Merge pull request #2097 from glotzerlab/speedup_mesh_read

Speeding up mesh construction

Author: joaander

CHANGELOG.rst

@@ -7,9 +7,6 @@ Change Log
 5.3.1 (not yet released)
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
-5.3.0 (2025-06-26)
-^^^^^^^^^^^^^^^^^^
-
 *Fixed*
 
 * Ensure that GPU devices have full unified memory capabilities
@@ -18,6 +15,11 @@ Change Log
   (`#2089 <https://github.com/glotzerlab/hoomd-blue/pull/2089>`__).
 * Install cuh headers
   (`#2091 <https://github.com/glotzerlab/hoomd-blue/pull/2091>`__).
+* Reduce the time needed to generate mesh bonds
+  (`#2097 <https://github.com/glotzerlab/hoomd-blue/pull/2097>`__).
+
+5.3.0 (2025-06-26)
+^^^^^^^^^^^^^^^^^^
 
 *Added*
 

hoomd/MeshGroupData.cc

@@ -125,6 +125,7 @@ void MeshGroupData<group_size, Group, name, snap>::initializeFromTriangleSnapsho
 
     if (group_size == 4)
         {
+        unsigned int bond_idx = 0;
         for (unsigned group_idx = 0; group_idx < snapshot.groups.size(); group_idx++)
             {
             std::vector<unsigned int> triag_tag(3);
@@ -169,20 +170,27 @@ void MeshGroupData<group_size, Group, name, snap>::initializeFromTriangleSnapsho
                     if (bonds[j].tag[0] == all_helper[i].tag[0]
                         && bonds[j].tag[1] == all_helper[i].tag[1])
                         {
-                        // all_helper[i].tag[3] = group_idx;
-                        all_helper[i].tag[3] = bonds[j].tag[2];
+                        unsigned int find_idx = all_helper[i].tag[2];
+                        all_groups[find_idx].tag[3] = bonds[j].tag[2];
+
+                        all_helper.erase(all_helper.begin() + i);
+                        i -= 1;
                         bonds.erase(bonds.begin() + j);
                         break;
                         }
                     }
                 }
             for (unsigned int i = 0; i < bonds.size(); ++i)
                 {
+                all_groups.push_back(bonds[i]);
                 all_helper.push_back(bonds[i]);
+                long unsigned int all_helper_size = all_helper.size() - 1;
+                all_helper[all_helper_size].tag[2] = bond_idx;
+                bond_idx++;
+
                 all_types.push_back(snapshot.type_id[group_idx]);
                 }
             }
-        all_groups = all_helper;
         }
     else // this part will be important later for dynamical bonding
         {