Refactor System class (espressomd#4816)

Description of changes:
- encapsulate several global variables inside the `System` class
   - new members: cell_system, integrator, electrostatics, magnetostatics, analysis, comfixed, galilei, bond_breakage
   - required for espressomd#4613
   - partial fix for espressomd#2628
- make energy/pressure/force calculation functions members of the `System` class
- fully encapsulate event hooks in the `System` class
- simplify checkpointing of the `System` class
- remove `EspressoSystemStandAlone` class
- API changes:
   - `espressomd.galilei.GalileiTransform` is now a member of the `System` class, accessible via `system.galilei`

doc/doxygen/Doxyfile.in

@@ -448,7 +448,7 @@ EXTRACT_PRIVATE        = NO
 # methods of a class will be included in the documentation.
 # The default value is: NO.
 
-EXTRACT_PRIV_VIRTUAL   = NO
+EXTRACT_PRIV_VIRTUAL   = YES
 
 # If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
 # scope will be included in the documentation.
@@ -468,7 +468,7 @@ EXTRACT_STATIC         = YES
 # for Java sources.
 # The default value is: YES.
 
-EXTRACT_LOCAL_CLASSES  = NO
+EXTRACT_LOCAL_CLASSES  = YES
 
 # This flag is only useful for Objective-C code. If set to YES, local methods,
 # which are defined in the implementation section but not in the interface are

src/core/CMakeLists.txt

@@ -30,20 +30,16 @@ add_library(
   dpd.cpp
   energy.cpp
   errorhandling.cpp
-  forcecap.cpp
   forces.cpp
   ghosts.cpp
+  global_ghost_flags.cpp
   immersed_boundaries.cpp
-  interactions.cpp
-  event.cpp
   integrate.cpp
   npt.cpp
-  partCfg_global.cpp
   particle_node.cpp
   polymer.cpp
   pressure.cpp
   rattle.cpp
-  rotate_system.cpp
   rotation.cpp
   Observable_stat.cpp
   thermostat.cpp
@@ -53,7 +49,6 @@ add_library(
   system/GpuParticleData.cpp
   system/System.cpp
   PartCfg.cpp
-  EspressoSystemStandAlone.cpp
   TabulatedPotential.cpp)
 add_library(espresso::core ALIAS espresso_core)
 set_target_properties(espresso_core PROPERTIES CXX_CLANG_TIDY

src/core/LocalBox.hpp

@@ -81,7 +81,6 @@ class LocalBox {
       boundaries[2u * dir + 1u] = -(node_index[dir] + 1 == node_grid[dir]);
     }
 
-    return {my_left, local_length, boundaries,
-            CellStructureType::CELL_STRUCTURE_REGULAR};
+    return {my_left, local_length, boundaries, CellStructureType::REGULAR};
   }
 };

src/core/Observable_stat.cpp

@@ -23,9 +23,7 @@
 
 #include "config/config.hpp"
 
-#include "bonded_interactions/bonded_interaction_data.hpp"
 #include "communication.hpp"
-#include "nonbonded_interactions/nonbonded_interaction_data.hpp"
 
 #include <utils/Span.hpp>
 #include <utils/index.hpp>
@@ -37,13 +35,9 @@
 #include <functional>
 #include <vector>
 
-static auto max_non_bonded_pairs() {
-  auto const n = static_cast<std::size_t>(max_seen_particle_type);
-  return (n * (n + 1)) / 2;
-}
-
-Observable_stat::Observable_stat(std::size_t chunk_size)
-    : m_chunk_size(chunk_size) {
+Observable_stat::Observable_stat(std::size_t chunk_size, std::size_t n_bonded,
+                                 int max_type)
+    : m_data{}, m_chunk_size{chunk_size} {
   // number of chunks for different interaction types
   constexpr std::size_t n_coulomb = 2;
   constexpr std::size_t n_dipolar = 2;
@@ -52,9 +46,9 @@ Observable_stat::Observable_stat(std::size_t chunk_size)
 #else
   constexpr std::size_t n_vs = 0;
 #endif
-  auto const n_bonded =
-      static_cast<std::size_t>(bonded_ia_params.get_next_key());
-  auto const n_non_bonded = max_non_bonded_pairs();
+  auto const n_non_bonded =
+      static_cast<std::size_t>(Utils::lower_triangular(max_type, max_type)) +
+      1ul;
   constexpr std::size_t n_ext_fields = 1; // reduction over all fields
   constexpr std::size_t n_kinetic = 1; // linear+angular kinetic contributions
 
@@ -80,8 +74,8 @@ Observable_stat::Observable_stat(std::size_t chunk_size)
 Utils::Span<double>
 Observable_stat::get_non_bonded_contribution(Utils::Span<double> base_pointer,
                                              int type1, int type2) const {
-  auto const offset = static_cast<std::size_t>(Utils::upper_triangular(
-      std::min(type1, type2), std::max(type1, type2), max_seen_particle_type));
+  auto const offset = static_cast<std::size_t>(
+      Utils::lower_triangular(std::max(type1, type2), std::min(type1, type2)));
   return {base_pointer.begin() + offset * m_chunk_size, m_chunk_size};
 }
 

src/core/Observable_stat.hpp

@@ -16,8 +16,8 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-#ifndef ESPRESSO_OBSERVABLE_STAT_HPP
-#define ESPRESSO_OBSERVABLE_STAT_HPP
+
+#pragma once
 
 #include <boost/range/algorithm/transform.hpp>
 #include <boost/range/numeric.hpp>
@@ -43,7 +43,7 @@ class Observable_stat {
                               int type2) const;
 
 public:
-  explicit Observable_stat(std::size_t chunk_size);
+  Observable_stat(std::size_t chunk_size, std::size_t n_bonded, int max_type);
 
   auto get_chunk_size() const { return m_chunk_size; }
 
@@ -121,5 +121,3 @@ class Observable_stat {
   /** MPI reduction. */
   void mpi_reduce();
 };
-
-#endif // ESPRESSO_OBSERVABLE_STAT_HPP

src/core/PartCfg.cpp

@@ -29,11 +29,6 @@
 #include <cstddef>
 
 void PartCfg::update() {
-  if (m_valid)
-    return;
-
-  auto const &box_geo = *System::get_system().box_geo;
-
   m_parts.clear();
 
   auto const ids = get_particle_ids();
@@ -51,12 +46,10 @@ void PartCfg::update() {
       m_parts.push_back(get_particle_data(id));
 
       auto &p = m_parts.back();
-      p.pos() += box_geo.image_shift(p.image_box());
+      p.pos() += m_box_geo.image_shift(p.image_box());
       p.image_box() = {};
     }
 
     offset += this_size;
   }
-
-  m_valid = true;
 }