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44 #include "gromacs/utility/smalloc.h"
46 #include "gromacs/fileio/gmxfio.h"
47 #include "gromacs/fileio/tpxio.h"
48 #include "gromacs/fileio/trxio.h"
49 #include "gromacs/fileio/trnio.h"
50 #include "gromacs/fileio/tngio.h"
51 #include "gromacs/fileio/tngio_for_tools.h"
52 #include "gromacs/commandline/pargs.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"
60 #include "gromacs/fileio/xvgr.h"
63 #include "gromacs/utility/fatalerror.h"
65 #define TIME_EXPLICIT 0
66 #define TIME_CONTINUE 1
71 #define FLAGS (TRX_READ_X | TRX_READ_V | TRX_READ_F)
73 static void scan_trj_files(char **fnms, int nfiles, real *readtime,
74 real *timestep, atom_id imax,
75 const output_env_t oenv)
77 /* Check start time of all files */
84 for (i = 0; i < nfiles; i++)
86 ok = read_first_frame(oenv, &status, fnms[i], &fr, FLAGS);
90 gmx_fatal(FARGS, "\nCouldn't read frame from file." );
94 readtime[i] = fr.time;
99 fprintf(stderr, "\nWARNING: Couldn't find a time in the frame.\n");
110 if (natoms != fr.natoms)
112 gmx_fatal(FARGS, "\nDifferent numbers of atoms (%d/%d) in files",
118 if (fr.natoms <= imax)
120 gmx_fatal(FARGS, "\nNot enough atoms (%d) for index group (%d)",
125 ok = read_next_frame(oenv, status, &fr);
128 timestep[i] = fr.time - readtime[i];
149 fprintf(stderr, "\n");
153 static void sort_files(char **fnms, real *settime, int nfile)
159 for (i = 0; i < nfile; i++)
162 for (j = i + 1; j < nfile; j++)
164 if (settime[j] < settime[minidx])
171 timeswap = settime[i];
172 settime[i] = settime[minidx];
173 settime[minidx] = timeswap;
175 fnms[i] = fnms[minidx];
176 fnms[minidx] = chptr;
181 static void edit_files(char **fnms, int nfiles, real *readtime, real *timestep,
182 real *settime, int *cont_type, gmx_bool bSetTime,
183 gmx_bool bSort, const output_env_t oenv)
187 char inputstring[STRLEN], *chptr;
191 fprintf(stderr, "\n\nEnter the new start time (%s) for each file.\n"
192 "There are two special options, both disable sorting:\n\n"
193 "c (continue) - The start time is taken from the end\n"
194 "of the previous file. Use it when your continuation run\n"
195 "restarts with t=0.\n\n"
196 "l (last) - The time in this file will be changed the\n"
197 "same amount as in the previous. Use it when the time in the\n"
198 "new run continues from the end of the previous one,\n"
199 "since this takes possible overlap into account.\n\n",
200 output_env_get_time_unit(oenv));
204 " File Current start (%s) New start (%s)\n"
205 "---------------------------------------------------------\n",
206 output_env_get_time_unit(oenv), output_env_get_time_unit(oenv));
208 for (i = 0; i < nfiles; i++)
210 fprintf(stderr, "%25s %10.3f %s ", fnms[i],
211 output_env_conv_time(oenv, readtime[i]), output_env_get_time_unit(oenv));
215 if (NULL == fgets(inputstring, STRLEN - 1, stdin))
217 gmx_fatal(FARGS, "Error reading user input" );
220 inputstring[strlen(inputstring)-1] = 0;
222 if (inputstring[0] == 'c' || inputstring[0] == 'C')
224 cont_type[i] = TIME_CONTINUE;
227 settime[i] = FLT_MAX;
229 else if (inputstring[0] == 'l' ||
230 inputstring[0] == 'L')
232 cont_type[i] = TIME_LAST;
235 settime[i] = FLT_MAX;
239 settime[i] = strtod(inputstring, &chptr)*
240 output_env_get_time_invfactor(oenv);
241 if (chptr == inputstring)
243 fprintf(stderr, "'%s' not recognized as a floating point number, 'c' or 'l'. "
244 "Try again: ", inputstring);
248 cont_type[i] = TIME_EXPLICIT;
255 if (cont_type[0] != TIME_EXPLICIT)
257 cont_type[0] = TIME_EXPLICIT;
263 for (i = 0; i < nfiles; i++)
265 settime[i] = readtime[i];
270 fprintf(stderr, "Sorting disabled.\n");
274 sort_files(fnms, settime, nfiles);
276 /* Write out the new order and start times */
277 fprintf(stderr, "\nSummary of files and start times used:\n\n"
278 " File Start time Time step\n"
279 "---------------------------------------------------------\n");
280 for (i = 0; i < nfiles; i++)
282 switch (cont_type[i])
285 fprintf(stderr, "%25s %10.3f %s %10.3f %s",
287 output_env_conv_time(oenv, settime[i]), output_env_get_time_unit(oenv),
288 output_env_conv_time(oenv, timestep[i]), output_env_get_time_unit(oenv));
290 cont_type[i-1] == TIME_EXPLICIT && settime[i] == settime[i-1])
292 fprintf(stderr, " WARNING: same Start time as previous");
294 fprintf(stderr, "\n");
297 fprintf(stderr, "%25s Continue from last file\n", fnms[i]);
300 fprintf(stderr, "%25s Change by same amount as last file\n",
305 fprintf(stderr, "\n");
307 settime[nfiles] = FLT_MAX;
308 cont_type[nfiles] = TIME_EXPLICIT;
309 readtime[nfiles] = FLT_MAX;
312 static void do_demux(int nset, char *fnms[], char *fnms_out[], int nval,
313 real **value, real *time, real dt_remd, int isize,
314 atom_id index[], real dt, const output_env_t oenv)
316 int i, j, k, natoms, nnn;
317 t_trxstatus **fp_in, **fp_out;
318 gmx_bool bCont, *bSet;
319 real t, first_time = 0;
327 for (i = 0; (i < nset); i++)
329 nnn = read_first_frame(oenv, &(fp_in[i]), fnms[i], &(trx[i]),
334 first_time = trx[i].time;
336 else if (natoms != nnn)
338 gmx_fatal(FARGS, "Trajectory file %s has %d atoms while previous trajs had %d atoms", fnms[i], nnn, natoms);
344 else if (t != trx[i].time)
346 gmx_fatal(FARGS, "Trajectory file %s has time %f while previous trajs had time %f", fnms[i], trx[i].time, t);
351 for (i = 0; (i < nset); i++)
353 fp_out[i] = open_trx(fnms_out[i], "w");
356 if (gmx_nint(time[k] - t) != 0)
358 gmx_fatal(FARGS, "First time in demuxing table does not match trajectories");
362 while ((k+1 < nval) && ((trx[0].time - time[k+1]) > dt_remd*0.1))
368 fprintf(debug, "trx[0].time = %g, time[k] = %g\n", trx[0].time, time[k]);
370 for (i = 0; (i < nset); i++)
374 for (i = 0; (i < nset); i++)
376 j = gmx_nint(value[i][k]);
377 range_check(j, 0, nset);
380 gmx_fatal(FARGS, "Demuxing the same replica %d twice at time %f",
385 if (dt == 0 || bRmod(trx[i].time, first_time, dt))
389 write_trxframe_indexed(fp_out[j], &trx[i], isize, index, NULL);
393 write_trxframe(fp_out[j], &trx[i], NULL);
399 for (i = 0; (i < nset); i++)
401 bCont = bCont && read_next_frame(oenv, fp_in[i], &trx[i]);
406 for (i = 0; (i < nset); i++)
409 close_trx(fp_out[i]);
413 int gmx_trjcat(int argc, char *argv[])
417 "[THISMODULE] concatenates several input trajectory files in sorted order. ",
418 "In case of double time frames the one in the later file is used. ",
419 "By specifying [TT]-settime[tt] you will be asked for the start time ",
420 "of each file. The input files are taken from the command line, ",
421 "such that a command like [TT]gmx trjcat -f *.trr -o fixed.trr[tt] should do ",
422 "the trick. Using [TT]-cat[tt], you can simply paste several files ",
423 "together without removal of frames with identical time stamps.[PAR]",
424 "One important option is inferred when the output file is amongst the",
425 "input files. In that case that particular file will be appended to",
426 "which implies you do not need to store double the amount of data.",
427 "Obviously the file to append to has to be the one with lowest starting",
428 "time since one can only append at the end of a file.[PAR]",
429 "If the [TT]-demux[tt] option is given, the N trajectories that are",
430 "read, are written in another order as specified in the [TT].xvg[tt] file.",
431 "The [TT].xvg[tt] file should contain something like:[PAR]",
432 "[TT]0 0 1 2 3 4 5[BR]",
433 "2 1 0 2 3 5 4[tt][BR]",
434 "Where the first number is the time, and subsequent numbers point to",
435 "trajectory indices.",
436 "The frames corresponding to the numbers present at the first line",
437 "are collected into the output trajectory. If the number of frames in",
438 "the trajectory does not match that in the [TT].xvg[tt] file then the program",
439 "tries to be smart. Beware."
