Bug Summary

File:gromacs/selection/compiler.cpp
Location:line 2235, column 53
Description:Access to field 'isize' results in a dereference of a null pointer (loaded from variable 'g')

Annotated Source Code

1/*
2 * This file is part of the GROMACS molecular simulation package.
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34 */
35/*! \internal \file
36 * \brief Selection compilation and optimization.
37 *
38 * \todo
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.
42 *
43 * \todo
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.
47 *
48 * \author Teemu Murtola <teemu.murtola@gmail.com>
49 * \ingroup module_selection
50 */
51/*! \internal
52 * \page page_module_selection_compiler Selection compilation
53 *
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
58 * functions expect.
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
62 * called.
63 *
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.
71 *
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75 * been replaced by the result of the evaluation.
76 *
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
86 * here.
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
98 * other fields.
99 * -# The gmx::SelectionTreeElement::evaluate field is set to the correct
100 * evaluation function from evaluate.h.
101 * .
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.
135 *
136 * The actual evaluation of the selection is described in the documentation
137 * of the functions in evaluate.h.
138 *
139 * \todo
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.
143 *
144 *
145 * \section selcompiler_tree Element tree after compilation
146 *
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.
152 *
153 *
154 * \subsection selcompiler_tree_root Root elements
155 *
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.
176 *
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.
181 *
182 * Selection names are stored as after parsing (see \ref selparser_tree_root).
183 *
184 *
185 * \subsection selcompiler_tree_const Constant elements
186 *
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.
194 *
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.
199 *
200 * \ref SEL_CONST elements have no children.
201 *
202 *
203 * \subsection selcompiler_tree_method Method evaluation elements
204 *
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
217 * calculated.
218 *
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.
225 *
226 *
227 * \subsection selcompiler_tree_subexpr Subexpression elements
228 *
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
237 * help in debugging.
238 *
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.
244 *
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.
248 *
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.
255 *
256 *
257 * \subsection selcompiler_tree_bool Boolean elements
258 *
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.
264 *
265 *
266 * \subsection selcompiler_tree_arith Arithmetic elements
267 *
268 * Constant and static expressions in \ref SEL_ARITHMETIC elements have been
269 * calculated.
270 * Currently, no other processing is done.
271 */
272#include "compiler.h"
273
274#include <algorithm>
275
276#include <math.h>
277#include <stdarg.h>
278
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"
287
288#include "evaluate.h"
289#include "keywords.h"
290#include "mempool.h"
291#include "selectioncollection-impl.h"
292#include "selelem.h"
293
294using std::min;
295using gmx::SelectionTreeElement;
296using gmx::SelectionTreeElementPointer;
297
298/*! \internal \brief
299 * Compiler flags.
300 */
301enum
302{
303 /*! \brief
304 * Whether a subexpression needs to evaluated for all atoms.
305 *
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.
309 */
310 SEL_CDATA_FULLEVAL = 1,
311 /*! \brief
312 * Whether the whole subexpression should be treated as static.
313 *
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.
316 */
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,
328 /*! \brief
329 * Whether a static subexpression needs to support multiple evaluations.
330 *
331 * This flag may only be set on \ref SEL_SUBEXPR elements that also have
332 * SEL_CDATA_SIMPLESUBEXPR.
333 */
334 SEL_CDATA_STATICMULTIEVALSUBEXPR = 64,
335 /** Whether this expression is a part of a common subexpression. */
336 SEL_CDATA_COMMONSUBEXPR = 128
337};
338
339/*! \internal \brief
340 * Internal data structure used by the compiler.
341 */
342typedef struct t_compiler_data
343{
344 /** The real evaluation method. */
345 gmx::sel_evalfunc evaluate;
346 /** Number of references to a \ref SEL_SUBEXPR element. */
347 int refcount;
348 /** Flags for specifying how to treat this element during compilation. */
349 int flags;
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;
354} t_compiler_data;
355
356
357/********************************************************************
358 * COMPILER UTILITY FUNCTIONS
359 ********************************************************************/
360
361/*! \brief
362 * Helper method for printing out debug information about a min/max group.
363 */
364static void
365print_group_info(FILE *fp, const char *name,
366 const SelectionTreeElement &sel,
367 gmx_ana_index_t *g)
368{
369 fprintf(fp, " %s=", name);
370 if (!g)
371 {
372 fprintf(fp, "(null)");
373 }
374 else if (sel.cdata->flags & SEL_CDATA_MINMAXALLOC)
375 {
376 fprintf(fp, "(%d atoms, %p)", g->isize, (void*)g);
377 }
378 else if (sel.v.type == GROUP_VALUE && g == sel.v.u.g)
379 {
380 fprintf(fp, "(static, %p)", (void*)g);
381 }
382 else
383 {
384 fprintf(fp, "%p", (void*)g);
385 }
386}
387
388/*!
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.
392 */
393void
394_gmx_selelem_print_compiler_info(FILE *fp, const SelectionTreeElement &sel,
395 int level)
396{
397 if (!sel.cdata)
398 {
399 return;
400 }
401 fprintf(fp, "%*c cdata: flg=", level*2+1, ' ');
402 if (sel.cdata->flags & SEL_CDATA_FULLEVAL)
403 {
404 fprintf(fp, "F");
405 }
406 if (!(sel.cdata->flags & SEL_CDATA_STATIC))
407 {
408 fprintf(fp, "D");
409 }
410 if (sel.cdata->flags & SEL_CDATA_STATICEVAL)
411 {
412 fprintf(fp, "S");
413 }
414 if (sel.cdata->flags & SEL_CDATA_EVALMAX)
415 {
416 fprintf(fp, "M");
417 }
418 if (sel.cdata->flags & SEL_CDATA_MINMAXALLOC)
419 {
420 fprintf(fp, "A");
421 }
422 if (sel.cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
423 {
424 fprintf(fp, "Ss");
425 }
426 if (sel.cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR)
427 {
428 fprintf(fp, "Sm");
429 }
430 if (sel.cdata->flags & SEL_CDATA_COMMONSUBEXPR)
431 {
432 fprintf(fp, "Sc");
433 }
434 if (!sel.cdata->flags)
435 {
436 fprintf(fp, "0");
437 }
438 if (sel.cdata->refcount > 0)
439 {
440 fprintf(fp, " refc=%d", sel.cdata->refcount);
441 }
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);
446 fprintf(fp, "\n");
447}
448
449namespace gmx
450{
451
452void SelectionTreeElement::freeCompilerData()
453{
454 if (cdata)
455 {
456 evaluate = cdata->evaluate;
457 if (cdata->flags & SEL_CDATA_MINMAXALLOC)
458 {
459 gmx_ana_index_deinit(cdata->gmin);
460 gmx_ana_index_deinit(cdata->gmax);
461 sfree(cdata->gmin)save_free("cdata->gmin", "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 461, (cdata->gmin));
462 sfree(cdata->gmax)save_free("cdata->gmax", "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 462, (cdata->gmax));
463 }
464 sfree(cdata)save_free("cdata", "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 464, (cdata));
465 }
466 cdata = NULL__null;
467}
468
469} // namespace gmx
470
471/*! \brief
472 * Allocates memory for storing the evaluated value of a selection element.
473 *
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.
477 *
478 * If called more than once, memory is (re)allocated to ensure that the
479 * maximum of the \p isize values can be stored.
480 *
481 * Allocation of POS_VALUE selection elements is a special case, and is
482 * handled by alloc_selection_pos_data().
483 */
484static void
485alloc_selection_data(const SelectionTreeElementPointer &sel,
486 int isize, bool bChildEval)
487{
488 int nalloc;
489
490 GMX_RELEASE_ASSERT(sel->v.type != POS_VALUE,((void) ((sel->v.type != POS_VALUE) ? (void)0 : ::gmx::internal
::assertHandler("sel->v.type != POS_VALUE", "Wrong allocation method called"
, __PRETTY_FUNCTION__, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 491)))
491 "Wrong allocation method called")((void) ((sel->v.type != POS_VALUE) ? (void)0 : ::gmx::internal
::assertHandler("sel->v.type != POS_VALUE", "Wrong allocation method called"
, __PRETTY_FUNCTION__, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 491)));
492 if (sel->mempool)
493 {
494 return;
495 }
496 /* Find out the number of elements to allocate */
497 if (sel->flags & SEL_SINGLEVAL2)
498 {
499 nalloc = 1;
500 }
501 else if (sel->flags & SEL_ATOMVAL4)
502 {
503 nalloc = isize;
504 }
505 else /* sel->flags should contain SEL_VARNUMVAL */
506 {
507 // TODO: Consider whether the bChildEval is any longer necessary.
508 if (!bChildEval)
509 {
510 return;
511 }
512 SelectionTreeElementPointer child = sel;
513 if (sel->type == SEL_SUBEXPRREF)
514 {
515 GMX_RELEASE_ASSERT(sel->child && sel->child->type == SEL_SUBEXPR,((void) ((sel->child && sel->child->type == SEL_SUBEXPR
) ? (void)0 : ::gmx::internal::assertHandler("sel->child && sel->child->type == SEL_SUBEXPR"
, "Subexpression expected for subexpression reference", __PRETTY_FUNCTION__
, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 516)))
516 "Subexpression expected for subexpression reference")((void) ((sel->child && sel->child->type == SEL_SUBEXPR
) ? (void)0 : ::gmx::internal::assertHandler("sel->child && sel->child->type == SEL_SUBEXPR"
, "Subexpression expected for subexpression reference", __PRETTY_FUNCTION__
, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 516)));
517 child = sel->child->child;
518 GMX_RELEASE_ASSERT(child,((void) ((child) ? (void)0 : ::gmx::internal::assertHandler("child"
, "Subexpression elements should always have a child element"
, __PRETTY_FUNCTION__, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 519)))
519 "Subexpression elements should always have a child element")((void) ((child) ? (void)0 : ::gmx::internal::assertHandler("child"
, "Subexpression elements should always have a child element"
, __PRETTY_FUNCTION__, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 519)));
520 }
521 nalloc = child->v.nr;
522 }
523 /* Allocate memory for sel->v.u if needed */
524 if (sel->flags & SEL_ALLOCVAL(1<<8))
525 {
526 _gmx_selvalue_reserve(&sel->v, nalloc);
527 }
528 /* Reserve memory inside group structure if SEL_ALLOCDATA is set. */
529 if ((sel->flags & SEL_ALLOCDATA(1<<9)) && sel->v.type == GROUP_VALUE)
530 {
531 gmx_ana_index_reserve(sel->v.u.g, isize);
532 }
533}
534
535/*! \brief
536 * Allocates memory for storing the evaluated value of a selection element.
537 *
538 * \param sel Selection element to initialize.
539 *
540 * Allocation of POS_VALUE selection elements is a special case, and is
541 * handled by this function instead of by alloc_selection_data().
542 */
543static void
544alloc_selection_pos_data(const SelectionTreeElementPointer &sel)
545{
546 int nalloc, isize;
547
548 GMX_RELEASE_ASSERT(sel->v.type == POS_VALUE,((void) ((sel->v.type == POS_VALUE) ? (void)0 : ::gmx::internal
::assertHandler("sel->v.type == POS_VALUE", "Wrong allocation method called"
, __PRETTY_FUNCTION__, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 549)))
549 "Wrong allocation method called")((void) ((sel->v.type == POS_VALUE) ? (void)0 : ::gmx::internal
::assertHandler("sel->v.type == POS_VALUE", "Wrong allocation method called"
, __PRETTY_FUNCTION__, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 549)));
550 GMX_RELEASE_ASSERT(!(sel->flags & SEL_ATOMVAL),((void) ((!(sel->flags & 4)) ? (void)0 : ::gmx::internal
::assertHandler("!(sel->flags & SEL_ATOMVAL)", "Per-atom evaluated positions not implemented"
, __PRETTY_FUNCTION__, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 551)))
551 "Per-atom evaluated positions not implemented")((void) ((!(sel->flags & 4)) ? (void)0 : ::gmx::internal
::assertHandler("!(sel->flags & SEL_ATOMVAL)", "Per-atom evaluated positions not implemented"
, __PRETTY_FUNCTION__, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 551)));
552 if (sel->mempool)
553 {
554 return;
555 }
556
557 SelectionTreeElementPointer child = sel;
558 if (sel->type == SEL_SUBEXPRREF)
559 {
560 GMX_RELEASE_ASSERT(sel->child && sel->child->type == SEL_SUBEXPR,((void) ((sel->child && sel->child->type == SEL_SUBEXPR
) ? (void)0 : ::gmx::internal::assertHandler("sel->child && sel->child->type == SEL_SUBEXPR"
, "Subexpression expected for subexpression reference", __PRETTY_FUNCTION__
, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 561)))
561 "Subexpression expected for subexpression reference")((void) ((sel->child && sel->child->type == SEL_SUBEXPR
) ? (void)0 : ::gmx::internal::assertHandler("sel->child && sel->child->type == SEL_SUBEXPR"
, "Subexpression expected for subexpression reference", __PRETTY_FUNCTION__
, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 561)));
562 child = sel->child->child;
563 GMX_RELEASE_ASSERT(child,((void) ((child) ? (void)0 : ::gmx::internal::assertHandler("child"
, "Subexpression elements should always have a child element"
, __PRETTY_FUNCTION__, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 564)))
564 "Subexpression elements should always have a child element")((void) ((child) ? (void)0 : ::gmx::internal::assertHandler("child"
, "Subexpression elements should always have a child element"
, __PRETTY_FUNCTION__, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 564)));
565 }
566 nalloc = child->v.u.p->count();
567 isize = child->v.u.p->m.b.nra;
568
569 /* For positions, we want to allocate just a single structure
570 * for nalloc positions. */
571 if (sel->flags & SEL_ALLOCVAL(1<<8))
572 {
573 _gmx_selvalue_reserve(&sel->v, 1);
574 }
575 sel->v.nr = 1;
576 /* Reserve memory inside position structure if SEL_ALLOCDATA is set. */
577 if (sel->flags & SEL_ALLOCDATA(1<<9))
578 {
579 gmx_ana_pos_reserve(sel->v.u.p, nalloc, isize);
580 }
581}
582
583/*! \brief
584 * Replace the evaluation function of each element in the subtree.
585 *
586 * \param sel Root of the selection subtree to process.
587 * \param[in] eval The new evaluation function.
588 */
589static void
590set_evaluation_function(const SelectionTreeElementPointer &sel,
591 gmx::sel_evalfunc eval)
592{
593 sel->evaluate = eval;
594 if (sel->type != SEL_SUBEXPRREF)
595 {
596 SelectionTreeElementPointer child = sel->child;
597 while (child)
598 {
599 set_evaluation_function(child, eval);
600 child = child->next;
601 }
602 }
603}
604
605
606/********************************************************************
607 * POSITION KEYWORD DEFAULT INITIALIZATION
608 ********************************************************************/
609
610/*! \brief
611 * Initializes default values for position keyword evaluation.
612 *
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.
618 */
619static void
620init_pos_keyword_defaults(SelectionTreeElement *root,
621 const char *spost, const char *rpost,
622 const gmx::internal::SelectionData *sel)
623{
624 /* Selections use largest static group by default, while
625 * reference positions use the whole residue/molecule. */
626 if (root->type == SEL_EXPRESSION)
627 {
628 bool bSelection = (sel != NULL__null);
629 int flags = bSelection ? POS_COMPLMAX2 : POS_COMPLWHOLE4;
630 if (bSelection)
631 {
632 if (sel->hasFlag(gmx::efSelection_DynamicMask))
633 {
634 flags |= POS_MASKONLY32;
635 }
636 if (sel->hasFlag(gmx::efSelection_EvaluateVelocities))
637 {
638 flags |= POS_VELOCITIES64;
639 }
640 if (sel->hasFlag(gmx::efSelection_EvaluateForces))
641 {
642 flags |= POS_FORCES128;
643 }
644 }
645 _gmx_selelem_set_kwpos_type(root, bSelection ? spost : rpost);
646 _gmx_selelem_set_kwpos_flags(root, flags);
647 }
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)
651 {
652 sel = NULL__null;
653 }
654 /* Recurse into children */
655 SelectionTreeElementPointer child = root->child;
656 while (child)
657 {
658 init_pos_keyword_defaults(child.get(), spost, rpost, sel);
659 child = child->next;
660 }
661}
662
663
664/********************************************************************
665 * SUBEXPRESSION PROCESSING
666 ********************************************************************/
667
668/*! \brief
669 * Reverses the chain of selection elements starting at \p root.
670 *
671 * \param root First selection in the whole selection chain.
672 * \returns The new first element for the chain.
673 */
674static SelectionTreeElementPointer
675reverse_selelem_chain(const SelectionTreeElementPointer &root)
676{
677 SelectionTreeElementPointer prev;
678 SelectionTreeElementPointer item = root;
679 while (item)
680 {
681 SelectionTreeElementPointer next = item->next;
682 item->next = prev;
683 prev = item;
684 item = next;
685 }
686 return prev;
687}
688
689/*! \brief
690 * Removes subexpressions that don't have any references.
691 *
692 * \param root First selection in the whole selection chain.
693 * \returns The new first element for the chain.
694 *
695 * The elements are processed in reverse order to correctly detect
696 * subexpressions only referred to by other subexpressions.
697 */
698static SelectionTreeElementPointer
699remove_unused_subexpressions(SelectionTreeElementPointer root)
700{
701 if (!root)
702 {
703 return SelectionTreeElementPointer();
704 }
705 root = reverse_selelem_chain(root);
706 while (root->child->type == SEL_SUBEXPR && root->child.unique())
707 {
708 // Frees the root element.
709 root = root->next;
710 }
711 SelectionTreeElementPointer prev = root;
712 SelectionTreeElementPointer item = root->next;
713 while (item)
714 {
715 SelectionTreeElementPointer next = item->next;
716 if (item->child->type == SEL_SUBEXPR && item->child.unique())
717 {
718 // Frees the current item when it goes out of scope.
719 prev->next = next;
720 }
721 else
722 {
723 prev = item;
724 }
725 item = next;
726 }
727 return reverse_selelem_chain(root);
728}
729
730/*! \brief
731 * Creates a name with a running number for a subexpression.
732 *
733 * \param[in,out] sel The subexpression to be named.
734 * \param[in] i Running number for the subexpression.
735 *
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().
741 */
742static void
743create_subexpression_name(const SelectionTreeElementPointer &sel, int i)
744{
745 std::string name(gmx::formatString("SubExpr %d", i));
746 sel->setName(name);
747}
748
749/*! \brief
750 * Processes and extracts subexpressions from a given selection subtree.
751 *
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.
755 *
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.
761 */
762static SelectionTreeElementPointer
763extract_item_subselections(const SelectionTreeElementPointer &sel,
764 int *subexprn)
765{
766 SelectionTreeElementPointer root;
767 SelectionTreeElementPointer subexpr;
768 SelectionTreeElementPointer child = sel->child;
769
770 while (child)
771 {
772 if (!root)
773 {
774 root = subexpr = extract_item_subselections(child, subexprn);
775 }
776 else
777 {
778 subexpr->next = extract_item_subselections(child, subexprn);
779 }
780 while (subexpr && subexpr->next)
781 {
782 subexpr = subexpr->next;
783 }
784 /* The latter check excludes variable references. */
785 if (child->type == SEL_SUBEXPRREF && child->child->type != SEL_SUBEXPR)
786 {
787 /* Create the root element for the subexpression */
788 if (!root)
789 {
790 root.reset(new SelectionTreeElement(SEL_ROOT));
791 subexpr = root;
792 }
793 else
794 {
795 subexpr->next.reset(new SelectionTreeElement(SEL_ROOT));
796 subexpr = subexpr->next;
797 }
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(1 | (2 | 4 | 8) | 16));
807 subexpr->child->flags |= (child->flags & SEL_VALFLAGMASK(1 | (2 | 4 | 8) | 16));
808 }
809 if (child->type == SEL_SUBEXPRREF)
810 {
811 child->setName(child->child->name());
812 }
813 child = child->next;
814 }
815
816 return root;
817}
818
819/*! \brief
820 * Extracts subexpressions of the selection chain.
821 *
822 * \param sel First selection in the whole selection chain.
823 * \returns The new first element for the chain.
824 *
825 * Finds all the subexpressions (and their subexpressions) in the
826 * selection chain starting from \p sel and creates \ref SEL_SUBEXPR
827 * elements for them.
828 * \ref SEL_ROOT elements are also created for each subexpression
829 * and inserted into the selection chain before the expressions that
830 * refer to them.
831 */
832static SelectionTreeElementPointer
833extract_subexpressions(SelectionTreeElementPointer sel)
834{
835 SelectionTreeElementPointer root;
836 SelectionTreeElementPointer next = sel;
837 int subexprn = 0;
838 while (next)
839 {
840 SelectionTreeElementPointer item
841 = extract_item_subselections(next, &subexprn);
842 if (item)
843 {
844 if (!root)
845 {
846 root = item;
847 }
848 else
849 {
850 sel->next = item;
851 }
852 while (item->next)
853 {
854 item = item->next;
855 }
856 item->next = next;
857 }
858 else if (!root)
859 {
860 root = next;
861 }
862 sel = next;
863 next = next->next;
864 }
865 return root;
866}
867
868
869/********************************************************************
870 * BOOLEAN OPERATION REORDERING
871 ********************************************************************/
872
873/*! \brief
874 * Removes redundant boolean selection elements.
875 *
876 * \param sel Root of the selection subtree to optimize.
877 *
878 * This function merges similar boolean operations (e.g., (A or B) or C becomes
879 * a single OR operation with three operands).
880 */
881static void
882optimize_boolean_expressions(const SelectionTreeElementPointer &sel)
883{
884 /* Do recursively for children */
885 if (sel->type != SEL_SUBEXPRREF)
886 {
887 SelectionTreeElementPointer prev;
888 SelectionTreeElementPointer child = sel->child;
889 while (child)
890 {
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)
895 {
896 /* Move the doubly negated expression up two levels */
897 if (!prev)
898 {
899 sel->child = child->child->child;
900 prev = sel->child;
901 }
902 else
903 {
904 prev->next = child->child->child;
905 prev = prev->next;
906 }
907 child->child->child->next = child->next;
908 // Discards the two negations.
909 child = prev;
910 }
911 prev = child;
912 child = child->next;
913 }
914 }
915 if (sel->type != SEL_BOOLEAN || sel->u.boolt == BOOL_NOT)
916 {
917 return;
918 }
919 /* Merge subsequent binary operations */
920 SelectionTreeElementPointer prev;
921 SelectionTreeElementPointer child = sel->child;
922 while (child)
923 {
924 if (child->type == SEL_BOOLEAN && child->u.boolt == sel->u.boolt)
925 {
926 if (!prev)
927 {
928 sel->child = child->child;
929 prev = sel->child;
930 }
931 else
932 {
933 prev->next = child->child;
934 }
935 while (prev->next)
936 {
937 prev = prev->next;
938 }
939 prev->next = child->next;
940 // Discards the old child.
941 child = prev->next;
942 }
943 else
944 {
945 prev = child;
946 child = child->next;
947 }
948 }
949}
950
951/*! \brief
952 * Reorders children of boolean expressions such that static selections
953 * come first.
954 *
955 * \param sel Root of the selection subtree to reorder.
956 *
957 * The relative order of static expressions does not change.
958 * The same is true for the dynamic expressions.
