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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
virtual bool areNeighbors (unsigned int i, unsigned int j) const
Returns whether atoms with indices i andj are neighbors.
virtual bool areNeighbors (SBAtom * atomI, SBAtom * atomJ) const
Returns whether atoms atomI andatomJ 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 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 ~SBSNeighborSearchParticleSystem ()
Destructor.

Public Functions inherited from SBSNeighborSearch#

See SBSNeighborSearch

Type Name
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 * particleSystem, const SBQuantity::length & cutoffDistance)
Protected constructor.
SBSNeighborSearchParticleSystem (SBParticleSystem * particleSystem, 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 areNeighbors [1/2]#

Returns whether atoms with indices i andj are neighbors. 

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

Determines whether two particles identified by their indices are neighbors.

Parameters:

  • i Index of the first particle.
  • j Index of the second particle.

Returns:

true if the particles are neighbors; otherwise false.

function areNeighbors [2/2]#

Returns whether atoms atomI andatomJ are neighbors. 

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

Determines whether two atoms are neighbors.

Parameters:

  • atomI Pointer to the first atom.
  • atomJ Pointer to the second atom.

Returns:

true if the atoms are neighbors; otherwise false.

function getNeighborVector#

Returns the neighbor list for the i-th particle. 

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

Returns the neighbor list for the specified particle index.

Parameters:

  • i Index of the particle whose neighbor list is requested.

Returns:

Pointer to a constant vector of neighbor atoms for particle 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

Appends to the provided vector all atoms located within a given radius of a position.

Parameters:

  • neighborVector Vector that will receive the neighboring atoms (appended to the existing contents).
  • position Center position around which to search for neighbors.
  • radius Maximum distance from the position to consider an atom a neighbor.

function getNeighbors [2/2]#

Appends to neighborVector all atoms inside thebox . 

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

Appends to the provided vector all atoms located inside a specified axis-aligned bounding box.

Parameters:

  • neighborVector Vector that will receive the neighboring atoms (appended to the existing contents).
  • box Axis-aligned bounding box defining the region to search for atoms.

function initializeNeighborLists#

Initializes the neighbor lists. 

virtual void SBSNeighborSearchParticleSystem::initializeNeighborLists ()

Initializes the neighbor lists for all particles.

function onDynamicalEvent#

Handles dynamical model events. 

void SBSNeighborSearchParticleSystem::onDynamicalEvent (
    SBDynamicalEvent * dynamicalEvent
)

Handles dynamical model events that affect the particle system, such as atom addition or removal.

Parameters:

  • dynamicalEvent Pointer to the event describing the dynamical change.

function print#

Prints debugging information. 

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

Prints debugging information for the neighbor search object.

Parameters:

  • offset Number of spaces to indent each line of output.

Implements SBSNeighborSearch::print

function updateNeighborLists#

Updates the neighbor lists. 

virtual void SBSNeighborSearchParticleSystem::updateNeighborLists ()

Updates the neighbor lists for all particles.

function ~SBSNeighborSearchParticleSystem#

Destructor. 

virtual SBSNeighborSearchParticleSystem::~SBSNeighborSearchParticleSystem ()

Destroys the neighbor search object and releases all associated resources.

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 * particleSystem,
    const SBQuantity::length & cutoffDistance
)

Constructs a neighbor search algorithm for a particle system with a specified cutoff distance.

Parameters:

  • p Pointer to the particle system the neighbor search will be attached to.
  • c The cutoff distance used for neighbor detection.

function SBSNeighborSearchParticleSystem [2/2]#

Protected constructor. 

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

Constructs a neighbor search algorithm for a particle system with a specified cutoff distance and internal data pointer.

Parameters:

  • p Pointer to the particle system the neighbor search will be attached to.
  • c The cutoff distance used for neighbor detection.
  • dataPointer Pointer to the internal data structure used by the neighbor search algorithm.