Merge pull request #387 from OpenBioSim/feature_somd2_logger

Use SOMD2 logger for dynamics warnings

Author: lohedges

doc/source/changelog.rst

@@ -21,6 +21,8 @@ organisation on `GitHub <https://github.com/openbiosim/sire>`__.
 
 * Fix ``delta`` parameter in soft-core Coulomb potential.
 
+* When possible, use the ``SOMD2`` logger for dynamics warnings.
+
 `2025.3.0 <https://github.com/openbiosim/sire/compare/2025.2.0...2025.3.0>`__ - November 2025
 ---------------------------------------------------------------------------------------------
 

src/sire/mol/_dynamics.py

@@ -304,6 +304,14 @@ def __init__(self, mols=None, map=None, **kwargs):
         else:
             self._pressure = None
 
+        # Try importing the SOMD2 logger.
+        try:
+            from somd2 import _logger as somd2_logger
+
+            self._somd2_logger = somd2_logger
+        except:
+            self._somd2_logger = None
+
     def is_null(self):
         return self._sire_mols is None
 
@@ -953,14 +961,19 @@ def _rebuild_and_minimise(self):
 
         from ..utils import Console
 
-        Console.warning(
+        msg = (
             "Something went wrong when running dynamics. The system will be "
             "minimised, and then dynamics will be attempted again. If an "
             "error still occurs, then it is likely that the step size is too "
             "large, the molecules are over-constrained, or there is something "
-            "more fundemental going wrong..."
+            "more fundamental going wrong..."
         )
 
+        if self._somd2_logger is not None:
+            self._somd2_logger.warning(msg)
+        else:
+            Console.warning(msg)
+
         # rebuild the molecules
         from ..convert import to