Class SBSNeighborSearchParticleSystemPBC#

ClassList > SBSNeighborSearchParticleSystemPBC

#include <SBSNeighborSearchParticleSystemPBC.hpp>

Inherits the following classes: SBSNeighborSearch

Inherited by the following classes: SBSNeighborSearchParticleSystemGridPBC

Public Functions#

Type	Name
SBVector< SBAtom * > *	getNeighborVector (unsigned int i)
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	initializeNeighborLists ()
void	onDynamicalEvent (SBDynamicalEvent * dynamicalEvent)
virtual void	print (unsigned int offset=0) override const Prints debugging information.
virtual void	updateNeighborLists ()
virtual	~SBSNeighborSearchParticleSystemPBC ()

Public Functions inherited from SBSNeighborSearch#

See SBSNeighborSearch

Type	Name
virtual void	print (unsigned int offset=0) const Prints debugging information.
virtual	~SBSNeighborSearch ()

Public Functions inherited from SBCReferenceTarget#

See SBCReferenceTarget

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

Protected Attributes#

Type	Name
SBIAPosition3 *	boxPBC
SBQuantity::length *	boxSizeX
SBQuantity::length *	boxSizeY
SBQuantity::length *	boxSizeZ
SBQuantity::squareLength *	cutoffDistanceSquared
SBQuantity::inverseLength *	inverseCutoffDistance
SBBuffer< SBVector< SBAtom * > * > *	neighborVectorBuffer The buffer containing the neighbor lists associated to each atom.
SBPointer< SBParticleSystem > *	particleSystem The particle system the neighbor search algorithm is attached to.

Protected Attributes inherited from SBCReferenceTarget#

See SBCReferenceTarget

Type	Name
SBCReferenceTargetData *	dataPointer

Protected Functions#

Type	Name
	SBSNeighborSearchParticleSystemPBC (SBParticleSystem * p, const SBQuantity::length & cutoffDistance)

Protected Functions inherited from SBSNeighborSearch#

See SBSNeighborSearch

Type	Name
	SBSNeighborSearch ()

Protected Functions inherited from SBCReferenceTarget#

See SBCReferenceTarget

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

Detailed Description#

This class is the base class of neighbor search algorithms that can be applied to particle systems with periodic boundary conditions.

Short name: SBNeighborSearchParticleSystemPBC

Public Functions Documentation#

function getNeighborVector#

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

function getNeighbors [1/2]#

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

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

function initializeNeighborLists#

virtual void SBSNeighborSearchParticleSystemPBC::initializeNeighborLists ()

function onDynamicalEvent#

void SBSNeighborSearchParticleSystemPBC::onDynamicalEvent (
    SBDynamicalEvent * dynamicalEvent
)

function print#

Prints debugging information.

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

Implements SBSNeighborSearch::print

function updateNeighborLists#

virtual void SBSNeighborSearchParticleSystemPBC::updateNeighborLists ()

function ~SBSNeighborSearchParticleSystemPBC#

virtual SBSNeighborSearchParticleSystemPBC::~SBSNeighborSearchParticleSystemPBC ()

Protected Attributes Documentation#

variable boxPBC#

SBIAPosition3* boxPBC;

variable boxSizeX#

SBQuantity::length* boxSizeX;

variable boxSizeY#

SBQuantity::length* boxSizeY;

variable boxSizeZ#

SBQuantity::length* boxSizeZ;

variable cutoffDistanceSquared#

SBQuantity::squareLength* cutoffDistanceSquared;

variable inverseCutoffDistance#

SBQuantity::inverseLength* inverseCutoffDistance;

variable neighborVectorBuffer#

The buffer containing the neighbor lists associated to each atom.

SBBuffer<SBVector<SBAtom*>*>* neighborVectorBuffer;

variable particleSystem#

The particle system the neighbor search algorithm is attached to.

SBPointer<SBParticleSystem>* particleSystem;

Protected Functions Documentation#

function SBSNeighborSearchParticleSystemPBC#

SBSNeighborSearchParticleSystemPBC::SBSNeighborSearchParticleSystemPBC (
    SBParticleSystem * p,
    const SBQuantity::length & cutoffDistance
)