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37 * Implements functions in selelem.h.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_selection
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/exceptions.h"
49 #include "gromacs/utility/gmxassert.h"
50 #include "gromacs/utility/smalloc.h"
51 #include "gromacs/utility/stringutil.h"
58 * \param[in] sel Selection for which the string is requested
59 * \returns Pointer to a string that corresponds to \p sel->type.
61 * The return value points to a string constant and should not be \p free'd.
63 * The function returns NULL if \p sel->type is not one of the valid values.
66 _gmx_selelem_type_str(const gmx::SelectionTreeElement &sel)
70 case SEL_CONST: return "CONST";
71 case SEL_EXPRESSION: return "EXPR";
72 case SEL_BOOLEAN: return "BOOL";
73 case SEL_ARITHMETIC: return "ARITH";
74 case SEL_ROOT: return "ROOT";
75 case SEL_SUBEXPR: return "SUBEXPR";
76 case SEL_SUBEXPRREF: return "REF";
77 case SEL_GROUPREF: return "GROUPREF";
78 case SEL_MODIFIER: return "MODIFIER";
84 * \param[in] val Value structore for which the string is requested.
85 * \returns Pointer to a string that corresponds to \p val->type,
86 * NULL if the type value is invalid.
88 * The return value points to a string constant and should not be \p free'd.
91 _gmx_sel_value_type_str(const gmx_ana_selvalue_t *val)
95 case NO_VALUE: return "NONE";
96 case INT_VALUE: return "INT";
97 case REAL_VALUE: return "REAL";
98 case STR_VALUE: return "STR";
99 case POS_VALUE: return "VEC";
100 case GROUP_VALUE: return "GROUP";
105 /*! \copydoc _gmx_selelem_type_str() */
107 _gmx_selelem_boolean_type_str(const gmx::SelectionTreeElement &sel)
111 case BOOL_NOT: return "NOT"; break;
112 case BOOL_AND: return "AND"; break;
113 case BOOL_OR: return "OR"; break;
114 case BOOL_XOR: return "XOR"; break;
123 SelectionTreeElement::SelectionTreeElement(e_selelem_t type)
126 this->flags = (type != SEL_ROOT) ? SEL_ALLOCVAL : 0;
127 if (type == SEL_BOOLEAN)
129 this->v.type = GROUP_VALUE;
130 this->flags |= SEL_ALLOCDATA;
134 this->v.type = NO_VALUE;
136 _gmx_selvalue_clear(&this->v);
137 std::memset(&this->u, 0, sizeof(this->u));
138 this->evaluate = NULL;
139 this->mempool = NULL;
143 SelectionTreeElement::~SelectionTreeElement()
145 /* Free the children.
146 * Must be done before freeing other data, because the children may hold
147 * references to data in this element. */
151 freeExpressionData();
155 void SelectionTreeElement::freeValues()
158 if ((flags & SEL_ALLOCDATA) && v.u.ptr)
160 /* The number of position/group structures is constant, so the
161 * backup of using sel->v.nr should work for them.
162 * For strings, we report an error if we don't know the allocation
164 int n = (v.nalloc > 0) ? v.nalloc : v.nr;
168 GMX_RELEASE_ASSERT(v.nalloc != 0,
169 "SEL_ALLOCDATA should only be set for allocated "
171 for (int i = 0; i < n; ++i)
177 for (int i = 0; i < n; ++i)
179 gmx_ana_index_deinit(&v.u.g[i]);
182 default: /* No special handling for other types */
188 if (v.type == POS_VALUE)
197 _gmx_selvalue_setstore(&v, NULL);
198 if (type == SEL_SUBEXPRREF && u.param)
200 u.param->val.u.ptr = NULL;
205 SelectionTreeElement::freeExpressionData()
207 if (type == SEL_EXPRESSION || type == SEL_MODIFIER)
209 _gmx_selelem_free_method(u.expr.method, u.expr.mdata);
211 u.expr.method = NULL;
212 /* Free position data */
215 /* Free position calculation data */
218 gmx_ana_poscalc_free(u.expr.pc);
222 if (type == SEL_ARITHMETIC)
224 sfree(u.arith.opstr);
225 u.arith.opstr = NULL;
227 if (type == SEL_SUBEXPR || type == SEL_ROOT
228 || (type == SEL_CONST && v.type == GROUP_VALUE))
230 gmx_ana_index_deinit(&u.cgrp);
232 if (type == SEL_GROUPREF)
238 void SelectionTreeElement::mempoolReserve(int count)
247 v.u.i = static_cast<int *>(
248 _gmx_sel_mempool_alloc(mempool, sizeof(*v.u.i)*count));
252 v.u.r = static_cast<real *>(
253 _gmx_sel_mempool_alloc(mempool, sizeof(*v.u.r)*count));
257 _gmx_sel_mempool_alloc_group(mempool, v.u.g, count);
261 GMX_THROW(gmx::InternalError("Memory pooling not implemented for requested type"));
265 void SelectionTreeElement::mempoolRelease()
275 _gmx_sel_mempool_free(mempool, v.u.ptr);
276 _gmx_selvalue_setstore(&v, NULL);
282 _gmx_sel_mempool_free_group(mempool, v.u.g);
287 GMX_THROW(gmx::InternalError("Memory pooling not implemented for requested type"));
291 void SelectionTreeElement::fillNameIfMissing(const char *selectionText)
293 GMX_RELEASE_ASSERT(type == SEL_ROOT,
294 "Should not be called for non-root elements");
297 // Check whether the actual selection given was from an external group,
298 // and if so, use the name of the external group.
299 SelectionTreeElementPointer child = this->child;
300 while (child->type == SEL_MODIFIER)
302 if (!child->child || child->child->type != SEL_SUBEXPRREF
303 || !child->child->child)
307 child = child->child->child;
309 if (child->type == SEL_EXPRESSION
310 && child->child && child->child->type == SEL_SUBEXPRREF
311 && child->child->child)
313 if (child->child->child->type == SEL_CONST
314 && child->child->child->v.type == GROUP_VALUE)
316 setName(child->child->child->name());
319 // If the group reference is still unresolved, leave the name empty
320 // and fill it later.
321 if (child->child->child->type == SEL_GROUPREF)
326 // If there still is no name, use the selection string.
327 setName(selectionText);
331 void SelectionTreeElement::resolveIndexGroupReference(gmx_ana_indexgrps_t *grps)
333 GMX_RELEASE_ASSERT(type == SEL_GROUPREF,
334 "Should only be called for index group reference elements");
337 std::string message = formatString(
338 "Cannot match '%s', because index groups are not available.",
340 GMX_THROW(InconsistentInputError(message));
343 gmx_ana_index_t foundGroup;
344 std::string foundName;
345 if (u.gref.name != NULL)
347 if (!gmx_ana_indexgrps_find(&foundGroup, &foundName, grps, u.gref.name))
349 std::string message = formatString(
350 "Cannot match '%s', because no such index group can be found.",
352 GMX_THROW(InconsistentInputError(message));
357 if (!gmx_ana_indexgrps_extract(&foundGroup, &foundName, grps, u.gref.id))
359 std::string message = formatString(
360 "Cannot match '%s', because no such index group can be found.",
362 GMX_THROW(InconsistentInputError(message));
366 if (!gmx_ana_index_check_sorted(&foundGroup))
368 flags |= SEL_UNSORTED;
369 // TODO: Add this test elsewhere, where it does not break valid use cases.
371 gmx_ana_index_deinit(&foundGroup);
372 std::string message = formatString(
373 "Group '%s' ('%s') cannot be used in selections, "
374 "because atom indices in it are not sorted and/or "
375 "it contains duplicate atoms.",
376 foundName.c_str(), name().c_str());
377 GMX_THROW(InconsistentInputError(message));
383 gmx_ana_index_set(&u.cgrp, foundGroup.isize, foundGroup.index,
384 foundGroup.nalloc_index);
391 * \param[in,out] sel Selection element to set the type for.
392 * \param[in] vtype Value type for the selection element.
394 * If the new type is \ref GROUP_VALUE or \ref POS_VALUE, the
395 * \ref SEL_ALLOCDATA flag is also set.
397 * This function should only be called at most once for each element,
398 * preferably right after calling _gmx_selelem_create().
401 _gmx_selelem_set_vtype(const gmx::SelectionTreeElementPointer &sel,
404 GMX_RELEASE_ASSERT(sel->type != SEL_BOOLEAN || vtype == GROUP_VALUE,
405 "Boolean elements must have a group value");
406 GMX_RELEASE_ASSERT(sel->v.type == NO_VALUE || vtype == sel->v.type,
407 "_gmx_selelem_set_vtype() called more than once");
409 if (vtype == GROUP_VALUE || vtype == POS_VALUE)
411 sel->flags |= SEL_ALLOCDATA;
416 * \param[in] method Method to free.
417 * \param[in] mdata Method data to free.
420 _gmx_selelem_free_method(gmx_ana_selmethod_t *method, void *mdata)
422 sel_freefunc free_func = NULL;
424 /* Save the pointer to the free function. */
425 if (method && method->free)
427 free_func = method->free;
430 /* Free the method itself.
431 * Has to be done before freeing the method data, because parameter
432 * values are typically stored in the method data, and here we may
438 /* Free the memory allocated for the parameters that are not managed
439 * by the selection method itself. */
440 for (i = 0; i < method->nparams; ++i)
442 gmx_ana_selparam_t *param = &method->param[i];
444 if (param->val.u.ptr)
446 if (param->val.type == GROUP_VALUE)
448 for (j = 0; j < param->val.nr; ++j)
450 gmx_ana_index_deinit(¶m->val.u.g[j]);
453 else if (param->val.type == POS_VALUE)
455 if (param->val.nalloc > 0)
457 delete[] param->val.u.p;
458 _gmx_selvalue_setstore(¶m->val, NULL);
462 if (param->val.nalloc > 0)
464 sfree(param->val.u.ptr);
468 sfree(method->param);
471 /* Free method data. */
486 * \param[in] fp File handle to receive the output.
