search

ReactionMechanismGenerator / RMG-Py

Python version of the amazing Reaction Mechanism Generator (RMG).
http://reactionmechanismgenerator.github.io/RMG-Py/
Other
382 stars 226 forks source link

Import chemkin library error #1594

Closed AH9316 closed 1 year ago

AH9316 commented 5 years ago

Topic

General area which your question is related to.

Context

We try to import the library into RMG database. The RMG shows us that "NotImplementedError: Can't check isomorphism of lists with 4 species/molecules".

Question

How to fix it?

alongd commented 5 years ago

My guess is that you probably have reactions with more than three reactants or products. Our solver does not support these, and looks like the parser was set not to process them. If this is not the case, or if you're unsure, paste the complete error trace message you get, and upload the files you are converting

AH9316 commented 5 years ago

Thank you for your response. We checked the reactions and we found that there is one reaction,which is "C7H16<=>CH3+2C2H4+C2H5", causes this error. We imported chemkin library successfully when we commented it out. In my opinion, I don't think the reason for this error is that we have more than 3 products in the right hand side of the reaction equation, because we successfully imported library with other reactions that have more than 3 products.

Below are the chemkin file and species dictionary we create, hope it can help you guys to improve RMG import function and figure out why this error appears. chemkin_speciesdictionary.zip

alongd commented 5 years ago

Could you try replacing "C7H16<=>CH3+2C2H4+C2H5" with "C7H16<=>CH3+C2H4+C2H4+C2H5" just for the exercise? Perhaps the coefficient before C2H4 was problematic, and if so maybe RMG should give a more helpful error message in the future

AH9316 commented 5 years ago

It does not work and the RMG shows the same error: "NotImplementedError: Can't check isomorphism of lists with 4 species/molecules Exception NotImplementedError: NotImplementedError("Can't check isomorphism of lists with 4 species/molecules",) in 'rmgpy.reaction.isomorphic_species_lists' ignored NotImplementedError: Can't check isomorphism of lists with 4 species/molecules Exception NotImplementedError: NotImplementedError("Can't check isomorphism of lists with 4 species/molecules",) in 'rmgpy.reaction.isomorphic_species_lists' ignored"

alongd commented 5 years ago

OK, so seems like the error message is informative enough after all.

AH9316 commented 5 years ago

As a user, personally, this error message is not very obviously. We actually spend a lot of time yesterday to find this reaction. When I first saw this message, I thought there is something wrong with my species dictionary. RMG is a very powerful software, we actually got good results using mechanisms that generated by RMG. And we still get some problems with some big molecular, such as benzene, toluene. I hope we can see the version 2.4.0 soon at the end of May.

github-actions[bot] commented 1 year ago

This issue 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 issue, otherwise it will automatically be closed in 30 days.