Logging in YAMMBS

Developer summary of what is logged.

Logger behavior

  • Modules use logging.getLogger(__name__).

  • YAMMBS does not configure root logging.

  • Runtime package code currently does not emit ERROR / EXCEPTION / CRITICAL.

Core minimization modules

yammbs/_minimize.py

  • DEBUG

    • Initial energy.

    • Initial positions.

    • Final energy.

    • Per-record completion (with qcarchive_id and final energy).

  • WARNING

    • Record skipped due to unassigned valence.

    • Record skipped due to ValueError during setup.

yammbs/torsion/_minimize.py

  • DEBUG

    • Input mapping/pool setup for torsion minimization.

    • Setup details (method, input payload, molecule/system creation).

    • Restraint construction details.

    • Initial/final dihedral diagnostics.

    • Initial/final energies (excluding restraint).

    • Per-record completion (with torsion_id and final energy).

  • WARNING

    • Record skipped due to unassigned valence.

    • Record skipped due to setup RuntimeError / ValueError.

Other modules

  • yammbs/_forcefields.py: INFO for SMIRNOFF constraint deregistration.

  • yammbs/_store.py: WARNING when TFD calculation fails.

  • yammbs/torsion/inputs.py: INFO on QCSubmit-to-YAMMBS conversion.

  • yammbs/torsion/analysis.py: WARNING for missing MM data.

  • yammbs/torsion/_store.py: INFO for torsion workflow stages; WARNING for missing QM/MM data.