Merge pull request #212 from OceanBioME/jsw/refactor-PISCES

Refactors to improve code clarity and make changing parameterisations easier

Manifest.toml

@@ -1,8 +1,8 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.10.4"
+julia_version = "1.10.2"
 manifest_format = "2.0"
-project_hash = "37e11a3bdd396c973917441db34ded05b97faa85"
+project_hash = "d9a7ed1497e9d29249634fa08034c82fcc96d9c4"
 
 [[deps.AbstractFFTs]]
 deps = ["LinearAlgebra"]
@@ -115,9 +115,9 @@ version = "0.9.2+0"
 
 [[deps.CUDA_Runtime_Discovery]]
 deps = ["Libdl"]
-git-tree-sha1 = "f3b237289a5a77c759b2dd5d4c2ff641d67c4030"
+git-tree-sha1 = "33576c7c1b2500f8e7e6baa082e04563203b3a45"
 uuid = "1af6417a-86b4-443c-805f-a4643ffb695f"
-version = "0.3.4"
+version = "0.3.5"
 
 [[deps.CUDA_Runtime_jll]]
 deps = ["Artifacts", "CUDA_Driver_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"]
@@ -171,7 +171,7 @@ weakdeps = ["Dates", "LinearAlgebra"]
 [[deps.CompilerSupportLibraries_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
-version = "1.1.1+0"
+version = "1.1.0+0"
 
 [[deps.CompositionsBase]]
 git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad"
@@ -183,17 +183,18 @@ weakdeps = ["InverseFunctions"]
     CompositionsBaseInverseFunctionsExt = "InverseFunctions"
 
 [[deps.ConstructionBase]]
-deps = ["LinearAlgebra"]
-git-tree-sha1 = "a33b7ced222c6165f624a3f2b55945fac5a598d9"
+git-tree-sha1 = "76219f1ed5771adbb096743bff43fb5fdd4c1157"
 uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
-version = "1.5.7"
+version = "1.5.8"
 
     [deps.ConstructionBase.extensions]
     ConstructionBaseIntervalSetsExt = "IntervalSets"
+    ConstructionBaseLinearAlgebraExt = "LinearAlgebra"
     ConstructionBaseStaticArraysExt = "StaticArrays"
 
     [deps.ConstructionBase.weakdeps]
     IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953"
+    LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
     StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 
 [[deps.Crayons]]
@@ -202,10 +203,10 @@ uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f"
 version = "4.1.1"
 
 [[deps.CubedSphere]]
-deps = ["Elliptic", "FFTW", "Printf", "ProgressBars", "SpecialFunctions", "TaylorSeries", "Test"]
-git-tree-sha1 = "10134667d7d3569b191a65801514271b8a93b292"
+deps = ["TaylorSeries"]
+git-tree-sha1 = "51bb25de518b4c62b7cdf26e5fbb84601bb27a60"
 uuid = "7445602f-e544-4518-8976-18f8e8ae6cdb"
-version = "0.2.5"
+version = "0.3.0"
 
 [[deps.DataAPI]]
 git-tree-sha1 = "abe83f3a2f1b857aac70ef8b269080af17764bbe"
@@ -265,11 +266,6 @@ deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
 uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 version = "1.6.0"
 
-[[deps.Elliptic]]
-git-tree-sha1 = "71c79e77221ab3a29918aaf6db4f217b89138608"
-uuid = "b305315f-e792-5b7a-8f41-49f472929428"
-version = "1.0.1"
-
 [[deps.ExprTools]]
 git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec"
 uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04"
@@ -313,9 +309,9 @@ version = "6.2.1+6"
 
 [[deps.GPUArrays]]
 deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"]
-git-tree-sha1 = "a74c3f1cf56a3dfcdef0605f8cdb7015926aae30"
+git-tree-sha1 = "62ee71528cca49be797076a76bdc654a170a523e"
 uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7"
-version = "10.3.0"
+version = "10.3.1"
 
 [[deps.GPUArraysCore]]
 deps = ["Adapt"]
@@ -384,10 +380,10 @@ version = "1.4.2"
     Parsers = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
 
 [[deps.IntelOpenMP_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "14eb2b542e748570b56446f4c50fbfb2306ebc45"
+deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl"]
+git-tree-sha1 = "10bd689145d2c3b2a9844005d01087cc1194e79e"
 uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0"
-version = "2024.2.0+0"
+version = "2024.2.1+0"
 
 [[deps.InteractiveUtils]]
 deps = ["Markdown"]
@@ -408,11 +404,6 @@ git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038"
 uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f"
 version = "1.3.0"
 
-[[deps.IrrationalConstants]]
-git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2"
-uuid = "92d709cd-6900-40b7-9082-c6be49f344b6"
-version = "0.2.2"
-
 [[deps.IterativeSolvers]]
 deps = ["LinearAlgebra", "Printf", "Random", "RecipesBase", "SparseArrays"]
 git-tree-sha1 = "59545b0a2b27208b0650df0a46b8e3019f85055b"
@@ -425,16 +416,16 @@ uuid = "82899510-4779-5014-852e-03e436cf321d"
 version = "1.0.0"
 
 [[deps.JLD2]]
-deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "PrecompileTools", "Reexport", "Requires", "TranscodingStreams", "UUIDs", "Unicode"]
-git-tree-sha1 = "67d4690d32c22e28818a434b293a374cc78473d3"
+deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "PrecompileTools", "Requires", "TranscodingStreams"]
+git-tree-sha1 = "a0746c21bdc986d0dc293efa6b1faee112c37c28"
 uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-version = "0.4.51"
+version = "0.4.53"
 
 [[deps.JLLWrappers]]
 deps = ["Artifacts", "Preferences"]
-git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca"
+git-tree-sha1 = "f389674c99bfcde17dc57454011aa44d5a260a40"
 uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
-version = "1.5.0"
+version = "1.6.0"
 
 [[deps.JuliaNVTXCallbacks_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -443,16 +434,20 @@ uuid = "9c1d0b0a-7046-5b2e-a33f-ea22f176ac7e"
 version = "0.2.1+0"
 
 [[deps.KernelAbstractions]]
-deps = ["Adapt", "Atomix", "InteractiveUtils", "LinearAlgebra", "MacroTools", "PrecompileTools", "Requires", "SparseArrays", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"]
-git-tree-sha1 = "0fac59881e91c7233a9b0d47f4b7d9432e534f0f"
+deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"]
+git-tree-sha1 = "cb1cff88ef2f3a157cbad75bbe6b229e1975e498"
 uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
-version = "0.9.23"
+version = "0.9.25"
 
     [deps.KernelAbstractions.extensions]
     EnzymeExt = "EnzymeCore"
+    LinearAlgebraExt = "LinearAlgebra"
+    SparseArraysExt = "SparseArrays"
 
     [deps.KernelAbstractions.weakdeps]
     EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869"
+    LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+    SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [[deps.LLVM]]
 deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Requires", "Unicode"]
@@ -536,22 +531,6 @@ version = "1.17.0+0"
 deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"]
 uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
-[[deps.LogExpFunctions]]
-deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"]
-git-tree-sha1 = "a2d09619db4e765091ee5c6ffe8872849de0feea"
-uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
-version = "0.3.28"
-
-    [deps.LogExpFunctions.extensions]
-    LogExpFunctionsChainRulesCoreExt = "ChainRulesCore"
-    LogExpFunctionsChangesOfVariablesExt = "ChangesOfVariables"
-    LogExpFunctionsInverseFunctionsExt = "InverseFunctions"
-
-    [deps.LogExpFunctions.weakdeps]
-    ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-    ChangesOfVariables = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0"
-    InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112"
-
 [[deps.Logging]]
 uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
 
@@ -635,9 +614,9 @@ version = "2023.1.10"
 
 [[deps.NCDatasets]]
 deps = ["CFTime", "CommonDataModel", "DataStructures", "Dates", "DiskArrays", "NetCDF_jll", "NetworkOptions", "Printf"]
-git-tree-sha1 = "a640912695952b074672edb5f9aaee2f7f9fd59a"
+git-tree-sha1 = "77df6d3708ec0eb3441551e1f20f7503b37c2393"
 uuid = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
-version = "0.14.4"
+version = "0.14.5"
 
 [[deps.NVTX]]
 deps = ["Colors", "JuliaNVTXCallbacks_jll", "Libdl", "NVTX_jll"]
@@ -669,16 +648,17 @@ version = "1.2.0"
 
 [[deps.Oceananigans]]
 deps = ["Adapt", "CUDA", "Crayons", "CubedSphere", "Dates", "Distances", "DocStringExtensions", "FFTW", "Glob", "IncompleteLU", "InteractiveUtils", "IterativeSolvers", "JLD2", "KernelAbstractions", "LinearAlgebra", "Logging", "MPI", "NCDatasets", "OffsetArrays", "OrderedCollections", "Pkg", "Printf", "Random", "Rotations", "SeawaterPolynomials", "SparseArrays", "Statistics", "StructArrays"]
-git-tree-sha1 = "ed415deb1d80c2a15c9b8bf0c7df04c6dec9d6c3"
+git-tree-sha1 = "9b1b114e7853bd744ad3feff93232a1e5747ffa1"
 uuid = "9e8cae18-63c1-5223-a75c-80ca9d6e9a09"
-version = "0.91.8"
+version = "0.91.13"
 
