src/gromacs/selection/sm_distance.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Implements distance-based selection methods.
  38  *
  39  * This file implements the \p distance, \p mindistance and \p within
  40  * selection methods.
  41  *
  42  * \author Teemu Murtola <teemu.murtola@gmail.com>
  43  * \ingroup module_selection
  44  */
  45 #include "gmxpre.h"
  46
  47 #include "gromacs/legacyheaders/macros.h"
  48 #include "gromacs/math/vec.h"
  49 #include "gromacs/selection/nbsearch.h"
  50 #include "gromacs/selection/position.h"
  51 #include "gromacs/utility/exceptions.h"
  52
  53 #include "selmethod.h"
  54
  55 /*! \internal
  56  * \brief
  57  * Data structure for distance-based selection method.
  58  *
  59  * The same data structure is used by all the distance-based methods.
  60  *
  61  * \ingroup module_selection
  62  */
  63 struct t_methoddata_distance
  64 {
  65     t_methoddata_distance() : cutoff(-1.0)
  66     {
  67     }
  68
  69     /** Cutoff distance. */
  70     real                             cutoff;
  71     /** Positions of the reference points. */
  72     gmx_ana_pos_t                    p;
  73     /** Neighborhood search data. */
  74     gmx::AnalysisNeighborhood        nb;
  75     /** Neighborhood search for an invididual frame. */
  76     gmx::AnalysisNeighborhoodSearch  nbsearch;
  77 };
  78
  79 /*! \brief
  80  * Allocates data for distance-based selection methods.
  81  *
  82  * \param[in]     npar  Not used (should be 2).
  83  * \param[in,out] param Method parameters (should point to one of the distance
  84  *   parameter arrays).
  85  * \returns       Pointer to the allocated data (\c t_methoddata_distance).
  86  *
  87  * Allocates memory for a \c t_methoddata_distance structure and
  88  * initializes the parameter as follows:
  89  *  - the first parameter defines the value for
  90  *    \c t_methoddata_distance::cutoff.
  91  *  - the second parameter defines the reference positions and the value is
  92  *    stored in \c t_methoddata_distance::p.
  93  */
  94 static void *
  95 init_data_common(int npar, gmx_ana_selparam_t *param);
  96 /*! \brief
  97  * Initializes a distance-based selection method.
  98  *
  99  * \param   top   Not used.
 100  * \param   npar  Not used (should be 2).
 101  * \param   param Method parameters (should point to one of the distance
 102  *   parameter arrays).
 103  * \param   data  Pointer to \c t_methoddata_distance to initialize.
 104  * \returns 0 on success, a non-zero error code on failure.
 105  *
 106  * Initializes the neighborhood search data structure
 107  * (\c t_methoddata_distance::nb).
 108  * Also checks that the cutoff is valid.
 109  */
 110 static void
 111 init_common(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
 112 /** Frees the data allocated for a distance-based selection method. */
 113 static void
 114 free_data_common(void *data);
 115 /*! \brief
 116  * Initializes the evaluation of a distance-based within selection method for a
 117  * frame.
 118  *
 119  * \param[in]  top  Not used.
 120  * \param[in]  fr   Current frame.
 121  * \param[in]  pbc  PBC structure.
 122  * \param      data Should point to a \c t_methoddata_distance.
 123  * \returns    0 on success, a non-zero error code on error.
 124  *
 125  * Initializes the neighborhood search for the current frame.
 126  */
 127 static void
 128 init_frame_common(t_topology *top, t_trxframe * fr, t_pbc *pbc, void *data);
 129 /** Evaluates the \p distance selection method. */
 130 static void
 131 evaluate_distance(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
 132                   gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
 133 /** Evaluates the \p within selection method. */
 134 static void
 135 evaluate_within(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
 136                 gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
 137
 138 /** Parameters for the \p distance selection method. */
 139 static gmx_ana_selparam_t smparams_distance[] = {
 140     {"cutoff", {REAL_VALUE, 1, {NULL}}, NULL, SPAR_OPTIONAL},
 141     {"from",   {POS_VALUE,  1, {NULL}}, NULL, SPAR_DYNAMIC},
 142 };
 143
 144 /** Parameters for the \p mindistance selection method. */
 145 static gmx_ana_selparam_t smparams_mindistance[] = {
 146     {"cutoff", {REAL_VALUE, 1, {NULL}}, NULL, SPAR_OPTIONAL},
 147     {"from",   {POS_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
 148 };
 149
 150 /** Parameters for the \p within selection method. */
 151 static gmx_ana_selparam_t smparams_within[] = {
 152     {NULL, {REAL_VALUE,  1, {NULL}}, NULL, 0},
 153     {"of", {POS_VALUE,  -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
 154 };
 155
 156 /** Help text for the distance selection methods. */
 157 static const char *help_distance[] = {
 158     "DISTANCE-BASED SELECTION KEYWORDS",
 159     "",
 160     "::",
 161     "",
 162     "  distance from POS [cutoff REAL]",
