#include <AutoPasContainer.h>

Inheritance diagram for AutoPasContainer:

Public Member Functions
	AutoPasContainer (double cutoff)

void	readXML (XMLfileUnits &xmlconfig) override

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

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

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

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

unsigned long	getNumberOfParticles () override

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

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

double	getSkin () 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

double *	getCellLength () override

double *	getHaloSize () override

size_t	getTotalSize () override

void	printSubInfo (int offset) override

std::string	getName () override

void	setCutoff (double cutoff) override

std::vector< Molecule >	getInvalidParticles () override

bool	isInvalidParticleReturner () override

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

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

virtual int	getHaloWidthNumCells ()

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

virtual bool	requiresForceExchange () const

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

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

A wrapper for the AutoPas library.

Member Function Documentation

◆ addHaloParticle()

bool AutoPasContainer::addHaloParticle	(	Molecule &	particle,
		bool	inBoxCheckedAlready = `false`,
		bool	checkWhetherDuplicate = `false`,
		const bool &	rebuildCaches = `false`
	)

overridevirtual

add a single Molecule to the ParticleContainer, ensures that it is added in the halo.

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

Reimplemented from ParticleContainer.

◆ addParticle()

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

overridevirtual

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

overridevirtual

adds a whole vector of particles

Parameters

particles reference to a vector of pointers to particles

Implements ParticleContainer.

◆ clear()

void AutoPasContainer::clear ( )

overridevirtual

Delete all molecules in container.

Implements ParticleContainer.

◆ deleteMolecule()

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

overridevirtual

Implements ParticleContainer.

◆ deleteOuterParticles()

void AutoPasContainer::deleteOuterParticles ( )

overridevirtual

delete all Particles which are not within the bounding box

Implements ParticleContainer.

◆ get_halo_L()

double AutoPasContainer::get_halo_L ( int index ) const

overridevirtual

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.

◆ getCellLength()

double * AutoPasContainer::getCellLength ( )

overridevirtual

Implements ParticleContainer.

◆ getConfigurationAsString()

std::string AutoPasContainer::getConfigurationAsString ( )

overridevirtual

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 AutoPasContainer::getCutoff ( ) const

overridevirtual

Implements ParticleContainer.

◆ getEnergy()

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

overridevirtual

Implements ParticleContainer.

◆ getHaloSize()

double * AutoPasContainer::getHaloSize ( )

overridevirtual

Return the size of the halo

Returns

Reimplemented from ParticleContainer.

◆ getInvalidParticles()

std::vector<Molecule> AutoPasContainer::getInvalidParticles ( )

inlineoverridevirtual

Reimplemented from ParticleContainer.

◆ getMoleculeAtPosition()

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

overridevirtual

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 AutoPasContainer::getName ( )

inlineoverridevirtual

Implements MemoryProfilable.

◆ getNumberOfParticles()

unsigned long AutoPasContainer::getNumberOfParticles ( )

overridevirtual

Returns: the number of particles stored in this container

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

Implements ParticleContainer.

◆ getSkin()

double AutoPasContainer::getSkin ( ) const

overridevirtual

Reimplemented from ParticleContainer.

◆ getTotalSize()

size_t AutoPasContainer::getTotalSize ( )

inlineoverridevirtual

Implements MemoryProfilable.

◆ initCubicGrid()

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

overridevirtual

Implements ParticleContainer.

◆ isInvalidParticleReturner()

bool AutoPasContainer::isInvalidParticleReturner ( )

inlineoverridevirtual

Reimplemented from ParticleContainer.

◆ iterator()

ParticleIterator AutoPasContainer::iterator ( ParticleIterator::Type t )

overridevirtual

Implements ParticleContainer.

◆ printSubInfo()

void AutoPasContainer::printSubInfo ( int offset )

inlineoverridevirtual

Implements MemoryProfilable.

◆ readXML()

void AutoPasContainer::readXML ( XMLfileUnits & xmlconfig )

overridevirtual

This function parses parameters for the AutoPas container. The following xml object structure is handled by this method:

<datastructure type="AutoPas">
 <allowedTraversals>STRINGLIST</allowedTraversals>
 <allowedContainers>STRINGLIST</allowedContainers>
 <selectorStrategy>STRING</selectorStrategy>
 <tuningStrategy>STRING</tuningStrategy>
 <extrapolationMethod>STRING</extrapolationMethod>
 <dataLayouts>STRINGLIST</dataLayouts>
 <newton3>STRINGLIST</newton3>
 <tuningAcquisitionFunction>STRING</tuningAcquisitionFunction>
 <maxEvidence>INTEGER</maxEvidence>
 <tuningPhasesWithoutTest>INTEGER</tuningPhasesWithoutTest>
 <evidenceForPrediction>INTEGER</evidenceForPrediction>
 <tuningSamples>INTEGER</tuningSamples>
 <tuningInterval>INTEGER</tuningInterval>
 <rebuildFrequency>INTEGER</rebuildFrequency>
 <skin>DOUBLE</skin>
 <optimumRange>DOUBLE</optimumRange>
 <blacklistRange>DOUBLE</blacklistRange>
 <useAVXFunctor>BOOL</useAVXFunctor>
 <verletClusterSize>INTEGER</verletClusterSize>
</datastructure>

If you are using MPI-parallel simulations, tuningSamples should be a multiple of rebuildFrequency! A list of the different Options can be found here: https://www5.in.tum.de/AutoPas/doxygen_doc/master/namespaceautopas_1_1options.html For multiple options, a comma separated list of strings is possible. Auto-Tuning is then performed on all possible combinations of those.

Parameters

xmlconfig

Implements ParticleContainer.

◆ rebuild()

bool AutoPasContainer::rebuild	(	double	bBoxMin[3],
		double	bBoxMax[3]
	)

overridevirtual

rebuild the datastructure

Load-balancing decompositions change the position and size of the local region during runtime. Therefore, the datastructure needs to be rebuild completely. This method basically does what the constructor does as well, with the difference, that there are already particles stored, and particles which don't belong to the new region have to be deleted after rebuild @parameter bBoxMin minimum of the box @parameter bBoxMax maximum of the box

Todo:: return sendHaloAndLeavingTogether, (always false) for simplicity.

Reimplemented from ParticleContainer.

◆ regionIterator()

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

overridevirtual

Implements ParticleContainer.

◆ setCutoff()

void AutoPasContainer::setCutoff ( double rc )

inlineoverridevirtual

set the cutoff

Parameters

rc

Reimplemented from ParticleContainer.

◆ traverseCells()

void AutoPasContainer::traverseCells ( CellProcessor & cellProcessor )

overridevirtual

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 AutoPasContainer::traverseNonInnermostCells ( CellProcessor & cellProcessor )

overridevirtual

Implements ParticleContainer.

◆ traversePartialInnermostCells()

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

overridevirtual

Implements ParticleContainer.

◆ update()

void AutoPasContainer::update ( )

overridevirtual

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 AutoPasContainer::updateBoundaryAndHaloMoleculeCaches ( )

overridevirtual

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 AutoPasContainer::updateInnerMoleculeCaches ( )

overridevirtual

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 AutoPasContainer::updateMoleculeCaches ( )

overridevirtual

Update the caches of the molecules.

Implements ParticleContainer.

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

src/particleContainer/AutoPasContainer.h
src/particleContainer/AutoPasContainer.cpp

Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ addHaloParticle()

◆ addParticle()

◆ addParticles()

◆ clear()

◆ deleteMolecule()

◆ deleteOuterParticles()

◆ get_halo_L()

◆ getCellLength()

◆ getConfigurationAsString()

◆ getCutoff()

◆ getEnergy()

◆ getHaloSize()

◆ getInvalidParticles()

◆ getMoleculeAtPosition()

◆ getName()

◆ getNumberOfParticles()

◆ getSkin()

◆ getTotalSize()

◆ initCubicGrid()

◆ isInvalidParticleReturner()

◆ iterator()

◆ printSubInfo()

◆ readXML()

◆ rebuild()

◆ regionIterator()

◆ setCutoff()

◆ traverseCells()

◆ traverseNonInnermostCells()

◆ traversePartialInnermostCells()

◆ update()

◆ updateBoundaryAndHaloMoleculeCaches()

◆ updateInnerMoleculeCaches()

◆ updateMoleculeCaches()