/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013, 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
#include <boost/shared_ptr.hpp>
-#include "../legacyheaders/typedefs.h"
-#include "../utility/common.h"
-#include "../utility/gmxassert.h"
+#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"
-#include "indexutil.h"
-
-struct gmx_ana_pos_t;
+struct t_blocka;
+struct t_pbc;
namespace gmx
{
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_(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;
+ }
+
+ /*! \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_;
+
+ //! 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.
*
*
* 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. However, the returned search objects can only
- * be used within a single thread. It is also possible to create multiple
- * concurrent searches within a single thread.
+ * 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
- * Support for exclusions.
- * The 4.5/4.6 C API had very low-level support for exclusions, which was not
- * very convenient to use, and hadn't been tested much. The internal code that
- * it used to do the exclusion during the search itself is still there, but it
- * needs more thought on what would be a convenient way to initialize it.
- * Can be implemented once there is need for it in some calling code.
+ * Generalize the exclusion machinery to make it easier to use for other cases
+ * than atom-atom exclusions from the topology.
*
* \inpublicapi
* \ingroup module_selection
~AnalysisNeighborhood();
/*! \brief
- * Set cutoff distance for the neighborhood searching.
+ * Sets cutoff distance for the neighborhood searching.
*
* \param[in] cutoff Cutoff distance for the search
* (<=0 stands for no cutoff).
* 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.
*
/*! \brief
* Initializes neighborhood search for a set of positions.
*
- * \param[in] pbc PBC information for the frame.
- * \param[in] n Number of reference positions for the frame.
- * \param[in] x \p n reference positions for the frame.
+ * \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.
- */
- AnalysisNeighborhoodSearch
- initSearch(const t_pbc *pbc, int n, const rvec x[]);
- /*! \brief
- * Initializes neighborhood search for a set of positions.
*
- * \param[in] pbc PBC information for the frame.
- * \param[in] p Reference positions for the frame.
- * \returns Search object that can be used to find positions from
- * \p p 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 gmx_ana_pos_t *p);
+ initSearch(const t_pbc *pbc,
+ const AnalysisNeighborhoodPositions &positions);
private:
class Impl;
{
public:
//! Initializes an invalid pair.
- AnalysisNeighborhoodPair() : refIndex_(-1), testIndex_(0) {}
+ AnalysisNeighborhoodPair() : refIndex_(-1), testIndex_(0), distance2_(0.0) {}
//! Initializes a pair object with the given data.
- AnalysisNeighborhoodPair(int refIndex, int testIndex)
- : refIndex_(refIndex), testIndex_(testIndex)
+ AnalysisNeighborhoodPair(int refIndex, int testIndex, real distance2)
+ : refIndex_(refIndex), testIndex_(testIndex), distance2_(distance2)
{
}
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
* 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.
- * Currently, it is not possible to call startPairSearch() while a previous
- * AnalysisNeighborhoodPairSearch object obtained from startPairSearch() of the
- * same instance still exists.
+ * 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.
+ * 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
/*! \brief
* Check whether a point is within a neighborhood.
*
- * \param[in] x Test position.
- * \returns true if the test position is within the cutoff of any
- * reference position.
- */
- bool isWithin(const rvec x) const;
- /*! \brief
- * Check whether a point is within a neighborhood.
- *
- * \param[in] p Test positions.
- * \param[in] i Use the i'th position in \p p for testing.
- * \returns true if the test position is within the cutoff of any
- * reference position.
- */
- bool isWithin(const gmx_ana_pos_t *p, int i) const;
- /*! \brief
- * Calculates the minimum distance from the reference points.
- *
- * \param[in] x Test position.
- * \returns The distance to the nearest reference position, or the
- * cutoff value if there are no reference positions within the
- * cutoff.
+ * \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.
*/
- real minimumDistance(const rvec x) const;
+ bool isWithin(const AnalysisNeighborhoodPositions &positions) const;
/*! \brief
* Calculates the minimum distance from the reference points.
*
- * \param[in] p Test positions.
- * \param[in] i Use the i'th position in \p p for testing.
+ * \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 gmx_ana_pos_t *p, int i) const;
- /*! \brief
- * Finds the closest reference point.
- *
- * \param[in] x Test position.
- * \returns The reference index identifies the reference position
- * that is closest to the test position.
- * The test index is always zero. The returned pair is invalid if
- * no reference position is within the cutoff.
- */
- AnalysisNeighborhoodPair nearestPoint(const rvec x) const;
+ real minimumDistance(const AnalysisNeighborhoodPositions &positions) const;
/*! \brief
* Finds the closest reference point.
*
- * \param[in] p Test positions.
- * \param[in] i Use the i'th position in \p p for testing.
+ * \param[in] positions Set of test positions to use.
* \returns The reference index identifies the reference position
- * that is closest to the test position.
- * The test index is always \p i. The returned pair is invalid if
+ * 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 gmx_ana_pos_t *p, int i) const;
+ AnalysisNeighborhoodPair
+ nearestPoint(const AnalysisNeighborhoodPositions &positions) const;
/*! \brief
* Start a search to find reference positions within a cutoff.
*
- * \param[in] x Test position to search the neighbors for.
+ * \param[in] positions Set of test positions to use.
* \returns Initialized search object to loop through all reference
* positions within the configured cutoff.
- *
- * In the AnalysisNeighborhoodPair objects returned by the search, the
- * test index is always zero.
- */
- AnalysisNeighborhoodPairSearch startPairSearch(const rvec x);
- /*! \brief
- * Start a search to find reference positions within a cutoff.
- *
- * \param[in] p Test positions.
- * \param[in] i Use the i'th position in \p p for testing.
- * \returns Initialized search object to loop through all reference
- * positions within the configured cutoff.
- *
- * In the AnalysisNeighborhoodPair objects returned by the search, the
- * test index is always \p i.
+ * \throws std::bad_alloc if out of memory.
*/
- AnalysisNeighborhoodPairSearch startPairSearch(const gmx_ana_pos_t *p, int i);
+ AnalysisNeighborhoodPairSearch
+ startPairSearch(const AnalysisNeighborhoodPositions &positions) const;
private:
+ typedef internal::AnalysisNeighborhoodSearchImpl Impl;
+
ImplPointer impl_;
};
* \code
gmx::AnalysisNeighborhood nb;
nb.setCutoff(cutoff);
- gmx::AnalysisNeighborhoodSearch search = nb.initSearch(pbc, nref, xref);
- gmx::AnalysisNeighborhoodPairSearch pairSearch = search.startPairSearch(x);
+ 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))
{
* \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_;
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff