Merge pull request #102 from ReactionMechanismGenerator/0diverr

Don't crush if RMG's reaction_system.simulate() fails

Author: alongd

t3/main.py

@@ -38,7 +38,12 @@
 from rmgpy.species import Species
 from rmgpy.thermo import NASAPolynomial, NASA, ThermoData, Wilhoit
 
-from arc.common import get_ordinal_indicator, key_by_val, read_yaml_file, save_yaml_file
+from arc.common import (get_number_with_ordinal_indicator,
+                        get_ordinal_indicator,
+                        key_by_val,
+                        read_yaml_file,
+                        save_yaml_file,
+                        )
 from arc.exceptions import ConverterError
 from arc.main import ARC
 from arc.species.species import ARCSpecies, check_label
@@ -637,13 +642,14 @@ def run_rmg(self):
         if rmg_exception_encountered:
             self.rmg_exceptions_counter += 1
             if self.rmg_exceptions_counter > max_rmg_exceptions_allowed:
-                self.logger.error(f'This is the {self.rmg_exceptions_counter} exception raised by RMG.\n'
-                                  f'Cannot allow more than {max_rmg_exceptions_allowed} RMG exceptions during a T3 run.\n'
-                                  f'Not allowing additional exceptions, terminating.')
+                self.logger.error(f'This is the {get_number_with_ordinal_indicator(self.rmg_exceptions_counter)} '
+                                  f'exception raised by RMG.\nCannot allow more than {max_rmg_exceptions_allowed} '
+                                  f'RMG exceptions during a T3 run.\nNot allowing additional exceptions, terminating.')
                 raise ValueError('Terminating due to RMG exceptions.')
             else:
                 self.logger.warning(f'RMG did not converge. '
-                                    f'This is the {self.rmg_exceptions_counter} exception raised by RMG.\n'
+                                    f'This is the {get_number_with_ordinal_indicator(self.rmg_exceptions_counter)} '
+                                    f'exception raised by RMG.\n'
                                     f'The maximum number of exceptions allowed is {max_rmg_exceptions_allowed}.')
 
         elapsed_time = time_lapse(tic)

t3/simulate/rmg_constantTP.py

@@ -198,21 +198,24 @@ def simulate(self):
             if reaction_system.const_spc_names is not None:
                 reaction_system.get_const_spc_indices(self.rmg_model.reaction_model.core.species)
 
-            reaction_system.simulate(
-                core_species=self.rmg_model.reaction_model.core.species,
-                core_reactions=self.rmg_model.reaction_model.core.reactions,
-                edge_species=self.rmg_model.reaction_model.edge.species,
-                edge_reactions=self.rmg_model.reaction_model.edge.reactions,
-                surface_species=[],
-                surface_reactions=[],
-                pdep_networks=pdep_networks,
-                sensitivity=True if reaction_system.sensitive_species else False,
-                sens_worksheet=sens_worksheet,
-                model_settings=model_settings,
-                simulator_settings=simulator_settings,
-                conditions={'T': reaction_system.sens_conditions['T'], 'P': reaction_system.sens_conditions['P']},
-                prune=False,
-            )
+            try:
+                reaction_system.simulate(
+                    core_species=self.rmg_model.reaction_model.core.species,
+                    core_reactions=self.rmg_model.reaction_model.core.reactions,
+                    edge_species=self.rmg_model.reaction_model.edge.species,
+                    edge_reactions=self.rmg_model.reaction_model.edge.reactions,
+                    surface_species=[],
+                    surface_reactions=[],
+                    pdep_networks=pdep_networks,
+                    sensitivity=True if reaction_system.sensitive_species else False,
+                    sens_worksheet=sens_worksheet,
+                    model_settings=model_settings,
+                    simulator_settings=simulator_settings,
+                    conditions={'T': reaction_system.sens_conditions['T'], 'P': reaction_system.sens_conditions['P']},
+                    prune=False,
+                )
+            except ZeroDivisionError as e:
+                self.logger.warning(f'Cannot simulate reaction system, got:\n{e}')
 
             if reaction_system.sensitive_species:
                 plot_sensitivity(self.rmg_model.output_directory, index, reaction_system.sensitive_species)