OceanBioME.jl
OceanBioME.jl: A flexible environment for modelling the coupled interactions between ocean biogeochemistry and physics - Published in JOSS (2023)
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Published in Journal of Open Source Software
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🌊 🦠 🌿 A fast and flexible modelling environment written in Julia for modelling the coupled interactions between ocean biogeochemistry, carbonate chemistry, and physics
Basic Info
- Host: GitHub
- Owner: OceanBioME
- License: mit
- Language: Julia
- Default Branch: main
- Homepage: https://oceanbiome.github.io/OceanBioME.jl/
- Size: 282 MB
Statistics
- Stars: 64
- Watchers: 8
- Forks: 23
- Open Issues: 34
- Releases: 35
Topics
Metadata Files
README.md
Ocean Biogeochemical Modelling Environment
Description
OceanBioME is a flexible biogeochemical modelling environment written in Julia for modelling the coupled interactions between ocean biology, carbonate chemistry, and physics. OceanBioME can be run as a stand-alone box model, or coupled with Oceananigans.jl to run as a 1D column model or with 2 and 3D physics.
OceanBioME was developed with generous support from the Centre for Climate Repair CCR and the Gordon and Betty Moore Foundation as a tool to study the effectiveness and impacts of ocean carbon dioxide removal (CDR) strategies.
Installation:
First, download and install Julia
From the Julia prompt (REPL), type:
julia
julia> using Pkg
julia> Pkg.add("OceanBioME")
Running your first model
As a simple example lets run a Nutrient-Phytoplankton-Zooplankton-Detritus (NPZD) model in a two-dimensional simulation of a buoyancy front. This example requires Oceananigans, so we install that first:
```julia 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.outputwriters[:tracers] = JLD2Writer(model, model.tracers, filename = "buoyancyfront.jld2", schedule = TimeInterval(24minute), overwrite_existing = true)
run!(simulation) ```
We can then visualise this:
```julia # 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 ```https://github.com/OceanBioME/OceanBioME.jl/assets/26657828/d4a5dbc9-ffff-4ef0-8431-b9afc951142f
In this example OceanBioME is providing the biogeochemistry and the remainder is taken care of by Oceananigans.
For comprehensive documentation of the physics modelling see
Oceananigans' Documentation, and for
biogeochemistry and other features we provide read below.
Using GPU
To run the same example on a GPU we just need to construct the grid on the GPU; the rest is taken care of!
Just replace CPU() with GPU() in the grid construction with everything else left unchanged:
julia
grid = RectilinearGrid(GPU(), size = (256, 32), extent = (500meters, 100meters), topology = (Bounded, Flat, Bounded))
Documentation
See the documentation for full description of the software package and more examples, as well as full descriptions of the included models and parametrisations.
Contributing
If you're interested in contributing to the development of OceanBioME we would appreciate your help!
If you'd like to work on a new feature, or if you're new to open source and want to crowd-source projects that fit your interests, please start a discussion.
For more information check out our contributor's guide.
Citing
If you use OceanBioME as part of your research, teaching, or other activities, we would be grateful if you could cite our work below and mention the package by name.
bibtex
@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}
}
If on top of citing the JOSS paper above, you need to cite a specific version of the package then please cite its corresponding version from the Zenodo archive.
Owner
- Name: OceanBioME
- Login: OceanBioME
- Kind: organization
- Email: js2430@damtp.cam.ac.uk
- Location: United Kingdom
- Website: https://oceanbiome.github.io/OceanBioME.jl
- Repositories: 2
- Profile: https://github.com/OceanBioME
Organisaiton for OceanBioME.jl, a flexible ocean biogeochemical modelling enviroment
JOSS Publication
OceanBioME.jl: A flexible environment for modelling the coupled interactions between ocean biogeochemistry and physics
Authors
Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom, Centre for Climate Repair, Cambridge, United Kingdom
Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom, Centre for Climate Repair, Cambridge, United Kingdom
Australian National University, Australia, Australian Research Council Centre for Climate Extremes
Massachusetts Institute of Technology, USA
Massachusetts Institute of Technology, USA
Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom, Centre for Climate Repair, Cambridge, United Kingdom
Editor
Kristen Thyng
Tags
julia biogeochemistry climate ocean carbonCitation (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"
GitHub Events
Total
- Fork event: 3
- Create event: 27
- Commit comment event: 20
- Release event: 6
- Issues event: 25
- Watch event: 17
- Delete event: 12
- Member event: 2
- Issue comment event: 119
- Push event: 163
- Pull request review comment event: 23
- Pull request review event: 35
- Pull request event: 30
Last Year
- Fork event: 3
- Create event: 27
- Commit comment event: 20
- Release event: 6
- Issues event: 25
- Watch event: 17
- Delete event: 12
- Member event: 2
- Issue comment event: 119
- Push event: 164
- Pull request review comment event: 23
- Pull request review event: 35
- Pull request event: 30
Committers
Last synced: 5 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Jago Stong-Wright | j****w@p****m | 1,386 |
| Navid C. Constantinou | n****y | 304 |
| ciadht | c****9@c****k | 90 |
| johnryantaylor | j****r@g****m | 79 |
| coding-code123 | h****s@o****m | 76 |
| ali-ramadhan | a****n@g****m | 36 |
| Pietro Monticone | 3****e | 22 |
| Si Chen | s****0@c****k | 11 |
| Si Chen | c****1@g****m | 5 |
| simone-silvestri | s****0@g****m | 3 |
| M. A. Kowalski | m****0@c****k | 3 |
| iury simoes-sousa | i****t@p****e | 1 |
| Jago Strong-Wright | j****0@l****r | 1 |
Committer Domains (Top 20 + Academic)
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Last synced: 4 months ago
All Time
- Total issues: 74
- Total pull requests: 216
- Average time to close issues: 2 months
- Average time to close pull requests: 10 days
- Total issue authors: 15
- Total pull request authors: 14
- Average comments per issue: 4.05
- Average comments per pull request: 2.65
- Merged pull requests: 158
- Bot issues: 0
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Past Year
- Issues: 30
- Pull requests: 48
- Average time to close issues: 11 days
- Average time to close pull requests: 18 days
- Issue authors: 8
- Pull request authors: 6
- Average comments per issue: 0.77
- Average comments per pull request: 1.75
- Merged pull requests: 24
- Bot issues: 0
- Bot pull requests: 0
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- jagoosw (24)
- MarionBWeinzierl (11)
- ali-ramadhan (10)
- johnryantaylor (9)
- navidcy (6)
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- glwagner (2)
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- emmabeniston (1)
- JuliaTagBot (1)
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- ciadht (30)
- navidcy (29)
- johnryantaylor (16)
- ali-ramadhan (7)
- syou83syou83 (3)
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Packages
- Total packages: 3
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Total downloads:
- julia 50 total
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Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 0
(may contain duplicates) - Total versions: 107
proxy.golang.org: github.com/oceanbiome/oceanbiome.jl
- Documentation: https://pkg.go.dev/github.com/oceanbiome/oceanbiome.jl#section-documentation
- License: mit
-
Latest release: v0.14.3
published 5 months ago
Rankings
proxy.golang.org: github.com/OceanBioME/OceanBioME.jl
- Documentation: https://pkg.go.dev/github.com/OceanBioME/OceanBioME.jl#section-documentation
- License: mit
-
Latest release: v0.14.3
published 5 months ago
Rankings
juliahub.com: OceanBioME
🌊 🦠 🌿 A fast and flexible modelling environment written in Julia for modelling the coupled interactions between ocean biogeochemistry, carbonate chemistry, and physics
- Homepage: https://oceanbiome.github.io/OceanBioME.jl/
- Documentation: https://docs.juliahub.com/General/OceanBioME/stable/
- License: MIT
-
Latest release: 0.14.2
published 6 months ago
Rankings
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- actions/checkout v2 composite
- julia-actions/setup-julia v1 composite
- actions/cache v1 composite
- actions/checkout v2 composite
- codecov/codecov-action v1 composite
- julia-actions/julia-buildpkg v1 composite
- julia-actions/julia-processcoverage v1 composite
- julia-actions/julia-runtest v1 composite
- julia-actions/setup-julia v1 composite
- JuliaRegistries/TagBot v1 composite
- actions/checkout v2 composite