to_rms issue

[NUSCondy]

Hi @alongd ,

This issue seems to be related with RMS module. I have tried two different tests, one use AramcoMech_2.0 and the other is an example case. Both encountered bugs, shown below:

**Traceback (most recent call last):
File "/home/zhuqiren/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/pseudo_python_cli.py", line 308, in main
python(**vars(ns))
File "/home/zhuqiren/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/pseudo_python_cli.py", line 59, in python
scope = runpy.run_path(script, run_name="main")
File "/home/zhuqiren/anaconda3/envs/rmg_env/lib/python3.7/runpy.py", line 263, in run_path
pkg_name=pkg_name, script_name=fname)
File "/home/zhuqiren/anaconda3/envs/rmg_env/lib/python3.7/runpy.py", line 96, in _run_module_code
mod_name, mod_spec, pkg_name, script_name)
File "/home/zhuqiren/anaconda3/envs/rmg_env/lib/python3.7/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/home/zhuqiren/RMG-Py/rmg.py", line 118, in
main()
File "/home/zhuqiren/RMG-Py/rmg.py", line 112, in main
rmg.execute(kwargs)
File "/home/zhuqiren/RMG-Py/rmgpy/rmg/main.py", line 755, in execute
trimolecular_react=self.trimolecular_react)
File "/home/zhuqiren/RMG-Py/rmgpy/rmg/model.py", line 679, in enlarge
self.update_unimolecular_reaction_networks()
File "/home/zhuqiren/RMG-Py/rmgpy/rmg/model.py", line 1872, in update_unimolecular_reaction_networks
network.update(self, self.pressure_dependence)
File "/home/zhuqiren/RMG-Py/rmgpy/rmg/pdep.py", line 893, in update
reaction_model.add_reaction_to_edge(net_reaction)
File "/home/zhuqiren/RMG-Py/rmgpy/rmg/model.py", line 1478, in add_reaction_to_edge
self.edge.phase_system.phases["Default"].add_reaction(rxn)
File "/home/zhuqiren/RMG-Py/rmgpy/rmg/reactors.py", line 217, in add_reaction
self.reactions.append(to_rms(rxn, species_names=self.names, rms_species_list=self.species))
File "/home/zhuqiren/RMG-Py/rmgpy/rmg/reactors.py", line 467, in to_rms
kinetics = to_rms(obj.kinetics)
File "/home/zhuqiren/RMG-Py/rmgpy/rmg/reactors.py", line 483, in to_rms
raise ValueError(f"Couldn't convert object of type {errortype} to an RMS object")
ValueError: Couldn't convert object of type <class 'NoneType'> to an RMS object

****Traceback (most recent call last):
File "/home/zhuqiren/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/pseudo_python_cli.py", line 308, in main
python(**vars(ns))
File "/home/zhuqiren/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/pseudo_python_cli.py", line 59, in python
scope = runpy.run_path(script, run_name="main")
File "/home/zhuqiren/anaconda3/envs/rmg_env/lib/python3.7/runpy.py", line 263, in run_path
pkg_name=pkg_name, script_name=fname)
File "/home/zhuqiren/anaconda3/envs/rmg_env/lib/python3.7/runpy.py", line 96, in _run_module_code
mod_name, mod_spec, pkg_name, script_name)
File "/home/zhuqiren/anaconda3/envs/rmg_env/lib/python3.7/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/home/zhuqiren/RMG-Py/rmg.py", line 118, in
main()
File "/home/zhuqiren/RMG-Py/rmg.py", line 112, in main
rmg.execute(kwargs)
File "/home/zhuqiren/RMG-Py/rmgpy/rmg/main.py", line 695, in execute
self.initialize(kwargs)
File "/home/zhuqiren/RMG-Py/rmgpy/rmg/main.py", line 577, in initialize
self.reaction_model.add_reaction_library_to_edge(library)
File "/home/zhuqiren/RMG-Py/rmgpy/rmg/model.py", line 1725, in add_reaction_library_to_edge
self.add_reaction_to_edge(rxn)
File "/home/zhuqiren/RMG-Py/rmgpy/rmg/model.py", line 1478, in add_reaction_to_edge
self.edge.phase_system.phases["Default"].add_reaction(rxn)
File "/home/zhuqiren/RMG-Py/rmgpy/rmg/reactors.py", line 217, in add_reaction
self.reactions.append(to_rms(rxn, species_names=self.names, rms_species_list=self.species))
File "/home/zhuqiren/RMG-Py/rmgpy/rmg/reactors.py", line 467, in to_rms
kinetics = to_rms(obj.kinetics)
File "/home/zhuqiren/RMG-Py/rmgpy/rmg/reactors.py", line 416, in to_rms
efficiencies = {spc.label: float(val) for spc, val in obj.efficiencies.items() if val != 1}
File "/home/zhuqiren/RMG-Py/rmgpy/rmg/reactors.py", line 416, in
efficiencies = {spc.label: float(val) for spc, val in obj.efficiencies.items() if val != 1}
AttributeError: 'rmgpy.molecule.molecule.Molecule' object has no attribute 'label'

The input files are attached
input1.txt
inputAramco.txt
:

[alongd]

@mjohnson541, would you know?

[NUSCondy]

Hi,
FYI, for the ethane example case, if I comment the pressure dependence options, it becomes good again.
For the one using AramcoMech_2.0, such a change doesn't work.

[mjohnson541]

We're working on these in #2208. I think the second one is at least fixed on that branch.

[NUSCondy]

Hi,

FYI, I have tried to build an ethane oxidation mechanism using Aramcomech_2.0 thermo and kinetics library with RMG I installed in Sept 2020. It seems that it is okay with that old version.

[NUSCondy]

Hi @mjohnson541,
Is this issue fixed on the latest version or on other branch?

[mjohnson541]

Sorry, I must've missed this, I think this is fixed on the other branch, which hopefully will be on main soon.

[NUSCondy]

Hi @mjohnson541 ,
It is good to hear that. I also have a question about to_rms option. Since sensitivity analysis or simulation on model is optional, is it necessary to construct rms object when using RMG with these options not chosen?

[mjohnson541]

So RMG has to simulate the model as a part of mechanism generation. Before adding RMS, RMG relied on its own internal simulation codes that weren't particularly well optimized and were difficult to extend. Using RMS allows us to write new reactors easily and include simulations where the rate constants aren't constant efficiently. The long term plan is to switch over all the reactors over to RMS.

[NUSCondy]

Got it! Thank you for the explanation!

[github-actions]

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