3 * This source code is part of
7 * GROningen MAchine for Chemical Simulations
10 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
11 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
12 * Copyright (c) 2001-2004, The GROMACS development team,
13 * check out http://www.gromacs.org for more information.
15 * This program is free software; you can redistribute it and/or
16 * modify it under the terms of the GNU General Public License
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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
[])
418 "[TT]trjcat[tt] concatenates several input trajectory files in sorted order. ",
419 "In case of double time frames the one in the later file is used. ",
420 "By specifying [TT]-settime[tt] you will be asked for the start time ",
421 "of each file. The input files are taken from the command line, ",
422 "such that a command like [TT]trjcat -f *.trr -o fixed.trr[tt] should do ",
423 "the trick. Using [TT]-cat[tt], you can simply paste several files ",
424 "together without removal of frames with identical time stamps.[PAR]",
425 "One important option is inferred when the output file is amongst the",
426 "input files. In that case that particular file will be appended to",
427 "which implies you do not need to store double the amount of data.",
428 "Obviously the file to append to has to be the one with lowest starting",
429 "time since one can only append at the end of a file.[PAR]",
430 "If the [TT]-demux[tt] option is given, the N trajectories that are",
431 "read, are written in another order as specified in the [TT].xvg[tt] file.",
432 "The [TT].xvg[tt] file should contain something like:[PAR]",
433 "[TT]0 0 1 2 3 4 5[BR]",
434 "2 1 0 2 3 5 4[tt][BR]",
435 "Where the first number is the time, and subsequent numbers point to",
436 "trajectory indices.",
437 "The frames corresponding to the numbers present at the first line",
438 "are collected into the output trajectory. If the number of frames in",
439 "the trajectory does not match that in the [TT].xvg[tt] file then the program",
440 "tries to be smart. Beware."
442 static gmx_bool bVels
= TRUE
;
444 static gmx_bool bCat
= FALSE
;
445 static gmx_bool bSort
= TRUE
;
446 static gmx_bool bKeepLast
= FALSE
;
447 static gmx_bool bKeepLastAppend
= FALSE
;
448 static gmx_bool bOverwrite
= FALSE
;
449 static gmx_bool bSetTime
= FALSE
;
450 static gmx_bool bDeMux
;
451 static real begin
= -1;
452 static real end
= -1;
458 { "-b", FALSE
, etTIME
,
459 { &begin
}, "First time to use (%t)" },
460 { "-e", FALSE
, etTIME
,
461 { &end
}, "Last time to use (%t)" },
462 { "-dt", FALSE
, etTIME
,
463 { &dt
}, "Only write frame when t MOD dt = first time (%t)" },
464 { "-prec", FALSE
, etINT
,
465 { &prec
}, "Precision for [TT].xtc[tt] and [TT].gro[tt] writing in number of decimal places" },
466 { "-vel", FALSE
, etBOOL
,
467 { &bVels
}, "Read and write velocities if possible" },
468 { "-settime", FALSE
, etBOOL
,
469 { &bSetTime
}, "Change starting time interactively" },
470 { "-sort", FALSE
, etBOOL
,
471 { &bSort
}, "Sort trajectory files (not frames)" },
472 { "-keeplast", FALSE
, etBOOL
,
473 { &bKeepLast
}, "Keep overlapping frames at end of trajectory" },
474 { "-overwrite", FALSE
, etBOOL
,
475 { &bOverwrite
}, "Overwrite overlapping frames during appending" },
476 { "-cat", FALSE
, etBOOL
,
477 { &bCat
}, "Do not discard double time frames" }
479 #define npargs asize(pa)
480 int ftpin
, i
, frame
, frame_out
, step
= 0, trjout
= 0;
484 t_trxframe fr
, frout
;
485 char **fnms
, **fnms_out
, *in_file
, *out_file
;
487 t_trxstatus
*trxout
= NULL
;
488 gmx_bool bNewFile
, bIndex
, bWrite
;
489 int earliersteps
, nfile_in
, nfile_out
, *cont_type
, last_ok_step
;
490 real
*readtime
, *timest
, *settime
;
491 real first_time
= 0, lasttime
= NOTSET
, last_ok_t
= -1, timestep
;
492 real last_frame_time
, searchtime
;
494 atom_id
*index
= NULL
, imax
;
496 real
**val
= NULL
, *t
= NULL
, dt_remd
;
503 { efTRX
, "-f", NULL
, ffRDMULT
},
504 { efTRO
, "-o", NULL
, ffWRMULT
},
505 { efNDX
, "-n", "index", ffOPTRD
},
506 { efXVG
, "-demux", "remd", ffOPTRD
}
509 #define NFILE asize(fnm)
511 parse_common_args(&argc
, argv
, PCA_BE_NICE
| PCA_TIME_UNIT
, NFILE
, fnm
,
512 asize(pa
), pa
, asize(desc
), desc
, 0, NULL
, &oenv
);
514 bIndex
= ftp2bSet(efNDX
, NFILE
, fnm
);
515 bDeMux
= ftp2bSet(efXVG
, NFILE
, fnm
);
516 bSort
= bSort
&& !bDeMux
;
521 printf("Select group for output\n");
522 rd_index(ftp2fn(efNDX
, NFILE
, fnm
), 1, &isize
, &index
, &grpname
);
525 for (i
= 1; i
< isize
; i
++)
527 imax
= max(imax
, index
[i
]);
534 val
= read_xvg_time(opt2fn("-demux", NFILE
, fnm
), TRUE
,
535 opt2parg_bSet("-b", npargs
, pa
), begin
,
536 opt2parg_bSet("-e", npargs
, pa
), end
, 1, &nset
, &n
,
538 printf("Read %d sets of %d points, dt = %g\n\n", nset
, n
, dt_remd
);
541 fprintf(debug
, "Dump of replica_index.xvg\n");
542 for (i
= 0; (i
< n
); i
++)
544 fprintf(debug
, "%10g", t
[i
]);
545 for (j
= 0; (j
< nset
); j
++)
547 fprintf(debug
, " %3d", gmx_nint(val
[j
][i
]));
549 fprintf(debug
, "\n");
553 /* prec is in nr of decimal places, xtcprec is a multiplication factor: */
555 for (i
= 0; i
< prec
; i
++)
560 nfile_in
= opt2fns(&fnms
, "-f", NFILE
, fnm
);
563 gmx_fatal(FARGS
, "No input files!" );
566 if (bDeMux
&& (nfile_in
!= nset
))
568 gmx_fatal(FARGS
, "You have specified %d files and %d entries in the demux table", nfile_in
, nset
);
571 nfile_out
= opt2fns(&fnms_out
, "-o", NFILE
, fnm
);
574 gmx_fatal(FARGS
, "No output files!");
576 if ((nfile_out
> 1) && !bDeMux
)
578 gmx_fatal(FARGS
, "Don't know what to do with more than 1 output file if not demultiplexing");
580 else if (bDeMux
&& (nfile_out
!= nset
) && (nfile_out
!= 1))
582 gmx_fatal(FARGS
, "Number of output files should be 1 or %d (#input files), not %d", nset
, nfile_out
);
586 if (nfile_out
!= nset
)
588 char *buf
= strdup(fnms_out
[0]);
589 snew(fnms_out
, nset
);
590 for (i
= 0; (i
< nset
); i
++)
592 snew(fnms_out
[i
], strlen(buf
)+32);
593 sprintf(fnms_out
[i
], "%d_%s", i
, buf
);
597 do_demux(nfile_in
, fnms
, fnms_out
, n
, val
, t
, dt_remd
, isize
, index
, dt
, oenv
);
601 snew(readtime
, nfile_in
+1);
602 snew(timest
, nfile_in
+1);
603 scan_trj_files(fnms
, nfile_in
, readtime
, timest
, imax
, oenv
);
605 snew(settime
, nfile_in
+1);
606 snew(cont_type
, nfile_in
+1);
607 edit_files(fnms
, nfile_in
, readtime
, timest
, settime
, cont_type
, bSetTime
, bSort
,
610 /* Check whether the output file is amongst the input files
611 * This has to be done after sorting etc.
613 out_file
= fnms_out
[0];
615 for (i
= 0; ((i
< nfile_in
) && (n_append
== -1)); i
++)
617 if (strcmp(fnms
[i
], out_file
) == 0)
624 fprintf(stderr
, "Will append to %s rather than creating a new file\n",
627 else if (n_append
!= -1)
629 gmx_fatal(FARGS
, "Can only append to the first file which is %s (not %s)",
634 /* Not checking input format, could be dangerous :-) */
635 /* Not checking output format, equally dangerous :-) */
639 /* the default is not to change the time at all,
640 * but this is overridden by the edit_files routine
646 trxout
= open_trx(out_file
, "w");
647 memset(&frout
, 0, sizeof(frout
));
653 if (!read_first_frame(oenv
, &status
, out_file
, &fr
, FLAGS
))
655 gmx_fatal(FARGS
, "Reading first frame from %s", out_file
);
658 stfio
= trx_get_fileio(status
);
659 if (!bKeepLast
&& !bOverwrite
)
661 fprintf(stderr
, "\n\nWARNING: Appending without -overwrite implies -keeplast "
662 "between the first two files. \n"
663 "If the trajectories have an overlap and have not been written binary \n"
664 "reproducible this will produce an incorrect trajectory!\n\n");
666 /* Fails if last frame is incomplete
667 * We can't do anything about it without overwriting
669 if (gmx_fio_getftp(stfio
) == efXTC
)
672 xdr_xtc_get_last_frame_time(gmx_fio_getfp(stfio
),
673 gmx_fio_getxdr(stfio
),
678 gmx_fatal(FARGS
, "Error reading last frame. Maybe seek not supported." );
683 while (read_next_frame(oenv
, status
, &fr
))
689 bKeepLastAppend
= TRUE
;
691 trxout
= open_trx(out_file
, "a");
695 if (gmx_fio_getftp(stfio
) != efXTC
)
697 gmx_fatal(FARGS
, "Overwrite only supported for XTC." );
700 xdr_xtc_get_last_frame_time(gmx_fio_getfp(stfio
),
701 gmx_fio_getxdr(stfio
),
705 gmx_fatal(FARGS
, "Error reading last frame. Maybe seek not supported." );
707 /* xtc_seek_time broken for trajectories containing only 1 or 2 frames
708 * or when seek time = 0 */
709 if (nfile_in
> 1 && settime
[1] < last_frame_time
+timest
[0]*0.5)
711 /* Jump to one time-frame before the start of next
713 searchtime
= settime
[1]-timest
[0]*1.25;
717 searchtime
= last_frame_time
;
719 if (xtc_seek_time(stfio
, searchtime
, fr
.natoms
, TRUE
))
721 gmx_fatal(FARGS
, "Error seeking to append position.");
723 read_next_frame(oenv
, status
, &fr
);
724 if (fabs(searchtime
- fr
.time
) > timest
[0]*0.5)
726 gmx_fatal(FARGS
, "Error seeking: attempted to seek to %f but got %f.",
727 searchtime
, fr
.time
);
730 fpos
= gmx_fio_ftell(stfio
);
732 trxout
= open_trx(out_file
, "r+");
733 if (gmx_fio_seek(trx_get_fileio(trxout
), fpos
))
735 gmx_fatal(FARGS
, "Error seeking to append position.");
738 printf("\n Will append after %f \n", lasttime
);
741 /* Lets stitch up some files */
742 timestep
= timest
[0];
743 for (i
= n_append
+1; (i
< nfile_in
); i
++)
747 /* set the next time from the last frame in previous file */
752 if (cont_type
[i
] == TIME_CONTINUE
)
755 begin
+= 0.5*timestep
;
756 settime
[i
] = frout
.time
;
757 cont_type
[i
] = TIME_EXPLICIT
;
759 else if (cont_type
[i
] == TIME_LAST
)
762 begin
+= 0.5*timestep
;
764 /* Or, if the time in the next part should be changed by the
765 * same amount, start at half a timestep from the last time
766 * so we dont repeat frames.
768 /* I don't understand the comment above, but for all the cases
769 * I tried the code seems to work properly. B. Hess 2008-4-2.
772 /* Or, if time is set explicitly, we check for overlap/gap */
773 if (cont_type
[i
] == TIME_EXPLICIT
)
775 if ( ( i
< nfile_in
) &&
776 ( frout
.time
< settime
[i
]-1.5*timestep
) )
778 fprintf(stderr
, "WARNING: Frames around t=%f %s have a different "
779 "spacing than the rest,\n"
780 "might be a gap or overlap that couldn't be corrected "
781 "automatically.\n", output_env_conv_time(oenv
, frout
.time
),
782 output_env_get_time_unit(oenv
));
787 /* if we don't have a timestep in the current file, use the old one */
790 timestep
= timest
[i
];
792 read_first_frame(oenv
, &status
, fnms
[i
], &fr
, FLAGS
);
796 fprintf(stderr
, "\nWARNING: Couldn't find a time in the frame.\n");
799 if (cont_type
[i
] == TIME_EXPLICIT
)
801 t_corr
= settime
[i
]-fr
.time
;
803 /* t_corr is the amount we want to change the time.
804 * If the user has chosen not to change the time for
805 * this part of the trajectory t_corr remains at
806 * the value it had in the last part, changing this
807 * by the same amount.
808 * If no value was given for the first trajectory part
809 * we let the time start at zero, see the edit_files routine.
815 if (lasttime
!= NOTSET
)
817 printf("lasttime %g\n", lasttime
);
822 /* copy the input frame to the output frame */
824 /* set the new time by adding the correct calculated above */
825 frout
.time
+= t_corr
;
826 /* quit if we have reached the end of what should be written */
827 if ((end
> 0) && (frout
.time
> end
+GMX_REAL_EPS
))
833 /* determine if we should write this frame (dt is handled elsewhere) */
834 if (bCat
) /* write all frames of all files */
838 else if (bKeepLast
|| (bKeepLastAppend
&& i
== 1))
839 /* write till last frame of this traj
840 and skip first frame(s) of next traj */
842 bWrite
= ( frout
.time
> lasttime
+0.5*timestep
);
844 else /* write till first frame of next traj */
846 bWrite
= ( frout
.time
< settime
[i
+1]-0.5*timestep
);
849 if (bWrite
&& (frout
.time
>= begin
) )
854 first_time
= frout
.time
;
856 lasttime
= frout
.time
;
857 if (dt
== 0 || bRmod(frout
.time
, first_time
, dt
))
860 last_ok_t
= frout
.time
;
863 fprintf(stderr
, "\nContinue writing frames from %s t=%g %s, "
865 fnms
[i
], output_env_conv_time(oenv
, frout
.time
), output_env_get_time_unit(oenv
),
872 write_trxframe_indexed(trxout
, &frout
, isize
, index
,
877 write_trxframe(trxout
, &frout
, NULL
);
879 if ( ((frame
% 10) == 0) || (frame
< 10) )
881 fprintf(stderr
, " -> frame %6d time %8.3f %s \r",
882 frame_out
, output_env_conv_time(oenv
, frout
.time
), output_env_get_time_unit(oenv
));
887 while (read_next_frame(oenv
, status
, &fr
));
891 earliersteps
+= step
;
897 fprintf(stderr
, "\nLast frame written was %d, time %f %s\n",
898 frame
, output_env_conv_time(oenv
, last_ok_t
), output_env_get_time_unit(oenv
));