959 */
960static void
961reorder_boolean_static_children(const SelectionTreeElementPointer &sel)
962{
963 /* Do recursively for children */
964 if (sel->type != SEL_SUBEXPRREF)
965 {
966 SelectionTreeElementPointer child = sel->child;
967 while (child)
968 {
969 reorder_boolean_static_children(child);
970 child = child->next;
971 }
972 }
973
974 /* Reorder boolean expressions such that static selections come first */
975 if (sel->type == SEL_BOOLEAN && (sel->flags & SEL_DYNAMIC16))
976 {
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;
983 while (child->next)
984 {
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_DYNAMIC16))
989 {
990 prev = next;
991 next = next->next;
992 }
993 /* next is now the first static expression after child */
994 if (!next)
995 {
996 break;
997 }
998 /* Reorder such that next comes after child */
999 if (prev != child)
1000 {
1001 prev->next = next->next;
1002 next->next = child->next;
1003 child->next = next;
1004 }
1005 else
1006 {
1007 prev = prev->next;
1008 }
1009 /* Advance child by one */
1010 child = next;
1011 }
1012
1013 sel->child = dummy->next;
1014 }
1015}
1016
1017
1018/********************************************************************
1019 * ARITHMETIC EXPRESSION PROCESSING
1020 ********************************************************************/
1021
1022/*! \brief
1023 * Processes arithmetic expressions to simplify and speed up evaluation.
1024 *
1025 * \param sel Root of the selection subtree to process.
1026 *
1027 * Currently, this function only converts integer constants to reals
1028 * within arithmetic expressions.
1029 */
1030static void
1031optimize_arithmetic_expressions(const SelectionTreeElementPointer &sel)
1032{
1033 /* Do recursively for children. */
1034 if (sel->type != SEL_SUBEXPRREF)
1035 {
1036 SelectionTreeElementPointer child = sel->child;
1037 while (child)
1038 {
1039 optimize_arithmetic_expressions(child);
1040 child = child->next;
1041 }
1042 }
1043
1044 if (sel->type != SEL_ARITHMETIC)
1045 {
1046 return;
1047 }
1048
1049 /* Convert integer constants to reals. */
1050 SelectionTreeElementPointer child = sel->child;
1051 while (child)
1052 {
1053 if (child->v.type == INT_VALUE)
1054 {
1055 real *r;
1056
1057 if (child->type != SEL_CONST)
1058 {
1059 GMX_THROW(gmx::InconsistentInputError("Non-constant integer expressions not implemented in arithmetic evaluation"))::boost::exception_detail::throw_exception_((gmx::InconsistentInputError
("Non-constant integer expressions not implemented in arithmetic evaluation"
)),__PRETTY_FUNCTION__,"/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
,1059);
1060 }
1061 snew(r, 1)gmx_snew_impl("r", "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 1061, (r), (1));
1062 r[0] = child->v.u.i[0];
1063 sfree(child->v.u.i)save_free("child->v.u.i", "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 1063, (child->v.u.i));
1064 child->v.u.r = r;
1065 child->v.type = REAL_VALUE;
1066 }
1067 else if (child->v.type != REAL_VALUE)
1068 {
1069 GMX_THROW(gmx::InternalError("Non-numerical value in arithmetic expression"))::boost::exception_detail::throw_exception_((gmx::InternalError
("Non-numerical value in arithmetic expression")),__PRETTY_FUNCTION__
,"/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
,1069);
1070 }
1071 child = child->next;
1072 }
1073}
1074
1075
1076/********************************************************************
1077 * EVALUATION PREPARATION COMPILER
1078 ********************************************************************/
1079
1080/*! \brief
1081 * Sets the evaluation functions for the selection (sub)tree.
1082 *
1083 * \param[in,out] sel Root of the selection subtree to process.
1084 *
1085 * This function sets the evaluation function
1086 * (gmx::SelectionTreeElement::evaluate) for the selection elements.
1087 */
1088static void
1089init_item_evalfunc(const SelectionTreeElementPointer &sel)
1090{
1091 /* Process children. */
1092 if (sel->type != SEL_SUBEXPRREF)
1093 {
1094 SelectionTreeElementPointer child = sel->child;
1095 while (child)
1096 {
1097 init_item_evalfunc(child);
1098 child = child->next;
1099 }
1100 }
1101
1102 /* Set the evaluation function */
1103 switch (sel->type)
1104 {
1105 case SEL_CONST:
1106 if (sel->v.type == GROUP_VALUE)
1107 {
1108 sel->evaluate = &_gmx_sel_evaluate_static;
1109 }
1110 break;
1111
1112 case SEL_EXPRESSION:
1113 if (!(sel->flags & SEL_DYNAMIC16) && sel->u.expr.method
1114 && sel->u.expr.method->init_frame)
1115 {
1116 sel->flags |= SEL_INITFRAME(1<<10);
1117 }
1118 sel->evaluate = &_gmx_sel_evaluate_method;
1119 break;
1120
1121 case SEL_ARITHMETIC:
1122 sel->evaluate = &_gmx_sel_evaluate_arithmetic;
1123 break;
1124
1125 case SEL_MODIFIER:
1126 if (sel->v.type != NO_VALUE)
1127 {
1128 sel->evaluate = &_gmx_sel_evaluate_modifier;
1129 }
1130 break;
1131
1132 case SEL_BOOLEAN:
1133 switch (sel->u.boolt)
1134 {
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;
1138 case BOOL_XOR:
1139 GMX_THROW(gmx::NotImplementedError("xor expressions not implemented"))::boost::exception_detail::throw_exception_((gmx::NotImplementedError
("xor expressions not implemented")),__PRETTY_FUNCTION__,"/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
,1139);
1140 }
1141 break;
1142
1143 case SEL_ROOT:
1144 sel->evaluate = &_gmx_sel_evaluate_root;
1145 break;
1146
1147 case SEL_SUBEXPR:
1148 if ((sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
1149 && !(sel->cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR))
1150 {
1151 sel->evaluate = &_gmx_sel_evaluate_subexpr_simple;
1152 }
1153 else
1154 {
1155 sel->evaluate = &_gmx_sel_evaluate_subexpr;
1156 }
1157 break;
1158
1159 case SEL_SUBEXPRREF:
1160 sel->evaluate = ((sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
1161 ? &_gmx_sel_evaluate_subexprref_simple
1162 : &_gmx_sel_evaluate_subexprref);
1163 break;
1164
1165 case SEL_GROUPREF:
1166 GMX_THROW(gmx::APIError("Unresolved group reference in compilation"))::boost::exception_detail::throw_exception_((gmx::APIError("Unresolved group reference in compilation"
)),__PRETTY_FUNCTION__,"/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
,1166);
1167 }
1168 sel->cdata->evaluate = sel->evaluate;
1169}
1170
1171/*! \brief
1172 * Sets the memory pool for selection elements that can use it.
1173 *
1174 * \param sel Root of the selection subtree to process.
1175 * \param[in] mempool Memory pool to use.
1176 */
1177static void
1178setup_memory_pooling(const SelectionTreeElementPointer &sel,
1179 gmx_sel_mempool_t *mempool)
1180{
1181 if (sel->type != SEL_SUBEXPRREF)
1182 {
1183 SelectionTreeElementPointer child = sel->child;
1184 while (child)
1185 {
1186 if ((sel->type == SEL_BOOLEAN && (child->flags & SEL_DYNAMIC16))
1187 || (sel->type == SEL_ARITHMETIC && child->type != SEL_CONST
1188 && !(child->flags & SEL_SINGLEVAL2))
1189 || (sel->type == SEL_SUBEXPR
1190 && !(sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)))
1191 {
1192 child->mempool = mempool;
1193 if (child->type == SEL_SUBEXPRREF
1194 && (child->child->cdata->flags & SEL_CDATA_SIMPLESUBEXPR))
1195 {
1196 child->child->child->mempool = mempool;
1197 }
1198 }
1199 setup_memory_pooling(child, mempool);
1200 child = child->next;
1201 }
1202 }
1203}
1204
1205/*! \brief
1206 * Prepares the selection (sub)tree for evaluation.
1207 *
1208 * \param[in,out] sel Root of the selection subtree to prepare.
1209 *
1210 * It also allocates memory for the \p sel->v.u.g or \p sel->v.u.p
1211 * structure if required.
1212 */
1213static void
1214init_item_evaloutput(const SelectionTreeElementPointer &sel)
1215{
1216 GMX_ASSERT(!(sel->child == NULL &&
1217 (sel->type == SEL_SUBEXPRREF || sel->type == SEL_SUBEXPR)),
1218 "Subexpression elements should always have a child element");
1219
1220 /* Process children. */
1221 if (sel->type != SEL_SUBEXPRREF)
1222 {
1223 SelectionTreeElementPointer child = sel->child;
1224 while (child)
1225 {
1226 init_item_evaloutput(child);
1227 child = child->next;
1228 }
1229 }
1230
1231 if (sel->type == SEL_SUBEXPR
1232 && (sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
1233 && !(sel->cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR))
1234 {
1235 sel->flags &= ~(SEL_ALLOCVAL(1<<8) | SEL_ALLOCDATA(1<<9));
1236 if (sel->v.type == GROUP_VALUE || sel->v.type == POS_VALUE)
1237 {
1238 _gmx_selvalue_setstore(&sel->v, sel->child->v.u.ptr);
1239 }
1240 }
1241 else if (sel->type == SEL_SUBEXPR
1242 && (sel->cdata->flags & SEL_CDATA_FULLEVAL))
1243 {
1244 sel->evaluate = &_gmx_sel_evaluate_subexpr_staticeval;
1245 sel->cdata->evaluate = sel->evaluate;
1246 sel->child->mempool = NULL__null;
1247 sel->flags &= ~(SEL_ALLOCVAL(1<<8) | SEL_ALLOCDATA(1<<9));
1248 if (sel->v.type == GROUP_VALUE || sel->v.type == POS_VALUE)
1249 {
1250 _gmx_selvalue_setstore(&sel->v, sel->child->v.u.ptr);
1251 }
1252 }
1253 else if (sel->type == SEL_SUBEXPRREF
1254 && (sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR))
1255 {
1256 if (sel->v.u.ptr)
1257 {
1258 _gmx_selvalue_setstore(&sel->child->v, sel->v.u.ptr);
1259 sel->child->child->freeValues();
1260 sel->child->child->flags &= ~(SEL_ALLOCVAL(1<<8) | SEL_ALLOCDATA(1<<9));
1261 sel->child->child->flags |= (sel->flags & SEL_ALLOCDATA(1<<9));
1262 _gmx_selvalue_setstore(&sel->child->child->v, sel->v.u.ptr);
1263 }
1264 else if (sel->v.type == GROUP_VALUE || sel->v.type == POS_VALUE)
1265 {
1266 _gmx_selvalue_setstore(&sel->v, sel->child->child->v.u.ptr);
1267 }
1268 sel->flags &= ~(SEL_ALLOCVAL(1<<8) | SEL_ALLOCDATA(1<<9));
1269 }
1270
1271 /* Make sure that the group/position structure is allocated. */
1272 if (!sel->v.u.ptr && (sel->flags & SEL_ALLOCVAL(1<<8)))
1273 {
1274 if (sel->v.type == GROUP_VALUE || sel->v.type == POS_VALUE)
1275 {
1276 _gmx_selvalue_reserve(&sel->v, 1);
1277 sel->v.nr = 1;
1278 }
1279 }
1280}
1281
1282
1283/********************************************************************
1284 * COMPILER DATA INITIALIZATION
1285 ********************************************************************/
1286
1287/*! \brief
1288 * Allocates memory for the compiler data and initializes the structure.
1289 *
1290 * \param sel Root of the selection subtree to process.
