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

#include <CellStructure.hpp>

Inheritance diagram for CellStructure:

Collaboration diagram for CellStructure:

Classes
struct	AoSoA_pack

Public Types
using	ForceType = Kokkos::View< double **[3], Kokkos::LayoutRight >

using	VirialType = Kokkos::View< double *[3], Kokkos::LayoutRight >

using	memory_space = Kokkos::HostSpace

using	ListAlgorithm = Cabana::HalfNeighborTag

using	ListType = CustomVerletList< Kokkos::HostSpace, ListAlgorithm, Cabana::VerletLayout2D, Cabana::TeamVectorOpTag >

Public Member Functions
	CellStructure (BoxGeometry const &box)

virtual	~CellStructure ()

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

std::size_t	count_local_particles () const

bool	use_parallel_for_each_local_particle () const
	whether to use parallel version of for_each_local_particle

void	for_each_local_particle (ParticleUnaryOp &&f, bool parallel=true) const
	Run a kernel on all local particles.

void	for_each_ghost_particle (ParticleUnaryOp &&f) const
	Run a kernel on all ghost particles.

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.

int	get_cached_max_local_particle_id () const

std::size_t	get_num_local_particles_cached () const

int	get_local_pair_bond_numbers () const

int	get_local_angle_bond_numbers () const

int	get_local_dihedral_bond_numbers () const

void	set_local_bond_numbers (int p, int a, int d)

void	clear_new_bonds ()

void	add_new_bond (int bond_id, std::vector< int > const &particle_ids)

void	rebuild_bond_list ()

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 and torques from ghost particles to real particles.

void	ghosts_reset_forces ()
	Set forces and torques on all ghosts to zero.

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.

auto	resolve_bond_partners (std::span< const int > partner_ids)
	Resolve ids to particles.

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.

auto	get_max_id () const

void	set_kokkos_handle (std::shared_ptr< KokkosHandle > handle)

void	rebuild_local_properties (double pair_cutoff)

void	reset_local_properties ()

void	reset_local_force ()

auto &	get_id_to_index ()

auto &	get_local_force ()

auto &	get_local_torque ()

auto &	get_local_virial ()

auto &	get_aosoa ()

auto const &	get_unique_particles () const

auto const &	get_verlet_list_cabana () const

auto &	bond_state ()

auto const &	bond_state () const

void	clear_local_properties ()

void	clear_bond_properties ()

auto	is_verlet_list_cabana_rebuild_needed () const

void	update_bond_storage (int &pair_count, int &angle_count, int &dihedral_count, Particle const &p)
	Update bond storage(m__bond_list_kokkos and m__bond_id_kokkos).

auto	prepare_verlet_list_cabana (double cutoff)
	Reset local properties of the Verlet list.

void	rebuild_verlet_list_cabana (auto &&kernel, bool rebuild_verlet_list)

void	set_index_map ()

void	cell_list_loop (auto &&kernel)

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

Static Public Attributes
static constexpr auto	vector_length = 1

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 169 of file CellStructure.hpp.

Member Typedef Documentation

◆ ForceType

using CellStructure::ForceType = Kokkos::View<double **[3], Kokkos::LayoutRight>

Definition at line 173 of file CellStructure.hpp.

◆ ListAlgorithm

using CellStructure::ListAlgorithm = Cabana::HalfNeighborTag

Definition at line 176 of file CellStructure.hpp.

◆ ListType

using CellStructure::ListType = CustomVerletList<Kokkos::HostSpace, ListAlgorithm, Cabana::VerletLayout2D, Cabana::TeamVectorOpTag>

Definition at line 177 of file CellStructure.hpp.

◆ memory_space

using CellStructure::memory_space = Kokkos::HostSpace

Definition at line 175 of file CellStructure.hpp.

◆ VirialType

using CellStructure::VirialType = Kokkos::View<double *[3], Kokkos::LayoutRight>

Definition at line 174 of file CellStructure.hpp.

Constructor & Destructor Documentation

◆ CellStructure()

CellStructure::CellStructure ( BoxGeometry const & box )

Definition at line 310 of file CellStructure.cpp.

◆ ~CellStructure()

CellStructure::~CellStructure ( )

virtual

Definition at line 78 of file CellStructure.cpp.

References clear_local_properties().

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 383 of file CellStructure.cpp.

