Jonathan Zheng

(Reopening due to accidental close!) Hi Pegah, thank you for writing. I wanted to let you know that the `RMG-website` repo is for issues related to the website hosted at...

Hi Hao-Wei, do you mean the `maximum_radical_electrons` for explorer jobs? I think that's different from this - this isn't network exploration, but rather, simply searching the kinetics libraries and families...

Hi Hao-Wei, thank you for the suggestion. This was helpful to learn about the species constraints. For transparency, Hao-Wei and I tried running the above code snippet including the species...

Thank you, Xiaorui, these are excellent ideas. I'll profile to figure out where, exactly, it is getting stuck, and for which families. I have a follow-up concern. Even if you...

After fixing and allowing `resonance=False` to propagate through (see PR #2632), you can turn off resonance and it will allow reactions to be generated at a reasonable time. That might...

It is getting stuck due to the reverse reaction of `1,4_Linear_birad_scission`. Specifically due to the double bonds:  This time-out issue occurs even with much simpler nitro-containing species. The simplest...

Some more benchmarking: |SMILES|# double bonds|resonance on?|time to generate 1,4_linear_birad_scission rxns (sec)| |-|-|-|-| |`C=C([N+](=O)[O-])`|1|yes|1| |`C=C([N+](=O)[O-])`|1|no|0.01| |`C=C([N+](=O)[O-])C=C`|2|yes|216| |`C=C([N+](=O)[O-])C=C`|2|no|0.04| |`C=CC=C([N+](=O)[O-])C=C`|3|yes|1451| |`C=CC=C([N+](=O)[O-])C=C`|3|no|0.1| |`c1ccccc1`|aromatic|yes|0.6| |`c1ccccc1[N+](=O)[O-]`|aromatic|yes|1320| |`c1ccccc1[N+](=O)[O-]`|aromatic|no|2| |`c1ccc([N+](=O)[O-])cc1[N+](=O)[O-]`|aromatic|yes|did not finish after 2 hours| |`c1ccc([N+](=O)[O-])cc1[N+](=O)[O-]`|aromatic|no|0.1| Just...

Right now the `resonance` flag is not exposed through the RMG interface, and also, right now it does not properly propagate if disabled. We have a pull request #2632 that...

Unfortunately we haven't yet exposed a way for users to change this setting without modifying the codebase. As a quick check could you see if setting `resonance=True` to `resonance=False` in...

Sorry for the late response - we no longer support RMG-Java in RMG-Py and should remove the feature from the website as well (#281).