Bug Summary

File:gromacs/fileio/trxio.c
Location:line 974, column 13
Description:Value stored to 'fio' 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#include "trxio.h"
38
39#ifdef HAVE_CONFIG_H1
40#include <config.h>
41#endif
42
43#include <assert.h>
44#include <math.h>
45
46#include "typedefs.h"
47#ifdef GMX_USE_PLUGINS
48#include "vmdio.h"
49#endif
50#include "gromacs/utility/smalloc.h"
51#include "pbc.h"
52#include "gmxfio.h"
53#include "trxio.h"
54#include "tpxio.h"
55#include "trnio.h"
56#include "tngio.h"
57#include "tngio_for_tools.h"
58#include "names.h"
59#include "gromacs/math/vec.h"
60#include "gromacs/utility/futil.h"
61#include "xtcio.h"
62#include "pdbio.h"
63#include "confio.h"
64#include "checkpoint.h"
65#include "xdrf.h"
66
67#include "gromacs/fileio/timecontrol.h"
68#include "gromacs/utility/fatalerror.h"
69
70/* defines for frame counter output */
71#define SKIP110 10
72#define SKIP2100 100
73#define SKIP31000 1000
74
75struct t_trxstatus
76{
77 int __frame;
78 t_trxframe *xframe;
79 int nxframe;
80 t_fileio *fio;
81 tng_trajectory_t tng;
82 int NATOMS;
83 double DT, BOX[3];
84 gmx_bool bReadBox;
85 char *persistent_line; /* Persistent line for reading g96 trajectories */
86};
87
88/* utility functions */
89
90gmx_bool bRmod_fd(double a, double b, double c, gmx_bool bDouble)
91{
92 int iq;
93 double tol;
94
95 tol = 2*(bDouble ? GMX_DOUBLE_EPS1.11022302E-16 : GMX_FLOAT_EPS5.96046448E-08);
96
97 iq = (int)((a - b + tol*a)/c);
98
99 if (fabs(a - b - c*iq) <= tol*fabs(a))
100 {
101 return TRUE1;
102 }
103 else
104 {
105 return FALSE0;
106 }
107}
108
109
110
111int check_times2(real t, real t0, gmx_bool bDouble)
112{
113 int r;
114
115#ifndef GMX_DOUBLE
116 /* since t is float, we can not use double precision for bRmod */
117 bDouble = FALSE0;
118#endif
119
120 r = -1;
121 if ((!bTimeSet(TBEGIN) || (t >= rTimeValue(TBEGIN))) &&
122 (!bTimeSet(TEND) || (t <= rTimeValue(TEND))))
123 {
124 if (bTimeSet(TDELTA) && !bRmod_fd(t, t0, rTimeValue(TDELTA), bDouble))
125 {
126 r = -1;
127 }
128 else
129 {
130 r = 0;
131 }
132 }
133 else if (bTimeSet(TEND) && (t >= rTimeValue(TEND)))
134 {
135 r = 1;
136 }
137 if (debug)
138 {
139 fprintf(debug, "t=%g, t0=%g, b=%g, e=%g, dt=%g: r=%d\n",
140 t, t0, rTimeValue(TBEGIN), rTimeValue(TEND), rTimeValue(TDELTA), r);
141 }
142 return r;
143}
144
145int check_times(real t)
146{
147 return check_times2(t, t, FALSE0);
148}
149
150static void initcount(t_trxstatus *status)
151{
152 status->__frame = -1;
153}
154
155static void status_init(t_trxstatus *status)
156{
157 status->nxframe = 0;
158 status->xframe = NULL((void*)0);
159 status->fio = NULL((void*)0);
160 status->__frame = -1;
161 status->persistent_line = NULL((void*)0);
162 status->tng = NULL((void*)0);
163}
164
165
166int nframes_read(t_trxstatus *status)
167{
168 return status->__frame;
169}
170
171static void printcount_(t_trxstatus *status, const output_env_t oenv,
172 const char *l, real t)
173{
174 if ((status->__frame < 2*SKIP110 || status->__frame % SKIP110 == 0) &&
175 (status->__frame < 2*SKIP2100 || status->__frame % SKIP2100 == 0) &&
176 (status->__frame < 2*SKIP31000 || status->__frame % SKIP31000 == 0))
177 {
178 fprintf(stderrstderr, "\r%-14s %6d time %8.3f ", l, status->__frame,
179 output_env_conv_time(oenv, t));
180 }
181}
182
183static void printcount(t_trxstatus *status, const output_env_t oenv, real t,
184 gmx_bool bSkip)
185{
186 status->__frame++;
187 printcount_(status, oenv, bSkip ? "Skipping frame" : "Reading frame", t);
188}
189
190static void printlast(t_trxstatus *status, const output_env_t oenv, real t)
191{
192 printcount_(status, oenv, "Last frame", t);
193 fprintf(stderrstderr, "\n");
194}
195
196static void printincomp(t_trxstatus *status, t_trxframe *fr)
197{
198 if (fr->not_ok & HEADER_NOT_OK(1<<0))
199 {
200 fprintf(stderrstderr, "WARNING: Incomplete header: nr %d time %g\n",
201 status->__frame+1, fr->time);
202 }
203 else if (fr->not_ok)
204 {
205 fprintf(stderrstderr, "WARNING: Incomplete frame: nr %d time %g\n",
206 status->__frame+1, fr->time);
207 }
208}
209
210int prec2ndec(real prec)
211{
212 if (prec <= 0)
213 {
214 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c",
214, "DEATH HORROR prec (%g) <= 0 in prec2ndec", prec);
215 }
216
217 return (int)(log(prec)/log(10.0)+0.5);
218}
219
220real ndec2prec(int ndec)
221{
222 return pow(10.0, ndec);
223}
224
225t_fileio *trx_get_fileio(t_trxstatus *status)
226{
227 return status->fio;
228}
229
230float trx_get_time_of_final_frame(t_trxstatus *status)
231{
232 t_fileio *stfio = trx_get_fileio(status);
233 int filetype = gmx_fio_getftp(stfio);
234 int bOK;
235 float lasttime = -1;
236
237 if (filetype == efXTC)
238 {
239 lasttime =
240 xdr_xtc_get_last_frame_time(gmx_fio_getfp(stfio),
241 gmx_fio_getxdr(stfio),
242 status->xframe->natoms, &bOK);
243 if (!bOK)
244 {
245 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c",
245, "Error reading last frame. Maybe seek not supported." );
246 }
247 }
248 else if (filetype == efTNG)
249 {
250 tng_trajectory_t tng = status->tng;
251 if (!tng)
252 {
253 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c",
253, "Error opening TNG file.");
254 }
255 lasttime = gmx_tng_get_time_of_final_frame(tng);
256 }
257 else
258 {
259 gmx_incons("Only supported for TNG and XTC")_gmx_error("incons", "Only supported for TNG and XTC", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c"
, 259);
260 }
261 return lasttime;
262}
263
264void clear_trxframe(t_trxframe *fr, gmx_bool bFirst)
265{
266 fr->not_ok = 0;
267 fr->bTitle = FALSE0;
268 fr->bStep = FALSE0;
269 fr->bTime = FALSE0;
270 fr->bLambda = FALSE0;
271 fr->bFepState = FALSE0;
272 fr->bAtoms = FALSE0;
273 fr->bPrec = FALSE0;
274 fr->bX = FALSE0;
275 fr->bV = FALSE0;
276 fr->bF = FALSE0;
277 fr->bBox = FALSE0;
278 if (bFirst)
279 {
280 fr->flags = 0;
281 fr->bDouble = FALSE0;
282 fr->natoms = -1;
283 fr->t0 = 0;
284 fr->tpf = 0;
285 fr->tppf = 0;
286 fr->title = NULL((void*)0);
287 fr->step = 0;
288 fr->time = 0;
289 fr->lambda = 0;
290 fr->fep_state = 0;
291 fr->atoms = NULL((void*)0);
292 fr->prec = 0;
293 fr->x = NULL((void*)0);
294 fr->v = NULL((void*)0);
295 fr->f = NULL((void*)0);
296 clear_mat(fr->box);
297 fr->bPBC = FALSE0;
298 fr->ePBC = -1;
299 }
300}
301
302void set_trxframe_ePBC(t_trxframe *fr, int ePBC)
303{
304 fr->bPBC = (ePBC == -1);
305 fr->ePBC = ePBC;
306}
307
308int write_trxframe_indexed(t_trxstatus *status, t_trxframe *fr, int nind,
309 const atom_id *ind, gmx_conect gc)
310{
311 char title[STRLEN4096];
312 rvec *xout = NULL((void*)0), *vout = NULL((void*)0), *fout = NULL((void*)0);
313 int i, ftp = -1;
314 real prec;
315
316 if (fr->bPrec)
317 {
318 prec = fr->prec;
319 }
320 else
321 {
322 prec = 1000.0;
323 }
324
325 if (status->tng)
326 {
327 ftp = efTNG;
328 }
329 else if (status->fio)
330 {
331 ftp = gmx_fio_getftp(status->fio);
332 }
333 else
334 {
335 gmx_incons("No input file available")_gmx_error("incons", "No input file available", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c"
, 335);
336 }
337
338 switch (ftp)
339 {
340 case efTRJ:
341 case efTRR:
342 case efTNG:
343 break;
344 default:
345 if (!fr->bX)
346 {
347 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c",
347, "Need coordinates to write a %s trajectory",
348 ftp2ext(ftp));
349 }
350 break;
351 }
352
353 switch (ftp)
354 {
355 case efTRJ:
356 case efTRR:
357 case efTNG:
358 if (fr->bV)
359 {
360 snew(vout, nind)(vout) = save_calloc("vout", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c"
, 360, (nind), sizeof(*(vout)));
361 for (i = 0; i < nind; i++)
362 {
363 copy_rvec(fr->v[ind[i]], vout[i]);
364 }
365 }
366 if (fr->bF)
367 {
368 snew(fout, nind)(fout) = save_calloc("fout", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c"
, 368, (nind), sizeof(*(fout)));
369 for (i = 0; i < nind; i++)
370 {
371 copy_rvec(fr->f[ind[i]], fout[i]);
372 }
373 }
374 /* no break */
375 case efXTC:
376 if (fr->bX)
377 {
378 snew(xout, nind)(xout) = save_calloc("xout", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c"
, 378, (nind), sizeof(*(xout)));
379 for (i = 0; i < nind; i++)
380 {
381 copy_rvec(fr->x[ind[i]], xout[i]);
382 }
383 }
384 break;
385 default:
386 break;
387 }
388
389 switch (ftp)
390 {
391 case efTNG:
392 gmx_write_tng_from_trxframe(status->tng, fr, nind);
393 break;
394 case efXTC:
395 write_xtc(status->fio, nind, fr->step, fr->time, fr->box, xout, prec);
396 break;
397 case efTRJ:
398 case efTRR:
399 fwrite_trn(status->fio, nframes_read(status),
400 fr->time, fr->step, fr->box, nind, xout, vout, fout);
401 break;
402 case efGRO:
403 case efPDB:
404 case efBRK:
405 case efENT:
406 if (!fr->bAtoms)
407 {
408 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c",
408, "Can not write a %s file without atom names",
409 ftp2ext(ftp));
410 }
411 sprintf(title, "frame t= %.3f", fr->time);
412 if (ftp == efGRO)
413 {
414 write_hconf_indexed_p(gmx_fio_getfp(status->fio), title, fr->atoms, nind, ind,
415 prec2ndec(prec),
416 fr->x, fr->bV ? fr->v : NULL((void*)0), fr->box);
417 }
418 else
419 {
420 write_pdbfile_indexed(gmx_fio_getfp(status->fio), title, fr->atoms,
421 fr->x, -1, fr->box, ' ', fr->step, nind, ind, gc, TRUE1);
422 }
423 break;
424 case efG96:
425 write_g96_conf(gmx_fio_getfp(status->fio), fr, nind, ind);
426 break;
427 default:
428 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c",
428, "Sorry, write_trxframe_indexed can not write %s",
429 ftp2ext(ftp));
430 break;
431 }
432
433 switch (ftp)
434 {
435 case efTRN:
436 case efTRJ:
437 case efTRR:
438 case efTNG:
439 if (vout)
440 {
441 sfree(vout)save_free("vout", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c"
, 441, (vout));
442 }
443 if (fout)
444 {
445 sfree(fout)save_free("fout", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c"
, 445, (fout));
446 }
447 /* no break */
448 case efXTC:
449 sfree(xout)save_free("xout", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c"
, 449, (xout));
450 break;
451 default:
452 break;
453 }
454
455 return 0;
456}
457
458void trjtools_gmx_prepare_tng_writing(const char *filename,
459 char filemode,
460 t_trxstatus *in,
461 t_trxstatus **out,
462 const char *infile,
463 const int natoms,
464 const gmx_mtop_t *mtop,
465 const atom_id *index,
466 const char *index_group_name)
467{
468 if (filemode != 'w' && filemode != 'a')
469 {
470 gmx_incons("Sorry, can only prepare for TNG output.")_gmx_error("incons", "Sorry, can only prepare for TNG output."
