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43 #include "gromacs/commandline/pargs.h"
44 #include "gromacs/fileio/confio.h"
45 #include "gromacs/fileio/g96io.h"
46 #include "gromacs/fileio/gmxfio.h"
47 #include "gromacs/fileio/pdbio.h"
48 #include "gromacs/fileio/tngio_for_tools.h"
49 #include "gromacs/fileio/tpxio.h"
50 #include "gromacs/fileio/trnio.h"
51 #include "gromacs/fileio/trxio.h"
52 #include "gromacs/fileio/xtcio.h"
53 #include "gromacs/fileio/xvgr.h"
54 #include "gromacs/gmxana/gmx_ana.h"
55 #include "gromacs/legacyheaders/copyrite.h"
56 #include "gromacs/legacyheaders/macros.h"
57 #include "gromacs/legacyheaders/names.h"
58 #include "gromacs/legacyheaders/typedefs.h"
59 #include "gromacs/legacyheaders/viewit.h"
60 #include "gromacs/math/do_fit.h"
61 #include "gromacs/math/vec.h"
62 #include "gromacs/pbcutil/pbc.h"
63 #include "gromacs/pbcutil/rmpbc.h"
64 #include "gromacs/topology/index.h"
65 #include "gromacs/topology/topology.h"
66 #include "gromacs/utility/fatalerror.h"
67 #include "gromacs/utility/futil.h"
68 #include "gromacs/utility/smalloc.h"
71 euSel, euRect, euTric, euCompact, euNR
75 static void calc_pbc_cluster(int ecenter, int nrefat, t_topology *top, int ePBC,
76 rvec x[], atom_id index[], matrix box)
78 int m, i, j, j0, j1, jj, ai, aj;
81 rvec dx, xtest, box_center;
82 int nmol, imol_center;
84 gmx_bool *bMol, *bTmp;
85 rvec *m_com, *m_shift;
93 calc_box_center(ecenter, box, box_center);
95 /* Initiate the pbc structure */
96 memset(&pbc, 0, sizeof(pbc));
97 set_pbc(&pbc, ePBC, box);
99 /* Convert atom index to molecular */
101 molind = top->mols.index;
107 snew(bTmp, top->atoms.nr);
109 for (i = 0; (i < nrefat); i++)
111 /* Mark all molecules in the index */
114 /* Binary search assuming the molecules are sorted */
119 if (ai < molind[j0+1])
123 else if (ai >= molind[j1])
130 if (ai < molind[jj+1])
142 /* Double check whether all atoms in all molecules that are marked are part
143 * of the cluster. Simultaneously compute the center of geometry.
145 min_dist2 = 10*sqr(trace(box));
148 for (i = 0; i < nmol; i++)
150 for (j = molind[i]; j < molind[i+1]; j++)
152 if (bMol[i] && !bTmp[j])
154 gmx_fatal(FARGS, "Molecule %d marked for clustering but not atom %d in it - check your index!", i+1, j+1);
156 else if (!bMol[i] && bTmp[j])
158 gmx_fatal(FARGS, "Atom %d marked for clustering but not molecule %d - this is an internal error...", j+1, i+1);
162 /* Make molecule whole, move 2nd and higher atom to same periodicity as 1st atom in molecule */
165 pbc_dx(&pbc, x[j], x[j-1], dx);
166 rvec_add(x[j-1], dx, x[j]);
168 /* Compute center of geometry of molecule - m_com[i] was zeroed when we did snew() on it! */
169 rvec_inc(m_com[i], x[j]);
174 /* Normalize center of geometry */
175 fac = 1.0/(molind[i+1]-molind[i]);
176 for (m = 0; (m < DIM); m++)
180 /* Determine which molecule is closest to the center of the box */
181 pbc_dx(&pbc, box_center, m_com[i], dx);
182 tmp_r2 = iprod(dx, dx);
184 if (tmp_r2 < min_dist2)
189 cluster[ncluster++] = i;
196 fprintf(stderr, "No molecules selected in the cluster\n");
199 else if (imol_center == -1)
201 fprintf(stderr, "No central molecules could be found\n");
206 added[nadded++] = imol_center;
207 bMol[imol_center] = FALSE;
209 while (nadded < ncluster)
211 /* Find min distance between cluster molecules and those remaining to be added */
212 min_dist2 = 10*sqr(trace(box));
215 /* Loop over added mols */
216 for (i = 0; i < nadded; i++)
219 /* Loop over all mols */
220 for (j = 0; j < ncluster; j++)
223 /* check those remaining to be added */
226 pbc_dx(&pbc, m_com[aj], m_com[ai], dx);
227 tmp_r2 = iprod(dx, dx);
228 if (tmp_r2 < min_dist2)
238 /* Add the best molecule */
239 added[nadded++] = jmin;
241 /* Calculate the shift from the ai molecule */
242 pbc_dx(&pbc, m_com[jmin], m_com[imin], dx);
243 rvec_add(m_com[imin], dx, xtest);
244 rvec_sub(xtest, m_com[jmin], m_shift[jmin]);
245 rvec_inc(m_com[jmin], m_shift[jmin]);
247 for (j = molind[jmin]; j < molind[jmin+1]; j++)
249 rvec_inc(x[j], m_shift[jmin]);
251 fprintf(stdout, "\rClustering iteration %d of %d...", nadded, ncluster);
261 fprintf(stdout, "\n");
264 static void put_molecule_com_in_box(int unitcell_enum, int ecenter,
266 int natoms, t_atom atom[],
267 int ePBC, matrix box, rvec x[])
271 rvec com, new_com, shift, dx, box_center;
276 calc_box_center(ecenter, box, box_center);
277 set_pbc(&pbc, ePBC, box);
280 gmx_fatal(FARGS, "There are no molecule descriptions. I need a .tpr file for this pbc option.");
282 for (i = 0; (i < mols->nr); i++)
287 for (j = mols->index[i]; (j < mols->index[i+1] && j < natoms); j++)
290 for (d = 0; d < DIM; d++)
296 /* calculate final COM */
297 svmul(1.0/mtot, com, com);
299 /* check if COM is outside box */
300 copy_rvec(com, new_com);
301 switch (unitcell_enum)
304 put_atoms_in_box(ePBC, box, 1, &new_com);
307 put_atoms_in_triclinic_unitcell(ecenter, box, 1, &new_com);
310 put_atoms_in_compact_unitcell(ePBC, ecenter, box, 1, &new_com);
313 rvec_sub(new_com, com, shift);
314 if (norm2(shift) > 0)
318 fprintf(debug, "\nShifting position of molecule %d "
319 "by %8.3f %8.3f %8.3f\n", i+1,
320 shift[XX], shift[YY], shift[ZZ]);
322 for (j = mols->index[i]; (j < mols->index[i+1] && j < natoms); j++)
324 rvec_inc(x[j], shift);
330 static void put_residue_com_in_box(int unitcell_enum, int ecenter,
331 int natoms, t_atom atom[],
332 int ePBC, matrix box, rvec x[])
334 atom_id i, j, res_start, res_end, res_nat;
338 rvec box_center, com, new_com, shift;
340 calc_box_center(ecenter, box, box_center);
346 for (i = 0; i < natoms+1; i++)
348 if (i == natoms || (presnr != atom[i].resind && presnr != NOTSET))
350 /* calculate final COM */
352 res_nat = res_end - res_start;
353 svmul(1.0/mtot, com, com);
355 /* check if COM is outside box */
356 copy_rvec(com, new_com);
357 switch (unitcell_enum)
360 put_atoms_in_box(ePBC, box, 1, &new_com);
363 put_atoms_in_triclinic_unitcell(ecenter, box, 1, &new_com);
366 put_atoms_in_compact_unitcell(ePBC, ecenter, box, 1, &new_com);
369 rvec_sub(new_com, com, shift);
374 fprintf(debug, "\nShifting position of residue %d (atoms %d-%d) "
375 "by %g,%g,%g\n", atom[res_start].resind+1,
376 res_start+1, res_end+1, shift[XX], shift[YY], shift[ZZ]);
378 for (j = res_start; j < res_end; j++)
380 rvec_inc(x[j], shift);
386 /* remember start of new residue */
393 for (d = 0; d < DIM; d++)
399 presnr = atom[i].resind;
404 static void center_x(int ecenter, rvec x[], matrix box, int n, int nc, atom_id ci[])
407 rvec cmin, cmax, box_center, dx;
411 copy_rvec(x[ci[0]], cmin);
412 copy_rvec(x[ci[0]], cmax);
413 for (i = 0; i < nc; i++)
416 for (m = 0; m < DIM; m++)
418 if (x[ai][m] < cmin[m])
422 else if (x[ai][m] > cmax[m])
428 calc_box_center(ecenter, box, box_center);
429 for (m = 0; m < DIM; m++)
431 dx[m] = box_center[m]-(cmin[m]+cmax[m])*0.5;
434 for (i = 0; i < n; i++)
441 static void mk_filenm(char *base, const char *ext, int ndigit, int file_nr,
447 strcpy(out_file, base);
458 strncat(out_file, "00000000000", ndigit-nd);
460 sprintf(nbuf, "%d.", file_nr);
461 strcat(out_file, nbuf);
462 strcat(out_file, ext);
465 void check_trn(const char *fn)
467 if (fn2ftp(fn) != efTRR)
469 gmx_fatal(FARGS, "%s is not a trajectory file, exiting\n", fn);
473 void do_trunc(const char *fn, real t0)
486 gmx_fatal(FARGS, "You forgot to set the truncation time");
489 /* Check whether this is a .trr file */
492 in = open_trn(fn, "r");
493 fp = gmx_fio_getfp(in);
496 fprintf(stderr, "Sorry, can not trunc %s, truncation of this filetype is not supported\n", fn);
502 fpos = gmx_fio_ftell(in);
504 while (!bStop && fread_trnheader(in, &sh, &bOK))
506 fread_htrn(in, &sh, NULL, NULL, NULL, NULL);
507 fpos = gmx_ftell(fp);
511 gmx_fseek(fp, fpos, SEEK_SET);
517 fprintf(stderr, "Do you REALLY want to truncate this trajectory (%s) at:\n"
518 "frame %d, time %g, bytes %ld ??? (type YES if so)\n",
519 fn, j, t, (long int)fpos);
520 if (1 != scanf("%s", yesno))
522 gmx_fatal(FARGS, "Error reading user input");
524 if (strcmp(yesno, "YES") == 0)
526 fprintf(stderr, "Once again, I'm gonna DO this...\n");
528 if (0 != gmx_truncate(fn, fpos))
530 gmx_fatal(FARGS, "Error truncating file %s", fn);
535 fprintf(stderr, "Ok, I'll forget about it\n");
540 fprintf(stderr, "Already at end of file (t=%g)...\n", t);
546 /*! \brief Read a full molecular topology if useful and available.
548 * If the input trajectory file is not in TNG format, and the output
549 * file is in TNG format, then we want to try to read a full topology
550 * (if available), so that we can write molecule information to the
551 * output file. The full topology provides better molecule information
552 * than is available from the normal t_topology data used by GROMACS
555 * Also, the t_topology is only read under (different) particular
556 * conditions. If both apply, then a .tpr file might be read
557 * twice. Trying to fix this redundancy while trjconv is still an
558 * all-purpose tool does not seem worthwhile.
560 * Because of the way gmx_prepare_tng_writing is implemented, the case
561 * where the input TNG file has no molecule information will never
562 * lead to an output TNG file having molecule information. Since
563 * molecule information will generally be present if the input TNG
564 * file was written by a GROMACS tool, this seems like reasonable
566 static gmx_mtop_t *read_mtop_for_tng(const char *tps_file,
567 const char *input_file,
568 const char *output_file)
570 gmx_mtop_t *mtop = NULL;
572 if (fn2bTPX(tps_file) &&
573 efTNG != fn2ftp(input_file) &&
574 efTNG == fn2ftp(output_file))
576 int temp_natoms = -1;
578 read_tpx(tps_file, NULL, NULL, &temp_natoms,
579 NULL, NULL, NULL, mtop);
585 int gmx_trjconv(int argc, char *argv[])
587 const char *desc[] = {
588 "[THISMODULE] can convert trajectory files in many ways:",
590 "* from one format to another",
591 "* select a subset of atoms",
592 "* change the periodicity representation",
593 "* keep multimeric molecules together",
594 "* center atoms in the box",
595 "* fit atoms to reference structure",
596 "* reduce the number of frames",
597 "* change the timestamps of the frames ([TT]-t0[tt] and [TT]-timestep[tt])",
598 "* cut the trajectory in small subtrajectories according",
599 " to information in an index file. This allows subsequent analysis of",
600 " the subtrajectories that could, for example, be the result of a",
601 " cluster analysis. Use option [TT]-sub[tt].",
602 " This assumes that the entries in the index file are frame numbers and",
603 " dumps each group in the index file to a separate trajectory file.",
604 "* select frames within a certain range of a quantity given",
605 " in an [REF].xvg[ref] file.",
607 "[gmx-trjcat] is better suited for concatenating multiple trajectory files.",
610 "The following formats are supported for input and output:",
611 "[REF].xtc[ref], [REF].trr[ref], [REF].gro[ref], [TT].g96[tt]",
612 "and [REF].pdb[ref].",
613 "The file formats are detected from the file extension.",
614 "The precision of [REF].xtc[ref] and [REF].gro[ref] output is taken from the",
615 "input file for [REF].xtc[ref], [REF].gro[ref] and [REF].pdb[ref],",
616 "and from the [TT]-ndec[tt] option for other input formats. The precision",
617 "is always taken from [TT]-ndec[tt], when this option is set.",
618 "All other formats have fixed precision. [REF].trr[ref]",
619 "output can be single or double precision, depending on the precision",
620 "of the [THISMODULE] binary.",
621 "Note that velocities are only supported in",
622 "[REF].trr[ref], [REF].gro[ref] and [TT].g96[tt] files.[PAR]",
624 "Option [TT]-sep[tt] can be used to write every frame to a separate",
625 "[TT].gro, .g96[tt] or [REF].pdb[ref] file. By default, all frames all written to one file.",
626 "[REF].pdb[ref] files with all frames concatenated can be viewed with",
627 "[TT]rasmol -nmrpdb[tt].[PAR]",
629 "It is possible to select part of your trajectory and write it out",
630 "to a new trajectory file in order to save disk space, e.g. for leaving",
631 "out the water from a trajectory of a protein in water.",
632 "[BB]ALWAYS[bb] put the original trajectory on tape!",
633 "We recommend to use the portable [REF].xtc[ref] format for your analysis",
634 "to save disk space and to have portable files.[PAR]",
636 "There are two options for fitting the trajectory to a reference",
637 "either for essential dynamics analysis, etc.",
638 "The first option is just plain fitting to a reference structure",
639 "in the structure file. The second option is a progressive fit",
640 "in which the first timeframe is fitted to the reference structure ",
641 "in the structure file to obtain and each subsequent timeframe is ",
642 "fitted to the previously fitted structure. This way a continuous",
643 "trajectory is generated, which might not be the case when using the",
644 "regular fit method, e.g. when your protein undergoes large",
645 "conformational transitions.[PAR]",
647 "Option [TT]-pbc[tt] sets the type of periodic boundary condition",
650 " * [TT]mol[tt] puts the center of mass of molecules in the box,",
651 " and requires a run input file to be supplied with [TT]-s[tt].",
652 " * [TT]res[tt] puts the center of mass of residues in the box.",
653 " * [TT]atom[tt] puts all the atoms in the box.",
654 " * [TT]nojump[tt] checks if atoms jump across the box and then puts",
655 " them back. This has the effect that all molecules",
656 " will remain whole (provided they were whole in the initial",
657 " conformation). [BB]Note[bb] that this ensures a continuous trajectory but",
658 " molecules may diffuse out of the box. The starting configuration",
659 " for this procedure is taken from the structure file, if one is",
660 " supplied, otherwise it is the first frame.",
661 " * [TT]cluster[tt] clusters all the atoms in the selected index",
662 " such that they are all closest to the center of mass of the cluster,",
663 " which is iteratively updated. [BB]Note[bb] that this will only give meaningful",
664 " results if you in fact have a cluster. Luckily that can be checked",
665 " afterwards using a trajectory viewer. Note also that if your molecules",
666 " are broken this will not work either.",
668 " The separate option [TT]-clustercenter[tt] can be used to specify an",
669 " approximate center for the cluster. This is useful e.g. if you have",
670 " two big vesicles, and you want to maintain their relative positions.",
671 " * [TT]whole[tt] only makes broken molecules whole.",
674 "Option [TT]-ur[tt] sets the unit cell representation for options",
675 "[TT]mol[tt], [TT]res[tt] and [TT]atom[tt] of [TT]-pbc[tt].",
676 "All three options give different results for triclinic boxes and",
677 "identical results for rectangular boxes.",
678 "[TT]rect[tt] is the ordinary brick shape.",
679 "[TT]tric[tt] is the triclinic unit cell.",
680 "[TT]compact[tt] puts all atoms at the closest distance from the center",
681 "of the box. This can be useful for visualizing e.g. truncated octahedra",
682 "or rhombic dodecahedra. The center for options [TT]tric[tt] and [TT]compact[tt]",
683 "is [TT]tric[tt] (see below), unless the option [TT]-boxcenter[tt]",
684 "is set differently.[PAR]",
686 "Option [TT]-center[tt] centers the system in the box. The user can",
687 "select the group which is used to determine the geometrical center.",
688 "Option [TT]-boxcenter[tt] sets the location of the center of the box",
689 "for options [TT]-pbc[tt] and [TT]-center[tt]. The center options are:",
690 "[TT]tric[tt]: half of the sum of the box vectors,",
691 "[TT]rect[tt]: half of the box diagonal,",
692 "[TT]zero[tt]: zero.",
693 "Use option [TT]-pbc mol[tt] in addition to [TT]-center[tt] when you",
694 "want all molecules in the box after the centering.[PAR]",
696 "Option [TT]-box[tt] sets the size of the new box. This option only works",
697 "for leading dimensions and is thus generally only useful for rectangular boxes.",
698 "If you want to modify only some of the dimensions, e.g. when reading from",
699 "a trajectory, you can use -1 for those dimensions that should stay the same",
701 "It is not always possible to use combinations of [TT]-pbc[tt],",
702 "[TT]-fit[tt], [TT]-ur[tt] and [TT]-center[tt] to do exactly what",
703 "you want in one call to [THISMODULE]. Consider using multiple",
704 "calls, and check out the GROMACS website for suggestions.[PAR]",
706 "With [TT]-dt[tt], it is possible to reduce the number of ",
707 "frames in the output. This option relies on the accuracy of the times",
708 "in your input trajectory, so if these are inaccurate use the",
709 "[TT]-timestep[tt] option to modify the time (this can be done",
710 "simultaneously). For making smooth movies, the program [gmx-filter]",
711 "can reduce the number of frames while using low-pass frequency",
712 "filtering, this reduces aliasing of high frequency motions.[PAR]",
714 "Using [TT]-trunc[tt] [THISMODULE] can truncate [REF].trr[ref] in place, i.e.",
715 "without copying the file. This is useful when a run has crashed",
716 "during disk I/O (i.e. full disk), or when two contiguous",
717 "trajectories must be concatenated without having double frames.[PAR]",
719 "Option [TT]-dump[tt] can be used to extract a frame at or near",
720 "one specific time from your trajectory, but only works reliably",
721 "if the time interval between frames is uniform.[PAR]",
723 "Option [TT]-drop[tt] reads an [REF].xvg[ref] file with times and values.",
724 "When options [TT]-dropunder[tt] and/or [TT]-dropover[tt] are set,",
725 "frames with a value below and above the value of the respective options",
726 "will not be written."
742 const char *pbc_opt[epNR + 1] =
744 NULL, "none", "mol", "res", "atom", "nojump", "cluster", "whole",
749 const char *unitcell_opt[euNR+1] =
750 { NULL, "rect", "tric", "compact", NULL };
754 ecSel, ecTric, ecRect, ecZero, ecNR
756 const char *center_opt[ecNR+1] =
757 { NULL, "tric", "rect", "zero", NULL };
763 efSel, efNone, efFit, efFitXY, efReset, efResetXY, efPFit, efNR
765 const char *fit[efNR + 1] =
767 NULL, "none", "rot+trans", "rotxy+transxy", "translation", "transxy",
771 static gmx_bool bSeparate = FALSE, bVels = TRUE, bForce = FALSE, bCONECT = FALSE;
772 static gmx_bool bCenter = FALSE;
773 static int skip_nr = 1, ndec = 3, nzero = 0;
774 static real tzero = 0, delta_t = 0, timestep = 0, ttrunc = -1, tdump = -1, split_t = 0;
775 static rvec newbox = {0, 0, 0}, shift = {0, 0, 0}, trans = {0, 0, 0};
776 static char *exec_command = NULL;
777 static real dropunder = 0, dropover = 0;
778 static gmx_bool bRound = FALSE;
783 { "-skip", FALSE, etINT,
784 { &skip_nr }, "Only write every nr-th frame" },
785 { "-dt", FALSE, etTIME,
787 "Only write frame when t MOD dt = first time (%t)" },
788 { "-round", FALSE, etBOOL,
789 { &bRound }, "Round measurements to nearest picosecond"},
790 { "-dump", FALSE, etTIME,
791 { &tdump }, "Dump frame nearest specified time (%t)" },
792 { "-t0", FALSE, etTIME,
794 "Starting time (%t) (default: don't change)" },
795 { "-timestep", FALSE, etTIME,
797 "Change time step between input frames (%t)" },
798 { "-pbc", FALSE, etENUM,
800 "PBC treatment (see help text for full description)" },
801 { "-ur", FALSE, etENUM,
802 { unitcell_opt }, "Unit-cell representation" },
803 { "-center", FALSE, etBOOL,
804 { &bCenter }, "Center atoms in box" },
805 { "-boxcenter", FALSE, etENUM,
806 { center_opt }, "Center for -pbc and -center" },
807 { "-box", FALSE, etRVEC,
809 "Size for new cubic box (default: read from input)" },
810 { "-trans", FALSE, etRVEC,
812 "All coordinates will be translated by trans. This "
813 "can advantageously be combined with -pbc mol -ur "
815 { "-shift", FALSE, etRVEC,
817 "All coordinates will be shifted by framenr*shift" },
818 { "-fit", FALSE, etENUM,
820 "Fit molecule to ref structure in the structure file" },
821 { "-ndec", FALSE, etINT,
823 "Precision for .xtc and .gro writing in number of "
825 { "-vel", FALSE, etBOOL,
826 { &bVels }, "Read and write velocities if possible" },
827 { "-force", FALSE, etBOOL,
828 { &bForce }, "Read and write forces if possible" },
829 { "-trunc", FALSE, etTIME,
831 "Truncate input trajectory file after this time (%t)" },
832 { "-exec", FALSE, etSTR,
834 "Execute command for every output frame with the "
835 "frame number as argument" },
836 { "-split", FALSE, etTIME,
838 "Start writing new file when t MOD split = first "
840 { "-sep", FALSE, etBOOL,
842 "Write each frame to a separate .gro, .g96 or .pdb "
844 { "-nzero", FALSE, etINT,
846 "If the -sep flag is set, use these many digits "
847 "for the file numbers and prepend zeros as needed" },
848 { "-dropunder", FALSE, etREAL,
849 { &dropunder }, "Drop all frames below this value" },
850 { "-dropover", FALSE, etREAL,
851 { &dropover }, "Drop all frames above this value" },
852 { "-conect", FALSE, etBOOL,
854 "Add conect records when writing [REF].pdb[ref] files. Useful "
855 "for visualization of non-standard molecules, e.g. "
856 "coarse grained ones" }
858 #define NPA asize(pa)
861 t_trxstatus *trxout = NULL;
863 int ftp, ftpin = 0, file_nr;
864 t_trxframe fr, frout;
866 rvec *xmem = NULL, *vmem = NULL, *fmem = NULL;
867 rvec *xp = NULL, x_shift, hbox, box_center, dx;
868 real xtcpr, lambda, *w_rls = NULL;
869 int m, i, d, frame, outframe, natoms, nout, ncent, nre, newstep = 0, model_nr;
872 gmx_mtop_t *mtop = NULL;
873 gmx_conect gc = NULL;
875 t_atoms *atoms = NULL, useatoms;
877 atom_id *index, *cindex;
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;
885 t_trxstatus **clust_status = NULL;
886 int *clust_status_id = NULL;
888 int *nfwritten = NULL;
889 int ndrop = 0, ncol, drop0 = 0, drop1 = 0, dropuse = 0;
891 real tshift = 0, t0 = -1, dt = 0.001, prec;
892 gmx_bool bFit, bFitXY, bPFit, bReset;
894 gmx_rmpbc_t gpbc = NULL;
895 gmx_bool bRmPBC, bPBCWhole, bPBCcomRes, bPBCcomMol, bPBCcomAtom, bPBC, bNoJump, bCluster;
896 gmx_bool bCopy, bDoIt, bIndex, bTDump, bSetTime, bTPS = FALSE, bDTset = FALSE;
897 gmx_bool bExec, bTimeStep = FALSE, bDumpFrame = FALSE, bSetPrec, bNeedPrec;
