#include "gromacs/utility/smalloc.h"
#if GMX_USE_PLUGINS
-#include "gromacs/fileio/vmdio.h"
+# include "gromacs/fileio/vmdio.h"
#endif
/* defines for frame counter output */
-#define SKIP1 10
-#define SKIP2 100
+#define SKIP1 10
+#define SKIP2 100
#define SKIP3 1000
struct t_trxstatus
{
- int flags; /* flags for read_first/next_frame */
- int __frame;
- real t0; /* time of the first frame, needed *
- * for skipping frames with -dt */
- real tf; /* internal frame time */
- t_trxframe *xframe;
- t_fileio *fio;
- gmx_tng_trajectory_t tng;
- int natoms;
- double DT, BOX[3];
- gmx_bool bReadBox;
- char *persistent_line; /* Persistent line for reading g96 trajectories */
+ int flags; /* flags for read_first/next_frame */
+ int __frame;
+ real t0; /* time of the first frame, needed *
+ * for skipping frames with -dt */
+ real tf; /* internal frame time */
+ t_trxframe* xframe;
+ t_fileio* fio;
+ gmx_tng_trajectory_t tng;
+ int natoms;
+ double DT, BOX[3];
+ gmx_bool bReadBox;
+ char* persistent_line; /* Persistent line for reading g96 trajectories */
#if GMX_USE_PLUGINS
- gmx_vmdplugin_t *vmdplugin;
+ gmx_vmdplugin_t* vmdplugin;
#endif
};
int iq;
double tol;
- tol = 2*(bDouble ? GMX_DOUBLE_EPS : GMX_FLOAT_EPS);
+ tol = 2 * (bDouble ? GMX_DOUBLE_EPS : GMX_FLOAT_EPS);
- iq = static_cast<int>((a - b + tol*a)/c);
+ iq = static_cast<int>((a - b + tol * a) / c);
- return fabs(a - b - c*iq) <= tol*fabs(a);
+ return fabs(a - b - c * iq) <= tol * fabs(a);
}
-
int check_times2(real t, real t0, gmx_bool bDouble)
{
- int r;
+ int r;
#if !GMX_DOUBLE
/* since t is float, we can not use double precision for bRmod */
#endif
r = -1;
- if ((!bTimeSet(TBEGIN) || (t >= rTimeValue(TBEGIN))) &&
- (!bTimeSet(TEND) || (t <= rTimeValue(TEND))))
+ if ((!bTimeSet(TBEGIN) || (t >= rTimeValue(TBEGIN))) && (!bTimeSet(TEND) || (t <= rTimeValue(TEND))))
{
if (bTimeSet(TDELTA) && !bRmod_fd(t, t0, rTimeValue(TDELTA), bDouble))
{
}
if (debug)
{
- fprintf(debug, "t=%g, t0=%g, b=%g, e=%g, dt=%g: r=%d\n",
- t, t0, rTimeValue(TBEGIN), rTimeValue(TEND), rTimeValue(TDELTA), r);
+ fprintf(debug, "t=%g, t0=%g, b=%g, e=%g, dt=%g: r=%d\n", t, t0, rTimeValue(TBEGIN),
+ rTimeValue(TEND), rTimeValue(TDELTA), r);
}
return r;
}
return check_times2(t, t, FALSE);
}
-static void initcount(t_trxstatus *status)
+static void initcount(t_trxstatus* status)
{
status->__frame = -1;
}
-static void status_init(t_trxstatus *status)
+static void status_init(t_trxstatus* status)
{
status->flags = 0;
status->xframe = nullptr;
}
-int nframes_read(t_trxstatus *status)
+int nframes_read(t_trxstatus* status)
{
return status->__frame;
}
-static void printcount_(t_trxstatus *status, const gmx_output_env_t *oenv,
- const char *l, real t)
+static void printcount_(t_trxstatus* status, const gmx_output_env_t* oenv, const char* l, real t)
{
- if ((status->__frame < 2*SKIP1 || status->__frame % SKIP1 == 0) &&
- (status->__frame < 2*SKIP2 || status->__frame % SKIP2 == 0) &&
- (status->__frame < 2*SKIP3 || status->__frame % SKIP3 == 0) &&
- output_env_get_trajectory_io_verbosity(oenv) != 0)
+ if ((status->__frame < 2 * SKIP1 || status->__frame % SKIP1 == 0)
+ && (status->__frame < 2 * SKIP2 || status->__frame % SKIP2 == 0)
+ && (status->__frame < 2 * SKIP3 || status->__frame % SKIP3 == 0)
+ && output_env_get_trajectory_io_verbosity(oenv) != 0)
{
- fprintf(stderr, "\r%-14s %6d time %8.3f ", l, status->__frame,
- output_env_conv_time(oenv, t));
+ fprintf(stderr, "\r%-14s %6d time %8.3f ", l, status->__frame, output_env_conv_time(oenv, t));
fflush(stderr);
}
}
-static void printcount(t_trxstatus *status, const gmx_output_env_t *oenv, real t,
- gmx_bool bSkip)
+static void printcount(t_trxstatus* status, const gmx_output_env_t* oenv, real t, gmx_bool bSkip)
{
status->__frame++;
printcount_(status, oenv, bSkip ? "Skipping frame" : "Reading frame", t);
}
-static void printlast(t_trxstatus *status, const gmx_output_env_t *oenv, real t)
+static void printlast(t_trxstatus* status, const gmx_output_env_t* oenv, real t)
{
printcount_(status, oenv, "Last frame", t);
fprintf(stderr, "\n");
fflush(stderr);
}
-static void printincomp(t_trxstatus *status, t_trxframe *fr)
+static void printincomp(t_trxstatus* status, t_trxframe* fr)
{
if (fr->not_ok & HEADER_NOT_OK)
{
- fprintf(stderr, "WARNING: Incomplete header: nr %d time %g\n",
- status->__frame+1, fr->time);
+ fprintf(stderr, "WARNING: Incomplete header: nr %d time %g\n", status->__frame + 1, fr->time);
}
else if (fr->not_ok)
{
- fprintf(stderr, "WARNING: Incomplete frame: nr %d time %g\n",
- status->__frame+1, fr->time);
+ fprintf(stderr, "WARNING: Incomplete frame: nr %d time %g\n", status->__frame + 1, fr->time);
}
fflush(stderr);
}
gmx_fatal(FARGS, "DEATH HORROR prec (%g) <= 0 in prec2ndec", prec);
}
- return gmx::roundToInt(log(prec)/log(10.0));
+ return gmx::roundToInt(log(prec) / log(10.0));
}
real ndec2prec(int ndec)
return pow(10.0, ndec);
}
-t_fileio *trx_get_fileio(t_trxstatus *status)
+t_fileio* trx_get_fileio(t_trxstatus* status)
{
return status->fio;
}
-float trx_get_time_of_final_frame(t_trxstatus *status)
+float trx_get_time_of_final_frame(t_trxstatus* status)
{
- t_fileio *stfio = trx_get_fileio(status);
+ t_fileio* stfio = trx_get_fileio(status);
int filetype = gmx_fio_getftp(stfio);
gmx_bool bOK;
float lasttime = -1;
if (filetype == efXTC)
{
- lasttime =
- xdr_xtc_get_last_frame_time(gmx_fio_getfp(stfio),
- gmx_fio_getxdr(stfio),
- status->natoms, &bOK);
+ lasttime = xdr_xtc_get_last_frame_time(gmx_fio_getfp(stfio), gmx_fio_getxdr(stfio),
+ status->natoms, &bOK);
if (!bOK)
{
- gmx_fatal(FARGS, "Error reading last frame. Maybe seek not supported." );
+ gmx_fatal(FARGS, "Error reading last frame. Maybe seek not supported.");
}
}
else if (filetype == efTNG)
return lasttime;
}
-void clear_trxframe(t_trxframe *fr, gmx_bool bFirst)
+void clear_trxframe(t_trxframe* fr, gmx_bool bFirst)
{
fr->not_ok = 0;
fr->bStep = FALSE;
fr->v = nullptr;
fr->f = nullptr;
clear_mat(fr->box);
- fr->bPBC = FALSE;
- fr->ePBC = -1;
+ fr->bPBC = FALSE;
+ fr->ePBC = -1;
}
}
-void set_trxframe_ePBC(t_trxframe *fr, int ePBC)
+void set_trxframe_ePBC(t_trxframe* fr, int ePBC)
{
fr->bPBC = (ePBC == -1);
fr->ePBC = ePBC;
}
-int write_trxframe_indexed(t_trxstatus *status, const t_trxframe *fr, int nind,
- const int *ind, gmx_conect gc)
+int write_trxframe_indexed(t_trxstatus* status, const t_trxframe* fr, int nind, const int* ind, gmx_conect gc)
{
char title[STRLEN];
rvec *xout = nullptr, *vout = nullptr, *fout = nullptr;
switch (ftp)
{
case efTRR:
- case efTNG:
- break;
+ case efTNG: break;
default:
if (!fr->bX)
{
- gmx_fatal(FARGS, "Need coordinates to write a %s trajectory",
- ftp2ext(ftp));
+ gmx_fatal(FARGS, "Need coordinates to write a %s trajectory", ftp2ext(ftp));
}
break;
}
}
}
break;
- default:
- break;
+ default: break;
}
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;
+ 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;
case efTRR:
- gmx_trr_write_frame(status->fio, nframes_read(status),
- fr->time, fr->step, fr->box, nind, xout, vout, fout);
+ gmx_trr_write_frame(status->fio, nframes_read(status), fr->time, fr->step, fr->box,
+ nind, xout, vout, fout);
break;
case efGRO:
case efPDB:
case efENT:
if (!fr->bAtoms)
{
- gmx_fatal(FARGS, "Can not write a %s file without atom names",
- ftp2ext(ftp));
+ gmx_fatal(FARGS, "Can not write a %s file without atom names", ftp2ext(ftp));
}
sprintf(title, "frame t= %.3f", fr->time);
if (ftp == efGRO)
}
else
{
- write_pdbfile_indexed(gmx_fio_getfp(status->fio), title, fr->atoms,
- fr->x, -1, fr->box, ' ', fr->step, nind, ind, gc, FALSE);
+ write_pdbfile_indexed(gmx_fio_getfp(status->fio), title, fr->atoms, fr->x, -1,
+ fr->box, ' ', fr->step, nind, ind, gc, FALSE);
}
break;
case efG96:
sprintf(title, "frame t= %.3f", fr->time);
write_g96_conf(gmx_fio_getfp(status->fio), title, fr, nind, ind);
break;
- default:
- gmx_fatal(FARGS, "Sorry, write_trxframe_indexed can not write %s",
- ftp2ext(ftp));
+ default: gmx_fatal(FARGS, "Sorry, write_trxframe_indexed can not write %s", ftp2ext(ftp));
}
switch (ftp)
}
sfree(xout);
break;
- case efXTC:
- sfree(xout);
- break;
- default:
- break;
+ case efXTC: sfree(xout); break;
+ default: break;
}
return 0;
}
-t_trxstatus *
-trjtools_gmx_prepare_tng_writing(const char *filename,
- char filemode,
- t_trxstatus *in,
- const char *infile,
- const int natoms,
- const gmx_mtop_t *mtop,
- gmx::ArrayRef<const int> index,
- const char *index_group_name)
+t_trxstatus* trjtools_gmx_prepare_tng_writing(const char* filename,
+ char filemode,
+ t_trxstatus* in,
+ const char* infile,
+ const int natoms,
+ const gmx_mtop_t* mtop,
+ gmx::ArrayRef<const int> index,
+ const char* index_group_name)
{
if (filemode != 'w' && filemode != 'a')
{
gmx_incons("Sorry, can only prepare for TNG output.");
}
- t_trxstatus *out;
+ t_trxstatus* out;
snew(out, 1);
status_init(out);
if (in != nullptr)
{
- gmx_prepare_tng_writing(filename,
- filemode,
- &in->tng,
- &out->tng,
- natoms,
- mtop,
- index,
+ gmx_prepare_tng_writing(filename, filemode, &in->tng, &out->tng, natoms, mtop, index,
index_group_name);
}
else if ((infile) && (efTNG == fn2ftp(infile)))
gmx_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,
+ gmx_prepare_tng_writing(filename, filemode, &tng_in, &out->tng, natoms, mtop, index,
index_group_name);
}
else
{
// we start from a file that is not a tng file or have been unable to load the
// input file, so we need to populate the fields independently of it
- gmx_prepare_tng_writing(filename,
- filemode,
- nullptr,
- &out->tng,
- natoms,
- mtop,
- index,
+ gmx_prepare_tng_writing(filename, filemode, nullptr, &out->tng, natoms, mtop, index,
index_group_name);
}
return out;
}
-void write_tng_frame(t_trxstatus *status,
- t_trxframe *frame)
+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)
+int write_trxframe(t_trxstatus* status, t_trxframe* fr, gmx_conect gc)
{
char title[STRLEN];
title[0] = '\0';
switch (gmx_fio_getftp(status->fio))
{
- case efTRR:
- break;
+ case efTRR: break;
default:
if (!fr->bX)
{
break;
case efTRR:
gmx_trr_write_frame(status->fio, fr->step, fr->time, fr->lambda, fr->box, fr->natoms,
- fr->bX ? fr->x : nullptr, fr->bV ? fr->v : nullptr, fr->bF ? fr->f : nullptr);
+ fr->bX ? fr->x : nullptr, fr->bV ? fr->v : nullptr,
+ fr->bF ? fr->f : nullptr);
break;
case efGRO:
case efPDB:
sprintf(title, "frame t= %.3f", fr->time);
if (gmx_fio_getftp(status->fio) == efGRO)
{
- write_hconf_p(gmx_fio_getfp(status->fio), title, fr->atoms,
- fr->x, fr->bV ? fr->v : nullptr, fr->box);
+ write_hconf_p(gmx_fio_getfp(status->fio), title, fr->atoms, fr->x,
+ fr->bV ? fr->v : nullptr, fr->box);
}
else
{
- write_pdbfile(gmx_fio_getfp(status->fio), title,
- fr->atoms, fr->x, fr->bPBC ? fr->ePBC : -1, fr->box,
- ' ', fr->step, gc);
+ write_pdbfile(gmx_fio_getfp(status->fio), title, fr->atoms, fr->x,
+ fr->bPBC ? fr->ePBC : -1, fr->box, ' ', fr->step, gc);
}
break;
- case efG96:
- write_g96_conf(gmx_fio_getfp(status->fio), title, fr, -1, nullptr);
- break;
+ case efG96: write_g96_conf(gmx_fio_getfp(status->fio), title, fr, -1, nullptr); break;
default:
gmx_fatal(FARGS, "Sorry, write_trxframe can not write %s",
ftp2ext(gmx_fio_getftp(status->fio)));
return 0;
}
-int write_trx(t_trxstatus *status, int nind, const int *ind, const t_atoms *atoms,
- int step, real time, matrix box, rvec x[], rvec *v,
- gmx_conect gc)
+int write_trx(t_trxstatus* status,
+ int nind,
+ const int* ind,
+ const t_atoms* atoms,
+ int step,
+ real time,
+ matrix box,
+ rvec x[],
+ rvec* v,
+ gmx_conect gc)
{
t_trxframe fr;
fr.bTime = TRUE;
fr.time = time;
fr.bAtoms = atoms != nullptr;
- fr.atoms = const_cast<t_atoms *>(atoms);
+ fr.atoms = const_cast<t_atoms*>(atoms);
fr.bX = TRUE;
fr.x = x;
fr.bV = v != nullptr;
return write_trxframe_indexed(status, &fr, nind, ind, gc);
}
-void close_trx(t_trxstatus *status)
+void close_trx(t_trxstatus* status)
{
if (status == nullptr)
{
sfree(status);
}
-t_trxstatus *open_trx(const char *outfile, const char *filemode)
+t_trxstatus* open_trx(const char* outfile, const char* filemode)
{
- t_trxstatus *stat;
+ t_trxstatus* stat;
if (filemode[0] != 'w' && filemode[0] != 'a' && filemode[1] != '+')
{
gmx_fatal(FARGS, "Sorry, write_trx can only write");
return stat;
}
-static gmx_bool gmx_next_frame(t_trxstatus *status, t_trxframe *fr)
+static gmx_bool gmx_next_frame(t_trxstatus* status, t_trxframe* fr)
{
gmx_trr_header_t sh;
gmx_bool bOK, bRet;
return bRet;
}
-static gmx_bool pdb_next_x(t_trxstatus *status, FILE *fp, t_trxframe *fr)
+static gmx_bool pdb_next_x(t_trxstatus* status, FILE* fp, t_trxframe* fr)
{
t_atoms atoms;
- t_symtab *symtab;
+ t_symtab* symtab;
matrix boxpdb;
// Initiate model_nr to -1 rather than NOTSET.
// It is not worthwhile introducing extra variables in the
// read_pdbfile call to verify that a model_nr was read.
- int ePBC, model_nr = -1, na;
- char title[STRLEN], *time, *step;
- double dbl;
+ int ePBC, model_nr = -1, na;
+ char title[STRLEN], *time, *step;
+ double dbl;
atoms.nr = fr->natoms;
atoms.atom = nullptr;
/* the other pointers in atoms should not be accessed if these are NULL */
snew(symtab, 1);
open_symtab(symtab);
- na = read_pdbfile(fp, title, &model_nr, &atoms, symtab, fr->x, &ePBC, boxpdb, TRUE, nullptr);
+ na = read_pdbfile(fp, title, &model_nr, &atoms, symtab, fr->x, &ePBC, boxpdb, TRUE, nullptr);
free_symtab(symtab);
sfree(symtab);
set_trxframe_ePBC(fr, ePBC);
fr->step = 0;
step = std::strstr(title, " step= ");
- fr->bStep = ((step != nullptr) && sscanf(step+7, "%" SCNd64, &fr->step) == 1);
+ fr->bStep = ((step != nullptr) && sscanf(step + 7, "%" SCNd64, &fr->step) == 1);
dbl = 0.0;
time = std::strstr(title, " t= ");
- fr->bTime = ((time != nullptr) && sscanf(time+4, "%lf", &dbl) == 1);
+ fr->bTime = ((time != nullptr) && sscanf(time + 4, "%lf", &dbl) == 1);
fr->time = dbl;
if (na == 0)
}
}
-static int pdb_first_x(t_trxstatus *status, FILE *fp, t_trxframe *fr)
+static int pdb_first_x(t_trxstatus* status, FILE* fp, t_trxframe* fr)
{
initcount(status);
return fr->natoms;
}
-bool read_next_frame(const gmx_output_env_t *oenv, t_trxstatus *status, t_trxframe *fr)
+bool read_next_frame(const gmx_output_env_t* oenv, t_trxstatus* status, t_trxframe* fr)
{
real pt;
int ct;
bool bRet = false;
int ftp;
- pt = status->tf;
+ pt = status->tf;
do
{
}
switch (ftp)
{
- case efTRR:
- bRet = gmx_next_frame(status, fr);
- break;
+ case efTRR: bRet = gmx_next_frame(status, fr); break;
case efCPT:
/* Checkpoint files can not contain mulitple frames */
break;
case efG96:
{
- t_symtab *symtab = nullptr;
- read_g96_conf(gmx_fio_getfp(status->fio), nullptr, nullptr, fr,
- symtab, status->persistent_line);
+ t_symtab* symtab = nullptr;
+ read_g96_conf(gmx_fio_getfp(status->fio), nullptr, nullptr, fr, symtab,
+ status->persistent_line);
bRet = (fr->natoms > 0);
break;
}
{
if (xtc_seek_time(status->fio, rTimeValue(TBEGIN), fr->natoms, TRUE))
{
- gmx_fatal(FARGS, "Specified frame (time %f) doesn't exist or file corrupt/inconsistent.",
+ gmx_fatal(FARGS,
+ "Specified frame (time %f) doesn't exist or file "
+ "corrupt/inconsistent.",
rTimeValue(TBEGIN));
}
initcount(status);
}
- bRet = (read_next_xtc(status->fio, fr->natoms, &fr->step, &fr->time, fr->box,
- fr->x, &fr->prec, &bOK) != 0);
+ bRet = (read_next_xtc(status->fio, fr->natoms, &fr->step, &fr->time, fr->box, fr->x,
+ &fr->prec, &bOK)
+ != 0);
fr->bPrec = (bRet && fr->prec > 0);
fr->bStep = bRet;
fr->bTime = bRet;
fr->not_ok = DATA_NOT_OK;
}
break;
- case efTNG:
- bRet = gmx_read_next_tng_frame(status->tng, fr, nullptr, 0);
- break;
- case efPDB:
- bRet = pdb_next_x(status, gmx_fio_getfp(status->fio), fr);
- break;
- case efGRO:
- bRet = gro_next_x_or_v(gmx_fio_getfp(status->fio), fr);
- break;
+ case efTNG: bRet = gmx_read_next_tng_frame(status->tng, fr, nullptr, 0); break;
+ case efPDB: bRet = pdb_next_x(status, gmx_fio_getfp(status->fio), fr); break;
+ case efGRO: bRet = gro_next_x_or_v(gmx_fio_getfp(status->fio), fr); break;
default:
#if GMX_USE_PLUGINS
bRet = read_next_vmd_frame(status->vmdplugin, fr);
#else
gmx_fatal(FARGS, "DEATH HORROR in read_next_frame ftp=%s,status=%s",
- ftp2ext(gmx_fio_getftp(status->fio)),
- gmx_fio_getname(status->fio));
+ ftp2ext(gmx_fio_getftp(status->fio)), gmx_fio_getname(status->fio));
#endif
}
status->tf = fr->time;
if (bRet)
{
- bMissingData = ((((status->flags & TRX_NEED_X) != 0) && !fr->bX) ||
- (((status->flags & TRX_NEED_V) != 0) && !fr->bV) ||
- (((status->flags & TRX_NEED_F) != 0) && !fr->bF));
- bSkip = FALSE;
+ bMissingData = ((((status->flags & TRX_NEED_X) != 0) && !fr->bX)
+ || (((status->flags & TRX_NEED_V) != 0) && !fr->bV)
+ || (((status->flags & TRX_NEED_F) != 0) && !fr->bF));
+ bSkip = FALSE;
if (!bMissingData)
{
ct = check_times2(fr->time, status->t0, fr->bDouble);
}
}
- }
- while (bRet && (bMissingData || bSkip));
+ } while (bRet && (bMissingData || bSkip));
if (!bRet)
{
return bRet;
}
-bool read_first_frame(const gmx_output_env_t *oenv, t_trxstatus **status,
- const char *fn, t_trxframe *fr, int flags)
+bool read_first_frame(const gmx_output_env_t* oenv, t_trxstatus** status, const char* fn, t_trxframe* fr, int flags)
{
- t_fileio *fio = nullptr;
- gmx_bool bFirst, bOK;
- int ftp = fn2ftp(fn);
+ t_fileio* fio = nullptr;
+ gmx_bool bFirst, bOK;
+ int ftp = fn2ftp(fn);
clear_trxframe(fr, TRUE);
snew((*status), 1);
- status_init( *status );
+ status_init(*status);
initcount(*status);
(*status)->flags = flags;
}
switch (ftp)
{
- case efTRR:
- break;
+ case efTRR: break;
case efCPT:
read_checkpoint_trxframe(fio, fr);
bFirst = FALSE;
if (!(*status)->persistent_line)
{
/* allocate the persistent line */
- snew((*status)->persistent_line, STRLEN+1);
+ snew((*status)->persistent_line, STRLEN + 1);
}
- t_symtab *symtab = nullptr;
+ t_symtab* symtab = nullptr;
read_g96_conf(gmx_fio_getfp(fio), fn, nullptr, fr, symtab, (*status)->persistent_line);
gmx_fio_close(fio);
clear_trxframe(fr, FALSE);
break;
}
case efXTC:
- if (read_first_xtc(fio, &fr->natoms, &fr->step, &fr->time, fr->box, &fr->x,
- &fr->prec, &bOK) == 0)
+ if (read_first_xtc(fio, &fr->natoms, &fr->step, &fr->time, fr->box, &fr->x, &fr->prec, &bOK) == 0)
{
- GMX_RELEASE_ASSERT(!bOK, "Inconsistent results - OK status from read_first_xtc, but 0 atom coords read");
+ GMX_RELEASE_ASSERT(!bOK,
+ "Inconsistent results - OK status from read_first_xtc, but 0 "
+ "atom coords read");
fr->not_ok = DATA_NOT_OK;
}
if (fr->not_ok)
break;
default:
#if GMX_USE_PLUGINS
- fprintf(stderr, "The file format of %s is not a known trajectory format to GROMACS.\n"
+ fprintf(stderr,
+ "The file format of %s is not a known trajectory format to GROMACS.\n"
"Please make sure that the file is a trajectory!\n"
- "GROMACS will now assume it to be a trajectory and will try to open it using the VMD plug-ins.\n"
- "This will only work in case the VMD plugins are found and it is a trajectory format supported by VMD.\n", fn);
+ "GROMACS will now assume it to be a trajectory and will try to open it using "
+ "the VMD plug-ins.\n"
+ "This will only work in case the VMD plugins are found and it is a trajectory "
+ "format supported by VMD.\n",
+ fn);
gmx_fio_fp_close(fio); /*only close the file without removing FIO entry*/
if (!read_first_vmd_frame(fn, &(*status)->vmdplugin, fr))
{
gmx_fatal(FARGS, "Not supported in read_first_frame: %s", fn);
}
#else
- gmx_fatal(FARGS, "Not supported in read_first_frame: %s. Please make sure that the file is a trajectory.\n"
- "GROMACS is not compiled with plug-in support. Thus it cannot read non-GROMACS trajectory formats using the VMD plug-ins.\n"
- "Please compile with plug-in support if you want to read non-GROMACS trajectory formats.\n", fn);
+ gmx_fatal(FARGS,
+ "Not supported in read_first_frame: %s. Please make sure that the file is a "
+ "trajectory.\n"
+ "GROMACS is not compiled with plug-in support. Thus it cannot read "
+ "non-GROMACS trajectory formats using the VMD plug-ins.\n"
+ "Please compile with plug-in support if you want to read non-GROMACS "
+ "trajectory formats.\n",
+ fn);
#endif
}
(*status)->tf = fr->time;
return FALSE;
}
- if (bFirst ||
- (!(flags & TRX_DONT_SKIP) && check_times(fr->time) < 0))
+ if (bFirst || (!(flags & TRX_DONT_SKIP) && check_times(fr->time) < 0))
{
/* Read a frame when no frame was read or the first was skipped */
if (!read_next_frame(oenv, *status, fr))
/***** C O O R D I N A T E S T U F F *****/
-int read_first_x(const gmx_output_env_t *oenv, t_trxstatus **status, const char *fn,
- real *t, rvec **x, matrix box)
+int read_first_x(const gmx_output_env_t* oenv, t_trxstatus** status, const char* fn, real* t, rvec** x, matrix box)
{
t_trxframe fr;
return (*status)->xframe->natoms;
}
-gmx_bool read_next_x(const gmx_output_env_t *oenv, t_trxstatus *status, real *t,
- rvec x[], matrix box)
+gmx_bool read_next_x(const gmx_output_env_t* oenv, t_trxstatus* status, real* t, rvec x[], matrix box)
{
gmx_bool bRet;
return bRet;
}
-void rewind_trj(t_trxstatus *status)
+void rewind_trj(t_trxstatus* status)
{
initcount(status);
/***** T O P O L O G Y S T U F F ******/
-t_topology *read_top(const char *fn, int *ePBC)
+t_topology* read_top(const char* fn, int* ePBC)
{
int epbc, natoms;
- t_topology *top;
+ t_topology* top;
snew(top, 1);
epbc = read_tpx_top(fn, nullptr, nullptr, &natoms, nullptr, nullptr, top);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff