DatabaseError with Thermo Parameters for F

[studies9]

DatabaseError related to thermo parameter estimation for fluorine-containing molecules in RMG-Py. Specifically, the error message is:
DatabaseError: Unable to determine thermo parameters for atom {'*': <Atom 'F'>} in molecule <Molecule "OOC(F)F">: no data for node R or any of its ancestors in database group.

I encounter this issue both with and without a seed mechanism. For instance, when using a seed mechanism, I receive the following error:
DatabaseError: Unable to determine thermo parameters for atom {'*': <Atom 'F'>} in molecule <Molecule "OCF">: no data for node R or any of its ancestors in database group.

[JacksonBurns]

Searching this molecule on rmg.mit.edu yields results - do you have the Fluorine library included in your thermoLibraries?

[studies9]

Data sources

database(
thermoLibraries = ['primaryThermoLibrary', 'Fluorine'],
reactionLibraries = [],
seedMechanisms = [],
kineticsDepositories = ['training'],
kineticsFamilies = 'default',
kineticsEstimator = 'rate rules',
)

List of species

species(
label='CH2F2',
reactive=True,
structure=SMILES("FCF"),
)
species(
label='O2',
reactive=True,
structure=SMILES("[O][O]"),
)

species(
label='Ar',
reactive=True,
structure=SMILES("[Ar]"),
)

Reaction systems

simpleReactor(
temperature=(600,'K'),
pressure=(1.0,'bar'),
initialMoleFractions={
"CH2F2": 0.025, "Ar": 0.95, "O2": 0.025,
},
terminationConversion={
'O2': 0.9999,
},
terminationTime=(1e12,'s'),
)

simulator(
atol=1e-16,
rtol=1e-8,
)

model(
toleranceKeepInEdge=1e-5,
toleranceMoveToCore=0.01,
toleranceInterruptSimulation=0.1,
maximumEdgeSpecies=100000
)

options(
units='si',
generateOutputHTML=False,
generatePlots=False,
saveEdgeSpecies=True,
saveSimulationProfiles=True,
)

[JacksonBurns]

Try adding the CHOF_G4 thermo library as well

[studies9]

The CHOF_G4 library is not available in our current RMG version. How can I obtain it?

[JacksonBurns]

You need to upgrade your version of RMG-database, see here if you installed form source: https://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/updatingSourceCode.html?highlight=update+database

[REACTION3]

Loading frequencies library from halogens_G4.py in /home/ubuntu/miniconda3/envs/rmg_env/share/rmgdatabase/statmech/libraries...
Error: Error while reading database '/home/ubuntu/miniconda3/envs/rmg_env/share/rmgdatabase/statmech/libraries/halogens_G4.py'.
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/rmg_env/bin/rmg.py", line 118, in
main()
File "/home/ubuntu/miniconda3/envs/rmg_env/bin/rmg.py", line 112, in main
rmg.execute(**kwargs)
File "/home/ubuntu/miniconda3/envs/rmg_env/lib/python3.7/site-packages/rmgpy/rmg/main.py", line 673, in execute
self.initialize(**kwargs)
File "/home/ubuntu/miniconda3/envs/rmg_env/lib/python3.7/site-packages/rmgpy/rmg/main.py", line 496, in initialize
self.load_database()
File "/home/ubuntu/miniconda3/envs/rmg_env/lib/python3.7/site-packages/rmgpy/rmg/main.py", line 374, in load_database
depository=False, # Don't bother loading the depository information, as we don't use it
File "/home/ubuntu/miniconda3/envs/rmg_env/lib/python3.7/site-packages/rmgpy/data/rmg.py", line 106, in load
self.load_statmech(os.path.join(path, 'statmech'), statmech_libraries, depository)
File "/home/ubuntu/miniconda3/envs/rmg_env/lib/python3.7/site-packages/rmgpy/data/rmg.py", line 197, in load_statmech
self.statmech.load(path, statmech_libraries, depository)
File "/home/ubuntu/miniconda3/envs/rmg_env/lib/python3.7/site-packages/rmgpy/data/statmech.py", line 517, in load
self.load_libraries(os.path.join(path, 'libraries'), libraries)
File "/home/ubuntu/miniconda3/envs/rmg_env/lib/python3.7/site-packages/rmgpy/data/statmech.py", line 541, in load_libraries
library.load(os.path.join(root, f), self.local_context, self.global_context)
File "/home/ubuntu/miniconda3/envs/rmg_env/lib/python3.7/site-packages/rmgpy/data/base.py", line 239, in load
exec(f.read(), global_context, local_context)
File "", line 18, in
TypeError: 'NoneType' object is not subscriptable

[rwest]

You probably need to update RMG-Py also, in order to read the new database.
The stack trace you post says the error is in File "/home/ubuntu/miniconda3/envs/rmg_env/lib/python3.7/site-packages/rmgpy/data/base.py", line 239, in load exec(f.read(), global_context, local_context)
But I think line 239 of the file rmgpy/data/base.py hasn't contained the code exec(f.read(), global_context, local_context) since May 2021.

In my experience, easiest to install an entire new version, in a brand new environment (give it a new name, not rmg_env). This greatly increases the chance of it working, and also decreases the chance of you messing up your old version.

[studies9]

Traceback (most recent call last):
File "/home/ubuntu/Downloads/RMG-Py/rmg.py", line 118, in
main()
File "/home/ubuntu/Downloads/RMG-Py/rmg.py", line 112, in main
rmg.execute(**kwargs)
File "/home/ubuntu/Downloads/RMG-Py/rmgpy/rmg/main.py", line 752, in execute
self.initialize(**kwargs)
File "/home/ubuntu/Downloads/RMG-Py/rmgpy/rmg/main.py", line 553, in initialize
self.reaction_model.add_species_to_edge(spec)
File "/home/ubuntu/Downloads/RMG-Py/rmgpy/rmg/model.py", line 1178, in add_species_to_edge
self.edge.phase_system.phases["Default"].add_species(spec)
File "/home/ubuntu/Downloads/RMG-Py/rmgpy/rmg/reactors.py", line 294, in add_species
spec = to_rms(spc)
File "/home/ubuntu/Downloads/RMG-Py/rmgpy/rmg/reactors.py", line 699, in to_rms
rad = rms.getspeciesradius(atomnums, bondnum)
NameError: name 'rms' is not defined
i have installed an entire new version, but then too this error comes up

[JacksonBurns]

It looks like you missed steps 11. and/or 12. in the installation instructions here: https://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/anacondaDeveloper.html
or you are not running RMG-Py from inside the correct conda environment.

An alternative is to install the Docker image, which avoids having to do this manual installation: https://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/index.html#recommended-install-docker