Add storage-agnostic function to add bonds between particles

.gitlab-ci.yml

@@ -373,36 +373,6 @@ tutorials-samples-no-gpu:
   rules:
     - if: $CI_PIPELINE_SOURCE == "schedule"
 
-rtx4090:
-  <<: *global_job_definition
-  stage: build
-  variables:
-     CC: 'gcc-12'
-     CXX: 'g++-12'
-     GCOV: 'gcov-12'
-     myconfig: 'maxset'
-     with_cuda: 'true'
-     with_coverage: 'false'
-     with_scafacos: 'true'
-     with_walberla: 'true'
-     with_walberla_avx: 'true'
-     with_stokesian_dynamics: 'true'
-     with_caliper: 'true'
-     build_type: 'Release'
-  script:
-    - bash maintainer/CI/build_cmake.sh
-    - cd build
-    - make check_samples
-    - make check_tutorials
-  tags:
-    - espresso
-    - cuda
-    - avx2
-    - sfb1313
-  rules:
-    - if: $CI_COMMIT_BRANCH == "python"
-      when: manual
-
 installation:
   <<: *global_job_definition
   stage: build

src/core/CMakeLists.txt

@@ -22,6 +22,7 @@
 add_library(
   espresso_core SHARED
   bond_error.cpp
+  bonds.cpp
   cells.cpp
   communication.cpp
   dpd.cpp

src/core/bonds.cpp

@@ -0,0 +1,36 @@
+/*
+ * Copyright (C) 2025 The ESPResSo project
+ *
+ * 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 "system/System.hpp"
+
+#include <vector>
+
+bool add_bond(System::System &system, int bond_id,
+              std::vector<int> const &particle_ids) {
+  Particle *p = system.cell_structure->get_local_particle(particle_ids[0]);
+  if (p) {
+    // The bond view is stored in the bond list of the primary particle.
+    // Thus the bond views's partner list only contains the other particle id.
+    BondView bond(bond_id, {particle_ids.data() + 1, particle_ids.size() - 1});
+    p->bonds().insert(bond);
+    return true;
+  }
+  return false;
+}

src/core/bonds.hpp

@@ -0,0 +1,35 @@
+/*
+ * Copyright (C) 2025 The ESPResSo project
+ *
+ * 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/>.
+ */
+
+#pragma once
+
+#include "system/System.hpp"
+
+#include <vector>
+
+constexpr bool use_one_sided_bond_storage = true;
+
+/**
+ * @brief Add a bond to a particle.
+ *
+ * The caller is responsible for calling
+ * @ref System::System::on_particle_change().
+ */
+bool add_bond(System::System &system, int bond_id,
+              std::vector<int> const &particle_ids);

src/core/collision_detection/BindAtPointOfCollision.cpp

@@ -86,7 +86,7 @@ void BindAtPointOfCollision::handle_collisions(
   auto const min_global_cut = system.get_min_global_cut();
   auto const &box_geo = *system.box_geo;
 
-  add_bind_centers(local_collision_queue, cell_structure, bond_centers);
+  add_bind_centers(local_collision_queue, system, bond_centers);
 
   // Gather the global collision queue, because only one node has a collision
   // across node boundaries in its queue.

src/core/collision_detection/BindCenters.cpp

@@ -58,7 +58,7 @@ void BindCenters::initialize(System::System &system) {
 
 void BindCenters::handle_collisions(
     System::System &system, std::vector<CollisionPair> &local_collision_queue) {
-  add_bind_centers(local_collision_queue, *system.cell_structure, bond_centers);
+  add_bind_centers(local_collision_queue, system, bond_centers);
 }
 
 } // namespace CollisionDetection

src/core/collision_detection/utils.hpp

@@ -27,6 +27,7 @@
 
 #include "BoxGeometry.hpp"
 #include "Particle.hpp"
+#include "bonds.hpp"
 #include "cell_system/CellStructure.hpp"
 #include "communication.hpp"
 #include "virtual_sites.hpp"
@@ -80,17 +81,19 @@ inline auto gather_collision_queue(std::vector<CollisionPair> const &local) {
 }
 
 inline void add_bind_centers(std::vector<CollisionPair> &collision_queue,
-                             CellStructure &cell_structure, int bond_centers) {
+                             System::System &system, int bond_id) {
   for (auto &c : collision_queue) {
     // Ensure that the bond is associated with the non-ghost particle
-    if (cell_structure.get_local_particle(c.first)->is_ghost()) {
+    if (system.cell_structure->get_local_particle(c.first)->is_ghost()) {
       std::swap(c.first, c.second);
     }
 
-    const int bondG[] = {c.second};
-
-    // Insert the bond for the non-ghost particle
-    get_part(cell_structure, c.first).bonds().insert({bond_centers, bondG});
+    // Because MPI rank 1's queue containing (@c p1_on_rank_1, @c p2_on_rank_2)
+    // doesn't guarantee that the same pair (with or without swapped order) is
+    // also queued on the MPI rank 2.
+    // Once we change bond storage, some syncing has to be done.
+    assert(use_one_sided_bond_storage);
+    ::add_bond(system, bond_id, {c.first, c.second});
   }
 }
 

src/script_interface/particle_data/ParticleHandle.cpp

@@ -30,6 +30,7 @@
 #include "core/BoxGeometry.hpp"
 #include "core/PropagationMode.hpp"
 #include "core/bonded_interactions/bonded_interaction_data.hpp"
+#include "core/bonds.hpp"
 #include "core/cell_system/CellStructure.hpp"
 #include "core/exclusions.hpp"
 #include "core/nonbonded_interactions/nonbonded_interaction_data.hpp"
@@ -580,13 +581,12 @@ Variant ParticleHandle::do_call_method(std::string const &name,
     return make_vector_of_variants(bonds_flat);
   }
   if (name == "add_bond") {
-    set_particle_property([&params](Particle &p) {
-      auto const bond_id = get_value<int>(params, "bond_id");
-      auto const part_id = get_value<std::vector<int>>(params, "part_id");
-      auto const bond_view =
-          BondView(bond_id, {part_id.data(), part_id.size()});
-      p.bonds().insert(bond_view);
-    });
+    auto const bond_id = get_value<int>(params, "bond_id");
+    auto const partner_ids = get_value<std::vector<int>>(params, "part_id");
+    std::vector<int> particle_ids = {m_pid};
+    std::ranges::copy(partner_ids, std::back_inserter(particle_ids));
+    ::add_bond(*get_system(), bond_id, particle_ids);
+    get_system()->on_particle_change();
   } else if (name == "del_bond") {
     set_particle_property([&params](Particle &p) {
       auto const bond_id = get_value<int>(params, "bond_id");