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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[],
77 rvec clust_com, matrix box, rvec clustercenter)
79 int m, i, j, j0, j1, jj, ai, aj;
82 rvec dx, xtest, box_center;
83 int nmol, imol_center;
85 gmx_bool *bMol, *bTmp;
86 rvec *m_com, *m_shift;
94 calc_box_center(ecenter, box, box_center);
96 /* Initiate the pbc structure */
97 memset(&pbc, 0, sizeof(pbc));
98 set_pbc(&pbc, ePBC, box);
100 /* Convert atom index to molecular */
102 molind = top->mols.index;
108 snew(bTmp, top->atoms.nr);
110 for (i = 0; (i < nrefat); i++)
112 /* Mark all molecules in the index */
115 /* Binary search assuming the molecules are sorted */
120 if (ai < molind[j0+1])
124 else if (ai >= molind[j1])
131 if (ai < molind[jj+1])
143 /* Double check whether all atoms in all molecules that are marked are part
144 * of the cluster. Simultaneously compute the center of geometry.
146 min_dist2 = 10*sqr(trace(box));
149 for (i = 0; i < nmol; i++)
151 for (j = molind[i]; j < molind[i+1]; j++)
153 if (bMol[i] && !bTmp[j])
155 gmx_fatal(FARGS, "Molecule %d marked for clustering but not atom %d in it - check your index!", i+1, j+1);
157 else if (!bMol[i] && bTmp[j])
159 gmx_fatal(FARGS, "Atom %d marked for clustering but not molecule %d - this is an internal error...", j+1, i+1);
163 /* Make molecule whole, move 2nd and higher atom to same periodicity as 1st atom in molecule */
166 pbc_dx(&pbc, x[j], x[j-1], dx);
167 rvec_add(x[j-1], dx, x[j]);
169 /* Compute center of geometry of molecule - m_com[i] was zeroed when we did snew() on it! */
170 rvec_inc(m_com[i], x[j]);
175 /* Normalize center of geometry */
176 fac = 1.0/(molind[i+1]-molind[i]);
177 for (m = 0; (m < DIM); m++)
181 /* Determine which molecule is closest to the center of the box */
182 pbc_dx(&pbc, box_center, m_com[i], dx);
183 tmp_r2 = iprod(dx, dx);
185 if (tmp_r2 < min_dist2)
190 cluster[ncluster++] = i;
197 fprintf(stderr, "No molecules selected in the cluster\n");
200 else if (imol_center == -1)
202 fprintf(stderr, "No central molecules could be found\n");
207 added[nadded++] = imol_center;
208 bMol[imol_center] = FALSE;
210 while (nadded < ncluster)
212 /* Find min distance between cluster molecules and those remaining to be added */
213 min_dist2 = 10*sqr(trace(box));
216 /* Loop over added mols */
217 for (i = 0; i < nadded; i++)
220 /* Loop over all mols */
221 for (j = 0; j < ncluster; j++)
224 /* check those remaining to be added */
227 pbc_dx(&pbc, m_com[aj], m_com[ai], dx);
228 tmp_r2 = iprod(dx, dx);
229 if (tmp_r2 < min_dist2)
239 /* Add the best molecule */
240 added[nadded++] = jmin;
242 /* Calculate the shift from the ai molecule */
243 pbc_dx(&pbc, m_com[jmin], m_com[imin], dx);
244 rvec_add(m_com[imin], dx, xtest);
245 rvec_sub(xtest, m_com[jmin], m_shift[jmin]);
246 rvec_inc(m_com[jmin], m_shift[jmin]);
248 for (j = molind[jmin]; j < molind[jmin+1]; j++)
250 rvec_inc(x[j], m_shift[jmin]);
252 fprintf(stdout, "\rClustering iteration %d of %d...", nadded, ncluster);
262 fprintf(stdout, "\n");
265 static void put_molecule_com_in_box(int unitcell_enum, int ecenter,
267 int natoms, t_atom atom[],
268 int ePBC, matrix box, rvec x[])
272 rvec com, new_com, shift, dx, box_center;
277 calc_box_center(ecenter, box, box_center);
278 set_pbc(&pbc, ePBC, box);
281 gmx_fatal(FARGS, "There are no molecule descriptions. I need a .tpr file for this pbc option.");
283 for (i = 0; (i < mols->nr); i++)
288 for (j = mols->index[i]; (j < mols->index[i+1] && j < natoms); j++)
291 for (d = 0; d < DIM; d++)
297 /* calculate final COM */
298 svmul(1.0/mtot, com, com);
300 /* check if COM is outside box */
301 copy_rvec(com, new_com);
302 switch (unitcell_enum)
305 put_atoms_in_box(ePBC, box, 1, &new_com);
308 put_atoms_in_triclinic_unitcell(ecenter, box, 1, &new_com);
311 put_atoms_in_compact_unitcell(ePBC, ecenter, box, 1, &new_com);
314 rvec_sub(new_com, com, shift);
315 if (norm2(shift) > 0)
319 fprintf (debug, "\nShifting position of molecule %d "
320 "by %8.3f %8.3f %8.3f\n", i+1, PR_VEC(shift));
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 %u-%u) "
375 "by %g,%g,%g\n", atom[res_start].resind+1,
376 res_start+1, res_end+1, PR_VEC(shift));
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) != efTRJ) && (fn2ftp(fn) != efTRR))
469 gmx_fatal(FARGS, "%s is not a trajectory file, exiting\n", fn);
473 #ifndef GMX_NATIVE_WINDOWS
474 void do_trunc(const char *fn, real t0)
