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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;
78 /** Allocates data for distance-based selection methods. */
80 init_data_common(int npar, gmx_ana_selparam_t *param);
81 /** Initializes a distance-based selection method. */
83 init_common(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
84 /** Frees the data allocated for a distance-based selection method. */
86 free_data_common(void *data);
87 /** Initializes the evaluation of a distance-based within selection method for a frame. */
89 init_frame_common(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data);
90 /** Evaluates the \p distance selection method. */
92 evaluate_distance(t_topology *top, t_trxframe *fr, t_pbc *pbc,
93 gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
94 /** Evaluates the \p within selection method. */
96 evaluate_within(t_topology *top, t_trxframe *fr, t_pbc *pbc,
97 gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
99 /** Parameters for the \p distance selection method. */
100 static gmx_ana_selparam_t smparams_distance[] = {
101 {"cutoff", {REAL_VALUE, 1, {NULL}}, NULL, SPAR_OPTIONAL},
102 {"from", {POS_VALUE, 1, {NULL}}, NULL, SPAR_DYNAMIC},
105 /** Parameters for the \p mindistance selection method. */
106 static gmx_ana_selparam_t smparams_mindistance[] = {
107 {"cutoff", {REAL_VALUE, 1, {NULL}}, NULL, SPAR_OPTIONAL},
108 {"from", {POS_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
111 /** Parameters for the \p within selection method. */
112 static gmx_ana_selparam_t smparams_within[] = {
113 {NULL, {REAL_VALUE, 1, {NULL}}, NULL, 0},
114 {"of", {POS_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
117 /** Help text for the distance selection methods. */
118 static const char *help_distance[] = {
119 "DISTANCE-BASED SELECTION KEYWORDS[PAR]",
121 "[TT]distance from POS [cutoff REAL][tt][BR]",
122 "[TT]mindistance from POS_EXPR [cutoff REAL][tt][BR]",
123 "[TT]within REAL of POS_EXPR[tt][PAR]",
125 "[TT]distance[tt] and [TT]mindistance[tt] calculate the distance from the",
126 "given position(s), the only difference being in that [TT]distance[tt]",
127 "only accepts a single position, while any number of positions can be",
128 "given for [TT]mindistance[tt], which then calculates the distance to the",
130 "[TT]within[tt] directly selects atoms that are within [TT]REAL[tt] of",
131 "[TT]POS_EXPR[tt].[PAR]",
133 "For the first two keywords, it is possible to specify a cutoff to speed",
134 "up the evaluation: all distances above the specified cutoff are",
135 "returned as equal to the cutoff.",
138 /** \internal Selection method data for the \p distance method. */
139 gmx_ana_selmethod_t sm_distance = {
140 "distance", REAL_VALUE, SMETH_DYNAMIC,
141 asize(smparams_distance), smparams_distance,
150 {"distance from POS [cutoff REAL]", asize(help_distance), help_distance},
153 /** \internal Selection method data for the \p distance method. */
154 gmx_ana_selmethod_t sm_mindistance = {
155 "mindistance", REAL_VALUE, SMETH_DYNAMIC,
156 asize(smparams_mindistance), smparams_mindistance,
165 {"mindistance from POS_EXPR [cutoff REAL]", asize(help_distance), help_distance},
168 /** \internal Selection method data for the \p within method. */
169 gmx_ana_selmethod_t sm_within = {
170 "within", GROUP_VALUE, SMETH_DYNAMIC,
171 asize(smparams_within), smparams_within,
180 {"within REAL of POS_EXPR", asize(help_distance), help_distance},
184 * \param[in] npar Not used (should be 2).
185 * \param[in,out] param Method parameters (should point to one of the distance
187 * \returns Pointer to the allocated data (\c t_methoddata_distance).
189 * Allocates memory for a \c t_methoddata_distance structure and
190 * initializes the parameter as follows:
191 * - the first parameter defines the value for
192 * \c t_methoddata_distance::cutoff.
193 * - the second parameter defines the reference positions and the value is
194 * stored in \c t_methoddata_distance::p.
197 init_data_common(int npar, gmx_ana_selparam_t *param)
199 t_methoddata_distance *data = new t_methoddata_distance();
200 param[0].val.u.r = &data->cutoff;
201 param[1].val.u.p = &data->p;
206 * \param top Not used.
207 * \param npar Not used (should be 2).
208 * \param param Method parameters (should point to one of the distance
210 * \param data Pointer to \c t_methoddata_distance to initialize.
211 * \returns 0 on success, a non-zero error code on failure.
213 * Initializes the neighborhood search data structure
214 * (\c t_methoddata_distance::nb).
215 * Also checks that the cutoff is valid.
218 init_common(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data)
220 t_methoddata_distance *d = (t_methoddata_distance *)data;
222 if ((param[0].flags & SPAR_SET) && d->cutoff <= 0)
224 GMX_THROW(gmx::InvalidInputError("Distance cutoff should be > 0"));
226 d->nb.setCutoff(d->cutoff);
230 * \param data Data to free (should point to a \c t_methoddata_distance).
232 * Frees the memory allocated for \c t_methoddata_distance::xref and
233 * \c t_methoddata_distance::nb.
236 free_data_common(void *data)
238 delete static_cast<t_methoddata_distance *>(data);
242 * \param[in] top Not used.
243 * \param[in] fr Current frame.
244 * \param[in] pbc PBC structure.
245 * \param data Should point to a \c t_methoddata_distance.
246 * \returns 0 on success, a non-zero error code on error.
248 * Initializes the neighborhood search for the current frame.
251 init_frame_common(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data)
253 t_methoddata_distance *d = (t_methoddata_distance *)data;
256 gmx::AnalysisNeighborhoodPositions pos(d->p.x, d->p.count());
257 d->nbsearch = d->nb.initSearch(pbc, pos);
261 * See sel_updatefunc_pos() for description of the parameters.
262 * \p data should point to a \c t_methoddata_distance.
264 * Calculates the distance of each position from \c t_methoddata_distance::p
265 * and puts them in \p out->u.r.
268 evaluate_distance(t_topology *top, t_trxframe *fr, t_pbc *pbc,
269 gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data)
271 t_methoddata_distance *d = (t_methoddata_distance *)data;
273 out->nr = pos->m.mapb.nra;
274 for (int b = 0; b < pos->count(); ++b)
276 real dist = d->nbsearch.minimumDistance(pos->x[b]);
277 for (int i = pos->m.mapb.index[b]; i < pos->m.mapb.index[b+1]; ++i)
285 * See sel_updatefunc() for description of the parameters.
286 * \p data should point to a \c t_methoddata_distance.
288 * Finds the atoms that are closer than the defined cutoff to
289 * \c t_methoddata_distance::xref and puts them in \p out.g.
292 evaluate_within(t_topology *top, t_trxframe *fr, t_pbc *pbc,
293 gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data)
295 t_methoddata_distance *d = (t_methoddata_distance *)data;
298 for (int b = 0; b < pos->count(); ++b)
300 if (d->nbsearch.isWithin(pos->x[b]))
302 gmx_ana_pos_add_to_group(out->u.g, pos, b);