Particle properties script interface (#4629)

Fixes #4616 

Description of changes:
- replace most of the particle property setters MPI callbacks by fully MPI-parallel code
   - a few MPI callbacks remain for properties that are relevant to reaction methods (position, velocity, type, charge), but these will be removed in the near future by #4617
   - some code duplication was introduced in `particle_node.cpp` and will be removed in the future, when the particle management will become more parallel (i.e. no more particle cache, id tracking and type tracking)
- remove 300 lines of C++ code
- deprecate `system.auto_exclusions(n)` in favor of `system.part.auto_exclusions(distance=n)`

src/core/Particle.hpp

@@ -467,8 +467,8 @@ struct Particle { // NOLINT(bugprone-exception-escape)
   constexpr auto &mass() const { return p.mass; }
 #endif
 #ifdef ROTATION
+  auto const &rotation() const { return p.rotation; }
   auto &rotation() { return p.rotation; }
-  auto rotation() const { return p.rotation; }
   bool can_rotate() const { return static_cast<bool>(p.rotation); }
   bool can_rotate_around(int const axis) const {
     detail::check_axis_idx_valid(axis);
@@ -498,8 +498,8 @@ struct Particle { // NOLINT(bugprone-exception-escape)
 #endif // EXTERNAL_FORCES
   auto calc_director() const { return r.calc_director(); }
 #else  // ROTATION
-  bool can_rotate() const { return false; }
-  bool can_rotate_around(int const axis) const { return false; }
+  auto can_rotate() const { return false; }
+  auto can_rotate_around(int const axis) const { return false; }
 #endif // ROTATION
 #ifdef DIPOLES
   auto const &dipm() const { return p.dipm; }
@@ -523,8 +523,9 @@ struct Particle { // NOLINT(bugprone-exception-escape)
   auto &mu_E() { return p.mu_E; }
 #endif
 #ifdef VIRTUAL_SITES
-  bool &virtual_flag() { return p.is_virtual; }
-  bool is_virtual() const { return p.is_virtual; }
+  auto &virtual_flag() { return p.is_virtual; }
+  auto const &virtual_flag() const { return p.is_virtual; }
+  auto is_virtual() const { return p.is_virtual; }
   void set_virtual(bool const virt_flag) { p.is_virtual = virt_flag; }
 #ifdef VIRTUAL_SITES_RELATIVE
   auto const &vs_relative() const { return p.vs_relative; }
@@ -542,6 +543,7 @@ struct Particle { // NOLINT(bugprone-exception-escape)
 #endif // ROTATION
 #endif // THERMOSTAT_PER_PARTICLE
 #ifdef EXTERNAL_FORCES
+  auto const &fixed() const { return p.ext_flag; }
   auto &fixed() { return p.ext_flag; }
   bool has_fixed_coordinates() const { return static_cast<bool>(p.ext_flag); }
   bool is_fixed_along(int const axis) const {
@@ -578,9 +580,6 @@ struct Particle { // NOLINT(bugprone-exception-escape)
 #ifdef EXCLUSIONS
   Utils::compact_vector<int> &exclusions() { return el; }
   Utils::compact_vector<int> const &exclusions() const { return el; }
-  std::vector<int> const exclusions_as_vector() const {
-    return {el.begin(), el.end()};
-  }
   bool has_exclusion(int pid) const {
     return std::find(el.begin(), el.end(), pid) != el.end();
   }

src/core/bond_breakage/bond_breakage.cpp

@@ -22,6 +22,7 @@
 #include "cells.hpp"
 #include "communication.hpp"
 #include "errorhandling.hpp"
+#include "event.hpp"
 #include "particle_data.hpp"
 
 #include <utils/mpi/gather_buffer.hpp>
@@ -153,20 +154,45 @@ ActionSet actions_for_breakage(QueueEntry const &e) {
   return {};
 }
 
+/**
+ * @brief Delete specific bond.
+ */
+static void remove_bond(Particle &p, BondView const &view) {
+  auto &bond_list = p.bonds();
+  auto it = std::find(bond_list.begin(), bond_list.end(), view);
+  if (it != bond_list.end()) {
+    bond_list.erase(it);
+  }
+}
+
+/**
+ * @brief Delete pair bonds to a specific partner
+ */
+static void remove_pair_bonds_to(Particle &p, int other_pid) {
+  std::vector<std::pair<int, int>> to_delete;
+  for (auto b : p.bonds()) {
+    if (b.partner_ids().size() == 1 and b.partner_ids()[0] == other_pid)
+      to_delete.emplace_back(std::pair<int, int>{b.bond_id(), other_pid});
+  }
+  for (auto const &b : to_delete) {
+    remove_bond(p, BondView(b.first, {&b.second, 1}));
+  }
+}
+
 // Handler for the different delete events
 class execute : public boost::static_visitor<> {
 public:
   void operator()(DeleteBond const &d) const {
-    auto p = cell_structure.get_local_particle(d.particle_id);
-    if (!p)
-      return;
-    local_remove_bond(*p, {d.bond_type, d.bond_partner_id});
+    if (auto p = ::cell_structure.get_local_particle(d.particle_id)) {
+      remove_bond(*p, BondView(d.bond_type, {&d.bond_partner_id, 1}));
+    }
+    on_particle_change();
   }
   void operator()(DeleteAllBonds const &d) const {
-    auto p = cell_structure.get_local_particle(d.particle_id_1);
-    if (!p)
-      return;
-    local_remove_pair_bonds_to(*p, d.particle_id_2);
+    if (auto p = ::cell_structure.get_local_particle(d.particle_id_1)) {
+      remove_pair_bonds_to(*p, d.particle_id_2);
+    }
+    on_particle_change();
   }
 };
 

src/core/collision.cpp

@@ -344,9 +344,7 @@ void place_vs_and_relate_to_particle(const int current_vs_pid,
   new_part.id() = current_vs_pid;
   new_part.pos() = pos;
   auto p_vs = cell_structure.add_particle(std::move(new_part));
-
-  local_vs_relate_to(*p_vs, get_part(relate_to));
-
+  vs_relate_to(*p_vs, get_part(relate_to));
   p_vs->set_virtual(true);
   p_vs->type() = collision_params.vs_particle_type;
 }