Fix buffer overflow. [closes #236]

doc/source/changelog.rst

@@ -26,6 +26,7 @@ organisation on `GitHub <https://github.com/openbiosim/sire>`__.
 * Add support for boresch restraints to PME.
 * Port SOMD torsion fix to PME code.
 * Fix issues with ``atomtype`` and ``atom`` records for dummy atoms in GROMACS topology files.
+* Fixed buffer overflow when computing molecule indices to excluded to/from ghost atom interactions.
 
 
 `2024.2.0 <https://github.com/openbiosim/sire/compare/2024.1.0...2024.2.0>`__ - June 2024

wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp

@@ -1578,14 +1578,14 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system,
     {
         // work out the molecule index for the from ghost atom
         int mol_from = 0;
-        while (start_indexes[mol_from] <= from_ghost_idx)
+        while (start_indexes[mol_from] <= from_ghost_idx and mol_from < nmols)
             mol_from++;
 
         for (const auto &to_ghost_idx : to_ghost_idxs)
         {
             // work out the molecule index for the to ghost atom
             int mol_to = 0;
-            while (start_indexes[mol_to] <= to_ghost_idx)
+            while (start_indexes[mol_to] <= to_ghost_idx and mol_to < nmols)
                 mol_to++;
 
             if (not excluded_ghost_pairs.contains(IndexPair(from_ghost_idx, to_ghost_idx)))