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Class SBSNeighborSearchParticleSystemGridPBC#

ClassList > SBSNeighborSearchParticleSystemGridPBC

This class describes a grid-based neighbor search algorithm that can be applied to particle systems with periodic boundary conditions (PBC). More...

  • #include "SBSNeighborSearchParticleSystemGridPBC.hpp"

Inherits the following classes: SBSNeighborSearchParticleSystemPBC

Public Functions#

Type Name
SBSNeighborSearchParticleSystemGridPBC (SBParticleSystem * p, const SBQuantity::length & cutoffDistance)
Constructs a neighbor search particle system grid with PBC for the given particle system and the given cutoff radius.
SB_DECLARE_DATA (SBSNeighborSearchParticleSystemGridPBC)
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 toradius from the specifiedposition .
virtual void getNeighbors (SBVector< SBAtom * > & neighborVector, const SBIAPosition3 & box) override const
Appends to neighborVector all atoms inside thebox .
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.
virtual void updateNeighborLists () override
Updates the neighbor lists.
virtual ~SBSNeighborSearchParticleSystemGridPBC ()
Destructor.

Public Functions inherited from SBSNeighborSearchParticleSystemPBC#

See SBSNeighborSearchParticleSystemPBC

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 toradius from the specifiedposition .
virtual void getNeighbors (SBVector< SBAtom * > & neighborVector, const SBIAPosition3 & box) const
Appends to neighborVector all atoms inside thebox .
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
SBPointerIndexer< SBAtom > const * atomIndexer
SBQuantity::length * cutoffDistance
The cutoff distance.
SBHashMap< GridKey, GridCell *, GridKeyFunctor, GridKeyComparator > * grid
SBVector< GridKey > * gridKeyVector

Protected Attributes inherited from SBSNeighborSearchParticleSystemPBC#

See SBSNeighborSearchParticleSystemPBC

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
SBSNeighborSearchParticleSystemGridPBC (SBParticleSystem * p, const SBQuantity::length & cutoffDistance, SBSNeighborSearchParticleSystemGridPBCData * dataPointer)
Protected constructor.
bool cellCrossesTheBox (GridKey & gridKey)
void checkCell (GridCell * gridCellJ, int i, std::set< unsigned int > & neighbors)
void checkCellsAroundBigBox (GridKey & gridKeyI, int i)
void checkCellsAroundCellByCell ()
void checkCellsAroundSmallBox (GridKey & gridKeyI, int i)
void checkCellsCross (GridCell * gridCellI, GridCell * gridCellJ)
void getCellCoordinates (SBPosition3 const & position, SBVector3 & coordinates)
void getMirrorCellKey (GridKey & gridKey, GridKey & gridKeyMirror)
bool isInTheBox (SBPosition3 const & position)
void updateLists ()

Protected Functions inherited from SBSNeighborSearchParticleSystemPBC#

See SBSNeighborSearchParticleSystemPBC

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: SBNeighborSearchParticleSystemGridPBC

Public Functions Documentation#

function SBSNeighborSearchParticleSystemGridPBC [2/2]#

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

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

function SB_DECLARE_DATA#

SBSNeighborSearchParticleSystemGridPBC::SB_DECLARE_DATA (
    SBSNeighborSearchParticleSystemGridPBC
)

function getNeighbors [1/2]#

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

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

Implements SBSNeighborSearchParticleSystemPBC::getNeighbors

function getNeighbors [2/2]#

Appends to neighborVector all atoms inside thebox . 

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

Implements SBSNeighborSearchParticleSystemPBC::getNeighbors

function initializeNeighborLists#

Initializes the neighbor lists. 

virtual void SBSNeighborSearchParticleSystemGridPBC::initializeNeighborLists () override

Implements SBSNeighborSearchParticleSystemPBC::initializeNeighborLists

function onDynamicalEvent#

Handles dynamical model events. 

void SBSNeighborSearchParticleSystemGridPBC::onDynamicalEvent (
    SBDynamicalEvent * dynamicalEvent
)

function print#

Prints debugging information. 

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

Implements SBSNeighborSearchParticleSystemPBC::print

function updateNeighborLists#

Updates the neighbor lists. 

virtual void SBSNeighborSearchParticleSystemGridPBC::updateNeighborLists () override

Important: this function does not appear to work at the moment. Please rebuild a grid at each step.

Implements SBSNeighborSearchParticleSystemPBC::updateNeighborLists

function ~SBSNeighborSearchParticleSystemGridPBC#

Destructor. 

virtual SBSNeighborSearchParticleSystemGridPBC::~SBSNeighborSearchParticleSystemGridPBC ()

Protected Attributes Documentation#

variable atomIndexer#

SBPointerIndexer<SBAtom> const* SBSNeighborSearchParticleSystemGridPBC::atomIndexer;

variable cutoffDistance#

The cutoff distance. 

SBQuantity::length* SBSNeighborSearchParticleSystemGridPBC::cutoffDistance;

variable grid#

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

variable gridKeyVector#

SBVector<GridKey>* SBSNeighborSearchParticleSystemGridPBC::gridKeyVector;

Protected Functions Documentation#

function SBSNeighborSearchParticleSystemGridPBC [1/2]#

Protected constructor. 

SBSNeighborSearchParticleSystemGridPBC::SBSNeighborSearchParticleSystemGridPBC (
    SBParticleSystem * p,
    const SBQuantity::length & cutoffDistance,
    SBSNeighborSearchParticleSystemGridPBCData * dataPointer
)

function cellCrossesTheBox#

bool SBSNeighborSearchParticleSystemGridPBC::cellCrossesTheBox (
    GridKey & gridKey
)

function checkCell#

void SBSNeighborSearchParticleSystemGridPBC::checkCell (
    GridCell * gridCellJ,
    int i,
    std::set< unsigned int > & neighbors
)

function checkCellsAroundBigBox#

void SBSNeighborSearchParticleSystemGridPBC::checkCellsAroundBigBox (
    GridKey & gridKeyI,
    int i
)

function checkCellsAroundCellByCell#

void SBSNeighborSearchParticleSystemGridPBC::checkCellsAroundCellByCell ()

function checkCellsAroundSmallBox#

void SBSNeighborSearchParticleSystemGridPBC::checkCellsAroundSmallBox (
    GridKey & gridKeyI,
    int i
)

function checkCellsCross#

void SBSNeighborSearchParticleSystemGridPBC::checkCellsCross (
    GridCell * gridCellI,
    GridCell * gridCellJ
)

function getCellCoordinates#

void SBSNeighborSearchParticleSystemGridPBC::getCellCoordinates (
    SBPosition3 const & position,
    SBVector3 & coordinates
)

function getMirrorCellKey#

void SBSNeighborSearchParticleSystemGridPBC::getMirrorCellKey (
    GridKey & gridKey,
    GridKey & gridKeyMirror
)

function isInTheBox#

bool SBSNeighborSearchParticleSystemGridPBC::isInTheBox (
    SBPosition3 const & position
)

function updateLists#

void SBSNeighborSearchParticleSystemGridPBC::updateLists ()