ESPResSo
Extensible Simulation Package for Research on Soft Matter Systems
|
#include "particle_node.hpp"
#include "BoxGeometry.hpp"
#include "Particle.hpp"
#include "cell_system/CellStructure.hpp"
#include "cells.hpp"
#include "communication.hpp"
#include "nonbonded_interactions/nonbonded_interaction_data.hpp"
#include "system/System.hpp"
#include <utils/Cache.hpp>
#include <utils/Vector.hpp>
#include <utils/keys.hpp>
#include <utils/mpi/gatherv.hpp>
#include <boost/mpi/collectives/all_gather.hpp>
#include <boost/mpi/collectives/all_reduce.hpp>
#include <boost/mpi/collectives/gather.hpp>
#include <boost/mpi/collectives/reduce.hpp>
#include <boost/mpi/collectives/scatter.hpp>
#include <algorithm>
#include <cmath>
#include <functional>
#include <iterator>
#include <span>
#include <stdexcept>
#include <string>
#include <unordered_map>
#include <unordered_set>
#include <utility>
#include <vector>
Go to the source code of this file.
Namespaces | |
namespace | anonymous_namespace{particle_node.cpp} |
Functions | |
static auto & | get_cell_structure () |
static auto | rebuild_needed () |
static void | mpi_synchronize_max_seen_pid_local () |
void | init_type_map (int type) |
static void | remove_id_from_map (int p_id, int type) |
static void | add_id_to_type_map (int p_id, int type) |
void | on_particle_type_change (int p_id, int old_type, int new_type) |
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. | |
static void | mpi_send_particle_data_local (int p_id) |
const Particle & | get_particle_data (int p_id) |
Get particle data. | |
static void | mpi_get_particles_local () |
static std::vector< Particle > | mpi_get_particles (std::span< const int > ids) |
Get multiple particles at once. | |
void | prefetch_particle_data (std::span< const int > in_ids) |
Fetch a range of particle into the fetch cache. | |
static void | mpi_who_has_local () |
static void | mpi_who_has_head () |
static void | build_particle_node () |
Rebuild the particle index. | |
static void | build_particle_node_parallel () |
Rebuild the particle index. | |
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) |
void | clear_particle_node () |
Invalidate particle_node. | |
static void | clear_particle_type_map () |
static int | calculate_max_seen_id () |
Calculate the largest particle id. | |
static bool | maybe_insert_particle (int p_id, Utils::Vector3d const &pos) |
Create a new particle and attach it to a cell. | |
static bool | maybe_move_particle (int p_id, Utils::Vector3d const &pos) |
Move particle to a new position. | |
void | remove_all_particles () |
Remove all particles. | |
void | remove_particle (int p_id) |
Remove particle with a given identity. | |
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. | |
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. | |
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 | |
constexpr auto | some_tag = 42 |
static bool | type_list_enable |
Enable particle type tracking in particle_type_map. | |
static std::unordered_map< int, std::unordered_set< int > > | particle_type_map |
Mapping particle types to lists of particle ids. | |
static std::unordered_map< int, int > | particle_node |
Mapping particle ids to MPI ranks. | |
static int | max_seen_pid = -1 |
Keep track of the largest particle id. | |
std::size_t const | anonymous_namespace{particle_node.cpp}::max_cache_size = (100ul * 1048576ul) / sizeof(Particle) |
Utils::Cache< int, Particle > | anonymous_namespace{particle_node.cpp}::particle_fetch_cache (max_cache_size) |
|
static |
Definition at line 120 of file particle_node.cpp.
References particle_type_map.
Referenced by on_particle_type_change().
|
static |
Rebuild the particle index.
Definition at line 345 of file particle_node.cpp.
References mpi_call(), mpi_who_has_head(), and mpi_who_has_local().
Referenced by get_n_part(), get_particle_ids(), get_particle_node(), and particle_exists().
|
static |
Rebuild the particle index.
Definition at line 353 of file particle_node.cpp.
References mpi_who_has_head(), mpi_who_has_local(), and this_node.
Referenced by get_maximal_particle_id(), get_particle_ids_parallel(), get_particle_node_parallel(), and make_new_particle().
|
static |
Calculate the largest particle id.
Traversing the particle_node to find the largest particle id scales with O(N). Consider using the cached value in max_seen_pid if possible. This function is only necessary when the cached value is invalidated, for example when removing the particle which has the largest id.
Definition at line 421 of file particle_node.cpp.
References particle_node.
Referenced by remove_particle().
void clear_particle_node | ( | ) |
Invalidate particle_node.
This has to be done at the beginning of the integration.
Definition at line 402 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().
|
static |
Definition at line 407 of file particle_node.cpp.
References particle_type_map.
Referenced by remove_all_particles().
std::size_t fetch_cache_max_size | ( | ) |
Return the maximal number of particles that are kept in the fetch cache.
Definition at line 157 of file particle_node.cpp.
References anonymous_namespace{particle_node.cpp}::particle_fetch_cache.
|
static |
Definition at line 66 of file particle_node.cpp.
References System::System::cell_structure, and System::get_system().
Referenced by ScriptInterface::Particles::ParticleHandle::do_call_method(), ScriptInterface::Particles::ParticleHandle::do_construct(), get_particle_data(), init_type_map(), maybe_insert_particle(), mpi_send_particle_data_local(), mpi_who_has_head(), mpi_who_has_local(), on_particle_type_change(), remove_all_particles(), remove_particle(), and set_particle_pos().
int get_maximal_particle_id | ( | ) |
Get maximal particle id.
Definition at line 599 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().
int get_n_part | ( | ) |
Get number of particles.
Definition at line 607 of file particle_node.cpp.
References build_particle_node(), and particle_node.
Referenced by ScriptInterface::Particles::ParticleList::do_call_method().
const Particle & get_particle_data | ( | int | p_id | ) |
Get particle data.
p_id | the identity of the particle to fetch |
Definition at line 172 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().
std::vector< int > get_particle_ids | ( | ) |
Get all particle ids.
Definition at line 580 of file particle_node.cpp.
References build_particle_node(), Utils::keys(), and particle_node.
Referenced by ScriptInterface::Particles::ParticleList::do_call_method(), ScriptInterface::System::System::get_internal_state(), and ScriptInterface::System::System::set_internal_state().
std::vector< int > get_particle_ids_parallel | ( | ) |
Definition at line 590 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().
int get_particle_node | ( | int | p_id | ) |
Get the MPI rank which owns the a specific particle.
p_id | identity of the particle |
Definition at line 361 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().
int get_particle_node_parallel | ( | int | p_id | ) |
Definition at line 379 of file particle_node.cpp.
References build_particle_node_parallel(), particle_node, rebuild_needed(), and this_node.
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 546 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().
void init_type_map | ( | int | type | ) |
Definition at line 89 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().
void invalidate_fetch_cache | ( | ) |
Invalidate the fetch cache for get_particle_data.
Definition at line 156 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().
void make_new_particle | ( | int | p_id, |
Utils::Vector3d const & | pos | ||
) |
Create a new particle and attach it to a cell.
p_id | The identity of the particle to create. |
pos | The particle position. |
Definition at line 515 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(), System::System::on_particle_change(), particle_node, rebuild_needed(), and this_node.
|
static |
Create a new particle and attach it to a cell.
p_id | The identity of the particle to create. |
pos | The particle position. |
Definition at line 433 of file particle_node.cpp.
References System::System::box_geo, get_cell_structure(), and System::get_system().
Referenced by make_new_particle().
|
static |
Move particle to a new position.
p_id | The identity of the particle to move. |
pos | The new particle position. |
Definition at line 454 of file particle_node.cpp.
References System::get_system().
Referenced by set_particle_pos().
|
static |
Get multiple particles at once.
WARNING Particles are returned in an arbitrary order.
ids | The ids of the particles that should be returned. |
Definition at line 221 of file particle_node.cpp.
References comm_cart, Utils::Mpi::gatherv(), get_particle_node(), mpi_call(), mpi_get_particles_local(), and this_node.
Referenced by prefetch_particle_data().
|
static |
Definition at line 195 of file particle_node.cpp.
References comm_cart, and Utils::Mpi::gatherv().
Referenced by mpi_get_particles().
|
static |
Definition at line 159 of file particle_node.cpp.
References comm_cart, and get_cell_structure().
Referenced by get_particle_data().
|
static |
Definition at line 85 of file particle_node.cpp.
References comm_cart, and max_seen_pid.
Referenced by make_new_particle(), mpi_who_has_head(), mpi_who_has_local(), and remove_particle().
|
static |
Definition at line 312 of file particle_node.cpp.
References comm_cart, get_cell_structure(), max_seen_pid, mpi_synchronize_max_seen_pid_local(), particle_node, some_tag, and this_node.
Referenced by build_particle_node(), and build_particle_node_parallel().
|
static |
Definition at line 289 of file particle_node.cpp.
References comm_cart, get_cell_structure(), mpi_synchronize_max_seen_pid_local(), and some_tag.
Referenced by build_particle_node(), and build_particle_node_parallel().
int number_of_particles_with_type | ( | int | type | ) |
Definition at line 563 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().
void on_particle_type_change | ( | int | p_id, |
int | old_type, | ||
int | new_type | ||
) |
Definition at line 126 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().
bool particle_exists | ( | int | p_id | ) |
Check if particle exists.
p_id | identity of the particle |
Definition at line 574 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_construct().
void prefetch_particle_data | ( | std::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.
ids | Ids of the particles that should be fetched. |
Definition at line 264 of file particle_node.cpp.
References comm_cart, mpi_get_particles(), and anonymous_namespace{particle_node.cpp}::particle_fetch_cache.
Referenced by ScriptInterface::Particles::ParticleSlice::do_call_method().
|
static |
Definition at line 79 of file particle_node.cpp.
References comm_cart, and particle_node.
Referenced by get_maximal_particle_id(), get_particle_ids_parallel(), get_particle_node_parallel(), and make_new_particle().
void remove_all_particles | ( | ) |
Remove all particles.
Definition at line 469 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().
|
static |
Definition at line 114 of file particle_node.cpp.
References particle_type_map.
Referenced by on_particle_type_change(), and remove_particle().
void remove_particle | ( | int | p_id | ) |
Remove particle with a given identity.
Also removes all bonds to the particle.
p_id | identity of the particle to remove |
Definition at line 476 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(), and ScriptInterface::Particles::ParticleHandle::do_call_method().
void set_particle_pos | ( | int | p_id, |
Utils::Vector3d const & | pos | ||
) |
Move particle to a new position.
p_id | The identity of the particle to move. |
pos | The new particle position. |
Definition at line 533 of file particle_node.cpp.
References comm_cart, get_cell_structure(), System::get_system(), maybe_move_particle(), System::System::on_particle_change(), Cells::RESORT_GLOBAL, and this_node.
Referenced by ReactionMethods::ReactionAlgorithm::displacement_mc_move(), and ScriptInterface::Particles::ParticleHandle::ParticleHandle().
|
static |
Keep track of the largest particle id.
This book-keeping variable is necessary to make particle insertion run in constant time. Traversing the particle_node to find the largest particle id scales with O(N) and traversing the local cells in parallel followed by a reduction scales with O(N^2).
Definition at line 77 of file particle_node.cpp.
Referenced by clear_particle_node(), get_maximal_particle_id(), make_new_particle(), mpi_synchronize_max_seen_pid_local(), mpi_who_has_head(), and remove_particle().
|
static |
Mapping particle ids to MPI ranks.
Definition at line 64 of file particle_node.cpp.
Referenced by calculate_max_seen_id(), clear_particle_node(), get_n_part(), get_particle_ids(), get_particle_ids_parallel(), get_particle_node(), get_particle_node_parallel(), make_new_particle(), mpi_who_has_head(), particle_exists(), rebuild_needed(), and remove_particle().
|
static |
Mapping particle types to lists of particle ids.
Definition at line 61 of file particle_node.cpp.
Referenced by add_id_to_type_map(), clear_particle_type_map(), get_random_p_id(), init_type_map(), number_of_particles_with_type(), on_particle_type_change(), and remove_id_from_map().
|
constexpr |
Definition at line 55 of file particle_node.cpp.
Referenced by mpi_who_has_head(), and mpi_who_has_local().
|
static |
Enable particle type tracking in particle_type_map.
Definition at line 58 of file particle_node.cpp.
Referenced by init_type_map(), on_particle_type_change(), and remove_particle().