Bug Summary

File:gromacs/fileio/enxio.c
Location:line 1052, column 13
Description:Value stored to 'bOK1' is never read

Annotated Source Code

1/*
2 * This file is part of the GROMACS molecular simulation package.
3 *
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
10 *
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
15 *
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
20 *
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
25 *
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
33 *
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
36 */
37#ifdef HAVE_CONFIG_H1
38#include <config.h>
39#endif
40
41#include <stdlib.h>
42#include <string.h>
43
44#include "gromacs/utility/futil.h"
45#include "gromacs/utility/fatalerror.h"
46#include "gromacs/utility/smalloc.h"
47#include "gmxfio.h"
48#include "enxio.h"
49#include "gromacs/math/vec.h"
50#include "xdrf.h"
51#include "macros.h"
52
53/* The source code in this file should be thread-safe.
54 Please keep it that way. */
55
56/* This number should be increased whenever the file format changes! */
57static const int enx_version = 5;
58
59const char *enx_block_id_name[] = {
60 "Averaged orientation restraints",
61 "Instantaneous orientation restraints",
62 "Orientation restraint order tensor(s)",
63 "Distance restraints",
64 "Free energy data",
65 "BAR histogram",
66 "Delta H raw data"
67};
68
69
70/* Stuff for reading pre 4.1 energy files */
71typedef struct {
72 gmx_bool bOldFileOpen; /* Is this an open old file? */
73 gmx_bool bReadFirstStep; /* Did we read the first step? */
74 int first_step; /* First step in the energy file */
75 int step_prev; /* Previous step */
76 int nsum_prev; /* Previous step sum length */
77 t_energy *ener_prev; /* Previous energy sums */
78} ener_old_t;
79
80struct ener_file
81{
82 ener_old_t eo;
83 t_fileio *fio;
84 int framenr;
85 real frametime;
86};
87
88static void enxsubblock_init(t_enxsubblock *sb)
89{
90 sb->nr = 0;
91#ifdef GMX_DOUBLE
92 sb->type = xdr_datatype_double;
93#else
94 sb->type = xdr_datatype_float;
95#endif
96 sb->fval = NULL((void*)0);
97 sb->dval = NULL((void*)0);
98 sb->ival = NULL((void*)0);
99 sb->lval = NULL((void*)0);
100 sb->cval = NULL((void*)0);
101 sb->sval = NULL((void*)0);
102 sb->fval_alloc = 0;
103 sb->dval_alloc = 0;
104 sb->ival_alloc = 0;
105 sb->lval_alloc = 0;
106 sb->cval_alloc = 0;
107 sb->sval_alloc = 0;
108}
109
110static void enxsubblock_free(t_enxsubblock *sb)
111{
112 if (sb->fval_alloc)
113 {
114 sfree(sb->fval)save_free("sb->fval", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 114, (sb->fval));
115 sb->fval_alloc = 0;
116 sb->fval = NULL((void*)0);
117 }
118 if (sb->dval_alloc)
119 {
120 sfree(sb->dval)save_free("sb->dval", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 120, (sb->dval));
121 sb->dval_alloc = 0;
122 sb->dval = NULL((void*)0);
123 }
124 if (sb->ival_alloc)
125 {
126 sfree(sb->ival)save_free("sb->ival", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 126, (sb->ival));
127 sb->ival_alloc = 0;
128 sb->ival = NULL((void*)0);
129 }
130 if (sb->lval_alloc)
131 {
132 sfree(sb->lval)save_free("sb->lval", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 132, (sb->lval));
133 sb->lval_alloc = 0;
134 sb->lval = NULL((void*)0);
135 }
136 if (sb->cval_alloc)
137 {
138 sfree(sb->cval)save_free("sb->cval", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 138, (sb->cval));
139 sb->cval_alloc = 0;
140 sb->cval = NULL((void*)0);
141 }
142 if (sb->sval_alloc)
143 {
144 int i;
145
146 for (i = 0; i < sb->sval_alloc; i++)
147 {
148 if (sb->sval[i])
149 {
150 sfree(sb->sval[i])save_free("sb->sval[i]", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 150, (sb->sval[i]));
151 }
152 }
153 sfree(sb->sval)save_free("sb->sval", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 153, (sb->sval));
154 sb->sval_alloc = 0;
155 sb->sval = NULL((void*)0);
156 }
157}
158
159/* allocate the appropriate amount of memory for the given type and nr */
160static void enxsubblock_alloc(t_enxsubblock *sb)
161{
162 /* allocate the appropriate amount of memory */
163 switch (sb->type)
164 {
165 case xdr_datatype_float:
166 if (sb->nr > sb->fval_alloc)
167 {
168 srenew(sb->fval, sb->nr)(sb->fval) = save_realloc("sb->fval", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 168, (sb->fval), (sb->nr), sizeof(*(sb->fval)));
169 sb->fval_alloc = sb->nr;
170 }
171 break;
172 case xdr_datatype_double:
173 if (sb->nr > sb->dval_alloc)
174 {
175 srenew(sb->dval, sb->nr)(sb->dval) = save_realloc("sb->dval", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 175, (sb->dval), (sb->nr), sizeof(*(sb->dval)));
176 sb->dval_alloc = sb->nr;
177 }
178 break;
179 case xdr_datatype_int:
180 if (sb->nr > sb->ival_alloc)
181 {
182 srenew(sb->ival, sb->nr)(sb->ival) = save_realloc("sb->ival", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 182, (sb->ival), (sb->nr), sizeof(*(sb->ival)));
183 sb->ival_alloc = sb->nr;
184 }
185 break;
186 case xdr_datatype_int64:
187 if (sb->nr > sb->lval_alloc)
188 {
189 srenew(sb->lval, sb->nr)(sb->lval) = save_realloc("sb->lval", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 189, (sb->lval), (sb->nr), sizeof(*(sb->lval)));
190 sb->lval_alloc = sb->nr;
191 }
192 break;
193 case xdr_datatype_char:
194 if (sb->nr > sb->cval_alloc)
195 {
196 srenew(sb->cval, sb->nr)(sb->cval) = save_realloc("sb->cval", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 196, (sb->cval), (sb->nr), sizeof(*(sb->cval)));
197 sb->cval_alloc = sb->nr;
198 }
199 break;
200 case xdr_datatype_string:
201 if (sb->nr > sb->sval_alloc)
202 {
203 int i;
204
205 srenew(sb->sval, sb->nr)(sb->sval) = save_realloc("sb->sval", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 205, (sb->sval), (sb->nr), sizeof(*(sb->sval)));
206 for (i = sb->sval_alloc; i < sb->nr; i++)
207 {
208 sb->sval[i] = NULL((void*)0);
209 }
210 sb->sval_alloc = sb->nr;
211 }
212 break;
213 default:
214 gmx_incons("Unknown block type: this file is corrupted or from the future")_gmx_error("incons", "Unknown block type: this file is corrupted or from the future"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c", 214
);
215 }
216}
217
218static void enxblock_init(t_enxblock *eb)
219{
220 eb->id = enxOR;
221 eb->nsub = 0;
222 eb->sub = NULL((void*)0);
223 eb->nsub_alloc = 0;
224}
225
226static void enxblock_free(t_enxblock *eb)
227{
228 if (eb->nsub_alloc > 0)
229 {
230 int i;
231 for (i = 0; i < eb->nsub_alloc; i++)
232 {
233 enxsubblock_free(&(eb->sub[i]));
234 }
235 sfree(eb->sub)save_free("eb->sub", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 235, (eb->sub));
236 eb->nsub_alloc = 0;
237 eb->sub = NULL((void*)0);
238 }
239}
240
241void init_enxframe(t_enxframe *fr)
242{
243 fr->e_alloc = 0;
244 fr->ener = NULL((void*)0);
245
246 /*fr->d_alloc=0;*/
247 fr->ener = NULL((void*)0);
248
249 /*fr->ndisre=0;*/
250
251 fr->nblock = 0;
252 fr->nblock_alloc = 0;
253 fr->block = NULL((void*)0);
254}
255
256
257void free_enxframe(t_enxframe *fr)
258{
259 int b;
260
261 if (fr->e_alloc)
262 {
263 sfree(fr->ener)save_free("fr->ener", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 263, (fr->ener));
264 }
265 for (b = 0; b < fr->nblock_alloc; b++)
266 {
267 enxblock_free(&(fr->block[b]));
268 }
269 sfree(fr->block)save_free("fr->block", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 269, (fr->block));
270}
271
272void add_blocks_enxframe(t_enxframe *fr, int n)
273{
274 fr->nblock = n;
275 if (n > fr->nblock_alloc)
276 {
277 int b;
278
279 srenew(fr->block, n)(fr->block) = save_realloc("fr->block", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 279, (fr->block), (n), sizeof(*(fr->block)));
280 for (b = fr->nblock_alloc; b < fr->nblock; b++)
281 {
282 enxblock_init(&(fr->block[b]));
283 }
284 fr->nblock_alloc = n;
285 }
286}
287
288t_enxblock *find_block_id_enxframe(t_enxframe *ef, int id, t_enxblock *prev)
289{
290 gmx_off_t starti = 0;
291 gmx_off_t i;
292
293 if (prev)
294 {
295 starti = (prev - ef->block) + 1;
296 }
297 for (i = starti; i < ef->nblock; i++)
298 {
299 if (ef->block[i].id == id)
300 {
301 return &(ef->block[i]);
302 }
303 }
304 return NULL((void*)0);
305}
306
307void add_subblocks_enxblock(t_enxblock *eb, int n)
308{
309 eb->nsub = n;
310 if (eb->nsub > eb->nsub_alloc)
311 {
312 int b;
313
314 srenew(eb->sub, n)(eb->sub) = save_realloc("eb->sub", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 314, (eb->sub), (n), sizeof(*(eb->sub)));
315 for (b = eb->nsub_alloc; b < n; b++)
316 {
317 enxsubblock_init(&(eb->sub[b]));
318 }
319 eb->nsub_alloc = n;
320 }
321}
322
323static void enx_warning(const char *msg)
324{
325 if (getenv("GMX_ENX_NO_FATAL") != NULL((void*)0))
326 {
327 gmx_warning(msg);
328 }
329 else
330 {
331 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c",
331, "%s\n%s",
332 msg,
333 "If you want to use the correct frames before the corrupted frame and avoid this fatal error set the env.var. GMX_ENX_NO_FATAL");
334 }
335}
336
337static void edr_strings(XDR *xdr, gmx_bool bRead, int file_version,
338 int n, gmx_enxnm_t **nms)
339{
340 int i;
341 gmx_enxnm_t *nm;
342
343 if (*nms == NULL((void*)0))
344 {
345 snew(*nms, n)(*nms) = save_calloc("*nms", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 345, (n), sizeof(*(*nms)));
346 }
347 for (i = 0; i < n; i++)
348 {
349 nm = &(*nms)[i];
350 if (bRead)
351 {
352 if (nm->name)
353 {
354 sfree(nm->name)save_free("nm->name", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 354, (nm->name));
355 nm->name = NULL((void*)0);
356 }
357 if (nm->unit)
358 {
359 sfree(nm->unit)save_free("nm->unit", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 359, (nm->unit));
360 nm->unit = NULL((void*)0);
361 }
362 }
363 if (!xdr_string(xdr, &(nm->name), STRLEN4096))
364 {
365 gmx_file("Cannot write energy names to file; maybe you are out of disk space?")_gmx_error("file", "Cannot write energy names to file; maybe you are out of disk space?"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c", 365
);
366 }
367 if (file_version >= 2)
368 {
369 if (!xdr_string(xdr, &(nm->unit), STRLEN4096))
370 {
371 gmx_file("Cannot write energy names to file; maybe you are out of disk space?")_gmx_error("file", "Cannot write energy names to file; maybe you are out of disk space?"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c", 371
);
372 }
373 }
374 else
375 {
376 nm->unit = strdup("kJ/mol")(__extension__ (__builtin_constant_p ("kJ/mol") && ((
size_t)(const void *)(("kJ/mol") + 1) - (size_t)(const void *
)("kJ/mol") == 1) ? (((const char *) ("kJ/mol"))[0] == '\0' ?
(char *) calloc ((size_t) 1, (size_t) 1) : ({ size_t __len =
strlen ("kJ/mol") + 1; char *__retval = (char *) malloc (__len
); if (__retval != ((void*)0)) __retval = (char *) memcpy (__retval
, "kJ/mol", __len); __retval; })) : __strdup ("kJ/mol")));
377 }
378 }
379}
380
381void do_enxnms(ener_file_t ef, int *nre, gmx_enxnm_t **nms)
382{
383 int magic = -55555;
384 XDR *xdr;
385 gmx_bool bRead = gmx_fio_getread(ef->fio);
386 int file_version;
387 int i;
388
389 gmx_fio_checktype(ef->fio);
390
391 xdr = gmx_fio_getxdr(ef->fio);
392
393 if (!xdr_int(xdr, &magic))
394 {
395 if (!bRead)
396 {
397 gmx_file("Cannot write energy names to file; maybe you are out of disk space?")_gmx_error("file", "Cannot write energy names to file; maybe you are out of disk space?"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c", 397
);
398 }
399 *nre = 0;
400 return;
401 }
402 if (magic > 0)
403 {
404 /* Assume this is an old edr format */
405 file_version = 1;
406 *nre = magic;
407 ef->eo.bOldFileOpen = TRUE1;
408 ef->eo.bReadFirstStep = FALSE0;
409 srenew(ef->eo.ener_prev, *nre)(ef->eo.ener_prev) = save_realloc("ef->eo.ener_prev", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 409, (ef->eo.ener_prev), (*nre), sizeof(*(ef->eo.ener_prev
)));
410 }
411 else
412 {
413 ef->eo.bOldFileOpen = FALSE0;
414
415 if (magic != -55555)
416 {
417 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c",
417, "Energy names magic number mismatch, this is not a GROMACS edr file");
418 }
419 file_version = enx_version;
420 xdr_int(xdr, &file_version);
421 if (file_version > enx_version)
422 {
423 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c",
423, "reading tpx file (%s) version %d with version %d program", gmx_fio_getname(ef->fio), file_version, enx_version);
424 }
425 xdr_int(xdr, nre);
426 }
427 if (file_version != enx_version)
428 {
429 fprintf(stderrstderr, "Note: enx file_version %d, software version %d\n",
430 file_version, enx_version);
431 }
432
433 edr_strings(xdr, bRead, file_version, *nre, nms);
434}
435
436static gmx_bool do_eheader(ener_file_t ef, int *file_version, t_enxframe *fr,
437 int nre_test, gmx_bool *bWrongPrecision, gmx_bool *bOK)
438{
439 int magic = -7777777;
440 real first_real_to_check;
441 int b, i, zero = 0, dum = 0;
442 gmx_bool bRead = gmx_fio_getread(ef->fio);
443 int tempfix_nr = 0;
444 int ndisre = 0;
445 int startb = 0;
446#ifndef GMX_DOUBLE
447 xdr_datatype dtreal = xdr_datatype_float;
448#else
449 xdr_datatype dtreal = xdr_datatype_double;
450#endif
451
452 if (bWrongPrecision)
453 {
454 *bWrongPrecision = FALSE0;
455 }
456
457 *bOK = TRUE1;
458 /* The original energy frame started with a real,
459 * so we have to use a real for compatibility.
460 * This is VERY DIRTY code, since do_eheader can be called
461 * with the wrong precision set and then we could read r > -1e10,
462 * while actually the intention was r < -1e10.
463 * When nre_test >= 0, do_eheader should therefore terminate
464 * before the number of i/o calls starts depending on what has been read
465 * (which is the case for for instance the block sizes for variable
466 * number of blocks, where this number is read before).
467 */
468 first_real_to_check = -2e10;
469 if (!gmx_fio_do_real(ef->fio, first_real_to_check)gmx_fio_doe_real(ef->fio, &first_real_to_check, ("first_real_to_check"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c",
469))
470 {
471 return FALSE0;
472 }
473 if (first_real_to_check > -1e10)
474 {
475 /* Assume we are reading an old format */
476 *file_version = 1;
477 fr->t = first_real_to_check;
478 if (!gmx_fio_do_int(ef->fio, dum)gmx_fio_doe_int(ef->fio, &dum, ("dum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 478))
479 {
480 *bOK = FALSE0;
481 }
482 fr->step = dum;
483 }
484 else
485 {
486 if (!gmx_fio_do_int(ef->fio, magic)gmx_fio_doe_int(ef->fio, &magic, ("magic"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 486))
487 {
488 *bOK = FALSE0;
489 }
490 if (magic != -7777777)
491 {
492 enx_warning("Energy header magic number mismatch, this is not a GROMACS edr file");
493 *bOK = FALSE0;
494 return FALSE0;
495 }
496 *file_version = enx_version;
497 if (!gmx_fio_do_int(ef->fio, *file_version)gmx_fio_doe_int(ef->fio, &*file_version, ("*file_version"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c",
497))
498 {
499 *bOK = FALSE0;
500 }
501 if (*bOK && *file_version > enx_version)
502 {
503 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c",
503, "reading tpx file (%s) version %d with version %d program", gmx_fio_getname(ef->fio), file_version, enx_version);
504 }
505 if (!gmx_fio_do_double(ef->fio, fr->t)gmx_fio_doe_double(ef->fio, &fr->t, ("fr->t"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 505))
506 {
507 *bOK = FALSE0;
508 }
509 if (!gmx_fio_do_int64(ef->fio, fr->step)gmx_fio_doe_int64(ef->fio, &fr->step, ("fr->step"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c",
509))
510 {
511 *bOK = FALSE0;
512 }
513 if (!bRead && fr->nsum == 1)
514 {
515 /* Do not store sums of length 1,
516 * since this does not add information.
517 */
518 if (!gmx_fio_do_int(ef->fio, zero)gmx_fio_doe_int(ef->fio, &zero, ("zero"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 518))
519 {
520 *bOK = FALSE0;
521 }
522 }
523 else
524 {
525 if (!gmx_fio_do_int(ef->fio, fr->nsum)gmx_fio_doe_int(ef->fio, &fr->nsum, ("fr->nsum")
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c", 525
))
526 {
527 *bOK = FALSE0;
528 }
529 }
530 if (*file_version >= 3)
531 {
532 if (!gmx_fio_do_int64(ef->fio, fr->nsteps)gmx_fio_doe_int64(ef->fio, &fr->nsteps, ("fr->nsteps"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c",
532))
533 {
534 *bOK = FALSE0;
535 }
536 }
537 else
538 {
539 fr->nsteps = max(1, fr->nsum)(((1) > (fr->nsum)) ? (1) : (fr->nsum) );
540 }
541 if (*file_version >= 5)
542 {
543 if (!gmx_fio_do_double(ef->fio, fr->dt)gmx_fio_doe_double(ef->fio, &fr->dt, ("fr->dt"),
"/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c", 543
))
544 {
545 *bOK = FALSE0;
546 }
547 }
548 else
549 {
550 fr->dt = 0;
551 }
552 }
553 if (!gmx_fio_do_int(ef->fio, fr->nre)gmx_fio_doe_int(ef->fio, &fr->nre, ("fr->nre"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 553))
554 {
555 *bOK = FALSE0;
556 }
557 if (*file_version < 4)
558 {
559 if (!gmx_fio_do_int(ef->fio, ndisre)gmx_fio_doe_int(ef->fio, &ndisre, ("ndisre"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 559))
560 {
561 *bOK = FALSE0;
562 }
563 }
564 else
565 {
566 /* now reserved for possible future use */
567 if (!gmx_fio_do_int(ef->fio, dum)gmx_fio_doe_int(ef->fio, &dum, ("dum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 567))
568 {
569 *bOK = FALSE0;
570 }
571 }
572
573 if (!gmx_fio_do_int(ef->fio, fr->nblock)gmx_fio_doe_int(ef->fio, &fr->nblock, ("fr->nblock"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c",
573))
574 {
575 *bOK = FALSE0;
576 }
577 if (fr->nblock < 0)
578 {
579 *bOK = FALSE0;
580 }
581
582 if (ndisre != 0)
583 {
584 if (*file_version >= 4)
585 {
586 enx_warning("Distance restraint blocks in old style in new style file");
587 *bOK = FALSE0;
588 return FALSE0;
589 }
590 fr->nblock += 1;
591 }
592
593
594 /* Frames could have nre=0, so we can not rely only on the fr->nre check */
595 if (bRead && nre_test >= 0 &&
596 ((fr->nre > 0 && fr->nre != nre_test) ||
597 fr->nre < 0 || ndisre < 0 || fr->nblock < 0))
598 {
599 *bWrongPrecision = TRUE1;
600 return *bOK;
601 }
602
603 /* we now know what these should be, or we've already bailed out because
604 of wrong precision */
605 if (*file_version == 1 && (fr->t < 0 || fr->t > 1e20 || fr->step < 0 ) )
606 {
607 enx_warning("edr file with negative step number or unreasonable time (and without version number).");
608 *bOK = FALSE0;
609 return FALSE0;
610 }
611
612
613 if (*bOK && bRead)
614 {
615 add_blocks_enxframe(fr, fr->nblock);
616 }
617
618 startb = 0;
619 if (ndisre > 0)
620 {
621 /* sub[0] is the instantaneous data, sub[1] is time averaged */
622 add_subblocks_enxblock(&(fr->block[0]), 2);
623 fr->block[0].id = enxDISRE;
624 fr->block[0].sub[0].nr = ndisre;
625 fr->block[0].sub[1].nr = ndisre;
626 fr->block[0].sub[0].type = dtreal;
627 fr->block[0].sub[1].type = dtreal;
628 startb++;
629 }
630
631 /* read block header info */
632 for (b = startb; b < fr->nblock; b++)
633 {
634 if (*file_version < 4)
635 {
636 /* blocks in old version files always have 1 subblock that
637 consists of reals. */
638 int nrint;
639
640 if (bRead)
641 {
642 add_subblocks_enxblock(&(fr->block[b]), 1);
643 }
644 else
645 {
646 if (fr->block[b].nsub != 1)
647 {
648 gmx_incons("Writing an old version .edr file with too many subblocks")_gmx_error("incons", "Writing an old version .edr file with too many subblocks"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c", 648
);
649 }
650 if (fr->block[b].sub[0].type != dtreal)
651 {
652 gmx_incons("Writing an old version .edr file the wrong subblock type")_gmx_error("incons", "Writing an old version .edr file the wrong subblock type"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c", 652
);
653 }
654 }
655 nrint = fr->block[b].sub[0].nr;
656
657 if (!gmx_fio_do_int(ef->fio, nrint)gmx_fio_doe_int(ef->fio, &nrint, ("nrint"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 657))
658 {
659 *bOK = FALSE0;
660 }
661 fr->block[b].id = b - startb;
662 fr->block[b].sub[0].nr = nrint;
663 fr->block[b].sub[0].type = dtreal;
664 }
665 else
666 {
667 int i;
668 /* in the new version files, the block header only contains
669 the ID and the number of subblocks */
670 int nsub = fr->block[b].nsub;
671 *bOK = *bOK && gmx_fio_do_int(ef->fio, fr->block[b].id)gmx_fio_doe_int(ef->fio, &fr->block[b].id, ("fr->block[b].id"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c",
671);
672 *bOK = *bOK && gmx_fio_do_int(ef->fio, nsub)gmx_fio_doe_int(ef->fio, &nsub, ("nsub"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 672);
673
674 fr->block[b].nsub = nsub;
675 if (bRead)
676 {
677 add_subblocks_enxblock(&(fr->block[b]), nsub);
678 }
679
680 /* read/write type & size for each subblock */
681 for (i = 0; i < nsub; i++)
682 {
683 t_enxsubblock *sub = &(fr->block[b].sub[i]); /* shortcut */
684 int typenr = sub->type;
685
686 *bOK = *bOK && gmx_fio_do_int(ef->fio, typenr)gmx_fio_doe_int(ef->fio, &typenr, ("typenr"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 686);