1291 */
1292static void
1293init_item_compilerdata(const SelectionTreeElementPointer &sel)
1294{
1295 /* Allocate the compiler data structure */
1296 snew(sel->cdata, 1)gmx_snew_impl("sel->cdata", "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 1296, (sel->cdata), (1));
1297
1298 /* Store the real evaluation method because the compiler will replace it */
1299 sel->cdata->evaluate = sel->evaluate;
1300
1301 /* This will be computed separately. */
1302 sel->cdata->refcount = 0;
1303
1304 /* Initialize the flags */
1305 sel->cdata->flags = SEL_CDATA_STATICEVAL;
1306 if (!(sel->flags & SEL_DYNAMIC16))
1307 {
1308 sel->cdata->flags |= SEL_CDATA_STATIC;
1309 }
1310 if (sel->type == SEL_SUBEXPR)
1311 {
1312 sel->cdata->flags |= SEL_CDATA_EVALMAX;
1313 }
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)
1318 {
1319 SelectionTreeElementPointer child = sel->child;
1320 while (child)
1321 {
1322 if (!(child->flags & SEL_ATOMVAL4) && child->child)
1323 {
1324 child->child->cdata->flags |= SEL_CDATA_FULLEVAL;
1325 }
1326 child = child->next;
1327 }
1328 }
1329 else if (sel->type == SEL_ROOT && sel->child->type == SEL_SUBEXPRREF)
1330 {
1331 sel->child->child->cdata->flags |= SEL_CDATA_FULLEVAL;
1332 }
1333
1334 /* Initialize children */
1335 if (sel->type != SEL_SUBEXPRREF)
1336 {
1337 SelectionTreeElementPointer child = sel->child;
1338 while (child)
1339 {
1340 init_item_compilerdata(child);
1341 child = child->next;
1342 }
1343 }
1344
1345 /* Determine whether we should evaluate the minimum or the maximum
1346 * for the children of this element. */
1347 if (sel->type == SEL_BOOLEAN)
1348 {
1349 bool bEvalMax;
1350
1351 bEvalMax = (sel->u.boolt == BOOL_AND);
1352 SelectionTreeElementPointer child = sel->child;
1353 while (child)
1354 {
1355 if (bEvalMax)
1356 {
1357 child->cdata->flags |= SEL_CDATA_EVALMAX;
1358 }
1359 else if (child->type == SEL_BOOLEAN && child->u.boolt == BOOL_NOT)
1360 {
1361 child->child->cdata->flags |= SEL_CDATA_EVALMAX;
1362 }
1363 child = child->next;
1364 }
1365 }
1366 else if (sel->type == SEL_EXPRESSION || sel->type == SEL_MODIFIER
1367 || sel->type == SEL_SUBEXPR)
1368 {
1369 SelectionTreeElementPointer child = sel->child;
1370 while (child)
1371 {
1372 child->cdata->flags |= SEL_CDATA_EVALMAX;
1373 child = child->next;
1374 }
1375 }
1376}
1377
1378/*! \brief
1379 * Initializes the static evaluation flag for a selection subtree.
1380 *
1381 * \param[in,out] sel Root of the selection subtree to process.
1382 *
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.
1386 *
1387 * reorder_boolean_static_children() should have been called.
1388 */
1389static void
1390init_item_staticeval(const SelectionTreeElementPointer &sel)
1391{
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))
1396 {
1397 return;
1398 }
1399
1400 /* Propagate the bStaticEval flag to children if it is not set */
1401 if (!(sel->cdata->flags & SEL_CDATA_STATICEVAL))
1402 {
1403 SelectionTreeElementPointer child = sel->child;
1404 while (child)
1405 {
1406 if ((sel->type != SEL_EXPRESSION && sel->type != SEL_MODIFIER)
1407 || (child->flags & SEL_ATOMVAL4))
1408 {
1409 if (child->cdata->flags & SEL_CDATA_STATICEVAL)
1410 {
1411 child->cdata->flags &= ~SEL_CDATA_STATICEVAL;
1412 init_item_staticeval(child);
1413 }
1414 }
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_DYNAMIC16)
1418 && (sel->type == SEL_EXPRESSION || sel->type == SEL_MODIFIER)
1419 && (child->flags & SEL_ATOMVAL4))
1420 {
1421 child->flags |= SEL_DYNAMIC16;
1422 child->cdata->flags &= ~SEL_CDATA_STATIC;
1423 }
1424 child = child->next;
1425 }
1426 }
1427 else /* bStaticEval is set */
1428 {
1429 /* For boolean expressions, any expression after the first dynamic
1430 * expression should not have bStaticEval. */
1431 if (sel->type == SEL_BOOLEAN)
1432 {
1433 SelectionTreeElementPointer child = sel->child;
1434 while (child && !(child->flags & SEL_DYNAMIC16))
1435 {
1436 child = child->next;
1437 }
1438 if (child)
1439 {
1440 child = child->next;
1441 }
1442 while (child)
1443 {
1444 child->cdata->flags &= ~SEL_CDATA_STATICEVAL;
1445 child = child->next;
1446 }
1447 }
1448
1449 /* Process the children */
1450 SelectionTreeElementPointer child = sel->child;
1451 while (child)
1452 {
1453 init_item_staticeval(child);
1454 child = child->next;
1455 }
1456 }
1457}
1458
1459/*! \brief
1460 * Compute reference counts for subexpressions.
1461 *
1462 * \param sel Root of the selection subtree to process.
1463 */
1464static void
1465init_item_subexpr_refcount(const SelectionTreeElementPointer &sel)
1466{
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)
1470 {
1471 sel->child->cdata->refcount = 0;
1472 }
1473
1474 if (sel->type == SEL_SUBEXPRREF)
1475 {
1476 ++sel->child->cdata->refcount;
1477 }
1478 else
1479 {
1480 SelectionTreeElementPointer child = sel->child;
1481 while (child)
1482 {
1483 init_item_subexpr_refcount(child);
1484 child = child->next;
1485 }
1486 }
1487}
1488
1489/*! \brief
1490 * Initializes compiler flags for subexpressions.
1491 *
1492 * \param sel Root of the selection subtree to process.
1493 */
1494static void
1495init_item_subexpr_flags(const SelectionTreeElementPointer &sel)
1496{
1497 if (sel->type == SEL_SUBEXPR)
1498 {
1499 if (sel->cdata->refcount == 1)
1500 {
1501 sel->cdata->flags |= SEL_CDATA_SIMPLESUBEXPR;
1502 }
1503 else if (!(sel->cdata->flags & SEL_CDATA_FULLEVAL))
1504 {
1505 sel->cdata->flags |= SEL_CDATA_COMMONSUBEXPR;
1506 }
1507 }
1508 else if (sel->type == SEL_SUBEXPRREF
1509 && (sel->child->cdata->flags & SEL_CDATA_SIMPLESUBEXPR))
1510 {
1511 /* See similar condition in init_item_staticeval(). */
1512 if ((sel->flags & SEL_ATOMVAL4)
1513 && (sel->flags & SEL_DYNAMIC16)
1514 && !(sel->child->flags & SEL_DYNAMIC16))
1515 {
1516 sel->child->cdata->flags |= SEL_CDATA_STATICMULTIEVALSUBEXPR;
1517 }
1518 else
1519 {
1520 sel->cdata->flags |= SEL_CDATA_SIMPLESUBEXPR;
1521 }
1522 }
1523
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)))
1529 {
1530 SelectionTreeElementPointer child = sel->child;
1531 while (child)
1532 {
1533 if (!(child->cdata->flags & SEL_CDATA_COMMONSUBEXPR))
1534 {
1535 if (sel->type != SEL_EXPRESSION || (child->flags & SEL_ATOMVAL4))
1536 {
1537 child->cdata->flags |=
1538 (sel->cdata->flags & SEL_CDATA_COMMONSUBEXPR);
1539 }
1540 init_item_subexpr_flags(child);
1541 }
1542 child = child->next;
1543 }
1544 }
1545}
1546
1547/*! \brief
1548 * Initializes the gmin and gmax fields of the compiler data structure.
1549 *
1550 * \param sel Root of the selection subtree to process.
1551 */
1552static void
1553init_item_minmax_groups(const SelectionTreeElementPointer &sel)
1554{
1555 /* Process children. */
1556 if (sel->type != SEL_SUBEXPRREF)
1557 {
1558 SelectionTreeElementPointer child = sel->child;
1559 while (child)
1560 {
1561 init_item_minmax_groups(child);
1562 child = child->next;
1563 }
1564 }
1565
1566 /* Initialize the minimum and maximum evaluation groups. */
1567 if (sel->type != SEL_ROOT && sel->v.type != NO_VALUE)
1568 {
1569 if (sel->v.type == GROUP_VALUE
1570 && (sel->cdata->flags & SEL_CDATA_STATIC))
1571 {
1572 sel->cdata->gmin = sel->v.u.g;
1573 sel->cdata->gmax = sel->v.u.g;
1574 }
1575 else if (sel->type == SEL_SUBEXPR
1576 && ((sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
1577 || (sel->cdata->flags & SEL_CDATA_FULLEVAL)))
1578 {
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;
1583 }
1584 else
1585 {
1586 sel->cdata->flags |= SEL_CDATA_MINMAXALLOC | SEL_CDATA_DOMINMAX;
1587 snew(sel->cdata->gmin, 1)gmx_snew_impl("sel->cdata->gmin", "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 1587, (sel->cdata->gmin), (1));
1588 snew(sel->cdata->gmax, 1)gmx_snew_impl("sel->cdata->gmax", "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 1588, (sel->cdata->gmax), (1));
1589 }
1590 }
1591}
1592
1593
1594/********************************************************************
1595 * EVALUATION GROUP INITIALIZATION
1596 ********************************************************************/
1597
1598/*! \brief
1599 * Initializes evaluation groups for root items.
1600 *
1601 * \param[in,out] sc Selection collection data.
1602 *
1603 * The evaluation group of each \ref SEL_ROOT element corresponding to a
1604 * selection in \p sc is set to NULL. The evaluation grop for \ref SEL_ROOT
1605 * elements corresponding to subexpressions that need full evaluation is set
1606 * to \c sc->gall.
1607 */
1608static void
1609initialize_evalgrps(gmx_ana_selcollection_t *sc)
1610{
1611 SelectionTreeElementPointer root = sc->root;
1612 while (root)
1613 {
1614 GMX_RELEASE_ASSERT(root->child,((void) ((root->child) ? (void)0 : ::gmx::internal::assertHandler
("root->child", "Root elements should always have a child"
, __PRETTY_FUNCTION__, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 1615)))
1615 "Root elements should always have a child")((void) ((root->child) ? (void)0 : ::gmx::internal::assertHandler
("root->child", "Root elements should always have a child"
, __PRETTY_FUNCTION__, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 1615)));
1616 if (root->child->type != SEL_SUBEXPR
1617 || (root->child->v.type != GROUP_VALUE && !(root->flags & SEL_ATOMVAL4)))
1618 {
1619 gmx_ana_index_set(&root->u.cgrp, -1, 0, 0);
1620 }
1621 else if (root->child->cdata->flags & SEL_CDATA_FULLEVAL)
1622 {
1623 gmx_ana_index_set(&root->u.cgrp, sc->gall.isize, sc->gall.index, 0);
1624 }
1625 root = root->next;
1626 }
1627}
1628
1629
1630/********************************************************************
1631 * STATIC ANALYSIS
1632 ********************************************************************/
1633
1634/*! \brief
1635 * Marks a subtree completely dynamic or undoes such a change.
1636 *
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.
1641 *
1642 * Does not descend into parameters of methods unless the parameters
1643 * are evaluated for each atom.
1644 */
1645static void
1646mark_subexpr_dynamic(const SelectionTreeElementPointer &sel,
1647 bool bDynamic)
1648{
1649 if (!bDynamic && !(sel->flags & SEL_DYNAMIC16))
1650 {
1651 sel->cdata->flags |= SEL_CDATA_STATIC;
1652 }
1653 else
1654 {
1655 sel->cdata->flags &= ~SEL_CDATA_STATIC;
1656 }
1657 SelectionTreeElementPointer child = sel->child;
1658 while (child)
1659 {
1660 if (sel->type != SEL_EXPRESSION || child->type != SEL_SUBEXPRREF
1661 || (child->u.param->flags & SPAR_ATOMVAL32))
1662 {
1663 mark_subexpr_dynamic(child, bDynamic);
1664 }
1665 child = child->next;
1666 }
1667}
1668
1669/*! \brief
1670 * Frees memory for subexpressions that are no longer needed.
1671 *
1672 * \param sel Selection subtree to check.
1673 *
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.
1680 */
1681static void
1682release_subexpr_memory(const SelectionTreeElementPointer &sel)
1683{
1684 if (sel->type == SEL_SUBEXPRREF)
1685 {
1686 const SelectionTreeElementPointer &subexpr = sel->child;
1687 if (subexpr.use_count() == 2)
1688 {
1689 release_subexpr_memory(subexpr);
1690 // Free children.
1691 subexpr->child.reset();
1692 subexpr->freeValues();
1693 subexpr->freeExpressionData();
1694 subexpr->freeCompilerData();
1695 }
1696 }
1697 else
1698 {
1699 SelectionTreeElementPointer child = sel->child;
1700 while (child)
1701 {
1702 release_subexpr_memory(child);
1703 child = child->next;
1704 }
1705 }
1706}
1707
1708/*! \brief
1709 * Makes an evaluated selection element static.
1710 *
1711 * \param sel Selection element to make static.
1712 *
1713 * The evaluated value becomes the value of the static element.
1714 * The element type is changed to SEL_CONST and the children are
1715 * deleted.
1716 */
1717static void
1718make_static(const SelectionTreeElementPointer &sel)
1719{
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))
1724 {
1725 if (sel->child->child->flags & SEL_ALLOCDATA(1<<9))
1726 {
1727 sel->flags |= SEL_ALLOCDATA(1<<9);
1728 sel->child->child->flags &= ~SEL_ALLOCDATA(1<<9);
1729 }
1730 if (sel->child->child->flags & SEL_ALLOCVAL(1<<8))
1731 {
1732 sel->flags |= SEL_ALLOCVAL(1<<8);
1733 sel->v.nalloc = sel->child->child->v.nalloc;
1734 sel->child->child->flags &= ~SEL_ALLOCVAL(1<<8);
1735 sel->child->child->v.nalloc = -1;
1736 }
1737 }
1738 /* Free the children. */
1739 release_subexpr_memory(sel);
1740 sel->child.reset();
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__null;
1746 sel->cdata->evaluate = NULL__null;
1747 /* Set the group value.
1748 * freeExpressionData() frees the cgrp group, so we can just override it.
1749 * */
1750 if (sel->v.type == GROUP_VALUE)
1751 {
1752 gmx_ana_index_set(&sel->u.cgrp, sel->v.u.g->isize, sel->v.u.g->index, 0);
1753 }
1754}
1755
1756/*! \brief
1757 * Evaluates a constant expression during analyze_static().
1758 *
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.
1763 */
1764static void
1765process_const(gmx_sel_evaluate_t *data,
1766 const SelectionTreeElementPointer &sel,
1767 gmx_ana_index_t *g)
1768{
1769 if (sel->v.type == GROUP_VALUE)
1770 {
1771 if (sel->cdata->evaluate)
1772 {
1773 sel->cdata->evaluate(data, sel, g);
1774 }
1775 }
1776 /* Other constant expressions do not need evaluation */
1777}
1778
1779/*! \brief
1780 * Sets the parameter value pointer for \ref SEL_SUBEXPRREF params.
1781 *
1782 * \param[in,out] sel Selection to process.
1783 *
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.
1791 */
1792static void
1793store_param_val(const SelectionTreeElementPointer &sel)
1794{
1795 /* Return immediately if there is no parameter. */
1796 if (sel->type != SEL_SUBEXPRREF || !sel->u.param)
1797 {
1798 return;
1799 }
1800
1801 /* Or if the value does not need storing. */
1802 if (!(sel->u.param->flags & (SPAR_VARNUM16 | SPAR_ATOMVAL32)))
1803 {
1804 return;
1805 }
1806
1807 if (sel->v.type == INT_VALUE || sel->v.type == REAL_VALUE
1808 || sel->v.type == STR_VALUE)
1809 {
1810 _gmx_selvalue_setstore(&sel->u.param->val, sel->v.u.ptr);
1811 }
1812}
1813
1814/*! \brief
1815 * Handles the initialization of a selection method during analyze_static() pass.
1816 *
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.
1821 *
1822 * Calls sel_initfunc() (and possibly sel_outinitfunc()) to initialize the
1823 * method.
1824 * If no \ref SPAR_ATOMVAL parameters are present, multiple initialization
1825 * is prevented by using \ref SEL_METHODINIT and \ref SEL_OUTINIT flags.
1826 */
1827static void
1828init_method(const SelectionTreeElementPointer &sel, t_topology *top, int isize)
1829{
1830 /* Find out whether there are any atom-valued parameters */
1831 bool bAtomVal = false;
1832 SelectionTreeElementPointer child = sel->child;
1833 while (child)
1834 {
1835 if (child->flags & SEL_ATOMVAL4)
1836 {
1837 bAtomVal = true;
1838 }
1839 child = child->next;
1840 }
1841
1842 /* Initialize the method */
1843 if (sel->u.expr.method->init
1844 && (bAtomVal || !(sel->flags & SEL_METHODINIT(1<<12))))
1845 {
1846 sel->flags |= SEL_METHODINIT(1<<12);
1847 sel->u.expr.method->init(top, sel->u.expr.method->nparams,
1848 sel->u.expr.method->param, sel->u.expr.mdata);
1849 }
1850 if (bAtomVal || !(sel->flags & SEL_OUTINIT(1<<13)))
1851 {
1852 sel->flags |= SEL_OUTINIT(1<<13);
1853 if (sel->u.expr.method->outinit)
1854 {
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_VARNUMVAL8))
1858 {
1859 alloc_selection_data(sel, isize, true);
1860 }
1861 }
1862 else
1863 {
1864 GMX_RELEASE_ASSERT(sel->v.type != POS_VALUE,((void) ((sel->v.type != POS_VALUE) ? (void)0 : ::gmx::internal
::assertHandler("sel->v.type != POS_VALUE", "Output initialization must be provided for "
"position-valued selection methods", __PRETTY_FUNCTION__, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 1866)))
1865 "Output initialization must be provided for "((void) ((sel->v.type != POS_VALUE) ? (void)0 : ::gmx::internal
::assertHandler("sel->v.type != POS_VALUE", "Output initialization must be provided for "
"position-valued selection methods", __PRETTY_FUNCTION__, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 1866)))
1866 "position-valued selection methods")((void) ((sel->v.type != POS_VALUE) ? (void)0 : ::gmx::internal
::assertHandler("sel->v.type != POS_VALUE", "Output initialization must be provided for "
"position-valued selection methods", __PRETTY_FUNCTION__, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 1866)));
1867 GMX_RELEASE_ASSERT(!(sel->flags & SEL_VARNUMVAL),((void) ((!(sel->flags & 8)) ? (void)0 : ::gmx::internal
::assertHandler("!(sel->flags & SEL_VARNUMVAL)", "Output initialization must be provided for "
"SMETH_VARNUMVAL selection methods", __PRETTY_FUNCTION__, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 1869)))
1868 "Output initialization must be provided for "((void) ((!(sel->flags & 8)) ? (void)0 : ::gmx::internal
::assertHandler("!(sel->flags & SEL_VARNUMVAL)", "Output initialization must be provided for "
"SMETH_VARNUMVAL selection methods", __PRETTY_FUNCTION__, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 1869)))
1869 "SMETH_VARNUMVAL selection methods")((void) ((!(sel->flags & 8)) ? (void)0 : ::gmx::internal
::assertHandler("!(sel->flags & SEL_VARNUMVAL)", "Output initialization must be provided for "
"SMETH_VARNUMVAL selection methods", __PRETTY_FUNCTION__, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 1869)));
1870 alloc_selection_data(sel, isize, true);
1871 if ((sel->flags & SEL_DYNAMIC16)
1872 && sel->v.type != GROUP_VALUE && sel->v.type != POS_VALUE)
1873 {
1874 sel->v.nr = isize;
1875 }
1876 /* If the method is char-valued, pre-allocate the strings. */
1877 if (sel->u.expr.method->flags & SMETH_CHARVAL64)
1878 {
1879 int i;
1880
1881 /* A sanity check */
1882 if (sel->v.type != STR_VALUE)
1883 {
1884 GMX_THROW(gmx::InternalError("Char-valued selection method in non-string element"))::boost::exception_detail::throw_exception_((gmx::InternalError
("Char-valued selection method in non-string element")),__PRETTY_FUNCTION__
,"/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
,1884);
1885 }
1886 sel->flags |= SEL_ALLOCDATA(1<<9);
1887 for (i = 0; i < isize; ++i)
1888 {
1889 if (sel->v.u.s[i] == NULL__null)
1890 {
1891 snew(sel->v.u.s[i], 2)gmx_snew_impl("sel->v.u.s[i]", "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 1891, (sel->v.u.s[i]), (2));
1892 }
1893 }
1894 }
1895 }
1896 /* Clear the values for dynamic output to avoid valgrind warnings. */
1897 if ((sel->flags & SEL_DYNAMIC16) && sel->v.type == REAL_VALUE)
1898 {
1899 int i;
1900
1901 for (i = 0; i < sel->v.nr; ++i)
1902 {
1903 sel->v.u.r[i] = 0.0;
1904 }
1905 }
1906 }
1907}
1908
1909/*! \brief
1910 * Evaluates the static part of a boolean expression.
1911 *
1912 * \param[in] data Evaluation data.
1913 * \param[in,out] sel Boolean selection element whose children should be
1914 * processed.
1915 * \param[in] g The evaluation group.
1916 * \returns 0 on success, a non-zero error code on error.
1917 *
1918 * reorder_item_static_children() should have been called.
1919 */
1920static void
1921evaluate_boolean_static_part(gmx_sel_evaluate_t *data,
1922 const SelectionTreeElementPointer &sel,
1923 gmx_ana_index_t *g)
1924{
1925 /* Find the last static subexpression */
1926 SelectionTreeElementPointer child = sel->child;
1927 while (child->next && (child->next->cdata->flags & SEL_CDATA_STATIC))
1928 {
1929 child = child->next;
1930 }
1931 if (!(child->cdata->flags & SEL_CDATA_STATIC))
1932 {
1933 return;
1934 }
1935
1936 /* Evalute the static part if there is more than one expression */
1937 if (child != sel->child)
1938 {
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_FLAGSSET1 | SEL_SINGLEVAL2 | SEL_ALLOCVAL(1<<8) | SEL_ALLOCDATA(1<<9);
1945 _gmx_selelem_set_vtype(child, GROUP_VALUE);
1946 child->evaluate = NULL__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;
1953 child->next = next;
1954 // Frees the old static subexpressions.
1955 sel->child = child;
1956 }
1957 else if (child->evaluate)
1958 {
1959 child->evaluate(data, child, g);
1960 }
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__null;
1969 if (sel->u.boolt == BOOL_NOT
1970 || ((sel->cdata->flags & SEL_CDATA_STATICEVAL)
1971 && sel->u.boolt == BOOL_OR))
1972 {
1973 child->cdata->evaluate = NULL__null;
1974 }
1975 else
1976 {
1977 child->cdata->evaluate = &_gmx_sel_evaluate_static;
1978 /* The cgrp has only been allocated if it originated from an
1979 * external index group. In that case, we need special handling
1980 * to preserve the name of the group and to not leak memory.
1981 * If cgrp has been set in make_static(), it is not allocated,
1982 * and hence we can overwrite it safely. */
1983 if (child->u.cgrp.nalloc_index > 0)
1984 {
1985 gmx_ana_index_copy(&child->u.cgrp, child->v.u.g, false);
1986 gmx_ana_index_squeeze(&child->u.cgrp);
1987 }
1988 else
1989 {
1990 gmx_ana_index_copy(&child->u.cgrp, child->v.u.g, true);
1991 }
1992 }
1993}
1994
1995/*! \brief
1996 * Evaluates the minimum and maximum groups for a boolean expression.
1997 *
1998 * \param[in] sel \ref SEL_BOOLEAN element currently being evaluated.
1999 * \param[in] g Group for which \p sel has been evaluated.
2000 * \param[out] gmin Largest subset of the possible values of \p sel.
2001 * \param[out] gmax Smallest superset of the possible values of \p sel.
2002 *
2003 * This is a helper function for analyze_static() that is called for
2004 * dynamic \ref SEL_BOOLEAN elements after they have been evaluated.
