ParticleCellBase Class Reference

ParticleCellBase defines the interface for cells used by the LinkedCells data structure to store molecule data. More...

#include <ParticleCellBase.h>

Inheritance diagram for ParticleCellBase:

Public Member Functions
virtual void	deallocateAllParticles ()=0
virtual bool	addParticle (Molecule &particle, bool checkWhetherDuplicate=false)=0
	Add a particle to the cell. More...
virtual bool	isEmpty () const =0
	Check if current cell contains no molecules. More...
bool	isNotEmpty () const
	Check if current cell contains molecules. More...
bool	deleteMoleculeByID (unsigned long molid)
	Remove moleulce from the cell based on molecule ID. More...
virtual bool	deleteMoleculeByIndex (size_t index)=0
virtual int	getMoleculeCount () const =0
virtual void	preUpdateLeavingMolecules ()=0
virtual void	updateLeavingMoleculesBase (ParticleCellBase &otherCell)=0
virtual void	postUpdateLeavingMolecules ()=0
virtual void	getRegion (double lowCorner[3], double highCorner[3], std::vector< Molecule * > &particlePtrs, bool removeFromContainer=false)=0
virtual void	buildSoACaches ()=0
virtual void	increaseMoleculeStorage (size_t numMols)=0
virtual bool	testPointInCell (const double point[3]) const
virtual bool	testInBox (const Molecule &particle) const
virtual size_t	getMoleculeVectorDynamicSize () const =0
virtual void	prefetchForForce () const
unsigned long	initCubicGrid (std::array< unsigned long, 3 > numMoleculesPerDimension, std::array< double, 3 > simBoxLength, Random &RNG)
virtual void	moleculesAtNew (size_t i, Molecule *&multipurposePointer)=0
virtual void	moleculesAtConstNew (size_t i, Molecule *&multipurposePointer) const =0
virtual void	getLeavingMolecules (std::vector< Molecule > &appendBuffer)
bool	isHaloCell () const final
bool	isBoundaryCell () const final
bool	isInnerCell () const final
bool	isInnerMostCell () const final
void	assignCellToHaloRegion ()
void	assignCellToBoundaryRegion ()
void	assignCellToInnerRegion ()
void	assignCellToInnerMostAndInnerRegion ()
void	skipCellFromHaloRegion ()
void	skipCellFromBoundaryRegion ()
void	skipCellFromInnerRegion ()
void	skipCellFromInnerMostRegion ()
double	getBoxMin (int d) const
double	getBoxMax (int d) const
std::array< double, 3 >	getBoxMinArray () const
std::array< double, 3 >	getBoxMaxArray () const
void	setBoxMin (const double b[3])
void	setBoxMax (const double b[3])
Public Member Functions inherited from Cell
unsigned long	getCellIndex () const
void	setCellIndex (unsigned long cellIndex)

Static Public Attributes
static CellBorderAndFlagManager	_cellBorderAndFlagManager

Protected Member Functions
virtual bool	findMoleculeByID (size_t &index, unsigned long molid) const =0
	Find the index of a molecule in a cell based on its molecule ID. More...

Additional Inherited Members
Protected Attributes inherited from Cell
unsigned long	_cellIndex
	the index of a cell. On one process every index must be unique.

Detailed Description

ParticleCellBase defines the interface for cells used by the LinkedCells data structure to store molecule data.

Member Function Documentation

addParticle()

virtual bool ParticleCellBase::addParticle ( Molecule &  particle, bool  checkWhetherDuplicate = false  )

pure virtual

Add a particle to the cell.

Parameters

particle	the particle to be added
checkWhetherDuplicate	if true, check if a molecule with the same molecule IDs already exists in the cell

Returns

true, if inserted

Implemented in FullParticleCell, and ParticleCellRMM.

assignCellToBoundaryRegion()

void ParticleCellBase::assignCellToBoundaryRegion ( )

inlinevirtual

Implements Cell.

assignCellToHaloRegion()

void ParticleCellBase::assignCellToHaloRegion ( )

inlinevirtual

Implements Cell.

assignCellToInnerMostAndInnerRegion()

void ParticleCellBase::assignCellToInnerMostAndInnerRegion ( )

inlinevirtual

Implements Cell.

assignCellToInnerRegion()

void ParticleCellBase::assignCellToInnerRegion ( )

inlinevirtual

Implements Cell.

deallocateAllParticles()

virtual void ParticleCellBase::deallocateAllParticles ( )

pure virtual

Implemented in FullParticleCell.

deleteMoleculeByID()

bool ParticleCellBase::deleteMoleculeByID

(

unsigned long

molid

)

Remove moleulce from the cell based on molecule ID.

Parameters

molid

molecule ID of the molecule to be deleted

Returns

true if molecules was deleted

findMoleculeByID()

virtual bool ParticleCellBase::findMoleculeByID ( size_t &  index, unsigned long  molid  ) const

protectedpure virtual

Find the index of a molecule in a cell based on its molecule ID.

Parameters

index	index of the molecule in the cell data structure
molid	molecule ID of the molecule to be searched in the cell

Returns

true if molecule was found

Implemented in FullParticleCell, and ParticleCellRMM.

getBoxMax()

double ParticleCellBase::getBoxMax ( int  d ) const

inlinevirtual

Implements Cell.

getBoxMin()

double ParticleCellBase::getBoxMin ( int  d ) const

inlinevirtual

Implements Cell.

getMoleculeCount()

virtual int ParticleCellBase::getMoleculeCount ( ) const

pure virtual

Implemented in FullParticleCell.

isBoundaryCell()

bool ParticleCellBase::isBoundaryCell ( ) const

inlinefinalvirtual

Implements Cell.

isEmpty()

virtual bool ParticleCellBase::isEmpty ( ) const

pure virtual

Check if current cell contains no molecules.

Returns

true if no molecules are in the cell, false otherwise

Implemented in FullParticleCell, and ParticleCellRMM.

isHaloCell()

bool ParticleCellBase::isHaloCell ( ) const

inlinefinalvirtual

Implements Cell.

isInnerCell()

bool ParticleCellBase::isInnerCell ( ) const

inlinefinalvirtual

Implements Cell.

isInnerMostCell()

bool ParticleCellBase::isInnerMostCell ( ) const

inlinefinalvirtual

Implements Cell.

isNotEmpty()

bool ParticleCellBase::isNotEmpty ( ) const

inline

Check if current cell contains molecules.

Returns

true if molecules are in the cell, false otherwise

setBoxMax()

void ParticleCellBase::setBoxMax ( const double  b[3] )

inlinevirtual

Implements Cell.

setBoxMin()

void ParticleCellBase::setBoxMin ( const double  b[3] )

inlinevirtual

Implements Cell.

skipCellFromBoundaryRegion()

void ParticleCellBase::skipCellFromBoundaryRegion ( )

inlinevirtual

Implements Cell.

skipCellFromHaloRegion()

void ParticleCellBase::skipCellFromHaloRegion ( )

inlinevirtual

Implements Cell.

skipCellFromInnerMostRegion()

void ParticleCellBase::skipCellFromInnerMostRegion ( )

inlinevirtual

Implements Cell.

skipCellFromInnerRegion()

void ParticleCellBase::skipCellFromInnerRegion ( )

inlinevirtual

Implements Cell.

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The documentation for this class was generated from the following files:

• src/particleContainer/ParticleCellBase.h
• src/particleContainer/ParticleCellBase.cpp