Bug Summary

File:gromacs/gmxana/gmx_trjconv.c
Location:line 961, column 9
Description:Value stored to 'bFitXY' 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 <math.h>
42#include <stdlib.h>
43#include <string.h>
44
45#include "copyrite.h"
46#include "macros.h"
47#include "gromacs/utility/smalloc.h"
48#include "typedefs.h"
49#include "gromacs/fileio/gmxfio.h"
50#include "gromacs/fileio/tpxio.h"
51#include "gromacs/fileio/trxio.h"
52#include "gromacs/fileio/trnio.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 "viewit.h"
65#include "gromacs/fileio/xvgr.h"
66#include "gmx_ana.h"
67
68#include "gromacs/math/do_fit.h"
69#include "gromacs/utility/fatalerror.h"
70
71#ifdef HAVE_UNISTD_H
72#include <unistd.h>
73#endif
74
75enum {
76 euSel, euRect, euTric, euCompact, euNR
77};
78
79
80static void calc_pbc_cluster(int ecenter, int nrefat, t_topology *top, int ePBC,
81 rvec x[], atom_id index[], matrix box)
82{
83 int m, i, j, j0, j1, jj, ai, aj;
84 int imin, jmin;
85 real fac, min_dist2;
86 rvec dx, xtest, box_center;
87 int nmol, imol_center;
88 atom_id *molind;
89 gmx_bool *bMol, *bTmp;
90 rvec *m_com, *m_shift;
91 t_pbc pbc;
92 real *com_dist2;
93 int *cluster;
94 int *added;
95 int ncluster, nadded;
96 real tmp_r2;
97
98 calc_box_center(ecenter, box, box_center);
99
100 /* Initiate the pbc structure */
101 memset(&pbc, 0, sizeof(pbc));
102 set_pbc(&pbc, ePBC, box);
103
104 /* Convert atom index to molecular */
105 nmol = top->mols.nr;
106 molind = top->mols.index;
107 snew(bMol, nmol)(bMol) = save_calloc("bMol", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 107, (nmol), sizeof(*(bMol)));
108 snew(m_com, nmol)(m_com) = save_calloc("m_com", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 108, (nmol), sizeof(*(m_com)));
109 snew(m_shift, nmol)(m_shift) = save_calloc("m_shift", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 109, (nmol), sizeof(*(m_shift)));
110 snew(cluster, nmol)(cluster) = save_calloc("cluster", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 110, (nmol), sizeof(*(cluster)));
111 snew(added, nmol)(added) = save_calloc("added", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 111, (nmol), sizeof(*(added)));
112 snew(bTmp, top->atoms.nr)(bTmp) = save_calloc("bTmp", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 112, (top->atoms.nr), sizeof(*(bTmp)));
113
114 for (i = 0; (i < nrefat); i++)
115 {
116 /* Mark all molecules in the index */
117 ai = index[i];
118 bTmp[ai] = TRUE1;
119 /* Binary search assuming the molecules are sorted */
120 j0 = 0;
121 j1 = nmol-1;
122 while (j0 < j1)
123 {
124 if (ai < molind[j0+1])
125 {
126 j1 = j0;
127 }
128 else if (ai >= molind[j1])
129 {
130 j0 = j1;
131 }
132 else
133 {
134 jj = (j0+j1)/2;
135 if (ai < molind[jj+1])
136 {
137 j1 = jj;
138 }
139 else
140 {
141 j0 = jj;
142 }
143 }
144 }
145 bMol[j0] = TRUE1;
146 }
147 /* Double check whether all atoms in all molecules that are marked are part
148 * of the cluster. Simultaneously compute the center of geometry.
149 */
150 min_dist2 = 10*sqr(trace(box));
151 imol_center = -1;
152 ncluster = 0;
153 for (i = 0; i < nmol; i++)
154 {
155 for (j = molind[i]; j < molind[i+1]; j++)
156 {
157 if (bMol[i] && !bTmp[j])
158 {
159 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 159, "Molecule %d marked for clustering but not atom %d in it - check your index!", i+1, j+1);
160 }
161 else if (!bMol[i] && bTmp[j])
162 {
163 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 163, "Atom %d marked for clustering but not molecule %d - this is an internal error...", j+1, i+1);
164 }
165 else if (bMol[i])
166 {
167 /* Make molecule whole, move 2nd and higher atom to same periodicity as 1st atom in molecule */
168 if (j > molind[i])
169 {
170 pbc_dx(&pbc, x[j], x[j-1], dx);
171 rvec_add(x[j-1], dx, x[j]);
172 }
173 /* Compute center of geometry of molecule - m_com[i] was zeroed when we did snew() on it! */
174 rvec_inc(m_com[i], x[j]);
175 }
176 }
177 if (bMol[i])
178 {
179 /* Normalize center of geometry */
180 fac = 1.0/(molind[i+1]-molind[i]);
181 for (m = 0; (m < DIM3); m++)
182 {
183 m_com[i][m] *= fac;
184 }
185 /* Determine which molecule is closest to the center of the box */
186 pbc_dx(&pbc, box_center, m_com[i], dx);
187 tmp_r2 = iprod(dx, dx);
188
189 if (tmp_r2 < min_dist2)
190 {
191 min_dist2 = tmp_r2;
192 imol_center = i;
193 }
194 cluster[ncluster++] = i;
195 }
196 }
197 sfree(bTmp)save_free("bTmp", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 197, (bTmp));
198
199 if (ncluster <= 0)
200 {
201 fprintf(stderrstderr, "No molecules selected in the cluster\n");
202 return;
203 }
204 else if (imol_center == -1)
205 {
206 fprintf(stderrstderr, "No central molecules could be found\n");
207 return;
208 }
209
210 nadded = 0;
211 added[nadded++] = imol_center;
212 bMol[imol_center] = FALSE0;
213
214 while (nadded < ncluster)
215 {
216 /* Find min distance between cluster molecules and those remaining to be added */
217 min_dist2 = 10*sqr(trace(box));
218 imin = -1;
219 jmin = -1;
220 /* Loop over added mols */
221 for (i = 0; i < nadded; i++)
222 {
223 ai = added[i];
224 /* Loop over all mols */
225 for (j = 0; j < ncluster; j++)
226 {
227 aj = cluster[j];
228 /* check those remaining to be added */
229 if (bMol[aj])
230 {
231 pbc_dx(&pbc, m_com[aj], m_com[ai], dx);
232 tmp_r2 = iprod(dx, dx);
233 if (tmp_r2 < min_dist2)
234 {
235 min_dist2 = tmp_r2;
236 imin = ai;
237 jmin = aj;
238 }
239 }
240 }
241 }
242
243 /* Add the best molecule */
244 added[nadded++] = jmin;
245 bMol[jmin] = FALSE0;
246 /* Calculate the shift from the ai molecule */
247 pbc_dx(&pbc, m_com[jmin], m_com[imin], dx);
248 rvec_add(m_com[imin], dx, xtest);
249 rvec_sub(xtest, m_com[jmin], m_shift[jmin]);
250 rvec_inc(m_com[jmin], m_shift[jmin]);
251
252 for (j = molind[jmin]; j < molind[jmin+1]; j++)
253 {
254 rvec_inc(x[j], m_shift[jmin]);
255 }
256 fprintf(stdoutstdout, "\rClustering iteration %d of %d...", nadded, ncluster);
257 fflush(stdoutstdout);
258 }
259
260 sfree(added)save_free("added", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 260, (added));
261 sfree(cluster)save_free("cluster", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 261, (cluster));
262 sfree(bMol)save_free("bMol", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 262, (bMol));
263 sfree(m_com)save_free("m_com", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 263, (m_com));
264 sfree(m_shift)save_free("m_shift", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 264, (m_shift));
265
266 fprintf(stdoutstdout, "\n");
267}
268
269static void put_molecule_com_in_box(int unitcell_enum, int ecenter,
270 t_block *mols,
271 int natoms, t_atom atom[],
272 int ePBC, matrix box, rvec x[])
273{
274 atom_id i, j;
275 int d;
276 rvec com, new_com, shift, dx, box_center;
277 real m;
278 double mtot;
279 t_pbc pbc;
280
281 calc_box_center(ecenter, box, box_center);
282 set_pbc(&pbc, ePBC, box);
283 if (mols->nr <= 0)
284 {
285 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 285, "There are no molecule descriptions. I need a .tpr file for this pbc option.");
286 }
287 for (i = 0; (i < mols->nr); i++)
288 {
289 /* calc COM */
290 clear_rvec(com);
291 mtot = 0;
292 for (j = mols->index[i]; (j < mols->index[i+1] && j < natoms); j++)
293 {
294 m = atom[j].m;
295 for (d = 0; d < DIM3; d++)
296 {
297 com[d] += m*x[j][d];
298 }
299 mtot += m;
300 }
301 /* calculate final COM */
302 svmul(1.0/mtot, com, com);
303
304 /* check if COM is outside box */
305 copy_rvec(com, new_com);
306 switch (unitcell_enum)
307 {
308 case euRect:
309 put_atoms_in_box(ePBC, box, 1, &new_com);
310 break;
311 case euTric:
312 put_atoms_in_triclinic_unitcell(ecenter, box, 1, &new_com);
313 break;
314 case euCompact:
315 put_atoms_in_compact_unitcell(ePBC, ecenter, box, 1, &new_com);
316 break;
317 }
318 rvec_sub(new_com, com, shift);
319 if (norm2(shift) > 0)
320 {
321 if (debug)
322 {
323 fprintf(debug, "\nShifting position of molecule %d "
324 "by %8.3f %8.3f %8.3f\n", i+1,
325 shift[XX0], shift[YY1], shift[ZZ2]);
326 }
327 for (j = mols->index[i]; (j < mols->index[i+1] && j < natoms); j++)
328 {
329 rvec_inc(x[j], shift);
330 }
331 }
332 }
333}
334
335static void put_residue_com_in_box(int unitcell_enum, int ecenter,
336 int natoms, t_atom atom[],
337 int ePBC, matrix box, rvec x[])
338{
339 atom_id i, j, res_start, res_end, res_nat;
340 int d, presnr;
341 real m;
342 double mtot;
343 rvec box_center, com, new_com, shift;
344
345 calc_box_center(ecenter, box, box_center);
346
347 presnr = NOTSET-12345;
348 res_start = 0;
349 clear_rvec(com);
350 mtot = 0;
351 for (i = 0; i < natoms+1; i++)
352 {
353 if (i == natoms || (presnr != atom[i].resind && presnr != NOTSET-12345))
354 {
355 /* calculate final COM */
356 res_end = i;
357 res_nat = res_end - res_start;
358 svmul(1.0/mtot, com, com);
359
360 /* check if COM is outside box */
361 copy_rvec(com, new_com);
362 switch (unitcell_enum)
363 {
364 case euRect:
365 put_atoms_in_box(ePBC, box, 1, &new_com);
366 break;
367 case euTric:
368 put_atoms_in_triclinic_unitcell(ecenter, box, 1, &new_com);
369 break;
370 case euCompact:
371 put_atoms_in_compact_unitcell(ePBC, ecenter, box, 1, &new_com);
372 break;
373 }
374 rvec_sub(new_com, com, shift);
375 if (norm2(shift))
376 {
377 if (debug)
378 {
379 fprintf(debug, "\nShifting position of residue %d (atoms %u-%u) "
380 "by %g,%g,%g\n", atom[res_start].resind+1,
381 res_start+1, res_end+1, shift[XX0], shift[YY1], shift[ZZ2]);
382 }
383 for (j = res_start; j < res_end; j++)
384 {
385 rvec_inc(x[j], shift);
386 }
387 }
388 clear_rvec(com);
389 mtot = 0;
390
391 /* remember start of new residue */
392 res_start = i;
393 }
394 if (i < natoms)
395 {
396 /* calc COM */
397 m = atom[i].m;
398 for (d = 0; d < DIM3; d++)
399 {
400 com[d] += m*x[i][d];
401 }
402 mtot += m;
403
404 presnr = atom[i].resind;
405 }
406 }
407}
408
409static void center_x(int ecenter, rvec x[], matrix box, int n, int nc, atom_id ci[])
410{
411 int i, m, ai;
412 rvec cmin, cmax, box_center, dx;
413
414 if (nc > 0)
415 {
416 copy_rvec(x[ci[0]], cmin);
417 copy_rvec(x[ci[0]], cmax);
418 for (i = 0; i < nc; i++)
419 {
420 ai = ci[i];
421 for (m = 0; m < DIM3; m++)
422 {
423 if (x[ai][m] < cmin[m])
424 {
425 cmin[m] = x[ai][m];
426 }
427 else if (x[ai][m] > cmax[m])
428 {
429 cmax[m] = x[ai][m];
430 }
431 }
432 }
433 calc_box_center(ecenter, box, box_center);
434 for (m = 0; m < DIM3; m++)
435 {
436 dx[m] = box_center[m]-(cmin[m]+cmax[m])*0.5;
437 }
438
439 for (i = 0; i < n; i++)
440 {
441 rvec_inc(x[i], dx);
442 }
443 }
444}
445
446static void mk_filenm(char *base, const char *ext, int ndigit, int file_nr,
447 char out_file[])
448{
449 char nbuf[128];
450 int nd = 0, fnr;
451
452 strcpy(out_file, base);
453 fnr = file_nr;
454 do
455 {
456 fnr /= 10;
457 nd++;
458 }
459 while (fnr > 0);
460
461 if (nd < ndigit)
462 {
463 strncat(out_file, "00000000000", ndigit-nd)__builtin_strncat (out_file, "00000000000", ndigit-nd);
464 }
465 sprintf(nbuf, "%d.", file_nr);
466 strcat(out_file, nbuf);
467 strcat(out_file, ext);
468}
469
470void check_trn(const char *fn)
471{
472 if ((fn2ftp(fn) != efTRJ) && (fn2ftp(fn) != efTRR))
473 {
474 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 474, "%s is not a trajectory file, exiting\n", fn);
475 }
476}
477
478#ifndef GMX_NATIVE_WINDOWS
479void do_trunc(const char *fn, real t0)
480{
481 t_fileio *in;
482 FILE *fp;
483 gmx_bool bStop, bOK;
484 t_trnheader sh;
485 gmx_off_t fpos;
486 char yesno[256];
487 int j;
488 real t = 0;
489
490 if (t0 == -1)
491 {
492 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 492, "You forgot to set the truncation time");
493 }
494
495 /* Check whether this is a .trj file */
496 check_trn(fn);
497
498 in = open_trn(fn, "r");
499 fp = gmx_fio_getfp(in);
500 if (fp == NULL((void*)0))
501 {
502 fprintf(stderrstderr, "Sorry, can not trunc %s, truncation of this filetype is not supported\n", fn);
503 close_trn(in);
504 }
505 else
506 {
507 j = 0;
508 fpos = gmx_fio_ftell(in);
509 bStop = FALSE0;
510 while (!bStop && fread_trnheader(in, &sh, &bOK))
511 {
512 fread_htrn(in, &sh, NULL((void*)0), NULL((void*)0), NULL((void*)0), NULL((void*)0));
513 fpos = gmx_ftell(fp);
514 t = sh.t;
515 if (t >= t0)
516 {
517 gmx_fseek(fp, fpos, SEEK_SET0);
518 bStop = TRUE1;
519 }
520 }
521 if (bStop)
522 {
523 fprintf(stderrstderr, "Do you REALLY want to truncate this trajectory (%s) at:\n"
524 "frame %d, time %g, bytes %ld ??? (type YES if so)\n",
525 fn, j, t, (long int)fpos);
526 if (1 != scanf("%s", yesno))
527 {
528 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 528, "Error reading user input");
529 }
530 if (strcmp(yesno, "YES")__extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p
(yesno) && __builtin_constant_p ("YES") && (
__s1_len = strlen (yesno), __s2_len = strlen ("YES"), (!((size_t
)(const void *)((yesno) + 1) - (size_t)(const void *)(yesno) ==
1) || __s1_len >= 4) && (!((size_t)(const void *)
(("YES") + 1) - (size_t)(const void *)("YES") == 1) || __s2_len
>= 4)) ? __builtin_strcmp (yesno, "YES") : (__builtin_constant_p
(yesno) && ((size_t)(const void *)((yesno) + 1) - (size_t
)(const void *)(yesno) == 1) && (__s1_len = strlen (yesno
), __s1_len < 4) ? (__builtin_constant_p ("YES") &&
((size_t)(const void *)(("YES") + 1) - (size_t)(const void *
)("YES") == 1) ? __builtin_strcmp (yesno, "YES") : (__extension__
({ const unsigned char *__s2 = (const unsigned char *) (const
char *) ("YES"); int __result = (((const unsigned char *) (const
char *) (yesno))[0] - __s2[0]); if (__s1_len > 0 &&
__result == 0) { __result = (((const unsigned char *) (const
char *) (yesno))[1] - __s2[1]); if (__s1_len > 1 &&
__result == 0) { __result = (((const unsigned char *) (const
char *) (yesno))[2] - __s2[2]); if (__s1_len > 2 &&
__result == 0) __result = (((const unsigned char *) (const char
*) (yesno))[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p
("YES") && ((size_t)(const void *)(("YES") + 1) - (size_t
)(const void *)("YES") == 1) && (__s2_len = strlen ("YES"
), __s2_len < 4) ? (__builtin_constant_p (yesno) &&
((size_t)(const void *)((yesno) + 1) - (size_t)(const void *
)(yesno) == 1) ? __builtin_strcmp (yesno, "YES") : (- (__extension__
({ const unsigned char *__s2 = (const unsigned char *) (const
char *) (yesno); int __result = (((const unsigned char *) (const
char *) ("YES"))[0] - __s2[0]); if (__s2_len > 0 &&
__result == 0) { __result = (((const unsigned char *) (const
char *) ("YES"))[1] - __s2[1]); if (__s2_len > 1 &&
__result == 0) { __result = (((const unsigned char *) (const
char *) ("YES"))[2] - __s2[2]); if (__s2_len > 2 &&
__result == 0) __result = (((const unsigned char *) (const char
*) ("YES"))[3] - __s2[3]); } } __result; })))) : __builtin_strcmp
(yesno, "YES")))); }) == 0)
531 {
532 fprintf(stderrstderr, "Once again, I'm gonna DO this...\n");
533 close_trn(in);
534 if (0 != truncate(fn, fpos))
535 {
536 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 536, "Error truncating file %s", fn);
537 }
538 }
539 else
540 {
541 fprintf(stderrstderr, "Ok, I'll forget about it\n");
542 }
543 }
544 else
545 {
546 fprintf(stderrstderr, "Already at end of file (t=%g)...\n", t);
547 close_trn(in);
548 }
549 }
550}
551#endif
552
553/*! \brief Read a full molecular topology if useful and available.
554 *
555 * If the input trajectory file is not in TNG format, and the output
556 * file is in TNG format, then we want to try to read a full topology
557 * (if available), so that we can write molecule information to the
558 * output file. The full topology provides better molecule information
559 * than is available from the normal t_topology data used by GROMACS
560 * tools.
561 *
562 * Also, the t_topology is only read under (different) particular
563 * conditions. If both apply, then a .tpr file might be read
564 * twice. Trying to fix this redundancy while trjconv is still an
565 * all-purpose tool does not seem worthwhile.
566 *
567 * Because of the way gmx_prepare_tng_writing is implemented, the case
568 * where the input TNG file has no molecule information will never
569 * lead to an output TNG file having molecule information. Since
570 * molecule information will generally be present if the input TNG
571 * file was written by a GROMACS tool, this seems like reasonable
572 * behaviour. */
573static gmx_mtop_t *read_mtop_for_tng(const char *tps_file,
574 const char *input_file,
575 const char *output_file)
576{
577 gmx_mtop_t *mtop = NULL((void*)0);
578
579 if (fn2bTPX(tps_file) &&
580 efTNG != fn2ftp(input_file) &&
581 efTNG == fn2ftp(output_file))
582 {
583 int temp_natoms = -1;
584 snew(mtop, 1)(mtop) = save_calloc("mtop", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 584, (1), sizeof(*(mtop)));
585 read_tpx(tps_file, NULL((void*)0), NULL((void*)0), &temp_natoms,
586 NULL((void*)0), NULL((void*)0), NULL((void*)0), mtop);
587 }
588
589 return mtop;
590}
591
592int gmx_trjconv(int argc, char *argv[])
593{
594 const char *desc[] = {
595 "[THISMODULE] can convert trajectory files in many ways:[BR]",
596 "* from one format to another[BR]",
597 "* select a subset of atoms[BR]",
598 "* change the periodicity representation[BR]",
599 "* keep multimeric molecules together[BR]",
600 "* center atoms in the box[BR]",
601 "* fit atoms to reference structure[BR]",
602 "* reduce the number of frames[BR]",
603 "* change the timestamps of the frames ",
604 "([TT]-t0[tt] and [TT]-timestep[tt])[BR]",
605 "* cut the trajectory in small subtrajectories according",
606 "to information in an index file. This allows subsequent analysis of",
607 "the subtrajectories that could, for example, be the result of a",
608 "cluster analysis. Use option [TT]-sub[tt].",
609 "This assumes that the entries in the index file are frame numbers and",
610 "dumps each group in the index file to a separate trajectory file.[BR]",
611 "* select frames within a certain range of a quantity given",
612 "in an [TT].xvg[tt] file.[PAR]",
613
614 "[gmx-trjcat] is better suited for concatenating multiple trajectory files.",
615 "[PAR]",
616
617 "The following formats are supported for input and output:",
618 "[TT].xtc[tt], [TT].trr[tt], [TT].trj[tt], [TT].gro[tt], [TT].g96[tt]",
619 "and [TT].pdb[tt].",
620 "The file formats are detected from the file extension.",
621 "The precision of [TT].xtc[tt] and [TT].gro[tt] output is taken from the",
622 "input file for [TT].xtc[tt], [TT].gro[tt] and [TT].pdb[tt],",
623 "and from the [TT]-ndec[tt] option for other input formats. The precision",
624 "is always taken from [TT]-ndec[tt], when this option is set.",
625 "All other formats have fixed precision. [TT].trr[tt] and [TT].trj[tt]",
626 "output can be single or double precision, depending on the precision",
627 "of the [THISMODULE] binary.",
628 "Note that velocities are only supported in",
629 "[TT].trr[tt], [TT].trj[tt], [TT].gro[tt] and [TT].g96[tt] files.[PAR]",
630
631 "Option [TT]-sep[tt] can be used to write every frame to a separate",
632 "[TT].gro, .g96[tt] or [TT].pdb[tt] file. By default, all frames all written to one file.",
633 "[TT].pdb[tt] files with all frames concatenated can be viewed with",
634 "[TT]rasmol -nmrpdb[tt].[PAR]",
635
636 "It is possible to select part of your trajectory and write it out",
637 "to a new trajectory file in order to save disk space, e.g. for leaving",
638 "out the water from a trajectory of a protein in water.",
639 "[BB]ALWAYS[bb] put the original trajectory on tape!",
640 "We recommend to use the portable [TT].xtc[tt] format for your analysis",
641 "to save disk space and to have portable files.[PAR]",
642
643 "There are two options for fitting the trajectory to a reference",
644 "either for essential dynamics analysis, etc.",
645 "The first option is just plain fitting to a reference structure",
646 "in the structure file. The second option is a progressive fit",
647 "in which the first timeframe is fitted to the reference structure ",
648 "in the structure file to obtain and each subsequent timeframe is ",
649 "fitted to the previously fitted structure. This way a continuous",
650 "trajectory is generated, which might not be the case when using the",
651 "regular fit method, e.g. when your protein undergoes large",
652 "conformational transitions.[PAR]",
653
654 "Option [TT]-pbc[tt] sets the type of periodic boundary condition",
655 "treatment:[BR]",
656 "[TT]* mol[tt] puts the center of mass of molecules in the box,",
657 "and requires a run input file to be supplied with [TT]-s[tt].[BR]",
658 "[TT]* res[tt] puts the center of mass of residues in the box.[BR]",
659 "[TT]* atom[tt] puts all the atoms in the box.[BR]",
660 "[TT]* nojump[tt] checks if atoms jump across the box and then puts",
661 "them back. This has the effect that all molecules",
662 "will remain whole (provided they were whole in the initial",
663 "conformation). [BB]Note[bb] that this ensures a continuous trajectory but",
664 "molecules may diffuse out of the box. The starting configuration",
665 "for this procedure is taken from the structure file, if one is",
666 "supplied, otherwise it is the first frame.[BR]",
667 "[TT]* cluster[tt] clusters all the atoms in the selected index",
668 "such that they are all closest to the center of mass of the cluster,",
669 "which is iteratively updated. [BB]Note[bb] that this will only give meaningful",
670 "results if you in fact have a cluster. Luckily that can be checked",
671 "afterwards using a trajectory viewer. Note also that if your molecules",
672 "are broken this will not work either.[BR]",
673 "The separate option [TT]-clustercenter[tt] can be used to specify an",
674 "approximate center for the cluster. This is useful e.g. if you have",
675 "two big vesicles, and you want to maintain their relative positions.[BR]",
676 "[TT]* whole[tt] only makes broken molecules whole.[PAR]",
677
678 "Option [TT]-ur[tt] sets the unit cell representation for options",
679 "[TT]mol[tt], [TT]res[tt] and [TT]atom[tt] of [TT]-pbc[tt].",
680 "All three options give different results for triclinic boxes and",
681 "identical results for rectangular boxes.",
682 "[TT]rect[tt] is the ordinary brick shape.",
683 "[TT]tric[tt] is the triclinic unit cell.",
684 "[TT]compact[tt] puts all atoms at the closest distance from the center",
685 "of the box. This can be useful for visualizing e.g. truncated octahedra",
686 "or rhombic dodecahedra. The center for options [TT]tric[tt] and [TT]compact[tt]",
687 "is [TT]tric[tt] (see below), unless the option [TT]-boxcenter[tt]",
688 "is set differently.[PAR]",
689
690 "Option [TT]-center[tt] centers the system in the box. The user can",
691 "select the group which is used to determine the geometrical center.",
692 "Option [TT]-boxcenter[tt] sets the location of the center of the box",
693 "for options [TT]-pbc[tt] and [TT]-center[tt]. The center options are:",
694 "[TT]tric[tt]: half of the sum of the box vectors,",
695 "[TT]rect[tt]: half of the box diagonal,",
696 "[TT]zero[tt]: zero.",
697 "Use option [TT]-pbc mol[tt] in addition to [TT]-center[tt] when you",
698 "want all molecules in the box after the centering.[PAR]",
699
700 "It is not always possible to use combinations of [TT]-pbc[tt],",
701 "[TT]-fit[tt], [TT]-ur[tt] and [TT]-center[tt] to do exactly what",
702 "you want in one call to [THISMODULE]. Consider using multiple",
703 "calls, and check out the GROMACS website for suggestions.[PAR]",
704
705 "With [TT]-dt[tt], it is possible to reduce the number of ",
706 "frames in the output. This option relies on the accuracy of the times",
707 "in your input trajectory, so if these are inaccurate use the",
708 "[TT]-timestep[tt] option to modify the time (this can be done",
709 "simultaneously). For making smooth movies, the program [gmx-filter]",
710 "can reduce the number of frames while using low-pass frequency",
711 "filtering, this reduces aliasing of high frequency motions.[PAR]",
712
713 "Using [TT]-trunc[tt] [THISMODULE] can truncate [TT].trj[tt] in place, i.e.",
714 "without copying the file. This is useful when a run has crashed",
715 "during disk I/O (i.e. full disk), or when two contiguous",
716 "trajectories must be concatenated without having double frames.[PAR]",
717
718 "Option [TT]-dump[tt] can be used to extract a frame at or near",
719 "one specific time from your trajectory.[PAR]",
720
721 "Option [TT]-drop[tt] reads an [TT].xvg[tt] file with times and values.",
722 "When options [TT]-dropunder[tt] and/or [TT]-dropover[tt] are set,",
723 "frames with a value below and above the value of the respective options",
724 "will not be written."
725 };
726
727 int pbc_enum;
728 enum
729 {
730 epSel,
731 epNone,
732 epComMol,
733 epComRes,
734 epComAtom,
735 epNojump,
736 epCluster,
737 epWhole,
738 epNR
739 };
740 const char *pbc_opt[epNR + 1] =
741 {
742 NULL((void*)0), "none", "mol", "res", "atom", "nojump", "cluster", "whole",
743 NULL((void*)0)
744 };
745
746 int unitcell_enum;
747 const char *unitcell_opt[euNR+1] =
748 { NULL((void*)0), "rect", "tric", "compact", NULL((void*)0) };
749
750 enum
751 {
752 ecSel, ecTric, ecRect, ecZero, ecNR
753 };
754 const char *center_opt[ecNR+1] =
755 { NULL((void*)0), "tric", "rect", "zero", NULL((void*)0) };
756 int ecenter;
757
758 int fit_enum;
759 enum
760 {
761 efSel, efNone, efFit, efFitXY, efReset, efResetXY, efPFit, efNR
762 };
763 const char *fit[efNR + 1] =
764 {
765 NULL((void*)0), "none", "rot+trans", "rotxy+transxy", "translation", "transxy",
766 "progressive", NULL((void*)0)
767 };
768
769 static gmx_bool bSeparate = FALSE0, bVels = TRUE1, bForce = FALSE0, bCONECT = FALSE0;
770 static gmx_bool bCenter = FALSE0;
771 static int skip_nr = 1, ndec = 3, nzero = 0;
772 static real tzero = 0, delta_t = 0, timestep = 0, ttrunc = -1, tdump = -1, split_t = 0;
773 static rvec newbox = {0, 0, 0}, shift = {0, 0, 0}, trans = {0, 0, 0};
774 static char *exec_command = NULL((void*)0);
775 static real dropunder = 0, dropover = 0;
776 static gmx_bool bRound = FALSE0;
777
778 t_pargs
779 pa[] =
780 {
781 { "-skip", FALSE0, etINT,
782 { &skip_nr }, "Only write every nr-th frame" },
783 { "-dt", FALSE0, etTIME,
784 { &delta_t },
785 "Only write frame when t MOD dt = first time (%t)" },
786 { "-round", FALSE0, etBOOL,
787 { &bRound }, "Round measurements to nearest picosecond"},
788 { "-dump", FALSE0, etTIME,
789 { &tdump }, "Dump frame nearest specified time (%t)" },
790 { "-t0", FALSE0, etTIME,
791 { &tzero },
792 "Starting time (%t) (default: don't change)" },
793 { "-timestep", FALSE0, etTIME,
794 { &timestep },
795 "Change time step between input frames (%t)" },
796 { "-pbc", FALSE0, etENUM,
797 { pbc_opt },
798 "PBC treatment (see help text for full description)" },
799 { "-ur", FALSE0, etENUM,
800 { unitcell_opt }, "Unit-cell representation" },
801 { "-center", FALSE0, etBOOL,
802 { &bCenter }, "Center atoms in box" },
803 { "-boxcenter", FALSE0, etENUM,
804 { center_opt }, "Center for -pbc and -center" },
805 { "-box", FALSE0, etRVEC,
806 { newbox },
807 "Size for new cubic box (default: read from input)" },
808 { "-trans", FALSE0, etRVEC,
809 { trans },
810 "All coordinates will be translated by trans. This "
811 "can advantageously be combined with -pbc mol -ur "
812 "compact." },
813 { "-shift", FALSE0, etRVEC,
814 { shift },
815 "All coordinates will be shifted by framenr*shift" },
816 { "-fit", FALSE0, etENUM,
817 { fit },
818 "Fit molecule to ref structure in the structure file" },
819 { "-ndec", FALSE0, etINT,
820 { &ndec },
821 "Precision for .xtc and .gro writing in number of "
822 "decimal places" },
823 { "-vel", FALSE0, etBOOL,
824 { &bVels }, "Read and write velocities if possible" },
825 { "-force", FALSE0, etBOOL,
826 { &bForce }, "Read and write forces if possible" },
827#ifndef GMX_NATIVE_WINDOWS
828 { "-trunc", FALSE0, etTIME,
829 { &ttrunc },
830 "Truncate input trajectory file after this time (%t)" },
831#endif
832 { "-exec", FALSE0, etSTR,
833 { &exec_command },
834 "Execute command for every output frame with the "
835 "frame number as argument" },
836 { "-split", FALSE0, etTIME,
837 { &split_t },
838 "Start writing new file when t MOD split = first "
839 "time (%t)" },
840 { "-sep", FALSE0, etBOOL,
841 { &bSeparate },
842 "Write each frame to a separate .gro, .g96 or .pdb "
843 "file" },
844 { "-nzero", FALSE0, etINT,
845 { &nzero },
846 "If the -sep flag is set, use these many digits "
847 "for the file numbers and prepend zeros as needed" },
848 { "-dropunder", FALSE0, etREAL,
849 { &dropunder }, "Drop all frames below this value" },
850 { "-dropover", FALSE0, etREAL,
851 { &dropover }, "Drop all frames above this value" },
852 { "-conect", FALSE0, etBOOL,
853 { &bCONECT },
854 "Add conect records when writing [TT].pdb[tt] files. Useful "
855 "for visualization of non-standard molecules, e.g. "
856 "coarse grained ones" }
857 };
858#define NPA((int)(sizeof(pa)/sizeof((pa)[0]))) asize(pa)((int)(sizeof(pa)/sizeof((pa)[0])))
859
860 FILE *out = NULL((void*)0);
861 t_trxstatus *trxout = NULL((void*)0);
862 t_trxstatus *trxin;
863 int ftp, ftpin = 0, file_nr;
864 t_trxframe fr, frout;
865 int flags;
866 rvec *xmem = NULL((void*)0), *vmem = NULL((void*)0), *fmem = NULL((void*)0);
867 rvec *xp = NULL((void*)0), x_shift, hbox, box_center, dx;
868 real xtcpr, lambda, *w_rls = NULL((void*)0);
869 int m, i, d, frame, outframe, natoms, nout, ncent, nre, newstep = 0, model_nr;
870#define SKIP10 10
871 t_topology top;
872 gmx_mtop_t *mtop = NULL((void*)0);
873 gmx_conect gc = NULL((void*)0);
874 int ePBC = -1;
875 t_atoms *atoms = NULL((void*)0), useatoms;
876 matrix top_box;
877 atom_id *index, *cindex;
878 char *grpnm;
879 int *frindex, nrfri;
880 char *frname;
881 int ifit, irms, my_clust = -1;
882 atom_id *ind_fit, *ind_rms;
883 char *gn_fit, *gn_rms;
884 t_cluster_ndx *clust = NULL((void*)0);
885 t_trxstatus **clust_status = NULL((void*)0);
886 int *clust_status_id = NULL((void*)0);
887 int ntrxopen = 0;
888 int *nfwritten = NULL((void*)0);
889 int ndrop = 0, ncol, drop0 = 0, drop1 = 0, dropuse = 0;
890 double **dropval;
891 real tshift = 0, t0 = -1, dt = 0.001, prec;
892 gmx_bool bFit, bFitXY, bPFit, bReset;
893 int nfitdim;
894 gmx_rmpbc_t gpbc = NULL((void*)0);
895 gmx_bool bRmPBC, bPBCWhole, bPBCcomRes, bPBCcomMol, bPBCcomAtom, bPBC, bNoJump, bCluster;
896 gmx_bool bCopy, bDoIt, bIndex, bTDump, bSetTime, bTPS = FALSE0, bDTset = FALSE0;
897 gmx_bool bExec, bTimeStep = FALSE0, bDumpFrame = FALSE0, bSetPrec, bNeedPrec;
898 gmx_bool bHaveFirstFrame, bHaveNextFrame, bSetBox, bSetUR, bSplit = FALSE0;
899 gmx_bool bSubTraj = FALSE0, bDropUnder = FALSE0, bDropOver = FALSE0, bTrans = FALSE0;
900 gmx_bool bWriteFrame, bSplitHere;
901 const char *top_file, *in_file, *out_file = NULL((void*)0);
902 char out_file2[256], *charpt;
903 char *outf_base = NULL((void*)0);
904 const char *outf_ext = NULL((void*)0);
905 char top_title[256], title[256], command[256], filemode[5];
906 int xdr = 0;
907 gmx_bool bWarnCompact = FALSE0;
908 const char *warn;
909 output_env_t oenv;
910
911 t_filenm fnm[] = {
912 { efTRX, "-f", NULL((void*)0), ffREAD1<<1 },
913 { efTRO, "-o", NULL((void*)0), ffWRITE1<<2 },
914 { efTPS, NULL((void*)0), NULL((void*)0), ffOPTRD(1<<1 | 1<<3) },
915 { efNDX, NULL((void*)0), NULL((void*)0), ffOPTRD(1<<1 | 1<<3) },
916 { efNDX, "-fr", "frames", ffOPTRD(1<<1 | 1<<3) },
917 { efNDX, "-sub", "cluster", ffOPTRD(1<<1 | 1<<3) },
918 { efXVG, "-drop", "drop", ffOPTRD(1<<1 | 1<<3) }
919 };
920#define NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))) asize(fnm)((int)(sizeof(fnm)/sizeof((fnm)[0])))
921
922 if (!parse_common_args(&argc, argv,
923 PCA_CAN_BEGIN(1<<6) | PCA_CAN_END(1<<7) | PCA_CAN_VIEW(1<<5) |
924 PCA_TIME_UNIT(1<<15) | PCA_BE_NICE(1<<13),
925 NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm, NPA((int)(sizeof(pa)/sizeof((pa)[0]))), pa, asize(desc)((int)(sizeof(desc)/sizeof((desc)[0]))), desc,
926 0, NULL((void*)0), &oenv))
927 {
928 return 0;
929 }
930
931 top_file = ftp2fn(efTPS, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
932 init_top(&top);
933
934 /* Check command line */
935 in_file = opt2fn("-f", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
936
937 if (ttrunc != -1)
938 {
939#ifndef GMX_NATIVE_WINDOWS
940 do_trunc(in_file, ttrunc);
941#endif
942 }
943 else
944 {
945 /* mark active cmdline options */
946 bSetBox = opt2parg_bSet("-box", NPA((int)(sizeof(pa)/sizeof((pa)[0]))), pa);
947 bSetTime = opt2parg_bSet("-t0", NPA((int)(sizeof(pa)/sizeof((pa)[0]))), pa);
948 bSetPrec = opt2parg_bSet("-ndec", NPA((int)(sizeof(pa)/sizeof((pa)[0]))), pa);
949 bSetUR = opt2parg_bSet("-ur", NPA((int)(sizeof(pa)/sizeof((pa)[0]))), pa);
950 bExec = opt2parg_bSet("-exec", NPA((int)(sizeof(pa)/sizeof((pa)[0]))), pa);
951 bTimeStep = opt2parg_bSet("-timestep", NPA((int)(sizeof(pa)/sizeof((pa)[0]))), pa);
952 bTDump = opt2parg_bSet("-dump", NPA((int)(sizeof(pa)/sizeof((pa)[0]))), pa);
953 bDropUnder = opt2parg_bSet("-dropunder", NPA((int)(sizeof(pa)/sizeof((pa)[0]))), pa);
954 bDropOver = opt2parg_bSet("-dropover", NPA((int)(sizeof(pa)/sizeof((pa)[0]))), pa);
955 bTrans = opt2parg_bSet("-trans", NPA((int)(sizeof(pa)/sizeof((pa)[0]))), pa);
956 bSplit = (split_t != 0);
957
958 /* parse enum options */
959 fit_enum = nenum(fit);
960 bFit = (fit_enum == efFit || fit_enum == efFitXY);
961 bFitXY = fit_enum == efFitXY;
Value stored to 'bFitXY' is never read
962 bReset = (fit_enum == efReset || fit_enum == efResetXY);
963 bPFit = fit_enum == efPFit;
964 pbc_enum = nenum(pbc_opt);
965 bPBCWhole = pbc_enum == epWhole;
966 bPBCcomRes = pbc_enum == epComRes;
967 bPBCcomMol = pbc_enum == epComMol;
968 bPBCcomAtom = pbc_enum == epComAtom;
969 bNoJump = pbc_enum == epNojump;
970 bCluster = pbc_enum == epCluster;
971 bPBC = pbc_enum != epNone;
972 unitcell_enum = nenum(unitcell_opt);
973 ecenter = nenum(center_opt) - ecTric;
974
975 /* set and check option dependencies */
976 if (bPFit)
977 {
978 bFit = TRUE1; /* for pfit, fit *must* be set */
979 }
980 if (bFit)
981 {
982 bReset = TRUE1; /* for fit, reset *must* be set */
983 }
984 nfitdim = 0;
985 if (bFit || bReset)
986 {
987 nfitdim = (fit_enum == efFitXY || fit_enum == efResetXY) ? 2 : 3;
988 }
989 bRmPBC = bFit || bPBCWhole || bPBCcomRes || bPBCcomMol;
990
991 if (bSetUR)
992 {
993 if (!(bPBCcomRes || bPBCcomMol || bPBCcomAtom))
994 {
995 fprintf(stderrstderr,
996 "WARNING: Option for unitcell representation (-ur %s)\n"
997 " only has effect in combination with -pbc %s, %s or %s.\n"
998 " Ingoring unitcell representation.\n\n",
999 unitcell_opt[0], pbc_opt[2], pbc_opt[3], pbc_opt[4]);
1000 bSetUR = FALSE0;
1001 }
1002 }
1003 if (bFit && bPBC)
1004 {
1005 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1005, "PBC condition treatment does not work together with rotational fit.\n"
1006 "Please do the PBC condition treatment first and then run trjconv in a second step\n"
1007 "for the rotational fit.\n"
1008 "First doing the rotational fit and then doing the PBC treatment gives incorrect\n"
1009 "results!");
1010 }
1011
1012 /* ndec is in nr of decimal places, prec is a multiplication factor: */
1013 prec = 1;
1014 for (i = 0; i < ndec; i++)
1015 {
1016 prec *= 10;
1017 }
1018
1019 bIndex = ftp2bSet(efNDX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
1020
1021
1022 /* Determine output type */
1023 out_file = opt2fn("-o", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
1024 ftp = fn2ftp(out_file);
1025 fprintf(stderrstderr, "Will write %s: %s\n", ftp2ext(ftp), ftp2desc(ftp));
1026 bNeedPrec = (ftp == efXTC || ftp == efGRO);
1027 if (bVels)
1028 {
1029 /* check if velocities are possible in input and output files */
1030 ftpin = fn2ftp(in_file);
1031 bVels = (ftp == efTRR || ftp == efTRJ || ftp == efGRO || ftp == efG96)
1032 && (ftpin == efTRR || ftpin == efTRJ || ftpin == efGRO || ftpin == efG96 ||
1033 ftpin == efCPT);
1034 }
1035 if (bSeparate || bSplit)
1036 {
1037 outf_ext = strrchr(out_file, '.');
1038 if (outf_ext == NULL((void*)0))
1039 {
1040 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1040, "Output file name '%s' does not contain a '.'", out_file);
1041 }
1042 outf_base = strdup(out_file)(__extension__ (__builtin_constant_p (out_file) && ((
size_t)(const void *)((out_file) + 1) - (size_t)(const void *
)(out_file) == 1) ? (((const char *) (out_file))[0] == '\0' ?
(char *) calloc ((size_t) 1, (size_t) 1) : ({ size_t __len =
strlen (out_file) + 1; char *__retval = (char *) malloc (__len
); if (__retval != ((void*)0)) __retval = (char *) memcpy (__retval
, out_file, __len); __retval; })) : __strdup (out_file)));
1043 outf_base[outf_ext - out_file] = '\0';
1044 }
1045
1046 bSubTraj = opt2bSet("-sub", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
1047 if (bSubTraj)
1048 {
1049 if ((ftp != efXTC) && (ftp != efTRR))
1050 {
1051 /* It seems likely that other trajectory file types
1052 * could work here. */
1053 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1053, "Can only use the sub option with output file types "
1054 "xtc and trr");
1055 }
1056 clust = cluster_index(NULL((void*)0), opt2fn("-sub", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm));
1057
1058 /* Check for number of files disabled, as FOPEN_MAX is not the correct
1059 * number to check for. In my linux box it is only 16.
1060 */
1061 if (0 && (clust->clust->nr > FOPEN_MAX16-4))
1062 {
1063 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1063, "Can not open enough (%d) files to write all the"
1064 " trajectories.\ntry splitting the index file in %d parts.\n"
1065 "FOPEN_MAX = %d",
1066 clust->clust->nr, 1+clust->clust->nr/FOPEN_MAX16, FOPEN_MAX16);
1067 }
1068 gmx_warning("The -sub option could require as many open output files as there are\n"
1069 "index groups in the file (%d). If you get I/O errors opening new files,\n"
1070 "try reducing the number of index groups in the file, and perhaps\n"
1071 "using trjconv -sub several times on different chunks of your index file.\n",
1072 clust->clust->nr);
1073
1074 snew(clust_status, clust->clust->nr)(clust_status) = save_calloc("clust_status", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1074, (clust->clust->nr), sizeof(*(clust_status)));
1075 snew(clust_status_id, clust->clust->nr)(clust_status_id) = save_calloc("clust_status_id", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1075, (clust->clust->nr), sizeof(*(clust_status_id)));
1076 snew(nfwritten, clust->clust->nr)(nfwritten) = save_calloc("nfwritten", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1076, (clust->clust->nr), sizeof(*(nfwritten)));
1077 for (i = 0; (i < clust->clust->nr); i++)
1078 {
1079 clust_status[i] = NULL((void*)0);
1080 clust_status_id[i] = -1;
1081 }
1082 bSeparate = bSplit = FALSE0;
1083 }
1084 /* skipping */
1085 if (skip_nr <= 0)
1086 {
1087 }
1088
1089 mtop = read_mtop_for_tng(top_file, in_file, out_file);
1090
1091 /* Determine whether to read a topology */
1092 bTPS = (ftp2bSet(efTPS, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm) ||
1093 bRmPBC || bReset || bPBCcomMol || bCluster ||
1094 (ftp == efGRO) || (ftp == efPDB) || bCONECT);
1095
1096 /* Determine if when can read index groups */
1097 bIndex = (bIndex || bTPS);
1098
1099 if (bTPS)
1100 {
1101 read_tps_conf(top_file, top_title, &top, &ePBC, &xp, NULL((void*)0), top_box,
1102 bReset || bPBCcomRes);
1103 atoms = &top.atoms;
1104
1105 if (0 == top.mols.nr && (bCluster || bPBCcomMol))
1106 {
1107 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1107, "Option -pbc %s requires a .tpr file for the -s option", pbc_opt[pbc_enum]);
1108 }
1109
1110 /* top_title is only used for gro and pdb,
1111 * the header in such a file is top_title t= ...
