[alexxy/gromacs.git] / src / gromacs / selection / nbsearch.h

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/*! \file
 * \brief API for neighborhood searching for analysis.
 *
 * The main part of the API is the class gmx::AnalysisNeighborhood.
 * See \ref page_analysisnbsearch for an overview.
 *
 * The classes within this file can be used independently of the other parts
 * of the selection module.
 *
 * \author Teemu Murtola <teemu.murtola@gmail.com>
 * \inpublicapi
 * \ingroup module_selection
 */
#ifndef GMX_SELECTION_NBSEARCH_H
#define GMX_SELECTION_NBSEARCH_H

#include <memory>
#include <vector>

#include "gromacs/math/vec.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/real.h"

struct t_blocka;
struct t_pbc;

namespace gmx
{

namespace internal
{
class AnalysisNeighborhoodSearchImpl;
class AnalysisNeighborhoodPairSearchImpl;
}; // namespace internal

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 AnalysisNeighborhoodPositions
{
public:
    /*! \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_(nullptr),
        indices_(nullptr)
    {
    }
    /*! \brief
     * Initializes positions from an array of position vectors.
     */
    AnalysisNeighborhoodPositions(const rvec x[], int count) :
        count_(count),
        index_(-1),
        x_(x),
        exclusionIds_(nullptr),
        indices_(nullptr)
    {
    }
    /*! \brief
     * Initializes positions from a vector of position vectors.
     */
    AnalysisNeighborhoodPositions(const std::vector<RVec>& x) :
        count_(ssize(x)),
        index_(-1),
        x_(as_rvec_array(x.data())),
        exclusionIds_(nullptr),
        indices_(nullptr)
    {
    }

    /*! \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(ArrayRef<const int> ids)
    {
        GMX_ASSERT(ssize(ids) == count_, "Exclusion id array should match the number of positions");
        exclusionIds_ = ids.data();
        return *this;
    }
    /*! \brief
     * Sets indices that select a subset of all positions from the array.
     *
     * If called, selected positions from the array of positions passed to
     * the constructor is used instead of the whole array.
     * All returned indices from AnalysisNeighborhoodPair objects are
     * indices to the \p indices array passed here.
     */
    AnalysisNeighborhoodPositions& indexed(ArrayRef<const int> indices)
    {
        count_   = ssize(indices);
        indices_ = indices.data();
        return *this;
    }

    /*! \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.
     *
     * If used together with indexed(), \p index references the index array
     * passed to indexed() instead of the position array.
     */
    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_;
    const int*  indices_;

    //! To access the positions for initialization.
    friend class internal::AnalysisNeighborhoodSearchImpl;
    //! To access the positions for initialization.
    friend class internal::AnalysisNeighborhoodPairSearchImpl;
};

/*! \brief
 * Neighborhood searching for analysis tools.
 *
 * See \ref page_analysisnbsearch for an overview.
 *
 * 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();

    /*! \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;

    /*! \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);

private:
    class Impl;

    PrivateImplPointer<Impl> impl_;
};

/*! \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), dx_() {}
    //! Initializes a pair object with the given data.
    AnalysisNeighborhoodPair(int refIndex, int testIndex, real distance2, const rvec dx) :
        refIndex_(refIndex),
        testIndex_(testIndex),
        distance2_(distance2),
        dx_()
    {
        copy_rvec(dx, dx_);
    }

    /*! \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_;
    }
    /*! \brief
     * Returns the shortest vector between the pair of positions.
     *
     * The vector is from the test position to the reference position.
     */
    const rvec& dx() const
    {
        GMX_ASSERT(isValid(), "Accessing invalid object");
        return dx_;
    }

private:
    int  refIndex_;
    int  testIndex_;
    real distance2_;
    rvec dx_;
};

/*! \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 removing minimumDistance(), as nearestPoint() already returns the
 * distance.
 *
 * \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 std::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
     * Checks 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
     * Starts a search to find all reference position pairs within a cutoff.
     *
     * \returns   Initialized search object to loop through all reference
     *     position pairs within the configured cutoff.
     * \throws    std::bad_alloc if out of memory.
     *
     * This works as if the reference positions were passed to
     * startPairSearch(), except that it only returns each pair once,
     * instead of returning both i-j and j-i pairs, as startPairSearch()
     * does.  i-i pairs are not returned.  Note that the order of ref/test
     * indices in the returned pairs is not predictable.  That is, one of
     * i-j or j-i is always returned, but there is no control which one.
     */
    AnalysisNeighborhoodPairSearch startSelfPairSearch() const;

    /*! \brief
     * Starts 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.
     *
     * If you want to pass the same positions here as you used for the
     * reference positions, consider using startSelfPairSearch().
     * It can be up to 50% faster.
     */
    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 std::shared_ptr<internal::AnalysisNeighborhoodPairSearchImpl> ImplPointer;

    /*! \brief
     * Internally initialize the search.
     *
     * Used to implement AnalysisNeighborhoodSearch::startPairSearch().
     * Cannot be called from user code.
     */
    explicit AnalysisNeighborhoodPairSearch(const ImplPointer& impl);

    /*! \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:
    ImplPointer impl_;
};

} // namespace gmx

#endif