#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/selection/position.h"
+#include "gromacs/topology/block.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
*
* \param[in] mode Search mode to use.
* \param[in] bXY Whether to use 2D searching.
+ * \param[in] excls Exclusions.
* \param[in] pbc PBC information.
* \param[in] positions Set of reference positions.
*/
void init(AnalysisNeighborhood::SearchMode mode,
bool bXY,
+ const t_blocka *excls,
const t_pbc *pbc,
const AnalysisNeighborhoodPositions &positions);
PairSearchImplPointer getPairSearch();
int nref_;
//! Reference point positions.
const rvec *xref_;
- //! Reference position ids (NULL if not available).
- const int *refid_;
+ //! Reference position exclusion IDs.
+ const int *refExclusionIds_;
+ //! Exclusions.
+ const t_blocka *excls_;
//! PBC data.
t_pbc pbc_;
- //! Number of excluded reference positions for current test particle.
- int nexcl_;
- //! Exclusions for current test particle.
- int *excl_;
-
//! Whether grid searching is actually used for the current positions.
bool bGrid_;
//! Array allocated for storing in-unit-cell reference positions.
explicit AnalysisNeighborhoodPairSearchImpl(const AnalysisNeighborhoodSearchImpl &search)
: search_(search)
{
+ testExclusionIds_ = NULL;
+ nexcl_ = 0;
+ excl_ = NULL;
clear_rvec(xtest_);
clear_ivec(testcell_);
reset(-1);
const AnalysisNeighborhoodSearchImpl &search_;
//! Reference to the test positions.
ConstArrayRef<rvec> testPositions_;
+ //! Reference to the test exclusion indices.
+ const int *testExclusionIds_;
+ //! Number of excluded reference positions for current test particle.
+ int nexcl_;
+ //! Exclusions for current test particle.
+ const int *excl_;
//! Index of the currently active test position in \p testPositions_.
int testIndex_;
//! Stores test position during a pair loop.
cutoff2_ = sqr(cutoff_);
bXY_ = false;
- nref_ = 0;
- xref_ = NULL;
- refid_ = NULL;
+ nref_ = 0;
+ xref_ = NULL;
+ refExclusionIds_ = NULL;
std::memset(&pbc_, 0, sizeof(pbc_));
- nexcl_ = 0;
- excl_ = NULL;
-
bGrid_ = false;
xref_alloc_ = NULL;
void AnalysisNeighborhoodSearchImpl::init(
AnalysisNeighborhood::SearchMode mode,
bool bXY,
+ const t_blocka *excls,
const t_pbc *pbc,
const AnalysisNeighborhoodPositions &positions)
{
{
xref_ = positions.x_;
}
- // TODO: Once exclusions are supported, this may need to be initialized.
- refid_ = NULL;
-}
-
-#if 0
-/*! \brief
- * Sets the exclusions for the next neighborhood search.
- *
- * \param[in,out] d Neighborhood search data structure.
- * \param[in] nexcl Number of reference positions to exclude from next
- * search.
- * \param[in] excl Indices of reference positions to exclude.
- *
- * The set exclusions remain in effect until the next call of this function.
- */
-void
-gmx_ana_nbsearch_set_excl(gmx_ana_nbsearch_t *d, int nexcl, int excl[])
-{
-
- d->nexcl = nexcl;
- d->excl = excl;
+ excls_ = excls;
+ refExclusionIds_ = NULL;
+ if (excls != NULL)
+ {
+ // TODO: Check that the IDs are ascending, or remove the limitation.
+ refExclusionIds_ = positions.exclusionIds_;
+ GMX_RELEASE_ASSERT(refExclusionIds_ != NULL,
+ "Exclusion IDs must be set for reference positions "
+ "when exclusions are enabled");
+ }
}
-#endif
/********************************************************************
* AnalysisNeighborhoodPairSearchImpl
1, &xtest_);
search_.mapPointToGridCell(xtest_, testcell_);
}
+ if (search_.excls_ != NULL)
+ {
+ const int exclIndex = testExclusionIds_[testIndex];
+ if (exclIndex < search_.excls_->nr)
+ {
+ const int startIndex = search_.excls_->index[exclIndex];
+ nexcl_ = search_.excls_->index[exclIndex + 1] - startIndex;
+ excl_ = &search_.excls_->a[startIndex];
+ }
+ else
+ {
+ nexcl_ = 0;
+ excl_ = NULL;
+ }
+ }
}
previ_ = -1;
prevr2_ = 0.0;
bool AnalysisNeighborhoodPairSearchImpl::isExcluded(int j)
{
- if (exclind_ < search_.nexcl_)
+ if (exclind_ < nexcl_)
{
- if (search_.refid_)
+ const int refId = search_.refExclusionIds_[j];
+ while (exclind_ < nexcl_ && excl_[exclind_] < refId)
{
- while (exclind_ < search_.nexcl_
- && search_.excl_[exclind_] < search_.refid_[j])
- {
- ++exclind_;
- }
- if (exclind_ < search_.nexcl_
- && search_.refid_[j] == search_.excl_[exclind_])
- {
- ++exclind_;
- return true;
- }
+ ++exclind_;
}
- else
+ if (exclind_ < nexcl_ && refId == excl_[exclind_])
{
- while (search_.bGrid_ && exclind_ < search_.nexcl_
- && search_.excl_[exclind_] < j)
- {
- ++exclind_;
- }
- if (search_.excl_[exclind_] == j)
- {
- ++exclind_;
- return true;
- }
+ ++exclind_;
+ return true;
}
}
return false;
void AnalysisNeighborhoodPairSearchImpl::startSearch(
const AnalysisNeighborhoodPositions &positions)
{
+ testExclusionIds_ = positions.exclusionIds_;
+ GMX_RELEASE_ASSERT(search_.excls_ == NULL || testExclusionIds_ != NULL,
+ "Exclusion IDs must be set when exclusions are enabled");
if (positions.index_ < 0)
{
testPositions_ = ConstArrayRef<rvec>(positions.x_, positions.count_);
typedef AnalysisNeighborhoodSearch::ImplPointer SearchImplPointer;
typedef std::vector<SearchImplPointer> SearchList;
- Impl() : cutoff_(0), mode_(eSearchMode_Automatic), bXY_(false)
+ Impl() : cutoff_(0), excls_(NULL), mode_(eSearchMode_Automatic), bXY_(false)
{
}
~Impl()
tMPI::mutex createSearchMutex_;
SearchList searchList_;
real cutoff_;
+ const t_blocka *excls_;
SearchMode mode_;
bool bXY_;
};
impl_->bXY_ = bXY;
}
+void AnalysisNeighborhood::setTopologyExclusions(const t_blocka *excls)
+{
+ GMX_RELEASE_ASSERT(impl_->searchList_.empty(),
+ "Changing the exclusions after initSearch() not currently supported");
+ impl_->excls_ = excls;
+}
+
void AnalysisNeighborhood::setMode(SearchMode mode)
{
impl_->mode_ = mode;
const AnalysisNeighborhoodPositions &positions)
{
Impl::SearchImplPointer search(impl_->getSearch());
- search->init(mode(), impl_->bXY_, pbc, positions);
+ search->init(mode(), impl_->bXY_, impl_->excls_, pbc, positions);
return AnalysisNeighborhoodSearch(search);
}
#include <boost/shared_ptr.hpp>
#include "../math/vectypes.h"
+#include "../utility/arrayref.h"
#include "../utility/common.h"
#include "../utility/gmxassert.h"
#include "../utility/real.h"
+struct t_blocka;
struct t_pbc;
namespace gmx
* to methods that accept positions.
*/
AnalysisNeighborhoodPositions(const rvec &x)
- : count_(1), index_(-1), x_(&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)
+ : 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.
*
int count_;
int index_;
const rvec *x_;
+ const int *exclusionIds_;
//! To access the positions for initialization.
friend class internal::AnalysisNeighborhoodSearchImpl;
* 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
* 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.
*
#include <algorithm>
#include <limits>
+#include <numeric>
#include <vector>
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/random/random.h"
+#include "gromacs/topology/block.h"
#include "gromacs/utility/smalloc.h"
#include "testutils/testasserts.h"
struct RefPair
{
RefPair(int refIndex, real distance)
- : refIndex(refIndex), distance(distance), bFound(false)
+ : refIndex(refIndex), distance(distance), bFound(false),
+ bExcluded(false)
{
}
int refIndex;
real distance;
+ // The variables below are state variables that are only used
+ // during the actual testing after creating a copy of the reference
+ // pair list, not as part of the reference data.
+ // Simpler to have just a single structure for both purposes.
bool bFound;
+ bool bExcluded;
};
struct TestPosition
}
}
+/********************************************************************
+ * ExclusionsHelper
+ */
+
+class ExclusionsHelper
+{
+ public:
+ static void markExcludedPairs(RefPairList *refPairs, int testIndex,
+ const t_blocka *excls);
+
+ ExclusionsHelper(int refPosCount, int testPosCount);
+
+ void generateExclusions();
+
+ const t_blocka *exclusions() const { return &excls_; }
+
+ gmx::ConstArrayRef<int> refPosIds() const
+ {
+ return gmx::ConstArrayRef<int>(exclusionIds_.begin(),
+ exclusionIds_.begin() + refPosCount_);
+ }
+ gmx::ConstArrayRef<int> testPosIds() const
+ {
+ return gmx::ConstArrayRef<int>(exclusionIds_.begin(),
+ exclusionIds_.begin() + testPosCount_);
+ }
+
+ private:
+ int refPosCount_;
+ int testPosCount_;
+ std::vector<int> exclusionIds_;
+ std::vector<int> exclsIndex_;
+ std::vector<int> exclsAtoms_;
+ t_blocka excls_;
+};
+
+// static
+void ExclusionsHelper::markExcludedPairs(RefPairList *refPairs, int testIndex,
+ const t_blocka *excls)
+{
+ int count = 0;
+ for (int i = excls->index[testIndex]; i < excls->index[testIndex + 1]; ++i)
+ {
+ const int excludedIndex = excls->a[i];
+ NeighborhoodSearchTestData::RefPair searchPair(excludedIndex, 0.0);
+ RefPairList::iterator excludedRefPair
+ = std::lower_bound(refPairs->begin(), refPairs->end(), searchPair);
+ if (excludedRefPair != refPairs->end()
+ && excludedRefPair->refIndex == excludedIndex)
+ {
+ excludedRefPair->bFound = true;
+ excludedRefPair->bExcluded = true;
+ ++count;
+ }
+ }
+}
+
+ExclusionsHelper::ExclusionsHelper(int refPosCount, int testPosCount)
+ : refPosCount_(refPosCount), testPosCount_(testPosCount)
+{
+ // Generate an array of 0, 1, 2, ...
+ // TODO: Make the tests work also with non-trivial exclusion IDs,
+ // and test that.
+ exclusionIds_.resize(std::max(refPosCount, testPosCount), 1);
+ exclusionIds_[0] = 0;
+ std::partial_sum(exclusionIds_.begin(), exclusionIds_.end(),
+ exclusionIds_.begin());
+
+ excls_.nr = 0;
+ excls_.index = NULL;
+ excls_.nra = 0;
+ excls_.a = NULL;
+ excls_.nalloc_index = 0;
+ excls_.nalloc_a = 0;
+}
+
+void ExclusionsHelper::generateExclusions()
+{
+ // TODO: Consider a better set of test data, where the density of the
+ // particles would be higher, or where the exclusions would not be random,
+ // to make a higher percentage of the exclusions to actually be within the
+ // cutoff.
+ exclsIndex_.reserve(testPosCount_ + 1);
+ exclsAtoms_.reserve(testPosCount_ * 20);
+ exclsIndex_.push_back(0);
+ for (int i = 0; i < testPosCount_; ++i)
+ {
+ for (int j = 0; j < 20; ++j)
+ {
+ exclsAtoms_.push_back(i + j*3);
+ }
+ exclsIndex_.push_back(exclsAtoms_.size());
+ }
+ excls_.nr = exclsIndex_.size();
+ excls_.index = &exclsIndex_[0];
+ excls_.nra = exclsAtoms_.size();
+ excls_.a = &exclsAtoms_[0];
+}
+
/********************************************************************
* NeighborhoodSearchTest
*/
const NeighborhoodSearchTestData &data);
void testPairSearch(gmx::AnalysisNeighborhoodSearch *search,
const NeighborhoodSearchTestData &data);
+ void testPairSearchFull(gmx::AnalysisNeighborhoodSearch *search,
+ const NeighborhoodSearchTestData &data,
+ const gmx::AnalysisNeighborhoodPositions &pos,
+ const t_blocka *excls);
gmx::AnalysisNeighborhood nb_;
};
}
}
+/*! \brief
+ * Helper function to check that all expected pairs were found.
+ */
+static void checkAllPairsFound(const RefPairList &refPairs)
+{
+ // This could be elegantly expressed with Google Mock matchers, but that
+ // has a significant effect on the runtime of the tests...
