src/gromacs/selection/sm_position.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Implements position evaluation selection methods.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_selection
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "gromacs/legacyheaders/macros.h"
  45 #include "gromacs/selection/indexutil.h"
  46 #include "gromacs/selection/position.h"
  47 #include "gromacs/utility/cstringutil.h"
  48 #include "gromacs/utility/smalloc.h"
  49
  50 #include "keywords.h"
  51 #include "poscalc.h"
  52 #include "selelem.h"
  53 #include "selmethod.h"
  54
  55 /*! \internal \brief
  56  * Data structure for position keyword evaluation.
  57  */
  58 typedef struct
  59 {
  60     /** Position calculation collection to use. */
  61     gmx::PositionCalculationCollection *pcc;
  62     /** Index group for which the center should be evaluated. */
  63     gmx_ana_index_t                     g;
  64     /** Position evaluation data structure. */
  65     gmx_ana_poscalc_t                  *pc;
  66     /** true if periodic boundary conditions should be used. */
  67     bool                                bPBC;
  68     /** Type of positions to calculate. */
  69     char                               *type;
  70     /** Flags for the position calculation. */
  71     int                                 flags;
  72 } t_methoddata_pos;
  73
  74 /** Allocates data for position evaluation selection methods. */
  75 static void *
  76 init_data_pos(int npar, gmx_ana_selparam_t *param);
  77 /** Sets the position calculation collection for position evaluation selection methods. */
  78 static void
  79 set_poscoll_pos(gmx::PositionCalculationCollection *pcc, void *data);
  80 /*! \brief
  81  * Initializes position evaluation keywords.
  82  *
  83  * \param[in] top   Not used.
  84  * \param[in] npar  Not used.
  85  * \param[in] param Not used.
  86  * \param[in,out] data  Should point to \c t_methoddata_pos.
  87  * \returns       0 on success, a non-zero error code on error.
  88  *
  89  * The \c t_methoddata_pos::type field should have been initialized
  90  * externally using _gmx_selelem_set_kwpos_type().
  91  */
  92 static void
  93 init_kwpos(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
  94 /*! \brief
  95  * Initializes the \p cog selection method.
  96  *
  97  * \param[in]     top   Topology data structure.
  98  * \param[in]     npar  Not used.
  99  * \param[in]     param Not used.
 100  * \param[in,out] data  Should point to \c t_methoddata_pos.
 101  * \returns       0 on success, a non-zero error code on error.
 102  */
 103 static void
 104 init_cog(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
 105 /*! \brief
 106  * Initializes the \p cog selection method.
 107  *
 108  * \param[in]     top   Topology data structure.
 109  * \param[in]     npar  Not used.
 110  * \param[in]     param Not used.
 111  * \param[in,out] data  Should point to \c t_methoddata_pos.
 112  * \returns       0 on success, a non-zero error code on error.
 113  */
 114 static void
 115 init_com(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
 116 /*! \brief
 117  * Initializes output for position evaluation selection methods.
 118  *
 119  * \param[in]     top   Topology data structure.
 120  * \param[in,out] out   Pointer to output data structure.
 121  * \param[in,out] data  Should point to \c t_methoddata_pos.
 122  * \returns       0 for success.
 123  */
 124 static void
 125 init_output_pos(t_topology *top, gmx_ana_selvalue_t *out, void *data);
 126 /** Frees the data allocated for position evaluation selection methods. */
 127 static void
 128 free_data_pos(void *data);
 129 /** Evaluates position evaluation selection methods. */
 130 static void
 131 evaluate_pos(t_topology * /* top */, t_trxframe *fr, t_pbc *pbc, gmx_ana_index_t * /* g */, gmx_ana_selvalue_t *out, void *data);
 132
 133 /** Parameters for position keyword evaluation. */
 134 static gmx_ana_selparam_t smparams_keyword_pos[] = {
 135     {NULL,   {GROUP_VALUE, 1, {NULL}}, NULL, SPAR_DYNAMIC},
 136 };
 137
 138 /** Parameters for the \p cog and \p com selection methods. */
 139 static gmx_ana_selparam_t smparams_com[] = {
 140     {"of",   {GROUP_VALUE, 1, {NULL}}, NULL, SPAR_DYNAMIC},
 141     {"pbc",  {NO_VALUE,    0, {NULL}}, NULL, 0},
 142 };
 143
 144 /** Selection method data for position keyword evaluation. */
 145 gmx_ana_selmethod_t sm_keyword_pos = {
 146     "kw_pos", POS_VALUE, SMETH_DYNAMIC | SMETH_VARNUMVAL | SMETH_ALLOW_UNSORTED,
 147     asize(smparams_keyword_pos), smparams_keyword_pos,
 148     &init_data_pos,
 149     &set_poscoll_pos,
 150     &init_kwpos,
 151     &init_output_pos,
 152     &free_data_pos,
 153     NULL,
 154     &evaluate_pos,
 155     NULL,
 156     {NULL, NULL, 0, NULL},
 157 };
 158
 159 /** Selection method data for the \p cog method. */
 160 gmx_ana_selmethod_t sm_cog = {
 161     "cog", POS_VALUE, SMETH_DYNAMIC | SMETH_SINGLEVAL,
 162     asize(smparams_com), smparams_com,
 163     &init_data_pos,
 164     &set_poscoll_pos,
 165     &init_cog,
 166     &init_output_pos,
 167     &free_data_pos,
 168     NULL,
 169     &evaluate_pos,
 170     NULL,
 171     {"cog of ATOM_EXPR [pbc]", NULL, 0, NULL},
 172 };
 173
 174 /** Selection method data for the \p com method. */
 175 gmx_ana_selmethod_t sm_com = {
 176     "com", POS_VALUE, SMETH_REQTOP | SMETH_DYNAMIC | SMETH_SINGLEVAL,
 177     asize(smparams_com), smparams_com,
 178     &init_data_pos,
 179     &set_poscoll_pos,
 180     &init_com,
 181     &init_output_pos,
 182     &free_data_pos,
 183     NULL,
 184     &evaluate_pos,
 185     NULL,
 186     {"com of ATOM_EXPR [pbc]", NULL, 0, NULL},
 187 };
 188
 189 /*!
 190  * \param[in]     npar  Should be 1 or 2.
 191  * \param[in,out] param Method parameters (should point to
 192  *   \ref smparams_keyword_pos or \ref smparams_com).
 193  * \returns       Pointer to the allocated data (\c t_methoddata_pos).
 194  *
 195  * Allocates memory for a \c t_methoddata_pos structure and initializes
 196  * the first parameter to define the value for \c t_methoddata_pos::g.
 197  * If a second parameter is present, it is used for setting the
 198  * \c t_methoddata_pos::bPBC flag.
 199  */
 200 static void *
 201 init_data_pos(int npar, gmx_ana_selparam_t *param)
 202 {
 203     t_methoddata_pos *data;
 204
 205     snew(data, 1);
 206     param[0].val.u.g = &data->g;
 207     if (npar > 1)
 208     {
 209         param[1].val.u.b = &data->bPBC;
 210     }
 211     data->pc       = NULL;
 212     data->bPBC     = false;
 213     data->type     = NULL;
 214     data->flags    = -1;
 215     return data;
 216 }
 217
 218 /*!
 219  * \param[in]     pcc   Position calculation collection to use.
 220  * \param[in,out] data  Should point to \c t_methoddata_pos.
 221  */
 222 static void
 223 set_poscoll_pos(gmx::PositionCalculationCollection *pcc, void *data)
 224 {
 225     ((t_methoddata_pos *)data)->pcc = pcc;
 226 }
 227
 228 bool
 229 _gmx_selelem_is_default_kwpos(const gmx::SelectionTreeElement &sel)
 230 {
 231     if (sel.type != SEL_EXPRESSION || !sel.u.expr.method
 232         || sel.u.expr.method->name != sm_keyword_pos.name)
 233     {
 234         return false;
 235     }
 236
 237     t_methoddata_pos *d = static_cast<t_methoddata_pos *>(sel.u.expr.mdata);
 238     return d->type == NULL;
 239 }
 240
 241 /*!
 242  * \param[in,out] sel   Selection element to initialize.
 243  * \param[in]     type  One of the enum values acceptable for
 244  *     PositionCalculationCollection::typeFromEnum().
 245  *
 246  * Initializes the reference position type for position evaluation.
 247  * If called multiple times, the first setting takes effect, and later calls
 248  * are neglected.
 249  */
 250 void
 251 _gmx_selelem_set_kwpos_type(gmx::SelectionTreeElement *sel, const char *type)
 252 {
 253     t_methoddata_pos *d = (t_methoddata_pos *)sel->u.expr.mdata;
 254
 255     if (sel->type != SEL_EXPRESSION || !sel->u.expr.method
 256         || sel->u.expr.method->name != sm_keyword_pos.name)
 257     {
 258         return;
 259     }
 260     if (!d->type && type)
 261     {
 262         d->type  = gmx_strdup(type);
 263         /* FIXME: It would be better not to have the string here hardcoded. */
 264         if (type[0] != 'a')
 265         {
 266             sel->u.expr.method->flags |= SMETH_REQTOP;
 267         }
 268     }
 269 }
 270
 271 /*!
