Read core species from external dictionary

Sometimes there are too many species to comfortably fit in one input file. This lets you outsource them to an external species dictionary so the input.py file can stay small enough to handle.

Author: sevyharris

rmgpy/rmg/input.py

@@ -40,6 +40,7 @@
 from rmgpy.data.vaporLiquidMassTransfer import (
     liquidVolumetricMassTransferCoefficientPowerLaw,
 )
+from rmgpy.chemkin import load_species_dictionary
 from rmgpy.exceptions import DatabaseError, InputError
 from rmgpy.molecule import Molecule
 from rmgpy.molecule.fragment import Fragment
@@ -190,6 +191,16 @@ def convert_binding_energies(binding_energies):
     return new_dict
 
 
+def core_species_file(species_dictionary_file):
+    # all species here are assumed to be reactive
+    rmg.species_core_file = species_dictionary_file
+    new_species_dict = load_species_dictionary(species_dictionary_file)
+    for key in new_species_dict:
+        label = new_species_dict[key].label
+        structure = new_species_dict[key].molecule[0]
+        species(label, structure, reactive=True, cut=False, size_threshold=None)
+
+
 def species(label, structure, reactive=True, cut=False, size_threshold=None):
     logging.debug('Found {0} species "{1}" ({2})'.format('reactive' if reactive else 'nonreactive',
                                                          label,
@@ -1560,6 +1571,7 @@ def read_input_file(path, rmg0):
         'False': False,
         'database': database,
         'catalystProperties': catalyst_properties,
+        'coreSpeciesFile': core_species_file,
         'species': species,
         'forbidden': forbidden,
         'SMARTS': smarts,