(0.12.0) Implements PISCES model

[jagoosw]

To do (for me but others feel free to open a PR into this branch doing them if you want to):

• Correct setup_velocity_fields and check that function field passing works and check open_bottom is working - addressed in Fixes setup_sinking_velocities and adds tests #210
• Implement yearly maximum silicate
• Implement dust deposition (?) remove dust, should be some general implementation to add as an additional forcing, like river inputs
• Implement day length
• Implement calcite saturation fields
  - [ ] Implement mixed layer field - going todo this in Oceanostics
• Implement euphotic depth field
• Check latitude is being put into the functions right
• Modify the darkness residents time to consider variable vertical diffusivity
• Add testing
• Fix box model to pass correct position when Flat dimension has non-trivial position - accidentally addressed in main (725cc5b)
• Update validation scripts for new air-sea flux
• GPU!
• Documentation pages (WIP: https://oceanbiome.github.io/OceanBioME.jl/previews/PR178/model_components/biogeochemical/PISCES/PISCES/)
• Document changes from Amount 2015 (WIP: https://oceanbiome.github.io/OceanBioME.jl/previews/PR178/model_components/biogeochemical/PISCES/notable_differences/)

I also imagine that there are a lot of GPU issues, and a lot of formatting needs to be changed

CC: @hannahmw1 @ciadht

[jagoosw]

@johnryantaylor I think this is now ready to merge. You can see the (brief) documentation I've written here https://oceanbiome.github.io/OceanBioME.jl/previews/PR178/model_components/biogeochemical/PISCES/PISCES/

with notes on what is different to Aumount, 2015 here https://oceanbiome.github.io/OceanBioME.jl/previews/PR178/model_components/biogeochemical/PISCES/notable_differences/

Is there anything else you think needs doing?

[jagoosw]

@ciadht @hannahmw1, I'm probably going to merge this soon. Thank you for all your work, it was really helpful and I'm not sure I'd have had the dedication to track down all of the bugs that you found.

If there's anything else you think we need todo before we merge let me know! But no worries if you don't want to look through it all (I've changed the code quite a lot, mainly to make it work on GPU).

[hannahmw1]

Hi Jago, Thanks for keeping us in the loop - exciting to hear its nearly ready to be merged! Hope all goes well with the merge and future of PISCES. Hannah

…

________________________________ From: Jago Strong-Wright ***@***.***> Sent: 04 October 2024 17:17 To: OceanBioME/OceanBioME.jl ***@***.***> Cc: hannahmw1 ***@***.***>; Mention ***@***.***> Subject: Re: [OceanBioME/OceanBioME.jl] Implements `PISCES` model (PR #178) @ciadht<https://github.com/ciadht> @hannahmw1<https://github.com/hannahmw1>, I'm probably going to merge this soon. Thank you for all your work, it was really helpful and I'm not sure I'd have had the dedication to track down all of the bugs that you found. If there's anything else you think we need todo before we merge let me know! But no worries if you don't want to look through it all (I've changed the code quite a lot, mainly to make it work on GPU). — Reply to this email directly, view it on GitHub<#178 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BCJ3NJMOCYDI5W3FS34Q4NTZZ3ESXAVCNFSM6AAAAABKTERLBWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOJUGE4DIOBQGY>. You are receiving this because you were mentioned.

[ciadht]

Hi Jago,

This all looks fantastic! Great to see PISCES becoming a part of OceanBioME!

I'm just writing my presentation at the moment and I wondered if you could let me know what happened with the Paris meeting just so I can add it to the end?

Thanks,
Ciadh

[jagoosw]

Great to hear from you both!

@ciadht I'll message you on slack about it

[jagoosw]

This PR probably isn't API breaking but there are some major internal changes to support discrete form models so going to bump minor version