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36 * \brief Selection compilation and optimization.
39 * Better error handling and memory management in error situations.
40 * At least, the main compilation function leaves the selection collection in
41 * a bad state if an error occurs.
44 * The memory usage could still be optimized.
45 * Use of memory pooling could still be extended, and a lot of redundant
46 * gmin/gmax data could be eliminated for complex arithmetic expressions.
48 * \author Teemu Murtola <teemu.murtola@gmail.com>
49 * \ingroup module_selection
52 * \page page_module_selection_compiler Selection compilation
54 * The compiler takes the selection element tree from the selection parser
55 * (see \ref page_module_selection_parser) as input.
56 * The selection parser is quite independent of selection evaluation details,
57 * and the compiler processes the tree to conform to what the evaluation
59 * For better control and optimization possibilities, the compilation is
60 * done on all selections simultaneously.
61 * Hence, all the selections should be parsed before the compiler can be
64 * The compiler initializes all fields in gmx::SelectionTreeElement not
65 * initialized by the parser: gmx::SelectionTreeElement::v (some fields have
66 * already been initialized by the parser),
67 * gmx::SelectionTreeElement::evaluate, and gmx::SelectionTreeElement::u
68 * (again, some elements have been initialized in the parser).
69 * The gmx::SelectionTreeElement::cdata field is used during the compilation to store
70 * internal data, but the data is freed when the compiler returns.
72 * In addition to initializing the elements, the compiler reorganizes the tree
73 * to simplify and optimize evaluation. The compiler also evaluates the static
74 * parts of the selection: in the end of the compilation, static parts have
75 * been replaced by the result of the evaluation.
77 * The compiler is invoked using gmx::SelectionCompiler.
78 * The gmx::SelectionCompiler::compile() method does the compilation in several
79 * passes over the gmx::SelectionTreeElement tree.
80 * -# Defaults are set for the position type and flags of position calculation
81 * methods that were not explicitly specified in the user input.
82 * -# Subexpressions are extracted: a separate root is created for each
83 * subexpression, and placed before the expression is first used.
84 * Currently, only variables and expressions used to evaluate parameter
85 * values are extracted, but common subexpression could also be detected
87 * -# A second pass (in fact, multiple passes because of interdependencies)
88 * with simple reordering and initialization is done:
89 * -# Boolean expressions are combined such that one element can evaluate,
90 * e.g., "A and B and C". The subexpressions in boolean expression are
91 * reordered such that static expressions come first without otherwise
92 * altering the relative order of the expressions.
93 * -# The compiler data structure is allocated for each element, and
94 * the fields are initialized, with the exception of the contents of
95 * \c gmax and \c gmin fields. This is the part that needs multiple
96 * passes, because some flags are set recursively based on which elements
97 * refer to an element, and these flags need to be set to initialize
99 * -# The gmx::SelectionTreeElement::evaluate field is set to the correct
100 * evaluation function from evaluate.h.
102 * -# The evaluation function of all elements is replaced with the
103 * analyze_static() function to be able to initialize the element before
104 * the actual evaluation function is called.
105 * The evaluation machinery is then called to initialize the whole tree,
106 * while simultaneously evaluating the static expressions.
107 * During the evaluation, track is kept of the smallest and largest
108 * possible selections, and these are stored in the internal compiler
109 * data structure for each element.
110 * To be able to do this for all possible values of dynamical expressions,
111 * special care needs to be taken with boolean expressions because they
112 * are short-circuiting. This is done through the
113 * \c SEL_CDATA_EVALMAX flag, which makes dynamic child expressions
114 * of \c BOOL_OR expressions evaluate to empty groups, while subexpressions
115 * of \c BOOL_AND are evaluated to largest possible groups.
116 * Memory is also allocated to store the results of the evaluation.
117 * For each element, analyze_static() calls the actual evaluation function
118 * after the element has been properly initialized.
119 * -# Another evaluation pass is done over subexpressions with more than
120 * one reference to them. These cannot be completely processed during the
121 * first pass, because it is not known whether later references require
122 * additional evaluation of static expressions.
123 * -# Unused subexpressions are removed. For efficiency reasons (and to avoid
124 * some checks), this is actually done several times already earlier in
125 * the compilation process.
126 * -# Most of the processing is now done, and the next pass simply sets the
127 * evaluation group of root elements to the largest selection as determined
128 * in pass 4. For root elements of subexpressions that should not be
129 * evaluated before they are referred to, the evaluation group/function is
130 * cleared. At the same time, position calculation data is initialized for
131 * for selection method elements that require it. Compiler data is also
132 * freed as it is no longer needed.
133 * -# A final pass initializes the total masses and charges in the
134 * \c gmx_ana_selection_t data structures.
136 * The actual evaluation of the selection is described in the documentation
137 * of the functions in evaluate.h.
140 * Some combinations of method parameter flags are not yet properly treated by
141 * the compiler or the evaluation functions in evaluate.cpp. All the ones used by
142 * currently implemented methods should work, but new combinations might not.
145 * \section selcompiler_tree Element tree after compilation
147 * After the compilation, the selection element tree is suitable for
148 * gmx_ana_selcollection_evaluate().
149 * Enough memory has been allocated for gmx::SelectionTreeElement::v
150 * (and gmx::SelectionTreeElement::cgrp for \ref SEL_SUBEXPR elements) to allow
151 * the selection to be evaluated without allocating any memory.
154 * \subsection selcompiler_tree_root Root elements
156 * The top level of the tree consists of a chain of \ref SEL_ROOT elements.
157 * These are used for two purposes:
158 * -# A selection that should be evaluated.
159 * These elements appear in the same order as the selections in the input.
160 * For these elements, gmx::SelectionTreeElement::v has been set to the
161 * maximum possible group that the selection can evaluate to (only for
162 * dynamic selections), and gmx::SelectionTreeElement::cgrp has been set to
163 * use a NULL group for evaluation.
164 * -# A subexpression that appears in one or more selections.
165 * Each selection that gives a value for a method parameter is a
166 * potential subexpression, as is any variable value.
167 * Only subexpressions that require evaluation for each frame are left
168 * after the selection is compiled.
169 * Each subexpression appears in the chain before any references to it.
170 * For these elements, gmx::SelectionTreeElement::cgrp has been set to the
171 * group that should be used to evaluate the subexpression.
172 * If gmx::SelectionTreeElement::cgrp is empty, the total evaluation group
173 * is not known in advance or it is more efficient to evaluate the
174 * subexpression only when it is referenced. If this is the case,
175 * gmx::SelectionTreeElement::evaluate is also NULL.
177 * The children of the \ref SEL_ROOT elements can be used to distinguish
178 * the two types of root elements from each other; the rules are the same
179 * as for the parsed tree (see \ref selparser_tree_root).
180 * Subexpressions are treated as if they had been provided through variables.
182 * Selection names are stored as after parsing (see \ref selparser_tree_root).
185 * \subsection selcompiler_tree_const Constant elements
187 * All (sub)selections that do not require particle positions have been
188 * replaced with \ref SEL_CONST elements.
189 * Constant elements from the parser are also retained if present in
190 * dynamic parts of the selections.
191 * Several constant elements with a NULL gmx::SelectionTreeElement::evaluate
192 * are left for debugging purposes; of these, only the ones for \ref BOOL_OR
193 * expressions are used during evaluation.
195 * The value is stored in gmx::SelectionTreeElement::v, and for group values
196 * with an evaluation function set, also in gmx::SelectionTreeElement::cgrp.
197 * For \ref GROUP_VALUE elements, unnecessary atoms (i.e., atoms that
198 * could never be selected) have been removed from the value.
200 * \ref SEL_CONST elements have no children.
203 * \subsection selcompiler_tree_method Method evaluation elements
205 * All selection methods that need to be evaluated dynamically are described
206 * by a \ref SEL_EXPRESSION element. The gmx::SelectionTreeElement::method and
207 * gmx::SelectionTreeElement::mdata fields have already been initialized by the parser,
208 * and the compiler only calls the initialization functions in the method
209 * data structure to do some additional initialization of these fields at
210 * appropriate points. If the gmx::SelectionTreeElement::pc data field has been
211 * created by the parser, the compiler initializes the data structure properly
212 * once the required positions are known. If the gmx::SelectionTreeElement::pc
213 * field is NULL after the parser, but the method provides only
214 * sel_updatefunc_pos(), an appropriate position calculation data structure is
215 * created. If gmx::SelectionTreeElement::pc is not NULL,
216 * gmx::SelectionTreeElement::pos is also initialized to hold the positions
219 * Children of these elements are of type \ref SEL_SUBEXPRREF, and describe
220 * parameter values that need to be evaluated for each frame. See the next
221 * section for more details.
222 * \ref SEL_CONST children can also appear, and stand for parameters that get
223 * their value from a static expression. These elements are present only for
224 * debugging purposes: they always have a NULL evaluation function.
227 * \subsection selcompiler_tree_subexpr Subexpression elements
229 * As described in \ref selcompiler_tree_root, subexpressions are created
230 * for each variable and each expression that gives a value to a selection
231 * method parameter. As the only child of the \ref SEL_ROOT element,
232 * these elements have a \ref SEL_SUBEXPR element. The \ref SEL_SUBEXPR
233 * element has a single child, which evaluates the actual expression.
234 * After compilation, only subexpressions that require particle positions
235 * for evaluation are left.
236 * For non-variable subexpression, automatic names have been generated to
239 * For \ref SEL_SUBEXPR elements, memory has been allocated for
240 * gmx::SelectionTreeElement::cgrp to store the group for which the expression
241 * has been evaluated during the current frame. This is only done if full
242 * subexpression evaluation by _gmx_sel_evaluate_subexpr() is needed; the other
243 * evaluation functions do not require this memory.
245 * \ref SEL_SUBEXPRREF elements are used to describe references to
246 * subexpressions. They have always a single child, which is the
247 * \ref SEL_SUBEXPR element being referenced.
249 * If a subexpression is used only once, the evaluation has been optimized by
250 * setting the child of the \ref SEL_SUBEXPR element to evaluate the value of
251 * \ref SEL_SUBEXPRREF directly (in the case of memory pooling, this is managed
252 * by the evaluation functions). In such cases, the evaluation routines for the
253 * \ref SEL_SUBEXPRREF and \ref SEL_SUBEXPR elements only propagate some status
254 * information, but do not unnecessarily copy the values.
257 * \subsection selcompiler_tree_bool Boolean elements
259 * \ref SEL_BOOLEAN elements have been merged such that one element
260 * may carry out evaluation of more than one operation of the same type.
261 * The static parts of the expressions have been evaluated, and are placed
262 * in the first child. These are followed by the dynamic expressions, in the
263 * order provided by the user.
266 * \subsection selcompiler_tree_arith Arithmetic elements
268 * Constant and static expressions in \ref SEL_ARITHMETIC elements have been
270 * Currently, no other processing is done.
272 #include "compiler.h"
279 #include "gromacs/legacyheaders/vec.h"
281 #include "gromacs/selection/indexutil.h"
282 #include "gromacs/selection/poscalc.h"
283 #include "gromacs/selection/selection.h"
284 #include "gromacs/selection/selmethod.h"
285 #include "gromacs/utility/exceptions.h"
286 #include "gromacs/utility/smalloc.h"
287 #include "gromacs/utility/stringutil.h"
289 #include "evaluate.h"
290 #include "keywords.h"
292 #include "selectioncollection-impl.h"
296 using gmx::SelectionTreeElement;
297 using gmx::SelectionTreeElementPointer;
305 * Whether a subexpression needs to evaluated for all atoms.
307 * This flag is set for \ref SEL_SUBEXPR elements that are used to
308 * evaluate non-atom-valued selection method parameters, as well as
309 * those that are used directly as values of selections.
311 SEL_CDATA_FULLEVAL = 1,
313 * Whether the whole subexpression should be treated as static.
315 * This flag is always false if \ref SEL_DYNAMIC is set for the element,
316 * but it is also false for static elements within common subexpressions.
318 SEL_CDATA_STATIC = 2,
319 /** Whether the subexpression will always be evaluated in the same group. */
320 SEL_CDATA_STATICEVAL = 4,
321 /** Whether the compiler evaluation routine should return the maximal selection. */
322 SEL_CDATA_EVALMAX = 8,
323 /** Whether memory has been allocated for \p gmin and \p gmax. */
324 SEL_CDATA_MINMAXALLOC = 16,
325 /** Whether to update \p gmin and \p gmax in static analysis. */
326 SEL_CDATA_DOMINMAX = 256,
327 /** Whether the subexpression uses simple pass evaluation functions. */
328 SEL_CDATA_SIMPLESUBEXPR = 32,
330 * Whether a static subexpression needs to support multiple evaluations.
332 * This flag may only be set on \ref SEL_SUBEXPR elements that also have
333 * SEL_CDATA_SIMPLESUBEXPR.
335 SEL_CDATA_STATICMULTIEVALSUBEXPR = 64,
336 /** Whether this expression is a part of a common subexpression. */
337 SEL_CDATA_COMMONSUBEXPR = 128
341 * Internal data structure used by the compiler.
343 typedef struct t_compiler_data
345 /** The real evaluation method. */
346 gmx::sel_evalfunc evaluate;
347 /** Number of references to a \ref SEL_SUBEXPR element. */
349 /** Flags for specifying how to treat this element during compilation. */
351 /** Smallest selection that can be selected by the subexpression. */
352 gmx_ana_index_t *gmin;
353 /** Largest selection that can be selected by the subexpression. */
354 gmx_ana_index_t *gmax;
358 /********************************************************************
359 * COMPILER UTILITY FUNCTIONS
360 ********************************************************************/
363 * Helper method for printing out debug information about a min/max group.
366 print_group_info(FILE *fp, const char *name,
367 const SelectionTreeElement &sel,
370 fprintf(fp, " %s=", name);
373 fprintf(fp, "(null)");
375 else if (sel.cdata->flags & SEL_CDATA_MINMAXALLOC)
377 fprintf(fp, "(%d atoms, %p)", g->isize, (void*)g);
379 else if (sel.v.type == GROUP_VALUE && g == sel.v.u.g)
381 fprintf(fp, "(static, %p)", (void*)g);
385 fprintf(fp, "%p", (void*)g);
390 * \param[in] fp File handle to receive the output.
391 * \param[in] sel Selection element to print.
392 * \param[in] level Indentation level, starting from zero.
395 _gmx_selelem_print_compiler_info(FILE *fp, const SelectionTreeElement &sel,
402 fprintf(fp, "%*c cdata: flg=", level*2+1, ' ');
403 if (sel.cdata->flags & SEL_CDATA_FULLEVAL)
407 if (!(sel.cdata->flags & SEL_CDATA_STATIC))
411 if (sel.cdata->flags & SEL_CDATA_STATICEVAL)
415 if (sel.cdata->flags & SEL_CDATA_EVALMAX)
419 if (sel.cdata->flags & SEL_CDATA_MINMAXALLOC)
423 if (sel.cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
427 if (sel.cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR)
431 if (sel.cdata->flags & SEL_CDATA_COMMONSUBEXPR)
435 if (!sel.cdata->flags)
439 if (sel.cdata->refcount > 0)
441 fprintf(fp, " refc=%d", sel.cdata->refcount);
443 fprintf(fp, " eval=");
444 _gmx_sel_print_evalfunc_name(fp, sel.cdata->evaluate);
445 print_group_info(fp, "gmin", sel, sel.cdata->gmin);
446 print_group_info(fp, "gmax", sel, sel.cdata->gmax);
453 void SelectionTreeElement::freeCompilerData()
457 evaluate = cdata->evaluate;
458 if (cdata->flags & SEL_CDATA_MINMAXALLOC)
460 gmx_ana_index_deinit(cdata->gmin);
461 gmx_ana_index_deinit(cdata->gmax);
473 * Allocates memory for storing the evaluated value of a selection element.
475 * \param sel Selection element to initialize
476 * \param[in] isize Maximum evaluation group size.
477 * \param[in] bChildEval true if children have already been processed.
479 * If called more than once, memory is (re)allocated to ensure that the
480 * maximum of the \p isize values can be stored.
482 * Allocation of POS_VALUE selection elements is a special case, and is
483 * handled by alloc_selection_pos_data().
486 alloc_selection_data(const SelectionTreeElementPointer &sel,
487 int isize, bool bChildEval)
491 GMX_RELEASE_ASSERT(sel->v.type != POS_VALUE,
492 "Wrong allocation method called");
497 /* Find out the number of elements to allocate */
498 if (sel->flags & SEL_SINGLEVAL)
502 else if (sel->flags & SEL_ATOMVAL)
506 else /* sel->flags should contain SEL_VARNUMVAL */
508 // TODO: Consider whether the bChildEval is any longer necessary.
513 SelectionTreeElementPointer child = sel;
514 if (sel->type == SEL_SUBEXPRREF)
516 GMX_RELEASE_ASSERT(sel->child && sel->child->type == SEL_SUBEXPR,
517 "Subexpression expected for subexpression reference");
518 child = sel->child->child;
519 GMX_RELEASE_ASSERT(child,
520 "Subexpression elements should always have a child element");
522 nalloc = child->v.nr;
524 /* Allocate memory for sel->v.u if needed */
525 if (sel->flags & SEL_ALLOCVAL)
527 _gmx_selvalue_reserve(&sel->v, nalloc);
529 /* Reserve memory inside group structure if SEL_ALLOCDATA is set. */
530 if ((sel->flags & SEL_ALLOCDATA) && sel->v.type == GROUP_VALUE)
532 gmx_ana_index_reserve(sel->v.u.g, isize);
537 * Allocates memory for storing the evaluated value of a selection element.
539 * \param sel Selection element to initialize.
541 * Allocation of POS_VALUE selection elements is a special case, and is
542 * handled by this function instead of by alloc_selection_data().
545 alloc_selection_pos_data(const SelectionTreeElementPointer &sel)
549 GMX_RELEASE_ASSERT(sel->v.type == POS_VALUE,
550 "Wrong allocation method called");
551 GMX_RELEASE_ASSERT(!(sel->flags & SEL_ATOMVAL),
552 "Per-atom evaluated positions not implemented");
558 SelectionTreeElementPointer child = sel;
559 if (sel->type == SEL_SUBEXPRREF)
561 GMX_RELEASE_ASSERT(sel->child && sel->child->type == SEL_SUBEXPR,
562 "Subexpression expected for subexpression reference");
563 child = sel->child->child;
564 GMX_RELEASE_ASSERT(child,
565 "Subexpression elements should always have a child element");
567 nalloc = child->v.u.p->count();
568 isize = child->v.u.p->m.b.nra;
570 /* For positions, we want to allocate just a single structure
571 * for nalloc positions. */
572 if (sel->flags & SEL_ALLOCVAL)
574 _gmx_selvalue_reserve(&sel->v, 1);
577 /* Reserve memory inside position structure if SEL_ALLOCDATA is set. */
578 if (sel->flags & SEL_ALLOCDATA)
580 gmx_ana_pos_reserve(sel->v.u.p, nalloc, isize);
585 * Replace the evaluation function of each element in the subtree.
587 * \param sel Root of the selection subtree to process.
588 * \param[in] eval The new evaluation function.
591 set_evaluation_function(const SelectionTreeElementPointer &sel,
592 gmx::sel_evalfunc eval)
594 sel->evaluate = eval;
595 if (sel->type != SEL_SUBEXPRREF)
597 SelectionTreeElementPointer child = sel->child;
600 set_evaluation_function(child, eval);
607 /********************************************************************
608 * POSITION KEYWORD DEFAULT INITIALIZATION
609 ********************************************************************/
612 * Initializes default values for position keyword evaluation.
614 * \param[in,out] root Root of the element tree to initialize.
615 * \param[in] spost Default output position type.
616 * \param[in] rpost Default reference position type.
617 * \param[in] sel Selection that the element evaluates the positions
618 * for, or NULL if the element is an internal element.
621 init_pos_keyword_defaults(SelectionTreeElement *root,
622 const char *spost, const char *rpost,
623 const gmx::internal::SelectionData *sel)
625 /* Selections use largest static group by default, while
626 * reference positions use the whole residue/molecule. */
627 if (root->type == SEL_EXPRESSION)
629 bool bSelection = (sel != NULL);
630 int flags = bSelection ? POS_COMPLMAX : POS_COMPLWHOLE;
633 if (sel->hasFlag(gmx::efSelection_DynamicMask))
635 flags |= POS_MASKONLY;
637 if (sel->hasFlag(gmx::efSelection_EvaluateVelocities))
639 flags |= POS_VELOCITIES;
641 if (sel->hasFlag(gmx::efSelection_EvaluateForces))
646 _gmx_selelem_set_kwpos_type(root, bSelection ? spost : rpost);
647 _gmx_selelem_set_kwpos_flags(root, flags);
649 /* Change the defaults once we are no longer processing modifiers */
650 if (root->type != SEL_ROOT && root->type != SEL_MODIFIER
651 && root->type != SEL_SUBEXPRREF && root->type != SEL_SUBEXPR)
655 /* Recurse into children */
656 SelectionTreeElementPointer child = root->child;
659 init_pos_keyword_defaults(child.get(), spost, rpost, sel);
665 /********************************************************************
666 * SUBEXPRESSION PROCESSING
667 ********************************************************************/
670 * Reverses the chain of selection elements starting at \p root.
672 * \param root First selection in the whole selection chain.
673 * \returns The new first element for the chain.
