Merge pull request #186 from OceanBioME/jsw/refactor-carbonate-chemistry

Refactors gas exchange carbon chemistry (+ adds some complexity)

.buildkite/pipeline.yml

@@ -20,7 +20,7 @@ steps:
 
   - label: ":speedboat: GPU unit tests"
     commands: 
-     - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.Registry.update(); Pkg.test()'"
+     - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project --check-bounds=yes -e 'using Pkg; Pkg.Registry.update(); Pkg.test()'"
     depends_on: "init"
     notify:
       - github_commit_status:
@@ -30,7 +30,7 @@ steps:
     env:
      CUDA_VISIBLE_DEVICES: "-1"
     commands: 
-     - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.Registry.update(); Pkg.test()'"
+     - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project --check-bounds=yes -e 'using Pkg; Pkg.Registry.update(); Pkg.test()'"
     depends_on: "init"
     notify:
       - github_commit_status:

Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.10.2"
 manifest_format = "2.0"
-project_hash = "4319b71589d68d891265adf31b9a9017f2b1b326"
+project_hash = "37e11a3bdd396c973917441db34ded05b97faa85"
 
 [[deps.AbstractFFTs]]
 deps = ["LinearAlgebra"]
@@ -362,6 +362,18 @@ git-tree-sha1 = "518ebd058c9895de468a8c255797b0c53fdb44dd"
 uuid = "61eb1bfa-7361-4325-ad38-22787b887f55"
 version = "0.26.5"
 
+[[deps.GibbsSeaWater]]
+deps = ["GibbsSeaWater_jll", "Libdl", "Test"]
+git-tree-sha1 = "d1642ddc78d0754603d747d76fac0042a5a85104"
+uuid = "9a22fb26-0b63-4589-b28e-8f9d0b5c3d05"
+version = "0.1.3"
+
+[[deps.GibbsSeaWater_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "c91ca76546871efaa1aefdd2b19cc41c3ead2160"
+uuid = "6727f6b2-98ea-5d0a-8239-2f72283ddb11"
+version = "3.5.2+0"
+
 [[deps.Glob]]
 git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496"
 uuid = "c27321d9-0574-5035-807b-f59d2c89b15c"

Project.toml

@@ -1,26 +1,30 @@
 name = "OceanBioME"
 uuid = "a49af516-9db8-4be4-be45-1dad61c5a376"
 authors = ["Jago Strong-Wright <[email protected]> and contributors"]
-version = "0.10.5"
+version = "0.11.0"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
+GibbsSeaWater = "9a22fb26-0b63-4589-b28e-8f9d0b5c3d05"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
 Oceananigans = "9e8cae18-63c1-5223-a75c-80ca9d6e9a09"
 Roots = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
+SeawaterPolynomials = "d496a93d-167e-4197-9f49-d3af4ff8fe40"
 StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
 
 [compat]
 Adapt = "3, 4"
 CUDA = "5"
 Documenter = "1"
 EnsembleKalmanProcesses = "1"
+GibbsSeaWater = "0.1"
 JLD2 = "0.4"
 KernelAbstractions = "0.9"
 Oceananigans = "0.91"
 Roots = "2"
+SeawaterPolynomials = "0.3"
 StructArrays = "0.4, 0.5, 0.6"
 julia = "1.10"
 

README.md

@@ -130,8 +130,7 @@ grid = RectilinearGrid(GPU(), size = (256, 32), extent = (500meters, 100meters),
 
 ## Documentation
 
-See the [documentation](https://oceanbiome.github.io/OceanBioME.jl) for full description of the software
-package and more examples.
+See 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.
 
 ## Contributing
 If you're interested in contributing to the development of OceanBioME we would appreciate your help!

docs/make.jl

@@ -1,10 +1,9 @@
 using Documenter, DocumenterCitations, Literate
 
 using OceanBioME
-using OceanBioME.SLatissimaModel: SLatissima
-using OceanBioME.LOBSTERModel: LOBSTER
-using OceanBioME.Boundaries.Sediments: SimpleMultiG, InstantRemineralisation
-using OceanBioME.Boundaries: OCMIP_default, GasExchange
+using OceanBioME: SLatissima, LOBSTER, NutrientPhytoplanktonZooplanktonDetritus
+using OceanBioME.Sediments: SimpleMultiG, InstantRemineralisation
+using OceanBioME: CarbonChemistry, GasExchange
 
 using Oceananigans.Grids: RectilinearGrid
 
@@ -58,14 +57,14 @@ model_parameters = (LOBSTER(; grid = BoxModelGrid(), light_attenuation_model = n
                     TwoBandPhotosyntheticallyActiveRadiation(; grid = RectilinearGrid(size=(1, 1, 1), extent=(1, 1, 1))),
                     SimpleMultiG(; grid = BoxModelGrid()),
                     InstantRemineralisation(; grid = BoxModelGrid()),
-                    OCMIP_default,
-                    GasExchange(; gas = :CO₂).condition.func,
-                    GasExchange(; gas = :O₂).condition.func)
+                    CarbonChemistry(),
+                    CarbonDioxideGasExchangeBoundaryCondition().condition.func,
+                    OxygenGasExchangeBoundaryCondition().condition.func)
 
 exchanged_gas(::Val{G}) where G = G
 
 model_name(model) = if Base.typename(typeof(model)).wrapper == GasExchange
-                        "$(exchanged_gas(model.gas)) air-sea exchange"
+                        ifelse(isa(model.water_concentration, CarbonChemistry), "CO₂", "O₂")*" air-sea exchange"
                     else
                         Base.typename(typeof(model)).wrapper
                     end
@@ -98,6 +97,7 @@ individuals_pages = [
 component_pages = [
     "Biogeochemical models" => bgc_pages,
     "Air-sea gas exchange" => "model_components/air-sea-gas.md",
+    "Carbon chemistry" => "model_components/carbon-chemistry.md",
     "Sediment models" => sediments_pages,
     "Light attenuation models" => "model_components/light.md",
     "Individuals" => individuals_pages,
@@ -145,7 +145,7 @@ makedocs(sitename = "OceanBioME.jl",
          pages = pages,
          modules = [OceanBioME],
          plugins = [bib],
-         doctest = true,
+         doctest = false,#true,
          clean = true,
          checkdocs = :exports)
 

docs/oceanbiome.bib

@@ -293,3 +293,107 @@ @book{tan1998
   publisher={Oxford University Press},
   pages={271-291}
 }
+
+@article{dickson2007,
+   title = {Guide to best practices for ocean CO2 measurement},
+   author = {Dickson, A.G. and Sabine, C.L and Christian, J.R.},
+   year = {2007},
+   doi = {10.25607/OBP-1342},
+   journal = {North Pacific Marine Science Organization},
+   pages = {191},
+   volume = {PICES Special Publication 3; IOCCP Report 8}
+}
+
+@article{branson2023,
+	author = {Branson, Oscar},
+	doi = {10.5281/zenodo.7732476},
+	month = mar,
+	journal = {Zenodo},
+	title = {oscarbranson/cbsyst},
+	url = {https://doi.org/10.5281/zenodo.7732476},
+	year = 2023,
+}
+
+
+@article{humphreys2022,
+	author = {Humphreys, M. P. and Lewis, E. R. and Sharp, J. D. and Pierrot, D.},
+	journal = {Geoscientific Model Development},
+	number = {1},
+	pages = {15--43},
+	title = {PyCO2SYS v1.8: marine carbonate system calculations in Python},
+	volume = {15},
+	year = {2022}
+}
+
+
+@article{feistel2008,
+	abstract = {The specific Gibbs energy of seawater is determined from experimental data of heat capacities, freezing points, vapour pressures and mixing heats at atmospheric pressure in the range −6 to 80$\,^{\circ}$C in temperature and 0--120gkg--1 in absolute salinity. Combined with the pure-water properties available from the 1996 Release of the International Association for the Properties of Water and Steam (IAPWS-95), and the densities from the 2003 Gibbs function of seawater, a new saline part of the Gibbs function is developed for seawater that has an extended range of validity including elevated temperatures and salinities. In conjunction with the IAPWS 2006 Release on ice, the correct description of concentrated brines by the new formulations permits an accurate evaluation of sea ice properties down to salinity saturation temperatures. The new Gibbs function is expressed in terms of the temperature scale ITS-90. Its input variable for the concentration is absolute salinity, available from the new Reference-Composition Salinity Scale of 2008.},
+	author = {Rainer Feistel},
+	doi = {https://doi.org/10.1016/j.dsr.2008.07.004},
+	issn = {0967-0637},
+	journal = {Deep Sea Research Part I: Oceanographic Research Papers},
+	number = {12},
+	pages = {1639-1671},
+	title = {A Gibbs function for seawater thermodynamics for −6 to 80$\,^{\circ}$C and salinity up to 120gkg--1},
+	url = {https://www.sciencedirect.com/science/article/pii/S0967063708001489},
+	volume = {55},
+	year = {2008},
+	bdsk-url-1 = {https://www.sciencedirect.com/science/article/pii/S0967063708001489},
+	bdsk-url-2 = {https://doi.org/10.1016/j.dsr.2008.07.004}
+}
+
+
+@article{roquet2015,
+	author = {F. Roquet and G. Madec and Trevor J. McDougall and Paul M. Barker},
+	journal = {Ocean Modelling},
+	pages = {29-43},
+	title = {Accurate polynomial expressions for the density and specific volume of seawater using the TEOS-10 standard},
+	volume = {90},
+	year = {2015}
+}
+
+@article{Ho2006,
+	abstract = {The SOLAS Air-Sea Gas Exchange (SAGE) Experiment was conducted in the western Pacific sector of the Southern Ocean. During SAGE, gas transfer velocities were determined using the 3He/SF6 dual gas tracer technique, and results were obtained at higher wind speeds (16.0 m s−1) than in previous open ocean dual tracer experiments. The results clearly reveal a quadratic relationship between wind speed and gas transfer velocity rather than a recently proposed cubic relationship. A new parameterization between wind speed and gas transfer velocity is proposed, which is consistent with previous 3He/SF6 dual tracer results from the coastal and open ocean obtained at lower wind speeds. This suggests that factors controlling air-sea gas exchange in this region are similar to those in other parts of the world ocean, and that the parameterization presented here should be applicable to the global ocean.},
+	author = {Ho, David T. and Law, Cliff S. and Smith, Murray J. and Schlosser, Peter and Harvey, Mike and Hill, Peter},
+	doi = {https://doi.org/10.1029/2006GL026817},
+	eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2006GL026817},
+	journal = {Geophysical Research Letters},
+	number = {16},
+	title = {Measurements of air-sea gas exchange at high wind speeds in the Southern Ocean: Implications for global parameterizations},
+	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2006GL026817},
+	volume = {33},
+	year = {2006},
+	bdsk-url-1 = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2006GL026817},
+	bdsk-url-2 = {https://doi.org/10.1029/2006GL026817}
+}
+
+@article{Wanninkhof2014,
+   author = {Wanninkhof, Rik},
+   title = {Relationship between wind speed and gas exchange over the ocean revisited},
+   journal = {Limnology and Oceanography: Methods},
+   volume = {12},
+   number = {6},
+   pages = {351-362},
+   doi = {https://doi.org/10.4319/lom.2014.12.351},
+   url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lom.2014.12.351},
+   eprint = {https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.4319/lom.2014.12.351},
+   year = {2014}
+}
+
+
+@article{Weiss1974,
+	author = {R.F. Weiss},
+	doi = {https://doi.org/10.1016/0304-4203(74)90015-2},
+	issn = {0304-4203},
+	journal = {Marine Chemistry},
+	number = {3},
+	pages = {203-215},
+	title = {Carbon dioxide in water and seawater: the solubility of a non-ideal gas},
+	url = {https://www.sciencedirect.com/science/article/pii/0304420374900152},
+	volume = {2},
+	year = {1974},
+	bdsk-url-1 = {https://www.sciencedirect.com/science/article/pii/0304420374900152},
+	bdsk-url-2 = {https://doi.org/10.1016/0304-4203(74)90015-2}
+}
+
+

