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48 #ifdef GMX_USE_PLUGINS
51 #include "gromacs/utility/smalloc.h"
58 #include "tngio_for_tools.h"
65 #include "checkpoint.h"
68 #include "gromacs/fileio/timecontrol.h"
69 #include "gromacs/legacyheaders/gmx_fatal.h"
71 /* defines for frame counter output */
86 char *persistent_line; /* Persistent line for reading g96 trajectories */
89 /* utility functions */
91 gmx_bool bRmod_fd(double a, double b, double c, gmx_bool bDouble)
96 tol = 2*(bDouble ? GMX_DOUBLE_EPS : GMX_FLOAT_EPS);
98 iq = (int)((a - b + tol*a)/c);
100 if (fabs(a - b - c*iq) <= tol*fabs(a))
112 int check_times2(real t, real t0, gmx_bool bDouble)
117 /* since t is float, we can not use double precision for bRmod */
122 if ((!bTimeSet(TBEGIN) || (t >= rTimeValue(TBEGIN))) &&
123 (!bTimeSet(TEND) || (t <= rTimeValue(TEND))))
125 if (bTimeSet(TDELTA) && !bRmod_fd(t, t0, rTimeValue(TDELTA), bDouble))
134 else if (bTimeSet(TEND) && (t >= rTimeValue(TEND)))
140 fprintf(debug, "t=%g, t0=%g, b=%g, e=%g, dt=%g: r=%d\n",
141 t, t0, rTimeValue(TBEGIN), rTimeValue(TEND), rTimeValue(TDELTA), r);
146 int check_times(real t)
148 return check_times2(t, t, FALSE);
151 static void initcount(t_trxstatus *status)
153 status->__frame = -1;
156 static void status_init(t_trxstatus *status)
159 status->xframe = NULL;
161 status->__frame = -1;
162 status->persistent_line = NULL;
167 int nframes_read(t_trxstatus *status)
169 return status->__frame;
172 static void printcount_(t_trxstatus *status, const output_env_t oenv,
173 const char *l, real t)
175 if ((status->__frame < 2*SKIP1 || status->__frame % SKIP1 == 0) &&
176 (status->__frame < 2*SKIP2 || status->__frame % SKIP2 == 0) &&
177 (status->__frame < 2*SKIP3 || status->__frame % SKIP3 == 0))
179 fprintf(stderr, "\r%-14s %6d time %8.3f ", l, status->__frame,
180 output_env_conv_time(oenv, t));
184 static void printcount(t_trxstatus *status, const output_env_t oenv, real t,
188 printcount_(status, oenv, bSkip ? "Skipping frame" : "Reading frame", t);
191 static void printlast(t_trxstatus *status, const output_env_t oenv, real t)
193 printcount_(status, oenv, "Last frame", t);
194 fprintf(stderr, "\n");
197 static void printincomp(t_trxstatus *status, t_trxframe *fr)
199 if (fr->not_ok & HEADER_NOT_OK)
201 fprintf(stderr, "WARNING: Incomplete header: nr %d time %g\n",
202 status->__frame+1, fr->time);
206 fprintf(stderr, "WARNING: Incomplete frame: nr %d time %g\n",
207 status->__frame+1, fr->time);
211 int prec2ndec(real prec)
215 gmx_fatal(FARGS, "DEATH HORROR prec (%g) <= 0 in prec2ndec", prec);
218 return (int)(log(prec)/log(10.0)+0.5);
221 real ndec2prec(int ndec)
223 return pow(10.0, ndec);
226 t_fileio *trx_get_fileio(t_trxstatus *status)
231 float trx_get_time_of_final_frame(t_trxstatus *status)
233 t_fileio *stfio = trx_get_fileio(status);
234 int filetype = gmx_fio_getftp(stfio);
238 if (filetype == efXTC)
241 xdr_xtc_get_last_frame_time(gmx_fio_getfp(stfio),
242 gmx_fio_getxdr(stfio),
243 status->xframe->natoms, &bOK);
246 gmx_fatal(FARGS, "Error reading last frame. Maybe seek not supported." );
249 else if (filetype == efTNG)
251 tng_trajectory_t tng = status->tng;
254 gmx_fatal(FARGS, "Error opening TNG file.");
256 lasttime = gmx_tng_get_time_of_final_frame(tng);
260 gmx_incons("Only supported for TNG and XTC");
265 void clear_trxframe(t_trxframe *fr, gmx_bool bFirst)
272 fr->bFepState = FALSE;
303 void set_trxframe_ePBC(t_trxframe *fr, int ePBC)
305 fr->bPBC = (ePBC == -1);
309 int write_trxframe_indexed(t_trxstatus *status, t_trxframe *fr, int nind,
310 const atom_id *ind, gmx_conect gc)
313 rvec *xout = NULL, *vout = NULL, *fout = NULL;
330 else if (status->fio)
332 ftp = gmx_fio_getftp(status->fio);
336 gmx_incons("No input file available");
348 gmx_fatal(FARGS, "Need coordinates to write a %s trajectory",
362 for (i = 0; i < nind; i++)
364 copy_rvec(fr->v[ind[i]], vout[i]);
370 for (i = 0; i < nind; i++)
372 copy_rvec(fr->f[ind[i]], fout[i]);
380 for (i = 0; i < nind; i++)
382 copy_rvec(fr->x[ind[i]], xout[i]);
393 gmx_write_tng_from_trxframe(status->tng, fr, nind);
396 write_xtc(status->fio, nind, fr->step, fr->time, fr->box, xout, prec);
400 fwrite_trn(status->fio, nframes_read(status),
401 fr->time, fr->step, fr->box, nind, xout, vout, fout);
409 gmx_fatal(FARGS, "Can not write a %s file without atom names",
412 sprintf(title, "frame t= %.3f", fr->time);
415 write_hconf_indexed_p(gmx_fio_getfp(status->fio), title, fr->atoms, nind, ind,
417 fr->x, fr->bV ? fr->v : NULL, fr->box);
421 write_pdbfile_indexed(gmx_fio_getfp(status->fio), title, fr->atoms,
422 fr->x, -1, fr->box, ' ', fr->step, nind, ind, gc, TRUE);
426 write_g96_conf(gmx_fio_getfp(status->fio), fr, nind, ind);
429 gmx_fatal(FARGS, "Sorry, write_trxframe_indexed can not write %s",
459 void trjtools_gmx_prepare_tng_writing(const char *filename,
465 const gmx_mtop_t *mtop,
466 const atom_id *index,
467 const char *index_group_name)
469 if (filemode != 'w' && filemode != 'a')
471 gmx_incons("Sorry, can only prepare for TNG output.");
482 gmx_prepare_tng_writing(filename,
491 else if (efTNG == fn2ftp(infile))
493 tng_trajectory_t tng_in;
494 gmx_tng_open(infile, 'r', &tng_in);
496 gmx_prepare_tng_writing(filename,
507 void write_tng_frame(t_trxstatus *status,
510 gmx_write_tng_from_trxframe(status->tng, frame, -1);
513 int write_trxframe(t_trxstatus *status, t_trxframe *fr, gmx_conect gc)
529 gmx_tng_set_compression_precision(status->tng, prec);
530 write_tng_frame(status, fr);
535 switch (gmx_fio_getftp(status->fio))
543 gmx_fatal(FARGS, "Need coordinates to write a %s trajectory",
544 ftp2ext(gmx_fio_getftp(status->fio)));
549 switch (gmx_fio_getftp(status->fio))
552 write_xtc(status->fio, fr->natoms, fr->step, fr->time, fr->box, fr->x, prec);
556 fwrite_trn(status->fio, fr->step, fr->time, fr->lambda, fr->box, fr->natoms,
557 fr->bX ? fr->x : NULL, fr->bV ? fr->v : NULL, fr->bF ? fr->f : NULL);
565 gmx_fatal(FARGS, "Can not write a %s file without atom names",
566 ftp2ext(gmx_fio_getftp(status->fio)));
568 sprintf(title, "frame t= %.3f", fr->time);
569 if (gmx_fio_getftp(status->fio) == efGRO)
571 write_hconf_p(gmx_fio_getfp(status->fio), title, fr->atoms,
572 prec2ndec(prec), fr->x, fr->bV ? fr->v : NULL, fr->box);
576 write_pdbfile(gmx_fio_getfp(status->fio), title,
577 fr->atoms, fr->x, fr->bPBC ? fr->ePBC : -1, fr->box,
578 ' ', fr->step, gc, TRUE);
582 write_g96_conf(gmx_fio_getfp(status->fio), fr, -1, NULL);
585 gmx_fatal(FARGS, "Sorry, write_trxframe can not write %s",
586 ftp2ext(gmx_fio_getftp(status->fio)));
593 int write_trx(t_trxstatus *status, int nind, const atom_id *ind, t_atoms *atoms,
