#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);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff