Refactor ScriptInterface

Give each member of ScriptInterface::System a handle to the core
System class. Refactor AutoParameters serialization. The System
class can now handle checkpointing of its ObjectHandle members.

src/core/analysis/statistics.cpp

@@ -140,13 +140,12 @@ double mindist(System::System const &system, std::vector<int> const &set1,
   return std::sqrt(mindist_sq);
 }
 
-Utils::Vector3d calc_linear_momentum(bool include_particles,
+Utils::Vector3d calc_linear_momentum(System::System const &system,
+                                     bool include_particles,
                                      bool include_lbfluid) {
   Utils::Vector3d momentum{};
-  auto const &system = System::get_system();
-  auto &cell_structure = *system.cell_structure;
   if (include_particles) {
-    auto const particles = cell_structure.local_particles();
+    auto const particles = system.cell_structure->local_particles();
     momentum =
         std::accumulate(particles.begin(), particles.end(), Utils::Vector3d{},
                         [](Utils::Vector3d const &m, Particle const &p) {

src/core/analysis/statistics.hpp

@@ -127,8 +127,10 @@ Utils::Vector9d moment_of_inertia_matrix(System::System const &system,
                                          int p_type);
 
 /** Calculate total momentum of the system (particles & LB fluid).
+ *  @param system              particle system
  *  @param include_particles   Add particles momentum
  *  @param include_lbfluid     Add LB fluid momentum
  */
-Utils::Vector3d calc_linear_momentum(bool include_particles,
+Utils::Vector3d calc_linear_momentum(System::System const &system,
+                                     bool include_particles,
                                      bool include_lbfluid);

src/core/nonbonded_interactions/nonbonded_interaction_data.cpp

@@ -24,7 +24,6 @@
 #include "nonbonded_interactions/nonbonded_interaction_data.hpp"
 
 #include "electrostatics/coulomb.hpp"
-#include "system/System.hpp"
 
 #include <algorithm>
 #include <cassert>
@@ -123,7 +122,3 @@ double InteractionsNonBonded::maximal_cutoff() const {
   }
   return max_cut_nonbonded;
 }
-
-void InteractionsNonBonded::on_non_bonded_ia_change() {
-  System::get_system().on_non_bonded_ia_change();
-}

src/core/nonbonded_interactions/nonbonded_interaction_data.hpp

@@ -427,7 +427,6 @@ class InteractionsNonBonded {
 
   void set_ia_param(int i, int j, std::shared_ptr<IA_parameters> const &ia) {
     m_nonbonded_ia_params[get_ia_param_key(i, j)] = ia;
-    on_non_bonded_ia_change();
   }
 
   auto get_max_seen_particle_type() const { return max_seen_particle_type; }
@@ -437,6 +436,4 @@ class InteractionsNonBonded {
 
   /** @brief Get maximal cutoff. */
   double maximal_cutoff() const;
-
-  void on_non_bonded_ia_change();
 };

src/python/espressomd/analyze.py

@@ -82,7 +82,7 @@ def acf_1d(signal, n_with_padding, n):
 
 @script_interface_register
 class _ObservableStat(ScriptInterfaceHelper):
-    _so_name = "ScriptInterface::Analysis::ObservableStat"
+    _so_name = "Analysis::ObservableStat"
     _so_creation_policy = "GLOBAL"
 
     def _generate_summary(self, obj, dim, calc_sp):
@@ -381,7 +381,7 @@ class Analysis(ScriptInterfaceHelper):
             and [1] contains the values of the rdf.
 
     """
-    _so_name = "ScriptInterface::Analysis::Analysis"
+    _so_name = "Analysis::Analysis"
     _so_creation_policy = "GLOBAL"
     _so_bind_methods = (
         "linear_momentum",
@@ -395,6 +395,11 @@ class Analysis(ScriptInterfaceHelper):
         "structure_factor",
         "distribution")
 
+    def __init__(self, **kwargs):
+        super().__init__(**kwargs)
+        self.obs_stat = _ObservableStat()
+        self.call_method("register_observable_stat", leaf=self.obs_stat)
+
     def min_dist(self, p1='default', p2='default'):
         """
         Minimal distance between two sets of particle types.
@@ -459,10 +464,9 @@ def pressure(self):
             * ``"external_fields"``: external fields contribution
 
         """
-        obs_stat = _ObservableStat()
-        observable = obs_stat.call_method("calculate_scalar_pressure")
+        observable = self.obs_stat.call_method("calculate_scalar_pressure")
         utils.handle_errors("calculate_pressure() failed")
-        return obs_stat._generate_summary(observable, 9, True)
+        return self.obs_stat._generate_summary(observable, 9, True)
 
     def pressure_tensor(self):
         """
@@ -502,10 +506,9 @@ def pressure_tensor(self):
             * ``"external_fields"``: external fields contribution
 
         """
-        obs_stat = _ObservableStat()
-        observable = obs_stat.call_method("calculate_pressure_tensor")
+        observable = self.obs_stat.call_method("calculate_pressure_tensor")
         utils.handle_errors("calculate_pressure() failed")
-        return obs_stat._generate_summary(observable, 9, False)
+        return self.obs_stat._generate_summary(observable, 9, False)
 
     def energy(self):
         """
@@ -551,10 +554,9 @@ def energy(self):
         >>> print(energy["external_fields"])
 
         """
-        obs_stat = _ObservableStat()
-        observable = obs_stat.call_method("calculate_energy")
+        observable = self.obs_stat.call_method("calculate_energy")
         utils.handle_errors("calculate_energy() failed")
-        return obs_stat._generate_summary(observable, 1, False)
+        return self.obs_stat._generate_summary(observable, 1, False)
 
     def particle_energy(self, particle):
         """

src/python/espressomd/system.py

@@ -247,8 +247,8 @@ def __getstate__(self):
             checkpointable_properties.append("_active_virtual_sites_handle")
         checkpointable_properties += [
             "non_bonded_inter", "bonded_inter", "cell_system", "lees_edwards",
-            "part", "analysis", "auto_update_accumulators",
-            "comfixed", "constraints", "galilei", "bond_breakage"
+            "part", "auto_update_accumulators",
+            "constraints", "bond_breakage"
         ]
         if has_features("COLLISION_DETECTION"):
             checkpointable_properties.append("collision_detection")

src/script_interface/ObjectContainer.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 SCRIPT_INTERFACE_OBJECT_CONTAINER_HPP
-#define SCRIPT_INTERFACE_OBJECT_CONTAINER_HPP
+
+#pragma once
 
 #include "script_interface/auto_parameters/AutoParameters.hpp"
 
@@ -38,5 +38,3 @@ using ObjectContainer = std::conditional_t<
     AutoParameters<Container<ManagedType, BaseType>, BaseType>, BaseType>;
 
 } // namespace ScriptInterface
-
-#endif

src/script_interface/ObjectHandle.cpp

@@ -52,20 +52,20 @@ Variant ObjectHandle::call_method(const std::string &name,
 std::string ObjectHandle::serialize() const {
   ObjectState state;
 
-  auto const params = this->get_parameters();
+  auto const params = serialize_parameters();
   state.params.resize(params.size());
 
-  PackVisitor v;
+  PackVisitor visit;
 
   /* Pack parameters and keep track of ObjectRef parameters */
   boost::transform(params, state.params.begin(),
-                   [&v](auto const &kv) -> PackedMap::value_type {
-                     return {kv.first, boost::apply_visitor(v, kv.second)};
+                   [&visit](auto const &kv) -> PackedMap::value_type {
+                     return {kv.first, boost::apply_visitor(visit, kv.second)};
                    });
 
   /* Packed Object parameters */
-  state.objects.resize(v.objects().size());
-  boost::transform(v.objects(), state.objects.begin(), [](auto const &kv) {
+  state.objects.resize(visit.objects().size());
+  boost::transform(visit.objects(), state.objects.begin(), [](auto const &kv) {
     return std::make_pair(kv.first, kv.second->serialize());
   });
 

src/script_interface/ObjectHandle.hpp

@@ -17,8 +17,8 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef SCRIPT_INTERFACE_SCRIPT_INTERFACE_BASE_HPP
-#define SCRIPT_INTERFACE_SCRIPT_INTERFACE_BASE_HPP
+#pragma once
+
 #include "Variant.hpp"
 
 #include <utils/Span.hpp>
@@ -27,6 +27,7 @@
 
 #include <memory>
 #include <string>
+#include <utility>
 #include <vector>
 
 namespace ScriptInterface {
@@ -156,9 +157,18 @@ class ObjectHandle {
    */
   static ObjectRef deserialize(const std::string &state, Context &ctx);
 
+  /**
+   * @brief Serialize parameters.
+   * Can be overriden to e.g. serialize parameters in a specific order.
+   */
+  virtual std::vector<std::pair<std::string, Variant>>
+  serialize_parameters() const {
+    auto const params = this->get_parameters();
+    return {params.begin(), params.end()};
+  }
+
 private:
   virtual std::string get_internal_state() const { return {}; }
   virtual void set_internal_state(std::string const &state) {}
 };
 } /* namespace ScriptInterface */
-#endif

src/script_interface/ObjectList.hpp

@@ -19,8 +19,7 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef SCRIPT_INTERFACE_OBJECT_LIST_HPP
-#define SCRIPT_INTERFACE_OBJECT_LIST_HPP
+#pragma once
 
 #include "script_interface/ObjectContainer.hpp"
 #include "script_interface/ScriptInterface.hpp"
@@ -160,4 +159,3 @@ class ObjectList : public ObjectContainer<ObjectList, ManagedType, BaseType> {
   }
 };
 } // Namespace ScriptInterface
-#endif

src/script_interface/ObjectMap.hpp

@@ -19,8 +19,7 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef SCRIPT_INTERFACE_OBJECT_MAP_HPP
-#define SCRIPT_INTERFACE_OBJECT_MAP_HPP
+#pragma once
 
 #include "script_interface/ObjectContainer.hpp"
 #include "script_interface/ScriptInterface.hpp"
@@ -194,4 +193,3 @@ class ObjectMap : public ObjectContainer<ObjectMap, ManagedType, BaseType> {
   }
 };
 } // Namespace ScriptInterface
-#endif

src/script_interface/ObjectState.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_SCRIPT_INTERFACE_OBJECTSTATE_HPP
-#define ESPRESSO_SCRIPT_INTERFACE_OBJECTSTATE_HPP
+
+#pragma once
 
 #include "packed_variant.hpp"
 
@@ -48,5 +48,3 @@ struct ObjectState {
   }
 };
 } // namespace ScriptInterface
-
-#endif

src/script_interface/Variant.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 SCRIPT_INTERFACE_VARIANT_HPP
-#define SCRIPT_INTERFACE_VARIANT_HPP
+
+#pragma once
 
 #include "None.hpp"
 
@@ -127,5 +127,3 @@ template <class T> bool is_type(Variant const &v) {
 
 inline bool is_none(Variant const &v) { return is_type<None>(v); }
 } // namespace ScriptInterface
-
-#endif