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46 #include "gromacs/fileio/gmxfio.h"
47 #include "gromacs/fileio/tpxio.h"
48 #include "gromacs/fileio/trxio.h"
49 #include "gromacs/fileio/trnio.h"
50 #include "gromacs/fileio/tngio_for_tools.h"
51 #include "gromacs/utility/futil.h"
52 #include "gromacs/fileio/pdbio.h"
53 #include "gromacs/fileio/confio.h"
55 #include "gromacs/topology/index.h"
56 #include "gromacs/math/vec.h"
57 #include "gromacs/fileio/xtcio.h"
61 #include "gromacs/commandline/pargs.h"
62 #include "gromacs/fileio/xvgr.h"
63 #include "gromacs/math/do_fit.h"
64 #include "gromacs/pbcutil/pbc.h"
65 #include "gromacs/pbcutil/rmpbc.h"
66 #include "gromacs/topology/topology.h"
67 #include "gromacs/utility/fatalerror.h"
68 #include "gromacs/utility/smalloc.h"
75 euSel, euRect, euTric, euCompact, euNR
79 static void calc_pbc_cluster(int ecenter, int nrefat, t_topology *top, int ePBC,
80 rvec x[], atom_id index[], matrix box)
82 int m, i, j, j0, j1, jj, ai, aj;
85 rvec dx, xtest, box_center;
86 int nmol, imol_center;
88 gmx_bool *bMol, *bTmp;
89 rvec *m_com, *m_shift;
97 calc_box_center(ecenter, box, box_center);
99 /* Initiate the pbc structure */
100 memset(&pbc, 0, sizeof(pbc));
101 set_pbc(&pbc, ePBC, box);
103 /* Convert atom index to molecular */
105 molind = top->mols.index;
111 snew(bTmp, top->atoms.nr);
113 for (i = 0; (i < nrefat); i++)
115 /* Mark all molecules in the index */
118 /* Binary search assuming the molecules are sorted */
123 if (ai < molind[j0+1])
127 else if (ai >= molind[j1])
134 if (ai < molind[jj+1])
146 /* Double check whether all atoms in all molecules that are marked are part
147 * of the cluster. Simultaneously compute the center of geometry.
149 min_dist2 = 10*sqr(trace(box));
152 for (i = 0; i < nmol; i++)
154 for (j = molind[i]; j < molind[i+1]; j++)
156 if (bMol[i] && !bTmp[j])
158 gmx_fatal(FARGS, "Molecule %d marked for clustering but not atom %d in it - check your index!", i+1, j+1);
160 else if (!bMol[i] && bTmp[j])
162 gmx_fatal(FARGS, "Atom %d marked for clustering but not molecule %d - this is an internal error...", j+1, i+1);
166 /* Make molecule whole, move 2nd and higher atom to same periodicity as 1st atom in molecule */
169 pbc_dx(&pbc, x[j], x[j-1], dx);
170 rvec_add(x[j-1], dx, x[j]);
172 /* Compute center of geometry of molecule - m_com[i] was zeroed when we did snew() on it! */
173 rvec_inc(m_com[i], x[j]);
178 /* Normalize center of geometry */
179 fac = 1.0/(molind[i+1]-molind[i]);
180 for (m = 0; (m < DIM); m++)
184 /* Determine which molecule is closest to the center of the box */
185 pbc_dx(&pbc, box_center, m_com[i], dx);
186 tmp_r2 = iprod(dx, dx);
188 if (tmp_r2 < min_dist2)
193 cluster[ncluster++] = i;
200 fprintf(stderr, "No molecules selected in the cluster\n");
203 else if (imol_center == -1)
205 fprintf(stderr, "No central molecules could be found\n");
210 added[nadded++] = imol_center;
211 bMol[imol_center] = FALSE;
213 while (nadded < ncluster)
215 /* Find min distance between cluster molecules and those remaining to be added */
216 min_dist2 = 10*sqr(trace(box));
219 /* Loop over added mols */
220 for (i = 0; i < nadded; i++)
223 /* Loop over all mols */
224 for (j = 0; j < ncluster; j++)
227 /* check those remaining to be added */
230 pbc_dx(&pbc, m_com[aj], m_com[ai], dx);
231 tmp_r2 = iprod(dx, dx);
232 if (tmp_r2 < min_dist2)
242 /* Add the best molecule */
243 added[nadded++] = jmin;
245 /* Calculate the shift from the ai molecule */
246 pbc_dx(&pbc, m_com[jmin], m_com[imin], dx);
247 rvec_add(m_com[imin], dx, xtest);
248 rvec_sub(xtest, m_com[jmin], m_shift[jmin]);
249 rvec_inc(m_com[jmin], m_shift[jmin]);
251 for (j = molind[jmin]; j < molind[jmin+1]; j++)
253 rvec_inc(x[j], m_shift[jmin]);
255 fprintf(stdout, "\rClustering iteration %d of %d...", nadded, ncluster);
265 fprintf(stdout, "\n");
268 static void put_molecule_com_in_box(int unitcell_enum, int ecenter,
270 int natoms, t_atom atom[],
271 int ePBC, matrix box, rvec x[])
275 rvec com, new_com, shift, dx, box_center;
280 calc_box_center(ecenter, box, box_center);
