fix(orca): implement NMD parsing, guard trsh against None - #1026
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## main #1026 +/- ##
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It's looking good @Mia1Gohary , just two comments for fixing! |
Orca's parse_normal_mode_displacement() was a stub returning (None, None). trsh_negative_freq() then called len(None) on any species with a genuine imaginary frequency, crashing the whole ARC process instead of nudging the geometry and re-optimizing. Implement real parsing of Orca's VIBRATIONAL FREQUENCIES / NORMAL MODES blocks, and add a defensive None check in trsh.py so any adapter lacking this capability degrades gracefully instead of crashing. Validated against CR_1's r1 freq job on zeus: correctly identified and parsed the -33.01 cm^-1 imaginary mode; live run confirmed freq troubleshooting completes (freq: True) where it previously crashed.
Reuse the Orca frequency parser when reading normal mode displacements, while retaining zero. Move the n-cetane checks into a dedicated test and verify that frequencies remain aligned with Cartesian displacement vectors.
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Return no normal modes when an Orca output ends inside the normal-mode matrix or contains an incomplete row. Add regression coverage for truncation, successful Orca parsing and troubleshooting, and supported Orca outputs without a normal-mode block.
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Orca's parse_normal_mode_displacement() was a stub returning (None, None). trsh_negative_freq() then called len(None) on any species with a genuine imaginary frequency, crashing the whole ARC process instead of nudging the geometry and re-optimizing.
Implement real parsing of Orca's VIBRATIONAL FREQUENCIES / NORMAL MODES blocks, and add a defensive None check in trsh.py so any adapter lacking this capability degrades gracefully instead of crashing.
Validated against CR_1's r1 freq job on zeus: correctly identified and parsed the -33.01 cm^-1 imaginary mode; live run confirmed freq troubleshooting completes (freq: True) where it previously crashed.