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ReactionMechanismGenerator / RMG-Py

Python version of the amazing Reaction Mechanism Generator (RMG).
http://reactionmechanismgenerator.github.io/RMG-Py/
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How to solve the problem where the desired component does not exist in the library? #2659

Closed mioxchan closed 6 months ago

mioxchan commented 6 months ago

This is my first time using RMG. When I input the component: ammonium dinitrate, the result shows an error. The component I need does not exist in the library. How can I solve this problem? 6d45a50aa053bf6461fee5cd9564fb5 589e7ef7cbd2e4b16f0093fdb7fb26f 5641b324c2578ed5744ff2ae17c1514

JacksonBurns commented 6 months ago

@mioxchan thanks for using RMG! I believe this error is because, while your molecule as a whole is neutral its component fragments are not, which RMG is not able to handle. @rwest could you confirm?

rwest commented 6 months ago

I think that's right, Jackson. This representation works: N.O=[N+]([O-])N[N+](=O)[O-] which I found by entering the SMILES from https://www.chemeo.com/cid/80-144-3/Ammonium-Dinitrate In this case the two fragments are both neutral (the H is moved across). Although this representation doesn't crash RMG, I would not expect RMG to do a good job (at all) at predicting its properties or reactions.

In general, RMG does not yet support ions.

JacksonBurns commented 6 months ago

@rwest thanks for confirming!

@mioxchan please see the link in the answer above which works for a variation in the species you requested. Note though that RMG won't be able to make good estimates for this and species like it, since RMG doesn't really work with ions. This won't change in the near term.

mioxchan commented 6 months ago

@rwest @JacksonBurns Thanks Your response was timely. I showed a great interest in it. May I ask where beginners like me can systematically learn RMG？

JacksonBurns commented 6 months ago

I'm happy to help! I recommend looking at the example input files in the documentation (https://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/examples.html) and also our video tutorial series from last year (https://youtu.be/S4aHvLShcAY?feature=shared).