675 static SelectionTreeElementPointer
676 reverse_selelem_chain(const SelectionTreeElementPointer &root)
678 SelectionTreeElementPointer prev;
679 SelectionTreeElementPointer item = root;
682 SelectionTreeElementPointer next = item->next;
691 * Removes subexpressions that don't have any references.
693 * \param root First selection in the whole selection chain.
694 * \returns The new first element for the chain.
696 * The elements are processed in reverse order to correctly detect
697 * subexpressions only referred to by other subexpressions.
699 static SelectionTreeElementPointer
700 remove_unused_subexpressions(SelectionTreeElementPointer root)
704 return SelectionTreeElementPointer();
706 root = reverse_selelem_chain(root);
707 while (root->child->type == SEL_SUBEXPR && root->child.unique())
709 // Frees the root element.
712 SelectionTreeElementPointer prev = root;
713 SelectionTreeElementPointer item = root->next;
716 SelectionTreeElementPointer next = item->next;
717 if (item->child->type == SEL_SUBEXPR && item->child.unique())
719 // Frees the current item when it goes out of scope.
728 return reverse_selelem_chain(root);
732 * Creates a name with a running number for a subexpression.
734 * \param[in,out] sel The subexpression to be named.
735 * \param[in] i Running number for the subexpression.
737 * The name of the selection becomes "SubExpr N", where N is \p i;
738 * Memory is allocated for the name and the name is stored both as the
739 * name of the subexpression element and as
740 * gmx::SelectionTreeElement::u::cgrp::name; the latter is freed by
741 * _gmx_selelem_free().
744 create_subexpression_name(const SelectionTreeElementPointer &sel, int i)
746 std::string name(gmx::formatString("SubExpr %d", i));
751 * Processes and extracts subexpressions from a given selection subtree.
753 * \param sel Root of the subtree to process.
754 * \param subexprn Pointer to a subexpression counter.
755 * \returns Pointer to a chain of subselections, or NULL if none were found.
757 * This function finds recursively all \ref SEL_SUBEXPRREF elements below
758 * the given root element and ensures that their children are within
759 * \ref SEL_SUBEXPR elements. It also creates a chain of \ref SEL_ROOT elements
760 * that contain the subexpression as their children and returns the first
761 * of these root elements.
763 static SelectionTreeElementPointer
764 extract_item_subselections(const SelectionTreeElementPointer &sel,
767 SelectionTreeElementPointer root;
768 SelectionTreeElementPointer subexpr;
769 SelectionTreeElementPointer child = sel->child;
775 root = subexpr = extract_item_subselections(child, subexprn);
779 subexpr->next = extract_item_subselections(child, subexprn);
781 while (subexpr && subexpr->next)
783 subexpr = subexpr->next;
785 /* The latter check excludes variable references. */
786 if (child->type == SEL_SUBEXPRREF && child->child->type != SEL_SUBEXPR)
788 /* Create the root element for the subexpression */
791 root.reset(new SelectionTreeElement(SEL_ROOT));
796 subexpr->next.reset(new SelectionTreeElement(SEL_ROOT));
797 subexpr = subexpr->next;
799 /* Create the subexpression element and
800 * move the actual subexpression under the created element. */
801 subexpr->child.reset(new SelectionTreeElement(SEL_SUBEXPR));
802 _gmx_selelem_set_vtype(subexpr->child, child->v.type);
803 subexpr->child->child = child->child;
804 child->child = subexpr->child;
805 create_subexpression_name(subexpr->child, ++*subexprn);
806 /* Set the flags for the created elements */
807 subexpr->flags |= (child->flags & SEL_VALFLAGMASK);
808 subexpr->child->flags |= (child->flags & SEL_VALFLAGMASK);
810 if (child->type == SEL_SUBEXPRREF)
812 child->setName(child->child->name());
821 * Extracts subexpressions of the selection chain.
823 * \param sel First selection in the whole selection chain.
824 * \returns The new first element for the chain.
826 * Finds all the subexpressions (and their subexpressions) in the
827 * selection chain starting from \p sel and creates \ref SEL_SUBEXPR
829 * \ref SEL_ROOT elements are also created for each subexpression
830 * and inserted into the selection chain before the expressions that
833 static SelectionTreeElementPointer
834 extract_subexpressions(SelectionTreeElementPointer sel)
836 SelectionTreeElementPointer root;
837 SelectionTreeElementPointer next = sel;
841 SelectionTreeElementPointer item
842 = extract_item_subselections(next, &subexprn);
870 /********************************************************************
871 * BOOLEAN OPERATION REORDERING
872 ********************************************************************/
875 * Removes redundant boolean selection elements.
877 * \param sel Root of the selection subtree to optimize.
879 * This function merges similar boolean operations (e.g., (A or B) or C becomes
880 * a single OR operation with three operands).
883 optimize_boolean_expressions(const SelectionTreeElementPointer &sel)
885 /* Do recursively for children */
886 if (sel->type != SEL_SUBEXPRREF)
888 SelectionTreeElementPointer prev;
889 SelectionTreeElementPointer child = sel->child;
892 optimize_boolean_expressions(child);
893 /* Remove double negations */
894 if (child->type == SEL_BOOLEAN && child->u.boolt == BOOL_NOT
895 && child->child->type == SEL_BOOLEAN && child->child->u.boolt == BOOL_NOT)
897 /* Move the doubly negated expression up two levels */
900 sel->child = child->child->child;
905 prev->next = child->child->child;
908 child->child->child->next = child->next;
909 // Discards the two negations.
916 if (sel->type != SEL_BOOLEAN || sel->u.boolt == BOOL_NOT)
920 /* Merge subsequent binary operations */
921 SelectionTreeElementPointer prev;
922 SelectionTreeElementPointer child = sel->child;
925 if (child->type == SEL_BOOLEAN && child->u.boolt == sel->u.boolt)
929 sel->child = child->child;
934 prev->next = child->child;
940 prev->next = child->next;
941 // Discards the old child.
953 * Reorders children of boolean expressions such that static selections
956 * \param sel Root of the selection subtree to reorder.
958 * The relative order of static expressions does not change.
959 * The same is true for the dynamic expressions.
962 reorder_boolean_static_children(const SelectionTreeElementPointer &sel)
964 /* Do recursively for children */
965 if (sel->type != SEL_SUBEXPRREF)
967 SelectionTreeElementPointer child = sel->child;
970 reorder_boolean_static_children(child);
975 /* Reorder boolean expressions such that static selections come first */
976 if (sel->type == SEL_BOOLEAN && (sel->flags & SEL_DYNAMIC))
978 // Add a dummy head element that precedes the first child.
979 SelectionTreeElementPointer dummy(
980 new SelectionTreeElement(SEL_BOOLEAN));
981 dummy->next = sel->child;
982 SelectionTreeElementPointer prev = dummy;
983 SelectionTreeElementPointer child = dummy;
986 /* child is the last handled static expression */
987 /* prev is the last handled non-static expression */
988 SelectionTreeElementPointer next = prev->next;
989 while (next && (next->flags & SEL_DYNAMIC))
994 /* next is now the first static expression after child */
999 /* Reorder such that next comes after child */
1002 prev->next = next->next;
1003 next->next = child->next;
1010 /* Advance child by one */
1014 sel->child = dummy->next;
1019 /********************************************************************
1020 * ARITHMETIC EXPRESSION PROCESSING
1021 ********************************************************************/
1024 * Processes arithmetic expressions to simplify and speed up evaluation.
1026 * \param sel Root of the selection subtree to process.
1028 * Currently, this function only converts integer constants to reals
1029 * within arithmetic expressions.
1032 optimize_arithmetic_expressions(const SelectionTreeElementPointer &sel)
1034 /* Do recursively for children. */
1035 if (sel->type != SEL_SUBEXPRREF)
1037 SelectionTreeElementPointer child = sel->child;
1040 optimize_arithmetic_expressions(child);
1041 child = child->next;
1045 if (sel->type != SEL_ARITHMETIC)
1050 /* Convert integer constants to reals. */
1051 SelectionTreeElementPointer child = sel->child;
1054 if (child->v.type == INT_VALUE)
1058 if (child->type != SEL_CONST)
1060 GMX_THROW(gmx::InconsistentInputError("Non-constant integer expressions not implemented in arithmetic evaluation"));
1063 r[0] = child->v.u.i[0];
1064 sfree(child->v.u.i);
1066 child->v.type = REAL_VALUE;
1068 else if (child->v.type != REAL_VALUE)
1070 GMX_THROW(gmx::InternalError("Non-numerical value in arithmetic expression"));
1072 child = child->next;
1077 /********************************************************************
1078 * EVALUATION PREPARATION COMPILER
1079 ********************************************************************/
1082 * Sets the evaluation functions for the selection (sub)tree.
1084 * \param[in,out] sel Root of the selection subtree to process.
1086 * This function sets the evaluation function
1087 * (gmx::SelectionTreeElement::evaluate) for the selection elements.
1090 init_item_evalfunc(const SelectionTreeElementPointer &sel)
1092 /* Process children. */
1093 if (sel->type != SEL_SUBEXPRREF)
1095 SelectionTreeElementPointer child = sel->child;
1098 init_item_evalfunc(child);
1099 child = child->next;
1103 /* Set the evaluation function */
1107 if (sel->v.type == GROUP_VALUE)
1109 sel->evaluate = &_gmx_sel_evaluate_static;
1113 case SEL_EXPRESSION:
1114 if (!(sel->flags & SEL_DYNAMIC) && sel->u.expr.method
1115 && sel->u.expr.method->init_frame)
1117 sel->flags |= SEL_INITFRAME;
1119 sel->evaluate = &_gmx_sel_evaluate_method;
1122 case SEL_ARITHMETIC:
1123 sel->evaluate = &_gmx_sel_evaluate_arithmetic;
1127 if (sel->v.type != NO_VALUE)
1129 sel->evaluate = &_gmx_sel_evaluate_modifier;
1134 switch (sel->u.boolt)
1136 case BOOL_NOT: sel->evaluate = &_gmx_sel_evaluate_not; break;
1137 case BOOL_AND: sel->evaluate = &_gmx_sel_evaluate_and; break;
1138 case BOOL_OR: sel->evaluate = &_gmx_sel_evaluate_or; break;
1140 GMX_THROW(gmx::NotImplementedError("xor expressions not implemented"));
1145 sel->evaluate = &_gmx_sel_evaluate_root;
1149 if ((sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
1150 && !(sel->cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR))
1152 sel->evaluate = &_gmx_sel_evaluate_subexpr_simple;
1156 sel->evaluate = &_gmx_sel_evaluate_subexpr;
1160 case SEL_SUBEXPRREF:
1161 sel->evaluate = ((sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
1162 ? &_gmx_sel_evaluate_subexprref_simple
1163 : &_gmx_sel_evaluate_subexprref);
1167 GMX_THROW(gmx::APIError("Unresolved group reference in compilation"));
1169 sel->cdata->evaluate = sel->evaluate;
1173 * Sets the memory pool for selection elements that can use it.
1175 * \param sel Root of the selection subtree to process.
1176 * \param[in] mempool Memory pool to use.
1179 setup_memory_pooling(const SelectionTreeElementPointer &sel,
1180 gmx_sel_mempool_t *mempool)
1182 if (sel->type != SEL_SUBEXPRREF)
1184 SelectionTreeElementPointer child = sel->child;
1187 if ((sel->type == SEL_BOOLEAN && (child->flags & SEL_DYNAMIC))
1188 || (sel->type == SEL_ARITHMETIC && child->type != SEL_CONST
1189 && !(child->flags & SEL_SINGLEVAL))
1190 || (sel->type == SEL_SUBEXPR
1191 && !(sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)))
1193 child->mempool = mempool;
1194 if (child->type == SEL_SUBEXPRREF
1195 && (child->child->cdata->flags & SEL_CDATA_SIMPLESUBEXPR))
1197 child->child->child->mempool = mempool;
1200 setup_memory_pooling(child, mempool);
1201 child = child->next;
1207 * Prepares the selection (sub)tree for evaluation.
1209 * \param[in,out] sel Root of the selection subtree to prepare.
1211 * It also allocates memory for the \p sel->v.u.g or \p sel->v.u.p
1212 * structure if required.
1215 init_item_evaloutput(const SelectionTreeElementPointer &sel)
1217 GMX_ASSERT(!(sel->child == NULL &&
1218 (sel->type == SEL_SUBEXPRREF || sel->type == SEL_SUBEXPR)),
1219 "Subexpression elements should always have a child element");
1221 /* Process children. */
1222 if (sel->type != SEL_SUBEXPRREF)
1224 SelectionTreeElementPointer child = sel->child;
1227 init_item_evaloutput(child);
1228 child = child->next;
1232 if (sel->type == SEL_SUBEXPR
1233 && (sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
1234 && !(sel->cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR))
1236 sel->flags &= ~(SEL_ALLOCVAL | SEL_ALLOCDATA);
1237 if (sel->v.type == GROUP_VALUE || sel->v.type == POS_VALUE)
1239 _gmx_selvalue_setstore(&sel->v, sel->child->v.u.ptr);
1242 else if (sel->type == SEL_SUBEXPR
1243 && (sel->cdata->flags & SEL_CDATA_FULLEVAL))
1245 sel->evaluate = &_gmx_sel_evaluate_subexpr_staticeval;
1246 sel->cdata->evaluate = sel->evaluate;
1247 sel->child->mempool = NULL;
1248 sel->flags &= ~(SEL_ALLOCVAL | SEL_ALLOCDATA);
1249 if (sel->v.type == GROUP_VALUE || sel->v.type == POS_VALUE)
1251 _gmx_selvalue_setstore(&sel->v, sel->child->v.u.ptr);
1254 else if (sel->type == SEL_SUBEXPRREF
1255 && (sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR))
1259 _gmx_selvalue_setstore(&sel->child->v, sel->v.u.ptr);
1260 sel->child->child->freeValues();
1261 sel->child->child->flags &= ~(SEL_ALLOCVAL | SEL_ALLOCDATA);
1262 sel->child->child->flags |= (sel->flags & SEL_ALLOCDATA);
1263 _gmx_selvalue_setstore(&sel->child->child->v, sel->v.u.ptr);
1265 else if (sel->v.type == GROUP_VALUE || sel->v.type == POS_VALUE)
1267 _gmx_selvalue_setstore(&sel->v, sel->child->child->v.u.ptr);
1269 sel->flags &= ~(SEL_ALLOCVAL | SEL_ALLOCDATA);
1272 /* Make sure that the group/position structure is allocated. */
1273 if (!sel->v.u.ptr && (sel->flags & SEL_ALLOCVAL))
1275 if (sel->v.type == GROUP_VALUE || sel->v.type == POS_VALUE)
1277 _gmx_selvalue_reserve(&sel->v, 1);
1284 /********************************************************************
1285 * COMPILER DATA INITIALIZATION
1286 ********************************************************************/
1289 * Allocates memory for the compiler data and initializes the structure.
1291 * \param sel Root of the selection subtree to process.
1294 init_item_compilerdata(const SelectionTreeElementPointer &sel)
1296 /* Allocate the compiler data structure */
1297 snew(sel->cdata, 1);
1299 /* Store the real evaluation method because the compiler will replace it */
1300 sel->cdata->evaluate = sel->evaluate;
1302 /* This will be computed separately. */
1303 sel->cdata->refcount = 0;
1305 /* Initialize the flags */
1306 sel->cdata->flags = SEL_CDATA_STATICEVAL;
1307 if (!(sel->flags & SEL_DYNAMIC))
1309 sel->cdata->flags |= SEL_CDATA_STATIC;
1311 if (sel->type == SEL_SUBEXPR)
1313 sel->cdata->flags |= SEL_CDATA_EVALMAX;
1315 /* Set the full evaluation flag for subexpressions that require it;
1316 * the subexpression has already been initialized, so we can simply
1317 * access its compilation flags.*/
1318 if (sel->type == SEL_EXPRESSION || sel->type == SEL_MODIFIER)
1320 SelectionTreeElementPointer child = sel->child;
1323 if (!(child->flags & SEL_ATOMVAL) && child->child)
1325 child->child->cdata->flags |= SEL_CDATA_FULLEVAL;
1327 child = child->next;
1330 else if (sel->type == SEL_ROOT && sel->child->type == SEL_SUBEXPRREF)
1332 sel->child->child->cdata->flags |= SEL_CDATA_FULLEVAL;
1335 /* Initialize children */
1336 if (sel->type != SEL_SUBEXPRREF)
1338 SelectionTreeElementPointer child = sel->child;
1341 init_item_compilerdata(child);
1342 child = child->next;
1346 /* Determine whether we should evaluate the minimum or the maximum
1347 * for the children of this element. */
1348 if (sel->type == SEL_BOOLEAN)
1352 bEvalMax = (sel->u.boolt == BOOL_AND);
1353 SelectionTreeElementPointer child = sel->child;
1358 child->cdata->flags |= SEL_CDATA_EVALMAX;
1360 else if (child->type == SEL_BOOLEAN && child->u.boolt == BOOL_NOT)
1362 child->child->cdata->flags |= SEL_CDATA_EVALMAX;
1364 child = child->next;
1367 else if (sel->type == SEL_EXPRESSION || sel->type == SEL_MODIFIER
1368 || sel->type == SEL_SUBEXPR)
1370 SelectionTreeElementPointer child = sel->child;
1373 child->cdata->flags |= SEL_CDATA_EVALMAX;
1374 child = child->next;
1380 * Initializes the static evaluation flag for a selection subtree.
1382 * \param[in,out] sel Root of the selection subtree to process.
1384 * Sets the \c bStaticEval in the compiler data structure:
1385 * for any element for which the evaluation group may depend on the trajectory
1386 * frame, the flag is cleared.
1388 * reorder_boolean_static_children() should have been called.
1391 init_item_staticeval(const SelectionTreeElementPointer &sel)
1393 /* Subexpressions with full evaluation should always have bStaticEval,
1394 * so don't do anything if a reference to them is encountered. */
1395 if (sel->type == SEL_SUBEXPRREF
1396 && (sel->child->cdata->flags & SEL_CDATA_FULLEVAL))
1401 /* Propagate the bStaticEval flag to children if it is not set */
1402 if (!(sel->cdata->flags & SEL_CDATA_STATICEVAL))
1404 SelectionTreeElementPointer child = sel->child;
1407 if ((sel->type != SEL_EXPRESSION && sel->type != SEL_MODIFIER)
1408 || (child->flags & SEL_ATOMVAL))
1410 if (child->cdata->flags & SEL_CDATA_STATICEVAL)
1412 child->cdata->flags &= ~SEL_CDATA_STATICEVAL;
1413 init_item_staticeval(child);
1416 /* If an expression is evaluated for a dynamic group, then also
1417 * atom-valued parameters need to be evaluated every time. */
1418 if ((sel->flags & SEL_DYNAMIC)
1419 && (sel->type == SEL_EXPRESSION || sel->type == SEL_MODIFIER)
1420 && (child->flags & SEL_ATOMVAL))
1422 child->flags |= SEL_DYNAMIC;
1423 child->cdata->flags &= ~SEL_CDATA_STATIC;
1425 child = child->next;
1428 else /* bStaticEval is set */
1430 /* For boolean expressions, any expression after the first dynamic
1431 * expression should not have bStaticEval. */
1432 if (sel->type == SEL_BOOLEAN)
1434 SelectionTreeElementPointer child = sel->child;
1435 while (child && !(child->flags & SEL_DYNAMIC))
1437 child = child->next;
1441 child = child->next;
1445 child->cdata->flags &= ~SEL_CDATA_STATICEVAL;
1446 child = child->next;
1450 /* Process the children */
1451 SelectionTreeElementPointer child = sel->child;
1454 init_item_staticeval(child);
1455 child = child->next;
1461 * Compute reference counts for subexpressions.
1463 * \param sel Root of the selection subtree to process.
1466 init_item_subexpr_refcount(const SelectionTreeElementPointer &sel)
1468 // Reset the counter when the subexpression is first encountered.
1469 if (sel->type == SEL_ROOT && sel->child->type == SEL_SUBEXPR
1470 && sel->child->cdata)
1472 sel->child->cdata->refcount = 0;
1475 if (sel->type == SEL_SUBEXPRREF)
1477 ++sel->child->cdata->refcount;
1481 SelectionTreeElementPointer child = sel->child;
1484 init_item_subexpr_refcount(child);
1485 child = child->next;
1491 * Initializes compiler flags for subexpressions.
1493 * \param sel Root of the selection subtree to process.
1496 init_item_subexpr_flags(const SelectionTreeElementPointer &sel)
1498 if (sel->type == SEL_SUBEXPR)
1500 if (sel->cdata->refcount == 1)
1502 sel->cdata->flags |= SEL_CDATA_SIMPLESUBEXPR;
1504 else if (!(sel->cdata->flags & SEL_CDATA_FULLEVAL))
1506 sel->cdata->flags |= SEL_CDATA_COMMONSUBEXPR;
1509 else if (sel->type == SEL_SUBEXPRREF
1510 && (sel->child->cdata->flags & SEL_CDATA_SIMPLESUBEXPR))
1512 /* See similar condition in init_item_staticeval(). */
1513 if ((sel->flags & SEL_ATOMVAL)
1514 && (sel->flags & SEL_DYNAMIC)
1515 && !(sel->child->flags & SEL_DYNAMIC))
1517 sel->child->cdata->flags |= SEL_CDATA_STATICMULTIEVALSUBEXPR;
1521 sel->cdata->flags |= SEL_CDATA_SIMPLESUBEXPR;
1525 /* Process children, but only follow subexpression references if the
1526 * common subexpression flag needs to be propagated. */
1527 if (sel->type != SEL_SUBEXPRREF
1528 || ((sel->cdata->flags & SEL_CDATA_COMMONSUBEXPR)
1529 && !(sel->child->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)))
1531 SelectionTreeElementPointer child = sel->child;
1534 if (!(child->cdata->flags & SEL_CDATA_COMMONSUBEXPR))
1536 if (sel->type != SEL_EXPRESSION || (child->flags & SEL_ATOMVAL))
1538 child->cdata->flags |=
1539 (sel->cdata->flags & SEL_CDATA_COMMONSUBEXPR);
1541 init_item_subexpr_flags(child);
1543 child = child->next;
1549 * Initializes the gmin and gmax fields of the compiler data structure.
1551 * \param sel Root of the selection subtree to process.
1554 init_item_minmax_groups(const SelectionTreeElementPointer &sel)
1556 /* Process children. */
1557 if (sel->type != SEL_SUBEXPRREF)
1559 SelectionTreeElementPointer child = sel->child;
1562 init_item_minmax_groups(child);
1563 child = child->next;
1567 /* Initialize the minimum and maximum evaluation groups. */
1568 if (sel->type != SEL_ROOT && sel->v.type != NO_VALUE)
1570 if (sel->v.type == GROUP_VALUE
1571 && (sel->cdata->flags & SEL_CDATA_STATIC))
1573 sel->cdata->gmin = sel->v.u.g;
1574 sel->cdata->gmax = sel->v.u.g;
1576 else if (sel->type == SEL_SUBEXPR
1577 && ((sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
1578 || (sel->cdata->flags & SEL_CDATA_FULLEVAL)))
1580 GMX_ASSERT(sel->child,
1581 "Subexpression elements should always have a child element");
1582 sel->cdata->gmin = sel->child->cdata->gmin;
1583 sel->cdata->gmax = sel->child->cdata->gmax;
1587 sel->cdata->flags |= SEL_CDATA_MINMAXALLOC | SEL_CDATA_DOMINMAX;
1588 snew(sel->cdata->gmin, 1);
1589 snew(sel->cdata->gmax, 1);
1595 /********************************************************************
1596 * EVALUATION GROUP INITIALIZATION
1597 ********************************************************************/
1600 * Initializes evaluation groups for root items.
1602 * \param[in,out] sc Selection collection data.
1604 * The evaluation group of each \ref SEL_ROOT element corresponding to a
1605 * selection in \p sc is set to NULL. The evaluation grop for \ref SEL_ROOT
1606 * elements corresponding to subexpressions that need full evaluation is set
1610 initialize_evalgrps(gmx_ana_selcollection_t *sc)
1612 SelectionTreeElementPointer root = sc->root;
1615 GMX_RELEASE_ASSERT(root->child,
1616 "Root elements should always have a child");
1617 if (root->child->type != SEL_SUBEXPR
1618 || (root->child->v.type != GROUP_VALUE && !(root->flags & SEL_ATOMVAL)))
1620 gmx_ana_index_set(&root->u.cgrp, -1, 0, 0);
1622 else if (root->child->cdata->flags & SEL_CDATA_FULLEVAL)
1624 gmx_ana_index_set(&root->u.cgrp, sc->gall.isize, sc->gall.index, 0);
1631 /********************************************************************
1633 ********************************************************************/
1636 * Marks a subtree completely dynamic or undoes such a change.
1638 * \param sel Selection subtree to mark.
1639 * \param[in] bDynamic If true, the \p bStatic flag of the whole
1640 * selection subtree is cleared. If false, the flag is restored to
1641 * using \ref SEL_DYNAMIC.
1643 * Does not descend into parameters of methods unless the parameters
1644 * are evaluated for each atom.
1647 mark_subexpr_dynamic(const SelectionTreeElementPointer &sel,
1650 if (!bDynamic && !(sel->flags & SEL_DYNAMIC))
1652 sel->cdata->flags |= SEL_CDATA_STATIC;
1656 sel->cdata->flags &= ~SEL_CDATA_STATIC;
1658 SelectionTreeElementPointer child = sel->child;
1661 if (sel->type != SEL_EXPRESSION || child->type != SEL_SUBEXPRREF
1662 || (child->u.param->flags & SPAR_ATOMVAL))
1664 mark_subexpr_dynamic(child, bDynamic);
1666 child = child->next;
1671 * Frees memory for subexpressions that are no longer needed.
1673 * \param sel Selection subtree to check.
1675 * Checks whether the subtree rooted at \p sel refers to any \ref SEL_SUBEXPR
1676 * elements that are not referred to by anything else except their own root
1677 * element. If such elements are found, all memory allocated for them is freed
1678 * except the actual element. The element is left because otherwise a dangling
1679 * pointer would be left at the root element, which is not traversed by this
1680 * function. Later compilation passes remove the stub elements.
1683 release_subexpr_memory(const SelectionTreeElementPointer &sel)
1685 if (sel->type == SEL_SUBEXPRREF)
1687 const SelectionTreeElementPointer &subexpr = sel->child;
1688 if (subexpr.use_count() == 2)
1690 release_subexpr_memory(subexpr);
1692 subexpr->child.reset();
1693 subexpr->freeValues();
1694 subexpr->freeExpressionData();
1695 subexpr->freeCompilerData();
1700 SelectionTreeElementPointer child = sel->child;
1703 release_subexpr_memory(child);
1704 child = child->next;
1710 * Makes an evaluated selection element static.
1712 * \param sel Selection element to make static.
1714 * The evaluated value becomes the value of the static element.
1715 * The element type is changed to SEL_CONST and the children are
1719 make_static(const SelectionTreeElementPointer &sel)
1721 /* If this is a subexpression reference and the data is stored in the
1722 * child, we transfer data ownership before doing anything else. */
1723 if (sel->type == SEL_SUBEXPRREF
1724 && (sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR))
1726 if (sel->child->child->flags & SEL_ALLOCDATA)
1728 sel->flags |= SEL_ALLOCDATA;
1729 sel->child->child->flags &= ~SEL_ALLOCDATA;
1731 if (sel->child->child->flags & SEL_ALLOCVAL)
1733 sel->flags |= SEL_ALLOCVAL;
1734 sel->v.nalloc = sel->child->child->v.nalloc;
1735 sel->child->child->flags &= ~SEL_ALLOCVAL;
1736 sel->child->child->v.nalloc = -1;
1739 /* Free the children. */
1740 release_subexpr_memory(sel);
1742 /* Free the expression data as it is no longer needed */
1743 sel->freeExpressionData();
1744 /* Make the item static */
1745 sel->type = SEL_CONST;
1746 sel->evaluate = NULL;
1747 sel->cdata->evaluate = NULL;
1748 /* Set the group value.
1749 * freeExpressionData() frees the cgrp group, so we can just override it.
1751 if (sel->v.type == GROUP_VALUE)
1753 gmx_ana_index_set(&sel->u.cgrp, sel->v.u.g->isize, sel->v.u.g->index, 0);
1758 * Evaluates a constant expression during analyze_static().
1760 * \param[in] data Evaluation data.
1761 * \param[in,out] sel Selection to process.
1762 * \param[in] g The evaluation group.
1763 * \returns 0 on success, a non-zero error code on error.
1766 process_const(gmx_sel_evaluate_t *data,
1767 const SelectionTreeElementPointer &sel,
1770 if (sel->v.type == GROUP_VALUE)
1772 if (sel->cdata->evaluate)
1774 sel->cdata->evaluate(data, sel, g);
1777 /* Other constant expressions do not need evaluation */
1781 * Sets the parameter value pointer for \ref SEL_SUBEXPRREF params.
1783 * \param[in,out] sel Selection to process.
1785 * Copies the value pointer of \p sel to \c sel->u.param if one is present
1786 * and should receive the value from the compiler
1787 * (most parameter values are handled during parsing).
1788 * If \p sel is not of type \ref SEL_SUBEXPRREF, or if \c sel->u.param is NULL,
1789 * the function does nothing.
1790 * Also, if the \c sel->u.param does not have \ref SPAR_VARNUM or
1791 * \ref SPAR_ATOMVAL, the function returns immediately.
1794 store_param_val(const SelectionTreeElementPointer &sel)
1796 /* Return immediately if there is no parameter. */
1797 if (sel->type != SEL_SUBEXPRREF || !sel->u.param)
1802 /* Or if the value does not need storing. */
1803 if (!(sel->u.param->flags & (SPAR_VARNUM | SPAR_ATOMVAL)))
1808 if (sel->v.type == INT_VALUE || sel->v.type == REAL_VALUE
1809 || sel->v.type == STR_VALUE)
1811 _gmx_selvalue_setstore(&sel->u.param->val, sel->v.u.ptr);
1816 * Handles the initialization of a selection method during analyze_static() pass.
1818 * \param[in,out] sel Selection element to process.
1819 * \param[in] top Topology structure.
1820 * \param[in] isize Size of the evaluation group for the element.
1821 * \returns 0 on success, a non-zero error code on return.
1823 * Calls sel_initfunc() (and possibly sel_outinitfunc()) to initialize the
1825 * If no \ref SPAR_ATOMVAL parameters are present, multiple initialization
1826 * is prevented by using \ref SEL_METHODINIT and \ref SEL_OUTINIT flags.
1829 init_method(const SelectionTreeElementPointer &sel, t_topology *top, int isize)
1831 /* Find out whether there are any atom-valued parameters */
1832 bool bAtomVal = false;
1833 SelectionTreeElementPointer child = sel->child;
1836 if (child->flags & SEL_ATOMVAL)
1840 child = child->next;
1843 /* Initialize the method */
1844 if (sel->u.expr.method->init
1845 && (bAtomVal || !(sel->flags & SEL_METHODINIT)))
1847 sel->flags |= SEL_METHODINIT;
1848 sel->u.expr.method->init(top, sel->u.expr.method->nparams,
1849 sel->u.expr.method->param, sel->u.expr.mdata);
1851 if (bAtomVal || !(sel->flags & SEL_OUTINIT))
1853 sel->flags |= SEL_OUTINIT;
1854 if (sel->u.expr.method->outinit)
1856 sel->u.expr.method->outinit(top, &sel->v, sel->u.expr.mdata);
1857 if (sel->v.type != POS_VALUE && sel->v.type != GROUP_VALUE
1858 && !(sel->flags & SEL_VARNUMVAL))
1860 alloc_selection_data(sel, isize, true);
1865 GMX_RELEASE_ASSERT(sel->v.type != POS_VALUE,
1866 "Output initialization must be provided for "
1867 "position-valued selection methods");
1868 GMX_RELEASE_ASSERT(!(sel->flags & SEL_VARNUMVAL),
1869 "Output initialization must be provided for "
1870 "SMETH_VARNUMVAL selection methods");
1871 alloc_selection_data(sel, isize, true);
1872 if ((sel->flags & SEL_DYNAMIC)
1873 && sel->v.type != GROUP_VALUE && sel->v.type != POS_VALUE)
1877 /* If the method is char-valued, pre-allocate the strings. */
1878 if (sel->u.expr.method->flags & SMETH_CHARVAL)
1882 /* A sanity check */
1883 if (sel->v.type != STR_VALUE)
1885 GMX_THROW(gmx::InternalError("Char-valued selection method in non-string element"));
1887 sel->flags |= SEL_ALLOCDATA;
1888 for (i = 0; i < isize; ++i)
1890 if (sel->v.u.s[i] == NULL)
1892 snew(sel->v.u.s[i], 2);
1897 /* Clear the values for dynamic output to avoid valgrind warnings. */
1898 if ((sel->flags & SEL_DYNAMIC) && sel->v.type == REAL_VALUE)
1902 for (i = 0; i < sel->v.nr; ++i)
1904 sel->v.u.r[i] = 0.0;
1911 * Evaluates the static part of a boolean expression.