2005 * It uses the minimum and maximum groups of the children to calculate
2006 * the minimum and maximum groups for \p sel, and also updates the static
2007 * part of \p sel (which is in the first child) if the children give
2008 * cause for this.
2009 *
2010 * This function may allocate some extra memory for \p gmin and \p gmax,
2011 * but as these groups are freed at the end of analyze_static() (which is
2012 * reached shortly after this function returns), this should not be a major
2013 * problem.
2014 */
2015static void
2016evaluate_boolean_minmax_grps(const SelectionTreeElementPointer &sel,
2017 gmx_ana_index_t *g,
2018 gmx_ana_index_t *gmin, gmx_ana_index_t *gmax)
2019{
2020 SelectionTreeElementPointer child;
2021
2022 switch (sel->u.boolt)
2023 {
2024 case BOOL_NOT:
2025 gmx_ana_index_reserve(gmin, g->isize);
2026 gmx_ana_index_reserve(gmax, g->isize);
2027 gmx_ana_index_difference(gmax, g, sel->child->cdata->gmin);
2028 gmx_ana_index_difference(gmin, g, sel->child->cdata->gmax);
2029 break;
2030
2031 case BOOL_AND:
2032 gmx_ana_index_copy(gmin, sel->child->cdata->gmin, true);
2033 gmx_ana_index_copy(gmax, sel->child->cdata->gmax, true);
2034 child = sel->child->next;
2035 while (child && gmax->isize > 0)
2036 {
2037 gmx_ana_index_intersection(gmin, gmin, child->cdata->gmin);
2038 gmx_ana_index_intersection(gmax, gmax, child->cdata->gmax);
2039 child = child->next;
2040 }
2041 /* Update the static part if other expressions limit it */
2042 if ((sel->child->cdata->flags & SEL_CDATA_STATIC)
2043 && sel->child->v.u.g->isize > gmax->isize)
2044 {
2045 gmx_ana_index_copy(sel->child->v.u.g, gmax, false);
2046 gmx_ana_index_squeeze(sel->child->v.u.g);
2047 if (sel->child->u.cgrp.isize > 0)
2048 {
2049 gmx_ana_index_copy(&sel->child->u.cgrp, gmax, false);
2050 gmx_ana_index_squeeze(&sel->child->u.cgrp);
2051 }
2052 }
2053 break;
2054
2055 case BOOL_OR:
2056 /* We can assume here that the gmin of children do not overlap
2057 * because of the way _gmx_sel_evaluate_or() works. */
2058 gmx_ana_index_reserve(gmin, g->isize);
2059 gmx_ana_index_reserve(gmax, g->isize);
2060 gmx_ana_index_copy(gmin, sel->child->cdata->gmin, false);
2061 gmx_ana_index_copy(gmax, sel->child->cdata->gmax, false);
2062 child = sel->child->next;
2063 while (child && gmin->isize < g->isize)
2064 {
2065 gmx_ana_index_merge(gmin, gmin, child->cdata->gmin);
2066 gmx_ana_index_union(gmax, gmax, child->cdata->gmax);
2067 child = child->next;
2068 }
2069 /* Update the static part if other expressions have static parts
2070 * that are not included. */
2071 if ((sel->child->cdata->flags & SEL_CDATA_STATIC)
2072 && sel->child->v.u.g->isize < gmin->isize)
2073 {
2074 GMX_RELEASE_ASSERT(sel->child->type == SEL_CONST,((void) ((sel->child->type == SEL_CONST) ? (void)0 : ::
gmx::internal::assertHandler("sel->child->type == SEL_CONST"
, "The first child should have already been evaluated " "to a constant expression"
, __PRETTY_FUNCTION__, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 2076)))
2075 "The first child should have already been evaluated "((void) ((sel->child->type == SEL_CONST) ? (void)0 : ::
gmx::internal::assertHandler("sel->child->type == SEL_CONST"
, "The first child should have already been evaluated " "to a constant expression"
, __PRETTY_FUNCTION__, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 2076)))
2076 "to a constant expression")((void) ((sel->child->type == SEL_CONST) ? (void)0 : ::
gmx::internal::assertHandler("sel->child->type == SEL_CONST"
, "The first child should have already been evaluated " "to a constant expression"
, __PRETTY_FUNCTION__, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 2076)));
2077 gmx_ana_index_reserve(sel->child->v.u.g, gmin->isize);
2078 gmx_ana_index_copy(sel->child->v.u.g, gmin, false);
2079 if (sel->child->u.cgrp.nalloc_index > 0)
2080 {
2081 gmx_ana_index_reserve(&sel->child->u.cgrp, gmin->isize);
2082 gmx_ana_index_copy(&sel->child->u.cgrp, gmin, false);
2083 }
2084 else
2085 {
2086 GMX_RELEASE_ASSERT(sel->child->u.cgrp.index == sel->child->v.u.g->index,((void) ((sel->child->u.cgrp.index == sel->child->
v.u.g->index) ? (void)0 : ::gmx::internal::assertHandler("sel->child->u.cgrp.index == sel->child->v.u.g->index"
, "If not allocated, the static group should equal the value"
, __PRETTY_FUNCTION__, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 2087)))
2087 "If not allocated, the static group should equal the value")((void) ((sel->child->u.cgrp.index == sel->child->
v.u.g->index) ? (void)0 : ::gmx::internal::assertHandler("sel->child->u.cgrp.index == sel->child->v.u.g->index"
, "If not allocated, the static group should equal the value"
, __PRETTY_FUNCTION__, "/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
, 2087)));
2088 sel->child->u.cgrp.isize = sel->child->v.u.g->isize;
2089 }
2090 }
2091 break;
2092
2093 case BOOL_XOR: /* Should not be reached */
2094 GMX_THROW(gmx::NotImplementedError("xor expressions not implemented"))::boost::exception_detail::throw_exception_((gmx::NotImplementedError
("xor expressions not implemented")),__PRETTY_FUNCTION__,"/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
,2094);
2095 break;
2096 }
2097}
2098
2099/*! \brief
2100 * Evaluates the static parts of \p sel and analyzes the structure.
2101 *
2102 * \param[in] data Evaluation data.
2103 * \param[in,out] sel Selection currently being evaluated.
2104 * \param[in] g Group for which \p sel should be evaluated.
2105 * \returns 0 on success, a non-zero error code on error.
2106 *
2107 * This function is used as the replacement for the
2108 * gmx::SelectionTreeElement::evaluate function pointer.
2109 * It does the single most complex task in the compiler: after all elements
2110 * have been processed, the \p gmin and \p gmax fields of \p t_compiler_data
2111 * have been properly initialized, enough memory has been allocated for
2112 * storing the value of each expression, and the static parts of the
2113 * expressions have been evaluated.
2114 * The above is exactly true only for elements other than subexpressions:
2115 * another pass is required for subexpressions that are referred to more than
2116 * once and whose evaluation group is not known in advance.
2117 */
2118static void
2119analyze_static(gmx_sel_evaluate_t *data,
2120 const SelectionTreeElementPointer &sel,
2121 gmx_ana_index_t *g)
2122{
2123 bool bDoMinMax;
2124
2125 if (sel->type != SEL_ROOT && g)
1
Assuming pointer value is null
→
2
←
Taking false branch
→
2126 {
2127 alloc_selection_data(sel, g->isize, false);
2128 }
2129
2130 bDoMinMax = (sel->cdata->flags & SEL_CDATA_DOMINMAX);
2131 if (sel->type != SEL_SUBEXPR && bDoMinMax)
2132 {
2133 gmx_ana_index_deinit(sel->cdata->gmin);
2134 gmx_ana_index_deinit(sel->cdata->gmax);
2135 }
2136
2137 /* TODO: This switch is awfully long... */
2138 switch (sel->type)
3
←
Control jumps to 'case SEL_SUBEXPR:' at line 2224
→
2139 {
2140 case SEL_CONST:
2141 process_const(data, sel, g);
2142 break;
2143
2144 case SEL_EXPRESSION:
2145 case SEL_MODIFIER:
2146 _gmx_sel_evaluate_method_params(data, sel, g);
2147 init_method(sel, data->top, g ? g->isize : 0);
2148 if (!(sel->flags & SEL_DYNAMIC16))
2149 {
2150 sel->cdata->evaluate(data, sel, g);
2151 if (sel->cdata->flags & SEL_CDATA_STATIC)
2152 {
2153 make_static(sel);
2154 }
2155 }
2156 else
2157 {
2158 /* Modifiers need to be evaluated even though they process
2159 * positions to get the modified output groups from the
2160 * maximum possible selections. */
2161 if (sel->type == SEL_MODIFIER)
2162 {
2163 sel->cdata->evaluate(data, sel, g);
2164 }
2165 if (bDoMinMax && g)
2166 {
2167 gmx_ana_index_copy(sel->cdata->gmax, g, true);
2168 }
2169 }
2170 break;
2171
2172 case SEL_BOOLEAN:
2173 if (!(sel->flags & SEL_DYNAMIC16))
2174 {
2175 sel->cdata->evaluate(data, sel, g);
2176 if (sel->cdata->flags & SEL_CDATA_STATIC)
2177 {
2178 make_static(sel);
2179 }
2180 }
2181 else
2182 {
2183 /* Evalute the static part if there is more than one expression */
2184 evaluate_boolean_static_part(data, sel, g);
2185
2186 /* Evaluate the selection.
2187 * If the type is boolean, we must explicitly handle the
2188 * static part evaluated in evaluate_boolean_static_part()
2189 * here because g may be larger. */
2190 if (sel->u.boolt == BOOL_AND && sel->child->type == SEL_CONST)
2191 {
2192 sel->cdata->evaluate(data, sel, sel->child->v.u.g);
2193 }
2194 else
2195 {
2196 sel->cdata->evaluate(data, sel, g);
2197 }
2198
2199 /* Evaluate minimal and maximal selections */
2200 evaluate_boolean_minmax_grps(sel, g, sel->cdata->gmin,
2201 sel->cdata->gmax);
2202 }
2203 break;
2204
2205 case SEL_ARITHMETIC:
2206 sel->cdata->evaluate(data, sel, g);
2207 if (!(sel->flags & SEL_DYNAMIC16))
2208 {
2209 if (sel->cdata->flags & SEL_CDATA_STATIC)
2210 {
2211 make_static(sel);
2212 }
2213 }
2214 else if (bDoMinMax)
2215 {
2216 gmx_ana_index_copy(sel->cdata->gmax, g, true);
2217 }
2218 break;
2219
2220 case SEL_ROOT:
2221 sel->cdata->evaluate(data, sel, g);
2222 break;
2223
2224 case SEL_SUBEXPR:
2225 if (((sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR) &&
4
←
Taking false branch
→
2226 !(sel->cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR))
2227 || (sel->cdata->flags & SEL_CDATA_FULLEVAL))
2228 {
2229 sel->cdata->evaluate(data, sel, g);
2230 _gmx_selvalue_setstore(&sel->v, sel->child->v.u.ptr);
2231 }
2232 else if (sel->u.cgrp.isize == 0)
5
←
Taking true branch
→
2233 {
2234 GMX_ASSERT(g, "group cannot be null");
2235 gmx_ana_index_reserve(&sel->u.cgrp, g->isize);
6
←
Access to field 'isize' results in a dereference of a null pointer (loaded from variable 'g')
2236 sel->cdata->evaluate(data, sel, g);
2237 if (bDoMinMax)
2238 {
2239 gmx_ana_index_copy(sel->cdata->gmin, sel->child->cdata->gmin, true);
2240 gmx_ana_index_copy(sel->cdata->gmax, sel->child->cdata->gmax, true);
2241 }
2242 }
2243 else
2244 {
2245 int isize = gmx_ana_index_difference_size(g, &sel->u.cgrp);
2246 if (isize > 0)
2247 {
2248 isize += sel->u.cgrp.isize;
2249 gmx_ana_index_reserve(&sel->u.cgrp, isize);
2250 alloc_selection_data(sel, isize, false);
2251 }
2252 sel->cdata->evaluate(data, sel, g);
2253 if (isize > 0 && bDoMinMax)
2254 {
2255 gmx_ana_index_reserve(sel->cdata->gmin,
2256 sel->cdata->gmin->isize
2257 + sel->child->cdata->gmin->isize);
2258 gmx_ana_index_reserve(sel->cdata->gmax,
2259 sel->cdata->gmax->isize
2260 + sel->child->cdata->gmax->isize);
2261 gmx_ana_index_merge(sel->cdata->gmin, sel->cdata->gmin,
2262 sel->child->cdata->gmin);
2263 gmx_ana_index_merge(sel->cdata->gmax, sel->cdata->gmax,
2264 sel->child->cdata->gmax);
2265 }
2266 }
2267 break;
2268
2269 case SEL_SUBEXPRREF:
2270 if (!g && !(sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR))
2271 {
2272 /* The subexpression should have been evaluated if g is NULL
2273 * (i.e., this is a method parameter or a direct value of a
2274 * selection). */
2275 if (sel->v.type == POS_VALUE)
2276 {
2277 alloc_selection_pos_data(sel);
2278 }
2279 else
2280 {
2281 alloc_selection_data(sel, sel->child->cdata->gmax->isize, true);
2282 }
2283 }
2284 sel->cdata->evaluate(data, sel, g);
2285 if ((sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
2286 && (sel->child->child->flags & SEL_ALLOCVAL(1<<8)))
2287 {
2288 _gmx_selvalue_setstore(&sel->v, sel->child->child->v.u.ptr);
2289 }
2290 /* Store the parameter value if required */
2291 store_param_val(sel);
2292 if (!(sel->flags & SEL_DYNAMIC16))
2293 {
2294 if (sel->cdata->flags & SEL_CDATA_STATIC)
2295 {
2296 make_static(sel);
2297 }
2298 }
2299 else if (bDoMinMax)
2300 {
2301 if ((sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR) || !g)
2302 {
2303 gmx_ana_index_copy(sel->cdata->gmin, sel->child->cdata->gmin, true);
2304 gmx_ana_index_copy(sel->cdata->gmax, sel->child->cdata->gmax, true);
2305 }
2306 else
2307 {
2308 gmx_ana_index_reserve(sel->cdata->gmin,
2309 min(g->isize, sel->child->cdata->gmin->isize));
2310 gmx_ana_index_reserve(sel->cdata->gmax,
2311 min(g->isize, sel->child->cdata->gmax->isize));
2312 gmx_ana_index_intersection(sel->cdata->gmin,
2313 sel->child->cdata->gmin, g);
2314 gmx_ana_index_intersection(sel->cdata->gmax,
2315 sel->child->cdata->gmax, g);
2316 }
2317 }
2318 break;
2319
2320 case SEL_GROUPREF: /* Should not be reached */
2321 GMX_THROW(gmx::APIError("Unresolved group reference in compilation"))::boost::exception_detail::throw_exception_((gmx::APIError("Unresolved group reference in compilation"
)),__PRETTY_FUNCTION__,"/home/alexxy/Develop/gromacs/src/gromacs/selection/compiler.cpp"
,2321);
2322 }
2323
2324 /* Update the minimal and maximal evaluation groups */
2325 if (bDoMinMax)
2326 {
2327 gmx_ana_index_squeeze(sel->cdata->gmin);
2328 gmx_ana_index_squeeze(sel->cdata->gmax);
2329 }
2330
2331 /* Replace the result of the evaluation */
2332 /* This is not necessary for subexpressions or for boolean negations
2333 * because the evaluation function already has done it properly. */
2334 if (sel->v.type == GROUP_VALUE && (sel->flags & SEL_DYNAMIC16)
2335 && sel->type != SEL_SUBEXPR
2336 && !(sel->type == SEL_BOOLEAN && sel->u.boolt == BOOL_NOT))
2337 {
2338 if (sel->cdata->flags & SEL_CDATA_EVALMAX)
2339 {
2340 gmx_ana_index_copy(sel->v.u.g, sel->cdata->gmax, false);
2341 }
2342 else
2343 {
2344 gmx_ana_index_copy(sel->v.u.g, sel->cdata->gmin, false);
2345 }
2346 }
2347}
2348
2349
2350/********************************************************************
2351 * EVALUATION GROUP INITIALIZATION
2352 ********************************************************************/
2353
2354/*! \brief
2355 * Initializes the evaluation group for a \ref SEL_ROOT element.
2356 *
2357 * \param root Root element to initialize.
2358 * \param[in] gall Group of all atoms.
2359 *
2360 * Checks whether it is necessary to evaluate anything through the root
2361 * element, and either clears the evaluation function or initializes the
2362 * evaluation group.
2363 */
2364static void
2365init_root_item(const SelectionTreeElementPointer &root,
2366 gmx_ana_index_t *gall)
2367{
2368 const SelectionTreeElementPointer &expr = root->child;
2369 /* Subexpressions with non-static evaluation group should not be
2370 * evaluated by the root, and neither should be single-reference
2371 * subexpressions that don't evaluate for all atoms. */
2372 if (expr->type == SEL_SUBEXPR
2373 && (!(root->child->cdata->flags & SEL_CDATA_STATICEVAL)
2374 || ((root->child->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
2375 && !(root->child->cdata->flags & SEL_CDATA_FULLEVAL))))
2376 {
2377 root->evaluate = NULL__null;
2378 if (root->cdata)
2379 {
2380 root->cdata->evaluate = NULL__null;
2381 }
2382 }
2383
2384 /* Set the evaluation group */
2385 if (root->evaluate)
2386 {
2387 /* Non-atom-valued non-group expressions don't care about the group, so
2388 * don't allocate any memory for it. */
2389 if ((expr->flags & SEL_VARNUMVAL8)
2390 || ((expr->flags & SEL_SINGLEVAL2) && expr->v.type != GROUP_VALUE))
2391 {
2392 gmx_ana_index_set(&root->u.cgrp, -1, NULL__null, 0);
2393 }
2394 else if (expr->cdata->gmax->isize == gall->isize)
2395 {
2396 /* Save some memory by only referring to the global group. */
2397 gmx_ana_index_set(&root->u.cgrp, gall->isize, gall->index, 0);
2398 }
2399 else
2400 {
2401 gmx_ana_index_copy(&root->u.cgrp, expr->cdata->gmax, true);
2402 }
2403 /* For selections, store the maximum group for
2404 * gmx_ana_selcollection_evaluate_fin() as the value of the root
2405 * element (unused otherwise). */
2406 if (expr->type != SEL_SUBEXPR && expr->v.u.p->m.mapb.a != NULL__null)
2407 {
2408 SelectionTreeElementPointer child = expr;
2409
2410 /* TODO: This code is copied from parsetree.c; it would be better
2411 * to have this hardcoded only in one place. */
2412 while (child->type == SEL_MODIFIER)
2413 {
2414 child = child->child;
2415 if (child->type == SEL_SUBEXPRREF)
2416 {
2417 child = child->child->child;
2418 }
2419 }
2420 if (child->type == SEL_SUBEXPRREF)
2421 {
2422 child = child->child->child;
2423 }
2424 if (child->child->flags & SEL_DYNAMIC16)
2425 {
2426 gmx_ana_index_t g;
2427 gmx_ana_index_set(&g, expr->v.u.p->m.mapb.nra, expr->v.u.p->m.mapb.a, 0);
2428 _gmx_selelem_set_vtype(root, GROUP_VALUE);
2429 root->flags |= (SEL_ALLOCVAL(1<<8) | SEL_ALLOCDATA(1<<9));
2430 _gmx_selvalue_reserve(&root->v, 1);
2431 gmx_ana_index_copy(root->v.u.g, &g, true);
2432 }
2433 }
2434 }
2435 else
2436 {
2437 gmx_ana_index_clear(&root->u.cgrp);
2438 }
2439}
2440
2441
2442/********************************************************************
2443 * FINAL SUBEXPRESSION OPTIMIZATION
2444 ********************************************************************/
2445
2446/*! \brief
2447 * Optimizes subexpression evaluation.
2448 *
2449 * \param sel Root of the selection subtree to process.
2450 *
2451 * Optimizes away some unnecessary evaluation of subexpressions that are only
2452 * referenced once.
2453 */
2454static void
2455postprocess_item_subexpressions(const SelectionTreeElementPointer &sel)
2456{
2457 GMX_ASSERT(!(sel->child == NULL &&
2458 (sel->type == SEL_SUBEXPRREF || sel->type == SEL_SUBEXPR)),
2459 "Subexpression elements should always have a child element");
2460
2461 /* Process children. */
2462 if (sel->type != SEL_SUBEXPRREF)
2463 {
2464 SelectionTreeElementPointer child = sel->child;
2465 while (child)
2466 {
2467 postprocess_item_subexpressions(child);
2468 child = child->next;
2469 }
2470 }
2471
2472 /* Replace the evaluation function of statically evaluated subexpressions
2473 * for which the static group was not known in advance. */
2474 if (sel->type == SEL_SUBEXPR && sel->cdata->refcount > 1
2475 && (sel->cdata->flags & SEL_CDATA_STATICEVAL)
2476 && !(sel->cdata->flags & SEL_CDATA_FULLEVAL))
2477 {
2478 /* We need to free memory allocated for the group, because it is no
2479 * longer needed (and would be lost on next call to the evaluation
2480 * function). */
2481 gmx_ana_index_deinit(&sel->u.cgrp);
2482
2483 sel->evaluate = &_gmx_sel_evaluate_subexpr_staticeval;
2484 sel->cdata->evaluate = sel->evaluate;
2485
2486 sel->child->freeValues();
2487 sel->child->mempool = NULL__null;
2488 _gmx_selvalue_setstore(&sel->child->v, sel->v.u.ptr);
2489 sel->child->flags &= ~(SEL_ALLOCVAL(1<<8) | SEL_ALLOCDATA(1<<9));
2490 }
2491
2492 /* Adjust memory allocation flags for subexpressions that are used only
2493 * once. This is not strictly necessary, but we do it to have the memory
2494 * managed consistently for all types of subexpressions. */
2495 if (sel->type == SEL_SUBEXPRREF
2496 && (sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR))
2497 {
2498 if (sel->child->child->flags & SEL_ALLOCVAL(1<<8))
2499 {
2500 sel->flags |= SEL_ALLOCVAL(1<<8);
2501 sel->flags |= (sel->child->child->flags & SEL_ALLOCDATA(1<<9));
2502 sel->v.nalloc = sel->child->child->v.nalloc;
2503 sel->child->child->flags &= ~(SEL_ALLOCVAL(1<<8) | SEL_ALLOCDATA(1<<9));
2504 sel->child->child->v.nalloc = -1;
2505 }
2506 }
2507
2508 /* Do the same for subexpressions that are evaluated at once for all atoms. */
2509 if (sel->type == SEL_SUBEXPR
2510 && !(sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
2511 && (sel->cdata->flags & SEL_CDATA_FULLEVAL))
2512 {
2513 sel->flags |= SEL_ALLOCVAL(1<<8);
2514 sel->flags |= (sel->child->flags & SEL_ALLOCDATA(1<<9));
2515 sel->v.nalloc = sel->child->v.nalloc;
2516 sel->child->flags &= ~(SEL_ALLOCVAL(1<<8) | SEL_ALLOCDATA(1<<9));
2517 sel->child->v.nalloc = -1;
2518 }
2519
2520 /* For static subexpressions with a dynamic evaluation group, there is
2521 * no need to evaluate them again, as the SEL_SUBEXPRREF takes care of
2522 * everything during evaluation. */
2523 if (sel->type == SEL_SUBEXPR
2524 && (sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
2525 && (sel->cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR))
2526 {
2527 sel->evaluate = NULL__null;
2528 sel->cdata->evaluate = NULL__null;
2529 }
2530}
2531
2532
2533/********************************************************************
2534 * COM CALCULATION INITIALIZATION
2535 ********************************************************************/
2536
2537/*! \brief
2538 * Initializes COM/COG calculation for method expressions that require it.
