Bug Summary

File:gromacs/gmxana/gmx_trjcat.c
Location:line 603, column 9
Description:Function call argument is an uninitialized value

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 <math.h>
42#include <stdlib.h>
43#include <string.h>
44
45#include "macros.h"
46#include "gromacs/utility/smalloc.h"
47#include "typedefs.h"
48#include "gromacs/fileio/gmxfio.h"
49#include "gromacs/fileio/tpxio.h"
50#include "gromacs/fileio/trxio.h"
51#include "gromacs/fileio/trnio.h"
52#include "gromacs/fileio/tngio.h"
53#include "gromacs/fileio/tngio_for_tools.h"
54#include "gromacs/commandline/pargs.h"
55#include "gromacs/utility/futil.h"
56#include "gromacs/fileio/pdbio.h"
57#include "gromacs/fileio/confio.h"
58#include "names.h"
59#include "index.h"
60#include "gromacs/math/vec.h"
61#include "gromacs/fileio/xtcio.h"
62#include "rmpbc.h"
63#include "pbc.h"
64#include "gromacs/fileio/xvgr.h"
65#include "gmx_ana.h"
66
67#include "gromacs/utility/fatalerror.h"
68
69#define TIME_EXPLICIT0 0
70#define TIME_CONTINUE1 1
71#define TIME_LAST2 2
72#ifndef FLT_MAX1e36
73#define FLT_MAX1e36 1e36
74#endif
75#define FLAGS((1<<0) | (1<<2) | (1<<4)) (TRX_READ_X(1<<0) | TRX_READ_V(1<<2) | TRX_READ_F(1<<4))
76
77static void scan_trj_files(char **fnms, int nfiles, real *readtime,
78 real *timestep, atom_id imax,
79 const output_env_t oenv)
80{
81 /* Check start time of all files */
82 int i, natoms = 0;
83 t_trxstatus *status;
84 real t;
85 t_trxframe fr;
86 gmx_bool ok;
87
88 for (i = 0; i < nfiles; i++)
89 {
90 ok = read_first_frame(oenv, &status, fnms[i], &fr, FLAGS((1<<0) | (1<<2) | (1<<4)));
91
92 if (!ok)
93 {
94 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 94, "\nCouldn't read frame from file." );
95 }
96 if (fr.bTime)
97 {
98 readtime[i] = fr.time;
99 }
100 else
101 {
102 readtime[i] = 0;
103 fprintf(stderrstderr, "\nWARNING: Couldn't find a time in the frame.\n");
104 }
105
106 if (i == 0)
107 {
108 natoms = fr.natoms;
109 }
110 else
111 {
112 if (imax == NO_ATID(atom_id)(~0))
113 {
114 if (natoms != fr.natoms)
115 {
116 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 116, "\nDifferent numbers of atoms (%d/%d) in files",
117 natoms, fr.natoms);
118 }
119 }
120 else
121 {
122 if (fr.natoms <= imax)
123 {
124 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 124, "\nNot enough atoms (%d) for index group (%d)",
125 fr.natoms, imax);
126 }
127 }
128 }
129 ok = read_next_frame(oenv, status, &fr);
130 if (ok && fr.bTime)
131 {
132 timestep[i] = fr.time - readtime[i];
133 }
134 else
135 {
136 timestep[i] = 0;
137 }
138
139 close_trj(status);
140 if (fr.bX)
141 {
142 sfree(fr.x)save_free("fr.x", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 142, (fr.x));
143 }
144 if (fr.bV)
145 {
146 sfree(fr.v)save_free("fr.v", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 146, (fr.v));
147 }
148 if (fr.bF)
149 {
150 sfree(fr.f)save_free("fr.f", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 150, (fr.f));
151 }
152 }
153 fprintf(stderrstderr, "\n");
154
155}
156
157static void sort_files(char **fnms, real *settime, int nfile)
158{
159 int i, j, minidx;
160 real timeswap;
161 char *chptr;
162
163 for (i = 0; i < nfile; i++)
164 {
165 minidx = i;
166 for (j = i + 1; j < nfile; j++)
167 {
168 if (settime[j] < settime[minidx])
169 {
170 minidx = j;
171 }
172 }
173 if (minidx != i)
174 {
175 timeswap = settime[i];
176 settime[i] = settime[minidx];
177 settime[minidx] = timeswap;
178 chptr = fnms[i];
179 fnms[i] = fnms[minidx];
180 fnms[minidx] = chptr;
181 }
182 }
183}
184
185static void edit_files(char **fnms, int nfiles, real *readtime, real *timestep,
186 real *settime, int *cont_type, gmx_bool bSetTime,
187 gmx_bool bSort, const output_env_t oenv)
188{
189 int i;
190 gmx_bool ok;
191 char inputstring[STRLEN4096], *chptr;
192
193 if (bSetTime)
194 {
195 fprintf(stderrstderr, "\n\nEnter the new start time (%s) for each file.\n"
196 "There are two special options, both disable sorting:\n\n"
