Verlet Lists container. More...

#include <VerletLists.h>

Inheritance diagram for autopas::VerletLists< Particle_T >:

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Collaboration diagram for autopas::VerletLists< Particle_T >:

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Public Types
enum	BuildVerletListType { VerletAoS , VerletSoA }
	Enum that specifies how the verlet lists should be build. More...

Public Types inherited from autopas::ParticleContainerInterface< Particle_T >
using	ParticleType = Particle_T
	Type of the Particle.

Public Member Functions
	VerletLists (const std::array< double, 3 > &boxMin, const std::array< double, 3 > &boxMax, const double cutoff, const double skin, const unsigned int rebuildFrequency, const BuildVerletListType buildVerletListType=BuildVerletListType::VerletSoA, const double cellSizeFactor=1.0)
	Constructor of the VerletLists class.

ContainerOption	getContainerType () const override
	Get the ContainerType.

void	computeInteractions (TraversalInterface *traversal) override
	Iterates over all particle multiples (e.g.

VerletListHelpers< Particle_T >::NeighborListAoSType &	getVerletListsAoS ()
	get the actual neighbor list

void	rebuildNeighborLists (TraversalInterface *traversal) override
	Rebuilds the verlet lists, marks them valid and resets the internal counter.

Public Member Functions inherited from autopas::VerletListsLinkedBase< Particle_T >
	VerletListsLinkedBase (const std::array< double, 3 > &boxMin, const std::array< double, 3 > &boxMax, const double cutoff, const double skin, const unsigned int rebuildFrequency, const std::set< TraversalOption > &applicableTraversals, const double cellSizeFactor)
	Constructor of the VerletListsLinkedBase class.

CellType	getParticleCellTypeEnum () const override
	Get the ParticleCell type as an Enum.

void	setStepsSinceLastRebuild (size_t stepsSinceLastRebuild) override
	Set the number of time-steps since last neighbor list rebuild.

void	reserve (size_t numParticles, size_t numParticlesHaloEstimate) override
	Reserve memory for a given number of particles in the container and logic layers.

void	addParticleImpl (const Particle_T &p) override
	Adds a particle to the container.

void	addHaloParticleImpl (const Particle_T &haloParticle) override
	Adds a particle to the container that lies in the halo region of the container.

size_t	size () const override
	Get the total number of particles saved in the container (owned + halo + dummy).

size_t	getNumberOfParticles (IteratorBehavior behavior) const override
	Get the number of particles with respect to the specified IteratorBehavior.

void	deleteHaloParticles () override
	Deletes all halo particles.

void	deleteAllParticles () override
	Deletes all particles.

std::tuple< const Particle_T *, size_t, size_t >	getParticle (size_t cellIndex, size_t particleIndex, IteratorBehavior iteratorBehavior, const std::array< double, 3 > &boxMin, const std::array< double, 3 > &boxMax) const override
	Fetch the pointer to a particle, identified via a cell and particle index.

std::tuple< const Particle_T *, size_t, size_t >	getParticle (size_t cellIndex, size_t particleIndex, IteratorBehavior iteratorBehavior) const override
	Fetch the pointer to a particle, identified via a cell and particle index.

template<bool regionIter>
std::tuple< const Particle_T *, size_t, size_t >	getParticleImpl (size_t cellIndex, size_t particleIndex, IteratorBehavior iteratorBehavior, const std::array< double, 3 > &boxMin, const std::array< double, 3 > &boxMax) const
	Container specific implementation for getParticle.

bool	deleteParticle (Particle_T &particle) override
	Deletes the given particle as long as this does not compromise the validity of the container.

bool	deleteParticle (size_t cellIndex, size_t particleIndex) override
	Deletes the particle at the given index positions as long as this does not compromise the validity of the container.

std::vector< Particle_T >	updateContainer (bool keepNeighborListsValid) override
	Updates the container.

bool	updateHaloParticle (const Particle_T &haloParticle) override
	Searches the provided halo particle and updates the found particle.

ContainerIterator< Particle_T, true, false >	begin (IteratorBehavior behavior=IteratorBehavior::ownedOrHalo, typename ContainerIterator< Particle_T, true, false >::ParticleVecType *additionalVectors=nullptr) override
	Iterate over all particles using for(auto iter = container.begin(); iter.isValid(); ++iter) .

ContainerIterator< Particle_T, false, false >	begin (IteratorBehavior behavior=IteratorBehavior::ownedOrHalo, typename ContainerIterator< Particle_T, false, false >::ParticleVecType *additionalVectors=nullptr) const override
	Iterate over all particles using for(auto iter = container.begin(); iter.isValid(); ++iter) .

template<typename Lambda >
void	forEach (Lambda forEachLambda, IteratorBehavior behavior)
	Execute code on all particles in this container as defined by a lambda function.

template<typename Lambda , typename A >
void	reduce (Lambda reduceLambda, A &result, IteratorBehavior behavior)
	Reduce properties of particles as defined by a lambda function.

ContainerIterator< Particle_T, true, true >	getRegionIterator (const std::array< double, 3 > &lowerCorner, const std::array< double, 3 > &higherCorner, IteratorBehavior behavior, typename ContainerIterator< Particle_T, true, true >::ParticleVecType *additionalVectors=nullptr) override
	Iterate over all particles in a specified region for(auto iter = container.getRegionIterator(lowCorner, highCorner);iter.isValid();++iter) .

ContainerIterator< Particle_T, false, true >	getRegionIterator (const std::array< double, 3 > &lowerCorner, const std::array< double, 3 > &higherCorner, IteratorBehavior behavior, typename ContainerIterator< Particle_T, false, true >::ParticleVecType *additionalVectors=nullptr) const override
	Iterate over all particles in a specified region for(auto iter = container.getRegionIterator(lowCorner, highCorner);iter.isValid();++iter) .

template<typename Lambda >
void	forEachInRegion (Lambda forEachLambda, const std::array< double, 3 > &lowerCorner, const std::array< double, 3 > &higherCorner, IteratorBehavior behavior)
	Execute code on all particles in this container in a certain region as defined by a lambda function.

template<typename Lambda , typename A >
void	reduceInRegion (Lambda reduceLambda, A &result, const std::array< double, 3 > &lowerCorner, const std::array< double, 3 > &higherCorner, IteratorBehavior behavior)
	Execute code on all particles in this container in a certain region as defined by a lambda function.

const std::array< std::size_t, 3 > &	getCellsPerDimension () const
	Get the dimension of the used cellblock including the haloboxes.

TraversalSelectorInfo	getTraversalSelectorInfo () const override
	Generates a traversal selector info for this container.

const std::array< double, 3 > &	getBoxMax () const final
	Get the upper corner of the container without halo.

const std::array< double, 3 > &	getBoxMin () const final
	Get the lower corner of the container without halo.

double	getCutoff () const final
	Return the cutoff of the container.

void	setCutoff (double cutoff) final
	Set the cutoff of the container.

double	getVerletSkin () const final
	Return the verletSkin of the container verletSkin.

double	getInteractionLength () const final
	Return the interaction length (cutoff+skin) of the container.

Public Member Functions inherited from autopas::ParticleContainerInterface< Particle_T >
virtual CellType	getParticleCellTypeEnum () const =0
	Get the ParticleCell type as an Enum.

	ParticleContainerInterface (double skin)
	Constructor.

virtual	~ParticleContainerInterface ()=default
	Destructor of ParticleContainerInterface.

	ParticleContainerInterface (const ParticleContainerInterface &obj)=delete
	Delete the copy constructor to prevent unwanted copies.

ParticleContainerInterface &	operator= (const ParticleContainerInterface &other)=delete
	Delete the copy assignment operator to prevent unwanted copies.

virtual ContainerOption	getContainerType () const =0
	Get the ContainerType.

virtual void	reserve (size_t numParticles, size_t numParticlesHaloEstimate)=0
	Reserve memory for a given number of particles in the container and logic layers.

template<bool checkInBox = true>
void	addParticle (const Particle_T &p)
	Adds a particle to the container.

template<bool checkInBox = true>
void	addHaloParticle (const Particle_T &haloParticle)
	Adds a particle to the container that lies in the halo region of the container.

virtual bool	updateHaloParticle (const Particle_T &haloParticle)=0
	Update a halo particle of the container with the given haloParticle.

virtual void	rebuildNeighborLists (TraversalInterface *traversal)=0
	Rebuilds the neighbor lists for the next traversals.

virtual void	deleteHaloParticles ()=0
	Deletes all halo particles.

virtual void	deleteAllParticles ()=0
	Deletes all particles.

virtual size_t	getNumberOfParticles (IteratorBehavior behavior=IteratorBehavior::owned) const =0
	Get the number of particles with respect to the specified IteratorBehavior.

virtual size_t	size () const =0
	Get the total number of particles saved in the container (owned + halo + dummy).

virtual ContainerIterator< ParticleType, true, false >	begin (IteratorBehavior behavior=autopas::IteratorBehavior::ownedOrHalo, typename ContainerIterator< ParticleType, true, false >::ParticleVecType *additionalVectors=nullptr)=0
	Iterate over all particles using for(auto iter = container.begin(); iter.isValid(); ++iter) .

virtual ContainerIterator< ParticleType, false, false >	begin (IteratorBehavior behavior=autopas::IteratorBehavior::ownedOrHalo, typename ContainerIterator< ParticleType, false, false >::ParticleVecType *additionalVectors=nullptr) const =0
	Iterate over all particles using for(auto iter = container.begin(); iter.isValid(); ++iter) .

virtual ContainerIterator< ParticleType, false, false >	cbegin (IteratorBehavior behavior=autopas::IteratorBehavior::ownedOrHalo, typename ContainerIterator< ParticleType, false, false >::ParticleVecType *additionalVectors=nullptr) const final
	Iterate over all particles using for(auto iter = container.begin(); iter.isValid(); ++iter) .

virtual ContainerIterator< ParticleType, true, true >	getRegionIterator (const std::array< double, 3 > &lowerCorner, const std::array< double, 3 > &higherCorner, IteratorBehavior behavior, typename ContainerIterator< ParticleType, true, true >::ParticleVecType *additionalVectors=nullptr)=0
	Iterate over all particles in a specified region for(auto iter = container.getRegionIterator(lowCorner, highCorner);iter.isValid();++iter) .

virtual ContainerIterator< ParticleType, false, true >	getRegionIterator (const std::array< double, 3 > &lowerCorner, const std::array< double, 3 > &higherCorner, IteratorBehavior behavior, typename ContainerIterator< ParticleType, false, true >::ParticleVecType *additionalVectors=nullptr) const =0
	Iterate over all particles in a specified region for(auto iter = container.getRegionIterator(lowCorner, highCorner);iter.isValid();++iter) .

constexpr bool	end () const
	Dummy to make range-based for loops work.

virtual void	computeInteractions (TraversalInterface *traversal)=0
	Iterates over all particle multiples (e.g.

virtual const std::array< double, 3 > &	getBoxMax () const =0
	Get the upper corner of the container without halo.

virtual const std::array< double, 3 > &	getBoxMin () const =0
	Get the lower corner of the container without halo.

virtual double	getCutoff () const =0
	Return the cutoff of the container.

virtual void	setCutoff (double cutoff)=0
	Set the cutoff of the container.

virtual double	getVerletSkin () const =0
	Return the verletSkin of the container verletSkin.

virtual size_t	getStepsSinceLastRebuild () const
	Return the number of time-steps since last neighbor list rebuild.

virtual void	setStepsSinceLastRebuild (size_t stepsSinceLastRebuild)
	Set the number of time-steps since last neighbor list rebuild.

virtual double	getInteractionLength () const =0
	Return the interaction length (cutoff+skin) of the container.

virtual std::vector< ParticleType >	updateContainer (bool keepNeighborListsValid)=0
	Updates the container.

virtual TraversalSelectorInfo	getTraversalSelectorInfo () const =0
	Generates a traversal selector info for this container.

std::set< TraversalOption >	getAllTraversals (const InteractionTypeOption interactionType) const
	Generates a list of all traversals that are theoretically applicable to this container.

virtual std::tuple< const Particle_T *, size_t, size_t >	getParticle (size_t cellIndex, size_t particleIndex, IteratorBehavior iteratorBehavior) const =0
	Fetch the pointer to a particle, identified via a cell and particle index.

virtual std::tuple< const Particle_T *, size_t, size_t >	getParticle (size_t cellIndex, size_t particleIndex, IteratorBehavior iteratorBehavior, const std::array< double, 3 > &boxMin, const std::array< double, 3 > &boxMax) const =0
	Fetch the pointer to a particle, identified via a cell and particle index.

std::tuple< Particle_T *, size_t, size_t >	getParticle (size_t cellIndex, size_t particleIndex, IteratorBehavior iteratorBehavior, const std::array< double, 3 > &boxMin, const std::array< double, 3 > &boxMax)
	Fetch the pointer to a particle, identified via a cell and particle index.

std::tuple< Particle_T *, size_t, size_t >	getParticle (size_t cellIndex, size_t particleIndex, IteratorBehavior iteratorBehavior)
	Fetch the pointer to a particle, identified via a cell and particle index.

virtual bool	deleteParticle (Particle_T &particle)=0
	Deletes the given particle as long as this does not compromise the validity of the container.

virtual bool	deleteParticle (size_t cellIndex, size_t particleIndex)=0
	Deletes the particle at the given index positions as long as this does not compromise the validity of the container.

Protected Member Functions
virtual void	updateVerletListsAoS (bool useNewton3)
	Update the verlet lists for AoS usage.

size_t	generateAoSNeighborLists ()
	Clears and then generates the AoS neighbor lists.

void	generateSoAListFromAoSVerletLists ()
	Fills SoA neighbor list with particle indices.

virtual void	addParticleImpl (const Particle_T &p)=0
	Adds a particle to the container.

virtual void	addHaloParticleImpl (const Particle_T &haloParticle)=0
	Adds a particle to the container that lies in the halo region of the container.

Additional Inherited Members
Protected Attributes inherited from autopas::VerletListsLinkedBase< Particle_T >
LinkedCells< Particle_T >	_linkedCells
	internal linked cells storage, handles Particle storage and used to build verlet lists

std::atomic< bool >	_neighborListIsValid {false}
	specifies if the neighbor list is currently valid

bool	_verletBuiltNewton3 {false}
	specifies if the current verlet list was built for newton3

Protected Attributes inherited from autopas::ParticleContainerInterface< Particle_T >
size_t	_stepsSinceLastRebuild {0}
	Stores the number of time-steps since last neighbor list rebuild.

double	_skin
	Skin distance a particle is allowed to move in one time-step.

Detailed Description

template<class Particle_T>
class autopas::VerletLists< Particle_T >

Verlet Lists container.

The VerletLists class uses neighborhood lists to calculate pairwise interactions of particles. It is optimized for a constant, i.e. particle independent, cutoff radius of the interaction. Cells are created using a cell size of at least cutoff + skin radius.

Template Parameters

Particle_T

Member Enumeration Documentation

◆ BuildVerletListType

template<class Particle_T >

enum autopas::VerletLists::BuildVerletListType

Enum that specifies how the verlet lists should be build.

Enumerator
VerletAoS	Build it using AoS.
VerletSoA	Build it using AoS.

Constructor & Destructor Documentation

◆ VerletLists()

template<class Particle_T >

autopas::VerletLists< Particle_T >::VerletLists	(	const std::array< double, 3 > &	boxMin,
		const std::array< double, 3 > &	boxMax,
		const double	cutoff,
		const double	skin,
		const unsigned int	rebuildFrequency,
		const BuildVerletListType	buildVerletListType = `BuildVerletListType::VerletSoA`,
		const double	cellSizeFactor = `1.0`
	)

inline

Constructor of the VerletLists class.

The neighbor lists are build using a search radius of cutoff + skin.

Parameters

boxMin	The lower corner of the domain.
boxMax	The upper corner of the domain.
cutoff	The cutoff radius of the interaction.
skin	The skin radius per timestep.
rebuildFrequency	rebuild fequency.
buildVerletListType	Specifies how the verlet list should be build, see BuildVerletListType
cellSizeFactor	cell size factor ralative to cutoff

Member Function Documentation

◆ computeInteractions()

template<class Particle_T >

void autopas::VerletLists< Particle_T >::computeInteractions ( TraversalInterface * traversal )

inlineoverridevirtual

Iterates over all particle multiples (e.g.

pairs, triplets) in the container using the given traversal.

Parameters

traversal The traversal to use for the iteration.

Implements autopas::ParticleContainerInterface< Particle_T >.

◆ generateAoSNeighborLists()

template<class Particle_T >

size_t autopas::VerletLists< Particle_T >::generateAoSNeighborLists ( )

inlineprotected

Clears and then generates the AoS neighbor lists.

The Id Map is used to map the id of a particle to the actual particle.

Returns: Number of particles in the container

◆ getContainerType()

template<class Particle_T >

ContainerOption autopas::VerletLists< Particle_T >::getContainerType ( ) const

inlineoverridevirtual

Get the ContainerType.

Returns: ContainerOption of the type of this container.

Implements autopas::ParticleContainerInterface< Particle_T >.

◆ getVerletListsAoS()

template<class Particle_T >

VerletListHelpers< Particle_T >::NeighborListAoSType & autopas::VerletLists< Particle_T >::getVerletListsAoS ( )

inline

get the actual neighbor list

Returns: the neighbor list

◆ rebuildNeighborLists()

template<class Particle_T >

void autopas::VerletLists< Particle_T >::rebuildNeighborLists ( TraversalInterface * traversal )

inlineoverridevirtual

Rebuilds the verlet lists, marks them valid and resets the internal counter.

Note: This function will be called in computeInteractions()!

Parameters

traversal

Implements autopas::ParticleContainerInterface< Particle_T >.

◆ updateVerletListsAoS()

template<class Particle_T >

virtual void autopas::VerletLists< Particle_T >::updateVerletListsAoS ( bool useNewton3 )

inlineprotectedvirtual

Update the verlet lists for AoS usage.

Parameters

useNewton3

Todo:: autotune traversal

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

autopas/containers/verletListsCellBased/verletLists/VerletLists.h

Public Types

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ BuildVerletListType

Constructor & Destructor Documentation

◆ VerletLists()

Member Function Documentation

◆ computeInteractions()

◆ generateAoSNeighborLists()

◆ getContainerType()

◆ getVerletListsAoS()

◆ rebuildNeighborLists()

◆ updateVerletListsAoS()