#include "trxio.h"
#include "tpxio.h"
#include "trnio.h"
+#include "tngio.h"
+#include "tngio_for_tools.h"
#include "names.h"
#include "vec.h"
#include "futil.h"
struct t_trxstatus
{
- int __frame;
- t_trxframe *xframe;
- int nxframe;
- t_fileio *fio;
- eFileFormat eFF;
- int NATOMS;
- double DT, BOX[3];
- gmx_bool bReadBox;
- char *persistent_line; /* Persistent line for reading g96 trajectories */
+ int __frame;
+ t_trxframe *xframe;
+ int nxframe;
+ t_fileio *fio;
+ tng_trajectory_t tng;
+ eFileFormat eFF;
+ int NATOMS;
+ double DT, BOX[3];
+ gmx_bool bReadBox;
+ char *persistent_line; /* Persistent line for reading g96 trajectories */
};
/* utility functions */
status->fio = NULL;
status->__frame = -1;
status->persistent_line = NULL;
+ status->tng = NULL;
}
return (int)(log(prec)/log(10.0)+0.5);
}
+real ndec2prec(int ndec)
+{
+ return pow(10.0, ndec);
+}
t_fileio *trx_get_fileio(t_trxstatus *status)
{
return status->fio;
}
-
+tng_trajectory_t trx_get_tng(t_trxstatus *status)
+{
+ return status->tng;
+}
void clear_trxframe(t_trxframe *fr, gmx_bool bFirst)
{
- fr->not_ok = 0;
- fr->bTitle = FALSE;
- fr->bStep = FALSE;
- fr->bTime = FALSE;
- fr->bLambda = FALSE;
+ fr->not_ok = 0;
+ fr->bTitle = FALSE;
+ fr->bStep = FALSE;
+ fr->bTime = FALSE;
+ fr->bLambda = FALSE;
fr->bFepState = FALSE;
- fr->bAtoms = FALSE;
- fr->bPrec = FALSE;
- fr->bX = FALSE;
- fr->bV = FALSE;
- fr->bF = FALSE;
- fr->bBox = FALSE;
+ fr->bAtoms = FALSE;
+ fr->bPrec = FALSE;
+ fr->bX = FALSE;
+ fr->bV = FALSE;
+ fr->bF = FALSE;
+ fr->bBox = FALSE;
if (bFirst)
{
- fr->flags = 0;
- fr->bDouble = FALSE;
- fr->natoms = -1;
- fr->t0 = 0;
- fr->tpf = 0;
- fr->tppf = 0;
- fr->title = NULL;
- fr->step = 0;
- fr->time = 0;
- fr->lambda = 0;
+ fr->flags = 0;
+ fr->bDouble = FALSE;
+ fr->natoms = -1;
+ fr->t0 = 0;
+ fr->tpf = 0;
+ fr->tppf = 0;
+ fr->title = NULL;
+ fr->step = 0;
+ fr->time = 0;
+ fr->lambda = 0;
fr->fep_state = 0;
- fr->atoms = NULL;
- fr->prec = 0;
- fr->x = NULL;
- fr->v = NULL;
- fr->f = NULL;
+ fr->atoms = NULL;
+ fr->prec = 0;
+ fr->x = NULL;
+ fr->v = NULL;
+ fr->f = NULL;
clear_mat(fr->box);
fr->bPBC = FALSE;
fr->ePBC = -1;
{
char title[STRLEN];
rvec *xout = NULL, *vout = NULL, *fout = NULL;
- int i;
+ int i, ftp = -1;
real prec;
if (fr->bPrec)
prec = 1000.0;
}
- switch (gmx_fio_getftp(status->fio))
+ if (status->tng)
+ {
+ ftp = efTNG;
+ }
+ else if (status->fio)
+ {
+ ftp = gmx_fio_getftp(status->fio);
+ }
+ else
+ {
+ gmx_incons("No input file available");
+ }
+
+ switch (ftp)
{
case efTRJ:
case efTRR:
+ case efTNG:
break;
default:
if (!fr->bX)
{
gmx_fatal(FARGS, "Need coordinates to write a %s trajectory",
- ftp2ext(gmx_fio_getftp(status->fio)));
+ ftp2ext(ftp));
}
break;
}
- switch (gmx_fio_getftp(status->fio))
+ switch (ftp)
{
case efTRJ:
case efTRR:
+ case efTNG:
if (fr->bV)
{
snew(vout, nind);
break;
}
- switch (gmx_fio_getftp(status->fio))
+ switch (ftp)
{
+ case efTNG:
+ gmx_write_tng_from_trxframe(status->tng, fr, nind);
+ break;
case efXTC:
write_xtc(status->fio, nind, fr->step, fr->time, fr->box, xout, prec);
break;
if (!fr->bAtoms)
{
gmx_fatal(FARGS, "Can not write a %s file without atom names",
- ftp2ext(gmx_fio_getftp(status->fio)));
+ ftp2ext(ftp));
}
sprintf(title, "frame t= %.3f", fr->time);
- if (gmx_fio_getftp(status->fio) == efGRO)
+ if (ftp == efGRO)
{
write_hconf_indexed_p(gmx_fio_getfp(status->fio), title, fr->atoms, nind, ind,
prec2ndec(prec),
break;
default:
gmx_fatal(FARGS, "Sorry, write_trxframe_indexed can not write %s",
- ftp2ext(gmx_fio_getftp(status->fio)));
+ ftp2ext(ftp));
break;
}
- switch (gmx_fio_getftp(status->fio))
+ switch (ftp)
{
case efTRN:
case efTRJ:
case efTRR:
+ case efTNG:
if (vout)
{
sfree(vout);
return 0;
}
+void trjtools_gmx_prepare_tng_writing(const char *filename,
+ char filemode,
+ t_trxstatus *in,
+ t_trxstatus **out,
+ const char *infile,
+ const int natoms,
+ const gmx_mtop_t *mtop,
+ const atom_id *index,
+ const char *index_group_name)
+{
+ if (filemode != 'w' && filemode != 'a')
+ {
+ gmx_incons("Sorry, can only prepare for TNG output.");
+ }
+
+ if (*out == NULL)
+ {
+ snew((*out), 1);
+ }
+ status_init(*out);
+
+ if (in != NULL)
+ {
+ gmx_prepare_tng_writing(filename,
+ filemode,
+ &in->tng,
+ &(*out)->tng,
+ natoms,
+ mtop,
+ index,
+ index_group_name);
+ }
+ else if (efTNG == fn2ftp(infile))
+ {
+ tng_trajectory_t tng_in;
+ gmx_tng_open(infile, 'r', &tng_in);
+
+ gmx_prepare_tng_writing(filename,
+ filemode,
+ &tng_in,
+ &(*out)->tng,
+ natoms,
+ mtop,
+ index,
+ index_group_name);
+ }
+}
+
+void write_tng_frame(t_trxstatus *status,
+ t_trxframe *frame)
+{
+ gmx_write_tng_from_trxframe(status->tng, frame, -1);
+}
+
int write_trxframe(t_trxstatus *status, t_trxframe *fr, gmx_conect gc)
{
char title[STRLEN];
prec = 1000.0;
}
+ if (status->tng)
+ {
+ gmx_tng_set_compression_precision(status->tng, prec);
+ write_tng_frame(status, fr);
+
+ return 0;
+ }
+
switch (gmx_fio_getftp(status->fio))
{
case efTRJ:
void close_trx(t_trxstatus *status)
{
- gmx_fio_close(status->fio);
+ gmx_tng_close(&status->tng);
+ if (status->fio)
+ {
+ gmx_fio_close(status->fio);
+ }
sfree(status);
}
int ct;
gmx_bool bOK, bRet, bMissingData = FALSE, bSkip = FALSE;
int dummy = 0;
+ int ftp;
bRet = FALSE;
pt = fr->time;
fr->tppf = fr->tpf;
fr->tpf = fr->time;
- switch (gmx_fio_getftp(status->fio))
+ if (status->tng)
+ {
+ /* Special treatment for TNG files */
+ ftp = efTNG;
+ }
+ else
+ {
+ ftp = gmx_fio_getftp(status->fio);
+ }
+ switch (ftp)
{
case efTRJ:
case efTRR:
fr->not_ok = DATA_NOT_OK;
}
break;
+ case efTNG:
+ bRet = gmx_read_next_tng_frame(status->tng, fr, NULL, 0);
+ break;
case efPDB:
bRet = pdb_next_x(status, gmx_fio_getfp(status->fio), fr);
break;
int read_first_frame(const output_env_t oenv, t_trxstatus **status,
const char *fn, t_trxframe *fr, int flags)
{
- t_fileio *fio;
- gmx_bool bFirst, bOK;
- int dummy = 0;
+ t_fileio *fio;
+ gmx_bool bFirst, bOK;
+ int dummy = 0;
+ int ftp = fn2ftp(fn);
+ gmx_int64_t *tng_ids;
clear_trxframe(fr, TRUE);
fr->flags = flags;
(*status)->nxframe = 1;
initcount(*status);
- fio = (*status)->fio = gmx_fio_open(fn, "r");
- switch (gmx_fio_getftp(fio))
+ if (efTNG == ftp)
+ {
+ /* Special treatment for TNG files */
+ gmx_tng_open(fn, 'r', &(*status)->tng);
+ }
+ else
+ {
+ fio = (*status)->fio = gmx_fio_open(fn, "r");
+ }
+ switch (ftp)
{
case efTRJ:
case efTRR:
}
bFirst = FALSE;
break;
+ case efTNG:
+ fr->step = -1;
+ if (!gmx_read_next_tng_frame((*status)->tng, fr, NULL, 0))
+ {
+ fr->not_ok = DATA_NOT_OK;
+ fr->natoms = 0;
+ printincomp(*status, fr);
+ }
+ else
+ {
+ printcount(*status, oenv, fr->time, FALSE);
+ }
+ bFirst = FALSE;
+ break;
case efPDB:
pdb_first_x(*status, gmx_fio_getfp(fio), fr);
if (fr->natoms)
void close_trj(t_trxstatus *status)
{
- gmx_fio_close(status->fio);
+ gmx_tng_close(&status->tng);
+ if (status->fio)
+ {
+ gmx_fio_close(status->fio);
+ }
+
/* The memory in status->xframe is lost here,
* but the read_first_x/read_next_x functions are deprecated anyhow.
* read_first_frame/read_next_frame and close_trx should be used.
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff