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39 * Implements functions in evaluate.h.
42 * One of the major bottlenecks for selection performance is that all the
43 * evaluation is carried out for atoms.
44 * There are several cases when the evaluation could be done for residues
45 * or molecules instead, including keywords that select by residue and
46 * cases where residue centers are used as reference positions.
47 * Implementing this would require a mechanism for recognizing whether
48 * something can be evaluated by residue/molecule instead by atom, and
49 * converting selections by residue/molecule into selections by atom
52 * \author Teemu Murtola <teemu.murtola@gmail.com>
53 * \ingroup module_selection
63 #include "gromacs/math/utilities.h"
64 #include "gromacs/math/vec.h"
65 #include "gromacs/selection/indexutil.h"
66 #include "gromacs/selection/selection.h"
67 #include "gromacs/utility/exceptions.h"
68 #include "gromacs/utility/gmxassert.h"
69 #include "gromacs/utility/smalloc.h"
73 #include "selectioncollection_impl.h"
75 #include "selmethod.h"
77 using gmx::SelectionTreeElement;
78 using gmx::SelectionTreeElementPointer;
84 * Reserves memory for a selection element from the evaluation memory pool.
86 * This class implements RAII semantics for allocating memory for selection
87 * element values from a selection evaluation memory pool.
89 * \ingroup module_selection
91 class MempoolSelelemReserver
94 //! Constructs a reserver without initial reservation.
95 MempoolSelelemReserver() {}
97 * Constructs a reserver with initial reservation.
99 * \param[in,out] sel Selection element for which to reserve.
100 * \param[in] count Number of values to reserve.
104 MempoolSelelemReserver(const SelectionTreeElementPointer& sel, int count)
108 //! Frees any memory allocated using this reserver.
109 ~MempoolSelelemReserver()
113 sel_->mempoolRelease();
118 * Reserves memory for selection element values using this reserver.
120 * \param[in,out] sel Selection element for which to reserve.
121 * \param[in] count Number of values to reserve.
123 * Allocates space to store \p count output values in \p sel from the
124 * memory pool associated with \p sel, or from the heap if there is no
125 * memory pool. Type of values to allocate is automatically determined
128 void reserve(const SelectionTreeElementPointer& sel, int count)
130 GMX_RELEASE_ASSERT(!sel_, "Can only reserve one element with one instance");
131 sel->mempoolReserve(count);
136 SelectionTreeElementPointer sel_;
140 * Reserves memory for an index group from the evaluation memory pool.
142 * This class implements RAII semantics for allocating memory for an index
143 * group from a selection evaluation memory pool.
145 * \ingroup module_selection
147 class MempoolGroupReserver
151 * Creates a reserver associated with a given memory pool.
153 * \param mp Memory pool from which to reserve memory.
155 explicit MempoolGroupReserver(gmx_sel_mempool_t* mp) : mp_(mp), g_(nullptr) {}
156 //! Frees any memory allocated using this reserver.
157 ~MempoolGroupReserver()
161 _gmx_sel_mempool_free_group(mp_, g_);
166 * Reserves memory for an index group using this reserver.
168 * \param[in,out] g Index group to reserve.
169 * \param[in] count Number of atoms to reserve space for.
171 * Allocates memory from the memory pool to store \p count atoms in
174 void reserve(gmx_ana_index_t* g, int count)
176 GMX_RELEASE_ASSERT(g_ == nullptr, "Can only reserve one element with one instance");
177 _gmx_sel_mempool_alloc_group(mp_, g, count);
182 gmx_sel_mempool_t* mp_;
187 * Assigns a temporary value for a selection element.
189 * This class implements RAII semantics for temporarily assigning the value
190 * pointer of a selection element to point to a different location.
192 * \ingroup module_selection
194 class SelelemTemporaryValueAssigner
197 //! Constructs an assigner without an initial assignment.
198 SelelemTemporaryValueAssigner() : old_ptr_(nullptr), old_nalloc_(0) {}
200 * Constructs an assigner with an initial assignment.
202 * \param[in,out] sel Selection element for which to assign.
203 * \param[in] vsource Element to which \p sel values will point to.
207 SelelemTemporaryValueAssigner(const SelectionTreeElementPointer& sel, const SelectionTreeElement& vsource)
209 assign(sel, vsource);
211 //! Undoes any temporary assignment done using this assigner.
212 ~SelelemTemporaryValueAssigner()
216 _gmx_selvalue_setstore_alloc(&sel_->v, old_ptr_, old_nalloc_);
221 * Assigns a temporary value pointer.
223 * \param[in,out] sel Selection element for which to assign.
224 * \param[in] vsource Element to which \p sel values will point to.
226 * Assigns the value pointer in \p sel to point to the values in
227 * \p vsource, i.e., any access/modification to values in \p sel
228 * actually accesses values in \p vsource.
230 void assign(const SelectionTreeElementPointer& sel, const SelectionTreeElement& vsource)
232 GMX_RELEASE_ASSERT(!sel_, "Can only assign one element with one instance");
233 GMX_RELEASE_ASSERT(sel->v.type == vsource.v.type, "Mismatching selection value types");
234 _gmx_selvalue_getstore_and_release(&sel->v, &old_ptr_, &old_nalloc_);
235 _gmx_selvalue_setstore(&sel->v, vsource.v.u.ptr);
240 SelectionTreeElementPointer sel_;
246 * Expands a value array from one-per-position to one-per-atom.
248 * \param[in,out] value Array to expand.
249 * \param[in,out] nr Number of values in \p value.
250 * \param[in] pos Position data.
251 * \tparam T Value type of the array to expand.
253 * On input, \p value contains one value for each position in \p pos (and `*nr`
254 * must match). On output, \p value will contain a value for each atom used to
255 * evaluate `pos`: each input value is replicated to all atoms that make up the
256 * corresponding position.
257 * The operation is done in-place.
262 void expandValueForPositions(T value[], int* nr, gmx_ana_pos_t* pos)
264 GMX_RELEASE_ASSERT(*nr == pos->count(),
265 "Position update method did not return the correct number of values");
266 *nr = pos->m.mapb.nra;
267 // Loop over the positions in reverse order so that the expansion can be
268 // done in-place (assumes that each position has at least one atom, which
269 // should always be the case).
270 int outputIndex = pos->m.mapb.nra;
271 for (int i = pos->count() - 1; i >= 0; --i)
273 const int atomCount = pos->m.mapb.index[i + 1] - pos->m.mapb.index[i];
274 outputIndex -= atomCount;
275 GMX_ASSERT(outputIndex >= i, "In-place algorithm would overwrite data not yet used");
276 std::fill(&value[outputIndex], &value[outputIndex + atomCount], value[i]);
283 * \param[in] fp File handle to receive the output.
284 * \param[in] evalfunc Function pointer to print.
286 void _gmx_sel_print_evalfunc_name(FILE* fp, gmx::sel_evalfunc evalfunc)
292 else if (evalfunc == &_gmx_sel_evaluate_root)
296 else if (evalfunc == &_gmx_sel_evaluate_static)
298 fprintf(fp, "static");
300 else if (evalfunc == &_gmx_sel_evaluate_subexpr_simple)
302 fprintf(fp, "subexpr_simple");
304 else if (evalfunc == &_gmx_sel_evaluate_subexpr_staticeval)
306 fprintf(fp, "subexpr_staticeval");
308 else if (evalfunc == &_gmx_sel_evaluate_subexpr)
310 fprintf(fp, "subexpr");
312 else if (evalfunc == &_gmx_sel_evaluate_subexprref_simple)
314 fprintf(fp, "ref_simple");
316 else if (evalfunc == &_gmx_sel_evaluate_subexprref)
320 else if (evalfunc == &_gmx_sel_evaluate_method)
322 fprintf(fp, "method");
324 else if (evalfunc == &_gmx_sel_evaluate_modifier)
328 else if (evalfunc == &_gmx_sel_evaluate_not)
332 else if (evalfunc == &_gmx_sel_evaluate_and)
336 else if (evalfunc == &_gmx_sel_evaluate_or)
340 else if (evalfunc == &_gmx_sel_evaluate_arithmetic)
342 fprintf(fp, "arithmetic");
346 fprintf(fp, "%p", reinterpret_cast<void*>(evalfunc));
351 * \param[out] data Evaluation data structure to initialize.
352 * \param[in] mp Memory pool for intermediate evaluation values.
353 * \param[in] gall Index group with all the atoms.
354 * \param[in] top Topology structure for evaluation.
355 * \param[in] fr New frame for evaluation.
356 * \param[in] pbc New PBC information for evaluation.
358 void _gmx_sel_evaluate_init(gmx_sel_evaluate_t* data,
359 gmx_sel_mempool_t* mp,
360 gmx_ana_index_t* gall,
361 const gmx_mtop_t* top,
373 * Recursively initializes the flags for evaluation.
375 * \param[in,out] sel Selection element to clear.
377 * The \ref SEL_INITFRAME flag is set for \ref SEL_EXPRESSION elements whose
378 * method defines the \p init_frame callback (see sel_framefunc()), and
379 * cleared for other elements.
381 * The \ref SEL_EVALFRAME flag is cleared for all elements.
383 static void init_frame_eval(SelectionTreeElementPointer sel)
387 sel->flags &= ~(SEL_INITFRAME | SEL_EVALFRAME);
388 if (sel->type == SEL_EXPRESSION)
390 if (sel->u.expr.method && sel->u.expr.method->init_frame)
392 sel->flags |= SEL_INITFRAME;
395 if (sel->child && sel->type != SEL_SUBEXPRREF)
397 init_frame_eval(sel->child);
406 SelectionEvaluator::SelectionEvaluator() {}
409 * \param[in,out] coll The selection collection to evaluate.
410 * \param[in] fr Frame for which the evaluation should be carried out.
411 * \param[in] pbc PBC data, or NULL if no PBC should be used.
412 * \returns 0 on successful evaluation, a non-zero error code on error.
414 * This functions sets the global variables for topology, frame and PBC,
415 * clears some information in the selection to initialize the evaluation
416 * for a new frame, and evaluates \p sel and all the selections pointed by
417 * the \p next pointers of \p sel.
419 * This is the only function that user code should call if they want to
420 * evaluate a selection for a new frame.
422 // NOLINTNEXTLINE readability-convert-member-functions-to-static
423 void SelectionEvaluator::evaluate(SelectionCollection* coll, t_trxframe* fr, t_pbc* pbc)
425 gmx_ana_selcollection_t* sc = &coll->impl_->sc_;
426 gmx_sel_evaluate_t data;
428 _gmx_sel_evaluate_init(&data, sc->mempool, &sc->gall, sc->top, fr, pbc);
429 init_frame_eval(sc->root);
430 SelectionTreeElementPointer sel = sc->root;
433 /* Clear the evaluation group of subexpressions */
434 if (sel->child && sel->child->type == SEL_SUBEXPR && sel->child->evaluate != nullptr)
436 sel->child->u.cgrp.isize = 0;
437 /* Not strictly necessary, because the value will be overwritten
438 * during first evaluation of the subexpression anyways, but we
439 * clear the group for clarity. Note that this is _not_ done during
440 * compilation because of some additional complexities involved
441 * (see compiler.cpp), so it should not be relied upon in
442 * _gmx_sel_evaluate_subexpr(). */
443 if (sel->child->v.type == GROUP_VALUE)
445 sel->child->v.u.g->isize = 0;
450 sel->evaluate(&data, sel, nullptr);
454 /* Update selection information */
455 SelectionDataList::const_iterator isel;
456 for (isel = sc->sel.begin(); isel != sc->sel.end(); ++isel)
458 internal::SelectionData& sel = **isel;
459 sel.refreshMassesAndCharges(sc->top);
460 sel.updateCoveredFractionForFrame();
465 * \param[in,out] coll The selection collection to evaluate.
466 * \param[in] nframes Total number of frames.
468 // NOLINTNEXTLINE readability-convert-member-functions-to-static
469 void SelectionEvaluator::evaluateFinal(SelectionCollection* coll, int nframes)
471 gmx_ana_selcollection_t* sc = &coll->impl_->sc_;
473 SelectionDataList::const_iterator isel;
474 for (isel = sc->sel.begin(); isel != sc->sel.end(); ++isel)
476 internal::SelectionData& sel = **isel;
477 sel.restoreOriginalPositions(sc->top);
478 sel.computeAverageCoveredFraction(nframes);
485 * \param[in] data Data for the current frame.
486 * \param[in] sel Selection element being evaluated.
487 * \param[in] g Group for which \p sel should be evaluated.
488 * \returns 0 on success, a non-zero error code on error.
490 * Evaluates each child of \p sel in \p g.
492 void _gmx_sel_evaluate_children(gmx_sel_evaluate_t* data,
493 const gmx::SelectionTreeElementPointer& sel,
496 SelectionTreeElementPointer child = sel->child;
501 child->evaluate(data, child, g);
507 void _gmx_sel_evaluate_root(gmx_sel_evaluate_t* data,
508 const gmx::SelectionTreeElementPointer& sel,
509 gmx_ana_index_t* /* g */)
511 if (sel->u.cgrp.isize == 0 || !sel->child->evaluate)
516 sel->child->evaluate(data, sel->child, sel->u.cgrp.isize < 0 ? nullptr : &sel->u.cgrp);
519 void _gmx_sel_evaluate_static(gmx_sel_evaluate_t* /* data */,
520 const gmx::SelectionTreeElementPointer& sel,
523 if (sel->flags & SEL_UNSORTED)
525 // This only works if g contains all the atoms, but that is currently
526 // the only supported case.
527 gmx_ana_index_copy(sel->v.u.g, &sel->u.cgrp, false);
531 gmx_ana_index_intersection(sel->v.u.g, &sel->u.cgrp, g);
536 /*********************************************************************
537 * SUBEXPRESSION EVALUATION
538 *********************************************************************/
541 * \param[in] data Data for the current frame.
542 * \param[in] sel Selection element being evaluated.
543 * \param[in] g Group for which \p sel should be evaluated.
544 * \returns 0 on success, a non-zero error code on error.
546 * Evaluates the child element (there should be exactly one) in \p g.
547 * The compiler has taken care that the child actually stores the evaluated
548 * value in the value pointer of this element.
550 * This function is used as gmx::SelectionTreeElement::evaluate for
551 * \ref SEL_SUBEXPR elements that are used only once, and hence do not need
552 * full subexpression handling.
554 void _gmx_sel_evaluate_subexpr_simple(gmx_sel_evaluate_t* data,
555 const gmx::SelectionTreeElementPointer& sel,
558 if (sel->child->evaluate)
560 sel->child->evaluate(data, sel->child, g);
562 sel->v.nr = sel->child->v.nr;
566 * \param[in] data Data for the current frame.
567 * \param[in] sel Selection element being evaluated.
568 * \param[in] g Group for which \p sel should be evaluated.
569 * \returns 0 on success, a non-zero error code on error.
571 * If this is the first call for this frame, evaluates the child element
572 * there should be exactly one in \p g.
573 * The compiler has taken care that the child actually stores the evaluated
574 * value in the value pointer of this element.
575 * Assumes that \p g is persistent for the duration of the whole evaluation.
577 * This function is used as gmx::SelectionTreeElement::evaluate for
578 * \ref SEL_SUBEXPR elements that have a static evaluation group, and hence do
579 * not need full subexpression handling.
581 void _gmx_sel_evaluate_subexpr_staticeval(gmx_sel_evaluate_t* data,
582 const gmx::SelectionTreeElementPointer& sel,
585 if (sel->u.cgrp.isize == 0)
587 sel->child->evaluate(data, sel->child, g);
588 sel->v.nr = sel->child->v.nr;
591 sel->u.cgrp.isize = -1;
595 gmx_ana_index_set(&sel->u.cgrp, g->isize, g->index, 0);
601 * \param[in] data Data for the current frame.
602 * \param[in] sel Selection element being evaluated.
603 * \param[in] g Group for which \p sel should be evaluated.
604 * \returns 0 on success, a non-zero error code on error.
606 * Finds the part of \p g for which the subexpression
607 * has not yet been evaluated by comparing \p g to \p sel->u.cgrp.
608 * If the part is not empty, the child expression is evaluated for this
609 * part, and the results merged to the old values of the child.
610 * The value of \p sel itself is undefined after the call.
613 * The call to gmx_ana_index_difference() can take quite a lot of unnecessary
614 * time if the subexpression is evaluated either several times for the same
615 * group or for completely distinct groups.
616 * However, in the majority of cases, these situations occur when
617 * _gmx_sel_evaluate_subexpr_staticeval() can be used, so this should not be a
620 void _gmx_sel_evaluate_subexpr(gmx_sel_evaluate_t* data,
621 const gmx::SelectionTreeElementPointer& sel,
624 gmx_ana_index_t gmiss;
626 MempoolGroupReserver gmissreserver(data->mp);
627 if (sel->u.cgrp.isize == 0)
630 SelelemTemporaryValueAssigner assigner(sel->child, *sel);
631 sel->child->evaluate(data, sel->child, g);
633 gmx_ana_index_copy(&sel->u.cgrp, g, false);
638 gmissreserver.reserve(&gmiss, g->isize);
639 gmx_ana_index_difference(&gmiss, g, &sel->u.cgrp);
643 MempoolSelelemReserver reserver(sel->child, gmiss.isize);
644 /* Evaluate the missing values for the child */
645 sel->child->evaluate(data, sel->child, &gmiss);
646 /* Merge the missing values to the existing ones. */
647 if (sel->v.type == GROUP_VALUE)
649 gmx_ana_index_merge(sel->v.u.g, sel->child->v.u.g, sel->v.u.g);
655 i = sel->u.cgrp.isize - 1;
657 /* TODO: This switch is kind of ugly, but it may be difficult to
658 * do this portably without C++ templates. */
662 for (k = sel->u.cgrp.isize + gmiss.isize - 1; k >= 0; k--)
664 if (i < 0 || (j >= 0 && sel->u.cgrp.index[i] < gmiss.index[j]))
666 sel->v.u.i[k] = sel->child->v.u.i[j--];
670 sel->v.u.i[k] = sel->v.u.i[i--];
676 for (k = sel->u.cgrp.isize + gmiss.isize - 1; k >= 0; k--)
678 if (i < 0 || (j >= 0 && sel->u.cgrp.index[i] < gmiss.index[j]))
680 sel->v.u.r[k] = sel->child->v.u.r[j--];
684 sel->v.u.r[k] = sel->v.u.r[i--];
690 // Note: with the currently allowed syntax, this case is never
692 for (k = sel->u.cgrp.isize + gmiss.isize - 1; k >= 0; k--)
694 if (i < 0 || (j >= 0 && sel->u.cgrp.index[i] < gmiss.index[j]))
696 sel->v.u.s[k] = sel->child->v.u.s[j--];
700 sel->v.u.s[k] = sel->v.u.s[i--];
706 /* TODO: Implement this */
707 GMX_THROW(gmx::NotImplementedError(
708 "position subexpressions not implemented properly"));
711 case GROUP_VALUE: GMX_THROW(gmx::InternalError("Invalid subexpression type"));
714 gmx_ana_index_merge(&sel->u.cgrp, &sel->u.cgrp, &gmiss);
719 * \param[in] data Data for the current frame.
720 * \param[in] sel Selection element being evaluated.
721 * \param[in] g Group for which \p sel should be evaluated.
722 * \returns 0 for success.
724 * Sets the value pointers of the child and its child to point to the same
725 * memory as the value pointer of this element to avoid copying, and then
726 * evaluates evaluates the child.
728 * This function is used as gmx::SelectionTreeElement:evaluate for
729 * \ref SEL_SUBEXPRREF elements for which the \ref SEL_SUBEXPR does not have
732 void _gmx_sel_evaluate_subexprref_simple(gmx_sel_evaluate_t* data,
733 const gmx::SelectionTreeElementPointer& sel,
738 _gmx_selvalue_setstore(&sel->child->v, sel->v.u.ptr);
739 _gmx_selvalue_setstore_alloc(&sel->child->child->v, sel->v.u.ptr, sel->child->child->v.nalloc);
740 sel->child->evaluate(data, sel->child, g);
742 sel->v.nr = sel->child->v.nr;
745 sel->u.param->val.nr = sel->v.nr;
746 if (sel->u.param->nvalptr)
748 *sel->u.param->nvalptr = sel->u.param->val.nr;
754 * \param[in] data Data for the current frame.
755 * \param[in] sel Selection element being evaluated.
756 * \param[in] g Group for which \p sel should be evaluated.
757 * \returns 0 on success, a non-zero error code on error.
759 * If the value type is \ref POS_VALUE, the value of the child is simply
760 * copied to set the value of \p sel (the child subexpression should
761 * already have been evaluated by its root).
762 * If the value type is something else, the child is evaluated for the
763 * group \p g, and the value of the child is then copied.
764 * There should be only one child element.
766 * This function is used as gmx::SelectionTreeElement::evaluate for
767 * \ref SEL_SUBEXPRREF elements.