687 *bOK = *bOK && gmx_fio_do_int(ef->fio, sub->nr)gmx_fio_doe_int(ef->fio, &sub->nr, ("sub->nr"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 687);
688
689 sub->type = (xdr_datatype)typenr;
690 }
691 }
692 }
693 if (!gmx_fio_do_int(ef->fio, fr->e_size)gmx_fio_doe_int(ef->fio, &fr->e_size, ("fr->e_size"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c",
693))
694 {
695 *bOK = FALSE0;
696 }
697
698 /* now reserved for possible future use */
699 if (!gmx_fio_do_int(ef->fio, dum)gmx_fio_doe_int(ef->fio, &dum, ("dum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 699))
700 {
701 *bOK = FALSE0;
702 }
703
704 /* Do a dummy int to keep the format compatible with the old code */
705 if (!gmx_fio_do_int(ef->fio, dum)gmx_fio_doe_int(ef->fio, &dum, ("dum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 705))
706 {
707 *bOK = FALSE0;
708 }
709
710 if (*bOK && *file_version == 1 && nre_test < 0)
711 {
712 if (!ef->eo.bReadFirstStep)
713 {
714 ef->eo.bReadFirstStep = TRUE1;
715 ef->eo.first_step = fr->step;
716 ef->eo.step_prev = fr->step;
717 ef->eo.nsum_prev = 0;
718 }
719
720 fr->nsum = fr->step - ef->eo.first_step + 1;
721 fr->nsteps = fr->step - ef->eo.step_prev;
722 fr->dt = 0;
723 }
724
725 return *bOK;
726}
727
728void free_enxnms(int n, gmx_enxnm_t *nms)
729{
730 int i;
731
732 for (i = 0; i < n; i++)
733 {
734 sfree(nms[i].name)save_free("nms[i].name", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 734, (nms[i].name));
735 sfree(nms[i].unit)save_free("nms[i].unit", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 735, (nms[i].unit));
736 }
737
738 sfree(nms)save_free("nms", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 738, (nms));
739}
740
741void close_enx(ener_file_t ef)
742{
743 if (gmx_fio_close(ef->fio) != 0)
744 {
745 gmx_file("Cannot close energy file; it might be corrupt, or maybe you are out of disk space?")_gmx_error("file", "Cannot close energy file; it might be corrupt, or maybe you are out of disk space?"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c", 745
);
746 }
747}
748
749static gmx_bool empty_file(const char *fn)
750{
751 FILE *fp;
752 char dum;
753 int ret;
754 gmx_bool bEmpty;
755
756 fp = gmx_fio_fopen(fn, "r");
757 ret = fread(&dum, sizeof(dum), 1, fp);
758 bEmpty = feof(fp);
759 gmx_fio_fclose(fp);
760
761 return bEmpty;
762}
763
764
765ener_file_t open_enx(const char *fn, const char *mode)
766{
767 int nre, i;
768 gmx_enxnm_t *nms = NULL((void*)0);
769 int file_version = -1;
770 t_enxframe *fr;
771 gmx_bool bWrongPrecision, bOK = TRUE1;
772 struct ener_file *ef;
773
774 snew(ef, 1)(ef) = save_calloc("ef", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 774, (1), sizeof(*(ef)));
775
776 if (mode[0] == 'r')
777 {
778 ef->fio = gmx_fio_open(fn, mode);
779 gmx_fio_checktype(ef->fio);
780 gmx_fio_setprecision(ef->fio, FALSE0);
781 do_enxnms(ef, &nre, &nms);
782 snew(fr, 1)(fr) = save_calloc("fr", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 782, (1), sizeof(*(fr)));
783 do_eheader(ef, &file_version, fr, nre, &bWrongPrecision, &bOK);
784 if (!bOK)
785 {
786 gmx_file("Cannot read energy file header. Corrupt file?")_gmx_error("file", "Cannot read energy file header. Corrupt file?"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c", 786
);
787 }
788
789 /* Now check whether this file is in single precision */
790 if (!bWrongPrecision &&
791 ((fr->e_size && (fr->nre == nre) &&
792 (nre*4*(long int)sizeof(float) == fr->e_size)) ) )
793 {
794 fprintf(stderrstderr, "Opened %s as single precision energy file\n", fn);
795 free_enxnms(nre, nms);
796 }
797 else
798 {
799 gmx_fio_rewind(ef->fio);
800 gmx_fio_checktype(ef->fio);
801 gmx_fio_setprecision(ef->fio, TRUE1);
802 do_enxnms(ef, &nre, &nms);
803 do_eheader(ef, &file_version, fr, nre, &bWrongPrecision, &bOK);
804 if (!bOK)
805 {
806 gmx_file("Cannot write energy file header; maybe you are out of disk space?")_gmx_error("file", "Cannot write energy file header; maybe you are out of disk space?"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c", 806
);
807 }
808
809 if (((fr->e_size && (fr->nre == nre) &&
810 (nre*4*(long int)sizeof(double) == fr->e_size)) ))
811 {
812 fprintf(stderrstderr, "Opened %s as double precision energy file\n",
813 fn);
814 }
815 else
816 {
817 if (empty_file(fn))
818 {
819 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c",
819, "File %s is empty", fn);
820 }
821 else
822 {
823 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c",
823, "Energy file %s not recognized, maybe different CPU?",
824 fn);
825 }
826 }
827 free_enxnms(nre, nms);
828 }
829 free_enxframe(fr);
830 sfree(fr)save_free("fr", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 830, (fr));
831 gmx_fio_rewind(ef->fio);
832 }
833 else
834 {
835 ef->fio = gmx_fio_open(fn, mode);
836 }
837
838 ef->framenr = 0;
839 ef->frametime = 0;
840 return ef;
841}
842
843t_fileio *enx_file_pointer(const ener_file_t ef)
844{
845 return ef->fio;
846}
847
848static void convert_full_sums(ener_old_t *ener_old, t_enxframe *fr)
849{
850 int nstep_all;
851 int ne, ns, i;
852 double esum_all, eav_all;
853
854 if (fr->nsum > 0)
855 {
856 ne = 0;
857 ns = 0;
