*/
#include "gromacs/selection/nbsearch.h"
-#include <math.h>
+#include <cmath>
+#include <cstring>
#include <algorithm>
#include <vector>
#include "thread_mpi/mutex.h"
+#include "gromacs/legacyheaders/names.h"
+
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/selection/position.h"
#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringutil.h"
namespace gmx
{
* Initializes the search with a given box and reference positions.
*
* \param[in] mode Search mode to use.
+ * \param[in] bXY Whether to use 2D searching.
* \param[in] pbc PBC information.
* \param[in] positions Set of reference positions.
*/
void init(AnalysisNeighborhood::SearchMode mode,
+ bool bXY,
const t_pbc *pbc,
const AnalysisNeighborhoodPositions &positions);
PairSearchImplPointer getPairSearch();
* \param[in] pbc Information about the box.
* \returns false if grid search is not suitable.
*/
- bool initGridCells(const t_pbc *pbc);
+ bool initGridCells(const t_pbc &pbc);
/*! \brief
* Sets ua a search grid for a given box.
*
* \param[in] pbc Information about the box.
* \returns false if grid search is not suitable.
*/
- bool initGrid(const t_pbc *pbc);
+ bool initGrid(const t_pbc &pbc);
/*! \brief
* Maps a point into a grid cell.
*
real cutoff_;
//! The cutoff squared.
real cutoff2_;
+ //! Whether to do searching in XY plane only.
+ bool bXY_;
//! Number of reference points for the current frame.
int nref_;
//! Reference position ids (NULL if not available).
const int *refid_;
//! PBC data.
- t_pbc *pbc_;
+ t_pbc pbc_;
//! Number of excluded reference positions for current test particle.
int nexcl_;
rvec xtest_;
//! Stores the previous returned position during a pair loop.
int previ_;
+ //! Stores the pair distance corresponding to previ_;
+ real prevr2_;
//! Stores the current exclusion index during loops.
int exclind_;
//! Stores the test particle cell index during loops.
bTryGrid_ = false;
}
cutoff2_ = sqr(cutoff_);
+ bXY_ = false;
nref_ = 0;
xref_ = NULL;
refid_ = NULL;
- pbc_ = NULL;
+ std::memset(&pbc_, 0, sizeof(pbc_));
nexcl_ = 0;
excl_ = NULL;
}
}
-bool AnalysisNeighborhoodSearchImpl::initGridCells(const t_pbc *pbc)
+bool AnalysisNeighborhoodSearchImpl::initGridCells(const t_pbc &pbc)
{
const real targetsize =
- pow(pbc->box[XX][XX] * pbc->box[YY][YY] * pbc->box[ZZ][ZZ]
+ pow(pbc.box[XX][XX] * pbc.box[YY][YY] * pbc.box[ZZ][ZZ]
* 10 / nref_, static_cast<real>(1./3.));
int cellCount = 1;
for (int dd = 0; dd < DIM; ++dd)
{
- ncelldim_[dd] = static_cast<int>(pbc->box[dd][dd] / targetsize);
+ ncelldim_[dd] = static_cast<int>(pbc.box[dd][dd] / targetsize);
cellCount *= ncelldim_[dd];
if (ncelldim_[dd] < 3)
{
return true;
}
-bool AnalysisNeighborhoodSearchImpl::initGrid(const t_pbc *pbc)
+bool AnalysisNeighborhoodSearchImpl::initGrid(const t_pbc &pbc)
{
/* TODO: This check could be improved. */
- if (0.5*pbc->max_cutoff2 < cutoff2_)
+ if (0.5*pbc.max_cutoff2 < cutoff2_)
{
return false;
}
return false;
}
- bTric_ = TRICLINIC(pbc->box);
+ bTric_ = TRICLINIC(pbc.box);
if (bTric_)
{
for (int dd = 0; dd < DIM; ++dd)
{
- svmul(1.0 / ncelldim_[dd], pbc->box[dd], cellbox_[dd]);
+ svmul(1.0 / ncelldim_[dd], pbc.box[dd], cellbox_[dd]);
}
m_inv_ur0(cellbox_, recipcell_);
}
{
for (int dd = 0; dd < DIM; ++dd)
{
- cellbox_[dd][dd] = pbc->box[dd][dd] / ncelldim_[dd];
+ cellbox_[dd][dd] = pbc.box[dd][dd] / ncelldim_[dd];
recipcell_[dd][dd] = 1.0 / cellbox_[dd][dd];
}
}
void AnalysisNeighborhoodSearchImpl::init(
AnalysisNeighborhood::SearchMode mode,
+ bool bXY,
const t_pbc *pbc,
const AnalysisNeighborhoodPositions &positions)
{
GMX_RELEASE_ASSERT(positions.index_ == -1,
"Individual indexed positions not supported as reference");
- pbc_ = const_cast<t_pbc *>(pbc);
+ bXY_ = bXY;
+ if (bXY_ && pbc->ePBC != epbcNONE)
+ {
+ if (pbc->ePBC != epbcXY && pbc->ePBC != epbcXYZ)
+ {
+ std::string message =
+ formatString("Computations in the XY plane are not supported with PBC type '%s'",
+ EPBC(pbc->ePBC));
+ GMX_THROW(NotImplementedError(message));
+ }
+ if (std::fabs(pbc->box[ZZ][XX]) > GMX_REAL_EPS*pbc->box[ZZ][ZZ] ||
+ std::fabs(pbc->box[ZZ][YY]) > GMX_REAL_EPS*pbc->box[ZZ][ZZ])
+ {
+ GMX_THROW(NotImplementedError("Computations in the XY plane are not supported when the last box vector is not parallel to the Z axis"));
+ }
+ set_pbc(&pbc_, epbcXY, const_cast<rvec *>(pbc->box));
+ }
+ else if (pbc != NULL)
+ {
+ pbc_ = *pbc;
+ }
+ else
+ {
+ pbc_.ePBC = epbcNONE;
+ }
nref_ = positions.count_;
// TODO: Consider whether it would be possible to support grid searching in
// more cases.