2539 *
2540 * \param sel Selection subtree to process.
2541 * \param[in,out] pcc Position calculation collection to use.
2542 * \param[in] type Default position calculation type.
2543 * \param[in] flags Flags for default position calculation.
2544 *
2545 * Searches recursively through the selection tree for dynamic
2546 * \ref SEL_EXPRESSION elements that define the \c gmx_ana_selmethod_t::pupdate
2547 * function.
2548 * For each such element found, position calculation is initialized
2549 * for the maximal evaluation group.
2550 * The type of the calculation is determined by \p type and \p flags.
2551 * No calculation is initialized if \p type equals \ref POS_ATOM and
2552 * the method also defines the \c gmx_ana_selmethod_t::update method.
2553 */
2554static void
2555init_item_comg(const SelectionTreeElementPointer &sel,
2556 gmx::PositionCalculationCollection *pcc,
2557 e_poscalc_t type, int flags)
2558{
2559 /* Initialize COM calculation for dynamic selections now that we know the maximal evaluation group */
2560 if (sel->type == SEL_EXPRESSION && sel->u.expr.method
2561 && sel->u.expr.method->pupdate)
2562 {
2563 if (!sel->u.expr.method->update || type != POS_ATOM)
2564 {
2565 /* Create a default calculation if one does not yet exist */
2566 int cflags = 0;
2567 if (!(sel->cdata->flags & SEL_CDATA_STATICEVAL))
2568 {
2569 cflags |= POS_DYNAMIC16;
2570 }
2571 if (!sel->u.expr.pc)
2572 {
2573 cflags |= flags;
2574 sel->u.expr.pc = pcc->createCalculation(type, cflags);
2575 }
2576 else
2577 {
2578 gmx_ana_poscalc_set_flags(sel->u.expr.pc, cflags);
2579 }
2580 gmx_ana_poscalc_set_maxindex(sel->u.expr.pc, sel->cdata->gmax);
2581 sel->u.expr.pos = new gmx_ana_pos_t();
2582 gmx_ana_poscalc_init_pos(sel->u.expr.pc, sel->u.expr.pos);
2583 }
2584 }
2585
2586 /* Call recursively for all children unless the children have already been processed */
2587 if (sel->type != SEL_SUBEXPRREF)
2588 {
2589 SelectionTreeElementPointer child = sel->child;
2590 while (child)
2591 {
2592 init_item_comg(child, pcc, type, flags);
2593 child = child->next;
2594 }
2595 }
2596}
2597
2598
2599/********************************************************************
2600 * COMPILER DATA FREEING
2601 ********************************************************************/
2602
2603/*! \brief
2604 * Frees the allocated compiler data recursively.
2605 *
2606 * \param sel Root of the selection subtree to process.
2607 *
2608 * Frees the data allocated for the compilation process.
2609 */
2610static void
2611free_item_compilerdata(const SelectionTreeElementPointer &sel)
2612{
2613 /* Free compilation data */
2614 sel->freeCompilerData();
2615
2616 /* Call recursively for all children unless the children have already been processed */
2617 if (sel->type != SEL_SUBEXPRREF)
2618 {
2619 SelectionTreeElementPointer child = sel->child;
2620 while (child)
2621 {
2622 free_item_compilerdata(child);
2623 child = child->next;
2624 }
2625 }
2626}
2627
2628
2629/********************************************************************
2630 * MAIN COMPILATION FUNCTION
2631 ********************************************************************/
2632
2633namespace gmx
2634{
2635
2636SelectionCompiler::SelectionCompiler()
2637{
2638}
2639
2640/*!
2641 * \param[in,out] coll Selection collection to be compiled.
2642 * \returns 0 on successful compilation, a non-zero error code on error.
2643 *
2644 * Before compilation, the selection collection should have been initialized
2645 * with gmx_ana_selcollection_parse_*().
2646 * The compiled selection collection can be passed to
2647 * gmx_ana_selcollection_evaluate() to evaluate the selection for a frame.
2648 * If an error occurs, \p sc is cleared.
2649 *
2650 * The covered fraction information in \p sc is initialized to
2651 * \ref CFRAC_NONE.
2652 */
2653void
2654SelectionCompiler::compile(SelectionCollection *coll)
2655{
2656 gmx_ana_selcollection_t *sc = &coll->impl_->sc_;
2657 gmx_sel_evaluate_t evaldata;
2658 SelectionTreeElementPointer item;
2659 e_poscalc_t post;
2660 size_t i;
2661 int flags;
2662 bool bDebug = (coll->impl_->debugLevel_ >= 2
2663 && coll->impl_->debugLevel_ != 3);
2664
2665 /* FIXME: Clean up the collection on exceptions */
2666
2667 sc->mempool = _gmx_sel_mempool_create();
2668 _gmx_sel_evaluate_init(&evaldata, sc->mempool, &sc->gall,
2669 sc->top, NULL__null, NULL__null);
2670
2671 /* Clear the symbol table because it is not possible to parse anything
2672 * after compilation, and variable references in the symbol table can
2673 * also mess up the compilation and/or become invalid.
2674 */
2675 coll->impl_->clearSymbolTable();
2676
2677 /* Loop through selections and initialize position keyword defaults if no
2678 * other value has been provided.
2679 */
2680 for (i = 0; i < sc->sel.size(); ++i)
2681 {
2682 gmx::internal::SelectionData &sel = *sc->sel[i];
2683 init_pos_keyword_defaults(&sel.rootElement(),
2684 coll->impl_->spost_.c_str(),
2685 coll->impl_->rpost_.c_str(),
2686 &sel);
2687 }
2688
2689 /* Remove any unused variables. */
2690 sc->root = remove_unused_subexpressions(sc->root);
2691 /* Extract subexpressions into separate roots */
2692 sc->root = extract_subexpressions(sc->root);
2693
2694 /* Initialize the evaluation callbacks and process the tree structure
2695 * to conform to the expectations of the callback functions. */
2696 /* Also, initialize and allocate the compiler data structure */
2697 // TODO: Processing the tree in reverse root order would be better,
2698 // as it would make dependency handling easier (all subexpression
2699 // references would be processed before the actual subexpression) and
2700 // could remove the need for most of these extra loops.
2701 item = sc->root;
2702 while (item)
2703 {
2704 /* Process boolean and arithmetic expressions. */
2705 optimize_boolean_expressions(item);
2706 reorder_boolean_static_children(item);
2707 optimize_arithmetic_expressions(item);
2708 /* Initialize the compiler data */
2709 init_item_compilerdata(item);
2710 item = item->next;
2711 }
2712 // Initialize the static evaluation compiler flags.
2713 // Requires the FULLEVAL compiler flag for the whole tree.
2714 item = sc->root;
2715 while (item)
2716 {
2717 init_item_staticeval(item);
2718 init_item_subexpr_refcount(item);
2719 item = item->next;
2720 }
2721 /* Initialize subexpression flags.
2722 * Requires compiler flags for the full tree. */
2723 item = sc->root;
2724 while (item)
2725 {
2726 init_item_subexpr_flags(item);
2727 item = item->next;
2728 }
2729 /* Initialize evaluation.
2730 * Requires subexpression flags. */
2731 item = sc->root;
2732 while (item)
2733 {
2734 init_item_evalfunc(item);
2735 setup_memory_pooling(item, sc->mempool);
2736 init_item_evaloutput(item);
2737 item = item->next;
2738 }
2739 /* Initialize minimum/maximum index groups.
2740 * Requires evaluation output for the full tree. */
2741 item = sc->root;
2742 while (item)
2743 {
2744 init_item_minmax_groups(item);
2745 item = item->next;
2746 }
2747 /* Initialize the evaluation index groups */
2748 initialize_evalgrps(sc);
2749
2750 if (bDebug)
2751 {
2752 fprintf(stderrstderr, "\nTree after initial compiler processing:\n");
2753 coll->printTree(stderrstderr, false);
2754 }
2755
2756 /* Evaluate all static parts of the selection and analyze the tree
2757 * to allocate enough memory to store the value of each dynamic subtree. */
2758 item = sc->root;
2759 while (item)
2760 {
2761 if (item->child->cdata->flags & SEL_CDATA_COMMONSUBEXPR)
2762 {
2763 mark_subexpr_dynamic(item->child, true);
2764 }
2765 set_evaluation_function(item, &analyze_static);
2766 item->evaluate(&evaldata, item, NULL__null);
2767 item = item->next;
2768 }
2769
2770 /* At this point, static subexpressions no longer have references to them,
2771 * so they can be removed. */
2772 sc->root = remove_unused_subexpressions(sc->root);
2773 // Update the reference counts for consistency (only used for the
2774 // debugging output below).
2775 item = sc->root;
2776 while (item)
2777 {
2778 init_item_subexpr_refcount(item);
2779 item = item->next;
2780 }
2781
2782 if (bDebug)
2783 {
2784 fprintf(stderrstderr, "\nTree after first analysis pass:\n");
2785 coll->printTree(stderrstderr, false);
2786 }
2787
2788 /* Do a second pass to evaluate static parts of common subexpressions */
2789 item = sc->root;
2790 while (item)
2791 {
2792 if (item->child->cdata->flags & SEL_CDATA_COMMONSUBEXPR)
2793 {
2794 bool bMinMax = item->child->cdata->flags & SEL_CDATA_DOMINMAX;
2795
2796 mark_subexpr_dynamic(item->child, false);
2797 item->child->u.cgrp.isize = 0;
2798 /* We won't clear item->child->v.u.g here, because it may
2799 * be static, and hence actually point to item->child->cdata->gmax,
2800 * which is used below. We could also check whether this is the
2801 * case and only clear the group otherwise, but because the value
2802 * is actually overwritten immediately in the evaluate call, we
2803 * won't, because similar problems may arise if gmax handling ever
2804 * changes and the check were not updated.
2805 * For the same reason, we clear the min/max flag so that the
2806 * evaluation group doesn't get messed up. */
2807 set_evaluation_function(item, &analyze_static);
2808 item->child->cdata->flags &= ~SEL_CDATA_DOMINMAX;
2809 item->evaluate(&evaldata, item->child, item->child->cdata->gmax);
2810 if (bMinMax)
2811 {
2812 item->child->cdata->flags |= SEL_CDATA_DOMINMAX;
2813 }
2814 }
2815 item = item->next;
2816 }
2817
2818 /* We need a yet another pass of subexpression removal to remove static
2819 * subexpressions referred to by common dynamic subexpressions. */
2820 sc->root = remove_unused_subexpressions(sc->root);
2821 // Update the reference counts, used by postprocess_item_subexpressions().
2822 item = sc->root;
2823 while (item)
2824 {
2825 init_item_subexpr_refcount(item);
2826 item = item->next;
2827 }
2828
2829 if (bDebug)
2830 {
2831 fprintf(stderrstderr, "\nTree after second analysis pass:\n");
2832 coll->printTree(stderrstderr, false);
2833 }
2834
2835 /* Initialize evaluation groups, position calculations for methods, perform
2836 * some final optimization, and free the memory allocated for the
2837 * compilation. */
2838 /* By default, use whole residues/molecules. */
2839 flags = POS_COMPLWHOLE4;
2840 PositionCalculationCollection::typeFromEnum(coll->impl_->rpost_.c_str(),
2841 &post, &flags);
2842 item = sc->root;
2843 while (item)
2844 {
2845 init_root_item(item, &sc->gall);
2846 postprocess_item_subexpressions(item);
2847 init_item_comg(item, &sc->pcc, post, flags);
2848 free_item_compilerdata(item);
2849 item = item->next;
2850 }
2851
2852 /* Allocate memory for the evaluation memory pool. */
2853 _gmx_sel_mempool_reserve(sc->mempool, 0);
2854
2855 /* Finish up by calculating total masses and charges. */
2856 for (i = 0; i < sc->sel.size(); ++i)
2857 {
2858 sc->sel[i]->initializeMassesAndCharges(sc->top);
2859 }
2860}
2861
2862} // namespace gmx