1913 * \param[in] data Evaluation data.
1914 * \param[in,out] sel Boolean selection element whose children should be
1916 * \param[in] g The evaluation group.
1917 * \returns 0 on success, a non-zero error code on error.
1919 * reorder_item_static_children() should have been called.
1922 evaluate_boolean_static_part(gmx_sel_evaluate_t *data,
1923 const SelectionTreeElementPointer &sel,
1926 /* Find the last static subexpression */
1927 SelectionTreeElementPointer child = sel->child;
1928 while (child->next && (child->next->cdata->flags & SEL_CDATA_STATIC))
1930 child = child->next;
1932 if (!(child->cdata->flags & SEL_CDATA_STATIC))
1937 /* Evalute the static part if there is more than one expression */
1938 if (child != sel->child)
1940 SelectionTreeElementPointer next = child->next;
1941 child->next.reset();
1942 sel->cdata->evaluate(data, sel, g);
1943 /* Replace the subexpressions with the result */
1944 child.reset(new SelectionTreeElement(SEL_CONST));
1945 child->flags = SEL_FLAGSSET | SEL_SINGLEVAL | SEL_ALLOCVAL | SEL_ALLOCDATA;
1946 _gmx_selelem_set_vtype(child, GROUP_VALUE);
1947 child->evaluate = NULL;
1948 _gmx_selvalue_reserve(&child->v, 1);
1949 gmx_ana_index_copy(child->v.u.g, sel->v.u.g, true);
1950 init_item_compilerdata(child);
1951 init_item_minmax_groups(child);
1952 child->cdata->flags &= ~SEL_CDATA_STATICEVAL;
1953 child->cdata->flags |= sel->cdata->flags & SEL_CDATA_STATICEVAL;
1955 // Frees the old static subexpressions.
1958 else if (child->evaluate)
1960 child->evaluate(data, child, g);
1962 /* Set the evaluation function for the constant element.
1963 * We never need to evaluate the element again during compilation,
1964 * but we may need to evaluate the static part again if the
1965 * expression is not an OR with a static evaluation group.
1966 * If we reach here with a NOT expression, the NOT expression
1967 * is also static, and will be made a constant later, so don't waste
1968 * time copying the group. */
1969 child->evaluate = NULL;
1970 if (sel->u.boolt == BOOL_NOT
1971 || ((sel->cdata->flags & SEL_CDATA_STATICEVAL)
1972 && sel->u.boolt == BOOL_OR))
1974 child->cdata->evaluate = NULL;
1978 child->cdata->evaluate = &_gmx_sel_evaluate_static;
1979 /* The cgrp has only been allocated if it originated from an
1980 * external index group. In that case, we need special handling
1981 * to preserve the name of the group and to not leak memory.
1982 * If cgrp has been set in make_static(), it is not allocated,
1983 * and hence we can overwrite it safely. */
1984 if (child->u.cgrp.nalloc_index > 0)
1986 gmx_ana_index_copy(&child->u.cgrp, child->v.u.g, false);
1987 gmx_ana_index_squeeze(&child->u.cgrp);
1991 gmx_ana_index_copy(&child->u.cgrp, child->v.u.g, true);
1997 * Evaluates the minimum and maximum groups for a boolean expression.
1999 * \param[in] sel \ref SEL_BOOLEAN element currently being evaluated.
2000 * \param[in] g Group for which \p sel has been evaluated.
2001 * \param[out] gmin Largest subset of the possible values of \p sel.
2002 * \param[out] gmax Smallest superset of the possible values of \p sel.
2004 * This is a helper function for analyze_static() that is called for
2005 * dynamic \ref SEL_BOOLEAN elements after they have been evaluated.
2006 * It uses the minimum and maximum groups of the children to calculate
2007 * the minimum and maximum groups for \p sel, and also updates the static
2008 * part of \p sel (which is in the first child) if the children give
2011 * This function may allocate some extra memory for \p gmin and \p gmax,
2012 * but as these groups are freed at the end of analyze_static() (which is
2013 * reached shortly after this function returns), this should not be a major
2017 evaluate_boolean_minmax_grps(const SelectionTreeElementPointer &sel,
2019 gmx_ana_index_t *gmin, gmx_ana_index_t *gmax)
2021 SelectionTreeElementPointer child;
2023 switch (sel->u.boolt)
2026 gmx_ana_index_reserve(gmin, g->isize);
2027 gmx_ana_index_reserve(gmax, g->isize);
2028 gmx_ana_index_difference(gmax, g, sel->child->cdata->gmin);
2029 gmx_ana_index_difference(gmin, g, sel->child->cdata->gmax);
2033 gmx_ana_index_copy(gmin, sel->child->cdata->gmin, true);
2034 gmx_ana_index_copy(gmax, sel->child->cdata->gmax, true);
2035 child = sel->child->next;
2036 while (child && gmax->isize > 0)
2038 gmx_ana_index_intersection(gmin, gmin, child->cdata->gmin);
2039 gmx_ana_index_intersection(gmax, gmax, child->cdata->gmax);
2040 child = child->next;
2042 /* Update the static part if other expressions limit it */
2043 if ((sel->child->cdata->flags & SEL_CDATA_STATIC)
2044 && sel->child->v.u.g->isize > gmax->isize)
2046 gmx_ana_index_copy(sel->child->v.u.g, gmax, false);
2047 gmx_ana_index_squeeze(sel->child->v.u.g);
2048 if (sel->child->u.cgrp.isize > 0)
2050 gmx_ana_index_copy(&sel->child->u.cgrp, gmax, false);
2051 gmx_ana_index_squeeze(&sel->child->u.cgrp);
2057 /* We can assume here that the gmin of children do not overlap
2058 * because of the way _gmx_sel_evaluate_or() works. */
2059 gmx_ana_index_reserve(gmin, g->isize);
2060 gmx_ana_index_reserve(gmax, g->isize);
2061 gmx_ana_index_copy(gmin, sel->child->cdata->gmin, false);
2062 gmx_ana_index_copy(gmax, sel->child->cdata->gmax, false);
2063 child = sel->child->next;
2064 while (child && gmin->isize < g->isize)
2066 gmx_ana_index_merge(gmin, gmin, child->cdata->gmin);
2067 gmx_ana_index_union(gmax, gmax, child->cdata->gmax);
2068 child = child->next;
2070 /* Update the static part if other expressions have static parts
2071 * that are not included. */
2072 if ((sel->child->cdata->flags & SEL_CDATA_STATIC)
2073 && sel->child->v.u.g->isize < gmin->isize)
2075 GMX_RELEASE_ASSERT(sel->child->type == SEL_CONST,
2076 "The first child should have already been evaluated "
2077 "to a constant expression");
2078 gmx_ana_index_reserve(sel->child->v.u.g, gmin->isize);
2079 gmx_ana_index_copy(sel->child->v.u.g, gmin, false);
2080 if (sel->child->u.cgrp.nalloc_index > 0)
2082 gmx_ana_index_reserve(&sel->child->u.cgrp, gmin->isize);
2083 gmx_ana_index_copy(&sel->child->u.cgrp, gmin, false);
2087 GMX_RELEASE_ASSERT(sel->child->u.cgrp.index == sel->child->v.u.g->index,
2088 "If not allocated, the static group should equal the value");
2089 sel->child->u.cgrp.isize = sel->child->v.u.g->isize;
2094 case BOOL_XOR: /* Should not be reached */
2095 GMX_THROW(gmx::NotImplementedError("xor expressions not implemented"));
2101 * Evaluates the static parts of \p sel and analyzes the structure.
2103 * \param[in] data Evaluation data.
2104 * \param[in,out] sel Selection currently being evaluated.
2105 * \param[in] g Group for which \p sel should be evaluated.
2106 * \returns 0 on success, a non-zero error code on error.
2108 * This function is used as the replacement for the
2109 * gmx::SelectionTreeElement::evaluate function pointer.
2110 * It does the single most complex task in the compiler: after all elements
2111 * have been processed, the \p gmin and \p gmax fields of \p t_compiler_data
2112 * have been properly initialized, enough memory has been allocated for
2113 * storing the value of each expression, and the static parts of the
2114 * expressions have been evaluated.
2115 * The above is exactly true only for elements other than subexpressions:
2116 * another pass is required for subexpressions that are referred to more than
2117 * once and whose evaluation group is not known in advance.
2120 analyze_static(gmx_sel_evaluate_t *data,
2121 const SelectionTreeElementPointer &sel,
2126 if (sel->type != SEL_ROOT && g)
2128 alloc_selection_data(sel, g->isize, false);
2131 bDoMinMax = (sel->cdata->flags & SEL_CDATA_DOMINMAX);
2132 if (sel->type != SEL_SUBEXPR && bDoMinMax)
2134 gmx_ana_index_deinit(sel->cdata->gmin);
2135 gmx_ana_index_deinit(sel->cdata->gmax);
2138 /* TODO: This switch is awfully long... */
2142 process_const(data, sel, g);
2145 case SEL_EXPRESSION:
2147 _gmx_sel_evaluate_method_params(data, sel, g);
2148 init_method(sel, data->top, g ? g->isize : 0);
2149 if (!(sel->flags & SEL_DYNAMIC))
2151 sel->cdata->evaluate(data, sel, g);
2152 if (sel->cdata->flags & SEL_CDATA_STATIC)
2159 /* Modifiers need to be evaluated even though they process
2160 * positions to get the modified output groups from the
2161 * maximum possible selections. */
2162 if (sel->type == SEL_MODIFIER)
2164 sel->cdata->evaluate(data, sel, g);
2168 gmx_ana_index_copy(sel->cdata->gmax, g, true);
2174 if (!(sel->flags & SEL_DYNAMIC))
2176 sel->cdata->evaluate(data, sel, g);
2177 if (sel->cdata->flags & SEL_CDATA_STATIC)
2184 /* Evalute the static part if there is more than one expression */
2185 evaluate_boolean_static_part(data, sel, g);
2187 /* Evaluate the selection.
2188 * If the type is boolean, we must explicitly handle the
2189 * static part evaluated in evaluate_boolean_static_part()
2190 * here because g may be larger. */
2191 if (sel->u.boolt == BOOL_AND && sel->child->type == SEL_CONST)
2193 sel->cdata->evaluate(data, sel, sel->child->v.u.g);
2197 sel->cdata->evaluate(data, sel, g);
2200 /* Evaluate minimal and maximal selections */
2201 evaluate_boolean_minmax_grps(sel, g, sel->cdata->gmin,
2206 case SEL_ARITHMETIC:
2207 sel->cdata->evaluate(data, sel, g);
2208 if (!(sel->flags & SEL_DYNAMIC))
2210 if (sel->cdata->flags & SEL_CDATA_STATIC)
2217 gmx_ana_index_copy(sel->cdata->gmax, g, true);
2222 sel->cdata->evaluate(data, sel, g);
2226 if (((sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR) &&
2227 !(sel->cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR))
2228 || (sel->cdata->flags & SEL_CDATA_FULLEVAL))
2230 sel->cdata->evaluate(data, sel, g);
2231 _gmx_selvalue_setstore(&sel->v, sel->child->v.u.ptr);
2233 else if (sel->u.cgrp.isize == 0)
2235 GMX_ASSERT(g, "group cannot be null");
2236 gmx_ana_index_reserve(&sel->u.cgrp, g->isize);
2237 sel->cdata->evaluate(data, sel, g);
2240 gmx_ana_index_copy(sel->cdata->gmin, sel->child->cdata->gmin, true);
2241 gmx_ana_index_copy(sel->cdata->gmax, sel->child->cdata->gmax, true);
2246 int isize = gmx_ana_index_difference_size(g, &sel->u.cgrp);
2249 isize += sel->u.cgrp.isize;
2250 gmx_ana_index_reserve(&sel->u.cgrp, isize);
2251 alloc_selection_data(sel, isize, false);
2253 sel->cdata->evaluate(data, sel, g);
2254 if (isize > 0 && bDoMinMax)
2256 gmx_ana_index_reserve(sel->cdata->gmin,
2257 sel->cdata->gmin->isize
2258 + sel->child->cdata->gmin->isize);
2259 gmx_ana_index_reserve(sel->cdata->gmax,
2260 sel->cdata->gmax->isize
2261 + sel->child->cdata->gmax->isize);
2262 gmx_ana_index_merge(sel->cdata->gmin, sel->cdata->gmin,
2263 sel->child->cdata->gmin);
2264 gmx_ana_index_merge(sel->cdata->gmax, sel->cdata->gmax,
2265 sel->child->cdata->gmax);
2270 case SEL_SUBEXPRREF:
2271 if (!g && !(sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR))
2273 /* The subexpression should have been evaluated if g is NULL
2274 * (i.e., this is a method parameter or a direct value of a
2276 if (sel->v.type == POS_VALUE)
2278 alloc_selection_pos_data(sel);
2282 alloc_selection_data(sel, sel->child->cdata->gmax->isize, true);
2285 sel->cdata->evaluate(data, sel, g);
2286 if ((sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
2287 && (sel->child->child->flags & SEL_ALLOCVAL))
2289 _gmx_selvalue_setstore(&sel->v, sel->child->child->v.u.ptr);
2291 /* Store the parameter value if required */
2292 store_param_val(sel);
2293 if (!(sel->flags & SEL_DYNAMIC))
2295 if (sel->cdata->flags & SEL_CDATA_STATIC)
2302 if ((sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR) || !g)
2304 gmx_ana_index_copy(sel->cdata->gmin, sel->child->cdata->gmin, true);
2305 gmx_ana_index_copy(sel->cdata->gmax, sel->child->cdata->gmax, true);
2309 gmx_ana_index_reserve(sel->cdata->gmin,
2310 min(g->isize, sel->child->cdata->gmin->isize));
2311 gmx_ana_index_reserve(sel->cdata->gmax,
2312 min(g->isize, sel->child->cdata->gmax->isize));
2313 gmx_ana_index_intersection(sel->cdata->gmin,
2314 sel->child->cdata->gmin, g);
2315 gmx_ana_index_intersection(sel->cdata->gmax,
2316 sel->child->cdata->gmax, g);
2321 case SEL_GROUPREF: /* Should not be reached */
2322 GMX_THROW(gmx::APIError("Unresolved group reference in compilation"));
2325 /* Update the minimal and maximal evaluation groups */
2328 gmx_ana_index_squeeze(sel->cdata->gmin);
2329 gmx_ana_index_squeeze(sel->cdata->gmax);
2332 /* Replace the result of the evaluation */
2333 /* This is not necessary for subexpressions or for boolean negations
2334 * because the evaluation function already has done it properly. */
2335 if (sel->v.type == GROUP_VALUE && (sel->flags & SEL_DYNAMIC)
2336 && sel->type != SEL_SUBEXPR
2337 && !(sel->type == SEL_BOOLEAN && sel->u.boolt == BOOL_NOT))
2339 if (sel->cdata->flags & SEL_CDATA_EVALMAX)
2341 gmx_ana_index_copy(sel->v.u.g, sel->cdata->gmax, false);
2345 gmx_ana_index_copy(sel->v.u.g, sel->cdata->gmin, false);
2351 /********************************************************************
2352 * EVALUATION GROUP INITIALIZATION
2353 ********************************************************************/
2356 * Initializes the evaluation group for a \ref SEL_ROOT element.
2358 * \param root Root element to initialize.
2359 * \param[in] gall Group of all atoms.
2361 * Checks whether it is necessary to evaluate anything through the root
2362 * element, and either clears the evaluation function or initializes the
2366 init_root_item(const SelectionTreeElementPointer &root,
2367 gmx_ana_index_t *gall)
2369 const SelectionTreeElementPointer &expr = root->child;
2370 /* Subexpressions with non-static evaluation group should not be
2371 * evaluated by the root, and neither should be single-reference
2372 * subexpressions that don't evaluate for all atoms. */
2373 if (expr->type == SEL_SUBEXPR
2374 && (!(root->child->cdata->flags & SEL_CDATA_STATICEVAL)
2375 || ((root->child->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
2376 && !(root->child->cdata->flags & SEL_CDATA_FULLEVAL))))
2378 root->evaluate = NULL;
2381 root->cdata->evaluate = NULL;
2385 /* Set the evaluation group */
2388 /* Non-atom-valued non-group expressions don't care about the group, so
2389 * don't allocate any memory for it. */
2390 if ((expr->flags & SEL_VARNUMVAL)
2391 || ((expr->flags & SEL_SINGLEVAL) && expr->v.type != GROUP_VALUE))
2393 gmx_ana_index_set(&root->u.cgrp, -1, NULL, 0);
2395 else if (expr->cdata->gmax->isize == gall->isize)
2397 /* Save some memory by only referring to the global group. */
2398 gmx_ana_index_set(&root->u.cgrp, gall->isize, gall->index, 0);
2402 gmx_ana_index_copy(&root->u.cgrp, expr->cdata->gmax, true);
2404 /* For selections, store the maximum group for
2405 * gmx_ana_selcollection_evaluate_fin() as the value of the root
2406 * element (unused otherwise). */
2407 if (expr->type != SEL_SUBEXPR && expr->v.u.p->m.mapb.a != NULL)
2409 SelectionTreeElementPointer child = expr;
2411 /* TODO: This code is copied from parsetree.c; it would be better
2412 * to have this hardcoded only in one place. */
2413 while (child->type == SEL_MODIFIER)
2415 child = child->child;
2416 if (child->type == SEL_SUBEXPRREF)
2418 child = child->child->child;
2421 if (child->type == SEL_SUBEXPRREF)
2423 child = child->child->child;
2425 if (child->child->flags & SEL_DYNAMIC)
2428 gmx_ana_index_set(&g, expr->v.u.p->m.mapb.nra, expr->v.u.p->m.mapb.a, 0);
2429 _gmx_selelem_set_vtype(root, GROUP_VALUE);
2430 root->flags |= (SEL_ALLOCVAL | SEL_ALLOCDATA);
2431 _gmx_selvalue_reserve(&root->v, 1);
2432 gmx_ana_index_copy(root->v.u.g, &g, true);
2438 gmx_ana_index_clear(&root->u.cgrp);
2443 /********************************************************************
2444 * FINAL SUBEXPRESSION OPTIMIZATION
2445 ********************************************************************/
2448 * Optimizes subexpression evaluation.
2450 * \param sel Root of the selection subtree to process.
2452 * Optimizes away some unnecessary evaluation of subexpressions that are only
2456 postprocess_item_subexpressions(const SelectionTreeElementPointer &sel)
2458 GMX_ASSERT(!(sel->child == NULL &&
2459 (sel->type == SEL_SUBEXPRREF || sel->type == SEL_SUBEXPR)),
2460 "Subexpression elements should always have a child element");
2462 /* Process children. */
2463 if (sel->type != SEL_SUBEXPRREF)
2465 SelectionTreeElementPointer child = sel->child;
2468 postprocess_item_subexpressions(child);
2469 child = child->next;
2473 /* Replace the evaluation function of statically evaluated subexpressions
2474 * for which the static group was not known in advance. */
2475 if (sel->type == SEL_SUBEXPR && sel->cdata->refcount > 1
2476 && (sel->cdata->flags & SEL_CDATA_STATICEVAL)
2477 && !(sel->cdata->flags & SEL_CDATA_FULLEVAL))
2479 /* We need to free memory allocated for the group, because it is no
2480 * longer needed (and would be lost on next call to the evaluation
2482 gmx_ana_index_deinit(&sel->u.cgrp);
2484 sel->evaluate = &_gmx_sel_evaluate_subexpr_staticeval;
2485 sel->cdata->evaluate = sel->evaluate;
2487 sel->child->freeValues();
2488 sel->child->mempool = NULL;
2489 _gmx_selvalue_setstore(&sel->child->v, sel->v.u.ptr);
2490 sel->child->flags &= ~(SEL_ALLOCVAL | SEL_ALLOCDATA);
2493 /* Adjust memory allocation flags for subexpressions that are used only
2494 * once. This is not strictly necessary, but we do it to have the memory
2495 * managed consistently for all types of subexpressions. */
2496 if (sel->type == SEL_SUBEXPRREF
2497 && (sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR))
2499 if (sel->child->child->flags & SEL_ALLOCVAL)
2501 sel->flags |= SEL_ALLOCVAL;
2502 sel->flags |= (sel->child->child->flags & SEL_ALLOCDATA);
2503 sel->v.nalloc = sel->child->child->v.nalloc;
2504 sel->child->child->flags &= ~(SEL_ALLOCVAL | SEL_ALLOCDATA);
2505 sel->child->child->v.nalloc = -1;
2509 /* Do the same for subexpressions that are evaluated at once for all atoms. */
2510 if (sel->type == SEL_SUBEXPR
2511 && !(sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
2512 && (sel->cdata->flags & SEL_CDATA_FULLEVAL))
2514 sel->flags |= SEL_ALLOCVAL;
2515 sel->flags |= (sel->child->flags & SEL_ALLOCDATA);
2516 sel->v.nalloc = sel->child->v.nalloc;
2517 sel->child->flags &= ~(SEL_ALLOCVAL | SEL_ALLOCDATA);
2518 sel->child->v.nalloc = -1;
2521 /* For static subexpressions with a dynamic evaluation group, there is
2522 * no need to evaluate them again, as the SEL_SUBEXPRREF takes care of
2523 * everything during evaluation. */
2524 if (sel->type == SEL_SUBEXPR
2525 && (sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
2526 && (sel->cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR))
2528 sel->evaluate = NULL;
2529 sel->cdata->evaluate = NULL;
2534 /********************************************************************
2535 * COM CALCULATION INITIALIZATION
2536 ********************************************************************/
2539 * Initializes COM/COG calculation for method expressions that require it.
2541 * \param sel Selection subtree to process.
2542 * \param[in,out] pcc Position calculation collection to use.
2543 * \param[in] type Default position calculation type.
2544 * \param[in] flags Flags for default position calculation.
2546 * Searches recursively through the selection tree for dynamic
2547 * \ref SEL_EXPRESSION elements that define the \c gmx_ana_selmethod_t::pupdate
2549 * For each such element found, position calculation is initialized
2550 * for the maximal evaluation group.
2551 * The type of the calculation is determined by \p type and \p flags.
2552 * No calculation is initialized if \p type equals \ref POS_ATOM and
2553 * the method also defines the \c gmx_ana_selmethod_t::update method.
2556 init_item_comg(const SelectionTreeElementPointer &sel,
2557 gmx::PositionCalculationCollection *pcc,
2558 e_poscalc_t type, int flags)
2560 /* Initialize COM calculation for dynamic selections now that we know the maximal evaluation group */
2561 if (sel->type == SEL_EXPRESSION && sel->u.expr.method
2562 && sel->u.expr.method->pupdate)
2564 if (!sel->u.expr.method->update || type != POS_ATOM)
2566 /* Create a default calculation if one does not yet exist */
2568 if (!(sel->cdata->flags & SEL_CDATA_STATICEVAL))
2570 cflags |= POS_DYNAMIC;
2572 if (!sel->u.expr.pc)
2575 sel->u.expr.pc = pcc->createCalculation(type, cflags);
2579 gmx_ana_poscalc_set_flags(sel->u.expr.pc, cflags);
2581 gmx_ana_poscalc_set_maxindex(sel->u.expr.pc, sel->cdata->gmax);
2582 sel->u.expr.pos = new gmx_ana_pos_t();
2583 gmx_ana_poscalc_init_pos(sel->u.expr.pc, sel->u.expr.pos);
2587 /* Call recursively for all children unless the children have already been processed */
2588 if (sel->type != SEL_SUBEXPRREF)
2590 SelectionTreeElementPointer child = sel->child;
2593 init_item_comg(child, pcc, type, flags);
2594 child = child->next;
2600 /********************************************************************
2601 * COMPILER DATA FREEING
2602 ********************************************************************/
2605 * Frees the allocated compiler data recursively.
2607 * \param sel Root of the selection subtree to process.
2609 * Frees the data allocated for the compilation process.
2612 free_item_compilerdata(const SelectionTreeElementPointer &sel)
2614 /* Free compilation data */
2615 sel->freeCompilerData();
2617 /* Call recursively for all children unless the children have already been processed */
2618 if (sel->type != SEL_SUBEXPRREF)
2620 SelectionTreeElementPointer child = sel->child;
2623 free_item_compilerdata(child);
2624 child = child->next;
2630 /********************************************************************
2631 * MAIN COMPILATION FUNCTION
2632 ********************************************************************/
2637 SelectionCompiler::SelectionCompiler()
2642 * \param[in,out] coll Selection collection to be compiled.
2643 * \returns 0 on successful compilation, a non-zero error code on error.
2645 * Before compilation, the selection collection should have been initialized
2646 * with gmx_ana_selcollection_parse_*().
2647 * The compiled selection collection can be passed to
2648 * gmx_ana_selcollection_evaluate() to evaluate the selection for a frame.
2649 * If an error occurs, \p sc is cleared.
2651 * The covered fraction information in \p sc is initialized to
2655 SelectionCompiler::compile(SelectionCollection *coll)
2657 gmx_ana_selcollection_t *sc = &coll->impl_->sc_;
2658 gmx_sel_evaluate_t evaldata;
2659 SelectionTreeElementPointer item;
2663 bool bDebug = (coll->impl_->debugLevel_ >= 2
2664 && coll->impl_->debugLevel_ != 3);
2666 /* FIXME: Clean up the collection on exceptions */
2668 sc->mempool = _gmx_sel_mempool_create();
2669 _gmx_sel_evaluate_init(&evaldata, sc->mempool, &sc->gall,
2670 sc->top, NULL, NULL);
2672 /* Clear the symbol table because it is not possible to parse anything
2673 * after compilation, and variable references in the symbol table can
2674 * also mess up the compilation and/or become invalid.
2676 coll->impl_->clearSymbolTable();
2678 /* Loop through selections and initialize position keyword defaults if no
2679 * other value has been provided.
2681 for (i = 0; i < sc->sel.size(); ++i)
2683 gmx::internal::SelectionData &sel = *sc->sel[i];
2684 init_pos_keyword_defaults(&sel.rootElement(),
2685 coll->impl_->spost_.c_str(),
2686 coll->impl_->rpost_.c_str(),
2690 /* Remove any unused variables. */
2691 sc->root = remove_unused_subexpressions(sc->root);
2692 /* Extract subexpressions into separate roots */
2693 sc->root = extract_subexpressions(sc->root);
2695 /* Initialize the evaluation callbacks and process the tree structure
2696 * to conform to the expectations of the callback functions. */
2697 /* Also, initialize and allocate the compiler data structure */
2698 // TODO: Processing the tree in reverse root order would be better,
2699 // as it would make dependency handling easier (all subexpression
2700 // references would be processed before the actual subexpression) and
2701 // could remove the need for most of these extra loops.
2705 /* Process boolean and arithmetic expressions. */
2706 optimize_boolean_expressions(item);
2707 reorder_boolean_static_children(item);
2708 optimize_arithmetic_expressions(item);
2709 /* Initialize the compiler data */
2710 init_item_compilerdata(item);
2713 // Initialize the static evaluation compiler flags.
2714 // Requires the FULLEVAL compiler flag for the whole tree.
2718 init_item_staticeval(item);
2719 init_item_subexpr_refcount(item);
2722 /* Initialize subexpression flags.
2723 * Requires compiler flags for the full tree. */
2727 init_item_subexpr_flags(item);
2730 /* Initialize evaluation.
2731 * Requires subexpression flags. */
2735 init_item_evalfunc(item);
2736 setup_memory_pooling(item, sc->mempool);
2737 init_item_evaloutput(item);
2740 /* Initialize minimum/maximum index groups.
2741 * Requires evaluation output for the full tree. */
2745 init_item_minmax_groups(item);
2748 /* Initialize the evaluation index groups */
2749 initialize_evalgrps(sc);
2753 fprintf(stderr, "\nTree after initial compiler processing:\n");
2754 coll->printTree(stderr, false);
2757 /* Evaluate all static parts of the selection and analyze the tree
2758 * to allocate enough memory to store the value of each dynamic subtree. */
2762 if (item->child->cdata->flags & SEL_CDATA_COMMONSUBEXPR)
2764 mark_subexpr_dynamic(item->child, true);
2766 set_evaluation_function(item, &analyze_static);
2767 item->evaluate(&evaldata, item, NULL);
2771 /* At this point, static subexpressions no longer have references to them,
2772 * so they can be removed. */
2773 sc->root = remove_unused_subexpressions(sc->root);
2774 // Update the reference counts for consistency (only used for the
2775 // debugging output below).
2779 init_item_subexpr_refcount(item);
2785 fprintf(stderr, "\nTree after first analysis pass:\n");
2786 coll->printTree(stderr, false);
2789 /* Do a second pass to evaluate static parts of common subexpressions */
2793 if (item->child->cdata->flags & SEL_CDATA_COMMONSUBEXPR)
2795 bool bMinMax = item->child->cdata->flags & SEL_CDATA_DOMINMAX;
2797 mark_subexpr_dynamic(item->child, false);
2798 item->child->u.cgrp.isize = 0;
2799 /* We won't clear item->child->v.u.g here, because it may
2800 * be static, and hence actually point to item->child->cdata->gmax,
2801 * which is used below. We could also check whether this is the
2802 * case and only clear the group otherwise, but because the value
2803 * is actually overwritten immediately in the evaluate call, we
2804 * won't, because similar problems may arise if gmax handling ever
2805 * changes and the check were not updated.
2806 * For the same reason, we clear the min/max flag so that the
2807 * evaluation group doesn't get messed up. */
2808 set_evaluation_function(item, &analyze_static);
2809 item->child->cdata->flags &= ~SEL_CDATA_DOMINMAX;
2810 item->evaluate(&evaldata, item->child, item->child->cdata->gmax);
2813 item->child->cdata->flags |= SEL_CDATA_DOMINMAX;
2819 /* We need a yet another pass of subexpression removal to remove static
2820 * subexpressions referred to by common dynamic subexpressions. */
2821 sc->root = remove_unused_subexpressions(sc->root);
2822 // Update the reference counts, used by postprocess_item_subexpressions().
2826 init_item_subexpr_refcount(item);
2832 fprintf(stderr, "\nTree after second analysis pass:\n");
2833 coll->printTree(stderr, false);
2836 /* Initialize evaluation groups, position calculations for methods, perform
2837 * some final optimization, and free the memory allocated for the
2839 /* By default, use whole residues/molecules. */
2840 flags = POS_COMPLWHOLE;
2841 PositionCalculationCollection::typeFromEnum(coll->impl_->rpost_.c_str(),
2846 init_root_item(item, &sc->gall);
2847 postprocess_item_subexpressions(item);
2848 init_item_comg(item, &sc->pcc, post, flags);
2849 free_item_compilerdata(item);
2853 /* Allocate memory for the evaluation memory pool. */
2854 _gmx_sel_mempool_reserve(sc->mempool, 0);
2856 /* Finish up by calculating total masses and charges. */
2857 for (i = 0; i < sc->sel.size(); ++i)
2859 sc->sel[i]->initializeMassesAndCharges(sc->top);