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37 * Implements position evaluation selection methods.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_selection
44 #include "gromacs/legacyheaders/macros.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"
50 #include "gromacs/utility/cstringutil.h"
51 #include "gromacs/utility/smalloc.h"
57 * Data structure for position keyword evaluation.
61 /** Position calculation collection to use. */
62 gmx::PositionCalculationCollection *pcc;
63 /** Index group for which the center should be evaluated. */
65 /** Position evaluation data structure. */
66 gmx_ana_poscalc_t *pc;
67 /** true if periodic boundary conditions should be used. */
69 /** Type of positions to calculate. */
71 /** Flags for the position calculation. */
75 /** Allocates data for position evaluation selection methods. */
77 init_data_pos(int npar, gmx_ana_selparam_t *param);
78 /** Sets the position calculation collection for position evaluation selection methods. */
80 set_poscoll_pos(gmx::PositionCalculationCollection *pcc, void *data);
82 * Initializes position evaluation keywords.
84 * \param[in] top Not used.
85 * \param[in] npar Not used.
86 * \param[in] param Not used.
87 * \param[in,out] data Should point to \c t_methoddata_pos.
88 * \returns 0 on success, a non-zero error code on error.
90 * The \c t_methoddata_pos::type field should have been initialized
91 * externally using _gmx_selelem_set_kwpos_type().
94 init_kwpos(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
96 * Initializes the \p cog selection method.
98 * \param[in] top Topology data structure.
99 * \param[in] npar Not used.
100 * \param[in] param Not used.
101 * \param[in,out] data Should point to \c t_methoddata_pos.
102 * \returns 0 on success, a non-zero error code on error.
105 init_cog(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
107 * Initializes the \p cog selection method.
109 * \param[in] top Topology data structure.
110 * \param[in] npar Not used.
111 * \param[in] param Not used.
112 * \param[in,out] data Should point to \c t_methoddata_pos.
113 * \returns 0 on success, a non-zero error code on error.
116 init_com(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
118 * Initializes output for position evaluation selection methods.
120 * \param[in] top Topology data structure.
121 * \param[in,out] out Pointer to output data structure.
122 * \param[in,out] data Should point to \c t_methoddata_pos.
123 * \returns 0 for success.
126 init_output_pos(t_topology *top, gmx_ana_selvalue_t *out, void *data);
127 /** Frees the data allocated for position evaluation selection methods. */
129 free_data_pos(void *data);
130 /** Evaluates position evaluation selection methods. */
132 evaluate_pos(t_topology * /* top */, t_trxframe *fr, t_pbc *pbc, gmx_ana_index_t * /* g */, gmx_ana_selvalue_t *out, void *data);
134 /** Parameters for position keyword evaluation. */
135 static gmx_ana_selparam_t smparams_keyword_pos[] = {
136 {NULL, {GROUP_VALUE, 1, {NULL}}, NULL, SPAR_DYNAMIC},
139 /** Parameters for the \p cog and \p com selection methods. */
140 static gmx_ana_selparam_t smparams_com[] = {
141 {"of", {GROUP_VALUE, 1, {NULL}}, NULL, SPAR_DYNAMIC},
142 {"pbc", {NO_VALUE, 0, {NULL}}, NULL, 0},
145 /** Selection method data for position keyword evaluation. */
146 gmx_ana_selmethod_t sm_keyword_pos = {
147 "kw_pos", POS_VALUE, SMETH_DYNAMIC | SMETH_VARNUMVAL | SMETH_ALLOW_UNSORTED,
148 asize(smparams_keyword_pos), smparams_keyword_pos,
160 /** Selection method data for the \p cog method. */
161 gmx_ana_selmethod_t sm_cog = {
162 "cog", POS_VALUE, SMETH_DYNAMIC | SMETH_SINGLEVAL,
163 asize(smparams_com), smparams_com,
172 {"cog of ATOM_EXPR [pbc]", 0, NULL},
175 /** Selection method data for the \p com method. */
176 gmx_ana_selmethod_t sm_com = {
177 "com", POS_VALUE, SMETH_REQTOP | SMETH_DYNAMIC | SMETH_SINGLEVAL,
178 asize(smparams_com), smparams_com,
187 {"com of ATOM_EXPR [pbc]", 0, NULL},
191 * \param[in] npar Should be 1 or 2.
192 * \param[in,out] param Method parameters (should point to
193 * \ref smparams_keyword_pos or \ref smparams_com).
194 * \returns Pointer to the allocated data (\c t_methoddata_pos).
196 * Allocates memory for a \c t_methoddata_pos structure and initializes
197 * the first parameter to define the value for \c t_methoddata_pos::g.