441 static gmx_bool bVels = TRUE;
442 static gmx_bool bCat = FALSE;
443 static gmx_bool bSort = TRUE;
444 static gmx_bool bKeepLast = FALSE;
445 static gmx_bool bKeepLastAppend = FALSE;
446 static gmx_bool bOverwrite = FALSE;
447 static gmx_bool bSetTime = FALSE;
448 static gmx_bool bDeMux;
449 static real begin = -1;
450 static real end = -1;
456 { "-b", FALSE, etTIME,
457 { &begin }, "First time to use (%t)" },
458 { "-e", FALSE, etTIME,
459 { &end }, "Last time to use (%t)" },
460 { "-dt", FALSE, etTIME,
461 { &dt }, "Only write frame when t MOD dt = first time (%t)" },
462 { "-vel", FALSE, etBOOL,
463 { &bVels }, "Read and write velocities if possible" },
464 { "-settime", FALSE, etBOOL,
465 { &bSetTime }, "Change starting time interactively" },
466 { "-sort", FALSE, etBOOL,
467 { &bSort }, "Sort trajectory files (not frames)" },
468 { "-keeplast", FALSE, etBOOL,
469 { &bKeepLast }, "Keep overlapping frames at end of trajectory" },
470 { "-overwrite", FALSE, etBOOL,
471 { &bOverwrite }, "Overwrite overlapping frames during appending" },
472 { "-cat", FALSE, etBOOL,
473 { &bCat }, "Do not discard double time frames" }
475 #define npargs asize(pa)
476 int ftpin, i, frame, frame_out, step = 0, trjout = 0;
477 t_trxstatus *status, *trxout = NULL;
480 t_trxframe fr, frout;
481 char **fnms, **fnms_out, *in_file, *out_file;
483 gmx_bool bNewFile, bIndex, bWrite;
484 int earliersteps, nfile_in, nfile_out, *cont_type, last_ok_step;
485 real *readtime, *timest, *settime;
486 real first_time = 0, lasttime = NOTSET, last_ok_t = -1, timestep;
487 real last_frame_time, searchtime;
489 atom_id *index = NULL, imax;
491 real **val = NULL, *t = NULL, dt_remd;
492 int n, nset, ftpout = -1, prevEndStep = 0, filetype;
498 { efTRX, "-f", NULL, ffRDMULT },
499 { efTRO, "-o", NULL, ffWRMULT },
500 { efNDX, "-n", "index", ffOPTRD },
501 { efXVG, "-demux", "remd", ffOPTRD }
504 #define NFILE asize(fnm)
506 if (!parse_common_args(&argc, argv, PCA_BE_NICE | PCA_TIME_UNIT, NFILE, fnm,
507 asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
512 bIndex = ftp2bSet(efNDX, NFILE, fnm);
513 bDeMux = ftp2bSet(efXVG, NFILE, fnm);
514 bSort = bSort && !bDeMux;
519 printf("Select group for output\n");
520 rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
523 for (i = 1; i < isize; i++)
525 imax = max(imax, index[i]);
532 val = read_xvg_time(opt2fn("-demux", NFILE, fnm), TRUE,
533 opt2parg_bSet("-b", npargs, pa), begin,
534 opt2parg_bSet("-e", npargs, pa), end, 1, &nset, &n,
536 printf("Read %d sets of %d points, dt = %g\n\n", nset, n, dt_remd);
539 fprintf(debug, "Dump of replica_index.xvg\n");
540 for (i = 0; (i < n); i++)
542 fprintf(debug, "%10g", t[i]);
543 for (j = 0; (j < nset); j++)
545 fprintf(debug, " %3d", gmx_nint(val[j][i]));
547 fprintf(debug, "\n");
552 nfile_in = opt2fns(&fnms, "-f", NFILE, fnm);
555 gmx_fatal(FARGS, "No input files!" );
558 if (bDeMux && (nfile_in != nset))
560 gmx_fatal(FARGS, "You have specified %d files and %d entries in the demux table", nfile_in, nset);
563 ftpin = fn2ftp(fnms[0]);
565 for (i = 1; i < nfile_in; i++)
567 if (ftpin != fn2ftp(fnms[i]))
569 gmx_fatal(FARGS, "All input files must be of the same format");
573 nfile_out = opt2fns(&fnms_out, "-o", NFILE, fnm);
576 gmx_fatal(FARGS, "No output files!");
578 if ((nfile_out > 1) && !bDeMux)
580 gmx_fatal(FARGS, "Don't know what to do with more than 1 output file if not demultiplexing");
582 else if (bDeMux && (nfile_out != nset) && (nfile_out != 1))
584 gmx_fatal(FARGS, "Number of output files should be 1 or %d (#input files), not %d", nset, nfile_out);
588 if (nfile_out != nset)
590 char *buf = strdup(fnms_out[0]);
591 snew(fnms_out, nset);
592 for (i = 0; (i < nset); i++)
594 snew(fnms_out[i], strlen(buf)+32);
595 sprintf(fnms_out[i], "%d_%s", i, buf);
599 do_demux(nfile_in, fnms, fnms_out, n, val, t, dt_remd, isize, index, dt, oenv);
603 snew(readtime, nfile_in+1);
604 snew(timest, nfile_in+1);
605 scan_trj_files(fnms, nfile_in, readtime, timest, imax, oenv);
607 snew(settime, nfile_in+1);
608 snew(cont_type, nfile_in+1);
609 edit_files(fnms, nfile_in, readtime, timest, settime, cont_type, bSetTime, bSort,
612 /* Check whether the output file is amongst the input files
613 * This has to be done after sorting etc.
615 out_file = fnms_out[0];
616 ftpout = fn2ftp(out_file);
618 for (i = 0; ((i < nfile_in) && (n_append == -1)); i++)
620 if (strcmp(fnms[i], out_file) == 0)
627 fprintf(stderr, "Will append to %s rather than creating a new file\n",
630 else if (n_append != -1)
632 gmx_fatal(FARGS, "Can only append to the first file which is %s (not %s)",
637 /* Not checking input format, could be dangerous :-) */
638 /* Not checking output format, equally dangerous :-) */
642 /* the default is not to change the time at all,
643 * but this is overridden by the edit_files routine
653 trjtools_gmx_prepare_tng_writing(out_file, 'w', NULL, &trxout,
654 fnms[0], isize, NULL, index, grpname);
658 trjtools_gmx_prepare_tng_writing(out_file, 'w', NULL, &trxout,
659 fnms[0], -1, NULL, NULL, NULL);
664 trxout = open_trx(out_file, "w");
666 memset(&frout, 0, sizeof(frout));
672 if (!read_first_frame(oenv, &status, out_file, &fr, FLAGS))
674 gmx_fatal(FARGS, "Reading first frame from %s", out_file);
677 stfio = trx_get_fileio(status);
678 if (!bKeepLast && !bOverwrite)
680 fprintf(stderr, "\n\nWARNING: Appending without -overwrite implies -keeplast "
681 "between the first two files. \n"
682 "If the trajectories have an overlap and have not been written binary \n"
683 "reproducible this will produce an incorrect trajectory!\n\n");
685 filetype = gmx_fio_getftp(stfio);
686 /* Fails if last frame is incomplete
687 * We can't do anything about it without overwriting
689 if (filetype == efXTC || filetype == efTNG)
691 lasttime = trx_get_time_of_final_frame(status);
696 while (read_next_frame(oenv, status, &fr))
702 bKeepLastAppend = TRUE;
704 trxout = open_trx(out_file, "a");
708 if (gmx_fio_getftp(stfio) != efXTC)
710 gmx_fatal(FARGS, "Overwrite only supported for XTC." );
712 last_frame_time = trx_get_time_of_final_frame(status);
714 /* xtc_seek_time broken for trajectories containing only 1 or 2 frames
715 * or when seek time = 0 */
716 if (nfile_in > 1 && settime[1] < last_frame_time+timest[0]*0.5)
718 /* Jump to one time-frame before the start of next
720 searchtime = settime[1]-timest[0]*1.25;
724 searchtime = last_frame_time;
726 if (xtc_seek_time(stfio, searchtime, fr.natoms, TRUE))
728 gmx_fatal(FARGS, "Error seeking to append position.");
730 read_next_frame(oenv, status, &fr);
731 if (fabs(searchtime - fr.time) > timest[0]*0.5)
733 gmx_fatal(FARGS, "Error seeking: attempted to seek to %f but got %f.",
734 searchtime, fr.time);
737 fpos = gmx_fio_ftell(stfio);
739 trxout = open_trx(out_file, "r+");
740 if (gmx_fio_seek(trx_get_fileio(trxout), fpos))
742 gmx_fatal(FARGS, "Error seeking to append position.");
745 printf("\n Will append after %f \n", lasttime);
748 /* Lets stitch up some files */
749 timestep = timest[0];
750 for (i = n_append+1; (i < nfile_in); i++)
754 /* set the next time from the last frame in previous file */
757 /* When writing TNG the step determine which frame to write. Use an
758 * offset to be able to increase steps properly when changing files. */
761 prevEndStep = frout.step;
766 if (cont_type[i] == TIME_CONTINUE)
769 begin += 0.5*timestep;
770 settime[i] = frout.time;
771 cont_type[i] = TIME_EXPLICIT;
773 else if (cont_type[i] == TIME_LAST)
776 begin += 0.5*timestep;
778 /* Or, if the time in the next part should be changed by the
779 * same amount, start at half a timestep from the last time
780 * so we dont repeat frames.
782 /* I don't understand the comment above, but for all the cases
783 * I tried the code seems to work properly. B. Hess 2008-4-2.
786 /* Or, if time is set explicitly, we check for overlap/gap */
787 if (cont_type[i] == TIME_EXPLICIT)
789 if ( ( i < nfile_in ) &&
790 ( frout.time < settime[i]-1.5*timestep ) )
792 fprintf(stderr, "WARNING: Frames around t=%f %s have a different "
793 "spacing than the rest,\n"
794 "might be a gap or overlap that couldn't be corrected "
795 "automatically.\n", output_env_conv_time(oenv, frout.time),
796 output_env_get_time_unit(oenv));
801 /* if we don't have a timestep in the current file, use the old one */
804 timestep = timest[i];
806 read_first_frame(oenv, &status, fnms[i], &fr, FLAGS);
810 fprintf(stderr, "\nWARNING: Couldn't find a time in the frame.\n");
813 if (cont_type[i] == TIME_EXPLICIT)
815 t_corr = settime[i]-fr.time;
817 /* t_corr is the amount we want to change the time.
818 * If the user has chosen not to change the time for
819 * this part of the trajectory t_corr remains at
820 * the value it had in the last part, changing this
821 * by the same amount.
822 * If no value was given for the first trajectory part
823 * we let the time start at zero, see the edit_files routine.
829 if (lasttime != NOTSET)
831 printf("lasttime %g\n", lasttime);
836 /* copy the input frame to the output frame */
838 /* set the new time by adding the correct calculated above */
839 frout.time += t_corr;
842 frout.step += prevEndStep;
844 /* quit if we have reached the end of what should be written */
845 if ((end > 0) && (frout.time > end+GMX_REAL_EPS))
851 /* determine if we should write this frame (dt is handled elsewhere) */
852 if (bCat) /* write all frames of all files */
856 else if (bKeepLast || (bKeepLastAppend && i == 1))
857 /* write till last frame of this traj
858 and skip first frame(s) of next traj */
860 bWrite = ( frout.time > lasttime+0.5*timestep );
862 else /* write till first frame of next traj */
864 bWrite = ( frout.time < settime[i+1]-0.5*timestep );
867 if (bWrite && (frout.time >= begin) )
872 first_time = frout.time;
874 lasttime = frout.time;
875 if (dt == 0 || bRmod(frout.time, first_time, dt))
878 last_ok_t = frout.time;
881 fprintf(stderr, "\nContinue writing frames from %s t=%g %s, "
883 fnms[i], output_env_conv_time(oenv, frout.time), output_env_get_time_unit(oenv),
890 write_trxframe_indexed(trxout, &frout, isize, index,
895 write_trxframe(trxout, &frout, NULL);
897 if ( ((frame % 10) == 0) || (frame < 10) )
899 fprintf(stderr, " -> frame %6d time %8.3f %s \r",
900 frame_out, output_env_conv_time(oenv, frout.time), output_env_get_time_unit(oenv));
905 while (read_next_frame(oenv, status, &fr));
909 earliersteps += step;
915 fprintf(stderr, "\nLast frame written was %d, time %f %s\n",
916 frame, output_env_conv_time(oenv, last_ok_t), output_env_get_time_unit(oenv));