     [deps.Oceananigans.extensions]
     OceananigansEnzymeExt = "Enzyme"
-    OceananigansMakieExt = "MakieCore"
+    OceananigansMakieExt = ["MakieCore", "Makie"]
 
     [deps.Oceananigans.weakdeps]
     Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9"
+    Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
     MakieCore = "20f20a25-4f0e-4fdf-b5d1-57303727442b"
 
 [[deps.OffsetArrays]]
@@ -695,11 +675,6 @@ deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
 uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"
 version = "0.3.23+4"
 
-[[deps.OpenLibm_jll]]
-deps = ["Artifacts", "Libdl"]
-uuid = "05823500-19ac-5b8b-9628-191a04bc5112"
-version = "0.8.1+2"
-
 [[deps.OpenMPI_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML", "Zlib_jll"]
 git-tree-sha1 = "bfce6d523861a6c562721b262c0d1aaeead2647f"
@@ -708,15 +683,9 @@ version = "5.0.5+0"
 
 [[deps.OpenSSL_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "a028ee3cb5641cccc4c24e90c36b0a4f7707bdf5"
+git-tree-sha1 = "1b35263570443fdd9e76c76b7062116e2f374ab8"
 uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95"
-version = "3.0.14+0"
-
-[[deps.OpenSpecFun_jll]]
-deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1"
-uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e"
-version = "0.5.5+0"
+version = "3.0.15+0"
 
 [[deps.OrderedCollections]]
 git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5"
@@ -768,12 +737,6 @@ version = "2.3.2"
 deps = ["Unicode"]
 uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
-[[deps.ProgressBars]]
-deps = ["Printf"]
-git-tree-sha1 = "b437cdb0385ed38312d91d9c00c20f3798b30256"
-uuid = "49802e3a-d2f1-5c88-81d8-b72133a6f568"
-version = "1.5.1"
-
 [[deps.Quaternions]]
 deps = ["LinearAlgebra", "Random", "RealDot"]
 git-tree-sha1 = "994cc27cdacca10e68feb291673ec3a76aa2fae9"
@@ -825,9 +788,9 @@ version = "1.3.0"
 
 [[deps.Roots]]
 deps = ["Accessors", "ChainRulesCore", "CommonSolve", "Printf"]
-git-tree-sha1 = "3484138c9fa4296a0cf46a74ca3f97b59d12b1d0"
+git-tree-sha1 = "48a7925c1d971b03bb81183b99d82c1dc7a3562f"
 uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
-version = "2.1.6"
+version = "2.1.8"
 
     [deps.Roots.extensions]
     RootsForwardDiffExt = "ForwardDiff"
@@ -862,9 +825,9 @@ uuid = "6c6a2e73-6563-6170-7368-637461726353"
 version = "1.2.1"
 
 [[deps.SeawaterPolynomials]]
-git-tree-sha1 = "6d85acd6de472f8e6da81c61c7c5b6280a55e0bc"
+git-tree-sha1 = "78f965a2f0cd5250a20c9aba9979346dd2b35734"
 uuid = "d496a93d-167e-4197-9f49-d3af4ff8fe40"
-version = "0.3.4"
+version = "0.3.5"
 
 [[deps.SentinelArrays]]
 deps = ["Dates", "Random"]
@@ -889,16 +852,6 @@ deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"]
 uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 version = "1.10.0"
 
-[[deps.SpecialFunctions]]
-deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"]
-git-tree-sha1 = "2f5d4697f21388cbe1ff299430dd169ef97d7e14"
-uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
-version = "2.4.0"
-weakdeps = ["ChainRulesCore"]
-
-    [deps.SpecialFunctions.extensions]
-    SpecialFunctionsChainRulesCoreExt = "ChainRulesCore"
-
 [[deps.StaticArrays]]
 deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"]
 git-tree-sha1 = "eeafab08ae20c62c44c8399ccb9354a04b80db50"
@@ -974,15 +927,21 @@ version = "1.10.0"
 
 [[deps.TaylorSeries]]
 deps = ["LinearAlgebra", "Markdown", "Requires", "SparseArrays"]
-git-tree-sha1 = "1c7170668366821b0c4c4fe03ee78f8d6cf36e2c"
+git-tree-sha1 = "90c9bc500f4c5cdd235c81503ec91b2048f06423"
 uuid = "6aa5eb33-94cf-58f4-a9d0-e4b2c4fc25ea"
-version = "0.16.0"
+version = "0.17.8"
 
     [deps.TaylorSeries.extensions]
     TaylorSeriesIAExt = "IntervalArithmetic"
+    TaylorSeriesJLD2Ext = "JLD2"
+    TaylorSeriesRATExt = "RecursiveArrayTools"
+    TaylorSeriesSAExt = "StaticArrays"
 
     [deps.TaylorSeries.weakdeps]
     IntervalArithmetic = "d1acc4aa-44c8-5952-acd4-ba5d80a2a253"
+    JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
+    RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
+    StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 
 [[deps.Test]]
 deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
@@ -1013,9 +972,9 @@ version = "0.2.1"
 
 [[deps.UnsafeAtomicsLLVM]]
 deps = ["LLVM", "UnsafeAtomics"]
-git-tree-sha1 = "4073c836c2befcb041e5fe306cb6abf621eb3140"
+git-tree-sha1 = "2d17fabcd17e67d7625ce9c531fb9f40b7c42ce4"
 uuid = "d80eeb9a-aca5-4d75-85e5-170c8b632249"
-version = "0.2.0"
+version = "0.2.1"
 
 [[deps.XML2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"]

Project.toml

@@ -22,7 +22,7 @@ EnsembleKalmanProcesses = "1"
 GibbsSeaWater = "0.1"
 JLD2 = "0.4"
 KernelAbstractions = "0.9"
-Oceananigans = "0.91"
+Oceananigans = "0.91.9"
 Roots = "2"
 SeawaterPolynomials = "0.3"
 StructArrays = "0.4, 0.5, 0.6"

docs/make.jl

@@ -77,10 +77,14 @@ end
 
 parameter_pages = ["$name" => "generated/$(name)_parameters.md" for name in model_names]
 
+pisces_pages = ["PISCES" => "model_components/biogeochemical/PISCES/PISCES.md",
+                "Queries" => "model_components/biogeochemical/PISCES/notable_differences.md"]
+
 bgc_pages = [
     "Overview" => "model_components/biogeochemical/index.md",
     "LOBSTER" => "model_components/biogeochemical/LOBSTER.md",
-    "NPZD" => "model_components/biogeochemical/NPZ.md"
+    "NPZD" => "model_components/biogeochemical/NPZ.md",
+    "PISCES" => pisces_pages
 ]
 
 sediments_pages = [

docs/oceanbiome.bib

@@ -396,4 +396,17 @@ @article{Weiss1974
 	bdsk-url-2 = {https://doi.org/10.1016/0304-4203(74)90015-2}
 }
 
-
+@article{Aumont2015,
+   abstract = {PISCES-v2 (Pelagic Interactions Scheme for Carbon and Ecosystem Studies volume 2) is a biogeochemical model which simulates the lower trophic levels of marine ecosystems (phytoplankton, microzooplankton and mesozooplankton) and the biogeochemical cycles of carbon and of the main nutrients (P, N, Fe, and Si). The model is intended to be used for both regional and global configurations at high or low spatial resolutions as well as for short-term (seasonal, interannual) and long-term (climate change, paleoceanography) analyses. There are 24 prognostic variables (tracers) including two phytoplankton compartments (diatoms and nanophytoplankton), two zooplankton size classes (microzooplankton and mesozooplankton) and a description of the carbonate chemistry. Formulations in PISCES-v2 are based on a mixed Monod-quota formalism. On the one hand, stoichiometry of C / N / P is fixed and growth rate of phytoplankton is limited by the external availability in N, P and Si. On the other hand, the iron and silicon quotas are variable and the growth rate of phytoplankton is limited by the internal availability in Fe. Various parameterizations can be activated in PISCES-v2, setting, for instance, the complexity of iron chemistry or the description of particulate organic materials. So far, PISCES-v2 has been coupled to the Nucleus for European Modelling of the Ocean (NEMO) and Regional Ocean Modeling System (ROMS) systems. A full description of PISCES-v2 and of its optional functionalities is provided here. The results of a quasi-steady-state simulation are presented and evaluated against diverse observational and satellite-derived data. Finally, some of the new functionalities of PISCES-v2 are tested in a series of sensitivity experiments.},
+   author = {O. Aumont and C. Ethé and A. Tagliabue and L. Bopp and M. Gehlen},
+   doi = {10.5194/gmd-8-2465-2015},
+   issn = {19919603},
+   issue = {8},
+   journal = {Geoscientific Model Development},
+   month = {8},
+   pages = {2465-2513},
+   publisher = {Copernicus GmbH},
+   title = {PISCES-v2: An ocean biogeochemical model for carbon and ecosystem studies},
+   volume = {8},
+   year = {2015},
+}