594 int step, real time, matrix box, rvec x[], rvec *v,
599 clear_trxframe(&fr, TRUE);
604 fr.bAtoms = atoms != NULL;
611 copy_mat(box, fr.box);
613 return write_trxframe_indexed(status, &fr, nind, ind, gc);
616 void close_trx(t_trxstatus *status)
618 gmx_tng_close(&status->tng);
621 gmx_fio_close(status->fio);
626 t_trxstatus *open_trx(const char *outfile, const char *filemode)
629 if (filemode[0] != 'w' && filemode[0] != 'a' && filemode[1] != '+')
631 gmx_fatal(FARGS, "Sorry, write_trx can only write");
637 stat->fio = gmx_fio_open(outfile, filemode);
641 static gmx_bool gmx_next_frame(t_trxstatus *status, t_trxframe *fr)
648 if (fread_trnheader(status->fio, &sh, &bOK))
650 fr->bDouble = sh.bDouble;
651 fr->natoms = sh.natoms;
657 fr->bFepState = TRUE;
658 fr->lambda = sh.lambda;
659 fr->bBox = sh.box_size > 0;
660 if (fr->flags & (TRX_READ_X | TRX_NEED_X))
664 snew(fr->x, sh.natoms);
666 fr->bX = sh.x_size > 0;
668 if (fr->flags & (TRX_READ_V | TRX_NEED_V))
672 snew(fr->v, sh.natoms);
674 fr->bV = sh.v_size > 0;
676 if (fr->flags & (TRX_READ_F | TRX_NEED_F))
680 snew(fr->f, sh.natoms);
682 fr->bF = sh.f_size > 0;
684 if (fread_htrn(status->fio, &sh, fr->box, fr->x, fr->v, fr->f))
690 fr->not_ok = DATA_NOT_OK;
696 fr->not_ok = HEADER_NOT_OK;
702 static gmx_bool pdb_next_x(t_trxstatus *status, FILE *fp, t_trxframe *fr)
706 int ePBC, model_nr, na;
707 char title[STRLEN], *time;
710 atoms.nr = fr->natoms;
712 atoms.pdbinfo = NULL;
713 /* the other pointers in atoms should not be accessed if these are NULL */
715 na = read_pdbfile(fp, title, &model_nr, &atoms, fr->x, &ePBC, boxpdb, TRUE, NULL);
716 set_trxframe_ePBC(fr, ePBC);
717 if (nframes_read(status) == 0)
719 fprintf(stderr, " '%s', %d atoms\n", title, fr->natoms);
724 fr->bBox = (boxpdb[XX][XX] != 0.0);
727 copy_mat(boxpdb, fr->box);
730 if (model_nr != NOTSET)
735 time = strstr(title, " t= ");
739 sscanf(time+4, "%lf", &dbl);
740 fr->time = (real)dbl;
745 /* this is a bit dirty, but it will work: if no time is read from
746 comment line in pdb file, set time to current frame number */
749 fr->time = (real)fr->step;
753 fr->time = (real)nframes_read(status);
762 if (na != fr->natoms)
764 gmx_fatal(FARGS, "Number of atoms in pdb frame %d is %d instead of %d",
765 nframes_read(status), na, fr->natoms);
771 static int pdb_first_x(t_trxstatus *status, FILE *fp, t_trxframe *fr)
775 fprintf(stderr, "Reading frames from pdb file");
777 get_pdb_coordnum(fp, &fr->natoms);
780 gmx_fatal(FARGS, "\nNo coordinates in pdb file\n");
783 snew(fr->x, fr->natoms);
784 pdb_next_x(status, fp, fr);
789 gmx_bool read_next_frame(const output_env_t oenv, t_trxstatus *status, t_trxframe *fr)
793 gmx_bool bOK, bRet, bMissingData = FALSE, bSkip = FALSE;
802 clear_trxframe(fr, FALSE);
808 /* Special treatment for TNG files */
813 ftp = gmx_fio_getftp(status->fio);
819 bRet = gmx_next_frame(status, fr);
822 /* Checkpoint files can not contain mulitple frames */
825 read_g96_conf(gmx_fio_getfp(status->fio), NULL, fr,
826 status->persistent_line);
827 bRet = (fr->natoms > 0);
831 * Sometimes is off by one frame
832 * and sometimes reports frame not present/file not seekable
834 /* DvdS 2005-05-31: this has been fixed along with the increased
835 * accuracy of the control over -b and -e options.
837 if (bTimeSet(TBEGIN) && (fr->time < rTimeValue(TBEGIN)))
839 if (xtc_seek_time(status->fio, rTimeValue(TBEGIN), fr->natoms, TRUE))
841 gmx_fatal(FARGS, "Specified frame (time %f) doesn't exist or file corrupt/inconsistent.",
846 bRet = read_next_xtc(status->fio, fr->natoms, &fr->step, &fr->time, fr->box,
847 fr->x, &fr->prec, &bOK);
848 fr->bPrec = (bRet && fr->prec > 0);
855 /* Actually the header could also be not ok,
856 but from bOK from read_next_xtc this can't be distinguished */
857 fr->not_ok = DATA_NOT_OK;
861 bRet = gmx_read_next_tng_frame(status->tng, fr, NULL, 0);
864 bRet = pdb_next_x(status, gmx_fio_getfp(status->fio), fr);
867 bRet = gro_next_x_or_v(gmx_fio_getfp(status->fio), fr);
870 #ifdef GMX_USE_PLUGINS
871 bRet = read_next_vmd_frame(fr);
873 gmx_fatal(FARGS, "DEATH HORROR in read_next_frame ftp=%s,status=%s",
874 ftp2ext(gmx_fio_getftp(status->fio)),
875 gmx_fio_getname(status->fio));
881 bMissingData = (((fr->flags & TRX_NEED_X) && !fr->bX) ||
882 ((fr->flags & TRX_NEED_V) && !fr->bV) ||
883 ((fr->flags & TRX_NEED_F) && !fr->bF));
887 ct = check_times2(fr->time, fr->t0, fr->bDouble);
888 if (ct == 0 || ((fr->flags & TRX_DONT_SKIP) && ct < 0))
890 printcount(status, oenv, fr->time, FALSE);
898 printcount(status, oenv, fr->time, TRUE);
905 while (bRet && (bMissingData || bSkip));
909 printlast(status, oenv, pt);
912 printincomp(status, fr);
919 int read_first_frame(const output_env_t oenv, t_trxstatus **status,
920 const char *fn, t_trxframe *fr, int flags)
923 gmx_bool bFirst, bOK;
925 int ftp = fn2ftp(fn);
926 gmx_int64_t *tng_ids;
928 clear_trxframe(fr, TRUE);
935 status_init( *status );
936 (*status)->nxframe = 1;
941 /* Special treatment for TNG files */
942 gmx_tng_open(fn, 'r', &(*status)->tng);
946 fio = (*status)->fio = gmx_fio_open(fn, "r");
954 read_checkpoint_trxframe(fio, fr);
958 /* Can not rewind a compressed file, so open it twice */
959 if (!(*status)->persistent_line)
961 /* allocate the persistent line */
962 snew((*status)->persistent_line, STRLEN+1);
964 read_g96_conf(gmx_fio_getfp(fio), fn, fr, (*status)->persistent_line);
966 clear_trxframe(fr, FALSE);
967 if (flags & (TRX_READ_X | TRX_NEED_X))
969 snew(fr->x, fr->natoms);
971 if (flags & (TRX_READ_V | TRX_NEED_V))
973 snew(fr->v, fr->natoms);
975 fio = (*status)->fio = gmx_fio_open(fn, "r");
978 if (read_first_xtc(fio, &fr->natoms, &fr->step, &fr->time, fr->box, &fr->x,
979 &fr->prec, &bOK) == 0)
982 fr->not_ok = DATA_NOT_OK;
987 printincomp(*status, fr);
991 fr->bPrec = (fr->prec > 0);
996 printcount(*status, oenv, fr->time, FALSE);
1002 if (!gmx_read_next_tng_frame((*status)->tng, fr, NULL, 0))
1004 fr->not_ok = DATA_NOT_OK;
1006 printincomp(*status, fr);
1010 printcount(*status, oenv, fr->time, FALSE);
1015 pdb_first_x(*status, gmx_fio_getfp(fio), fr);
1018 printcount(*status, oenv, fr->time, FALSE);
1023 if (gro_first_x_or_v(gmx_fio_getfp(fio), fr))
1025 printcount(*status, oenv, fr->time, FALSE);
1030 #ifdef GMX_USE_PLUGINS
1031 fprintf(stderr, "The file format of %s is not a known trajectory format to GROMACS.\n"
1032 "Please make sure that the file is a trajectory!\n"
1033 "GROMACS will now assume it to be a trajectory and will try to open it using the VMD plug-ins.\n"
1034 "This will only work in case the VMD plugins are found and it is a trajectory format supported by VMD.\n", fn);
1035 gmx_fio_fp_close(fio); /*only close the file without removing FIO entry*/
1036 if (!read_first_vmd_frame(fn, fr))
1038 gmx_fatal(FARGS, "Not supported in read_first_frame: %s", fn);
1041 gmx_fatal(FARGS, "Not supported in read_first_frame: %s. Please make sure that the file is a trajectory.\n"
1042 "GROMACS is not compiled with plug-in support. Thus it cannot read non-GROMACS trajectory formats using the VMD plug-ins.\n"
1043 "Please compile with plug-in support if you want to read non-GROMACS trajectory formats.\n", fn);
1048 /* Return FALSE if we read a frame that's past the set ending time. */
1049 if (!bFirst && (!(fr->flags & TRX_DONT_SKIP) && check_times(fr->time) > 0))
1056 (!(fr->flags & TRX_DONT_SKIP) && check_times(fr->time) < 0))
1058 /* Read a frame when no frame was read or the first was skipped */
1059 if (!read_next_frame(oenv, *status, fr))
1066 return (fr->natoms > 0);
1069 /***** C O O R D I N A T E S T U F F *****/
1071 int read_first_x(const output_env_t oenv, t_trxstatus **status, const char *fn,
1072 real *t, rvec **x, matrix box)
1076 read_first_frame(oenv, status, fn, &fr, TRX_NEED_X);
1078 snew((*status)->xframe, 1);
1079 (*status)->nxframe = 1;
1080 (*(*status)->xframe) = fr;
1081 *t = (*status)->xframe->time;
1082 *x = (*status)->xframe->x;
1083 copy_mat((*status)->xframe->box, box);
1085 return (*status)->xframe->natoms;
1088 gmx_bool read_next_x(const output_env_t oenv, t_trxstatus *status, real *t,
1089 rvec x[], matrix box)
1093 status->xframe->x = x;
1094 /*xframe[status].x = x;*/
1095 bRet = read_next_frame(oenv, status, status->xframe);
1096 *t = status->xframe->time;
1097 copy_mat(status->xframe->box, box);
1102 void close_trj(t_trxstatus *status)
1104 gmx_tng_close(&status->tng);
1107 gmx_fio_close(status->fio);
1110 /* The memory in status->xframe is lost here,
1111 * but the read_first_x/read_next_x functions are deprecated anyhow.
1112 * read_first_frame/read_next_frame and close_trx should be used.
1117 void rewind_trj(t_trxstatus *status)
1121 gmx_fio_rewind(status->fio);
1124 /***** T O P O L O G Y S T U F F ******/
1126 t_topology *read_top(const char *fn, int *ePBC)
1132 epbc = read_tpx_top(fn, NULL, NULL, &natoms, NULL, NULL, NULL, top);