858 for (i = 0; i < fr->nre; i++)
859 {
860 if (fr->ener[i].e != 0)
861 {
862 ne++;
863 }
864 if (fr->ener[i].esum != 0)
865 {
866 ns++;
867 }
868 }
869 if (ne > 0 && ns == 0)
870 {
871 /* We do not have all energy sums */
872 fr->nsum = 0;
873 }
874 }
875
876 /* Convert old full simulation sums to sums between energy frames */
877 nstep_all = fr->step - ener_old->first_step + 1;
878 if (fr->nsum > 1 && fr->nsum == nstep_all && ener_old->nsum_prev > 0)
879 {
880 /* Set the new sum length: the frame step difference */
881 fr->nsum = fr->step - ener_old->step_prev;
882 for (i = 0; i < fr->nre; i++)
883 {
884 esum_all = fr->ener[i].esum;
885 eav_all = fr->ener[i].eav;
886 fr->ener[i].esum = esum_all - ener_old->ener_prev[i].esum;
887 fr->ener[i].eav = eav_all - ener_old->ener_prev[i].eav
888 - dsqr(ener_old->ener_prev[i].esum/(nstep_all - fr->nsum)
889 - esum_all/nstep_all)*
890 (nstep_all - fr->nsum)*nstep_all/(double)fr->nsum;
891 ener_old->ener_prev[i].esum = esum_all;
892 ener_old->ener_prev[i].eav = eav_all;
893 }
894 ener_old->nsum_prev = nstep_all;
895 }
896 else if (fr->nsum > 0)
897 {
898 if (fr->nsum != nstep_all)
899 {
900 fprintf(stderrstderr, "\nWARNING: something is wrong with the energy sums, will not use exact averages\n");
901 ener_old->nsum_prev = 0;
902 }
903 else
904 {
905 ener_old->nsum_prev = nstep_all;
906 }
907 /* Copy all sums to ener_prev */
908 for (i = 0; i < fr->nre; i++)
909 {
910 ener_old->ener_prev[i].esum = fr->ener[i].esum;
911 ener_old->ener_prev[i].eav = fr->ener[i].eav;
912 }
913 }
914
915 ener_old->step_prev = fr->step;
916}
917
918gmx_bool do_enx(ener_file_t ef, t_enxframe *fr)
919{
920 int file_version = -1;
921 int i, b;
922 gmx_bool bRead, bOK, bOK1, bSane;
923 real tmp1, tmp2, rdum;
924 char buf[22];
925 /*int d_size;*/
926
927 bOK = TRUE1;
928 bRead = gmx_fio_getread(ef->fio);
929 if (!bRead)
930 {
931 fr->e_size = fr->nre*sizeof(fr->ener[0].e)*4;
932 /*d_size = fr->ndisre*(sizeof(real)*2);*/
933 }
934 gmx_fio_checktype(ef->fio);
935
936 if (!do_eheader(ef, &file_version, fr, -1, NULL((void*)0), &bOK))
937 {
938 if (bRead)
939 {
940 fprintf(stderrstderr, "\rLast energy frame read %d time %8.3f ",
941 ef->framenr-1, ef->frametime);
942 if (!bOK)
943 {
944 fprintf(stderrstderr,
945 "\nWARNING: Incomplete energy frame: nr %d time %8.3f\n",
946 ef->framenr, fr->t);
947 }
948 }
949 else
950 {
951 gmx_file("Cannot write energy file header; maybe you are out of disk space?")_gmx_error("file", "Cannot write energy file header; maybe you are out of disk space?"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c", 951
);
952 }
953 return FALSE0;
954 }
955 if (bRead)
956 {
957 if ((ef->framenr < 20 || ef->framenr % 10 == 0) &&
958 (ef->framenr < 200 || ef->framenr % 100 == 0) &&
959 (ef->framenr < 2000 || ef->framenr % 1000 == 0))
960 {
961 fprintf(stderrstderr, "\rReading energy frame %6d time %8.3f ",
962 ef->framenr, fr->t);
963 }
964 ef->framenr++;
965 ef->frametime = fr->t;
966 }
967 /* Check sanity of this header */
968 bSane = fr->nre > 0;
969 for (b = 0; b < fr->nblock; b++)
970 {
971 bSane = bSane || (fr->block[b].nsub > 0);
972 }
973 if (!((fr->step >= 0) && bSane))
974 {
975 fprintf(stderrstderr, "\nWARNING: there may be something wrong with energy file %s\n",
976 gmx_fio_getname(ef->fio));
977 fprintf(stderrstderr, "Found: step=%s, nre=%d, nblock=%d, time=%g.\n"
978 "Trying to skip frame expect a crash though\n",
979 gmx_step_str(fr->step, buf), fr->nre, fr->nblock, fr->t);
980 }
981 if (bRead && fr->nre > fr->e_alloc)
982 {
983 srenew(fr->ener, fr->nre)(fr->ener) = save_realloc("fr->ener", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 983, (fr->ener), (fr->nre), sizeof(*(fr->ener)));
984 for (i = fr->e_alloc; (i < fr->nre); i++)
985 {
986 fr->ener[i].e = 0;
987 fr->ener[i].eav = 0;
988 fr->ener[i].esum = 0;
989 }
990 fr->e_alloc = fr->nre;
991 }
992
993 for (i = 0; i < fr->nre; i++)
994 {
995 bOK = bOK && gmx_fio_do_real(ef->fio, fr->ener[i].e)gmx_fio_doe_real(ef->fio, &fr->ener[i].e, ("fr->ener[i].e"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c",
995);
996
997 /* Do not store sums of length 1,
998 * since this does not add information.
999 */
1000 if (file_version == 1 ||
1001 (bRead && fr->nsum > 0) || fr->nsum > 1)
1002 {
1003 tmp1 = fr->ener[i].eav;
1004 bOK = bOK && gmx_fio_do_real(ef->fio, tmp1)gmx_fio_doe_real(ef->fio, &tmp1, ("tmp1"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 1004);
1005 if (bRead)
1006 {
1007 fr->ener[i].eav = tmp1;
1008 }
1009
1010 /* This is to save only in single precision (unless compiled in DP) */
1011 tmp2 = fr->ener[i].esum;
1012 bOK = bOK && gmx_fio_do_real(ef->fio, tmp2)gmx_fio_doe_real(ef->fio, &tmp2, ("tmp2"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 1012);
1013 if (bRead)
1014 {
1015 fr->ener[i].esum = tmp2;
1016 }
1017
1018 if (file_version == 1)
1019 {
1020 /* Old, unused real */
1021 rdum = 0;
1022 bOK = bOK && gmx_fio_do_real(ef->fio, rdum)gmx_fio_doe_real(ef->fio, &rdum, ("rdum"), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 1022);
1023 }
1024 }
1025 }
1026
1027 /* Here we can not check for file_version==1, since one could have
1028 * continued an old format simulation with a new one with mdrun -append.
1029 */
1030 if (bRead && ef->eo.bOldFileOpen)
1031 {
1032 /* Convert old full simulation sums to sums between energy frames */
1033 convert_full_sums(&(ef->eo), fr);
1034 }
1035 /* read the blocks */
1036 for (b = 0; b < fr->nblock; b++)
1037 {
1038 /* now read the subblocks. */
1039 int nsub = fr->block[b].nsub; /* shortcut */
1040 int i;
1041
1042 for (i = 0; i < nsub; i++)
1043 {
1044 t_enxsubblock *sub = &(fr->block[b].sub[i]); /* shortcut */
1045
1046 if (bRead)
1047 {
1048 enxsubblock_alloc(sub);
1049 }
1050
1051 /* read/write data */
1052 bOK1 = TRUE1;
Value stored to 'bOK1' is never read
1053 switch (sub->type)
1054 {
1055 case xdr_datatype_float:
1056 bOK1 = gmx_fio_ndo_float(ef->fio, sub->fval, sub->nr)gmx_fio_ndoe_float(ef->fio, sub->fval, sub->nr, ("sub->fval"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c",
1056);
1057 break;
1058 case xdr_datatype_double:
1059 bOK1 = gmx_fio_ndo_double(ef->fio, sub->dval, sub->nr)gmx_fio_ndoe_double(ef->fio, sub->dval, sub->nr, ("sub->dval"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c",
1059);
1060 break;
1061 case xdr_datatype_int:
1062 bOK1 = gmx_fio_ndo_int(ef->fio, sub->ival, sub->nr)gmx_fio_ndoe_int(ef->fio, sub->ival, sub->nr, ("sub->ival"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c",
1062);
1063 break;
1064 case xdr_datatype_int64:
1065 bOK1 = gmx_fio_ndo_int64(ef->fio, sub->lval, sub->nr)gmx_fio_ndoe_int64(ef->fio, sub->lval, sub->nr, ("sub->lval"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c",
1065);
1066 break;
1067 case xdr_datatype_char:
1068 bOK1 = gmx_fio_ndo_uchar(ef->fio, sub->cval, sub->nr)gmx_fio_ndoe_uchar(ef->fio, sub->cval, sub->nr, ("sub->cval"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c",
1068);
1069 break;
1070 case xdr_datatype_string:
1071 bOK1 = gmx_fio_ndo_string(ef->fio, sub->sval, sub->nr)gmx_fio_ndoe_string(ef->fio, sub->sval, sub->nr, ("sub->sval"
), "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c",
1071);
1072 break;
1073 default:
1074 gmx_incons("Reading unknown block data type: this file is corrupted or from the future")_gmx_error("incons", "Reading unknown block data type: this file is corrupted or from the future"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c", 1074
);
1075 }
1076 bOK = bOK && bOK1;
1077 }
1078 }
1079
1080 if (!bRead)
1081 {
1082 if (gmx_fio_flush(ef->fio) != 0)
1083 {
1084 gmx_file("Cannot write energy file; maybe you are out of disk space?")_gmx_error("file", "Cannot write energy file; maybe you are out of disk space?"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c", 1084
);
1085 }
1086 }
1087
1088 if (!bOK)
1089 {
1090 if (bRead)
1091 {
1092 fprintf(stderrstderr, "\nLast energy frame read %d",
1093 ef->framenr-1);
1094 fprintf(stderrstderr, "\nWARNING: Incomplete energy frame: nr %d time %8.3f\n",
1095 ef->framenr, fr->t);
1096 }
1097 else
1098 {
1099 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c",
1099, "could not write energies");
1100 }
1101 return FALSE0;
1102 }
1103
1104 return TRUE1;
1105}
1106
1107static real find_energy(const char *name, int nre, gmx_enxnm_t *enm,
1108 t_enxframe *fr)
1109{
1110 int i;
1111
1112 for (i = 0; i < nre; i++)
1113 {
1114 if (strcmp(enm[i].name, name)__extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p
(enm[i].name) && __builtin_constant_p (name) &&
(__s1_len = strlen (enm[i].name), __s2_len = strlen (name), (
!((size_t)(const void *)((enm[i].name) + 1) - (size_t)(const void
*)(enm[i].name) == 1) || __s1_len >= 4) && (!((size_t
)(const void *)((name) + 1) - (size_t)(const void *)(name) ==
1) || __s2_len >= 4)) ? __builtin_strcmp (enm[i].name, name
) : (__builtin_constant_p (enm[i].name) && ((size_t)(
const void *)((enm[i].name) + 1) - (size_t)(const void *)(enm
[i].name) == 1) && (__s1_len = strlen (enm[i].name), __s1_len
< 4) ? (__builtin_constant_p (name) && ((size_t)(
const void *)((name) + 1) - (size_t)(const void *)(name) == 1
) ? __builtin_strcmp (enm[i].name, name) : (__extension__ ({ const
unsigned char *__s2 = (const unsigned char *) (const char *)
(name); int __result = (((const unsigned char *) (const char
*) (enm[i].name))[0] - __s2[0]); if (__s1_len > 0 &&
__result == 0) { __result = (((const unsigned char *) (const
char *) (enm[i].name))[1] - __s2[1]); if (__s1_len > 1 &&
__result == 0) { __result = (((const unsigned char *) (const
char *) (enm[i].name))[2] - __s2[2]); if (__s1_len > 2 &&
__result == 0) __result = (((const unsigned char *) (const char
*) (enm[i].name))[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p
(name) && ((size_t)(const void *)((name) + 1) - (size_t