898 gmx_bool bHaveFirstFrame, bHaveNextFrame, bSetBox, bSetUR, bSplit = FALSE;
899 gmx_bool bSubTraj = FALSE, bDropUnder = FALSE, bDropOver = FALSE, bTrans = FALSE;
900 gmx_bool bWriteFrame, bSplitHere;
901 const char *top_file, *in_file, *out_file = NULL;
902 char out_file2[256], *charpt;
903 char *outf_base = NULL;
904 const char *outf_ext = NULL;
905 char top_title[256], title[256], command[256], filemode[5];
907 gmx_bool bWarnCompact = FALSE;
912 { efTRX, "-f", NULL, ffREAD },
913 { efTRO, "-o", NULL, ffWRITE },
914 { efTPS, NULL, NULL, ffOPTRD },
915 { efNDX, NULL, NULL, ffOPTRD },
916 { efNDX, "-fr", "frames", ffOPTRD },
917 { efNDX, "-sub", "cluster", ffOPTRD },
918 { efXVG, "-drop", "drop", ffOPTRD }
920 #define NFILE asize(fnm)
922 if (!parse_common_args(&argc, argv,
923 PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW |
925 NFILE, fnm, NPA, pa, asize(desc), desc,
931 top_file = ftp2fn(efTPS, NFILE, fnm);
934 /* Check command line */
935 in_file = opt2fn("-f", NFILE, fnm);
939 do_trunc(in_file, ttrunc);
943 /* mark active cmdline options */
944 bSetBox = opt2parg_bSet("-box", NPA, pa);
945 bSetTime = opt2parg_bSet("-t0", NPA, pa);
946 bSetPrec = opt2parg_bSet("-ndec", NPA, pa);
947 bSetUR = opt2parg_bSet("-ur", NPA, pa);
948 bExec = opt2parg_bSet("-exec", NPA, pa);
949 bTimeStep = opt2parg_bSet("-timestep", NPA, pa);
950 bTDump = opt2parg_bSet("-dump", NPA, pa);
951 bDropUnder = opt2parg_bSet("-dropunder", NPA, pa);
952 bDropOver = opt2parg_bSet("-dropover", NPA, pa);
953 bTrans = opt2parg_bSet("-trans", NPA, pa);
954 bSplit = (split_t != 0);
956 /* parse enum options */
957 fit_enum = nenum(fit);
958 bFit = (fit_enum == efFit || fit_enum == efFitXY);
959 bFitXY = fit_enum == efFitXY;
960 bReset = (fit_enum == efReset || fit_enum == efResetXY);
961 bPFit = fit_enum == efPFit;
962 pbc_enum = nenum(pbc_opt);
963 bPBCWhole = pbc_enum == epWhole;
964 bPBCcomRes = pbc_enum == epComRes;
965 bPBCcomMol = pbc_enum == epComMol;
966 bPBCcomAtom = pbc_enum == epComAtom;
967 bNoJump = pbc_enum == epNojump;
968 bCluster = pbc_enum == epCluster;
969 bPBC = pbc_enum != epNone;
970 unitcell_enum = nenum(unitcell_opt);
971 ecenter = nenum(center_opt) - ecTric;
973 /* set and check option dependencies */
976 bFit = TRUE; /* for pfit, fit *must* be set */
980 bReset = TRUE; /* for fit, reset *must* be set */
985 nfitdim = (fit_enum == efFitXY || fit_enum == efResetXY) ? 2 : 3;
987 bRmPBC = bFit || bPBCWhole || bPBCcomRes || bPBCcomMol;
991 if (!(bPBCcomRes || bPBCcomMol || bPBCcomAtom))
994 "WARNING: Option for unitcell representation (-ur %s)\n"
995 " only has effect in combination with -pbc %s, %s or %s.\n"
996 " Ingoring unitcell representation.\n\n",
997 unitcell_opt[0], pbc_opt[2], pbc_opt[3], pbc_opt[4]);
1003 gmx_fatal(FARGS, "PBC condition treatment does not work together with rotational fit.\n"
1004 "Please do the PBC condition treatment first and then run trjconv in a second step\n"
1005 "for the rotational fit.\n"
1006 "First doing the rotational fit and then doing the PBC treatment gives incorrect\n"
1010 /* ndec is in nr of decimal places, prec is a multiplication factor: */
1012 for (i = 0; i < ndec; i++)
1017 bIndex = ftp2bSet(efNDX, NFILE, fnm);
1020 /* Determine output type */
1021 out_file = opt2fn("-o", NFILE, fnm);
1022 ftp = fn2ftp(out_file);
1023 fprintf(stderr, "Will write %s: %s\n", ftp2ext(ftp), ftp2desc(ftp));
1024 bNeedPrec = (ftp == efXTC || ftp == efGRO);
1027 /* check if velocities are possible in input and output files */
1028 ftpin = fn2ftp(in_file);
1029 bVels = (ftp == efTRR || ftp == efGRO ||
1030 ftp == efG96 || ftp == efTNG)
1031 && (ftpin == efTRR || ftpin == efGRO ||
1032 ftpin == efG96 || ftpin == efTNG || ftpin == efCPT);
1034 if (bSeparate || bSplit)
1036 outf_ext = strrchr(out_file, '.');
1037 if (outf_ext == NULL)
1039 gmx_fatal(FARGS, "Output file name '%s' does not contain a '.'", out_file);
1041 outf_base = gmx_strdup(out_file);
1042 outf_base[outf_ext - out_file] = '\0';
1045 bSubTraj = opt2bSet("-sub", NFILE, fnm);
1048 if ((ftp != efXTC) && (ftp != efTRR))
1050 /* It seems likely that other trajectory file types
1051 * could work here. */
1052 gmx_fatal(FARGS, "Can only use the sub option with output file types "
1055 clust = cluster_index(NULL, opt2fn("-sub", NFILE, fnm));
1057 /* Check for number of files disabled, as FOPEN_MAX is not the correct
1058 * number to check for. In my linux box it is only 16.
