Inheritance diagram for ParticleContainerToBasisWrapper:

Public Member Functions
void	readXML (XMLfileUnits &xmlconfig) override

void	setBoundingBox (std::shared_ptr< Object > object)

bool	addParticle (Molecule &particle, bool inBoxCheckedAlready=false, bool checkWhetherDuplicate=false, const bool &rebuildCaches=false) override
	add a single Molecule to the ParticleContainer. More...

Basis &	getBasis ()
	return reference to internal basis object.

void	clear () override
	Delete all molecules in container. More...

unsigned long	getNumberOfParticles () override

double	getBoundingBoxMin (int dimension) const override
	returns one coordinate of the lower corner of the bounding box More...

double	getBoundingBoxMax (int dimension) const override
	returns one coordinate of the higher corner of the bounding box More...

bool	isInBoundingBox (double r[3]) const override
	checks, whether given coordinates are within the bounding box More...

void	update () override
	do necessary updates resulting from changed particle positions More...

void	addParticles (std::vector< Molecule > &particles, bool checkWhetherDuplicate=false) override
	adds a whole vector of particles More...

void	traverseCells (CellProcessor &cellProcessor) override
	traverse pairs which are close to each other More...

void	traverseNonInnermostCells (CellProcessor &cellProcessor) override

void	traversePartialInnermostCells (CellProcessor &cellProcessor, unsigned int stage, int stageCount) override

ParticleIterator	iterator (ParticleIterator::Type t) override

RegionParticleIterator	regionIterator (const double startCorner[3], const double endCorner[3], ParticleIterator::Type t) override

void	deleteOuterParticles () override
	delete all Particles which are not within the bounding box More...

double	get_halo_L (int index) const override
	returns the width of the halo stripe (for the given dimension index) More...

double	getCutoff () const override

void	deleteMolecule (ParticleIterator &moleculeIter, const bool &rebuildCaches) override

double	getEnergy (ParticlePairsHandler particlePairsHandler, Molecule m1, CellProcessor &cellProcessor) override

void	updateInnerMoleculeCaches () override
	Update the caches of the molecules, that lie in inner cells. The caches of boundary and halo cells is not updated. This method is used for a multi-step scheme of overlapping mpi communication. More...

void	updateBoundaryAndHaloMoleculeCaches () override
	Update the caches of the molecules, that lie in the boundary or halo cells. The caches of boundary and halo cells is updated, the caches of the inner cells are not updated. This method is used for a multi-step scheme of overlapping mpi communication. More...

void	updateMoleculeCaches () override
	Update the caches of the molecules. More...

std::variant< ParticleIterator, SingleCellIterator< ParticleCell > >	getMoleculeAtPosition (const double pos[3]) override
	Gets a molecule by its position. More...

unsigned long	initCubicGrid (std::array< unsigned long, 3 > numMoleculesPerDimension, std::array< double, 3 > simBoxLength, size_t seed_offset) override

size_t	getTotalSize () override

void	printSubInfo (int offset) override

std::string	getName () override

double *	getCellLength () override

string	getConfigurationAsString () override

Public Member Functions inherited from ParticleContainer
	ParticleContainer (double bBoxMin[3], double bBoxMax[3])
	The constructor. More...

	ParticleContainer ()
	Default constructor.

virtual	~ParticleContainer ()
	The destructor.

virtual bool	rebuild (double bBoxMin[3], double bBoxMax[3])
	rebuild the datastructure More...

virtual bool	addHaloParticle (Molecule &particle, bool inBoxCheckedAlready=false, bool checkWhetherDuplicate=false, const bool &rebuildCaches=false)
	add a single Molecule to the ParticleContainer, ensures that it is added in the halo. More...

virtual int	getHaloWidthNumCells ()

virtual double	getSkin () const

virtual bool	requiresForceExchange () const

virtual double *	getHaloSize ()

virtual std::vector< unsigned long >	getParticleCellStatistics ()

virtual void	setCutoff (double rc)

virtual std::vector< Molecule >	getInvalidParticles ()

virtual bool	isInvalidParticleReturner ()

Additional Inherited Members
Protected Attributes inherited from ParticleContainer
double	_boundingBoxMin [3]
	coordinates of the left, lower, front corner of the bounding box

double	_boundingBoxMax [3]
	coordinates of the right, upper, back corner of the bounding box

Detailed Description

The ParticleContainerToBasisWrapper class is there to read in any phase space input and save it into a Basis object instead of a regular particle container, so it can be used for the grid filler.

Warning: While providing all interface methods the ParticleContainerToBasisWrapper is not a fully working particle container!

Todo:: Find a better way to reuse all the different I/O classes and their readPhase space methods. Maybe bring back the Dummy domain decomposition?

Member Function Documentation

◆ addParticle()

bool ParticleContainerToBasisWrapper::addParticle	(	Molecule &	particle,
		bool	inBoxCheckedAlready = `false`,
		bool	checkWhetherDuplicate = `false`,
		const bool &	rebuildCaches = `false`
	)

inlineoverridevirtual

add a single Molecule to the ParticleContainer.

Note: a copy of the particle is pushed. Destroying the argument is responsibility of the programmer.

Parameters

particle	reference to the particle which has to be added
inBoxCheckedAlready	- if true, spare check whether molecule is in bounding box
checkWhetherDuplicate	- if true, check whether molecule already exists and don't insert it.
rebuildCaches	specifies, whether the caches should be rebuild

Returns: true if successful, false if particle outside domain

Implements ParticleContainer.

◆ addParticles()

void ParticleContainerToBasisWrapper::addParticles	(	std::vector< Molecule > &	particles,
		bool	checkWhetherDuplicate = `false`
	)

inlineoverridevirtual

adds a whole vector of particles

Parameters

particles reference to a vector of pointers to particles

Implements ParticleContainer.

◆ clear()

void ParticleContainerToBasisWrapper::clear ( )

inlineoverridevirtual

Delete all molecules in container.

Implements ParticleContainer.

◆ deleteMolecule()

void ParticleContainerToBasisWrapper::deleteMolecule	(	ParticleIterator &	moleculeIter,
		const bool &	rebuildCaches
	)

inlineoverridevirtual

Implements ParticleContainer.

◆ deleteOuterParticles()

void ParticleContainerToBasisWrapper::deleteOuterParticles ( )

inlineoverridevirtual

delete all Particles which are not within the bounding box

Implements ParticleContainer.

◆ get_halo_L()

double ParticleContainerToBasisWrapper::get_halo_L ( int index ) const

inlineoverridevirtual

returns the width of the halo stripe (for the given dimension index)

Todo:: remove this method, because a halo_L shouldn't be necessary for every ParticleContainer e.g. replace it by the cutoff-radius

Implements ParticleContainer.

◆ getBoundingBoxMax()

double ParticleContainerToBasisWrapper::getBoundingBoxMax ( int dimension ) const

inlineoverridevirtual

returns one coordinate of the higher corner of the bounding box

Parameters

dimension the coordinate which should be returned

Reimplemented from ParticleContainer.

◆ getBoundingBoxMin()

double ParticleContainerToBasisWrapper::getBoundingBoxMin ( int dimension ) const

inlineoverridevirtual

returns one coordinate of the lower corner of the bounding box

Parameters

dimension the coordinate which should be returned

Reimplemented from ParticleContainer.

◆ getCellLength()

double* ParticleContainerToBasisWrapper::getCellLength ( )

inlineoverridevirtual

Implements ParticleContainer.

◆ getConfigurationAsString()

string ParticleContainerToBasisWrapper::getConfigurationAsString ( )

inlineoverridevirtual

Return a string representation of the algorithmic configuration of the container. Only used for logging / output.

Note

: Formatting rules:

The whole configuration should be enclosed in curly brackets.
Different elements should be separated by a comma sourrounded by spaces: " , ".
Every element should be in the form "key: value"

Returns

Implements ParticleContainer.

◆ getCutoff()

double ParticleContainerToBasisWrapper::getCutoff ( ) const

inlineoverridevirtual

Implements ParticleContainer.

◆ getEnergy()

double ParticleContainerToBasisWrapper::getEnergy	(	ParticlePairsHandler *	particlePairsHandler,
		Molecule *	m1,
		CellProcessor &	cellProcessor
	)

inlineoverridevirtual

Implements ParticleContainer.

◆ getMoleculeAtPosition()

std::variant<ParticleIterator, SingleCellIterator<ParticleCell> > ParticleContainerToBasisWrapper::getMoleculeAtPosition ( const double pos[3] )

inlineoverridevirtual

Gets a molecule by its position.

Parameters

pos	Molecule position

Returns: Iterator to the molecule. The iterator is invalid if no molecule was found.

Implements ParticleContainer.

◆ getName()

std::string ParticleContainerToBasisWrapper::getName ( )

inlineoverridevirtual

Implements MemoryProfilable.

◆ getNumberOfParticles()

unsigned long ParticleContainerToBasisWrapper::getNumberOfParticles ( )

inlineoverridevirtual

Returns: the number of particles stored in this container

This number may include particles which are outside of the bounding box

Implements ParticleContainer.

◆ getTotalSize()

size_t ParticleContainerToBasisWrapper::getTotalSize ( )

inlineoverridevirtual

Implements MemoryProfilable.

◆ initCubicGrid()

unsigned long ParticleContainerToBasisWrapper::initCubicGrid	(	std::array< unsigned long, 3 >	numMoleculesPerDimension,
		std::array< double, 3 >	simBoxLength,
		size_t	seed_offset
	)

inlineoverridevirtual

Implements ParticleContainer.

◆ isInBoundingBox()

bool ParticleContainerToBasisWrapper::isInBoundingBox ( double r[3] ) const

inlineoverridevirtual

checks, whether given coordinates are within the bounding box

Parameters

r	the coordinates to check

Returns: true if coordinates within bounding box, false otherwise

Reimplemented from ParticleContainer.

◆ iterator()

ParticleIterator ParticleContainerToBasisWrapper::iterator ( ParticleIterator::Type t )

inlineoverridevirtual

Implements ParticleContainer.

◆ printSubInfo()

void ParticleContainerToBasisWrapper::printSubInfo ( int offset )

inlineoverridevirtual

Implements MemoryProfilable.

◆ readXML()

void ParticleContainerToBasisWrapper::readXML ( XMLfileUnits & xmlconfig )

inlineoverridevirtual

Implements ParticleContainer.

◆ regionIterator()

RegionParticleIterator ParticleContainerToBasisWrapper::regionIterator	(	const double	startCorner[3],
		const double	endCorner[3],
		ParticleIterator::Type	t
	)

inlineoverridevirtual

Implements ParticleContainer.

◆ traverseCells()

void ParticleContainerToBasisWrapper::traverseCells ( CellProcessor & cellProcessor )

inlineoverridevirtual

traverse pairs which are close to each other

Only interactions between particles which have a distance which is not larger than the cutoff radius are to be considered.
This method has to be implemented in derived classes Precondition: All Particles of the process + halo molecules are stored Task: Run over all pairs (Each pair exactely once!) of particles (within cutoffradius) Important: Some pairs might be "duplicated": All pairs which cross the boundary occur twice (second time at the periodic image). Those pairs are from the point of view of the datastructure two different pairs, but they both times connect the same particles. For a pair which occurs twice, it has to be made sure, that one gets the status "original pair" and the other one "duplicated pair". For each pair found, there is an action executed, but it is a different action for original and duplicated pairs. Details about how to handle pairs can be found in the documentation for the class ParticlePairsHandler

Parameters

particlePairsHandler specified concrete action to be done for each pair

Implements ParticleContainer.

◆ traverseNonInnermostCells()

void ParticleContainerToBasisWrapper::traverseNonInnermostCells ( CellProcessor & cellProcessor )

inlineoverridevirtual

Implements ParticleContainer.

◆ traversePartialInnermostCells()

void ParticleContainerToBasisWrapper::traversePartialInnermostCells	(	CellProcessor &	cellProcessor,
		unsigned int	stage,
		int	stageCount
	)

inlineoverridevirtual

Implements ParticleContainer.

◆ update()

void ParticleContainerToBasisWrapper::update ( )

inlineoverridevirtual

do necessary updates resulting from changed particle positions

For some implementations of the interface ParticleContainer, the place where particles are stored might e.g. depend on the spacial position of the particle. So when some externel method (e.g. Leap-Frog) changes the spacial position of a particle, the representation within the particleContainer becomes invalid. This method restores a valid representation.

Implements ParticleContainer.

◆ updateBoundaryAndHaloMoleculeCaches()

void ParticleContainerToBasisWrapper::updateBoundaryAndHaloMoleculeCaches ( )

inlineoverridevirtual

Update the caches of the molecules, that lie in the boundary or halo cells. The caches of boundary and halo cells is updated, the caches of the inner cells are not updated. This method is used for a multi-step scheme of overlapping mpi communication.

Implements ParticleContainer.

◆ updateInnerMoleculeCaches()

void ParticleContainerToBasisWrapper::updateInnerMoleculeCaches ( )

inlineoverridevirtual

Update the caches of the molecules, that lie in inner cells. The caches of boundary and halo cells is not updated. This method is used for a multi-step scheme of overlapping mpi communication.

Implements ParticleContainer.

◆ updateMoleculeCaches()

void ParticleContainerToBasisWrapper::updateMoleculeCaches ( )

inlineoverridevirtual

Update the caches of the molecules.

Implements ParticleContainer.

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

src/utils/generator/ReplicaFiller.cpp

Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ addParticle()

◆ addParticles()

◆ clear()

◆ deleteMolecule()

◆ deleteOuterParticles()

◆ get_halo_L()

◆ getBoundingBoxMax()

◆ getBoundingBoxMin()

◆ getCellLength()

◆ getConfigurationAsString()

◆ getCutoff()

◆ getEnergy()

◆ getMoleculeAtPosition()

◆ getName()

◆ getNumberOfParticles()

◆ getTotalSize()

◆ initCubicGrid()

◆ isInBoundingBox()

◆ iterator()

◆ printSubInfo()

◆ readXML()

◆ regionIterator()

◆ traverseCells()

◆ traverseNonInnermostCells()

◆ traversePartialInnermostCells()

◆ update()

◆ updateBoundaryAndHaloMoleculeCaches()

◆ updateInnerMoleculeCaches()

◆ updateMoleculeCaches()