src/gromacs/selection/sm_merge.cpp

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  37 /*! \internal \file
  38  * \brief
  39  * Implements the \p merge and \p plus selection modifiers.
  40  *
  41  * \author Teemu Murtola <teemu.murtola@gmail.com>
  42  * \ingroup module_selection
  43  */
  44 #include "gmxpre.h"
  45
  46 #include "gromacs/math/vec.h"
  47 #include "gromacs/utility/arraysize.h"
  48 #include "gromacs/utility/basedefinitions.h"
  49 #include "gromacs/utility/exceptions.h"
  50 #include "gromacs/utility/smalloc.h"
  51
  52 #include "position.h"
  53 #include "selmethod.h"
  54 #include "selmethod_impl.h"
  55
  56 /*! \internal \brief
  57  * Data structure for the merging selection modifiers.
  58  */
  59 typedef struct methoddata_merge
  60 {
  61     /** Input positions. */
  62     gmx_ana_pos_t p1;
  63     /** Other input positions. */
  64     gmx_ana_pos_t p2;
  65     /** Stride for merging (\c stride values from \c p1 for each in \c p2). */
  66     int stride;
  67 } t_methoddata_merge;
  68
  69 /** Allocates data for the merging selection modifiers. */
  70 static void* init_data_merge(int npar, gmx_ana_selparam_t* param);
  71 /*! \brief
  72  * Initializes data for the merging selection modifiers.
  73  *
  74  * \param[in] top   Not used.
  75  * \param[in] npar  Not used (should be 2 or 3).
  76  * \param[in] param Method parameters (should point to \ref smparams_merge).
  77  * \param[in] data  Should point to a \p t_methoddata_merge.
  78  * \returns   0 if everything is successful, -1 on error.
  79  */
  80 static void init_merge(const gmx_mtop_t* top, int npar, gmx_ana_selparam_t* param, void* data);
  81 /** Initializes output for the \p merge selection modifier. */
  82 static void init_output_merge(const gmx_mtop_t* top, gmx_ana_selvalue_t* out, void* data);
  83 /** Initializes output for the \p plus selection modifier. */
  84 static void init_output_plus(const gmx_mtop_t* top, gmx_ana_selvalue_t* out, void* data);
  85 /** Frees the memory allocated for the merging selection modifiers. */
  86 static void free_data_merge(void* data);
  87 /*! \brief
  88  * Evaluates the \p merge selection modifier.
  89  *
  90  * \param[in]  context Not used.
  91  * \param[in]  p     Positions to merge (should point to \p data->p1).
  92  * \param[out] out   Output data structure (\p out->u.p is used).
  93  * \param[in]  data  Should point to a \p t_methoddata_merge.
  94  */
  95 static void evaluate_merge(const gmx::SelMethodEvalContext& context,
  96                            gmx_ana_pos_t*                   p,
  97                            gmx_ana_selvalue_t*              out,
  98                            void*                            data);
  99 /*! \brief
 100  * Evaluates the \p plus selection modifier.
 101  *
 102  * \param[in]  context Not used.
 103  * \param[in]  p     Positions to merge (should point to \p data->p1).
 104  * \param[out] out   Output data structure (\p out->u.p is used).
 105  * \param[in]  data  Should point to a \p t_methoddata_merge.
 106  */
 107 static void evaluate_plus(const gmx::SelMethodEvalContext& context,
 108                           gmx_ana_pos_t*                   p,
 109                           gmx_ana_selvalue_t*              out,
 110                           void*                            data);
 111
 112 /** Parameters for the merging selection modifiers. */
 113 static gmx_ana_selparam_t smparams_merge[] = {
 114     { nullptr, { POS_VALUE, -1, { nullptr } }, nullptr, SPAR_DYNAMIC | SPAR_VARNUM },
 115     { nullptr, { POS_VALUE, -1, { nullptr } }, nullptr, SPAR_DYNAMIC | SPAR_VARNUM },
 116     { "stride", { INT_VALUE, 1, { nullptr } }, nullptr, SPAR_OPTIONAL },
 117 };
 118
 119 //! Help title for the merging selection modifiers.
 120 static const char helptitle_merge[] = "Merging selections";
 121 //! Help text for the merging selection modifiers.
 122 static const char* const help_merge[] = {
 123     "::",
 124     "",
 125     "  POSEXPR merge POSEXPR [stride INT]",
 126     "  POSEXPR merge POSEXPR [merge POSEXPR ...]",
 127     "  POSEXPR plus POSEXPR [plus POSEXPR ...]",
 128     "",
 129     "Basic selection keywords can only create selections where each atom",
 130     "occurs at most once. The [TT]merge[tt] and [TT]plus[tt] selection",
 131     "keywords can be used to work around this limitation. Both create",
 132     "a selection that contains the positions from all the given position",
 133     "expressions, even if they contain duplicates.",
 134     "The difference between the two is that [TT]merge[tt] expects two or more",
 135     "selections with the same number of positions, and the output contains",
 136     "the input positions selected from each expression in turn, i.e.,",
 137     "the output is like A1 B1 A2 B2 and so on. It is also possible to merge",
 138     "selections of unequal size as long as the size of the first is a",
 139     "multiple of the second one. The [TT]stride[tt] parameter can be used",
 140     "to explicitly provide this multiplicity.",
 141     "[TT]plus[tt] simply concatenates the positions after each other, and",
 142     "can work also with selections of different sizes.",
 143     "These keywords are valid only at the selection level, not in any",
 144     "subexpressions.",
 145 };
 146
 147 /** Selection method data for the \p plus modifier. */
 148 gmx_ana_selmethod_t sm_merge = {
 149     "merge",
 150     POS_VALUE,
 151     SMETH_MODIFIER,
 152     asize(smparams_merge),
 153     smparams_merge,
 154     &init_data_merge,
 155     nullptr,
 156     &init_merge,
 157     &init_output_merge,
 158     &free_data_merge,
 159     nullptr,
 160     nullptr,
 161     &evaluate_merge,
 162     { "merge POSEXPR", helptitle_merge, asize(help_merge), help_merge },
 163 };
 164
 165 /** Selection method data for the \p plus modifier. */
 166 gmx_ana_selmethod_t sm_plus = {
 167     "plus",
 168     POS_VALUE,
 169     SMETH_MODIFIER,
 170     asize(smparams_merge) - 1,
 171     smparams_merge,
 172     &init_data_merge,
 173     nullptr,
 174     &init_merge,
 175     &init_output_plus,
 176     &free_data_merge,
 177     nullptr,
 178     nullptr,
 179     &evaluate_plus,
 180     { "plus POSEXPR", helptitle_merge, asize(help_merge), help_merge },
 181 };
 182
 183 /*!
 184  * \param[in]     npar  Should be 2 for \c plus and 3 for \c merge.
 185  * \param[in,out] param Method parameters (should point to a copy of
 186  *   \ref smparams_merge).
 187  * \returns Pointer to the allocated data (\p t_methoddata_merge).
 188  *
 189  * Allocates memory for a \p t_methoddata_merge structure.
 190  */
 191 static void* init_data_merge(int npar, gmx_ana_selparam_t* param)
 192 {
 193     t_methoddata_merge* data = new t_methoddata_merge();
 194     data->stride             = 0;
 195     param[0].val.u.p         = &data->p1;
 196     param[1].val.u.p         = &data->p2;
 197     if (npar > 2)
 198     {
 199         param[2].val.u.i = &data->stride;
 200     }
 201     return data;
 202 }
 203
 204 static void init_merge(const gmx_mtop_t* /* top */, int /* npar */, gmx_ana_selparam_t* /* param */, void* data)
 205 {
 206     t_methoddata_merge* d = static_cast<t_methoddata_merge*>(data);
 207
 208     if (d->stride < 0)
 209     {
 210         GMX_THROW(gmx::InvalidInputError("Stride for merging should be positive"));
 211     }
 212     /* If no stride given, deduce it from the input sizes */
 213     if (d->stride == 0)
 214     {
 215         d->stride = d->p1.count() / d->p2.count();
 216     }
 217     if (d->p1.count() != d->stride * d->p2.count())
 218     {
 219         GMX_THROW(gmx::InconsistentInputError(
 220                 "The number of positions to be merged are not compatible"));
 221     }
 222 }
 223
 224 /*! \brief
 225  * Does common initialization to all merging modifiers.
 226  *
 227  * \param[in]     top   Topology data structure.
 228  * \param[in,out] out   Pointer to output data structure.
 229  * \param[in,out] data  Should point to \c t_methoddata_merge.
 230  */
 231 static void init_output_common(const gmx_mtop_t* top, gmx_ana_selvalue_t* out, void* data)
 232 {
 233     t_methoddata_merge* d = static_cast<t_methoddata_merge*>(data);
 234
 235     GMX_UNUSED_VALUE(top);
 236     if (d->p1.m.type != d->p2.m.type)
 237     {
 238         /* TODO: Maybe we could pick something else here? */
 239         out->u.p->m.type = INDEX_UNKNOWN;
 240     }
 241     else
 242     {
 243         out->u.p->m.type = d->p1.m.type;
 244     }
 245     gmx_ana_pos_reserve_for_append(out->u.p, d->p1.count() + d->p2.count(),
 246                                    d->p1.m.b.nra + d->p2.m.b.nra, d->p1.v != nullptr, d->p1.f != nullptr);
 247     gmx_ana_pos_empty_init(out->u.p);
 248 }
 249
 250 /*!
 251  * \param[in]     top   Topology data structure.
 252  * \param[in,out] out   Pointer to output data structure.
 253  * \param[in,out] data  Should point to \c t_methoddata_merge.
 254  */
 255 static void init_output_merge(const gmx_mtop_t* top, gmx_ana_selvalue_t* out, void* data)
 256 {
 257     t_methoddata_merge* d = static_cast<t_methoddata_merge*>(data);
 258     int                 i, j;
 259
 260     init_output_common(top, out, data);
 261     for (i = 0; i < d->p2.count(); ++i)
 262     {
 263         for (j = 0; j < d->stride; ++j)
 264         {
 265             gmx_ana_pos_append_init(out->u.p, &d->p1, d->stride * i + j);
 266         }
 267         gmx_ana_pos_append_init(out->u.p, &d->p2, i);
 268     }
 269 }
 270
 271 /*!
 272  * \param[in]     top   Topology data structure.
 273  * \param[in,out] out   Pointer to output data structure.
 274  * \param[in,out] data  Should point to \c t_methoddata_merge.
 275  */
 276 static void init_output_plus(const gmx_mtop_t* top, gmx_ana_selvalue_t* out, void* data)
 277 {
 278     t_methoddata_merge* d = static_cast<t_methoddata_merge*>(data);
 279     int                 i;
 280
 281     init_output_common(top, out, data);
 282     for (i = 0; i < d->p1.count(); ++i)
 283     {
 284         gmx_ana_pos_append_init(out->u.p, &d->p1, i);
 285     }
 286     for (i = 0; i < d->p2.count(); ++i)
 287     {
 288         gmx_ana_pos_append_init(out->u.p, &d->p2, i);
 289     }
 290 }
 291
 292 /*!
 293  * \param data Data to free (should point to a \p t_methoddata_merge).
 294  *
 295  * Frees the memory allocated for \c t_methoddata_merge.
 296  */
 297 static void free_data_merge(void* data)
 298 {
 299     t_methoddata_merge* d = static_cast<t_methoddata_merge*>(data);
 300     delete d;
 301 }
 302
 303 static void evaluate_merge(const gmx::SelMethodEvalContext& /*context*/,
 304                            gmx_ana_pos_t* /* p */,
 305                            gmx_ana_selvalue_t* out,
 306                            void*               data)
 307 {
 308     t_methoddata_merge* d = static_cast<t_methoddata_merge*>(data);
 309     int                 i, j;
 310     int                 refid;
 311
 312     if (d->p1.count() != d->stride * d->p2.count())
 313     {
 314         GMX_THROW(gmx::InconsistentInputError(
 315                 "The number of positions to be merged are not compatible"));
 316     }
 317     gmx_ana_pos_empty(out->u.p);
 318     for (i = 0; i < d->p2.count(); ++i)
 319     {
 320         for (j = 0; j < d->stride; ++j)
 321         {
 322             refid = d->p1.m.refid[d->stride * i + j];
 323             if (refid != -1)
 324             {
 325                 refid = (d->stride + 1) * (refid / d->stride) + (refid % d->stride);
 326             }
 327             gmx_ana_pos_append(out->u.p, &d->p1, d->stride * i + j, refid);
 328         }
 329         refid = (d->stride + 1) * d->p2.m.refid[i] + d->stride;
 330         gmx_ana_pos_append(out->u.p, &d->p2, i, refid);
 331     }
 332     gmx_ana_pos_append_finish(out->u.p);
 333 }
 334
 335 static void evaluate_plus(const gmx::SelMethodEvalContext& /*context*/,
 336                           gmx_ana_pos_t* /* p */,
 337                           gmx_ana_selvalue_t* out,
 338                           void*               data)
 339 {
 340     t_methoddata_merge* d = static_cast<t_methoddata_merge*>(data);
 341     int                 i;
 342     int                 refid;
 343
 344     gmx_ana_pos_empty(out->u.p);
 345     for (i = 0; i < d->p1.count(); ++i)
 346     {
 347         refid = d->p1.m.refid[i];
 348         gmx_ana_pos_append(out->u.p, &d->p1, i, refid);
 349     }
 350     for (i = 0; i < d->p2.count(); ++i)
 351     {
 352         refid = d->p2.m.refid[i];
 353         if (refid != -1)
 354         {
 355             refid += d->p1.m.b.nr;
 356         }
 357         gmx_ana_pos_append(out->u.p, &d->p2, i, refid);
 358     }
 359     gmx_ana_pos_append_finish(out->u.p);
 360 }