+ for (RefPairList::const_iterator i = refPairs.begin(); i != refPairs.end(); ++i)
+ {
+ if (!i->bFound)
+ {
+ ADD_FAILURE()
+ << "Some pairs within the cutoff were not found.";
+ break;
+ }
+ }
+}
+
void NeighborhoodSearchTest::testPairSearch(
gmx::AnalysisNeighborhoodSearch *search,
const NeighborhoodSearchTestData &data)
{
- NeighborhoodSearchTestData::TestPositionList::const_iterator i;
- // TODO: Test also searching all the test positions in a single search;
- // currently the implementation just contains this loop, though, but in
- // the future that may trigger a different code path.
- for (i = data.testPositions_.begin(); i != data.testPositions_.end(); ++i)
+ testPairSearchFull(search, data, data.testPositions(), NULL);
+}
+
+void NeighborhoodSearchTest::testPairSearchFull(
+ gmx::AnalysisNeighborhoodSearch *search,
+ const NeighborhoodSearchTestData &data,
+ const gmx::AnalysisNeighborhoodPositions &pos,
+ const t_blocka *excls)
+{
+ // TODO: Some parts of this code do not work properly if pos does not
+ // contain all the test positions.
+ std::set<int> remainingTestPositions;
+ for (size_t i = 0; i < data.testPositions_.size(); ++i)
+ {
+ remainingTestPositions.insert(i);
+ }
+ gmx::AnalysisNeighborhoodPairSearch pairSearch
+ = search->startPairSearch(pos);
+ gmx::AnalysisNeighborhoodPair pair;
+ // TODO: There is an ordering assumption here that may break in the future:
+ // all pairs for a test position are assumed to be returned consencutively.
+ RefPairList refPairs;
+ int prevTestPos = -1;
+ while (pairSearch.findNextPair(&pair))
{
- RefPairList refPairs = i->refPairs;
- gmx::AnalysisNeighborhoodPairSearch pairSearch
- = search->startPairSearch(i->x);
- gmx::AnalysisNeighborhoodPair pair;
- while (pairSearch.findNextPair(&pair))
+ if (pair.testIndex() != prevTestPos)
{
- EXPECT_EQ(0, pair.testIndex());
- NeighborhoodSearchTestData::RefPair searchPair(pair.refIndex(),
- sqrt(pair.distance2()));
- RefPairList::iterator foundRefPair
- = std::lower_bound(refPairs.begin(), refPairs.end(), searchPair);
- if (foundRefPair == refPairs.end() || foundRefPair->refIndex != pair.refIndex())
+ if (prevTestPos != -1)
{
- ADD_FAILURE()
- << "Expected: Position " << pair.refIndex()
- << " is within cutoff.\n"
- << " Actual: It is not.";
+ checkAllPairsFound(refPairs);
}
- else if (foundRefPair->bFound)
+ const int testIndex = pair.testIndex();
+ if (remainingTestPositions.count(testIndex) == 0)
{
ADD_FAILURE()
- << "Expected: Position " << pair.refIndex()
- << " is returned only once.\n"
- << " Actual: It is returned multiple times.";
+ << "Pairs for test position " << testIndex
+ << " are returned more than once.";
}
- else
+ remainingTestPositions.erase(testIndex);
+ refPairs = data.testPositions_[testIndex].refPairs;
+ if (excls != NULL)
{
- foundRefPair->bFound = true;
- EXPECT_REAL_EQ_TOL(foundRefPair->distance, searchPair.distance,
- gmx::test::ulpTolerance(64));
+ ExclusionsHelper::markExcludedPairs(&refPairs, testIndex, excls);
}
+ prevTestPos = testIndex;
}
- for (RefPairList::const_iterator j = refPairs.begin(); j != refPairs.end(); ++j)
+
+ NeighborhoodSearchTestData::RefPair searchPair(pair.refIndex(),
+ sqrt(pair.distance2()));
+ RefPairList::iterator foundRefPair
+ = std::lower_bound(refPairs.begin(), refPairs.end(), searchPair);
+ if (foundRefPair == refPairs.end() || foundRefPair->refIndex != pair.refIndex())
{
- if (!j->bFound)
- {
- ADD_FAILURE()
- << "Expected: All pairs within cutoff will be returned.\n"
- << " Actual: Position " << j->refIndex << " is not found.";
- break;
- }
+ ADD_FAILURE()
+ << "Expected: Pair (ref: " << pair.refIndex() << ", test: "
+ << pair.testIndex() << ") is not within the cutoff.\n"
+ << " Actual: It is returned.";
+ }
+ else if (foundRefPair->bExcluded)
+ {
+ ADD_FAILURE()
+ << "Expected: Pair (ref: " << pair.refIndex() << ", test: "
+ << pair.testIndex() << ") is excluded from the search.\n"
+ << " Actual: It is returned.";
+ }
+ else if (foundRefPair->bFound)
+ {
+ ADD_FAILURE()
+ << "Expected: Pair (ref: " << pair.refIndex() << ", test: "
+ << pair.testIndex() << ") is returned only once.\n"
+ << " Actual: It is returned multiple times.";
+ }
+ else
+ {
+ foundRefPair->bFound = true;
+ EXPECT_REAL_EQ_TOL(foundRefPair->distance, searchPair.distance,
+ gmx::test::ulpTolerance(64))
+ << "Distance computed by the neighborhood search does not match.";
+ }
+ }
+ checkAllPairsFound(refPairs);
+ for (std::set<int>::const_iterator i = remainingTestPositions.begin();
+ i != remainingTestPositions.end(); ++i)
+ {
+ if (!data.testPositions_[*i].refPairs.empty())
+ {
+ ADD_FAILURE()
+ << "Expected: Pairs would be returned for test position " << *i << ".\n"
+ << " Actual: None were returned.";
+ break;
}
}
}
testPairSearch(&search2, data);
gmx::AnalysisNeighborhoodPair pair;
- pairSearch1.findNextPair(&pair);
+ ASSERT_TRUE(pairSearch1.findNextPair(&pair))
+ << "Test data did not contain any pairs for position 0 (problem in the test).";
EXPECT_EQ(0, pair.testIndex());
{
NeighborhoodSearchTestData::RefPair searchPair(pair.refIndex(), sqrt(pair.distance2()));
EXPECT_TRUE(data.containsPair(0, searchPair));
}
- pairSearch2.findNextPair(&pair);
+ ASSERT_TRUE(pairSearch2.findNextPair(&pair))
+ << "Test data did not contain any pairs for position 1 (problem in the test).";
EXPECT_EQ(1, pair.testIndex());
{
NeighborhoodSearchTestData::RefPair searchPair(pair.refIndex(), sqrt(pair.distance2()));
}
}
+TEST_F(NeighborhoodSearchTest, SimpleSearchExclusions)
+{
+ const NeighborhoodSearchTestData &data = RandomBoxFullPBCData::get();
+
+ ExclusionsHelper helper(data.refPosCount_, data.testPositions_.size());
+ helper.generateExclusions();
+
+ nb_.setCutoff(data.cutoff_);
+ nb_.setTopologyExclusions(helper.exclusions());
+ nb_.setMode(gmx::AnalysisNeighborhood::eSearchMode_Simple);
+ gmx::AnalysisNeighborhoodSearch search =
+ nb_.initSearch(&data.pbc_,
+ data.refPositions().exclusionIds(helper.refPosIds()));
+ ASSERT_EQ(gmx::AnalysisNeighborhood::eSearchMode_Simple, search.mode());
+
+ testPairSearchFull(&search, data,
+ data.testPositions().exclusionIds(helper.testPosIds()),
+ helper.exclusions());
+}
+
+TEST_F(NeighborhoodSearchTest, GridSearchExclusions)
+{
+ const NeighborhoodSearchTestData &data = RandomBoxFullPBCData::get();
+
+ ExclusionsHelper helper(data.refPosCount_, data.testPositions_.size());
+ helper.generateExclusions();
+
+ nb_.setCutoff(data.cutoff_);
+ nb_.setTopologyExclusions(helper.exclusions());
+ nb_.setMode(gmx::AnalysisNeighborhood::eSearchMode_Grid);
+ gmx::AnalysisNeighborhoodSearch search =
+ nb_.initSearch(&data.pbc_,
+ data.refPositions().exclusionIds(helper.refPosIds()));
+ ASSERT_EQ(gmx::AnalysisNeighborhood::eSearchMode_Grid, search.mode());
+
+ testPairSearchFull(&search, data,
+ data.testPositions().exclusionIds(helper.testPosIds()),
+ helper.exclusions());
+}
+
} // namespace
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff