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Create YAML file outputs in RMG for use in Cantera #2321

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Create YAML file outputs in RMG for use in Cantera #2321

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d286485
Save cantera files that were made from chemkin files to a separate fo…
rwest Jun 6, 2024
0adcae3
Rename yml to yaml_rms, because it was specific to RMS
Nora-Khalil Jun 15, 2022
23315b7
Enable Cantera-YAML writing.
Nora-Khalil Jun 13, 2022
becf208
Minor: Fix a Cython declaration in a Reaction method.
rwest Aug 2, 2024
133a100
Reworking the Elements blocks in cantera yaml writer.
rwest Aug 2, 2024
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2 changes: 1 addition & 1 deletion rmgpy/reaction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1429,7 +1429,7 @@ def is_balanced(self):
from rmgpy.molecule.element import element_list
from rmgpy.molecule.fragment import CuttingLabel, Fragment

cython.declare(reactant_elements=dict, product_elements=dict, molecule=Graph, atom=Vertex, element=Element,
cython.declare(reactant_elements=dict, product_elements=dict, molecule=Molecule, atom=Atom, element=Element,
reactants_net_charge=cython.int, products_net_charge=cython.int)

reactant_elements = {}
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6 changes: 4 additions & 2 deletions rmgpy/rmg/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,8 @@
from rmgpy.thermo.thermoengine import submit
from rmgpy.tools.plot import plot_sensitivity
from rmgpy.tools.uncertainty import Uncertainty, process_local_results
from rmgpy.yml import RMSWriter
from rmgpy.yaml_rms import RMSWriter
from rmgpy.yaml_cantera import CanteraWriter
from rmgpy.rmg.reactors import Reactor

################################################################################
Expand Down Expand Up @@ -757,6 +758,7 @@ def register_listeners(self):

self.attach(ChemkinWriter(self.output_directory))
self.attach(RMSWriter(self.output_directory))
self.attach(CanteraWriter(self.output_directory))

if self.generate_output_html:
self.attach(OutputHTMLWriter(self.output_directory))
Expand Down Expand Up @@ -1788,7 +1790,7 @@ def generate_cantera_files(self, chemkin_file, **kwargs):
"""
transport_file = os.path.join(os.path.dirname(chemkin_file), "tran.dat")
file_name = os.path.splitext(os.path.basename(chemkin_file))[0] + ".yaml"
out_name = os.path.join(self.output_directory, "cantera", file_name)
out_name = os.path.join(self.output_directory, "cantera_from_ck", file_name)
if "surface_file" in kwargs:
out_name = out_name.replace("-gas.", ".")
cantera_dir = os.path.dirname(out_name)
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