Amending LOBSTER functions in OceanBioME after calling in source code

[kgrabb]

Hi Oceananigans community,

I am new to using Oceananigans and am trying to amend some of the functions and equations within LOBSTER in OceanBioME. Right now, LOBSTER.jl defines nitrification rate as a constant 'nitrification_rate::FT = 5.8e-7, # 1/s'.

However, I would like to amend the nitrification rate to depend on pH, ideally by adding an equation such as 'nitrification_rate = -2e-6*pH + 2e-5', which also requires pH to be solved for before defining the nitrification rate. Ideally I would like to not amend the LOBSTER source code, but somehow amend this equation after calling in LOBSTER. I have heard that there may be ways to do this by re-declaring a second version of LOBSTER, somehow making it a field, and/or adding a forcing function to amend the nitrification rate. However, I do not have experience with any of these actions, so suggestions (and/or new ideas) are welcomed!

Thank you!
Kalina

[simone-silvestri]

This may be a question more suited for OceanBIOME.jl since you would need to interact with the source code of that package rather than Oceananigans.
However, at first glance, without redefining the LOBSTER type, there is no easy way that I can find to pass a function, since you are forced to pass a type that is consistent with the other variable inputs (in this case, FT).

What you can do in your script is change how the LOBSTER type acts. From what I see, the nitrification rate is used in these three functions:

• for the O2
  https://github.com/OceanBioME/OceanBioME.jl/blob/27629676f66118ed4046bfde6b69be5799cb3fee/src/Models/AdvectedPopulations/LOBSTER/oxygen_chemistry.jl#L2-L15
• for the NO3
  https://github.com/OceanBioME/OceanBioME.jl/blob/27629676f66118ed4046bfde6b69be5799cb3fee/src/Models/AdvectedPopulations/LOBSTER/core.jl#L12-L20
• for the NH4
  https://github.com/OceanBioME/OceanBioME.jl/blob/27629676f66118ed4046bfde6b69be5799cb3fee/src/Models/AdvectedPopulations/LOBSTER/core.jl#L22-L45

If you import LOBSTER in your script, for example, with

import OceanBIOME.Models.AdvectedPopulations.LOBSTERModel: LOBSTER

you can redefine what these functions do locally

@inline function (bgc::LOBSTER)(::Val{:NO₃}, x, y, z, t, NO₃, NH₄, P, Z, sPOM, bPOM, DOM, PAR)
    μₚ = bgc.maximum_phytoplankton_growthrate
    kₚₐᵣ = bgc.light_half_saturation
    ψ = bgc.nitrate_ammonia_inhibition
    kₙₒ₃ = bgc.nitrate_half_saturation
    μₙ = # Here I do what I want with nitrate....

    return μₙ*NH₄ - μₚ*Lₚₐᵣ(PAR, kₚₐᵣ)*Lₙₒ₃(NO₃, NH₄, ψ, kₙₒ₃)*P
end

However, here the question is how you would access PH to compute your nitrate rate, which does not seem to be a parameter passed to this function. How I would go about it is to open an issue in OceanBIOME and eventually a PR that leads to (1) the possibility of passing differently typed inputs in LOBSTER (so you can pass a simple function as your nitrification_rate) and (2) making sure all the variables you need (in this case PH) are available where you need them (in this case where you need to compute your nitrification rate).

Maybe @jagoosw can chime in here.

[jagoosw]

Hi @kgrabb,

Thanks for reaching out its great to hear you're using OceanBioME!

We actually have a PR about to be merged that changes LOBSTER so its much easier to make changes like this OceanBioME/OceanBioME.jl#276

Simone's solution seems like a good interim, or if you wanted to use the branch (you can write ] add https://github.com/OceanBioME/OceanBioME.jl#jsw/iron-limitation) then you can make a new "nutrients" like in this file, which could be the exact same except for the nitrifcation function. You would also need to get the pH some how which you could either do as an auxiliary field or you can compute it inline from the carbon chemistry.

I'm happy to help with this and will try to merge that PR asap to make things easier.

[kgrabb]

Thank you @simone-silvestri and @jagoosw for the quick reply! I will work through the suggestions you made and chime in again if I have follow-up questions. Good to know in the future I can post directly to OceanBioME.