)(const void *)(name) == 1) && (__s2_len = strlen (name
), __s2_len < 4) ? (__builtin_constant_p (enm[i].name) &&
((size_t)(const void *)((enm[i].name) + 1) - (size_t)(const void
*)(enm[i].name) == 1) ? __builtin_strcmp (enm[i].name, name)
: (- (__extension__ ({ const unsigned char *__s2 = (const unsigned
char *) (const char *) (enm[i].name); int __result = (((const
unsigned char *) (const char *) (name))[0] - __s2[0]); if (__s2_len
> 0 && __result == 0) { __result = (((const unsigned
char *) (const char *) (name))[1] - __s2[1]); if (__s2_len >
1 && __result == 0) { __result = (((const unsigned char
*) (const char *) (name))[2] - __s2[2]); if (__s2_len > 2
&& __result == 0) __result = (((const unsigned char *
) (const char *) (name))[3] - __s2[3]); } } __result; })))) :
__builtin_strcmp (enm[i].name, name)))); }) == 0)
1115 {
1116 return fr->ener[i].e;
1117 }
1118 }
1119
1120 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c",
1120, "Could not find energy term named '%s'", name);
1121
1122 return 0;
1123}
1124
1125
1126void get_enx_state(const char *fn, real t, gmx_groups_t *groups, t_inputrec *ir,
1127 t_state *state)
1128{
1129 /* Should match the names in mdebin.c */
1130 static const char *boxvel_nm[] = {
1131 "Box-Vel-XX", "Box-Vel-YY", "Box-Vel-ZZ",
1132 "Box-Vel-YX", "Box-Vel-ZX", "Box-Vel-ZY"
1133 };
1134
1135 static const char *pcouplmu_nm[] = {
1136 "Pcoupl-Mu-XX", "Pcoupl-Mu-YY", "Pcoupl-Mu-ZZ",
1137 "Pcoupl-Mu-YX", "Pcoupl-Mu-ZX", "Pcoupl-Mu-ZY"
1138 };
1139 static const char *baro_nm[] = {
1140 "Barostat"
1141 };
1142
1143
1144 int ind0[] = { XX0, YY1, ZZ2, YY1, ZZ2, ZZ2 };
1145 int ind1[] = { XX0, YY1, ZZ2, XX0, XX0, YY1 };
1146 int nre, nfr, i, j, ni, npcoupl;
1147 char buf[STRLEN4096];
1148 const char *bufi;
1149 gmx_enxnm_t *enm = NULL((void*)0);
1150 t_enxframe *fr;
1151 ener_file_t in;
1152
1153 in = open_enx(fn, "r");
1154 do_enxnms(in, &nre, &enm);
1155 snew(fr, 1)(fr) = save_calloc("fr", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 1155, (1), sizeof(*(fr)));
1156 nfr = 0;
1157 while ((nfr == 0 || fr->t != t) && do_enx(in, fr))
1158 {
1159 nfr++;
1160 }
1161 close_enx(in);
1162 fprintf(stderrstderr, "\n");
1163
1164 if (nfr == 0 || fr->t != t)
1165 {
1166 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c",
1166, "Could not find frame with time %f in '%s'", t, fn);
1167 }
1168
1169 npcoupl = TRICLINIC(ir->compress)(ir->compress[1][0] != 0 || ir->compress[2][0] != 0 || ir
->compress[2][1] != 0) ? 6 : 3;
1170 if (ir->epc == epcPARRINELLORAHMAN)
1171 {
1172 clear_mat(state->boxv);
1173 for (i = 0; i < npcoupl; i++)
1174 {
1175 state->boxv[ind0[i]][ind1[i]] =
1176 find_energy(boxvel_nm[i], nre, enm, fr);
1177 }
1178 fprintf(stderrstderr, "\nREAD %d BOX VELOCITIES FROM %s\n\n", npcoupl, fn);
1179 }
1180
1181 if (ir->etc == etcNOSEHOOVER)
1182 {
1183 char cns[20];
1184
1185 cns[0] = '\0';
1186
1187 for (i = 0; i < state->ngtc; i++)
1188 {
1189 ni = groups->grps[egcTC].nm_ind[i];
1190 bufi = *(groups->grpname[ni]);
1191 for (j = 0; (j < state->nhchainlength); j++)
1192 {
1193 if (IR_NVT_TROTTER(ir)((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) &&
((!((ir)->epc == epcMTTK)) && ((ir)->etc == etcNOSEHOOVER
))))
1194 {
1195 sprintf(cns, "-%d", j);
1196 }
1197 sprintf(buf, "Xi%s-%s", cns, bufi);
1198 state->nosehoover_xi[i] = find_energy(buf, nre, enm, fr);
1199 sprintf(buf, "vXi%s-%s", cns, bufi);
1200 state->nosehoover_vxi[i] = find_energy(buf, nre, enm, fr);
1201 }
1202
1203 }
1204 fprintf(stderrstderr, "\nREAD %d NOSE-HOOVER Xi chains FROM %s\n\n", state->ngtc, fn);
1205
1206 if (IR_NPT_TROTTER(ir)((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) &&
(((ir)->epc == epcMTTK) && ((ir)->etc == etcNOSEHOOVER
))) || IR_NPH_TROTTER(ir)((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) &&
(((ir)->epc == epcMTTK) && (!(((ir)->etc == etcNOSEHOOVER
))))))
1207 {
1208 for (i = 0; i < state->nnhpres; i++)
1209 {
1210 bufi = baro_nm[0]; /* All barostat DOF's together for now */
1211 for (j = 0; (j < state->nhchainlength); j++)
1212 {
1213 sprintf(buf, "Xi-%d-%s", j, bufi);
1214 state->nhpres_xi[i] = find_energy(buf, nre, enm, fr);
1215 sprintf(buf, "vXi-%d-%s", j, bufi);
1216 state->nhpres_vxi[i] = find_energy(buf, nre, enm, fr);
1217 }
1218 }
1219 fprintf(stderrstderr, "\nREAD %d NOSE-HOOVER BAROSTAT Xi chains FROM %s\n\n", state->nnhpres, fn);
1220 }
1221 }
1222
1223 free_enxnms(nre, enm);
1224 free_enxframe(fr);
1225 sfree(fr)save_free("fr", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/enxio.c"
, 1225, (fr));
1226}