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37 * Implements functions in selelem.h.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_selection
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/exceptions.h"
51 #include "gromacs/utility/gmxassert.h"
52 #include "gromacs/utility/smalloc.h"
53 #include "gromacs/utility/stringutil.h"
58 #include "selmethod.h"
61 * \param[in] sel Selection for which the string is requested
62 * \returns Pointer to a string that corresponds to \p sel->type.
64 * The return value points to a string constant and should not be \p free'd.
66 * The function returns NULL if \p sel->type is not one of the valid values.
69 _gmx_selelem_type_str(const gmx::SelectionTreeElement &sel)
74 case SEL_CONST: p = "CONST"; break;
75 case SEL_EXPRESSION: p = "EXPR"; break;
76 case SEL_BOOLEAN: p = "BOOL"; break;
77 case SEL_ARITHMETIC: p = "ARITH"; break;
78 case SEL_ROOT: p = "ROOT"; break;
79 case SEL_SUBEXPR: p = "SUBEXPR"; break;
80 case SEL_SUBEXPRREF: p = "REF"; break;
81 case SEL_GROUPREF: p = "GROUPREF"; break;
82 case SEL_MODIFIER: p = "MODIFIER"; break;
83 // No default clause so we intentionally get compiler errors
84 // if new selection choices are added later.
90 * \param[in] val Value structore for which the string is requested.
91 * \returns Pointer to a string that corresponds to \p val->type,
92 * NULL if the type value is invalid.
94 * The return value points to a string constant and should not be \p free'd.
97 _gmx_sel_value_type_str(const gmx_ana_selvalue_t *val)
102 case NO_VALUE: p = "NONE"; break;
103 case INT_VALUE: p = "INT"; break;
104 case REAL_VALUE: p = "REAL"; break;
105 case STR_VALUE: p = "STR"; break;
106 case POS_VALUE: p = "VEC"; break;
107 case GROUP_VALUE: p = "GROUP"; break;
108 // No default clause so we intentionally get compiler errors
109 // if new selection choices are added later.
114 /*! \copydoc _gmx_selelem_type_str() */
116 _gmx_selelem_boolean_type_str(const gmx::SelectionTreeElement &sel)
118 const char *p = NULL;
121 case BOOL_NOT: p = "NOT"; break;
122 case BOOL_AND: p = "AND"; break;
123 case BOOL_OR: p = "OR"; break;
124 case BOOL_XOR: p = "XOR"; break;
125 // No default clause so we intentionally get compiler errors
126 // if new selection choices are added later.
135 SelectionTreeElement::SelectionTreeElement(e_selelem_t type)
138 this->flags = (type != SEL_ROOT) ? SEL_ALLOCVAL : 0;
139 if (type == SEL_BOOLEAN)
141 this->v.type = GROUP_VALUE;
142 this->flags |= SEL_ALLOCDATA;
146 this->v.type = NO_VALUE;
148 _gmx_selvalue_clear(&this->v);
149 std::memset(&this->u, 0, sizeof(this->u));
150 this->evaluate = NULL;
151 this->mempool = NULL;
155 SelectionTreeElement::~SelectionTreeElement()
157 /* Free the children.
158 * Must be done before freeing other data, because the children may hold
159 * references to data in this element. */
163 freeExpressionData();
167 void SelectionTreeElement::freeValues()
170 if ((flags & SEL_ALLOCDATA) && v.u.ptr)
172 /* The number of position/group structures is constant, so the
173 * backup of using sel->v.nr should work for them.
174 * For strings, we report an error if we don't know the allocation
176 int n = (v.nalloc > 0) ? v.nalloc : v.nr;
180 GMX_RELEASE_ASSERT(v.nalloc != 0,
181 "SEL_ALLOCDATA should only be set for allocated "
183 for (int i = 0; i < n; ++i)
189 for (int i = 0; i < n; ++i)
191 gmx_ana_index_deinit(&v.u.g[i]);
194 default: /* No special handling for other types */
200 if (v.type == POS_VALUE)
209 _gmx_selvalue_setstore(&v, NULL);
210 if (type == SEL_SUBEXPRREF && u.param)
212 u.param->val.u.ptr = NULL;
217 SelectionTreeElement::freeExpressionData()
219 if (type == SEL_EXPRESSION || type == SEL_MODIFIER)
221 _gmx_selelem_free_method(u.expr.method, u.expr.mdata);
223 u.expr.method = NULL;
224 /* Free position data */
227 /* Free position calculation data */
230 gmx_ana_poscalc_free(u.expr.pc);
234 if (type == SEL_ARITHMETIC)
236 sfree(u.arith.opstr);
237 u.arith.opstr = NULL;
239 if (type == SEL_SUBEXPR || type == SEL_ROOT
240 || (type == SEL_CONST && v.type == GROUP_VALUE))
242 gmx_ana_index_deinit(&u.cgrp);
244 if (type == SEL_GROUPREF)
250 void SelectionTreeElement::mempoolReserve(int count)
259 v.u.i = static_cast<int *>(
260 _gmx_sel_mempool_alloc(mempool, sizeof(*v.u.i)*count));
264 v.u.r = static_cast<real *>(
265 _gmx_sel_mempool_alloc(mempool, sizeof(*v.u.r)*count));
269 _gmx_sel_mempool_alloc_group(mempool, v.u.g, count);
273 GMX_THROW(gmx::InternalError("Memory pooling not implemented for requested type"));
277 void SelectionTreeElement::mempoolRelease()
287 _gmx_sel_mempool_free(mempool, v.u.ptr);
288 _gmx_selvalue_setstore(&v, NULL);
294 _gmx_sel_mempool_free_group(mempool, v.u.g);
299 GMX_THROW(gmx::InternalError("Memory pooling not implemented for requested type"));
303 void SelectionTreeElement::fillNameIfMissing(const char *selectionText)
305 GMX_RELEASE_ASSERT(type == SEL_ROOT,
306 "Should not be called for non-root elements");
309 // Check whether the actual selection given was from an external group,
310 // and if so, use the name of the external group.
311 SelectionTreeElementPointer child = this->child;
312 while (child->type == SEL_MODIFIER)
314 if (!child->child || child->child->type != SEL_SUBEXPRREF
315 || !child->child->child)
319 child = child->child->child;
321 if (child->type == SEL_EXPRESSION
322 && child->child && child->child->type == SEL_SUBEXPRREF
323 && child->child->child)
325 if (child->child->child->type == SEL_CONST
326 && child->child->child->v.type == GROUP_VALUE)
328 setName(child->child->child->name());
331 // If the group reference is still unresolved, leave the name empty
332 // and fill it later.
333 if (child->child->child->type == SEL_GROUPREF)
338 // If there still is no name, use the selection string.
339 setName(selectionText);
343 void SelectionTreeElement::checkUnsortedAtoms(
344 bool bUnsortedAllowed, ExceptionInitializer *errors) const
346 const bool bUnsortedSupported
347 = (type == SEL_CONST && v.type == GROUP_VALUE)
348 || type == SEL_ROOT || type == SEL_SUBEXPR || type == SEL_SUBEXPRREF
349 // TODO: Consolidate.
350 || type == SEL_MODIFIER
351 || (type == SEL_EXPRESSION && (u.expr.method->flags & SMETH_ALLOW_UNSORTED));
353 // TODO: For some complicated selections, this may result in the same
354 // index group reference being flagged as an error multiple times for the
356 SelectionTreeElementPointer child = this->child;
359 child->checkUnsortedAtoms(bUnsortedAllowed && bUnsortedSupported,
364 // The logic here is simplified by the fact that only constant groups can
365 // currently be the root cause of SEL_UNSORTED being set, so only those
366 // need to be considered in triggering the error.