197 "c (continue) - The start time is taken from the end\n"
198 "of the previous file. Use it when your continuation run\n"
199 "restarts with t=0.\n\n"
200 "l (last) - The time in this file will be changed the\n"
201 "same amount as in the previous. Use it when the time in the\n"
202 "new run continues from the end of the previous one,\n"
203 "since this takes possible overlap into account.\n\n",
204 output_env_get_time_unit(oenv));
205
206 fprintf(
207 stderrstderr,
208 " File Current start (%s) New start (%s)\n"
209 "---------------------------------------------------------\n",
210 output_env_get_time_unit(oenv), output_env_get_time_unit(oenv));
211
212 for (i = 0; i < nfiles; i++)
213 {
214 fprintf(stderrstderr, "%25s %10.3f %s ", fnms[i],
215 output_env_conv_time(oenv, readtime[i]), output_env_get_time_unit(oenv));
216 ok = FALSE0;
217 do
218 {
219 if (NULL((void*)0) == fgets(inputstring, STRLEN4096 - 1, stdinstdin))
220 {
221 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 221, "Error reading user input" );
222 }
223
224 inputstring[strlen(inputstring)-1] = 0;
225
226 if (inputstring[0] == 'c' || inputstring[0] == 'C')
227 {
228 cont_type[i] = TIME_CONTINUE1;
229 bSort = FALSE0;
230 ok = TRUE1;
231 settime[i] = FLT_MAX1e36;
232 }
233 else if (inputstring[0] == 'l' ||
234 inputstring[0] == 'L')
235 {
236 cont_type[i] = TIME_LAST2;
237 bSort = FALSE0;
238 ok = TRUE1;
239 settime[i] = FLT_MAX1e36;
240 }
241 else
242 {
243 settime[i] = strtod(inputstring, &chptr)*
244 output_env_get_time_invfactor(oenv);
245 if (chptr == inputstring)
246 {
247 fprintf(stderrstderr, "'%s' not recognized as a floating point number, 'c' or 'l'. "
248 "Try again: ", inputstring);
249 }
250 else
251 {
252 cont_type[i] = TIME_EXPLICIT0;
253 ok = TRUE1;
254 }
255 }
256 }
257 while (!ok);
258 }
259 if (cont_type[0] != TIME_EXPLICIT0)
260 {
261 cont_type[0] = TIME_EXPLICIT0;
262 settime[0] = 0;
263 }
264 }
265 else
266 {
267 for (i = 0; i < nfiles; i++)
268 {
269 settime[i] = readtime[i];
270 }
271 }
272 if (!bSort)
273 {
274 fprintf(stderrstderr, "Sorting disabled.\n");
275 }
276 else
277 {
278 sort_files(fnms, settime, nfiles);
279 }
280 /* Write out the new order and start times */
281 fprintf(stderrstderr, "\nSummary of files and start times used:\n\n"
282 " File Start time Time step\n"
283 "---------------------------------------------------------\n");
284 for (i = 0; i < nfiles; i++)
285 {
286 switch (cont_type[i])
287 {
288 case TIME_EXPLICIT0:
289 fprintf(stderrstderr, "%25s %10.3f %s %10.3f %s",
290 fnms[i],
291 output_env_conv_time(oenv, settime[i]), output_env_get_time_unit(oenv),
292 output_env_conv_time(oenv, timestep[i]), output_env_get_time_unit(oenv));
293 if (i > 0 &&
294 cont_type[i-1] == TIME_EXPLICIT0 && settime[i] == settime[i-1])
295 {
296 fprintf(stderrstderr, " WARNING: same Start time as previous");
297 }
298 fprintf(stderrstderr, "\n");
299 break;
300 case TIME_CONTINUE1:
301 fprintf(stderrstderr, "%25s Continue from last file\n", fnms[i]);
302 break;
303 case TIME_LAST2:
304 fprintf(stderrstderr, "%25s Change by same amount as last file\n",
305 fnms[i]);
306 break;
307 }
308 }
309 fprintf(stderrstderr, "\n");
310
311 settime[nfiles] = FLT_MAX1e36;
312 cont_type[nfiles] = TIME_EXPLICIT0;
313 readtime[nfiles] = FLT_MAX1e36;
314}
315
316static void do_demux(int nset, char *fnms[], char *fnms_out[], int nval,
317 real **value, real *time, real dt_remd, int isize,
318 atom_id index[], real dt, const output_env_t oenv)
319{
320 int i, j, k, natoms, nnn;
321 t_trxstatus **fp_in, **fp_out;
322 gmx_bool bCont, *bSet;
323 real t, first_time = 0;
324 t_trxframe *trx;
325
326 snew(fp_in, nset)(fp_in) = save_calloc("fp_in", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 326, (nset), sizeof(*(fp_in)));
327 snew(trx, nset)(trx) = save_calloc("trx", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 327, (nset), sizeof(*(trx)));
328 snew(bSet, nset)(bSet) = save_calloc("bSet", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 328, (nset), sizeof(*(bSet)));
