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.
SBCContainerVector< SBAtom * > const *	getNeighborVector (unsigned int i) const Returns the neighbor vector of atom `i` .
SBCContainerVector< SBAtom * > const *	getNeighborVector (SBAtom * atom) const Returns the neighbor vector of atom `atom` .
virtual void	getNeighbors (SBCContainerVector< 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 (SBCContainerVector< 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 () Builds the reference target.
unsigned int	getMemoryFootprint () const Returns the memory footprint.
void	printReferencesToOwners () const Prints the references to the owners of this reference target.
virtual	~SBCReferenceTarget () Destructor.

Protected Attributes inherited from SBCReferenceTarget#

See SBCReferenceTarget

Type	Name
SBCReferenceTargetData *	dataPointer A pointer to the private data.

Protected Functions inherited from SBCReferenceTarget#

See SBCReferenceTarget

Type	Name
	SBCReferenceTarget (SBCReferenceTargetData * dataPointer) Protected constructor.
void	removeAllReferenceOwners () Stops all the reference owners from referencing this reference target.

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 .

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

function getNeighborVector [2/2]#

Returns the neighbor vector of atom atom .

SBCContainerVector < 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 (
    SBCContainerVector < 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 (
    SBCContainerVector < 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 ()