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Could not determine representative localized structures #1598
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So now, I am confused. Does it mean that with one SMILES, we can generate several different structures, and now the RMG cannot determine which one to use? Looking forward to the solution, it is very important for us to get a model with gasoline and 2-Ethylhexyl-nitrate blend. |
Yes, SMILES represent localized structures, while many species have delocalization (resonance). In this case, the only difference is whether the benzene ring is represented with alternating S/D bonds or with aromatic bonds (with bond orders of 1.5). |
@mliu49, it seems to me that in filtration.py, |
I've discovered that Unfortunately, I haven't been able to create an easily replicable test case. I can't seem to recreate the error by creating the molecule from scratch in an ipython notebook. Running the input file does generate the error consistently though, and sorting atoms for each molecule in |
As a general user is there any easy way to fix this problem since I have no idea how to actually sort atoms for each molecule in mol_list. Thanks! |
Sorry, that wasn't necessarily intended to be a user fix. If you really want and are comfortable with editing code, you can add the following lines here:
The purpose of my comment was primarily to help us debug this issue. Once we do find the root cause, we'll patch it and you can update your local version. |
@alongd I updated RMG with "conda update rmg rmgdatabase -c rmg" command, but I still get the same error. When I installed RMG, I followed "For Basic Users: Binary installation using Anaconda for Unix-Based Systems" guide. Should I install RMG again by following "For Developers: Installation by Source Using Anaconda Environment" guide so that this error will disappear? |
Yes, the developer installation is able to be updated by the user (so it should solve your issue). The basic version is updated periodically, the next update should be son (end of May or early June). So go ahead and install the developer version. |
Fixed by #1600 |
Topic
General area which your question is related to.
Context
With running one RMG simulation, I get an error:
Question
What does this error mean? Does this mean RMG cannot generate the above species' structure? And how to fix this problem? I attach the input file below,
input_gasoline_C8H17NO3_baseline_T_0.01_C_0.95_725_.zip
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