329 natoms = -1;
330 t = -1;
331 for (i = 0; (i < nset); i++)
332 {
333 nnn = read_first_frame(oenv, &(fp_in[i]), fnms[i], &(trx[i]),
334 TRX_NEED_X(1<<1));
335 if (natoms == -1)
336 {
337 natoms = nnn;
338 first_time = trx[i].time;
339 }
340 else if (natoms != nnn)
341 {
342 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 342, "Trajectory file %s has %d atoms while previous trajs had %d atoms", fnms[i], nnn, natoms);
343 }
344 if (t == -1)
345 {
346 t = trx[i].time;
347 }
348 else if (t != trx[i].time)
349 {
350 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 350, "Trajectory file %s has time %f while previous trajs had time %f", fnms[i], trx[i].time, t);
351 }
352 }
353
354 snew(fp_out, nset)(fp_out) = save_calloc("fp_out", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 354, (nset), sizeof(*(fp_out)));
355 for (i = 0; (i < nset); i++)
356 {
357 fp_out[i] = open_trx(fnms_out[i], "w");
358 }
359 k = 0;
360 if (gmx_nint(time[k] - t) != 0)
361 {
362 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 362, "First time in demuxing table does not match trajectories");
363 }
364 do
365 {
366 while ((k+1 < nval) && ((trx[0].time - time[k+1]) > dt_remd*0.1))
367 {
368 k++;
369 }
370 if (debug)
371 {
372 fprintf(debug, "trx[0].time = %g, time[k] = %g\n", trx[0].time, time[k]);
373 }
374 for (i = 0; (i < nset); i++)
375 {
376 bSet[i] = FALSE0;
377 }
378 for (i = 0; (i < nset); i++)
379 {
380 j = gmx_nint(value[i][k]);
381 range_check(j, 0, nset)_range_check(j, 0, nset, ((void*)0),"j", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 381);
382 if (bSet[j])
383 {
384 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 384, "Demuxing the same replica %d twice at time %f",
385 j, trx[0].time);
386 }
387 bSet[j] = TRUE1;
388
389 if (dt == 0 || bRmod(trx[i].time, first_time, dt)bRmod_fd(trx[i].time, first_time, dt, 0))
390 {
391 if (index)
392 {
393 write_trxframe_indexed(fp_out[j], &trx[i], isize, index, NULL((void*)0));
394 }
395 else
396 {
397 write_trxframe(fp_out[j], &trx[i], NULL((void*)0));
398 }
399 }
400 }
401
402 bCont = (k < nval);
403 for (i = 0; (i < nset); i++)
404 {
405 bCont = bCont && read_next_frame(oenv, fp_in[i], &trx[i]);
406 }
407 }
408 while (bCont);
409
410 for (i = 0; (i < nset); i++)
411 {
412 close_trx(fp_in[i]);
413 close_trx(fp_out[i]);
414 }
415}
416
417int gmx_trjcat(int argc, char *argv[])
418{
419 const char *desc[] =
420 {
421 "[THISMODULE] concatenates several input trajectory files in sorted order. ",
422 "In case of double time frames the one in the later file is used. ",
423 "By specifying [TT]-settime[tt] you will be asked for the start time ",
424 "of each file. The input files are taken from the command line, ",
425 "such that a command like [TT]gmx trjcat -f *.trr -o fixed.trr[tt] should do ",
426 "the trick. Using [TT]-cat[tt], you can simply paste several files ",
427 "together without removal of frames with identical time stamps.[PAR]",
428 "One important option is inferred when the output file is amongst the",
429 "input files. In that case that particular file will be appended to",
430 "which implies you do not need to store double the amount of data.",
431 "Obviously the file to append to has to be the one with lowest starting",
432 "time since one can only append at the end of a file.[PAR]",
433 "If the [TT]-demux[tt] option is given, the N trajectories that are",
434 "read, are written in another order as specified in the [TT].xvg[tt] file.",
435 "The [TT].xvg[tt] file should contain something like:[PAR]",
436 "[TT]0 0 1 2 3 4 5[BR]",
437 "2 1 0 2 3 5 4[tt][BR]",
438 "Where the first number is the time, and subsequent numbers point to",
439 "trajectory indices.",
440 "The frames corresponding to the numbers present at the first line",
441 "are collected into the output trajectory. If the number of frames in",
442 "the trajectory does not match that in the [TT].xvg[tt] file then the program",
443 "tries to be smart. Beware."
444 };
445 static gmx_bool bVels = TRUE1;
446 static gmx_bool bCat = FALSE0;
447 static gmx_bool bSort = TRUE1;
448 static gmx_bool bKeepLast = FALSE0;
449 static gmx_bool bKeepLastAppend = FALSE0;
450 static gmx_bool bOverwrite = FALSE0;
451 static gmx_bool bSetTime = FALSE0;
452 static gmx_bool bDeMux;
453 static real begin = -1;
454 static real end = -1;
455 static real dt = 0;
456
457 t_pargs
458 pa[] =
459 {
460 { "-b", FALSE0, etTIME,
461 { &begin }, "First time to use (%t)" },
462 { "-e", FALSE0, etTIME,
463 { &end }, "Last time to use (%t)" },
464 { "-dt", FALSE0, etTIME,
465 { &dt }, "Only write frame when t MOD dt = first time (%t)" },
466 { "-vel", FALSE0, etBOOL,
467 { &bVels }, "Read and write velocities if possible" },
468 { "-settime", FALSE0, etBOOL,
469 { &bSetTime }, "Change starting time interactively" },
470 { "-sort", FALSE0, etBOOL,
471 { &bSort }, "Sort trajectory files (not frames)" },
472 { "-keeplast", FALSE0, etBOOL,
473 { &bKeepLast }, "Keep overlapping frames at end of trajectory" },
474 { "-overwrite", FALSE0, etBOOL,
475 { &bOverwrite }, "Overwrite overlapping frames during appending" },
476 { "-cat", FALSE0, etBOOL,
477 { &bCat }, "Do not discard double time frames" }
478 };
479#define npargs((int)(sizeof(pa)/sizeof((pa)[0]))) asize(pa)((int)(sizeof(pa)/sizeof((pa)[0])))
480 int ftpin, i, frame, frame_out, step = 0, trjout = 0;
481 t_trxstatus *status, *trxout = NULL((void*)0);
482 rvec *x, *v;
483 real t_corr;
484 t_trxframe fr, frout;
485 char **fnms, **fnms_out, *in_file, *out_file;
486 int n_append;
487 gmx_bool bNewFile, bIndex, bWrite;
488 int earliersteps, nfile_in, nfile_out, *cont_type, last_ok_step;
489 real *readtime, *timest, *settime;
490 real first_time = 0, lasttime = NOTSET-12345, last_ok_t = -1, timestep;
491 real last_frame_time, searchtime;
492 int isize, j;
1
'isize' declared without an initial value
→
493 atom_id *index = NULL((void*)0), imax;
494 char *grpname;
495 real **val = NULL((void*)0), *t = NULL((void*)0), dt_remd;
496 int n, nset, ftpout = -1, prevEndStep = 0, filetype;
497 gmx_bool bOK;
498 gmx_off_t fpos;
499 output_env_t oenv;
500 t_filenm fnm[] =
501 {
502 { efTRX, "-f", NULL((void*)0), ffRDMULT(1<<1 | 1<<5) },
503 { efTRO, "-o", NULL((void*)0), ffWRMULT(1<<2 | 1<<5) },
504 { efNDX, "-n", "index", ffOPTRD(1<<1 | 1<<3) },
505 { efXVG, "-demux", "remd", ffOPTRD(1<<1 | 1<<3) }
506 };
507
508#define NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))) asize(fnm)((int)(sizeof(fnm)/sizeof((fnm)[0])))
509
510 if (!parse_common_args(&argc, argv, PCA_BE_NICE(1<<13) | PCA_TIME_UNIT(1<<15), NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm,
2
←
Taking false branch
→
511 asize(pa)((int)(sizeof(pa)/sizeof((pa)[0]))), pa, asize(desc)((int)(sizeof(desc)/sizeof((desc)[0]))), desc, 0, NULL((void*)0), &oenv))
512 {
513 return 0;
514 }
515
516 bIndex = ftp2bSet(efNDX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
517 bDeMux = ftp2bSet(efXVG, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
518 bSort = bSort && !bDeMux;
3
←
Assuming 'bDeMux' is not equal to 0
→
519
520 imax = NO_ATID(atom_id)(~0);
521 if (bIndex)
4
←
Assuming 'bIndex' is 0
→
5
←
Taking false branch
→
522 {
523 printf("Select group for output\n");
524 rd_index(ftp2fn(efNDX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), 1, &isize, &index, &grpname);
525 /* scan index */
526 imax = index[0];
527 for (i = 1; i < isize; i++)
528 {
529 imax = max(imax, index[i])(((imax) > (index[i])) ? (imax) : (index[i]) );
530 }
531 }
532 if (bDeMux)
6
←
Taking true branch
→
533 {
534 nset = 0;
535 dt_remd = 0;
536 val = read_xvg_time(opt2fn("-demux", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), TRUE1,
537 opt2parg_bSet("-b", npargs((int)(sizeof(pa)/sizeof((pa)[0]))), pa), begin,
538 opt2parg_bSet("-e", npargs((int)(sizeof(pa)/sizeof((pa)[0]))), pa), end, 1, &nset, &n,
539 &dt_remd, &t);
540 printf("Read %d sets of %d points, dt = %g\n\n", nset, n, dt_remd);
541 if (debug)
7
←
Assuming 'debug' is null
→
8
←
Taking false branch
→
542 {
543 fprintf(debug, "Dump of replica_index.xvg\n");
544 for (i = 0; (i < n); i++)
545 {
546 fprintf(debug, "%10g", t[i]);
547 for (j = 0; (j < nset); j++)
548 {
549 fprintf(debug, " %3d", gmx_nint(val[j][i]));
550 }
551 fprintf(debug, "\n");
552 }
553 }
554 }
555
556 nfile_in = opt2fns(&fnms, "-f", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
557 if (!nfile_in)
9
←
Assuming 'nfile_in' is not equal to 0
→
10
←
Taking false branch
→
558 {
559 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 559, "No input files!" );
560 }
561
562 if (bDeMux && (nfile_in != nset))
11
←
Taking false branch
→
563 {
564 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 564, "You have specified %d files and %d entries in the demux table", nfile_in, nset);
565 }
566
567 ftpin = fn2ftp(fnms[0]);
568
569 for (i = 1; i < nfile_in; i++)
12
←
Assuming 'i' is >= 'nfile_in'
→
13
←
Loop condition is false. Execution continues on line 577
→
570 {
571 if (ftpin != fn2ftp(fnms[i]))
572 {
573 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 573, "All input files must be of the same format");
574 }
575 }
576
577 nfile_out = opt2fns(&fnms_out, "-o", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
578 if (!nfile_out)
14
←
Assuming 'nfile_out' is not equal to 0
→
15
←
Taking false branch
→
579 {
580 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 580, "No output files!");
581 }
582 if ((nfile_out > 1) && !bDeMux)
16
←
Assuming 'nfile_out' is <= 1
→
583 {
584 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 584, "Don't know what to do with more than 1 output file if not demultiplexing");
585 }
586 else if (bDeMux && (nfile_out != nset) && (nfile_out != 1))
587 {
588 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 588, "Number of output files should be 1 or %d (#input files), not %d", nset, nfile_out);
589 }
590 if (bDeMux)
17
←
Taking true branch
→
591 {
592 if (nfile_out != nset)
18
←
Taking false branch
→
593 {
594 char *buf = strdup(fnms_out[0])(__extension__ (__builtin_constant_p (fnms_out[0]) &&
((size_t)(const void *)((fnms_out[0]) + 1) - (size_t)(const void
*)(fnms_out[0]) == 1) ? (((const char *) (fnms_out[0]))[0] ==
'\0' ? (char *) calloc ((size_t) 1, (size_t) 1) : ({ size_t __len
= strlen (fnms_out[0]) + 1; char *__retval = (char *) malloc
(__len); if (__retval != ((void*)0)) __retval = (char *) memcpy
(__retval, fnms_out[0], __len); __retval; })) : __strdup (fnms_out
[0])));
595 snew(fnms_out, nset)(fnms_out) = save_calloc("fnms_out", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 595, (nset), sizeof(*(fnms_out)));
596 for (i = 0; (i < nset); i++)
597 {
598 snew(fnms_out[i], strlen(buf)+32)(fnms_out[i]) = save_calloc("fnms_out[i]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 598, (strlen(buf)+32), sizeof(*(fnms_out[i])));
599 sprintf(fnms_out[i], "%d_%s", i, buf);
600 }
601 sfree(buf)save_free("buf", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 601, (buf));
602 }
603 do_demux(nfile_in, fnms, fnms_out, n, val, t, dt_remd, isize, index, dt, oenv);
19
←
Function call argument is an uninitialized value
604 }
605 else
606 {
607 snew(readtime, nfile_in+1)(readtime) = save_calloc("readtime", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 607, (nfile_in+1), sizeof(*(readtime)));
608 snew(timest, nfile_in+1)(timest) = save_calloc("timest", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 608, (nfile_in+1), sizeof(*(timest)));
609 scan_trj_files(fnms, nfile_in, readtime, timest, imax, oenv);
610
611 snew(settime, nfile_in+1)(settime) = save_calloc("settime", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 611, (nfile_in+1), sizeof(*(settime)));
612 snew(cont_type, nfile_in+1)(cont_type) = save_calloc("cont_type", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 612, (nfile_in+1), sizeof(*(cont_type)));
613 edit_files(fnms, nfile_in, readtime, timest, settime, cont_type, bSetTime, bSort,
614 oenv);
615
616 /* Check whether the output file is amongst the input files
617 * This has to be done after sorting etc.
618 */
619 out_file = fnms_out[0];
620 ftpout = fn2ftp(out_file);
621 n_append = -1;
622 for (i = 0; ((i < nfile_in) && (n_append == -1)); i++)
623 {
624 if (strcmp(fnms[i], out_file)__extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p
(fnms[i]) && __builtin_constant_p (out_file) &&
(__s1_len = strlen (fnms[i]), __s2_len = strlen (out_file), (
!((size_t)(const void *)((fnms[i]) + 1) - (size_t)(const void
*)(fnms[i]) == 1) || __s1_len >= 4) && (!((size_t
)(const void *)((out_file) + 1) - (size_t)(const void *)(out_file
) == 1) || __s2_len >= 4)) ? __builtin_strcmp (fnms[i], out_file
) : (__builtin_constant_p (fnms[i]) && ((size_t)(const
void *)((fnms[i]) + 1) - (size_t)(const void *)(fnms[i]) == 1
) && (__s1_len = strlen (fnms[i]), __s1_len < 4) ?
(__builtin_constant_p (out_file) && ((size_t)(const void
*)((out_file) + 1) - (size_t)(const void *)(out_file) == 1) ?
__builtin_strcmp (fnms[i], out_file) : (__extension__ ({ const
unsigned char *__s2 = (const unsigned char *) (const char *)
(out_file); int __result = (((const unsigned char *) (const char
*) (fnms[i]))[0] - __s2[0]); if (__s1_len > 0 && __result
== 0) { __result = (((const unsigned char *) (const char *) (
fnms[i]))[1] - __s2[1]); if (__s1_len > 1 && __result
== 0) { __result = (((const unsigned char *) (const char *) (
fnms[i]))[2] - __s2[2]); if (__s1_len > 2 && __result
== 0) __result = (((const unsigned char *) (const char *) (fnms
[i]))[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p
(out_file) && ((size_t)(const void *)((out_file) + 1
) - (size_t)(const void *)(out_file) == 1) && (__s2_len
= strlen (out_file), __s2_len < 4) ? (__builtin_constant_p
(fnms[i]) && ((size_t)(const void *)((fnms[i]) + 1) -
(size_t)(const void *)(fnms[i]) == 1) ? __builtin_strcmp (fnms
[i], out_file) : (- (__extension__ ({ const unsigned char *__s2
= (const unsigned char *) (const char *) (fnms[i]); int __result
= (((const unsigned char *) (const char *) (out_file))[0] - __s2
[0]); if (__s2_len > 0 && __result == 0) { __result
= (((const unsigned char *) (const char *) (out_file))[1] - __s2
[1]); if (__s2_len > 1 && __result == 0) { __result
= (((const unsigned char *) (const char *) (out_file))[2] - __s2
[2]); if (__s2_len > 2 && __result == 0) __result =
(((const unsigned char *) (const char *) (out_file))[3] - __s2
[3]); } } __result; })))) : __builtin_strcmp (fnms[i], out_file
)))); }) == 0)
625 {
626 n_append = i;
627 }
628 }
629 if (n_append == 0)
630 {
631 fprintf(stderrstderr, "Will append to %s rather than creating a new file\n",
632 out_file);
633 }
634 else if (n_append != -1)
635 {
636 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 636, "Can only append to the first file which is %s (not %s)",
637 fnms[0], out_file);
638 }
639 earliersteps = 0;
640
641 /* Not checking input format, could be dangerous :-) */
642 /* Not checking output format, equally dangerous :-) */
643
644 frame = -1;
645 frame_out = -1;
646 /* the default is not to change the time at all,
647 * but this is overridden by the edit_files routine
648 */
649 t_corr = 0;
650
651 if (n_append == -1)
652 {
653 if (ftpout == efTNG)
654 {
655 if (bIndex)
656 {
657 trjtools_gmx_prepare_tng_writing(out_file, 'w', NULL((void*)0), &trxout,
658 fnms[0], isize, NULL((void*)0), index, grpname);
659 }
660 else
661 {
662 trjtools_gmx_prepare_tng_writing(out_file, 'w', NULL((void*)0), &trxout,
663 fnms[0], -1, NULL((void*)0), NULL((void*)0), NULL((void*)0));
664 }
665 }
666 else
667 {
668 trxout = open_trx(out_file, "w");
669 }
670 memset(&frout, 0, sizeof(frout));
671 }
672 else
673 {
674 t_fileio *stfio;
675
676 if (!read_first_frame(oenv, &status, out_file, &fr, FLAGS((1<<0) | (1<<2) | (1<<4))))
677 {
678 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 678, "Reading first frame from %s", out_file);
679 }
680
681 stfio = trx_get_fileio(status);
682 if (!bKeepLast && !bOverwrite)
683 {
684 fprintf(stderrstderr, "\n\nWARNING: Appending without -overwrite implies -keeplast "
685 "between the first two files. \n"
686 "If the trajectories have an overlap and have not been written binary \n"
687 "reproducible this will produce an incorrect trajectory!\n\n");
688
689 filetype = gmx_fio_getftp(stfio);
690 /* Fails if last frame is incomplete
691 * We can't do anything about it without overwriting
692 * */
693 if (filetype == efXTC || filetype == efTNG)
694 {
695 lasttime = trx_get_time_of_final_frame(status);
696 fr.time = lasttime;
697 }
698 else
699 {
700 while (read_next_frame(oenv, status, &fr))
701 {
702 ;
703 }
704 lasttime = fr.time;
705 }
706 bKeepLastAppend = TRUE1;
707 close_trj(status);
708 trxout = open_trx(out_file, "a");
709 }
710 else if (bOverwrite)
711 {
712 if (gmx_fio_getftp(stfio) != efXTC)
713 {
714 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 714, "Overwrite only supported for XTC." );
715 }
716 last_frame_time = trx_get_time_of_final_frame(status);
717
718 /* xtc_seek_time broken for trajectories containing only 1 or 2 frames
719 * or when seek time = 0 */
720 if (nfile_in > 1 && settime[1] < last_frame_time+timest[0]*0.5)
721 {
722 /* Jump to one time-frame before the start of next
723 * trajectory file */
724 searchtime = settime[1]-timest[0]*1.25;
725 }
726 else
727 {
728 searchtime = last_frame_time;
729 }
730 if (xtc_seek_time(stfio, searchtime, fr.natoms, TRUE1))
731 {
732 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 732, "Error seeking to append position.");
733 }
734 read_next_frame(oenv, status, &fr);
735 if (fabs(searchtime - fr.time) > timest[0]*0.5)
736 {
737 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 737, "Error seeking: attempted to seek to %f but got %f.",
738 searchtime, fr.time);
739 }
740 lasttime = fr.time;
741 fpos = gmx_fio_ftell(stfio);
742 close_trj(status);
743 trxout = open_trx(out_file, "r+");
744 if (gmx_fio_seek(trx_get_fileio(trxout), fpos))
745 {
746 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjcat.c"
, 746, "Error seeking to append position.");
747 }
748 }
749 printf("\n Will append after %f \n", lasttime);
750 frout = fr;
751 }
752 /* Lets stitch up some files */
753 timestep = timest[0];
754 for (i = n_append+1; (i < nfile_in); i++)
755 {
756 /* Open next file */
757
758 /* set the next time from the last frame in previous file */
759 if (i > 0)
760 {
761 /* When writing TNG the step determine which frame to write. Use an
762 * offset to be able to increase steps properly when changing files. */
763 if (ftpout == efTNG)
764 {
765 prevEndStep = frout.step;
766 }
767
768 if (frame_out >= 0)
769 {
770 if (cont_type[i] == TIME_CONTINUE1)
771 {
772 begin = frout.time;
773 begin += 0.5*timestep;
774 settime[i] = frout.time;
775 cont_type[i] = TIME_EXPLICIT0;
776 }
777 else if (cont_type[i] == TIME_LAST2)
778 {
779 begin = frout.time;
780 begin += 0.5*timestep;
781 }
782 /* Or, if the time in the next part should be changed by the
783 * same amount, start at half a timestep from the last time
784 * so we dont repeat frames.
785 */
786 /* I don't understand the comment above, but for all the cases
787 * I tried the code seems to work properly. B. Hess 2008-4-2.
788 */
789 }
790 /* Or, if time is set explicitly, we check for overlap/gap */
791 if (cont_type[i] == TIME_EXPLICIT0)
792 {
793 if ( ( i < nfile_in ) &&
794 ( frout.time < settime[i]-1.5*timestep ) )
795 {
796 fprintf(stderrstderr, "WARNING: Frames around t=%f %s have a different "
797 "spacing than the rest,\n"
798 "might be a gap or overlap that couldn't be corrected "
799 "automatically.\n", output_env_conv_time(oenv, frout.time),
800 output_env_get_time_unit(oenv));
801 }
802 }
803 }
804
805 /* if we don't have a timestep in the current file, use the old one */
806 if (timest[i] != 0)
807 {
808 timestep = timest[i];
809 }
810 read_first_frame(oenv, &status, fnms[i], &fr, FLAGS((1<<0) | (1<<2) | (1<<4)));
811 if (!fr.bTime)
812 {
813 fr.time = 0;
814 fprintf(stderrstderr, "\nWARNING: Couldn't find a time in the frame.\n");
815 }
816
817 if (cont_type[i] == TIME_EXPLICIT0)
818 {
819 t_corr = settime[i]-fr.time;
820 }
821 /* t_corr is the amount we want to change the time.
822 * If the user has chosen not to change the time for
823 * this part of the trajectory t_corr remains at
824 * the value it had in the last part, changing this
825 * by the same amount.
826 * If no value was given for the first trajectory part
827 * we let the time start at zero, see the edit_files routine.
828 */
829
830 bNewFile = TRUE1;
831
832 printf("\n");
833 if (lasttime != NOTSET-12345)
834 {
835 printf("lasttime %g\n", lasttime);
836 }
837
838 do
839 {
840 /* copy the input frame to the output frame */
841 frout = fr;
842 /* set the new time by adding the correct calculated above */
843 frout.time += t_corr;
844 if (ftpout == efTNG)
845 {
846 frout.step += prevEndStep;
847 }
848 /* quit if we have reached the end of what should be written */
849 if ((end > 0) && (frout.time > end+GMX_REAL_EPS5.96046448E-08))
850 {
851 i = nfile_in;
852 break;
853 }
854
855 /* determine if we should write this frame (dt is handled elsewhere) */
856 if (bCat) /* write all frames of all files */
857 {
858 bWrite = TRUE1;
859 }
860 else if (bKeepLast || (bKeepLastAppend && i == 1))
861 /* write till last frame of this traj
862 and skip first frame(s) of next traj */
863 {
864 bWrite = ( frout.time > lasttime+0.5*timestep );
865 }
866 else /* write till first frame of next traj */
867 {
868 bWrite = ( frout.time < settime[i+1]-0.5*timestep );
869 }
870
871 if (bWrite && (frout.time >= begin) )
872 {
873 frame++;
874 if (frame_out == -1)
875 {
876 first_time = frout.time;
877 }
878 lasttime = frout.time;
879 if (dt == 0 || bRmod(frout.time, first_time, dt)bRmod_fd(frout.time, first_time, dt, 0))
880 {
881 frame_out++;
882 last_ok_t = frout.time;
883 if (bNewFile)
884 {
885 fprintf(stderrstderr, "\nContinue writing frames from %s t=%g %s, "
886 "frame=%d \n",
887 fnms[i], output_env_conv_time(oenv, frout.time), output_env_get_time_unit(oenv),
888 frame);
889 bNewFile = FALSE0;
890 }
891
892 if (bIndex)
893 {
894 write_trxframe_indexed(trxout, &frout, isize, index,
895 NULL((void*)0));
896 }
897 else
898 {
899 write_trxframe(trxout, &frout, NULL((void*)0));
900 }
901 if ( ((frame % 10) == 0) || (frame < 10) )
902 {
903 fprintf(stderrstderr, " -> frame %6d time %8.3f %s \r",
904 frame_out, output_env_conv_time(oenv, frout.time), output_env_get_time_unit(oenv));
905 }
906 }
907 }
908 }
909 while (read_next_frame(oenv, status, &fr));
910
911 close_trj(status);
912
913 earliersteps += step;
914 }
915 if (trxout)
916 {
917 close_trx(trxout);
918 }
919 fprintf(stderrstderr, "\nLast frame written was %d, time %f %s\n",
920 frame, output_env_conv_time(oenv, last_ok_t), output_env_get_time_unit(oenv));
921 }
922
923 return 0;
924}