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36 * \brief API for neighborhood searching for analysis.
38 * The main part of the API is the class gmx::AnalysisNeighborhood.
39 * See \ref page_analysisnbsearch for an overview.
41 * The classes within this file can be used independently of the other parts
42 * of the selection module.
44 * \author Teemu Murtola <teemu.murtola@gmail.com>
46 * \ingroup module_selection
48 #ifndef GMX_SELECTION_NBSEARCH_H
49 #define GMX_SELECTION_NBSEARCH_H
54 #include "gromacs/math/vec.h"
55 #include "gromacs/math/vectypes.h"
56 #include "gromacs/utility/arrayref.h"
57 #include "gromacs/utility/classhelpers.h"
58 #include "gromacs/utility/gmxassert.h"
59 #include "gromacs/utility/real.h"
69 class AnalysisNeighborhoodSearchImpl;
70 class AnalysisNeighborhoodPairSearchImpl;
73 class AnalysisNeighborhoodSearch;
74 class AnalysisNeighborhoodPairSearch;
77 * Input positions for neighborhood searching.
79 * This class supports uniformly specifying sets of positions for various
80 * methods in the analysis neighborhood searching classes
81 * (AnalysisNeighborhood and AnalysisNeighborhoodSearch).
83 * Note that copies are not made: only a reference to the positions passed to
84 * the constructors are kept. The caller is responsible to ensure that those
85 * positions remain in scope as long as the neighborhood search object requires
88 * Also note that in addition to constructors here, Selection and
89 * SelectionPosition provide conversions operators to this type. It is done
90 * this way to not introduce a cyclic dependency between the selection code and
91 * the neighborhood search code, which in turn allows splitting this search
92 * code into a separate lower-level module if desired at some point.
94 * Methods in this class do not throw.
97 * \ingroup module_selection
99 class AnalysisNeighborhoodPositions
103 * Initializes positions from a single position vector.
105 * For positions initialized this way, AnalysisNeighborhoodPair always
106 * returns zero in the corresponding index.
108 * This constructor is not explicit to allow directly passing an rvec
109 * to methods that accept positions.
111 AnalysisNeighborhoodPositions(const rvec &x)
112 : count_(1), index_(-1), x_(&x), exclusionIds_(nullptr), indices_(nullptr)
116 * Initializes positions from an array of position vectors.
118 AnalysisNeighborhoodPositions(const rvec x[], int count)
119 : count_(count), index_(-1), x_(x), exclusionIds_(nullptr), indices_(nullptr)
123 * Initializes positions from a vector of position vectors.
125 AnalysisNeighborhoodPositions(const std::vector<RVec> &x)
126 : count_(x.size()), index_(-1), x_(as_rvec_array(x.data())),
127 exclusionIds_(nullptr), indices_(nullptr)
132 * Sets indices to use for mapping exclusions to these positions.
134 * The exclusion IDs can always be set, but they are ignored unless
135 * actual exclusions have been set with
136 * AnalysisNeighborhood::setTopologyExclusions().
138 AnalysisNeighborhoodPositions &
139 exclusionIds(ArrayRef<const int> ids)
141 GMX_ASSERT(static_cast<int>(ids.size()) == count_,
142 "Exclusion id array should match the number of positions");
143 exclusionIds_ = ids.data();
147 * Sets indices that select a subset of all positions from the array.
149 * If called, selected positions from the array of positions passed to
150 * the constructor is used instead of the whole array.
151 * All returned indices from AnalysisNeighborhoodPair objects are
152 * indices to the \p indices array passed here.
154 AnalysisNeighborhoodPositions &
155 indexed(ArrayRef<const int> indices)
157 count_ = indices.size();
158 indices_ = indices.data();
163 * Selects a single position to use from an array.
165 * If called, a single position from the array of positions passed to
166 * the constructor is used instead of the whole array.
167 * In contrast to the AnalysisNeighborhoodPositions(const rvec &)
168 * constructor, AnalysisNeighborhoodPair objects return \p index
171 * If used together with indexed(), \p index references the index array
172 * passed to indexed() instead of the position array.
174 AnalysisNeighborhoodPositions &selectSingleFromArray(int index)
176 GMX_ASSERT(index >= 0 && index < count_, "Invalid position index");
185 const int *exclusionIds_;
188 //! To access the positions for initialization.
189 friend class internal::AnalysisNeighborhoodSearchImpl;
190 //! To access the positions for initialization.
191 friend class internal::AnalysisNeighborhoodPairSearchImpl;
195 * Neighborhood searching for analysis tools.
197 * See \ref page_analysisnbsearch for an overview.
199 * To use the search, create an object of this type, call setCutoff() to
200 * initialize it, and then repeatedly call initSearch() to start a search with
201 * different sets of reference positions. For each set of reference positions,
202 * use methods in the returned AnalysisNeighborhoodSearch to find the reference
203 * positions that are within the given cutoff from a provided position.
205 * initSearch() is thread-safe and can be called from multiple threads. Each
206 * call returns a different instance of the search object that can be used
207 * independently of the others. The returned AnalysisNeighborhoodSearch
208 * objects are also thread-safe, and can be used concurrently from multiple
209 * threads. It is also possible to create multiple concurrent searches within
213 * Generalize the exclusion machinery to make it easier to use for other cases
214 * than atom-atom exclusions from the topology.
217 * \ingroup module_selection
219 class AnalysisNeighborhood
222 //! Searching algorithm to use.
225 //! Select algorithm based on heuristic efficiency considerations.
226 eSearchMode_Automatic,
227 //! Use a simple loop over all pairs.
229 //! Use grid-based searching whenever possible.
233 //! Creates an uninitialized neighborhood search.
234 AnalysisNeighborhood();
235 ~AnalysisNeighborhood();
238 * Sets cutoff distance for the neighborhood searching.
240 * \param[in] cutoff Cutoff distance for the search
241 * (<=0 stands for no cutoff).
243 * Currently, can only be called before the first call to initSearch().
244 * If this method is not called, no cutoff is used in the searches.
248 void setCutoff(real cutoff);
250 * Sets the search to only happen in the XY plane.
252 * Z component of the coordinates is not used in the searching,
253 * and returned distances are computed in the XY plane.
254 * Only boxes with the third box vector parallel to the Z axis are
255 * currently implemented.
259 void setXYMode(bool bXY);
261 * Sets atom exclusions from a topology.
263 * The \p excls structure specifies the exclusions from test positions
264 * to reference positions, i.e., a block starting at `excls->index[i]`
265 * specifies the exclusions for test position `i`, and the indices in
266 * `excls->a` are indices of the reference positions. If `excls->nr`
267 * is smaller than a test position id, then such test positions do not
268 * have any exclusions.
269 * It is assumed that the indices within a block of indices in
270 * `excls->a` is ascending.
274 * \see AnalysisNeighborhoodPositions::exclusionIds()
276 void setTopologyExclusions(const t_blocka *excls);
278 * Sets the algorithm to use for searching.
280 * \param[in] mode Search mode to use.
282 * Note that if \p mode is \ref eSearchMode_Grid, it is still only a
283 * suggestion: grid-based searching may not be possible with the
284 * provided input, in which case a simple search is still used.
285 * This is mainly useful for testing purposes to force a mode.
289 void setMode(SearchMode mode);
290 //! Returns the currently active search mode.
291 SearchMode mode() const;
294 * Initializes neighborhood search for a set of positions.
296 * \param[in] pbc PBC information for the frame.
297 * \param[in] positions Set of reference positions to use.
298 * \returns Search object that can be used to find positions from
299 * \p x within the given cutoff.
300 * \throws std::bad_alloc if out of memory.
302 * Currently, the input positions cannot use
303 * AnalysisNeighborhoodPositions::selectSingleFromArray().
305 AnalysisNeighborhoodSearch
306 initSearch(const t_pbc *pbc,
307 const AnalysisNeighborhoodPositions &positions);
312 PrivateImplPointer<Impl> impl_;
316 * Value type to represent a pair of positions found in neighborhood searching.
318 * Methods in this class do not throw.
321 * \ingroup module_selection
323 class AnalysisNeighborhoodPair
326 //! Initializes an invalid pair.
327 AnalysisNeighborhoodPair() : refIndex_(-1), testIndex_(0), distance2_(0.0), dx_()
330 //! Initializes a pair object with the given data.
331 AnalysisNeighborhoodPair(int refIndex, int testIndex, real distance2,
333 : refIndex_(refIndex), testIndex_(testIndex), distance2_(distance2), dx_()
339 * Whether this pair is valid.
341 * If isValid() returns false, other methods should not be called.
343 bool isValid() const { return refIndex_ >= 0; }
346 * Returns the index of the reference position in the pair.
348 * This index is always the index into the position array provided to
349 * AnalysisNeighborhood::initSearch().
353 GMX_ASSERT(isValid(), "Accessing invalid object");
357 * Returns the index of the test position in the pair.
359 * The contents of this index depends on the context (method call) that
361 * If there was no array in the call, this index is zero.
363 int testIndex() const
365 GMX_ASSERT(isValid(), "Accessing invalid object");
369 * Returns the squared distance between the pair of positions.
371 real distance2() const
373 GMX_ASSERT(isValid(), "Accessing invalid object");
377 * Returns the shortest vector between the pair of positions.
379 * The vector is from the test position to the reference position.
381 const rvec &dx() const
383 GMX_ASSERT(isValid(), "Accessing invalid object");
395 * Initialized neighborhood search with a fixed set of reference positions.
397 * An instance of this class is obtained through
398 * AnalysisNeighborhood::initSearch(), and can be used to do multiple searches
399 * against the provided set of reference positions.
400 * It is possible to create concurrent pair searches (including from different
401 * threads), as well as call other methods in this class while a pair search is
404 * This class works like a pointer: copies of it point to the same search.
405 * In general, avoid creating copies, and only use the copy/assignment support
406 * for moving the variable around. With C++11, this class would best be
409 * Methods in this class do not throw unless otherwise indicated.
412 * Make it such that reset() is not necessary to call in code that repeatedly
413 * assigns the result of AnalysisNeighborhood::initSearch() to the same
414 * variable (see sm_distance.cpp).
417 * Consider removing minimumDistance(), as nearestPoint() already returns the
421 * \ingroup module_selection
423 class AnalysisNeighborhoodSearch
427 * Internal short-hand type for a pointer to the implementation class.
429 * shared_ptr is used here to automatically keep a reference count to
430 * track whether an implementation class is still used outside the
431 * AnalysisNeighborhood object. Ownership currently always stays with
432 * AnalysisNeighborhood; it always keeps one instance of the pointer.
434 typedef std::shared_ptr<internal::AnalysisNeighborhoodSearchImpl>
438 * Initializes an invalid search.
440 * Such an object cannot be used for searching. It needs to be
441 * assigned a value from AnalysisNeighborhood::initSearch() before it
442 * can be used. Provided to allow declaring a variable to hold the
443 * search before calling AnalysisNeighborhood::initSearch().
445 AnalysisNeighborhoodSearch();
447 * Internally initialize the search.
449 * Used to implement AnalysisNeighborhood::initSearch().
450 * Cannot be called from user code.
452 explicit AnalysisNeighborhoodSearch(const ImplPointer &impl);
455 * Clears this search.
457 * Equivalent to \c "*this = AnalysisNeighborhoodSearch();".
458 * Currently, this is necessary to avoid unnecessary memory allocation
459 * if the previous search variable is still in scope when you want to
460 * call AnalysisNeighborhood::initSearch() again.
465 * Returns the searching algorithm that this search is using.
467 * The return value is never AnalysisNeighborhood::eSearchMode_Automatic.
469 AnalysisNeighborhood::SearchMode mode() const;
472 * Checks whether a point is within a neighborhood.
474 * \param[in] positions Set of test positions to use.
475 * \returns true if any of the test positions is within the cutoff of
476 * any reference position.
478 bool isWithin(const AnalysisNeighborhoodPositions &positions) const;
480 * Calculates the minimum distance from the reference points.
482 * \param[in] positions Set of test positions to use.
483 * \returns The distance to the nearest reference position, or the
484 * cutoff value if there are no reference positions within the
487 real minimumDistance(const AnalysisNeighborhoodPositions &positions) const;
489 * Finds the closest reference point.
491 * \param[in] positions Set of test positions to use.
492 * \returns The reference index identifies the reference position
493 * that is closest to the test positions.
494 * The test index identifies the test position that is closest to
495 * the provided test position. The returned pair is invalid if
496 * no reference position is within the cutoff.
498 AnalysisNeighborhoodPair
499 nearestPoint(const AnalysisNeighborhoodPositions &positions) const;
502 * Starts a search to find all reference position pairs within a cutoff.
504 * \returns Initialized search object to loop through all reference
505 * position pairs within the configured cutoff.
506 * \throws std::bad_alloc if out of memory.
508 * This works as if the reference positions were passed to
509 * startPairSearch(), except that it only returns each pair once,
510 * instead of returning both i-j and j-i pairs, as startPairSearch()
511 * does. i-i pairs are not returned. Note that the order of ref/test
512 * indices in the returned pairs is not predictable. That is, one of
513 * i-j or j-i is always returned, but there is no control which one.
515 AnalysisNeighborhoodPairSearch
516 startSelfPairSearch() const;
519 * Starts a search to find reference positions within a cutoff.
521 * \param[in] positions Set of test positions to use.
522 * \returns Initialized search object to loop through all reference
523 * positions within the configured cutoff.
524 * \throws std::bad_alloc if out of memory.
526 * If you want to pass the same positions here as you used for the
527 * reference positions, consider using startSelfPairSearch().
528 * It can be up to 50% faster.
530 AnalysisNeighborhoodPairSearch
531 startPairSearch(const AnalysisNeighborhoodPositions &positions) const;
534 typedef internal::AnalysisNeighborhoodSearchImpl Impl;
540 * Initialized neighborhood pair search with a fixed set of positions.
542 * This class is used to loop through pairs of neighbors within the cutoff
543 * provided to AnalysisNeighborhood. The following code demonstrates its use:
545 gmx::AnalysisNeighborhood nb;
546 nb.setCutoff(cutoff);
547 gmx::AnalysisNeighborhoodPositions refPos(xref, nref);
548 gmx::AnalysisNeighborhoodSearch search = nb.initSearch(pbc, refPos);
549 gmx::AnalysisNeighborhoodPairSearch pairSearch = search.startPairSearch(selection);
550 gmx::AnalysisNeighborhoodPair pair;
551 while (pairSearch.findNextPair(&pair))
553 // <do something for each found pair the information in pair>
557 * It is not possible to use a single search object from multiple threads
560 * This class works like a pointer: copies of it point to the same search.
561 * In general, avoid creating copies, and only use the copy/assignment support
562 * for moving the variable around. With C++11, this class would best be
565 * Methods in this class do not throw.
568 * \ingroup module_selection
570 class AnalysisNeighborhoodPairSearch
574 * Internal short-hand type for a pointer to the implementation class.
576 * See AnalysisNeighborhoodSearch::ImplPointer for rationale of using
577 * shared_ptr and ownership semantics.
579 typedef std::shared_ptr<internal::AnalysisNeighborhoodPairSearchImpl>
583 * Internally initialize the search.
585 * Used to implement AnalysisNeighborhoodSearch::startPairSearch().
586 * Cannot be called from user code.
588 explicit AnalysisNeighborhoodPairSearch(const ImplPointer &impl);
591 * Finds the next pair within the cutoff.
593 * \param[out] pair Information about the found pair.
594 * \returns false if there were no more pairs.
596 * If the method returns false, \p pair will be invalid.
598 * \see AnalysisNeighborhoodPair
599 * \see AnalysisNeighborhoodSearch::startPairSearch()
601 bool findNextPair(AnalysisNeighborhoodPair *pair);
603 * Skip remaining pairs for a test position in the search.
605 * When called after findNextPair(), makes subsequent calls to
606 * findNextPair() skip any pairs that have the same test position as
607 * that previously returned.
608 * This is useful if the caller wants to search whether any reference
609 * position within the cutoff satisfies some condition. This method
610 * can be used to skip remaining pairs after the first such position
611 * has been found if the remaining pairs would not have an effect on
614 void skipRemainingPairsForTestPosition();