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status](https://badge.buildkite.com/3d79ccbf2cba42de1d4e54a2f31cc6f99d377198bf63334d0d.svg)](https://buildkite.com/oceanbiome/oceanbiome)\n[![codecov](https://codecov.io/gh/OceanBioME/OceanBioME.jl/branch/main/graph/badge.svg?token=3DIW4R7N3R)](https://codecov.io/gh/OceanBioME/OceanBioME.jl)\n# *Ocean* *Bio*geochemical *M*odelling *E*nvironment\n\n## Description\nOceanBioME 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](https://github.com/cliMA/oceananigans.jl/) to run as a 1D column model or with 2 and 3D physics. \n\nOceanBioME was developed with generous support from the Centre for Climate Repair [CCR](https://www.climaterepair.cam.ac.uk) and the Gordon and Betty Moore Foundation as a tool to study the effectiveness and impacts of ocean carbon dioxide removal (CDR) strategies.\n\n## Installation:\n\nFirst, [download and install Julia](https://julialang.org/downloads/)\n\nFrom the Julia prompt (REPL), type:\n```julia\njulia\u003e using Pkg\njulia\u003e Pkg.add(\"OceanBioME\")\n```\n\n## Running your first model\nAs 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:\n\n```julia\nusing Pkg; Pkg.add(\"Oceananigans\")\n\nusing OceanBioME, Oceananigans\nusing Oceananigans.Units\n\ngrid = RectilinearGrid(CPU(), size = (160, 32), extent = (10000meters, 500meters), topology = (Bounded, Flat, Bounded))\n\nbiogeochemistry = NutrientPhytoplanktonZooplanktonDetritus(; grid) \n\nmodel = NonhydrostaticModel(; grid, biogeochemistry,\n                              advection = WENO(),\n                              closure = AnisotropicMinimumDissipation(),\n\t\t\t      buoyancy = SeawaterBuoyancy(constant_salinity = true))\n\n@inline front(x, z, μ, δ) = μ + δ * tanh((x - 7000 + 4 * z) / 500)\n\nPᵢ(x, z) = ifelse(z \u003e -50, 0.03, 0.01)\nNᵢ(x, z) = front(x, z, 2.5, -2)\nTᵢ(x, z) = front(x, z, 9, 0.05)\n\nset!(model, N = Nᵢ, P = Pᵢ, Z = Pᵢ, T = Tᵢ)\n\nsimulation = Simulation(model; Δt = 50, stop_time = 4days)\n\nsimulation.output_writers[:tracers] = JLD2Writer(model, model.tracers,\n                                                 filename = \"buoyancy_front.jld2\",\n                                                 schedule = TimeInterval(24minute),\n                                                 overwrite_existing = true)\n\nrun!(simulation)\n```\n\n\u003cdetails\u003e\n\u003csummary\u003eWe can then visualise this:\u003c/summary\u003e\n\n```julia\n# Before running the visualization code below, make sure CairoMakie is installed:\nusing Pkg; Pkg.add(\"CairoMakie\")\n\nT = FieldTimeSeries(\"buoyancy_front.jld2\", \"T\")\nN = FieldTimeSeries(\"buoyancy_front.jld2\", \"N\")\nP = FieldTimeSeries(\"buoyancy_front.jld2\", \"P\")\n\nxc, yc, zc = nodes(T)\n\ntimes = T.times\n\nusing CairoMakie\n\nn = Observable(1)\n\nT_lims = (8.94, 9.06)\nN_lims = (0, 4.5)\nP_lims = (0.007, 0.02)\n\nTₙ = @lift interior(T[$n], :, 1, :)\nNₙ = @lift interior(N[$n], :, 1, :)\nPₙ = @lift interior(P[$n], :, 1, :)\n\nfig = Figure(size = (1000, 520), fontsize = 20)\n\ntitle = @lift \"t = $(prettytime(times[$n]))\"\nLabel(fig[0, :], title)\n\naxis_kwargs = (xlabel = \"x (m)\", ylabel = \"z (m)\", width = 770, yticks = [-400, -200, 0])\nax1 = Axis(fig[1, 1]; title = \"Temperature (°C)\", axis_kwargs...)\nax2 = Axis(fig[2, 1]; title = \"Nutrients concentration (mmol N / m³)\",axis_kwargs...)\nax3 = Axis(fig[3, 1]; title = \"Phytoplankton concentration (mmol N / m³)\", axis_kwargs...)\n\nhm1 = heatmap!(ax1, xc, zc, Tₙ, colorrange = T_lims, colormap = Reverse(:lajolla), interpolate = true)\nhm2 = heatmap!(ax2, xc, zc, Nₙ, colorrange = N_lims, colormap = Reverse(:bamako), interpolate = true)\nhm3 = heatmap!(ax3, xc, zc, Pₙ, colorrange = P_lims, colormap = Reverse(:bamako), interpolate = true)\n\nColorbar(fig[1, 2], hm1, ticks = [8.95, 9.0, 9.05])\nColorbar(fig[2, 2], hm2, ticks = [0, 2, 4])\nColorbar(fig[3, 2], hm3, ticks = [0.01, 0.02, 0.03])\n\nrowgap!(fig.layout, 0)\n\nrecord(fig, \"buoyancy_front.gif\", 1:length(times)) do i\n    n[] = i\nend\n```\n\u003c/details\u003e\n\nhttps://github.com/OceanBioME/OceanBioME.jl/assets/26657828/d4a5dbc9-ffff-4ef0-8431-b9afc951142f\n\nIn this example `OceanBioME` is providing the `biogeochemistry` and the remainder is taken care of by `Oceananigans`.\nFor comprehensive documentation of the physics modelling see\n[Oceananigans' Documentation](https://clima.github.io/OceananigansDocumentation/stable/), and for\nbiogeochemistry and other features we provide read below.\n\n## Using GPU\n\nTo run the same example on a GPU we just need to construct the `grid` on the GPU; the rest is taken care of!\n\nJust replace `CPU()` with `GPU()` in the grid construction with everything else left unchanged:\n\n```julia\ngrid = RectilinearGrid(GPU(), size = (256, 32), extent = (500meters, 100meters), topology = (Bounded, Flat, Bounded))\n```\n\n## Documentation\n\nSee the [documentation](https://oceanbiome.github.io/OceanBioME.jl) for full description of the software package and more examples, as well as full descriptions of the included models and parametrisations.\n\n## Contributing\nIf you're interested in contributing to the development of OceanBioME we would appreciate your help!\n\nIf 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.\n\nFor more information check out our [contributor's guide](https://oceanbiome.github.io/OceanBioME.jl/stable/contributing/).\n\n## Citing\n\nIf 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.\n\n```bibtex\n@article{OceanBioMEJOSS,\n  doi = {10.21105/joss.05669},\n  url = {https://doi.org/10.21105/joss.05669},\n  year = {2023},\n  publisher = {The Open Journal},\n  volume = {8},\n  number = {90},\n  pages = {5669},\n  author = {Jago Strong-Wright and Si Chen and Navid C. 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Taylor},\n  title = {{OceanBioME.jl: A flexible environment for modelling the coupled interactions between ocean biogeochemistry and physics}},\n  journal = {Journal of Open Source Software}\n}\n```\n\nIf 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](https://zenodo.org/doi/10.5281/zenodo.8403489).\n","funding_links":[],"readme_doi_urls":["https://doi.org/10.21105/joss.05669","https://doi.org/10.5281/zenodo.10038575"],"works":{"https://doi.org/10.21105/joss.05669":{"id":"https://openalex.org/W4387376940","doi":"https://doi.org/10.21105/joss.05669","title":"OceanBioME.jl: A flexible environment for modelling the coupled interactions between ocean biogeochemistry and physics","display_name":"OceanBioME.jl: A flexible environment for modelling the coupled interactions between ocean biogeochemistry and physics","publication_year":2023,"publication_date":"2023-10-05","ids":{"openalex":"https://openalex.org/W4387376940","doi":"https://doi.org/10.21105/joss.05669"},"language":"en","primary_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.05669","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.05669.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"Journal of open source software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},"type":"article","type_crossref":"journal-article","open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://joss.theoj.org/papers/10.21105/joss.05669.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083672658","display_name":"Jago Strong-Wright","orcid":"https://orcid.org/0000-0002-7174-5283"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jago Strong-Wright","raw_affiliation_string":"","raw_affiliation_strings":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019805606","display_name":"Si Chen","orcid":"https://orcid.org/0009-0002-1296-7166"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Si Chen","raw_affiliation_string":"","raw_affiliation_strings":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023610195","display_name":"Navid C. 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