281 set_pbc(&pbc, ePBC, box);
284 gmx_fatal(FARGS, "There are no molecule descriptions. I need a .tpr file for this pbc option.");
286 for (i = 0; (i < mols->nr); i++)
291 for (j = mols->index[i]; (j < mols->index[i+1] && j < natoms); j++)
294 for (d = 0; d < DIM; d++)
300 /* calculate final COM */
301 svmul(1.0/mtot, com, com);
303 /* check if COM is outside box */
304 copy_rvec(com, new_com);
305 switch (unitcell_enum)
308 put_atoms_in_box(ePBC, box, 1, &new_com);
311 put_atoms_in_triclinic_unitcell(ecenter, box, 1, &new_com);
314 put_atoms_in_compact_unitcell(ePBC, ecenter, box, 1, &new_com);
317 rvec_sub(new_com, com, shift);
318 if (norm2(shift) > 0)
322 fprintf(debug, "\nShifting position of molecule %d "
323 "by %8.3f %8.3f %8.3f\n", i+1,
324 shift[XX], shift[YY], shift[ZZ]);
326 for (j = mols->index[i]; (j < mols->index[i+1] && j < natoms); j++)
328 rvec_inc(x[j], shift);
334 static void put_residue_com_in_box(int unitcell_enum, int ecenter,
335 int natoms, t_atom atom[],
336 int ePBC, matrix box, rvec x[])
338 atom_id i, j, res_start, res_end, res_nat;
342 rvec box_center, com, new_com, shift;
344 calc_box_center(ecenter, box, box_center);
350 for (i = 0; i < natoms+1; i++)
352 if (i == natoms || (presnr != atom[i].resind && presnr != NOTSET))
354 /* calculate final COM */
356 res_nat = res_end - res_start;
357 svmul(1.0/mtot, com, com);
359 /* check if COM is outside box */
360 copy_rvec(com, new_com);
361 switch (unitcell_enum)
364 put_atoms_in_box(ePBC, box, 1, &new_com);
367 put_atoms_in_triclinic_unitcell(ecenter, box, 1, &new_com);
370 put_atoms_in_compact_unitcell(ePBC, ecenter, box, 1, &new_com);
373 rvec_sub(new_com, com, shift);
378 fprintf(debug, "\nShifting position of residue %d (atoms %u-%u) "
379 "by %g,%g,%g\n", atom[res_start].resind+1,
380 res_start+1, res_end+1, shift[XX], shift[YY], shift[ZZ]);
382 for (j = res_start; j < res_end; j++)
384 rvec_inc(x[j], shift);
390 /* remember start of new residue */
397 for (d = 0; d < DIM; d++)
403 presnr = atom[i].resind;
408 static void center_x(int ecenter, rvec x[], matrix box, int n, int nc, atom_id ci[])
411 rvec cmin, cmax, box_center, dx;
415 copy_rvec(x[ci[0]], cmin);
416 copy_rvec(x[ci[0]], cmax);
417 for (i = 0; i < nc; i++)
420 for (m = 0; m < DIM; m++)
422 if (x[ai][m] < cmin[m])
426 else if (x[ai][m] > cmax[m])
432 calc_box_center(ecenter, box, box_center);
433 for (m = 0; m < DIM; m++)
435 dx[m] = box_center[m]-(cmin[m]+cmax[m])*0.5;
438 for (i = 0; i < n; i++)
445 static void mk_filenm(char *base, const char *ext, int ndigit, int file_nr,
451 strcpy(out_file, base);
462 strncat(out_file, "00000000000", ndigit-nd);
464 sprintf(nbuf, "%d.", file_nr);
465 strcat(out_file, nbuf);
466 strcat(out_file, ext);
469 void check_trn(const char *fn)
471 if ((fn2ftp(fn) != efTRJ) && (fn2ftp(fn) != efTRR))
473 gmx_fatal(FARGS, "%s is not a trajectory file, exiting\n", fn);
477 #ifndef GMX_NATIVE_WINDOWS
478 void do_trunc(const char *fn, real t0)
491 gmx_fatal(FARGS, "You forgot to set the truncation time");
494 /* Check whether this is a .trj file */
497 in = open_trn(fn, "r");
498 fp = gmx_fio_getfp(in);
501 fprintf(stderr, "Sorry, can not trunc %s, truncation of this filetype is not supported\n", fn);
507 fpos = gmx_fio_ftell(in);
509 while (!bStop && fread_trnheader(in, &sh, &bOK))
511 fread_htrn(in, &sh, NULL, NULL, NULL, NULL);
512 fpos = gmx_ftell(fp);
516 gmx_fseek(fp, fpos, SEEK_SET);
522 fprintf(stderr, "Do you REALLY want to truncate this trajectory (%s) at:\n"
523 "frame %d, time %g, bytes %ld ??? (type YES if so)\n",
524 fn, j, t, (long int)fpos);
525 if (1 != scanf("%s", yesno))
527 gmx_fatal(FARGS, "Error reading user input");
529 if (strcmp(yesno, "YES") == 0)
531 fprintf(stderr, "Once again, I'm gonna DO this...\n");
533 if (0 != truncate(fn, fpos))
535 gmx_fatal(FARGS, "Error truncating file %s", fn);
540 fprintf(stderr, "Ok, I'll forget about it\n");
545 fprintf(stderr, "Already at end of file (t=%g)...\n", t);
552 /*! \brief Read a full molecular topology if useful and available.