1060 if (0 && (clust->clust->nr > FOPEN_MAX-4))
1062 gmx_fatal(FARGS, "Can not open enough (%d) files to write all the"
1063 " trajectories.\ntry splitting the index file in %d parts.\n"
1065 clust->clust->nr, 1+clust->clust->nr/FOPEN_MAX, FOPEN_MAX);
1067 gmx_warning("The -sub option could require as many open output files as there are\n"
1068 "index groups in the file (%d). If you get I/O errors opening new files,\n"
1069 "try reducing the number of index groups in the file, and perhaps\n"
1070 "using trjconv -sub several times on different chunks of your index file.\n",
1073 snew(clust_status, clust->clust->nr);
1074 snew(clust_status_id, clust->clust->nr);
1075 snew(nfwritten, clust->clust->nr);
1076 for (i = 0; (i < clust->clust->nr); i++)
1078 clust_status[i] = NULL;
1079 clust_status_id[i] = -1;
1081 bSeparate = bSplit = FALSE;
1088 mtop = read_mtop_for_tng(top_file, in_file, out_file);
1090 /* Determine whether to read a topology */
1091 bTPS = (ftp2bSet(efTPS, NFILE, fnm) ||
1092 bRmPBC || bReset || bPBCcomMol || bCluster ||
1093 (ftp == efGRO) || (ftp == efPDB) || bCONECT);
1095 /* Determine if when can read index groups */
1096 bIndex = (bIndex || bTPS);
1100 read_tps_conf(top_file, top_title, &top, &ePBC, &xp, NULL, top_box,
1101 bReset || bPBCcomRes);
1104 if (0 == top.mols.nr && (bCluster || bPBCcomMol))
1106 gmx_fatal(FARGS, "Option -pbc %s requires a .tpr file for the -s option", pbc_opt[pbc_enum]);
1109 /* top_title is only used for gro and pdb,
1110 * the header in such a file is top_title t= ...
1111 * to prevent a double t=, remove it from top_title
1113 if ((charpt = strstr(top_title, " t= ")))
1120 gc = gmx_conect_generate(&top);
1124 gpbc = gmx_rmpbc_init(&top.idef, ePBC, top.atoms.nr);
1128 /* get frame number index */
1130 if (opt2bSet("-fr", NFILE, fnm))
1132 printf("Select groups of frame number indices:\n");
1133 rd_index(opt2fn("-fr", NFILE, fnm), 1, &nrfri, (atom_id **)&frindex, &frname);
1136 for (i = 0; i < nrfri; i++)
1138 fprintf(debug, "frindex[%4d]=%4d\n", i, frindex[i]);
1143 /* get index groups etc. */
1146 printf("Select group for %s fit\n",
1147 bFit ? "least squares" : "translational");
1148 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
1149 1, &ifit, &ind_fit, &gn_fit);
1155 gmx_fatal(FARGS, "Need at least 2 atoms to fit!\n");
1159 fprintf(stderr, "WARNING: fitting with only 2 atoms is not unique\n");
1165 printf("Select group for clustering\n");
1166 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
1167 1, &ifit, &ind_fit, &gn_fit);
1174 printf("Select group for centering\n");
1175 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
1176 1, &ncent, &cindex, &grpnm);
1178 printf("Select group for output\n");
1179 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
1180 1, &nout, &index, &grpnm);
1184 /* no index file, so read natoms from TRX */
1185 if (!read_first_frame(oenv, &trxin, in_file, &fr, TRX_DONT_SKIP))
1187 gmx_fatal(FARGS, "Could not read a frame from %s", in_file);
1192 snew(index, natoms);
1193 for (i = 0; i < natoms; i++)
1207 snew(w_rls, atoms->nr);
1208 for (i = 0; (i < ifit); i++)
1210 w_rls[ind_fit[i]] = atoms->atom[ind_fit[i]].m;
1213 /* Restore reference structure and set to origin,
1214 store original location (to put structure back) */
1217 gmx_rmpbc(gpbc, top.atoms.nr, top_box, xp);
1219 copy_rvec(xp[index[0]], x_shift);
1220 reset_x_ndim(nfitdim, ifit, ind_fit, atoms->nr, NULL, xp, w_rls);
1221 rvec_dec(x_shift, xp[index[0]]);
1225 clear_rvec(x_shift);
1228 if (bDropUnder || bDropOver)
1230 /* Read the .xvg file with the drop values */
1231 fprintf(stderr, "\nReading drop file ...");
1232 ndrop = read_xvg(opt2fn("-drop", NFILE, fnm), &dropval, &ncol);
1233 fprintf(stderr, " %d time points\n", ndrop);
1234 if (ndrop == 0 || ncol < 2)
1236 gmx_fatal(FARGS, "Found no data points in %s",
1237 opt2fn("-drop", NFILE, fnm));
1243 /* Make atoms struct for output in GRO or PDB files */
1244 if ((ftp == efGRO) || ((ftp == efG96) && bTPS) || (ftp == efPDB))
1246 /* get memory for stuff to go in .pdb file, and initialize
1247 * the pdbinfo structure part if the input has it.
1249 init_t_atoms(&useatoms, atoms->nr, (atoms->pdbinfo != NULL));
1250 sfree(useatoms.resinfo);
1251 useatoms.resinfo = atoms->resinfo;
1252 for (i = 0; (i < nout); i++)
1254 useatoms.atomname[i] = atoms->atomname[index[i]];
1255 useatoms.atom[i] = atoms->atom[index[i]];
1256 if (atoms->pdbinfo != NULL)
1258 useatoms.pdbinfo[i] = atoms->pdbinfo[index[i]];
1260 useatoms.nres = max(useatoms.nres, useatoms.atom[i].resind+1);
1264 /* select what to read */
1275 flags = flags | TRX_READ_V;
1279 flags = flags | TRX_READ_F;
1282 /* open trx file for reading */
1283 bHaveFirstFrame = read_first_frame(oenv, &trxin, in_file, &fr, flags);
1286 fprintf(stderr, "\nPrecision of %s is %g (nm)\n", in_file, 1/fr.prec);
1290 if (bSetPrec || !fr.bPrec)
1292 fprintf(stderr, "\nSetting output precision to %g (nm)\n", 1/prec);
1296 fprintf(stderr, "Using output precision of %g (nm)\n", 1/prec);
1300 if (bHaveFirstFrame)
1302 set_trxframe_ePBC(&fr, ePBC);
1308 tshift = tzero-fr.time;
1318 /* check if index is meaningful */
1319 for (i = 0; i < nout; i++)
1321 if (index[i] >= natoms)
1324 "Index[%d] %d is larger than the number of atoms in the\n"
1325 "trajectory file (%d). There is a mismatch in the contents\n"
1326 "of your -f, -s and/or -n files.", i, index[i]+1, natoms);
1328 bCopy = bCopy || (i != index[i]);
1332 /* open output for writing */
1333 strcpy(filemode, "w");
1337 trjtools_gmx_prepare_tng_writing(out_file,
1350 if (!bSplit && !bSubTraj)
1352 trxout = open_trx(out_file, filemode);
1358 if (( !bSeparate && !bSplit ) && !bSubTraj)
1360 out = gmx_ffopen(out_file, filemode);
1364 gmx_incons("Illegal output file format");
1380 /* Start the big loop over frames */
1387 /* Main loop over frames */
1398 /*if (frame >= clust->clust->nra)
1399 gmx_fatal(FARGS,"There are more frames in the trajectory than in the cluster index file\n");*/
1400 if (frame > clust->maxframe)
1406 my_clust = clust->inv_clust[frame];
1408 if ((my_clust < 0) || (my_clust >= clust->clust->nr) ||
1409 (my_clust == NO_ATID))
1417 /* generate new box */
1418 if (fr.bBox == FALSE)
1422 for (m = 0; m < DIM; m++)
1426 fr.box[m][m] = newbox[m];
1430 if (fr.bBox == FALSE)
1432 gmx_fatal(FARGS, "Cannot preserve a box that does not exist.\n");
1440 for (i = 0; i < natoms; i++)
1442 rvec_inc(fr.x[i], trans);
1448 /* determine timestep */
1461 /* This is not very elegant, as one can not dump a frame after
1462 * a timestep with is more than twice as small as the first one. */
1463 bDumpFrame = (fr.time > tdump-0.5*dt) && (fr.time <= tdump+0.5*dt);
1470 /* determine if an atom jumped across the box and reset it if so */
1471 if (bNoJump && (bTPS || frame != 0))
1473 for (d = 0; d < DIM; d++)
1475 hbox[d] = 0.5*fr.box[d][d];
1477 for (i = 0; i < natoms; i++)
1481 rvec_dec(fr.x[i], x_shift);
1483 for (m = DIM-1; m >= 0; m--)
1487 while (fr.x[i][m]-xp[i][m] <= -hbox[m])
1489 for (d = 0; d <= m; d++)
1491 fr.x[i][d] += fr.box[m][d];
1494 while (fr.x[i][m]-xp[i][m] > hbox[m])
1496 for (d = 0; d <= m; d++)
1498 fr.x[i][d] -= fr.box[m][d];
1507 calc_pbc_cluster(ecenter, ifit, &top, ePBC, fr.x, ind_fit, fr.box);
1512 /* Now modify the coords according to the flags,
1513 for normal fit, this is only done for output frames */
1516 gmx_rmpbc_trxfr(gpbc, &fr);
1519 reset_x_ndim(nfitdim, ifit, ind_fit, natoms, NULL, fr.x, w_rls);
1520 do_fit(natoms, w_rls, xp, fr.x);
1523 /* store this set of coordinates for future use */
1524 if (bPFit || bNoJump)
1530 for (i = 0; (i < natoms); i++)
1532 copy_rvec(fr.x[i], xp[i]);
1533 rvec_inc(fr.x[i], x_shift);
1539 /* see if we have a frame from the frame index group */
1540 for (i = 0; i < nrfri && !bDumpFrame; i++)
1542 bDumpFrame = frame == frindex[i];
1545 if (debug && bDumpFrame)
1547 fprintf(debug, "dumping %d\n", frame);
1551 ( ( !bTDump && !frindex && frame % skip_nr == 0 ) || bDumpFrame );
1553 if (bWriteFrame && (bDropUnder || bDropOver))
1555 while (dropval[0][drop1] < fr.time && drop1+1 < ndrop)
1560 if (fabs(dropval[0][drop0] - fr.time)
1561 < fabs(dropval[0][drop1] - fr.time))
1569 if ((bDropUnder && dropval[1][dropuse] < dropunder) ||
1570 (bDropOver && dropval[1][dropuse] > dropover))
1572 bWriteFrame = FALSE;
1578 /* We should avoid modifying the input frame,
1579 * but since here we don't have the output frame yet,
1580 * we introduce a temporary output frame time variable.
1584 frout_time = fr.time;
1589 frout_time = tzero + frame*timestep;
1594 frout_time += tshift;
1599 fprintf(stderr, "\nDumping frame at t= %g %s\n",
1600 output_env_conv_time(oenv, frout_time), output_env_get_time_unit(oenv));
1603 /* check for writing at each delta_t */
1604 bDoIt = (delta_t == 0);
1609 bDoIt = bRmod(frout_time, tzero, delta_t);
1613 /* round() is not C89 compatible, so we do this: */
1614 bDoIt = bRmod(floor(frout_time+0.5), floor(tzero+0.5),
1615 floor(delta_t+0.5));
1619 if (bDoIt || bTDump)
1621 /* print sometimes */
1622 if ( ((outframe % SKIP) == 0) || (outframe < SKIP) )
1624 fprintf(stderr, " -> frame %6d time %8.3f \r",
1625 outframe, output_env_conv_time(oenv, frout_time));
1630 /* Now modify the coords according to the flags,
1631 for PFit we did this already! */
1635 gmx_rmpbc_trxfr(gpbc, &fr);
1640 reset_x_ndim(nfitdim, ifit, ind_fit, natoms, NULL, fr.x, w_rls);
1643 do_fit_ndim(nfitdim, natoms, w_rls, xp, fr.x);
1647 for (i = 0; i < natoms; i++)
1649 rvec_inc(fr.x[i], x_shift);
1656 center_x(ecenter, fr.x, fr.box, natoms, ncent, cindex);
1662 switch (unitcell_enum)
1665 put_atoms_in_box(ePBC, fr.box, natoms, fr.x);
1668 put_atoms_in_triclinic_unitcell(ecenter, fr.box, natoms, fr.x);
1671 warn = put_atoms_in_compact_unitcell(ePBC, ecenter, fr.box,
1673 if (warn && !bWarnCompact)
1675 fprintf(stderr, "\n%s\n", warn);
1676 bWarnCompact = TRUE;
1683 put_residue_com_in_box(unitcell_enum, ecenter,
1684 natoms, atoms->atom, ePBC, fr.box, fr.x);
1688 put_molecule_com_in_box(unitcell_enum, ecenter,
1690 natoms, atoms->atom, ePBC, fr.box, fr.x);
1692 /* Copy the input trxframe struct to the output trxframe struct */
1694 frout.time = frout_time;
1695 frout.bV = (frout.bV && bVels);
1696 frout.bF = (frout.bF && bForce);
1697 frout.natoms = nout;
1698 if (bNeedPrec && (bSetPrec || !fr.bPrec))
1714 for (i = 0; i < nout; i++)
1716 copy_rvec(fr.x[index[i]], frout.x[i]);
1719 copy_rvec(fr.v[index[i]], frout.v[i]);
1723 copy_rvec(fr.f[index[i]], frout.f[i]);
1728 if (opt2parg_bSet("-shift", NPA, pa))
1730 for (i = 0; i < nout; i++)
1732 for (d = 0; d < DIM; d++)
1734 frout.x[i][d] += outframe*shift[d];
1741 bSplitHere = bSplit && bRmod(frout.time, tzero, split_t);
1745 /* round() is not C89 compatible, so we do this: */
1746 bSplitHere = bSplit && bRmod(floor(frout.time+0.5),
1748 floor(split_t+0.5));
1750 if (bSeparate || bSplitHere)
1752 mk_filenm(outf_base, ftp2ext(ftp), nzero, file_nr, out_file2);
1758 write_tng_frame(trxout, &frout);
1759 // TODO when trjconv behaves better: work how to read and write lambda
1769 trxout = open_trx(out_file2, filemode);
1776 if (clust_status_id[my_clust] == -1)
1778 sprintf(buf, "%s.%s", clust->grpname[my_clust], ftp2ext(ftp));
1779 clust_status[my_clust] = open_trx(buf, "w");
1780 clust_status_id[my_clust] = 1;
1783 else if (clust_status_id[my_clust] == -2)
1785 gmx_fatal(FARGS, "File %s.xtc should still be open (%d open .xtc files)\n" "in order to write frame %d. my_clust = %d",
1786 clust->grpname[my_clust], ntrxopen, frame,
1789 write_trxframe(clust_status[my_clust], &frout, gc);
1790 nfwritten[my_clust]++;
1791 if (nfwritten[my_clust] ==
1792 (clust->clust->index[my_clust+1]-
1793 clust->clust->index[my_clust]))
1795 close_trx(clust_status[my_clust]);
1796 clust_status[my_clust] = NULL;
1797 clust_status_id[my_clust] = -2;
1801 gmx_fatal(FARGS, "Less than zero open .xtc files!");
1808 write_trxframe(trxout, &frout, gc);
1814 sprintf(title, "Generated by trjconv : %s t= %9.5f",
1815 top_title, frout.time);
1816 if (bSeparate || bSplitHere)
1818 out = gmx_ffopen(out_file2, "w");
1823 write_hconf_p(out, title, &useatoms, prec2ndec(frout.prec),
1824 frout.x, frout.bV ? frout.v : NULL, frout.box);
1827 fprintf(out, "REMARK GENERATED BY TRJCONV\n");
1828 sprintf(title, "%s t= %9.5f", top_title, frout.time);
1829 /* if reading from pdb, we want to keep the original
1830 model numbering else we write the output frame
1831 number plus one, because model 0 is not allowed in pdb */
1832 if (ftpin == efPDB && fr.bStep && fr.step > model_nr)
1840 write_pdbfile(out, title, &useatoms, frout.x,
1841 frout.ePBC, frout.box, ' ', model_nr, gc, TRUE);
1844 frout.title = title;
1845 if (bSeparate || bTDump)
1847 frout.bTitle = TRUE;
1850 frout.bAtoms = TRUE;
1852 frout.atoms = &useatoms;
1853 frout.bStep = FALSE;
1854 frout.bTime = FALSE;
1858 frout.bTitle = (outframe == 0);
1859 frout.bAtoms = FALSE;
1863 write_g96_conf(out, &frout, -1, NULL);
1865 if (bSeparate || bSplitHere)
1872 gmx_fatal(FARGS, "DHE, ftp=%d\n", ftp);
1874 if (bSeparate || bSplitHere)
1879 /* execute command */
1883 sprintf(c, "%s %d", exec_command, file_nr-1);
1884 /*fprintf(stderr,"Executing '%s'\n",c);*/
1887 gmx_fatal(FARGS, "Error executing command: %s", c);
1894 bHaveNextFrame = read_next_frame(oenv, trxin, &fr);
1896 while (!(bTDump && bDumpFrame) && bHaveNextFrame);
1899 if (!bHaveFirstFrame || (bTDump && !bDumpFrame))
1901 fprintf(stderr, "\nWARNING no output, "
1902 "last frame read at t=%g\n", fr.time);
1904 fprintf(stderr, "\n");
1911 gmx_rmpbc_done(gpbc);
1918 else if (out != NULL)
1924 for (i = 0; (i < clust->clust->nr); i++)
1926 if (clust_status_id[i] >= 0)
1928 close_trx(clust_status[i]);
1936 do_view(oenv, out_file, NULL);