Explicit valence for atom # 9 C greater than permitted

[arnab37]

I was running RMG calculation on a mixture of molecular nitrogen, methane and water at very high temperature and low pressure ranges to see any growth kinetics (formation of PAHs and N-PAHs). I think the RMG calculation is stuck for the last few hours. I am attaching the input file for your review. The messages that are printed during the run as follows:

---

After model enlargement:
    The model core has 41 species and 0 reactions
    The model edge has 0 species and 0 reactions


Initialization complete. Starting model generation.

conditions choosen for reactor 0 were: T = 2500.0 K, P = 6.907755278982137e-05 bar,
Generating initial reactions...
For reaction generation 1 process is used.
[17:26:46] Explicit valence for atom # 7 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:26:46] Explicit valence for atom # 7 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:26:46] Explicit valence for atom # 7 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:26:46] Explicit valence for atom # 7 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:26:46] Explicit valence for atom # 7 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:26:46] Explicit valence for atom # 7 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:26:46] Explicit valence for atom # 7 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:26:47] Explicit valence for atom # 6 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:26:47] Explicit valence for atom # 6 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:26:47] Explicit valence for atom # 6 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:26:47] Explicit valence for atom # 7 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:26:47] Explicit valence for atom # 7 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:26:47] Explicit valence for atom # 7 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:26:47] Explicit valence for atom # 7 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:26:47] Explicit valence for atom # 7 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:26:47] Explicit valence for atom # 6 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:26:47] Explicit valence for atom # 6 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:26:47] Explicit valence for atom # 6 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:27:06] Explicit valence for atom # 10 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:27:06] Explicit valence for atom # 10 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:27:06] Explicit valence for atom # 10 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:27:06] Explicit valence for atom # 10 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:27:06] Explicit valence for atom # 10 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:27:06] Explicit valence for atom # 10 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:27:06] Explicit valence for atom # 9 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:27:06] Explicit valence for atom # 9 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:27:06] Explicit valence for atom # 10 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:27:06] Explicit valence for atom # 9 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:27:06] Explicit valence for atom # 7 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
[17:27:06] Explicit valence for atom # 7 C greater than permitted
Warning: Unable to check aromaticity by converting to RDKit Mol.
Trying to use OpenBabel to check aromaticity.
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I followed the previous issues (#1278, #929, etc.). However, I was not able to implement generate_resonance_structures module. Thus, I don't know if that will help or not. Any suggestion to improve the calculation would be really helpful.

input_N2_CH4.txt