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+ * the research papers on the package. Check out http://www.gromacs.org.
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/*! \internal \file
* \brief
* This file implements the \p distance, \p mindistance and \p within
* selection methods.
*
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/pbc.h"
-#include "gromacs/legacyheaders/smalloc.h"
-#include "gromacs/legacyheaders/vec.h"
+#include "gmxpre.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
#include "gromacs/selection/nbsearch.h"
#include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
#include "gromacs/utility/exceptions.h"
-/*! \internal \brief
+#include "selmethod.h"
+
+/*! \internal
+ * \brief
* Data structure for distance-based selection method.
*
* The same data structure is used by all the distance-based methods.
+ *
+ * \ingroup module_selection
*/
-typedef struct
+struct t_methoddata_distance
{
+ t_methoddata_distance() : cutoff(-1.0)
+ {
+ }
+
/** Cutoff distance. */
- real cutoff;
+ real cutoff;
/** Positions of the reference points. */
- gmx_ana_pos_t p;
+ gmx_ana_pos_t p;
/** Neighborhood search data. */
- gmx_ana_nbsearch_t *nb;
-} t_methoddata_distance;
+ gmx::AnalysisNeighborhood nb;
+ /** Neighborhood search for an invididual frame. */
+ gmx::AnalysisNeighborhoodSearch nbsearch;
+};
-/** Allocates data for distance-based selection methods. */
+/*! \brief
+ * Allocates data for distance-based selection methods.
+ *
+ * \param[in] npar Not used (should be 2).
+ * \param[in,out] param Method parameters (should point to one of the distance
+ * parameter arrays).
+ * \returns Pointer to the allocated data (\c t_methoddata_distance).
+ *
+ * Allocates memory for a \c t_methoddata_distance structure and
+ * initializes the parameter as follows:
+ * - the first parameter defines the value for
+ * \c t_methoddata_distance::cutoff.
+ * - the second parameter defines the reference positions and the value is
+ * stored in \c t_methoddata_distance::p.
+ */
static void *
init_data_common(int npar, gmx_ana_selparam_t *param);
-/** Initializes a distance-based selection method. */
+/*! \brief
+ * Initializes a distance-based selection method.
+ *
+ * \param top Not used.
+ * \param npar Not used (should be 2).
+ * \param param Method parameters (should point to one of the distance
+ * parameter arrays).
+ * \param data Pointer to \c t_methoddata_distance to initialize.
+ * \returns 0 on success, a non-zero error code on failure.
+ *
+ * Initializes the neighborhood search data structure
+ * (\c t_methoddata_distance::nb).
+ * Also checks that the cutoff is valid.
+ */
static void
init_common(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
/** Frees the data allocated for a distance-based selection method. */
static void
free_data_common(void *data);
-/** Initializes the evaluation of a distance-based within selection method for a frame. */
+/*! \brief
+ * Initializes the evaluation of a distance-based within selection method for a
+ * frame.
+ *
+ * \param[in] top Not used.
+ * \param[in] fr Current frame.
+ * \param[in] pbc PBC structure.
+ * \param data Should point to a \c t_methoddata_distance.
+ * \returns 0 on success, a non-zero error code on error.
+ *
+ * Initializes the neighborhood search for the current frame.
+ */
static void
-init_frame_common(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data);
+init_frame_common(t_topology *top, t_trxframe * fr, t_pbc *pbc, void *data);
/** Evaluates the \p distance selection method. */
static void
-evaluate_distance(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_distance(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
/** Evaluates the \p within selection method. */
static void
-evaluate_within(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_within(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
/** Parameters for the \p distance selection method. */
"returned as equal to the cutoff.",
};
-/** \internal Selection method data for the \p distance method. */
+/** Selection method data for the \p distance method. */
gmx_ana_selmethod_t sm_distance = {
"distance", REAL_VALUE, SMETH_DYNAMIC,
asize(smparams_distance), smparams_distance,
{"distance from POS [cutoff REAL]", asize(help_distance), help_distance},
};
-/** \internal Selection method data for the \p distance method. */
+/** Selection method data for the \p distance method. */
gmx_ana_selmethod_t sm_mindistance = {
"mindistance", REAL_VALUE, SMETH_DYNAMIC,
asize(smparams_mindistance), smparams_mindistance,
{"mindistance from POS_EXPR [cutoff REAL]", asize(help_distance), help_distance},
};
-/** \internal Selection method data for the \p within method. */
+/** Selection method data for the \p within method. */
gmx_ana_selmethod_t sm_within = {
"within", GROUP_VALUE, SMETH_DYNAMIC,
asize(smparams_within), smparams_within,
{"within REAL of POS_EXPR", asize(help_distance), help_distance},
};
-/*!
- * \param[in] npar Not used (should be 2).
- * \param[in,out] param Method parameters (should point to one of the distance
- * parameter arrays).
- * \returns Pointer to the allocated data (\c t_methoddata_distance).
- *
- * Allocates memory for a \c t_methoddata_distance structure and
- * initializes the parameter as follows:
- * - the first parameter defines the value for
- * \c t_methoddata_distance::cutoff.
- * - the second parameter defines the reference positions and the value is
- * stored in \c t_methoddata_distance::p.
- */
static void *
-init_data_common(int npar, gmx_ana_selparam_t *param)
+init_data_common(int /* npar */, gmx_ana_selparam_t *param)
{
- t_methoddata_distance *data;
-
- snew(data, 1);
- data->cutoff = -1;
+ t_methoddata_distance *data = new t_methoddata_distance();
param[0].val.u.r = &data->cutoff;
param[1].val.u.p = &data->p;
return data;
}
-/*!
- * \param top Not used.
- * \param npar Not used (should be 2).
- * \param param Method parameters (should point to one of the distance
- * parameter arrays).
- * \param data Pointer to \c t_methoddata_distance to initialize.
- * \returns 0 on success, a non-zero error code on failure.
- *
- * Initializes the neighborhood search data structure
- * (\c t_methoddata_distance::nb).
- * Also checks that the cutoff is valid.
- */
static void
-init_common(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data)
+init_common(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
{
- t_methoddata_distance *d = (t_methoddata_distance *)data;
+ t_methoddata_distance *d = static_cast<t_methoddata_distance *>(data);
if ((param[0].flags & SPAR_SET) && d->cutoff <= 0)
{
GMX_THROW(gmx::InvalidInputError("Distance cutoff should be > 0"));
}
- d->nb = gmx_ana_nbsearch_create(d->cutoff, d->p.nr);
+ d->nb.setCutoff(d->cutoff);
}
/*!
static void
free_data_common(void *data)
{
- t_methoddata_distance *d = (t_methoddata_distance *)data;
-
- if (d->nb)
- {
- gmx_ana_nbsearch_free(d->nb);
- }
- sfree(d);
+ delete static_cast<t_methoddata_distance *>(data);
}
-/*!
- * \param[in] top Not used.
- * \param[in] fr Current frame.
- * \param[in] pbc PBC structure.
- * \param data Should point to a \c t_methoddata_distance.
- * \returns 0 on success, a non-zero error code on error.
- *
- * Initializes the neighborhood search for the current frame.
- */
static void
-init_frame_common(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data)
+init_frame_common(t_topology * /* top */, t_trxframe * /* fr */, t_pbc *pbc, void *data)
{
- t_methoddata_distance *d = (t_methoddata_distance *)data;
+ t_methoddata_distance *d = static_cast<t_methoddata_distance *>(data);
- gmx_ana_nbsearch_pos_init(d->nb, pbc, &d->p);
+ d->nbsearch.reset();
+ gmx::AnalysisNeighborhoodPositions pos(d->p.x, d->p.count());
+ d->nbsearch = d->nb.initSearch(pbc, pos);
}
/*!
* and puts them in \p out->u.r.
*/
static void
-evaluate_distance(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_distance(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data)
{
- t_methoddata_distance *d = (t_methoddata_distance *)data;
- int b, i;
- real n;
+ t_methoddata_distance *d = static_cast<t_methoddata_distance *>(data);
- out->nr = pos->g->isize;
- for (b = 0; b < pos->nr; ++b)
+ out->nr = pos->m.mapb.nra;
+ for (int b = 0; b < pos->count(); ++b)
{
- n = gmx_ana_nbsearch_pos_mindist(d->nb, pos, b);
- for (i = pos->m.mapb.index[b]; i < pos->m.mapb.index[b+1]; ++i)
+ real dist = d->nbsearch.minimumDistance(pos->x[b]);
+ for (int i = pos->m.mapb.index[b]; i < pos->m.mapb.index[b+1]; ++i)
{
- out->u.r[i] = n;
+ out->u.r[i] = dist;
}
}
}
* \c t_methoddata_distance::xref and puts them in \p out.g.
*/
static void
-evaluate_within(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_within(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data)
{
- t_methoddata_distance *d = (t_methoddata_distance *)data;
- int b;
+ t_methoddata_distance *d = static_cast<t_methoddata_distance *>(data);
out->u.g->isize = 0;
- for (b = 0; b < pos->nr; ++b)
+ for (int b = 0; b < pos->count(); ++b)
{
- if (gmx_ana_nbsearch_pos_is_within(d->nb, pos, b))
+ if (d->nbsearch.isWithin(pos->x[b]))
{
- gmx_ana_pos_append(NULL, out->u.g, pos, b, 0);
+ gmx_ana_pos_add_to_group(out->u.g, pos, b);
}
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff