Describes a cell structure / cell system. More...

#include <CellStructure.hpp>

Inheritance diagram for CellStructure:

Collaboration diagram for CellStructure:

Public Member Functions
	CellStructure (BoxGeometry const &box)

void	update_particle_index (int id, Particle *p)
	Update local particle index.

void	update_particle_index (Particle &p)
	Update local particle index.

void	update_particle_index (ParticleList &pl)
	Update local particle index.

void	clear_particle_index ()
	Clear the particles index.

Particle *	get_local_particle (int id)
	Get a local particle by id.

const Particle *	get_local_particle (int id) const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

template<class InputRange , class OutputIterator >
void	get_local_particles (InputRange ids, OutputIterator out)

CellStructureType	decomposition_type () const

Utils::Vector3d	max_cutoff () const
	Maximal cutoff supported by current cell system.

Utils::Vector3d	max_range () const
	Maximal pair range supported by current cell system.

ParticleRange	local_particles () const

ParticleRange	ghost_particles () const

Particle *	add_particle (Particle &&p)
	Add a particle.

Particle *	add_local_particle (Particle &&p)
	Add a particle.

void	remove_particle (int id)
	Remove a particle.

int	get_max_local_particle_id () const
	Get the maximal particle id on this node.

void	remove_all_particles ()
	Remove all particles from the cell system.

ParticleDecomposition const &	decomposition () const
	Get the underlying particle decomposition.

void	set_resort_particles (Cells::Resort level)
	Increase the local resort level at least to `level`.

unsigned	get_resort_particles () const
	Get the currently scheduled resort level.

void	clear_resort_particles ()
	Set the resort level to sorted.

bool	check_resort_required (Utils::Vector3d const &additional_offset={}) const
	Check whether a particle has moved further than half the skin since the last Verlet list update, thus requiring a resort.

auto	get_le_pos_offset_at_last_resort () const

void	ghosts_count ()
	Synchronize number of ghosts.

void	ghosts_update (unsigned data_parts)
	Update ghost particles.

void	update_ghosts_and_resort_particle (unsigned data_parts)
	Update ghost particles, with particle resort if needed.

void	ghosts_reduce_forces ()
	Add forces from ghost particles to real particles.

void	ghosts_reduce_rattle_correction ()
	Add rattle corrections from ghost particles to real particles.

void	resort_particles (bool global_flag)
	Resort particles.

auto	is_verlet_skin_set () const
	Whether the Verlet skin is set.

auto	get_verlet_skin () const
	Get the Verlet skin.

void	set_verlet_skin (double value)
	Set the Verlet skin.

void	set_verlet_skin_heuristic ()
	Set the Verlet skin using a heuristic.

void	update_verlet_stats (int n_steps, int n_verlet_updates)

auto	get_verlet_reuse () const
	Average number of integration steps the Verlet list was re-used.

void	set_atom_decomposition ()
	Set the particle decomposition to AtomDecomposition.

void	set_regular_decomposition (double range, std::optional< std::pair< int, int > > fully_connected_boundary)
	Set the particle decomposition to RegularDecomposition.

void	set_hybrid_decomposition (double cutoff_regular, std::set< int > n_square_types)
	Set the particle decomposition to HybridDecomposition.

template<class BondKernel >
void	bond_loop (BondKernel const &bond_kernel)
	Bonded pair loop.

template<class PairKernel >
void	non_bonded_loop (PairKernel pair_kernel)
	Non-bonded pair loop.

template<class PairKernel , class VerletCriterion >
void	non_bonded_loop (PairKernel pair_kernel, const VerletCriterion &verlet_criterion)
	Non-bonded pair loop with potential use of verlet lists.

void	check_particle_index () const
	Check that particle index is commensurate with particles.

void	check_particle_sorting () const
	Check that particles are in the correct cell.

Cell *	find_current_cell (const Particle &p)
	Find cell a particle is stored in.

template<class Kernel >
bool	run_on_particle_short_range_neighbors (Particle const &p, Kernel &kernel)
	Run kernel on all particles inside local cell and its neighbors.

Public Member Functions inherited from System::Leaf< CellStructure >
void	bind_system (std::shared_ptr< System > const &system)

void	detach_system (std::shared_ptr< System > const &system)

Public Attributes
bool	use_verlet_list = true

Additional Inherited Members
Protected Member Functions inherited from System::Leaf< CellStructure >
auto &	get_system ()

auto &	get_system () const

Protected Attributes inherited from System::Leaf< CellStructure >
std::weak_ptr< System >	m_system

Detailed Description

Describes a cell structure / cell system.

Contains information about the communication of cell contents (particles, ghosts, ...) between different nodes and the relation between particle positions and the cell system. All other properties of the cell system which are not common between different cell systems have to be stored in separate structures.

Definition at line 134 of file CellStructure.hpp.

Constructor & Destructor Documentation

◆ CellStructure()

CellStructure::CellStructure ( BoxGeometry const & box )

Definition at line 54 of file CellStructure.cpp.

Member Function Documentation

◆ add_local_particle()

Particle * CellStructure::add_local_particle ( Particle && p )

Add a particle.

Moves a particle into the cell system, if it belongs to this node. Otherwise this does not have an effect and the particle is discarded. This can be used to add a particle without knowledge where it should be placed by calling the function on all nodes, it will then add the particle in exactly one place.

Parameters

p	Particle to add.

Returns: Pointer to particle if it is local, null otherwise.

Definition at line 128 of file CellStructure.cpp.

◆ add_particle()

Particle * CellStructure::add_particle ( Particle && p )

Add a particle.

Moves a particle into the cell system. This adds a particle to the local node, irrespective of where it belongs.

Parameters

p	Particle to add.

Returns: Pointer to the particle in the cell system.

Definition at line 139 of file CellStructure.cpp.

References decomposition(), ParticleDecomposition::local_cells(), Cells::RESORT_GLOBAL, Cells::RESORT_LOCAL, and set_resort_particles().

Referenced by Mpiio::mpi_mpiio_common_read(), and CollisionDetection::place_vs_and_relate_to_particle().

◆ bond_loop()

template<class BondKernel >

void CellStructure::bond_loop ( BondKernel const & bond_kernel )

inline

Bonded pair loop.

Parameters

bond_kernel Kernel to apply

Definition at line 652 of file CellStructure.hpp.

References local_particles().

Referenced by add_oif_global_forces(), calc_oif_mesh(), and compute_correction_vector().

◆ check_particle_index()

void CellStructure::check_particle_index ( ) const

Check that particle index is commensurate with particles.

For each local particles is checked that has a correct entry in the particles index, and that there are no excess (non-existing) particles in the index.

Definition at line 57 of file CellStructure.cpp.

References get_local_particle(), get_max_local_particle_id(), Particle::id(), and local_particles().

Referenced by resort_particles().

◆ check_particle_sorting()

void CellStructure::check_particle_sorting ( ) const

Check that particles are in the correct cell.

This checks for all local particles that the result of particles_to_cell is the cell the particles is actually in, e.g. that the particles are sorted according to particles_to_cell.

Definition at line 90 of file CellStructure.cpp.

References decomposition(), and ParticleDecomposition::local_cells().

Referenced by resort_particles().

◆ check_resort_required()

bool CellStructure::check_resort_required ( Utils::Vector3d const & additional_offset = {} ) const

inline

Check whether a particle has moved further than half the skin since the last Verlet list update, thus requiring a resort.

Parameters

additional_offset Offset which is added to the distance the particle has travelled when comparing to half the Verlet skin (e.g., for Lees-Edwards BC).

Returns: Whether a resort is needed.

Definition at line 394 of file CellStructure.hpp.

Referenced by correct_position_shake(), and vs_relative_update_particles().

◆ clear_particle_index()

void CellStructure::clear_particle_index ( )

inline

Clear the particles index.

Definition at line 204 of file CellStructure.hpp.

◆ clear_resort_particles()

void CellStructure::clear_resort_particles ( )

inline

Set the resort level to sorted.

Definition at line 383 of file CellStructure.hpp.

References Cells::RESORT_NONE.

Referenced by update_ghosts_and_resort_particle().

◆ decomposition()

ParticleDecomposition const & CellStructure::decomposition ( ) const

inline

Get the underlying particle decomposition.

Should be used solely for informative purposes.

Returns: The active particle decomposition.

Definition at line 357 of file CellStructure.hpp.

Referenced by add_particle(), check_particle_sorting(), ghost_particles(), ghosts_count(), ghosts_reduce_forces(), ghosts_reduce_rattle_correction(), ghosts_update(), local_particles(), max_cutoff(), max_range(), remove_all_particles(), remove_particle(), and run_on_particle_short_range_neighbors().

◆ decomposition_type()

CellStructureType CellStructure::decomposition_type ( ) const

inline

Definition at line 262 of file CellStructure.hpp.

◆ find_current_cell()

Cell * CellStructure::find_current_cell ( const Particle & p )

inline

Find cell a particle is stored in.

For local particles, this returns the cell they are stored in, otherwise nullptr is returned.

Parameters

p	Particle to find cell for

Returns: Cell for particle or nullptr.

Definition at line 710 of file CellStructure.hpp.

References get_resort_particles(), and Particle::is_ghost().

Referenced by run_on_particle_short_range_neighbors().

◆ get_le_pos_offset_at_last_resort()

auto CellStructure::get_le_pos_offset_at_last_resort ( ) const

inline

Definition at line 403 of file CellStructure.hpp.

◆ get_local_particle() [1/2]

Particle * CellStructure::get_local_particle ( int id )

inline

Get a local particle by id.

Parameters

id	Particle to get.

Returns: Pointer to particle if it is local, nullptr otherwise.

Definition at line 237 of file CellStructure.hpp.

Referenced by BondBreakage::actions_for_breakage(), CollisionDetection::add_bind_centers(), check_particle_index(), ScriptInterface::Analysis::check_topology(), GatherParticleTraits< T >::fetch(), get_ibm_particle_position(), get_local_particles(), CollisionDetection::get_part(), ScriptInterface::Particles::get_real_particle(), get_reference_particle(), ScriptInterface::Particles::local_add_exclusion(), ScriptInterface::Particles::local_remove_exclusion(), BondBreakage::execute::operator()(), BondBreakage::execute::operator()(), BondBreakage::execute::operator()(), update_ghosts_and_resort_particle(), and vs_relative_pressure_tensor().

◆ get_local_particle() [2/2]

const Particle * CellStructure::get_local_particle ( int id ) const

inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 247 of file CellStructure.hpp.

◆ get_local_particles()

template<class InputRange , class OutputIterator >

void CellStructure::get_local_particles	(	InputRange	ids,
		OutputIterator	out
	)

inline

Definition at line 257 of file CellStructure.hpp.

References get_local_particle().

◆ get_max_local_particle_id()

int CellStructure::get_max_local_particle_id ( ) const

Get the maximal particle id on this node.

This returns the highest particle id on this node, or -1 if there are no particles on this node.

Definition at line 153 of file CellStructure.cpp.

Referenced by check_particle_index().

◆ get_resort_particles()

unsigned CellStructure::get_resort_particles ( ) const

inline

Get the currently scheduled resort level.

Definition at line 378 of file CellStructure.hpp.

Referenced by find_current_cell().

◆ get_verlet_reuse()

auto CellStructure::get_verlet_reuse ( ) const

inline

Average number of integration steps the Verlet list was re-used.

Definition at line 471 of file CellStructure.hpp.

◆ get_verlet_skin()

auto CellStructure::get_verlet_skin ( ) const

inline

Get the Verlet skin.

Definition at line 454 of file CellStructure.hpp.

Referenced by lb_tracers_propagate().

◆ ghost_particles()

ParticleRange CellStructure::ghost_particles ( ) const

inline

Definition at line 274 of file CellStructure.hpp.

References decomposition(), and Cells::particles().

Referenced by correct_position_shake(), correct_velocity_shake(), lb_tracers_add_particle_force_to_fluid(), update_ghosts_and_resort_particle(), and vs_relative_back_transfer_forces_and_torques().

◆ ghosts_count()

void CellStructure::ghosts_count ( )

Synchronize number of ghosts.

Definition at line 186 of file CellStructure.cpp.

References decomposition(), System::Leaf< CellStructure >::get_system(), ghost_communicator(), and GHOSTTRANS_PARTNUM.

Referenced by update_ghosts_and_resort_particle().

◆ ghosts_reduce_forces()

void CellStructure::ghosts_reduce_forces ( )

Add forces from ghost particles to real particles.

Definition at line 194 of file CellStructure.cpp.

References decomposition(), System::Leaf< CellStructure >::get_system(), ghost_communicator(), and GHOSTTRANS_FORCE.

Referenced by ICCStar::iteration(), and vs_relative_back_transfer_forces_and_torques().

◆ ghosts_reduce_rattle_correction()

void CellStructure::ghosts_reduce_rattle_correction ( )

Add rattle corrections from ghost particles to real particles.

Definition at line 199 of file CellStructure.cpp.

References decomposition(), System::Leaf< CellStructure >::get_system(), ghost_communicator(), and GHOSTTRANS_RATTLE.

Referenced by correct_position_shake(), and correct_velocity_shake().

◆ ghosts_update()

void CellStructure::ghosts_update ( unsigned data_parts )

Update ghost particles.

Update ghost particles with data from the real particles.

Parameters

data_parts Particle parts to update, combination of Cells::DataPart

Definition at line 190 of file CellStructure.cpp.

References decomposition(), System::Leaf< CellStructure >::get_system(), ghost_communicator(), and map_data_parts().

Referenced by correct_position_shake(), correct_velocity_shake(), ICCStar::iteration(), update_ghosts_and_resort_particle(), and vs_relative_update_particles().

◆ is_verlet_skin_set()

auto CellStructure::is_verlet_skin_set ( ) const

inline

Whether the Verlet skin is set.

Definition at line 451 of file CellStructure.hpp.

Referenced by set_verlet_skin_heuristic().

◆ local_particles()

ParticleRange CellStructure::local_particles ( ) const

inline

Definition at line 270 of file CellStructure.hpp.

References decomposition(), and Cells::particles().

Referenced by bond_loop(), calc_total_charge(), check_particle_index(), correct_position_shake(), correct_velocity_shake(), lb_tracers_add_particle_force_to_fluid(), lb_tracers_propagate(), ScriptInterface::System::rescale_particles(), ScriptInterface::System::rotate_system(), vs_relative_back_transfer_forces_and_torques(), vs_relative_pressure_tensor(), and vs_relative_update_particles().

◆ max_cutoff()

Utils::Vector3d CellStructure::max_cutoff ( ) const

inline

Maximal cutoff supported by current cell system.

Definition at line 265 of file CellStructure.hpp.

References decomposition(), and ParticleDecomposition::max_cutoff().

Referenced by set_verlet_skin_heuristic().

◆ max_range()

Utils::Vector3d CellStructure::max_range ( ) const

inline

Maximal pair range supported by current cell system.

Definition at line 268 of file CellStructure.hpp.

References decomposition(), and ParticleDecomposition::max_range().

Referenced by set_verlet_skin_heuristic().

◆ non_bonded_loop() [1/2]

template<class PairKernel >

void CellStructure::non_bonded_loop ( PairKernel pair_kernel )

inline

Non-bonded pair loop.

Parameters

pair_kernel Kernel to apply

Definition at line 661 of file CellStructure.hpp.

Referenced by force_calc_icc().

◆ non_bonded_loop() [2/2]

template<class PairKernel , class VerletCriterion >

void CellStructure::non_bonded_loop	(	PairKernel	pair_kernel,
		const VerletCriterion &	verlet_criterion
	)

inline

Non-bonded pair loop with potential use of verlet lists.

Parameters

pair_kernel	Kernel to apply
verlet_criterion	Filter for verlet lists.

Definition at line 671 of file CellStructure.hpp.

References use_verlet_list.

◆ remove_all_particles()

void CellStructure::remove_all_particles ( )

Remove all particles from the cell system.

This allows linear time removal of all particles from the system, removing each particle individually would be quadratic.

Definition at line 160 of file CellStructure.cpp.

References decomposition(), and ParticleDecomposition::local_cells().

Referenced by Mpiio::mpi_mpiio_common_read().

◆ remove_particle()

void CellStructure::remove_particle ( int id )

Remove a particle.

Removes a particle and all bonds pointing to it. This is a collective call.

Parameters

id	Id of particle to remove.

Definition at line 101 of file CellStructure.cpp.

References Utils::contains(), decomposition(), ParticleDecomposition::local_cells(), and update_particle_index().

◆ resort_particles()

void CellStructure::resort_particles ( bool global_flag )

Resort particles.

Definition at line 219 of file CellStructure.cpp.

References check_particle_index(), check_particle_sorting(), and System::Leaf< CellStructure >::get_system().

Referenced by update_ghosts_and_resort_particle().

◆ run_on_particle_short_range_neighbors()

template<class Kernel >

bool CellStructure::run_on_particle_short_range_neighbors	(	Particle const &	p,
		Kernel &	kernel
	)

inline

Run kernel on all particles inside local cell and its neighbors.

Parameters

p	Particle to find cell for
kernel	Function with signature `double(Particle const&, Particle const&, Utils::Vector3d const&)`

Returns: false if cell is not found, otherwise true

Definition at line 729 of file CellStructure.hpp.

References ParticleDecomposition::box(), decomposition(), find_current_cell(), and ParticleDecomposition::minimum_image_distance().

◆ set_atom_decomposition()

void CellStructure::set_atom_decomposition ( )

Set the particle decomposition to AtomDecomposition.

Definition at line 241 of file CellStructure.cpp.

References comm_cart, System::Leaf< CellStructure >::get_system(), and NSQUARE.

◆ set_hybrid_decomposition()

void CellStructure::set_hybrid_decomposition	(	double	cutoff_regular,
		std::set< int >	n_square_types
	)

Set the particle decomposition to HybridDecomposition.

Parameters

cutoff_regular	Interaction cutoff_regular.
n_square_types	Particle types to put into n_square decomposition.

Definition at line 264 of file CellStructure.cpp.

References comm_cart, System::Leaf< CellStructure >::get_system(), and HYBRID.

◆ set_regular_decomposition()

void CellStructure::set_regular_decomposition	(	double	range,
		std::optional< std::pair< int, int > >	fully_connected_boundary
	)

Set the particle decomposition to RegularDecomposition.

Parameters

range	Interaction range.
fully_connected_boundary	neighbor cell directions for Lees-Edwards.

Definition at line 252 of file CellStructure.cpp.

References comm_cart, System::Leaf< CellStructure >::get_system(), and REGULAR.

◆ set_resort_particles()

void CellStructure::set_resort_particles ( Cells::Resort level )

inline

Increase the local resort level at least to level.

Definition at line 370 of file CellStructure.hpp.

Referenced by add_particle(), correct_position_shake(), lb_tracers_propagate(), ScriptInterface::System::rotate_system(), and vs_relative_update_particles().

◆ set_verlet_skin()

void CellStructure::set_verlet_skin ( double value )

Set the Verlet skin.

Definition at line 278 of file CellStructure.cpp.

References System::Leaf< CellStructure >::get_system().

Referenced by set_verlet_skin_heuristic().

◆ set_verlet_skin_heuristic()

void CellStructure::set_verlet_skin_heuristic ( )

Set the Verlet skin using a heuristic.

Definition at line 285 of file CellStructure.cpp.

References System::Leaf< CellStructure >::get_system(), is_verlet_skin_set(), max_cutoff(), max_range(), and set_verlet_skin().

◆ update_ghosts_and_resort_particle()

void CellStructure::update_ghosts_and_resort_particle ( unsigned data_parts )

Update ghost particles, with particle resort if needed.

Update ghost particles with data from the real particles. Resort particles if a resort is due.

Parameters

data_parts Particle parts to update, combination of Cells::DataPart

Definition at line 299 of file CellStructure.cpp.

References clear_resort_particles(), comm_cart, Cells::DATA_PART_BONDS, Cells::DATA_PART_PROPERTIES, get_local_particle(), ghost_particles(), ghosts_count(), ghosts_update(), Cells::RESORT_GLOBAL, Cells::RESORT_NONE, resort_particles(), and update_particle_index().

Referenced by correct_position_shake(), lb_tracers_add_particle_force_to_fluid(), and ScriptInterface::System::rotate_system().

◆ update_particle_index() [1/3]

void CellStructure::update_particle_index	(	int	id,
		Particle *	p
	)

inline

Update local particle index.

Update the entry for a particle in the local particle index.

Parameters

id	Entry to update.
p	Pointer to the particle.

Definition at line 167 of file CellStructure.hpp.

References Particle::id().

Referenced by anonymous_namespace{CellStructure.cpp}::UpdateParticleIndexVisitor::operator()(), anonymous_namespace{CellStructure.cpp}::UpdateParticleIndexVisitor::operator()(), remove_particle(), update_ghosts_and_resort_particle(), update_particle_index(), and update_particle_index().

◆ update_particle_index() [2/3]

void CellStructure::update_particle_index ( Particle & p )

inline

Update local particle index.

Update the entry for a particle in the local particle index.

Parameters

p	Pointer to the particle.

Definition at line 186 of file CellStructure.hpp.

References Particle::id(), and update_particle_index().

◆ update_particle_index() [3/3]

void CellStructure::update_particle_index ( ParticleList & pl )

inline

Update local particle index.

Parameters

pl	List of particles whose index entries should be updated.

Definition at line 195 of file CellStructure.hpp.

References update_particle_index().

◆ update_verlet_stats()

void CellStructure::update_verlet_stats	(	int	n_steps,
		int	n_verlet_updates
	)

inline

Definition at line 462 of file CellStructure.hpp.

Member Data Documentation

◆ use_verlet_list

bool CellStructure::use_verlet_list = true

Definition at line 156 of file CellStructure.hpp.

Referenced by non_bonded_loop().

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

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CellStructure()

Member Function Documentation

◆ add_local_particle()

◆ add_particle()

◆ bond_loop()

◆ check_particle_index()

◆ check_particle_sorting()

◆ check_resort_required()

◆ clear_particle_index()

◆ clear_resort_particles()

◆ decomposition()

◆ decomposition_type()

◆ find_current_cell()

◆ get_le_pos_offset_at_last_resort()

◆ get_local_particle() [1/2]

◆ get_local_particle() [2/2]

◆ get_local_particles()

◆ get_max_local_particle_id()

◆ get_resort_particles()

◆ get_verlet_reuse()

◆ get_verlet_skin()

◆ ghost_particles()

◆ ghosts_count()

◆ ghosts_reduce_forces()

◆ ghosts_reduce_rattle_correction()

◆ ghosts_update()

◆ is_verlet_skin_set()

◆ local_particles()

◆ max_cutoff()

◆ max_range()

◆ non_bonded_loop() [1/2]

◆ non_bonded_loop() [2/2]

◆ remove_all_particles()

◆ remove_particle()

◆ resort_particles()

◆ run_on_particle_short_range_neighbors()

◆ set_atom_decomposition()

◆ set_hybrid_decomposition()

◆ set_regular_decomposition()

◆ set_resort_particles()

◆ set_verlet_skin()

◆ set_verlet_skin_heuristic()

◆ update_ghosts_and_resort_particle()

◆ update_particle_index() [1/3]

◆ update_particle_index() [2/3]

◆ update_particle_index() [3/3]

◆ update_verlet_stats()

Member Data Documentation

◆ use_verlet_list