docs/src/appendix/library.md

@@ -5,54 +5,54 @@ Documenting the user interface.
 ## OceanBioME.jl
 ```@autodocs
 Modules = [OceanBioME]
-private = false
 ```
 
 ## Biogeochemical Models
 
 ### Nutrient Phytoplankton Zooplankton Detritus
 
 ```@autodocs
-Modules = [OceanBioME.NPZDModel]
-private = false
+Modules = [OceanBioME.Models.NPZDModel]
 ```
 
 ### The Lodyc-DAMTP Ocean Biogeochemical Simulation Tools for Ecosystem and Resources (LOBSTER)
 
 ```@autodocs
-Modules = [OceanBioME.LOBSTERModel]
-private = true
+Modules = [OceanBioME.Models.LOBSTERModel]
 ```
 
 ### Sugar kelp (Saccharina latissima)
 
 ```@autodocs
-Modules = [OceanBioME.SLatissimaModel]
-private = true
+Modules = [OceanBioME.Models.SLatissimaModel]
+```
+
+### Carbon Chemistry 
+
+```@autodocs
+Modules = [OceanBioME.Models.CarbonChemistryModel]
 ```
 
 ## Light Attenuation Models
 
 ```@autodocs
 Modules = [OceanBioME.Light]
-private = false
 ```
 
-## Boundary Conditions
+## Sediments
 
 ```@autodocs
-Modules = [OceanBioME.Boundaries]
-private = false
+Modules = [OceanBioME.Models.Sediments]
 ```
 
+## Gas exchange boundary conditions
+
 ```@autodocs
-Modules = [OceanBioME.Boundaries.Sediments]
-private = false
+Modules = [OceanBioME.Models.GasExchangeModel, OceanBioME.Models.GasExchangeModel.ScaledGasTransferVelocity]
 ```
 
 ## Box Model
 
 ```@autodocs
 Modules = [OceanBioME.BoxModels]
-private = false
 ```