cells.cpp

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/*
 * Copyright (C) 2010-2022 The ESPResSo project
 * Copyright (C) 2002,2003,2004,2005,2006,2007,2008,2009,2010
 *   Max-Planck-Institute for Polymer Research, Theory Group
 *
 * 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/>.
 */
/** \file
 *
 *  This file contains functions for the cell system.
 *
 *  Implementation of cells.hpp.
 */
 
#include "cells.hpp"
 
#include "cell_system/Cell.hpp"
#include "cell_system/CellStructure.hpp"
#include "cell_system/CellStructureType.hpp"
#include "cell_system/HybridDecomposition.hpp"
 
#include "Particle.hpp"
#include "communication.hpp"
#include "errorhandling.hpp"
#include "particle_node.hpp"
#include "system/System.hpp"
 
#include <utils/Vector.hpp>
#include <utils/math/sqr.hpp>
 
#include <boost/serialization/set.hpp>
 
#include <algorithm>
#include <functional>
#include <optional>
#include <stdexcept>
#include <utility>
#include <vector>
 
/**
 * @brief Get pairs of particles that are closer than a distance and fulfill a
 * filter criterion.
 *
 * It uses link_cell to get pairs out of the cellsystem
 * by a simple distance criterion and applies the filter on both particles.
 *
 * Pairs are sorted so that first.id < second.id
 */
template <class Filter>
static auto get_pairs_filtered(System::System const &system,
                               double const distance, Filter filter) {
  std::vector<std::pair<int, int>> ret;
  auto const cutoff2 = Utils::sqr(distance);
  auto const pair_kernel = [cutoff2, &filter, &ret](Particle const &p1,
                                                    Particle const &p2,
                                                    Distance const &d) {
    if (d.dist2 < cutoff2 and filter(p1) and filter(p2))
      ret.emplace_back(p1.id(), p2.id());
  };
 
  system.cell_structure->non_bonded_loop(pair_kernel);
 
  /* Sort pairs */
  for (auto &pair : ret) {
    if (pair.first > pair.second)
      std::swap(pair.first, pair.second);
  }
 
  return ret;
}
static auto get_pairs_filtered(System::System const &system, {…}
 
namespace detail {
static auto get_max_neighbor_search_range(System::System const &system) {
  auto const &cell_structure = *system.cell_structure;
  return std::ranges::min(cell_structure.max_range());
}
static void search_distance_sanity_check_max_range(System::System const &system,
                                                   double const distance) {
  /* get_pairs_filtered() finds pairs via the non_bonded_loop. The maximum
   * finding range is therefore limited by the decomposition that is used.
   */
  auto const max_range = get_max_neighbor_search_range(system);
  if (distance > max_range) {
    throw std::domain_error("pair search distance " + std::to_string(distance) +
                            " bigger than the decomposition range " +
                            std::to_string(max_range));
  }
}
static void
search_distance_sanity_check_cell_structure(System::System const &system,
                                            double const) {
  auto const &cell_structure = *system.cell_structure;
  if (cell_structure.decomposition_type() == CellStructureType::HYBRID) {
    throw std::runtime_error("Cannot search for neighbors in the hybrid "
                             "decomposition cell system");
  }
}
static void search_neighbors_sanity_checks(System::System const &system,
                                           double const distance) {
  search_distance_sanity_check_max_range(system, distance);
  search_distance_sanity_check_cell_structure(system, distance);
}
} // namespace detail
 
std::optional<std::vector<int>>
get_short_range_neighbors(System::System const &system, int const pid,
                          double const distance) {
  detail::search_neighbors_sanity_checks(system, distance);
  std::vector<int> ret;
  auto const cutoff2 = Utils::sqr(distance);
  auto const kernel = [cutoff2, &ret](Particle const &, Particle const &p2,
                                      Utils::Vector3d const &vec) {
    if (vec.norm2() < cutoff2) {
      ret.emplace_back(p2.id());
    }
  };
  auto &cell_structure = *system.cell_structure;
  auto const p = cell_structure.get_local_particle(pid);
  if (p and not p->is_ghost()) {
    cell_structure.run_on_particle_short_range_neighbors(*p, kernel);
    return {ret};
  }
  return {};
}
get_short_range_neighbors(System::System const &system, int const pid, {…}
 
/**
 * @brief Get pointers to all interacting neighbors of a central particle.
 */
static auto get_interacting_neighbors(System::System const &system,
                                      Particle const &p) {
  auto &cell_structure = *system.cell_structure;
  auto const distance = std::ranges::min(cell_structure.max_range());
  detail::search_neighbors_sanity_checks(system, distance);
  std::vector<Particle const *> ret;
  auto const cutoff2 = Utils::sqr(distance);
  auto const kernel = [cutoff2, &ret](Particle const &, Particle const &p2,
                                      Utils::Vector3d const &vec) {
    if (vec.norm2() < cutoff2) {
      ret.emplace_back(&p2);
    }
  };
  cell_structure.run_on_particle_short_range_neighbors(p, kernel);
  return ret;
}
static auto get_interacting_neighbors(System::System const &system, {…}
 
std::vector<std::pair<int, int>> get_pairs(System::System const &system,
                                           double const distance) {
  detail::search_neighbors_sanity_checks(system, distance);
  return get_pairs_filtered(system, distance,
                            [](Particle const &) { return true; });
}
std::vector<std::pair<int, int>> get_pairs(System::System const &system, {…}
 
std::vector<std::pair<int, int>>
get_pairs_of_types(System::System const &system, double const distance,
                   std::vector<int> const &types) {
  detail::search_neighbors_sanity_checks(system, distance);
  return get_pairs_filtered(system, distance, [types](Particle const &p) {
    return std::ranges::any_of(
        types, [target = p.type()](int const type) { return type == target; });
  });
}
get_pairs_of_types(System::System const &system, double const distance, {…}
 
std::vector<PairInfo> non_bonded_loop_trace(System::System const &system,
                                            int const rank) {
  std::vector<PairInfo> pairs;
  auto const pair_kernel = [&pairs, rank](Particle const &p1,
                                          Particle const &p2,
                                          Distance const &d) {
    pairs.emplace_back(p1.id(), p2.id(), p1.pos(), p2.pos(), d.vec21, rank);
  };
  system.cell_structure->non_bonded_loop(pair_kernel);
  return pairs;
}
std::vector<PairInfo> non_bonded_loop_trace(System::System const &system, {…}
 
std::vector<NeighborPIDs> get_neighbor_pids(System::System const &system) {
  std::vector<NeighborPIDs> ret;
  auto kernel = [&ret](Particle const &p,
                       std::vector<Particle const *> const &neighbors) {
    std::vector<int> neighbor_pids;
    neighbor_pids.reserve(neighbors.size());
    for (auto const &neighbor : neighbors) {
      neighbor_pids.emplace_back(neighbor->id());
    }
    ret.emplace_back(p.id(), neighbor_pids);
  };
  auto &cell_structure = *system.cell_structure;
  for (auto const &p : cell_structure.local_particles()) {
    kernel(p, get_interacting_neighbors(system, p));
  }
  return ret;
}
std::vector<NeighborPIDs> get_neighbor_pids(System::System const &system) {…}