198 * If a second parameter is present, it is used for setting the
199 * \c t_methoddata_pos::bPBC flag.
202 init_data_pos(int npar, gmx_ana_selparam_t *param)
204 t_methoddata_pos *data;
207 param[0].val.u.g = &data->g;
210 param[1].val.u.b = &data->bPBC;
220 * \param[in] pcc Position calculation collection to use.
221 * \param[in,out] data Should point to \c t_methoddata_pos.
224 set_poscoll_pos(gmx::PositionCalculationCollection *pcc, void *data)
226 ((t_methoddata_pos *)data)->pcc = pcc;
230 * \param[in,out] sel Selection element to initialize.
231 * \param[in] type One of the enum values acceptable for
232 * PositionCalculationCollection::typeFromEnum().
234 * Initializes the reference position type for position evaluation.
235 * If called multiple times, the first setting takes effect, and later calls
239 _gmx_selelem_set_kwpos_type(gmx::SelectionTreeElement *sel, const char *type)
241 t_methoddata_pos *d = (t_methoddata_pos *)sel->u.expr.mdata;
243 if (sel->type != SEL_EXPRESSION || !sel->u.expr.method
244 || sel->u.expr.method->name != sm_keyword_pos.name)
248 if (!d->type && type)
250 d->type = gmx_strdup(type);
251 /* FIXME: It would be better not to have the string here hardcoded. */
254 sel->u.expr.method->flags |= SMETH_REQTOP;
260 * \param[in,out] sel Selection element to initialize.
261 * \param[in] flags Default completion flags
262 * (see PositionCalculationCollection::typeFromEnum()).
264 * Initializes the flags for position evaluation.
265 * If called multiple times, the first setting takes effect, and later calls
269 _gmx_selelem_set_kwpos_flags(gmx::SelectionTreeElement *sel, int flags)
271 t_methoddata_pos *d = (t_methoddata_pos *)sel->u.expr.mdata;
273 if (sel->type != SEL_EXPRESSION || !sel->u.expr.method
274 || sel->u.expr.method->name != sm_keyword_pos.name)
285 init_kwpos(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
287 t_methoddata_pos *d = (t_methoddata_pos *)data;
289 if (!(param[0].flags & SPAR_DYNAMIC))
291 d->flags &= ~(POS_DYNAMIC | POS_MASKONLY);
293 else if (!(d->flags & POS_MASKONLY))
295 d->flags |= POS_DYNAMIC;
297 d->pc = d->pcc->createCalculationFromEnum(d->type, d->flags);
298 gmx_ana_poscalc_set_maxindex(d->pc, &d->g);
302 init_cog(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
304 t_methoddata_pos *d = (t_methoddata_pos *)data;
306 d->flags = (param[0].flags & SPAR_DYNAMIC) ? POS_DYNAMIC : 0;
307 d->pc = d->pcc->createCalculation(d->bPBC ? POS_ALL_PBC : POS_ALL, d->flags);
308 gmx_ana_poscalc_set_maxindex(d->pc, &d->g);
312 init_com(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
314 t_methoddata_pos *d = (t_methoddata_pos *)data;
316 d->flags = (param[0].flags & SPAR_DYNAMIC) ? POS_DYNAMIC : 0;
317 d->flags |= POS_MASS;
318 d->pc = d->pcc->createCalculation(d->bPBC ? POS_ALL_PBC : POS_ALL, d->flags);
319 gmx_ana_poscalc_set_maxindex(d->pc, &d->g);
323 init_output_pos(t_topology * /* top */, gmx_ana_selvalue_t *out, void *data)
325 t_methoddata_pos *d = (t_methoddata_pos *)data;
327 gmx_ana_poscalc_init_pos(d->pc, out->u.p);
331 * \param data Data to free (should point to a \c t_methoddata_pos).
333 * Frees the memory allocated for \c t_methoddata_pos::g and
334 * \c t_methoddata_pos::pc.
337 free_data_pos(void *data)
339 t_methoddata_pos *d = (t_methoddata_pos *)data;
342 gmx_ana_poscalc_free(d->pc);
347 * See sel_updatefunc() for description of the parameters.
348 * \p data should point to a \c t_methoddata_pos.
350 * Calculates the positions using \c t_methoddata_pos::pc for the index group
351 * in \c t_methoddata_pos::g and stores the results in \p out->u.p.
354 evaluate_pos(t_topology * /* top */, t_trxframe *fr, t_pbc *pbc,
355 gmx_ana_index_t * /* g */, gmx_ana_selvalue_t *out, void *data)
357 t_methoddata_pos *d = (t_methoddata_pos *)data;
359 gmx_ana_poscalc_update(d->pc, out->u.p, &d->g, fr, pbc);