Class SBSNeighborSearchParticleSystem#

ClassList > SBSNeighborSearchParticleSystem

This class is the base class of neighbor search algorithms that can be applied to particle systems. More...

#include "SBSNeighborSearchParticleSystem.hpp"

Inherits the following classes: SBSNeighborSearch

Inherited by the following classes: SBSNeighborSearchParticleSystemGrid

Public Functions#

Type	Name
	SB_DECLARE_DATA (SBSNeighborSearchParticleSystem)
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) Returns the neighbor list for the i-th particle.
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 () Initializes the neighbor lists.
void	onDynamicalEvent (SBDynamicalEvent * dynamicalEvent) Handles dynamical model events.
virtual void	print (unsigned int offset=0) override const Prints debugging information.
virtual void	updateNeighborLists () Updates the neighbor lists.
virtual	~SBSNeighborSearchParticleSystem () Destructor.

Public Functions inherited from SBSNeighborSearch#

See SBSNeighborSearch

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

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#

Type	Name
SBQuantity::squareLength *	cutoffDistanceSquared The squared cutoff distance.
SBQuantity::inverseLength *	inverseCutoffDistance The inverse cutoff distance.
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 A pointer to the private data.

Protected Functions#

Type	Name
	SBSNeighborSearchParticleSystem (SBParticleSystem * p, const SBQuantity::length & cutoffDistance) Protected constructor.
	SBSNeighborSearchParticleSystem (SBParticleSystem * p, const SBQuantity::length & cutoffDistance, SBSNeighborSearchParticleSystemData * dataPointer) Protected constructor.

Protected Functions inherited from SBSNeighborSearch#

See SBSNeighborSearch

Type	Name
	SBSNeighborSearch () Protected constructor.
	SBSNeighborSearch (SBSNeighborSearchData * dataPointer) Protected constructor.

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#

Short name: SBNeighborSearchParticleSystem

Public Functions Documentation#

function SB_DECLARE_DATA#

SBSNeighborSearchParticleSystem::SB_DECLARE_DATA (
    SBSNeighborSearchParticleSystem
)

function areNeighbors [1/2]#

Returns whether atoms with indices i andj are neighbors.

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

function areNeighbors [2/2]#

Returns whether atoms atomI andatomJ are neighbors.

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

function getNeighborVector#

Returns the neighbor list for the i-th particle.

SBVector< SBAtom * > const * SBSNeighborSearchParticleSystem::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 SBSNeighborSearchParticleSystem::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 SBSNeighborSearchParticleSystem::getNeighbors (
    SBVector< SBAtom * > & neighborVector,
    const SBIAPosition3 & box
) const

function initializeNeighborLists#

Initializes the neighbor lists.

virtual void SBSNeighborSearchParticleSystem::initializeNeighborLists ()

function onDynamicalEvent#

Handles dynamical model events.

void SBSNeighborSearchParticleSystem::onDynamicalEvent (
    SBDynamicalEvent * dynamicalEvent
)

function print#

Prints debugging information.

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

Implements SBSNeighborSearch::print

function updateNeighborLists#

Updates the neighbor lists.

virtual void SBSNeighborSearchParticleSystem::updateNeighborLists ()

function ~SBSNeighborSearchParticleSystem#

Destructor.

virtual SBSNeighborSearchParticleSystem::~SBSNeighborSearchParticleSystem ()

Protected Attributes Documentation#

variable cutoffDistanceSquared#

The squared cutoff distance.

SBQuantity::squareLength* SBSNeighborSearchParticleSystem::cutoffDistanceSquared;

variable inverseCutoffDistance#

The inverse cutoff distance.

SBQuantity::inverseLength* SBSNeighborSearchParticleSystem::inverseCutoffDistance;

variable neighborVectorBuffer#

The buffer containing the neighbor lists associated to each atom.

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

variable particleSystem#

The particle system the neighbor search algorithm is attached to.

SBPointer<SBParticleSystem>* SBSNeighborSearchParticleSystem::particleSystem;

Protected Functions Documentation#

function SBSNeighborSearchParticleSystem [1/2]#

Protected constructor.

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

function SBSNeighborSearchParticleSystem [2/2]#

Protected constructor.

SBSNeighborSearchParticleSystem::SBSNeighborSearchParticleSystem (
    SBParticleSystem * p,
    const SBQuantity::length & cutoffDistance,
    SBSNeighborSearchParticleSystemData * dataPointer
)