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45 #include "gromacs/fileio/gmxfio.h"
46 #include "gromacs/fileio/tpxio.h"
47 #include "gromacs/fileio/trxio.h"
48 #include "gromacs/fileio/trnio.h"
50 #include "gromacs/fileio/futil.h"
51 #include "gromacs/fileio/pdbio.h"
52 #include "gromacs/fileio/confio.h"
56 #include "gromacs/fileio/xtcio.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, PR_VEC(shift));
321 for (j = mols->index[i]; (j < mols->index[i+1] && j < natoms); j++)
323 rvec_inc(x[j], shift);
329 static void put_residue_com_in_box(int unitcell_enum, int ecenter,
330 int natoms, t_atom atom[],
331 int ePBC, matrix box, rvec x[])
333 atom_id i, j, res_start, res_end, res_nat;
337 rvec box_center, com, new_com, shift;
339 calc_box_center(ecenter, box, box_center);
345 for (i = 0; i < natoms+1; i++)
347 if (i == natoms || (presnr != atom[i].resind && presnr != NOTSET))
349 /* calculate final COM */
351 res_nat = res_end - res_start;
352 svmul(1.0/mtot, com, com);
354 /* check if COM is outside box */
355 copy_rvec(com, new_com);
356 switch (unitcell_enum)
359 put_atoms_in_box(ePBC, box, 1, &new_com);
362 put_atoms_in_triclinic_unitcell(ecenter, box, 1, &new_com);
365 put_atoms_in_compact_unitcell(ePBC, ecenter, box, 1, &new_com);
368 rvec_sub(new_com, com, shift);
373 fprintf (debug, "\nShifting position of residue %d (atoms %u-%u) "
374 "by %g,%g,%g\n", atom[res_start].resind+1,
375 res_start+1, res_end+1, PR_VEC(shift));
377 for (j = res_start; j < res_end; j++)
379 rvec_inc(x[j], shift);
385 /* remember start of new residue */
392 for (d = 0; d < DIM; d++)
398 presnr = atom[i].resind;
403 static void center_x(int ecenter, rvec x[], matrix box, int n, int nc, atom_id ci[])
406 rvec cmin, cmax, box_center, dx;
410 copy_rvec(x[ci[0]], cmin);
411 copy_rvec(x[ci[0]], cmax);
412 for (i = 0; i < nc; i++)
415 for (m = 0; m < DIM; m++)
417 if (x[ai][m] < cmin[m])
421 else if (x[ai][m] > cmax[m])
427 calc_box_center(ecenter, box, box_center);
428 for (m = 0; m < DIM; m++)
430 dx[m] = box_center[m]-(cmin[m]+cmax[m])*0.5;
433 for (i = 0; i < n; i++)
440 static void mk_filenm(char *base, const char *ext, int ndigit, int file_nr,
446 strcpy(out_file, base);
457 strncat(out_file, "00000000000", ndigit-nd);
459 sprintf(nbuf, "%d.", file_nr);
460 strcat(out_file, nbuf);
461 strcat(out_file, ext);
464 void check_trn(const char *fn)
466 if ((fn2ftp(fn) != efTRJ) && (fn2ftp(fn) != efTRR))
468 gmx_fatal(FARGS, "%s is not a trajectory file, exiting\n", fn);
472 #ifndef GMX_NATIVE_WINDOWS
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 .trj 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 != 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);
547 int gmx_trjconv(int argc, char *argv[])
549 const char *desc[] = {
550 "[TT]trjconv[tt] can convert trajectory files in many ways:[BR]",
551 "[BB]1.[bb] from one format to another[BR]",
552 "[BB]2.[bb] select a subset of atoms[BR]",
553 "[BB]3.[bb] change the periodicity representation[BR]",
554 "[BB]4.[bb] keep multimeric molecules together[BR]",
555 "[BB]5.[bb] center atoms in the box[BR]",
556 "[BB]6.[bb] fit atoms to reference structure[BR]",
557 "[BB]7.[bb] reduce the number of frames[BR]",
558 "[BB]8.[bb] change the timestamps of the frames ",
559 "([TT]-t0[tt] and [TT]-timestep[tt])[BR]",
560 "[BB]9.[bb] cut the trajectory in small subtrajectories according",
561 "to information in an index file. This allows subsequent analysis of",
562 "the subtrajectories that could, for example, be the result of a",
563 "cluster analysis. Use option [TT]-sub[tt].",
564 "This assumes that the entries in the index file are frame numbers and",
565 "dumps each group in the index file to a separate trajectory file.[BR]",
566 "[BB]10.[bb] select frames within a certain range of a quantity given",
567 "in an [TT].xvg[tt] file.[PAR]",
569 "The program [TT]trjcat[tt] is better suited for concatenating multiple trajectory files.",
572 "Currently seven formats are supported for input and output:",
573 "[TT].xtc[tt], [TT].trr[tt], [TT].trj[tt], [TT].gro[tt], [TT].g96[tt],",
574 "[TT].pdb[tt] and [TT].g87[tt].",
575 "The file formats are detected from the file extension.",
576 "The precision of [TT].xtc[tt] and [TT].gro[tt] output is taken from the",
577 "input file for [TT].xtc[tt], [TT].gro[tt] and [TT].pdb[tt],",
578 "and from the [TT]-ndec[tt] option for other input formats. The precision",
579 "is always taken from [TT]-ndec[tt], when this option is set.",
580 "All other formats have fixed precision. [TT].trr[tt] and [TT].trj[tt]",
581 "output can be single or double precision, depending on the precision",
582 "of the [TT]trjconv[tt] binary.",
583 "Note that velocities are only supported in",
584 "[TT].trr[tt], [TT].trj[tt], [TT].gro[tt] and [TT].g96[tt] files.[PAR]",
586 "Option [TT]-app[tt] can be used to",
587 "append output to an existing trajectory file.",
588 "No checks are performed to ensure integrity",
589 "of the resulting combined trajectory file.[PAR]",
591 "Option [TT]-sep[tt] can be used to write every frame to a separate",
592 "[TT].gro, .g96[tt] or [TT].pdb[tt] file. By default, all frames all written to one file.",
593 "[TT].pdb[tt] files with all frames concatenated can be viewed with",
594 "[TT]rasmol -nmrpdb[tt].[PAR]",
596 "It is possible to select part of your trajectory and write it out",
597 "to a new trajectory file in order to save disk space, e.g. for leaving",
598 "out the water from a trajectory of a protein in water.",
599 "[BB]ALWAYS[bb] put the original trajectory on tape!",
600 "We recommend to use the portable [TT].xtc[tt] format for your analysis",
601 "to save disk space and to have portable files.[PAR]",
603 "There are two options for fitting the trajectory to a reference",
604 "either for essential dynamics analysis, etc.",
605 "The first option is just plain fitting to a reference structure",
606 "in the structure file. The second option is a progressive fit",
607 "in which the first timeframe is fitted to the reference structure ",
608 "in the structure file to obtain and each subsequent timeframe is ",
609 "fitted to the previously fitted structure. This way a continuous",
610 "trajectory is generated, which might not be the case when using the",
611 "regular fit method, e.g. when your protein undergoes large",
612 "conformational transitions.[PAR]",
614 "Option [TT]-pbc[tt] sets the type of periodic boundary condition",
616 "[TT]* mol[tt] puts the center of mass of molecules in the box,",
617 "and requires a run input file to be supplied with [TT]-s[tt].[BR]",
618 "[TT]* res[tt] puts the center of mass of residues in the box.[BR]",
619 "[TT]* atom[tt] puts all the atoms in the box.[BR]",
620 "[TT]* nojump[tt] checks if atoms jump across the box and then puts",
621 "them back. This has the effect that all molecules",
622 "will remain whole (provided they were whole in the initial",
623 "conformation). [BB]Note[bb] that this ensures a continuous trajectory but",
624 "molecules may diffuse out of the box. The starting configuration",
625 "for this procedure is taken from the structure file, if one is",
626 "supplied, otherwise it is the first frame.[BR]",
627 "[TT]* cluster[tt] clusters all the atoms in the selected index",
628 "such that they are all closest to the center of mass of the cluster,",
629 "which is iteratively updated. [BB]Note[bb] that this will only give meaningful",
630 "results if you in fact have a cluster. Luckily that can be checked",
631 "afterwards using a trajectory viewer. Note also that if your molecules",
632 "are broken this will not work either.[BR]",
633 "The separate option [TT]-clustercenter[tt] can be used to specify an",
634 "approximate center for the cluster. This is useful e.g. if you have",
635 "two big vesicles, and you want to maintain their relative positions.[BR]",
636 "[TT]* whole[tt] only makes broken molecules whole.[PAR]",
638 "Option [TT]-ur[tt] sets the unit cell representation for options",
639 "[TT]mol[tt], [TT]res[tt] and [TT]atom[tt] of [TT]-pbc[tt].",
640 "All three options give different results for triclinic boxes and",
641 "identical results for rectangular boxes.",
642 "[TT]rect[tt] is the ordinary brick shape.",
643 "[TT]tric[tt] is the triclinic unit cell.",
644 "[TT]compact[tt] puts all atoms at the closest distance from the center",
645 "of the box. This can be useful for visualizing e.g. truncated octahedra",
646 "or rhombic dodecahedra. The center for options [TT]tric[tt] and [TT]compact[tt]",
647 "is [TT]tric[tt] (see below), unless the option [TT]-boxcenter[tt]",
648 "is set differently.[PAR]",
650 "Option [TT]-center[tt] centers the system in the box. The user can",
651 "select the group which is used to determine the geometrical center.",
652 "Option [TT]-boxcenter[tt] sets the location of the center of the box",
653 "for options [TT]-pbc[tt] and [TT]-center[tt]. The center options are:",
654 "[TT]tric[tt]: half of the sum of the box vectors,",
655 "[TT]rect[tt]: half of the box diagonal,",
656 "[TT]zero[tt]: zero.",
657 "Use option [TT]-pbc mol[tt] in addition to [TT]-center[tt] when you",
658 "want all molecules in the box after the centering.[PAR]",
660 "It is not always possible to use combinations of [TT]-pbc[tt],",
661 "[TT]-fit[tt], [TT]-ur[tt] and [TT]-center[tt] to do exactly what",
662 "you want in one call to [TT]trjconv[tt]. Consider using multiple",
663 "calls, and check out the GROMACS website for suggestions.[PAR]",
665 "With [TT]-dt[tt], it is possible to reduce the number of ",
666 "frames in the output. This option relies on the accuracy of the times",
667 "in your input trajectory, so if these are inaccurate use the",
668 "[TT]-timestep[tt] option to modify the time (this can be done",
669 "simultaneously). For making smooth movies, the program [TT]g_filter[tt]",
670 "can reduce the number of frames while using low-pass frequency",
671 "filtering, this reduces aliasing of high frequency motions.[PAR]",
673 "Using [TT]-trunc[tt] [TT]trjconv[tt] can truncate [TT].trj[tt] in place, i.e.",
674 "without copying the file. This is useful when a run has crashed",
675 "during disk I/O (i.e. full disk), or when two contiguous",
676 "trajectories must be concatenated without having double frames.[PAR]",
678 "Option [TT]-dump[tt] can be used to extract a frame at or near",
679 "one specific time from your trajectory.[PAR]",
681 "Option [TT]-drop[tt] reads an [TT].xvg[tt] file with times and values.",
682 "When options [TT]-dropunder[tt] and/or [TT]-dropover[tt] are set,",
683 "frames with a value below and above the value of the respective options",
684 "will not be written."
700 const char *pbc_opt[epNR + 1] =
702 NULL, "none", "mol", "res", "atom", "nojump", "cluster", "whole",
707 const char *unitcell_opt[euNR+1] =
708 { NULL, "rect", "tric", "compact", NULL };
712 ecSel, ecTric, ecRect, ecZero, ecNR
714 const char *center_opt[ecNR+1] =
715 { NULL, "tric", "rect", "zero", NULL };
721 efSel, efNone, efFit, efFitXY, efReset, efResetXY, efPFit, efNR
723 const char *fit[efNR + 1] =
725 NULL, "none", "rot+trans", "rotxy+transxy", "translation", "transxy",
729 static gmx_bool bAppend = FALSE, bSeparate = FALSE, bVels = TRUE, bForce = FALSE, bCONECT = FALSE;
730 static gmx_bool bCenter = FALSE;
731 static int skip_nr = 1, ndec = 3, nzero = 0;
732 static real tzero = 0, delta_t = 0, timestep = 0, ttrunc = -1, tdump = -1, split_t = 0;
733 static rvec newbox = {0, 0, 0}, shift = {0, 0, 0}, trans = {0, 0, 0};
734 static char *exec_command = NULL;
735 static real dropunder = 0, dropover = 0;
736 static gmx_bool bRound = FALSE;
741 { "-skip", FALSE, etINT,
742 { &skip_nr }, "Only write every nr-th frame" },
743 { "-dt", FALSE, etTIME,
745 "Only write frame when t MOD dt = first time (%t)" },
746 { "-round", FALSE, etBOOL,
747 { &bRound }, "Round measurements to nearest picosecond"},
748 { "-dump", FALSE, etTIME,
749 { &tdump }, "Dump frame nearest specified time (%t)" },
750 { "-t0", FALSE, etTIME,
752 "Starting time (%t) (default: don't change)" },
753 { "-timestep", FALSE, etTIME,
755 "Change time step between input frames (%t)" },
756 { "-pbc", FALSE, etENUM,
758 "PBC treatment (see help text for full description)" },
759 { "-ur", FALSE, etENUM,
760 { unitcell_opt }, "Unit-cell representation" },
761 { "-center", FALSE, etBOOL,
762 { &bCenter }, "Center atoms in box" },
763 { "-boxcenter", FALSE, etENUM,
764 { center_opt }, "Center for -pbc and -center" },
765 { "-box", FALSE, etRVEC,
767 "Size for new cubic box (default: read from input)" },
768 { "-trans", FALSE, etRVEC,
770 "All coordinates will be translated by trans. This "
771 "can advantageously be combined with -pbc mol -ur "
773 { "-shift", FALSE, etRVEC,
775 "All coordinates will be shifted by framenr*shift" },
776 { "-fit", FALSE, etENUM,
778 "Fit molecule to ref structure in the structure file" },
779 { "-ndec", FALSE, etINT,
781 "Precision for .xtc and .gro writing in number of "
783 { "-vel", FALSE, etBOOL,
784 { &bVels }, "Read and write velocities if possible" },
785 { "-force", FALSE, etBOOL,
786 { &bForce }, "Read and write forces if possible" },
787 #ifndef GMX_NATIVE_WINDOWS
788 { "-trunc", FALSE, etTIME,
790 "Truncate input trajectory file after this time (%t)" },
792 { "-exec", FALSE, etSTR,
794 "Execute command for every output frame with the "
795 "frame number as argument" },
796 { "-app", FALSE, etBOOL,
797 { &bAppend }, "Append output" },
798 { "-split", FALSE, etTIME,
800 "Start writing new file when t MOD split = first "
802 { "-sep", FALSE, etBOOL,
804 "Write each frame to a separate .gro, .g96 or .pdb "
806 { "-nzero", FALSE, etINT,
808 "If the -sep flag is set, use these many digits "
809 "for the file numbers and prepend zeros as needed" },
810 { "-dropunder", FALSE, etREAL,
811 { &dropunder }, "Drop all frames below this value" },
812 { "-dropover", FALSE, etREAL,
813 { &dropover }, "Drop all frames above this value" },
814 { "-conect", FALSE, etBOOL,
816 "Add conect records when writing [TT].pdb[tt] files. Useful "
817 "for visualization of non-standard molecules, e.g. "
818 "coarse grained ones" }
820 #define NPA asize(pa)
823 t_trxstatus *trxout = NULL;
825 int ftp, ftpin = 0, file_nr;
826 t_trxframe fr, frout;
828 rvec *xmem = NULL, *vmem = NULL, *fmem = NULL;
829 rvec *xp = NULL, x_shift, hbox, box_center, dx;
830 real xtcpr, lambda, *w_rls = NULL;
831 int m, i, d, frame, outframe, natoms, nout, ncent, nre, newstep = 0, model_nr;
834 gmx_conect gc = NULL;
836 t_atoms *atoms = NULL, useatoms;
838 atom_id *index, *cindex;
842 int ifit, irms, my_clust = -1;
843 atom_id *ind_fit, *ind_rms;
844 char *gn_fit, *gn_rms;
845 t_cluster_ndx *clust = NULL;
846 t_trxstatus **clust_status = NULL;
847 int *clust_status_id = NULL;
849 int *nfwritten = NULL;
850 int ndrop = 0, ncol, drop0 = 0, drop1 = 0, dropuse = 0;
852 real tshift = 0, t0 = -1, dt = 0.001, prec;
853 gmx_bool bFit, bFitXY, bPFit, bReset;
855 gmx_rmpbc_t gpbc = NULL;
856 gmx_bool bRmPBC, bPBCWhole, bPBCcomRes, bPBCcomMol, bPBCcomAtom, bPBC, bNoJump, bCluster;
857 gmx_bool bCopy, bDoIt, bIndex, bTDump, bSetTime, bTPS = FALSE, bDTset = FALSE;
858 gmx_bool bExec, bTimeStep = FALSE, bDumpFrame = FALSE, bSetPrec, bNeedPrec;
859 gmx_bool bHaveFirstFrame, bHaveNextFrame, bSetBox, bSetUR, bSplit = FALSE;
860 gmx_bool bSubTraj = FALSE, bDropUnder = FALSE, bDropOver = FALSE, bTrans = FALSE;
861 gmx_bool bWriteFrame, bSplitHere;
862 const char *top_file, *in_file, *out_file = NULL;
863 char out_file2[256], *charpt;
864 char *outf_base = NULL;
865 const char *outf_ext = NULL;
866 char top_title[256], title[256], command[256], filemode[5];
868 gmx_bool bWarnCompact = FALSE;
873 { efTRX, "-f", NULL, ffREAD },
874 { efTRO, "-o", NULL, ffWRITE },
875 { efTPS, NULL, NULL, ffOPTRD },
876 { efNDX, NULL, NULL, ffOPTRD },
877 { efNDX, "-fr", "frames", ffOPTRD },
878 { efNDX, "-sub", "cluster", ffOPTRD },
879 { efXVG, "-drop", "drop", ffOPTRD }
881 #define NFILE asize(fnm)
883 if (!parse_common_args(&argc, argv,
884 PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW |
885 PCA_TIME_UNIT | PCA_BE_NICE,
886 NFILE, fnm, NPA, pa, asize(desc), desc,
892 top_file = ftp2fn(efTPS, NFILE, fnm);
895 /* Check command line */
896 in_file = opt2fn("-f", NFILE, fnm);
900 #ifndef GMX_NATIVE_WINDOWS
901 do_trunc(in_file, ttrunc);
906 /* mark active cmdline options */
907 bSetBox = opt2parg_bSet("-box", NPA, pa);
908 bSetTime = opt2parg_bSet("-t0", NPA, pa);
909 bSetPrec = opt2parg_bSet("-ndec", NPA, pa);
910 bSetUR = opt2parg_bSet("-ur", NPA, pa);
911 bExec = opt2parg_bSet("-exec", NPA, pa);
912 bTimeStep = opt2parg_bSet("-timestep", NPA, pa);
913 bTDump = opt2parg_bSet("-dump", NPA, pa);
914 bDropUnder = opt2parg_bSet("-dropunder", NPA, pa);
915 bDropOver = opt2parg_bSet("-dropover", NPA, pa);
916 bTrans = opt2parg_bSet("-trans", NPA, pa);
917 bSplit = (split_t != 0);
919 /* parse enum options */
920 fit_enum = nenum(fit);
921 bFit = (fit_enum == efFit || fit_enum == efFitXY);
922 bFitXY = fit_enum == efFitXY;
923 bReset = (fit_enum == efReset || fit_enum == efResetXY);
924 bPFit = fit_enum == efPFit;
925 pbc_enum = nenum(pbc_opt);
926 bPBCWhole = pbc_enum == epWhole;
927 bPBCcomRes = pbc_enum == epComRes;
928 bPBCcomMol = pbc_enum == epComMol;
929 bPBCcomAtom = pbc_enum == epComAtom;
930 bNoJump = pbc_enum == epNojump;
931 bCluster = pbc_enum == epCluster;
932 bPBC = pbc_enum != epNone;
933 unitcell_enum = nenum(unitcell_opt);
934 ecenter = nenum(center_opt) - ecTric;
936 /* set and check option dependencies */
939 bFit = TRUE; /* for pfit, fit *must* be set */
943 bReset = TRUE; /* for fit, reset *must* be set */
948 nfitdim = (fit_enum == efFitXY || fit_enum == efResetXY) ? 2 : 3;
950 bRmPBC = bFit || bPBCWhole || bPBCcomRes || bPBCcomMol;
954 if (!(bPBCcomRes || bPBCcomMol || bPBCcomAtom))
957 "WARNING: Option for unitcell representation (-ur %s)\n"
958 " only has effect in combination with -pbc %s, %s or %s.\n"
959 " Ingoring unitcell representation.\n\n",
960 unitcell_opt[0], pbc_opt[2], pbc_opt[3], pbc_opt[4]);
966 gmx_fatal(FARGS, "PBC condition treatment does not work together with rotational fit.\n"
967 "Please do the PBC condition treatment first and then run trjconv in a second step\n"
968 "for the rotational fit.\n"
969 "First doing the rotational fit and then doing the PBC treatment gives incorrect\n"
973 /* ndec is in nr of decimal places, prec is a multiplication factor: */
975 for (i = 0; i < ndec; i++)
980 bIndex = ftp2bSet(efNDX, NFILE, fnm);
983 /* Determine output type */
984 out_file = opt2fn("-o", NFILE, fnm);
985 ftp = fn2ftp(out_file);
986 fprintf(stderr, "Will write %s: %s\n", ftp2ext(ftp), ftp2desc(ftp));
987 bNeedPrec = (ftp == efXTC || ftp == efGRO);
990 /* check if velocities are possible in input and output files */
991 ftpin = fn2ftp(in_file);
992 bVels = (ftp == efTRR || ftp == efTRJ || ftp == efGRO || ftp == efG96)
993 && (ftpin == efTRR || ftpin == efTRJ || ftpin == efGRO || ftpin == efG96 ||
996 if (bSeparate || bSplit)
998 outf_ext = strrchr(out_file, '.');
999 if (outf_ext == NULL)
1001 gmx_fatal(FARGS, "Output file name '%s' does not contain a '.'", out_file);
1003 outf_base = strdup(out_file);
1004 outf_base[outf_ext - out_file] = '\0';
1007 bSubTraj = opt2bSet("-sub", NFILE, fnm);
1010 if ((ftp != efXTC) && (ftp != efTRR))
1012 /* It seems likely that other trajectory file types
1013 * could work here. */
1014 gmx_fatal(FARGS, "Can only use the sub option with output file types "
1017 clust = cluster_index(NULL, opt2fn("-sub", NFILE, fnm));
1019 /* Check for number of files disabled, as FOPEN_MAX is not the correct
1020 * number to check for. In my linux box it is only 16.
1022 if (0 && (clust->clust->nr > FOPEN_MAX-4))
1024 gmx_fatal(FARGS, "Can not open enough (%d) files to write all the"
1025 " trajectories.\ntry splitting the index file in %d parts.\n"
1027 clust->clust->nr, 1+clust->clust->nr/FOPEN_MAX, FOPEN_MAX);
1029 gmx_warning("The -sub option could require as many open output files as there are\n"
1030 "index groups in the file (%d). If you get I/O errors opening new files,\n"
1031 "try reducing the number of index groups in the file, and perhaps\n"
1032 "using trjconv -sub several times on different chunks of your index file.\n",
1035 snew(clust_status, clust->clust->nr);
1036 snew(clust_status_id, clust->clust->nr);
1037 snew(nfwritten, clust->clust->nr);
1038 for (i = 0; (i < clust->clust->nr); i++)
1040 clust_status[i] = NULL;
1041 clust_status_id[i] = -1;
1043 bSeparate = bSplit = FALSE;
1050 /* Determine whether to read a topology */
1051 bTPS = (ftp2bSet(efTPS, NFILE, fnm) ||
1052 bRmPBC || bReset || bPBCcomMol || bCluster ||
1053 (ftp == efGRO) || (ftp == efPDB) || bCONECT);
1055 /* Determine if when can read index groups */
1056 bIndex = (bIndex || bTPS);
1060 read_tps_conf(top_file, top_title, &top, &ePBC, &xp, NULL, top_box,
1061 bReset || bPBCcomRes);
1064 if (0 == top.mols.nr && (bCluster || bPBCcomMol))
1066 gmx_fatal(FARGS, "Option -pbc %s requires a .tpr file for the -s option", pbc_opt[pbc_enum]);
1069 /* top_title is only used for gro and pdb,
1070 * the header in such a file is top_title t= ...
1071 * to prevent a double t=, remove it from top_title
1073 if ((charpt = strstr(top_title, " t= ")))
1080 gc = gmx_conect_generate(&top);
1084 gpbc = gmx_rmpbc_init(&top.idef, ePBC, top.atoms.nr);
1088 /* get frame number index */
1090 if (opt2bSet("-fr", NFILE, fnm))
1092 printf("Select groups of frame number indices:\n");
1093 rd_index(opt2fn("-fr", NFILE, fnm), 1, &nrfri, (atom_id **)&frindex, &frname);
1096 for (i = 0; i < nrfri; i++)
1098 fprintf(debug, "frindex[%4d]=%4d\n", i, frindex[i]);
1103 /* get index groups etc. */
1106 printf("Select group for %s fit\n",
1107 bFit ? "least squares" : "translational");
1108 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
1109 1, &ifit, &ind_fit, &gn_fit);
1115 gmx_fatal(FARGS, "Need at least 2 atoms to fit!\n");
1119 fprintf(stderr, "WARNING: fitting with only 2 atoms is not unique\n");
1125 printf("Select group for clustering\n");
1126 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
1127 1, &ifit, &ind_fit, &gn_fit);
1134 printf("Select group for centering\n");
1135 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
1136 1, &ncent, &cindex, &grpnm);
1138 printf("Select group for output\n");
1139 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
1140 1, &nout, &index, &grpnm);
1144 /* no index file, so read natoms from TRX */
1145 if (!read_first_frame(oenv, &status, in_file, &fr, TRX_DONT_SKIP))
1147 gmx_fatal(FARGS, "Could not read a frame from %s", in_file);
1152 snew(index, natoms);
1153 for (i = 0; i < natoms; i++)
1167 snew(w_rls, atoms->nr);
1168 for (i = 0; (i < ifit); i++)
1170 w_rls[ind_fit[i]] = atoms->atom[ind_fit[i]].m;
1173 /* Restore reference structure and set to origin,
1174 store original location (to put structure back) */
1177 gmx_rmpbc(gpbc, top.atoms.nr, top_box, xp);
1179 copy_rvec(xp[index[0]], x_shift);
1180 reset_x_ndim(nfitdim, ifit, ind_fit, atoms->nr, NULL, xp, w_rls);
1181 rvec_dec(x_shift, xp[index[0]]);
1185 clear_rvec(x_shift);
1188 if (bDropUnder || bDropOver)
1190 /* Read the .xvg file with the drop values */
1191 fprintf(stderr, "\nReading drop file ...");
1192 ndrop = read_xvg(opt2fn("-drop", NFILE, fnm), &dropval, &ncol);
1193 fprintf(stderr, " %d time points\n", ndrop);
1194 if (ndrop == 0 || ncol < 2)
1196 gmx_fatal(FARGS, "Found no data points in %s",
1197 opt2fn("-drop", NFILE, fnm));
1203 /* Make atoms struct for output in GRO or PDB files */
1204 if ((ftp == efGRO) || ((ftp == efG96) && bTPS) || (ftp == efPDB))
1206 /* get memory for stuff to go in .pdb file */
1207 init_t_atoms(&useatoms, atoms->nr, FALSE);
1208 sfree(useatoms.resinfo);
1209 useatoms.resinfo = atoms->resinfo;
1210 for (i = 0; (i < nout); i++)
1212 useatoms.atomname[i] = atoms->atomname[index[i]];
1213 useatoms.atom[i] = atoms->atom[index[i]];
1214 useatoms.nres = max(useatoms.nres, useatoms.atom[i].resind+1);
1218 /* select what to read */
1219 if (ftp == efTRR || ftp == efTRJ)
1229 flags = flags | TRX_READ_V;
1233 flags = flags | TRX_READ_F;
1236 /* open trx file for reading */
1237 bHaveFirstFrame = read_first_frame(oenv, &status, in_file, &fr, flags);
1240 fprintf(stderr, "\nPrecision of %s is %g (nm)\n", in_file, 1/fr.prec);
1244 if (bSetPrec || !fr.bPrec)
1246 fprintf(stderr, "\nSetting output precision to %g (nm)\n", 1/prec);
1250 fprintf(stderr, "Using output precision of %g (nm)\n", 1/prec);
1254 if (bHaveFirstFrame)
1256 set_trxframe_ePBC(&fr, ePBC);
1262 tshift = tzero-fr.time;
1269 /* open output for writing */
1270 if ((bAppend) && (gmx_fexist(out_file)))
1272 strcpy(filemode, "a");
1273 fprintf(stderr, "APPENDING to existing file %s\n", out_file);
1277 strcpy(filemode, "w");
1286 if (!bSplit && !bSubTraj)
1288 trxout = open_trx(out_file, filemode);
1294 if (( !bSeparate && !bSplit ) && !bSubTraj)
1296 out = ffopen(out_file, filemode);
1304 /* check if index is meaningful */
1305 for (i = 0; i < nout; i++)
1307 if (index[i] >= natoms)
1310 "Index[%d] %d is larger than the number of atoms in the\n"
1311 "trajectory file (%d). There is a mismatch in the contents\n"
1312 "of your -f, -s and/or -n files.", i, index[i]+1, natoms);
1314 bCopy = bCopy || (i != index[i]);
1332 fprintf(gmx_fio_getfp(trx_get_fileio(trxout)),
1333 "Generated by %s. #atoms=%d, a BOX is"
1334 " stored in this file.\n", ShortProgram(), nout);
1337 /* Start the big loop over frames */
1344 /* Main loop over frames */
1355 /*if (frame >= clust->clust->nra)
1356 gmx_fatal(FARGS,"There are more frames in the trajectory than in the cluster index file\n");*/
1357 if (frame > clust->maxframe)
1363 my_clust = clust->inv_clust[frame];
1365 if ((my_clust < 0) || (my_clust >= clust->clust->nr) ||
1366 (my_clust == NO_ATID))
1374 /* generate new box */
1376 for (m = 0; m < DIM; m++)
1378 fr.box[m][m] = newbox[m];
1384 for (i = 0; i < natoms; i++)
1386 rvec_inc(fr.x[i], trans);
1392 /* determine timestep */
1405 /* This is not very elegant, as one can not dump a frame after
1406 * a timestep with is more than twice as small as the first one. */
1407 bDumpFrame = (fr.time > tdump-0.5*dt) && (fr.time <= tdump+0.5*dt);
1414 /* determine if an atom jumped across the box and reset it if so */
1415 if (bNoJump && (bTPS || frame != 0))
1417 for (d = 0; d < DIM; d++)
1419 hbox[d] = 0.5*fr.box[d][d];
1421 for (i = 0; i < natoms; i++)
1425 rvec_dec(fr.x[i], x_shift);
1427 for (m = DIM-1; m >= 0; m--)
1431 while (fr.x[i][m]-xp[i][m] <= -hbox[m])
1433 for (d = 0; d <= m; d++)
1435 fr.x[i][d] += fr.box[m][d];
1438 while (fr.x[i][m]-xp[i][m] > hbox[m])
1440 for (d = 0; d <= m; d++)
1442 fr.x[i][d] -= fr.box[m][d];
1451 calc_pbc_cluster(ecenter, ifit, &top, ePBC, fr.x, ind_fit, fr.box);
1456 /* Now modify the coords according to the flags,
1457 for normal fit, this is only done for output frames */
1460 gmx_rmpbc_trxfr(gpbc, &fr);
1463 reset_x_ndim(nfitdim, ifit, ind_fit, natoms, NULL, fr.x, w_rls);
1464 do_fit(natoms, w_rls, xp, fr.x);
1467 /* store this set of coordinates for future use */
1468 if (bPFit || bNoJump)
1474 for (i = 0; (i < natoms); i++)
1476 copy_rvec(fr.x[i], xp[i]);
1477 rvec_inc(fr.x[i], x_shift);
1483 /* see if we have a frame from the frame index group */
1484 for (i = 0; i < nrfri && !bDumpFrame; i++)
1486 bDumpFrame = frame == frindex[i];
1489 if (debug && bDumpFrame)
1491 fprintf(debug, "dumping %d\n", frame);
1495 ( ( !bTDump && !frindex && frame % skip_nr == 0 ) || bDumpFrame );
1497 if (bWriteFrame && (bDropUnder || bDropOver))
1499 while (dropval[0][drop1] < fr.time && drop1+1 < ndrop)
1504 if (fabs(dropval[0][drop0] - fr.time)
1505 < fabs(dropval[0][drop1] - fr.time))
1513 if ((bDropUnder && dropval[1][dropuse] < dropunder) ||
1514 (bDropOver && dropval[1][dropuse] > dropover))
1516 bWriteFrame = FALSE;
1526 fr.time = tzero+frame*timestep;
1536 fprintf(stderr, "\nDumping frame at t= %g %s\n",
1537 output_env_conv_time(oenv, fr.time), output_env_get_time_unit(oenv));
1540 /* check for writing at each delta_t */
1541 bDoIt = (delta_t == 0);
1546 bDoIt = bRmod(fr.time, tzero, delta_t);
1550 /* round() is not C89 compatible, so we do this: */
1551 bDoIt = bRmod(floor(fr.time+0.5), floor(tzero+0.5),
1552 floor(delta_t+0.5));
1556 if (bDoIt || bTDump)
1558 /* print sometimes */
1559 if ( ((outframe % SKIP) == 0) || (outframe < SKIP) )
1561 fprintf(stderr, " -> frame %6d time %8.3f \r",
1562 outframe, output_env_conv_time(oenv, fr.time));
1567 /* Now modify the coords according to the flags,
1568 for PFit we did this already! */
1572 gmx_rmpbc_trxfr(gpbc, &fr);
1577 reset_x_ndim(nfitdim, ifit, ind_fit, natoms, NULL, fr.x, w_rls);
1580 do_fit_ndim(nfitdim, natoms, w_rls, xp, fr.x);
1584 for (i = 0; i < natoms; i++)
1586 rvec_inc(fr.x[i], x_shift);
1593 center_x(ecenter, fr.x, fr.box, natoms, ncent, cindex);
1599 switch (unitcell_enum)
1602 put_atoms_in_box(ePBC, fr.box, natoms, fr.x);
1605 put_atoms_in_triclinic_unitcell(ecenter, fr.box, natoms, fr.x);
1608 warn = put_atoms_in_compact_unitcell(ePBC, ecenter, fr.box,
1610 if (warn && !bWarnCompact)
1612 fprintf(stderr, "\n%s\n", warn);
1613 bWarnCompact = TRUE;
1620 put_residue_com_in_box(unitcell_enum, ecenter,
1621 natoms, atoms->atom, ePBC, fr.box, fr.x);
1625 put_molecule_com_in_box(unitcell_enum, ecenter,
1627 natoms, atoms->atom, ePBC, fr.box, fr.x);
1629 /* Copy the input trxframe struct to the output trxframe struct */
1631 frout.bV = (frout.bV && bVels);
1632 frout.bF = (frout.bF && bForce);
1633 frout.natoms = nout;
1634 if (bNeedPrec && (bSetPrec || !fr.bPrec))
1650 for (i = 0; i < nout; i++)
1652 copy_rvec(fr.x[index[i]], frout.x[i]);
1655 copy_rvec(fr.v[index[i]], frout.v[i]);
1659 copy_rvec(fr.f[index[i]], frout.f[i]);
1664 if (opt2parg_bSet("-shift", NPA, pa))
1666 for (i = 0; i < nout; i++)
1668 for (d = 0; d < DIM; d++)
1670 frout.x[i][d] += outframe*shift[d];
1677 bSplitHere = bSplit && bRmod(fr.time, tzero, split_t);
1681 /* round() is not C89 compatible, so we do this: */
1682 bSplitHere = bSplit && bRmod(floor(fr.time+0.5),
1684 floor(split_t+0.5));
1686 if (bSeparate || bSplitHere)
1688 mk_filenm(outf_base, ftp2ext(ftp), nzero, file_nr, out_file2);
1703 trxout = open_trx(out_file2, filemode);
1710 if (clust_status_id[my_clust] == -1)
1712 sprintf(buf, "%s.%s", clust->grpname[my_clust], ftp2ext(ftp));
1713 clust_status[my_clust] = open_trx(buf, "w");
1714 clust_status_id[my_clust] = 1;
1717 else if (clust_status_id[my_clust] == -2)
1719 gmx_fatal(FARGS, "File %s.xtc should still be open (%d open .xtc files)\n" "in order to write frame %d. my_clust = %d",
1720 clust->grpname[my_clust], ntrxopen, frame,
1723 write_trxframe(clust_status[my_clust], &frout, gc);
1724 nfwritten[my_clust]++;
1725 if (nfwritten[my_clust] ==
1726 (clust->clust->index[my_clust+1]-
1727 clust->clust->index[my_clust]))
1729 close_trx(clust_status[my_clust]);
1730 clust_status[my_clust] = NULL;
1731 clust_status_id[my_clust] = -2;
1735 gmx_fatal(FARGS, "Less than zero open .xtc files!");
1742 write_trxframe(trxout, &frout, gc);
1748 sprintf(title, "Generated by trjconv : %s t= %9.5f",
1749 top_title, fr.time);
1750 if (bSeparate || bSplitHere)
1752 out = ffopen(out_file2, "w");
1757 write_hconf_p(out, title, &useatoms, prec2ndec(frout.prec),
1758 frout.x, frout.bV ? frout.v : NULL, frout.box);
1761 fprintf(out, "REMARK GENERATED BY TRJCONV\n");
1762 sprintf(title, "%s t= %9.5f", top_title, frout.time);
1763 /* if reading from pdb, we want to keep the original
1764 model numbering else we write the output frame
1765 number plus one, because model 0 is not allowed in pdb */
1766 if (ftpin == efPDB && fr.bStep && fr.step > model_nr)
1774 write_pdbfile(out, title, &useatoms, frout.x,
1775 frout.ePBC, frout.box, ' ', model_nr, gc, TRUE);
1778 frout.title = title;
1779 if (bSeparate || bTDump)
1781 frout.bTitle = TRUE;
1784 frout.bAtoms = TRUE;
1786 frout.atoms = &useatoms;
1787 frout.bStep = FALSE;
1788 frout.bTime = FALSE;
1792 frout.bTitle = (outframe == 0);
1793 frout.bAtoms = FALSE;
1797 write_g96_conf(out, &frout, -1, NULL);
1806 gmx_fatal(FARGS, "DHE, ftp=%d\n", ftp);
1808 if (bSeparate || bSplitHere)
1813 /* execute command */
1817 sprintf(c, "%s %d", exec_command, file_nr-1);
1818 /*fprintf(stderr,"Executing '%s'\n",c);*/
1819 #ifdef GMX_NO_SYSTEM
1820 printf("Warning-- No calls to system(3) supported on this platform.");
1821 printf("Warning-- Skipping execution of 'system(\"%s\")'.", c);
1825 gmx_fatal(FARGS, "Error executing command: %s", c);
1833 bHaveNextFrame = read_next_frame(oenv, status, &fr);
1835 while (!(bTDump && bDumpFrame) && bHaveNextFrame);
1838 if (!bHaveFirstFrame || (bTDump && !bDumpFrame))
1840 fprintf(stderr, "\nWARNING no output, "
1841 "last frame read at t=%g\n", fr.time);
1843 fprintf(stderr, "\n");
1850 gmx_rmpbc_done(gpbc);
1857 else if (out != NULL)
1863 for (i = 0; (i < clust->clust->nr); i++)
1865 if (clust_status_id[i] >= 0)
1867 close_trx(clust_status[i]);
1873 do_view(oenv, out_file, NULL);