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45 #include "gromacs/commandline/pargs.h"
46 #include "gromacs/fileio/confio.h"
47 #include "gromacs/fileio/gmxfio.h"
48 #include "gromacs/fileio/pdbio.h"
49 #include "gromacs/fileio/tngio.h"
50 #include "gromacs/fileio/trxio.h"
51 #include "gromacs/fileio/xtcio.h"
52 #include "gromacs/fileio/xvgr.h"
53 #include "gromacs/gmxana/gmx_ana.h"
54 #include "gromacs/math/vec.h"
55 #include "gromacs/mdtypes/md_enums.h"
56 #include "gromacs/topology/index.h"
57 #include "gromacs/trajectory/trajectoryframe.h"
58 #include "gromacs/utility/arraysize.h"
59 #include "gromacs/utility/fatalerror.h"
60 #include "gromacs/utility/futil.h"
61 #include "gromacs/utility/smalloc.h"
63 #define TIME_EXPLICIT 0
64 #define TIME_CONTINUE 1
69 #define FLAGS (TRX_READ_X | TRX_READ_V | TRX_READ_F)
71 static void scan_trj_files(char **fnms, int nfiles, real *readtime,
72 real *timestep, int imax,
73 const gmx_output_env_t *oenv)
75 /* Check start time of all files */
81 for (i = 0; i < nfiles; i++)
83 ok = read_first_frame(oenv, &status, fnms[i], &fr, FLAGS);
87 gmx_fatal(FARGS, "\nCouldn't read frame from file." );
91 readtime[i] = fr.time;
96 fprintf(stderr, "\nWARNING: Couldn't find a time in the frame.\n");
107 if (natoms != fr.natoms)
109 gmx_fatal(FARGS, "\nDifferent numbers of atoms (%d/%d) in files",
115 if (fr.natoms <= imax)
117 gmx_fatal(FARGS, "\nNot enough atoms (%d) for index group (%d)",
122 ok = read_next_frame(oenv, status, &fr);
125 timestep[i] = fr.time - readtime[i];
146 fprintf(stderr, "\n");
150 static void sort_files(char **fnms, real *settime, int nfile)
156 for (i = 0; i < nfile; i++)
159 for (j = i + 1; j < nfile; j++)
161 if (settime[j] < settime[minidx])
168 timeswap = settime[i];
169 settime[i] = settime[minidx];
170 settime[minidx] = timeswap;
172 fnms[i] = fnms[minidx];
173 fnms[minidx] = chptr;
178 static void edit_files(char **fnms, int nfiles, real *readtime, real *timestep,
179 real *settime, int *cont_type, gmx_bool bSetTime,
180 gmx_bool bSort, const gmx_output_env_t *oenv)
184 char inputstring[STRLEN], *chptr;
188 fprintf(stderr, "\n\nEnter the new start time (%s) for each file.\n"
189 "There are two special options, both disable sorting:\n\n"
190 "c (continue) - The start time is taken from the end\n"
191 "of the previous file. Use it when your continuation run\n"
192 "restarts with t=0.\n\n"
193 "l (last) - The time in this file will be changed the\n"
194 "same amount as in the previous. Use it when the time in the\n"
195 "new run continues from the end of the previous one,\n"
196 "since this takes possible overlap into account.\n\n",
197 output_env_get_time_unit(oenv));
201 " File Current start (%s) New start (%s)\n"
202 "---------------------------------------------------------\n",
203 output_env_get_time_unit(oenv), output_env_get_time_unit(oenv));
205 for (i = 0; i < nfiles; i++)
207 fprintf(stderr, "%25s %10.3f %s ", fnms[i],
208 output_env_conv_time(oenv, readtime[i]), output_env_get_time_unit(oenv));
212 if (nullptr == fgets(inputstring, STRLEN - 1, stdin))
214 gmx_fatal(FARGS, "Error reading user input" );
217 inputstring[std::strlen(inputstring)-1] = 0;
219 if (inputstring[0] == 'c' || inputstring[0] == 'C')
221 cont_type[i] = TIME_CONTINUE;
224 settime[i] = FLT_MAX;
226 else if (inputstring[0] == 'l' ||
227 inputstring[0] == 'L')
229 cont_type[i] = TIME_LAST;
232 settime[i] = FLT_MAX;
236 settime[i] = strtod(inputstring, &chptr)*
237 output_env_get_time_invfactor(oenv);
238 if (chptr == inputstring)
240 fprintf(stderr, "'%s' not recognized as a floating point number, 'c' or 'l'. "
241 "Try again: ", inputstring);
245 cont_type[i] = TIME_EXPLICIT;
252 if (cont_type[0] != TIME_EXPLICIT)
254 cont_type[0] = TIME_EXPLICIT;
260 for (i = 0; i < nfiles; i++)
262 settime[i] = readtime[i];
267 fprintf(stderr, "Sorting disabled.\n");
271 sort_files(fnms, settime, nfiles);
273 /* Write out the new order and start times */
274 fprintf(stderr, "\nSummary of files and start times used:\n\n"
275 " File Start time Time step\n"
276 "---------------------------------------------------------\n");
277 for (i = 0; i < nfiles; i++)
279 switch (cont_type[i])
282 fprintf(stderr, "%25s %10.3f %s %10.3f %s",
284 output_env_conv_time(oenv, settime[i]), output_env_get_time_unit(oenv),
285 output_env_conv_time(oenv, timestep[i]), output_env_get_time_unit(oenv));
287 cont_type[i-1] == TIME_EXPLICIT && settime[i] == settime[i-1])
289 fprintf(stderr, " WARNING: same Start time as previous");
291 fprintf(stderr, "\n");
294 fprintf(stderr, "%25s Continue from last file\n", fnms[i]);
297 fprintf(stderr, "%25s Change by same amount as last file\n",
302 fprintf(stderr, "\n");
304 settime[nfiles] = FLT_MAX;
305 cont_type[nfiles] = TIME_EXPLICIT;
306 readtime[nfiles] = FLT_MAX;
309 static void do_demux(int nset, char *fnms[], char *fnms_out[], int nval,
310 real **value, real *time, real dt_remd, int isize,
311 int index[], real dt, const gmx_output_env_t *oenv)
313 int i, j, k, natoms, nnn;
314 t_trxstatus **fp_in, **fp_out;
315 gmx_bool bCont, *bSet;
316 real t, first_time = 0;
324 for (i = 0; (i < nset); i++)
326 nnn = read_first_frame(oenv, &(fp_in[i]), fnms[i], &(trx[i]),
331 first_time = trx[i].time;
333 else if (natoms != nnn)
335 gmx_fatal(FARGS, "Trajectory file %s has %d atoms while previous trajs had %d atoms", fnms[i], nnn, natoms);
341 else if (t != trx[i].time)
343 gmx_fatal(FARGS, "Trajectory file %s has time %f while previous trajs had time %f", fnms[i], trx[i].time, t);
348 for (i = 0; (i < nset); i++)
350 fp_out[i] = open_trx(fnms_out[i], "w");
353 if (std::round(time[k] - t) != 0)
355 gmx_fatal(FARGS, "First time in demuxing table does not match trajectories");
359 while ((k+1 < nval) && ((trx[0].time - time[k+1]) > dt_remd*0.1))
365 fprintf(debug, "trx[0].time = %g, time[k] = %g\n", trx[0].time, time[k]);
367 for (i = 0; (i < nset); i++)
371 for (i = 0; (i < nset); i++)
373 j = std::round(value[i][k]);
374 range_check(j, 0, nset);
377 gmx_fatal(FARGS, "Demuxing the same replica %d twice at time %f",
382 if (dt == 0 || bRmod(trx[i].time, first_time, dt))
386 write_trxframe_indexed(fp_out[j], &trx[i], isize, index, nullptr);
390 write_trxframe(fp_out[j], &trx[i], nullptr);
396 for (i = 0; (i < nset); i++)
398 bCont = bCont && read_next_frame(oenv, fp_in[i], &trx[i]);
403 for (i = 0; (i < nset); i++)
406 close_trx(fp_out[i]);
410 int gmx_trjcat(int argc, char *argv[])
414 "[THISMODULE] concatenates several input trajectory files in sorted order. ",
415 "In case of double time frames the one in the later file is used. ",
416 "By specifying [TT]-settime[tt] you will be asked for the start time ",
417 "of each file. The input files are taken from the command line, ",
418 "such that a command like [TT]gmx trjcat -f *.trr -o fixed.trr[tt] should do ",
419 "the trick. Using [TT]-cat[tt], you can simply paste several files ",
420 "together without removal of frames with identical time stamps.[PAR]",
421 "One important option is inferred when the output file is amongst the",
422 "input files. In that case that particular file will be appended to",
423 "which implies you do not need to store double the amount of data.",
424 "Obviously the file to append to has to be the one with lowest starting",
425 "time since one can only append at the end of a file.[PAR]",
426 "If the [TT]-demux[tt] option is given, the N trajectories that are",
427 "read, are written in another order as specified in the [REF].xvg[ref] file.",
428 "The [REF].xvg[ref] file should contain something like::",
433 "The first number is the time, and subsequent numbers point to",
434 "trajectory indices.",
435 "The frames corresponding to the numbers present at the first line",
436 "are collected into the output trajectory. If the number of frames in",
437 "the trajectory does not match that in the [REF].xvg[ref] file then the program",
438 "tries to be smart. Beware."
