src/gromacs/selection/sm_distance.cpp

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  37 /*! \internal \file
  38  * \brief
  39  * Implements distance-based selection methods.
  40  *
  41  * This file implements the \p distance, \p mindistance and \p within
  42  * selection methods.
  43  *
  44  * \author Teemu Murtola <teemu.murtola@gmail.com>
  45  * \ingroup module_selection
  46  */
  47 #include "gmxpre.h"
  48
  49 #include "gromacs/math/vec.h"
  50 #include "gromacs/selection/nbsearch.h"
  51 #include "gromacs/utility/arraysize.h"
  52 #include "gromacs/utility/exceptions.h"
  53
  54 #include "position.h"
  55 #include "selmethod.h"
  56 #include "selmethod_impl.h"
  57
  58 /*! \internal
  59  * \brief
  60  * Data structure for distance-based selection method.
  61  *
  62  * The same data structure is used by all the distance-based methods.
  63  *
  64  * \ingroup module_selection
  65  */
  66 struct t_methoddata_distance
  67 {
  68     t_methoddata_distance() : cutoff(-1.0) {}
  69
  70     /** Cutoff distance. */
  71     real cutoff;
  72     /** Positions of the reference points. */
  73     gmx_ana_pos_t p;
  74     /** Neighborhood search data. */
  75     gmx::AnalysisNeighborhood nb;
  76     /** Neighborhood search for an invididual frame. */
  77     gmx::AnalysisNeighborhoodSearch nbsearch;
  78 };
  79
  80 /*! \brief
  81  * Allocates data for distance-based selection methods.
  82  *
  83  * \param[in]     npar  Not used (should be 2).
  84  * \param[in,out] param Method parameters (should point to one of the distance
  85  *   parameter arrays).
  86  * \returns       Pointer to the allocated data (\c t_methoddata_distance).
  87  *
  88  * Allocates memory for a \c t_methoddata_distance structure and
  89  * initializes the parameter as follows:
  90  *  - the first parameter defines the value for
  91  *    \c t_methoddata_distance::cutoff.
  92  *  - the second parameter defines the reference positions and the value is
  93  *    stored in \c t_methoddata_distance::p.
  94  */
  95 static void* 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 init_common(const gmx_mtop_t* top, int npar, gmx_ana_selparam_t* param, void* data);
 111 /** Frees the data allocated for a distance-based selection method. */
 112 static void free_data_common(void* data);
 113 /*! \brief
 114  * Initializes the evaluation of a distance-based within selection method for a
 115  * frame.
 116  *
 117  * \param[in]  context Evaluation context.
 118  * \param      data    Should point to a \c t_methoddata_distance.
 119  * \returns    0 on success, a non-zero error code on error.
 120  *
 121  * Initializes the neighborhood search for the current frame.
 122  */
 123 static void init_frame_common(const gmx::SelMethodEvalContext& context, void* data);
 124 /** Evaluates the \p distance selection method. */
 125 static void evaluate_distance(const gmx::SelMethodEvalContext& /*context*/,
 126                               gmx_ana_pos_t*      pos,
 127                               gmx_ana_selvalue_t* out,
 128                               void*               data);
 129 /** Evaluates the \p within selection method. */
 130 static void evaluate_within(const gmx::SelMethodEvalContext& /*context*/,
 131                             gmx_ana_pos_t*      pos,
 132                             gmx_ana_selvalue_t* out,
 133                             void*               data);
 134
 135 /** Parameters for the \p distance selection method. */
 136 static gmx_ana_selparam_t smparams_distance[] = {
 137     { "cutoff", { REAL_VALUE, 1, { nullptr } }, nullptr, SPAR_OPTIONAL },
 138     { "from", { POS_VALUE, 1, { nullptr } }, nullptr, SPAR_DYNAMIC },
 139 };
 140
 141 /** Parameters for the \p mindistance selection method. */
 142 static gmx_ana_selparam_t smparams_mindistance[] = {
 143     { "cutoff", { REAL_VALUE, 1, { nullptr } }, nullptr, SPAR_OPTIONAL },
 144     { "from", { POS_VALUE, -1, { nullptr } }, nullptr, SPAR_DYNAMIC | SPAR_VARNUM },
 145 };
 146
 147 /** Parameters for the \p within selection method. */
 148 static gmx_ana_selparam_t smparams_within[] = {
 149     { nullptr, { REAL_VALUE, 1, { nullptr } }, nullptr, 0 },
 150     { "of", { POS_VALUE, -1, { nullptr } }, nullptr, SPAR_DYNAMIC | SPAR_VARNUM },
 151 };
 152
 153 //! Help title for distance selection methods.
 154 static const char helptitle_distance[] = "Selecting based on distance";
 155 //! Help text for distance selection methods.
