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46 #include "gromacs/commandline/pargs.h"
47 #include "gromacs/fileio/confio.h"
48 #include "gromacs/fileio/gmxfio.h"
49 #include "gromacs/fileio/pdbio.h"
50 #include "gromacs/fileio/tngio.h"
51 #include "gromacs/fileio/trxio.h"
52 #include "gromacs/fileio/xtcio.h"
53 #include "gromacs/fileio/xvgr.h"
54 #include "gromacs/gmxana/gmx_ana.h"
55 #include "gromacs/math/vec.h"
56 #include "gromacs/mdtypes/md_enums.h"
57 #include "gromacs/topology/index.h"
58 #include "gromacs/trajectory/trajectoryframe.h"
59 #include "gromacs/utility/arrayref.h"
60 #include "gromacs/utility/arraysize.h"
61 #include "gromacs/utility/fatalerror.h"
62 #include "gromacs/utility/futil.h"
63 #include "gromacs/utility/smalloc.h"
64 #include "gromacs/utility/stringutil.h"
66 #define TIME_EXPLICIT 0
67 #define TIME_CONTINUE 1
72 #define FLAGS (TRX_READ_X | TRX_READ_V | TRX_READ_F)
74 static void scan_trj_files(gmx::ArrayRef<const std::string> files,
76 real *timestep, int imax,
77 const gmx_output_env_t *oenv)
79 /* Check start time of all files */
85 for (gmx::index i = 0; i < files.size(); i++)
87 ok = read_first_frame(oenv, &status, files[i].c_str(), &fr, FLAGS);
91 gmx_fatal(FARGS, "\nCouldn't read frame from file." );
95 readtime[i] = fr.time;
100 fprintf(stderr, "\nWARNING: Couldn't find a time in the frame.\n");
111 if (natoms != fr.natoms)
113 gmx_fatal(FARGS, "\nDifferent numbers of atoms (%d/%d) in files",
119 if (fr.natoms <= imax)
121 gmx_fatal(FARGS, "\nNot enough atoms (%d) for index group (%d)",
126 ok = read_next_frame(oenv, status, &fr);
129 timestep[i] = fr.time - readtime[i];
150 fprintf(stderr, "\n");
154 static void sort_files(gmx::ArrayRef<std::string> files, real *settime)
156 for (gmx::index i = 0; i < files.size(); i++)
158 gmx::index minidx = i;
159 for (gmx::index j = i + 1; j < files.size(); j++)
161 if (settime[j] < settime[minidx])
168 real timeswap = settime[i];
169 settime[i] = settime[minidx];
170 settime[minidx] = timeswap;
171 std::swap(files[i], files[minidx]);
176 static void edit_files(gmx::ArrayRef<std::string> files,
177 real *readtime, real *timestep,
178 real *settime, int *cont_type, gmx_bool bSetTime,
179 gmx_bool bSort, const gmx_output_env_t *oenv)
182 char inputstring[STRLEN], *chptr;
184 auto timeUnit = output_env_get_time_unit(oenv);
187 fprintf(stderr, "\n\nEnter the new start time (%s) for each file.\n"
188 "There are two special options, both disable sorting:\n\n"
189 "c (continue) - The start time is taken from the end\n"
190 "of the previous file. Use it when your continuation run\n"
191 "restarts with t=0.\n\n"
192 "l (last) - The time in this file will be changed the\n"
193 "same amount as in the previous. Use it when the time in the\n"
194 "new run continues from the end of the previous one,\n"
195 "since this takes possible overlap into account.\n\n",
200 " File Current start (%s) New start (%s)\n"
201 "---------------------------------------------------------\n",
202 timeUnit.c_str(), timeUnit.c_str());
204 for (gmx::index i = 0; i < files.size(); i++)
206 fprintf(stderr, "%25s %10.3f %s ", files[i].c_str(),
207 output_env_conv_time(oenv, readtime[i]), timeUnit.c_str());
211 if (nullptr == fgets(inputstring, STRLEN - 1, stdin))
213 gmx_fatal(FARGS, "Error reading user input" );
216 inputstring[std::strlen(inputstring)-1] = 0;
218 if (inputstring[0] == 'c' || inputstring[0] == 'C')
220 cont_type[i] = TIME_CONTINUE;
223 settime[i] = FLT_MAX;
225 else if (inputstring[0] == 'l' ||
226 inputstring[0] == 'L')
228 cont_type[i] = TIME_LAST;
231 settime[i] = FLT_MAX;
235 settime[i] = strtod(inputstring, &chptr)*
236 output_env_get_time_invfactor(oenv);
237 if (chptr == inputstring)
239 fprintf(stderr, "'%s' not recognized as a floating point number, 'c' or 'l'. "
240 "Try again: ", inputstring);
244 cont_type[i] = TIME_EXPLICIT;
251 if (cont_type[0] != TIME_EXPLICIT)
253 cont_type[0] = TIME_EXPLICIT;
259 for (gmx::index i = 0; i < files.size(); i++)
261 settime[i] = readtime[i];
266 fprintf(stderr, "Sorting disabled.\n");
270 sort_files(files, settime);
272 /* Write out the new order and start times */
273 fprintf(stderr, "\nSummary of files and start times used:\n\n"
274 " File Start time Time step\n"
275 "---------------------------------------------------------\n");
276 for (gmx::index i = 0; i < files.size(); i++)
278 switch (cont_type[i])
281 fprintf(stderr, "%25s %10.3f %s %10.3f %s",
283 output_env_conv_time(oenv, settime[i]), timeUnit.c_str(),
284 output_env_conv_time(oenv, timestep[i]), timeUnit.c_str());
286 cont_type[i-1] == TIME_EXPLICIT && settime[i] == settime[i-1])
288 fprintf(stderr, " WARNING: same Start time as previous");
290 fprintf(stderr, "\n");
293 fprintf(stderr, "%25s Continue from last file\n", files[i].c_str());
296 fprintf(stderr, "%25s Change by same amount as last file\n",
301 fprintf(stderr, "\n");
303 settime[files.size()] = FLT_MAX;
304 cont_type[files.size()] = TIME_EXPLICIT;
305 readtime[files.size()] = FLT_MAX;
308 static void do_demux(gmx::ArrayRef<const std::string> inFiles,
309 gmx::ArrayRef<const std::string> outFiles, int nval,
310 real **value, real *time, real dt_remd, int isize,
311 int index[], real dt, const gmx_output_env_t *oenv)
314 t_trxstatus **fp_in, **fp_out;
315 gmx_bool bCont, *bSet;
316 real t, first_time = 0;
319 snew(fp_in, inFiles.size());
320 snew(trx, inFiles.size());
321 snew(bSet, inFiles.size());
324 for (gmx::index i = 0; i < inFiles.size(); i++)
326 read_first_frame(oenv, &(fp_in[i]), inFiles[i].c_str(), &(trx[i]),
330 natoms = trx[i].natoms;
331 first_time = trx[i].time;
333 else if (natoms != trx[i].natoms)
335 gmx_fatal(FARGS, "Trajectory file %s has %d atoms while previous trajs had %d atoms", inFiles[i].c_str(), trx[i].natoms, natoms);
341 else if (t != trx[i].time)
343 gmx_fatal(FARGS, "Trajectory file %s has time %f while previous trajs had time %f", inFiles[i].c_str(), trx[i].time, t);
347 snew(fp_out, inFiles.size());
348 for (gmx::index i = 0; i < inFiles.size(); i++)
350 fp_out[i] = open_trx(outFiles[i].c_str(), "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 (gmx::index i = 0; i < inFiles.size(); i++)
371 for (gmx::index i = 0; i < inFiles.size(); i++)
373 int j = std::round(value[i][k]);
374 range_check(j, 0, inFiles.size());
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 (gmx::index i = 0; i < inFiles.size(); i++)
398 bCont = bCont && read_next_frame(oenv, fp_in[i], &trx[i]);
403 for (gmx::index i = 0; i < inFiles.size(); 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;
477 gmx_bool bNewFile, bIndex, bWrite;
479 real *readtime, *timest, *settime;
480 real first_time = 0, lasttime = 0, last_ok_t = -1, timestep;
481 gmx_bool lastTimeSet = FALSE;
482 real last_frame_time, searchtime;
484 int *index = nullptr, imax;
486 real **val = nullptr, *t = nullptr, dt_remd;
487 int n, nset, ftpout = -1, prevEndStep = 0, filetype;
489 gmx_output_env_t *oenv;
492 { efTRX, "-f", nullptr, ffRDMULT },
493 { efTRO, "-o", nullptr, ffWRMULT },
494 { efNDX, "-n", "index", ffOPTRD },
495 { efXVG, "-demux", "remd", ffOPTRD }
498 #define NFILE asize(fnm)
500 if (!parse_common_args(&argc, argv, PCA_TIME_UNIT, NFILE, fnm,
501 asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
505 auto timeUnit = output_env_get_time_unit(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 gmx::ArrayRef<const std::string> inFiles = opt2fns("-f", NFILE, fnm);
550 gmx_fatal(FARGS, "No input files!" );
553 if (bDeMux && static_cast<int>(inFiles.size()) != nset)
555 gmx_fatal(FARGS, "You have specified %zu files and %d entries in the demux table", inFiles.size(), nset);
558 ftpin = fn2ftp(inFiles[0].c_str());
560 if (ftpin != efTRR && ftpin != efXTC && ftpin != efTNG)
562 gmx_fatal(FARGS, "gmx trjcat can only handle binary trajectory formats (trr, xtc, tng)");
565 for (const std::string &inFile : inFiles)
567 if (ftpin != fn2ftp(inFile.c_str()))
569 gmx_fatal(FARGS, "All input files must be of the same (trr, xtc or tng) format");
573 gmx::ArrayRef<const std::string> outFiles = opt2fns("-o", NFILE, fnm);
574 if (outFiles.empty())
576 gmx_fatal(FARGS, "No output files!");
578 if ((outFiles.size() > 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 && static_cast<int>(outFiles.size()) != nset && outFiles.size() != 1)
584 gmx_fatal(FARGS, "Number of output files should be 1 or %d (#input files), not %zu", nset, outFiles.size());
588 auto outFilesDemux = gmx::copyOf(outFiles);
589 if (static_cast<int>(outFilesDemux.size()) != nset)
591 std::string name = outFilesDemux[0];
592 outFilesDemux.resize(nset);
593 for (i = 0; (i < nset); i++)
595 outFilesDemux[0] = gmx::formatString("%d_%s", i, name.c_str());
598 do_demux(inFiles, outFilesDemux, n, val, t, dt_remd, isize, index, dt, oenv);
602 snew(readtime, inFiles.size() + 1);
603 snew(timest, inFiles.size() + 1);
604 scan_trj_files(inFiles, readtime, timest, imax, oenv);
606 snew(settime, inFiles.size() + 1);
607 snew(cont_type, inFiles.size() + 1);
608 auto inFilesEdited = gmx::copyOf(inFiles);
609 edit_files(inFilesEdited, 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 const char *out_file = outFiles[0].c_str();
616 ftpout = fn2ftp(out_file);
618 for (size_t i = 0; i < inFilesEdited.size() && n_append == -1; i++)
620 if (std::strcmp(inFilesEdited[i].c_str(), 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)",
633 inFilesEdited[0].c_str(), out_file);
636 /* Not checking input format, could be dangerous :-) */
637 /* Not checking output format, equally dangerous :-) */
641 /* the default is not to change the time at all,
642 * but this is overridden by the edit_files routine
652 gmx_fatal(FARGS, "When writing TNG the input file format must also be TNG");
656 trxout = trjtools_gmx_prepare_tng_writing(out_file, 'w', nullptr,
657 inFilesEdited[0].c_str(), isize, nullptr, index, grpname);
661 trxout = trjtools_gmx_prepare_tng_writing(out_file, 'w', nullptr,
662 inFilesEdited[0].c_str(), -1, nullptr, nullptr, nullptr);
667 trxout = open_trx(out_file, "w");
669 std::memset(&frout, 0, sizeof(frout));
675 if (!read_first_frame(oenv, &status, out_file, &fr, FLAGS))
677 gmx_fatal(FARGS, "Reading first frame from %s", out_file);
680 stfio = trx_get_fileio(status);
681 if (!bKeepLast && !bOverwrite)
683 fprintf(stderr, "\n\nWARNING: Appending without -overwrite implies -keeplast "
684 "between the first two files. \n"
685 "If the trajectories have an overlap and have not been written binary \n"
686 "reproducible this will produce an incorrect trajectory!\n\n");
688 filetype = gmx_fio_getftp(stfio);
689 /* Fails if last frame is incomplete
690 * We can't do anything about it without overwriting
692 if (filetype == efXTC || filetype == efTNG)
694 lasttime = trx_get_time_of_final_frame(status);
699 while (read_next_frame(oenv, status, &fr))
706 bKeepLastAppend = TRUE;
708 trxout = open_trx(out_file, "a");
712 if (gmx_fio_getftp(stfio) != efXTC)
714 gmx_fatal(FARGS, "Overwrite only supported for XTC." );
716 last_frame_time = trx_get_time_of_final_frame(status);
718 /* xtc_seek_time broken for trajectories containing only 1 or 2 frames
719 * or when seek time = 0 */
720 if (inFilesEdited.size() > 1 && settime[1] < last_frame_time+timest[0]*0.5)
722 /* Jump to one time-frame before the start of next
724 searchtime = settime[1]-timest[0]*1.25;
728 searchtime = last_frame_time;
730 if (xtc_seek_time(stfio, searchtime, fr.natoms, TRUE))
732 gmx_fatal(FARGS, "Error seeking to append position.");
734 read_next_frame(oenv, status, &fr);
735 if (std::abs(searchtime - fr.time) > timest[0]*0.5)
737 gmx_fatal(FARGS, "Error seeking: attempted to seek to %f but got %f.",
738 searchtime, fr.time);
742 fpos = gmx_fio_ftell(stfio);
744 trxout = open_trx(out_file, "r+");
745 if (gmx_fio_seek(trx_get_fileio(trxout), fpos))
747 gmx_fatal(FARGS, "Error seeking to append position.");
752 printf("\n Will append after %f \n", lasttime);
756 /* Lets stitch up some files */
757 timestep = timest[0];
758 for (size_t i = n_append + 1; i < inFilesEdited.size(); i++)
762 /* set the next time from the last frame in previous file */
765 /* When writing TNG the step determine which frame to write. Use an
766 * offset to be able to increase steps properly when changing files. */
769 prevEndStep = frout.step;
774 if (cont_type[i] == TIME_CONTINUE)
777 begin += 0.5*timestep;
778 settime[i] = frout.time;
779 cont_type[i] = TIME_EXPLICIT;
781 else if (cont_type[i] == TIME_LAST)
784 begin += 0.5*timestep;
786 /* Or, if the time in the next part should be changed by the
787 * same amount, start at half a timestep from the last time
788 * so we dont repeat frames.
790 /* I don't understand the comment above, but for all the cases
791 * I tried the code seems to work properly. B. Hess 2008-4-2.
794 /* Or, if time is set explicitly, we check for overlap/gap */
795 if (cont_type[i] == TIME_EXPLICIT)
797 if (i < inFilesEdited.size() &&
798 frout.time < settime[i] - 1.5*timestep)
800 fprintf(stderr, "WARNING: Frames around t=%f %s have a different "
801 "spacing than the rest,\n"
802 "might be a gap or overlap that couldn't be corrected "
803 "automatically.\n", output_env_conv_time(oenv, frout.time),
809 /* if we don't have a timestep in the current file, use the old one */
812 timestep = timest[i];
814 read_first_frame(oenv, &status, inFilesEdited[i].c_str(), &fr, FLAGS);
818 fprintf(stderr, "\nWARNING: Couldn't find a time in the frame.\n");
821 if (cont_type[i] == TIME_EXPLICIT)
823 t_corr = settime[i]-fr.time;
825 /* t_corr is the amount we want to change the time.
826 * If the user has chosen not to change the time for
827 * this part of the trajectory t_corr remains at
828 * the value it had in the last part, changing this
829 * by the same amount.
830 * If no value was given for the first trajectory part
831 * we let the time start at zero, see the edit_files routine.
842 printf("lasttime %g\n", lasttime);
846 /* copy the input frame to the output frame */
848 /* set the new time by adding the correct calculated above */
849 frout.time += t_corr;
852 frout.step += prevEndStep;
854 /* quit if we have reached the end of what should be written */
855 if ((end > 0) && (frout.time > end+GMX_REAL_EPS))
857 i = inFilesEdited.size();
861 /* determine if we should write this frame (dt is handled elsewhere) */
862 if (bCat) /* write all frames of all files */
866 else if (bKeepLast || (bKeepLastAppend && i == 1))
867 /* write till last frame of this traj
868 and skip first frame(s) of next traj */
870 bWrite = ( frout.time > lasttime+0.5*timestep );
872 else /* write till first frame of next traj */
874 bWrite = ( frout.time < settime[i+1]-0.5*timestep );
877 if (bWrite && (frout.time >= begin) )
882 first_time = frout.time;
884 lasttime = frout.time;
886 if (dt == 0 || bRmod(frout.time, first_time, dt))
889 last_ok_t = frout.time;
892 fprintf(stderr, "\nContinue writing frames from %s t=%g %s, "
894 inFilesEdited[i].c_str(),
895 output_env_conv_time(oenv, frout.time), timeUnit.c_str(),
902 write_trxframe_indexed(trxout, &frout, isize, index,
907 write_trxframe(trxout, &frout, nullptr);
909 if ( ((frame % 10) == 0) || (frame < 10) )
911 fprintf(stderr, " -> frame %6d time %8.3f %s \r",
912 frame_out, output_env_conv_time(oenv, frout.time), timeUnit.c_str());
918 while (read_next_frame(oenv, status, &fr));
926 fprintf(stderr, "\nLast frame written was %d, time %f %s\n",
927 frame, output_env_conv_time(oenv, last_ok_t), timeUnit.c_str());