gmx::AnalysisNeighborhood Class Reference

#include <gromacs/selection/nbsearch.h>

Description

Neighborhood searching for analysis tools.

See Neighborhood search for analysis tools for an overview.

To use the search, create an object of this type, call setCutoff() to initialize it, and then repeatedly call initSearch() to start a search with different sets of reference positions. For each set of reference positions, use methods in the returned AnalysisNeighborhoodSearch to find the reference positions that are within the given cutoff from a provided position.

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. 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:

Generalize the exclusion machinery to make it easier to use for other cases than atom-atom exclusions from the topology.

Examples:

template.cpp.

Public Types
enum	SearchMode { eSearchMode_Automatic, eSearchMode_Simple, eSearchMode_Grid }
	Searching algorithm to use. More...

Public Member Functions
	AnalysisNeighborhood ()
	Creates an uninitialized neighborhood search.
void	setCutoff (real cutoff)
	Sets cutoff distance for the neighborhood searching. More...
void	setXYMode (bool bXY)
	Sets the search to only happen in the XY plane. More...
void	setTopologyExclusions (const ListOfLists< int > *excls)
	Sets atom exclusions from a topology. More...
void	setMode (SearchMode mode)
	Sets the algorithm to use for searching. More...
SearchMode	mode () const
	Returns the currently active search mode.
AnalysisNeighborhoodSearch	initSearch (const t_pbc *pbc, const AnalysisNeighborhoodPositions &positions)
	Initializes neighborhood search for a set of positions. More...

Member Enumeration Documentation

enum gmx::AnalysisNeighborhood::SearchMode

Searching algorithm to use.

Enumerator
eSearchMode_Automatic	Select algorithm based on heuristic efficiency considerations.
eSearchMode_Simple	Use a simple loop over all pairs.
eSearchMode_Grid	Use grid-based searching whenever possible.

Member Function Documentation

AnalysisNeighborhoodSearch gmx::AnalysisNeighborhood::initSearch	(	const t_pbc *	pbc,
		const AnalysisNeighborhoodPositions &	positions
	)

Initializes neighborhood search for a set of positions.

Parameters

[in]	pbc	PBC information for the frame.
[in]	positions	Set of reference positions to use.

Returns

Search object that can be used to find positions from x within the given cutoff.

Exceptions

std::bad_alloc

if out of memory.

Currently, the input positions cannot use AnalysisNeighborhoodPositions::selectSingleFromArray().

Examples:

template.cpp.

void gmx::AnalysisNeighborhood::setCutoff

(

real

cutoff

)

Sets cutoff distance for the neighborhood searching.

Parameters

[in]

cutoff

Cutoff distance for the search (<=0 stands for no cutoff).

Currently, can only be called before the first call to initSearch(). If this method is not called, no cutoff is used in the searches.

Does not throw.

Examples:

template.cpp.

void gmx::AnalysisNeighborhood::setMode

(

SearchMode

mode

)

Sets the algorithm to use for searching.

Parameters

[in]

mode

Search mode to use.

Note that if mode is eSearchMode_Grid, it is still only a suggestion: grid-based searching may not be possible with the provided input, in which case a simple search is still used. This is mainly useful for testing purposes to force a mode.

Does not throw.

void gmx::AnalysisNeighborhood::setTopologyExclusions

(

const ListOfLists< int > *

excls

)

Sets atom exclusions from a topology.

The 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 Also

AnalysisNeighborhoodPositions::exclusionIds()

void gmx::AnalysisNeighborhood::setXYMode

(

bool

bXY

)

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.

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The documentation for this class was generated from the following files:

• api/legacy/include/gromacs/selection/nbsearch.h
• src/gromacs/selection/nbsearch.cpp