 163     "  mindistance from POS_EXPR [cutoff REAL]",
 164     "  within REAL of POS_EXPR",
 165     "",
 166     "[TT]distance[tt] and [TT]mindistance[tt] calculate the distance from the",
 167     "given position(s), the only difference being in that [TT]distance[tt]",
 168     "only accepts a single position, while any number of positions can be",
 169     "given for [TT]mindistance[tt], which then calculates the distance to the",
 170     "closest position.",
 171     "[TT]within[tt] directly selects atoms that are within [TT]REAL[tt] of",
 172     "[TT]POS_EXPR[tt].[PAR]",
 173
 174     "For the first two keywords, it is possible to specify a cutoff to speed",
 175     "up the evaluation: all distances above the specified cutoff are",
 176     "returned as equal to the cutoff.",
 177 };
 178
 179 /** Selection method data for the \p distance method. */
 180 gmx_ana_selmethod_t sm_distance = {
 181     "distance", REAL_VALUE, SMETH_DYNAMIC,
 182     asize(smparams_distance), smparams_distance,
 183     &init_data_common,
 184     NULL,
 185     &init_common,
 186     NULL,
 187     &free_data_common,
 188     &init_frame_common,
 189     NULL,
 190     &evaluate_distance,
 191     {"distance from POS [cutoff REAL]", asize(help_distance), help_distance},
 192 };
 193
 194 /** Selection method data for the \p distance method. */
 195 gmx_ana_selmethod_t sm_mindistance = {
 196     "mindistance", REAL_VALUE, SMETH_DYNAMIC,
 197     asize(smparams_mindistance), smparams_mindistance,
 198     &init_data_common,
 199     NULL,
 200     &init_common,
 201     NULL,
 202     &free_data_common,
 203     &init_frame_common,
 204     NULL,
 205     &evaluate_distance,
 206     {"mindistance from POS_EXPR [cutoff REAL]", asize(help_distance), help_distance},
 207 };
 208
 209 /** Selection method data for the \p within method. */
 210 gmx_ana_selmethod_t sm_within = {
 211     "within", GROUP_VALUE, SMETH_DYNAMIC,
 212     asize(smparams_within), smparams_within,
 213     &init_data_common,
 214     NULL,
 215     &init_common,
 216     NULL,
 217     &free_data_common,
 218     &init_frame_common,
 219     NULL,
 220     &evaluate_within,
 221     {"within REAL of POS_EXPR", asize(help_distance), help_distance},
 222 };
 223
 224 static void *
 225 init_data_common(int /* npar */, gmx_ana_selparam_t *param)
 226 {
 227     t_methoddata_distance *data = new t_methoddata_distance();
 228     param[0].val.u.r = &data->cutoff;
 229     param[1].val.u.p = &data->p;
 230     return data;
 231 }
 232
 233 static void
 234 init_common(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
 235 {
 236     t_methoddata_distance *d = static_cast<t_methoddata_distance *>(data);
 237
 238     if ((param[0].flags & SPAR_SET) && d->cutoff <= 0)
 239     {
 240         GMX_THROW(gmx::InvalidInputError("Distance cutoff should be > 0"));
 241     }
 242     d->nb.setCutoff(d->cutoff);
 243 }
 244
 245 /*!
 246  * \param data Data to free (should point to a \c t_methoddata_distance).
 247  *
 248  * Frees the memory allocated for \c t_methoddata_distance::xref and
 249  * \c t_methoddata_distance::nb.
 250  */
 251 static void
 252 free_data_common(void *data)
 253 {
 254     delete static_cast<t_methoddata_distance *>(data);
 255 }
 256
 257 static void
 258 init_frame_common(t_topology * /* top */, t_trxframe * /* fr */, t_pbc *pbc, void *data)
 259 {
 260     t_methoddata_distance *d = static_cast<t_methoddata_distance *>(data);
 261
 262     d->nbsearch.reset();
 263     gmx::AnalysisNeighborhoodPositions pos(d->p.x, d->p.count());
 264     d->nbsearch = d->nb.initSearch(pbc, pos);
 265 }
 266
 267 /*!
 268  * See sel_updatefunc_pos() for description of the parameters.
 269  * \p data should point to a \c t_methoddata_distance.
 270  *
 271  * Calculates the distance of each position from \c t_methoddata_distance::p
 272  * and puts them in \p out->u.r.
 273  */
 274 static void
 275 evaluate_distance(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
 276                   gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data)
 277 {
 278     t_methoddata_distance *d = static_cast<t_methoddata_distance *>(data);
 279
 280     out->nr = pos->count();
 281     for (int i = 0; i < pos->count(); ++i)
 282     {
 283         out->u.r[i] = d->nbsearch.minimumDistance(pos->x[i]);
 284     }
 285 }
 286
 287 /*!
 288  * See sel_updatefunc() for description of the parameters.
 289  * \p data should point to a \c t_methoddata_distance.
 290  *
 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.
 293  */
 294 static void
 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)
 297 {
 298     t_methoddata_distance *d = static_cast<t_methoddata_distance *>(data);
 299
 300     out->u.g->isize = 0;
 301     for (int b = 0; b < pos->count(); ++b)
 302     {
 303         if (d->nbsearch.isWithin(pos->x[b]))
 304         {
 305             gmx_ana_pos_add_to_group(out->u.g, pos, b);
 306         }
 307     }
 308 }