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33 * Implements distance-based selection methods.
35 * This file implements the \p distance, \p mindistance and \p within
38 * \author Teemu Murtola <teemu.murtola@cbr.su.se>
39 * \ingroup module_selection
50 #include "gromacs/selection/nbsearch.h"
51 #include "gromacs/selection/position.h"
52 #include "gromacs/selection/selmethod.h"
53 #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.
62 /** Cutoff distance. */
64 /** Positions of the reference points. */
66 /** Neighborhood search data. */
67 gmx_ana_nbsearch_t *nb;
68 } t_methoddata_distance;
70 /** Allocates data for distance-based selection methods. */
72 init_data_common(int npar, gmx_ana_selparam_t *param);
73 /** Initializes a distance-based selection method. */
75 init_common(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
76 /** Frees the data allocated for a distance-based selection method. */
78 free_data_common(void *data);
79 /** Initializes the evaluation of a distance-based within selection method for a frame. */
81 init_frame_common(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data);
82 /** Evaluates the \p distance selection method. */
84 evaluate_distance(t_topology *top, t_trxframe *fr, t_pbc *pbc,
85 gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
86 /** Evaluates the \p within selection method. */
88 evaluate_within(t_topology *top, t_trxframe *fr, t_pbc *pbc,
89 gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
91 /** Parameters for the \p distance selection method. */
92 static gmx_ana_selparam_t smparams_distance[] = {
93 {"cutoff", {REAL_VALUE, 1, {NULL}}, NULL, SPAR_OPTIONAL},
94 {"from", {POS_VALUE, 1, {NULL}}, NULL, SPAR_DYNAMIC},
97 /** Parameters for the \p mindistance selection method. */
98 static gmx_ana_selparam_t smparams_mindistance[] = {
99 {"cutoff", {REAL_VALUE, 1, {NULL}}, NULL, SPAR_OPTIONAL},
100 {"from", {POS_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
103 /** Parameters for the \p within selection method. */
104 static gmx_ana_selparam_t smparams_within[] = {
105 {NULL, {REAL_VALUE, 1, {NULL}}, NULL, 0},
106 {"of", {POS_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
109 /** Help text for the distance selection methods. */
110 static const char *help_distance[] = {
111 "DISTANCE-BASED SELECTION KEYWORDS[PAR]",
113 "[TT]distance from POS [cutoff REAL][tt][BR]",
114 "[TT]mindistance from POS_EXPR [cutoff REAL][tt][BR]",
115 "[TT]within REAL of POS_EXPR[tt][PAR]",
117 "[TT]distance[tt] and [TT]mindistance[tt] calculate the distance from the",
118 "given position(s), the only difference being in that [TT]distance[tt]",
119 "only accepts a single position, while any number of positions can be",
120 "given for [TT]mindistance[tt], which then calculates the distance to the",
122 "[TT]within[tt] directly selects atoms that are within [TT]REAL[tt] of",
123 "[TT]POS_EXPR[tt].[PAR]",
125 "For the first two keywords, it is possible to specify a cutoff to speed",
126 "up the evaluation: all distances above the specified cutoff are",
127 "returned as equal to the cutoff.",
130 /** \internal Selection method data for the \p distance method. */
131 gmx_ana_selmethod_t sm_distance = {
132 "distance", REAL_VALUE, SMETH_DYNAMIC,
133 asize(smparams_distance), smparams_distance,
142 {"distance from POS [cutoff REAL]", asize(help_distance), help_distance},
145 /** \internal Selection method data for the \p distance method. */
146 gmx_ana_selmethod_t sm_mindistance = {
147 "mindistance", REAL_VALUE, SMETH_DYNAMIC,
148 asize(smparams_mindistance), smparams_mindistance,
157 {"mindistance from POS_EXPR [cutoff REAL]", asize(help_distance), help_distance},
160 /** \internal Selection method data for the \p within method. */
161 gmx_ana_selmethod_t sm_within = {
162 "within", GROUP_VALUE, SMETH_DYNAMIC,
163 asize(smparams_within), smparams_within,
172 {"within REAL of POS_EXPR", asize(help_distance), help_distance},
176 * \param[in] npar Not used (should be 2).
177 * \param[in,out] param Method parameters (should point to one of the distance
179 * \returns Pointer to the allocated data (\c t_methoddata_distance).
181 * Allocates memory for a \c t_methoddata_distance structure and
182 * initializes the parameter as follows:
183 * - the first parameter defines the value for
184 * \c t_methoddata_distance::cutoff.
185 * - the second parameter defines the reference positions and the value is
186 * stored in \c t_methoddata_distance::p.
189 init_data_common(int npar, gmx_ana_selparam_t *param)
191 t_methoddata_distance *data;
195 param[0].val.u.r = &data->cutoff;
196 param[1].val.u.p = &data->p;
201 * \param top Not used.
202 * \param npar Not used (should be 2).
203 * \param param Method parameters (should point to one of the distance
205 * \param data Pointer to \c t_methoddata_distance to initialize.
206 * \returns 0 on success, a non-zero error code on failure.
208 * Initializes the neighborhood search data structure
209 * (\c t_methoddata_distance::nb).
210 * Also checks that the cutoff is valid.
213 init_common(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data)
215 t_methoddata_distance *d = (t_methoddata_distance *)data;
217 if ((param[0].flags & SPAR_SET) && d->cutoff <= 0)
219 GMX_THROW(gmx::InvalidInputError("Distance cutoff should be > 0"));
221 d->nb = gmx_ana_nbsearch_create(d->cutoff, d->p.nr);
225 * \param data Data to free (should point to a \c t_methoddata_distance).
227 * Frees the memory allocated for \c t_methoddata_distance::xref and
228 * \c t_methoddata_distance::nb.
231 free_data_common(void *data)
233 t_methoddata_distance *d = (t_methoddata_distance *)data;
237 gmx_ana_nbsearch_free(d->nb);
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;
255 gmx_ana_nbsearch_pos_init(d->nb, pbc, &d->p);
259 * See sel_updatefunc_pos() for description of the parameters.
260 * \p data should point to a \c t_methoddata_distance.
262 * Calculates the distance of each position from \c t_methoddata_distance::p
263 * and puts them in \p out->u.r.
266 evaluate_distance(t_topology *top, t_trxframe *fr, t_pbc *pbc,
267 gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data)
269 t_methoddata_distance *d = (t_methoddata_distance *)data;
273 out->nr = pos->g->isize;
274 for (b = 0; b < pos->nr; ++b)
276 n = gmx_ana_nbsearch_pos_mindist(d->nb, pos, b);
277 for (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;
299 for (b = 0; b < pos->nr; ++b)
301 if (gmx_ana_nbsearch_pos_is_within(d->nb, pos, b))
303 gmx_ana_pos_append(NULL, out->u.g, pos, b, 0);