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37 * Implements position evaluation selection methods.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_selection
42 #include "gromacs/legacyheaders/macros.h"
43 #include "gromacs/legacyheaders/smalloc.h"
44 #include "gromacs/legacyheaders/string2.h"
46 #include "gromacs/selection/indexutil.h"
47 #include "gromacs/selection/poscalc.h"
48 #include "gromacs/selection/position.h"
49 #include "gromacs/selection/selmethod.h"
55 * Data structure for position keyword evaluation.
59 /** Position calculation collection to use. */
60 gmx::PositionCalculationCollection *pcc;
61 /** Index group for which the center should be evaluated. */
63 /** Position evaluation data structure. */
64 gmx_ana_poscalc_t *pc;
65 /** true if periodic boundary conditions should be used. */
67 /** Type of positions to calculate. */
69 /** Flags for the position calculation. */
73 /** Allocates data for position evaluation selection methods. */
75 init_data_pos(int npar, gmx_ana_selparam_t *param);
76 /** Sets the position calculation collection for position evaluation selection methods. */
78 set_poscoll_pos(gmx::PositionCalculationCollection *pcc, void *data);
80 * Initializes position evaluation keywords.
82 * \param[in] top Not used.
83 * \param[in] npar Not used.
84 * \param[in] param Not used.
85 * \param[in,out] data Should point to \c t_methoddata_pos.
86 * \returns 0 on success, a non-zero error code on error.
88 * The \c t_methoddata_pos::type field should have been initialized
89 * externally using _gmx_selelem_set_kwpos_type().
92 init_kwpos(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
93 /*! Initializes the \p cog selection method.
95 * \param[in] top Topology data structure.
96 * \param[in] npar Not used.
97 * \param[in] param Not used.
98 * \param[in,out] data Should point to \c t_methoddata_pos.
99 * \returns 0 on success, a non-zero error code on error.
102 init_cog(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
104 * Initializes the \p cog selection method.
106 * \param[in] top Topology data structure.
107 * \param[in] npar Not used.
108 * \param[in] param Not used.
109 * \param[in,out] data Should point to \c t_methoddata_pos.
110 * \returns 0 on success, a non-zero error code on error.
113 init_com(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
115 * Initializes output for position evaluation selection methods.
117 * \param[in] top Topology data structure.
118 * \param[in,out] out Pointer to output data structure.
119 * \param[in,out] data Should point to \c t_methoddata_pos.
120 * \returns 0 for success.
123 init_output_pos(t_topology *top, gmx_ana_selvalue_t *out, void *data);
124 /** Frees the data allocated for position evaluation selection methods. */
126 free_data_pos(void *data);
127 /** Evaluates position evaluation selection methods. */
129 evaluate_pos(t_topology * /* top */, t_trxframe *fr, t_pbc *pbc, gmx_ana_index_t * /* g */, gmx_ana_selvalue_t *out, void *data);
131 /** Parameters for position keyword evaluation. */
132 static gmx_ana_selparam_t smparams_keyword_pos[] = {
133 {NULL, {GROUP_VALUE, 1, {NULL}}, NULL, SPAR_DYNAMIC},
136 /** Parameters for the \p cog and \p com selection methods. */
137 static gmx_ana_selparam_t smparams_com[] = {
138 {"of", {GROUP_VALUE, 1, {NULL}}, NULL, SPAR_DYNAMIC},
139 {"pbc", {NO_VALUE, 0, {NULL}}, NULL, 0},
142 /** \internal Selection method data for position keyword evaluation. */
143 gmx_ana_selmethod_t sm_keyword_pos = {
144 "kw_pos", POS_VALUE, SMETH_DYNAMIC | SMETH_VARNUMVAL,
145 asize(smparams_keyword_pos), smparams_keyword_pos,
157 /** \internal Selection method data for the \p cog method. */
158 gmx_ana_selmethod_t sm_cog = {
159 "cog", POS_VALUE, SMETH_DYNAMIC | SMETH_SINGLEVAL,
160 asize(smparams_com), smparams_com,
169 {"cog of ATOM_EXPR [pbc]", 0, NULL},
172 /** \internal Selection method data for the \p com method. */
173 gmx_ana_selmethod_t sm_com = {
174 "com", POS_VALUE, SMETH_REQTOP | SMETH_DYNAMIC | SMETH_SINGLEVAL,
175 asize(smparams_com), smparams_com,
184 {"com of ATOM_EXPR [pbc]", 0, NULL},
188 * \param[in] npar Should be 1 or 2.
189 * \param[in,out] param Method parameters (should point to
190 * \ref smparams_keyword_pos or \ref smparams_com).
191 * \returns Pointer to the allocated data (\c t_methoddata_pos).
193 * Allocates memory for a \c t_methoddata_pos structure and initializes
194 * the first parameter to define the value for \c t_methoddata_pos::g.
195 * If a second parameter is present, it is used for setting the
196 * \c t_methoddata_pos::bPBC flag.
199 init_data_pos(int npar, gmx_ana_selparam_t *param)
201 t_methoddata_pos *data;
204 param[0].val.u.g = &data->g;
207 param[1].val.u.b = &data->bPBC;
217 * \param[in] pcc Position calculation collection to use.
218 * \param[in,out] data Should point to \c t_methoddata_pos.
221 set_poscoll_pos(gmx::PositionCalculationCollection *pcc, void *data)
223 ((t_methoddata_pos *)data)->pcc = pcc;
227 * \param[in,out] sel Selection element to initialize.
228 * \param[in] type One of the enum values acceptable for
229 * PositionCalculationCollection::typeFromEnum().
231 * Initializes the reference position type for position evaluation.
232 * If called multiple times, the first setting takes effect, and later calls
236 _gmx_selelem_set_kwpos_type(gmx::SelectionTreeElement *sel, const char *type)
238 t_methoddata_pos *d = (t_methoddata_pos *)sel->u.expr.mdata;
240 if (sel->type != SEL_EXPRESSION || !sel->u.expr.method
241 || sel->u.expr.method->name != sm_keyword_pos.name)
245 if (!d->type && type)
247 d->type = strdup(type);
248 /* FIXME: It would be better not to have the string here hardcoded. */
251 sel->u.expr.method->flags |= SMETH_REQTOP;
257 * \param[in,out] sel Selection element to initialize.
258 * \param[in] flags Default completion flags
259 * (see PositionCalculationCollection::typeFromEnum()).
261 * Initializes the flags for position evaluation.
262 * If called multiple times, the first setting takes effect, and later calls
266 _gmx_selelem_set_kwpos_flags(gmx::SelectionTreeElement *sel, int flags)
268 t_methoddata_pos *d = (t_methoddata_pos *)sel->u.expr.mdata;
270 if (sel->type != SEL_EXPRESSION || !sel->u.expr.method
271 || sel->u.expr.method->name != sm_keyword_pos.name)
282 init_kwpos(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
284 t_methoddata_pos *d = (t_methoddata_pos *)data;
286 if (!(param[0].flags & SPAR_DYNAMIC))
288 d->flags &= ~(POS_DYNAMIC | POS_MASKONLY);
290 else if (!(d->flags & POS_MASKONLY))
292 d->flags |= POS_DYNAMIC;
294 d->pc = d->pcc->createCalculationFromEnum(d->type, d->flags);
295 gmx_ana_poscalc_set_maxindex(d->pc, &d->g);
299 init_cog(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
301 t_methoddata_pos *d = (t_methoddata_pos *)data;
303 d->flags = (param[0].flags & SPAR_DYNAMIC) ? POS_DYNAMIC : 0;
304 d->pc = d->pcc->createCalculation(d->bPBC ? POS_ALL_PBC : POS_ALL, d->flags);
305 gmx_ana_poscalc_set_maxindex(d->pc, &d->g);
309 init_com(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
311 t_methoddata_pos *d = (t_methoddata_pos *)data;
313 d->flags = (param[0].flags & SPAR_DYNAMIC) ? POS_DYNAMIC : 0;
314 d->flags |= POS_MASS;
315 d->pc = d->pcc->createCalculation(d->bPBC ? POS_ALL_PBC : POS_ALL, d->flags);
316 gmx_ana_poscalc_set_maxindex(d->pc, &d->g);
320 init_output_pos(t_topology * /* top */, gmx_ana_selvalue_t *out, void *data)
322 t_methoddata_pos *d = (t_methoddata_pos *)data;
324 gmx_ana_poscalc_init_pos(d->pc, out->u.p);
328 * \param data Data to free (should point to a \c t_methoddata_pos).
330 * Frees the memory allocated for \c t_methoddata_pos::g and
331 * \c t_methoddata_pos::pc.
334 free_data_pos(void *data)
336 t_methoddata_pos *d = (t_methoddata_pos *)data;
339 gmx_ana_poscalc_free(d->pc);
344 * See sel_updatefunc() for description of the parameters.
345 * \p data should point to a \c t_methoddata_pos.
347 * Calculates the positions using \c t_methoddata_pos::pc for the index group
348 * in \c t_methoddata_pos::g and stores the results in \p out->u.p.
351 evaluate_pos(t_topology * /* top */, t_trxframe *fr, t_pbc *pbc,
352 gmx_ana_index_t * /* g */, gmx_ana_selvalue_t *out, void *data)
354 t_methoddata_pos *d = (t_methoddata_pos *)data;
356 gmx_ana_poscalc_update(d->pc, out->u.p, &d->g, fr, pbc);