◆ add_new_bond()

void CellStructure::add_new_bond	(	int	bond_id,
		std::vector< int > const &	particle_ids
	)

Definition at line 429 of file CellStructure.cpp.

References get_id_to_index().

◆ 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 393 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 842 of file CellStructure.hpp.

References local_particles().

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

◆ bond_state() [1/2]

auto & CellStructure::bond_state ( )

inline

Definition at line 743 of file CellStructure.hpp.

◆ bond_state() [2/2]

auto const & CellStructure::bond_state ( ) const

inline

Definition at line 744 of file CellStructure.hpp.

◆ cell_list_loop()

void CellStructure::cell_list_loop ( auto && kernel )

inline

Definition at line 792 of file CellStructure.hpp.

Referenced by cabana_short_range().

◆ 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 313 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 346 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

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 625 of file CellStructure.cpp.

References Utils::Vector< T, N >::norm2(), reduce_over_local_particles(), and Utils::sqr().

Referenced by correct_position_shake(), and vs_relative_update_particles().

◆ clear_bond_properties()

void CellStructure::clear_bond_properties ( )

Definition at line 98 of file CellStructure.cpp.

Referenced by remove_all_particles().

◆ clear_local_properties()

void CellStructure::clear_local_properties ( )

Definition at line 84 of file CellStructure.cpp.

Referenced by ~CellStructure().

◆ clear_new_bonds()

void CellStructure::clear_new_bonds ( )

Definition at line 428 of file CellStructure.cpp.

◆ clear_particle_index()

void CellStructure::clear_particle_index ( )

inline

Clear the particles index.

Definition at line 270 of file CellStructure.hpp.

◆ clear_resort_particles()

void CellStructure::clear_resort_particles ( )

inline

Set the resort level to sorted.

Definition at line 503 of file CellStructure.hpp.

References Cells::RESORT_NONE.

Referenced by update_ghosts_and_resort_particle().

◆ count_local_particles()

std::size_t CellStructure::count_local_particles ( ) const

inline

Definition at line 344 of file CellStructure.hpp.

Referenced by anonymous_namespace{p3m_heffte.impl.hpp}::AssignForces< cao >::operator()(), and set_index_map().

◆ 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 477 of file CellStructure.hpp.

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

◆ decomposition_type()

CellStructureType CellStructure::decomposition_type ( ) const

inline

Definition at line 328 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 900 of file CellStructure.hpp.

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

Referenced by run_on_particle_short_range_neighbors().

◆ for_each_ghost_particle()

void CellStructure::for_each_ghost_particle ( ParticleUnaryOp && f ) const

inline

Run a kernel on all ghost particles.

The kernel is assumed to be thread-safe.

Definition at line 374 of file CellStructure.hpp.

References ghost_particles().

Referenced by force_calc_icc(), and ghosts_reset_forces().

◆ for_each_local_particle()

void CellStructure::for_each_local_particle	(	ParticleUnaryOp &&	f,
		bool	parallel = `true`
	)		const

inline

Run a kernel on all local particles.

The kernel is assumed to be thread-safe.

Definition at line 359 of file CellStructure.hpp.

References decomposition(), local_particles(), and use_parallel_for_each_local_particle().

Referenced by force_calc_icc(), force_capping(), get_pid_for_vs_com(), integrator_step_1(), integrator_step_2(), reinit_dip_fld(), vs_com_back_transfer_forces_and_torques(), vs_com_update_particles(), vs_relative_back_transfer_forces_and_torques(), and vs_relative_update_particles().

◆ get_aosoa()

auto & CellStructure::get_aosoa ( )

inline

Definition at line 740 of file CellStructure.hpp.

Referenced by anonymous_namespace{p3m_heffte.impl.hpp}::AssignForces< cao >::operator()(), reset_local_properties(), update_aosoa_charges(), and update_cabana_state().

◆ get_cached_max_local_particle_id()

int CellStructure::get_cached_max_local_particle_id ( ) const

inline

Definition at line 445 of file CellStructure.hpp.

Referenced by cabana_short_range(), rebuild_local_properties(), and update_cabana_state().

◆ get_id_to_index()

auto & CellStructure::get_id_to_index ( )

inline

Definition at line 732 of file CellStructure.hpp.

Referenced by add_new_bond(), cabana_short_range(), rebuild_local_properties(), and update_cabana_state().

◆ get_le_pos_offset_at_last_resort()

auto CellStructure::get_le_pos_offset_at_last_resort ( ) const

inline

Definition at line 516 of file CellStructure.hpp.

◆ get_local_angle_bond_numbers()

int CellStructure::get_local_angle_bond_numbers ( ) const

Definition at line 417 of file CellStructure.cpp.

Referenced by cabana_short_range().

◆ get_local_dihedral_bond_numbers()

int CellStructure::get_local_dihedral_bond_numbers ( ) const

Definition at line 420 of file CellStructure.cpp.

Referenced by cabana_short_range().

◆ get_local_force()

auto & CellStructure::get_local_force ( )

inline

Definition at line 733 of file CellStructure.hpp.

Referenced by anonymous_namespace{dp3m_heffte.impl.hpp}::AssignForcesDip< cao >::operator()(), anonymous_namespace{p3m_heffte.impl.hpp}::AssignForces< cao >::operator()(), rebuild_local_properties(), reset_local_force(), and reset_local_properties().

◆ get_local_pair_bond_numbers()

int CellStructure::get_local_pair_bond_numbers ( ) const

Definition at line 414 of file CellStructure.cpp.

Referenced by cabana_short_range().

◆ 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 303 of file CellStructure.hpp.

◆ 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 313 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 323 of file CellStructure.hpp.

References get_local_particle().

Referenced by resolve_bond_partners().

◆ get_local_torque()

auto & CellStructure::get_local_torque ( )

inline

Definition at line 735 of file CellStructure.hpp.

Referenced by anonymous_namespace{dp3m_heffte.impl.hpp}::AssignTorques< cao >::operator()(), rebuild_local_properties(), and reset_local_properties().

◆ get_local_virial()

auto & CellStructure::get_local_virial ( )

inline

Definition at line 738 of file CellStructure.hpp.

Referenced by reset_local_properties().

◆ get_max_id()

auto CellStructure::get_max_id ( ) const

inline

Definition at line 725 of file CellStructure.hpp.

◆ 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 407 of file CellStructure.cpp.

Referenced by check_particle_index().

◆ get_num_local_particles_cached()

std::size_t CellStructure::get_num_local_particles_cached ( ) const

inline

Definition at line 448 of file CellStructure.hpp.

Referenced by rebuild_local_properties().

◆ get_resort_particles()

unsigned CellStructure::get_resort_particles ( ) const

inline

Get the currently scheduled resort level.

Definition at line 498 of file CellStructure.hpp.

Referenced by cabana_short_range(), and find_current_cell().

◆ get_unique_particles()

auto const & CellStructure::get_unique_particles ( ) const

inline

Definition at line 741 of file CellStructure.hpp.

Referenced by cabana_short_range(), anonymous_namespace{dp3m_heffte.impl.hpp}::AssignTorques< cao >::operator()(), anonymous_namespace{dp3m_heffte.impl.hpp}::AssignForcesDip< cao >::operator()(), rebuild_local_properties(), update_aosoa_charges(), and update_cabana_state().

◆ get_verlet_list_cabana()

auto const & CellStructure::get_verlet_list_cabana ( ) const

inline

Definition at line 742 of file CellStructure.hpp.

Referenced by cabana_short_range().

◆ get_verlet_reuse()

auto CellStructure::get_verlet_reuse ( ) const

inline

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

Definition at line 589 of file CellStructure.hpp.

◆ get_verlet_skin()

auto CellStructure::get_verlet_skin ( ) const

inline

Get the Verlet skin.

Definition at line 572 of file CellStructure.hpp.

Referenced by lb_tracers_propagate().

◆ ghost_particles()

ParticleRange CellStructure::ghost_particles ( ) const

inline

Definition at line 340 of file CellStructure.hpp.

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

Referenced by correct_position_shake(), correct_velocity_shake(), for_each_ghost_particle(), lb_tracers_add_particle_force_to_fluid(), set_index_map(), and update_ghosts_and_resort_particle().

◆ ghosts_count()

void CellStructure::ghosts_count ( )

Synchronize number of ghosts.

Definition at line 463 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 and torques from ghost particles to real particles.

Definition at line 471 of file CellStructure.cpp.

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

Referenced by vs_com_back_transfer_forces_and_torques(), 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 476 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_reset_forces()

void CellStructure::ghosts_reset_forces ( )

inline

Set forces and torques on all ghosts to zero.

Definition at line 552 of file CellStructure.hpp.

References for_each_ghost_particle(), and Particle::force_and_torque().

Referenced by lb_tracers_add_particle_force_to_fluid(), vs_com_back_transfer_forces_and_torques(), and vs_relative_back_transfer_forces_and_torques().

◆ 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 467 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(), update_ghosts_and_resort_particle(), vs_com_update_particles(), and vs_relative_update_particles().

◆ is_verlet_list_cabana_rebuild_needed()

auto CellStructure::is_verlet_list_cabana_rebuild_needed ( ) const

inline

Definition at line 748 of file CellStructure.hpp.

Referenced by prepare_verlet_list_cabana(), and rebuild_verlet_list_cabana().

◆ is_verlet_skin_set()

auto CellStructure::is_verlet_skin_set ( ) const

inline

Whether the Verlet skin is set.

Definition at line 569 of file CellStructure.hpp.

Referenced by set_verlet_skin_heuristic().

◆ local_particles()

ParticleRange CellStructure::local_particles ( ) const

inline

Definition at line 336 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(), for_each_local_particle(), integrator_step_1(), integrator_step_2(), lb_tracers_add_particle_force_to_fluid(), lb_tracers_propagate(), SteepestDescent::propagate(), ScriptInterface::System::rescale_particles(), ScriptInterface::System::rotate_system(), and vs_relative_pressure_tensor().

◆ max_cutoff()

Utils::Vector3d CellStructure::max_cutoff ( ) const

inline

Maximal cutoff supported by current cell system.

Definition at line 331 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 334 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 851 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 861 of file CellStructure.hpp.

References use_verlet_list.

◆ prepare_verlet_list_cabana()

auto CellStructure::prepare_verlet_list_cabana ( double cutoff )

inline

Reset local properties of the Verlet list.

Parameters

cutoff Pair interaction cutoff.

Returns: True if a rebuild is needed.

Definition at line 767 of file CellStructure.hpp.

References is_verlet_list_cabana_rebuild_needed(), rebuild_local_properties(), reset_local_properties(), and set_index_map().

Referenced by update_cabana_state().

◆ rebuild_bond_list()

void CellStructure::rebuild_bond_list ( )

Definition at line 433 of file CellStructure.cpp.

◆ rebuild_local_properties()

void CellStructure::rebuild_local_properties ( double pair_cutoff )

Definition at line 135 of file CellStructure.cpp.

References estimate_max_counts(), get_cached_max_local_particle_id(), get_id_to_index(), get_local_force(), get_local_torque(), get_num_local_particles_cached(), System::Leaf< CellStructure >::get_system(), and get_unique_particles().

Referenced by prepare_verlet_list_cabana().

◆ rebuild_verlet_list_cabana()

void CellStructure::rebuild_verlet_list_cabana	(	auto &&	kernel,
		bool	rebuild_verlet_list
	)

inline

Definition at line 781 of file CellStructure.hpp.

References is_verlet_list_cabana_rebuild_needed().

◆ 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 436 of file CellStructure.cpp.

References clear_bond_properties(), 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 357 of file CellStructure.cpp.

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

◆ reset_local_force()

void CellStructure::reset_local_force ( )

Definition at line 188 of file CellStructure.cpp.

References get_local_force().

Referenced by force_calc_icc().

◆ reset_local_properties()

void CellStructure::reset_local_properties ( )

Definition at line 195 of file CellStructure.cpp.

References get_aosoa(), get_local_force(), get_local_torque(), and get_local_virial().

Referenced by prepare_verlet_list_cabana().

◆ resolve_bond_partners()

auto CellStructure::resolve_bond_partners ( std::span< const int > partner_ids )

inline

Resolve ids to particles.

Exceptions

BondResolutionError if one of the ids was not found.

Parameters

partner_ids Ids to resolve.

Returns: Vector of Particle pointers.

Definition at line 600 of file CellStructure.hpp.

References get_local_particles().

Referenced by update_bond_storage().

◆ resort_particles()

void CellStructure::resort_particles ( bool global_flag )

Resort particles.

Definition at line 496 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 919 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 518 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 541 of file CellStructure.cpp.

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

◆ set_index_map()

void CellStructure::set_index_map ( )

Definition at line 244 of file CellStructure.cpp.

References Particle::bonds(), count_local_particles(), enumerate_local_particles(), get_local_particle(), ghost_particles(), Particle::id(), and set_local_bond_numbers().

Referenced by prepare_verlet_list_cabana().

◆ set_kokkos_handle()

void CellStructure::set_kokkos_handle ( std::shared_ptr< KokkosHandle > handle )

Definition at line 100 of file CellStructure.cpp.

◆ set_local_bond_numbers()

void CellStructure::set_local_bond_numbers	(	int	p,
		int	a,
		int	d
	)

Definition at line 423 of file CellStructure.cpp.

Referenced by set_index_map().

◆ 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 529 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 490 of file CellStructure.hpp.

Referenced by add_particle(), correct_position_shake(), lb_tracers_propagate(), SteepestDescent::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 555 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 563 of file CellStructure.cpp.

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

◆ update_bond_storage()

void CellStructure::update_bond_storage	(	int &	pair_count,
		int &	angle_count,
		int &	dihedral_count,
		Particle const &	p
	)

Update bond storage(m_*_bond_list_kokkos and m_*_bond_id_kokkos).

Parameters

pair_count	Index for pair bond storage.
angle_count	Index for angle bond storage.
dihedral_count	Index for dihedral bond storage.
p	Particle pointer.

Definition at line 206 of file CellStructure.cpp.

References bond_resolution_error(), Particle::bonds(), Particle::id(), and resolve_bond_partners().

◆ 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 577 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 233 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 252 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 261 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 580 of file CellStructure.hpp.

◆ use_parallel_for_each_local_particle()

bool CellStructure::use_parallel_for_each_local_particle ( ) const

inline

whether to use parallel version of for_each_local_particle

Definition at line 353 of file CellStructure.hpp.

Referenced by enumerate_local_particles(), and for_each_local_particle().

Member Data Documentation

◆ use_verlet_list

bool CellStructure::use_verlet_list = true

Definition at line 222 of file CellStructure.hpp.

Referenced by cabana_short_range(), and non_bonded_loop().

◆ vector_length

constexpr auto CellStructure::vector_length = 1

staticconstexpr

Definition at line 171 of file CellStructure.hpp.

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

Classes

Public Types

Public Member Functions

Public Attributes

Static Public Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ForceType

◆ ListAlgorithm

◆ ListType

◆ memory_space

◆ VirialType

Constructor & Destructor Documentation

◆ CellStructure()

◆ ~CellStructure()

Member Function Documentation

◆ add_local_particle()

◆ add_new_bond()

◆ add_particle()

◆ bond_loop()

◆ bond_state() [1/2]

◆ bond_state() [2/2]

◆ cell_list_loop()

◆ check_particle_index()

◆ check_particle_sorting()

◆ check_resort_required()

◆ clear_bond_properties()

◆ clear_local_properties()

◆ clear_new_bonds()

◆ clear_particle_index()

◆ clear_resort_particles()

◆ count_local_particles()

◆ decomposition()

◆ decomposition_type()

◆ find_current_cell()

◆ for_each_ghost_particle()

◆ for_each_local_particle()

◆ get_aosoa()

◆ get_cached_max_local_particle_id()

◆ get_id_to_index()

◆ get_le_pos_offset_at_last_resort()

◆ get_local_angle_bond_numbers()

◆ get_local_dihedral_bond_numbers()

◆ get_local_force()

◆ get_local_pair_bond_numbers()

◆ get_local_particle() [1/2]

◆ get_local_particle() [2/2]

◆ get_local_particles()

◆ get_local_torque()

◆ get_local_virial()

◆ get_max_id()

◆ get_max_local_particle_id()

◆ get_num_local_particles_cached()

◆ get_resort_particles()

◆ get_unique_particles()

◆ get_verlet_list_cabana()

◆ get_verlet_reuse()

◆ get_verlet_skin()

◆ ghost_particles()

◆ ghosts_count()

◆ ghosts_reduce_forces()

◆ ghosts_reduce_rattle_correction()

◆ ghosts_reset_forces()

◆ ghosts_update()

◆ is_verlet_list_cabana_rebuild_needed()

◆ is_verlet_skin_set()

◆ local_particles()

◆ max_cutoff()

◆ max_range()

◆ non_bonded_loop() [1/2]

◆ non_bonded_loop() [2/2]

◆ prepare_verlet_list_cabana()

◆ rebuild_bond_list()

◆ rebuild_local_properties()

◆ rebuild_verlet_list_cabana()

◆ remove_all_particles()

◆ remove_particle()

◆ reset_local_force()

◆ reset_local_properties()