add requires_rms to pdep, thermo filtering, and process_new_rxns

Author: JacksonBurns

rmgpy/rmg/main.py

@@ -841,7 +841,7 @@ def execute(self, initialize=True, **kwargs):
             )
 
         if not np.isinf(self.model_settings_list[0].thermo_tol_keep_spc_in_edge):
-            self.reaction_model.thermo_filter_down(maximum_edge_species=self.model_settings_list[0].maximum_edge_species)
+            self.reaction_model.thermo_filter_down(maximum_edge_species=self.model_settings_list[0].maximum_edge_species, requires_rms=requires_rms)
 
         logging.info("Completed initial enlarge edge step.\n")
 
@@ -1108,7 +1108,7 @@ def execute(self, initialize=True, **kwargs):
                             reactor_done = False
 
                         if not np.isinf(self.model_settings_list[0].thermo_tol_keep_spc_in_edge):
-                            self.reaction_model.thermo_filter_down(maximum_edge_species=model_settings.maximum_edge_species)
+                            self.reaction_model.thermo_filter_down(maximum_edge_species=model_settings.maximum_edge_species, requires_rms=requires_rms)
 
                         max_num_spcs_hit = len(self.reaction_model.core.species) >= model_settings.max_num_species
 

rmgpy/rmg/model.py

@@ -643,7 +643,7 @@ def enlarge(self, new_object=None, react_edge=False, unimolecular_react=None, bi
                 pdep_network, new_species = new_object
                 new_reactions.extend(pdep_network.explore_isomer(new_species))
 
-                self.process_new_reactions(new_reactions, new_species, pdep_network)
+                self.process_new_reactions(new_reactions, new_species, pdep_network, requires_rms=requires_rms)
 
             else:
                 raise TypeError(
@@ -667,7 +667,7 @@ def enlarge(self, new_object=None, react_edge=False, unimolecular_react=None, bi
                         if len(products) == 1 and products[0] == species:
                             new_reactions = network.explore_isomer(species)
 
-                            self.process_new_reactions(new_reactions, species, network)
+                            self.process_new_reactions(new_reactions, species, network, requires_rms=requires_rms)
                             network.update_configurations(self)
                             index = 0
                             break
@@ -692,7 +692,7 @@ def enlarge(self, new_object=None, react_edge=False, unimolecular_react=None, bi
                     # Identify a core species which was used to generate the reaction
                     # This is only used to determine the reaction direction for processing
                     spc = spcTuple[0]
-                    self.process_new_reactions(rxnList, spc)
+                    self.process_new_reactions(rxnList, spc, requires_rms=requires_rms)
 
         ################################################################
         # Begin processing the new species and reactions
@@ -704,7 +704,7 @@ def enlarge(self, new_object=None, react_edge=False, unimolecular_react=None, bi
 
         # Do thermodynamic filtering
         if not np.isinf(self.thermo_tol_keep_spc_in_edge) and self.new_species_list != []:
-            self.thermo_filter_species(self.new_species_list)
+            self.thermo_filter_species(self.new_species_list, requires_rms=requires_rms)
 
         # Update unimolecular (pressure dependent) reaction networks
         if self.pressure_dependence:
@@ -1131,7 +1131,7 @@ def add_species_to_core(self, spec, requires_rms=False):
             if spec in self.edge.species:
                 # remove forbidden species from edge
                 logging.info("Species {0} was Forbidden and not added to Core...Removing from Edge.".format(spec))
-                self.remove_species_from_edge(self.reaction_systems, spec)
+                self.remove_species_from_edge(self.reaction_systems, spec, requires_rms=requires_rms)
                 # remove any empty pdep networks as a result of species removal
                 if self.pressure_dependence:
                     self.remove_empty_pdep_networks()
@@ -1207,7 +1207,7 @@ def set_thermodynamic_filtering_parameters(
         self.reaction_systems = reaction_systems
         self.maximum_edge_species = maximum_edge_species
 
-    def thermo_filter_species(self, spcs):
+    def thermo_filter_species(self, spcs, requires_rms=False):
         """
         checks Gibbs energy of the species in species against the
         maximum allowed Gibbs energy
@@ -1222,13 +1222,13 @@ def thermo_filter_species(self, spcs):
                     "greater than the thermo_tol_keep_spc_in_edge of "
                     "{3} ".format(spc, G, Gn, self.thermo_tol_keep_spc_in_edge)
                 )
-                self.remove_species_from_edge(self.reaction_systems, spc)
+                self.remove_species_from_edge(self.reaction_systems, spc, requires_rms=requires_rms)
 
         # Delete any networks that became empty as a result of pruning
         if self.pressure_dependence:
             self.remove_empty_pdep_networks()
 
-    def thermo_filter_down(self, maximum_edge_species, min_species_exist_iterations_for_prune=0):
+    def thermo_filter_down(self, maximum_edge_species, min_species_exist_iterations_for_prune=0, requires_rms=False):
         """
         removes species from the edge based on their Gibbs energy until maximum_edge_species
         is reached under the constraint that all removed species are older than
@@ -1270,7 +1270,7 @@ def thermo_filter_down(self, maximum_edge_species, min_species_exist_iterations_
                 logging.info(
                     "Removing species {0} from edge to meet maximum number of edge species, Gibbs " "number is {1}".format(spc, Gns[rInds[i]])
                 )
-                self.remove_species_from_edge(self.reaction_systems, spc)
+                self.remove_species_from_edge(self.reaction_systems, spc, requires_rms=requires_rms)
 
             # Delete any networks that became empty as a result of pruning
             if self.pressure_dependence:
@@ -1643,9 +1643,9 @@ def add_seed_mechanism_to_core(self, seed_mechanism, react=False, requires_rms=F
                 # This unimolecular library reaction is flagged as `elementary_high_p` and has Arrhenius type kinetics.
                 # We should calculate a pressure-dependent rate for it
                 if len(rxn.reactants) == 1:
-                    self.process_new_reactions(new_reactions=[rxn], new_species=rxn.reactants[0])
+                    self.process_new_reactions(new_reactions=[rxn], new_species=rxn.reactants[0], requires_rms=requires_rms)
                 else:
-                    self.process_new_reactions(new_reactions=[rxn], new_species=rxn.products[0])
+                    self.process_new_reactions(new_reactions=[rxn], new_species=rxn.products[0], requires_rms=requires_rms)
 
         # Perform species constraints and forbidden species checks
 
@@ -1693,7 +1693,7 @@ def add_seed_mechanism_to_core(self, seed_mechanism, react=False, requires_rms=F
                     submit(spec, self.solvent_name)
 
                 rxn.fix_barrier_height(force_positive=True)
-            self.add_reaction_to_core(rxn)
+            self.add_reaction_to_core(rxn, requires_rms=requires_rms)
 
         # Check we didn't introduce unmarked duplicates
         self.mark_chemkin_duplicates()
@@ -1765,9 +1765,9 @@ def add_reaction_library_to_edge(self, reaction_library, requires_rms=False):
                 # This unimolecular library reaction is flagged as `elementary_high_p` and has Arrhenius type kinetics.
                 # We should calculate a pressure-dependent rate for it
                 if len(rxn.reactants) == 1:
-                    self.process_new_reactions(new_reactions=[rxn], new_species=rxn.reactants[0])
+                    self.process_new_reactions(new_reactions=[rxn], new_species=rxn.reactants[0], requires_rms=requires_rms)
                 else:
-                    self.process_new_reactions(new_reactions=[rxn], new_species=rxn.products[0])
+                    self.process_new_reactions(new_reactions=[rxn], new_species=rxn.products[0], requires_rms=requires_rms)
 
         # Perform species constraints and forbidden species checks
         for spec in self.new_species_list:

rmgpy/rmg/pdep.py

@@ -917,7 +917,7 @@ def update(self, reaction_model, pdep_settings):
                                              f'from the {rxn.library} library, and was not added to the model')
                                 break
                         else:
-                            reaction_model.add_reaction_to_core(net_reaction)
+                            reaction_model.add_reaction_to_core(net_reaction, requires_rms=True)
                     else:
                         # Check whether netReaction already exists in the edge as a LibraryReaction
                         for rxn in reaction_model.edge.reactions:
@@ -929,7 +929,7 @@ def update(self, reaction_model, pdep_settings):
                                              f'from the {rxn.library} library, and was not added to the model')
                                 break
                         else:
-                            reaction_model.add_reaction_to_edge(net_reaction)
+                            reaction_model.add_reaction_to_edge(net_reaction, requires_rms=True)
 
                 # Set/update the net reaction kinetics using interpolation model
                 kdata = K[:, :, i, j].copy()