CellStructure.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/>.
 */
 
#include "cell_system/CellStructure.hpp"
 
#include "cell_system/AtomDecomposition.hpp"
#include "cell_system/HybridDecomposition.hpp"
#include "cell_system/ParticleDecomposition.hpp"
#include "cell_system/RegularDecomposition.hpp"
 
#include "BoxGeometry.hpp"
#include "LocalBox.hpp"
#include "Particle.hpp"
#include "cell_system/CellStructureType.hpp"
#include "communication.hpp"
#include "lees_edwards/lees_edwards.hpp"
#include "system/System.hpp"
 
#include <utils/contains.hpp>
 
#include <boost/mpi/collectives/all_reduce.hpp>
#include <boost/variant.hpp>
 
#include <algorithm>
#include <cassert>
#include <cstddef>
#include <iterator>
#include <memory>
#include <optional>
#include <set>
#include <stdexcept>
#include <string>
#include <utility>
#include <vector>
 
CellStructure::CellStructure(BoxGeometry const &box)
    : m_decomposition{std::make_unique<AtomDecomposition>(box)} {}
CellStructure::CellStructure(BoxGeometry const &box) {…}
 
void CellStructure::check_particle_index() const {
  auto const max_id = get_max_local_particle_id();
 
  for (auto const &p : local_particles()) {
    auto const id = p.id();
 
    if (id < 0 || id > max_id) {
      throw std::runtime_error("Particle id out of bounds.");
    }
 
    if (get_local_particle(id) != &p) {
      throw std::runtime_error("Invalid local particle index entry.");
    }
  }
 
  /* checks: local particle id */
  std::size_t local_part_cnt = 0u;
  for (int n = 0; n < get_max_local_particle_id() + 1; n++) {
    if (get_local_particle(n) != nullptr) {
      local_part_cnt++;
      if (get_local_particle(n)->id() != n) {
        throw std::runtime_error("local_particles part has corrupted id.");
      }
    }
  }
 
  if (local_part_cnt != local_particles().size()) {
    throw std::runtime_error(
        std::to_string(local_particles().size()) + " parts in cells but " +
        std::to_string(local_part_cnt) + " parts in local_particles");
  }
}
void CellStructure::check_particle_index() const  {…}
 
void CellStructure::check_particle_sorting() const {
  for (auto cell : decomposition().local_cells()) {
    for (auto const &p : cell->particles()) {
      if (particle_to_cell(p) != cell) {
        throw std::runtime_error("misplaced particle with id " +
                                 std::to_string(p.id()));
      }
    }
  }
}
void CellStructure::check_particle_sorting() const  {…}
 
void CellStructure::remove_particle(int id) {
  auto remove_all_bonds_to = [id](BondList &bl) {
    for (auto it = bl.begin(); it != bl.end();) {
      if (Utils::contains(it->partner_ids(), id)) {
        it = bl.erase(it);
      } else {
        std::advance(it, 1);
      }
    }
  };
 
  for (auto c : decomposition().local_cells()) {
    auto &parts = c->particles();
 
    for (auto it = parts.begin(); it != parts.end();) {
      if (it->id() == id) {
        it = parts.erase(it);
        update_particle_index(id, nullptr);
        update_particle_index(parts);
      } else {
        remove_all_bonds_to(it->bonds());
        it++;
      }
    }
  }
}
void CellStructure::remove_particle(int id) {…}
 
Particle *CellStructure::add_local_particle(Particle &&p) {
  auto const sort_cell = particle_to_cell(p);
  if (sort_cell) {
 
    return std::addressof(
        append_indexed_particle(sort_cell->particles(), std::move(p)));
  }
 
  return {};
}
Particle *CellStructure::add_local_particle(Particle &&p) {…}
 
Particle *CellStructure::add_particle(Particle &&p) {
  auto const sort_cell = particle_to_cell(p);
  /* There is always at least one cell, so if the particle
   * does not belong to a cell on this node we can put it there. */
  auto cell = sort_cell ? sort_cell : decomposition().local_cells()[0];
 
  /* If the particle isn't local a global resort may be
   * needed, otherwise a local resort if sufficient. */
  set_resort_particles(sort_cell ? Cells::RESORT_LOCAL : Cells::RESORT_GLOBAL);
 
  return std::addressof(
      append_indexed_particle(cell->particles(), std::move(p)));
}
Particle *CellStructure::add_particle(Particle &&p) {…}
 
int CellStructure::get_max_local_particle_id() const {
  auto it = std::find_if(m_particle_index.rbegin(), m_particle_index.rend(),
                         [](const Particle *p) { return p != nullptr; });
 
  return (it != m_particle_index.rend()) ? (*it)->id() : -1;
}
int CellStructure::get_max_local_particle_id() const  {…}
 
void CellStructure::remove_all_particles() {
  for (auto c : decomposition().local_cells()) {
    c->particles().clear();
  }
 
  m_particle_index.clear();
}
void CellStructure::remove_all_particles() {…}
 
/* Map the data parts flags from cells to those used internally
 * by the ghost communication */
unsigned map_data_parts(unsigned data_parts) {
  using namespace Cells;
 
  /* clang-format off */
  return GHOSTTRANS_NONE
         | ((data_parts & DATA_PART_PROPERTIES) ? GHOSTTRANS_PROPRTS : 0u)
         | ((data_parts & DATA_PART_POSITION) ? GHOSTTRANS_POSITION : 0u)
         | ((data_parts & DATA_PART_MOMENTUM) ? GHOSTTRANS_MOMENTUM : 0u)
         | ((data_parts & DATA_PART_FORCE) ? GHOSTTRANS_FORCE : 0u)
#ifdef BOND_CONSTRAINT
         | ((data_parts & DATA_PART_RATTLE) ? GHOSTTRANS_RATTLE : 0u)
#endif
         | ((data_parts & DATA_PART_BONDS) ? GHOSTTRANS_BONDS : 0u);
  /* clang-format on */
}
unsigned map_data_parts(unsigned data_parts) {…}
 
void CellStructure::ghosts_count() {
  ghost_communicator(decomposition().exchange_ghosts_comm(),
                     *get_system().box_geo, GHOSTTRANS_PARTNUM);
}
void CellStructure::ghosts_count() {…}
void CellStructure::ghosts_update(unsigned data_parts) {
  ghost_communicator(decomposition().exchange_ghosts_comm(),
                     *get_system().box_geo, map_data_parts(data_parts));
}
void CellStructure::ghosts_update(unsigned data_parts) {…}
void CellStructure::ghosts_reduce_forces() {
  ghost_communicator(decomposition().collect_ghost_force_comm(),
                     *get_system().box_geo, GHOSTTRANS_FORCE);
}
void CellStructure::ghosts_reduce_forces() {…}
#ifdef BOND_CONSTRAINT
void CellStructure::ghosts_reduce_rattle_correction() {
  ghost_communicator(decomposition().collect_ghost_force_comm(),
                     *get_system().box_geo, GHOSTTRANS_RATTLE);
}
void CellStructure::ghosts_reduce_rattle_correction() {…}
#endif
 
namespace {
/**
 * @brief Apply a @ref ParticleChange to a particle index.
 */
struct UpdateParticleIndexVisitor {
  CellStructure *cs;
 
  void operator()(RemovedParticle rp) const {
    cs->update_particle_index(rp.id, nullptr);
  }
  void operator()(RemovedParticle rp) const  {…}
  void operator()(ModifiedList mp) const { cs->update_particle_index(mp.pl); }
};
struct UpdateParticleIndexVisitor {…};
} // namespace
namespace { {…}
 
void CellStructure::resort_particles(bool global_flag) {
  invalidate_ghosts();
 
  static std::vector<ParticleChange> diff;
  diff.clear();
 
  m_decomposition->resort(global_flag, diff);
 
  for (auto d : diff) {
    boost::apply_visitor(UpdateParticleIndexVisitor{this}, d);
  }
 
  auto const &lebc = get_system().box_geo->lees_edwards_bc();
  m_rebuild_verlet_list = true;
  m_le_pos_offset_at_last_resort = lebc.pos_offset;
 
#ifdef ADDITIONAL_CHECKS
  check_particle_index();
  check_particle_sorting();
#endif
}
void CellStructure::resort_particles(bool global_flag) {…}
 
void CellStructure::set_atom_decomposition() {
  auto &system = get_system();
  auto &local_geo = *system.local_geo;
  auto const &box_geo = *system.box_geo;
  set_particle_decomposition(
      std::make_unique<AtomDecomposition>(::comm_cart, box_geo));
  m_type = CellStructureType::NSQUARE;
  local_geo.set_cell_structure_type(m_type);
  system.on_cell_structure_change();
}
void CellStructure::set_atom_decomposition() {…}
 
void CellStructure::set_regular_decomposition(
    double range, std::optional<std::pair<int, int>> fully_connected_boundary) {
  auto &system = get_system();
  auto &local_geo = *system.local_geo;
  auto const &box_geo = *system.box_geo;
  set_particle_decomposition(std::make_unique<RegularDecomposition>(
      ::comm_cart, range, box_geo, local_geo, fully_connected_boundary));
  m_type = CellStructureType::REGULAR;
  local_geo.set_cell_structure_type(m_type);
  system.on_cell_structure_change();
}
void CellStructure::set_regular_decomposition( {…}
 
void CellStructure::set_hybrid_decomposition(double cutoff_regular,
                                             std::set<int> n_square_types) {
  auto &system = get_system();
  auto &local_geo = *system.local_geo;
  auto const &box_geo = *system.box_geo;
  set_particle_decomposition(std::make_unique<HybridDecomposition>(
      ::comm_cart, cutoff_regular, m_verlet_skin,
      [&system]() { return system.get_global_ghost_flags(); }, box_geo,
      local_geo, n_square_types));
  m_type = CellStructureType::HYBRID;
  local_geo.set_cell_structure_type(m_type);
  system.on_cell_structure_change();
}
void CellStructure::set_hybrid_decomposition(double cutoff_regular, {…}
 
void CellStructure::set_verlet_skin(double value) {
  assert(value >= 0.);
  m_verlet_skin = value;
  m_verlet_skin_set = true;
  get_system().on_verlet_skin_change();
}
void CellStructure::set_verlet_skin(double value) {…}
 
void CellStructure::set_verlet_skin_heuristic() {
  assert(not is_verlet_skin_set());
  auto const max_cut = get_system().maximal_cutoff();
  if (max_cut <= 0.) {
    throw std::runtime_error(
        "cannot automatically determine skin, please set it manually");
  }
  /* maximal skin that can be used without resorting is the maximal
   * range of the cell system minus what is needed for interactions. */
  auto const max_range = std::ranges::min(max_cutoff());
  auto const new_skin = std::min(0.4 * max_cut, max_range - max_cut);
  set_verlet_skin(new_skin);
}
void CellStructure::set_verlet_skin_heuristic() {…}
 
void CellStructure::update_ghosts_and_resort_particle(unsigned data_parts) {
  /* data parts that are only updated on resort */
  auto constexpr resort_only_parts =
      Cells::DATA_PART_PROPERTIES | Cells::DATA_PART_BONDS;
 
  auto const global_resort = boost::mpi::all_reduce(
      ::comm_cart, m_resort_particles, std::bit_or<unsigned>());
 
  if (global_resort != Cells::RESORT_NONE) {
    auto const do_global_resort = (global_resort & Cells::RESORT_GLOBAL) != 0;
 
    /* Resort cell system */
    resort_particles(do_global_resort);
    ghosts_count();
    ghosts_update(data_parts);
 
    /* Add the ghost particles to the index if we don't already
     * have them. */
    for (auto &p : ghost_particles()) {
      if (get_local_particle(p.id()) == nullptr) {
        update_particle_index(p.id(), &p);
      }
    }
 
    /* Particles are now sorted */
    clear_resort_particles();
  } else {
    /* Communication step: ghost information */
    ghosts_update(data_parts & ~resort_only_parts);
  }
}
void CellStructure::update_ghosts_and_resort_particle(unsigned data_parts) {…}