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c", 470
);
471 }
472
473 if (*out == NULL((void*)0))
474 {
475 snew((*out), 1)((*out)) = save_calloc("(*out)", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c"
, 475, (1), sizeof(*((*out))));
476 }
477 status_init(*out);
478
479 if (in != NULL((void*)0))
480 {
481 gmx_prepare_tng_writing(filename,
482 filemode,
483 &in->tng,
484 &(*out)->tng,
485 natoms,
486 mtop,
487 index,
488 index_group_name);
489 }
490 else if (efTNG == fn2ftp(infile))
491 {
492 tng_trajectory_t tng_in;
493 gmx_tng_open(infile, 'r', &tng_in);
494
495 gmx_prepare_tng_writing(filename,
496 filemode,
497 &tng_in,
498 &(*out)->tng,
499 natoms,
500 mtop,
501 index,
502 index_group_name);
503 }
504}
505
506void write_tng_frame(t_trxstatus *status,
507 t_trxframe *frame)
508{
509 gmx_write_tng_from_trxframe(status->tng, frame, -1);
510}
511
512int write_trxframe(t_trxstatus *status, t_trxframe *fr, gmx_conect gc)
513{
514 char title[STRLEN4096];
515 real prec;
516
517 if (fr->bPrec)
518 {
519 prec = fr->prec;
520 }
521 else
522 {
523 prec = 1000.0;
524 }
525
526 if (status->tng)
527 {
528 gmx_tng_set_compression_precision(status->tng, prec);
529 write_tng_frame(status, fr);
530
531 return 0;
532 }
533
534 switch (gmx_fio_getftp(status->fio))
535 {
536 case efTRJ:
537 case efTRR:
538 break;
539 default:
540 if (!fr->bX)
541 {
542 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c",
542, "Need coordinates to write a %s trajectory",
543 ftp2ext(gmx_fio_getftp(status->fio)));
544 }
545 break;
546 }
547
548 switch (gmx_fio_getftp(status->fio))
549 {
550 case efXTC:
551 write_xtc(status->fio, fr->natoms, fr->step, fr->time, fr->box, fr->x, prec);
552 break;
553 case efTRJ:
554 case efTRR:
555 fwrite_trn(status->fio, fr->step, fr->time, fr->lambda, fr->box, fr->natoms,
556 fr->bX ? fr->x : NULL((void*)0), fr->bV ? fr->v : NULL((void*)0), fr->bF ? fr->f : NULL((void*)0));
557 break;
558 case efGRO:
559 case efPDB:
560 case efBRK:
561 case efENT:
562 if (!fr->bAtoms)
563 {
564 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c",
564, "Can not write a %s file without atom names",
565 ftp2ext(gmx_fio_getftp(status->fio)));
566 }
567 sprintf(title, "frame t= %.3f", fr->time);
568 if (gmx_fio_getftp(status->fio) == efGRO)
569 {
570 write_hconf_p(gmx_fio_getfp(status->fio), title, fr->atoms,
571 prec2ndec(prec), fr->x, fr->bV ? fr->v : NULL((void*)0), fr->box);
572 }
573 else
574 {
575 write_pdbfile(gmx_fio_getfp(status->fio), title,
576 fr->atoms, fr->x, fr->bPBC ? fr->ePBC : -1, fr->box,
577 ' ', fr->step, gc, TRUE1);
578 }
579 break;
580 case efG96:
581 write_g96_conf(gmx_fio_getfp(status->fio), fr, -1, NULL((void*)0));
582 break;
583 default:
584 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c",
584, "Sorry, write_trxframe can not write %s",
585 ftp2ext(gmx_fio_getftp(status->fio)));
586 break;
587 }
588
589 return 0;
590}
591
592int write_trx(t_trxstatus *status, int nind, const atom_id *ind, t_atoms *atoms,
593 int step, real time, matrix box, rvec x[], rvec *v,
594 gmx_conect gc)
595{
596 t_trxframe fr;
597
598 clear_trxframe(&fr, TRUE1);
599 fr.bStep = TRUE1;
600 fr.step = step;
601 fr.bTime = TRUE1;
602 fr.time = time;
603 fr.bAtoms = atoms != NULL((void*)0);
604 fr.atoms = atoms;
605 fr.bX = TRUE1;
606 fr.x = x;
607 fr.bV = v != NULL((void*)0);
608 fr.v = v;
609 fr.bBox = TRUE1;
610 copy_mat(box, fr.box);
611
612 return write_trxframe_indexed(status, &fr, nind, ind, gc);
613}
614
615void close_trx(t_trxstatus *status)
616{
617 gmx_tng_close(&status->tng);
618 if (status->fio)
619 {
620 gmx_fio_close(status->fio);
621 }
622 sfree(status)save_free("status", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c"
, 622, (status));
623}
624
625t_trxstatus *open_trx(const char *outfile, const char *filemode)
626{
627 t_trxstatus *stat;
628 if (filemode[0] != 'w' && filemode[0] != 'a' && filemode[1] != '+')
629 {
630 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c",
630, "Sorry, write_trx can only write");
631 }
632
633 snew(stat, 1)(stat) = save_calloc("stat", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c"
, 633, (1), sizeof(*(stat)));
634 status_init(stat);
635
636 stat->fio = gmx_fio_open(outfile, filemode);
637 return stat;
638}
639
640static gmx_bool gmx_next_frame(t_trxstatus *status, t_trxframe *fr)
641{
642 t_trnheader sh;
643 gmx_bool bOK, bRet;
644
645 bRet = FALSE0;
646
647 if (fread_trnheader(status->fio, &sh, &bOK))
648 {
649 fr->bDouble = sh.bDouble;
650 fr->natoms = sh.natoms;
651 fr->bStep = TRUE1;
652 fr->step = sh.step;
653 fr->bTime = TRUE1;
654 fr->time = sh.t;
655 fr->bLambda = TRUE1;
656 fr->bFepState = TRUE1;
657 fr->lambda = sh.lambda;
658 fr->bBox = sh.box_size > 0;
659 if (fr->flags & (TRX_READ_X(1<<0) | TRX_NEED_X(1<<1)))
660 {
661 if (fr->x == NULL((void*)0))
662 {
663 snew(fr->x, sh.natoms)(fr->x) = save_calloc("fr->x", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c"
, 663, (sh.natoms), sizeof(*(fr->x)));
664 }
665 fr->bX = sh.x_size > 0;
666 }
667 if (fr->flags & (TRX_READ_V(1<<2) | TRX_NEED_V(1<<3)))
668 {
669 if (fr->v == NULL((void*)0))
670 {
671 snew(fr->v, sh.natoms)(fr->v) = save_calloc("fr->v", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c"
, 671, (sh.natoms), sizeof(*(fr->v)));
672 }
673 fr->bV = sh.v_size > 0;
674 }
675 if (fr->flags & (TRX_READ_F(1<<4) | TRX_NEED_F(1<<5)))
676 {
677 if (fr->f == NULL((void*)0))
678 {
679 snew(fr->f, sh.natoms)(fr->f) = save_calloc("fr->f", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c"
, 679, (sh.natoms), sizeof(*(fr->f)));
680 }
681 fr->bF = sh.f_size > 0;
682 }
683 if (fread_htrn(status->fio, &sh, fr->box, fr->x, fr->v, fr->f))
684 {
685 bRet = TRUE1;
686 }
687 else
688 {
689 fr->not_ok = DATA_NOT_OK(1<<1);
690 }
691 }
692 else
693 if (!bOK)
694 {
695 fr->not_ok = HEADER_NOT_OK(1<<0);
696 }
697
698 return bRet;
699}
700
701static gmx_bool pdb_next_x(t_trxstatus *status, FILE *fp, t_trxframe *fr)
702{
703 t_atoms atoms;
704 matrix boxpdb;
705 int ePBC, model_nr, na;
706 char title[STRLEN4096], *time;
707 double dbl;
708
709 atoms.nr = fr->natoms;
710 atoms.atom = NULL((void*)0);
711 atoms.pdbinfo = NULL((void*)0);
712 /* the other pointers in atoms should not be accessed if these are NULL */
713 model_nr = NOTSET-12345;
714 na = read_pdbfile(fp, title, &model_nr, &atoms, fr->x, &ePBC, boxpdb, TRUE1, NULL((void*)0));
715 set_trxframe_ePBC(fr, ePBC);
716 if (nframes_read(status) == 0)
717 {
718 fprintf(stderrstderr, " '%s', %d atoms\n", title, fr->natoms);
719 }
720 fr->bPrec = TRUE1;
721 fr->prec = 10000;
722 fr->bX = TRUE1;
723 fr->bBox = (boxpdb[XX0][XX0] != 0.0);
724 if (fr->bBox)
725 {
726 copy_mat(boxpdb, fr->box);
727 }
728
729 if (model_nr != NOTSET-12345)
730 {
731 fr->bStep = TRUE1;
732 fr->step = model_nr;
733 }
734 time = strstr(title, " t= ");
735 if (time)
736 {
737 fr->bTime = TRUE1;
738 sscanf(time+4, "%lf", &dbl);
739 fr->time = (real)dbl;
740 }
741 else
742 {
743 fr->bTime = FALSE0;
744 /* this is a bit dirty, but it will work: if no time is read from
745 comment line in pdb file, set time to current frame number */
746 if (fr->bStep)
747 {
748 fr->time = (real)fr->step;
749 }
750 else
751 {
752 fr->time = (real)nframes_read(status);
753 }
754 }
755 if (na == 0)
756 {
757 return FALSE0;
758 }
759 else
760 {
761 if (na != fr->natoms)
762 {
