particle_node.hpp File Reference

Particles creation and deletion. More...

#include "Particle.hpp"
#include <utils/Span.hpp>
#include <utils/Vector.hpp>
#include <cstddef>
#include <vector>

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Namespaces
namespace	type_tracking

Functions
const Particle &	get_particle_data (int p_id)
	Get particle data.
void	prefetch_particle_data (Utils::Span< const int > ids)
	Fetch a range of particle into the fetch cache.
void	invalidate_fetch_cache ()
	Invalidate the fetch cache for get_particle_data.
std::size_t	fetch_cache_max_size ()
	Return the maximal number of particles that are kept in the fetch cache.
void	clear_particle_node ()
	Invalidate particle_node.
void	make_new_particle (int p_id, Utils::Vector3d const &pos)
	Create a new particle and attach it to a cell.
void	set_particle_pos (int p_id, Utils::Vector3d const &pos)
	Move particle to a new position.
void	remove_particle (int p_id)
	Remove particle with a given identity.
void	remove_all_particles ()
	Remove all particles.
void	init_type_map (int type)
void	on_particle_type_change (int p_id, int old_type, int new_type)
int	get_random_p_id (int type, int random_index_in_type_map)
	Find a particle of given type and return its id.
int	number_of_particles_with_type (int type)
bool	particle_exists (int p_id)
	Check if particle exists.
int	get_particle_node (int p_id)
	Get the MPI rank which owns the a specific particle.
int	get_particle_node_parallel (int p_id)
std::vector< int >	get_particle_ids ()
	Get all particle ids.
std::vector< int >	get_particle_ids_parallel ()
int	get_maximal_particle_id ()
	Get maximal particle id.
int	get_n_part ()
	Get number of particles.

Variables
auto constexpr	type_tracking::any_type = -2
auto constexpr	type_tracking::new_part = -3

Detailed Description

Particles creation and deletion.

This file contains everything related to particle storage and tracking.

Implementation in particle_node.cpp.

Definition in file particle_node.hpp.

Function Documentation

clear_particle_node()

void clear_particle_node

(

)

Invalidate particle_node.

This has to be done at the beginning of the integration.

Definition at line 405 of file particle_node.cpp.

References max_seen_pid, and particle_node.

Referenced by System::System::on_cell_structure_change(), System::System::on_observable_calc(), and remove_all_particles().

fetch_cache_max_size()

std::size_t fetch_cache_max_size

(

)

Return the maximal number of particles that are kept in the fetch cache.

Definition at line 160 of file particle_node.cpp.

References anonymous_namespace{particle_node.cpp}::particle_fetch_cache.

get_maximal_particle_id()

int get_maximal_particle_id

(

)

Get maximal particle id.

Definition at line 603 of file particle_node.cpp.

References build_particle_node_parallel(), max_seen_pid, and rebuild_needed().

Referenced by ReactionMethods::ReactionAlgorithm::delete_particle(), ScriptInterface::Particles::ParticleList::do_call_method(), and ScriptInterface::Particles::ParticleHandle::do_construct().

get_n_part()

int get_n_part

(

)

Get number of particles.

Definition at line 611 of file particle_node.cpp.

References build_particle_node(), and particle_node.

Referenced by ScriptInterface::Particles::ParticleList::do_call_method().

get_particle_data()

const Particle & get_particle_data

(

int

p_id

)

Get particle data.

Parameters

p_id	the identity of the particle to fetch

Definition at line 175 of file particle_node.cpp.

References Communication::MpiCallbacks::call_all(), comm_cart, get_cell_structure(), get_particle_node(), mpi_send_particle_data_local(), Communication::mpiCallbacks(), anonymous_namespace{particle_node.cpp}::particle_fetch_cache, and this_node.

Referenced by ClusterAnalysis::Cluster::center_of_mass_subcluster(), PairCriteria::PairCriterion::decide(), ScriptInterface::Particles::ParticleHandle::do_call_method(), ClusterAnalysis::Cluster::fractal_dimension(), ClusterAnalysis::Cluster::longest_distance(), ScriptInterface::Particles::ParticleHandle::ParticleHandle(), ClusterAnalysis::Cluster::radius_of_gyration_subcluster(), and ClusterAnalysis::ClusterStructure::run_for_bonded_particles().

get_particle_ids()

std::vector< int > get_particle_ids

(

)

Get all particle ids.

Returns

Sorted ids of all existing particles.

Definition at line 584 of file particle_node.cpp.

References build_particle_node(), Utils::keys(), and particle_node.

Referenced by ScriptInterface::Particles::ParticleList::do_call_method(), ScriptInterface::Particles::ParticleList::get_internal_state(), and ScriptInterface::Particles::ParticleList::set_internal_state().

get_particle_ids_parallel()

std::vector< int > get_particle_ids_parallel

(

)

Definition at line 594 of file particle_node.cpp.

References build_particle_node_parallel(), comm_cart, Utils::keys(), particle_node, and rebuild_needed().

Referenced by ReactionMethods::ReactionAlgorithm::setup_bookkeeping_of_empty_pids().

get_particle_node()

int get_particle_node

(

int

p_id

)

Get the MPI rank which owns the a specific particle.

Parameters

p_id	identity of the particle

Returns

The MPI rank the particle is on.

Definition at line 364 of file particle_node.cpp.

References build_particle_node(), and particle_node.

Referenced by get_particle_data(), mpi_get_particles(), and ScriptInterface::Particles::ParticleHandle::ParticleHandle().

get_particle_node_parallel()

int get_particle_node_parallel

(

int

p_id

)

Definition at line 382 of file particle_node.cpp.

References build_particle_node_parallel(), particle_node, rebuild_needed(), and this_node.

get_random_p_id()

int get_random_p_id	(	int	type,
		int	random_index_in_type_map
	)

Find a particle of given type and return its id.

Definition at line 550 of file particle_node.cpp.

References comm_cart, and particle_type_map.

Referenced by ReactionMethods::ReactionAlgorithm::displacement_mc_move(), and ReactionMethods::ReactionAlgorithm::make_reaction_attempt().

init_type_map()

void init_type_map

(

int

type

)

Definition at line 92 of file particle_node.cpp.

References comm_cart, get_cell_structure(), System::get_system(), System::System::nonbonded_ias, particle_type_map, and type_list_enable.

Referenced by ReactionMethods::ReactionAlgorithm::add_reaction(), ScriptInterface::System::System::do_call_method(), and ScriptInterface::ReactionMethods::ReactionAlgorithm::do_call_method().

invalidate_fetch_cache()

void invalidate_fetch_cache

(

)

Invalidate the fetch cache for get_particle_data.

Definition at line 159 of file particle_node.cpp.

References anonymous_namespace{particle_node.cpp}::particle_fetch_cache.

Referenced by System::System::on_integration_start(), and System::System::on_particle_change().

make_new_particle()

void make_new_particle	(	int	p_id,
		Utils::Vector3d const &	pos
	)

Create a new particle and attach it to a cell.

Parameters

p_id	The identity of the particle to create.
pos	The particle position.

Definition at line 519 of file particle_node.cpp.

References build_particle_node_parallel(), comm_cart, System::get_system(), max_seen_pid, maybe_insert_particle(), mpi_synchronize_max_seen_pid_local(), node, System::System::on_particle_change(), particle_node, pos, rebuild_needed(), and this_node.

Referenced by ScriptInterface::Particles::ParticleHandle::do_construct().

number_of_particles_with_type()

int number_of_particles_with_type

(

int

type

)

Definition at line 567 of file particle_node.cpp.

References particle_type_map.

Referenced by ReactionMethods::ReactionAlgorithm::all_reactant_particles_exist(), ReactionMethods::ReactionAlgorithm::displacement_mc_move(), ReactionMethods::ReactionAlgorithm::make_displacement_mc_move_attempt(), and ReactionMethods::ReactionAlgorithm::make_reaction_attempt().

on_particle_type_change()

void on_particle_type_change	(	int	p_id,
		int	old_type,
		int	new_type
	)

Definition at line 129 of file particle_node.cpp.

References add_id_to_type_map(), type_tracking::any_type, get_cell_structure(), type_tracking::new_part, particle_type_map, remove_id_from_map(), and type_list_enable.

Referenced by ReactionMethods::ReactionAlgorithm::make_reaction_attempt(), ScriptInterface::Particles::ParticleHandle::ParticleHandle(), and ReactionMethods::ReactionAlgorithm::restore_old_system_state().

particle_exists()

bool particle_exists

(

int

p_id

)

Check if particle exists.

Parameters

p_id	identity of the particle

Returns

True iff the particle exists.

Definition at line 578 of file particle_node.cpp.

References build_particle_node(), and particle_node.

Referenced by ScriptInterface::Particles::ParticleList::do_call_method(), and ScriptInterface::Particles::ParticleSlice::do_call_method().

prefetch_particle_data()

void prefetch_particle_data

(

Utils::Span< const int >

ids

)

Fetch a range of particle into the fetch cache.

If the range is larger than the cache size, only the particle that fit into the cache are fetched.

The particles have to exist, an exception it throw if one of the the particles can not be found.

Parameters

ids	Ids of the particles that should be fetched.

Definition at line 267 of file particle_node.cpp.

References Utils::Span< T >::begin(), comm_cart, Utils::Span< T >::end(), mpi_get_particles(), and anonymous_namespace{particle_node.cpp}::particle_fetch_cache.

Referenced by ScriptInterface::Particles::ParticleSlice::do_call_method().

remove_all_particles()

void remove_all_particles

(

)

Remove all particles.

Definition at line 473 of file particle_node.cpp.

References clear_particle_node(), clear_particle_type_map(), get_cell_structure(), System::get_system(), and System::System::on_particle_change().

Referenced by ScriptInterface::Particles::ParticleList::do_call_method().

remove_particle()

void remove_particle

(

int

p_id

)

Remove particle with a given identity.

Also removes all bonds to the particle.

Parameters

p_id	identity of the particle to remove

Definition at line 480 of file particle_node.cpp.

References calculate_max_seen_id(), comm_cart, get_cell_structure(), System::get_system(), max_seen_pid, mpi_synchronize_max_seen_pid_local(), System::System::on_particle_change(), particle_node, remove_id_from_map(), this_node, and type_list_enable.

Referenced by ReactionMethods::ReactionAlgorithm::delete_particle(), ScriptInterface::Particles::ParticleHandle::do_call_method(), and ScriptInterface::Particles::ParticleHandle::do_construct().

set_particle_pos()

void set_particle_pos	(	int	p_id,
		Utils::Vector3d const &	pos
	)

Move particle to a new position.

Parameters

p_id	The identity of the particle to move.
pos	The new particle position.

Definition at line 537 of file particle_node.cpp.

References comm_cart, get_cell_structure(), System::get_system(), maybe_move_particle(), System::System::on_particle_change(), pos, Cells::RESORT_GLOBAL, and this_node.

Referenced by ReactionMethods::ReactionAlgorithm::displacement_mc_move(), and ScriptInterface::Particles::ParticleHandle::ParticleHandle().