Fix TS multiplicity from YAML input (#882)

## Issue
A TS species defined in input.yml with only is_ts: true and xyz (no
smiles/adjlist) could be assigned the wrong multiplicity, causing
Gaussian to reject the input with GL301. For example, a closed-shell TS
with 24 electrons was written as 0 2 (mult=2), which is electronically
impossible.
## Root cause                                             
ARCSpecies.from_dict (the path taken when main.py loads species from
YAML via ARCSpecies(species_dict=spc)) called mol_from_xyz to perceive a
2D graph from the TS geometry, then blindly assigned self.multiplicity =
self.mol.multiplicity. RMG's perception of TS-like geometries (partial
bonds, near-radical atoms) routinely returns spurious biradical
structures — for the failing case it returned O=[C][H][OH] with mult=2.
Direct construction (ARCSpecies(label=..., is_ts=True, xyz=...)) was
unaffected because __init__ routes through determine_multiplicity, which
skips the descriptor path for TSs and uses electron parity from xyz.

## Fix
In from_dict, when is_ts=True and xyz is available, fall back to
determine_multiplicity_from_xyz (electron-parity) instead of trusting
the perceived mol.multiplicity. Non-TS behavior is unchanged; TSs
without xyz still fall through to mol.multiplicity since there's no
parity signal.

## Test                                                   
Added a dict-construction assertion to test_determine_multiplicity for
the failing TS xyz — this is the path the bug actually went through. The
pre-existing direct-construction assertion was insufficient because it
bypassed from_dict entirely.

Author: alongd

arc/species/species.py

@@ -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()
+                    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:

arc/species/species_test.py

@@ -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)
+
+        # 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