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48 #include "gromacs/fileio/gmxfio.h"
49 #include "gromacs/fileio/tpxio.h"
50 #include "gromacs/fileio/trxio.h"
51 #include "gromacs/fileio/trnio.h"
52 #include "gromacs/fileio/tngio_for_tools.h"
53 #include "gromacs/utility/futil.h"
54 #include "gromacs/fileio/pdbio.h"
55 #include "gromacs/fileio/confio.h"
57 #include "gromacs/topology/index.h"
58 #include "gromacs/math/vec.h"
59 #include "gromacs/fileio/xtcio.h"
63 #include "gromacs/commandline/pargs.h"
64 #include "gromacs/fileio/xvgr.h"
65 #include "gromacs/math/do_fit.h"
66 #include "gromacs/pbcutil/pbc.h"
67 #include "gromacs/pbcutil/rmpbc.h"
68 #include "gromacs/topology/topology.h"
69 #include "gromacs/utility/fatalerror.h"
70 #include "gromacs/utility/smalloc.h"
77 euSel, euRect, euTric, euCompact, euNR
81 static void calc_pbc_cluster(int ecenter, int nrefat, t_topology *top, int ePBC,
82 rvec x[], atom_id index[], matrix box)
84 int m, i, j, j0, j1, jj, ai, aj;
87 rvec dx, xtest, box_center;
88 int nmol, imol_center;
90 gmx_bool *bMol, *bTmp;
91 rvec *m_com, *m_shift;
99 calc_box_center(ecenter, box, box_center);
101 /* Initiate the pbc structure */
102 memset(&pbc, 0, sizeof(pbc));
103 set_pbc(&pbc, ePBC, box);
105 /* Convert atom index to molecular */
107 molind = top->mols.index;
113 snew(bTmp, top->atoms.nr);
115 for (i = 0; (i < nrefat); i++)
117 /* Mark all molecules in the index */
120 /* Binary search assuming the molecules are sorted */
125 if (ai < molind[j0+1])
129 else if (ai >= molind[j1])
136 if (ai < molind[jj+1])
148 /* Double check whether all atoms in all molecules that are marked are part
149 * of the cluster. Simultaneously compute the center of geometry.
151 min_dist2 = 10*sqr(trace(box));
154 for (i = 0; i < nmol; i++)
156 for (j = molind[i]; j < molind[i+1]; j++)
158 if (bMol[i] && !bTmp[j])
160 gmx_fatal(FARGS, "Molecule %d marked for clustering but not atom %d in it - check your index!", i+1, j+1);
162 else if (!bMol[i] && bTmp[j])
164 gmx_fatal(FARGS, "Atom %d marked for clustering but not molecule %d - this is an internal error...", j+1, i+1);
168 /* Make molecule whole, move 2nd and higher atom to same periodicity as 1st atom in molecule */
171 pbc_dx(&pbc, x[j], x[j-1], dx);
172 rvec_add(x[j-1], dx, x[j]);
174 /* Compute center of geometry of molecule - m_com[i] was zeroed when we did snew() on it! */
175 rvec_inc(m_com[i], x[j]);
180 /* Normalize center of geometry */
181 fac = 1.0/(molind[i+1]-molind[i]);
182 for (m = 0; (m < DIM); m++)
186 /* Determine which molecule is closest to the center of the box */
187 pbc_dx(&pbc, box_center, m_com[i], dx);
188 tmp_r2 = iprod(dx, dx);
190 if (tmp_r2 < min_dist2)
195 cluster[ncluster++] = i;
202 fprintf(stderr, "No molecules selected in the cluster\n");
205 else if (imol_center == -1)
207 fprintf(stderr, "No central molecules could be found\n");
212 added[nadded++] = imol_center;
213 bMol[imol_center] = FALSE;
215 while (nadded < ncluster)
217 /* Find min distance between cluster molecules and those remaining to be added */
218 min_dist2 = 10*sqr(trace(box));
221 /* Loop over added mols */
222 for (i = 0; i < nadded; i++)
225 /* Loop over all mols */
226 for (j = 0; j < ncluster; j++)
229 /* check those remaining to be added */
232 pbc_dx(&pbc, m_com[aj], m_com[ai], dx);
233 tmp_r2 = iprod(dx, dx);
234 if (tmp_r2 < min_dist2)
244 /* Add the best molecule */
245 added[nadded++] = jmin;
247 /* Calculate the shift from the ai molecule */
248 pbc_dx(&pbc, m_com[jmin], m_com[imin], dx);
249 rvec_add(m_com[imin], dx, xtest);
250 rvec_sub(xtest, m_com[jmin], m_shift[jmin]);
251 rvec_inc(m_com[jmin], m_shift[jmin]);
253 for (j = molind[jmin]; j < molind[jmin+1]; j++)
255 rvec_inc(x[j], m_shift[jmin]);
257 fprintf(stdout, "\rClustering iteration %d of %d...", nadded, ncluster);
267 fprintf(stdout, "\n");
270 static void put_molecule_com_in_box(int unitcell_enum, int ecenter,
272 int natoms, t_atom atom[],
273 int ePBC, matrix box, rvec x[])
277 rvec com, new_com, shift, dx, box_center;
282 calc_box_center(ecenter, box, box_center);
283 set_pbc(&pbc, ePBC, box);
286 gmx_fatal(FARGS, "There are no molecule descriptions. I need a .tpr file for this pbc option.");
288 for (i = 0; (i < mols->nr); i++)
293 for (j = mols->index[i]; (j < mols->index[i+1] && j < natoms); j++)
296 for (d = 0; d < DIM; d++)
302 /* calculate final COM */
303 svmul(1.0/mtot, com, com);
305 /* check if COM is outside box */
306 copy_rvec(com, new_com);
307 switch (unitcell_enum)
310 put_atoms_in_box(ePBC, box, 1, &new_com);
313 put_atoms_in_triclinic_unitcell(ecenter, box, 1, &new_com);
316 put_atoms_in_compact_unitcell(ePBC, ecenter, box, 1, &new_com);
319 rvec_sub(new_com, com, shift);
320 if (norm2(shift) > 0)
324 fprintf(debug, "\nShifting position of molecule %d "
325 "by %8.3f %8.3f %8.3f\n", i+1,
326 shift[XX], shift[YY], shift[ZZ]);
328 for (j = mols->index[i]; (j < mols->index[i+1] && j < natoms); j++)
330 rvec_inc(x[j], shift);
336 static void put_residue_com_in_box(int unitcell_enum, int ecenter,
337 int natoms, t_atom atom[],
338 int ePBC, matrix box, rvec x[])
340 atom_id i, j, res_start, res_end, res_nat;
344 rvec box_center, com, new_com, shift;
346 calc_box_center(ecenter, box, box_center);
352 for (i = 0; i < natoms+1; i++)
354 if (i == natoms || (presnr != atom[i].resind && presnr != NOTSET))
356 /* calculate final COM */
358 res_nat = res_end - res_start;
359 svmul(1.0/mtot, com, com);
361 /* check if COM is outside box */
362 copy_rvec(com, new_com);
363 switch (unitcell_enum)
366 put_atoms_in_box(ePBC, box, 1, &new_com);
369 put_atoms_in_triclinic_unitcell(ecenter, box, 1, &new_com);
372 put_atoms_in_compact_unitcell(ePBC, ecenter, box, 1, &new_com);
375 rvec_sub(new_com, com, shift);
380 fprintf(debug, "\nShifting position of residue %d (atoms %u-%u) "
381 "by %g,%g,%g\n", atom[res_start].resind+1,
382 res_start+1, res_end+1, shift[XX], shift[YY], shift[ZZ]);
384 for (j = res_start; j < res_end; j++)
386 rvec_inc(x[j], shift);
392 /* remember start of new residue */
399 for (d = 0; d < DIM; d++)
405 presnr = atom[i].resind;
410 static void center_x(int ecenter, rvec x[], matrix box, int n, int nc, atom_id ci[])
413 rvec cmin, cmax, box_center, dx;
417 copy_rvec(x[ci[0]], cmin);
418 copy_rvec(x[ci[0]], cmax);
419 for (i = 0; i < nc; i++)
422 for (m = 0; m < DIM; m++)
424 if (x[ai][m] < cmin[m])
428 else if (x[ai][m] > cmax[m])
434 calc_box_center(ecenter, box, box_center);
435 for (m = 0; m < DIM; m++)
437 dx[m] = box_center[m]-(cmin[m]+cmax[m])*0.5;
440 for (i = 0; i < n; i++)
447 static void mk_filenm(char *base, const char *ext, int ndigit, int file_nr,
453 strcpy(out_file, base);
464 strncat(out_file, "00000000000", ndigit-nd);
466 sprintf(nbuf, "%d.", file_nr);
467 strcat(out_file, nbuf);
468 strcat(out_file, ext);
471 void check_trn(const char *fn)
473 if ((fn2ftp(fn) != efTRJ) && (fn2ftp(fn) != efTRR))
475 gmx_fatal(FARGS, "%s is not a trajectory file, exiting\n", fn);
479 #ifndef GMX_NATIVE_WINDOWS
480 void do_trunc(const char *fn, real t0)
493 gmx_fatal(FARGS, "You forgot to set the truncation time");
496 /* Check whether this is a .trj file */
499 in = open_trn(fn, "r");
500 fp = gmx_fio_getfp(in);
503 fprintf(stderr, "Sorry, can not trunc %s, truncation of this filetype is not supported\n", fn);
509 fpos = gmx_fio_ftell(in);
511 while (!bStop && fread_trnheader(in, &sh, &bOK))
513 fread_htrn(in, &sh, NULL, NULL, NULL, NULL);
514 fpos = gmx_ftell(fp);
518 gmx_fseek(fp, fpos, SEEK_SET);
524 fprintf(stderr, "Do you REALLY want to truncate this trajectory (%s) at:\n"
525 "frame %d, time %g, bytes %ld ??? (type YES if so)\n",
526 fn, j, t, (long int)fpos);
527 if (1 != scanf("%s", yesno))
529 gmx_fatal(FARGS, "Error reading user input");
531 if (strcmp(yesno, "YES") == 0)
533 fprintf(stderr, "Once again, I'm gonna DO this...\n");
535 if (0 != truncate(fn, fpos))
537 gmx_fatal(FARGS, "Error truncating file %s", fn);
542 fprintf(stderr, "Ok, I'll forget about it\n");
547 fprintf(stderr, "Already at end of file (t=%g)...\n", t);
554 /*! \brief Read a full molecular topology if useful and available.
556 * If the input trajectory file is not in TNG format, and the output
557 * file is in TNG format, then we want to try to read a full topology
558 * (if available), so that we can write molecule information to the
559 * output file. The full topology provides better molecule information
560 * than is available from the normal t_topology data used by GROMACS
563 * Also, the t_topology is only read under (different) particular
564 * conditions. If both apply, then a .tpr file might be read
565 * twice. Trying to fix this redundancy while trjconv is still an
566 * all-purpose tool does not seem worthwhile.
568 * Because of the way gmx_prepare_tng_writing is implemented, the case
569 * where the input TNG file has no molecule information will never
570 * lead to an output TNG file having molecule information. Since
571 * molecule information will generally be present if the input TNG
572 * file was written by a GROMACS tool, this seems like reasonable
574 static gmx_mtop_t *read_mtop_for_tng(const char *tps_file,
575 const char *input_file,
576 const char *output_file)
578 gmx_mtop_t *mtop = NULL;
580 if (fn2bTPX(tps_file) &&
581 efTNG != fn2ftp(input_file) &&
582 efTNG == fn2ftp(output_file))
584 int temp_natoms = -1;
586 read_tpx(tps_file, NULL, NULL, &temp_natoms,
587 NULL, NULL, NULL, mtop);
593 int gmx_trjconv(int argc, char *argv[])
595 const char *desc[] = {
596 "[THISMODULE] can convert trajectory files in many ways:[BR]",
597 "* from one format to another[BR]",
598 "* select a subset of atoms[BR]",
599 "* change the periodicity representation[BR]",
600 "* keep multimeric molecules together[BR]",
601 "* center atoms in the box[BR]",
602 "* fit atoms to reference structure[BR]",
603 "* reduce the number of frames[BR]",
604 "* change the timestamps of the frames ",
605 "([TT]-t0[tt] and [TT]-timestep[tt])[BR]",
606 "* cut the trajectory in small subtrajectories according",
607 "to information in an index file. This allows subsequent analysis of",
608 "the subtrajectories that could, for example, be the result of a",
609 "cluster analysis. Use option [TT]-sub[tt].",
610 "This assumes that the entries in the index file are frame numbers and",
611 "dumps each group in the index file to a separate trajectory file.[BR]",
612 "* select frames within a certain range of a quantity given",
613 "in an [TT].xvg[tt] file.[PAR]",
615 "[gmx-trjcat] is better suited for concatenating multiple trajectory files.",
618 "The following formats are supported for input and output:",
619 "[TT].xtc[tt], [TT].trr[tt], [TT].trj[tt], [TT].gro[tt], [TT].g96[tt]",
621 "The file formats are detected from the file extension.",
622 "The precision of [TT].xtc[tt] and [TT].gro[tt] output is taken from the",
623 "input file for [TT].xtc[tt], [TT].gro[tt] and [TT].pdb[tt],",
624 "and from the [TT]-ndec[tt] option for other input formats. The precision",
625 "is always taken from [TT]-ndec[tt], when this option is set.",
626 "All other formats have fixed precision. [TT].trr[tt] and [TT].trj[tt]",
627 "output can be single or double precision, depending on the precision",
628 "of the [THISMODULE] binary.",
629 "Note that velocities are only supported in",
630 "[TT].trr[tt], [TT].trj[tt], [TT].gro[tt] and [TT].g96[tt] files.[PAR]",
632 "Option [TT]-sep[tt] can be used to write every frame to a separate",
633 "[TT].gro, .g96[tt] or [TT].pdb[tt] file. By default, all frames all written to one file.",
634 "[TT].pdb[tt] files with all frames concatenated can be viewed with",
635 "[TT]rasmol -nmrpdb[tt].[PAR]",
637 "It is possible to select part of your trajectory and write it out",
638 "to a new trajectory file in order to save disk space, e.g. for leaving",
639 "out the water from a trajectory of a protein in water.",
640 "[BB]ALWAYS[bb] put the original trajectory on tape!",
641 "We recommend to use the portable [TT].xtc[tt] format for your analysis",
642 "to save disk space and to have portable files.[PAR]",
644 "There are two options for fitting the trajectory to a reference",
645 "either for essential dynamics analysis, etc.",
646 "The first option is just plain fitting to a reference structure",
647 "in the structure file. The second option is a progressive fit",
648 "in which the first timeframe is fitted to the reference structure ",
649 "in the structure file to obtain and each subsequent timeframe is ",
650 "fitted to the previously fitted structure. This way a continuous",
651 "trajectory is generated, which might not be the case when using the",
652 "regular fit method, e.g. when your protein undergoes large",
653 "conformational transitions.[PAR]",
655 "Option [TT]-pbc[tt] sets the type of periodic boundary condition",
657 "[TT]* mol[tt] puts the center of mass of molecules in the box,",
658 "and requires a run input file to be supplied with [TT]-s[tt].[BR]",
659 "[TT]* res[tt] puts the center of mass of residues in the box.[BR]",
660 "[TT]* atom[tt] puts all the atoms in the box.[BR]",
661 "[TT]* nojump[tt] checks if atoms jump across the box and then puts",
662 "them back. This has the effect that all molecules",
663 "will remain whole (provided they were whole in the initial",
664 "conformation). [BB]Note[bb] that this ensures a continuous trajectory but",
665 "molecules may diffuse out of the box. The starting configuration",
666 "for this procedure is taken from the structure file, if one is",
667 "supplied, otherwise it is the first frame.[BR]",
668 "[TT]* cluster[tt] clusters all the atoms in the selected index",
669 "such that they are all closest to the center of mass of the cluster,",
670 "which is iteratively updated. [BB]Note[bb] that this will only give meaningful",
671 "results if you in fact have a cluster. Luckily that can be checked",
672 "afterwards using a trajectory viewer. Note also that if your molecules",
673 "are broken this will not work either.[BR]",
674 "The separate option [TT]-clustercenter[tt] can be used to specify an",
675 "approximate center for the cluster. This is useful e.g. if you have",
676 "two big vesicles, and you want to maintain their relative positions.[BR]",
677 "[TT]* whole[tt] only makes broken molecules whole.[PAR]",
679 "Option [TT]-ur[tt] sets the unit cell representation for options",
680 "[TT]mol[tt], [TT]res[tt] and [TT]atom[tt] of [TT]-pbc[tt].",
681 "All three options give different results for triclinic boxes and",
682 "identical results for rectangular boxes.",
683 "[TT]rect[tt] is the ordinary brick shape.",
684 "[TT]tric[tt] is the triclinic unit cell.",
685 "[TT]compact[tt] puts all atoms at the closest distance from the center",
686 "of the box. This can be useful for visualizing e.g. truncated octahedra",
687 "or rhombic dodecahedra. The center for options [TT]tric[tt] and [TT]compact[tt]",
688 "is [TT]tric[tt] (see below), unless the option [TT]-boxcenter[tt]",
689 "is set differently.[PAR]",
691 "Option [TT]-center[tt] centers the system in the box. The user can",
692 "select the group which is used to determine the geometrical center.",
693 "Option [TT]-boxcenter[tt] sets the location of the center of the box",
694 "for options [TT]-pbc[tt] and [TT]-center[tt]. The center options are:",
695 "[TT]tric[tt]: half of the sum of the box vectors,",
696 "[TT]rect[tt]: half of the box diagonal,",
697 "[TT]zero[tt]: zero.",
698 "Use option [TT]-pbc mol[tt] in addition to [TT]-center[tt] when you",
699 "want all molecules in the box after the centering.[PAR]",
701 "Option [TT]-box[tt] sets the size of the new box. If you want to"
702 "modify only some of the dimensions, e.g. when reading from a trajectory,"
703 "you can use -1 for those dimensions that should stay the same"
705 "It is not always possible to use combinations of [TT]-pbc[tt],",
706 "[TT]-fit[tt], [TT]-ur[tt] and [TT]-center[tt] to do exactly what",
707 "you want in one call to [THISMODULE]. Consider using multiple",
708 "calls, and check out the GROMACS website for suggestions.[PAR]",
710 "With [TT]-dt[tt], it is possible to reduce the number of ",
711 "frames in the output. This option relies on the accuracy of the times",
712 "in your input trajectory, so if these are inaccurate use the",
713 "[TT]-timestep[tt] option to modify the time (this can be done",
714 "simultaneously). For making smooth movies, the program [gmx-filter]",
715 "can reduce the number of frames while using low-pass frequency",
716 "filtering, this reduces aliasing of high frequency motions.[PAR]",
718 "Using [TT]-trunc[tt] [THISMODULE] can truncate [TT].trj[tt] in place, i.e.",
719 "without copying the file. This is useful when a run has crashed",
720 "during disk I/O (i.e. full disk), or when two contiguous",
721 "trajectories must be concatenated without having double frames.[PAR]",
723 "Option [TT]-dump[tt] can be used to extract a frame at or near",
724 "one specific time from your trajectory.[PAR]",
726 "Option [TT]-drop[tt] reads an [TT].xvg[tt] file with times and values.",
727 "When options [TT]-dropunder[tt] and/or [TT]-dropover[tt] are set,",
728 "frames with a value below and above the value of the respective options",
729 "will not be written."
745 const char *pbc_opt[epNR + 1] =
747 NULL, "none", "mol", "res", "atom", "nojump", "cluster", "whole",
752 const char *unitcell_opt[euNR+1] =
753 { NULL, "rect", "tric", "compact", NULL };
757 ecSel, ecTric, ecRect, ecZero, ecNR
759 const char *center_opt[ecNR+1] =
760 { NULL, "tric", "rect", "zero", NULL };
766 efSel, efNone, efFit, efFitXY, efReset, efResetXY, efPFit, efNR
768 const char *fit[efNR + 1] =
770 NULL, "none", "rot+trans", "rotxy+transxy", "translation", "transxy",
774 static gmx_bool bSeparate = FALSE, bVels = TRUE, bForce = FALSE, bCONECT = FALSE;
775 static gmx_bool bCenter = FALSE;
776 static int skip_nr = 1, ndec = 3, nzero = 0;
777 static real tzero = 0, delta_t = 0, timestep = 0, ttrunc = -1, tdump = -1, split_t = 0;
778 static rvec newbox = {0, 0, 0}, shift = {0, 0, 0}, trans = {0, 0, 0};
779 static char *exec_command = NULL;
780 static real dropunder = 0, dropover = 0;
781 static gmx_bool bRound = FALSE;
786 { "-skip", FALSE, etINT,
787 { &skip_nr }, "Only write every nr-th frame" },
788 { "-dt", FALSE, etTIME,
790 "Only write frame when t MOD dt = first time (%t)" },
791 { "-round", FALSE, etBOOL,
792 { &bRound }, "Round measurements to nearest picosecond"},
793 { "-dump", FALSE, etTIME,
794 { &tdump }, "Dump frame nearest specified time (%t)" },
795 { "-t0", FALSE, etTIME,
797 "Starting time (%t) (default: don't change)" },
798 { "-timestep", FALSE, etTIME,
800 "Change time step between input frames (%t)" },
801 { "-pbc", FALSE, etENUM,
803 "PBC treatment (see help text for full description)" },
804 { "-ur", FALSE, etENUM,
805 { unitcell_opt }, "Unit-cell representation" },
806 { "-center", FALSE, etBOOL,
807 { &bCenter }, "Center atoms in box" },
808 { "-boxcenter", FALSE, etENUM,
809 { center_opt }, "Center for -pbc and -center" },
810 { "-box", FALSE, etRVEC,
812 "Size for new cubic box (default: read from input)" },
813 { "-trans", FALSE, etRVEC,
815 "All coordinates will be translated by trans. This "
816 "can advantageously be combined with -pbc mol -ur "
818 { "-shift", FALSE, etRVEC,
820 "All coordinates will be shifted by framenr*shift" },
821 { "-fit", FALSE, etENUM,
823 "Fit molecule to ref structure in the structure file" },
824 { "-ndec", FALSE, etINT,
826 "Precision for .xtc and .gro writing in number of "
828 { "-vel", FALSE, etBOOL,
829 { &bVels }, "Read and write velocities if possible" },
830 { "-force", FALSE, etBOOL,
831 { &bForce }, "Read and write forces if possible" },
832 #ifndef GMX_NATIVE_WINDOWS
833 { "-trunc", FALSE, etTIME,
835 "Truncate input trajectory file after this time (%t)" },
837 { "-exec", FALSE, etSTR,
839 "Execute command for every output frame with the "
840 "frame number as argument" },
841 { "-split", FALSE, etTIME,
843 "Start writing new file when t MOD split = first "
845 { "-sep", FALSE, etBOOL,
847 "Write each frame to a separate .gro, .g96 or .pdb "
849 { "-nzero", FALSE, etINT,
851 "If the -sep flag is set, use these many digits "
852 "for the file numbers and prepend zeros as needed" },
853 { "-dropunder", FALSE, etREAL,
854 { &dropunder }, "Drop all frames below this value" },
855 { "-dropover", FALSE, etREAL,
856 { &dropover }, "Drop all frames above this value" },
857 { "-conect", FALSE, etBOOL,
859 "Add conect records when writing [TT].pdb[tt] files. Useful "
860 "for visualization of non-standard molecules, e.g. "
861 "coarse grained ones" }
863 #define NPA asize(pa)
866 t_trxstatus *trxout = NULL;
868 int ftp, ftpin = 0, file_nr;
869 t_trxframe fr, frout;
871 rvec *xmem = NULL, *vmem = NULL, *fmem = NULL;
872 rvec *xp = NULL, x_shift, hbox, box_center, dx;
873 real xtcpr, lambda, *w_rls = NULL;
874 int m, i, d, frame, outframe, natoms, nout, ncent, nre, newstep = 0, model_nr;
877 gmx_mtop_t *mtop = NULL;
878 gmx_conect gc = NULL;
880 t_atoms *atoms = NULL, useatoms;
882 atom_id *index, *cindex;
886 int ifit, irms, my_clust = -1;
887 atom_id *ind_fit, *ind_rms;
888 char *gn_fit, *gn_rms;
889 t_cluster_ndx *clust = NULL;
890 t_trxstatus **clust_status = NULL;
891 int *clust_status_id = NULL;
893 int *nfwritten = NULL;
894 int ndrop = 0, ncol, drop0 = 0, drop1 = 0, dropuse = 0;
896 real tshift = 0, t0 = -1, dt = 0.001, prec;
897 gmx_bool bFit, bFitXY, bPFit, bReset;
899 gmx_rmpbc_t gpbc = NULL;
900 gmx_bool bRmPBC, bPBCWhole, bPBCcomRes, bPBCcomMol, bPBCcomAtom, bPBC, bNoJump, bCluster;
901 gmx_bool bCopy, bDoIt, bIndex, bTDump, bSetTime, bTPS = FALSE, bDTset = FALSE;
902 gmx_bool bExec, bTimeStep = FALSE, bDumpFrame = FALSE, bSetPrec, bNeedPrec;
903 gmx_bool bHaveFirstFrame, bHaveNextFrame, bSetBox, bSetUR, bSplit = FALSE;
904 gmx_bool bSubTraj = FALSE, bDropUnder = FALSE, bDropOver = FALSE, bTrans = FALSE;
905 gmx_bool bWriteFrame, bSplitHere;
906 const char *top_file, *in_file, *out_file = NULL;
907 char out_file2[256], *charpt;
908 char *outf_base = NULL;
909 const char *outf_ext = NULL;
910 char top_title[256], title[256], command[256], filemode[5];
912 gmx_bool bWarnCompact = FALSE;
917 { efTRX, "-f", NULL, ffREAD },
918 { efTRO, "-o", NULL, ffWRITE },
919 { efTPS, NULL, NULL, ffOPTRD },
920 { efNDX, NULL, NULL, ffOPTRD },
921 { efNDX, "-fr", "frames", ffOPTRD },
922 { efNDX, "-sub", "cluster", ffOPTRD },
923 { efXVG, "-drop", "drop", ffOPTRD }
925 #define NFILE asize(fnm)
927 if (!parse_common_args(&argc, argv,
928 PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW |
929 PCA_TIME_UNIT | PCA_BE_NICE,
930 NFILE, fnm, NPA, pa, asize(desc), desc,
936 top_file = ftp2fn(efTPS, NFILE, fnm);
939 /* Check command line */
940 in_file = opt2fn("-f", NFILE, fnm);
944 #ifndef GMX_NATIVE_WINDOWS
945 do_trunc(in_file, ttrunc);
950 /* mark active cmdline options */
951 bSetBox = opt2parg_bSet("-box", NPA, pa);
952 bSetTime = opt2parg_bSet("-t0", NPA, pa);
953 bSetPrec = opt2parg_bSet("-ndec", NPA, pa);
954 bSetUR = opt2parg_bSet("-ur", NPA, pa);
955 bExec = opt2parg_bSet("-exec", NPA, pa);
956 bTimeStep = opt2parg_bSet("-timestep", NPA, pa);
957 bTDump = opt2parg_bSet("-dump", NPA, pa);
958 bDropUnder = opt2parg_bSet("-dropunder", NPA, pa);
959 bDropOver = opt2parg_bSet("-dropover", NPA, pa);
960 bTrans = opt2parg_bSet("-trans", NPA, pa);
961 bSplit = (split_t != 0);
963 /* parse enum options */
964 fit_enum = nenum(fit);
965 bFit = (fit_enum == efFit || fit_enum == efFitXY);
966 bFitXY = fit_enum == efFitXY;
967 bReset = (fit_enum == efReset || fit_enum == efResetXY);
968 bPFit = fit_enum == efPFit;
969 pbc_enum = nenum(pbc_opt);
970 bPBCWhole = pbc_enum == epWhole;
971 bPBCcomRes = pbc_enum == epComRes;
972 bPBCcomMol = pbc_enum == epComMol;
973 bPBCcomAtom = pbc_enum == epComAtom;
974 bNoJump = pbc_enum == epNojump;
975 bCluster = pbc_enum == epCluster;
976 bPBC = pbc_enum != epNone;
977 unitcell_enum = nenum(unitcell_opt);
978 ecenter = nenum(center_opt) - ecTric;
980 /* set and check option dependencies */
983 bFit = TRUE; /* for pfit, fit *must* be set */
987 bReset = TRUE; /* for fit, reset *must* be set */
992 nfitdim = (fit_enum == efFitXY || fit_enum == efResetXY) ? 2 : 3;
994 bRmPBC = bFit || bPBCWhole || bPBCcomRes || bPBCcomMol;
998 if (!(bPBCcomRes || bPBCcomMol || bPBCcomAtom))
1001 "WARNING: Option for unitcell representation (-ur %s)\n"
1002 " only has effect in combination with -pbc %s, %s or %s.\n"
1003 " Ingoring unitcell representation.\n\n",
1004 unitcell_opt[0], pbc_opt[2], pbc_opt[3], pbc_opt[4]);
1010 gmx_fatal(FARGS, "PBC condition treatment does not work together with rotational fit.\n"
1011 "Please do the PBC condition treatment first and then run trjconv in a second step\n"
1012 "for the rotational fit.\n"
1013 "First doing the rotational fit and then doing the PBC treatment gives incorrect\n"
1017 /* ndec is in nr of decimal places, prec is a multiplication factor: */
1019 for (i = 0; i < ndec; i++)
1024 bIndex = ftp2bSet(efNDX, NFILE, fnm);
1027 /* Determine output type */
1028 out_file = opt2fn("-o", NFILE, fnm);
1029 ftp = fn2ftp(out_file);
1030 fprintf(stderr, "Will write %s: %s\n", ftp2ext(ftp), ftp2desc(ftp));
1031 bNeedPrec = (ftp == efXTC || ftp == efGRO);
1034 /* check if velocities are possible in input and output files */
1035 ftpin = fn2ftp(in_file);
1036 bVels = (ftp == efTRR || ftp == efTRJ || ftp == efGRO ||
1037 ftp == efG96 || ftp == efTNG)
1038 && (ftpin == efTRR || ftpin == efTRJ || ftpin == efGRO ||
1039 ftpin == efG96 || ftpin == efTNG || ftpin == efCPT);
1041 if (bSeparate || bSplit)
1043 outf_ext = strrchr(out_file, '.');
1044 if (outf_ext == NULL)
1046 gmx_fatal(FARGS, "Output file name '%s' does not contain a '.'", out_file);
1048 outf_base = strdup(out_file);
1049 outf_base[outf_ext - out_file] = '\0';
1052 bSubTraj = opt2bSet("-sub", NFILE, fnm);
1055 if ((ftp != efXTC) && (ftp != efTRR))
1057 /* It seems likely that other trajectory file types
1058 * could work here. */
1059 gmx_fatal(FARGS, "Can only use the sub option with output file types "
1062 clust = cluster_index(NULL, opt2fn("-sub", NFILE, fnm));
1064 /* Check for number of files disabled, as FOPEN_MAX is not the correct
1065 * number to check for. In my linux box it is only 16.
1067 if (0 && (clust->clust->nr > FOPEN_MAX-4))
1069 gmx_fatal(FARGS, "Can not open enough (%d) files to write all the"
1070 " trajectories.\ntry splitting the index file in %d parts.\n"
1072 clust->clust->nr, 1+clust->clust->nr/FOPEN_MAX, FOPEN_MAX);
1074 gmx_warning("The -sub option could require as many open output files as there are\n"
1075 "index groups in the file (%d). If you get I/O errors opening new files,\n"
1076 "try reducing the number of index groups in the file, and perhaps\n"
1077 "using trjconv -sub several times on different chunks of your index file.\n",
1080 snew(clust_status, clust->clust->nr);
1081 snew(clust_status_id, clust->clust->nr);
1082 snew(nfwritten, clust->clust->nr);
1083 for (i = 0; (i < clust->clust->nr); i++)
1085 clust_status[i] = NULL;
1086 clust_status_id[i] = -1;
1088 bSeparate = bSplit = FALSE;
1095 mtop = read_mtop_for_tng(top_file, in_file, out_file);
1097 /* Determine whether to read a topology */
1098 bTPS = (ftp2bSet(efTPS, NFILE, fnm) ||
1099 bRmPBC || bReset || bPBCcomMol || bCluster ||
1100 (ftp == efGRO) || (ftp == efPDB) || bCONECT);
1102 /* Determine if when can read index groups */
1103 bIndex = (bIndex || bTPS);
1107 read_tps_conf(top_file, top_title, &top, &ePBC, &xp, NULL, top_box,
1108 bReset || bPBCcomRes);
1111 if (0 == top.mols.nr && (bCluster || bPBCcomMol))
1113 gmx_fatal(FARGS, "Option -pbc %s requires a .tpr file for the -s option", pbc_opt[pbc_enum]);
1116 /* top_title is only used for gro and pdb,
1117 * the header in such a file is top_title t= ...
1118 * to prevent a double t=, remove it from top_title
1120 if ((charpt = strstr(top_title, " t= ")))
1127 gc = gmx_conect_generate(&top);
1131 gpbc = gmx_rmpbc_init(&top.idef, ePBC, top.atoms.nr);
1135 /* get frame number index */
1137 if (opt2bSet("-fr", NFILE, fnm))
1139 printf("Select groups of frame number indices:\n");
1140 rd_index(opt2fn("-fr", NFILE, fnm), 1, &nrfri, (atom_id **)&frindex, &frname);
1143 for (i = 0; i < nrfri; i++)
1145 fprintf(debug, "frindex[%4d]=%4d\n", i, frindex[i]);
1150 /* get index groups etc. */
1153 printf("Select group for %s fit\n",
1154 bFit ? "least squares" : "translational");
1155 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
1156 1, &ifit, &ind_fit, &gn_fit);
1162 gmx_fatal(FARGS, "Need at least 2 atoms to fit!\n");
1166 fprintf(stderr, "WARNING: fitting with only 2 atoms is not unique\n");
1172 printf("Select group for clustering\n");
1173 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
1174 1, &ifit, &ind_fit, &gn_fit);
1181 printf("Select group for centering\n");
1182 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
1183 1, &ncent, &cindex, &grpnm);
1185 printf("Select group for output\n");
1186 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
1187 1, &nout, &index, &grpnm);
1191 /* no index file, so read natoms from TRX */
1192 if (!read_first_frame(oenv, &trxin, in_file, &fr, TRX_DONT_SKIP))
1194 gmx_fatal(FARGS, "Could not read a frame from %s", in_file);
1199 snew(index, natoms);
1200 for (i = 0; i < natoms; i++)
1214 snew(w_rls, atoms->nr);
1215 for (i = 0; (i < ifit); i++)
1217 w_rls[ind_fit[i]] = atoms->atom[ind_fit[i]].m;
1220 /* Restore reference structure and set to origin,
1221 store original location (to put structure back) */
1224 gmx_rmpbc(gpbc, top.atoms.nr, top_box, xp);
1226 copy_rvec(xp[index[0]], x_shift);
1227 reset_x_ndim(nfitdim, ifit, ind_fit, atoms->nr, NULL, xp, w_rls);
1228 rvec_dec(x_shift, xp[index[0]]);
1232 clear_rvec(x_shift);
1235 if (bDropUnder || bDropOver)
1237 /* Read the .xvg file with the drop values */
1238 fprintf(stderr, "\nReading drop file ...");
1239 ndrop = read_xvg(opt2fn("-drop", NFILE, fnm), &dropval, &ncol);
1240 fprintf(stderr, " %d time points\n", ndrop);
1241 if (ndrop == 0 || ncol < 2)
1243 gmx_fatal(FARGS, "Found no data points in %s",
1244 opt2fn("-drop", NFILE, fnm));
1250 /* Make atoms struct for output in GRO or PDB files */
1251 if ((ftp == efGRO) || ((ftp == efG96) && bTPS) || (ftp == efPDB))
1253 /* get memory for stuff to go in .pdb file, and initialize
1254 * the pdbinfo structure part if the input has it.
1256 init_t_atoms(&useatoms, atoms->nr, (atoms->pdbinfo != NULL));
1257 sfree(useatoms.resinfo);
1258 useatoms.resinfo = atoms->resinfo;
1259 for (i = 0; (i < nout); i++)
1261 useatoms.atomname[i] = atoms->atomname[index[i]];
1262 useatoms.atom[i] = atoms->atom[index[i]];
1263 if (atoms->pdbinfo != NULL)
1265 useatoms.pdbinfo[i] = atoms->pdbinfo[index[i]];
1267 useatoms.nres = max(useatoms.nres, useatoms.atom[i].resind+1);
1271 /* select what to read */
1272 if (ftp == efTRR || ftp == efTRJ)
1282 flags = flags | TRX_READ_V;
1286 flags = flags | TRX_READ_F;
1289 /* open trx file for reading */
1290 bHaveFirstFrame = read_first_frame(oenv, &trxin, in_file, &fr, flags);
1293 fprintf(stderr, "\nPrecision of %s is %g (nm)\n", in_file, 1/fr.prec);
1297 if (bSetPrec || !fr.bPrec)
1299 fprintf(stderr, "\nSetting output precision to %g (nm)\n", 1/prec);
1303 fprintf(stderr, "Using output precision of %g (nm)\n", 1/prec);
1307 if (bHaveFirstFrame)
1309 set_trxframe_ePBC(&fr, ePBC);
1315 tshift = tzero-fr.time;
1325 /* check if index is meaningful */
1326 for (i = 0; i < nout; i++)
1328 if (index[i] >= natoms)
1331 "Index[%d] %d is larger than the number of atoms in the\n"
1332 "trajectory file (%d). There is a mismatch in the contents\n"
1333 "of your -f, -s and/or -n files.", i, index[i]+1, natoms);
1335 bCopy = bCopy || (i != index[i]);
1339 /* open output for writing */
1340 strcpy(filemode, "w");
1344 trjtools_gmx_prepare_tng_writing(out_file,
1358 if (!bSplit && !bSubTraj)
1360 trxout = open_trx(out_file, filemode);
1366 if (( !bSeparate && !bSplit ) && !bSubTraj)
1368 out = gmx_ffopen(out_file, filemode);
1372 gmx_incons("Illegal output file format");
1388 /* Start the big loop over frames */
1395 /* Main loop over frames */
1406 /*if (frame >= clust->clust->nra)
1407 gmx_fatal(FARGS,"There are more frames in the trajectory than in the cluster index file\n");*/
1408 if (frame > clust->maxframe)
1414 my_clust = clust->inv_clust[frame];
1416 if ((my_clust < 0) || (my_clust >= clust->clust->nr) ||
1417 (my_clust == NO_ATID))
1425 /* generate new box */
1427 for (m = 0; m < DIM; m++)
1431 fr.box[m][m] = newbox[m];
1438 for (i = 0; i < natoms; i++)
1440 rvec_inc(fr.x[i], trans);
1446 /* determine timestep */
1459 /* This is not very elegant, as one can not dump a frame after
1460 * a timestep with is more than twice as small as the first one. */
1461 bDumpFrame = (fr.time > tdump-0.5*dt) && (fr.time <= tdump+0.5*dt);
1468 /* determine if an atom jumped across the box and reset it if so */
1469 if (bNoJump && (bTPS || frame != 0))
1471 for (d = 0; d < DIM; d++)
1473 hbox[d] = 0.5*fr.box[d][d];
1475 for (i = 0; i < natoms; i++)
1479 rvec_dec(fr.x[i], x_shift);
1481 for (m = DIM-1; m >= 0; m--)
1485 while (fr.x[i][m]-xp[i][m] <= -hbox[m])
1487 for (d = 0; d <= m; d++)
1489 fr.x[i][d] += fr.box[m][d];
1492 while (fr.x[i][m]-xp[i][m] > hbox[m])
1494 for (d = 0; d <= m; d++)
1496 fr.x[i][d] -= fr.box[m][d];
1505 calc_pbc_cluster(ecenter, ifit, &top, ePBC, fr.x, ind_fit, fr.box);
1510 /* Now modify the coords according to the flags,
1511 for normal fit, this is only done for output frames */
1514 gmx_rmpbc_trxfr(gpbc, &fr);
1517 reset_x_ndim(nfitdim, ifit, ind_fit, natoms, NULL, fr.x, w_rls);
1518 do_fit(natoms, w_rls, xp, fr.x);
1521 /* store this set of coordinates for future use */
1522 if (bPFit || bNoJump)
1528 for (i = 0; (i < natoms); i++)
1530 copy_rvec(fr.x[i], xp[i]);
1531 rvec_inc(fr.x[i], x_shift);
1537 /* see if we have a frame from the frame index group */
1538 for (i = 0; i < nrfri && !bDumpFrame; i++)
1540 bDumpFrame = frame == frindex[i];
1543 if (debug && bDumpFrame)
1545 fprintf(debug, "dumping %d\n", frame);
1549 ( ( !bTDump && !frindex && frame % skip_nr == 0 ) || bDumpFrame );
1551 if (bWriteFrame && (bDropUnder || bDropOver))
1553 while (dropval[0][drop1] < fr.time && drop1+1 < ndrop)
1558 if (fabs(dropval[0][drop0] - fr.time)
1559 < fabs(dropval[0][drop1] - fr.time))
1567 if ((bDropUnder && dropval[1][dropuse] < dropunder) ||
1568 (bDropOver && dropval[1][dropuse] > dropover))
1570 bWriteFrame = FALSE;
1580 fr.time = tzero+frame*timestep;
1590 fprintf(stderr, "\nDumping frame at t= %g %s\n",
1591 output_env_conv_time(oenv, fr.time), output_env_get_time_unit(oenv));
1594 /* check for writing at each delta_t */
1595 bDoIt = (delta_t == 0);
1600 bDoIt = bRmod(fr.time, tzero, delta_t);
1604 /* round() is not C89 compatible, so we do this: */
1605 bDoIt = bRmod(floor(fr.time+0.5), floor(tzero+0.5),
1606 floor(delta_t+0.5));
1610 if (bDoIt || bTDump)
1612 /* print sometimes */
1613 if ( ((outframe % SKIP) == 0) || (outframe < SKIP) )
1615 fprintf(stderr, " -> frame %6d time %8.3f \r",
1616 outframe, output_env_conv_time(oenv, fr.time));
1621 /* Now modify the coords according to the flags,
1622 for PFit we did this already! */
1626 gmx_rmpbc_trxfr(gpbc, &fr);
1631 reset_x_ndim(nfitdim, ifit, ind_fit, natoms, NULL, fr.x, w_rls);
1634 do_fit_ndim(nfitdim, natoms, w_rls, xp, fr.x);
1638 for (i = 0; i < natoms; i++)
1640 rvec_inc(fr.x[i], x_shift);
1647 center_x(ecenter, fr.x, fr.box, natoms, ncent, cindex);
1653 switch (unitcell_enum)
1656 put_atoms_in_box(ePBC, fr.box, natoms, fr.x);
1659 put_atoms_in_triclinic_unitcell(ecenter, fr.box, natoms, fr.x);
1662 warn = put_atoms_in_compact_unitcell(ePBC, ecenter, fr.box,
1664 if (warn && !bWarnCompact)
1666 fprintf(stderr, "\n%s\n", warn);
1667 bWarnCompact = TRUE;
1674 put_residue_com_in_box(unitcell_enum, ecenter,
1675 natoms, atoms->atom, ePBC, fr.box, fr.x);
1679 put_molecule_com_in_box(unitcell_enum, ecenter,
1681 natoms, atoms->atom, ePBC, fr.box, fr.x);
1683 /* Copy the input trxframe struct to the output trxframe struct */
1685 frout.bV = (frout.bV && bVels);
1686 frout.bF = (frout.bF && bForce);
1687 frout.natoms = nout;
1688 if (bNeedPrec && (bSetPrec || !fr.bPrec))
1704 for (i = 0; i < nout; i++)
1706 copy_rvec(fr.x[index[i]], frout.x[i]);
1709 copy_rvec(fr.v[index[i]], frout.v[i]);
1713 copy_rvec(fr.f[index[i]], frout.f[i]);
1718 if (opt2parg_bSet("-shift", NPA, pa))
1720 for (i = 0; i < nout; i++)
1722 for (d = 0; d < DIM; d++)
1724 frout.x[i][d] += outframe*shift[d];
1731 bSplitHere = bSplit && bRmod(fr.time, tzero, split_t);
1735 /* round() is not C89 compatible, so we do this: */
1736 bSplitHere = bSplit && bRmod(floor(fr.time+0.5),
1738 floor(split_t+0.5));
1740 if (bSeparate || bSplitHere)
1742 mk_filenm(outf_base, ftp2ext(ftp), nzero, file_nr, out_file2);
1748 write_tng_frame(trxout, &frout);
1749 // TODO when trjconv behaves better: work how to read and write lambda
1760 trxout = open_trx(out_file2, filemode);
1767 if (clust_status_id[my_clust] == -1)
1769 sprintf(buf, "%s.%s", clust->grpname[my_clust], ftp2ext(ftp));
1770 clust_status[my_clust] = open_trx(buf, "w");
1771 clust_status_id[my_clust] = 1;
1774 else if (clust_status_id[my_clust] == -2)
1776 gmx_fatal(FARGS, "File %s.xtc should still be open (%d open .xtc files)\n" "in order to write frame %d. my_clust = %d",
1777 clust->grpname[my_clust], ntrxopen, frame,
1780 write_trxframe(clust_status[my_clust], &frout, gc);
1781 nfwritten[my_clust]++;
1782 if (nfwritten[my_clust] ==
1783 (clust->clust->index[my_clust+1]-
1784 clust->clust->index[my_clust]))
1786 close_trx(clust_status[my_clust]);
1787 clust_status[my_clust] = NULL;
1788 clust_status_id[my_clust] = -2;
1792 gmx_fatal(FARGS, "Less than zero open .xtc files!");
1799 write_trxframe(trxout, &frout, gc);
1805 sprintf(title, "Generated by trjconv : %s t= %9.5f",
1806 top_title, fr.time);
1807 if (bSeparate || bSplitHere)
1809 out = gmx_ffopen(out_file2, "w");
1814 write_hconf_p(out, title, &useatoms, prec2ndec(frout.prec),
1815 frout.x, frout.bV ? frout.v : NULL, frout.box);
1818 fprintf(out, "REMARK GENERATED BY TRJCONV\n");
1819 sprintf(title, "%s t= %9.5f", top_title, frout.time);
1820 /* if reading from pdb, we want to keep the original
1821 model numbering else we write the output frame
1822 number plus one, because model 0 is not allowed in pdb */
1823 if (ftpin == efPDB && fr.bStep && fr.step > model_nr)
1831 write_pdbfile(out, title, &useatoms, frout.x,
1832 frout.ePBC, frout.box, ' ', model_nr, gc, TRUE);
1835 frout.title = title;
1836 if (bSeparate || bTDump)
1838 frout.bTitle = TRUE;
1841 frout.bAtoms = TRUE;
1843 frout.atoms = &useatoms;
1844 frout.bStep = FALSE;
1845 frout.bTime = FALSE;
1849 frout.bTitle = (outframe == 0);
1850 frout.bAtoms = FALSE;
1854 write_g96_conf(out, &frout, -1, NULL);
1863 gmx_fatal(FARGS, "DHE, ftp=%d\n", ftp);
1865 if (bSeparate || bSplitHere)
1870 /* execute command */
1874 sprintf(c, "%s %d", exec_command, file_nr-1);
1875 /*fprintf(stderr,"Executing '%s'\n",c);*/
1876 #ifdef GMX_NO_SYSTEM
1877 printf("Warning-- No calls to system(3) supported on this platform.");
1878 printf("Warning-- Skipping execution of 'system(\"%s\")'.", c);
1882 gmx_fatal(FARGS, "Error executing command: %s", c);
1890 bHaveNextFrame = read_next_frame(oenv, trxin, &fr);
1892 while (!(bTDump && bDumpFrame) && bHaveNextFrame);
1895 if (!bHaveFirstFrame || (bTDump && !bDumpFrame))
1897 fprintf(stderr, "\nWARNING no output, "
1898 "last frame read at t=%g\n", fr.time);
1900 fprintf(stderr, "\n");
1907 gmx_rmpbc_done(gpbc);
1914 else if (out != NULL)
1920 for (i = 0; (i < clust->clust->nr); i++)
1922 if (clust_status_id[i] >= 0)
1924 close_trx(clust_status[i]);
1932 do_view(oenv, out_file, NULL);