554 * If the input trajectory file is not in TNG format, and the output
555 * file is in TNG format, then we want to try to read a full topology
556 * (if available), so that we can write molecule information to the
557 * output file. The full topology provides better molecule information
558 * than is available from the normal t_topology data used by GROMACS
561 * Also, the t_topology is only read under (different) particular
562 * conditions. If both apply, then a .tpr file might be read
563 * twice. Trying to fix this redundancy while trjconv is still an
564 * all-purpose tool does not seem worthwhile.
566 * Because of the way gmx_prepare_tng_writing is implemented, the case
567 * where the input TNG file has no molecule information will never
568 * lead to an output TNG file having molecule information. Since
569 * molecule information will generally be present if the input TNG
570 * file was written by a GROMACS tool, this seems like reasonable
572 static gmx_mtop_t *read_mtop_for_tng(const char *tps_file,
573 const char *input_file,
574 const char *output_file)
576 gmx_mtop_t *mtop = NULL;
578 if (fn2bTPX(tps_file) &&
579 efTNG != fn2ftp(input_file) &&
580 efTNG == fn2ftp(output_file))
582 int temp_natoms = -1;
584 read_tpx(tps_file, NULL, NULL, &temp_natoms,
585 NULL, NULL, NULL, mtop);
591 int gmx_trjconv(int argc, char *argv[])
593 const char *desc[] = {
594 "[THISMODULE] can convert trajectory files in many ways:[BR]",
595 "* from one format to another[BR]",
596 "* select a subset of atoms[BR]",
597 "* change the periodicity representation[BR]",
598 "* keep multimeric molecules together[BR]",
599 "* center atoms in the box[BR]",
600 "* fit atoms to reference structure[BR]",
601 "* reduce the number of frames[BR]",
602 "* change the timestamps of the frames ",
603 "([TT]-t0[tt] and [TT]-timestep[tt])[BR]",
604 "* cut the trajectory in small subtrajectories according",
605 "to information in an index file. This allows subsequent analysis of",
606 "the subtrajectories that could, for example, be the result of a",
607 "cluster analysis. Use option [TT]-sub[tt].",
608 "This assumes that the entries in the index file are frame numbers and",
609 "dumps each group in the index file to a separate trajectory file.[BR]",
610 "* select frames within a certain range of a quantity given",
611 "in an [TT].xvg[tt] file.[PAR]",
613 "[gmx-trjcat] is better suited for concatenating multiple trajectory files.",
616 "The following formats are supported for input and output:",
617 "[TT].xtc[tt], [TT].trr[tt], [TT].trj[tt], [TT].gro[tt], [TT].g96[tt]",
619 "The file formats are detected from the file extension.",
620 "The precision of [TT].xtc[tt] and [TT].gro[tt] output is taken from the",
621 "input file for [TT].xtc[tt], [TT].gro[tt] and [TT].pdb[tt],",
622 "and from the [TT]-ndec[tt] option for other input formats. The precision",
623 "is always taken from [TT]-ndec[tt], when this option is set.",
624 "All other formats have fixed precision. [TT].trr[tt] and [TT].trj[tt]",
625 "output can be single or double precision, depending on the precision",
626 "of the [THISMODULE] binary.",
627 "Note that velocities are only supported in",
628 "[TT].trr[tt], [TT].trj[tt], [TT].gro[tt] and [TT].g96[tt] files.[PAR]",
630 "Option [TT]-sep[tt] can be used to write every frame to a separate",
631 "[TT].gro, .g96[tt] or [TT].pdb[tt] file. By default, all frames all written to one file.",
632 "[TT].pdb[tt] files with all frames concatenated can be viewed with",
633 "[TT]rasmol -nmrpdb[tt].[PAR]",
635 "It is possible to select part of your trajectory and write it out",
636 "to a new trajectory file in order to save disk space, e.g. for leaving",
637 "out the water from a trajectory of a protein in water.",
638 "[BB]ALWAYS[bb] put the original trajectory on tape!",
639 "We recommend to use the portable [TT].xtc[tt] format for your analysis",
640 "to save disk space and to have portable files.[PAR]",
642 "There are two options for fitting the trajectory to a reference",
643 "either for essential dynamics analysis, etc.",
644 "The first option is just plain fitting to a reference structure",
645 "in the structure file. The second option is a progressive fit",
646 "in which the first timeframe is fitted to the reference structure ",
647 "in the structure file to obtain and each subsequent timeframe is ",
648 "fitted to the previously fitted structure. This way a continuous",
649 "trajectory is generated, which might not be the case when using the",
650 "regular fit method, e.g. when your protein undergoes large",
651 "conformational transitions.[PAR]",
653 "Option [TT]-pbc[tt] sets the type of periodic boundary condition",
655 "[TT]* mol[tt] puts the center of mass of molecules in the box,",
656 "and requires a run input file to be supplied with [TT]-s[tt].[BR]",
657 "[TT]* res[tt] puts the center of mass of residues in the box.[BR]",
658 "[TT]* atom[tt] puts all the atoms in the box.[BR]",
659 "[TT]* nojump[tt] checks if atoms jump across the box and then puts",
660 "them back. This has the effect that all molecules",
661 "will remain whole (provided they were whole in the initial",
662 "conformation). [BB]Note[bb] that this ensures a continuous trajectory but",
663 "molecules may diffuse out of the box. The starting configuration",
664 "for this procedure is taken from the structure file, if one is",
665 "supplied, otherwise it is the first frame.[BR]",
666 "[TT]* cluster[tt] clusters all the atoms in the selected index",
667 "such that they are all closest to the center of mass of the cluster,",
668 "which is iteratively updated. [BB]Note[bb] that this will only give meaningful",
669 "results if you in fact have a cluster. Luckily that can be checked",
670 "afterwards using a trajectory viewer. Note also that if your molecules",
671 "are broken this will not work either.[BR]",
672 "The separate option [TT]-clustercenter[tt] can be used to specify an",
673 "approximate center for the cluster. This is useful e.g. if you have",
674 "two big vesicles, and you want to maintain their relative positions.[BR]",
675 "[TT]* whole[tt] only makes broken molecules whole.[PAR]",
677 "Option [TT]-ur[tt] sets the unit cell representation for options",
678 "[TT]mol[tt], [TT]res[tt] and [TT]atom[tt] of [TT]-pbc[tt].",
679 "All three options give different results for triclinic boxes and",
680 "identical results for rectangular boxes.",
681 "[TT]rect[tt] is the ordinary brick shape.",
682 "[TT]tric[tt] is the triclinic unit cell.",
683 "[TT]compact[tt] puts all atoms at the closest distance from the center",
684 "of the box. This can be useful for visualizing e.g. truncated octahedra",
685 "or rhombic dodecahedra. The center for options [TT]tric[tt] and [TT]compact[tt]",
686 "is [TT]tric[tt] (see below), unless the option [TT]-boxcenter[tt]",
687 "is set differently.[PAR]",
689 "Option [TT]-center[tt] centers the system in the box. The user can",
690 "select the group which is used to determine the geometrical center.",
691 "Option [TT]-boxcenter[tt] sets the location of the center of the box",
692 "for options [TT]-pbc[tt] and [TT]-center[tt]. The center options are:",
693 "[TT]tric[tt]: half of the sum of the box vectors,",
694 "[TT]rect[tt]: half of the box diagonal,",
695 "[TT]zero[tt]: zero.",
696 "Use option [TT]-pbc mol[tt] in addition to [TT]-center[tt] when you",
697 "want all molecules in the box after the centering.[PAR]",
699 "Option [TT]-box[tt] sets the size of the new box. If you want to"
700 "modify only some of the dimensions, e.g. when reading from a trajectory,"
701 "you can use -1 for those dimensions that should stay the same"
703 "It is not always possible to use combinations of [TT]-pbc[tt],",
704 "[TT]-fit[tt], [TT]-ur[tt] and [TT]-center[tt] to do exactly what",
705 "you want in one call to [THISMODULE]. Consider using multiple",
706 "calls, and check out the GROMACS website for suggestions.[PAR]",
708 "With [TT]-dt[tt], it is possible to reduce the number of ",
709 "frames in the output. This option relies on the accuracy of the times",
710 "in your input trajectory, so if these are inaccurate use the",
711 "[TT]-timestep[tt] option to modify the time (this can be done",
712 "simultaneously). For making smooth movies, the program [gmx-filter]",
713 "can reduce the number of frames while using low-pass frequency",
714 "filtering, this reduces aliasing of high frequency motions.[PAR]",
716 "Using [TT]-trunc[tt] [THISMODULE] can truncate [TT].trj[tt] in place, i.e.",
717 "without copying the file. This is useful when a run has crashed",
718 "during disk I/O (i.e. full disk), or when two contiguous",
719 "trajectories must be concatenated without having double frames.[PAR]",
721 "Option [TT]-dump[tt] can be used to extract a frame at or near",
722 "one specific time from your trajectory.[PAR]",
724 "Option [TT]-drop[tt] reads an [TT].xvg[tt] file with times and values.",
725 "When options [TT]-dropunder[tt] and/or [TT]-dropover[tt] are set,",
726 "frames with a value below and above the value of the respective options",
727 "will not be written."