 156 static const char* const help_distance[] = {
 157     "::",
 158     "",
 159     "  distance from POS [cutoff REAL]",
 160     "  mindistance from POS_EXPR [cutoff REAL]",
 161     "  within REAL of POS_EXPR",
 162     "",
 163     "[TT]distance[tt] and [TT]mindistance[tt] calculate the distance from the",
 164     "given position(s), the only difference being in that [TT]distance[tt]",
 165     "only accepts a single position, while any number of positions can be",
 166     "given for [TT]mindistance[tt], which then calculates the distance to the",
 167     "closest position.",
 168     "[TT]within[tt] directly selects atoms that are within [TT]REAL[tt] of",
 169     "[TT]POS_EXPR[tt].[PAR]",
 170
 171     "For the first two keywords, it is possible to specify a cutoff to speed",
 172     "up the evaluation: all distances above the specified cutoff are",
 173     "returned as equal to the cutoff.",
 174 };
 175
 176 /** Selection method data for the \p distance method. */
 177 gmx_ana_selmethod_t sm_distance = {
 178     "distance",
 179     REAL_VALUE,
 180     SMETH_DYNAMIC,
 181     asize(smparams_distance),
 182     smparams_distance,
 183     &init_data_common,
 184     nullptr,
 185     &init_common,
 186     nullptr,
 187     &free_data_common,
 188     &init_frame_common,
 189     nullptr,
 190     &evaluate_distance,
 191     { "distance from POS [cutoff REAL]", helptitle_distance, 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",
 197     REAL_VALUE,
 198     SMETH_DYNAMIC,
 199     asize(smparams_mindistance),
 200     smparams_mindistance,
 201     &init_data_common,
 202     nullptr,
 203     &init_common,
 204     nullptr,
 205     &free_data_common,
 206     &init_frame_common,
 207     nullptr,
 208     &evaluate_distance,
 209     { "mindistance from POS_EXPR [cutoff REAL]", helptitle_distance, asize(help_distance), help_distance },
 210 };
 211
 212 /** Selection method data for the \p within method. */
 213 gmx_ana_selmethod_t sm_within = {
 214     "within",
 215     GROUP_VALUE,
 216     SMETH_DYNAMIC,
 217     asize(smparams_within),
 218     smparams_within,
 219     &init_data_common,
 220     nullptr,
 221     &init_common,
 222     nullptr,
 223     &free_data_common,
 224     &init_frame_common,
 225     nullptr,
 226     &evaluate_within,
 227     { "within REAL of POS_EXPR", helptitle_distance, asize(help_distance), help_distance },
 228 };
 229
 230 static void* init_data_common(int /* npar */, gmx_ana_selparam_t* param)
 231 {
 232     t_methoddata_distance* data = new t_methoddata_distance();
 233     param[0].val.u.r            = &data->cutoff;
 234     param[1].val.u.p            = &data->p;
 235     return data;
 236 }
 237
 238 static void init_common(const gmx_mtop_t* /* top */, int /* npar */, gmx_ana_selparam_t* param, void* data)
 239 {
 240     t_methoddata_distance* d = static_cast<t_methoddata_distance*>(data);
 241
 242     if ((param[0].flags & SPAR_SET) && d->cutoff <= 0)
 243     {
 244         GMX_THROW(gmx::InvalidInputError("Distance cutoff should be > 0"));
 245     }
 246     d->nb.setCutoff(d->cutoff);
 247 }
 248
 249 /*!
 250  * \param data Data to free (should point to a \c t_methoddata_distance).
 251  *
 252  * Frees the memory allocated for \c t_methoddata_distance::xref and
 253  * \c t_methoddata_distance::nb.
 254  */
 255 static void free_data_common(void* data)
 256 {
 257     delete static_cast<t_methoddata_distance*>(data);
 258 }
 259
 260 static void init_frame_common(const gmx::SelMethodEvalContext& context, void* data)
 261 {
 262     t_methoddata_distance* d = static_cast<t_methoddata_distance*>(data);
 263
 264     d->nbsearch.reset();
 265     gmx::AnalysisNeighborhoodPositions pos(d->p.x, d->p.count());
 266     d->nbsearch = d->nb.initSearch(context.pbc, pos);
 267 }
 268
 269 /*!
 270  * See sel_updatefunc_pos() for description of the parameters.
 271  * \p data should point to a \c t_methoddata_distance.
 272  *
 273  * Calculates the distance of each position from \c t_methoddata_distance::p
 274  * and puts them in \p out->u.r.
 275  */
 276 static void evaluate_distance(const gmx::SelMethodEvalContext& /*context*/,
 277                               gmx_ana_pos_t*      pos,
 278                               gmx_ana_selvalue_t* out,
 279                               void*               data)
 280 {
 281     t_methoddata_distance* d = static_cast<t_methoddata_distance*>(data);
 282
 283     out->nr = pos->count();
 284     for (int i = 0; i < pos->count(); ++i)
 285     {
 286         out->u.r[i] = d->nbsearch.minimumDistance(pos->x[i]);
 287     }
 288 }
 289
 290 /*!
 291  * See sel_updatefunc() for description of the parameters.
 292  * \p data should point to a \c t_methoddata_distance.
 293  *
 294  * Finds the atoms that are closer than the defined cutoff to
 295  * \c t_methoddata_distance::xref and puts them in \p out.g.
 296  */
 297 static void evaluate_within(const gmx::SelMethodEvalContext& /*context*/,
 298                             gmx_ana_pos_t*      pos,
 299                             gmx_ana_selvalue_t* out,
 300                             void*               data)
 301 {
 302     t_methoddata_distance* d = static_cast<t_methoddata_distance*>(data);
 303
 304     out->u.g->isize = 0;
 305     for (int b = 0; b < pos->count(); ++b)
 306     {
 307         if (d->nbsearch.isWithin(pos->x[b]))
 308         {
 309             gmx_ana_pos_add_to_group(out->u.g, pos, b);
 310         }
 311     }
 312 }