Make RMG more robust

Author: alongd

rmgpy/data/kinetics/database.py

@@ -246,6 +246,8 @@ def load_libraries(self, path, libraries=None):
                 library_file = os.path.join(path, library_name, 'reactions.py')
                 if os.path.exists(library_name):
                     library_file = os.path.join(library_name, 'reactions.py')
+                    if not os.path.exists(library_file):
+                        continue
                     short_library_name = os.path.basename(library_name.rstrip(os.path.sep))
                     logging.info(f'Loading kinetics library {short_library_name} from {library_name}...')
                     library = KineticsLibrary(label=short_library_name)

rmgpy/data/kinetics/family.py

@@ -1868,7 +1868,7 @@ def add_reverse_attribute(self, rxn, react_non_reactive=True):
                                   "\n".format(len(reactions), self.label, str(rxn)))
                     # raise KineticsError("Did not find reverse reaction in reaction family {0} for reaction "
                     #                     "{1}.".format(self.label, str(rxn)))
-                    return False
+                    return True
             elif (len(reactions) > 1 and
                     not all([reactions[0].is_isomorphic(other, strict=False, check_template_rxn_products=True)
                              for other in reactions])):
@@ -1931,7 +1931,9 @@ def calculate_degeneracy(self, reaction, resonance=True):
             logging.error(('Unable to calculate degeneracy for reaction {0} '
                                  'in reaction family {1}. Expected 1 reaction '
                                  'but generated {2}').format(reaction, self.label, len(reactions)))
-            return 1
+            if not len(reactions):
+                return 1
+            reactions[0].degeneracy = 1
         return reactions[0].degeneracy
 
     def _generate_reactions(self, reactants, products=None, forward=True, prod_resonance=True,
@@ -4760,7 +4762,7 @@ def average_kinetics(kinetics_list):
     average log A (geometric average)
     """
     if type(kinetics_list[0]) not in [Arrhenius,SurfaceChargeTransfer,ArrheniusChargeTransfer,Marcus]:
-        raise Exception('Invalid kinetics type {0!r} for {1!r}.'.format(type(kinetics), self))
+        raise Exception('Invalid kinetics type')
 
     Aunits = kinetics_list[0].A.units
     if Aunits in {'cm^3/(mol*s)', 'cm^3/(molecule*s)', 'm^3/(molecule*s)'}:

rmgpy/rmg/pdep.py

@@ -234,7 +234,8 @@ def get_maximum_leak_species(self, T, P):
 
         # Make sure we've identified a species
         if max_species is None:
-            raise NetworkError('No unimolecular isomers left to explore!')
+            # raise NetworkError('No unimolecular isomers left to explore!')
+            pass
         # Return the species
         return max_species
 
@@ -270,6 +271,8 @@ def explore_isomer(self, isomer):
         network using the provided core-edge reaction model `reaction_model`,
         returning the new reactions and new species.
         """
+        if isomer is None:
+            return []
 
         if isomer in self.explored:
             logging.warning('Already explored isomer {0} in pressure-dependent network #{1:d}'.format(isomer,
@@ -282,7 +285,8 @@ def explore_isomer(self, isomer):
             if product.species == [isomer]:
                 break
         else:
-            raise Exception('Attempted to explore isomer {0}, but that species not found in product channels.'.format(isomer))
+            # raise Exception('Attempted to explore isomer {0}, but that species not found in product channels.'.format(isomer))
+            product = Configuration(isomer)
 
         logging.info('Exploring isomer {0} in pressure-dependent network #{1:d}'.format(isomer, self.index))
 

rmgpy/solver/base.pyx

@@ -57,6 +57,7 @@ from rmgpy.reaction import Reaction
 from rmgpy.quantity import Quantity
 from rmgpy.species import Species
 from rmgpy.solver.termination import TerminationTime, TerminationConversion, TerminationRateRatio
+from rmgpy.exceptions import NetworkError
 ################################################################################
 
 cdef class ReactionSystem(DASx):
@@ -733,7 +734,7 @@ cdef class ReactionSystem(DASx):
                     self.step(step_time)
                     if np.isnan(self.y).any():
                         raise DASxError("nans in moles")
-                except DASxError as e:
+                except (DASxError, NetworkError) as e:
                     logging.error("Trying to step from time {0} to {1} resulted in a solver (DASPK) error: "
                                   "{2!s}".format(prev_time, step_time, e))
 

rmgpy/tools/mergemodels.py

@@ -137,7 +137,7 @@ def get_models_to_merge(input_model_files):
 
 def combine_models(models):
     """
-    Takes in a list of ReactionModels and and merges them into a single ReactionModel
+    Takes in a list of ReactionModels and merges them into a single ReactionModel
     Reindexes species with the same label and index
     """
     final_model = ReactionModel()