update loader tool to include surface mech paths

Author: sevyharris

rmgpy/tools/loader.py

@@ -50,6 +50,7 @@ def load_rmg_job(
     use_java=False,
     use_chemkin_names=False,
     check_duplicates=True,
+    surface_path=None,
 ):
     # The argument is an RMG-Py input file
     rmg = load_rmg_py_job(
@@ -59,13 +60,14 @@ def load_rmg_job(
         generate_images,
         use_chemkin_names=use_chemkin_names,
         check_duplicates=check_duplicates,
+        surface_path=surface_path,
     )
 
     return rmg
 
 
 def load_rmg_py_job(input_file, chemkin_file=None, species_dict=None, generate_images=True,
-                    use_chemkin_names=False, check_duplicates=True):
+                    use_chemkin_names=False, check_duplicates=True, surface_path=None):
     """
     Load the results of an RMG-Py job generated from the given `input_file`.
     """
@@ -83,7 +85,8 @@ def load_rmg_py_job(input_file, chemkin_file=None, species_dict=None, generate_i
         species_dict = os.path.join(os.path.dirname(input_file), 'chemkin', 'species_dictionary.txt')
     species_list, reaction_list = load_chemkin_file(chemkin_file, species_dict,
                                                     use_chemkin_names=use_chemkin_names,
-                                                    check_duplicates=check_duplicates)
+                                                    check_duplicates=check_duplicates,
+                                                    surface_path=surface_path)
 
     # Created "observed" versions of all reactive species that are not explicitly
     # identified as  "constant" species

rmgpy/tools/uncertainty.py

@@ -336,7 +336,7 @@ def load_database(self, kinetics_families='all', kinetics_depositories=None, the
                 family.add_rules_from_training(thermo_database=self.database.thermo)
                 family.fill_rules_by_averaging_up(verbose=True)
 
-    def load_model(self, chemkin_path, dictionary_path, transport_path=None):
+    def load_model(self, chemkin_path, dictionary_path, transport_path=None, surface_path=None):
         """
         Load a RMG-generated model into the Uncertainty class
         `chemkin_path`: path to the chem_annotated.inp CHEMKIN mechanism
@@ -351,7 +351,8 @@ def load_model(self, chemkin_path, dictionary_path, transport_path=None):
 
         self.species_list, self.reaction_list = load_chemkin_file(chemkin_path,
                                                                   dictionary_path=dictionary_path,
-                                                                  transport_path=transport_path)
+                                                                  transport_path=transport_path,
+                                                                  surface_path=surface_path)
 
     def retrieve_saturated_species_from_list(self, species):
         """