440 static gmx_bool bCat = FALSE;
441 static gmx_bool bSort = TRUE;
442 static gmx_bool bKeepLast = FALSE;
443 static gmx_bool bKeepLastAppend = FALSE;
444 static gmx_bool bOverwrite = FALSE;
445 static gmx_bool bSetTime = FALSE;
446 static gmx_bool bDeMux;
447 static real begin = -1;
448 static real end = -1;
454 { "-b", FALSE, etTIME,
455 { &begin }, "First time to use (%t)" },
456 { "-e", FALSE, etTIME,
457 { &end }, "Last time to use (%t)" },
458 { "-dt", FALSE, etTIME,
459 { &dt }, "Only write frame when t MOD dt = first time (%t)" },
460 { "-settime", FALSE, etBOOL,
461 { &bSetTime }, "Change starting time interactively" },
462 { "-sort", FALSE, etBOOL,
463 { &bSort }, "Sort trajectory files (not frames)" },
464 { "-keeplast", FALSE, etBOOL,
465 { &bKeepLast }, "Keep overlapping frames at end of trajectory" },
466 { "-overwrite", FALSE, etBOOL,
467 { &bOverwrite }, "Overwrite overlapping frames during appending" },
468 { "-cat", FALSE, etBOOL,
469 { &bCat }, "Do not discard double time frames" }
471 #define npargs asize(pa)
472 int ftpin, i, frame, frame_out;
473 t_trxstatus *status, *trxout = nullptr;
475 t_trxframe fr, frout;
476 char **fnms, **fnms_out, *out_file;
478 gmx_bool bNewFile, bIndex, bWrite;
479 int nfile_in, nfile_out, *cont_type;
480 real *readtime, *timest, *settime;
481 real first_time = 0, lasttime, last_ok_t = -1, timestep;
482 gmx_bool lastTimeSet = FALSE;
483 real last_frame_time, searchtime;
485 int *index = nullptr, imax;
487 real **val = nullptr, *t = nullptr, dt_remd;
488 int n, nset, ftpout = -1, prevEndStep = 0, filetype;
490 gmx_output_env_t *oenv;
493 { efTRX, "-f", nullptr, ffRDMULT },
494 { efTRO, "-o", nullptr, ffWRMULT },
495 { efNDX, "-n", "index", ffOPTRD },
496 { efXVG, "-demux", "remd", ffOPTRD }
499 #define NFILE asize(fnm)
501 if (!parse_common_args(&argc, argv, PCA_TIME_UNIT, NFILE, fnm,
502 asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
507 bIndex = ftp2bSet(efNDX, NFILE, fnm);
508 bDeMux = ftp2bSet(efXVG, NFILE, fnm);
509 bSort = bSort && !bDeMux;
514 printf("Select group for output\n");
515 rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
518 for (i = 1; i < isize; i++)
520 imax = std::max(imax, index[i]);
527 val = read_xvg_time(opt2fn("-demux", NFILE, fnm), TRUE,
528 opt2parg_bSet("-b", npargs, pa), begin,
529 opt2parg_bSet("-e", npargs, pa), end, 1, &nset, &n,
531 printf("Read %d sets of %d points, dt = %g\n\n", nset, n, dt_remd);
534 fprintf(debug, "Dump of replica_index.xvg\n");
535 for (i = 0; (i < n); i++)
537 fprintf(debug, "%10g", t[i]);
538 for (j = 0; (j < nset); j++)
540 fprintf(debug, " %3d", static_cast<int>(std::round(val[j][i])));
542 fprintf(debug, "\n");
547 nfile_in = opt2fns(&fnms, "-f", NFILE, fnm);
550 gmx_fatal(FARGS, "No input files!" );
553 if (bDeMux && (nfile_in != nset))
555 gmx_fatal(FARGS, "You have specified %d files and %d entries in the demux table", nfile_in, nset);
558 ftpin = fn2ftp(fnms[0]);
560 for (i = 1; i < nfile_in; i++)
562 if (ftpin != fn2ftp(fnms[i]))
564 gmx_fatal(FARGS, "All input files must be of the same format");
568 nfile_out = opt2fns(&fnms_out, "-o", NFILE, fnm);
571 gmx_fatal(FARGS, "No output files!");
573 if ((nfile_out > 1) && !bDeMux)
575 gmx_fatal(FARGS, "Don't know what to do with more than 1 output file if not demultiplexing");
577 else if (bDeMux && (nfile_out != nset) && (nfile_out != 1))
579 gmx_fatal(FARGS, "Number of output files should be 1 or %d (#input files), not %d", nset, nfile_out);
583 if (nfile_out != nset)
585 char *buf = gmx_strdup(fnms_out[0]);
586 snew(fnms_out, nset);
587 for (i = 0; (i < nset); i++)
589 snew(fnms_out[i], std::strlen(buf)+32);
590 sprintf(fnms_out[i], "%d_%s", i, buf);
594 do_demux(nfile_in, fnms, fnms_out, n, val, t, dt_remd, isize, index, dt, oenv);
