update Arkane statmech to handle xtb adapter

xtb does not save geometries to its frequency logs, so this redirects Arkane's statmech.py to use the geometry file in place of the frequency file for anything that depends on geometry. It also grabs the frequencies from the frequency log and combines them with the conformer object built by the geometry log to get a complete conformer object with all the modes.

Author: sevyharris

arkane/modelchem.py

@@ -285,7 +285,8 @@ def str_to_lot(s: str) -> Union[LevelOfTheory, CompositeLevelOfTheory]:
     'orca': ('orca',),
     'terachem': ('terachem',),
     'mopac': ('mopac',),
-    'psi4': ('psi4',)
+    'psi4': ('psi4',),
+    'xtb': ('xtb',)
 }
 _software_ids = {_name: _id for _id, _names in _valid_software_names.items() for _name in _names}
 

arkane/statmech.py

@@ -57,7 +57,7 @@
 
 from arkane.common import ArkaneSpecies, symbol_by_number, get_principal_moments_of_inertia
 from arkane.encorr.corr import get_atom_correction, get_bac
-from arkane.ess import ESSAdapter, ess_factory, _registered_ess_adapters, GaussianLog, QChemLog
+from arkane.ess import ESSAdapter, ess_factory, _registered_ess_adapters, GaussianLog, QChemLog, XTBLog
 from arkane.encorr.isodesmic import ErrorCancelingSpecies, IsodesmicRingScheme
 from arkane.modelchem import LevelOfTheory, CompositeLevelOfTheory, standardize_name
 from arkane.output import prettify
@@ -506,10 +506,22 @@ def create_log(log_path, check_for_errors=True):
                                  self.species.label))
 
         logging.debug('    Reading molecular degrees of freedom...')
-        conformer, unscaled_frequencies = statmech_log.load_conformer(symmetry=external_symmetry,
+        if isinstance(statmech_log, XTBLog):
+            # XTB frequencies log does not contain geometry information, so read the geometry from the geometry log
+            # frequencies from the frequencies log and combine them to create the conformer object
+            conformer, unscaled_frequencies = geom_log.load_conformer(symmetry=external_symmetry,
                                                                       spin_multiplicity=spin_multiplicity,
                                                                       optical_isomers=optical_isomers,
                                                                       label=self.species.label)
+            unscaled_frequencies = statmech_log._load_frequencies()
+            if unscaled_frequencies:
+                conformer.modes.append(HarmonicOscillator(frequencies=(unscaled_frequencies, "cm^-1")))
+        else:
+
+            conformer, unscaled_frequencies = statmech_log.load_conformer(symmetry=external_symmetry,
+                                                                          spin_multiplicity=spin_multiplicity,
+                                                                          optical_isomers=optical_isomers,
+                                                                          label=self.species.label)
 
         for mode in conformer.modes:
             if isinstance(mode, (Translation, IdealGasTranslation)):
@@ -695,7 +707,10 @@ def create_log(log_path, check_for_errors=True):
 
         # save supporting information for calculation
         self.supporting_info = [self.species.label]
-        optical_isomers_read, symmetry_read, point_group_read = statmech_log.get_symmetry_properties()
+        if isinstance(statmech_log, XTBLog):
+            optical_isomers_read, symmetry_read, point_group_read = geom_log.get_symmetry_properties()
+        else:
+            optical_isomers_read, symmetry_read, point_group_read = statmech_log.get_symmetry_properties()
         self.supporting_info.append(external_symmetry if external_symmetry else symmetry_read)
         self.supporting_info.append(optical_isomers if optical_isomers else optical_isomers_read)
         self.supporting_info.append(point_group_read)