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Add initial species in core before seed mechanism #2382

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Add initial species in core before seed mechanism #2382

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54775a8
add initial species in core before seed mechanism to make sure initia…
hwpang Mar 2, 2023
b772183
Move library to edge before adding initial species to core to make su…
hwpang Sep 12, 2023
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33 changes: 18 additions & 15 deletions rmgpy/rmg/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -614,23 +614,35 @@ def initialize(self, **kwargs):

# Initialize reaction model

# 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:
self.reaction_model.add_seed_mechanism_to_core(seed_mechanism, react=False)

# Reaction libraries: add species and reactions from reaction library to the edge so
# that RMG can find them if their rates are large enough
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")]:
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:
self.reaction_model.add_seed_mechanism_to_core(seed_mechanism, react=False)

# 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 @@ -690,15 +702,6 @@ 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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