598 snew(readtime, nfile_in+1);
599 snew(timest, nfile_in+1);
600 scan_trj_files(fnms, nfile_in, readtime, timest, imax, oenv);
602 snew(settime, nfile_in+1);
603 snew(cont_type, nfile_in+1);
604 edit_files(fnms, nfile_in, readtime, timest, settime, cont_type, bSetTime, bSort,
607 /* Check whether the output file is amongst the input files
608 * This has to be done after sorting etc.
610 out_file = fnms_out[0];
611 ftpout = fn2ftp(out_file);
613 for (i = 0; ((i < nfile_in) && (n_append == -1)); i++)
615 if (std::strcmp(fnms[i], out_file) == 0)
622 fprintf(stderr, "Will append to %s rather than creating a new file\n",
625 else if (n_append != -1)
627 gmx_fatal(FARGS, "Can only append to the first file which is %s (not %s)",
631 /* Not checking input format, could be dangerous :-) */
632 /* Not checking output format, equally dangerous :-) */
636 /* the default is not to change the time at all,
637 * but this is overridden by the edit_files routine
647 gmx_fatal(FARGS, "When writing TNG the input file format must also be TNG");
651 trjtools_gmx_prepare_tng_writing(out_file, 'w', nullptr, &trxout,
652 fnms[0], isize, nullptr, index, grpname);
656 trjtools_gmx_prepare_tng_writing(out_file, 'w', nullptr, &trxout,
657 fnms[0], -1, nullptr, nullptr, nullptr);
662 trxout = open_trx(out_file, "w");
664 std::memset(&frout, 0, sizeof(frout));
670 if (!read_first_frame(oenv, &status, out_file, &fr, FLAGS))
672 gmx_fatal(FARGS, "Reading first frame from %s", out_file);
675 stfio = trx_get_fileio(status);
676 if (!bKeepLast && !bOverwrite)
678 fprintf(stderr, "\n\nWARNING: Appending without -overwrite implies -keeplast "
679 "between the first two files. \n"
680 "If the trajectories have an overlap and have not been written binary \n"
681 "reproducible this will produce an incorrect trajectory!\n\n");
683 filetype = gmx_fio_getftp(stfio);
684 /* Fails if last frame is incomplete
685 * We can't do anything about it without overwriting
687 if (filetype == efXTC || filetype == efTNG)
689 lasttime = trx_get_time_of_final_frame(status);
694 while (read_next_frame(oenv, status, &fr))
701 bKeepLastAppend = TRUE;
703 trxout = open_trx(out_file, "a");
707 if (gmx_fio_getftp(stfio) != efXTC)
709 gmx_fatal(FARGS, "Overwrite only supported for XTC." );
711 last_frame_time = trx_get_time_of_final_frame(status);
713 /* xtc_seek_time broken for trajectories containing only 1 or 2 frames
714 * or when seek time = 0 */
715 if (nfile_in > 1 && settime[1] < last_frame_time+timest[0]*0.5)
717 /* Jump to one time-frame before the start of next
719 searchtime = settime[1]-timest[0]*1.25;
723 searchtime = last_frame_time;
725 if (xtc_seek_time(stfio, searchtime, fr.natoms, TRUE))
727 gmx_fatal(FARGS, "Error seeking to append position.");
729 read_next_frame(oenv, status, &fr);
730 if (std::abs(searchtime - fr.time) > timest[0]*0.5)
732 gmx_fatal(FARGS, "Error seeking: attempted to seek to %f but got %f.",
733 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.");
747 printf("\n Will append after %f \n", lasttime);
751 /* Lets stitch up some files */
752 timestep = timest[0];
753 for (i = n_append+1; (i < nfile_in); i++)
757 /* set the next time from the last frame in previous file */
760 /* When writing TNG the step determine which frame to write. Use an
761 * offset to be able to increase steps properly when changing files. */
764 prevEndStep = frout.step;
769 if (cont_type[i] == TIME_CONTINUE)
772 begin += 0.5*timestep;
773 settime[i] = frout.time;
774 cont_type[i] = TIME_EXPLICIT;
776 else if (cont_type[i] == TIME_LAST)
779 begin += 0.5*timestep;
781 /* Or, if the time in the next part should be changed by the
782 * same amount, start at half a timestep from the last time
783 * so we dont repeat frames.
785 /* I don't understand the comment above, but for all the cases
786 * I tried the code seems to work properly. B. Hess 2008-4-2.
789 /* Or, if time is set explicitly, we check for overlap/gap */
790 if (cont_type[i] == TIME_EXPLICIT)
792 if ( ( i < nfile_in ) &&
793 ( frout.time < settime[i]-1.5*timestep ) )
795 fprintf(stderr, "WARNING: Frames around t=%f %s have a different "
796 "spacing than the rest,\n"
797 "might be a gap or overlap that couldn't be corrected "
798 "automatically.\n", output_env_conv_time(oenv, frout.time),
799 output_env_get_time_unit(oenv));
804 /* if we don't have a timestep in the current file, use the old one */
807 timestep = timest[i];
809 read_first_frame(oenv, &status, fnms[i], &fr, FLAGS);
813 fprintf(stderr, "\nWARNING: Couldn't find a time in the frame.\n");
816 if (cont_type[i] == TIME_EXPLICIT)
818 t_corr = settime[i]-fr.time;
820 /* t_corr is the amount we want to change the time.
821 * If the user has chosen not to change the time for
822 * this part of the trajectory t_corr remains at
823 * the value it had in the last part, changing this
824 * by the same amount.
825 * If no value was given for the first trajectory part
826 * we let the time start at zero, see the edit_files routine.
837 printf("lasttime %g\n", lasttime);
841 /* copy the input frame to the output frame */
843 /* set the new time by adding the correct calculated above */
844 frout.time += t_corr;
847 frout.step += prevEndStep;
849 /* quit if we have reached the end of what should be written */
850 if ((end > 0) && (frout.time > end+GMX_REAL_EPS))
856 /* determine if we should write this frame (dt is handled elsewhere) */
857 if (bCat) /* write all frames of all files */
861 else if (bKeepLast || (bKeepLastAppend && i == 1))
862 /* write till last frame of this traj
863 and skip first frame(s) of next traj */
865 bWrite = ( frout.time > lasttime+0.5*timestep );
867 else /* write till first frame of next traj */
869 bWrite = ( frout.time < settime[i+1]-0.5*timestep );
872 if (bWrite && (frout.time >= begin) )
877 first_time = frout.time;
879 lasttime = frout.time;
881 if (dt == 0 || bRmod(frout.time, first_time, dt))
884 last_ok_t = frout.time;
887 fprintf(stderr, "\nContinue writing frames from %s t=%g %s, "
889 fnms[i], output_env_conv_time(oenv, frout.time), output_env_get_time_unit(oenv),
896 write_trxframe_indexed(trxout, &frout, isize, index,
901 write_trxframe(trxout, &frout, nullptr);
903 if ( ((frame % 10) == 0) || (frame < 10) )
905 fprintf(stderr, " -> frame %6d time %8.3f %s \r",
906 frame_out, output_env_conv_time(oenv, frout.time), output_env_get_time_unit(oenv));
912 while (read_next_frame(oenv, status, &fr));
920 fprintf(stderr, "\nLast frame written was %d, time %f %s\n",
921 frame, output_env_conv_time(oenv, last_ok_t), output_env_get_time_unit(oenv));