/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012, by the GROMACS development team, led by
- * David van der Spoel, Berk Hess, Erik Lindahl, and including many
- * others, as listed in the AUTHORS file in the top-level source
- * directory and at http://www.gromacs.org.
+ * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
* GROMACS is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* the research papers on the package. Check out http://www.gromacs.org.
*/
/*! \file
- * \brief API for neighborhood searching.
+ * \brief API for neighborhood searching for analysis.
*
- * The API is documented in more detail on a separate page:
- * \ref nbsearch
+ * The main part of the API is the class gmx::AnalysisNeighborhood.
+ * See the class documentation for usage.
*
- * The functions within this file can be used independently of the other parts
+ * The classes within this file can be used independently of the other parts
* of the library.
- * The library also uses the functions internally.
+ * The library also uses the classes internally.
*
* \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inpublicapi
* \ingroup module_selection
*/
#ifndef GMX_SELECTION_NBSEARCH_H
#define GMX_SELECTION_NBSEARCH_H
-#include "../legacyheaders/typedefs.h"
-
-#include "indexutil.h"
-
-struct gmx_ana_pos_t;
-
-/** Data structure for neighborhood searches. */
-typedef struct gmx_ana_nbsearch_t gmx_ana_nbsearch_t;
-
-/** Create a new neighborhood search data structure. */
-gmx_ana_nbsearch_t *
-gmx_ana_nbsearch_create(real cutoff, int maxn);
-/** Free memory allocated for neighborhood search. */
-void
-gmx_ana_nbsearch_free(gmx_ana_nbsearch_t *d);
-
-/** Initializes neighborhood search for a new frame. */
-void
-gmx_ana_nbsearch_init(gmx_ana_nbsearch_t *d, t_pbc *pbc, int n, const rvec x[]);
-/** Initializes neighborhood search for a frame using \c gmx_ana_pos_t. */
-void
-gmx_ana_nbsearch_pos_init(gmx_ana_nbsearch_t *d, t_pbc *pbc,
- const struct gmx_ana_pos_t *p);
-/** Sets the exclusions for the next neighborhood search. */
-void
-gmx_ana_nbsearch_set_excl(gmx_ana_nbsearch_t *d, int nexcl, int excl[]);
-/** Check whether a point is within a neighborhood. */
-bool
-gmx_ana_nbsearch_is_within(gmx_ana_nbsearch_t *d, const rvec x);
-/** Check whether a position is within a neighborhood. */
-bool
-gmx_ana_nbsearch_pos_is_within(gmx_ana_nbsearch_t *d,
- const struct gmx_ana_pos_t *p, int i);
-/** Calculates the minimun distance from the reference points. */
-real
-gmx_ana_nbsearch_mindist(gmx_ana_nbsearch_t *d, const rvec x);
-/** Calculates the minimun distance from the reference points. */
-real
-gmx_ana_nbsearch_pos_mindist(gmx_ana_nbsearch_t *d,
- const struct gmx_ana_pos_t *p, int i);
-/** Finds the first reference position within the cutoff. */
-bool
-gmx_ana_nbsearch_first_within(gmx_ana_nbsearch_t *d, const rvec x, int *jp);
-/** Finds the first reference position within the cutoff. */
-bool
-gmx_ana_nbsearch_pos_first_within(gmx_ana_nbsearch_t *d,
- const struct gmx_ana_pos_t *p, int i, int *jp);
-/** Finds the next reference position within the cutoff. */
-bool
-gmx_ana_nbsearch_next_within(gmx_ana_nbsearch_t *d, int *jp);
+#include <boost/shared_ptr.hpp>
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/common.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/real.h"
+
+struct t_blocka;
+struct t_pbc;
namespace gmx
{
-/*
- * C++ wrapper for neighborhood searching.
+namespace internal
+{
+class AnalysisNeighborhoodSearchImpl;
+class AnalysisNeighborhoodPairSearchImpl;
+};
+
+class AnalysisNeighborhoodSearch;
+class AnalysisNeighborhoodPairSearch;
+
+/*! \brief
+ * Input positions for neighborhood searching.
+ *
+ * This class supports uniformly specifying sets of positions for various
+ * methods in the analysis neighborhood searching classes
+ * (AnalysisNeighborhood and AnalysisNeighborhoodSearch).
+ *
+ * Note that copies are not made: only a reference to the positions passed to
+ * the constructors are kept. The caller is responsible to ensure that those
+ * positions remain in scope as long as the neighborhood search object requires
+ * access to them.
+ *
+ * Also note that in addition to constructors here, Selection and
+ * SelectionPosition provide conversions operators to this type. It is done
+ * this way to not introduce a cyclic dependency between the selection code and
+ * the neighborhood search code, which in turn allows splitting this search
+ * code into a separate lower-level module if desired at some point.
+ *
+ * Methods in this class do not throw.
*
+ * \inpublicapi
+ * \ingroup module_selection
*/
-class NeighborhoodSearch
+class AnalysisNeighborhoodPositions
{
public:
- NeighborhoodSearch(real cutoff, int maxn)
- : d_(gmx_ana_nbsearch_create(cutoff, maxn))
+ /*! \brief
+ * Initializes positions from a single position vector.
+ *
+ * For positions initialized this way, AnalysisNeighborhoodPair always
+ * returns zero in the corresponding index.
+ *
+ * This constructor is not explicit to allow directly passing an rvec
+ * to methods that accept positions.
+ */
+ AnalysisNeighborhoodPositions(const rvec &x)
+ : count_(1), index_(-1), x_(&x), exclusionIds_(NULL)
+ {
+ }
+ /*! \brief
+ * Initializes positions from an array of position vectors.
+ */
+ AnalysisNeighborhoodPositions(const rvec x[], int count)
+ : count_(count), index_(-1), x_(x), exclusionIds_(NULL)
+ {
+ }
+
+ /*! \brief
+ * Sets indices to use for mapping exclusions to these positions.
+ *
+ * The exclusion IDs can always be set, but they are ignored unless
+ * actual exclusions have been set with
+ * AnalysisNeighborhood::setTopologyExclusions().
+ */
+ AnalysisNeighborhoodPositions &
+ exclusionIds(ConstArrayRef<int> ids)
{
+ GMX_ASSERT(static_cast<int>(ids.size()) == count_,
+ "Exclusion id array should match the number of positions");
+ exclusionIds_ = ids.data();
+ return *this;
}
- ~NeighborhoodSearch() { gmx_ana_nbsearch_free(d_); }
- void init(t_pbc *pbc, int n, const rvec x[])
- { gmx_ana_nbsearch_init(d_, pbc, n, x); }
+ /*! \brief
+ * Selects a single position to use from an array.
+ *
+ * If called, a single position from the array of positions passed to
+ * the constructor is used instead of the whole array.
+ * In contrast to the AnalysisNeighborhoodPositions(const rvec &)
+ * constructor, AnalysisNeighborhoodPair objects return \p index
+ * instead of zero.
+ */
+ AnalysisNeighborhoodPositions &selectSingleFromArray(int index)
+ {
+ GMX_ASSERT(index >= 0 && index < count_, "Invalid position index");
+ index_ = index;
+ return *this;
+ }
+
+ private:
+ int count_;
+ int index_;
+ const rvec *x_;
+ const int *exclusionIds_;
- void init(t_pbc *pbc, const gmx_ana_pos_t *p)
- { gmx_ana_nbsearch_pos_init(d_, pbc, p); }
+ //! To access the positions for initialization.
+ friend class internal::AnalysisNeighborhoodSearchImpl;
+ //! To access the positions for initialization.
+ friend class internal::AnalysisNeighborhoodPairSearchImpl;
+};
- void setExclusions(int nexcl, atom_id *excl)
- { gmx_ana_nbsearch_set_excl(d_, nexcl, excl); }
+/*! \brief
+ * Neighborhood searching for analysis tools.
+ *
+ * This class implements neighborhood searching routines for analysis tools.
+ * The emphasis is in flexibility and ease of use; one main driver is to have
+ * a common implementation of grid-based searching to avoid replicating this in
+ * multiple tools (and to make more tools take advantage of the significant
+ * performance improvement this allows).
+ *
+ * To use the search, create an object of this type, call setCutoff() to
+ * initialize it, and then repeatedly call initSearch() to start a search with
+ * different sets of reference positions. For each set of reference positions,
+ * use methods in the returned AnalysisNeighborhoodSearch to find the reference
+ * positions that are within the given cutoff from a provided position.
+ *
+ * initSearch() is thread-safe and can be called from multiple threads. Each
+ * call returns a different instance of the search object that can be used
+ * independently of the others. The returned AnalysisNeighborhoodSearch
+ * objects are also thread-safe, and can be used concurrently from multiple
+ * threads. It is also possible to create multiple concurrent searches within
+ * a single thread.
+ *
+ * \todo
+ * Generalize the exclusion machinery to make it easier to use for other cases
+ * than atom-atom exclusions from the topology.
+ *
+ * \inpublicapi
+ * \ingroup module_selection
+ */
+class AnalysisNeighborhood
+{
+ public:
+ //! Searching algorithm to use.
+ enum SearchMode
+ {
+ //! Select algorithm based on heuristic efficiency considerations.
+ eSearchMode_Automatic,
+ //! Use a simple loop over all pairs.
+ eSearchMode_Simple,
+ //! Use grid-based searching whenever possible.
+ eSearchMode_Grid
+ };
+ //! Creates an uninitialized neighborhood search.
+ AnalysisNeighborhood();
+ ~AnalysisNeighborhood();
- bool isWithin(const rvec x)
- { return gmx_ana_nbsearch_is_within(d_, x); }
+ /*! \brief
+ * Sets cutoff distance for the neighborhood searching.
+ *
+ * \param[in] cutoff Cutoff distance for the search
+ * (<=0 stands for no cutoff).
+ *
+ * Currently, can only be called before the first call to initSearch().
+ * If this method is not called, no cutoff is used in the searches.
+ *
+ * Does not throw.
+ */
+ void setCutoff(real cutoff);
+ /*! \brief
+ * Sets the search to only happen in the XY plane.
+ *
+ * Z component of the coordinates is not used in the searching,
+ * and returned distances are computed in the XY plane.
+ * Only boxes with the third box vector parallel to the Z axis are
+ * currently implemented.
+ *
+ * Does not throw.
+ */
+ void setXYMode(bool bXY);
+ /*! \brief
+ * Sets atom exclusions from a topology.
+ *
+ * The \p excls structure specifies the exclusions from test positions
+ * to reference positions, i.e., a block starting at `excls->index[i]`
+ * specifies the exclusions for test position `i`, and the indices in
+ * `excls->a` are indices of the reference positions. If `excls->nr`
+ * is smaller than a test position id, then such test positions do not
+ * have any exclusions.
+ * It is assumed that the indices within a block of indices in
+ * `excls->a` is ascending.
+ *
+ * Does not throw.
+ *
+ * \see AnalysisNeighborhoodPositions::exclusionIds()
+ */
+ void setTopologyExclusions(const t_blocka *excls);
+ /*! \brief
+ * Sets the algorithm to use for searching.
+ *
+ * \param[in] mode Search mode to use.
+ *
+ * Note that if \p mode is \ref eSearchMode_Grid, it is still only a
+ * suggestion: grid-based searching may not be possible with the
+ * provided input, in which case a simple search is still used.
+ * This is mainly useful for testing purposes to force a mode.
+ *
+ * Does not throw.
+ */
+ void setMode(SearchMode mode);
+ //! Returns the currently active search mode.
+ SearchMode mode() const;
- bool isWithin(const gmx_ana_pos_t *p, int i)
- { return gmx_ana_nbsearch_pos_is_within(d_, p, i); }
+ /*! \brief
+ * Initializes neighborhood search for a set of positions.
+ *
+ * \param[in] pbc PBC information for the frame.
+ * \param[in] positions Set of reference positions to use.
+ * \returns Search object that can be used to find positions from
+ * \p x within the given cutoff.
+ * \throws std::bad_alloc if out of memory.
+ *
+ * Currently, the input positions cannot use
+ * AnalysisNeighborhoodPositions::selectSingleFromArray().
+ */
+ AnalysisNeighborhoodSearch
+ initSearch(const t_pbc *pbc,
+ const AnalysisNeighborhoodPositions &positions);
- real minimumDistance(const rvec x)
- { return gmx_ana_nbsearch_mindist(d_, x); }
+ private:
+ class Impl;
- real minimumDistance(const gmx_ana_pos_t *p, int i)
- { return gmx_ana_nbsearch_pos_mindist(d_, p, i); }
+ PrivateImplPointer<Impl> impl_;
+};
- bool firstWithin(const rvec x, int *jp)
- { return gmx_ana_nbsearch_first_within(d_, x, jp); }
+/*! \brief
+ * Value type to represent a pair of positions found in neighborhood searching.
+ *
+ * Methods in this class do not throw.
+ *
+ * \inpublicapi
+ * \ingroup module_selection
+ */
+class AnalysisNeighborhoodPair
+{
+ public:
+ //! Initializes an invalid pair.
+ AnalysisNeighborhoodPair() : refIndex_(-1), testIndex_(0), distance2_(0.0) {}
+ //! Initializes a pair object with the given data.
+ AnalysisNeighborhoodPair(int refIndex, int testIndex, real distance2)
+ : refIndex_(refIndex), testIndex_(testIndex), distance2_(distance2)
+ {
+ }
+
+ /*! \brief
+ * Whether this pair is valid.
+ *
+ * If isValid() returns false, other methods should not be called.
+ */
+ bool isValid() const { return refIndex_ >= 0; }
+
+ /*! \brief
+ * Returns the index of the reference position in the pair.
+ *
+ * This index is always the index into the position array provided to
+ * AnalysisNeighborhood::initSearch().
+ */
+ int refIndex() const
+ {
+ GMX_ASSERT(isValid(), "Accessing invalid object");
+ return refIndex_;
+ }
+ /*! \brief
+ * Returns the index of the test position in the pair.
+ *
+ * The contents of this index depends on the context (method call) that
+ * produces the pair.
+ * If there was no array in the call, this index is zero.
+ */
+ int testIndex() const
+ {
+ GMX_ASSERT(isValid(), "Accessing invalid object");
+ return testIndex_;
+ }
+ /*! \brief
+ * Returns the squared distance between the pair of positions.
+ */
+ real distance2() const
+ {
+ GMX_ASSERT(isValid(), "Accessing invalid object");
+ return distance2_;
+ }
+
+ private:
+ int refIndex_;
+ int testIndex_;
+ real distance2_;
+};
+
+/*! \brief
+ * Initialized neighborhood search with a fixed set of reference positions.
+ *
+ * An instance of this class is obtained through
+ * AnalysisNeighborhood::initSearch(), and can be used to do multiple searches
+ * against the provided set of reference positions.
+ * It is possible to create concurrent pair searches (including from different
+ * threads), as well as call other methods in this class while a pair search is
+ * in progress.
+ *
+ * This class works like a pointer: copies of it point to the same search.
+ * In general, avoid creating copies, and only use the copy/assignment support
+ * for moving the variable around. With C++11, this class would best be
+ * movable.
+ *
+ * Methods in this class do not throw unless otherwise indicated.
+ *
+ * \todo
+ * Make it such that reset() is not necessary to call in code that repeatedly
+ * assigns the result of AnalysisNeighborhood::initSearch() to the same
+ * variable (see sm_distance.cpp).
+ *
+ * \todo
+ * Consider merging nearestPoint() and minimumDistance() by adding the distance
+ * to AnalysisNeighborhoodPair.
+ *
+ * \inpublicapi
+ * \ingroup module_selection
+ */
+class AnalysisNeighborhoodSearch
+{
+ public:
+ /*! \brief
+ * Internal short-hand type for a pointer to the implementation class.
+ *
+ * shared_ptr is used here to automatically keep a reference count to
+ * track whether an implementation class is still used outside the
+ * AnalysisNeighborhood object. Ownership currently always stays with
+ * AnalysisNeighborhood; it always keeps one instance of the pointer.
+ */
+ typedef boost::shared_ptr<internal::AnalysisNeighborhoodSearchImpl>
+ ImplPointer;
+
+ /*! \brief
+ * Initializes an invalid search.
+ *
+ * Such an object cannot be used for searching. It needs to be
+ * assigned a value from AnalysisNeighborhood::initSearch() before it
+ * can be used. Provided to allow declaring a variable to hold the
+ * search before calling AnalysisNeighborhood::initSearch().
+ */
+ AnalysisNeighborhoodSearch();
+ /*! \brief
+ * Internally initialize the search.
+ *
+ * Used to implement AnalysisNeighborhood::initSearch().
+ * Cannot be called from user code.
+ */
+ explicit AnalysisNeighborhoodSearch(const ImplPointer &impl);
+
+ /*! \brief
+ * Clears this search.
+ *
+ * Equivalent to \c "*this = AnalysisNeighborhoodSearch();".
+ * Currently, this is necessary to avoid unnecessary memory allocation
+ * if the previous search variable is still in scope when you want to
+ * call AnalysisNeighborhood::initSearch() again.
+ */
+ void reset();
+
+ /*! \brief
+ * Returns the searching algorithm that this search is using.
+ *
+ * The return value is never AnalysisNeighborhood::eSearchMode_Automatic.
+ */
+ AnalysisNeighborhood::SearchMode mode() const;
+
+ /*! \brief
+ * Check whether a point is within a neighborhood.
+ *
+ * \param[in] positions Set of test positions to use.
+ * \returns true if any of the test positions is within the cutoff of
+ * any reference position.
+ */
+ bool isWithin(const AnalysisNeighborhoodPositions &positions) const;
+ /*! \brief
+ * Calculates the minimum distance from the reference points.
+ *
+ * \param[in] positions Set of test positions to use.
+ * \returns The distance to the nearest reference position, or the
+ * cutoff value if there are no reference positions within the
+ * cutoff.
+ */
+ real minimumDistance(const AnalysisNeighborhoodPositions &positions) const;
+ /*! \brief
+ * Finds the closest reference point.
+ *
+ * \param[in] positions Set of test positions to use.
+ * \returns The reference index identifies the reference position
+ * that is closest to the test positions.
+ * The test index identifies the test position that is closest to
+ * the provided test position. The returned pair is invalid if
+ * no reference position is within the cutoff.
+ */
+ AnalysisNeighborhoodPair
+ nearestPoint(const AnalysisNeighborhoodPositions &positions) const;
+
+ /*! \brief
+ * Start a search to find reference positions within a cutoff.
+ *
+ * \param[in] positions Set of test positions to use.
+ * \returns Initialized search object to loop through all reference
+ * positions within the configured cutoff.
+ * \throws std::bad_alloc if out of memory.
+ */
+ AnalysisNeighborhoodPairSearch
+ startPairSearch(const AnalysisNeighborhoodPositions &positions) const;
+
+ private:
+ typedef internal::AnalysisNeighborhoodSearchImpl Impl;
+
+ ImplPointer impl_;
+};
+
+/*! \brief
+ * Initialized neighborhood pair search with a fixed set of positions.
+ *
+ * This class is used to loop through pairs of neighbors within the cutoff
+ * provided to AnalysisNeighborhood. The following code demonstrates its use:
+ * \code
+ gmx::AnalysisNeighborhood nb;
+ nb.setCutoff(cutoff);
+ gmx::AnalysisNeighborhoodPositions refPos(xref, nref);
+ gmx::AnalysisNeighborhoodSearch search = nb.initSearch(pbc, refPos);
+ gmx::AnalysisNeighborhoodPairSearch pairSearch = search.startPairSearch(selection);
+ gmx::AnalysisNeighborhoodPair pair;
+ while (pairSearch.findNextPair(&pair))
+ {
+ // <do something for each found pair the information in pair>
+ }
+ * \endcode
+ *
+ * It is not possible to use a single search object from multiple threads
+ * concurrently.
+ *
+ * This class works like a pointer: copies of it point to the same search.
+ * In general, avoid creating copies, and only use the copy/assignment support
+ * for moving the variable around. With C++11, this class would best be
+ * movable.
+ *
+ * Methods in this class do not throw.
+ *
+ * \inpublicapi
+ * \ingroup module_selection
+ */
+class AnalysisNeighborhoodPairSearch
+{
+ public:
+ /*! \brief
+ * Internal short-hand type for a pointer to the implementation class.
+ *
+ * See AnalysisNeighborhoodSearch::ImplPointer for rationale of using
+ * shared_ptr and ownership semantics.
+ */
+ typedef boost::shared_ptr<internal::AnalysisNeighborhoodPairSearchImpl>
+ ImplPointer;
- bool firstWithin(const gmx_ana_pos_t *p, int i, int *jp)
- { return gmx_ana_nbsearch_pos_first_within(d_, p, i, jp); }
+ /*! \brief
+ * Internally initialize the search.
+ *
+ * Used to implement AnalysisNeighborhoodSearch::startPairSearch().
+ * Cannot be called from user code.
+ */
+ explicit AnalysisNeighborhoodPairSearch(const ImplPointer &impl);
- bool nextWithin(int *jp)
- { return gmx_ana_nbsearch_next_within(d_, jp); }
+ /*! \brief
+ * Finds the next pair within the cutoff.
+ *
+ * \param[out] pair Information about the found pair.
+ * \returns false if there were no more pairs.
+ *
+ * If the method returns false, \p pair will be invalid.
+ *
+ * \see AnalysisNeighborhoodPair
+ * \see AnalysisNeighborhoodSearch::startPairSearch()
+ */
+ bool findNextPair(AnalysisNeighborhoodPair *pair);
+ /*! \brief
+ * Skip remaining pairs for a test position in the search.
+ *
+ * When called after findNextPair(), makes subsequent calls to
+ * findNextPair() skip any pairs that have the same test position as
+ * that previously returned.
+ * This is useful if the caller wants to search whether any reference
+ * position within the cutoff satisfies some condition. This method
+ * can be used to skip remaining pairs after the first such position
+ * has been found if the remaining pairs would not have an effect on
+ * the outcome.
+ */
+ void skipRemainingPairsForTestPosition();
private:
- gmx_ana_nbsearch_t *d_;
+ ImplPointer impl_;
};
} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff