Fixing .kinetics.py file
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This is to read in somebody's chemkin file, and turn it into a thermo library. Eventually this should help you identify what the species are, but it doesn't do that quite yet.
Correct docstring in convertThermo.py file
Added some argument parsing, etc.
In order to let RMG calculate reactions etc. for the imported species, we need to make them into the right kind of species, estimate massage their thermo, etc. It is now at a point where you can expand the reaction model (I think)
Making a class, etc. and make it cope with conserved case in chemkin reader.
Reactions that include species whose chemical formula doesn't match anything in the chemkin file are deleted from the edge
Also give it a clue for 'mb'= Methyl butanoate, to test how much this helps. Gets from 59 to 89!
If you're using QTconsole, it displays them inline in various points. It also saves them in the species directory.
Helps you spot mistakes, and helps choose between alternatives.
This should avoid the "check absolutely everything" when you run low on species. When you match a species, you need to re-check the reactions that it is involved in, in case you can learn anything new from them.
(Presumably it was in the core??)
Move the "check reactions" into a separate function, and now we can put it inside a while loop, so that if one set of matches invalidates some reactions they are re-checked immediately.
Currently makes a new prunedVotes matrix, and prints it, but doesn't use it.
Currently set at 150 kJ/mol Perhaps should depend on how good other matches are.
Before it would use pruned votes for one-to-many check, and all votes for many-to-one. Now it's pruned in both directions.
May not even help, but this is the slowest function
This is reused several times, and should be its own function.
This should store all chemkin-defined reactions between identified species
I've seen bugs like this before. *sigh* :-( In this case it was skipping alternate reactions.
Hopefully this will be fixed one day... (ref ReactionMechanismGenerator#140 and ReactionMechanismGenerator#141)
These take a long time to make and I'm not currently using them, so by default don't make them.
Change the dictionary keys from variables to strings and add a comma to the end of "rmgPyKinetics".
Might create confusion when importing file, so using the underscore
rwest
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Jun 7, 2023
This is a combination of 12 commits, as we tried everything under the sun to debug the CI. But they all cancelled out when merged (apart from fixing a typo in a comment) - This is the 1st commit message: CI: trying to force ubuntu-20.04 instead of ubuntu-latest (temporary) While we figure out what's happening, let's try an older ubuntu. - This is commit message #2: fixup! CI: trying to force ubuntu-20.04 instead of ubuntu-latest (temporary) - This is the commit message #3: Switch back to ubuntu-latest But leave a 20.04 in the matrix build - This is the commit message #4: Trying libstdcxx-ng < 13 in Conda environment. Trying to debug. If this works it should be put in docker file too. Or, better, the real cause found and fixed. - This is the commit message #5: fix typo in env, undo ubuntu os changes, set gcc version in CI to 6 this system object of this version is being provided by gcc, and the runners no longer come prepackaged with it since its old (?) - This is the commit message #6: it wasn't the gcc version - This is the commit message #7: it was the julia version, 1.9.0 is brokey as reported at conda-forge/julia-feedstock#253 the latest release of julia (1.9.0) is brokey, don't use it (put !=1.9.0 in the environment file) - This is the commit message #8: make mac and ubuntu use the same cxx library - This is the commit message #9: but what if it was rdkit all along? - This is the commit message ReactionMechanismGenerator#10: Revert "but what if it was rdkit all along?" because it wasn't - This is the commit message ReactionMechanismGenerator#11: Revert "make mac and ubuntu use the same cxx library" cos it didn't work - This is the commit message ReactionMechanismGenerator#12: Revert "it was the julia version, 1.9.0 is brokey" but it wasn't
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This pull request is being automatically marked as stale because it has not received any interaction in the last 90 days. Please leave a comment if this is still a relevant pull request, otherwise it will automatically be closed in 30 days. |
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This pull request is being automatically marked as stale because it has not received any interaction in the last 90 days. Please leave a comment if this is still a relevant pull request, otherwise it will automatically be closed in 30 days. |
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The dot in the
.kinetics.py(the first one) might cause some confusion. Switched it to an underscore.A couple other fixes to the file printing, but should be working now.