743 const char *pbc_opt[epNR + 1] =
745 NULL, "none", "mol", "res", "atom", "nojump", "cluster", "whole",
750 const char *unitcell_opt[euNR+1] =
751 { NULL, "rect", "tric", "compact", NULL };
755 ecSel, ecTric, ecRect, ecZero, ecNR
757 const char *center_opt[ecNR+1] =
758 { NULL, "tric", "rect", "zero", NULL };
764 efSel, efNone, efFit, efFitXY, efReset, efResetXY, efPFit, efNR
766 const char *fit[efNR + 1] =
768 NULL, "none", "rot+trans", "rotxy+transxy", "translation", "transxy",
772 static gmx_bool bSeparate = FALSE, bVels = TRUE, bForce = FALSE, bCONECT = FALSE;
773 static gmx_bool bCenter = FALSE;
774 static int skip_nr = 1, ndec = 3, nzero = 0;
775 static real tzero = 0, delta_t = 0, timestep = 0, ttrunc = -1, tdump = -1, split_t = 0;
776 static rvec newbox = {0, 0, 0}, shift = {0, 0, 0}, trans = {0, 0, 0};
777 static char *exec_command = NULL;
778 static real dropunder = 0, dropover = 0;
779 static gmx_bool bRound = FALSE;
784 { "-skip", FALSE, etINT,
785 { &skip_nr }, "Only write every nr-th frame" },
786 { "-dt", FALSE, etTIME,
788 "Only write frame when t MOD dt = first time (%t)" },
789 { "-round", FALSE, etBOOL,
790 { &bRound }, "Round measurements to nearest picosecond"},
791 { "-dump", FALSE, etTIME,
792 { &tdump }, "Dump frame nearest specified time (%t)" },
793 { "-t0", FALSE, etTIME,
795 "Starting time (%t) (default: don't change)" },
796 { "-timestep", FALSE, etTIME,
798 "Change time step between input frames (%t)" },
799 { "-pbc", FALSE, etENUM,
801 "PBC treatment (see help text for full description)" },
802 { "-ur", FALSE, etENUM,
803 { unitcell_opt }, "Unit-cell representation" },
804 { "-center", FALSE, etBOOL,
805 { &bCenter }, "Center atoms in box" },
806 { "-boxcenter", FALSE, etENUM,
807 { center_opt }, "Center for -pbc and -center" },
808 { "-box", FALSE, etRVEC,
810 "Size for new cubic box (default: read from input)" },
811 { "-trans", FALSE, etRVEC,
813 "All coordinates will be translated by trans. This "
814 "can advantageously be combined with -pbc mol -ur "
816 { "-shift", FALSE, etRVEC,
818 "All coordinates will be shifted by framenr*shift" },
819 { "-fit", FALSE, etENUM,
821 "Fit molecule to ref structure in the structure file" },
822 { "-ndec", FALSE, etINT,
824 "Precision for .xtc and .gro writing in number of "
826 { "-vel", FALSE, etBOOL,
827 { &bVels }, "Read and write velocities if possible" },
828 { "-force", FALSE, etBOOL,
829 { &bForce }, "Read and write forces if possible" },
830 #ifndef GMX_NATIVE_WINDOWS
831 { "-trunc", FALSE, etTIME,
833 "Truncate input trajectory file after this time (%t)" },
835 { "-exec", FALSE, etSTR,
837 "Execute command for every output frame with the "
838 "frame number as argument" },
839 { "-split", FALSE, etTIME,
841 "Start writing new file when t MOD split = first "
843 { "-sep", FALSE, etBOOL,
845 "Write each frame to a separate .gro, .g96 or .pdb "
847 { "-nzero", FALSE, etINT,
849 "If the -sep flag is set, use these many digits "
850 "for the file numbers and prepend zeros as needed" },
851 { "-dropunder", FALSE, etREAL,
852 { &dropunder }, "Drop all frames below this value" },
853 { "-dropover", FALSE, etREAL,
854 { &dropover }, "Drop all frames above this value" },
855 { "-conect", FALSE, etBOOL,
857 "Add conect records when writing [TT].pdb[tt] files. Useful "
858 "for visualization of non-standard molecules, e.g. "
859 "coarse grained ones" }
861 #define NPA asize(pa)
864 t_trxstatus *trxout = NULL;
866 int ftp, ftpin = 0, file_nr;
867 t_trxframe fr, frout;
869 rvec *xmem = NULL, *vmem = NULL, *fmem = NULL;
870 rvec *xp = NULL, x_shift, hbox, box_center, dx;
871 real xtcpr, lambda, *w_rls = NULL;
872 int m, i, d, frame, outframe, natoms, nout, ncent, nre, newstep = 0, model_nr;
875 gmx_mtop_t *mtop = NULL;
876 gmx_conect gc = NULL;
878 t_atoms *atoms = NULL, useatoms;
880 atom_id *index, *cindex;
884 int ifit, irms, my_clust = -1;
885 atom_id *ind_fit, *ind_rms;
886 char *gn_fit, *gn_rms;
887 t_cluster_ndx *clust = NULL;
888 t_trxstatus **clust_status = NULL;
889 int *clust_status_id = NULL;
891 int *nfwritten = NULL;
892 int ndrop = 0, ncol, drop0 = 0, drop1 = 0, dropuse = 0;
894 real tshift = 0, t0 = -1, dt = 0.001, prec;
895 gmx_bool bFit, bFitXY, bPFit, bReset;
897 gmx_rmpbc_t gpbc = NULL;
898 gmx_bool bRmPBC, bPBCWhole, bPBCcomRes, bPBCcomMol, bPBCcomAtom, bPBC, bNoJump, bCluster;
899 gmx_bool bCopy, bDoIt, bIndex, bTDump, bSetTime, bTPS = FALSE, bDTset = FALSE;
900 gmx_bool bExec, bTimeStep = FALSE, bDumpFrame = FALSE, bSetPrec, bNeedPrec;
901 gmx_bool bHaveFirstFrame, bHaveNextFrame, bSetBox, bSetUR, bSplit = FALSE;
902 gmx_bool bSubTraj = FALSE, bDropUnder = FALSE, bDropOver = FALSE, bTrans = FALSE;
903 gmx_bool bWriteFrame, bSplitHere;
904 const char *top_file, *in_file, *out_file = NULL;
905 char out_file2[256], *charpt;
906 char *outf_base = NULL;
907 const char *outf_ext = NULL;
908 char top_title[256], title[256], command[256], filemode[5];
910 gmx_bool bWarnCompact = FALSE;
915 { efTRX, "-f", NULL, ffREAD },
916 { efTRO, "-o", NULL, ffWRITE },
917 { efTPS, NULL, NULL, ffOPTRD },
918 { efNDX, NULL, NULL, ffOPTRD },
919 { efNDX, "-fr", "frames", ffOPTRD },
920 { efNDX, "-sub", "cluster", ffOPTRD },
921 { efXVG, "-drop", "drop", ffOPTRD }
923 #define NFILE asize(fnm)
925 if (!parse_common_args(&argc, argv,
926 PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW |
927 PCA_TIME_UNIT | PCA_BE_NICE,
928 NFILE, fnm, NPA, pa, asize(desc), desc,
934 top_file = ftp2fn(efTPS, NFILE, fnm);
937 /* Check command line */
938 in_file = opt2fn("-f", NFILE, fnm);
942 #ifndef GMX_NATIVE_WINDOWS
943 do_trunc(in_file, ttrunc);
948 /* mark active cmdline options */
949 bSetBox = opt2parg_bSet("-box", NPA, pa);
950 bSetTime = opt2parg_bSet("-t0", NPA, pa);
951 bSetPrec = opt2parg_bSet("-ndec", NPA, pa);
952 bSetUR = opt2parg_bSet("-ur", NPA, pa);
953 bExec = opt2parg_bSet("-exec", NPA, pa);
954 bTimeStep = opt2parg_bSet("-timestep", NPA, pa);
955 bTDump = opt2parg_bSet("-dump", NPA, pa);
956 bDropUnder = opt2parg_bSet("-dropunder", NPA, pa);
957 bDropOver = opt2parg_bSet("-dropover", NPA, pa);
958 bTrans = opt2parg_bSet("-trans", NPA, pa);
959 bSplit = (split_t != 0);
961 /* parse enum options */
962 fit_enum = nenum(fit);
963 bFit = (fit_enum == efFit || fit_enum == efFitXY);
964 bFitXY = fit_enum == efFitXY;
965 bReset = (fit_enum == efReset || fit_enum == efResetXY);
966 bPFit = fit_enum == efPFit;
967 pbc_enum = nenum(pbc_opt);
968 bPBCWhole = pbc_enum == epWhole;
969 bPBCcomRes = pbc_enum == epComRes;
970 bPBCcomMol = pbc_enum == epComMol;
971 bPBCcomAtom = pbc_enum == epComAtom;
972 bNoJump = pbc_enum == epNojump;
973 bCluster = pbc_enum == epCluster;
974 bPBC = pbc_enum != epNone;
975 unitcell_enum = nenum(unitcell_opt);
976 ecenter = nenum(center_opt) - ecTric;
978 /* set and check option dependencies */
981 bFit = TRUE; /* for pfit, fit *must* be set */
985 bReset = TRUE; /* for fit, reset *must* be set */
990 nfitdim = (fit_enum == efFitXY || fit_enum == efResetXY) ? 2 : 3;
992 bRmPBC = bFit || bPBCWhole || bPBCcomRes || bPBCcomMol;
996 if (!(bPBCcomRes || bPBCcomMol || bPBCcomAtom))
999 "WARNING: Option for unitcell representation (-ur %s)\n"
1000 " only has effect in combination with -pbc %s, %s or %s.\n"
1001 " Ingoring unitcell representation.\n\n",
1002 unitcell_opt[0], pbc_opt[2], pbc_opt[3], pbc_opt[4]);
1008 gmx_fatal(FARGS, "PBC condition treatment does not work together with rotational fit.\n"
1009 "Please do the PBC condition treatment first and then run trjconv in a second step\n"
1010 "for the rotational fit.\n"
1011 "First doing the rotational fit and then doing the PBC treatment gives incorrect\n"
1015 /* ndec is in nr of decimal places, prec is a multiplication factor: */
1017 for (i = 0; i < ndec; i++)
1022 bIndex = ftp2bSet(efNDX, NFILE, fnm);
1025 /* Determine output type */
1026 out_file = opt2fn("-o", NFILE, fnm);
1027 ftp = fn2ftp(out_file);
1028 fprintf(stderr, "Will write %s: %s\n", ftp2ext(ftp), ftp2desc(ftp));
1029 bNeedPrec = (ftp == efXTC || ftp == efGRO);
1032 /* check if velocities are possible in input and output files */
1033 ftpin = fn2ftp(in_file);
1034 bVels = (ftp == efTRR || ftp == efTRJ || ftp == efGRO ||
1035 ftp == efG96 || ftp == efTNG)
1036 && (ftpin == efTRR || ftpin == efTRJ || ftpin == efGRO ||
1037 ftpin == efG96 || ftpin == efTNG || ftpin == efCPT);
1039 if (bSeparate || bSplit)
1041 outf_ext = strrchr(out_file, '.');
1042 if (outf_ext == NULL)
1044 gmx_fatal(FARGS, "Output file name '%s' does not contain a '.'", out_file);
1046 outf_base = gmx_strdup(out_file);
1047 outf_base[outf_ext - out_file] = '\0';
1050 bSubTraj = opt2bSet("-sub", NFILE, fnm);
1053 if ((ftp != efXTC) && (ftp != efTRR))
1055 /* It seems likely that other trajectory file types
1056 * could work here. */
1057 gmx_fatal(FARGS, "Can only use the sub option with output file types "
1060 clust = cluster_index(NULL, opt2fn("-sub", NFILE, fnm));
1062 /* Check for number of files disabled, as FOPEN_MAX is not the correct
1063 * number to check for. In my linux box it is only 16.
