Reaction pathway analysis documentation

[gpsimms]

Hey y'all:

I don't see any examples of code of reaction pathway analysis on the main site.  Does someone have some sample code, or any other documentation that can get me started on how one does this?

thanks

greg

[Nick Curtis]

Hi greg,
There is a minimal example in the documentation:
http://www.cantera.org/docs/sphinx/html/cython/examples/kinetics_reaction_path.html

However, recently a user (Tilman Bremer) has made a very nice tutorial on reaction pathway analysis w/ Cantera, which is much more fleshed out:
https://www.tilmanbremer.de/2017/06/tutorial-generating-reaction-path-diagrams-with-cantera-and-python/

Nick

[gpsimms]

Thank you Nick!

This is exactly what I was looking for.

greg

[Rosa Padilla]

I am new to Cantera and exploring the reaction pathway analysis. Are there any examples to run the reaction path analysis using Matlab?

[chandra vadhana]

Hi Rose,

Can you elaborate a bit more on what you are specifically looking for, in Matlab? Are you simulating system biology kind? 

Matlab has graph theory based approaches such as shortest distance and maximum flow based functions. 

Best,

Vadhana

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[Rosa Padilla]

Hi Vadhana,

Eventually I would like to use the reaction path analysis for an  ethanol reaction using e.g.  a batch reactor.  Is there a good example that integrates the reaction path analysis with a reactor?  Thank you very much!

I saw on the link below that this can only be used in python and was hoping to confirm.

https://www.tilmanbremer.de/2017/06/tutorial-generating-reaction-path-diagrams-with-cantera-and-python/ 

Regards,

Rosa

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[chandra vadhana]

Hi Rose,

I apologize, I am not so familiar with reactor based reaction path analysis diagrams. I thought, the latter was connected with reaction rate constants, selectivity and transition states and am not sure how that would change with different reactor set-ups. However, if there is a dependency from what you mention in your email,  you can try python based libraries such as RenView (visualization of various reactions with time dependencies too. The inputs will be the outputs from your reactor based simulations) and/or OpenMKM.  And, to generate reaction path diagrams in Matlab was challenging too from my experience. Matlab creates a network of reactants and if one wants to study the yield, selectivity, i guess, we need to write our own custom code using built-in functions in Matlab such as maxflow, shortestpath etc.

I am not sure if I answered your questions but trying to answer from my limited experience I gained in my Post-doc. And, I worked on systems biology using concepts in Reaction engineering. 

Regards

vadhana

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[chandra vadhana]

And sorry, I misspelt your name as Rose instead of Rosa... my bad!