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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75 * been replaced by the result of the evaluation.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/math/vec.h"
280 #include "gromacs/selection/indexutil.h"
281 #include "gromacs/selection/poscalc.h"
282 #include "gromacs/selection/selection.h"
283 #include "gromacs/selection/selmethod.h"
284 #include "gromacs/utility/exceptions.h"
285 #include "gromacs/utility/smalloc.h"
286 #include "gromacs/utility/stringutil.h"
288 #include "evaluate.h"
289 #include "keywords.h"
291 #include "selectioncollection-impl.h"
295 using gmx::SelectionTreeElement;
296 using gmx::SelectionTreeElementPointer;
304 * Whether a subexpression needs to evaluated for all atoms.
306 * This flag is set for \ref SEL_SUBEXPR elements that are used to
307 * evaluate non-atom-valued selection method parameters, as well as
308 * those that are used directly as values of selections.
310 SEL_CDATA_FULLEVAL = 1,
312 * Whether the whole subexpression should be treated as static.
314 * This flag is always false if \ref SEL_DYNAMIC is set for the element,
315 * but it is also false for static elements within common subexpressions.
317 SEL_CDATA_STATIC = 2,
318 /** Whether the subexpression will always be evaluated in the same group. */
319 SEL_CDATA_STATICEVAL = 4,
320 /** Whether the compiler evaluation routine should return the maximal selection. */
321 SEL_CDATA_EVALMAX = 8,
322 /** Whether memory has been allocated for \p gmin and \p gmax. */
323 SEL_CDATA_MINMAXALLOC = 16,
324 /** Whether to update \p gmin and \p gmax in static analysis. */
325 SEL_CDATA_DOMINMAX = 256,
326 /** Whether the subexpression uses simple pass evaluation functions. */
327 SEL_CDATA_SIMPLESUBEXPR = 32,
329 * Whether a static subexpression needs to support multiple evaluations.
331 * This flag may only be set on \ref SEL_SUBEXPR elements that also have
332 * SEL_CDATA_SIMPLESUBEXPR.
334 SEL_CDATA_STATICMULTIEVALSUBEXPR = 64,
335 /** Whether this expression is a part of a common subexpression. */
336 SEL_CDATA_COMMONSUBEXPR = 128
340 * Internal data structure used by the compiler.
342 typedef struct t_compiler_data
344 /** The real evaluation method. */
345 gmx::sel_evalfunc evaluate;
346 /** Number of references to a \ref SEL_SUBEXPR element. */
348 /** Flags for specifying how to treat this element during compilation. */
350 /** Smallest selection that can be selected by the subexpression. */
351 gmx_ana_index_t *gmin;
352 /** Largest selection that can be selected by the subexpression. */
353 gmx_ana_index_t *gmax;
357 /********************************************************************
358 * COMPILER UTILITY FUNCTIONS
359 ********************************************************************/
362 * Helper method for printing out debug information about a min/max group.
365 print_group_info(FILE *fp, const char *name,
366 const SelectionTreeElement &sel,
369 fprintf(fp, " %s=", name);
372 fprintf(fp, "(null)");
374 else if (sel.cdata->flags & SEL_CDATA_MINMAXALLOC)
376 fprintf(fp, "(%d atoms, %p)", g->isize, (void*)g);
378 else if (sel.v.type == GROUP_VALUE && g == sel.v.u.g)
380 fprintf(fp, "(static, %p)", (void*)g);
384 fprintf(fp, "%p", (void*)g);
389 * \param[in] fp File handle to receive the output.
390 * \param[in] sel Selection element to print.
391 * \param[in] level Indentation level, starting from zero.
394 _gmx_selelem_print_compiler_info(FILE *fp, const SelectionTreeElement &sel,
401 fprintf(fp, "%*c cdata: flg=", level*2+1, ' ');
402 if (sel.cdata->flags & SEL_CDATA_FULLEVAL)
406 if (!(sel.cdata->flags & SEL_CDATA_STATIC))
410 if (sel.cdata->flags & SEL_CDATA_STATICEVAL)
414 if (sel.cdata->flags & SEL_CDATA_EVALMAX)
418 if (sel.cdata->flags & SEL_CDATA_MINMAXALLOC)
422 if (sel.cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
426 if (sel.cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR)
430 if (sel.cdata->flags & SEL_CDATA_COMMONSUBEXPR)
434 if (!sel.cdata->flags)
438 if (sel.cdata->refcount > 0)
440 fprintf(fp, " refc=%d", sel.cdata->refcount);
442 fprintf(fp, " eval=");
443 _gmx_sel_print_evalfunc_name(fp, sel.cdata->evaluate);
444 print_group_info(fp, "gmin", sel, sel.cdata->gmin);
445 print_group_info(fp, "gmax", sel, sel.cdata->gmax);
452 void SelectionTreeElement::freeCompilerData()
456 evaluate = cdata->evaluate;
457 if (cdata->flags & SEL_CDATA_MINMAXALLOC)
459 gmx_ana_index_deinit(cdata->gmin);
460 gmx_ana_index_deinit(cdata->gmax);
472 * Allocates memory for storing the evaluated value of a selection element.
474 * \param sel Selection element to initialize
475 * \param[in] isize Maximum evaluation group size.
476 * \param[in] bChildEval true if children have already been processed.
478 * If called more than once, memory is (re)allocated to ensure that the
479 * maximum of the \p isize values can be stored.
481 * Allocation of POS_VALUE selection elements is a special case, and is
482 * handled by alloc_selection_pos_data().
485 alloc_selection_data(const SelectionTreeElementPointer &sel,
486 int isize, bool bChildEval)
490 GMX_RELEASE_ASSERT(sel->v.type != POS_VALUE,
491 "Wrong allocation method called");
496 /* Find out the number of elements to allocate */
497 if (sel->flags & SEL_SINGLEVAL)
501 else if (sel->flags & SEL_ATOMVAL)
505 else /* sel->flags should contain SEL_VARNUMVAL */
507 // TODO: Consider whether the bChildEval is any longer necessary.
512 SelectionTreeElementPointer child = sel;
513 if (sel->type == SEL_SUBEXPRREF)
515 GMX_RELEASE_ASSERT(sel->child && sel->child->type == SEL_SUBEXPR,
516 "Subexpression expected for subexpression reference");
517 child = sel->child->child;
518 GMX_RELEASE_ASSERT(child,
519 "Subexpression elements should always have a child element");
521 nalloc = child->v.nr;
523 /* Allocate memory for sel->v.u if needed */
524 if (sel->flags & SEL_ALLOCVAL)
526 _gmx_selvalue_reserve(&sel->v, nalloc);
528 /* Reserve memory inside group structure if SEL_ALLOCDATA is set. */
529 if ((sel->flags & SEL_ALLOCDATA) && sel->v.type == GROUP_VALUE)
531 gmx_ana_index_reserve(sel->v.u.g, isize);
536 * Allocates memory for storing the evaluated value of a selection element.
538 * \param sel Selection element to initialize.
540 * Allocation of POS_VALUE selection elements is a special case, and is
541 * handled by this function instead of by alloc_selection_data().
544 alloc_selection_pos_data(const SelectionTreeElementPointer &sel)
548 GMX_RELEASE_ASSERT(sel->v.type == POS_VALUE,
549 "Wrong allocation method called");
550 GMX_RELEASE_ASSERT(!(sel->flags & SEL_ATOMVAL),
551 "Per-atom evaluated positions not implemented");
557 SelectionTreeElementPointer child = sel;
558 if (sel->type == SEL_SUBEXPRREF)
560 GMX_RELEASE_ASSERT(sel->child && sel->child->type == SEL_SUBEXPR,
561 "Subexpression expected for subexpression reference");
562 child = sel->child->child;
563 GMX_RELEASE_ASSERT(child,
564 "Subexpression elements should always have a child element");
566 nalloc = child->v.u.p->count();
567 isize = child->v.u.p->m.b.nra;
569 /* For positions, we want to allocate just a single structure
570 * for nalloc positions. */
571 if (sel->flags & SEL_ALLOCVAL)
573 _gmx_selvalue_reserve(&sel->v, 1);
576 /* Reserve memory inside position structure if SEL_ALLOCDATA is set. */
577 if (sel->flags & SEL_ALLOCDATA)
579 gmx_ana_pos_reserve(sel->v.u.p, nalloc, isize);
584 * Replace the evaluation function of each element in the subtree.
586 * \param sel Root of the selection subtree to process.
587 * \param[in] eval The new evaluation function.
590 set_evaluation_function(const SelectionTreeElementPointer &sel,
591 gmx::sel_evalfunc eval)
593 sel->evaluate = eval;
594 if (sel->type != SEL_SUBEXPRREF)
596 SelectionTreeElementPointer child = sel->child;
599 set_evaluation_function(child, eval);
606 /********************************************************************
607 * POSITION KEYWORD DEFAULT INITIALIZATION
608 ********************************************************************/
611 * Initializes default values for position keyword evaluation.
613 * \param[in,out] root Root of the element tree to initialize.
614 * \param[in] spost Default output position type.
615 * \param[in] rpost Default reference position type.
616 * \param[in] sel Selection that the element evaluates the positions
617 * for, or NULL if the element is an internal element.
620 init_pos_keyword_defaults(SelectionTreeElement *root,
621 const char *spost, const char *rpost,
622 const gmx::internal::SelectionData *sel)
624 /* Selections use largest static group by default, while
625 * reference positions use the whole residue/molecule. */
626 if (root->type == SEL_EXPRESSION)
628 bool bSelection = (sel != NULL);
629 int flags = bSelection ? POS_COMPLMAX : POS_COMPLWHOLE;
632 if (sel->hasFlag(gmx::efSelection_DynamicMask))
634 flags |= POS_MASKONLY;
636 if (sel->hasFlag(gmx::efSelection_EvaluateVelocities))
638 flags |= POS_VELOCITIES;
640 if (sel->hasFlag(gmx::efSelection_EvaluateForces))
645 _gmx_selelem_set_kwpos_type(root, bSelection ? spost : rpost);
646 _gmx_selelem_set_kwpos_flags(root, flags);
648 /* Change the defaults once we are no longer processing modifiers */
649 if (root->type != SEL_ROOT && root->type != SEL_MODIFIER
650 && root->type != SEL_SUBEXPRREF && root->type != SEL_SUBEXPR)
654 /* Recurse into children */
655 SelectionTreeElementPointer child = root->child;
658 init_pos_keyword_defaults(child.get(), spost, rpost, sel);
664 /********************************************************************
665 * SUBEXPRESSION PROCESSING
666 ********************************************************************/
669 * Reverses the chain of selection elements starting at \p root.
671 * \param root First selection in the whole selection chain.
672 * \returns The new first element for the chain.
674 static SelectionTreeElementPointer
675 reverse_selelem_chain(const SelectionTreeElementPointer &root)
677 SelectionTreeElementPointer prev;
678 SelectionTreeElementPointer item = root;
681 SelectionTreeElementPointer next = item->next;
690 * Removes subexpressions that don't have any references.
692 * \param root First selection in the whole selection chain.
693 * \returns The new first element for the chain.
695 * The elements are processed in reverse order to correctly detect
696 * subexpressions only referred to by other subexpressions.
698 static SelectionTreeElementPointer
699 remove_unused_subexpressions(SelectionTreeElementPointer root)
703 return SelectionTreeElementPointer();
705 root = reverse_selelem_chain(root);
706 while (root->child->type == SEL_SUBEXPR && root->child.unique())
708 // Frees the root element.
711 SelectionTreeElementPointer prev = root;
712 SelectionTreeElementPointer item = root->next;
715 SelectionTreeElementPointer next = item->next;
716 if (item->child->type == SEL_SUBEXPR && item->child.unique())
718 // Frees the current item when it goes out of scope.
727 return reverse_selelem_chain(root);
731 * Creates a name with a running number for a subexpression.
733 * \param[in,out] sel The subexpression to be named.
734 * \param[in] i Running number for the subexpression.
736 * The name of the selection becomes "SubExpr N", where N is \p i;
737 * Memory is allocated for the name and the name is stored both as the
738 * name of the subexpression element and as
739 * gmx::SelectionTreeElement::u::cgrp::name; the latter is freed by
740 * _gmx_selelem_free().
743 create_subexpression_name(const SelectionTreeElementPointer &sel, int i)
745 std::string name(gmx::formatString("SubExpr %d", i));
750 * Processes and extracts subexpressions from a given selection subtree.
752 * \param sel Root of the subtree to process.
753 * \param subexprn Pointer to a subexpression counter.
754 * \returns Pointer to a chain of subselections, or NULL if none were found.
756 * This function finds recursively all \ref SEL_SUBEXPRREF elements below
757 * the given root element and ensures that their children are within
758 * \ref SEL_SUBEXPR elements. It also creates a chain of \ref SEL_ROOT elements
759 * that contain the subexpression as their children and returns the first
760 * of these root elements.
762 static SelectionTreeElementPointer
763 extract_item_subselections(const SelectionTreeElementPointer &sel,
766 SelectionTreeElementPointer root;
767 SelectionTreeElementPointer subexpr;
768 SelectionTreeElementPointer child = sel->child;
774 root = subexpr = extract_item_subselections(child, subexprn);
778 subexpr->next = extract_item_subselections(child, subexprn);
780 while (subexpr && subexpr->next)
782 subexpr = subexpr->next;
784 /* The latter check excludes variable references. */
785 if (child->type == SEL_SUBEXPRREF && child->child->type != SEL_SUBEXPR)
787 /* Create the root element for the subexpression */
790 root.reset(new SelectionTreeElement(SEL_ROOT));
795 subexpr->next.reset(new SelectionTreeElement(SEL_ROOT));
796 subexpr = subexpr->next;
798 /* Create the subexpression element and
799 * move the actual subexpression under the created element. */
800 subexpr->child.reset(new SelectionTreeElement(SEL_SUBEXPR));
801 _gmx_selelem_set_vtype(subexpr->child, child->v.type);
802 subexpr->child->child = child->child;
803 child->child = subexpr->child;
804 create_subexpression_name(subexpr->child, ++*subexprn);
805 /* Set the flags for the created elements */
806 subexpr->flags |= (child->flags & SEL_VALFLAGMASK);
807 subexpr->child->flags |= (child->flags & SEL_VALFLAGMASK);
809 if (child->type == SEL_SUBEXPRREF)
811 child->setName(child->child->name());
820 * Extracts subexpressions of the selection chain.
822 * \param sel First selection in the whole selection chain.
823 * \returns The new first element for the chain.
825 * Finds all the subexpressions (and their subexpressions) in the
826 * selection chain starting from \p sel and creates \ref SEL_SUBEXPR
828 * \ref SEL_ROOT elements are also created for each subexpression
829 * and inserted into the selection chain before the expressions that
832 static SelectionTreeElementPointer
833 extract_subexpressions(SelectionTreeElementPointer sel)
835 SelectionTreeElementPointer root;
836 SelectionTreeElementPointer next = sel;
840 SelectionTreeElementPointer item
841 = extract_item_subselections(next, &subexprn);
869 /********************************************************************
870 * BOOLEAN OPERATION REORDERING
871 ********************************************************************/
874 * Removes redundant boolean selection elements.
876 * \param sel Root of the selection subtree to optimize.
878 * This function merges similar boolean operations (e.g., (A or B) or C becomes
879 * a single OR operation with three operands).
882 optimize_boolean_expressions(const SelectionTreeElementPointer &sel)
884 /* Do recursively for children */
885 if (sel->type != SEL_SUBEXPRREF)
887 SelectionTreeElementPointer prev;
888 SelectionTreeElementPointer child = sel->child;
891 optimize_boolean_expressions(child);
892 /* Remove double negations */
893 if (child->type == SEL_BOOLEAN && child->u.boolt == BOOL_NOT
894 && child->child->type == SEL_BOOLEAN && child->child->u.boolt == BOOL_NOT)
896 /* Move the doubly negated expression up two levels */
899 sel->child = child->child->child;
904 prev->next = child->child->child;
907 child->child->child->next = child->next;
908 // Discards the two negations.
915 if (sel->type != SEL_BOOLEAN || sel->u.boolt == BOOL_NOT)
919 /* Merge subsequent binary operations */
920 SelectionTreeElementPointer prev;
921 SelectionTreeElementPointer child = sel->child;
924 if (child->type == SEL_BOOLEAN && child->u.boolt == sel->u.boolt)
928 sel->child = child->child;
933 prev->next = child->child;
939 prev->next = child->next;
940 // Discards the old child.
952 * Reorders children of boolean expressions such that static selections
955 * \param sel Root of the selection subtree to reorder.
957 * The relative order of static expressions does not change.
958 * The same is true for the dynamic expressions.
961 reorder_boolean_static_children(const SelectionTreeElementPointer &sel)
963 /* Do recursively for children */
964 if (sel->type != SEL_SUBEXPRREF)
966 SelectionTreeElementPointer child = sel->child;
969 reorder_boolean_static_children(child);
974 /* Reorder boolean expressions such that static selections come first */
975 if (sel->type == SEL_BOOLEAN && (sel->flags & SEL_DYNAMIC))
977 // Add a dummy head element that precedes the first child.
978 SelectionTreeElementPointer dummy(
979 new SelectionTreeElement(SEL_BOOLEAN));
980 dummy->next = sel->child;
981 SelectionTreeElementPointer prev = dummy;
982 SelectionTreeElementPointer child = dummy;
985 /* child is the last handled static expression */
986 /* prev is the last handled non-static expression */
987 SelectionTreeElementPointer next = prev->next;
988 while (next && (next->flags & SEL_DYNAMIC))
993 /* next is now the first static expression after child */
998 /* Reorder such that next comes after child */
1001 prev->next = next->next;
1002 next->next = child->next;
1009 /* Advance child by one */
1013 sel->child = dummy->next;
1018 /********************************************************************
1019 * ARITHMETIC EXPRESSION PROCESSING
1020 ********************************************************************/
1023 * Processes arithmetic expressions to simplify and speed up evaluation.
1025 * \param sel Root of the selection subtree to process.
1027 * Currently, this function only converts integer constants to reals
1028 * within arithmetic expressions.
1031 optimize_arithmetic_expressions(const SelectionTreeElementPointer &sel)
1033 /* Do recursively for children. */
1034 if (sel->type != SEL_SUBEXPRREF)
1036 SelectionTreeElementPointer child = sel->child;
1039 optimize_arithmetic_expressions(child);
1040 child = child->next;
1044 if (sel->type != SEL_ARITHMETIC)
1049 /* Convert integer constants to reals. */
1050 SelectionTreeElementPointer child = sel->child;
1053 if (child->v.type == INT_VALUE)
1057 if (child->type != SEL_CONST)
1059 GMX_THROW(gmx::InconsistentInputError("Non-constant integer expressions not implemented in arithmetic evaluation"));
1062 r[0] = child->v.u.i[0];
1063 sfree(child->v.u.i);
1065 child->v.type = REAL_VALUE;
1067 else if (child->v.type != REAL_VALUE)
1069 GMX_THROW(gmx::InternalError("Non-numerical value in arithmetic expression"));
1071 child = child->next;
1076 /********************************************************************
1077 * EVALUATION PREPARATION COMPILER
1078 ********************************************************************/
1081 * Sets the evaluation functions for the selection (sub)tree.
1083 * \param[in,out] sel Root of the selection subtree to process.
1085 * This function sets the evaluation function
1086 * (gmx::SelectionTreeElement::evaluate) for the selection elements.
1089 init_item_evalfunc(const SelectionTreeElementPointer &sel)
1091 /* Process children. */
1092 if (sel->type != SEL_SUBEXPRREF)
1094 SelectionTreeElementPointer child = sel->child;
1097 init_item_evalfunc(child);
1098 child = child->next;
1102 /* Set the evaluation function */
1106 if (sel->v.type == GROUP_VALUE)
1108 sel->evaluate = &_gmx_sel_evaluate_static;
1112 case SEL_EXPRESSION:
1113 if (!(sel->flags & SEL_DYNAMIC) && sel->u.expr.method
1114 && sel->u.expr.method->init_frame)
1116 sel->flags |= SEL_INITFRAME;
1118 sel->evaluate = &_gmx_sel_evaluate_method;
1121 case SEL_ARITHMETIC:
1122 sel->evaluate = &_gmx_sel_evaluate_arithmetic;
1126 if (sel->v.type != NO_VALUE)
1128 sel->evaluate = &_gmx_sel_evaluate_modifier;
1133 switch (sel->u.boolt)
1135 case BOOL_NOT: sel->evaluate = &_gmx_sel_evaluate_not; break;
1136 case BOOL_AND: sel->evaluate = &_gmx_sel_evaluate_and; break;
1137 case BOOL_OR: sel->evaluate = &_gmx_sel_evaluate_or; break;
1139 GMX_THROW(gmx::NotImplementedError("xor expressions not implemented"));
1144 sel->evaluate = &_gmx_sel_evaluate_root;
1148 if ((sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
1149 && !(sel->cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR))
1151 sel->evaluate = &_gmx_sel_evaluate_subexpr_simple;
1155 sel->evaluate = &_gmx_sel_evaluate_subexpr;
1159 case SEL_SUBEXPRREF:
1160 sel->evaluate = ((sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
1161 ? &_gmx_sel_evaluate_subexprref_simple
1162 : &_gmx_sel_evaluate_subexprref);
1166 GMX_THROW(gmx::APIError("Unresolved group reference in compilation"));
1168 sel->cdata->evaluate = sel->evaluate;
1172 * Sets the memory pool for selection elements that can use it.
1174 * \param sel Root of the selection subtree to process.
1175 * \param[in] mempool Memory pool to use.
1178 setup_memory_pooling(const SelectionTreeElementPointer &sel,
1179 gmx_sel_mempool_t *mempool)
1181 if (sel->type != SEL_SUBEXPRREF)
1183 SelectionTreeElementPointer child = sel->child;
1186 if ((sel->type == SEL_BOOLEAN && (child->flags & SEL_DYNAMIC))
1187 || (sel->type == SEL_ARITHMETIC && child->type != SEL_CONST
1188 && !(child->flags & SEL_SINGLEVAL))
1189 || (sel->type == SEL_SUBEXPR
1190 && !(sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)))
1192 child->mempool = mempool;
1193 if (child->type == SEL_SUBEXPRREF
1194 && (child->child->cdata->flags & SEL_CDATA_SIMPLESUBEXPR))
1196 child->child->child->mempool = mempool;
1199 setup_memory_pooling(child, mempool);
1200 child = child->next;
1206 * Prepares the selection (sub)tree for evaluation.
1208 * \param[in,out] sel Root of the selection subtree to prepare.
1210 * It also allocates memory for the \p sel->v.u.g or \p sel->v.u.p
1211 * structure if required.
1214 init_item_evaloutput(const SelectionTreeElementPointer &sel)
1216 GMX_ASSERT(!(sel->child == NULL &&
1217 (sel->type == SEL_SUBEXPRREF || sel->type == SEL_SUBEXPR)),
1218 "Subexpression elements should always have a child element");
1220 /* Process children. */
1221 if (sel->type != SEL_SUBEXPRREF)
1223 SelectionTreeElementPointer child = sel->child;
1226 init_item_evaloutput(child);
1227 child = child->next;
1231 if (sel->type == SEL_SUBEXPR
1232 && (sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
1233 && !(sel->cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR))
1235 sel->flags &= ~(SEL_ALLOCVAL | SEL_ALLOCDATA);
1236 if (sel->v.type == GROUP_VALUE || sel->v.type == POS_VALUE)
1238 _gmx_selvalue_setstore(&sel->v, sel->child->v.u.ptr);
1241 else if (sel->type == SEL_SUBEXPR
1242 && (sel->cdata->flags & SEL_CDATA_FULLEVAL))
1244 sel->evaluate = &_gmx_sel_evaluate_subexpr_staticeval;
1245 sel->cdata->evaluate = sel->evaluate;
1246 sel->child->mempool = NULL;
1247 sel->flags &= ~(SEL_ALLOCVAL | SEL_ALLOCDATA);
1248 if (sel->v.type == GROUP_VALUE || sel->v.type == POS_VALUE)
1250 _gmx_selvalue_setstore(&sel->v, sel->child->v.u.ptr);
1253 else if (sel->type == SEL_SUBEXPRREF
1254 && (sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR))
1258 _gmx_selvalue_setstore(&sel->child->v, sel->v.u.ptr);
1259 sel->child->child->freeValues();
1260 sel->child->child->flags &= ~(SEL_ALLOCVAL | SEL_ALLOCDATA);
1261 sel->child->child->flags |= (sel->flags & SEL_ALLOCDATA);
1262 _gmx_selvalue_setstore(&sel->child->child->v, sel->v.u.ptr);
1264 else if (sel->v.type == GROUP_VALUE || sel->v.type == POS_VALUE)
1266 _gmx_selvalue_setstore(&sel->v, sel->child->child->v.u.ptr);
1268 sel->flags &= ~(SEL_ALLOCVAL | SEL_ALLOCDATA);
1271 /* Make sure that the group/position structure is allocated. */
1272 if (!sel->v.u.ptr && (sel->flags & SEL_ALLOCVAL))
1274 if (sel->v.type == GROUP_VALUE || sel->v.type == POS_VALUE)
1276 _gmx_selvalue_reserve(&sel->v, 1);
1283 /********************************************************************
1284 * COMPILER DATA INITIALIZATION
1285 ********************************************************************/
1288 * Allocates memory for the compiler data and initializes the structure.
1290 * \param sel Root of the selection subtree to process.
1293 init_item_compilerdata(const SelectionTreeElementPointer &sel)
1295 /* Allocate the compiler data structure */
1296 snew(sel->cdata, 1);
1298 /* Store the real evaluation method because the compiler will replace it */
1299 sel->cdata->evaluate = sel->evaluate;
1301 /* This will be computed separately. */
1302 sel->cdata->refcount = 0;
1304 /* Initialize the flags */
1305 sel->cdata->flags = SEL_CDATA_STATICEVAL;
1306 if (!(sel->flags & SEL_DYNAMIC))
1308 sel->cdata->flags |= SEL_CDATA_STATIC;
1310 if (sel->type == SEL_SUBEXPR)
1312 sel->cdata->flags |= SEL_CDATA_EVALMAX;
1314 /* Set the full evaluation flag for subexpressions that require it;
1315 * the subexpression has already been initialized, so we can simply
1316 * access its compilation flags.*/
1317 if (sel->type == SEL_EXPRESSION || sel->type == SEL_MODIFIER)
1319 SelectionTreeElementPointer child = sel->child;
1322 if (!(child->flags & SEL_ATOMVAL) && child->child)
1324 child->child->cdata->flags |= SEL_CDATA_FULLEVAL;
1326 child = child->next;
1329 else if (sel->type == SEL_ROOT && sel->child->type == SEL_SUBEXPRREF)
1331 sel->child->child->cdata->flags |= SEL_CDATA_FULLEVAL;
1334 /* Initialize children */
1335 if (sel->type != SEL_SUBEXPRREF)
1337 SelectionTreeElementPointer child = sel->child;
1340 init_item_compilerdata(child);
1341 child = child->next;
1345 /* Determine whether we should evaluate the minimum or the maximum
1346 * for the children of this element. */
1347 if (sel->type == SEL_BOOLEAN)
1351 bEvalMax = (sel->u.boolt == BOOL_AND);
1352 SelectionTreeElementPointer child = sel->child;
1357 child->cdata->flags |= SEL_CDATA_EVALMAX;
1359 else if (child->type == SEL_BOOLEAN && child->u.boolt == BOOL_NOT)
1361 child->child->cdata->flags |= SEL_CDATA_EVALMAX;
1363 child = child->next;
1366 else if (sel->type == SEL_EXPRESSION || sel->type == SEL_MODIFIER
1367 || sel->type == SEL_SUBEXPR)
1369 SelectionTreeElementPointer child = sel->child;
1372 child->cdata->flags |= SEL_CDATA_EVALMAX;
1373 child = child->next;
1379 * Initializes the static evaluation flag for a selection subtree.
1381 * \param[in,out] sel Root of the selection subtree to process.
1383 * Sets the \c bStaticEval in the compiler data structure:
1384 * for any element for which the evaluation group may depend on the trajectory
1385 * frame, the flag is cleared.
1387 * reorder_boolean_static_children() should have been called.
1390 init_item_staticeval(const SelectionTreeElementPointer &sel)
1392 /* Subexpressions with full evaluation should always have bStaticEval,
1393 * so don't do anything if a reference to them is encountered. */
1394 if (sel->type == SEL_SUBEXPRREF
1395 && (sel->child->cdata->flags & SEL_CDATA_FULLEVAL))
1400 /* Propagate the bStaticEval flag to children if it is not set */
1401 if (!(sel->cdata->flags & SEL_CDATA_STATICEVAL))
1403 SelectionTreeElementPointer child = sel->child;
1406 if ((sel->type != SEL_EXPRESSION && sel->type != SEL_MODIFIER)
1407 || (child->flags & SEL_ATOMVAL))
1409 if (child->cdata->flags & SEL_CDATA_STATICEVAL)
1411 child->cdata->flags &= ~SEL_CDATA_STATICEVAL;
1412 init_item_staticeval(child);
1415 /* If an expression is evaluated for a dynamic group, then also
1416 * atom-valued parameters need to be evaluated every time. */
1417 if ((sel->flags & SEL_DYNAMIC)
1418 && (sel->type == SEL_EXPRESSION || sel->type == SEL_MODIFIER)
1419 && (child->flags & SEL_ATOMVAL))
1421 child->flags |= SEL_DYNAMIC;
1422 child->cdata->flags &= ~SEL_CDATA_STATIC;
1424 child = child->next;
1427 else /* bStaticEval is set */
1429 /* For boolean expressions, any expression after the first dynamic
1430 * expression should not have bStaticEval. */
1431 if (sel->type == SEL_BOOLEAN)
1433 SelectionTreeElementPointer child = sel->child;
1434 while (child && !(child->flags & SEL_DYNAMIC))
1436 child = child->next;
1440 child = child->next;
1444 child->cdata->flags &= ~SEL_CDATA_STATICEVAL;
1445 child = child->next;
1449 /* Process the children */
1450 SelectionTreeElementPointer child = sel->child;
1453 init_item_staticeval(child);
1454 child = child->next;
1460 * Compute reference counts for subexpressions.
1462 * \param sel Root of the selection subtree to process.
1465 init_item_subexpr_refcount(const SelectionTreeElementPointer &sel)
1467 // Reset the counter when the subexpression is first encountered.
1468 if (sel->type == SEL_ROOT && sel->child->type == SEL_SUBEXPR
1469 && sel->child->cdata)
1471 sel->child->cdata->refcount = 0;
1474 if (sel->type == SEL_SUBEXPRREF)
1476 ++sel->child->cdata->refcount;
1480 SelectionTreeElementPointer child = sel->child;
1483 init_item_subexpr_refcount(child);
1484 child = child->next;
1490 * Initializes compiler flags for subexpressions.
1492 * \param sel Root of the selection subtree to process.
1495 init_item_subexpr_flags(const SelectionTreeElementPointer &sel)
1497 if (sel->type == SEL_SUBEXPR)
1499 if (sel->cdata->refcount == 1)
1501 sel->cdata->flags |= SEL_CDATA_SIMPLESUBEXPR;
1503 else if (!(sel->cdata->flags & SEL_CDATA_FULLEVAL))
1505 sel->cdata->flags |= SEL_CDATA_COMMONSUBEXPR;
1508 else if (sel->type == SEL_SUBEXPRREF
1509 && (sel->child->cdata->flags & SEL_CDATA_SIMPLESUBEXPR))
1511 /* See similar condition in init_item_staticeval(). */
1512 if ((sel->flags & SEL_ATOMVAL)
1513 && (sel->flags & SEL_DYNAMIC)
1514 && !(sel->child->flags & SEL_DYNAMIC))
1516 sel->child->cdata->flags |= SEL_CDATA_STATICMULTIEVALSUBEXPR;
1520 sel->cdata->flags |= SEL_CDATA_SIMPLESUBEXPR;
1524 /* Process children, but only follow subexpression references if the
1525 * common subexpression flag needs to be propagated. */
1526 if (sel->type != SEL_SUBEXPRREF
1527 || ((sel->cdata->flags & SEL_CDATA_COMMONSUBEXPR)
1528 && !(sel->child->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)))
1530 SelectionTreeElementPointer child = sel->child;
1533 if (!(child->cdata->flags & SEL_CDATA_COMMONSUBEXPR))
1535 if (sel->type != SEL_EXPRESSION || (child->flags & SEL_ATOMVAL))
1537 child->cdata->flags |=
1538 (sel->cdata->flags & SEL_CDATA_COMMONSUBEXPR);
1540 init_item_subexpr_flags(child);
1542 child = child->next;
1548 * Initializes the gmin and gmax fields of the compiler data structure.
1550 * \param sel Root of the selection subtree to process.
1553 init_item_minmax_groups(const SelectionTreeElementPointer &sel)
1555 /* Process children. */
1556 if (sel->type != SEL_SUBEXPRREF)
1558 SelectionTreeElementPointer child = sel->child;
1561 init_item_minmax_groups(child);
1562 child = child->next;
1566 /* Initialize the minimum and maximum evaluation groups. */
1567 if (sel->type != SEL_ROOT && sel->v.type != NO_VALUE)
1569 if (sel->v.type == GROUP_VALUE
1570 && (sel->cdata->flags & SEL_CDATA_STATIC))
1572 sel->cdata->gmin = sel->v.u.g;
1573 sel->cdata->gmax = sel->v.u.g;
1575 else if (sel->type == SEL_SUBEXPR
1576 && ((sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
1577 || (sel->cdata->flags & SEL_CDATA_FULLEVAL)))
1579 GMX_ASSERT(sel->child,
1580 "Subexpression elements should always have a child element");
1581 sel->cdata->gmin = sel->child->cdata->gmin;
1582 sel->cdata->gmax = sel->child->cdata->gmax;
1586 sel->cdata->flags |= SEL_CDATA_MINMAXALLOC | SEL_CDATA_DOMINMAX;
1587 snew(sel->cdata->gmin, 1);
1588 snew(sel->cdata->gmax, 1);
1594 /********************************************************************
1595 * EVALUATION GROUP INITIALIZATION
1596 ********************************************************************/
1599 * Initializes evaluation groups for root items.
1601 * \param[in,out] sc Selection collection data.
1603 * The evaluation group of each \ref SEL_ROOT element corresponding to a
1604 * selection in \p sc is set to NULL. The evaluation group for \ref SEL_ROOT
1605 * elements corresponding to subexpressions that need full evaluation is set
1609 initialize_evalgrps(gmx_ana_selcollection_t *sc)
1611 SelectionTreeElementPointer root = sc->root;
1614 GMX_RELEASE_ASSERT(root->child,
1615 "Root elements should always have a child");
1616 if (root->child->type != SEL_SUBEXPR
1617 || (root->child->v.type != GROUP_VALUE && !(root->flags & SEL_ATOMVAL)))
1619 gmx_ana_index_set(&root->u.cgrp, -1, 0, 0);
1621 else if (root->child->cdata->flags & SEL_CDATA_FULLEVAL)
1623 gmx_ana_index_set(&root->u.cgrp, sc->gall.isize, sc->gall.index, 0);
1630 /********************************************************************
1632 ********************************************************************/
1635 * Marks a subtree completely dynamic or undoes such a change.
1637 * \param sel Selection subtree to mark.
1638 * \param[in] bDynamic If true, the \p bStatic flag of the whole
1639 * selection subtree is cleared. If false, the flag is restored to
1640 * using \ref SEL_DYNAMIC.
1642 * Does not descend into parameters of methods unless the parameters
1643 * are evaluated for each atom.
1646 mark_subexpr_dynamic(const SelectionTreeElementPointer &sel,
1649 if (!bDynamic && !(sel->flags & SEL_DYNAMIC))
1651 sel->cdata->flags |= SEL_CDATA_STATIC;
1655 sel->cdata->flags &= ~SEL_CDATA_STATIC;
1657 SelectionTreeElementPointer child = sel->child;
1660 if (sel->type != SEL_EXPRESSION || child->type != SEL_SUBEXPRREF
1661 || (child->u.param->flags & SPAR_ATOMVAL))
1663 mark_subexpr_dynamic(child, bDynamic);
1665 child = child->next;
1670 * Frees memory for subexpressions that are no longer needed.
1672 * \param sel Selection subtree to check.
1674 * Checks whether the subtree rooted at \p sel refers to any \ref SEL_SUBEXPR
1675 * elements that are not referred to by anything else except their own root
1676 * element. If such elements are found, all memory allocated for them is freed
1677 * except the actual element. The element is left because otherwise a dangling
1678 * pointer would be left at the root element, which is not traversed by this
1679 * function. Later compilation passes remove the stub elements.
1682 release_subexpr_memory(const SelectionTreeElementPointer &sel)
1684 if (sel->type == SEL_SUBEXPRREF)
1686 const SelectionTreeElementPointer &subexpr = sel->child;
1687 if (subexpr.use_count() == 2)
1689 release_subexpr_memory(subexpr);
1691 subexpr->child.reset();
1692 subexpr->freeValues();
1693 subexpr->freeExpressionData();
1694 subexpr->freeCompilerData();
1699 SelectionTreeElementPointer child = sel->child;
1702 release_subexpr_memory(child);
1703 child = child->next;
1709 * Makes an evaluated selection element static.
1711 * \param sel Selection element to make static.
1713 * The evaluated value becomes the value of the static element.
1714 * The element type is changed to SEL_CONST and the children are
1718 make_static(const SelectionTreeElementPointer &sel)
1720 /* If this is a subexpression reference and the data is stored in the
1721 * child, we transfer data ownership before doing anything else. */
1722 if (sel->type == SEL_SUBEXPRREF
1723 && (sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR))
1725 if (sel->child->child->flags & SEL_ALLOCDATA)
1727 sel->flags |= SEL_ALLOCDATA;
1728 sel->child->child->flags &= ~SEL_ALLOCDATA;
1730 if (sel->child->child->flags & SEL_ALLOCVAL)
1732 sel->flags |= SEL_ALLOCVAL;
1733 sel->v.nalloc = sel->child->child->v.nalloc;
1734 sel->child->child->flags &= ~SEL_ALLOCVAL;
1735 sel->child->child->v.nalloc = -1;
1738 /* Free the children. */
1739 release_subexpr_memory(sel);
1741 /* Free the expression data as it is no longer needed */
1742 sel->freeExpressionData();
1743 /* Make the item static */
1744 sel->type = SEL_CONST;
1745 sel->evaluate = NULL;
1746 sel->cdata->evaluate = NULL;
1747 /* Set the group value.
1748 * freeExpressionData() frees the cgrp group, so we can just override it.
1750 if (sel->v.type == GROUP_VALUE)
1752 gmx_ana_index_set(&sel->u.cgrp, sel->v.u.g->isize, sel->v.u.g->index, 0);
1757 * Evaluates a constant expression during analyze_static().
1759 * \param[in] data Evaluation data.
1760 * \param[in,out] sel Selection to process.
1761 * \param[in] g The evaluation group.
1762 * \returns 0 on success, a non-zero error code on error.
1765 process_const(gmx_sel_evaluate_t *data,
1766 const SelectionTreeElementPointer &sel,
1769 if (sel->v.type == GROUP_VALUE)
1771 if (sel->cdata->evaluate)
1773 sel->cdata->evaluate(data, sel, g);
1776 /* Other constant expressions do not need evaluation */
1780 * Sets the parameter value pointer for \ref SEL_SUBEXPRREF params.
1782 * \param[in,out] sel Selection to process.
1784 * Copies the value pointer of \p sel to \c sel->u.param if one is present
1785 * and should receive the value from the compiler
1786 * (most parameter values are handled during parsing).
1787 * If \p sel is not of type \ref SEL_SUBEXPRREF, or if \c sel->u.param is NULL,
1788 * the function does nothing.
1789 * Also, if the \c sel->u.param does not have \ref SPAR_VARNUM or
1790 * \ref SPAR_ATOMVAL, the function returns immediately.
1793 store_param_val(const SelectionTreeElementPointer &sel)
1795 /* Return immediately if there is no parameter. */
1796 if (sel->type != SEL_SUBEXPRREF || !sel->u.param)
1801 /* Or if the value does not need storing. */
1802 if (!(sel->u.param->flags & (SPAR_VARNUM | SPAR_ATOMVAL)))
1807 if (sel->v.type == INT_VALUE || sel->v.type == REAL_VALUE
1808 || sel->v.type == STR_VALUE)
1810 _gmx_selvalue_setstore(&sel->u.param->val, sel->v.u.ptr);
1815 * Handles the initialization of a selection method during analyze_static() pass.
1817 * \param[in,out] sel Selection element to process.
1818 * \param[in] top Topology structure.
1819 * \param[in] isize Size of the evaluation group for the element.
1820 * \returns 0 on success, a non-zero error code on return.
1822 * Calls sel_initfunc() (and possibly sel_outinitfunc()) to initialize the
1824 * If no \ref SPAR_ATOMVAL parameters are present, multiple initialization
1825 * is prevented by using \ref SEL_METHODINIT and \ref SEL_OUTINIT flags.
1828 init_method(const SelectionTreeElementPointer &sel, t_topology *top, int isize)
1830 /* Find out whether there are any atom-valued parameters */
1831 bool bAtomVal = false;
1832 SelectionTreeElementPointer child = sel->child;
1835 if (child->flags & SEL_ATOMVAL)
1839 child = child->next;
1842 /* Initialize the method */
1843 if (sel->u.expr.method->init
1844 && (bAtomVal || !(sel->flags & SEL_METHODINIT)))
1846 sel->flags |= SEL_METHODINIT;
1847 sel->u.expr.method->init(top, sel->u.expr.method->nparams,
1848 sel->u.expr.method->param, sel->u.expr.mdata);
1850 if (bAtomVal || !(sel->flags & SEL_OUTINIT))
1852 sel->flags |= SEL_OUTINIT;
1853 if (sel->u.expr.method->outinit)
1855 sel->u.expr.method->outinit(top, &sel->v, sel->u.expr.mdata);
1856 if (sel->v.type != POS_VALUE && sel->v.type != GROUP_VALUE
1857 && !(sel->flags & SEL_VARNUMVAL))
1859 alloc_selection_data(sel, isize, true);
1864 GMX_RELEASE_ASSERT(sel->v.type != POS_VALUE,
1865 "Output initialization must be provided for "
1866 "position-valued selection methods");
1867 GMX_RELEASE_ASSERT(!(sel->flags & SEL_VARNUMVAL),
1868 "Output initialization must be provided for "
1869 "SMETH_VARNUMVAL selection methods");
1870 alloc_selection_data(sel, isize, true);
1871 if ((sel->flags & SEL_DYNAMIC)
1872 && sel->v.type != GROUP_VALUE && sel->v.type != POS_VALUE)
1876 /* If the method is char-valued, pre-allocate the strings. */
1877 if (sel->u.expr.method->flags & SMETH_CHARVAL)
1881 /* A sanity check */
1882 if (sel->v.type != STR_VALUE)
1884 GMX_THROW(gmx::InternalError("Char-valued selection method in non-string element"));
1886 sel->flags |= SEL_ALLOCDATA;
1887 for (i = 0; i < isize; ++i)
1889 if (sel->v.u.s[i] == NULL)
1891 snew(sel->v.u.s[i], 2);
1896 /* Clear the values for dynamic output to avoid valgrind warnings. */
1897 if ((sel->flags & SEL_DYNAMIC) && sel->v.type == REAL_VALUE)
1901 for (i = 0; i < sel->v.nr; ++i)
1903 sel->v.u.r[i] = 0.0;
1910 * Evaluates the static part of a boolean expression.
1912 * \param[in] data Evaluation data.
1913 * \param[in,out] sel Boolean selection element whose children should be
1915 * \param[in] g The evaluation group.
1916 * \returns 0 on success, a non-zero error code on error.
1918 * reorder_item_static_children() should have been called.
1921 evaluate_boolean_static_part(gmx_sel_evaluate_t *data,
1922 const SelectionTreeElementPointer &sel,
1925 /* Find the last static subexpression */
1926 SelectionTreeElementPointer child = sel->child;
1927 while (child->next && (child->next->cdata->flags & SEL_CDATA_STATIC))
1929 child = child->next;
1931 if (!(child->cdata->flags & SEL_CDATA_STATIC))
1936 /* Evalute the static part if there is more than one expression */
1937 if (child != sel->child)
1939 SelectionTreeElementPointer next = child->next;
1940 child->next.reset();
1941 sel->cdata->evaluate(data, sel, g);
1942 /* Replace the subexpressions with the result */
1943 child.reset(new SelectionTreeElement(SEL_CONST));
1944 child->flags = SEL_FLAGSSET | SEL_SINGLEVAL | SEL_ALLOCVAL | SEL_ALLOCDATA;
1945 _gmx_selelem_set_vtype(child, GROUP_VALUE);
1946 child->evaluate = NULL;
1947 _gmx_selvalue_reserve(&child->v, 1);
1948 gmx_ana_index_copy(child->v.u.g, sel->v.u.g, true);
1949 init_item_compilerdata(child);
1950 init_item_minmax_groups(child);
1951 child->cdata->flags &= ~SEL_CDATA_STATICEVAL;
1952 child->cdata->flags |= sel->cdata->flags & SEL_CDATA_STATICEVAL;
1954 // Frees the old static subexpressions.
1957 else if (child->evaluate)
1959 child->evaluate(data, child, g);
1961 /* Set the evaluation function for the constant element.
1962 * We never need to evaluate the element again during compilation,
1963 * but we may need to evaluate the static part again if the
1964 * expression is not an OR with a static evaluation group.
1965 * If we reach here with a NOT expression, the NOT expression
1966 * is also static, and will be made a constant later, so don't waste
1967 * time copying the group. */
1968 child->evaluate = NULL;
1969 if (sel->u.boolt == BOOL_NOT
1970 || ((sel->cdata->flags & SEL_CDATA_STATICEVAL)
1971 && sel->u.boolt == BOOL_OR))
1973 child->cdata->evaluate = NULL;
1977 child->cdata->evaluate = &_gmx_sel_evaluate_static;
1978 /* The cgrp has only been allocated if it originated from an
1979 * external index group.
1980 * If cgrp has been set in make_static(), it is not allocated,
1981 * and hence we can overwrite it safely. */
1982 if (child->u.cgrp.nalloc_index > 0)
1984 gmx_ana_index_copy(&child->u.cgrp, child->v.u.g, false);
1985 gmx_ana_index_squeeze(&child->u.cgrp);
1989 gmx_ana_index_copy(&child->u.cgrp, child->v.u.g, true);
1995 * Evaluates the minimum and maximum groups for a boolean expression.
1997 * \param[in] sel \ref SEL_BOOLEAN element currently being evaluated.
1998 * \param[in] g Group for which \p sel has been evaluated.
1999 * \param[out] gmin Largest subset of the possible values of \p sel.
2000 * \param[out] gmax Smallest superset of the possible values of \p sel.
2002 * This is a helper function for analyze_static() that is called for
2003 * dynamic \ref SEL_BOOLEAN elements after they have been evaluated.
