Class SBMStructuralModelGrid#

ClassList > SBMStructuralModelGrid

This class describes a grid-based neighbor search algorithm that can be applied to atoms (atoms or pseudo-atoms). More...

#include <SBMStructuralModelGrid.hpp>

Inherits the following classes: SBCReferenceTarget

Public Functions#

Type	Name
	SBMStructuralModelGrid (const SBNodeIndexer & nodeIndexer, const SBQuantity::length & cutoffDistance) Constructs a neighbor search grid.
	SB_DECLARE_DATA (SBMStructuralModelGrid)
virtual bool	areNeighbors (unsigned int i, unsigned int j) const Returns whether atoms with indices `i` and`j` are neighbors.
virtual bool	areNeighbors (SBAtom * atomI, SBAtom * atomJ) const Returns whether atoms `atomI` and`atomJ` are neighbors.
SBVector< SBAtom * > const *	getNeighborVector (unsigned int i) const Returns the neighbor vector of atom `i` .
SBVector< SBAtom * > const *	getNeighborVector (SBAtom * atom) const Returns the neighbor vector of atom `atom` .
virtual void	getNeighbors (SBVector< SBAtom * > & neighborVector, const SBPosition3 & position, const SBQuantity::length & radius) const Appends to `neighborVector` all atoms that are at a distance smaller than or equal to`radius` from the specified`position` .
virtual void	getNeighbors (SBVector< SBAtom * > & neighborVector, const SBIAPosition3 & box) const Appends to `neighborVector` all atoms inside the`box` .
virtual void	print (unsigned int offset=0) const Prints debugging information.
virtual void	update () Updates the grid and neighbor lists.
virtual	~SBMStructuralModelGrid () Destroys the neighbor search grid.

Public Functions inherited from SBCReferenceTarget#

See SBCReferenceTarget

Type	Name
	SBCReferenceTarget ()
unsigned int	getMemoryFootprint () const
void	printReferencesToOwners () const
virtual	~SBCReferenceTarget ()

Protected Attributes inherited from SBCReferenceTarget#

See SBCReferenceTarget

Type	Name
SBCReferenceTargetData *	dataPointer

Protected Functions inherited from SBCReferenceTarget#

See SBCReferenceTarget

Type	Name
	SBCReferenceTarget (SBCReferenceTargetData * dataPointer)
void	removeAllReferenceOwners ()

Detailed Description#

This class may be used by developers to perform neighbor search between atoms . Internally, the neighbor search algorithm uses a grid to efficiently determine neighbors.

Short name: SBStructuralModelGrid

Public Functions Documentation#

function SBMStructuralModelGrid#

Constructs a neighbor search grid.

SBMStructuralModelGrid::SBMStructuralModelGrid (
    const SBNodeIndexer & nodeIndexer,
    const SBQuantity::length & cutoffDistance
)

This constructor initializes the neighbor search algorithm. After the grid is constructed, neighbor lists are available and can be retrieved using the getNeighborVector functions.

function SB_DECLARE_DATA#

SBMStructuralModelGrid::SB_DECLARE_DATA (
    SBMStructuralModelGrid
)

function areNeighbors [1/2]#

Returns whether atoms with indices i andj are neighbors.

virtual bool SBMStructuralModelGrid::areNeighbors (
    unsigned int i,
    unsigned int j
) const

function areNeighbors [2/2]#

Returns whether atoms atomI andatomJ are neighbors.

virtual bool SBMStructuralModelGrid::areNeighbors (
    SBAtom * atomI,
    SBAtom * atomJ
) const

function getNeighborVector [1/2]#

Returns the neighbor vector of atom i .

SBVector< SBAtom * > const * SBMStructuralModelGrid::getNeighborVector (
    unsigned int i
) const

function getNeighborVector [2/2]#

Returns the neighbor vector of atom atom .

SBVector< SBAtom * > const * SBMStructuralModelGrid::getNeighborVector (
    SBAtom * atom
) const

function getNeighbors [1/2]#

Appends to neighborVector all atoms that are at a distance smaller than or equal toradius from the specifiedposition .

virtual void SBMStructuralModelGrid::getNeighbors (
    SBVector< SBAtom * > & neighborVector,
    const SBPosition3 & position,
    const SBQuantity::length & radius
) const

function getNeighbors [2/2]#

Appends to neighborVector all atoms inside thebox .

virtual void SBMStructuralModelGrid::getNeighbors (
    SBVector< SBAtom * > & neighborVector,
    const SBIAPosition3 & box
) const

function print#

Prints debugging information.

virtual void SBMStructuralModelGrid::print (
    unsigned int offset=0
) const

function update#

Updates the grid and neighbor lists.

virtual void SBMStructuralModelGrid::update ()

function ~SBMStructuralModelGrid#

Destroys the neighbor search grid.

virtual SBMStructuralModelGrid::~SBMStructuralModelGrid ()