 272  * \param[in,out] sel   Selection element to initialize.
 273  * \param[in]     flags Default completion flags
 274  *     (see PositionCalculationCollection::typeFromEnum()).
 275  *
 276  * Initializes the flags for position evaluation.
 277  * If called multiple times, the first setting takes effect, and later calls
 278  * are neglected.
 279  */
 280 void
 281 _gmx_selelem_set_kwpos_flags(gmx::SelectionTreeElement *sel, int flags)
 282 {
 283     t_methoddata_pos *d = (t_methoddata_pos *)sel->u.expr.mdata;
 284
 285     if (sel->type != SEL_EXPRESSION || !sel->u.expr.method
 286         || sel->u.expr.method->name != sm_keyword_pos.name)
 287     {
 288         return;
 289     }
 290     if (d->flags == -1)
 291     {
 292         d->flags = flags;
 293     }
 294 }
 295
 296 static void
 297 init_kwpos(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
 298 {
 299     t_methoddata_pos *d = (t_methoddata_pos *)data;
 300
 301     if (!(param[0].flags & SPAR_DYNAMIC))
 302     {
 303         d->flags &= ~(POS_DYNAMIC | POS_MASKONLY);
 304     }
 305     else if (!(d->flags & POS_MASKONLY))
 306     {
 307         d->flags |= POS_DYNAMIC;
 308     }
 309     d->pc = d->pcc->createCalculationFromEnum(d->type, d->flags);
 310     gmx_ana_poscalc_set_maxindex(d->pc, &d->g);
 311 }
 312
 313 static void
 314 init_cog(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
 315 {
 316     t_methoddata_pos *d = (t_methoddata_pos *)data;
 317
 318     d->flags = (param[0].flags & SPAR_DYNAMIC) ? POS_DYNAMIC : 0;
 319     d->pc    = d->pcc->createCalculation(d->bPBC ? POS_ALL_PBC : POS_ALL, d->flags);
 320     gmx_ana_poscalc_set_maxindex(d->pc, &d->g);
 321 }
 322
 323 static void
 324 init_com(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
 325 {
 326     t_methoddata_pos *d = (t_methoddata_pos *)data;
 327
 328     d->flags  = (param[0].flags & SPAR_DYNAMIC) ? POS_DYNAMIC : 0;
 329     d->flags |= POS_MASS;
 330     d->pc     = d->pcc->createCalculation(d->bPBC ? POS_ALL_PBC : POS_ALL, d->flags);
 331     gmx_ana_poscalc_set_maxindex(d->pc, &d->g);
 332 }
 333
 334 static void
 335 init_output_pos(t_topology * /* top */, gmx_ana_selvalue_t *out, void *data)
 336 {
 337     t_methoddata_pos *d = (t_methoddata_pos *)data;
 338
 339     gmx_ana_poscalc_init_pos(d->pc, out->u.p);
 340 }
 341
 342 /*!
 343  * \param data Data to free (should point to a \c t_methoddata_pos).
 344  *
 345  * Frees the memory allocated for \c t_methoddata_pos::g and
 346  * \c t_methoddata_pos::pc.
 347  */
 348 static void
 349 free_data_pos(void *data)
 350 {
 351     t_methoddata_pos *d = (t_methoddata_pos *)data;
 352
 353     sfree(d->type);
 354     gmx_ana_poscalc_free(d->pc);
 355     sfree(d);
 356 }
 357
 358 /*!
 359  * See sel_updatefunc() for description of the parameters.
 360  * \p data should point to a \c t_methoddata_pos.
 361  *
 362  * Calculates the positions using \c t_methoddata_pos::pc for the index group
 363  * in \c t_methoddata_pos::g and stores the results in \p out->u.p.
 364  */
 365 static void
 366 evaluate_pos(t_topology * /* top */, t_trxframe *fr, t_pbc *pbc,
 367              gmx_ana_index_t * /* g */, gmx_ana_selvalue_t *out, void *data)
 368 {
 369     t_methoddata_pos *d = (t_methoddata_pos *)data;
 370
 371     gmx_ana_poscalc_update(d->pc, out->u.p, &d->g, fr, pbc);
 372 }