fix(orca): implement NMD parsing, guard trsh against None - #1026
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Mia1Gohary wants to merge 3 commits into
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fix(orca): implement NMD parsing, guard trsh against None#1026Mia1Gohary wants to merge 3 commits into
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #1026 +/- ##
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+ Coverage 63.25% 64.54% +1.28%
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Files 114 119 +5
Lines 38274 39886 +1612
Branches 10013 10326 +313
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+ Hits 24212 25744 +1532
- Misses 11158 11160 +2
- Partials 2904 2982 +78
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Mia1Gohary
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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.
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calvinp0
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Aug 26, 2026
calvinp0
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calvinp0
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It's looking good @Mia1Gohary , just two comments for fixing! |
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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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.