nbsearch.cpp File Reference

#include "gmxpre.h"
#include "gromacs/selection/nbsearch.h"
#include <cmath>
#include <cstring>
#include <algorithm>
#include <memory>
#include <mutex>
#include <string>
#include <vector>
#include "gromacs/math/functions.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/selection/position.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/listoflists.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/stringutil.h"

Include dependency graph for nbsearch.cpp:

Description

Implements neighborhood searching for analysis (from nbsearch.h).

High-level overview of the algorithm is at Neighborhood search for analysis tools.

Todo:

The grid implementation could still be optimized in several different ways:

• A better heuristic for selecting the grid size or falling back to a simple all-pairs search.
• A multi-level grid implementation could be used to be able to use small grids for short cutoffs with very inhomogeneous particle distributions without a memory cost.

Author

Teemu Murtola teemu.nosp@m..mur.nosp@m.tola@.nosp@m.gmai.nosp@m.l.com

Classes
class	gmx::anonymous_namespace{nbsearch.cpp}::MindistAction
	Search action find the minimum distance. More...

Functions
void	gmx::anonymous_namespace{nbsearch.cpp}::computeBoundingBox (int posCount, const rvec x[], rvec origin, rvec size)
	Computes the bounding box for a set of positions. More...
bool	gmx::anonymous_namespace{nbsearch.cpp}::withinAction (int, real, const rvec)
	Search action to find the next neighbor. More...