2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 2009,2010,2011,2012,2013 by the GROMACS development team.
5 * Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
6 * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
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 gmx_ana_index_reserve(sel->v.u.g, sel->u.cgrp.isize);
526 // This only works if g contains all the atoms, but that is currently
527 // the only supported case.
528 gmx_ana_index_copy(sel->v.u.g, &sel->u.cgrp, false);
532 gmx_ana_index_intersection(sel->v.u.g, &sel->u.cgrp, g);
537 /*********************************************************************
538 * SUBEXPRESSION EVALUATION
539 *********************************************************************/
542 * \param[in] data Data for the current frame.
543 * \param[in] sel Selection element being evaluated.
544 * \param[in] g Group for which \p sel should be evaluated.
545 * \returns 0 on success, a non-zero error code on error.
547 * Evaluates the child element (there should be exactly one) in \p g.
548 * The compiler has taken care that the child actually stores the evaluated
549 * value in the value pointer of this element.
551 * This function is used as gmx::SelectionTreeElement::evaluate for
552 * \ref SEL_SUBEXPR elements that are used only once, and hence do not need
553 * full subexpression handling.
555 void _gmx_sel_evaluate_subexpr_simple(gmx_sel_evaluate_t* data,
556 const gmx::SelectionTreeElementPointer& sel,
559 if (sel->child->evaluate)
561 sel->child->evaluate(data, sel->child, g);
563 sel->v.nr = sel->child->v.nr;
567 * \param[in] data Data for the current frame.
568 * \param[in] sel Selection element being evaluated.
569 * \param[in] g Group for which \p sel should be evaluated.
570 * \returns 0 on success, a non-zero error code on error.
572 * If this is the first call for this frame, evaluates the child element
573 * there should be exactly one in \p g.
574 * The compiler has taken care that the child actually stores the evaluated
575 * value in the value pointer of this element.
576 * Assumes that \p g is persistent for the duration of the whole evaluation.
578 * This function is used as gmx::SelectionTreeElement::evaluate for
579 * \ref SEL_SUBEXPR elements that have a static evaluation group, and hence do
580 * not need full subexpression handling.
582 void _gmx_sel_evaluate_subexpr_staticeval(gmx_sel_evaluate_t* data,
583 const gmx::SelectionTreeElementPointer& sel,
586 if (sel->u.cgrp.isize == 0)
588 sel->child->evaluate(data, sel->child, g);
589 sel->v.nr = sel->child->v.nr;
592 sel->u.cgrp.isize = -1;
596 gmx_ana_index_set(&sel->u.cgrp, g->isize, g->index, 0);
602 * \param[in] data Data for the current frame.
603 * \param[in] sel Selection element being evaluated.
604 * \param[in] g Group for which \p sel should be evaluated.
605 * \returns 0 on success, a non-zero error code on error.
607 * Finds the part of \p g for which the subexpression
608 * has not yet been evaluated by comparing \p g to \p sel->u.cgrp.
609 * If the part is not empty, the child expression is evaluated for this
610 * part, and the results merged to the old values of the child.
611 * The value of \p sel itself is undefined after the call.
614 * The call to gmx_ana_index_difference() can take quite a lot of unnecessary
615 * time if the subexpression is evaluated either several times for the same
616 * group or for completely distinct groups.
617 * However, in the majority of cases, these situations occur when
618 * _gmx_sel_evaluate_subexpr_staticeval() can be used, so this should not be a
621 void _gmx_sel_evaluate_subexpr(gmx_sel_evaluate_t* data,
622 const gmx::SelectionTreeElementPointer& sel,
625 gmx_ana_index_t gmiss;
627 MempoolGroupReserver gmissreserver(data->mp);
628 if (sel->u.cgrp.isize == 0)
631 SelelemTemporaryValueAssigner assigner(sel->child, *sel);
632 sel->child->evaluate(data, sel->child, g);
634 gmx_ana_index_copy(&sel->u.cgrp, g, false);
639 gmissreserver.reserve(&gmiss, g->isize);
640 gmx_ana_index_difference(&gmiss, g, &sel->u.cgrp);
644 MempoolSelelemReserver reserver(sel->child, gmiss.isize);
645 /* Evaluate the missing values for the child */
646 sel->child->evaluate(data, sel->child, &gmiss);
647 /* Merge the missing values to the existing ones. */
648 if (sel->v.type == GROUP_VALUE)
650 gmx_ana_index_merge(sel->v.u.g, sel->child->v.u.g, sel->v.u.g);
656 i = sel->u.cgrp.isize - 1;
658 /* TODO: This switch is kind of ugly, but it may be difficult to
659 * do this portably without C++ templates. */
663 for (k = sel->u.cgrp.isize + gmiss.isize - 1; k >= 0; k--)
665 if (i < 0 || (j >= 0 && sel->u.cgrp.index[i] < gmiss.index[j]))
667 sel->v.u.i[k] = sel->child->v.u.i[j--];
671 sel->v.u.i[k] = sel->v.u.i[i--];
677 for (k = sel->u.cgrp.isize + gmiss.isize - 1; k >= 0; k--)
679 if (i < 0 || (j >= 0 && sel->u.cgrp.index[i] < gmiss.index[j]))
681 sel->v.u.r[k] = sel->child->v.u.r[j--];
685 sel->v.u.r[k] = sel->v.u.r[i--];
691 // Note: with the currently allowed syntax, this case is never
693 for (k = sel->u.cgrp.isize + gmiss.isize - 1; k >= 0; k--)
695 if (i < 0 || (j >= 0 && sel->u.cgrp.index[i] < gmiss.index[j]))
697 sel->v.u.s[k] = sel->child->v.u.s[j--];
701 sel->v.u.s[k] = sel->v.u.s[i--];
707 /* TODO: Implement this */
708 GMX_THROW(gmx::NotImplementedError(
709 "position subexpressions not implemented properly"));
712 case GROUP_VALUE: GMX_THROW(gmx::InternalError("Invalid subexpression type"));
715 gmx_ana_index_merge(&sel->u.cgrp, &sel->u.cgrp, &gmiss);
720 * \param[in] data Data for the current frame.
721 * \param[in] sel Selection element being evaluated.
722 * \param[in] g Group for which \p sel should be evaluated.
723 * \returns 0 for success.
725 * Sets the value pointers of the child and its child to point to the same
726 * memory as the value pointer of this element to avoid copying, and then
727 * evaluates evaluates the child.
729 * This function is used as gmx::SelectionTreeElement:evaluate for
730 * \ref SEL_SUBEXPRREF elements for which the \ref SEL_SUBEXPR does not have
733 void _gmx_sel_evaluate_subexprref_simple(gmx_sel_evaluate_t* data,
734 const gmx::SelectionTreeElementPointer& sel,
739 _gmx_selvalue_setstore(&sel->child->v, sel->v.u.ptr);
740 _gmx_selvalue_setstore_alloc(&sel->child->child->v, sel->v.u.ptr, sel->child->child->v.nalloc);
741 sel->child->evaluate(data, sel->child, g);
743 sel->v.nr = sel->child->v.nr;
746 sel->u.param->val.nr = sel->v.nr;
747 if (sel->u.param->nvalptr)
749 *sel->u.param->nvalptr = sel->u.param->val.nr;
755 * \param[in] data Data for the current frame.
756 * \param[in] sel Selection element being evaluated.
757 * \param[in] g Group for which \p sel should be evaluated.
758 * \returns 0 on success, a non-zero error code on error.
760 * If the value type is \ref POS_VALUE, the value of the child is simply
761 * copied to set the value of \p sel (the child subexpression should
762 * already have been evaluated by its root).
763 * If the value type is something else, the child is evaluated for the
764 * group \p g, and the value of the child is then copied.
765 * There should be only one child element.
767 * This function is used as gmx::SelectionTreeElement::evaluate for
768 * \ref SEL_SUBEXPRREF elements.
770 void _gmx_sel_evaluate_subexprref(gmx_sel_evaluate_t* data,
771 const gmx::SelectionTreeElementPointer& sel,
776 if (g != nullptr && sel->child->evaluate != nullptr)
778 sel->child->evaluate(data, sel->child, g);
780 const SelectionTreeElementPointer& expr = sel->child;
786 sel->v.nr = expr->v.nr;
787 memcpy(sel->v.u.i, expr->v.u.i, sel->v.nr * sizeof(*sel->v.u.i));
791 sel->v.nr = g->isize;
792 /* Extract the values corresponding to g */
793 for (i = j = 0; i < g->isize; ++i, ++j)
795 while (sel->child->u.cgrp.index[j] < g->index[i])
799 sel->v.u.i[i] = expr->v.u.i[j];
807 sel->v.nr = expr->v.nr;
808 memcpy(sel->v.u.r, expr->v.u.r, sel->v.nr * sizeof(*sel->v.u.r));
812 sel->v.nr = g->isize;
813 /* Extract the values corresponding to g */
814 for (i = j = 0; i < g->isize; ++i, ++j)
816 while (sel->child->u.cgrp.index[j] < g->index[i])
820 sel->v.u.r[i] = expr->v.u.r[j];
828 sel->v.nr = expr->v.nr;
829 memcpy(sel->v.u.s, expr->v.u.s, sel->v.nr * sizeof(*sel->v.u.s));
833 sel->v.nr = g->isize;
834 /* Extract the values corresponding to g */
835 for (i = j = 0; i < g->isize; ++i, ++j)
837 while (sel->child->u.cgrp.index[j] < g->index[i])
841 sel->v.u.s[i] = expr->v.u.s[j];
847 /* Currently, there is no need to do anything fancy here,
848 * but some future extensions may need a more flexible
850 gmx_ana_pos_copy(sel->v.u.p, expr->v.u.p, false);
856 gmx_ana_index_copy(sel->v.u.g, expr->v.u.g, false);
860 gmx_ana_index_intersection(sel->v.u.g, expr->v.u.g, g);
864 default: /* should not be reached */
865 GMX_THROW(gmx::InternalError("Invalid subexpression reference type"));
867 /* Store the number of values if needed */
870 sel->u.param->val.nr = sel->v.nr;
871 if (sel->u.param->nvalptr)
873 *sel->u.param->nvalptr = sel->u.param->val.nr;
878 /********************************************************************
879 * METHOD EXPRESSION EVALUATION
880 ********************************************************************/
883 * \param[in] data Data for the current frame.
884 * \param[in] sel Selection element being evaluated.
885 * \param[in] g Group for which \p sel should be evaluated.
886 * \returns 0 on success, a non-zero error code on error.
888 * Evaluates each child of a \ref SEL_EXPRESSION element.
889 * The value of \p sel is not touched.
891 * This function is not used as gmx::SelectionTreeElement::evaluate,
892 * but is used internally.
894 void _gmx_sel_evaluate_method_params(gmx_sel_evaluate_t* data,
895 const gmx::SelectionTreeElementPointer& sel,
898 SelectionTreeElementPointer child = sel->child;
901 if (child->evaluate && !(child->flags & SEL_EVALFRAME))
903 if (child->flags & SEL_ATOMVAL)
905 child->evaluate(data, child, g);
909 child->flags |= SEL_EVALFRAME;
910 child->evaluate(data, child, nullptr);
918 * \param[in] data Data for the current frame.
919 * \param[in] sel Selection element being evaluated.
920 * \param[in] g Group for which \p sel should be evaluated.
921 * \returns 0 on success, a non-zero error code on error.
923 * Evaluates all child selections (using _gmx_sel_evaluate_method_params())
924 * to evaluate any parameter values.
925 * If this is the first time this expression is evaluated for
926 * the frame, sel_framefunc() callback is called if one is provided.
927 * If a reference position calculation has been initialized for this element,
928 * the positions are also updated, and sel_updatefunc_pos() is used to
929 * evaluate the value. Otherwise, sel_updatefunc() is used.
931 * This function is used as gmx::SelectionTreeElement::evaluate for
932 * \ref SEL_EXPRESSION elements.
934 void _gmx_sel_evaluate_method(gmx_sel_evaluate_t* data,
935 const gmx::SelectionTreeElementPointer& sel,
938 _gmx_sel_evaluate_method_params(data, sel, g);
939 gmx::SelMethodEvalContext context(data->top, data->fr, data->pbc);
940 if (sel->flags & SEL_INITFRAME)
942 sel->flags &= ~SEL_INITFRAME;
943 sel->u.expr.method->init_frame(context, sel->u.expr.mdata);
947 gmx_ana_poscalc_update(sel->u.expr.pc, sel->u.expr.pos, g, data->fr, data->pbc);
948 sel->u.expr.method->pupdate(context, sel->u.expr.pos, &sel->v, sel->u.expr.mdata);
949 if ((sel->flags & SEL_ATOMVAL) && sel->v.nr < g->isize)
954 expandValueForPositions(sel->v.u.r, &sel->v.nr, sel->u.expr.pos);
957 GMX_RELEASE_ASSERT(false, "Unimplemented value type for position update method");
963 sel->u.expr.method->update(context, g, &sel->v, sel->u.expr.mdata);
968 * \param[in] data Data for the current frame.
969 * \param[in] sel Selection element being evaluated.
970 * \param[in] g Group for which \p sel should be evaluated.
971 * \returns 0 on success, a non-zero error code on error.
973 * Evaluates all child selections (using _gmx_sel_evaluate_method_params())
974 * to evaluate any parameter values.
975 * If this is the first time this expression is evaluated for
976 * the frame, sel_framefunc() callback is called if one is provided.
977 * The modifier is then evaluated using sel_updatefunc_pos().
979 * This function is used as gmx::SelectionTreeElement::evaluate for
980 * \ref SEL_MODIFIER elements.
982 void _gmx_sel_evaluate_modifier(gmx_sel_evaluate_t* data,
983 const gmx::SelectionTreeElementPointer& sel,
986 _gmx_sel_evaluate_method_params(data, sel, g);
987 gmx::SelMethodEvalContext context(data->top, data->fr, data->pbc);
988 if (sel->flags & SEL_INITFRAME)
990 sel->flags &= ~SEL_INITFRAME;
991 sel->u.expr.method->init_frame(context, sel->u.expr.mdata);
993 if (sel->child && sel->child->v.type != POS_VALUE)
995 GMX_THROW(gmx::NotImplementedError("Non-position valued modifiers not implemented"));
997 sel->u.expr.method->pupdate(context, nullptr, &sel->v, sel->u.expr.mdata);
1001 /********************************************************************
1002 * BOOLEAN EXPRESSION EVALUATION
1003 ********************************************************************/
1006 * \param[in] data Data for the current frame.
1007 * \param[in] sel Selection element being evaluated.
1008 * \param[in] g Group for which \p sel should be evaluated.
1009 * \returns 0 on success, a non-zero error code on error.
1011 * Evaluates the child element (there should be only one) in the group
1012 * \p g, and then sets the value of \p sel to the complement of the
1015 * This function is used as gmx::SelectionTreeElement::evaluate for
1016 * \ref SEL_BOOLEAN elements with \ref BOOL_NOT.
1018 void _gmx_sel_evaluate_not(gmx_sel_evaluate_t* data,
1019 const gmx::SelectionTreeElementPointer& sel,
1022 MempoolSelelemReserver reserver(sel->child, g->isize);
1023 sel->child->evaluate(data, sel->child, g);
1024 gmx_ana_index_difference(sel->v.u.g, g, sel->child->v.u.g);
1028 * \param[in] data Data for the current frame.
1029 * \param[in] sel Selection element being evaluated.
1030 * \param[in] g Group for which \p sel should be evaluated.
1031 * \returns 0 on success, a non-zero error code on error.
1033 * Short-circuiting evaluation of logical AND expressions.
1035 * Starts by evaluating the first child element in the group \p g.
1036 * The each following child element is evaluated in the intersection
1037 * of all the previous values until all children have been evaluated
1038 * or the intersection becomes empty.
1039 * The value of \p sel is set to the intersection of all the (evaluated)
1042 * If the first child does not have an evaluation function, it is skipped
1043 * and the evaluation is started at the second child.
1044 * This happens if the first child is a constant expression and during
1045 * compilation it was detected that the evaluation group is always a subset
1046 * of the constant group
1047 * (currently, the compiler never detects this).
1049 * This function is used as gmx::SelectionTreeElement::evaluate for
1050 * \ref SEL_BOOLEAN elements with \ref BOOL_AND.
1052 void _gmx_sel_evaluate_and(gmx_sel_evaluate_t* data,
1053 const gmx::SelectionTreeElementPointer& sel,
1056 SelectionTreeElementPointer child = sel->child;
1057 /* Skip the first child if it does not have an evaluation function. */
1058 if (!child->evaluate)
1060 child = child->next;
1062 /* Evaluate the first child */
1064 MempoolSelelemReserver reserver(child, g->isize);
1065 child->evaluate(data, child, g);
1066 gmx_ana_index_copy(sel->v.u.g, child->v.u.g, false);
1068 child = child->next;
1069 while (child && sel->v.u.g->isize > 0)
1071 MempoolSelelemReserver reserver(child, sel->v.u.g->isize);
1072 child->evaluate(data, child, sel->v.u.g);
1073 gmx_ana_index_intersection(sel->v.u.g, sel->v.u.g, child->v.u.g);
1074 child = child->next;
1079 * \param[in] data Data for the current frame.
1080 * \param[in] sel Selection element being evaluated.
1081 * \param[in] g Group for which \p sel should be evaluated.
1082 * \returns 0 on success, a non-zero error code on error.
1084 * Short-circuiting evaluation of logical OR expressions.
1086 * Starts by evaluating the first child element in the group \p g.
1087 * For each subsequent child, finds the part of \p g that is not
1088 * included the value of any previous child, and evaluates the child
1089 * in that group until the last child is evaluated or all of \p g
1090 * is included in some child value.
1091 * The value of \p sel is set to the union of all the (evaluated)
1094 * If the first child does not have an evaluation function, its value is
1095 * used without evaluation.
1096 * This happens if the first child is a constant expression, the selection
1097 * has been compiled, and the evaluation group is the same for each frame.
1098 * In this case, the compiler has taken care of that the child value is a
1099 * subset of \p g, making it unnecessary to evaluate it.
1101 * This function is used as gmx::SelectionTreeElement::evaluate for
1102 * \ref SEL_BOOLEAN elements with \ref BOOL_OR.
1104 void _gmx_sel_evaluate_or(gmx_sel_evaluate_t* data,
1105 const gmx::SelectionTreeElementPointer& sel,
1108 gmx_ana_index_t tmp, tmp2;
1110 SelectionTreeElementPointer child = sel->child;
1111 if (child->evaluate)
1113 MempoolSelelemReserver reserver(child, g->isize);
1114 child->evaluate(data, child, g);
1115 gmx_ana_index_partition(sel->v.u.g, &tmp, g, child->v.u.g);
1119 gmx_ana_index_partition(sel->v.u.g, &tmp, g, child->v.u.g);
1121 child = child->next;
1122 while (child && tmp.isize > 0)
1125 MempoolSelelemReserver reserver(child, tmp.isize);
1126 child->evaluate(data, child, &tmp);
1127 gmx_ana_index_partition(&tmp, &tmp2, &tmp, child->v.u.g);
1129 sel->v.u.g->isize += tmp.isize;
1130 tmp.isize = tmp2.isize;
1131 tmp.index = tmp2.index;
1132 child = child->next;
1134 gmx_ana_index_sort(sel->v.u.g);
1138 /********************************************************************
1139 * ARITHMETIC EVALUATION
1140 ********************************************************************/
1143 * \param[in] data Data for the current frame.
1144 * \param[in] sel Selection element being evaluated.
1145 * \param[in] g Group for which \p sel should be evaluated.
1146 * \returns 0 on success, a non-zero error code on error.
1148 void _gmx_sel_evaluate_arithmetic(gmx_sel_evaluate_t* data,
1149 const gmx::SelectionTreeElementPointer& sel,
1153 real lval, rval = 0., val = 0.;
1155 const SelectionTreeElementPointer& left = sel->child;
1156 const SelectionTreeElementPointer& right = left->next;
1158 SelelemTemporaryValueAssigner assigner;
1159 MempoolSelelemReserver reserver;
1162 assigner.assign(left, *sel);
1165 reserver.reserve(right, g->isize);
1168 else if (right && right->mempool)
1170 assigner.assign(right, *sel);
1172 _gmx_sel_evaluate_children(data, sel, g);
1174 n = (sel->flags & SEL_SINGLEVAL) ? 1 : g->isize;
1177 bool bArithNeg = (sel->u.arith.type == ARITH_NEG);
1178 GMX_ASSERT(right || bArithNeg, "Right operand cannot be null except for negations");
1179 for (i = i1 = i2 = 0; i < n; ++i)
1181 lval = left->v.u.r[i1];
1184 rval = right->v.u.r[i2];
1186 switch (sel->u.arith.type)
1188 case ARITH_PLUS: val = lval + rval; break;
1189 case ARITH_MINUS: val = lval - rval; break;
1190 case ARITH_NEG: val = -lval; break;
1191 case ARITH_MULT: val = lval * rval; break;
1192 case ARITH_DIV: val = lval / rval; break;
1193 case ARITH_EXP: val = pow(lval, rval); break;
1195 sel->v.u.r[i] = val;
1196 if (!(left->flags & SEL_SINGLEVAL))
1200 if (!bArithNeg && !(right->flags & SEL_SINGLEVAL))