Class SBSNeighborSearchParticleSystemGrid#

ClassList > SBSNeighborSearchParticleSystemGrid

This class describes a grid-based neighbor search algorithm that can be applied to particle systems. More...

#include "SBSNeighborSearchParticleSystemGrid.hpp"

Inherits the following classes: SBSNeighborSearchParticleSystem

Public Functions#

Type	Name
	SBSNeighborSearchParticleSystemGrid (SBParticleSystem * p, const SBQuantity::length & cutoffDistance) Constructs a neighbor search particle system grid for the given particle system and the given cutoff radius.
	SB_DECLARE_DATA (SBSNeighborSearchParticleSystemGrid)
virtual bool	areNeighbors (unsigned int i, unsigned int j) override const Returns whether atoms with indices `i` and`j` are neighbors.
virtual bool	areNeighbors (SBAtom * atomI, SBAtom * atomJ) override const Returns whether atoms `atomI` and`atomJ` are neighbors.
virtual void	getNeighbors (SBVector< SBAtom * > & neighborVector, const SBPosition3 & position, const SBQuantity::length & radius) override 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) override const Appends to `neighborVector` all atoms inside the`box` .
bool	getParallelizationEnabled () const Returns whether the parallelization is enabled. By default, it is enabled and will be used if some criteria (e.g. the minimum number of atoms) are met.
virtual void	initializeNeighborLists () override Initializes the neighbor lists.
void	onDynamicalEvent (SBDynamicalEvent * dynamicalEvent) Handles dynamical model events.
virtual void	print (unsigned int offset=0) override const Prints debugging information.
void	setParallelizationEnabled (bool enabled) Sets whether the parallelization is enabled. If set to true then the parallel implementation will be used if some criteria (e.g. the minimum number of atoms) are met, else the serial implementation will be used.
virtual void	updateNeighborLists () override Updates the neighbor lists.
virtual	~SBSNeighborSearchParticleSystemGrid () Destructor.

Public Functions inherited from SBSNeighborSearchParticleSystem#

See SBSNeighborSearchParticleSystem

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
SBHashMap< GridKey, GridCell , GridKeyFunctor, GridKeyComparator >	grid
SBVector< GridKey > *	gridKeyVector
SBHashMap< std::pair< unsigned int, unsigned int >, bool > *	neighborMap Hashmap which caches whether two atoms are neighbors.

Protected Attributes inherited from SBSNeighborSearchParticleSystem#

See SBSNeighborSearchParticleSystem

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
	SBSNeighborSearchParticleSystemGrid (SBParticleSystem * p, const SBQuantity::length & cutoffDistance, SBSNeighborSearchParticleSystemGridData * dataPointer) Protected constructor.

Protected Functions inherited from SBSNeighborSearchParticleSystem#

See SBSNeighborSearchParticleSystem

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: SBNeighborSearchParticleSystemGrid

Public Functions Documentation#

function SBSNeighborSearchParticleSystemGrid [2/2]#

Constructs a neighbor search particle system grid for the given particle system and the given cutoff radius.

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

function SB_DECLARE_DATA#

SBSNeighborSearchParticleSystemGrid::SB_DECLARE_DATA (
    SBSNeighborSearchParticleSystemGrid
)

function areNeighbors [1/2]#

Returns whether atoms with indices i andj are neighbors.

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

Implements SBSNeighborSearchParticleSystem::areNeighbors

function areNeighbors [2/2]#

Returns whether atoms atomI andatomJ are neighbors.

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

Implements SBSNeighborSearchParticleSystem::areNeighbors

function getNeighbors [1/2]#

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

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

Implements SBSNeighborSearchParticleSystem::getNeighbors

function getNeighbors [2/2]#

Appends to neighborVector all atoms inside thebox .

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

Implements SBSNeighborSearchParticleSystem::getNeighbors

function getParallelizationEnabled#

Returns whether the parallelization is enabled. By default, it is enabled and will be used if some criteria (e.g. the minimum number of atoms) are met.

bool SBSNeighborSearchParticleSystemGrid::getParallelizationEnabled () const

function initializeNeighborLists#

Initializes the neighbor lists.

virtual void SBSNeighborSearchParticleSystemGrid::initializeNeighborLists () override

Implements SBSNeighborSearchParticleSystem::initializeNeighborLists

function onDynamicalEvent#

Handles dynamical model events.

void SBSNeighborSearchParticleSystemGrid::onDynamicalEvent (
    SBDynamicalEvent * dynamicalEvent
)

function print#

Prints debugging information.

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

Implements SBSNeighborSearchParticleSystem::print

function setParallelizationEnabled#

Sets whether the parallelization is enabled. If set to true then the parallel implementation will be used if some criteria (e.g. the minimum number of atoms) are met, else the serial implementation will be used.

void SBSNeighborSearchParticleSystemGrid::setParallelizationEnabled (
    bool enabled
)

function updateNeighborLists#

Updates the neighbor lists.

virtual void SBSNeighborSearchParticleSystemGrid::updateNeighborLists () override

Implements SBSNeighborSearchParticleSystem::updateNeighborLists

function ~SBSNeighborSearchParticleSystemGrid#

Destructor.

virtual SBSNeighborSearchParticleSystemGrid::~SBSNeighborSearchParticleSystemGrid ()

Protected Attributes Documentation#

variable grid#

SBHashMap<GridKey, GridCell*, GridKeyFunctor, GridKeyComparator>* SBSNeighborSearchParticleSystemGrid::grid;

variable gridKeyVector#

SBVector<GridKey>* SBSNeighborSearchParticleSystemGrid::gridKeyVector;

variable neighborMap#

Hashmap which caches whether two atoms are neighbors.

SBHashMap<std::pair<unsigned int, unsigned int>, bool>* SBSNeighborSearchParticleSystemGrid::neighborMap;

Protected Functions Documentation#

function SBSNeighborSearchParticleSystemGrid [1/2]#

Protected constructor.

SBSNeighborSearchParticleSystemGrid::SBSNeighborSearchParticleSystemGrid (
    SBParticleSystem * p,
    const SBQuantity::length & cutoffDistance,
    SBSNeighborSearchParticleSystemGridData * dataPointer
)