RMG-Py

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Improve SMILES translation for surface adsorbates

4

### Motivation or Problem I recently discovered (a happy accident) that you can put `*` in a SMILES string and RDKit will use it as a dummy atom, with an...

rwest

[Docs] Add CONTRIBUTING file with contributor guidelines

3

Related to larger issue of outdated docs in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2703. This PR serves to consolidate contributor guidelines in a `CONTRIBUTING.md` file [as described here.](https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/setting-guidelines-for-repository-contributors)

jonwzheng

Better drawing of poly-dentate adsorbates (with more than one surface site)

12

### Motivation or Problem Adsorbates with more than one surface site were drawn weirdly, with the second or third surface site often floating up in the air. Examples: ### Description...

rwest

Vd w bonds

10

### Motivation or Problem There are a couple of species that we currently cannot handle in RMG when generating mechanisms for heterogeneously catalyzed reactions, because we have no way to...

bjkreitz

Add and improve to_cantera methods for conversion to in-memory Cantera objects

1

Replaces https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2597 ### Motivation or Problem The conversion to Cantera YAML files currently implemented in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2321 involves converting things to Cantera objects in memory then having Cantera return the properties....

rwest

### Bug Description Hi, I'm trying to run a sensitivity analysis (SA) in RMG for 9 different conditions (range of T and P). I've noticed that when reaching 1 bar...

NellyMitnik

### Bug Description Arkane reports SA coefficients of PDep reactions, yet the units are reported in `J/mol`. I think it should be `mol/J` instead. We should also consider adding these...

alongd

UnboundLocalError: local variable 'optical_isomers' referenced before assignment

2

### Bug Description I ran Arkane (through ARC) and got this trace-back: ``` Traceback (most recent call last): File "/home/william.d/Code/ARC/ARC.py", line 69, in main() File "/home/william.d/Code/ARC/ARC.py", line 65, in main...

wanufey

bug installing RMG on M3 chip following step by step instructions.

5

### Bug Description Hello, I am having an issue installing RMG following the developer[ install instructions](https://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/anacondaDeveloper.html) ``` ['/Users/ayushmaantripathi/miniforge3/envs/rmg_env/bin/python', '-m', 'pip', 'install', '-U', '-r', '/Users/ayushmaantripathi/RMG-Py/condaenv.qx4fndti.requirements.txt', '--exists-action=b'] Pip subprocess output: Pip subprocess...

tripash30

Check for adsorbates in resonance structure generation

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### Motivation or Problem @kirkbadger18 observed an issue when generating mechanisms with adsorbates that contain N atoms. RMG seems to generate species that have formal charges, although the reaction templates...

bjkreitz