487 gmx_fatal(FARGS, "You forgot to set the truncation time");
490 /* Check whether this is a .trj file */
493 in = open_trn(fn, "r");
494 fp = gmx_fio_getfp(in);
497 fprintf(stderr, "Sorry, can not trunc %s, truncation of this filetype is not supported\n", fn);
503 fpos = gmx_fio_ftell(in);
505 while (!bStop && fread_trnheader(in, &sh, &bOK))
507 fread_htrn(in, &sh, NULL, NULL, NULL, NULL);
508 fpos = gmx_ftell(fp);
512 gmx_fseek(fp, fpos, SEEK_SET);
518 fprintf(stderr, "Do you REALLY want to truncate this trajectory (%s) at:\n"
519 "frame %d, time %g, bytes %ld ??? (type YES if so)\n",
520 fn, j, t, (long int)fpos);
521 if (1 != scanf("%s", yesno))
523 gmx_fatal(FARGS, "Error reading user input");
525 if (strcmp(yesno, "YES") == 0)
527 fprintf(stderr, "Once again, I'm gonna DO this...\n");
529 if (0 != truncate(fn, fpos))
531 gmx_fatal(FARGS, "Error truncating file %s", fn);
536 fprintf(stderr, "Ok, I'll forget about it\n");
541 fprintf(stderr, "Already at end of file (t=%g)...\n", t);
548 int gmx_trjconv(int argc, char *argv[])
550 const char *desc[] = {
551 "[TT]trjconv[tt] can convert trajectory files in many ways:[BR]",
552 "[BB]1.[bb] from one format to another[BR]",
553 "[BB]2.[bb] select a subset of atoms[BR]",
554 "[BB]3.[bb] change the periodicity representation[BR]",
555 "[BB]4.[bb] keep multimeric molecules together[BR]",
556 "[BB]5.[bb] center atoms in the box[BR]",
557 "[BB]6.[bb] fit atoms to reference structure[BR]",
558 "[BB]7.[bb] reduce the number of frames[BR]",
559 "[BB]8.[bb] change the timestamps of the frames ",
560 "([TT]-t0[tt] and [TT]-timestep[tt])[BR]",
561 "[BB]9.[bb] cut the trajectory in small subtrajectories according",
562 "to information in an index file. This allows subsequent analysis of",
563 "the subtrajectories that could, for example, be the result of a",
564 "cluster analysis. Use option [TT]-sub[tt].",
565 "This assumes that the entries in the index file are frame numbers and",
566 "dumps each group in the index file to a separate trajectory file.[BR]",
567 "[BB]10.[bb] select frames within a certain range of a quantity given",
568 "in an [TT].xvg[tt] file.[PAR]",
570 "The program [TT]trjcat[tt] is better suited for concatenating multiple trajectory files.",
573 "Currently seven formats are supported for input and output:",
574 "[TT].xtc[tt], [TT].trr[tt], [TT].trj[tt], [TT].gro[tt], [TT].g96[tt],",
575 "[TT].pdb[tt] and [TT].g87[tt].",
576 "The file formats are detected from the file extension.",
577 "The precision of [TT].xtc[tt] and [TT].gro[tt] output is taken from the",
578 "input file for [TT].xtc[tt], [TT].gro[tt] and [TT].pdb[tt],",
579 "and from the [TT]-ndec[tt] option for other input formats. The precision",
580 "is always taken from [TT]-ndec[tt], when this option is set.",
581 "All other formats have fixed precision. [TT].trr[tt] and [TT].trj[tt]",
582 "output can be single or double precision, depending on the precision",
583 "of the [TT]trjconv[tt] binary.",
584 "Note that velocities are only supported in",
585 "[TT].trr[tt], [TT].trj[tt], [TT].gro[tt] and [TT].g96[tt] files.[PAR]",
587 "Option [TT]-app[tt] can be used to",
588 "append output to an existing trajectory file.",
589 "No checks are performed to ensure integrity",
590 "of the resulting combined trajectory file.[PAR]",
592 "Option [TT]-sep[tt] can be used to write every frame to a separate",
593 "[TT].gro, .g96[tt] or [TT].pdb[tt] file. By default, all frames all written to one file.",
594 "[TT].pdb[tt] files with all frames concatenated can be viewed with",
595 "[TT]rasmol -nmrpdb[tt].[PAR]",
597 "It is possible to select part of your trajectory and write it out",
598 "to a new trajectory file in order to save disk space, e.g. for leaving",
599 "out the water from a trajectory of a protein in water.",
600 "[BB]ALWAYS[bb] put the original trajectory on tape!",
601 "We recommend to use the portable [TT].xtc[tt] format for your analysis",
602 "to save disk space and to have portable files.[PAR]",
604 "There are two options for fitting the trajectory to a reference",
605 "either for essential dynamics analysis, etc.",
606 "The first option is just plain fitting to a reference structure",
607 "in the structure file. The second option is a progressive fit",
608 "in which the first timeframe is fitted to the reference structure ",
609 "in the structure file to obtain and each subsequent timeframe is ",
610 "fitted to the previously fitted structure. This way a continuous",
611 "trajectory is generated, which might not be the case when using the",
612 "regular fit method, e.g. when your protein undergoes large",
613 "conformational transitions.[PAR]",
615 "Option [TT]-pbc[tt] sets the type of periodic boundary condition",
617 "[TT]* mol[tt] puts the center of mass of molecules in the box,",
618 "and requires a run input file to be supplied with [TT]-s[tt].[BR]",
619 "[TT]* res[tt] puts the center of mass of residues in the box.[BR]",
620 "[TT]* atom[tt] puts all the atoms in the box.[BR]",
621 "[TT]* nojump[tt] checks if atoms jump across the box and then puts",
622 "them back. This has the effect that all molecules",
623 "will remain whole (provided they were whole in the initial",
624 "conformation). [BB]Note[bb] that this ensures a continuous trajectory but",
625 "molecules may diffuse out of the box. The starting configuration",
626 "for this procedure is taken from the structure file, if one is",
627 "supplied, otherwise it is the first frame.[BR]",
628 "[TT]* cluster[tt] clusters all the atoms in the selected index",
629 "such that they are all closest to the center of mass of the cluster,",
630 "which is iteratively updated. [BB]Note[bb] that this will only give meaningful",
631 "results if you in fact have a cluster. Luckily that can be checked",
632 "afterwards using a trajectory viewer. Note also that if your molecules",
633 "are broken this will not work either.[BR]",
634 "The separate option [TT]-clustercenter[tt] can be used to specify an",
635 "approximate center for the cluster. This is useful e.g. if you have",
636 "two big vesicles, and you want to maintain their relative positions.[BR]",
637 "[TT]* whole[tt] only makes broken molecules whole.[PAR]",
639 "Option [TT]-ur[tt] sets the unit cell representation for options",
640 "[TT]mol[tt], [TT]res[tt] and [TT]atom[tt] of [TT]-pbc[tt].",
641 "All three options give different results for triclinic boxes and",
642 "identical results for rectangular boxes.",
643 "[TT]rect[tt] is the ordinary brick shape.",
644 "[TT]tric[tt] is the triclinic unit cell.",
645 "[TT]compact[tt] puts all atoms at the closest distance from the center",
646 "of the box. This can be useful for visualizing e.g. truncated octahedra",
647 "or rhombic dodecahedra. The center for options [TT]tric[tt] and [TT]compact[tt]",
648 "is [TT]tric[tt] (see below), unless the option [TT]-boxcenter[tt]",
649 "is set differently.[PAR]",
651 "Option [TT]-center[tt] centers the system in the box. The user can",
652 "select the group which is used to determine the geometrical center.",
653 "Option [TT]-boxcenter[tt] sets the location of the center of the box",
654 "for options [TT]-pbc[tt] and [TT]-center[tt]. The center options are:",
655 "[TT]tric[tt]: half of the sum of the box vectors,",
656 "[TT]rect[tt]: half of the box diagonal,",
657 "[TT]zero[tt]: zero.",
658 "Use option [TT]-pbc mol[tt] in addition to [TT]-center[tt] when you",
659 "want all molecules in the box after the centering.[PAR]",
661 "It is not always possible to use combinations of [TT]-pbc[tt],",
662 "[TT]-fit[tt], [TT]-ur[tt] and [TT]-center[tt] to do exactly what",
663 "you want in one call to [TT]trjconv[tt]. Consider using multiple",
664 "calls, and check out the GROMACS website for suggestions.[PAR]",
666 "With [TT]-dt[tt], it is possible to reduce the number of ",
667 "frames in the output. This option relies on the accuracy of the times",
668 "in your input trajectory, so if these are inaccurate use the",
669 "[TT]-timestep[tt] option to modify the time (this can be done",
670 "simultaneously). For making smooth movies, the program [TT]g_filter[tt]",
671 "can reduce the number of frames while using low-pass frequency",
672 "filtering, this reduces aliasing of high frequency motions.[PAR]",
674 "Using [TT]-trunc[tt] [TT]trjconv[tt] can truncate [TT].trj[tt] in place, i.e.",
675 "without copying the file. This is useful when a run has crashed",
676 "during disk I/O (i.e. full disk), or when two contiguous",
677 "trajectories must be concatenated without having double frames.[PAR]",
679 "Option [TT]-dump[tt] can be used to extract a frame at or near",
680 "one specific time from your trajectory.[PAR]",
682 "Option [TT]-drop[tt] reads an [TT].xvg[tt] file with times and values.",
683 "When options [TT]-dropunder[tt] and/or [TT]-dropover[tt] are set,",
684 "frames with a value below and above the value of the respective options",
685 "will not be written."
701 const char *pbc_opt[epNR + 1] =
703 NULL, "none", "mol", "res", "atom", "nojump", "cluster", "whole",
708 const char *unitcell_opt[euNR+1] =
709 { NULL, "rect", "tric", "compact", NULL };
713 ecSel, ecTric, ecRect, ecZero, ecNR
715 const char *center_opt[ecNR+1] =
716 { NULL, "tric", "rect", "zero", NULL };
722 efSel, efNone, efFit, efFitXY, efReset, efResetXY, efPFit, efNR
724 const char *fit[efNR + 1] =
726 NULL, "none", "rot+trans", "rotxy+transxy", "translation", "transxy",
730 static gmx_bool bAppend = FALSE, bSeparate = FALSE, bVels = TRUE, bForce = FALSE, bCONECT = FALSE;
731 static gmx_bool bCenter = FALSE;
732 static int skip_nr = 1, ndec = 3, nzero = 0;
733 static real tzero = 0, delta_t = 0, timestep = 0, ttrunc = -1, tdump = -1, split_t = 0;
734 static rvec newbox = {0, 0, 0}, shift = {0, 0, 0}, trans = {0, 0, 0};
735 static char *exec_command = NULL;
736 static real dropunder = 0, dropover = 0;
737 static gmx_bool bRound = FALSE;
738 static rvec clustercenter = {0, 0, 0};
743 { "-skip", FALSE, etINT,
744 { &skip_nr }, "Only write every nr-th frame" },
745 { "-dt", FALSE, etTIME,
747 "Only write frame when t MOD dt = first time (%t)" },
748 { "-round", FALSE, etBOOL,
749 { &bRound }, "Round measurements to nearest picosecond"},
750 { "-dump", FALSE, etTIME,
751 { &tdump }, "Dump frame nearest specified time (%t)" },
752 { "-t0", FALSE, etTIME,
754 "Starting time (%t) (default: don't change)" },
755 { "-timestep", FALSE, etTIME,
757 "Change time step between input frames (%t)" },
758 { "-pbc", FALSE, etENUM,
760 "PBC treatment (see help text for full description)" },
761 { "-ur", FALSE, etENUM,
762 { unitcell_opt }, "Unit-cell representation" },
763 { "-center", FALSE, etBOOL,
764 { &bCenter }, "Center atoms in box" },
765 { "-boxcenter", FALSE, etENUM,
766 { center_opt }, "Center for -pbc and -center" },
767 { "-box", FALSE, etRVEC,
769 "Size for new cubic box (default: read from input)" },
770 { "-clustercenter", FALSE, etRVEC,
772 "Optional starting point for pbc cluster option" },
773 { "-trans", FALSE, etRVEC,
775 "All coordinates will be translated by trans. This "
776 "can advantageously be combined with -pbc mol -ur "
778 { "-shift", FALSE, etRVEC,
780 "All coordinates will be shifted by framenr*shift" },
781 { "-fit", FALSE, etENUM,
783 "Fit molecule to ref structure in the structure file" },
784 { "-ndec", FALSE, etINT,
786 "Precision for .xtc and .gro writing in number of "
788 { "-vel", FALSE, etBOOL,
789 { &bVels }, "Read and write velocities if possible" },
790 { "-force", FALSE, etBOOL,
791 { &bForce }, "Read and write forces if possible" },
792 #ifndef GMX_NATIVE_WINDOWS
793 { "-trunc", FALSE, etTIME,
795 "Truncate input trajectory file after this time (%t)" },
797 { "-exec", FALSE, etSTR,
799 "Execute command for every output frame with the "
800 "frame number as argument" },
801 { "-app", FALSE, etBOOL,
802 { &bAppend }, "Append output" },
803 { "-split", FALSE, etTIME,
805 "Start writing new file when t MOD split = first "
807 { "-sep", FALSE, etBOOL,
809 "Write each frame to a separate .gro, .g96 or .pdb "
811 { "-nzero", FALSE, etINT,
813 "If the -sep flag is set, use these many digits "
814 "for the file numbers and prepend zeros as needed" },
815 { "-dropunder", FALSE, etREAL,
816 { &dropunder }, "Drop all frames below this value" },
817 { "-dropover", FALSE, etREAL,
818 { &dropover }, "Drop all frames above this value" },
819 { "-conect", FALSE, etBOOL,
821 "Add conect records when writing [TT].pdb[tt] files. Useful "
822 "for visualization of non-standard molecules, e.g. "
823 "coarse grained ones" }
825 #define NPA asize(pa)
828 t_trxstatus *trxout = NULL;
830 int ftp, ftpin = 0, file_nr;
831 t_trxframe fr, frout;
833 rvec *xmem = NULL, *vmem = NULL, *fmem = NULL;
834 rvec *xp = NULL, x_shift, hbox, box_center, dx;
835 real xtcpr, lambda, *w_rls = NULL;
836 int m, i, d, frame, outframe, natoms, nout, ncent, nre, newstep = 0, model_nr;
839 gmx_conect gc = NULL;
841 t_atoms *atoms = NULL, useatoms;
843 atom_id *index, *cindex;
847 int ifit, irms, my_clust = -1;
848 atom_id *ind_fit, *ind_rms;
849 char *gn_fit, *gn_rms;
850 t_cluster_ndx *clust = NULL;
851 t_trxstatus **clust_status = NULL;
852 int *clust_status_id = NULL;
854 int *nfwritten = NULL;
855 int ndrop = 0, ncol, drop0 = 0, drop1 = 0, dropuse = 0;
857 real tshift = 0, t0 = -1, dt = 0.001, prec;
858 gmx_bool bFit, bFitXY, bPFit, bReset;
860 gmx_rmpbc_t gpbc = NULL;
861 gmx_bool bRmPBC, bPBCWhole, bPBCcomRes, bPBCcomMol, bPBCcomAtom, bPBC, bNoJump, bCluster;
862 gmx_bool bCopy, bDoIt, bIndex, bTDump, bSetTime, bTPS = FALSE, bDTset = FALSE;
863 gmx_bool bExec, bTimeStep = FALSE, bDumpFrame = FALSE, bSetPrec, bNeedPrec;
864 gmx_bool bHaveFirstFrame, bHaveNextFrame, bSetBox, bSetUR, bSplit = FALSE;
865 gmx_bool bSubTraj = FALSE, bDropUnder = FALSE, bDropOver = FALSE, bTrans = FALSE;
866 gmx_bool bWriteFrame, bSplitHere;
867 const char *top_file, *in_file, *out_file = NULL;
868 char out_file2[256], *charpt;
869 char *outf_base = NULL;
870 const char *outf_ext = NULL;
871 char top_title[256], title[256], command[256], filemode[5];
873 gmx_bool bWarnCompact = FALSE;
878 { efTRX, "-f", NULL, ffREAD },
879 { efTRO, "-o", NULL, ffWRITE },
880 { efTPS, NULL, NULL, ffOPTRD },
881 { efNDX, NULL, NULL, ffOPTRD },
882 { efNDX, "-fr", "frames", ffOPTRD },
883 { efNDX, "-sub", "cluster", ffOPTRD },
884 { efXVG, "-drop", "drop", ffOPTRD }
886 #define NFILE asize(fnm)
888 parse_common_args(&argc, argv,
889 PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW |
890 PCA_TIME_UNIT | PCA_BE_NICE,
891 NFILE, fnm, NPA, pa, asize(desc), desc,
894 top_file = ftp2fn(efTPS, NFILE, fnm);
897 /* Check command line */
898 in_file = opt2fn("-f", NFILE, fnm);
902 #ifndef GMX_NATIVE_WINDOWS
903 do_trunc(in_file, ttrunc);
908 /* mark active cmdline options */
909 bSetBox = opt2parg_bSet("-box", NPA, pa);
910 bSetTime = opt2parg_bSet("-t0", NPA, pa);
911 bSetPrec = opt2parg_bSet("-ndec", NPA, pa);
912 bSetUR = opt2parg_bSet("-ur", NPA, pa);
913 bExec = opt2parg_bSet("-exec", NPA, pa);
914 bTimeStep = opt2parg_bSet("-timestep", NPA, pa);
915 bTDump = opt2parg_bSet("-dump", NPA, pa);
916 bDropUnder = opt2parg_bSet("-dropunder", NPA, pa);
917 bDropOver = opt2parg_bSet("-dropover", NPA, pa);
918 bTrans = opt2parg_bSet("-trans", NPA, pa);
919 bSplit = (split_t != 0);
921 /* parse enum options */
922 fit_enum = nenum(fit);
923 bFit = (fit_enum == efFit || fit_enum == efFitXY);
924 bFitXY = fit_enum == efFitXY;
925 bReset = (fit_enum == efReset || fit_enum == efResetXY);
926 bPFit = fit_enum == efPFit;
927 pbc_enum = nenum(pbc_opt);
928 bPBCWhole = pbc_enum == epWhole;
929 bPBCcomRes = pbc_enum == epComRes;
930 bPBCcomMol = pbc_enum == epComMol;
931 bPBCcomAtom = pbc_enum == epComAtom;
932 bNoJump = pbc_enum == epNojump;
933 bCluster = pbc_enum == epCluster;
934 bPBC = pbc_enum != epNone;
935 unitcell_enum = nenum(unitcell_opt);
936 ecenter = nenum(center_opt) - ecTric;
938 /* set and check option dependencies */
941 bFit = TRUE; /* for pfit, fit *must* be set */
945 bReset = TRUE; /* for fit, reset *must* be set */
950 nfitdim = (fit_enum == efFitXY || fit_enum == efResetXY) ? 2 : 3;
952 bRmPBC = bFit || bPBCWhole || bPBCcomRes || bPBCcomMol;
956 if (!(bPBCcomRes || bPBCcomMol || bPBCcomAtom))
959 "WARNING: Option for unitcell representation (-ur %s)\n"
960 " only has effect in combination with -pbc %s, %s or %s.\n"
961 " Ingoring unitcell representation.\n\n",
962 unitcell_opt[0], pbc_opt[2], pbc_opt[3], pbc_opt[4]);
968 gmx_fatal(FARGS, "PBC condition treatment does not work together with rotational fit.\n"
969 "Please do the PBC condition treatment first and then run trjconv in a second step\n"
970 "for the rotational fit.\n"
971 "First doing the rotational fit and then doing the PBC treatment gives incorrect\n"
975 /* ndec is in nr of decimal places, prec is a multiplication factor: */
977 for (i = 0; i < ndec; i++)
982 bIndex = ftp2bSet(efNDX, NFILE, fnm);
985 /* Determine output type */
986 out_file = opt2fn("-o", NFILE, fnm);
987 ftp = fn2ftp(out_file);
988 fprintf(stderr, "Will write %s: %s\n", ftp2ext(ftp), ftp2desc(ftp));
989 bNeedPrec = (ftp == efXTC || ftp == efGRO);
992 /* check if velocities are possible in input and output files */
993 ftpin = fn2ftp(in_file);
994 bVels = (ftp == efTRR || ftp == efTRJ || ftp == efGRO || ftp == efG96)
995 && (ftpin == efTRR || ftpin == efTRJ || ftpin == efGRO || ftpin == efG96 ||
998 if (bSeparate || bSplit)
1000 outf_ext = strrchr(out_file, '.');
1001 if (outf_ext == NULL)
1003 gmx_fatal(FARGS, "Output file name '%s' does not contain a '.'", out_file);
1005 outf_base = strdup(out_file);
1006 outf_base[outf_ext - out_file] = '\0';
1009 bSubTraj = opt2bSet("-sub", NFILE, fnm);
1012 if ((ftp != efXTC) && (ftp != efTRR))
1014 /* It seems likely that other trajectory file types
1015 * could work here. */
1016 gmx_fatal(FARGS, "Can only use the sub option with output file types "
1019 clust = cluster_index(NULL, opt2fn("-sub", NFILE, fnm));
1021 /* Check for number of files disabled, as FOPEN_MAX is not the correct
1022 * number to check for. In my linux box it is only 16.
1024 if (0 && (clust->clust->nr > FOPEN_MAX-4))
1026 gmx_fatal(FARGS, "Can not open enough (%d) files to write all the"
1027 " trajectories.\ntry splitting the index file in %d parts.\n"
1029 clust->clust->nr, 1+clust->clust->nr/FOPEN_MAX, FOPEN_MAX);
1031 gmx_warning("The -sub option could require as many open output files as there are\n"
1032 "index groups in the file (%d). If you get I/O errors opening new files,\n"
1033 "try reducing the number of index groups in the file, and perhaps\n"
1034 "using trjconv -sub several times on different chunks of your index file.\n",
1037 snew(clust_status, clust->clust->nr);
1038 snew(clust_status_id, clust->clust->nr);
1039 snew(nfwritten, clust->clust->nr);
1040 for (i = 0; (i < clust->clust->nr); i++)
1042 clust_status[i] = NULL;
1043 clust_status_id[i] = -1;
1045 bSeparate = bSplit = FALSE;
1052 /* Determine whether to read a topology */
1053 bTPS = (ftp2bSet(efTPS, NFILE, fnm) ||
1054 bRmPBC || bReset || bPBCcomMol || bCluster ||
1055 (ftp == efGRO) || (ftp == efPDB) || bCONECT);
1057 /* Determine if when can read index groups */
1058 bIndex = (bIndex || bTPS);
1062 read_tps_conf(top_file, top_title, &top, &ePBC, &xp, NULL, top_box,
1063 bReset || bPBCcomRes);
1066 if (0 == top.mols.nr && (bCluster || bPBCcomMol))
1068 gmx_fatal(FARGS, "Option -pbc %s requires a .tpr file for the -s option", pbc_opt[pbc_enum]);
1071 /* top_title is only used for gro and pdb,
1072 * the header in such a file is top_title t= ...
1073 * to prevent a double t=, remove it from top_title
1075 if ((charpt = strstr(top_title, " t= ")))
1082 gc = gmx_conect_generate(&top);
1086 gpbc = gmx_rmpbc_init(&top.idef, ePBC, top.atoms.nr, top_box);
1090 /* get frame number index */
1092 if (opt2bSet("-fr", NFILE, fnm))
1094 printf("Select groups of frame number indices:\n");
1095 rd_index(opt2fn("-fr", NFILE, fnm), 1, &nrfri, (atom_id **)&frindex, &frname);
1098 for (i = 0; i < nrfri; i++)
1100 fprintf(debug, "frindex[%4d]=%4d\n", i, frindex[i]);
1105 /* get index groups etc. */
1108 printf("Select group for %s fit\n",
1109 bFit ? "least squares" : "translational");
1110 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
1111 1, &ifit, &ind_fit, &gn_fit);
1117 gmx_fatal(FARGS, "Need at least 2 atoms to fit!\n");
1121 fprintf(stderr, "WARNING: fitting with only 2 atoms is not unique\n");
1127 printf("Select group for clustering\n");
1128 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
1129 1, &ifit, &ind_fit, &gn_fit);
1136 printf("Select group for centering\n");
1137 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
1138 1, &ncent, &cindex, &grpnm);
1140 printf("Select group for output\n");
1141 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
1142 1, &nout, &index, &grpnm);
1146 /* no index file, so read natoms from TRX */
1147 if (!read_first_frame(oenv, &status, in_file, &fr, TRX_DONT_SKIP))
1149 gmx_fatal(FARGS, "Could not read a frame from %s", in_file);
1154 snew(index, natoms);
1155 for (i = 0; i < natoms; i++)
1169 snew(w_rls, atoms->nr);
1170 for (i = 0; (i < ifit); i++)
1172 w_rls[ind_fit[i]] = atoms->atom[ind_fit[i]].m;
1175 /* Restore reference structure and set to origin,
1176 store original location (to put structure back) */
1179 gmx_rmpbc(gpbc, top.atoms.nr, top_box, xp);
1181 copy_rvec(xp[index[0]], x_shift);
1182 reset_x_ndim(nfitdim, ifit, ind_fit, atoms->nr, NULL, xp, w_rls);
1183 rvec_dec(x_shift, xp[index[0]]);
1187 clear_rvec(x_shift);
1190 if (bDropUnder || bDropOver)
1192 /* Read the .xvg file with the drop values */
1193 fprintf(stderr, "\nReading drop file ...");
1194 ndrop = read_xvg(opt2fn("-drop", NFILE, fnm), &dropval, &ncol);
1195 fprintf(stderr, " %d time points\n", ndrop);
1196 if (ndrop == 0 || ncol < 2)
1198 gmx_fatal(FARGS, "Found no data points in %s",
1199 opt2fn("-drop", NFILE, fnm));
1205 /* Make atoms struct for output in GRO or PDB files */
1206 if ((ftp == efGRO) || ((ftp == efG96) && bTPS) || (ftp == efPDB))
1208 /* get memory for stuff to go in .pdb file */
1209 init_t_atoms(&useatoms, atoms->nr, FALSE);
1210 sfree(useatoms.resinfo);
1211 useatoms.resinfo = atoms->resinfo;
1212 for (i = 0; (i < nout); i++)
1214 useatoms.atomname[i] = atoms->atomname[index[i]];
1215 useatoms.atom[i] = atoms->atom[index[i]];
1216 useatoms.nres = max(useatoms.nres, useatoms.atom[i].resind+1);
1220 /* select what to read */
1221 if (ftp == efTRR || ftp == efTRJ)
1231 flags = flags | TRX_READ_V;
1235 flags = flags | TRX_READ_F;
1238 /* open trx file for reading */
1239 bHaveFirstFrame = read_first_frame(oenv, &status, in_file, &fr, flags);
1242 fprintf(stderr, "\nPrecision of %s is %g (nm)\n", in_file, 1/fr.prec);
1246 if (bSetPrec || !fr.bPrec)
1248 fprintf(stderr, "\nSetting output precision to %g (nm)\n", 1/prec);
1252 fprintf(stderr, "Using output precision of %g (nm)\n", 1/prec);
1256 if (bHaveFirstFrame)
1258 set_trxframe_ePBC(&fr, ePBC);
1264 tshift = tzero-fr.time;
1271 /* open output for writing */
1272 if ((bAppend) && (gmx_fexist(out_file)))
1274 strcpy(filemode, "a");
1275 fprintf(stderr, "APPENDING to existing file %s\n", out_file);
1279 strcpy(filemode, "w");
1288 if (!bSplit && !bSubTraj)
1290 trxout = open_trx(out_file, filemode);
1296 if (( !bSeparate && !bSplit ) && !bSubTraj)
1298 out = ffopen(out_file, filemode);
1306 /* check if index is meaningful */
1307 for (i = 0; i < nout; i++)
1309 if (index[i] >= natoms)
1312 "Index[%d] %d is larger than the number of atoms in the\n"
1313 "trajectory file (%d). There is a mismatch in the contents\n"
1314 "of your -f, -s and/or -n files.", i, index[i]+1, natoms);
1316 bCopy = bCopy || (i != index[i]);
1334 fprintf(gmx_fio_getfp(trx_get_fileio(trxout)),
1335 "Generated by %s. #atoms=%d, a BOX is"
1336 " stored in this file.\n", Program(), nout);
1339 /* Start the big loop over frames */
1346 /* Main loop over frames */
1357 /*if (frame >= clust->clust->nra)
1358 gmx_fatal(FARGS,"There are more frames in the trajectory than in the cluster index file\n");*/
1359 if (frame > clust->maxframe)
1365 my_clust = clust->inv_clust[frame];
1367 if ((my_clust < 0) || (my_clust >= clust->clust->nr) ||
1368 (my_clust == NO_ATID))
1376 /* generate new box */
1378 for (m = 0; m < DIM; m++)
1380 fr.box[m][m] = newbox[m];
1386 for (i = 0; i < natoms; i++)
1388 rvec_inc(fr.x[i], trans);
1394 /* determine timestep */
1407 /* This is not very elegant, as one can not dump a frame after
1408 * a timestep with is more than twice as small as the first one. */
1409 bDumpFrame = (fr.time > tdump-0.5*dt) && (fr.time <= tdump+0.5*dt);
1416 /* determine if an atom jumped across the box and reset it if so */
1417 if (bNoJump && (bTPS || frame != 0))
1419 for (d = 0; d < DIM; d++)
1421 hbox[d] = 0.5*fr.box[d][d];
1423 for (i = 0; i < natoms; i++)
1427 rvec_dec(fr.x[i], x_shift);
1429 for (m = DIM-1; m >= 0; m--)
1433 while (fr.x[i][m]-xp[i][m] <= -hbox[m])
1435 for (d = 0; d <= m; d++)
1437 fr.x[i][d] += fr.box[m][d];
1440 while (fr.x[i][m]-xp[i][m] > hbox[m])
1442 for (d = 0; d <= m; d++)
1444 fr.x[i][d] -= fr.box[m][d];
1455 calc_pbc_cluster(ecenter, ifit, &top, ePBC, fr.x, ind_fit, com, fr.box, clustercenter);
1460 /* Now modify the coords according to the flags,
1461 for normal fit, this is only done for output frames */
1464 gmx_rmpbc_trxfr(gpbc, &fr);
1467 reset_x_ndim(nfitdim, ifit, ind_fit, natoms, NULL, fr.x, w_rls);
1468 do_fit(natoms, w_rls, xp, fr.x);
1471 /* store this set of coordinates for future use */
1472 if (bPFit || bNoJump)
1478 for (i = 0; (i < natoms); i++)
1480 copy_rvec(fr.x[i], xp[i]);
1481 rvec_inc(fr.x[i], x_shift);
1487 /* see if we have a frame from the frame index group */
1488 for (i = 0; i < nrfri && !bDumpFrame; i++)
1490 bDumpFrame = frame == frindex[i];
1493 if (debug && bDumpFrame)
1495 fprintf(debug, "dumping %d\n", frame);
1499 ( ( !bTDump && !frindex && frame % skip_nr == 0 ) || bDumpFrame );
1501 if (bWriteFrame && (bDropUnder || bDropOver))
1503 while (dropval[0][drop1] < fr.time && drop1+1 < ndrop)
1508 if (fabs(dropval[0][drop0] - fr.time)
1509 < fabs(dropval[0][drop1] - fr.time))
1517 if ((bDropUnder && dropval[1][dropuse] < dropunder) ||
1518 (bDropOver && dropval[1][dropuse] > dropover))
1520 bWriteFrame = FALSE;
1530 fr.time = tzero+frame*timestep;
1540 fprintf(stderr, "\nDumping frame at t= %g %s\n",
1541 output_env_conv_time(oenv, fr.time), output_env_get_time_unit(oenv));
1544 /* check for writing at each delta_t */
1545 bDoIt = (delta_t == 0);
1550 bDoIt = bRmod(fr.time, tzero, delta_t);
1554 /* round() is not C89 compatible, so we do this: */
1555 bDoIt = bRmod(floor(fr.time+0.5), floor(tzero+0.5),
1556 floor(delta_t+0.5));
1560 if (bDoIt || bTDump)
1562 /* print sometimes */
1563 if ( ((outframe % SKIP) == 0) || (outframe < SKIP) )
1565 fprintf(stderr, " -> frame %6d time %8.3f \r",
1566 outframe, output_env_conv_time(oenv, fr.time));
1571 /* Now modify the coords according to the flags,
1572 for PFit we did this already! */
1576 gmx_rmpbc_trxfr(gpbc, &fr);
1581 reset_x_ndim(nfitdim, ifit, ind_fit, natoms, NULL, fr.x, w_rls);
1584 do_fit_ndim(nfitdim, natoms, w_rls, xp, fr.x);
1588 for (i = 0; i < natoms; i++)
1590 rvec_inc(fr.x[i], x_shift);
1597 center_x(ecenter, fr.x, fr.box, natoms, ncent, cindex);
1603 switch (unitcell_enum)
1606 put_atoms_in_box(ePBC, fr.box, natoms, fr.x);
1609 put_atoms_in_triclinic_unitcell(ecenter, fr.box, natoms, fr.x);
1612 warn = put_atoms_in_compact_unitcell(ePBC, ecenter, fr.box,
1614 if (warn && !bWarnCompact)
1616 fprintf(stderr, "\n%s\n", warn);
1617 bWarnCompact = TRUE;
1624 put_residue_com_in_box(unitcell_enum, ecenter,
1625 natoms, atoms->atom, ePBC, fr.box, fr.x);
1629 put_molecule_com_in_box(unitcell_enum, ecenter,
1631 natoms, atoms->atom, ePBC, fr.box, fr.x);
1633 /* Copy the input trxframe struct to the output trxframe struct */
1635 frout.bV = (frout.bV && bVels);
1636 frout.bF = (frout.bF && bForce);
1637 frout.natoms = nout;
1638 if (bNeedPrec && (bSetPrec || !fr.bPrec))
1654 for (i = 0; i < nout; i++)
1656 copy_rvec(fr.x[index[i]], frout.x[i]);
1659 copy_rvec(fr.v[index[i]], frout.v[i]);
1663 copy_rvec(fr.f[index[i]], frout.f[i]);
1668 if (opt2parg_bSet("-shift", NPA, pa))
1670 for (i = 0; i < nout; i++)
1672 for (d = 0; d < DIM; d++)
1674 frout.x[i][d] += outframe*shift[d];
1681 bSplitHere = bSplit && bRmod(fr.time, tzero, split_t);
1685 /* round() is not C89 compatible, so we do this: */
1686 bSplitHere = bSplit && bRmod(floor(fr.time+0.5),
1688 floor(split_t+0.5));
1690 if (bSeparate || bSplitHere)
1692 mk_filenm(outf_base, ftp2ext(ftp), nzero, file_nr, out_file2);
1707 trxout = open_trx(out_file2, filemode);
1714 if (clust_status_id[my_clust] == -1)
1716 sprintf(buf, "%s.%s", clust->grpname[my_clust], ftp2ext(ftp));
1717 clust_status[my_clust] = open_trx(buf, "w");
1718 clust_status_id[my_clust] = 1;
1721 else if (clust_status_id[my_clust] == -2)
1723 gmx_fatal(FARGS, "File %s.xtc should still be open (%d open .xtc files)\n" "in order to write frame %d. my_clust = %d",
1724 clust->grpname[my_clust], ntrxopen, frame,
1727 write_trxframe(clust_status[my_clust], &frout, gc);
1728 nfwritten[my_clust]++;
1729 if (nfwritten[my_clust] ==
1730 (clust->clust->index[my_clust+1]-
1731 clust->clust->index[my_clust]))
1733 close_trx(clust_status[my_clust]);
1734 clust_status[my_clust] = NULL;
1735 clust_status_id[my_clust] = -2;
1739 gmx_fatal(FARGS, "Less than zero open .xtc files!");
1746 write_trxframe(trxout, &frout, gc);
1752 sprintf(title, "Generated by trjconv : %s t= %9.5f",
1753 top_title, fr.time);
1754 if (bSeparate || bSplitHere)
1756 out = ffopen(out_file2, "w");
1761 write_hconf_p(out, title, &useatoms, prec2ndec(frout.prec),
1762 frout.x, frout.bV ? frout.v : NULL, frout.box);
1765 fprintf(out, "REMARK GENERATED BY TRJCONV\n");
1766 sprintf(title, "%s t= %9.5f", top_title, frout.time);
1767 /* if reading from pdb, we want to keep the original
1768 model numbering else we write the output frame
1769 number plus one, because model 0 is not allowed in pdb */
1770 if (ftpin == efPDB && fr.bStep && fr.step > model_nr)
1778 write_pdbfile(out, title, &useatoms, frout.x,
1779 frout.ePBC, frout.box, ' ', model_nr, gc, TRUE);
1782 frout.title = title;
1783 if (bSeparate || bTDump)
1785 frout.bTitle = TRUE;
1788 frout.bAtoms = TRUE;
1790 frout.atoms = &useatoms;
1791 frout.bStep = FALSE;
1792 frout.bTime = FALSE;
1796 frout.bTitle = (outframe == 0);
1797 frout.bAtoms = FALSE;
1801 write_g96_conf(out, &frout, -1, NULL);
1810 gmx_fatal(FARGS, "DHE, ftp=%d\n", ftp);
1812 if (bSeparate || bSplitHere)
1817 /* execute command */
1821 sprintf(c, "%s %d", exec_command, file_nr-1);
1822 /*fprintf(stderr,"Executing '%s'\n",c);*/
1823 #ifdef GMX_NO_SYSTEM
1824 printf("Warning-- No calls to system(3) supported on this platform.");
1825 printf("Warning-- Skipping execution of 'system(\"%s\")'.", c);
1829 gmx_fatal(FARGS, "Error executing command: %s", c);
1837 bHaveNextFrame = read_next_frame(oenv, status, &fr);
1839 while (!(bTDump && bDumpFrame) && bHaveNextFrame);
1842 if (!bHaveFirstFrame || (bTDump && !bDumpFrame))
1844 fprintf(stderr, "\nWARNING no output, "
1845 "last frame read at t=%g\n", fr.time);
1847 fprintf(stderr, "\n");
1854 gmx_rmpbc_done(gpbc);
1861 else if (out != NULL)
1867 for (i = 0; (i < clust->clust->nr); i++)
1869 if (clust_status_id[i] >= 0)
1871 close_trx(clust_status[i]);
1877 do_view(oenv, out_file, NULL);