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49 #include "gromacs/commandline/pargs.h"
50 #include "gromacs/fileio/confio.h"
51 #include "gromacs/fileio/gmxfio.h"
52 #include "gromacs/fileio/pdbio.h"
53 #include "gromacs/fileio/tngio_for_tools.h"
54 #include "gromacs/fileio/tpxio.h"
55 #include "gromacs/fileio/trnio.h"
56 #include "gromacs/fileio/trxio.h"
57 #include "gromacs/fileio/xtcio.h"
58 #include "gromacs/fileio/xvgr.h"
59 #include "gromacs/gmxana/gmx_ana.h"
60 #include "gromacs/legacyheaders/copyrite.h"
61 #include "gromacs/legacyheaders/macros.h"
62 #include "gromacs/legacyheaders/names.h"
63 #include "gromacs/legacyheaders/typedefs.h"
64 #include "gromacs/legacyheaders/viewit.h"
65 #include "gromacs/math/do_fit.h"
66 #include "gromacs/math/vec.h"
67 #include "gromacs/pbcutil/pbc.h"
68 #include "gromacs/pbcutil/rmpbc.h"
69 #include "gromacs/topology/index.h"
70 #include "gromacs/topology/topology.h"
71 #include "gromacs/utility/fatalerror.h"
72 #include "gromacs/utility/futil.h"
73 #include "gromacs/utility/smalloc.h"
76 euSel, euRect, euTric, euCompact, euNR
80 static void calc_pbc_cluster(int ecenter, int nrefat, t_topology *top, int ePBC,
81 rvec x[], atom_id index[], matrix box)
83 int m, i, j, j0, j1, jj, ai, aj;
86 rvec dx, xtest, box_center;
87 int nmol, imol_center;
89 gmx_bool *bMol, *bTmp;
90 rvec *m_com, *m_shift;
98 calc_box_center(ecenter, box, box_center);
100 /* Initiate the pbc structure */
101 memset(&pbc, 0, sizeof(pbc));
102 set_pbc(&pbc, ePBC, box);
104 /* Convert atom index to molecular */
106 molind = top->mols.index;
112 snew(bTmp, top->atoms.nr);
114 for (i = 0; (i < nrefat); i++)
116 /* Mark all molecules in the index */
119 /* Binary search assuming the molecules are sorted */
124 if (ai < molind[j0+1])
128 else if (ai >= molind[j1])
135 if (ai < molind[jj+1])
147 /* Double check whether all atoms in all molecules that are marked are part
148 * of the cluster. Simultaneously compute the center of geometry.
150 min_dist2 = 10*sqr(trace(box));
153 for (i = 0; i < nmol; i++)
155 for (j = molind[i]; j < molind[i+1]; j++)
157 if (bMol[i] && !bTmp[j])
159 gmx_fatal(FARGS, "Molecule %d marked for clustering but not atom %d in it - check your index!", i+1, j+1);
161 else if (!bMol[i] && bTmp[j])
163 gmx_fatal(FARGS, "Atom %d marked for clustering but not molecule %d - this is an internal error...", j+1, i+1);
167 /* Make molecule whole, move 2nd and higher atom to same periodicity as 1st atom in molecule */
170 pbc_dx(&pbc, x[j], x[j-1], dx);
171 rvec_add(x[j-1], dx, x[j]);
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]);
179 /* Normalize center of geometry */
180 fac = 1.0/(molind[i+1]-molind[i]);
181 for (m = 0; (m < DIM); m++)
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);
189 if (tmp_r2 < min_dist2)
194 cluster[ncluster++] = i;
201 fprintf(stderr, "No molecules selected in the cluster\n");
204 else if (imol_center == -1)
206 fprintf(stderr, "No central molecules could be found\n");
211 added[nadded++] = imol_center;
212 bMol[imol_center] = FALSE;
214 while (nadded < ncluster)
216 /* Find min distance between cluster molecules and those remaining to be added */
217 min_dist2 = 10*sqr(trace(box));
220 /* Loop over added mols */
221 for (i = 0; i < nadded; i++)
224 /* Loop over all mols */
225 for (j = 0; j < ncluster; j++)
228 /* check those remaining to be added */
231 pbc_dx(&pbc, m_com[aj], m_com[ai], dx);
232 tmp_r2 = iprod(dx, dx);
233 if (tmp_r2 < min_dist2)
243 /* Add the best molecule */
244 added[nadded++] = jmin;
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]);
252 for (j = molind[jmin]; j < molind[jmin+1]; j++)
254 rvec_inc(x[j], m_shift[jmin]);
256 fprintf(stdout, "\rClustering iteration %d of %d...", nadded, ncluster);
266 fprintf(stdout, "\n");
269 static void put_molecule_com_in_box(int unitcell_enum, int ecenter,
271 int natoms, t_atom atom[],
272 int ePBC, matrix box, rvec x[])
276 rvec com, new_com, shift, dx, box_center;
281 calc_box_center(ecenter, box, box_center);
282 set_pbc(&pbc, ePBC, box);
285 gmx_fatal(FARGS, "There are no molecule descriptions. I need a .tpr file for this pbc option.");
287 for (i = 0; (i < mols->nr); i++)
292 for (j = mols->index[i]; (j < mols->index[i+1] && j < natoms); j++)
295 for (d = 0; d < DIM; d++)
301 /* calculate final COM */
302 svmul(1.0/mtot, com, com);
304 /* check if COM is outside box */
305 copy_rvec(com, new_com);
306 switch (unitcell_enum)
309 put_atoms_in_box(ePBC, box, 1, &new_com);
312 put_atoms_in_triclinic_unitcell(ecenter, box, 1, &new_com);
315 put_atoms_in_compact_unitcell(ePBC, ecenter, box, 1, &new_com);
318 rvec_sub(new_com, com, shift);
319 if (norm2(shift) > 0)
323 fprintf(debug, "\nShifting position of molecule %d "
324 "by %8.3f %8.3f %8.3f\n", i+1,
325 shift[XX], shift[YY], shift[ZZ]);
327 for (j = mols->index[i]; (j < mols->index[i+1] && j < natoms); j++)
329 rvec_inc(x[j], shift);
335 static void put_residue_com_in_box(int unitcell_enum, int ecenter,
336 int natoms, t_atom atom[],
337 int ePBC, matrix box, rvec x[])
339 atom_id i, j, res_start, res_end, res_nat;
343 rvec box_center, com, new_com, shift;
345 calc_box_center(ecenter, box, box_center);
351 for (i = 0; i < natoms+1; i++)
353 if (i == natoms || (presnr != atom[i].resind && presnr != NOTSET))
355 /* calculate final COM */
357 res_nat = res_end - res_start;
358 svmul(1.0/mtot, com, com);
360 /* check if COM is outside box */
361 copy_rvec(com, new_com);
362 switch (unitcell_enum)
365 put_atoms_in_box(ePBC, box, 1, &new_com);
368 put_atoms_in_triclinic_unitcell(ecenter, box, 1, &new_com);
371 put_atoms_in_compact_unitcell(ePBC, ecenter, box, 1, &new_com);
374 rvec_sub(new_com, com, shift);
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[XX], shift[YY], shift[ZZ]);
383 for (j = res_start; j < res_end; j++)
385 rvec_inc(x[j], shift);
391 /* remember start of new residue */
398 for (d = 0; d < DIM; d++)
404 presnr = atom[i].resind;
409 static void center_x(int ecenter, rvec x[], matrix box, int n, int nc, atom_id ci[])
412 rvec cmin, cmax, box_center, dx;
416 copy_rvec(x[ci[0]], cmin);
417 copy_rvec(x[ci[0]], cmax);
418 for (i = 0; i < nc; i++)
421 for (m = 0; m < DIM; m++)
423 if (x[ai][m] < cmin[m])
427 else if (x[ai][m] > cmax[m])
433 calc_box_center(ecenter, box, box_center);
434 for (m = 0; m < DIM; m++)
436 dx[m] = box_center[m]-(cmin[m]+cmax[m])*0.5;
439 for (i = 0; i < n; i++)
446 static void mk_filenm(char *base, const char *ext, int ndigit, int file_nr,
452 strcpy(out_file, base);
463 strncat(out_file, "00000000000", ndigit-nd);
465 sprintf(nbuf, "%d.", file_nr);
466 strcat(out_file, nbuf);
467 strcat(out_file, ext);
470 void check_trn(const char *fn)
472 if (fn2ftp(fn) != efTRR)
474 gmx_fatal(FARGS, "%s is not a trajectory file, exiting\n", fn);
478 #ifndef GMX_NATIVE_WINDOWS
479 void do_trunc(const char *fn, real t0)
492 gmx_fatal(FARGS, "You forgot to set the truncation time");
495 /* Check whether this is a .trr file */
498 in = open_trn(fn, "r");
499 fp = gmx_fio_getfp(in);
502 fprintf(stderr, "Sorry, can not trunc %s, truncation of this filetype is not supported\n", fn);
508 fpos = gmx_fio_ftell(in);
510 while (!bStop && fread_trnheader(in, &sh, &bOK))
512 fread_htrn(in, &sh, NULL, NULL, NULL, NULL);
513 fpos = gmx_ftell(fp);
517 gmx_fseek(fp, fpos, SEEK_SET);
523 fprintf(stderr, "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))
528 gmx_fatal(FARGS, "Error reading user input");
530 if (strcmp(yesno, "YES") == 0)
532 fprintf(stderr, "Once again, I'm gonna DO this...\n");
534 if (0 != truncate(fn, fpos))
536 gmx_fatal(FARGS, "Error truncating file %s", fn);
541 fprintf(stderr, "Ok, I'll forget about it\n");
546 fprintf(stderr, "Already at end of file (t=%g)...\n", t);
553 /*! \brief Read a full molecular topology if useful and available.
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
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.
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
573 static gmx_mtop_t *read_mtop_for_tng(const char *tps_file,
574 const char *input_file,
575 const char *output_file)
577 gmx_mtop_t *mtop = NULL;
579 if (fn2bTPX(tps_file) &&
580 efTNG != fn2ftp(input_file) &&
581 efTNG == fn2ftp(output_file))
583 int temp_natoms = -1;
585 read_tpx(tps_file, NULL, NULL, &temp_natoms,
586 NULL, NULL, NULL, mtop);
592 int gmx_trjconv(int argc, char *argv[])
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]",
614 "[gmx-trjcat] is better suited for concatenating multiple trajectory files.",
617 "The following formats are supported for input and output:",
618 "[TT].xtc[tt], [TT].trr[tt], [TT].gro[tt], [TT].g96[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]",
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].gro[tt] and [TT].g96[tt] files.[PAR]",
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]",
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]",
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]",
654 "Option [TT]-pbc[tt] sets the type of periodic boundary condition",
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]",
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]",
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]",
700 "Option [TT]-box[tt] sets the size of the new box. If you want to"
701 "modify only some of the dimensions, e.g. when reading from a trajectory,"
702 "you can use -1 for those dimensions that should stay the same"
704 "It is not always possible to use combinations of [TT]-pbc[tt],",
705 "[TT]-fit[tt], [TT]-ur[tt] and [TT]-center[tt] to do exactly what",
706 "you want in one call to [THISMODULE]. Consider using multiple",
707 "calls, and check out the GROMACS website for suggestions.[PAR]",
709 "With [TT]-dt[tt], it is possible to reduce the number of ",
710 "frames in the output. This option relies on the accuracy of the times",
711 "in your input trajectory, so if these are inaccurate use the",
712 "[TT]-timestep[tt] option to modify the time (this can be done",
713 "simultaneously). For making smooth movies, the program [gmx-filter]",
714 "can reduce the number of frames while using low-pass frequency",
715 "filtering, this reduces aliasing of high frequency motions.[PAR]",
717 "Using [TT]-trunc[tt] [THISMODULE] can truncate [TT].trr[tt] in place, i.e.",
718 "without copying the file. This is useful when a run has crashed",
719 "during disk I/O (i.e. full disk), or when two contiguous",
720 "trajectories must be concatenated without having double frames.[PAR]",
722 "Option [TT]-dump[tt] can be used to extract a frame at or near",
723 "one specific time from your trajectory.[PAR]",
725 "Option [TT]-drop[tt] reads an [TT].xvg[tt] file with times and values.",
726 "When options [TT]-dropunder[tt] and/or [TT]-dropover[tt] are set,",
727 "frames with a value below and above the value of the respective options",
728 "will not be written."
744 const char *pbc_opt[epNR + 1] =
746 NULL, "none", "mol", "res", "atom", "nojump", "cluster", "whole",
751 const char *unitcell_opt[euNR+1] =
752 { NULL, "rect", "tric", "compact", NULL };
756 ecSel, ecTric, ecRect, ecZero, ecNR
758 const char *center_opt[ecNR+1] =
759 { NULL, "tric", "rect", "zero", NULL };
765 efSel, efNone, efFit, efFitXY, efReset, efResetXY, efPFit, efNR
767 const char *fit[efNR + 1] =
769 NULL, "none", "rot+trans", "rotxy+transxy", "translation", "transxy",
773 static gmx_bool bSeparate = FALSE, bVels = TRUE, bForce = FALSE, bCONECT = FALSE;
774 static gmx_bool bCenter = FALSE;
775 static int skip_nr = 1, ndec = 3, nzero = 0;
776 static real tzero = 0, delta_t = 0, timestep = 0, ttrunc = -1, tdump = -1, split_t = 0;
777 static rvec newbox = {0, 0, 0}, shift = {0, 0, 0}, trans = {0, 0, 0};
778 static char *exec_command = NULL;
779 static real dropunder = 0, dropover = 0;
780 static gmx_bool bRound = FALSE;
785 { "-skip", FALSE, etINT,
786 { &skip_nr }, "Only write every nr-th frame" },
787 { "-dt", FALSE, etTIME,
789 "Only write frame when t MOD dt = first time (%t)" },
790 { "-round", FALSE, etBOOL,
791 { &bRound }, "Round measurements to nearest picosecond"},
792 { "-dump", FALSE, etTIME,
793 { &tdump }, "Dump frame nearest specified time (%t)" },
794 { "-t0", FALSE, etTIME,
796 "Starting time (%t) (default: don't change)" },
797 { "-timestep", FALSE, etTIME,
799 "Change time step between input frames (%t)" },
800 { "-pbc", FALSE, etENUM,
802 "PBC treatment (see help text for full description)" },
803 { "-ur", FALSE, etENUM,
804 { unitcell_opt }, "Unit-cell representation" },
805 { "-center", FALSE, etBOOL,
806 { &bCenter }, "Center atoms in box" },
807 { "-boxcenter", FALSE, etENUM,
808 { center_opt }, "Center for -pbc and -center" },
809 { "-box", FALSE, etRVEC,
811 "Size for new cubic box (default: read from input)" },
812 { "-trans", FALSE, etRVEC,
814 "All coordinates will be translated by trans. This "
815 "can advantageously be combined with -pbc mol -ur "
817 { "-shift", FALSE, etRVEC,
819 "All coordinates will be shifted by framenr*shift" },
820 { "-fit", FALSE, etENUM,
822 "Fit molecule to ref structure in the structure file" },
823 { "-ndec", FALSE, etINT,
825 "Precision for .xtc and .gro writing in number of "
827 { "-vel", FALSE, etBOOL,
828 { &bVels }, "Read and write velocities if possible" },
829 { "-force", FALSE, etBOOL,
830 { &bForce }, "Read and write forces if possible" },
831 #ifndef GMX_NATIVE_WINDOWS
832 { "-trunc", FALSE, etTIME,
834 "Truncate input trajectory file after this time (%t)" },
836 { "-exec", FALSE, etSTR,
838 "Execute command for every output frame with the "
839 "frame number as argument" },
840 { "-split", FALSE, etTIME,
842 "Start writing new file when t MOD split = first "
844 { "-sep", FALSE, etBOOL,
846 "Write each frame to a separate .gro, .g96 or .pdb "
848 { "-nzero", FALSE, etINT,
850 "If the -sep flag is set, use these many digits "
851 "for the file numbers and prepend zeros as needed" },
852 { "-dropunder", FALSE, etREAL,
853 { &dropunder }, "Drop all frames below this value" },
854 { "-dropover", FALSE, etREAL,
855 { &dropover }, "Drop all frames above this value" },
856 { "-conect", FALSE, etBOOL,
858 "Add conect records when writing [TT].pdb[tt] files. Useful "
859 "for visualization of non-standard molecules, e.g. "
860 "coarse grained ones" }
862 #define NPA asize(pa)
865 t_trxstatus *trxout = NULL;
867 int ftp, ftpin = 0, file_nr;
868 t_trxframe fr, frout;
870 rvec *xmem = NULL, *vmem = NULL, *fmem = NULL;
871 rvec *xp = NULL, x_shift, hbox, box_center, dx;
872 real xtcpr, lambda, *w_rls = NULL;
873 int m, i, d, frame, outframe, natoms, nout, ncent, nre, newstep = 0, model_nr;
876 gmx_mtop_t *mtop = NULL;
877 gmx_conect gc = NULL;
879 t_atoms *atoms = NULL, useatoms;
881 atom_id *index, *cindex;
885 int ifit, irms, my_clust = -1;
886 atom_id *ind_fit, *ind_rms;
887 char *gn_fit, *gn_rms;
888 t_cluster_ndx *clust = NULL;
889 t_trxstatus **clust_status = NULL;
890 int *clust_status_id = NULL;
892 int *nfwritten = NULL;
893 int ndrop = 0, ncol, drop0 = 0, drop1 = 0, dropuse = 0;
895 real tshift = 0, t0 = -1, dt = 0.001, prec;
896 gmx_bool bFit, bFitXY, bPFit, bReset;
898 gmx_rmpbc_t gpbc = NULL;
899 gmx_bool bRmPBC, bPBCWhole, bPBCcomRes, bPBCcomMol, bPBCcomAtom, bPBC, bNoJump, bCluster;
900 gmx_bool bCopy, bDoIt, bIndex, bTDump, bSetTime, bTPS = FALSE, bDTset = FALSE;
901 gmx_bool bExec, bTimeStep = FALSE, bDumpFrame = FALSE, bSetPrec, bNeedPrec;
902 gmx_bool bHaveFirstFrame, bHaveNextFrame, bSetBox, bSetUR, bSplit = FALSE;
903 gmx_bool bSubTraj = FALSE, bDropUnder = FALSE, bDropOver = FALSE, bTrans = FALSE;
904 gmx_bool bWriteFrame, bSplitHere;
905 const char *top_file, *in_file, *out_file = NULL;
906 char out_file2[256], *charpt;
907 char *outf_base = NULL;
908 const char *outf_ext = NULL;
909 char top_title[256], title[256], command[256], filemode[5];
911 gmx_bool bWarnCompact = FALSE;
916 { efTRX, "-f", NULL, ffREAD },
917 { efTRO, "-o", NULL, ffWRITE },
918 { efTPS, NULL, NULL, ffOPTRD },
919 { efNDX, NULL, NULL, ffOPTRD },
920 { efNDX, "-fr", "frames", ffOPTRD },
921 { efNDX, "-sub", "cluster", ffOPTRD },
922 { efXVG, "-drop", "drop", ffOPTRD }
924 #define NFILE asize(fnm)
926 if (!parse_common_args(&argc, argv,
927 PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW |
929 NFILE, fnm, NPA, pa, asize(desc), desc,
935 top_file = ftp2fn(efTPS, NFILE, fnm);
938 /* Check command line */
939 in_file = opt2fn("-f", NFILE, fnm);
943 #ifndef GMX_NATIVE_WINDOWS
944 do_trunc(in_file, ttrunc);
949 /* mark active cmdline options */
950 bSetBox = opt2parg_bSet("-box", NPA, pa);
951 bSetTime = opt2parg_bSet("-t0", NPA, pa);
952 bSetPrec = opt2parg_bSet("-ndec", NPA, pa);
953 bSetUR = opt2parg_bSet("-ur", NPA, pa);
954 bExec = opt2parg_bSet("-exec", NPA, pa);
955 bTimeStep = opt2parg_bSet("-timestep", NPA, pa);
956 bTDump = opt2parg_bSet("-dump", NPA, pa);
957 bDropUnder = opt2parg_bSet("-dropunder", NPA, pa);
958 bDropOver = opt2parg_bSet("-dropover", NPA, pa);
959 bTrans = opt2parg_bSet("-trans", NPA, pa);
960 bSplit = (split_t != 0);
962 /* parse enum options */
963 fit_enum = nenum(fit);
964 bFit = (fit_enum == efFit || fit_enum == efFitXY);
965 bFitXY = fit_enum == efFitXY;
966 bReset = (fit_enum == efReset || fit_enum == efResetXY);
967 bPFit = fit_enum == efPFit;
968 pbc_enum = nenum(pbc_opt);
969 bPBCWhole = pbc_enum == epWhole;
970 bPBCcomRes = pbc_enum == epComRes;
971 bPBCcomMol = pbc_enum == epComMol;
972 bPBCcomAtom = pbc_enum == epComAtom;
973 bNoJump = pbc_enum == epNojump;
974 bCluster = pbc_enum == epCluster;
975 bPBC = pbc_enum != epNone;
976 unitcell_enum = nenum(unitcell_opt);
977 ecenter = nenum(center_opt) - ecTric;
979 /* set and check option dependencies */
982 bFit = TRUE; /* for pfit, fit *must* be set */
986 bReset = TRUE; /* for fit, reset *must* be set */
991 nfitdim = (fit_enum == efFitXY || fit_enum == efResetXY) ? 2 : 3;
993 bRmPBC = bFit || bPBCWhole || bPBCcomRes || bPBCcomMol;
997 if (!(bPBCcomRes || bPBCcomMol || bPBCcomAtom))
1000 "WARNING: Option for unitcell representation (-ur %s)\n"
1001 " only has effect in combination with -pbc %s, %s or %s.\n"
1002 " Ingoring unitcell representation.\n\n",
1003 unitcell_opt[0], pbc_opt[2], pbc_opt[3], pbc_opt[4]);
1009 gmx_fatal(FARGS, "PBC condition treatment does not work together with rotational fit.\n"
1010 "Please do the PBC condition treatment first and then run trjconv in a second step\n"
1011 "for the rotational fit.\n"
1012 "First doing the rotational fit and then doing the PBC treatment gives incorrect\n"
1016 /* ndec is in nr of decimal places, prec is a multiplication factor: */
1018 for (i = 0; i < ndec; i++)
1023 bIndex = ftp2bSet(efNDX, NFILE, fnm);
1026 /* Determine output type */
1027 out_file = opt2fn("-o", NFILE, fnm);
1028 ftp = fn2ftp(out_file);
1029 fprintf(stderr, "Will write %s: %s\n", ftp2ext(ftp), ftp2desc(ftp));
1030 bNeedPrec = (ftp == efXTC || ftp == efGRO);
1033 /* check if velocities are possible in input and output files */
1034 ftpin = fn2ftp(in_file);
1035 bVels = (ftp == efTRR || ftp == efGRO ||
1036 ftp == efG96 || ftp == efTNG)
1037 && (ftpin == efTRR || ftpin == efGRO ||
1038 ftpin == efG96 || ftpin == efTNG || ftpin == efCPT);
1040 if (bSeparate || bSplit)
1042 outf_ext = strrchr(out_file, '.');
1043 if (outf_ext == NULL)
1045 gmx_fatal(FARGS, "Output file name '%s' does not contain a '.'", out_file);
1047 outf_base = gmx_strdup(out_file);
1048 outf_base[outf_ext - out_file] = '\0';
1051 bSubTraj = opt2bSet("-sub", NFILE, fnm);
1054 if ((ftp != efXTC) && (ftp != efTRR))
1056 /* It seems likely that other trajectory file types
1057 * could work here. */
1058 gmx_fatal(FARGS, "Can only use the sub option with output file types "
1061 clust = cluster_index(NULL, opt2fn("-sub", NFILE, fnm));
1063 /* Check for number of files disabled, as FOPEN_MAX is not the correct
1064 * number to check for. In my linux box it is only 16.
1066 if (0 && (clust->clust->nr > FOPEN_MAX-4))
1068 gmx_fatal(FARGS, "Can not open enough (%d) files to write all the"
1069 " trajectories.\ntry splitting the index file in %d parts.\n"
1071 clust->clust->nr, 1+clust->clust->nr/FOPEN_MAX, FOPEN_MAX);
1073 gmx_warning("The -sub option could require as many open output files as there are\n"
1074 "index groups in the file (%d). If you get I/O errors opening new files,\n"
1075 "try reducing the number of index groups in the file, and perhaps\n"
1076 "using trjconv -sub several times on different chunks of your index file.\n",
1079 snew(clust_status, clust->clust->nr);
1080 snew(clust_status_id, clust->clust->nr);
1081 snew(nfwritten, clust->clust->nr);
1082 for (i = 0; (i < clust->clust->nr); i++)
1084 clust_status[i] = NULL;
1085 clust_status_id[i] = -1;
1087 bSeparate = bSplit = FALSE;
1094 mtop = read_mtop_for_tng(top_file, in_file, out_file);
1096 /* Determine whether to read a topology */
1097 bTPS = (ftp2bSet(efTPS, NFILE, fnm) ||
1098 bRmPBC || bReset || bPBCcomMol || bCluster ||
1099 (ftp == efGRO) || (ftp == efPDB) || bCONECT);
1101 /* Determine if when can read index groups */
1102 bIndex = (bIndex || bTPS);
1106 read_tps_conf(top_file, top_title, &top, &ePBC, &xp, NULL, top_box,
1107 bReset || bPBCcomRes);
1110 if (0 == top.mols.nr && (bCluster || bPBCcomMol))
1112 gmx_fatal(FARGS, "Option -pbc %s requires a .tpr file for the -s option", pbc_opt[pbc_enum]);
1115 /* top_title is only used for gro and pdb,
1116 * the header in such a file is top_title t= ...
1117 * to prevent a double t=, remove it from top_title
1119 if ((charpt = strstr(top_title, " t= ")))
1126 gc = gmx_conect_generate(&top);
1130 gpbc = gmx_rmpbc_init(&top.idef, ePBC, top.atoms.nr);
1134 /* get frame number index */
1136 if (opt2bSet("-fr", NFILE, fnm))
1138 printf("Select groups of frame number indices:\n");
1139 rd_index(opt2fn("-fr", NFILE, fnm), 1, &nrfri, (atom_id **)&frindex, &frname);
1142 for (i = 0; i < nrfri; i++)
1144 fprintf(debug, "frindex[%4d]=%4d\n", i, frindex[i]);
1149 /* get index groups etc. */
1152 printf("Select group for %s fit\n",
1153 bFit ? "least squares" : "translational");
1154 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
1155 1, &ifit, &ind_fit, &gn_fit);
1161 gmx_fatal(FARGS, "Need at least 2 atoms to fit!\n");
1165 fprintf(stderr, "WARNING: fitting with only 2 atoms is not unique\n");
1171 printf("Select group for clustering\n");
1172 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
1173 1, &ifit, &ind_fit, &gn_fit);
1180 printf("Select group for centering\n");
1181 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
1182 1, &ncent, &cindex, &grpnm);
1184 printf("Select group for output\n");
1185 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
1186 1, &nout, &index, &grpnm);
1190 /* no index file, so read natoms from TRX */
1191 if (!read_first_frame(oenv, &trxin, in_file, &fr, TRX_DONT_SKIP))
1193 gmx_fatal(FARGS, "Could not read a frame from %s", in_file);
1198 snew(index, natoms);
1199 for (i = 0; i < natoms; i++)
1213 snew(w_rls, atoms->nr);
1214 for (i = 0; (i < ifit); i++)
1216 w_rls[ind_fit[i]] = atoms->atom[ind_fit[i]].m;
1219 /* Restore reference structure and set to origin,
1220 store original location (to put structure back) */
1223 gmx_rmpbc(gpbc, top.atoms.nr, top_box, xp);
1225 copy_rvec(xp[index[0]], x_shift);
1226 reset_x_ndim(nfitdim, ifit, ind_fit, atoms->nr, NULL, xp, w_rls);
1227 rvec_dec(x_shift, xp[index[0]]);
1231 clear_rvec(x_shift);
1234 if (bDropUnder || bDropOver)
1236 /* Read the .xvg file with the drop values */
1237 fprintf(stderr, "\nReading drop file ...");
1238 ndrop = read_xvg(opt2fn("-drop", NFILE, fnm), &dropval, &ncol);
1239 fprintf(stderr, " %d time points\n", ndrop);
1240 if (ndrop == 0 || ncol < 2)
1242 gmx_fatal(FARGS, "Found no data points in %s",
1243 opt2fn("-drop", NFILE, fnm));
1249 /* Make atoms struct for output in GRO or PDB files */
1250 if ((ftp == efGRO) || ((ftp == efG96) && bTPS) || (ftp == efPDB))
1252 /* get memory for stuff to go in .pdb file, and initialize
1253 * the pdbinfo structure part if the input has it.
1255 init_t_atoms(&useatoms, atoms->nr, (atoms->pdbinfo != NULL));
1256 sfree(useatoms.resinfo);
1257 useatoms.resinfo = atoms->resinfo;
1258 for (i = 0; (i < nout); i++)
1260 useatoms.atomname[i] = atoms->atomname[index[i]];
1261 useatoms.atom[i] = atoms->atom[index[i]];
1262 if (atoms->pdbinfo != NULL)
1264 useatoms.pdbinfo[i] = atoms->pdbinfo[index[i]];
1266 useatoms.nres = max(useatoms.nres, useatoms.atom[i].resind+1);
1270 /* select what to read */
1281 flags = flags | TRX_READ_V;
1285 flags = flags | TRX_READ_F;
1288 /* open trx file for reading */
1289 bHaveFirstFrame = read_first_frame(oenv, &trxin, in_file, &fr, flags);
1292 fprintf(stderr, "\nPrecision of %s is %g (nm)\n", in_file, 1/fr.prec);
1296 if (bSetPrec || !fr.bPrec)
1298 fprintf(stderr, "\nSetting output precision to %g (nm)\n", 1/prec);
1302 fprintf(stderr, "Using output precision of %g (nm)\n", 1/prec);
1306 if (bHaveFirstFrame)
1308 set_trxframe_ePBC(&fr, ePBC);
1314 tshift = tzero-fr.time;
1324 /* check if index is meaningful */
1325 for (i = 0; i < nout; i++)
1327 if (index[i] >= natoms)
1330 "Index[%d] %d is larger than the number of atoms in the\n"
1331 "trajectory file (%d). There is a mismatch in the contents\n"
1332 "of your -f, -s and/or -n files.", i, index[i]+1, natoms);
1334 bCopy = bCopy || (i != index[i]);
1338 /* open output for writing */
1339 strcpy(filemode, "w");
1343 trjtools_gmx_prepare_tng_writing(out_file,
1356 if (!bSplit && !bSubTraj)
1358 trxout = open_trx(out_file, filemode);
1364 if (( !bSeparate && !bSplit ) && !bSubTraj)
1366 out = gmx_ffopen(out_file, filemode);
1370 gmx_incons("Illegal output file format");
1386 /* Start the big loop over frames */
1393 /* Main loop over frames */
1404 /*if (frame >= clust->clust->nra)
1405 gmx_fatal(FARGS,"There are more frames in the trajectory than in the cluster index file\n");*/
1406 if (frame > clust->maxframe)
1412 my_clust = clust->inv_clust[frame];
1414 if ((my_clust < 0) || (my_clust >= clust->clust->nr) ||
1415 (my_clust == NO_ATID))
1423 /* generate new box */
1425 for (m = 0; m < DIM; m++)
1429 fr.box[m][m] = newbox[m];
1436 for (i = 0; i < natoms; i++)
1438 rvec_inc(fr.x[i], trans);
1444 /* determine timestep */
1457 /* This is not very elegant, as one can not dump a frame after
1458 * a timestep with is more than twice as small as the first one. */
1459 bDumpFrame = (fr.time > tdump-0.5*dt) && (fr.time <= tdump+0.5*dt);
1466 /* determine if an atom jumped across the box and reset it if so */
1467 if (bNoJump && (bTPS || frame != 0))
1469 for (d = 0; d < DIM; d++)
1471 hbox[d] = 0.5*fr.box[d][d];
1473 for (i = 0; i < natoms; i++)
1477 rvec_dec(fr.x[i], x_shift);
1479 for (m = DIM-1; m >= 0; m--)
1483 while (fr.x[i][m]-xp[i][m] <= -hbox[m])
1485 for (d = 0; d <= m; d++)
1487 fr.x[i][d] += fr.box[m][d];
1490 while (fr.x[i][m]-xp[i][m] > hbox[m])
1492 for (d = 0; d <= m; d++)
1494 fr.x[i][d] -= fr.box[m][d];
1503 calc_pbc_cluster(ecenter, ifit, &top, ePBC, fr.x, ind_fit, fr.box);
1508 /* Now modify the coords according to the flags,
1509 for normal fit, this is only done for output frames */
1512 gmx_rmpbc_trxfr(gpbc, &fr);
1515 reset_x_ndim(nfitdim, ifit, ind_fit, natoms, NULL, fr.x, w_rls);
1516 do_fit(natoms, w_rls, xp, fr.x);
1519 /* store this set of coordinates for future use */
1520 if (bPFit || bNoJump)
1526 for (i = 0; (i < natoms); i++)
1528 copy_rvec(fr.x[i], xp[i]);
1529 rvec_inc(fr.x[i], x_shift);
1535 /* see if we have a frame from the frame index group */
1536 for (i = 0; i < nrfri && !bDumpFrame; i++)
1538 bDumpFrame = frame == frindex[i];
1541 if (debug && bDumpFrame)
1543 fprintf(debug, "dumping %d\n", frame);
1547 ( ( !bTDump && !frindex && frame % skip_nr == 0 ) || bDumpFrame );
1549 if (bWriteFrame && (bDropUnder || bDropOver))
1551 while (dropval[0][drop1] < fr.time && drop1+1 < ndrop)
1556 if (fabs(dropval[0][drop0] - fr.time)
1557 < fabs(dropval[0][drop1] - fr.time))
1565 if ((bDropUnder && dropval[1][dropuse] < dropunder) ||
1566 (bDropOver && dropval[1][dropuse] > dropover))
1568 bWriteFrame = FALSE;
1578 fr.time = tzero+frame*timestep;
1588 fprintf(stderr, "\nDumping frame at t= %g %s\n",
1589 output_env_conv_time(oenv, fr.time), output_env_get_time_unit(oenv));
1592 /* check for writing at each delta_t */
1593 bDoIt = (delta_t == 0);
1598 bDoIt = bRmod(fr.time, tzero, delta_t);
1602 /* round() is not C89 compatible, so we do this: */
1603 bDoIt = bRmod(floor(fr.time+0.5), floor(tzero+0.5),
1604 floor(delta_t+0.5));
1608 if (bDoIt || bTDump)
1610 /* print sometimes */
1611 if ( ((outframe % SKIP) == 0) || (outframe < SKIP) )
1613 fprintf(stderr, " -> frame %6d time %8.3f \r",
1614 outframe, output_env_conv_time(oenv, fr.time));
1619 /* Now modify the coords according to the flags,
1620 for PFit we did this already! */
1624 gmx_rmpbc_trxfr(gpbc, &fr);
1629 reset_x_ndim(nfitdim, ifit, ind_fit, natoms, NULL, fr.x, w_rls);
1632 do_fit_ndim(nfitdim, natoms, w_rls, xp, fr.x);
1636 for (i = 0; i < natoms; i++)
1638 rvec_inc(fr.x[i], x_shift);
1645 center_x(ecenter, fr.x, fr.box, natoms, ncent, cindex);
1651 switch (unitcell_enum)
1654 put_atoms_in_box(ePBC, fr.box, natoms, fr.x);
1657 put_atoms_in_triclinic_unitcell(ecenter, fr.box, natoms, fr.x);
1660 warn = put_atoms_in_compact_unitcell(ePBC, ecenter, fr.box,
1662 if (warn && !bWarnCompact)
1664 fprintf(stderr, "\n%s\n", warn);
1665 bWarnCompact = TRUE;
1672 put_residue_com_in_box(unitcell_enum, ecenter,
1673 natoms, atoms->atom, ePBC, fr.box, fr.x);
1677 put_molecule_com_in_box(unitcell_enum, ecenter,
1679 natoms, atoms->atom, ePBC, fr.box, fr.x);
1681 /* Copy the input trxframe struct to the output trxframe struct */
1683 frout.bV = (frout.bV && bVels);
1684 frout.bF = (frout.bF && bForce);
1685 frout.natoms = nout;
1686 if (bNeedPrec && (bSetPrec || !fr.bPrec))
1702 for (i = 0; i < nout; i++)
1704 copy_rvec(fr.x[index[i]], frout.x[i]);
1707 copy_rvec(fr.v[index[i]], frout.v[i]);
1711 copy_rvec(fr.f[index[i]], frout.f[i]);
1716 if (opt2parg_bSet("-shift", NPA, pa))
1718 for (i = 0; i < nout; i++)
1720 for (d = 0; d < DIM; d++)
1722 frout.x[i][d] += outframe*shift[d];
1729 bSplitHere = bSplit && bRmod(fr.time, tzero, split_t);
1733 /* round() is not C89 compatible, so we do this: */
1734 bSplitHere = bSplit && bRmod(floor(fr.time+0.5),
1736 floor(split_t+0.5));
1738 if (bSeparate || bSplitHere)
1740 mk_filenm(outf_base, ftp2ext(ftp), nzero, file_nr, out_file2);
1746 write_tng_frame(trxout, &frout);
1747 // TODO when trjconv behaves better: work how to read and write lambda
1757 trxout = open_trx(out_file2, filemode);
1764 if (clust_status_id[my_clust] == -1)
1766 sprintf(buf, "%s.%s", clust->grpname[my_clust], ftp2ext(ftp));
1767 clust_status[my_clust] = open_trx(buf, "w");
1768 clust_status_id[my_clust] = 1;
1771 else if (clust_status_id[my_clust] == -2)
1773 gmx_fatal(FARGS, "File %s.xtc should still be open (%d open .xtc files)\n" "in order to write frame %d. my_clust = %d",
1774 clust->grpname[my_clust], ntrxopen, frame,
1777 write_trxframe(clust_status[my_clust], &frout, gc);
1778 nfwritten[my_clust]++;
1779 if (nfwritten[my_clust] ==
1780 (clust->clust->index[my_clust+1]-
1781 clust->clust->index[my_clust]))
1783 close_trx(clust_status[my_clust]);
1784 clust_status[my_clust] = NULL;
1785 clust_status_id[my_clust] = -2;
1789 gmx_fatal(FARGS, "Less than zero open .xtc files!");
1796 write_trxframe(trxout, &frout, gc);
1802 sprintf(title, "Generated by trjconv : %s t= %9.5f",
1803 top_title, fr.time);
1804 if (bSeparate || bSplitHere)
1806 out = gmx_ffopen(out_file2, "w");
1811 write_hconf_p(out, title, &useatoms, prec2ndec(frout.prec),
1812 frout.x, frout.bV ? frout.v : NULL, frout.box);
1815 fprintf(out, "REMARK GENERATED BY TRJCONV\n");
1816 sprintf(title, "%s t= %9.5f", top_title, frout.time);
1817 /* if reading from pdb, we want to keep the original
1818 model numbering else we write the output frame
1819 number plus one, because model 0 is not allowed in pdb */
1820 if (ftpin == efPDB && fr.bStep && fr.step > model_nr)
1828 write_pdbfile(out, title, &useatoms, frout.x,
1829 frout.ePBC, frout.box, ' ', model_nr, gc, TRUE);
1832 frout.title = title;
1833 if (bSeparate || bTDump)
1835 frout.bTitle = TRUE;
1838 frout.bAtoms = TRUE;
1840 frout.atoms = &useatoms;
1841 frout.bStep = FALSE;
1842 frout.bTime = FALSE;
1846 frout.bTitle = (outframe == 0);
1847 frout.bAtoms = FALSE;
1851 write_g96_conf(out, &frout, -1, NULL);
1860 gmx_fatal(FARGS, "DHE, ftp=%d\n", ftp);
1862 if (bSeparate || bSplitHere)
1867 /* execute command */
1871 sprintf(c, "%s %d", exec_command, file_nr-1);
1872 /*fprintf(stderr,"Executing '%s'\n",c);*/
1873 #ifdef GMX_NO_SYSTEM
1874 printf("Warning-- No calls to system(3) supported on this platform.");
1875 printf("Warning-- Skipping execution of 'system(\"%s\")'.", c);
1879 gmx_fatal(FARGS, "Error executing command: %s", c);
1887 bHaveNextFrame = read_next_frame(oenv, trxin, &fr);
1889 while (!(bTDump && bDumpFrame) && bHaveNextFrame);
1892 if (!bHaveFirstFrame || (bTDump && !bDumpFrame))
1894 fprintf(stderr, "\nWARNING no output, "
1895 "last frame read at t=%g\n", fr.time);
1897 fprintf(stderr, "\n");
1904 gmx_rmpbc_done(gpbc);
1911 else if (out != NULL)
1917 for (i = 0; (i < clust->clust->nr); i++)
1919 if (clust_status_id[i] >= 0)
1921 close_trx(clust_status[i]);
1929 do_view(oenv, out_file, NULL);