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10 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
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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"
49 #include "gromacs/commandline/pargs.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"
59 #include "gromacs/fileio/g87io.h"
62 #include "gromacs/fileio/xdrf.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;
443 static gmx_bool bCat = FALSE;
444 static gmx_bool bSort = TRUE;
445 static gmx_bool bKeepLast = FALSE;
446 static gmx_bool bKeepLastAppend = FALSE;
447 static gmx_bool bOverwrite = FALSE;
448 static gmx_bool bSetTime = FALSE;
449 static gmx_bool bDeMux;
450 static real begin = -1;
451 static real end = -1;
457 { "-b", FALSE, etTIME,
458 { &begin }, "First time to use (%t)" },
459 { "-e", FALSE, etTIME,
460 { &end }, "Last time to use (%t)" },
461 { "-dt", FALSE, etTIME,
462 { &dt }, "Only write frame when t MOD dt = first time (%t)" },
463 { "-prec", FALSE, etINT,
464 { &prec }, "Precision for [TT].xtc[tt] and [TT].gro[tt] writing in number of decimal places" },
465 { "-vel", FALSE, etBOOL,
466 { &bVels }, "Read and write velocities if possible" },
467 { "-settime", FALSE, etBOOL,
468 { &bSetTime }, "Change starting time interactively" },
469 { "-sort", FALSE, etBOOL,
470 { &bSort }, "Sort trajectory files (not frames)" },
471 { "-keeplast", FALSE, etBOOL,
472 { &bKeepLast }, "Keep overlapping frames at end of trajectory" },
473 { "-overwrite", FALSE, etBOOL,
474 { &bOverwrite }, "Overwrite overlapping frames during appending" },
475 { "-cat", FALSE, etBOOL,
476 { &bCat }, "Do not discard double time frames" }
478 #define npargs asize(pa)
479 int ftpin, i, frame, frame_out, step = 0, trjout = 0;
483 t_trxframe fr, frout;
484 char **fnms, **fnms_out, *in_file, *out_file;
486 t_trxstatus *trxout = NULL;
487 gmx_bool bNewFile, bIndex, bWrite;
488 int earliersteps, nfile_in, nfile_out, *cont_type, last_ok_step;
489 real *readtime, *timest, *settime;
490 real first_time = 0, lasttime = NOTSET, last_ok_t = -1, timestep;
491 real last_frame_time, searchtime;
493 atom_id *index = NULL, imax;
495 real **val = NULL, *t = NULL, dt_remd;
502 { efTRX, "-f", NULL, ffRDMULT },
503 { efTRO, "-o", NULL, ffWRMULT },
504 { efNDX, "-n", "index", ffOPTRD },
505 { efXVG, "-demux", "remd", ffOPTRD }
508 #define NFILE asize(fnm)
510 if (!parse_common_args(&argc, argv, PCA_BE_NICE | PCA_TIME_UNIT, NFILE, fnm,
511 asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
516 bIndex = ftp2bSet(efNDX, NFILE, fnm);
517 bDeMux = ftp2bSet(efXVG, NFILE, fnm);
518 bSort = bSort && !bDeMux;
523 printf("Select group for output\n");
524 rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
527 for (i = 1; i < isize; i++)
529 imax = max(imax, index[i]);
536 val = read_xvg_time(opt2fn("-demux", NFILE, fnm), TRUE,
537 opt2parg_bSet("-b", npargs, pa), begin,
538 opt2parg_bSet("-e", npargs, pa), end, 1, &nset, &n,
540 printf("Read %d sets of %d points, dt = %g\n\n", nset, n, dt_remd);
543 fprintf(debug, "Dump of replica_index.xvg\n");
544 for (i = 0; (i < n); i++)
546 fprintf(debug, "%10g", t[i]);
547 for (j = 0; (j < nset); j++)
549 fprintf(debug, " %3d", gmx_nint(val[j][i]));
551 fprintf(debug, "\n");
555 /* prec is in nr of decimal places, xtcprec is a multiplication factor: */
557 for (i = 0; i < prec; i++)
562 nfile_in = opt2fns(&fnms, "-f", NFILE, fnm);
565 gmx_fatal(FARGS, "No input files!" );
568 if (bDeMux && (nfile_in != nset))
570 gmx_fatal(FARGS, "You have specified %d files and %d entries in the demux table", nfile_in, nset);
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];
617 for (i = 0; ((i < nfile_in) && (n_append == -1)); i++)
619 if (strcmp(fnms[i], out_file) == 0)
626 fprintf(stderr, "Will append to %s rather than creating a new file\n",
629 else if (n_append != -1)
631 gmx_fatal(FARGS, "Can only append to the first file which is %s (not %s)",
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
648 trxout = open_trx(out_file, "w");
649 memset(&frout, 0, sizeof(frout));
655 if (!read_first_frame(oenv, &status, out_file, &fr, FLAGS))
657 gmx_fatal(FARGS, "Reading first frame from %s", out_file);
660 stfio = trx_get_fileio(status);
661 if (!bKeepLast && !bOverwrite)
663 fprintf(stderr, "\n\nWARNING: Appending without -overwrite implies -keeplast "
664 "between the first two files. \n"
665 "If the trajectories have an overlap and have not been written binary \n"
666 "reproducible this will produce an incorrect trajectory!\n\n");
668 /* Fails if last frame is incomplete
669 * We can't do anything about it without overwriting
671 if (gmx_fio_getftp(stfio) == efXTC)
674 xdr_xtc_get_last_frame_time(gmx_fio_getfp(stfio),
675 gmx_fio_getxdr(stfio),
680 gmx_fatal(FARGS, "Error reading last frame. Maybe seek not supported." );
685 while (read_next_frame(oenv, status, &fr))
691 bKeepLastAppend = TRUE;
693 trxout = open_trx(out_file, "a");
697 if (gmx_fio_getftp(stfio) != efXTC)
699 gmx_fatal(FARGS, "Overwrite only supported for XTC." );
702 xdr_xtc_get_last_frame_time(gmx_fio_getfp(stfio),
703 gmx_fio_getxdr(stfio),
707 gmx_fatal(FARGS, "Error reading last frame. Maybe seek not supported." );
709 /* xtc_seek_time broken for trajectories containing only 1 or 2 frames
710 * or when seek time = 0 */
711 if (nfile_in > 1 && settime[1] < last_frame_time+timest[0]*0.5)
713 /* Jump to one time-frame before the start of next
715 searchtime = settime[1]-timest[0]*1.25;
719 searchtime = last_frame_time;
721 if (xtc_seek_time(stfio, searchtime, fr.natoms, TRUE))
723 gmx_fatal(FARGS, "Error seeking to append position.");
725 read_next_frame(oenv, status, &fr);
726 if (fabs(searchtime - fr.time) > timest[0]*0.5)
728 gmx_fatal(FARGS, "Error seeking: attempted to seek to %f but got %f.",
729 searchtime, fr.time);
732 fpos = gmx_fio_ftell(stfio);
734 trxout = open_trx(out_file, "r+");
735 if (gmx_fio_seek(trx_get_fileio(trxout), fpos))
737 gmx_fatal(FARGS, "Error seeking to append position.");
740 printf("\n Will append after %f \n", lasttime);
743 /* Lets stitch up some files */
744 timestep = timest[0];
745 for (i = n_append+1; (i < nfile_in); i++)
749 /* set the next time from the last frame in previous file */
754 if (cont_type[i] == TIME_CONTINUE)
757 begin += 0.5*timestep;
758 settime[i] = frout.time;
759 cont_type[i] = TIME_EXPLICIT;
761 else if (cont_type[i] == TIME_LAST)
764 begin += 0.5*timestep;
766 /* Or, if the time in the next part should be changed by the
767 * same amount, start at half a timestep from the last time
768 * so we dont repeat frames.
770 /* I don't understand the comment above, but for all the cases
771 * I tried the code seems to work properly. B. Hess 2008-4-2.
774 /* Or, if time is set explicitly, we check for overlap/gap */
775 if (cont_type[i] == TIME_EXPLICIT)
777 if ( ( i < nfile_in ) &&
778 ( frout.time < settime[i]-1.5*timestep ) )
780 fprintf(stderr, "WARNING: Frames around t=%f %s have a different "
781 "spacing than the rest,\n"
782 "might be a gap or overlap that couldn't be corrected "
783 "automatically.\n", output_env_conv_time(oenv, frout.time),
784 output_env_get_time_unit(oenv));
789 /* if we don't have a timestep in the current file, use the old one */
792 timestep = timest[i];
794 read_first_frame(oenv, &status, fnms[i], &fr, FLAGS);
798 fprintf(stderr, "\nWARNING: Couldn't find a time in the frame.\n");
801 if (cont_type[i] == TIME_EXPLICIT)
803 t_corr = settime[i]-fr.time;
805 /* t_corr is the amount we want to change the time.
806 * If the user has chosen not to change the time for
807 * this part of the trajectory t_corr remains at
808 * the value it had in the last part, changing this
809 * by the same amount.
810 * If no value was given for the first trajectory part
811 * we let the time start at zero, see the edit_files routine.
817 if (lasttime != NOTSET)
819 printf("lasttime %g\n", lasttime);
824 /* copy the input frame to the output frame */
826 /* set the new time by adding the correct calculated above */
827 frout.time += t_corr;
828 /* quit if we have reached the end of what should be written */
829 if ((end > 0) && (frout.time > end+GMX_REAL_EPS))
835 /* determine if we should write this frame (dt is handled elsewhere) */
836 if (bCat) /* write all frames of all files */
840 else if (bKeepLast || (bKeepLastAppend && i == 1))
841 /* write till last frame of this traj
842 and skip first frame(s) of next traj */
844 bWrite = ( frout.time > lasttime+0.5*timestep );
846 else /* write till first frame of next traj */
848 bWrite = ( frout.time < settime[i+1]-0.5*timestep );
851 if (bWrite && (frout.time >= begin) )
856 first_time = frout.time;
858 lasttime = frout.time;
859 if (dt == 0 || bRmod(frout.time, first_time, dt))
862 last_ok_t = frout.time;
865 fprintf(stderr, "\nContinue writing frames from %s t=%g %s, "
867 fnms[i], output_env_conv_time(oenv, frout.time), output_env_get_time_unit(oenv),
874 write_trxframe_indexed(trxout, &frout, isize, index,
879 write_trxframe(trxout, &frout, NULL);
881 if ( ((frame % 10) == 0) || (frame < 10) )
883 fprintf(stderr, " -> frame %6d time %8.3f %s \r",
884 frame_out, output_env_conv_time(oenv, frout.time), output_env_get_time_unit(oenv));
889 while (read_next_frame(oenv, status, &fr));
893 earliersteps += step;
899 fprintf(stderr, "\nLast frame written was %d, time %f %s\n",
900 frame, output_env_conv_time(oenv, last_ok_t), output_env_get_time_unit(oenv));