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Fix TS multiplicity from YAML input #882

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Fix TS multiplicity from YAML input #882

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7 changes: 6 additions & 1 deletion arc/species/species.py
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Original file line number Diff line number Diff line change
Expand Up @@ -932,7 +932,12 @@ def from_dict(self, species_dict):
if self.bond_corrections:
self.long_thermo_description += f'Bond corrections: {self.bond_corrections}\n'
if self.multiplicity is None:
self.multiplicity = self.mol.multiplicity
if self.is_ts and self.get_xyz(generate=False):
self.determine_multiplicity_from_xyz()
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@samcogan21 samcogan21 May 2, 2026

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Might be worth adding a log line here- so it will be easier to debug if there's a multiplicity issue that still arises.

Something like:
logger.debug(f"TS species {self.label}: using xyz-based multiplicity {self.multiplicity} (ignored mol.multiplicity)") would make debugging much easier down the road, especially since a wrong multiplicity here causes Gaussian to reject the job entirely.

logger.debug(f'TS species {self.label}: using xyz-based multiplicity '
f'{self.multiplicity} (ignored mol.multiplicity)')
else:
self.multiplicity = self.mol.multiplicity
if self.charge is None:
self.charge = self.mol.get_net_charge()
if 'conformers' in species_dict:
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23 changes: 23 additions & 0 deletions arc/species/species_test.py
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Expand Up @@ -2188,6 +2188,29 @@ def test_determine_multiplicity(self):
ch_ts = ARCSpecies(label='C--H-TS', xyz='C 0 0 0\nH 1 2 5', is_ts=True)
self.assertEqual(ch_ts.multiplicity, 2)

ts_1_xyz = """H -2.99394700 1.00970200 0.09451400
O -4.10192200 0.13578500 -0.05953100
H -4.43761000 -0.35213100 0.70859500
C -2.22272000 0.16048700 -0.01004900
O -1.59892700 -0.79618100 0.08758500"""
ts_1_spc = ARCSpecies(label='TS1', is_ts=True, xyz=ts_1_xyz)
self.assertEqual(ts_1_spc.multiplicity, 1)

ts_1_spc_from_dict = ARCSpecies(species_dict={'label': 'TS1', 'is_ts': True, 'xyz': ts_1_xyz})
self.assertEqual(ts_1_spc_from_dict.multiplicity, 1)

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@samcogan21 samcogan21 May 2, 2026

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Can we add a known TS with a multiplicity of 2 (actual radical) to make sure the XYZ doesn't flatten it to 1?

# Test a known doublet TS from a Gaussian output file (NH3 + H = NH2 + H2).
# Verify that xyz-based electron counting (11 electrons → mult 2) wins over mol.multiplicity.
ts_doublet_path = os.path.join(ARC_TESTING_PATH, 'freq', 'TS_NH3+H=NH2+H2.out')
ts_doublet = ARCSpecies(label='TS_NH3+H', is_ts=True, xyz=ts_doublet_path)
self.assertIsNotNone(ts_doublet.mol)
self.assertEqual(ts_doublet.multiplicity, 2)
# Simulate a mol that incorrectly perceives multiplicity as 1, and verify xyz detection still gives 2.
ts_doublet.multiplicity = None
ts_doublet.mol.multiplicity = 1
ts_doublet.determine_multiplicity_from_xyz()
self.assertEqual(ts_doublet.multiplicity, 2)

def test_cluster_tsgs(self):
"""Test the cluster_tsgs() method."""
xyz_1 = """N 0.9177905887 0.5194617797 0.0000000000
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