OceanBioME.jl

A tool to study the effectiveness and impacts of ocean carbon dioxide removal strategies.
https://github.com/OceanBioME/OceanBioME.jl

Category: Emissions
Sub Category: Carbon Capture

Keywords

biogeochemical-models biogeochemistry climate julia ocean ocean-modelling ocean-sciences oceanography

Keywords from Contributors

climate-change data-assimilation energy-system-model climate-science

Last synced: about 1 hour ago
JSON representation

Repository metadata

🌊 🦠 🌿 A fast and flexible modelling environment written in Julia for modelling the coupled interactions between ocean biogeochemistry, carbonate chemistry, and physics

• Host: GitHub
• URL: https://github.com/OceanBioME/OceanBioME.jl
• Owner: OceanBioME
• License: mit
• Created: 2022-07-15T13:33:46.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2025-12-13T02:04:43.000Z (13 days ago)
• Last Synced: 2025-12-14T01:45:56.751Z (12 days ago)
• Topics: biogeochemical-models, biogeochemistry, climate, julia, ocean, ocean-modelling, ocean-sciences, oceanography
• Language: Julia
• Homepage: https://oceanbiome.github.io/OceanBioME.jl/
• Size: 310 MB
• Stars: 66
• Watchers: 6
• Forks: 24
• Open Issues: 33
• Releases: 48
• Metadata Files:
  • Readme: README.md
  • License: LICENSE
  • Citation: CITATION.cff

README.md

julia> using Pkg
julia> Pkg.add("OceanBioME")

using Pkg; Pkg.add("Oceananigans")

using OceanBioME, Oceananigans
using Oceananigans.Units

grid = RectilinearGrid(CPU(), size = (160, 32), extent = (10000meters, 500meters), topology = (Bounded, Flat, Bounded))

biogeochemistry = NutrientPhytoplanktonZooplanktonDetritus(; grid) 

model = NonhydrostaticModel(; grid, biogeochemistry,
                              advection = WENO(),
                              closure = AnisotropicMinimumDissipation(),
			      buoyancy = SeawaterBuoyancy(constant_salinity = true))

@inline front(x, z, μ, δ) = μ + δ * tanh((x - 7000 + 4 * z) / 500)

Pᵢ(x, z) = ifelse(z > -50, 0.03, 0.01)
Nᵢ(x, z) = front(x, z, 2.5, -2)
Tᵢ(x, z) = front(x, z, 9, 0.05)

set!(model, N = Nᵢ, P = Pᵢ, Z = Pᵢ, T = Tᵢ)

simulation = Simulation(model; Δt = 50, stop_time = 4days)

simulation.output_writers[:tracers] = JLD2Writer(model, model.tracers,
                                                 filename = "buoyancy_front.jld2",
                                                 schedule = TimeInterval(24minute),
                                                 overwrite_existing = true)

run!(simulation)

# Before running the visualization code below, make sure CairoMakie is installed:
using Pkg; Pkg.add("CairoMakie")

T = FieldTimeSeries("buoyancy_front.jld2", "T")
N = FieldTimeSeries("buoyancy_front.jld2", "N")
P = FieldTimeSeries("buoyancy_front.jld2", "P")

xc, yc, zc = nodes(T)

times = T.times

using CairoMakie

n = Observable(1)

T_lims = (8.94, 9.06)
N_lims = (0, 4.5)
P_lims = (0.007, 0.02)

Tₙ = @lift interior(T[$n], :, 1, :)
Nₙ = @lift interior(N[$n], :, 1, :)
Pₙ = @lift interior(P[$n], :, 1, :)

fig = Figure(size = (1000, 520), fontsize = 20)

title = @lift "t = $(prettytime(times[$n]))"
Label(fig[0, :], title)

axis_kwargs = (xlabel = "x (m)", ylabel = "z (m)", width = 770, yticks = [-400, -200, 0])
ax1 = Axis(fig[1, 1]; title = "Temperature (°C)", axis_kwargs...)
ax2 = Axis(fig[2, 1]; title = "Nutrients concentration (mmol N / m³)",axis_kwargs...)
ax3 = Axis(fig[3, 1]; title = "Phytoplankton concentration (mmol N / m³)", axis_kwargs...)

hm1 = heatmap!(ax1, xc, zc, Tₙ, colorrange = T_lims, colormap = Reverse(:lajolla), interpolate = true)
hm2 = heatmap!(ax2, xc, zc, Nₙ, colorrange = N_lims, colormap = Reverse(:bamako), interpolate = true)
hm3 = heatmap!(ax3, xc, zc, Pₙ, colorrange = P_lims, colormap = Reverse(:bamako), interpolate = true)

Colorbar(fig[1, 2], hm1, ticks = [8.95, 9.0, 9.05])
Colorbar(fig[2, 2], hm2, ticks = [0, 2, 4])
Colorbar(fig[3, 2], hm3, ticks = [0.01, 0.02, 0.03])

rowgap!(fig.layout, 0)

record(fig, "buoyancy_front.gif", 1:length(times)) do i
    n[] = i
end

grid = RectilinearGrid(GPU(), size = (256, 32), extent = (500meters, 100meters), topology = (Bounded, Flat, Bounded))

@article{OceanBioMEJOSS,
  doi = {10.21105/joss.05669},
  url = {https://doi.org/10.21105/joss.05669},
  year = {2023},
  publisher = {The Open Journal},
  volume = {8},
  number = {90},
  pages = {5669},
  author = {Jago Strong-Wright and Si Chen and Navid C. Constantinou and Simone Silvestri and Gregory LeClaire Wagner and John R. Taylor},
  title = {{OceanBioME.jl: A flexible environment for modelling the coupled interactions between ocean biogeochemistry and physics}},
  journal = {Journal of Open Source Software}
}

Citation (CITATION.cff)

cff-version: "1.2.0"
authors:
- family-names: Strong-Wright
  given-names: Jago
  orcid: "https://orcid.org/0000-0002-7174-5283"
- family-names: Chen
  given-names: Si
  orcid: "https://orcid.org/0009-0002-1296-7166"
- family-names: Constantinou
  given-names: Navid C
  orcid: "https://orcid.org/0000-0002-8149-4094"
- family-names: Silvestri
  given-names: Simone
  orcid: "https://orcid.org/0000-0002-7156-946X"
- family-names: Wagner
  given-names: Gregory LeClaire
  orcid: "https://orcid.org/0000-0001-5317-2445"
- family-names: Taylor
  given-names: John R
  orcid: "https://orcid.org/0000-0002-1292-3756"
contact:
- family-names: Strong-Wright
  given-names: Jago
  orcid: "https://orcid.org/0000-0002-7174-5283"
doi: 10.5281/zenodo.8403490
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Strong-Wright
    given-names: Jago
    orcid: "https://orcid.org/0000-0002-7174-5283"
  - family-names: Chen
    given-names: Si
    orcid: "https://orcid.org/0009-0002-1296-7166"
  - family-names: Constantinou
    given-names: Navid C
    orcid: "https://orcid.org/0000-0002-8149-4094"
  - family-names: Silvestri
    given-names: Simone
    orcid: "https://orcid.org/0000-0002-7156-946X"
  - family-names: Wagner
    given-names: Gregory LeClaire
    orcid: "https://orcid.org/0000-0001-5317-2445"
  - family-names: Taylor
    given-names: John R
    orcid: "https://orcid.org/0000-0002-1292-3756"
  date-published: 2023-10-05
  doi: 10.21105/joss.05669
  issn: 2475-9066
  issue: 90
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5669
  title: "OceanBioME.jl: A flexible environment for modelling the
    coupled interactions between ocean biogeochemistry and physics"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05669"
  volume: 8
title: "OceanBioME.jl: A flexible environment for modelling the coupled
  interactions between ocean biogeochemistry and physics"

Owner metadata

• Name: OceanBioME
• Login: OceanBioME
• Email: js2430@damtp.cam.ac.uk
• Kind: organization
• Description: Organisaiton for OceanBioME.jl, a flexible ocean biogeochemical modelling enviroment
• Website: https://oceanbiome.github.io/OceanBioME.jl
• Location: United Kingdom
• Twitter:
• Company:
• Icon url: https://avatars.githubusercontent.com/u/109746627?v=4
• Repositories: 2
• Last ynced at: 2023-07-12T17:32:06.599Z
• Profile URL: https://github.com/OceanBioME

GitHub Events

Total

• Create event: 39
• Commit comment event: 29
• Release event: 8
• Delete event: 23
• Member event: 2
• Pull request event: 43
• Fork event: 3
• Discussion event: 1
• Issues event: 36
• Watch event: 18
• Issue comment event: 158
• Push event: 304
• Pull request review comment event: 31
• Pull request review event: 44

Last Year

• Create event: 33
• Commit comment event: 24
• Release event: 6
• Delete event: 18
• Member event: 2
• Pull request event: 34
• Fork event: 2
• Discussion event: 1
• Issues event: 28
• Watch event: 14
• Issue comment event: 123
• Push event: 244
• Pull request review comment event: 29
• Pull request review event: 38

Committers metadata

Last synced: 4 days ago

Committer domains:

• cam.ac.uk: 2
• login-e-4.data.cluster: 1
• pm.me: 1
• julialang.org: 1
• charybdis.damtp.cam.ac.uk: 1

Issue and Pull Request metadata

Last synced: 5 days ago

Package metadata

• Total packages: 3
• Total downloads:
  • julia: 112 total
• Total dependent packages: 0 (may contain duplicates)
• Total dependent repositories: 0 (may contain duplicates)
• Total versions: 153

Dependencies

Score: 12.021668922531894