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add initial species in core before seed mechanism to make sure initia…
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…l species in phase.names
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hwpang authored and JacksonBurns committed Apr 16, 2023
1 parent 856f72a commit 0835cbf
Showing 1 changed file with 19 additions and 16 deletions.
35 changes: 19 additions & 16 deletions rmgpy/rmg/main.py
Original file line number Diff line number Diff line change
Expand Up @@ -585,6 +585,25 @@ def initialize(self, **kwargs):

# Initialize reaction model

# Also always add in a few bath gases (since RMG-Java does)
for label, smiles in [('Ar', '[Ar]'), ('He', '[He]'), ('Ne', '[Ne]'), ('N2', 'N#N')]:
molecule = Molecule().from_smiles(smiles)
spec, is_new = self.reaction_model.make_new_species(molecule, label=label, reactive=False)
if is_new:
self.initial_species.append(spec)

for spec in self.initial_species:
submit(spec, self.solvent)

# Add nonreactive species (e.g. bath gases) to core first
# This is necessary so that the PDep algorithm can identify the bath gas
for spec in self.initial_species:
if not spec.reactive:
self.reaction_model.enlarge(spec)
for spec in self.initial_species:
if spec.reactive:
self.reaction_model.enlarge(spec)

# Seed mechanisms: add species and reactions from seed mechanism
# DON'T generate any more reactions for the seed species at this time
for seed_mechanism in self.seed_mechanisms:
Expand All @@ -595,13 +614,6 @@ def initialize(self, **kwargs):
for library, option in self.reaction_libraries:
self.reaction_model.add_reaction_library_to_edge(library)

# Also always add in a few bath gases (since RMG-Java does)
for label, smiles in [('Ar', '[Ar]'), ('He', '[He]'), ('Ne', '[Ne]'), ('N2', 'N#N')]:
molecule = Molecule().from_smiles(smiles)
spec, is_new = self.reaction_model.make_new_species(molecule, label=label, reactive=False)
if is_new:
self.initial_species.append(spec)

# Perform species constraints and forbidden species checks on input species
for spec in self.initial_species:
if self.database.forbidden_structures.is_molecule_forbidden(spec.molecule[0]):
Expand Down Expand Up @@ -654,15 +666,6 @@ def initialize(self, **kwargs):
spec.get_liquid_volumetric_mass_transfer_coefficient_data()
spec.get_henry_law_constant_data()

# Add nonreactive species (e.g. bath gases) to core first
# This is necessary so that the PDep algorithm can identify the bath gas
for spec in self.initial_species:
if not spec.reactive:
self.reaction_model.enlarge(spec)
for spec in self.initial_species:
if spec.reactive:
self.reaction_model.enlarge(spec)

# chatelak: store constant SPC indices in the reactor attributes if any constant SPC provided in the input file
# advantages to write it here: this is run only once (as species indexes does not change over the generation)
if self.solvent is not None:
Expand Down

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