Questions about fixes/edits to sediment-related processes and biogeochemistry

[cha...@oregonstate.edu]

Hi all, 

I hope everyone is doing well! I'm a PhD student at Oregon State University whose work and background focuses on sediment biogeochemistry. I'm a newcomer to the Atlantis community and am being mentored by Dr. Isaac Kaplan. 

I'm interested in enhancing Atlantis's sediment modeling capabilities by incorporating approaches similar to those outlined in Berner 1969, Boudreau 1996, Soetaert et al. 1996 etc. I'm hoping that I can adjust/tweak Atlantis's sediment modeling capabilities to assess how changes to bottom trawling activity and management might affect carbon storage and how this may cascade through the California Current ecosystem.

One of the things I've noticed is that there were a number of "FIX" notes that are in the sediment-related portions of code (e.g. on compaction in atphysics.c, on tracer concentration calculations in atbioirrig.c, oxygen calculations and profile-setting, etc.), and I was wondering if anyone has fiddled with/fixed these in their own version/iterations of Atlantis and/or if you have updated or altered the nitrogen cycling (denitrification, nitrification, addition of other N-cycling processes like DNRA or anammox etc.). If you have, I would love to discuss these further with you. 

Thank you in advance!

Adrienne Chan

[Fulton, Beth (Environment, Hobart)]

OFFICIAL

G’day

 

Very happy for you to play with that bgc. It is reflective of how sediment biogeochemistry was modelled 25-30 years ago but has not benefited from any updates in approach since. Ok as a first order approximation but would benefit from extensive revision. Ti my knowledge no one has focused on addressing that aspect of the code.

 

If you are interested in elaborating it, you can play with it on your machine(s) and then we can integrate those changes once they’ve been reviewed. This can be done either via a new code modification protocol that has been devised for the git hub repository or vua the older approach of you working up the changes and then sending them to me to fold into the code.

 

Cheers

 

Beth

 

 

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