if (mode == AnalysisNeighborhood::eSearchMode_Simple
- || pbc_ == NULL || pbc_->ePBC != epbcXYZ)
+ || pbc_.ePBC != epbcXYZ)
{
bGrid_ = false;
}
{
copy_rvec(positions.x_[i], xref_alloc_[i]);
}
- put_atoms_in_triclinic_unitcell(ecenterTRIC, pbc_->box,
+ put_atoms_in_triclinic_unitcell(ecenterTRIC, pbc_.box,
nref_, xref_alloc_);
for (int i = 0; i < nref_; ++i)
{
copy_rvec(testPositions_[testIndex_], xtest_);
if (search_.bGrid_)
{
- put_atoms_in_triclinic_unitcell(ecenterTRIC, search_.pbc_->box,
+ put_atoms_in_triclinic_unitcell(ecenterTRIC,
+ const_cast<rvec *>(search_.pbc_.box),
1, &xtest_);
search_.mapPointToGridCell(xtest_, testcell_);
}
}
previ_ = -1;
+ prevr2_ = 0.0;
exclind_ = 0;
prevnbi_ = 0;
prevcai_ = -1;
{
if (search_.bGrid_)
{
+ GMX_RELEASE_ASSERT(!search_.bXY_, "Grid-based XY searches not implemented");
+
int nbi = prevnbi_;
int cai = prevcai_ + 1;
continue;
}
rvec dx;
- pbc_dx_aiuc(search_.pbc_, xtest_, search_.xref_[i], dx);
+ pbc_dx_aiuc(&search_.pbc_, xtest_, search_.xref_[i], dx);
const real r2 = norm2(dx);
if (r2 <= search_.cutoff2_)
{
prevnbi_ = nbi;
prevcai_ = cai;
previ_ = i;
+ prevr2_ = r2;
return true;
}
}
continue;
}
rvec dx;
- if (search_.pbc_)
+ if (search_.pbc_.ePBC != epbcNONE)
{
- pbc_dx(search_.pbc_, xtest_, search_.xref_[i], dx);
+ pbc_dx(&search_.pbc_, xtest_, search_.xref_[i], dx);
}
else
{
rvec_sub(xtest_, search_.xref_[i], dx);
}
- const real r2 = norm2(dx);
+ const real r2
+ = search_.bXY_
+ ? dx[XX]*dx[XX] + dx[YY]*dx[YY]
+ : norm2(dx);
if (r2 <= search_.cutoff2_)
{
if (action(i, r2))
{
- previ_ = i;
+ previ_ = i;
+ prevr2_ = r2;
return true;
}
}
}
else
{
- *pair = AnalysisNeighborhoodPair(previ_, testIndex_);
+ *pair = AnalysisNeighborhoodPair(previ_, testIndex_, prevr2_);
}
}
typedef AnalysisNeighborhoodSearch::ImplPointer SearchImplPointer;
typedef std::vector<SearchImplPointer> SearchList;
- Impl() : cutoff_(0), mode_(eSearchMode_Automatic)
+ Impl() : cutoff_(0), mode_(eSearchMode_Automatic), bXY_(false)
{
}
~Impl()
SearchList searchList_;
real cutoff_;
SearchMode mode_;
+ bool bXY_;
};
AnalysisNeighborhood::Impl::SearchImplPointer
impl_->cutoff_ = cutoff;
}
+void AnalysisNeighborhood::setXYMode(bool bXY)
+{
+ impl_->bXY_ = bXY;
+}
+
void AnalysisNeighborhood::setMode(SearchMode mode)
{
impl_->mode_ = mode;
const AnalysisNeighborhoodPositions &positions)
{
Impl::SearchImplPointer search(impl_->getSearch());
- search->init(mode(), pbc, positions);
+ search->init(mode(), impl_->bXY_, pbc, positions);
return AnalysisNeighborhoodSearch(search);
}
int closestPoint = -1;
MindistAction action(&closestPoint, &minDist2);
(void)pairSearch.searchNext(action);
- return AnalysisNeighborhoodPair(closestPoint, 0);
+ return AnalysisNeighborhoodPair(closestPoint, 0, minDist2);
}
AnalysisNeighborhoodPairSearch
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff