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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"
47 #include "gromacs/math/vec.h"
48 #include "gromacs/selection/nbsearch.h"
49 #include "gromacs/selection/position.h"
50 #include "gromacs/selection/selmethod.h"
51 #include "gromacs/utility/exceptions.h"
55 * Data structure for distance-based selection method.
57 * The same data structure is used by all the distance-based methods.
59 * \ingroup module_selection
61 struct t_methoddata_distance
63 t_methoddata_distance() : cutoff(-1.0)
67 /** Cutoff distance. */
69 /** Positions of the reference points. */
71 /** Neighborhood search data. */
72 gmx::AnalysisNeighborhood nb;
73 /** Neighborhood search for an invididual frame. */
74 gmx::AnalysisNeighborhoodSearch nbsearch;
78 * Allocates data for distance-based selection methods.
80 * \param[in] npar Not used (should be 2).
81 * \param[in,out] param Method parameters (should point to one of the distance
83 * \returns Pointer to the allocated data (\c t_methoddata_distance).
85 * Allocates memory for a \c t_methoddata_distance structure and
86 * initializes the parameter as follows:
87 * - the first parameter defines the value for
88 * \c t_methoddata_distance::cutoff.
89 * - the second parameter defines the reference positions and the value is
90 * stored in \c t_methoddata_distance::p.
93 init_data_common(int npar, gmx_ana_selparam_t *param);
95 * Initializes a distance-based selection method.
97 * \param top Not used.
98 * \param npar Not used (should be 2).
99 * \param param Method parameters (should point to one of the distance
101 * \param data Pointer to \c t_methoddata_distance to initialize.
102 * \returns 0 on success, a non-zero error code on failure.
104 * Initializes the neighborhood search data structure
105 * (\c t_methoddata_distance::nb).
106 * Also checks that the cutoff is valid.
109 init_common(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
110 /** Frees the data allocated for a distance-based selection method. */
112 free_data_common(void *data);
114 * Initializes the evaluation of a distance-based within selection method for a
117 * \param[in] top Not used.
118 * \param[in] fr Current frame.
119 * \param[in] pbc PBC structure.
120 * \param data Should point to a \c t_methoddata_distance.
121 * \returns 0 on success, a non-zero error code on error.
123 * Initializes the neighborhood search for the current frame.
126 init_frame_common(t_topology *top, t_trxframe * fr, t_pbc *pbc, void *data);
127 /** Evaluates the \p distance selection method. */
129 evaluate_distance(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
130 gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
131 /** Evaluates the \p within selection method. */
133 evaluate_within(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
134 gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
136 /** Parameters for the \p distance selection method. */
137 static gmx_ana_selparam_t smparams_distance[] = {
138 {"cutoff", {REAL_VALUE, 1, {NULL}}, NULL, SPAR_OPTIONAL},
139 {"from", {POS_VALUE, 1, {NULL}}, NULL, SPAR_DYNAMIC},
142 /** Parameters for the \p mindistance selection method. */
143 static gmx_ana_selparam_t smparams_mindistance[] = {
144 {"cutoff", {REAL_VALUE, 1, {NULL}}, NULL, SPAR_OPTIONAL},
145 {"from", {POS_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
148 /** Parameters for the \p within selection method. */
149 static gmx_ana_selparam_t smparams_within[] = {
150 {NULL, {REAL_VALUE, 1, {NULL}}, NULL, 0},
151 {"of", {POS_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
154 /** Help text for the distance selection methods. */
155 static const char *help_distance[] = {
156 "DISTANCE-BASED SELECTION KEYWORDS[PAR]",
158 "[TT]distance from POS [cutoff REAL][tt][BR]",
159 "[TT]mindistance from POS_EXPR [cutoff REAL][tt][BR]",
160 "[TT]within REAL of POS_EXPR[tt][PAR]",
162 "[TT]distance[tt] and [TT]mindistance[tt] calculate the distance from the",
163 "given position(s), the only difference being in that [TT]distance[tt]",
164 "only accepts a single position, while any number of positions can be",
165 "given for [TT]mindistance[tt], which then calculates the distance to the",
167 "[TT]within[tt] directly selects atoms that are within [TT]REAL[tt] of",
168 "[TT]POS_EXPR[tt].[PAR]",
170 "For the first two keywords, it is possible to specify a cutoff to speed",
171 "up the evaluation: all distances above the specified cutoff are",
172 "returned as equal to the cutoff.",
175 /** Selection method data for the \p distance method. */
176 gmx_ana_selmethod_t sm_distance = {
177 "distance", REAL_VALUE, SMETH_DYNAMIC,
178 asize(smparams_distance), smparams_distance,
187 {"distance from POS [cutoff REAL]", asize(help_distance), help_distance},
190 /** Selection method data for the \p distance method. */
191 gmx_ana_selmethod_t sm_mindistance = {
192 "mindistance", REAL_VALUE, SMETH_DYNAMIC,
193 asize(smparams_mindistance), smparams_mindistance,
202 {"mindistance from POS_EXPR [cutoff REAL]", asize(help_distance), help_distance},
205 /** Selection method data for the \p within method. */
206 gmx_ana_selmethod_t sm_within = {
207 "within", GROUP_VALUE, SMETH_DYNAMIC,
208 asize(smparams_within), smparams_within,
217 {"within REAL of POS_EXPR", asize(help_distance), help_distance},
221 init_data_common(int /* npar */, gmx_ana_selparam_t *param)
223 t_methoddata_distance *data = new t_methoddata_distance();
224 param[0].val.u.r = &data->cutoff;
225 param[1].val.u.p = &data->p;
230 init_common(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
232 t_methoddata_distance *d = static_cast<t_methoddata_distance *>(data);
234 if ((param[0].flags & SPAR_SET) && d->cutoff <= 0)
236 GMX_THROW(gmx::InvalidInputError("Distance cutoff should be > 0"));
238 d->nb.setCutoff(d->cutoff);
242 * \param data Data to free (should point to a \c t_methoddata_distance).
244 * Frees the memory allocated for \c t_methoddata_distance::xref and
245 * \c t_methoddata_distance::nb.
248 free_data_common(void *data)
250 delete static_cast<t_methoddata_distance *>(data);
254 init_frame_common(t_topology * /* top */, t_trxframe * /* fr */, t_pbc *pbc, void *data)
256 t_methoddata_distance *d = static_cast<t_methoddata_distance *>(data);
259 gmx::AnalysisNeighborhoodPositions pos(d->p.x, d->p.count());
260 d->nbsearch = d->nb.initSearch(pbc, pos);
264 * See sel_updatefunc_pos() for description of the parameters.
265 * \p data should point to a \c t_methoddata_distance.
267 * Calculates the distance of each position from \c t_methoddata_distance::p
268 * and puts them in \p out->u.r.
271 evaluate_distance(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
272 gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data)
274 t_methoddata_distance *d = static_cast<t_methoddata_distance *>(data);
276 out->nr = pos->m.mapb.nra;
277 for (int b = 0; b < pos->count(); ++b)
279 real dist = d->nbsearch.minimumDistance(pos->x[b]);
280 for (int i = pos->m.mapb.index[b]; i < pos->m.mapb.index[b+1]; ++i)
288 * See sel_updatefunc() for description of the parameters.
289 * \p data should point to a \c t_methoddata_distance.
291 * Finds the atoms that are closer than the defined cutoff to
292 * \c t_methoddata_distance::xref and puts them in \p out.g.
295 evaluate_within(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
296 gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data)
298 t_methoddata_distance *d = static_cast<t_methoddata_distance *>(data);
301 for (int b = 0; b < pos->count(); ++b)
303 if (d->nbsearch.isWithin(pos->x[b]))
305 gmx_ana_pos_add_to_group(out->u.g, pos, b);