void
TrajectoryAnalysisRunnerCommon::doneIndexGroups(SelectionCollection *selections)
{
if (impl_->grps_ != NULL)
{
selections->setIndexGroups(NULL);
gmx_ana_indexgrps_free(impl_->grps_);
impl_->grps_ = NULL;
}
}
TrajectoryAnalysisRunnerCommon::Impl::~Impl()
{
if (grps_ != NULL)
{
gmx_ana_indexgrps_free(grps_);
}
finishTrajectory();
if (fr)
{
// There doesn't seem to be a function for freeing frame data
sfree(fr->x);
sfree(fr->v);
sfree(fr->f);
sfree(fr);
}
if (oenv_ != NULL)
{
output_env_done(oenv_);
}
}
/*!
* \param[in,out] d Trajectory analysis data structure.
* \returns 0 on success, a non-zero error code on error.
*
* Initializes the selection data in \c gmx_ana_traj_t based on
* the selection options and/or index files provided on the command line.
*
* This function is called automatically by parse_trjana_args() and should
* not be called directly unless \ref ANA_USER_SELINIT is specified.
*
* \see ANA_USER_SELINIT
*/
int
gmx_ana_init_selections(gmx_ana_traj_t *d)
{
int rc;
int i;
int nr;
gmx_ana_indexgrps_t *grps;
int natoms;
bool bStdIn;
bool bInteractive;
bool bOk;
if (d->sel)
{
gmx_call("init_selections called more than once\n"
"perhaps you forgot ANA_USER_SELINIT");
return -1;
}
/* Check if we need some information from the topology */
if (gmx_ana_selcollection_requires_top(d->sc))
{
rc = load_topology(d, TRUE);
if (rc != 0)
{
return rc;
}
}
/* Load the topology and init the index groups */
gmx_ana_indexgrps_init(&grps, d->top, d->ndxfile);
/* Parse the selection */
rc = gmx_ana_selmethod_register_defaults(d->sc);
if (rc != 0)
{
gmx_fatal(FARGS, "default selection method registration failed");
return rc;
}
bStdIn = (d->selfile && d->selfile[0] == '-' && d->selfile[1] == 0)
|| (d->selection && d->selection[0] == 0)
|| (!d->selfile && !d->selection);
bInteractive = bStdIn && isatty(fileno(stdin));
if (bStdIn && bInteractive)
{
/* Parse from stdin */
/* First we parse the reference groups if there are any */
if (d->nrefgrps > 0)
{
fprintf(stderr, "\nSpecify ");
if (d->nrefgrps == 1)
{
fprintf(stderr, "a reference selection");
}
else
{
fprintf(stderr, "%d reference selections", d->nrefgrps);
}
fprintf(stderr, ":\n");
fprintf(stderr, "(one selection per line, use \\ for line continuation)\n");
rc = gmx_ana_selcollection_parse_stdin(d->sc, d->nrefgrps, grps, TRUE);
nr = gmx_ana_selcollection_get_count(d->sc);
if (rc != 0 || nr != d->nrefgrps)
{
gmx_ana_traj_free(d);
gmx_input("unrecoverable error in selection parsing");
return rc;
}
}
/* Then, we parse the analysis groups */
fprintf(stderr, "\nSpecify ");
if (d->nanagrps == 1)
{
fprintf(stderr, "a selection");
}
else if (d->nanagrps == -1)
{
fprintf(stderr, "any number of selections");
}
else
{
fprintf(stderr, "%d selections", d->nanagrps);
}
fprintf(stderr, " for analysis:\n");
fprintf(stderr, "(one selection per line, use \\ for line continuation%s)\n",
d->nanagrps == -1 ? ", Ctrl-D to end" : "");
rc = gmx_ana_selcollection_parse_stdin(d->sc, d->nanagrps, grps, TRUE);
fprintf(stderr, "\n");
}
else if (bStdIn)
{
rc = gmx_ana_selcollection_parse_stdin(d->sc, -1, grps, FALSE);
}
else if (d->selection)
{
rc = gmx_ana_selcollection_parse_str(d->sc, d->selection, grps);
}
else
{
rc = gmx_ana_selcollection_parse_file(d->sc, d->selfile, grps);
}
gmx_ana_indexgrps_free(grps);
if (rc != 0)
{
/* Free memory for memory leak checking */
gmx_ana_traj_free(d);
gmx_input("selection(s) could not be parsed");
return rc;
}
/* Check the number of groups */
nr = gmx_ana_selcollection_get_count(d->sc);
if (nr <= d->nrefgrps)
{
gmx_input("selection does not specify enough index groups");
return -1;
}
if (d->nanagrps <= 0)
{
d->nanagrps = nr - d->nrefgrps;
}
else if (nr != d->nrefgrps + d->nanagrps)
{
gmx_input("selection does not specify the correct number of index groups");
return -1;
}
if (d->flags & ANA_DEBUG_SELECTION)
{
gmx_ana_selcollection_print_tree(stderr, d->sc, FALSE);
}
if (gmx_ana_selcollection_requires_top(d->sc))
{
rc = load_topology(d, TRUE);
if (rc != 0)
{
return rc;
}
}
if (d->top)
{
natoms = -1;
}
else
{
rc = init_first_frame(d);
if (rc != 0)
{
return rc;
}
natoms = d->fr->natoms;
}
gmx_ana_selcollection_set_topology(d->sc, d->top, natoms);
rc = gmx_ana_selcollection_compile(d->sc);
if (rc != 0)
{
/* Free memory for memory leak checking */
gmx_ana_traj_free(d);
gmx_input("selection could not be compiled");
return rc;
}
/* Create the selection array */
d->ngrps = gmx_ana_selcollection_get_count(d->sc);
if (!(d->flags & ANA_USE_FULLGRPS))
{
d->ngrps -= d->nrefgrps;
}
snew(d->sel, d->ngrps);
for (i = 0; i < d->ngrps; ++i)
{
if (d->flags & ANA_USE_FULLGRPS)
{
d->sel[i] = gmx_ana_selcollection_get_selection(d->sc, i);
}
else
{
d->sel[i] = gmx_ana_selcollection_get_selection(d->sc, i + d->nrefgrps);
}
}
if (d->flags & ANA_DEBUG_SELECTION)
{
fprintf(stderr, "\n");
gmx_ana_selcollection_print_tree(stderr, d->sc, FALSE);
fprintf(stderr, "\n");
gmx_ana_poscalc_coll_print_tree(stderr, d->pcc);
fprintf(stderr, "\n");
}
/* Initialize the position evaluation */
gmx_ana_poscalc_init_eval(d->pcc);
if (d->flags & ANA_DEBUG_SELECTION)
{
gmx_ana_poscalc_coll_print_tree(stderr, d->pcc);
fprintf(stderr, "\n");
}
/* Check that dynamic selections are not provided if not allowed */
if (d->flags & ANA_NO_DYNSEL)
{
for (i = 0; i < d->nrefgrps + d->nanagrps; ++i)
{
gmx_ana_selection_t *sel;
sel = gmx_ana_selcollection_get_selection(d->sc, i);
if (sel->bDynamic)
{
gmx_fatal(FARGS, "%s does not support dynamic selections",
ShortProgram());
return -1;
}
}
}
/* Check that non-atom positions are not provided if not allowed.
* TODO: It would be better to have these checks in the parser. */
if (d->flags & ANA_ONLY_ATOMPOS)
{
for (i = 0; i < d->nanagrps; ++i)
{
gmx_ana_selection_t *sel;
sel = gmx_ana_selcollection_get_selection(d->sc, i + d->nrefgrps);
if (sel->p.m.type != INDEX_ATOM)
{
gmx_fatal(FARGS, "%s does not support non-atom positions",
ShortProgram());
return -1;
}
}
}
/* Create the names array */
snew(d->grpnames, d->ngrps);
for (i = 0; i < d->ngrps; ++i)
{
d->grpnames[i] = gmx_ana_selection_name(d->sel[i]);
}
return 0;
}