2004 * It uses the minimum and maximum groups of the children to calculate
2005 * the minimum and maximum groups for \p sel, and also updates the static
2006 * part of \p sel (which is in the first child) if the children give
2009 * This function may allocate some extra memory for \p gmin and \p gmax,
2010 * but as these groups are freed at the end of analyze_static() (which is
2011 * reached shortly after this function returns), this should not be a major
2015 evaluate_boolean_minmax_grps(const SelectionTreeElementPointer &sel,
2017 gmx_ana_index_t *gmin, gmx_ana_index_t *gmax)
2019 SelectionTreeElementPointer child;
2021 switch (sel->u.boolt)
2024 gmx_ana_index_reserve(gmin, g->isize);
2025 gmx_ana_index_reserve(gmax, g->isize);
2026 gmx_ana_index_difference(gmax, g, sel->child->cdata->gmin);
2027 gmx_ana_index_difference(gmin, g, sel->child->cdata->gmax);
2031 gmx_ana_index_copy(gmin, sel->child->cdata->gmin, true);
2032 gmx_ana_index_copy(gmax, sel->child->cdata->gmax, true);
2033 child = sel->child->next;
2034 while (child && gmax->isize > 0)
2036 gmx_ana_index_intersection(gmin, gmin, child->cdata->gmin);
2037 gmx_ana_index_intersection(gmax, gmax, child->cdata->gmax);
2038 child = child->next;
2040 /* Update the static part if other expressions limit it */
2041 if ((sel->child->cdata->flags & SEL_CDATA_STATIC)
2042 && sel->child->v.u.g->isize > gmax->isize)
2044 gmx_ana_index_copy(sel->child->v.u.g, gmax, false);
2045 gmx_ana_index_squeeze(sel->child->v.u.g);
2046 if (sel->child->u.cgrp.isize > 0)
2048 gmx_ana_index_copy(&sel->child->u.cgrp, gmax, false);
2049 gmx_ana_index_squeeze(&sel->child->u.cgrp);
2055 /* We can assume here that the gmin of children do not overlap
2056 * because of the way _gmx_sel_evaluate_or() works. */
2057 gmx_ana_index_reserve(gmin, g->isize);
2058 gmx_ana_index_reserve(gmax, g->isize);
2059 gmx_ana_index_copy(gmin, sel->child->cdata->gmin, false);
2060 gmx_ana_index_copy(gmax, sel->child->cdata->gmax, false);
2061 child = sel->child->next;
2062 while (child && gmin->isize < g->isize)
2064 gmx_ana_index_merge(gmin, gmin, child->cdata->gmin);
2065 gmx_ana_index_union(gmax, gmax, child->cdata->gmax);
2066 child = child->next;
2068 /* Update the static part if other expressions have static parts
2069 * that are not included. */
2070 if ((sel->child->cdata->flags & SEL_CDATA_STATIC)
2071 && sel->child->v.u.g->isize < gmin->isize)
2073 GMX_RELEASE_ASSERT(sel->child->type == SEL_CONST,
2074 "The first child should have already been evaluated "
2075 "to a constant expression");
2076 gmx_ana_index_reserve(sel->child->v.u.g, gmin->isize);
2077 gmx_ana_index_copy(sel->child->v.u.g, gmin, false);
2078 if (sel->child->u.cgrp.nalloc_index > 0)
2080 gmx_ana_index_reserve(&sel->child->u.cgrp, gmin->isize);
2081 gmx_ana_index_copy(&sel->child->u.cgrp, gmin, false);
2085 GMX_RELEASE_ASSERT(sel->child->u.cgrp.index == sel->child->v.u.g->index,
2086 "If not allocated, the static group should equal the value");
2087 sel->child->u.cgrp.isize = sel->child->v.u.g->isize;
2092 case BOOL_XOR: /* Should not be reached */
2093 GMX_THROW(gmx::NotImplementedError("xor expressions not implemented"));
2099 * Evaluates the static parts of \p sel and analyzes the structure.
2101 * \param[in] data Evaluation data.
2102 * \param[in,out] sel Selection currently being evaluated.
2103 * \param[in] g Group for which \p sel should be evaluated.
2104 * \returns 0 on success, a non-zero error code on error.
2106 * This function is used as the replacement for the
2107 * gmx::SelectionTreeElement::evaluate function pointer.
2108 * It does the single most complex task in the compiler: after all elements
2109 * have been processed, the \p gmin and \p gmax fields of \p t_compiler_data
2110 * have been properly initialized, enough memory has been allocated for
2111 * storing the value of each expression, and the static parts of the
2112 * expressions have been evaluated.
2113 * The above is exactly true only for elements other than subexpressions:
2114 * another pass is required for subexpressions that are referred to more than
2115 * once and whose evaluation group is not known in advance.
2118 analyze_static(gmx_sel_evaluate_t *data,
2119 const SelectionTreeElementPointer &sel,
2124 if (sel->type != SEL_ROOT && g)
2126 alloc_selection_data(sel, g->isize, false);
2129 bDoMinMax = (sel->cdata->flags & SEL_CDATA_DOMINMAX);
2130 if (sel->type != SEL_SUBEXPR && bDoMinMax)
2132 gmx_ana_index_deinit(sel->cdata->gmin);
2133 gmx_ana_index_deinit(sel->cdata->gmax);
2136 /* TODO: This switch is awfully long... */
2140 process_const(data, sel, g);
2143 case SEL_EXPRESSION:
2145 _gmx_sel_evaluate_method_params(data, sel, g);
2146 init_method(sel, data->top, g ? g->isize : 0);
2147 if (!(sel->flags & SEL_DYNAMIC))
2149 sel->cdata->evaluate(data, sel, g);
2150 if (sel->cdata->flags & SEL_CDATA_STATIC)
2157 /* Modifiers need to be evaluated even though they process
2158 * positions to get the modified output groups from the
2159 * maximum possible selections. */
2160 if (sel->type == SEL_MODIFIER)
2162 sel->cdata->evaluate(data, sel, g);
2166 gmx_ana_index_copy(sel->cdata->gmax, g, true);
2172 if (!(sel->flags & SEL_DYNAMIC))
2174 sel->cdata->evaluate(data, sel, g);
2175 if (sel->cdata->flags & SEL_CDATA_STATIC)
2182 /* Evalute the static part if there is more than one expression */
2183 evaluate_boolean_static_part(data, sel, g);
2185 /* Evaluate the selection.
2186 * If the type is boolean, we must explicitly handle the
2187 * static part evaluated in evaluate_boolean_static_part()
2188 * here because g may be larger. */
2189 if (sel->u.boolt == BOOL_AND && sel->child->type == SEL_CONST)
2191 sel->cdata->evaluate(data, sel, sel->child->v.u.g);
2195 sel->cdata->evaluate(data, sel, g);
2198 /* Evaluate minimal and maximal selections */
2199 evaluate_boolean_minmax_grps(sel, g, sel->cdata->gmin,
2204 case SEL_ARITHMETIC:
2205 sel->cdata->evaluate(data, sel, g);
2206 if (!(sel->flags & SEL_DYNAMIC))
2208 if (sel->cdata->flags & SEL_CDATA_STATIC)
2215 gmx_ana_index_copy(sel->cdata->gmax, g, true);
2220 sel->cdata->evaluate(data, sel, g);
2224 if (((sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR) &&
2225 !(sel->cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR))
2226 || (sel->cdata->flags & SEL_CDATA_FULLEVAL))
2228 sel->cdata->evaluate(data, sel, g);
2229 _gmx_selvalue_setstore(&sel->v, sel->child->v.u.ptr);
2231 else if (sel->u.cgrp.isize == 0)
2233 GMX_ASSERT(g, "group cannot be null");
2234 gmx_ana_index_reserve(&sel->u.cgrp, g->isize);
2235 sel->cdata->evaluate(data, sel, g);
2238 gmx_ana_index_copy(sel->cdata->gmin, sel->child->cdata->gmin, true);
2239 gmx_ana_index_copy(sel->cdata->gmax, sel->child->cdata->gmax, true);
2244 int isize = gmx_ana_index_difference_size(g, &sel->u.cgrp);
2247 isize += sel->u.cgrp.isize;
2248 gmx_ana_index_reserve(&sel->u.cgrp, isize);
2249 alloc_selection_data(sel, isize, false);
2251 sel->cdata->evaluate(data, sel, g);
2252 if (isize > 0 && bDoMinMax)
2254 gmx_ana_index_reserve(sel->cdata->gmin,
2255 sel->cdata->gmin->isize
2256 + sel->child->cdata->gmin->isize);
2257 gmx_ana_index_reserve(sel->cdata->gmax,
2258 sel->cdata->gmax->isize
2259 + sel->child->cdata->gmax->isize);
2260 gmx_ana_index_merge(sel->cdata->gmin, sel->cdata->gmin,
2261 sel->child->cdata->gmin);
2262 gmx_ana_index_merge(sel->cdata->gmax, sel->cdata->gmax,
2263 sel->child->cdata->gmax);
2268 case SEL_SUBEXPRREF:
2269 if (!g && !(sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR))
2271 /* The subexpression should have been evaluated if g is NULL
2272 * (i.e., this is a method parameter or a direct value of a
2274 if (sel->v.type == POS_VALUE)
2276 alloc_selection_pos_data(sel);
2280 alloc_selection_data(sel, sel->child->cdata->gmax->isize, true);
2283 sel->cdata->evaluate(data, sel, g);
2284 if ((sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
2285 && (sel->child->child->flags & SEL_ALLOCVAL))
2287 _gmx_selvalue_setstore(&sel->v, sel->child->child->v.u.ptr);
2289 /* Store the parameter value if required */
2290 store_param_val(sel);
2291 if (!(sel->flags & SEL_DYNAMIC))
2293 if (sel->cdata->flags & SEL_CDATA_STATIC)
2300 if ((sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR) || !g)
2302 gmx_ana_index_copy(sel->cdata->gmin, sel->child->cdata->gmin, true);
2303 gmx_ana_index_copy(sel->cdata->gmax, sel->child->cdata->gmax, true);
2307 gmx_ana_index_reserve(sel->cdata->gmin,
2308 min(g->isize, sel->child->cdata->gmin->isize));
2309 gmx_ana_index_reserve(sel->cdata->gmax,
2310 min(g->isize, sel->child->cdata->gmax->isize));
2311 gmx_ana_index_intersection(sel->cdata->gmin,
2312 sel->child->cdata->gmin, g);
2313 gmx_ana_index_intersection(sel->cdata->gmax,
2314 sel->child->cdata->gmax, g);
2319 case SEL_GROUPREF: /* Should not be reached */
2320 GMX_THROW(gmx::APIError("Unresolved group reference in compilation"));
2323 /* Update the minimal and maximal evaluation groups */
2326 gmx_ana_index_squeeze(sel->cdata->gmin);
2327 gmx_ana_index_squeeze(sel->cdata->gmax);
2330 /* Replace the result of the evaluation */
2331 /* This is not necessary for subexpressions or for boolean negations
2332 * because the evaluation function already has done it properly. */
2333 if (sel->v.type == GROUP_VALUE && (sel->flags & SEL_DYNAMIC)
2334 && sel->type != SEL_SUBEXPR
2335 && !(sel->type == SEL_BOOLEAN && sel->u.boolt == BOOL_NOT))
2337 if (sel->cdata->flags & SEL_CDATA_EVALMAX)
2339 gmx_ana_index_copy(sel->v.u.g, sel->cdata->gmax, false);
2343 gmx_ana_index_copy(sel->v.u.g, sel->cdata->gmin, false);
2349 /********************************************************************
2350 * EVALUATION GROUP INITIALIZATION
2351 ********************************************************************/
2354 * Initializes the evaluation group for a \ref SEL_ROOT element.
2356 * \param root Root element to initialize.
2357 * \param[in] gall Group of all atoms.
2359 * Checks whether it is necessary to evaluate anything through the root
2360 * element, and either clears the evaluation function or initializes the
2364 init_root_item(const SelectionTreeElementPointer &root,
2365 gmx_ana_index_t *gall)
2367 const SelectionTreeElementPointer &expr = root->child;
2368 /* Subexpressions with non-static evaluation group should not be
2369 * evaluated by the root, and neither should be single-reference
2370 * subexpressions that don't evaluate for all atoms. */
2371 if (expr->type == SEL_SUBEXPR
2372 && (!(root->child->cdata->flags & SEL_CDATA_STATICEVAL)
2373 || ((root->child->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
2374 && !(root->child->cdata->flags & SEL_CDATA_FULLEVAL))))
2376 root->evaluate = NULL;
2379 root->cdata->evaluate = NULL;
2383 /* Set the evaluation group */
2386 /* Non-atom-valued non-group expressions don't care about the group, so
2387 * don't allocate any memory for it. */
2388 if ((expr->flags & SEL_VARNUMVAL)
2389 || ((expr->flags & SEL_SINGLEVAL) && expr->v.type != GROUP_VALUE))
2391 gmx_ana_index_set(&root->u.cgrp, -1, NULL, 0);
2393 else if (expr->cdata->gmax->isize == gall->isize)
2395 /* Save some memory by only referring to the global group. */
2396 gmx_ana_index_set(&root->u.cgrp, gall->isize, gall->index, 0);
2400 gmx_ana_index_copy(&root->u.cgrp, expr->cdata->gmax, true);
2402 /* For selections, store the maximum group for
2403 * gmx_ana_selcollection_evaluate_fin() as the value of the root
2404 * element (unused otherwise). */
2405 if (expr->type != SEL_SUBEXPR && expr->v.u.p->m.mapb.a != NULL)
2407 SelectionTreeElementPointer child = expr;
2409 /* TODO: This code is copied from parsetree.c; it would be better
2410 * to have this hardcoded only in one place. */
2411 while (child->type == SEL_MODIFIER)
2413 child = child->child;
2414 if (child->type == SEL_SUBEXPRREF)
2416 child = child->child->child;
2419 if (child->type == SEL_SUBEXPRREF)
2421 child = child->child->child;
2423 if (child->child->flags & SEL_DYNAMIC)
2426 gmx_ana_index_set(&g, expr->v.u.p->m.mapb.nra, expr->v.u.p->m.mapb.a, 0);
2427 _gmx_selelem_set_vtype(root, GROUP_VALUE);
2428 root->flags |= (SEL_ALLOCVAL | SEL_ALLOCDATA);
2429 _gmx_selvalue_reserve(&root->v, 1);
2430 gmx_ana_index_copy(root->v.u.g, &g, true);
2436 gmx_ana_index_clear(&root->u.cgrp);
2441 /********************************************************************
2442 * REQUIRED ATOMS ANALYSIS
2443 ********************************************************************/
2446 * Finds the highest atom index required to evaluate a selection subtree.
2448 * \param[in] sel Root of the selection subtree to process.
2449 * \param[in,out] maxAtomIndex The highest atom index required to evaluate the
2450 * subtree. The existing value is never decreased, so multiple calls with
2451 * the same parameter will compute the maximum over several subtrees.
2453 * For evaluation that starts from a \ref SEL_ROOT element with a fixed group,
2454 * children will never extend the evaluation group except for method parameter
2455 * evaluation (which have their own root element), so it is sufficient to check
2456 * the root. However, children of \ref SEL_EXPRESSION elements (i.e., the
2457 * method parameters) may have been independently evaluated to a static group
2458 * that no longer has a separate root, so those need to be checked as well.
2460 * Position calculations are not considered here, but are analyzed through the
2461 * position calculation collection in the main compilation method.
2464 init_required_atoms(const SelectionTreeElementPointer &sel, int *maxAtomIndex)
2466 // Process children.
2467 if (sel->type != SEL_SUBEXPRREF)
2469 SelectionTreeElementPointer child = sel->child;
2472 init_required_atoms(child, maxAtomIndex);
2473 child = child->next;
2477 if (sel->type == SEL_ROOT
2478 || (sel->type == SEL_CONST && sel->v.type == GROUP_VALUE))
2480 if (sel->u.cgrp.isize > 0)
2483 std::max(*maxAtomIndex, gmx_ana_index_get_max_index(&sel->u.cgrp));
2489 /********************************************************************
2490 * FINAL SUBEXPRESSION OPTIMIZATION
2491 ********************************************************************/
2494 * Optimizes subexpression evaluation.
2496 * \param sel Root of the selection subtree to process.
2498 * Optimizes away some unnecessary evaluation of subexpressions that are only
2502 postprocess_item_subexpressions(const SelectionTreeElementPointer &sel)
2504 GMX_ASSERT(!(sel->child == NULL &&
2505 (sel->type == SEL_SUBEXPRREF || sel->type == SEL_SUBEXPR)),
2506 "Subexpression elements should always have a child element");
2508 /* Process children. */
2509 if (sel->type != SEL_SUBEXPRREF)
2511 SelectionTreeElementPointer child = sel->child;
2514 postprocess_item_subexpressions(child);
2515 child = child->next;
2519 /* Replace the evaluation function of statically evaluated subexpressions
2520 * for which the static group was not known in advance. */
2521 if (sel->type == SEL_SUBEXPR && sel->cdata->refcount > 1
2522 && (sel->cdata->flags & SEL_CDATA_STATICEVAL)
2523 && !(sel->cdata->flags & SEL_CDATA_FULLEVAL))
2525 /* We need to free memory allocated for the group, because it is no
2526 * longer needed (and would be lost on next call to the evaluation
2528 gmx_ana_index_deinit(&sel->u.cgrp);
2530 sel->evaluate = &_gmx_sel_evaluate_subexpr_staticeval;
2531 sel->cdata->evaluate = sel->evaluate;
2533 sel->child->freeValues();
2534 sel->child->mempool = NULL;
2535 _gmx_selvalue_setstore(&sel->child->v, sel->v.u.ptr);
2536 sel->child->flags &= ~(SEL_ALLOCVAL | SEL_ALLOCDATA);
2539 /* Adjust memory allocation flags for subexpressions that are used only
2540 * once. This is not strictly necessary, but we do it to have the memory
2541 * managed consistently for all types of subexpressions. */
2542 if (sel->type == SEL_SUBEXPRREF
2543 && (sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR))
2545 if (sel->child->child->flags & SEL_ALLOCVAL)
2547 sel->flags |= SEL_ALLOCVAL;
2548 sel->flags |= (sel->child->child->flags & SEL_ALLOCDATA);
2549 sel->v.nalloc = sel->child->child->v.nalloc;
2550 sel->child->child->flags &= ~(SEL_ALLOCVAL | SEL_ALLOCDATA);
2551 sel->child->child->v.nalloc = -1;
2555 /* Do the same for subexpressions that are evaluated at once for all atoms. */
2556 if (sel->type == SEL_SUBEXPR
2557 && !(sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
2558 && (sel->cdata->flags & SEL_CDATA_FULLEVAL))
2560 sel->flags |= SEL_ALLOCVAL;
2561 sel->flags |= (sel->child->flags & SEL_ALLOCDATA);
2562 sel->v.nalloc = sel->child->v.nalloc;
2563 sel->child->flags &= ~(SEL_ALLOCVAL | SEL_ALLOCDATA);
2564 sel->child->v.nalloc = -1;
2567 /* For static subexpressions with a dynamic evaluation group, there is
2568 * no need to evaluate them again, as the SEL_SUBEXPRREF takes care of
2569 * everything during evaluation. */
2570 if (sel->type == SEL_SUBEXPR
2571 && (sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
2572 && (sel->cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR))
2574 sel->evaluate = NULL;
2575 sel->cdata->evaluate = NULL;
2580 /********************************************************************
2581 * COM CALCULATION INITIALIZATION
2582 ********************************************************************/
2585 * Initializes COM/COG calculation for method expressions that require it.
2587 * \param sel Selection subtree to process.
2588 * \param[in,out] pcc Position calculation collection to use.
2589 * \param[in] type Default position calculation type.
2590 * \param[in] flags Flags for default position calculation.
2592 * Searches recursively through the selection tree for dynamic
2593 * \ref SEL_EXPRESSION elements that define the \c gmx_ana_selmethod_t::pupdate
2595 * For each such element found, position calculation is initialized
2596 * for the maximal evaluation group.
2597 * The type of the calculation is determined by \p type and \p flags.
2598 * No calculation is initialized if \p type equals \ref POS_ATOM and
2599 * the method also defines the \c gmx_ana_selmethod_t::update method.
2602 init_item_comg(const SelectionTreeElementPointer &sel,
2603 gmx::PositionCalculationCollection *pcc,
2604 e_poscalc_t type, int flags)
2606 /* Initialize COM calculation for dynamic selections now that we know the maximal evaluation group */
2607 if (sel->type == SEL_EXPRESSION && sel->u.expr.method
2608 && sel->u.expr.method->pupdate)
2610 if (!sel->u.expr.method->update || type != POS_ATOM)
2612 /* Create a default calculation if one does not yet exist */
2614 if (!(sel->cdata->flags & SEL_CDATA_STATICEVAL))
2616 cflags |= POS_DYNAMIC;
2618 if (!sel->u.expr.pc)
2621 sel->u.expr.pc = pcc->createCalculation(type, cflags);
2625 gmx_ana_poscalc_set_flags(sel->u.expr.pc, cflags);
2627 gmx_ana_poscalc_set_maxindex(sel->u.expr.pc, sel->cdata->gmax);
2628 sel->u.expr.pos = new gmx_ana_pos_t();
2629 gmx_ana_poscalc_init_pos(sel->u.expr.pc, sel->u.expr.pos);
2633 /* Call recursively for all children unless the children have already been processed */
2634 if (sel->type != SEL_SUBEXPRREF)
2636 SelectionTreeElementPointer child = sel->child;
2639 init_item_comg(child, pcc, type, flags);
2640 child = child->next;
2646 /********************************************************************
2647 * COMPILER DATA FREEING
2648 ********************************************************************/
2651 * Frees the allocated compiler data recursively.
2653 * \param sel Root of the selection subtree to process.
2655 * Frees the data allocated for the compilation process.
2658 free_item_compilerdata(const SelectionTreeElementPointer &sel)
2660 /* Free compilation data */
2661 sel->freeCompilerData();
2663 /* Call recursively for all children unless the children have already been processed */
2664 if (sel->type != SEL_SUBEXPRREF)
2666 SelectionTreeElementPointer child = sel->child;
2669 free_item_compilerdata(child);
2670 child = child->next;
2676 /********************************************************************
2677 * MAIN COMPILATION FUNCTION
2678 ********************************************************************/
2683 SelectionCompiler::SelectionCompiler()
2688 * \param[in,out] coll Selection collection to be compiled.
2689 * \returns 0 on successful compilation, a non-zero error code on error.
2691 * Before compilation, the selection collection should have been initialized
2692 * with gmx_ana_selcollection_parse_*().
2693 * The compiled selection collection can be passed to
2694 * gmx_ana_selcollection_evaluate() to evaluate the selection for a frame.
2695 * If an error occurs, \p sc is cleared.
2697 * The covered fraction information in \p sc is initialized to
2701 SelectionCompiler::compile(SelectionCollection *coll)
2703 gmx_ana_selcollection_t *sc = &coll->impl_->sc_;
2704 gmx_sel_evaluate_t evaldata;
2705 SelectionTreeElementPointer item;
2709 bool bDebug = (coll->impl_->debugLevel_ >= 2
2710 && coll->impl_->debugLevel_ != 3);
2712 /* FIXME: Clean up the collection on exceptions */
2714 sc->mempool = _gmx_sel_mempool_create();
2715 _gmx_sel_evaluate_init(&evaldata, sc->mempool, &sc->gall,
2716 sc->top, NULL, NULL);
2718 /* Clear the symbol table because it is not possible to parse anything
2719 * after compilation, and variable references in the symbol table can
2720 * also mess up the compilation and/or become invalid.
2722 coll->impl_->clearSymbolTable();
2724 /* Loop through selections and initialize position keyword defaults if no
2725 * other value has been provided.
2727 for (i = 0; i < sc->sel.size(); ++i)
2729 gmx::internal::SelectionData &sel = *sc->sel[i];
2730 init_pos_keyword_defaults(&sel.rootElement(),
2731 coll->impl_->spost_.c_str(),
2732 coll->impl_->rpost_.c_str(),
2736 /* Remove any unused variables. */
2737 sc->root = remove_unused_subexpressions(sc->root);
2738 /* Extract subexpressions into separate roots */
2739 sc->root = extract_subexpressions(sc->root);
2741 /* Initialize the evaluation callbacks and process the tree structure
2742 * to conform to the expectations of the callback functions. */
2743 /* Also, initialize and allocate the compiler data structure */
2744 // TODO: Processing the tree in reverse root order would be better,
2745 // as it would make dependency handling easier (all subexpression
2746 // references would be processed before the actual subexpression) and
2747 // could remove the need for most of these extra loops.
2751 /* Process boolean and arithmetic expressions. */
2752 optimize_boolean_expressions(item);
2753 reorder_boolean_static_children(item);
2754 optimize_arithmetic_expressions(item);
2755 /* Initialize the compiler data */
2756 init_item_compilerdata(item);
2759 // Initialize the static evaluation compiler flags.
2760 // Requires the FULLEVAL compiler flag for the whole tree.
2764 init_item_staticeval(item);
2765 init_item_subexpr_refcount(item);
2768 /* Initialize subexpression flags.
2769 * Requires compiler flags for the full tree. */
2773 init_item_subexpr_flags(item);
2776 /* Initialize evaluation.
2777 * Requires subexpression flags. */
2781 init_item_evalfunc(item);
2782 setup_memory_pooling(item, sc->mempool);
2783 init_item_evaloutput(item);
2786 /* Initialize minimum/maximum index groups.
2787 * Requires evaluation output for the full tree. */
2791 init_item_minmax_groups(item);
2794 /* Initialize the evaluation index groups */
2795 initialize_evalgrps(sc);
2799 fprintf(stderr, "\nTree after initial compiler processing:\n");
2800 coll->printTree(stderr, false);
2803 /* Evaluate all static parts of the selection and analyze the tree
2804 * to allocate enough memory to store the value of each dynamic subtree. */
2808 if (item->child->cdata->flags & SEL_CDATA_COMMONSUBEXPR)
2810 mark_subexpr_dynamic(item->child, true);
2812 set_evaluation_function(item, &analyze_static);
2813 item->evaluate(&evaldata, item, NULL);
2817 /* At this point, static subexpressions no longer have references to them,
2818 * so they can be removed. */
2819 sc->root = remove_unused_subexpressions(sc->root);
2820 // Update the reference counts for consistency (only used for the
2821 // debugging output below).
2825 init_item_subexpr_refcount(item);
2831 fprintf(stderr, "\nTree after first analysis pass:\n");
2832 coll->printTree(stderr, false);
2835 /* Do a second pass to evaluate static parts of common subexpressions */
2839 if (item->child->cdata->flags & SEL_CDATA_COMMONSUBEXPR)
2841 bool bMinMax = item->child->cdata->flags & SEL_CDATA_DOMINMAX;
2843 mark_subexpr_dynamic(item->child, false);
2844 item->child->u.cgrp.isize = 0;
2845 /* We won't clear item->child->v.u.g here, because it may
2846 * be static, and hence actually point to item->child->cdata->gmax,
2847 * which is used below. We could also check whether this is the
2848 * case and only clear the group otherwise, but because the value
2849 * is actually overwritten immediately in the evaluate call, we
2850 * won't, because similar problems may arise if gmax handling ever
2851 * changes and the check were not updated.
2852 * For the same reason, we clear the min/max flag so that the
2853 * evaluation group doesn't get messed up. */
2854 set_evaluation_function(item, &analyze_static);
2855 item->child->cdata->flags &= ~SEL_CDATA_DOMINMAX;
2856 item->evaluate(&evaldata, item->child, item->child->cdata->gmax);
2859 item->child->cdata->flags |= SEL_CDATA_DOMINMAX;
2865 /* We need a yet another pass of subexpression removal to remove static
2866 * subexpressions referred to by common dynamic subexpressions. */
2867 sc->root = remove_unused_subexpressions(sc->root);
2868 // Update the reference counts, used by postprocess_item_subexpressions().
2872 init_item_subexpr_refcount(item);
2878 fprintf(stderr, "\nTree after second analysis pass:\n");
2879 coll->printTree(stderr, false);
2882 // Initialize evaluation groups, maximum atom index needed for evaluation,
2883 // position calculations for methods, perform some final optimization, and
2884 // free the memory allocated for the compilation.
2885 coll->impl_->maxAtomIndex_ = 0;
2886 /* By default, use whole residues/molecules. */
2887 flags = POS_COMPLWHOLE;
2888 PositionCalculationCollection::typeFromEnum(coll->impl_->rpost_.c_str(),
2893 init_root_item(item, &sc->gall);
2894 postprocess_item_subexpressions(item);
2895 init_required_atoms(item, &coll->impl_->maxAtomIndex_);
2896 init_item_comg(item, &sc->pcc, post, flags);
2897 free_item_compilerdata(item);
2900 coll->impl_->maxAtomIndex_ =
2901 std::max(coll->impl_->maxAtomIndex_,
2902 sc->pcc.getHighestRequiredAtomIndex());
2904 /* Allocate memory for the evaluation memory pool. */
2905 _gmx_sel_mempool_reserve(sc->mempool, 0);
2907 /* Finish up by calculating total masses and charges. */
2908 for (i = 0; i < sc->sel.size(); ++i)
2910 sc->sel[i]->initializeMassesAndCharges(sc->top);