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47 #include "gromacs/fileio/checkpoint.h"
48 #include "gromacs/fileio/confio.h"
49 #include "gromacs/fileio/filetypes.h"
50 #include "gromacs/fileio/g96io.h"
51 #include "gromacs/fileio/gmxfio.h"
52 #include "gromacs/fileio/gmxfio-xdr.h"
53 #include "gromacs/fileio/groio.h"
54 #include "gromacs/fileio/oenv.h"
55 #include "gromacs/fileio/pdbio.h"
56 #include "gromacs/fileio/timecontrol.h"
57 #include "gromacs/fileio/tngio.h"
58 #include "gromacs/fileio/tpxio.h"
59 #include "gromacs/fileio/trrio.h"
60 #include "gromacs/fileio/xdrf.h"
61 #include "gromacs/fileio/xtcio.h"
62 #include "gromacs/math/vec.h"
63 #include "gromacs/mdtypes/md_enums.h"
64 #include "gromacs/topology/atoms.h"
65 #include "gromacs/topology/symtab.h"
66 #include "gromacs/topology/topology.h"
67 #include "gromacs/trajectory/trajectoryframe.h"
68 #include "gromacs/utility/fatalerror.h"
69 #include "gromacs/utility/futil.h"
70 #include "gromacs/utility/gmxassert.h"
71 #include "gromacs/utility/smalloc.h"
74 #include "gromacs/fileio/vmdio.h"
77 /* defines for frame counter output */
84 int flags; /* flags for read_first/next_frame */
86 real t0; /* time of the first frame, needed *
87 * for skipping frames with -dt */
88 real tf; /* internal frame time */
91 gmx_tng_trajectory_t tng;
95 char *persistent_line; /* Persistent line for reading g96 trajectories */
97 gmx_vmdplugin_t *vmdplugin;
101 /* utility functions */
103 gmx_bool bRmod_fd(double a, double b, double c, gmx_bool bDouble)
108 tol = 2*(bDouble ? GMX_DOUBLE_EPS : GMX_FLOAT_EPS);
110 iq = static_cast<int>((a - b + tol*a)/c);
112 return fabs(a - b - c*iq) <= tol*fabs(a);
117 int check_times2(real t, real t0, gmx_bool bDouble)
122 /* since t is float, we can not use double precision for bRmod */
127 if ((!bTimeSet(TBEGIN) || (t >= rTimeValue(TBEGIN))) &&
128 (!bTimeSet(TEND) || (t <= rTimeValue(TEND))))
130 if (bTimeSet(TDELTA) && !bRmod_fd(t, t0, rTimeValue(TDELTA), bDouble))
139 else if (bTimeSet(TEND) && (t >= rTimeValue(TEND)))
145 fprintf(debug, "t=%g, t0=%g, b=%g, e=%g, dt=%g: r=%d\n",
146 t, t0, rTimeValue(TBEGIN), rTimeValue(TEND), rTimeValue(TDELTA), r);
151 int check_times(real t)
153 return check_times2(t, t, FALSE);
156 static void initcount(t_trxstatus *status)
158 status->__frame = -1;
161 static void status_init(t_trxstatus *status)
164 status->xframe = nullptr;
165 status->fio = nullptr;
166 status->__frame = -1;
169 status->persistent_line = nullptr;
170 status->tng = nullptr;
174 int nframes_read(t_trxstatus *status)
176 return status->__frame;
179 static void printcount_(t_trxstatus *status, const gmx_output_env_t *oenv,
180 const char *l, real t)
182 if ((status->__frame < 2*SKIP1 || status->__frame % SKIP1 == 0) &&
183 (status->__frame < 2*SKIP2 || status->__frame % SKIP2 == 0) &&
184 (status->__frame < 2*SKIP3 || status->__frame % SKIP3 == 0) &&
185 output_env_get_trajectory_io_verbosity(oenv) != 0)
187 fprintf(stderr, "\r%-14s %6d time %8.3f ", l, status->__frame,
188 output_env_conv_time(oenv, t));
193 static void printcount(t_trxstatus *status, const gmx_output_env_t *oenv, real t,
197 printcount_(status, oenv, bSkip ? "Skipping frame" : "Reading frame", t);
200 static void printlast(t_trxstatus *status, const gmx_output_env_t *oenv, real t)
202 printcount_(status, oenv, "Last frame", t);
203 fprintf(stderr, "\n");
207 static void printincomp(t_trxstatus *status, t_trxframe *fr)
209 if (fr->not_ok & HEADER_NOT_OK)
211 fprintf(stderr, "WARNING: Incomplete header: nr %d time %g\n",
212 status->__frame+1, fr->time);
216 fprintf(stderr, "WARNING: Incomplete frame: nr %d time %g\n",
217 status->__frame+1, fr->time);
222 int prec2ndec(real prec)
226 gmx_fatal(FARGS, "DEATH HORROR prec (%g) <= 0 in prec2ndec", prec);
229 return static_cast<int>(log(prec)/log(10.0)+0.5);
232 real ndec2prec(int ndec)
234 return pow(10.0, ndec);
237 t_fileio *trx_get_fileio(t_trxstatus *status)
242 float trx_get_time_of_final_frame(t_trxstatus *status)
244 t_fileio *stfio = trx_get_fileio(status);
245 int filetype = gmx_fio_getftp(stfio);
249 if (filetype == efXTC)
252 xdr_xtc_get_last_frame_time(gmx_fio_getfp(stfio),
253 gmx_fio_getxdr(stfio),
254 status->natoms, &bOK);
257 gmx_fatal(FARGS, "Error reading last frame. Maybe seek not supported." );
260 else if (filetype == efTNG)
262 gmx_tng_trajectory_t tng = status->tng;
265 gmx_fatal(FARGS, "Error opening TNG file.");
267 lasttime = gmx_tng_get_time_of_final_frame(tng);
271 gmx_incons("Only supported for TNG and XTC");
276 void clear_trxframe(t_trxframe *fr, gmx_bool bFirst)
282 fr->bFepState = FALSE;
308 void set_trxframe_ePBC(t_trxframe *fr, int ePBC)
310 fr->bPBC = (ePBC == -1);
314 int write_trxframe_indexed(t_trxstatus *status, const t_trxframe *fr, int nind,
315 const int *ind, gmx_conect gc)
318 rvec *xout = nullptr, *vout = nullptr, *fout = nullptr;
335 else if (status->fio)
337 ftp = gmx_fio_getftp(status->fio);
341 gmx_incons("No input file available");
352 gmx_fatal(FARGS, "Need coordinates to write a %s trajectory",
365 for (i = 0; i < nind; i++)
367 copy_rvec(fr->v[ind[i]], vout[i]);
373 for (i = 0; i < nind; i++)
375 copy_rvec(fr->f[ind[i]], fout[i]);
381 for (i = 0; i < nind; i++)
383 copy_rvec(fr->x[ind[i]], xout[i]);
391 for (i = 0; i < nind; i++)
393 copy_rvec(fr->x[ind[i]], xout[i]);
404 gmx_write_tng_from_trxframe(status->tng, fr, nind);
407 write_xtc(status->fio, nind, fr->step, fr->time, fr->box, xout, prec);
410 gmx_trr_write_frame(status->fio, nframes_read(status),
411 fr->time, fr->step, fr->box, nind, xout, vout, fout);
419 gmx_fatal(FARGS, "Can not write a %s file without atom names",
422 sprintf(title, "frame t= %.3f", fr->time);
425 write_hconf_indexed_p(gmx_fio_getfp(status->fio), title, fr->atoms, nind, ind,
426 fr->x, fr->bV ? fr->v : nullptr, fr->box);
430 write_pdbfile_indexed(gmx_fio_getfp(status->fio), title, fr->atoms,
431 fr->x, -1, fr->box, ' ', fr->step, nind, ind, gc, TRUE, FALSE);
435 sprintf(title, "frame t= %.3f", fr->time);
436 write_g96_conf(gmx_fio_getfp(status->fio), title, fr, nind, ind);
439 gmx_fatal(FARGS, "Sorry, write_trxframe_indexed can not write %s",
468 trjtools_gmx_prepare_tng_writing(const char *filename,
473 const gmx_mtop_t *mtop,
475 const char *index_group_name)
477 if (filemode != 'w' && filemode != 'a')
479 gmx_incons("Sorry, can only prepare for TNG output.");
487 gmx_prepare_tng_writing(filename,
496 else if ((infile) && (efTNG == fn2ftp(infile)))
498 gmx_tng_trajectory_t tng_in;
499 gmx_tng_open(infile, 'r', &tng_in);
501 gmx_prepare_tng_writing(filename,
512 // we start from a file that is not a tng file or have been unable to load the
513 // input file, so we need to populate the fields independently of it
514 gmx_prepare_tng_writing(filename,
526 void write_tng_frame(t_trxstatus *status,
529 gmx_write_tng_from_trxframe(status->tng, frame, -1);
532 int write_trxframe(t_trxstatus *status, t_trxframe *fr, gmx_conect gc)
548 gmx_tng_set_compression_precision(status->tng, prec);
549 write_tng_frame(status, fr);
554 switch (gmx_fio_getftp(status->fio))
561 gmx_fatal(FARGS, "Need coordinates to write a %s trajectory",
562 ftp2ext(gmx_fio_getftp(status->fio)));
567 switch (gmx_fio_getftp(status->fio))
570 write_xtc(status->fio, fr->natoms, fr->step, fr->time, fr->box, fr->x, prec);
573 gmx_trr_write_frame(status->fio, fr->step, fr->time, fr->lambda, fr->box, fr->natoms,
574 fr->bX ? fr->x : nullptr, fr->bV ? fr->v : nullptr, fr->bF ? fr->f : nullptr);
582 gmx_fatal(FARGS, "Can not write a %s file without atom names",
583 ftp2ext(gmx_fio_getftp(status->fio)));
585 sprintf(title, "frame t= %.3f", fr->time);
586 if (gmx_fio_getftp(status->fio) == efGRO)
588 write_hconf_p(gmx_fio_getfp(status->fio), title, fr->atoms,
589 fr->x, fr->bV ? fr->v : nullptr, fr->box);
593 write_pdbfile(gmx_fio_getfp(status->fio), title,
594 fr->atoms, fr->x, fr->bPBC ? fr->ePBC : -1, fr->box,
595 ' ', fr->step, gc, TRUE);
599 write_g96_conf(gmx_fio_getfp(status->fio), title, fr, -1, nullptr);
602 gmx_fatal(FARGS, "Sorry, write_trxframe can not write %s",
603 ftp2ext(gmx_fio_getftp(status->fio)));
609 int write_trx(t_trxstatus *status, int nind, const int *ind, const t_atoms *atoms,
610 int step, real time, matrix box, rvec x[], rvec *v,
615 clear_trxframe(&fr, TRUE);
620 fr.bAtoms = atoms != nullptr;
621 fr.atoms = const_cast<t_atoms *>(atoms);
624 fr.bV = v != nullptr;
627 copy_mat(box, fr.box);
629 return write_trxframe_indexed(status, &fr, nind, ind, gc);
632 void close_trx(t_trxstatus *status)
634 if (status == nullptr)
638 gmx_tng_close(&status->tng);
641 gmx_fio_close(status->fio);
643 sfree(status->persistent_line);
645 sfree(status->vmdplugin);
647 /* The memory in status->xframe is lost here,
648 * but the read_first_x/read_next_x functions are deprecated anyhow.
649 * read_first_frame/read_next_frame and close_trx should be used.
654 t_trxstatus *open_trx(const char *outfile, const char *filemode)
657 if (filemode[0] != 'w' && filemode[0] != 'a' && filemode[1] != '+')
659 gmx_fatal(FARGS, "Sorry, write_trx can only write");
665 stat->fio = gmx_fio_open(outfile, filemode);
669 static gmx_bool gmx_next_frame(t_trxstatus *status, t_trxframe *fr)
676 if (gmx_trr_read_frame_header(status->fio, &sh, &bOK))
678 fr->bDouble = sh.bDouble;
679 fr->natoms = sh.natoms;
685 fr->bFepState = TRUE;
686 fr->lambda = sh.lambda;
687 fr->bBox = sh.box_size > 0;
688 if (status->flags & (TRX_READ_X | TRX_NEED_X))
690 if (fr->x == nullptr)
692 snew(fr->x, sh.natoms);
694 fr->bX = sh.x_size > 0;
696 if (status->flags & (TRX_READ_V | TRX_NEED_V))
698 if (fr->v == nullptr)
700 snew(fr->v, sh.natoms);
702 fr->bV = sh.v_size > 0;
704 if (status->flags & (TRX_READ_F | TRX_NEED_F))
706 if (fr->f == nullptr)
708 snew(fr->f, sh.natoms);
710 fr->bF = sh.f_size > 0;
712 if (gmx_trr_read_frame_data(status->fio, &sh, fr->box, fr->x, fr->v, fr->f))
718 fr->not_ok = DATA_NOT_OK;
723 fr->not_ok = HEADER_NOT_OK;
729 static gmx_bool pdb_next_x(t_trxstatus *status, FILE *fp, t_trxframe *fr)
734 // Initiate model_nr to -1 rather than NOTSET.
735 // It is not worthwhile introducing extra variables in the
736 // read_pdbfile call to verify that a model_nr was read.
737 int ePBC, model_nr = -1, na;
738 char title[STRLEN], *time, *step;
741 atoms.nr = fr->natoms;
742 atoms.atom = nullptr;
743 atoms.pdbinfo = nullptr;
744 /* the other pointers in atoms should not be accessed if these are NULL */
747 na = read_pdbfile(fp, title, &model_nr, &atoms, symtab, fr->x, &ePBC, boxpdb, TRUE, nullptr);
750 set_trxframe_ePBC(fr, ePBC);
751 if (nframes_read(status) == 0)
753 fprintf(stderr, " '%s', %d atoms\n", title, fr->natoms);
758 fr->bBox = (boxpdb[XX][XX] != 0.0);
761 copy_mat(boxpdb, fr->box);
765 step = std::strstr(title, " step= ");
766 fr->bStep = (step && sscanf(step+7, "%" SCNd64, &fr->step) == 1);
769 time = std::strstr(title, " t= ");
770 fr->bTime = (time && sscanf(time+4, "%lf", &dbl) == 1);
779 if (na != fr->natoms)
781 gmx_fatal(FARGS, "Number of atoms in pdb frame %d is %d instead of %d",
782 nframes_read(status), na, fr->natoms);
788 static int pdb_first_x(t_trxstatus *status, FILE *fp, t_trxframe *fr)
792 fprintf(stderr, "Reading frames from pdb file");
794 get_pdb_coordnum(fp, &fr->natoms);
797 gmx_fatal(FARGS, "\nNo coordinates in pdb file\n");
800 snew(fr->x, fr->natoms);
801 pdb_next_x(status, fp, fr);
806 bool read_next_frame(const gmx_output_env_t *oenv, t_trxstatus *status, t_trxframe *fr)
810 gmx_bool bOK, bMissingData = FALSE, bSkip = FALSE;
818 clear_trxframe(fr, FALSE);
822 /* Special treatment for TNG files */
827 ftp = gmx_fio_getftp(status->fio);
832 bRet = gmx_next_frame(status, fr);
835 /* Checkpoint files can not contain mulitple frames */
839 t_symtab *symtab = nullptr;
840 read_g96_conf(gmx_fio_getfp(status->fio), nullptr, nullptr, fr,
841 symtab, status->persistent_line);
842 bRet = (fr->natoms > 0);
846 if (bTimeSet(TBEGIN) && (status->tf < rTimeValue(TBEGIN)))
848 if (xtc_seek_time(status->fio, rTimeValue(TBEGIN), fr->natoms, TRUE))
850 gmx_fatal(FARGS, "Specified frame (time %f) doesn't exist or file corrupt/inconsistent.",
855 bRet = read_next_xtc(status->fio, fr->natoms, &fr->step, &fr->time, fr->box,
856 fr->x, &fr->prec, &bOK);
857 fr->bPrec = (bRet && fr->prec > 0);
864 /* Actually the header could also be not ok,
865 but from bOK from read_next_xtc this can't be distinguished */
866 fr->not_ok = DATA_NOT_OK;
870 bRet = gmx_read_next_tng_frame(status->tng, fr, nullptr, 0);
873 bRet = pdb_next_x(status, gmx_fio_getfp(status->fio), fr);
876 bRet = gro_next_x_or_v(gmx_fio_getfp(status->fio), fr);
880 bRet = read_next_vmd_frame(status->vmdplugin, fr);
882 gmx_fatal(FARGS, "DEATH HORROR in read_next_frame ftp=%s,status=%s",
883 ftp2ext(gmx_fio_getftp(status->fio)),
884 gmx_fio_getname(status->fio));
887 status->tf = fr->time;
891 bMissingData = (((status->flags & TRX_NEED_X) && !fr->bX) ||
892 ((status->flags & TRX_NEED_V) && !fr->bV) ||
893 ((status->flags & TRX_NEED_F) && !fr->bF));
897 ct = check_times2(fr->time, status->t0, fr->bDouble);
898 if (ct == 0 || ((status->flags & TRX_DONT_SKIP) && ct < 0))
900 printcount(status, oenv, fr->time, FALSE);
908 printcount(status, oenv, fr->time, TRUE);
915 while (bRet && (bMissingData || bSkip));
919 printlast(status, oenv, pt);
922 printincomp(status, fr);
929 bool read_first_frame(const gmx_output_env_t *oenv, t_trxstatus **status,
930 const char *fn, t_trxframe *fr, int flags)
932 t_fileio *fio = nullptr;
933 gmx_bool bFirst, bOK;
934 int ftp = fn2ftp(fn);
936 clear_trxframe(fr, TRUE);
942 status_init( *status );
944 (*status)->flags = flags;
948 /* Special treatment for TNG files */
949 gmx_tng_open(fn, 'r', &(*status)->tng);
953 fio = (*status)->fio = gmx_fio_open(fn, "r");
960 read_checkpoint_trxframe(fio, fr);
965 /* Can not rewind a compressed file, so open it twice */
966 if (!(*status)->persistent_line)
968 /* allocate the persistent line */
969 snew((*status)->persistent_line, STRLEN+1);
971 t_symtab *symtab = nullptr;
972 read_g96_conf(gmx_fio_getfp(fio), fn, nullptr, fr, symtab, (*status)->persistent_line);
974 clear_trxframe(fr, FALSE);
975 if (flags & (TRX_READ_X | TRX_NEED_X))
977 snew(fr->x, fr->natoms);
979 if (flags & (TRX_READ_V | TRX_NEED_V))
981 snew(fr->v, fr->natoms);
983 (*status)->fio = gmx_fio_open(fn, "r");
987 if (read_first_xtc(fio, &fr->natoms, &fr->step, &fr->time, fr->box, &fr->x,
988 &fr->prec, &bOK) == 0)
990 GMX_RELEASE_ASSERT(!bOK, "Inconsistent results - OK status from read_first_xtc, but 0 atom coords read");
991 fr->not_ok = DATA_NOT_OK;
996 printincomp(*status, fr);
1000 fr->bPrec = (fr->prec > 0);
1005 printcount(*status, oenv, fr->time, FALSE);
1011 if (!gmx_read_next_tng_frame((*status)->tng, fr, nullptr, 0))
1013 fr->not_ok = DATA_NOT_OK;
1015 printincomp(*status, fr);
1019 printcount(*status, oenv, fr->time, FALSE);
1024 pdb_first_x(*status, gmx_fio_getfp(fio), fr);
1027 printcount(*status, oenv, fr->time, FALSE);
1032 if (gro_first_x_or_v(gmx_fio_getfp(fio), fr))
1034 printcount(*status, oenv, fr->time, FALSE);
1040 fprintf(stderr, "The file format of %s is not a known trajectory format to GROMACS.\n"
1041 "Please make sure that the file is a trajectory!\n"
1042 "GROMACS will now assume it to be a trajectory and will try to open it using the VMD plug-ins.\n"
1043 "This will only work in case the VMD plugins are found and it is a trajectory format supported by VMD.\n", fn);
1044 gmx_fio_fp_close(fio); /*only close the file without removing FIO entry*/
1045 if (!read_first_vmd_frame(fn, &(*status)->vmdplugin, fr))
1047 gmx_fatal(FARGS, "Not supported in read_first_frame: %s", fn);
1050 gmx_fatal(FARGS, "Not supported in read_first_frame: %s. Please make sure that the file is a trajectory.\n"
1051 "GROMACS is not compiled with plug-in support. Thus it cannot read non-GROMACS trajectory formats using the VMD plug-ins.\n"
1052 "Please compile with plug-in support if you want to read non-GROMACS trajectory formats.\n", fn);
1056 (*status)->tf = fr->time;
1058 /* Return FALSE if we read a frame that's past the set ending time. */
1059 if (!bFirst && (!(flags & TRX_DONT_SKIP) && check_times(fr->time) > 0))
1061 (*status)->t0 = fr->time;
1066 (!(flags & TRX_DONT_SKIP) && check_times(fr->time) < 0))
1068 /* Read a frame when no frame was read or the first was skipped */
1069 if (!read_next_frame(oenv, *status, fr))
1074 (*status)->t0 = fr->time;
1076 /* We need the number of atoms for random-access XTC searching, even when
1077 * we don't have access to the actual frame data.
1079 (*status)->natoms = fr->natoms;
1081 return (fr->natoms > 0);
1084 /***** C O O R D I N A T E S T U F F *****/
1086 int read_first_x(const gmx_output_env_t *oenv, t_trxstatus **status, const char *fn,
1087 real *t, rvec **x, matrix box)
1091 read_first_frame(oenv, status, fn, &fr, TRX_NEED_X);
1093 snew((*status)->xframe, 1);
1094 (*(*status)->xframe) = fr;
1095 *t = (*status)->xframe->time;
1096 *x = (*status)->xframe->x;
1097 copy_mat((*status)->xframe->box, box);
1099 return (*status)->xframe->natoms;
1102 gmx_bool read_next_x(const gmx_output_env_t *oenv, t_trxstatus *status, real *t,
1103 rvec x[], matrix box)
1107 status->xframe->x = x;
1108 /*xframe[status].x = x;*/
1109 bRet = read_next_frame(oenv, status, status->xframe);
1110 *t = status->xframe->time;
1111 copy_mat(status->xframe->box, box);
1116 void rewind_trj(t_trxstatus *status)
1120 gmx_fio_rewind(status->fio);
1123 /***** T O P O L O G Y S T U F F ******/
1125 t_topology *read_top(const char *fn, int *ePBC)
1131 epbc = read_tpx_top(fn, nullptr, nullptr, &natoms, nullptr, nullptr, top);