487 * \param[in] sel Root of the selection subtree to print.
488 * \param[in] bValues If true, the evaluated values of selection elements
489 * are printed as well.
490 * \param[in] level Indentation level, starting from zero.
493 _gmx_selelem_print_tree(FILE *fp, const gmx::SelectionTreeElement &sel,
494 bool bValues, int level)
498 fprintf(fp, "%*c %s %s", level*2+1, '*',
499 _gmx_selelem_type_str(sel), _gmx_sel_value_type_str(&sel.v));
500 if (!sel.name().empty())
502 fprintf(fp, " \"%s\"", sel.name().c_str());
504 fprintf(fp, " flg=");
505 if (sel.flags & SEL_FLAGSSET)
509 if (sel.flags & SEL_SINGLEVAL)
513 if (sel.flags & SEL_ATOMVAL)
517 if (sel.flags & SEL_VARNUMVAL)
521 if (sel.flags & SEL_DYNAMIC)
525 if (!(sel.flags & SEL_VALFLAGMASK))
529 if (sel.flags & SEL_ALLOCVAL)
533 if (sel.flags & SEL_ALLOCDATA)
541 if (sel.type == SEL_CONST)
543 if (sel.v.type == INT_VALUE)
545 fprintf(fp, " %d", sel.v.u.i[0]);
547 else if (sel.v.type == REAL_VALUE)
549 fprintf(fp, " %f", sel.v.u.r[0]);
551 else if (sel.v.type == GROUP_VALUE)
553 const gmx_ana_index_t *g = sel.v.u.g;
554 if (!g || g->isize == 0)
558 fprintf(fp, " (%d atoms)", g->isize);
561 else if (sel.type == SEL_BOOLEAN)
563 fprintf(fp, " %s", _gmx_selelem_boolean_type_str(sel));
565 else if (sel.type == SEL_EXPRESSION
566 && sel.u.expr.method->name == sm_compare.name)
568 _gmx_selelem_print_compare_info(fp, sel.u.expr.mdata);
572 fprintf(fp, " eval=");
573 _gmx_sel_print_evalfunc_name(fp, sel.evaluate);
575 if (!(sel.flags & SEL_ALLOCVAL))
577 fprintf(fp, " (ext)");
581 if ((sel.type == SEL_CONST && sel.v.type == GROUP_VALUE) || sel.type == SEL_ROOT)
583 const gmx_ana_index_t *g = sel.v.u.g;
584 if (!g || g->isize == 0 || sel.evaluate != NULL)
590 fprintf(fp, "%*c group: (null)\n", level*2+1, ' ');
592 else if (g->isize > 0)
594 fprintf(fp, "%*c group:", level*2+1, ' ');
597 for (i = 0; i < g->isize; ++i)
599 fprintf(fp, " %d", g->index[i] + 1);
604 fprintf(fp, " %d atoms", g->isize);
609 else if (sel.type == SEL_EXPRESSION)
613 fprintf(fp, "%*c COM", level*2+3, '*');
620 _gmx_selelem_print_compiler_info(fp, sel, level);
623 if (bValues && sel.type != SEL_CONST && sel.type != SEL_ROOT && sel.v.u.ptr)
625 fprintf(fp, "%*c value: ", level*2+1, ' ');
629 /* In normal use, the pointer should never be NULL, but it's
630 * useful to have the check for debugging to avoid accidental
631 * segfaults when printing the selection tree. */
634 fprintf(fp, "(%f, %f, %f)",
635 sel.v.u.p->x[0][XX], sel.v.u.p->x[0][YY],
636 sel.v.u.p->x[0][ZZ]);
640 fprintf(fp, "(null)");
644 fprintf(fp, "%d atoms", sel.v.u.g->isize);
645 if (sel.v.u.g->isize < 20)
647 if (sel.v.u.g->isize > 0)
651 for (i = 0; i < sel.v.u.g->isize; ++i)
653 fprintf(fp, " %d", sel.v.u.g->index[i] + 1);
664 /* Print the subexpressions with one more level of indentation */
665 gmx::SelectionTreeElementPointer child = sel.child;
668 if (!(sel.type == SEL_SUBEXPRREF && child->type == SEL_SUBEXPR))
670 _gmx_selelem_print_tree(fp, *child, bValues, level+1);
677 * \param[in] root Root of the subtree to query.
678 * \returns true if \p root or any any of its elements require topology
679 * information, false otherwise.
682 _gmx_selelem_requires_top(const gmx::SelectionTreeElement &root)
684 if (root.type == SEL_EXPRESSION || root.type == SEL_MODIFIER)
686 if (root.u.expr.method && (root.u.expr.method->flags & SMETH_REQTOP))
690 if (root.u.expr.pc && gmx_ana_poscalc_requires_top(root.u.expr.pc))
695 gmx::SelectionTreeElementPointer child = root.child;
698 if (_gmx_selelem_requires_top(*child))