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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
47 #include "gromacs/math/vec.h"
48 #include "gromacs/selection/nbsearch.h"
49 #include "gromacs/utility/arraysize.h"
50 #include "gromacs/utility/exceptions.h"
53 #include "selmethod.h"
54 #include "selmethod_impl.h"
58 * Data structure for distance-based selection method.
60 * The same data structure is used by all the distance-based methods.
62 * \ingroup module_selection
64 struct t_methoddata_distance
66 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.
93 static void* 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.
108 static void init_common(const gmx_mtop_t* top, int npar, gmx_ana_selparam_t* param, void* data);
109 /** Frees the data allocated for a distance-based selection method. */
110 static void free_data_common(void* data);
112 * Initializes the evaluation of a distance-based within selection method for a
115 * \param[in] context Evaluation context.
116 * \param data Should point to a \c t_methoddata_distance.
117 * \returns 0 on success, a non-zero error code on error.
119 * Initializes the neighborhood search for the current frame.
121 static void init_frame_common(const gmx::SelMethodEvalContext& context, void* data);
122 /** Evaluates the \p distance selection method. */
123 static void evaluate_distance(const gmx::SelMethodEvalContext& /*context*/,
125 gmx_ana_selvalue_t* out,
127 /** Evaluates the \p within selection method. */
128 static void evaluate_within(const gmx::SelMethodEvalContext& /*context*/,
130 gmx_ana_selvalue_t* out,
133 /** Parameters for the \p distance selection method. */
134 static gmx_ana_selparam_t smparams_distance[] = {
135 { "cutoff", { REAL_VALUE, 1, { nullptr } }, nullptr, SPAR_OPTIONAL },
136 { "from", { POS_VALUE, 1, { nullptr } }, nullptr, SPAR_DYNAMIC },
139 /** Parameters for the \p mindistance selection method. */
140 static gmx_ana_selparam_t smparams_mindistance[] = {
141 { "cutoff", { REAL_VALUE, 1, { nullptr } }, nullptr, SPAR_OPTIONAL },
142 { "from", { POS_VALUE, -1, { nullptr } }, nullptr, SPAR_DYNAMIC | SPAR_VARNUM },
145 /** Parameters for the \p within selection method. */
146 static gmx_ana_selparam_t smparams_within[] = {
147 { nullptr, { REAL_VALUE, 1, { nullptr } }, nullptr, 0 },
148 { "of", { POS_VALUE, -1, { nullptr } }, nullptr, SPAR_DYNAMIC | SPAR_VARNUM },
151 //! Help title for distance selection methods.
152 static const char helptitle_distance[] = "Selecting based on distance";
153 //! Help text for distance selection methods.
154 static const char* const help_distance[] = {
157 " distance from POS [cutoff REAL]",
158 " mindistance from POS_EXPR [cutoff REAL]",
159 " within REAL of POS_EXPR",
161 "[TT]distance[tt] and [TT]mindistance[tt] calculate the distance from the",
162 "given position(s), the only difference being in that [TT]distance[tt]",
163 "only accepts a single position, while any number of positions can be",
164 "given for [TT]mindistance[tt], which then calculates the distance to the",
166 "[TT]within[tt] directly selects atoms that are within [TT]REAL[tt] of",
167 "[TT]POS_EXPR[tt].[PAR]",
169 "For the first two keywords, it is possible to specify a cutoff to speed",
170 "up the evaluation: all distances above the specified cutoff are",
171 "returned as equal to the cutoff.",
174 /** Selection method data for the \p distance method. */
175 gmx_ana_selmethod_t sm_distance = {
179 asize(smparams_distance),
189 { "distance from POS [cutoff REAL]", helptitle_distance, asize(help_distance), help_distance },
192 /** Selection method data for the \p distance method. */
193 gmx_ana_selmethod_t sm_mindistance = {
197 asize(smparams_mindistance),
198 smparams_mindistance,
207 { "mindistance from POS_EXPR [cutoff REAL]", helptitle_distance, asize(help_distance), help_distance },
210 /** Selection method data for the \p within method. */
211 gmx_ana_selmethod_t sm_within = {
215 asize(smparams_within),
225 { "within REAL of POS_EXPR", helptitle_distance, asize(help_distance), help_distance },
228 static void* init_data_common(int /* npar */, gmx_ana_selparam_t* param)
230 t_methoddata_distance* data = new t_methoddata_distance();
231 param[0].val.u.r = &data->cutoff;
232 param[1].val.u.p = &data->p;
236 static void init_common(const gmx_mtop_t* /* top */, int /* npar */, gmx_ana_selparam_t* param, void* data)
238 t_methoddata_distance* d = static_cast<t_methoddata_distance*>(data);
240 if ((param[0].flags & SPAR_SET) && d->cutoff <= 0)
242 GMX_THROW(gmx::InvalidInputError("Distance cutoff should be > 0"));
244 d->nb.setCutoff(d->cutoff);
248 * \param data Data to free (should point to a \c t_methoddata_distance).
250 * Frees the memory allocated for \c t_methoddata_distance::xref and
251 * \c t_methoddata_distance::nb.
253 static void free_data_common(void* data)
255 delete static_cast<t_methoddata_distance*>(data);
258 static void init_frame_common(const gmx::SelMethodEvalContext& context, void* data)
260 t_methoddata_distance* d = static_cast<t_methoddata_distance*>(data);
263 gmx::AnalysisNeighborhoodPositions pos(d->p.x, d->p.count());
264 d->nbsearch = d->nb.initSearch(context.pbc, pos);
268 * See sel_updatefunc_pos() for description of the parameters.
269 * \p data should point to a \c t_methoddata_distance.
271 * Calculates the distance of each position from \c t_methoddata_distance::p
272 * and puts them in \p out->u.r.
274 static void evaluate_distance(const gmx::SelMethodEvalContext& /*context*/,
276 gmx_ana_selvalue_t* out,
279 t_methoddata_distance* d = static_cast<t_methoddata_distance*>(data);
281 out->nr = pos->count();
282 for (int i = 0; i < pos->count(); ++i)
284 out->u.r[i] = d->nbsearch.minimumDistance(pos->x[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.
295 static void evaluate_within(const gmx::SelMethodEvalContext& /*context*/,
297 gmx_ana_selvalue_t* out,
300 t_methoddata_distance* d = static_cast<t_methoddata_distance*>(data);
303 for (int b = 0; b < pos->count(); ++b)
305 if (d->nbsearch.isWithin(pos->x[b]))
307 gmx_ana_pos_add_to_group(out->u.g, pos, b);