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

This allows the Cantera yaml writer to live alongside it

…ubstituted for 'yml' Attach the YAMLWriter listener Work on the yaml writing for cantera Renaming yml_test to cantera This is for writing Cantera yaml files updated set_cantera_kinetics in falloff.py spelled "high" wrong in set_cantera_kinetics added write_cantera_inputs to falloff.pyx for Troe reactions Fixing Lindemann and Troe deleted write_cantera_inputs, restructured using to_cantera > set_cantera_kinetics > to_cantera_kinetics for Lindemann and Troe reactions added efficiencies restructured cantera.py, now includes MultiArrhenius reactions added Chebyshev restructured and added in RMG equations added in Surface Arrhenius added sticking coefficient :) use_chemkin_identifier=True when making Cantera objects This uses the correct species names Dump yaml in the order of the dict, not alphabetical remove quotes from species names Handle duplicate reactions For MultiArrhenius and MultiPDepArrhenius kinetics we need to make more than one reaction in the list of reactions for Cantera yaml. (at least until this is implemented: Cantera/enhancements#132 ) added the beginnings of the catalysis edits still need to edit 'state' and fix 'vector<double>' error fixed for catalysis. Separates gas and surface reactions in the "reactions" section. Now just need to fix the bug with the C.Pt(22) stuff. Stay strong, shortie wip changes for stickingcoeffcient issue fixed "sites" v. "size" problem, yaml_writer now works for catalysis and gas phase. Time for pull request? Removing comments Trying cantera 2.5+ from conda-forge in environment.yml I suspected that the unit tests are failing because the new code can't work with cantera 2.3 from the RMG channel Trying Cantera 2.5+ from cantera channel in environment.yml Added in doc strings to methods. Removed unused imports Removed unused import from reaction.py renamed cantera.py to cantera_.py. Edited import statement in main.py to reflect this name change. Edited reaction.py so depreciated Cantera term is not used. Edited reactionTest.py so that test_falloff is successful for third body reactions Edited high_rate, low_rate in set_cantera_kinetics() for Lindemann reactions. Can now extract the high & low rate from the Cantera Lindemann object, which is necessary for reactionTest.py to pass successfully. restructed set_cantera_kinetics() and to_cantera_kinetics() for Lindemann reactions in falloff.pyx. Added Lindemann reaction checks in falloff.pyx Minor stylish change in falloff.py/ troe to cantera cleaning up falloff.pyx after rebase conflicts

…ubstituted for 'yml'

This is for writing Cantera yaml files

deleted write_cantera_inputs, restructured using to_cantera > set_cantera_kinetics > to_cantera_kinetics for Lindemann and Troe reactions

This uses the correct species names

For MultiArrhenius and MultiPDepArrhenius kinetics we need to make more than one reaction in the list of reactions for Cantera yaml. (at least until this is implemented: Cantera/enhancements#132 )

still need to edit 'state' and fix 'vector<double>' error

Separates gas and surface reactions in the "reactions" section. Now just need to fix the bug with the C.Pt(22) stuff. Stay strong, shortie

…and gas phase. Time for pull request?

I suspected that the unit tests are failing because the new code can't work with cantera 2.3 from the RMG channel

… to reflect this name change. Edited reaction.py so depreciated Cantera term is not used. Edited reactionTest.py so that test_falloff is successful for third body reactions

…actions. Can now extract the high & low rate from the Cantera Lindemann object, which is necessary for reactionTest.py to pass successfully.

…mann reactions in falloff.pyx. Added Lindemann reaction checks in falloff.pyx

Previously the if was always True

I think this is the same.

Because that's what it is

The call rate = ct.LindemannRate(low_rate, high_rate, falloff) was causing TypeError: Argument 'rate' has incorrect type (expected cantera._cantera.Arrhenius, got cantera._cantera.ArrheniusRate) I think the ct.LindemannRate expects an Arrhenius not an ArrheniusRate. Thdis was with cantera 2.6.0 py37hb93dfd8_0 cantera running on the Ubuntu CI

Still doing things mostly the same way, just renaming variables, combining some blocks, removing X from the gas phase,

Renamed some functions and (i think) simplified some loops

The call rmgpy/reaction.py:339: in rmgpy.reaction.Reaction.to_cantera rate = ct.TroeRate( was causing TypeError: Argument 'rate' has incorrect type (expected cantera._cantera.Arrhenius, got cantera._cantera.ArrheniusRate) I think the ct.LindemannRate expects an Arrhenius not an ArrheniusRate. Thdis was with cantera 2.6.0 py37hb93dfd8_0 cantera running on the Ubuntu CI

This was moved into the testing folder. I don't think any of the other changes were deliberate.

This had been done on a branch. Not sure if it is needed as things got moved in a confusing rebase.

I think final edits to this file were mostly just accidents in rebasing, and the version on main is probably ok.

I think this was a rebasing error.

This function is only used in one place for one very specific thing so I inlined it. It also had a vague name. I then commented it out, because I'm not clear why it's needed. If it is needed, we can restore it (and put a comment as to why)

The reactionTest.py is failing. From the failure I can't see why this would be the cause, but in the idea of change-one-thing-at-a-time I'm reverting the most recent change since I think the tests USED to pass. This reverts commit a8eaa3b.

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

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

Commits on Apr 1, 2024

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

Commits on Apr 1, 2024