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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"
44 #include "gromacs/selection/indexutil.h"
45 #include "gromacs/selection/poscalc.h"
46 #include "gromacs/selection/position.h"
47 #include "gromacs/selection/selmethod.h"
48 #include "gromacs/utility/cstringutil.h"
49 #include "gromacs/utility/smalloc.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);
94 * Initializes the \p cog selection method.
96 * \param[in] top Topology data structure.
97 * \param[in] npar Not used.
98 * \param[in] param Not used.
99 * \param[in,out] data Should point to \c t_methoddata_pos.
100 * \returns 0 on success, a non-zero error code on error.
103 init_cog(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
105 * Initializes the \p cog selection method.
107 * \param[in] top Topology data structure.
108 * \param[in] npar Not used.
109 * \param[in] param Not used.
110 * \param[in,out] data Should point to \c t_methoddata_pos.
111 * \returns 0 on success, a non-zero error code on error.
114 init_com(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
116 * Initializes output for position evaluation selection methods.
118 * \param[in] top Topology data structure.
119 * \param[in,out] out Pointer to output data structure.
120 * \param[in,out] data Should point to \c t_methoddata_pos.
121 * \returns 0 for success.
124 init_output_pos(t_topology *top, gmx_ana_selvalue_t *out, void *data);
125 /** Frees the data allocated for position evaluation selection methods. */
127 free_data_pos(void *data);
128 /** Evaluates position evaluation selection methods. */
130 evaluate_pos(t_topology * /* top */, t_trxframe *fr, t_pbc *pbc, gmx_ana_index_t * /* g */, gmx_ana_selvalue_t *out, void *data);
132 /** Parameters for position keyword evaluation. */
133 static gmx_ana_selparam_t smparams_keyword_pos[] = {
134 {NULL, {GROUP_VALUE, 1, {NULL}}, NULL, SPAR_DYNAMIC},
137 /** Parameters for the \p cog and \p com selection methods. */
138 static gmx_ana_selparam_t smparams_com[] = {
139 {"of", {GROUP_VALUE, 1, {NULL}}, NULL, SPAR_DYNAMIC},
140 {"pbc", {NO_VALUE, 0, {NULL}}, NULL, 0},
143 /** Selection method data for position keyword evaluation. */
144 gmx_ana_selmethod_t sm_keyword_pos = {
145 "kw_pos", POS_VALUE, SMETH_DYNAMIC | SMETH_VARNUMVAL,
146 asize(smparams_keyword_pos), smparams_keyword_pos,
158 /** Selection method data for the \p cog method. */
159 gmx_ana_selmethod_t sm_cog = {
160 "cog", POS_VALUE, SMETH_DYNAMIC | SMETH_SINGLEVAL,
161 asize(smparams_com), smparams_com,
170 {"cog of ATOM_EXPR [pbc]", 0, NULL},
173 /** Selection method data for the \p com method. */
174 gmx_ana_selmethod_t sm_com = {
175 "com", POS_VALUE, SMETH_REQTOP | SMETH_DYNAMIC | SMETH_SINGLEVAL,
176 asize(smparams_com), smparams_com,
185 {"com of ATOM_EXPR [pbc]", 0, NULL},
189 * \param[in] npar Should be 1 or 2.
190 * \param[in,out] param Method parameters (should point to
191 * \ref smparams_keyword_pos or \ref smparams_com).
192 * \returns Pointer to the allocated data (\c t_methoddata_pos).
194 * Allocates memory for a \c t_methoddata_pos structure and initializes
195 * the first parameter to define the value for \c t_methoddata_pos::g.
196 * If a second parameter is present, it is used for setting the
197 * \c t_methoddata_pos::bPBC flag.
200 init_data_pos(int npar, gmx_ana_selparam_t *param)
202 t_methoddata_pos *data;
205 param[0].val.u.g = &data->g;
208 param[1].val.u.b = &data->bPBC;
218 * \param[in] pcc Position calculation collection to use.
219 * \param[in,out] data Should point to \c t_methoddata_pos.
222 set_poscoll_pos(gmx::PositionCalculationCollection *pcc, void *data)
224 ((t_methoddata_pos *)data)->pcc = pcc;
228 * \param[in,out] sel Selection element to initialize.
229 * \param[in] type One of the enum values acceptable for
230 * PositionCalculationCollection::typeFromEnum().
232 * Initializes the reference position type for position evaluation.
233 * If called multiple times, the first setting takes effect, and later calls
237 _gmx_selelem_set_kwpos_type(gmx::SelectionTreeElement *sel, const char *type)
239 t_methoddata_pos *d = (t_methoddata_pos *)sel->u.expr.mdata;
241 if (sel->type != SEL_EXPRESSION || !sel->u.expr.method
242 || sel->u.expr.method->name != sm_keyword_pos.name)
246 if (!d->type && type)
248 d->type = gmx_strdup(type);
249 /* FIXME: It would be better not to have the string here hardcoded. */
252 sel->u.expr.method->flags |= SMETH_REQTOP;
258 * \param[in,out] sel Selection element to initialize.
259 * \param[in] flags Default completion flags
260 * (see PositionCalculationCollection::typeFromEnum()).
262 * Initializes the flags for position evaluation.
263 * If called multiple times, the first setting takes effect, and later calls
267 _gmx_selelem_set_kwpos_flags(gmx::SelectionTreeElement *sel, int flags)
269 t_methoddata_pos *d = (t_methoddata_pos *)sel->u.expr.mdata;
271 if (sel->type != SEL_EXPRESSION || !sel->u.expr.method
272 || sel->u.expr.method->name != sm_keyword_pos.name)
283 init_kwpos(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
285 t_methoddata_pos *d = (t_methoddata_pos *)data;
287 if (!(param[0].flags & SPAR_DYNAMIC))
289 d->flags &= ~(POS_DYNAMIC | POS_MASKONLY);
291 else if (!(d->flags & POS_MASKONLY))
293 d->flags |= POS_DYNAMIC;
295 d->pc = d->pcc->createCalculationFromEnum(d->type, d->flags);
296 gmx_ana_poscalc_set_maxindex(d->pc, &d->g);
300 init_cog(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
302 t_methoddata_pos *d = (t_methoddata_pos *)data;
304 d->flags = (param[0].flags & SPAR_DYNAMIC) ? POS_DYNAMIC : 0;
305 d->pc = d->pcc->createCalculation(d->bPBC ? POS_ALL_PBC : POS_ALL, d->flags);
306 gmx_ana_poscalc_set_maxindex(d->pc, &d->g);
310 init_com(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
312 t_methoddata_pos *d = (t_methoddata_pos *)data;
314 d->flags = (param[0].flags & SPAR_DYNAMIC) ? POS_DYNAMIC : 0;
315 d->flags |= POS_MASS;
316 d->pc = d->pcc->createCalculation(d->bPBC ? POS_ALL_PBC : POS_ALL, d->flags);
317 gmx_ana_poscalc_set_maxindex(d->pc, &d->g);
321 init_output_pos(t_topology * /* top */, gmx_ana_selvalue_t *out, void *data)
323 t_methoddata_pos *d = (t_methoddata_pos *)data;
325 gmx_ana_poscalc_init_pos(d->pc, out->u.p);
329 * \param data Data to free (should point to a \c t_methoddata_pos).
331 * Frees the memory allocated for \c t_methoddata_pos::g and
332 * \c t_methoddata_pos::pc.
335 free_data_pos(void *data)
337 t_methoddata_pos *d = (t_methoddata_pos *)data;
340 gmx_ana_poscalc_free(d->pc);
345 * See sel_updatefunc() for description of the parameters.
346 * \p data should point to a \c t_methoddata_pos.
348 * Calculates the positions using \c t_methoddata_pos::pc for the index group
349 * in \c t_methoddata_pos::g and stores the results in \p out->u.p.
352 evaluate_pos(t_topology * /* top */, t_trxframe *fr, t_pbc *pbc,
353 gmx_ana_index_t * /* g */, gmx_ana_selvalue_t *out, void *data)
355 t_methoddata_pos *d = (t_methoddata_pos *)data;
357 gmx_ana_poscalc_update(d->pc, out->u.p, &d->g, fr, pbc);