1065 if (0 && (clust->clust->nr > FOPEN_MAX-4))
1067 gmx_fatal(FARGS, "Can not open enough (%d) files to write all the"
1068 " trajectories.\ntry splitting the index file in %d parts.\n"
1070 clust->clust->nr, 1+clust->clust->nr/FOPEN_MAX, FOPEN_MAX);
1072 gmx_warning("The -sub option could require as many open output files as there are\n"
1073 "index groups in the file (%d). If you get I/O errors opening new files,\n"
1074 "try reducing the number of index groups in the file, and perhaps\n"
1075 "using trjconv -sub several times on different chunks of your index file.\n",
1078 snew(clust_status, clust->clust->nr);
1079 snew(clust_status_id, clust->clust->nr);
1080 snew(nfwritten, clust->clust->nr);
1081 for (i = 0; (i < clust->clust->nr); i++)
1083 clust_status[i] = NULL;
1084 clust_status_id[i] = -1;
1086 bSeparate = bSplit = FALSE;
1093 mtop = read_mtop_for_tng(top_file, in_file, out_file);
1095 /* Determine whether to read a topology */
1096 bTPS = (ftp2bSet(efTPS, NFILE, fnm) ||
1097 bRmPBC || bReset || bPBCcomMol || bCluster ||
1098 (ftp == efGRO) || (ftp == efPDB) || bCONECT);
1100 /* Determine if when can read index groups */
1101 bIndex = (bIndex || bTPS);
1105 read_tps_conf(top_file, top_title, &top, &ePBC, &xp, NULL, top_box,
1106 bReset || bPBCcomRes);
1109 if (0 == top.mols.nr && (bCluster || bPBCcomMol))
1111 gmx_fatal(FARGS, "Option -pbc %s requires a .tpr file for the -s option", pbc_opt[pbc_enum]);
1114 /* top_title is only used for gro and pdb,
1115 * the header in such a file is top_title t= ...
1116 * to prevent a double t=, remove it from top_title
1118 if ((charpt = strstr(top_title, " t= ")))
1125 gc = gmx_conect_generate(&top);
1129 gpbc = gmx_rmpbc_init(&top.idef, ePBC, top.atoms.nr);
1133 /* get frame number index */
1135 if (opt2bSet("-fr", NFILE, fnm))
1137 printf("Select groups of frame number indices:\n");
1138 rd_index(opt2fn("-fr", NFILE, fnm), 1, &nrfri, (atom_id **)&frindex, &frname);
1141 for (i = 0; i < nrfri; i++)
1143 fprintf(debug, "frindex[%4d]=%4d\n", i, frindex[i]);
1148 /* get index groups etc. */
1151 printf("Select group for %s fit\n",
1152 bFit ? "least squares" : "translational");
1153 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
1154 1, &ifit, &ind_fit, &gn_fit);
1160 gmx_fatal(FARGS, "Need at least 2 atoms to fit!\n");
1164 fprintf(stderr, "WARNING: fitting with only 2 atoms is not unique\n");
1170 printf("Select group for clustering\n");
1171 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
1172 1, &ifit, &ind_fit, &gn_fit);
1179 printf("Select group for centering\n");
1180 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
1181 1, &ncent, &cindex, &grpnm);
1183 printf("Select group for output\n");
1184 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
1185 1, &nout, &index, &grpnm);
1189 /* no index file, so read natoms from TRX */
1190 if (!read_first_frame(oenv, &trxin, in_file, &fr, TRX_DONT_SKIP))
1192 gmx_fatal(FARGS, "Could not read a frame from %s", in_file);
1197 snew(index, natoms);
1198 for (i = 0; i < natoms; i++)
1212 snew(w_rls, atoms->nr);
1213 for (i = 0; (i < ifit); i++)
1215 w_rls[ind_fit[i]] = atoms->atom[ind_fit[i]].m;
1218 /* Restore reference structure and set to origin,
1219 store original location (to put structure back) */
1222 gmx_rmpbc(gpbc, top.atoms.nr, top_box, xp);
1224 copy_rvec(xp[index[0]], x_shift);
1225 reset_x_ndim(nfitdim, ifit, ind_fit, atoms->nr, NULL, xp, w_rls);
1226 rvec_dec(x_shift, xp[index[0]]);
1230 clear_rvec(x_shift);
1233 if (bDropUnder || bDropOver)
1235 /* Read the .xvg file with the drop values */
1236 fprintf(stderr, "\nReading drop file ...");
1237 ndrop = read_xvg(opt2fn("-drop", NFILE, fnm), &dropval, &ncol);
1238 fprintf(stderr, " %d time points\n", ndrop);
1239 if (ndrop == 0 || ncol < 2)
1241 gmx_fatal(FARGS, "Found no data points in %s",
1242 opt2fn("-drop", NFILE, fnm));
1248 /* Make atoms struct for output in GRO or PDB files */
1249 if ((ftp == efGRO) || ((ftp == efG96) && bTPS) || (ftp == efPDB))
1251 /* get memory for stuff to go in .pdb file, and initialize
1252 * the pdbinfo structure part if the input has it.
1254 init_t_atoms(&useatoms, atoms->nr, (atoms->pdbinfo != NULL));
1255 sfree(useatoms.resinfo);
1256 useatoms.resinfo = atoms->resinfo;
1257 for (i = 0; (i < nout); i++)
1259 useatoms.atomname[i] = atoms->atomname[index[i]];
1260 useatoms.atom[i] = atoms->atom[index[i]];
1261 if (atoms->pdbinfo != NULL)
1263 useatoms.pdbinfo[i] = atoms->pdbinfo[index[i]];
1265 useatoms.nres = max(useatoms.nres, useatoms.atom[i].resind+1);
1269 /* select what to read */
1270 if (ftp == efTRR || ftp == efTRJ)
1280 flags = flags | TRX_READ_V;
1284 flags = flags | TRX_READ_F;
1287 /* open trx file for reading */
1288 bHaveFirstFrame = read_first_frame(oenv, &trxin, in_file, &fr, flags);
1291 fprintf(stderr, "\nPrecision of %s is %g (nm)\n", in_file, 1/fr.prec);
1295 if (bSetPrec || !fr.bPrec)
1297 fprintf(stderr, "\nSetting output precision to %g (nm)\n", 1/prec);
1301 fprintf(stderr, "Using output precision of %g (nm)\n", 1/prec);
1305 if (bHaveFirstFrame)
1307 set_trxframe_ePBC(&fr, ePBC);
1313 tshift = tzero-fr.time;
1323 /* check if index is meaningful */
1324 for (i = 0; i < nout; i++)
1326 if (index[i] >= natoms)
1329 "Index[%d] %d is larger than the number of atoms in the\n"
1330 "trajectory file (%d). There is a mismatch in the contents\n"
1331 "of your -f, -s and/or -n files.", i, index[i]+1, natoms);
1333 bCopy = bCopy || (i != index[i]);
1337 /* open output for writing */
1338 strcpy(filemode, "w");
1342 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
1758 trxout = open_trx(out_file2, filemode);
1765 if (clust_status_id[my_clust] == -1)
1767 sprintf(buf, "%s.%s", clust->grpname[my_clust], ftp2ext(ftp));
1768 clust_status[my_clust] = open_trx(buf, "w");
1769 clust_status_id[my_clust] = 1;
1772 else if (clust_status_id[my_clust] == -2)
1774 gmx_fatal(FARGS, "File %s.xtc should still be open (%d open .xtc files)\n" "in order to write frame %d. my_clust = %d",
1775 clust->grpname[my_clust], ntrxopen, frame,
1778 write_trxframe(clust_status[my_clust], &frout, gc);
1779 nfwritten[my_clust]++;
1780 if (nfwritten[my_clust] ==
1781 (clust->clust->index[my_clust+1]-
1782 clust->clust->index[my_clust]))
1784 close_trx(clust_status[my_clust]);
1785 clust_status[my_clust] = NULL;
1786 clust_status_id[my_clust] = -2;
1790 gmx_fatal(FARGS, "Less than zero open .xtc files!");
1797 write_trxframe(trxout, &frout, gc);
1803 sprintf(title, "Generated by trjconv : %s t= %9.5f",
1804 top_title, fr.time);
1805 if (bSeparate || bSplitHere)
1807 out = gmx_ffopen(out_file2, "w");
1812 write_hconf_p(out, title, &useatoms, prec2ndec(frout.prec),
1813 frout.x, frout.bV ? frout.v : NULL, frout.box);
1816 fprintf(out, "REMARK GENERATED BY TRJCONV\n");
1817 sprintf(title, "%s t= %9.5f", top_title, frout.time);
1818 /* if reading from pdb, we want to keep the original
1819 model numbering else we write the output frame
1820 number plus one, because model 0 is not allowed in pdb */
1821 if (ftpin == efPDB && fr.bStep && fr.step > model_nr)
1829 write_pdbfile(out, title, &useatoms, frout.x,
1830 frout.ePBC, frout.box, ' ', model_nr, gc, TRUE);
1833 frout.title = title;
1834 if (bSeparate || bTDump)
1836 frout.bTitle = TRUE;
1839 frout.bAtoms = TRUE;
1841 frout.atoms = &useatoms;
1842 frout.bStep = FALSE;
1843 frout.bTime = FALSE;
1847 frout.bTitle = (outframe == 0);
1848 frout.bAtoms = FALSE;
1852 write_g96_conf(out, &frout, -1, NULL);
1861 gmx_fatal(FARGS, "DHE, ftp=%d\n", ftp);
1863 if (bSeparate || bSplitHere)
1868 /* execute command */
1872 sprintf(c, "%s %d", exec_command, file_nr-1);
1873 /*fprintf(stderr,"Executing '%s'\n",c);*/
1874 #ifdef GMX_NO_SYSTEM
1875 printf("Warning-- No calls to system(3) supported on this platform.");
1876 printf("Warning-- Skipping execution of 'system(\"%s\")'.", c);
1880 gmx_fatal(FARGS, "Error executing command: %s", c);
1888 bHaveNextFrame = read_next_frame(oenv, trxin, &fr);
1890 while (!(bTDump && bDumpFrame) && bHaveNextFrame);
1893 if (!bHaveFirstFrame || (bTDump && !bDumpFrame))
1895 fprintf(stderr, "\nWARNING no output, "
1896 "last frame read at t=%g\n", fr.time);
1898 fprintf(stderr, "\n");
1905 gmx_rmpbc_done(gpbc);
1912 else if (out != NULL)
1918 for (i = 0; (i < clust->clust->nr); i++)
1920 if (clust_status_id[i] >= 0)
1922 close_trx(clust_status[i]);
1930 do_view(oenv, out_file, NULL);