367 if (!bUnsortedAllowed && (flags & SEL_UNSORTED)
368 && type == SEL_CONST && v.type == GROUP_VALUE)
370 std::string message = formatString(
371 "Group '%s' cannot be used in selections except "
372 "as a full value of the selection, "
373 "because atom indices in it are not sorted and/or "
374 "it contains duplicate atoms.",
376 errors->addNested(InconsistentInputError(message));
380 void SelectionTreeElement::resolveIndexGroupReference(
381 gmx_ana_indexgrps_t *grps, int natoms)
383 GMX_RELEASE_ASSERT(type == SEL_GROUPREF,
384 "Should only be called for index group reference elements");
387 std::string message = formatString(
388 "Cannot match '%s', because index groups are not available.",
390 GMX_THROW(InconsistentInputError(message));
393 gmx_ana_index_t foundGroup;
394 std::string foundName;
395 if (u.gref.name != NULL)
397 if (!gmx_ana_indexgrps_find(&foundGroup, &foundName, grps, u.gref.name))
399 std::string message = formatString(
400 "Cannot match '%s', because no such index group can be found.",
402 GMX_THROW(InconsistentInputError(message));
407 if (!gmx_ana_indexgrps_extract(&foundGroup, &foundName, grps, u.gref.id))
409 std::string message = formatString(
410 "Cannot match '%s', because no such index group can be found.",
412 GMX_THROW(InconsistentInputError(message));
416 if (!gmx_ana_index_check_sorted(&foundGroup))
418 flags |= SEL_UNSORTED;
423 gmx_ana_index_set(&u.cgrp, foundGroup.isize, foundGroup.index,
424 foundGroup.nalloc_index);
429 checkIndexGroup(natoms);
433 void SelectionTreeElement::checkIndexGroup(int natoms)
435 GMX_RELEASE_ASSERT(type == SEL_CONST && v.type == GROUP_VALUE,
436 "Should only be called for index group elements");
437 if (!gmx_ana_index_check_range(&u.cgrp, natoms))
439 std::string message = formatString(
440 "Group '%s' cannot be used in selections, because it "
441 "contains negative atom indices and/or references atoms "
442 "not present (largest allowed atom index is %d).",
443 name().c_str(), natoms);
444 GMX_THROW(InconsistentInputError(message));
451 * \param[in,out] sel Selection element to set the type for.
452 * \param[in] vtype Value type for the selection element.
454 * If the new type is \ref GROUP_VALUE or \ref POS_VALUE, the
455 * \ref SEL_ALLOCDATA flag is also set.
457 * This function should only be called at most once for each element,
458 * preferably right after calling _gmx_selelem_create().
461 _gmx_selelem_set_vtype(const gmx::SelectionTreeElementPointer &sel,
464 GMX_RELEASE_ASSERT(sel->type != SEL_BOOLEAN || vtype == GROUP_VALUE,
465 "Boolean elements must have a group value");
466 GMX_RELEASE_ASSERT(sel->v.type == NO_VALUE || vtype == sel->v.type,
467 "_gmx_selelem_set_vtype() called more than once");
469 if (vtype == GROUP_VALUE || vtype == POS_VALUE)
471 sel->flags |= SEL_ALLOCDATA;
476 * \param[in] method Method to free.
477 * \param[in] mdata Method data to free.
480 _gmx_selelem_free_method(gmx_ana_selmethod_t *method, void *mdata)
482 sel_freefunc free_func = NULL;
484 /* Save the pointer to the free function. */
485 if (method && method->free)
487 free_func = method->free;
490 /* Free the method itself.
491 * Has to be done before freeing the method data, because parameter
492 * values are typically stored in the method data, and here we may
498 /* Free the memory allocated for the parameters that are not managed
499 * by the selection method itself. */
500 for (i = 0; i < method->nparams; ++i)
502 gmx_ana_selparam_t *param = &method->param[i];
504 if (param->val.u.ptr)
506 if (param->val.type == GROUP_VALUE)
508 for (j = 0; j < param->val.nr; ++j)
510 gmx_ana_index_deinit(¶m->val.u.g[j]);
513 else if (param->val.type == POS_VALUE)
515 if (param->val.nalloc > 0)
517 delete[] param->val.u.p;
518 _gmx_selvalue_setstore(¶m->val, NULL);
522 if (param->val.nalloc > 0)
524 sfree(param->val.u.ptr);
528 sfree(method->param);
531 /* Free method data. */
546 * \param[in] fp File handle to receive the output.
547 * \param[in] sel Root of the selection subtree to print.
548 * \param[in] bValues If true, the evaluated values of selection elements
549 * are printed as well.
550 * \param[in] level Indentation level, starting from zero.
553 _gmx_selelem_print_tree(FILE *fp, const gmx::SelectionTreeElement &sel,
554 bool bValues, int level)
558 fprintf(fp, "%*c %s %s", level*2+1, '*',
559 _gmx_selelem_type_str(sel), _gmx_sel_value_type_str(&sel.v));
560 if (!sel.name().empty())
562 fprintf(fp, " \"%s\"", sel.name().c_str());
564 fprintf(fp, " flg=");
565 if (sel.flags & SEL_FLAGSSET)
569 if (sel.flags & SEL_SINGLEVAL)
573 if (sel.flags & SEL_ATOMVAL)
577 if (sel.flags & SEL_VARNUMVAL)
581 if (sel.flags & SEL_DYNAMIC)
585 if (!(sel.flags & SEL_VALFLAGMASK))
589 if (sel.flags & SEL_ALLOCVAL)
593 if (sel.flags & SEL_ALLOCDATA)
601 if (sel.type == SEL_CONST)
603 if (sel.v.type == INT_VALUE)
605 fprintf(fp, " %d", sel.v.u.i[0]);
607 else if (sel.v.type == REAL_VALUE)
609 fprintf(fp, " %f", sel.v.u.r[0]);
611 else if (sel.v.type == GROUP_VALUE)
613 const gmx_ana_index_t *g = sel.v.u.g;
614 if (!g || g->isize == 0)
618 fprintf(fp, " (%d atoms)", g->isize);
621 else if (sel.type == SEL_BOOLEAN)
623 fprintf(fp, " %s", _gmx_selelem_boolean_type_str(sel));
625 else if (sel.type == SEL_EXPRESSION
626 && sel.u.expr.method->name == sm_compare.name)
628 _gmx_selelem_print_compare_info(fp, sel.u.expr.mdata);
632 fprintf(fp, " eval=");
633 _gmx_sel_print_evalfunc_name(fp, sel.evaluate);
635 if (!(sel.flags & SEL_ALLOCVAL))
637 fprintf(fp, " (ext)");
641 if ((sel.type == SEL_CONST && sel.v.type == GROUP_VALUE) || sel.type == SEL_ROOT)
643 const gmx_ana_index_t *g = sel.v.u.g;
644 if (!g || g->isize == 0 || sel.evaluate != NULL)
650 fprintf(fp, "%*c group: (null)\n", level*2+1, ' ');
652 else if (g->isize > 0)
654 fprintf(fp, "%*c group:", level*2+1, ' ');
657 for (i = 0; i < g->isize; ++i)
659 fprintf(fp, " %d", g->index[i] + 1);
664 fprintf(fp, " %d atoms", g->isize);
669 else if (sel.type == SEL_EXPRESSION)
673 fprintf(fp, "%*c COM", level*2+3, '*');
680 _gmx_selelem_print_compiler_info(fp, sel, level);
683 if (bValues && sel.type != SEL_CONST && sel.type != SEL_ROOT && sel.v.u.ptr)
685 fprintf(fp, "%*c value: ", level*2+1, ' ');
689 /* In normal use, the pointer should never be NULL, but it's
690 * useful to have the check for debugging to avoid accidental
691 * segfaults when printing the selection tree. */
694 fprintf(fp, "(%f, %f, %f)",
695 sel.v.u.p->x[0][XX], sel.v.u.p->x[0][YY],
696 sel.v.u.p->x[0][ZZ]);
700 fprintf(fp, "(null)");
704 fprintf(fp, "%d atoms", sel.v.u.g->isize);
705 if (sel.v.u.g->isize < 20)
707 if (sel.v.u.g->isize > 0)
711 for (i = 0; i < sel.v.u.g->isize; ++i)
713 fprintf(fp, " %d", sel.v.u.g->index[i] + 1);
724 /* Print the subexpressions with one more level of indentation */
725 gmx::SelectionTreeElementPointer child = sel.child;
728 if (!(sel.type == SEL_SUBEXPRREF && child->type == SEL_SUBEXPR))
730 _gmx_selelem_print_tree(fp, *child, bValues, level+1);
737 * \param[in] root Root of the subtree to query.
738 * \returns true if \p root or any any of its elements require topology
739 * information, false otherwise.
742 _gmx_selelem_requires_top(const gmx::SelectionTreeElement &root)
744 if (root.type == SEL_EXPRESSION || root.type == SEL_MODIFIER)
746 if (root.u.expr.method && (root.u.expr.method->flags & SMETH_REQTOP))
750 if (root.u.expr.pc && gmx_ana_poscalc_requires_top(root.u.expr.pc))
755 gmx::SelectionTreeElementPointer child = root.child;
758 if (_gmx_selelem_requires_top(*child))