1112 * to prevent a double t=, remove it from top_title
1113 */
1114 if ((charpt = strstr(top_title, " t= ")))
1115 {
1116 charpt[0] = '\0';
1117 }
1118
1119 if (bCONECT)
1120 {
1121 gc = gmx_conect_generate(&top);
1122 }
1123 if (bRmPBC)
1124 {
1125 gpbc = gmx_rmpbc_init(&top.idef, ePBC, top.atoms.nr);
1126 }
1127 }
1128
1129 /* get frame number index */
1130 frindex = NULL((void*)0);
1131 if (opt2bSet("-fr", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm))
1132 {
1133 printf("Select groups of frame number indices:\n");
1134 rd_index(opt2fn("-fr", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), 1, &nrfri, (atom_id **)&frindex, &frname);
1135 if (debug)
1136 {
1137 for (i = 0; i < nrfri; i++)
1138 {
1139 fprintf(debug, "frindex[%4d]=%4d\n", i, frindex[i]);
1140 }
1141 }
1142 }
1143
1144 /* get index groups etc. */
1145 if (bReset)
1146 {
1147 printf("Select group for %s fit\n",
1148 bFit ? "least squares" : "translational");
1149 get_index(atoms, ftp2fn_null(efNDX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm),
1150 1, &ifit, &ind_fit, &gn_fit);
1151
1152 if (bFit)
1153 {
1154 if (ifit < 2)
1155 {
1156 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1156, "Need at least 2 atoms to fit!\n");
1157 }
1158 else if (ifit == 3)
1159 {
1160 fprintf(stderrstderr, "WARNING: fitting with only 2 atoms is not unique\n");
1161 }
1162 }
1163 }
1164 else if (bCluster)
1165 {
1166 printf("Select group for clustering\n");
1167 get_index(atoms, ftp2fn_null(efNDX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm),
1168 1, &ifit, &ind_fit, &gn_fit);
1169 }
1170
1171 if (bIndex)
1172 {
1173 if (bCenter)
1174 {
1175 printf("Select group for centering\n");
1176 get_index(atoms, ftp2fn_null(efNDX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm),
1177 1, &ncent, &cindex, &grpnm);
1178 }
1179 printf("Select group for output\n");
1180 get_index(atoms, ftp2fn_null(efNDX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm),
1181 1, &nout, &index, &grpnm);
1182 }
1183 else
1184 {
1185 /* no index file, so read natoms from TRX */
1186 if (!read_first_frame(oenv, &trxin, in_file, &fr, TRX_DONT_SKIP(1<<6)))
1187 {
1188 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1188, "Could not read a frame from %s", in_file);
1189 }
1190 natoms = fr.natoms;
1191 close_trj(trxin);
1192 sfree(fr.x)save_free("fr.x", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1192, (fr.x));
1193 snew(index, natoms)(index) = save_calloc("index", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1193, (natoms), sizeof(*(index)));
1194 for (i = 0; i < natoms; i++)
1195 {
1196 index[i] = i;
1197 }
1198 nout = natoms;
1199 if (bCenter)
1200 {
1201 ncent = nout;
1202 cindex = index;
1203 }
1204 }
1205
1206 if (bReset)
1207 {
1208 snew(w_rls, atoms->nr)(w_rls) = save_calloc("w_rls", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1208, (atoms->nr), sizeof(*(w_rls)));
1209 for (i = 0; (i < ifit); i++)
1210 {
1211 w_rls[ind_fit[i]] = atoms->atom[ind_fit[i]].m;
1212 }
1213
1214 /* Restore reference structure and set to origin,
1215 store original location (to put structure back) */
1216 if (bRmPBC)
1217 {
1218 gmx_rmpbc(gpbc, top.atoms.nr, top_box, xp);
1219 }
1220 copy_rvec(xp[index[0]], x_shift);
1221 reset_x_ndim(nfitdim, ifit, ind_fit, atoms->nr, NULL((void*)0), xp, w_rls);
1222 rvec_dec(x_shift, xp[index[0]]);
1223 }
1224 else
1225 {
1226 clear_rvec(x_shift);
1227 }
1228
1229 if (bDropUnder || bDropOver)
1230 {
1231 /* Read the .xvg file with the drop values */
1232 fprintf(stderrstderr, "\nReading drop file ...");
1233 ndrop = read_xvg(opt2fn("-drop", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), &dropval, &ncol);
1234 fprintf(stderrstderr, " %d time points\n", ndrop);
1235 if (ndrop == 0 || ncol < 2)
1236 {
1237 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1237, "Found no data points in %s",
1238 opt2fn("-drop", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm));
1239 }
1240 drop0 = 0;
1241 drop1 = 0;
1242 }
1243
1244 /* Make atoms struct for output in GRO or PDB files */
1245 if ((ftp == efGRO) || ((ftp == efG96) && bTPS) || (ftp == efPDB))
1246 {
1247 /* get memory for stuff to go in .pdb file */
1248 init_t_atoms(&useatoms, atoms->nr, FALSE0);
1249 sfree(useatoms.resinfo)save_free("useatoms.resinfo", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1249, (useatoms.resinfo));
1250 useatoms.resinfo = atoms->resinfo;
1251 for (i = 0; (i < nout); i++)
1252 {
1253 useatoms.atomname[i] = atoms->atomname[index[i]];
1254 useatoms.atom[i] = atoms->atom[index[i]];
1255 useatoms.nres = max(useatoms.nres, useatoms.atom[i].resind+1)(((useatoms.nres) > (useatoms.atom[i].resind+1)) ? (useatoms
.nres) : (useatoms.atom[i].resind+1) );
1256 }
1257 useatoms.nr = nout;
1258 }
1259 /* select what to read */
1260 if (ftp == efTRR || ftp == efTRJ)
1261 {
1262 flags = TRX_READ_X(1<<0);
1263 }
1264 else
1265 {
1266 flags = TRX_NEED_X(1<<1);
1267 }
1268 if (bVels)
1269 {
1270 flags = flags | TRX_READ_V(1<<2);
1271 }
1272 if (bForce)
1273 {
1274 flags = flags | TRX_READ_F(1<<4);
1275 }
1276
1277 /* open trx file for reading */
1278 bHaveFirstFrame = read_first_frame(oenv, &trxin, in_file, &fr, flags);
1279 if (fr.bPrec)
1280 {
1281 fprintf(stderrstderr, "\nPrecision of %s is %g (nm)\n", in_file, 1/fr.prec);
1282 }
1283 if (bNeedPrec)
1284 {
1285 if (bSetPrec || !fr.bPrec)
1286 {
1287 fprintf(stderrstderr, "\nSetting output precision to %g (nm)\n", 1/prec);
1288 }
1289 else
1290 {
1291 fprintf(stderrstderr, "Using output precision of %g (nm)\n", 1/prec);
1292 }
1293 }
1294
1295 if (bHaveFirstFrame)
1296 {
1297 set_trxframe_ePBC(&fr, ePBC);
1298
1299 natoms = fr.natoms;
1300
1301 if (bSetTime)
1302 {
1303 tshift = tzero-fr.time;
1304 }
1305 else
1306 {
1307 tzero = fr.time;
1308 }
1309
1310 bCopy = FALSE0;
1311 if (bIndex)
1312 {
1313 /* check if index is meaningful */
1314 for (i = 0; i < nout; i++)
1315 {
1316 if (index[i] >= natoms)
1317 {
1318 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1318,
1319 "Index[%d] %d is larger than the number of atoms in the\n"
1320 "trajectory file (%d). There is a mismatch in the contents\n"
1321 "of your -f, -s and/or -n files.", i, index[i]+1, natoms);
1322 }
1323 bCopy = bCopy || (i != index[i]);
1324 }
1325 }
1326
1327 /* open output for writing */
1328 strcpy(filemode, "w");
1329 switch (ftp)
1330 {
1331 case efTNG:
1332 trjtools_gmx_prepare_tng_writing(out_file,
1333 filemode[0],
1334 trxin,
1335 &trxout,
1336 NULL((void*)0),
1337 nout,
1338 mtop,
1339 index,
1340 grpnm);
1341 break;
1342 case efXTC:
1343 case efTRR:
1344 case efTRJ:
1345 out = NULL((void*)0);
1346 if (!bSplit && !bSubTraj)
1347 {
1348 trxout = open_trx(out_file, filemode);
1349 }
1350 break;
1351 case efGRO:
1352 case efG96:
1353 case efPDB:
1354 if (( !bSeparate && !bSplit ) && !bSubTraj)
1355 {
1356 out = gmx_ffopen(out_file, filemode);
1357 }
1358 break;
1359 default:
1360 gmx_incons("Illegal output file format")_gmx_error("incons", "Illegal output file format", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1360);
1361 }
1362
1363 if (bCopy)
1364 {
1365 snew(xmem, nout)(xmem) = save_calloc("xmem", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1365, (nout), sizeof(*(xmem)));
1366 if (bVels)
1367 {
1368 snew(vmem, nout)(vmem) = save_calloc("vmem", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1368, (nout), sizeof(*(vmem)));
1369 }
1370 if (bForce)
1371 {
1372 snew(fmem, nout)(fmem) = save_calloc("fmem", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1372, (nout), sizeof(*(fmem)));
1373 }
1374 }
1375
1376 /* Start the big loop over frames */
1377 file_nr = 0;
1378 frame = 0;
1379 outframe = 0;
1380 model_nr = 0;
1381 bDTset = FALSE0;
1382
1383 /* Main loop over frames */
1384 do
1385 {
1386 if (!fr.bStep)
1387 {
1388 /* set the step */
1389 fr.step = newstep;
1390 newstep++;
1391 }
1392 if (bSubTraj)
1393 {
1394 /*if (frame >= clust->clust->nra)
1395 gmx_fatal(FARGS,"There are more frames in the trajectory than in the cluster index file\n");*/
1396 if (frame > clust->maxframe)
1397 {
1398 my_clust = -1;
1399 }
1400 else
1401 {
1402 my_clust = clust->inv_clust[frame];
1403 }
1404 if ((my_clust < 0) || (my_clust >= clust->clust->nr) ||
1405 (my_clust == NO_ATID(atom_id)(~0)))
1406 {
1407 my_clust = -1;
1408 }
1409 }
1410
1411 if (bSetBox)
1412 {
1413 /* generate new box */
1414 clear_mat(fr.box);
1415 for (m = 0; m < DIM3; m++)
1416 {
1417 fr.box[m][m] = newbox[m];
1418 }
1419 }
1420
1421 if (bTrans)
1422 {
1423 for (i = 0; i < natoms; i++)
1424 {
1425 rvec_inc(fr.x[i], trans);
1426 }
1427 }
1428
1429 if (bTDump)
1430 {
1431 /* determine timestep */
1432 if (t0 == -1)
1433 {
1434 t0 = fr.time;
1435 }
1436 else
1437 {
1438 if (!bDTset)
1439 {
1440 dt = fr.time-t0;
1441 bDTset = TRUE1;
1442 }
1443 }
1444 /* This is not very elegant, as one can not dump a frame after
1445 * a timestep with is more than twice as small as the first one. */
1446 bDumpFrame = (fr.time > tdump-0.5*dt) && (fr.time <= tdump+0.5*dt);
1447 }
1448 else
1449 {
1450 bDumpFrame = FALSE0;
1451 }
1452
1453 /* determine if an atom jumped across the box and reset it if so */
1454 if (bNoJump && (bTPS || frame != 0))
1455 {
1456 for (d = 0; d < DIM3; d++)
1457 {
1458 hbox[d] = 0.5*fr.box[d][d];
1459 }
1460 for (i = 0; i < natoms; i++)
1461 {
1462 if (bReset)
1463 {
1464 rvec_dec(fr.x[i], x_shift);
1465 }
1466 for (m = DIM3-1; m >= 0; m--)
1467 {
1468 if (hbox[m] > 0)
1469 {
1470 while (fr.x[i][m]-xp[i][m] <= -hbox[m])
1471 {
1472 for (d = 0; d <= m; d++)
1473 {
1474 fr.x[i][d] += fr.box[m][d];
1475 }
1476 }
1477 while (fr.x[i][m]-xp[i][m] > hbox[m])
1478 {
1479 for (d = 0; d <= m; d++)
1480 {
1481 fr.x[i][d] -= fr.box[m][d];
1482 }
1483 }
1484 }
1485 }
1486 }
1487 }
1488 else if (bCluster)
1489 {
1490 calc_pbc_cluster(ecenter, ifit, &top, ePBC, fr.x, ind_fit, fr.box);
1491 }
1492
1493 if (bPFit)
1494 {
1495 /* Now modify the coords according to the flags,
1496 for normal fit, this is only done for output frames */
1497 if (bRmPBC)
1498 {
1499 gmx_rmpbc_trxfr(gpbc, &fr);
1500 }
1501
1502 reset_x_ndim(nfitdim, ifit, ind_fit, natoms, NULL((void*)0), fr.x, w_rls);
1503 do_fit(natoms, w_rls, xp, fr.x);
1504 }
1505
1506 /* store this set of coordinates for future use */
1507 if (bPFit || bNoJump)
1508 {
1509 if (xp == NULL((void*)0))
1510 {
1511 snew(xp, natoms)(xp) = save_calloc("xp", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1511, (natoms), sizeof(*(xp)));
1512 }
1513 for (i = 0; (i < natoms); i++)
1514 {
1515 copy_rvec(fr.x[i], xp[i]);
1516 rvec_inc(fr.x[i], x_shift);
1517 }
1518 }
1519
1520 if (frindex)
1521 {
1522 /* see if we have a frame from the frame index group */
1523 for (i = 0; i < nrfri && !bDumpFrame; i++)
1524 {
1525 bDumpFrame = frame == frindex[i];
1526 }
1527 }
1528 if (debug && bDumpFrame)
1529 {
1530 fprintf(debug, "dumping %d\n", frame);
1531 }
1532
1533 bWriteFrame =
1534 ( ( !bTDump && !frindex && frame % skip_nr == 0 ) || bDumpFrame );
1535
1536 if (bWriteFrame && (bDropUnder || bDropOver))
1537 {
1538 while (dropval[0][drop1] < fr.time && drop1+1 < ndrop)
1539 {
1540 drop0 = drop1;
1541 drop1++;
1542 }
1543 if (fabs(dropval[0][drop0] - fr.time)
1544 < fabs(dropval[0][drop1] - fr.time))
1545 {
1546 dropuse = drop0;
1547 }
1548 else
1549 {
1550 dropuse = drop1;
1551 }
1552 if ((bDropUnder && dropval[1][dropuse] < dropunder) ||
1553 (bDropOver && dropval[1][dropuse] > dropover))
1554 {
1555 bWriteFrame = FALSE0;
1556 }
1557 }
1558
1559 if (bWriteFrame)
1560 {
1561
1562 /* calc new time */
1563 if (bTimeStep)
1564 {
1565 fr.time = tzero+frame*timestep;
1566 }
1567 else
1568 if (bSetTime)
1569 {
1570 fr.time += tshift;
1571 }
1572
1573 if (bTDump)
1574 {
1575 fprintf(stderrstderr, "\nDumping frame at t= %g %s\n",
1576 output_env_conv_time(oenv, fr.time), output_env_get_time_unit(oenv));
1577 }
1578
1579 /* check for writing at each delta_t */
1580 bDoIt = (delta_t == 0);
1581 if (!bDoIt)
1582 {
1583 if (!bRound)
1584 {
1585 bDoIt = bRmod(fr.time, tzero, delta_t)bRmod_fd(fr.time, tzero, delta_t, 0);
1586 }
1587 else
1588 {
1589 /* round() is not C89 compatible, so we do this: */
1590 bDoIt = bRmod(floor(fr.time+0.5), floor(tzero+0.5),bRmod_fd(floor(fr.time+0.5), floor(tzero+0.5), floor(delta_t+
0.5), 0)
1591 floor(delta_t+0.5))bRmod_fd(floor(fr.time+0.5), floor(tzero+0.5), floor(delta_t+
0.5), 0);
1592 }
1593 }
1594
1595 if (bDoIt || bTDump)
1596 {
1597 /* print sometimes */
1598 if ( ((outframe % SKIP10) == 0) || (outframe < SKIP10) )
1599 {
1600 fprintf(stderrstderr, " -> frame %6d time %8.3f \r",
1601 outframe, output_env_conv_time(oenv, fr.time));
1602 }
1603
1604 if (!bPFit)
1605 {
1606 /* Now modify the coords according to the flags,
1607 for PFit we did this already! */
1608
1609 if (bRmPBC)
1610 {
1611 gmx_rmpbc_trxfr(gpbc, &fr);
1612 }
1613
1614 if (bReset)
1615 {
1616 reset_x_ndim(nfitdim, ifit, ind_fit, natoms, NULL((void*)0), fr.x, w_rls);
1617 if (bFit)
1618 {
1619 do_fit_ndim(nfitdim, natoms, w_rls, xp, fr.x);
1620 }
1621 if (!bCenter)
1622 {
1623 for (i = 0; i < natoms; i++)
1624 {
1625 rvec_inc(fr.x[i], x_shift);
1626 }
1627 }
1628 }
1629
1630 if (bCenter)
1631 {
1632 center_x(ecenter, fr.x, fr.box, natoms, ncent, cindex);
1633 }
1634 }
1635
1636 if (bPBCcomAtom)
1637 {
1638 switch (unitcell_enum)
1639 {
1640 case euRect:
1641 put_atoms_in_box(ePBC, fr.box, natoms, fr.x);
1642 break;
1643 case euTric:
1644 put_atoms_in_triclinic_unitcell(ecenter, fr.box, natoms, fr.x);
1645 break;
1646 case euCompact:
1647 warn = put_atoms_in_compact_unitcell(ePBC, ecenter, fr.box,
1648 natoms, fr.x);
1649 if (warn && !bWarnCompact)
1650 {
1651 fprintf(stderrstderr, "\n%s\n", warn);
1652 bWarnCompact = TRUE1;
1653 }
1654 break;
1655 }
1656 }
1657 if (bPBCcomRes)
1658 {
1659 put_residue_com_in_box(unitcell_enum, ecenter,
1660 natoms, atoms->atom, ePBC, fr.box, fr.x);
1661 }
1662 if (bPBCcomMol)
1663 {
1664 put_molecule_com_in_box(unitcell_enum, ecenter,
1665 &top.mols,
1666 natoms, atoms->atom, ePBC, fr.box, fr.x);
1667 }
1668 /* Copy the input trxframe struct to the output trxframe struct */
1669 frout = fr;
1670 frout.bV = (frout.bV && bVels);
1671 frout.bF = (frout.bF && bForce);
1672 frout.natoms = nout;
1673 if (bNeedPrec && (bSetPrec || !fr.bPrec))
1674 {
1675 frout.bPrec = TRUE1;
1676 frout.prec = prec;
1677 }
1678 if (bCopy)
1679 {
1680 frout.x = xmem;
1681 if (frout.bV)
1682 {
1683 frout.v = vmem;
1684 }
1685 if (frout.bF)
1686 {
1687 frout.f = fmem;
1688 }
1689 for (i = 0; i < nout; i++)
1690 {
1691 copy_rvec(fr.x[index[i]], frout.x[i]);
1692 if (frout.bV)
1693 {
1694 copy_rvec(fr.v[index[i]], frout.v[i]);
1695 }
1696 if (frout.bF)
1697 {
1698 copy_rvec(fr.f[index[i]], frout.f[i]);
1699 }
1700 }
1701 }
1702
1703 if (opt2parg_bSet("-shift", NPA((int)(sizeof(pa)/sizeof((pa)[0]))), pa))
1704 {
1705 for (i = 0; i < nout; i++)
1706 {
1707 for (d = 0; d < DIM3; d++)
1708 {
1709 frout.x[i][d] += outframe*shift[d];
1710 }
1711 }
1712 }
1713
1714 if (!bRound)
1715 {
1716 bSplitHere = bSplit && bRmod(fr.time, tzero, split_t)bRmod_fd(fr.time, tzero, split_t, 0);
1717 }
1718 else
1719 {
1720 /* round() is not C89 compatible, so we do this: */
1721 bSplitHere = bSplit && bRmod(floor(fr.time+0.5),bRmod_fd(floor(fr.time+0.5), floor(tzero+0.5), floor(split_t+
0.5), 0)
1722 floor(tzero+0.5),bRmod_fd(floor(fr.time+0.5), floor(tzero+0.5), floor(split_t+
0.5), 0)
1723 floor(split_t+0.5))bRmod_fd(floor(fr.time+0.5), floor(tzero+0.5), floor(split_t+
0.5), 0);
1724 }
1725 if (bSeparate || bSplitHere)
1726 {
1727 mk_filenm(outf_base, ftp2ext(ftp), nzero, file_nr, out_file2);
1728 }
1729
1730 switch (ftp)
1731 {
1732 case efTNG:
1733 write_tng_frame(trxout, &frout);
1734 // TODO when trjconv behaves better: work how to read and write lambda
1735 break;
1736 case efTRJ:
1737 case efTRR:
1738 case efXTC:
1739 if (bSplitHere)
1740 {
1741 if (trxout)
1742 {
1743 close_trx(trxout);
1744 }
1745 trxout = open_trx(out_file2, filemode);
1746 }
1747 if (bSubTraj)
1748 {
1749 if (my_clust != -1)
1750 {
1751 char buf[STRLEN4096];
1752 if (clust_status_id[my_clust] == -1)
1753 {
1754 sprintf(buf, "%s.%s", clust->grpname[my_clust], ftp2ext(ftp));
1755 clust_status[my_clust] = open_trx(buf, "w");
1756 clust_status_id[my_clust] = 1;
1757 ntrxopen++;
1758 }
1759 else if (clust_status_id[my_clust] == -2)
1760 {
1761 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1761, "File %s.xtc should still be open (%d open .xtc files)\n" "in order to write frame %d. my_clust = %d",
1762 clust->grpname[my_clust], ntrxopen, frame,
1763 my_clust);
1764 }
1765 write_trxframe(clust_status[my_clust], &frout, gc);
1766 nfwritten[my_clust]++;
1767 if (nfwritten[my_clust] ==
1768 (clust->clust->index[my_clust+1]-
1769 clust->clust->index[my_clust]))
1770 {
1771 close_trx(clust_status[my_clust]);
1772 clust_status[my_clust] = NULL((void*)0);
1773 clust_status_id[my_clust] = -2;
1774 ntrxopen--;
1775 if (ntrxopen < 0)
1776 {
1777 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1777, "Less than zero open .xtc files!");
1778 }
1779 }
1780 }
1781 }
1782 else
1783 {
1784 write_trxframe(trxout, &frout, gc);
1785 }
1786 break;
1787 case efGRO:
1788 case efG96:
1789 case efPDB:
1790 sprintf(title, "Generated by trjconv : %s t= %9.5f",
1791 top_title, fr.time);
1792 if (bSeparate || bSplitHere)
1793 {
1794 out = gmx_ffopen(out_file2, "w");
1795 }
1796 switch (ftp)
1797 {
1798 case efGRO:
1799 write_hconf_p(out, title, &useatoms, prec2ndec(frout.prec),
1800 frout.x, frout.bV ? frout.v : NULL((void*)0), frout.box);
1801 break;
1802 case efPDB:
1803 fprintf(out, "REMARK GENERATED BY TRJCONV\n");
1804 sprintf(title, "%s t= %9.5f", top_title, frout.time);
1805 /* if reading from pdb, we want to keep the original
1806 model numbering else we write the output frame
1807 number plus one, because model 0 is not allowed in pdb */
1808 if (ftpin == efPDB && fr.bStep && fr.step > model_nr)
1809 {
1810 model_nr = fr.step;
1811 }
1812 else
1813 {
1814 model_nr++;
1815 }
1816 write_pdbfile(out, title, &useatoms, frout.x,
1817 frout.ePBC, frout.box, ' ', model_nr, gc, TRUE1);
1818 break;
1819 case efG96:
1820 frout.title = title;
1821 if (bSeparate || bTDump)
1822 {
1823 frout.bTitle = TRUE1;
1824 if (bTPS)
1825 {
1826 frout.bAtoms = TRUE1;
1827 }
1828 frout.atoms = &useatoms;
1829 frout.bStep = FALSE0;
1830 frout.bTime = FALSE0;
1831 }
1832 else
1833 {
1834 frout.bTitle = (outframe == 0);
1835 frout.bAtoms = FALSE0;
1836 frout.bStep = TRUE1;
1837 frout.bTime = TRUE1;
1838 }
1839 write_g96_conf(out, &frout, -1, NULL((void*)0));
1840 }
1841 if (bSeparate)
1842 {
1843 gmx_ffclose(out);
1844 out = NULL((void*)0);
1845 }
1846 break;
1847 default:
1848 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1848, "DHE, ftp=%d\n", ftp);
1849 }
1850 if (bSeparate || bSplitHere)
1851 {
1852 file_nr++;
1853 }
1854
1855 /* execute command */
1856 if (bExec)
1857 {
1858 char c[255];
1859 sprintf(c, "%s %d", exec_command, file_nr-1);
1860 /*fprintf(stderr,"Executing '%s'\n",c);*/
1861#ifdef GMX_NO_SYSTEM
1862 printf("Warning-- No calls to system(3) supported on this platform.");
1863 printf("Warning-- Skipping execution of 'system(\"%s\")'.", c);
1864#else
1865 if (0 != system(c))
1866 {
1867 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1867, "Error executing command: %s", c);
1868 }
1869#endif
1870 }
1871 outframe++;
1872 }
1873 }
1874 frame++;
1875 bHaveNextFrame = read_next_frame(oenv, trxin, &fr);
1876 }
1877 while (!(bTDump && bDumpFrame) && bHaveNextFrame);
1878 }
1879
1880 if (!bHaveFirstFrame || (bTDump && !bDumpFrame))
1881 {
1882 fprintf(stderrstderr, "\nWARNING no output, "
1883 "last frame read at t=%g\n", fr.time);
1884 }
1885 fprintf(stderrstderr, "\n");
1886
1887 close_trj(trxin);
1888 sfree(outf_base)save_free("outf_base", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1888, (outf_base));
1889
1890 if (bRmPBC)
1891 {
1892 gmx_rmpbc_done(gpbc);
1893 }
1894
1895 if (trxout)
1896 {
1897 close_trx(trxout);
1898 }
1899 else if (out != NULL((void*)0))
1900 {
1901 gmx_ffclose(out);
1902 }
1903 if (bSubTraj)
1904 {
1905 for (i = 0; (i < clust->clust->nr); i++)
1906 {
1907 if (clust_status_id[i] >= 0)
1908 {
1909 close_trx(clust_status[i]);
1910 }
1911 }
1912 }
1913 }
1914
1915 sfree(mtop)save_free("mtop", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c"
, 1915, (mtop));
1916
1917 do_view(oenv, out_file, NULL((void*)0));
1918
1919 return 0;
1920}