763 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c",
763, "Number of atoms in pdb frame %d is %d instead of %d",
764 nframes_read(status), na, fr->natoms);
765 }
766 return TRUE1;
767 }
768}
769
770static int pdb_first_x(t_trxstatus *status, FILE *fp, t_trxframe *fr)
771{
772 initcount(status);
773
774 fprintf(stderrstderr, "Reading frames from pdb file");
775 frewind(fp);
776 get_pdb_coordnum(fp, &fr->natoms);
777 if (fr->natoms == 0)
778 {
779 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c",
779, "\nNo coordinates in pdb file\n");
780 }
781 frewind(fp);
782 snew(fr->x, fr->natoms)(fr->x) = save_calloc("fr->x", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c"
, 782, (fr->natoms), sizeof(*(fr->x)));
783 pdb_next_x(status, fp, fr);
784
785 return fr->natoms;
786}
787
788gmx_bool read_next_frame(const output_env_t oenv, t_trxstatus *status, t_trxframe *fr)
789{
790 real pt;
791 int ct;
792 gmx_bool bOK, bRet, bMissingData = FALSE0, bSkip = FALSE0;
793 int dummy = 0;
794 int ftp;
795
796 bRet = FALSE0;
797 pt = fr->time;
798
799 do
800 {
801 clear_trxframe(fr, FALSE0);
802 fr->tppf = fr->tpf;
803 fr->tpf = fr->time;
804
805 if (status->tng)
806 {
807 /* Special treatment for TNG files */
808 ftp = efTNG;
809 }
810 else
811 {
812 ftp = gmx_fio_getftp(status->fio);
813 }
814 switch (ftp)
815 {
816 case efTRJ:
817 case efTRR:
818 bRet = gmx_next_frame(status, fr);
819 break;
820 case efCPT:
821 /* Checkpoint files can not contain mulitple frames */
822 break;
823 case efG96:
824 read_g96_conf(gmx_fio_getfp(status->fio), NULL((void*)0), fr,
825 status->persistent_line);
826 bRet = (fr->natoms > 0);
827 break;
828 case efXTC:
829 /* B. Hess 2005-4-20
830 * Sometimes is off by one frame
831 * and sometimes reports frame not present/file not seekable
832 */
833 /* DvdS 2005-05-31: this has been fixed along with the increased
834 * accuracy of the control over -b and -e options.
835 */
836 if (bTimeSet(TBEGIN) && (fr->time < rTimeValue(TBEGIN)))
837 {
838 if (xtc_seek_time(status->fio, rTimeValue(TBEGIN), fr->natoms, TRUE1))
839 {
840 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c",
840, "Specified frame (time %f) doesn't exist or file corrupt/inconsistent.",
841 rTimeValue(TBEGIN));
842 }
843 initcount(status);
844 }
845 bRet = read_next_xtc(status->fio, fr->natoms, &fr->step, &fr->time, fr->box,
846 fr->x, &fr->prec, &bOK);
847 fr->bPrec = (bRet && fr->prec > 0);
848 fr->bStep = bRet;
849 fr->bTime = bRet;
850 fr->bX = bRet;
851 fr->bBox = bRet;
852 if (!bOK)
853 {
854 /* Actually the header could also be not ok,
855 but from bOK from read_next_xtc this can't be distinguished */
856 fr->not_ok = DATA_NOT_OK(1<<1);
857 }
858 break;
859 case efTNG:
860 bRet = gmx_read_next_tng_frame(status->tng, fr, NULL((void*)0), 0);
861 break;
862 case efPDB:
863 bRet = pdb_next_x(status, gmx_fio_getfp(status->fio), fr);
864 break;
865 case efGRO:
866 bRet = gro_next_x_or_v(gmx_fio_getfp(status->fio), fr);
867 break;
868 default:
869#ifdef GMX_USE_PLUGINS
870 bRet = read_next_vmd_frame(fr);
871#else
872 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c",
872, "DEATH HORROR in read_next_frame ftp=%s,status=%s",
873 ftp2ext(gmx_fio_getftp(status->fio)),
874 gmx_fio_getname(status->fio));
875#endif
876 }
877
878 if (bRet)
879 {
880 bMissingData = (((fr->flags & TRX_NEED_X(1<<1)) && !fr->bX) ||
881 ((fr->flags & TRX_NEED_V(1<<3)) && !fr->bV) ||
882 ((fr->flags & TRX_NEED_F(1<<5)) && !fr->bF));
883 bSkip = FALSE0;
884 if (!bMissingData)
885 {
886 ct = check_times2(fr->time, fr->t0, fr->bDouble);
887 if (ct == 0 || ((fr->flags & TRX_DONT_SKIP(1<<6)) && ct < 0))
888 {
889 printcount(status, oenv, fr->time, FALSE0);
890 }
891 else if (ct > 0)
892 {
893 bRet = FALSE0;
894 }
895 else
896 {
897 printcount(status, oenv, fr->time, TRUE1);
898 bSkip = TRUE1;
899 }
900 }
901 }
902
903 }
904 while (bRet && (bMissingData || bSkip));
905
906 if (!bRet)
907 {
908 printlast(status, oenv, pt);
909 if (fr->not_ok)
910 {
911 printincomp(status, fr);
912 }
913 }
914
915 return bRet;
916}
917
918int read_first_frame(const output_env_t oenv, t_trxstatus **status,
919 const char *fn, t_trxframe *fr, int flags)
920{
921 t_fileio *fio;
922 gmx_bool bFirst, bOK;
923 int dummy = 0;
924 int ftp = fn2ftp(fn);
925 gmx_int64_t *tng_ids;
926
927 clear_trxframe(fr, TRUE1);
928 fr->flags = flags;
929
930 bFirst = TRUE1;
931
932 snew((*status), 1)((*status)) = save_calloc("(*status)", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c"
, 932, (1), sizeof(*((*status))));
933
934 status_init( *status );
935 (*status)->nxframe = 1;
936 initcount(*status);
937
938 if (efTNG == ftp)
939 {
940 /* Special treatment for TNG files */
941 gmx_tng_open(fn, 'r', &(*status)->tng);
942 }
943 else
944 {
945 fio = (*status)->fio = gmx_fio_open(fn, "r");
946 }
947 switch (ftp)
948 {
949 case efTRJ:
950 case efTRR:
951 break;
952 case efCPT:
953 read_checkpoint_trxframe(fio, fr);
954 bFirst = FALSE0;
955 break;
956 case efG96:
957 /* Can not rewind a compressed file, so open it twice */
958 if (!(*status)->persistent_line)
959 {
960 /* allocate the persistent line */
961 snew((*status)->persistent_line, STRLEN+1)((*status)->persistent_line) = save_calloc("(*status)->persistent_line"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c", 961
, (4096 +1), sizeof(*((*status)->persistent_line)));
962 }
963 read_g96_conf(gmx_fio_getfp(fio), fn, fr, (*status)->persistent_line);
964 gmx_fio_close(fio);
965 clear_trxframe(fr, FALSE0);
966 if (flags & (TRX_READ_X(1<<0) | TRX_NEED_X(1<<1)))
967 {
968 snew(fr->x, fr->natoms)(fr->x) = save_calloc("fr->x", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c"
, 968, (fr->natoms), sizeof(*(fr->x)));
969 }
970 if (flags & (TRX_READ_V(1<<2) | TRX_NEED_V(1<<3)))
971 {
972 snew(fr->v, fr->natoms)(fr->v) = save_calloc("fr->v", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c"
, 972, (fr->natoms), sizeof(*(fr->v)));
973 }
974 fio = (*status)->fio = gmx_fio_open(fn, "r");
Value stored to 'fio' is never read
975 break;
976 case efXTC:
977 if (read_first_xtc(fio, &fr->natoms, &fr->step, &fr->time, fr->box, &fr->x,
978 &fr->prec, &bOK) == 0)
979 {
980 assert(!bOK)((void) (0));
981 fr->not_ok = DATA_NOT_OK(1<<1);
982 }
983 if (fr->not_ok)
984 {
985 fr->natoms = 0;
986 printincomp(*status, fr);
987 }
988 else
989 {
990 fr->bPrec = (fr->prec > 0);
991 fr->bStep = TRUE1;
992 fr->bTime = TRUE1;
993 fr->bX = TRUE1;
994 fr->bBox = TRUE1;
995 printcount(*status, oenv, fr->time, FALSE0);
996 }
997 bFirst = FALSE0;
998 break;
999 case efTNG:
1000 fr->step = -1;
1001 if (!gmx_read_next_tng_frame((*status)->tng, fr, NULL((void*)0), 0))
1002 {
1003 fr->not_ok = DATA_NOT_OK(1<<1);
1004 fr->natoms = 0;
1005 printincomp(*status, fr);
1006 }
1007 else
1008 {
1009 printcount(*status, oenv, fr->time, FALSE0);
1010 }
1011 bFirst = FALSE0;
1012 break;
1013 case efPDB:
1014 pdb_first_x(*status, gmx_fio_getfp(fio), fr);
1015 if (fr->natoms)
1016 {
1017 printcount(*status, oenv, fr->time, FALSE0);
1018 }
1019 bFirst = FALSE0;
1020 break;
1021 case efGRO:
1022 if (gro_first_x_or_v(gmx_fio_getfp(fio), fr))
1023 {
1024 printcount(*status, oenv, fr->time, FALSE0);
1025 }
1026 bFirst = FALSE0;
1027 break;
1028 default:
1029#ifdef GMX_USE_PLUGINS
1030 fprintf(stderrstderr, "The file format of %s is not a known trajectory format to GROMACS.\n"
1031 "Please make sure that the file is a trajectory!\n"
1032 "GROMACS will now assume it to be a trajectory and will try to open it using the VMD plug-ins.\n"
1033 "This will only work in case the VMD plugins are found and it is a trajectory format supported by VMD.\n", fn);
1034 gmx_fio_fp_close(fio); /*only close the file without removing FIO entry*/
1035 if (!read_first_vmd_frame(fn, fr))
1036 {
1037 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c",
1037, "Not supported in read_first_frame: %s", fn);
1038 }
1039#else
1040 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c",
1040, "Not supported in read_first_frame: %s. Please make sure that the file is a trajectory.\n"
1041 "GROMACS is not compiled with plug-in support. Thus it cannot read non-GROMACS trajectory formats using the VMD plug-ins.\n"
1042 "Please compile with plug-in support if you want to read non-GROMACS trajectory formats.\n", fn);
1043#endif
1044 break;
1045 }
1046
1047 /* Return FALSE if we read a frame that's past the set ending time. */
1048 if (!bFirst && (!(fr->flags & TRX_DONT_SKIP(1<<6)) && check_times(fr->time) > 0))
1049 {
1050 fr->t0 = fr->time;
1051 return FALSE0;
1052 }
1053
1054 if (bFirst ||
1055 (!(fr->flags & TRX_DONT_SKIP(1<<6)) && check_times(fr->time) < 0))
1056 {
1057 /* Read a frame when no frame was read or the first was skipped */
1058 if (!read_next_frame(oenv, *status, fr))
1059 {
1060 return FALSE0;
1061 }
1062 }
1063 fr->t0 = fr->time;
1064
1065 return (fr->natoms > 0);
1066}
1067
1068/***** C O O R D I N A T E S T U F F *****/
1069
1070int read_first_x(const output_env_t oenv, t_trxstatus **status, const char *fn,
1071 real *t, rvec **x, matrix box)
1072{
1073 t_trxframe fr;
1074
1075 read_first_frame(oenv, status, fn, &fr, TRX_NEED_X(1<<1));
1076
1077 snew((*status)->xframe, 1)((*status)->xframe) = save_calloc("(*status)->xframe", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c"
, 1077, (1), sizeof(*((*status)->xframe)));
1078 (*status)->nxframe = 1;
1079 (*(*status)->xframe) = fr;
1080 *t = (*status)->xframe->time;
1081 *x = (*status)->xframe->x;
1082 copy_mat((*status)->xframe->box, box);
1083
1084 return (*status)->xframe->natoms;
1085}
1086
1087gmx_bool read_next_x(const output_env_t oenv, t_trxstatus *status, real *t,
1088 rvec x[], matrix box)
1089{
1090 gmx_bool bRet;
1091
1092 status->xframe->x = x;
1093 /*xframe[status].x = x;*/
1094 bRet = read_next_frame(oenv, status, status->xframe);
1095 *t = status->xframe->time;
1096 copy_mat(status->xframe->box, box);
1097
1098 return bRet;
1099}
1100
1101void close_trj(t_trxstatus *status)
1102{
1103 gmx_tng_close(&status->tng);
1104 if (status->fio)
1105 {
1106 gmx_fio_close(status->fio);
1107 }
1108
1109 /* The memory in status->xframe is lost here,
1110 * but the read_first_x/read_next_x functions are deprecated anyhow.
1111 * read_first_frame/read_next_frame and close_trx should be used.
1112 */
1113 sfree(status)save_free("status", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c"
, 1113, (status));
1114}
1115
1116void rewind_trj(t_trxstatus *status)
1117{
1118 initcount(status);
1119
1120 gmx_fio_rewind(status->fio);
1121}
1122
1123/***** T O P O L O G Y S T U F F ******/
1124
1125t_topology *read_top(const char *fn, int *ePBC)
1126{
1127 int epbc, natoms;
1128 t_topology *top;
1129
1130 snew(top, 1)(top) = save_calloc("top", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c"
, 1130, (1), sizeof(*(top)));
1131 epbc = read_tpx_top(fn, NULL((void*)0), NULL((void*)0), &natoms, NULL((void*)0), NULL((void*)0), NULL((void*)0), top);
1132 if (ePBC)
1133 {
1134 *ePBC = epbc;
1135 }
1136
1137 return top;
1138}