Replies: 16 comments
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This sounds like a big first step in the right direction. Having a another repo called |
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I draft a repo on this matter here.
So basically the repository can simply give all auxiliary functions that are needed for the biogeochemical models, but not the interelationship functions, which can be defined as forcing functions and added to a list of examples on the documentation. I don't mind giving up this repository and merging or adding it to the organization if this is somehow a good starting point. |
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@iuryt that's a beautiful summary! That repository is a great starting point! All we need is the word geo I think... 😄 Reading your description I'm realizing there's another point to be made about "embedded" |
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Yeah.. I am not yet sure how this would work embedded. By now, what I have is just some functions that the user has to add as callbacks. Thinking more, it would be so the function automatically adds the callbacks to the simulation? const Δb=(g/ρₒ) * 0.03
h = Field{Center, Center, Nothing}(grid)
MixedLayerDepth(simulation, h, Δb)
# constants for the NP model
const μ₀ = 1/day # surface growth rate
const m = 0.015/day # mortality rate due to virus and zooplankton grazing
const Kw = 0.059 # meter^-1
const kn = 0.75
const kr = 0.5
# https://doi.org/10.1029/2017GB005850
const chl2c = 0.06 # average value for winter in North Atlantic
const α = 0.0538/day
const average = :growth
const shading = true
light_growth = Field{Center, Center, Center}(grid)
# time evolution of shortwave radiation (North Atlantic)
@inline Lₒ(t) = 116.5 * sin( 2π * ( t / days + 50 ) / 375.7 + 1.3 ) + 132.3
# evolution of the available light at the surface
@inline light_function(t, z) = 0.43 * Lₒ(t) * exp( z * Kw )
# light profile
@inline light_growth_function(light) = μ₀ * ( light * α ) / sqrt( μ₀^2 + ( light * α )^2 )
phytoplankton = ("P",) # list of phytoplankton tracers
LightGrowth(light_growth, h, simulation, phytoplankton, light_function, light_growth_function, time(simulation), average, shading, chl2c) |
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@iuryt https://github.com/iuryt/Bioceananigans.jl looks like an awesome start!!! 🚀 @glwagner arguably it could be biogeochemonanigans.jl or biogeocheminanigans.jl ? Would it be interesting to think about an interface that could be helpful for projects like https://github.com/openjournals/joss-reviews/issues/4207/https://github.com/JuliaOcean/PlanktonIndividuals.jl from @zhenwu0728 and @gaelforget too at some point? Note -
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I know chemistry! Ahaha I like those.
There are multiple possible places where one might update the I think we want to pursue code design that allows these paradigms to be interchanged. I think it's crucial that functionality developed "externally" can be "copy/pasted" into
I see very much what you're saying. There's an opportunity to also support biogeochemistry on Lagrangian particles. |
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That's an awesome idea @christophernhill ! I haven't yet used a Lagrangian formulation for biogeochemical models, but this it would be cool to have some way to support both on this. The name What about We can list some of the options and make a poll. Is it possible to create a poll on github? |
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I suggest we wait on this for the time being. We are in discussions to start a formal collaboration to develop the ocean biogeochemistry component of the CliMA model. We need to plan our strategy with the new collaborators who will join us. It will happen soon and we can then have a discussion with all people involved on what is the best strategy moving forward. |
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That sounds like a great idea @rafferrari . I would be happy to participate in this in the future if you are looking for people to get involved. |
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The more the merrier! Contributors are generally welcome on our end too. Links @christophernhill in his comment were broken. So just in case: PlanktonIndividuals.jl: A GPU supported individual-based phytoplankton life cycle model |
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@gaelforget it looks like you might have some Oceananigans examples which is super cool!! Can you point to them for us? Have you considered expanding to "online" capabilities? What are the pros and cons of that? |
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I agree, this issue is for planning purposes, but there's no timeline for setting up a new package. I think the package itself is easy, but designing the interface that allows different "biogeochemical models" to plug in to Oceananigans will require a bit more care. On the Oceananigans side, it seems like some necessary features of a
Perhaps further consultation will produce additional requirements. One big one that I see is for chemistry models that require subcycling or special numerical methods for time-stepping (ie stiff carbonate chemistry systems as in Smith et al 2018). Supporting those cases will be more challenging. I think our Lagrangian particles already (or are intended to) support dynamics-on-particles so there may not be much to do there on the Oceananigans side. |
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The two models we currently have some support for (offline) are I have examples for both models in https://gaelforget.github.io/ClimateModels.jl/dev/examples/ which you can run the JuliaClimate sandbox https://juliaclimate.github.io/Notebooks/ and generate the kind of model output that An online mode with models like For completeness, here is the reference to the JOSS paper on IndividualDisplacement.jl -- https://joss.theoj.org/papers/10.21105/joss.02813.pdf -- and the GitHub repo |
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I guess if you have a (julia) function that takes a particle time-step, given a velocity field (ie 3D array), then you can use PlanktonIndividuals.jl online with Oceananigans now, using the |
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For now, I will change the name of the package to |
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We're close to having this, I'm going to move this to a discussion. |
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There's been a bunch of interest in using Oceananigans for physical-biogeochemical interaction studies --- problems where systems of reacting tracers that represent either oceanic biological systems, chemical reactions and cycles, or both interact with turbulence and fluid dynamics simulated by Oceananigans.
In order to organize the community's work (and also to support some work at Clima on biogeochemistry in Oceananigans), I propose that we create a new package that interfaces with
Oceananigans--- could it be...Biogeoceananigans.jl... ? --- to:To achieve either of these there's no question we need a particular place to collaborate on re-useable code (rather than working independently). But also, I think the Oceananigans.jl repository is not the best repo to use to achieve the above goals, because it's big and complex, which might make it harder for potential developers to contribute and see their place. I also think it would slow development down, because, for example, we'll have to make sure all unit tests for differential operators pass before we can add a new biogeochemistry model implementation. I think development might be faster and more accessible if we do it in a different repo.
There are also some details to discuss regarding implementation. Oceananigans' design already supports reacting systems via
Forcing. OceananigansForcingare arbitrary functions of spatial coordinates, time, prognostic model fields, and forcing function parameters --- or alternatively, indicesi, j, k,grid,clock, and a NamedTuple of model fields that can be indexed into arbitrarily. @iuryt and @syou83syou83 (and perhaps others) have experimented in this direction.However, I think we might benefit from adding a model property to both
NonhydrostaticModelandHydrostaticFreeSurfaceModelthat's specifically dedicated tobiogeochemistry, and designing an interface that allows users / other packages (like Biogeoceananigans.jl) to build custombiogeochemistrytypes. One advantage I think is we'll have more flexibility in designing the code that hooks into Oceananigans than if we limit ourselves to usingmodel.forcing. I also think it will yield a cleaner and more interpretable user API: biogeochemistry models are sometimes complicated, so it's helpful to disentangle their specification from the specification of more "vanilla" forcing terms, like sponge layers, etc. We may want special time-stepping methods for some types of biogeochemistry in the future.I also think we can build an interface for
biogeochemistrythat uses similar or identical syntax toForcing(like requiring functions ofx, y, z, t, fields--- etc) because this will allow directly transferring code for biogeochemistry models that's first implemented as a system of forcing functions (a very common and useful development paradigm).What do others think about this? @iuryt @johnryantaylor @rafferrari @simone-silvestri @christophernhill @jm-c @sandreza
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