769 void _gmx_sel_evaluate_subexprref(gmx_sel_evaluate_t* data,
770 const gmx::SelectionTreeElementPointer& sel,
775 if (g != nullptr && sel->child->evaluate != nullptr)
777 sel->child->evaluate(data, sel->child, g);
779 const SelectionTreeElementPointer& expr = sel->child;
785 sel->v.nr = expr->v.nr;
786 memcpy(sel->v.u.i, expr->v.u.i, sel->v.nr * sizeof(*sel->v.u.i));
790 sel->v.nr = g->isize;
791 /* Extract the values corresponding to g */
792 for (i = j = 0; i < g->isize; ++i, ++j)
794 while (sel->child->u.cgrp.index[j] < g->index[i])
798 sel->v.u.i[i] = expr->v.u.i[j];
806 sel->v.nr = expr->v.nr;
807 memcpy(sel->v.u.r, expr->v.u.r, sel->v.nr * sizeof(*sel->v.u.r));
811 sel->v.nr = g->isize;
812 /* Extract the values corresponding to g */
813 for (i = j = 0; i < g->isize; ++i, ++j)
815 while (sel->child->u.cgrp.index[j] < g->index[i])
819 sel->v.u.r[i] = expr->v.u.r[j];
827 sel->v.nr = expr->v.nr;
828 memcpy(sel->v.u.s, expr->v.u.s, sel->v.nr * sizeof(*sel->v.u.s));
832 sel->v.nr = g->isize;
833 /* Extract the values corresponding to g */
834 for (i = j = 0; i < g->isize; ++i, ++j)
836 while (sel->child->u.cgrp.index[j] < g->index[i])
840 sel->v.u.s[i] = expr->v.u.s[j];
846 /* Currently, there is no need to do anything fancy here,
847 * but some future extensions may need a more flexible
849 gmx_ana_pos_copy(sel->v.u.p, expr->v.u.p, false);
855 gmx_ana_index_copy(sel->v.u.g, expr->v.u.g, false);
859 gmx_ana_index_intersection(sel->v.u.g, expr->v.u.g, g);
863 default: /* should not be reached */
864 GMX_THROW(gmx::InternalError("Invalid subexpression reference type"));
866 /* Store the number of values if needed */
869 sel->u.param->val.nr = sel->v.nr;
870 if (sel->u.param->nvalptr)
872 *sel->u.param->nvalptr = sel->u.param->val.nr;
877 /********************************************************************
878 * METHOD EXPRESSION EVALUATION
879 ********************************************************************/
882 * \param[in] data Data for the current frame.
883 * \param[in] sel Selection element being evaluated.
884 * \param[in] g Group for which \p sel should be evaluated.
885 * \returns 0 on success, a non-zero error code on error.
887 * Evaluates each child of a \ref SEL_EXPRESSION element.
888 * The value of \p sel is not touched.
890 * This function is not used as gmx::SelectionTreeElement::evaluate,
891 * but is used internally.
893 void _gmx_sel_evaluate_method_params(gmx_sel_evaluate_t* data,
894 const gmx::SelectionTreeElementPointer& sel,
897 SelectionTreeElementPointer child = sel->child;
900 if (child->evaluate && !(child->flags & SEL_EVALFRAME))
902 if (child->flags & SEL_ATOMVAL)
904 child->evaluate(data, child, g);
908 child->flags |= SEL_EVALFRAME;
909 child->evaluate(data, child, nullptr);
917 * \param[in] data Data for the current frame.
918 * \param[in] sel Selection element being evaluated.
919 * \param[in] g Group for which \p sel should be evaluated.
920 * \returns 0 on success, a non-zero error code on error.
922 * Evaluates all child selections (using _gmx_sel_evaluate_method_params())
923 * to evaluate any parameter values.
924 * If this is the first time this expression is evaluated for
925 * the frame, sel_framefunc() callback is called if one is provided.
926 * If a reference position calculation has been initialized for this element,
927 * the positions are also updated, and sel_updatefunc_pos() is used to
928 * evaluate the value. Otherwise, sel_updatefunc() is used.
930 * This function is used as gmx::SelectionTreeElement::evaluate for
931 * \ref SEL_EXPRESSION elements.
933 void _gmx_sel_evaluate_method(gmx_sel_evaluate_t* data,
934 const gmx::SelectionTreeElementPointer& sel,
937 _gmx_sel_evaluate_method_params(data, sel, g);
938 gmx::SelMethodEvalContext context(data->top, data->fr, data->pbc);
939 if (sel->flags & SEL_INITFRAME)
941 sel->flags &= ~SEL_INITFRAME;
942 sel->u.expr.method->init_frame(context, sel->u.expr.mdata);
946 gmx_ana_poscalc_update(sel->u.expr.pc, sel->u.expr.pos, g, data->fr, data->pbc);
947 sel->u.expr.method->pupdate(context, sel->u.expr.pos, &sel->v, sel->u.expr.mdata);
948 if ((sel->flags & SEL_ATOMVAL) && sel->v.nr < g->isize)
953 expandValueForPositions(sel->v.u.r, &sel->v.nr, sel->u.expr.pos);
956 GMX_RELEASE_ASSERT(false, "Unimplemented value type for position update method");
962 sel->u.expr.method->update(context, g, &sel->v, sel->u.expr.mdata);
967 * \param[in] data Data for the current frame.
968 * \param[in] sel Selection element being evaluated.
969 * \param[in] g Group for which \p sel should be evaluated.
970 * \returns 0 on success, a non-zero error code on error.
972 * Evaluates all child selections (using _gmx_sel_evaluate_method_params())
973 * to evaluate any parameter values.
974 * If this is the first time this expression is evaluated for
975 * the frame, sel_framefunc() callback is called if one is provided.
976 * The modifier is then evaluated using sel_updatefunc_pos().
978 * This function is used as gmx::SelectionTreeElement::evaluate for
979 * \ref SEL_MODIFIER elements.
981 void _gmx_sel_evaluate_modifier(gmx_sel_evaluate_t* data,
982 const gmx::SelectionTreeElementPointer& sel,
985 _gmx_sel_evaluate_method_params(data, sel, g);
986 gmx::SelMethodEvalContext context(data->top, data->fr, data->pbc);
987 if (sel->flags & SEL_INITFRAME)
989 sel->flags &= ~SEL_INITFRAME;
990 sel->u.expr.method->init_frame(context, sel->u.expr.mdata);
992 if (sel->child && sel->child->v.type != POS_VALUE)
994 GMX_THROW(gmx::NotImplementedError("Non-position valued modifiers not implemented"));
996 sel->u.expr.method->pupdate(context, nullptr, &sel->v, sel->u.expr.mdata);
1000 /********************************************************************
1001 * BOOLEAN EXPRESSION EVALUATION
1002 ********************************************************************/
1005 * \param[in] data Data for the current frame.
1006 * \param[in] sel Selection element being evaluated.
1007 * \param[in] g Group for which \p sel should be evaluated.
1008 * \returns 0 on success, a non-zero error code on error.
1010 * Evaluates the child element (there should be only one) in the group
1011 * \p g, and then sets the value of \p sel to the complement of the
1014 * This function is used as gmx::SelectionTreeElement::evaluate for
1015 * \ref SEL_BOOLEAN elements with \ref BOOL_NOT.
1017 void _gmx_sel_evaluate_not(gmx_sel_evaluate_t* data,
1018 const gmx::SelectionTreeElementPointer& sel,
1021 MempoolSelelemReserver reserver(sel->child, g->isize);
1022 sel->child->evaluate(data, sel->child, g);
1023 gmx_ana_index_difference(sel->v.u.g, g, sel->child->v.u.g);
1027 * \param[in] data Data for the current frame.
1028 * \param[in] sel Selection element being evaluated.
1029 * \param[in] g Group for which \p sel should be evaluated.
1030 * \returns 0 on success, a non-zero error code on error.
1032 * Short-circuiting evaluation of logical AND expressions.
1034 * Starts by evaluating the first child element in the group \p g.
1035 * The each following child element is evaluated in the intersection
1036 * of all the previous values until all children have been evaluated
1037 * or the intersection becomes empty.
1038 * The value of \p sel is set to the intersection of all the (evaluated)
1041 * If the first child does not have an evaluation function, it is skipped
1042 * and the evaluation is started at the second child.
1043 * This happens if the first child is a constant expression and during
1044 * compilation it was detected that the evaluation group is always a subset
1045 * of the constant group
1046 * (currently, the compiler never detects this).
1048 * This function is used as gmx::SelectionTreeElement::evaluate for
1049 * \ref SEL_BOOLEAN elements with \ref BOOL_AND.
1051 void _gmx_sel_evaluate_and(gmx_sel_evaluate_t* data,
1052 const gmx::SelectionTreeElementPointer& sel,
1055 SelectionTreeElementPointer child = sel->child;
1056 /* Skip the first child if it does not have an evaluation function. */
1057 if (!child->evaluate)
1059 child = child->next;
1061 /* Evaluate the first child */
1063 MempoolSelelemReserver reserver(child, g->isize);
1064 child->evaluate(data, child, g);
1065 gmx_ana_index_copy(sel->v.u.g, child->v.u.g, false);
1067 child = child->next;
1068 while (child && sel->v.u.g->isize > 0)
1070 MempoolSelelemReserver reserver(child, sel->v.u.g->isize);
1071 child->evaluate(data, child, sel->v.u.g);
1072 gmx_ana_index_intersection(sel->v.u.g, sel->v.u.g, child->v.u.g);
1073 child = child->next;
1078 * \param[in] data Data for the current frame.
1079 * \param[in] sel Selection element being evaluated.
1080 * \param[in] g Group for which \p sel should be evaluated.
1081 * \returns 0 on success, a non-zero error code on error.
1083 * Short-circuiting evaluation of logical OR expressions.
1085 * Starts by evaluating the first child element in the group \p g.
1086 * For each subsequent child, finds the part of \p g that is not
1087 * included the value of any previous child, and evaluates the child
1088 * in that group until the last child is evaluated or all of \p g
1089 * is included in some child value.
1090 * The value of \p sel is set to the union of all the (evaluated)
1093 * If the first child does not have an evaluation function, its value is
1094 * used without evaluation.
1095 * This happens if the first child is a constant expression, the selection
1096 * has been compiled, and the evaluation group is the same for each frame.
1097 * In this case, the compiler has taken care of that the child value is a
1098 * subset of \p g, making it unnecessary to evaluate it.
1100 * This function is used as gmx::SelectionTreeElement::evaluate for
1101 * \ref SEL_BOOLEAN elements with \ref BOOL_OR.
1103 void _gmx_sel_evaluate_or(gmx_sel_evaluate_t* data,
1104 const gmx::SelectionTreeElementPointer& sel,
1107 gmx_ana_index_t tmp, tmp2;
1109 SelectionTreeElementPointer child = sel->child;
1110 if (child->evaluate)
1112 MempoolSelelemReserver reserver(child, g->isize);
1113 child->evaluate(data, child, g);
1114 gmx_ana_index_partition(sel->v.u.g, &tmp, g, child->v.u.g);
1118 gmx_ana_index_partition(sel->v.u.g, &tmp, g, child->v.u.g);
1120 child = child->next;
1121 while (child && tmp.isize > 0)
1124 MempoolSelelemReserver reserver(child, tmp.isize);
1125 child->evaluate(data, child, &tmp);
1126 gmx_ana_index_partition(&tmp, &tmp2, &tmp, child->v.u.g);
1128 sel->v.u.g->isize += tmp.isize;
1129 tmp.isize = tmp2.isize;
1130 tmp.index = tmp2.index;
1131 child = child->next;
1133 gmx_ana_index_sort(sel->v.u.g);
1137 /********************************************************************
1138 * ARITHMETIC EVALUATION
1139 ********************************************************************/
1142 * \param[in] data Data for the current frame.
1143 * \param[in] sel Selection element being evaluated.
1144 * \param[in] g Group for which \p sel should be evaluated.
1145 * \returns 0 on success, a non-zero error code on error.
1147 void _gmx_sel_evaluate_arithmetic(gmx_sel_evaluate_t* data,
1148 const gmx::SelectionTreeElementPointer& sel,
1152 real lval, rval = 0., val = 0.;
1154 const SelectionTreeElementPointer& left = sel->child;
1155 const SelectionTreeElementPointer& right = left->next;
1157 SelelemTemporaryValueAssigner assigner;
1158 MempoolSelelemReserver reserver;
1161 assigner.assign(left, *sel);
1164 reserver.reserve(right, g->isize);
1167 else if (right && right->mempool)
1169 assigner.assign(right, *sel);
1171 _gmx_sel_evaluate_children(data, sel, g);
1173 n = (sel->flags & SEL_SINGLEVAL) ? 1 : g->isize;
1176 bool bArithNeg = (sel->u.arith.type == ARITH_NEG);
1177 GMX_ASSERT(right || bArithNeg, "Right operand cannot be null except for negations");
1178 for (i = i1 = i2 = 0; i < n; ++i)
1180 lval = left->v.u.r[i1];
1183 rval = right->v.u.r[i2];
1185 switch (sel->u.arith.type)
1187 case ARITH_PLUS: val = lval + rval; break;
1188 case ARITH_MINUS: val = lval - rval; break;
1189 case ARITH_NEG: val = -lval; break;
1190 case ARITH_MULT: val = lval * rval; break;
1191 case ARITH_DIV: val = lval / rval; break;
1192 case ARITH_EXP: val = pow(lval, rval); break;
1194 sel->v.u.r[i] = val;
1195 if (!(left->flags & SEL_SINGLEVAL))
1199 if (!bArithNeg && !(right->flags & SEL_SINGLEVAL))