Class SBSNeighborSearchParticleSystemPBC#

ClassList > SBSNeighborSearchParticleSystemPBC

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

#include "SBSNeighborSearchParticleSystemPBC.hpp"

Inherits the following classes: SBSNeighborSearch

Inherited by the following classes: SBSNeighborSearchParticleSystemGridPBC

Public Functions#

Type	Name
	SB_DECLARE_DATA (SBSNeighborSearchParticleSystemPBC)
SBVector< SBAtom * > *	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	~SBSNeighborSearchParticleSystemPBC () 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
SBIAPosition3 *	boxPBC The box's periodic boundary conditions bounds.
SBQuantity::length *	boxSizeX The box's size in x-direction.
SBQuantity::length *	boxSizeY The box's size in y-direction.
SBQuantity::length *	boxSizeZ The box's size in z-direction.
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
	SBSNeighborSearchParticleSystemPBC (SBParticleSystem * p, const SBQuantity::length & cutoffDistance) Protected constructor.
	SBSNeighborSearchParticleSystemPBC (SBParticleSystem * p, const SBQuantity::length & cutoffDistance, SBSNeighborSearchParticleSystemPBCData * 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: SBNeighborSearchParticleSystemPBC

Public Functions Documentation#

function SB_DECLARE_DATA#

SBSNeighborSearchParticleSystemPBC::SB_DECLARE_DATA (
    SBSNeighborSearchParticleSystemPBC
)

function getNeighborVector#

Returns the neighbor list for the i-th particle.

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#

Initializes the neighbor lists.

virtual void SBSNeighborSearchParticleSystemPBC::initializeNeighborLists ()

function onDynamicalEvent#

Handles dynamical model events.

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#

Updates the neighbor lists.

virtual void SBSNeighborSearchParticleSystemPBC::updateNeighborLists ()

function ~SBSNeighborSearchParticleSystemPBC#

Destructor.

virtual SBSNeighborSearchParticleSystemPBC::~SBSNeighborSearchParticleSystemPBC ()

Protected Attributes Documentation#

variable boxPBC#

The box's periodic boundary conditions bounds.

SBIAPosition3* SBSNeighborSearchParticleSystemPBC::boxPBC;

variable boxSizeX#

The box's size in x-direction.

SBQuantity::length* SBSNeighborSearchParticleSystemPBC::boxSizeX;

variable boxSizeY#

The box's size in y-direction.

SBQuantity::length* SBSNeighborSearchParticleSystemPBC::boxSizeY;

variable boxSizeZ#

The box's size in z-direction.

SBQuantity::length* SBSNeighborSearchParticleSystemPBC::boxSizeZ;

variable cutoffDistanceSquared#

The squared cutoff distance.

SBQuantity::squareLength* SBSNeighborSearchParticleSystemPBC::cutoffDistanceSquared;

variable inverseCutoffDistance#

The inverse cutoff distance.

SBQuantity::inverseLength* SBSNeighborSearchParticleSystemPBC::inverseCutoffDistance;

variable neighborVectorBuffer#

The buffer containing the neighbor lists associated to each atom.

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

variable particleSystem#

The particle system the neighbor search algorithm is attached to.

SBPointer<SBParticleSystem>* SBSNeighborSearchParticleSystemPBC::particleSystem;

Protected Functions Documentation#

function SBSNeighborSearchParticleSystemPBC [1/2]#

Protected constructor.

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

function SBSNeighborSearchParticleSystemPBC [2/2]#

Protected constructor.

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