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37 * Implements distance-based selection methods.
39 * This file implements the \p distance, \p mindistance and \p within
42 * \author Teemu Murtola <teemu.murtola@gmail.com>
43 * \ingroup module_selection
45 #include "gromacs/legacyheaders/macros.h"
46 #include "gromacs/legacyheaders/pbc.h"
47 #include "gromacs/legacyheaders/vec.h"
49 #include "gromacs/selection/nbsearch.h"
50 #include "gromacs/selection/position.h"
51 #include "gromacs/selection/selmethod.h"
52 #include "gromacs/utility/exceptions.h"
56 * Data structure for distance-based selection method.
58 * The same data structure is used by all the distance-based methods.
60 * \ingroup module_selection
62 struct t_methoddata_distance
64 t_methoddata_distance() : cutoff(-1.0)
68 /** Cutoff distance. */
70 /** Positions of the reference points. */
72 /** Neighborhood search data. */
73 gmx::AnalysisNeighborhood nb;
74 /** Neighborhood search for an invididual frame. */
75 gmx::AnalysisNeighborhoodSearch nbsearch;
79 * Allocates data for distance-based selection methods.
81 * \param[in] npar Not used (should be 2).
82 * \param[in,out] param Method parameters (should point to one of the distance
84 * \returns Pointer to the allocated data (\c t_methoddata_distance).
86 * Allocates memory for a \c t_methoddata_distance structure and
87 * initializes the parameter as follows:
88 * - the first parameter defines the value for
89 * \c t_methoddata_distance::cutoff.
90 * - the second parameter defines the reference positions and the value is
91 * stored in \c t_methoddata_distance::p.
94 init_data_common(int npar, gmx_ana_selparam_t *param);
96 * Initializes a distance-based selection method.
98 * \param top Not used.
99 * \param npar Not used (should be 2).
100 * \param param Method parameters (should point to one of the distance
102 * \param data Pointer to \c t_methoddata_distance to initialize.
103 * \returns 0 on success, a non-zero error code on failure.
105 * Initializes the neighborhood search data structure
106 * (\c t_methoddata_distance::nb).
107 * Also checks that the cutoff is valid.
110 init_common(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
111 /** Frees the data allocated for a distance-based selection method. */
113 free_data_common(void *data);
115 * Initializes the evaluation of a distance-based within selection method for a
118 * \param[in] top Not used.
119 * \param[in] fr Current frame.
120 * \param[in] pbc PBC structure.
121 * \param data Should point to a \c t_methoddata_distance.
122 * \returns 0 on success, a non-zero error code on error.
124 * Initializes the neighborhood search for the current frame.
127 init_frame_common(t_topology *top, t_trxframe * fr, t_pbc *pbc, void *data);
128 /** Evaluates the \p distance selection method. */
130 evaluate_distance(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
131 gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
132 /** Evaluates the \p within selection method. */
134 evaluate_within(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
135 gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
137 /** Parameters for the \p distance selection method. */
138 static gmx_ana_selparam_t smparams_distance[] = {
139 {"cutoff", {REAL_VALUE, 1, {NULL}}, NULL, SPAR_OPTIONAL},
140 {"from", {POS_VALUE, 1, {NULL}}, NULL, SPAR_DYNAMIC},
143 /** Parameters for the \p mindistance selection method. */
144 static gmx_ana_selparam_t smparams_mindistance[] = {
145 {"cutoff", {REAL_VALUE, 1, {NULL}}, NULL, SPAR_OPTIONAL},
146 {"from", {POS_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
149 /** Parameters for the \p within selection method. */
150 static gmx_ana_selparam_t smparams_within[] = {
151 {NULL, {REAL_VALUE, 1, {NULL}}, NULL, 0},
152 {"of", {POS_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
155 /** Help text for the distance selection methods. */
156 static const char *help_distance[] = {
157 "DISTANCE-BASED SELECTION KEYWORDS[PAR]",
159 "[TT]distance from POS [cutoff REAL][tt][BR]",
160 "[TT]mindistance from POS_EXPR [cutoff REAL][tt][BR]",
161 "[TT]within REAL of POS_EXPR[tt][PAR]",
163 "[TT]distance[tt] and [TT]mindistance[tt] calculate the distance from the",
164 "given position(s), the only difference being in that [TT]distance[tt]",
165 "only accepts a single position, while any number of positions can be",
166 "given for [TT]mindistance[tt], which then calculates the distance to the",
168 "[TT]within[tt] directly selects atoms that are within [TT]REAL[tt] of",
169 "[TT]POS_EXPR[tt].[PAR]",
171 "For the first two keywords, it is possible to specify a cutoff to speed",
172 "up the evaluation: all distances above the specified cutoff are",
173 "returned as equal to the cutoff.",
176 /** \internal Selection method data for the \p distance method. */
177 gmx_ana_selmethod_t sm_distance = {
178 "distance", REAL_VALUE, SMETH_DYNAMIC,
179 asize(smparams_distance), smparams_distance,
188 {"distance from POS [cutoff REAL]", asize(help_distance), help_distance},
191 /** \internal Selection method data for the \p distance method. */
192 gmx_ana_selmethod_t sm_mindistance = {
193 "mindistance", REAL_VALUE, SMETH_DYNAMIC,
194 asize(smparams_mindistance), smparams_mindistance,
203 {"mindistance from POS_EXPR [cutoff REAL]", asize(help_distance), help_distance},
206 /** \internal Selection method data for the \p within method. */
207 gmx_ana_selmethod_t sm_within = {
208 "within", GROUP_VALUE, SMETH_DYNAMIC,
209 asize(smparams_within), smparams_within,
218 {"within REAL of POS_EXPR", asize(help_distance), help_distance},
222 init_data_common(int /* npar */, gmx_ana_selparam_t *param)
224 t_methoddata_distance *data = new t_methoddata_distance();
225 param[0].val.u.r = &data->cutoff;
226 param[1].val.u.p = &data->p;
231 init_common(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
233 t_methoddata_distance *d = (t_methoddata_distance *)data;
235 if ((param[0].flags & SPAR_SET) && d->cutoff <= 0)
237 GMX_THROW(gmx::InvalidInputError("Distance cutoff should be > 0"));
239 d->nb.setCutoff(d->cutoff);
243 * \param data Data to free (should point to a \c t_methoddata_distance).
245 * Frees the memory allocated for \c t_methoddata_distance::xref and
246 * \c t_methoddata_distance::nb.
249 free_data_common(void *data)
251 delete static_cast<t_methoddata_distance *>(data);
255 init_frame_common(t_topology * /* top */, t_trxframe * /* fr */, t_pbc *pbc, void *data)
257 t_methoddata_distance *d = (t_methoddata_distance *)data;
260 gmx::AnalysisNeighborhoodPositions pos(d->p.x, d->p.count());
261 d->nbsearch = d->nb.initSearch(pbc, pos);
265 * See sel_updatefunc_pos() for description of the parameters.
266 * \p data should point to a \c t_methoddata_distance.
268 * Calculates the distance of each position from \c t_methoddata_distance::p
269 * and puts them in \p out->u.r.
272 evaluate_distance(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
273 gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data)
275 t_methoddata_distance *d = (t_methoddata_distance *)data;
277 out->nr = pos->m.mapb.nra;
278 for (int b = 0; b < pos->count(); ++b)
280 real dist = d->nbsearch.minimumDistance(pos->x[b]);
281 for (int i = pos->m.mapb.index[b]; i < pos->m.mapb.index[b+1]; ++i)
289 * See sel_updatefunc() for description of the parameters.
290 * \p data should point to a \c t_methoddata_distance.
292 * Finds the atoms that are closer than the defined cutoff to
293 * \c t_methoddata_distance::xref and puts them in \p out.g.
296 evaluate_within(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
297 gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data)
299 t_methoddata_distance *d = (t_methoddata_distance *)data;
302 for (int b = 0; b < pos->count(); ++b)
304 if (d->nbsearch.isWithin(pos->x[b]))
306 gmx_ana_pos_add_to_group(out->u.g, pos, b);