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core: Extract exclusion range neighbor search
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,154 @@ | ||
| /* | ||
| * Copyright (C) 2022-2023 The ESPResSo project | ||
| * | ||
| * This file is part of ESPResSo. | ||
| * | ||
| * ESPResSo is free software: you can redistribute it and/or modify | ||
| * it under the terms of the GNU General Public License as published by | ||
| * the Free Software Foundation, either version 3 of the License, or | ||
| * (at your option) any later version. | ||
| * | ||
| * ESPResSo is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU General Public License | ||
| * along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| */ | ||
|
|
||
| #include "reaction_methods/ExclusionRadius.hpp" | ||
|
|
||
| #include "cells.hpp" | ||
| #include "event.hpp" | ||
| #include "grid.hpp" | ||
| #include "particle_node.hpp" | ||
|
|
||
| #include <boost/mpi/collectives/all_reduce.hpp> | ||
| #include <boost/mpi/collectives/broadcast.hpp> | ||
| #include <boost/mpi/communicator.hpp> | ||
|
|
||
| #include <algorithm> | ||
| #include <cassert> | ||
| #include <functional> | ||
| #include <stdexcept> | ||
| #include <string> | ||
| #include <unordered_map> | ||
| #include <vector> | ||
|
|
||
| static auto get_real_particle(boost::mpi::communicator const &comm, int p_id) { | ||
| assert(p_id >= 0); | ||
| auto ptr = ::cell_structure.get_local_particle(p_id); | ||
| if (ptr != nullptr and ptr->is_ghost()) { | ||
| ptr = nullptr; | ||
| } | ||
| assert(boost::mpi::all_reduce(comm, static_cast<int>(ptr != nullptr), | ||
| std::plus<>()) == 1); | ||
| return ptr; | ||
| } | ||
|
|
||
| void ExclusionRadius::set_exclusion_range(double range) { | ||
| if (range < 0.) { | ||
| throw std::domain_error("Invalid value for exclusion range"); | ||
| } | ||
| exclusion_range = range; | ||
| recalc_derived_parameters(); | ||
| } | ||
|
|
||
| void ExclusionRadius::set_exclusion_radius_per_type(map_type const &map) { | ||
| for (auto const &[type, exclusion_radius] : map) { | ||
| if (exclusion_radius < 0.) { | ||
| throw std::domain_error("Invalid exclusion radius for type " + | ||
| std::to_string(type) + ": radius " + | ||
| std::to_string(exclusion_radius)); | ||
| } | ||
| } | ||
| exclusion_radius_per_type = map; | ||
| recalc_derived_parameters(); | ||
| } | ||
|
|
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| void ExclusionRadius::recalc_derived_parameters() { | ||
| m_max_exclusion_range = exclusion_range; | ||
| for (auto const &item : exclusion_radius_per_type) { | ||
| auto const radius = item.second; | ||
| m_max_exclusion_range = std::max(m_max_exclusion_range, 2. * radius); | ||
| } | ||
| } | ||
|
|
||
| /** | ||
| * Check if an inserted particle is too close to neighboring particles. | ||
| */ | ||
| bool ExclusionRadius::check_exclusion_range(int p_id, int p_type) { | ||
|
|
||
| /* Check the exclusion radius of the inserted particle */ | ||
| if (exclusion_radius_per_type.count(p_type) != 0) { | ||
| if (exclusion_radius_per_type[p_type] == 0.) { | ||
| return false; | ||
| } | ||
| } | ||
|
|
||
| auto p1_ptr = get_real_particle(m_comm, p_id); | ||
|
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| std::vector<int> particle_ids; | ||
| if (neighbor_search_order_n) { | ||
| auto all_ids = get_particle_ids_parallel(); | ||
| /* remove the inserted particle id */ | ||
| all_ids.erase(std::remove(all_ids.begin(), all_ids.end(), p_id), | ||
| all_ids.end()); | ||
| particle_ids = all_ids; | ||
| } else { | ||
| on_observable_calc(); | ||
| auto const local_ids = | ||
| get_short_range_neighbors(p_id, m_max_exclusion_range); | ||
| assert(p1_ptr == nullptr or !!local_ids); | ||
| if (local_ids) { | ||
| particle_ids = std::move(*local_ids); | ||
| } | ||
| } | ||
|
|
||
| auto within_exclusion_range = false; | ||
| if (p1_ptr != nullptr) { | ||
| auto &p1 = *p1_ptr; | ||
|
|
||
| /* Check if the inserted particle within any exclusion radius */ | ||
| for (auto const p2_id : particle_ids) { | ||
| if (auto const p2_ptr = ::cell_structure.get_local_particle(p2_id)) { | ||
| auto const &p2 = *p2_ptr; | ||
| double excluded_distance; | ||
| if (exclusion_radius_per_type.count(p_type) == 0 or | ||
| exclusion_radius_per_type.count(p2.type()) == 0) { | ||
| excluded_distance = exclusion_range; | ||
| } else if (exclusion_radius_per_type[p2.type()] == 0.) { | ||
| continue; | ||
| } else { | ||
| excluded_distance = exclusion_radius_per_type[p_type] + | ||
| exclusion_radius_per_type[p2.type()]; | ||
| } | ||
|
|
||
| auto const d_min = ::box_geo.get_mi_vector(p2.pos(), p1.pos()).norm(); | ||
|
|
||
| if (d_min < excluded_distance) { | ||
| within_exclusion_range = true; | ||
| break; | ||
| } | ||
| } | ||
| } | ||
| if (m_comm.rank() != 0) { | ||
| m_comm.send(0, 1, within_exclusion_range); | ||
| } | ||
| } else if (m_comm.rank() == 0) { | ||
| m_comm.recv(boost::mpi::any_source, 1, within_exclusion_range); | ||
| } | ||
| boost::mpi::broadcast(m_comm, within_exclusion_range, 0); | ||
| return within_exclusion_range; | ||
| } | ||
|
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| bool ExclusionRadius::check_exclusion_range(int pid) { | ||
| int type_local = 0; | ||
| if (auto p = get_real_particle(m_comm, pid)) { | ||
| type_local = p->type(); | ||
| } | ||
| auto const type = | ||
| boost::mpi::all_reduce(m_comm, type_local, std::plus<int>()); | ||
| return check_exclusion_range(pid, type); | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,43 @@ | ||
| /* | ||
| * Copyright (C) 2022-2023 The ESPResSo project | ||
| * | ||
| * This file is part of ESPResSo. | ||
| * | ||
| * ESPResSo is free software: you can redistribute it and/or modify | ||
| * it under the terms of the GNU General Public License as published by | ||
| * the Free Software Foundation, either version 3 of the License, or | ||
| * (at your option) any later version. | ||
| * | ||
| * ESPResSo is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU General Public License | ||
| * along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| */ | ||
|
|
||
| #pragma once | ||
|
|
||
| #include <boost/mpi/communicator.hpp> | ||
|
|
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| #include <unordered_map> | ||
|
|
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| class ExclusionRadius { | ||
| boost::mpi::communicator const &m_comm; | ||
| double m_max_exclusion_range = 0.; | ||
| void recalc_derived_parameters(); | ||
|
|
||
| public: | ||
| using map_type = std::unordered_map<int, double>; | ||
| explicit ExclusionRadius(boost::mpi::communicator const &comm) | ||
| : m_comm{comm} {} | ||
| void set_exclusion_range(double range); | ||
| void set_exclusion_radius_per_type(map_type const &map); | ||
| bool check_exclusion_range(int p_id, int p_type); | ||
| bool check_exclusion_range(int pid); | ||
|
|
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| bool neighbor_search_order_n = true; | ||
| double exclusion_range = 0.; | ||
| map_type exclusion_radius_per_type{}; | ||
| }; |
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