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47 #include "gromacs/utility/smalloc.h"
49 #include "gromacs/fileio/gmxfio.h"
50 #include "gromacs/fileio/tpxio.h"
51 #include "gromacs/fileio/trxio.h"
52 #include "gromacs/fileio/trnio.h"
53 #include "gromacs/fileio/tngio_for_tools.h"
54 #include "gromacs/commandline/pargs.h"
55 #include "gromacs/utility/futil.h"
56 #include "gromacs/fileio/pdbio.h"
57 #include "gromacs/fileio/confio.h"
60 #include "gromacs/math/vec.h"
61 #include "gromacs/fileio/xtcio.h"
62 #include "gromacs/pbcutil/rmpbc.h"
63 #include "gromacs/pbcutil/pbc.h"
65 #include "gromacs/fileio/xvgr.h"
68 #include "gromacs/math/do_fit.h"
69 #include "gromacs/utility/fatalerror.h"
76 euSel
, euRect
, euTric
, euCompact
, euNR
80 static void calc_pbc_cluster(int ecenter
, int nrefat
, t_topology
*top
, int ePBC
,
81 rvec x
[], atom_id index
[], matrix box
)
83 int m
, i
, j
, j0
, j1
, jj
, ai
, aj
;
86 rvec dx
, xtest
, box_center
;
87 int nmol
, imol_center
;
89 gmx_bool
*bMol
, *bTmp
;
90 rvec
*m_com
, *m_shift
;
98 calc_box_center(ecenter
, box
, box_center
);
100 /* Initiate the pbc structure */
101 memset(&pbc
, 0, sizeof(pbc
));
102 set_pbc(&pbc
, ePBC
, box
);
104 /* Convert atom index to molecular */
106 molind
= top
->mols
.index
;
112 snew(bTmp
, top
->atoms
.nr
);
114 for (i
= 0; (i
< nrefat
); i
++)
116 /* Mark all molecules in the index */
119 /* Binary search assuming the molecules are sorted */
124 if (ai
< molind
[j0
+1])
128 else if (ai
>= molind
[j1
])
135 if (ai
< molind
[jj
+1])
147 /* Double check whether all atoms in all molecules that are marked are part
148 * of the cluster. Simultaneously compute the center of geometry.
150 min_dist2
= 10*sqr(trace(box
));
153 for (i
= 0; i
< nmol
; i
++)
155 for (j
= molind
[i
]; j
< molind
[i
+1]; j
++)
157 if (bMol
[i
] && !bTmp
[j
])
159 gmx_fatal(FARGS
, "Molecule %d marked for clustering but not atom %d in it - check your index!", i
+1, j
+1);
161 else if (!bMol
[i
] && bTmp
[j
])
163 gmx_fatal(FARGS
, "Atom %d marked for clustering but not molecule %d - this is an internal error...", j
+1, i
+1);
167 /* Make molecule whole, move 2nd and higher atom to same periodicity as 1st atom in molecule */
170 pbc_dx(&pbc
, x
[j
], x
[j
-1], dx
);
171 rvec_add(x
[j
-1], dx
, x
[j
]);
173 /* Compute center of geometry of molecule - m_com[i] was zeroed when we did snew() on it! */
174 rvec_inc(m_com
[i
], x
[j
]);
179 /* Normalize center of geometry */
180 fac
= 1.0/(molind
[i
+1]-molind
[i
]);
181 for (m
= 0; (m
< DIM
); m
++)
185 /* Determine which molecule is closest to the center of the box */
186 pbc_dx(&pbc
, box_center
, m_com
[i
], dx
);
187 tmp_r2
= iprod(dx
, dx
);
189 if (tmp_r2
< min_dist2
)
194 cluster
[ncluster
++] = i
;
201 fprintf(stderr
, "No molecules selected in the cluster\n");
204 else if (imol_center
== -1)
206 fprintf(stderr
, "No central molecules could be found\n");
211 added
[nadded
++] = imol_center
;
212 bMol
[imol_center
] = FALSE
;
214 while (nadded
< ncluster
)
216 /* Find min distance between cluster molecules and those remaining to be added */
217 min_dist2
= 10*sqr(trace(box
));
220 /* Loop over added mols */
221 for (i
= 0; i
< nadded
; i
++)
224 /* Loop over all mols */
225 for (j
= 0; j
< ncluster
; j
++)
228 /* check those remaining to be added */
231 pbc_dx(&pbc
, m_com
[aj
], m_com
[ai
], dx
);
232 tmp_r2
= iprod(dx
, dx
);
233 if (tmp_r2
< min_dist2
)
243 /* Add the best molecule */
244 added
[nadded
++] = jmin
;
246 /* Calculate the shift from the ai molecule */
247 pbc_dx(&pbc
, m_com
[jmin
], m_com
[imin
], dx
);
248 rvec_add(m_com
[imin
], dx
, xtest
);
249 rvec_sub(xtest
, m_com
[jmin
], m_shift
[jmin
]);
250 rvec_inc(m_com
[jmin
], m_shift
[jmin
]);
252 for (j
= molind
[jmin
]; j
< molind
[jmin
+1]; j
++)
254 rvec_inc(x
[j
], m_shift
[jmin
]);
256 fprintf(stdout
, "\rClustering iteration %d of %d...", nadded
, ncluster
);
266 fprintf(stdout
, "\n");
269 static void put_molecule_com_in_box(int unitcell_enum
, int ecenter
,
271 int natoms
, t_atom atom
[],
272 int ePBC
, matrix box
, rvec x
[])
276 rvec com
, new_com
, shift
, dx
, box_center
;
281 calc_box_center(ecenter
, box
, box_center
);
282 set_pbc(&pbc
, ePBC
, box
);
285 gmx_fatal(FARGS
, "There are no molecule descriptions. I need a .tpr file for this pbc option.");
287 for (i
= 0; (i
< mols
->nr
); i
++)
292 for (j
= mols
->index
[i
]; (j
< mols
->index
[i
+1] && j
< natoms
); j
++)
295 for (d
= 0; d
< DIM
; d
++)
301 /* calculate final COM */
302 svmul(1.0/mtot
, com
, com
);
304 /* check if COM is outside box */
305 copy_rvec(com
, new_com
);
306 switch (unitcell_enum
)
309 put_atoms_in_box(ePBC
, box
, 1, &new_com
);
312 put_atoms_in_triclinic_unitcell(ecenter
, box
, 1, &new_com
);
315 put_atoms_in_compact_unitcell(ePBC
, ecenter
, box
, 1, &new_com
);
318 rvec_sub(new_com
, com
, shift
);
319 if (norm2(shift
) > 0)
323 fprintf(debug
, "\nShifting position of molecule %d "
324 "by %8.3f %8.3f %8.3f\n", i
+1,
325 shift
[XX
], shift
[YY
], shift
[ZZ
]);
327 for (j
= mols
->index
[i
]; (j
< mols
->index
[i
+1] && j
< natoms
); j
++)
329 rvec_inc(x
[j
], shift
);
335 static void put_residue_com_in_box(int unitcell_enum
, int ecenter
,
336 int natoms
, t_atom atom
[],
337 int ePBC
, matrix box
, rvec x
[])
339 atom_id i
, j
, res_start
, res_end
, res_nat
;
343 rvec box_center
, com
, new_com
, shift
;
345 calc_box_center(ecenter
, box
, box_center
);
351 for (i
= 0; i
< natoms
+1; i
++)
353 if (i
== natoms
|| (presnr
!= atom
[i
].resind
&& presnr
!= NOTSET
))
355 /* calculate final COM */
357 res_nat
= res_end
- res_start
;
358 svmul(1.0/mtot
, com
, com
);
360 /* check if COM is outside box */
361 copy_rvec(com
, new_com
);
362 switch (unitcell_enum
)
365 put_atoms_in_box(ePBC
, box
, 1, &new_com
);
368 put_atoms_in_triclinic_unitcell(ecenter
, box
, 1, &new_com
);
371 put_atoms_in_compact_unitcell(ePBC
, ecenter
, box
, 1, &new_com
);
374 rvec_sub(new_com
, com
, shift
);
379 fprintf(debug
, "\nShifting position of residue %d (atoms %u-%u) "
380 "by %g,%g,%g\n", atom
[res_start
].resind
+1,
381 res_start
+1, res_end
+1, shift
[XX
], shift
[YY
], shift
[ZZ
]);
383 for (j
= res_start
; j
< res_end
; j
++)
385 rvec_inc(x
[j
], shift
);
391 /* remember start of new residue */
398 for (d
= 0; d
< DIM
; d
++)
404 presnr
= atom
[i
].resind
;
409 static void center_x(int ecenter
, rvec x
[], matrix box
, int n
, int nc
, atom_id ci
[])
412 rvec cmin
, cmax
, box_center
, dx
;
416 copy_rvec(x
[ci
[0]], cmin
);
417 copy_rvec(x
[ci
[0]], cmax
);
418 for (i
= 0; i
< nc
; i
++)
421 for (m
= 0; m
< DIM
; m
++)
423 if (x
[ai
][m
] < cmin
[m
])
427 else if (x
[ai
][m
] > cmax
[m
])
433 calc_box_center(ecenter
, box
, box_center
);
434 for (m
= 0; m
< DIM
; m
++)
436 dx
[m
] = box_center
[m
]-(cmin
[m
]+cmax
[m
])*0.5;
439 for (i
= 0; i
< n
; i
++)
446 static void mk_filenm(char *base
, const char *ext
, int ndigit
, int file_nr
,
452 strcpy(out_file
, base
);
463 strncat(out_file
, "00000000000", ndigit
-nd
);
465 sprintf(nbuf
, "%d.", file_nr
);
466 strcat(out_file
, nbuf
);
467 strcat(out_file
, ext
);
470 void check_trn(const char *fn
)
472 if ((fn2ftp(fn
) != efTRJ
) && (fn2ftp(fn
) != efTRR
))
474 gmx_fatal(FARGS
, "%s is not a trajectory file, exiting\n", fn
);
478 #ifndef GMX_NATIVE_WINDOWS
479 void do_trunc(const char *fn
, real t0
)
492 gmx_fatal(FARGS
, "You forgot to set the truncation time");
495 /* Check whether this is a .trj file */
498 in
= open_trn(fn
, "r");
499 fp
= gmx_fio_getfp(in
);
502 fprintf(stderr
, "Sorry, can not trunc %s, truncation of this filetype is not supported\n", fn
);
508 fpos
= gmx_fio_ftell(in
);
510 while (!bStop
&& fread_trnheader(in
, &sh
, &bOK
))
512 fread_htrn(in
, &sh
, NULL
, NULL
, NULL
, NULL
);
513 fpos
= gmx_ftell(fp
);
517 gmx_fseek(fp
, fpos
, SEEK_SET
);
523 fprintf(stderr
, "Do you REALLY want to truncate this trajectory (%s) at:\n"
524 "frame %d, time %g, bytes %ld ??? (type YES if so)\n",
525 fn
, j
, t
, (long int)fpos
);
526 if (1 != scanf("%s", yesno
))
528 gmx_fatal(FARGS
, "Error reading user input");
530 if (strcmp(yesno
, "YES") == 0)
532 fprintf(stderr
, "Once again, I'm gonna DO this...\n");
534 if (0 != truncate(fn
, fpos
))
536 gmx_fatal(FARGS
, "Error truncating file %s", fn
);
541 fprintf(stderr
, "Ok, I'll forget about it\n");
546 fprintf(stderr
, "Already at end of file (t=%g)...\n", t
);
553 /*! \brief Read a full molecular topology if useful and available.
555 * If the input trajectory file is not in TNG format, and the output
556 * file is in TNG format, then we want to try to read a full topology
557 * (if available), so that we can write molecule information to the
558 * output file. The full topology provides better molecule information
559 * than is available from the normal t_topology data used by GROMACS
562 * Also, the t_topology is only read under (different) particular
563 * conditions. If both apply, then a .tpr file might be read
564 * twice. Trying to fix this redundancy while trjconv is still an
565 * all-purpose tool does not seem worthwhile.
567 * Because of the way gmx_prepare_tng_writing is implemented, the case
568 * where the input TNG file has no molecule information will never
569 * lead to an output TNG file having molecule information. Since
570 * molecule information will generally be present if the input TNG
571 * file was written by a GROMACS tool, this seems like reasonable
573 static gmx_mtop_t
*read_mtop_for_tng(const char *tps_file
,
574 const char *input_file
,
575 const char *output_file
)
577 gmx_mtop_t
*mtop
= NULL
;
579 if (fn2bTPX(tps_file
) &&
580 efTNG
!= fn2ftp(input_file
) &&
581 efTNG
== fn2ftp(output_file
))
583 int temp_natoms
= -1;
585 read_tpx(tps_file
, NULL
, NULL
, &temp_natoms
,
586 NULL
, NULL
, NULL
, mtop
);
592 int gmx_trjconv(int argc
, char *argv
[])
594 const char *desc
[] = {
595 "[THISMODULE] can convert trajectory files in many ways:[BR]",
596 "* from one format to another[BR]",
597 "* select a subset of atoms[BR]",
598 "* change the periodicity representation[BR]",
599 "* keep multimeric molecules together[BR]",
600 "* center atoms in the box[BR]",
601 "* fit atoms to reference structure[BR]",
602 "* reduce the number of frames[BR]",
603 "* change the timestamps of the frames ",
604 "([TT]-t0[tt] and [TT]-timestep[tt])[BR]",
605 "* cut the trajectory in small subtrajectories according",
606 "to information in an index file. This allows subsequent analysis of",
607 "the subtrajectories that could, for example, be the result of a",
608 "cluster analysis. Use option [TT]-sub[tt].",
609 "This assumes that the entries in the index file are frame numbers and",
610 "dumps each group in the index file to a separate trajectory file.[BR]",
611 "* select frames within a certain range of a quantity given",
612 "in an [TT].xvg[tt] file.[PAR]",
614 "[gmx-trjcat] is better suited for concatenating multiple trajectory files.",
617 "The following formats are supported for input and output:",
618 "[TT].xtc[tt], [TT].trr[tt], [TT].trj[tt], [TT].gro[tt], [TT].g96[tt]",
620 "The file formats are detected from the file extension.",
621 "The precision of [TT].xtc[tt] and [TT].gro[tt] output is taken from the",
622 "input file for [TT].xtc[tt], [TT].gro[tt] and [TT].pdb[tt],",
623 "and from the [TT]-ndec[tt] option for other input formats. The precision",
624 "is always taken from [TT]-ndec[tt], when this option is set.",
625 "All other formats have fixed precision. [TT].trr[tt] and [TT].trj[tt]",
626 "output can be single or double precision, depending on the precision",
627 "of the [THISMODULE] binary.",
628 "Note that velocities are only supported in",
629 "[TT].trr[tt], [TT].trj[tt], [TT].gro[tt] and [TT].g96[tt] files.[PAR]",
631 "Option [TT]-sep[tt] can be used to write every frame to a separate",
632 "[TT].gro, .g96[tt] or [TT].pdb[tt] file. By default, all frames all written to one file.",
633 "[TT].pdb[tt] files with all frames concatenated can be viewed with",
634 "[TT]rasmol -nmrpdb[tt].[PAR]",
636 "It is possible to select part of your trajectory and write it out",
637 "to a new trajectory file in order to save disk space, e.g. for leaving",
638 "out the water from a trajectory of a protein in water.",
639 "[BB]ALWAYS[bb] put the original trajectory on tape!",
640 "We recommend to use the portable [TT].xtc[tt] format for your analysis",
641 "to save disk space and to have portable files.[PAR]",
643 "There are two options for fitting the trajectory to a reference",
644 "either for essential dynamics analysis, etc.",
645 "The first option is just plain fitting to a reference structure",
646 "in the structure file. The second option is a progressive fit",
647 "in which the first timeframe is fitted to the reference structure ",
648 "in the structure file to obtain and each subsequent timeframe is ",
649 "fitted to the previously fitted structure. This way a continuous",
650 "trajectory is generated, which might not be the case when using the",
651 "regular fit method, e.g. when your protein undergoes large",
652 "conformational transitions.[PAR]",
654 "Option [TT]-pbc[tt] sets the type of periodic boundary condition",
656 "[TT]* mol[tt] puts the center of mass of molecules in the box,",
657 "and requires a run input file to be supplied with [TT]-s[tt].[BR]",
658 "[TT]* res[tt] puts the center of mass of residues in the box.[BR]",
659 "[TT]* atom[tt] puts all the atoms in the box.[BR]",
660 "[TT]* nojump[tt] checks if atoms jump across the box and then puts",
661 "them back. This has the effect that all molecules",
662 "will remain whole (provided they were whole in the initial",
663 "conformation). [BB]Note[bb] that this ensures a continuous trajectory but",
664 "molecules may diffuse out of the box. The starting configuration",
665 "for this procedure is taken from the structure file, if one is",
666 "supplied, otherwise it is the first frame.[BR]",
667 "[TT]* cluster[tt] clusters all the atoms in the selected index",
668 "such that they are all closest to the center of mass of the cluster,",
669 "which is iteratively updated. [BB]Note[bb] that this will only give meaningful",
670 "results if you in fact have a cluster. Luckily that can be checked",
671 "afterwards using a trajectory viewer. Note also that if your molecules",
672 "are broken this will not work either.[BR]",
673 "The separate option [TT]-clustercenter[tt] can be used to specify an",
674 "approximate center for the cluster. This is useful e.g. if you have",
675 "two big vesicles, and you want to maintain their relative positions.[BR]",
676 "[TT]* whole[tt] only makes broken molecules whole.[PAR]",
678 "Option [TT]-ur[tt] sets the unit cell representation for options",
679 "[TT]mol[tt], [TT]res[tt] and [TT]atom[tt] of [TT]-pbc[tt].",
680 "All three options give different results for triclinic boxes and",
681 "identical results for rectangular boxes.",
682 "[TT]rect[tt] is the ordinary brick shape.",
683 "[TT]tric[tt] is the triclinic unit cell.",
684 "[TT]compact[tt] puts all atoms at the closest distance from the center",
685 "of the box. This can be useful for visualizing e.g. truncated octahedra",
686 "or rhombic dodecahedra. The center for options [TT]tric[tt] and [TT]compact[tt]",
687 "is [TT]tric[tt] (see below), unless the option [TT]-boxcenter[tt]",
688 "is set differently.[PAR]",
690 "Option [TT]-center[tt] centers the system in the box. The user can",
691 "select the group which is used to determine the geometrical center.",
692 "Option [TT]-boxcenter[tt] sets the location of the center of the box",
693 "for options [TT]-pbc[tt] and [TT]-center[tt]. The center options are:",
694 "[TT]tric[tt]: half of the sum of the box vectors,",
695 "[TT]rect[tt]: half of the box diagonal,",
696 "[TT]zero[tt]: zero.",
697 "Use option [TT]-pbc mol[tt] in addition to [TT]-center[tt] when you",
698 "want all molecules in the box after the centering.[PAR]",
700 "It is not always possible to use combinations of [TT]-pbc[tt],",
701 "[TT]-fit[tt], [TT]-ur[tt] and [TT]-center[tt] to do exactly what",
702 "you want in one call to [THISMODULE]. Consider using multiple",
703 "calls, and check out the GROMACS website for suggestions.[PAR]",
705 "With [TT]-dt[tt], it is possible to reduce the number of ",
706 "frames in the output. This option relies on the accuracy of the times",
707 "in your input trajectory, so if these are inaccurate use the",
708 "[TT]-timestep[tt] option to modify the time (this can be done",
709 "simultaneously). For making smooth movies, the program [gmx-filter]",
710 "can reduce the number of frames while using low-pass frequency",
711 "filtering, this reduces aliasing of high frequency motions.[PAR]",
713 "Using [TT]-trunc[tt] [THISMODULE] can truncate [TT].trj[tt] in place, i.e.",
714 "without copying the file. This is useful when a run has crashed",
715 "during disk I/O (i.e. full disk), or when two contiguous",
716 "trajectories must be concatenated without having double frames.[PAR]",
718 "Option [TT]-dump[tt] can be used to extract a frame at or near",
719 "one specific time from your trajectory.[PAR]",
721 "Option [TT]-drop[tt] reads an [TT].xvg[tt] file with times and values.",
722 "When options [TT]-dropunder[tt] and/or [TT]-dropover[tt] are set,",
723 "frames with a value below and above the value of the respective options",
724 "will not be written."
740 const char *pbc_opt
[epNR
+ 1] =
742 NULL
, "none", "mol", "res", "atom", "nojump", "cluster", "whole",
747 const char *unitcell_opt
[euNR
+1] =
748 { NULL
, "rect", "tric", "compact", NULL
};
752 ecSel
, ecTric
, ecRect
, ecZero
, ecNR
754 const char *center_opt
[ecNR
+1] =
755 { NULL
, "tric", "rect", "zero", NULL
};
761 efSel
, efNone
, efFit
, efFitXY
, efReset
, efResetXY
, efPFit
, efNR
763 const char *fit
[efNR
+ 1] =
765 NULL
, "none", "rot+trans", "rotxy+transxy", "translation", "transxy",
769 static gmx_bool bSeparate
= FALSE
, bVels
= TRUE
, bForce
= FALSE
, bCONECT
= FALSE
;
770 static gmx_bool bCenter
= FALSE
;
771 static int skip_nr
= 1, ndec
= 3, nzero
= 0;
772 static real tzero
= 0, delta_t
= 0, timestep
= 0, ttrunc
= -1, tdump
= -1, split_t
= 0;
773 static rvec newbox
= {0, 0, 0}, shift
= {0, 0, 0}, trans
= {0, 0, 0};
774 static char *exec_command
= NULL
;
775 static real dropunder
= 0, dropover
= 0;
776 static gmx_bool bRound
= FALSE
;
781 { "-skip", FALSE
, etINT
,
782 { &skip_nr
}, "Only write every nr-th frame" },
783 { "-dt", FALSE
, etTIME
,
785 "Only write frame when t MOD dt = first time (%t)" },
786 { "-round", FALSE
, etBOOL
,
787 { &bRound
}, "Round measurements to nearest picosecond"},
788 { "-dump", FALSE
, etTIME
,
789 { &tdump
}, "Dump frame nearest specified time (%t)" },
790 { "-t0", FALSE
, etTIME
,
792 "Starting time (%t) (default: don't change)" },
793 { "-timestep", FALSE
, etTIME
,
795 "Change time step between input frames (%t)" },
796 { "-pbc", FALSE
, etENUM
,
798 "PBC treatment (see help text for full description)" },
799 { "-ur", FALSE
, etENUM
,
800 { unitcell_opt
}, "Unit-cell representation" },
801 { "-center", FALSE
, etBOOL
,
802 { &bCenter
}, "Center atoms in box" },
803 { "-boxcenter", FALSE
, etENUM
,
804 { center_opt
}, "Center for -pbc and -center" },
805 { "-box", FALSE
, etRVEC
,
807 "Size for new cubic box (default: read from input)" },
808 { "-trans", FALSE
, etRVEC
,
810 "All coordinates will be translated by trans. This "
811 "can advantageously be combined with -pbc mol -ur "
813 { "-shift", FALSE
, etRVEC
,
815 "All coordinates will be shifted by framenr*shift" },
816 { "-fit", FALSE
, etENUM
,
818 "Fit molecule to ref structure in the structure file" },
819 { "-ndec", FALSE
, etINT
,
821 "Precision for .xtc and .gro writing in number of "
823 { "-vel", FALSE
, etBOOL
,
824 { &bVels
}, "Read and write velocities if possible" },
825 { "-force", FALSE
, etBOOL
,
826 { &bForce
}, "Read and write forces if possible" },
827 #ifndef GMX_NATIVE_WINDOWS
828 { "-trunc", FALSE
, etTIME
,
830 "Truncate input trajectory file after this time (%t)" },
832 { "-exec", FALSE
, etSTR
,
834 "Execute command for every output frame with the "
835 "frame number as argument" },
836 { "-split", FALSE
, etTIME
,
838 "Start writing new file when t MOD split = first "
840 { "-sep", FALSE
, etBOOL
,
842 "Write each frame to a separate .gro, .g96 or .pdb "
844 { "-nzero", FALSE
, etINT
,
846 "If the -sep flag is set, use these many digits "
847 "for the file numbers and prepend zeros as needed" },
848 { "-dropunder", FALSE
, etREAL
,
849 { &dropunder
}, "Drop all frames below this value" },
850 { "-dropover", FALSE
, etREAL
,
851 { &dropover
}, "Drop all frames above this value" },
852 { "-conect", FALSE
, etBOOL
,
854 "Add conect records when writing [TT].pdb[tt] files. Useful "
855 "for visualization of non-standard molecules, e.g. "
856 "coarse grained ones" }
858 #define NPA asize(pa)
861 t_trxstatus
*trxout
= NULL
;
863 int ftp
, ftpin
= 0, file_nr
;
864 t_trxframe fr
, frout
;
866 rvec
*xmem
= NULL
, *vmem
= NULL
, *fmem
= NULL
;
867 rvec
*xp
= NULL
, x_shift
, hbox
, box_center
, dx
;
868 real xtcpr
, lambda
, *w_rls
= NULL
;
869 int m
, i
, d
, frame
, outframe
, natoms
, nout
, ncent
, nre
, newstep
= 0, model_nr
;
872 gmx_mtop_t
*mtop
= NULL
;
873 gmx_conect gc
= NULL
;
875 t_atoms
*atoms
= NULL
, useatoms
;
877 atom_id
*index
, *cindex
;
881 int ifit
, irms
, my_clust
= -1;
882 atom_id
*ind_fit
, *ind_rms
;
883 char *gn_fit
, *gn_rms
;
884 t_cluster_ndx
*clust
= NULL
;
885 t_trxstatus
**clust_status
= NULL
;
886 int *clust_status_id
= NULL
;
888 int *nfwritten
= NULL
;
889 int ndrop
= 0, ncol
, drop0
= 0, drop1
= 0, dropuse
= 0;
891 real tshift
= 0, t0
= -1, dt
= 0.001, prec
;
892 gmx_bool bFit
, bFitXY
, bPFit
, bReset
;
894 gmx_rmpbc_t gpbc
= NULL
;
895 gmx_bool bRmPBC
, bPBCWhole
, bPBCcomRes
, bPBCcomMol
, bPBCcomAtom
, bPBC
, bNoJump
, bCluster
;
896 gmx_bool bCopy
, bDoIt
, bIndex
, bTDump
, bSetTime
, bTPS
= FALSE
, bDTset
= FALSE
;
897 gmx_bool bExec
, bTimeStep
= FALSE
, bDumpFrame
= FALSE
, bSetPrec
, bNeedPrec
;
898 gmx_bool bHaveFirstFrame
, bHaveNextFrame
, bSetBox
, bSetUR
, bSplit
= FALSE
;
899 gmx_bool bSubTraj
= FALSE
, bDropUnder
= FALSE
, bDropOver
= FALSE
, bTrans
= FALSE
;
900 gmx_bool bWriteFrame
, bSplitHere
;
901 const char *top_file
, *in_file
, *out_file
= NULL
;
902 char out_file2
[256], *charpt
;
903 char *outf_base
= NULL
;
904 const char *outf_ext
= NULL
;
905 char top_title
[256], title
[256], command
[256], filemode
[5];
907 gmx_bool bWarnCompact
= FALSE
;
912 { efTRX
, "-f", NULL
, ffREAD
},
913 { efTRO
, "-o", NULL
, ffWRITE
},
914 { efTPS
, NULL
, NULL
, ffOPTRD
},
915 { efNDX
, NULL
, NULL
, ffOPTRD
},
916 { efNDX
, "-fr", "frames", ffOPTRD
},
917 { efNDX
, "-sub", "cluster", ffOPTRD
},
918 { efXVG
, "-drop", "drop", ffOPTRD
}
920 #define NFILE asize(fnm)
922 if (!parse_common_args(&argc
, argv
,
923 PCA_CAN_BEGIN
| PCA_CAN_END
| PCA_CAN_VIEW
|
924 PCA_TIME_UNIT
| PCA_BE_NICE
,
925 NFILE
, fnm
, NPA
, pa
, asize(desc
), desc
,
931 top_file
= ftp2fn(efTPS
, NFILE
, fnm
);
934 /* Check command line */
935 in_file
= opt2fn("-f", NFILE
, fnm
);
939 #ifndef GMX_NATIVE_WINDOWS
940 do_trunc(in_file
, ttrunc
);
945 /* mark active cmdline options */
946 bSetBox
= opt2parg_bSet("-box", NPA
, pa
);
947 bSetTime
= opt2parg_bSet("-t0", NPA
, pa
);
948 bSetPrec
= opt2parg_bSet("-ndec", NPA
, pa
);
949 bSetUR
= opt2parg_bSet("-ur", NPA
, pa
);
950 bExec
= opt2parg_bSet("-exec", NPA
, pa
);
951 bTimeStep
= opt2parg_bSet("-timestep", NPA
, pa
);
952 bTDump
= opt2parg_bSet("-dump", NPA
, pa
);
953 bDropUnder
= opt2parg_bSet("-dropunder", NPA
, pa
);
954 bDropOver
= opt2parg_bSet("-dropover", NPA
, pa
);
955 bTrans
= opt2parg_bSet("-trans", NPA
, pa
);
956 bSplit
= (split_t
!= 0);
958 /* parse enum options */
959 fit_enum
= nenum(fit
);
960 bFit
= (fit_enum
== efFit
|| fit_enum
== efFitXY
);
961 bFitXY
= fit_enum
== efFitXY
;
962 bReset
= (fit_enum
== efReset
|| fit_enum
== efResetXY
);
963 bPFit
= fit_enum
== efPFit
;
964 pbc_enum
= nenum(pbc_opt
);
965 bPBCWhole
= pbc_enum
== epWhole
;
966 bPBCcomRes
= pbc_enum
== epComRes
;
967 bPBCcomMol
= pbc_enum
== epComMol
;
968 bPBCcomAtom
= pbc_enum
== epComAtom
;
969 bNoJump
= pbc_enum
== epNojump
;
970 bCluster
= pbc_enum
== epCluster
;
971 bPBC
= pbc_enum
!= epNone
;
972 unitcell_enum
= nenum(unitcell_opt
);
973 ecenter
= nenum(center_opt
) - ecTric
;
975 /* set and check option dependencies */
978 bFit
= TRUE
; /* for pfit, fit *must* be set */
982 bReset
= TRUE
; /* for fit, reset *must* be set */
987 nfitdim
= (fit_enum
== efFitXY
|| fit_enum
== efResetXY
) ? 2 : 3;
989 bRmPBC
= bFit
|| bPBCWhole
|| bPBCcomRes
|| bPBCcomMol
;
993 if (!(bPBCcomRes
|| bPBCcomMol
|| bPBCcomAtom
))
996 "WARNING: Option for unitcell representation (-ur %s)\n"
997 " only has effect in combination with -pbc %s, %s or %s.\n"
998 " Ingoring unitcell representation.\n\n",
999 unitcell_opt
[0], pbc_opt
[2], pbc_opt
[3], pbc_opt
[4]);
1005 gmx_fatal(FARGS
, "PBC condition treatment does not work together with rotational fit.\n"
1006 "Please do the PBC condition treatment first and then run trjconv in a second step\n"
1007 "for the rotational fit.\n"
1008 "First doing the rotational fit and then doing the PBC treatment gives incorrect\n"
1012 /* ndec is in nr of decimal places, prec is a multiplication factor: */
1014 for (i
= 0; i
< ndec
; i
++)
1019 bIndex
= ftp2bSet(efNDX
, NFILE
, fnm
);
1022 /* Determine output type */
1023 out_file
= opt2fn("-o", NFILE
, fnm
);
1024 ftp
= fn2ftp(out_file
);
1025 fprintf(stderr
, "Will write %s: %s\n", ftp2ext(ftp
), ftp2desc(ftp
));
1026 bNeedPrec
= (ftp
== efXTC
|| ftp
== efGRO
);
1029 /* check if velocities are possible in input and output files */
1030 ftpin
= fn2ftp(in_file
);
1031 bVels
= (ftp
== efTRR
|| ftp
== efTRJ
|| ftp
== efGRO
|| ftp
== efG96
)
1032 && (ftpin
== efTRR
|| ftpin
== efTRJ
|| ftpin
== efGRO
|| ftpin
== efG96
||
1035 if (bSeparate
|| bSplit
)
1037 outf_ext
= strrchr(out_file
, '.');
1038 if (outf_ext
== NULL
)
1040 gmx_fatal(FARGS
, "Output file name '%s' does not contain a '.'", out_file
);
1042 outf_base
= strdup(out_file
);
1043 outf_base
[outf_ext
- out_file
] = '\0';
1046 bSubTraj
= opt2bSet("-sub", NFILE
, fnm
);
1049 if ((ftp
!= efXTC
) && (ftp
!= efTRR
))
1051 /* It seems likely that other trajectory file types
1052 * could work here. */
1053 gmx_fatal(FARGS
, "Can only use the sub option with output file types "
1056 clust
= cluster_index(NULL
, opt2fn("-sub", NFILE
, fnm
));
1058 /* Check for number of files disabled, as FOPEN_MAX is not the correct
1059 * number to check for. In my linux box it is only 16.
1061 if (0 && (clust
->clust
->nr
> FOPEN_MAX
-4))
1063 gmx_fatal(FARGS
, "Can not open enough (%d) files to write all the"
1064 " trajectories.\ntry splitting the index file in %d parts.\n"
1066 clust
->clust
->nr
, 1+clust
->clust
->nr
/FOPEN_MAX
, FOPEN_MAX
);
1068 gmx_warning("The -sub option could require as many open output files as there are\n"
1069 "index groups in the file (%d). If you get I/O errors opening new files,\n"
1070 "try reducing the number of index groups in the file, and perhaps\n"
1071 "using trjconv -sub several times on different chunks of your index file.\n",
1074 snew(clust_status
, clust
->clust
->nr
);
1075 snew(clust_status_id
, clust
->clust
->nr
);
1076 snew(nfwritten
, clust
->clust
->nr
);
1077 for (i
= 0; (i
< clust
->clust
->nr
); i
++)
1079 clust_status
[i
] = NULL
;
1080 clust_status_id
[i
] = -1;
1082 bSeparate
= bSplit
= FALSE
;
1089 mtop
= read_mtop_for_tng(top_file
, in_file
, out_file
);
1091 /* Determine whether to read a topology */
1092 bTPS
= (ftp2bSet(efTPS
, NFILE
, fnm
) ||
1093 bRmPBC
|| bReset
|| bPBCcomMol
|| bCluster
||
1094 (ftp
== efGRO
) || (ftp
== efPDB
) || bCONECT
);
1096 /* Determine if when can read index groups */
1097 bIndex
= (bIndex
|| bTPS
);
1101 read_tps_conf(top_file
, top_title
, &top
, &ePBC
, &xp
, NULL
, top_box
,
1102 bReset
|| bPBCcomRes
);
1105 if (0 == top
.mols
.nr
&& (bCluster
|| bPBCcomMol
))
1107 gmx_fatal(FARGS
, "Option -pbc %s requires a .tpr file for the -s option", pbc_opt
[pbc_enum
]);
1110 /* top_title is only used for gro and pdb,
1111 * the header in such a file is top_title t= ...
1112 * to prevent a double t=, remove it from top_title
1114 if ((charpt
= strstr(top_title
, " t= ")))
1121 gc
= gmx_conect_generate(&top
);
1125 gpbc
= gmx_rmpbc_init(&top
.idef
, ePBC
, top
.atoms
.nr
);
1129 /* get frame number index */
1131 if (opt2bSet("-fr", NFILE
, fnm
))
1133 printf("Select groups of frame number indices:\n");
1134 rd_index(opt2fn("-fr", NFILE
, fnm
), 1, &nrfri
, (atom_id
**)&frindex
, &frname
);
1137 for (i
= 0; i
< nrfri
; i
++)
1139 fprintf(debug
, "frindex[%4d]=%4d\n", i
, frindex
[i
]);
1144 /* get index groups etc. */
1147 printf("Select group for %s fit\n",
1148 bFit
? "least squares" : "translational");
1149 get_index(atoms
, ftp2fn_null(efNDX
, NFILE
, fnm
),
1150 1, &ifit
, &ind_fit
, &gn_fit
);
1156 gmx_fatal(FARGS
, "Need at least 2 atoms to fit!\n");
1160 fprintf(stderr
, "WARNING: fitting with only 2 atoms is not unique\n");
1166 printf("Select group for clustering\n");
1167 get_index(atoms
, ftp2fn_null(efNDX
, NFILE
, fnm
),
1168 1, &ifit
, &ind_fit
, &gn_fit
);
1175 printf("Select group for centering\n");
1176 get_index(atoms
, ftp2fn_null(efNDX
, NFILE
, fnm
),
1177 1, &ncent
, &cindex
, &grpnm
);
1179 printf("Select group for output\n");
1180 get_index(atoms
, ftp2fn_null(efNDX
, NFILE
, fnm
),
1181 1, &nout
, &index
, &grpnm
);
1185 /* no index file, so read natoms from TRX */
1186 if (!read_first_frame(oenv
, &trxin
, in_file
, &fr
, TRX_DONT_SKIP
))
1188 gmx_fatal(FARGS
, "Could not read a frame from %s", in_file
);
1193 snew(index
, natoms
);
1194 for (i
= 0; i
< natoms
; i
++)
1208 snew(w_rls
, atoms
->nr
);
1209 for (i
= 0; (i
< ifit
); i
++)
1211 w_rls
[ind_fit
[i
]] = atoms
->atom
[ind_fit
[i
]].m
;
1214 /* Restore reference structure and set to origin,
1215 store original location (to put structure back) */
1218 gmx_rmpbc(gpbc
, top
.atoms
.nr
, top_box
, xp
);
1220 copy_rvec(xp
[index
[0]], x_shift
);
1221 reset_x_ndim(nfitdim
, ifit
, ind_fit
, atoms
->nr
, NULL
, xp
, w_rls
);
1222 rvec_dec(x_shift
, xp
[index
[0]]);
1226 clear_rvec(x_shift
);
1229 if (bDropUnder
|| bDropOver
)
1231 /* Read the .xvg file with the drop values */
1232 fprintf(stderr
, "\nReading drop file ...");
1233 ndrop
= read_xvg(opt2fn("-drop", NFILE
, fnm
), &dropval
, &ncol
);
1234 fprintf(stderr
, " %d time points\n", ndrop
);
1235 if (ndrop
== 0 || ncol
< 2)
1237 gmx_fatal(FARGS
, "Found no data points in %s",
1238 opt2fn("-drop", NFILE
, fnm
));
1244 /* Make atoms struct for output in GRO or PDB files */
1245 if ((ftp
== efGRO
) || ((ftp
== efG96
) && bTPS
) || (ftp
== efPDB
))
1247 /* get memory for stuff to go in .pdb file */
1248 init_t_atoms(&useatoms
, atoms
->nr
, FALSE
);
1249 sfree(useatoms
.resinfo
);
1250 useatoms
.resinfo
= atoms
->resinfo
;
1251 for (i
= 0; (i
< nout
); i
++)
1253 useatoms
.atomname
[i
] = atoms
->atomname
[index
[i
]];
1254 useatoms
.atom
[i
] = atoms
->atom
[index
[i
]];
1255 useatoms
.nres
= max(useatoms
.nres
, useatoms
.atom
[i
].resind
+1);
1259 /* select what to read */
1260 if (ftp
== efTRR
|| ftp
== efTRJ
)
1270 flags
= flags
| TRX_READ_V
;
1274 flags
= flags
| TRX_READ_F
;
1277 /* open trx file for reading */
1278 bHaveFirstFrame
= read_first_frame(oenv
, &trxin
, in_file
, &fr
, flags
);
1281 fprintf(stderr
, "\nPrecision of %s is %g (nm)\n", in_file
, 1/fr
.prec
);
1285 if (bSetPrec
|| !fr
.bPrec
)
1287 fprintf(stderr
, "\nSetting output precision to %g (nm)\n", 1/prec
);
1291 fprintf(stderr
, "Using output precision of %g (nm)\n", 1/prec
);
1295 if (bHaveFirstFrame
)
1297 set_trxframe_ePBC(&fr
, ePBC
);
1303 tshift
= tzero
-fr
.time
;
1313 /* check if index is meaningful */
1314 for (i
= 0; i
< nout
; i
++)
1316 if (index
[i
] >= natoms
)
1319 "Index[%d] %d is larger than the number of atoms in the\n"
1320 "trajectory file (%d). There is a mismatch in the contents\n"
1321 "of your -f, -s and/or -n files.", i
, index
[i
]+1, natoms
);
1323 bCopy
= bCopy
|| (i
!= index
[i
]);
1327 /* open output for writing */
1328 strcpy(filemode
, "w");
1332 trjtools_gmx_prepare_tng_writing(out_file
,
1346 if (!bSplit
&& !bSubTraj
)
1348 trxout
= open_trx(out_file
, filemode
);
1354 if (( !bSeparate
&& !bSplit
) && !bSubTraj
)
1356 out
= gmx_ffopen(out_file
, filemode
);
1360 gmx_incons("Illegal output file format");
1376 /* Start the big loop over frames */
1383 /* Main loop over frames */
1394 /*if (frame >= clust->clust->nra)
1395 gmx_fatal(FARGS,"There are more frames in the trajectory than in the cluster index file\n");*/
1396 if (frame
> clust
->maxframe
)
1402 my_clust
= clust
->inv_clust
[frame
];
1404 if ((my_clust
< 0) || (my_clust
>= clust
->clust
->nr
) ||
1405 (my_clust
== NO_ATID
))
1413 /* generate new box */
1415 for (m
= 0; m
< DIM
; m
++)
1417 fr
.box
[m
][m
] = newbox
[m
];
1423 for (i
= 0; i
< natoms
; i
++)
1425 rvec_inc(fr
.x
[i
], trans
);
1431 /* determine timestep */
1444 /* This is not very elegant, as one can not dump a frame after
1445 * a timestep with is more than twice as small as the first one. */
1446 bDumpFrame
= (fr
.time
> tdump
-0.5*dt
) && (fr
.time
<= tdump
+0.5*dt
);
1453 /* determine if an atom jumped across the box and reset it if so */
1454 if (bNoJump
&& (bTPS
|| frame
!= 0))
1456 for (d
= 0; d
< DIM
; d
++)
1458 hbox
[d
] = 0.5*fr
.box
[d
][d
];
1460 for (i
= 0; i
< natoms
; i
++)
1464 rvec_dec(fr
.x
[i
], x_shift
);
1466 for (m
= DIM
-1; m
>= 0; m
--)
1470 while (fr
.x
[i
][m
]-xp
[i
][m
] <= -hbox
[m
])
1472 for (d
= 0; d
<= m
; d
++)
1474 fr
.x
[i
][d
] += fr
.box
[m
][d
];
1477 while (fr
.x
[i
][m
]-xp
[i
][m
] > hbox
[m
])
1479 for (d
= 0; d
<= m
; d
++)
1481 fr
.x
[i
][d
] -= fr
.box
[m
][d
];
1490 calc_pbc_cluster(ecenter
, ifit
, &top
, ePBC
, fr
.x
, ind_fit
, fr
.box
);
1495 /* Now modify the coords according to the flags,
1496 for normal fit, this is only done for output frames */
1499 gmx_rmpbc_trxfr(gpbc
, &fr
);
1502 reset_x_ndim(nfitdim
, ifit
, ind_fit
, natoms
, NULL
, fr
.x
, w_rls
);
1503 do_fit(natoms
, w_rls
, xp
, fr
.x
);
1506 /* store this set of coordinates for future use */
1507 if (bPFit
|| bNoJump
)
1513 for (i
= 0; (i
< natoms
); i
++)
1515 copy_rvec(fr
.x
[i
], xp
[i
]);
1516 rvec_inc(fr
.x
[i
], x_shift
);
1522 /* see if we have a frame from the frame index group */
1523 for (i
= 0; i
< nrfri
&& !bDumpFrame
; i
++)
1525 bDumpFrame
= frame
== frindex
[i
];
1528 if (debug
&& bDumpFrame
)
1530 fprintf(debug
, "dumping %d\n", frame
);
1534 ( ( !bTDump
&& !frindex
&& frame
% skip_nr
== 0 ) || bDumpFrame
);
1536 if (bWriteFrame
&& (bDropUnder
|| bDropOver
))
1538 while (dropval
[0][drop1
] < fr
.time
&& drop1
+1 < ndrop
)
1543 if (fabs(dropval
[0][drop0
] - fr
.time
)
1544 < fabs(dropval
[0][drop1
] - fr
.time
))
1552 if ((bDropUnder
&& dropval
[1][dropuse
] < dropunder
) ||
1553 (bDropOver
&& dropval
[1][dropuse
] > dropover
))
1555 bWriteFrame
= FALSE
;
1565 fr
.time
= tzero
+frame
*timestep
;
1575 fprintf(stderr
, "\nDumping frame at t= %g %s\n",
1576 output_env_conv_time(oenv
, fr
.time
), output_env_get_time_unit(oenv
));
1579 /* check for writing at each delta_t */
1580 bDoIt
= (delta_t
== 0);
1585 bDoIt
= bRmod(fr
.time
, tzero
, delta_t
);
1589 /* round() is not C89 compatible, so we do this: */
1590 bDoIt
= bRmod(floor(fr
.time
+0.5), floor(tzero
+0.5),
1591 floor(delta_t
+0.5));
1595 if (bDoIt
|| bTDump
)
1597 /* print sometimes */
1598 if ( ((outframe
% SKIP
) == 0) || (outframe
< SKIP
) )
1600 fprintf(stderr
, " -> frame %6d time %8.3f \r",
1601 outframe
, output_env_conv_time(oenv
, fr
.time
));
1606 /* Now modify the coords according to the flags,
1607 for PFit we did this already! */
1611 gmx_rmpbc_trxfr(gpbc
, &fr
);
1616 reset_x_ndim(nfitdim
, ifit
, ind_fit
, natoms
, NULL
, fr
.x
, w_rls
);
1619 do_fit_ndim(nfitdim
, natoms
, w_rls
, xp
, fr
.x
);
1623 for (i
= 0; i
< natoms
; i
++)
1625 rvec_inc(fr
.x
[i
], x_shift
);
1632 center_x(ecenter
, fr
.x
, fr
.box
, natoms
, ncent
, cindex
);
1638 switch (unitcell_enum
)
1641 put_atoms_in_box(ePBC
, fr
.box
, natoms
, fr
.x
);
1644 put_atoms_in_triclinic_unitcell(ecenter
, fr
.box
, natoms
, fr
.x
);
1647 warn
= put_atoms_in_compact_unitcell(ePBC
, ecenter
, fr
.box
,
1649 if (warn
&& !bWarnCompact
)
1651 fprintf(stderr
, "\n%s\n", warn
);
1652 bWarnCompact
= TRUE
;
1659 put_residue_com_in_box(unitcell_enum
, ecenter
,
1660 natoms
, atoms
->atom
, ePBC
, fr
.box
, fr
.x
);
1664 put_molecule_com_in_box(unitcell_enum
, ecenter
,
1666 natoms
, atoms
->atom
, ePBC
, fr
.box
, fr
.x
);
1668 /* Copy the input trxframe struct to the output trxframe struct */
1670 frout
.bV
= (frout
.bV
&& bVels
);
1671 frout
.bF
= (frout
.bF
&& bForce
);
1672 frout
.natoms
= nout
;
1673 if (bNeedPrec
&& (bSetPrec
|| !fr
.bPrec
))
1689 for (i
= 0; i
< nout
; i
++)
1691 copy_rvec(fr
.x
[index
[i
]], frout
.x
[i
]);
1694 copy_rvec(fr
.v
[index
[i
]], frout
.v
[i
]);
1698 copy_rvec(fr
.f
[index
[i
]], frout
.f
[i
]);
1703 if (opt2parg_bSet("-shift", NPA
, pa
))
1705 for (i
= 0; i
< nout
; i
++)
1707 for (d
= 0; d
< DIM
; d
++)
1709 frout
.x
[i
][d
] += outframe
*shift
[d
];
1716 bSplitHere
= bSplit
&& bRmod(fr
.time
, tzero
, split_t
);
1720 /* round() is not C89 compatible, so we do this: */
1721 bSplitHere
= bSplit
&& bRmod(floor(fr
.time
+0.5),
1723 floor(split_t
+0.5));
1725 if (bSeparate
|| bSplitHere
)
1727 mk_filenm(outf_base
, ftp2ext(ftp
), nzero
, file_nr
, out_file2
);
1733 write_tng_frame(trxout
, &frout
);
1734 // TODO when trjconv behaves better: work how to read and write lambda
1745 trxout
= open_trx(out_file2
, filemode
);
1752 if (clust_status_id
[my_clust
] == -1)
1754 sprintf(buf
, "%s.%s", clust
->grpname
[my_clust
], ftp2ext(ftp
));
1755 clust_status
[my_clust
] = open_trx(buf
, "w");
1756 clust_status_id
[my_clust
] = 1;
1759 else if (clust_status_id
[my_clust
] == -2)
1761 gmx_fatal(FARGS
, "File %s.xtc should still be open (%d open .xtc files)\n" "in order to write frame %d. my_clust = %d",
1762 clust
->grpname
[my_clust
], ntrxopen
, frame
,
1765 write_trxframe(clust_status
[my_clust
], &frout
, gc
);
1766 nfwritten
[my_clust
]++;
1767 if (nfwritten
[my_clust
] ==
1768 (clust
->clust
->index
[my_clust
+1]-
1769 clust
->clust
->index
[my_clust
]))
1771 close_trx(clust_status
[my_clust
]);
1772 clust_status
[my_clust
] = NULL
;
1773 clust_status_id
[my_clust
] = -2;
1777 gmx_fatal(FARGS
, "Less than zero open .xtc files!");
1784 write_trxframe(trxout
, &frout
, gc
);
1790 sprintf(title
, "Generated by trjconv : %s t= %9.5f",
1791 top_title
, fr
.time
);
1792 if (bSeparate
|| bSplitHere
)
1794 out
= gmx_ffopen(out_file2
, "w");
1799 write_hconf_p(out
, title
, &useatoms
, prec2ndec(frout
.prec
),
1800 frout
.x
, frout
.bV
? frout
.v
: NULL
, frout
.box
);
1803 fprintf(out
, "REMARK GENERATED BY TRJCONV\n");
1804 sprintf(title
, "%s t= %9.5f", top_title
, frout
.time
);
1805 /* if reading from pdb, we want to keep the original
1806 model numbering else we write the output frame
1807 number plus one, because model 0 is not allowed in pdb */
1808 if (ftpin
== efPDB
&& fr
.bStep
&& fr
.step
> model_nr
)
1816 write_pdbfile(out
, title
, &useatoms
, frout
.x
,
1817 frout
.ePBC
, frout
.box
, ' ', model_nr
, gc
, TRUE
);
1820 frout
.title
= title
;
1821 if (bSeparate
|| bTDump
)
1823 frout
.bTitle
= TRUE
;
1826 frout
.bAtoms
= TRUE
;
1828 frout
.atoms
= &useatoms
;
1829 frout
.bStep
= FALSE
;
1830 frout
.bTime
= FALSE
;
1834 frout
.bTitle
= (outframe
== 0);
1835 frout
.bAtoms
= FALSE
;
1839 write_g96_conf(out
, &frout
, -1, NULL
);
1848 gmx_fatal(FARGS
, "DHE, ftp=%d\n", ftp
);
1850 if (bSeparate
|| bSplitHere
)
1855 /* execute command */
1859 sprintf(c
, "%s %d", exec_command
, file_nr
-1);
1860 /*fprintf(stderr,"Executing '%s'\n",c);*/
1861 #ifdef GMX_NO_SYSTEM
1862 printf("Warning-- No calls to system(3) supported on this platform.");
1863 printf("Warning-- Skipping execution of 'system(\"%s\")'.", c
);
1867 gmx_fatal(FARGS
, "Error executing command: %s", c
);
1875 bHaveNextFrame
= read_next_frame(oenv
, trxin
, &fr
);
1877 while (!(bTDump
&& bDumpFrame
) && bHaveNextFrame
);
1880 if (!bHaveFirstFrame
|| (bTDump
&& !bDumpFrame
))
1882 fprintf(stderr
, "\nWARNING no output, "
1883 "last frame read at t=%g\n", fr
.time
);
1885 fprintf(stderr
, "\n");
1892 gmx_rmpbc_done(gpbc
);
1899 else if (out
!= NULL
)
1905 for (i
= 0; (i
< clust
->clust
->nr
); i
++)
1907 if (clust_status_id
[i
] >= 0)
1909 close_trx(clust_status
[i
]);
1917 do_view(oenv
, out_file
, NULL
);