Merge branch 'main' into jsw/add-some-flexibility-to-particle-interpo…

…lation

Manifest.toml

@@ -1,8 +1,8 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.10.2"
+julia_version = "1.10.5"
 manifest_format = "2.0"
-project_hash = "3c5ec406d66c67a7c97dba5d81a300057adf87ab"
+project_hash = "b7b68895e3965b7930805d42785ca0f68052cac9"
 
 [[deps.AbstractFFTs]]
 deps = ["LinearAlgebra"]
@@ -45,9 +45,9 @@ version = "0.1.38"
 
 [[deps.Adapt]]
 deps = ["LinearAlgebra", "Requires"]
-git-tree-sha1 = "6a55b747d1812e699320963ffde36f1ebdda4099"
+git-tree-sha1 = "d80af0733c99ea80575f612813fa6aa71022d33a"
 uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
-version = "4.0.4"
+version = "4.1.0"
 weakdeps = ["StaticArrays"]
 
     [deps.Adapt.extensions]
@@ -77,15 +77,15 @@ uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
 [[deps.Blosc_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Lz4_jll", "Zlib_jll", "Zstd_jll"]
-git-tree-sha1 = "19b98ee7e3db3b4eff74c5c9c72bf32144e24f10"
+git-tree-sha1 = "ef12cdd1c7fb7e1dfd6fa8fd60d4db6bc61d2f23"
 uuid = "0b7ba130-8d10-5ba8-a3d6-c5182647fed9"
-version = "1.21.5+0"
+version = "1.21.6+0"
 
 [[deps.Bzip2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "9e2a6b69137e6969bab0152632dcb3bc108c8bdd"
+git-tree-sha1 = "8873e196c2eb87962a2048b3b8e08946535864a1"
 uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0"
-version = "1.0.8+1"
+version = "1.0.8+2"
 
 [[deps.CEnum]]
 git-tree-sha1 = "389ad5c84de1ae7cf0e28e381131c98ea87d54fc"
@@ -168,7 +168,7 @@ weakdeps = ["Dates", "LinearAlgebra"]
 [[deps.CompilerSupportLibraries_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
-version = "1.1.0+0"
+version = "1.1.1+0"
 
 [[deps.CompositionsBase]]
 git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad"
@@ -239,9 +239,9 @@ version = "0.3.23"
 
 [[deps.Distances]]
 deps = ["LinearAlgebra", "Statistics", "StatsAPI"]
-git-tree-sha1 = "66c4c81f259586e8f002eacebc177e1fb06363b0"
+git-tree-sha1 = "c7e3a542b999843086e2f29dac96a618c105be1d"
 uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
-version = "0.10.11"
+version = "0.10.12"
 
     [deps.Distances.extensions]
     DistancesChainRulesCoreExt = "ChainRulesCore"
@@ -285,9 +285,9 @@ version = "3.3.10+1"
 
 [[deps.FileIO]]
 deps = ["Pkg", "Requires", "UUIDs"]
-git-tree-sha1 = "82d8afa92ecf4b52d78d869f038ebfb881267322"
+git-tree-sha1 = "62ca0547a14c57e98154423419d8a342dca75ca9"
 uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
-version = "1.16.3"
+version = "1.16.4"
 
 [[deps.FileWatching]]
 uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
@@ -417,15 +417,15 @@ version = "1.0.0"
 
 [[deps.JLD2]]
 deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "PrecompileTools", "Requires", "TranscodingStreams"]
-git-tree-sha1 = "a0746c21bdc986d0dc293efa6b1faee112c37c28"
+git-tree-sha1 = "783c1be5213a09609b23237a0c9e5dfd258ae6f2"
 uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-version = "0.4.53"
+version = "0.5.7"
 
 [[deps.JLLWrappers]]
 deps = ["Artifacts", "Preferences"]
-git-tree-sha1 = "f389674c99bfcde17dc57454011aa44d5a260a40"
+git-tree-sha1 = "be3dc50a92e5a386872a493a10050136d4703f9b"
 uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
-version = "1.6.0"
+version = "1.6.1"
 
 [[deps.JuliaNVTXCallbacks_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -435,9 +435,9 @@ version = "0.2.1+0"
 
 [[deps.KernelAbstractions]]
 deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"]
-git-tree-sha1 = "5126765c5847f74758c411c994312052eb7117ef"
+git-tree-sha1 = "e73a077abc7fe798fe940deabe30ef6c66bdde52"
 uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
-version = "0.9.27"
+version = "0.9.29"
 
     [deps.KernelAbstractions.extensions]
     EnzymeExt = "EnzymeCore"
@@ -450,10 +450,10 @@ version = "0.9.27"
     SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [[deps.LLVM]]
-deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Requires", "Unicode"]
-git-tree-sha1 = "4ad43cb0a4bb5e5b1506e1d1f48646d7e0c80363"
+deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Unicode"]
+git-tree-sha1 = "d422dfd9707bec6617335dc2ea3c5172a87d5908"
 uuid = "929cbde3-209d-540e-8aea-75f648917ca0"
-version = "9.1.2"
+version = "9.1.3"
 weakdeps = ["BFloat16s"]
 
     [deps.LLVM.extensions]
@@ -486,9 +486,9 @@ weakdeps = ["Serialization"]
     SerializationExt = ["Serialization"]
 
 [[deps.LaTeXStrings]]
-git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec"
+git-tree-sha1 = "dda21b8cbd6a6c40d9d02a73230f9d70fed6918c"
 uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
-version = "1.3.1"
+version = "1.4.0"
 
 [[deps.LazyArtifacts]]
 deps = ["Artifacts", "Pkg"]
@@ -523,9 +523,9 @@ uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 
 [[deps.Libiconv_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175"
+git-tree-sha1 = "61dfdba58e585066d8bce214c5a51eaa0539f269"
 uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531"
-version = "1.17.0+0"
+version = "1.17.0+1"
 
 [[deps.LinearAlgebra]]
 deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"]
@@ -574,9 +574,9 @@ version = "0.1.11"
 
 [[deps.MPItrampoline_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"]
-git-tree-sha1 = "fde81c9f9c94fe5fbeaed7b3f1330305cf9a327c"
+git-tree-sha1 = "70e830dab5d0775183c99fc75e4c24c614ed7142"
 uuid = "f1f71cc9-e9ae-5b93-9b94-4fe0e1ad3748"
-version = "5.5.0+0"
+version = "5.5.1+0"
 
 [[deps.MacroTools]]
 deps = ["Markdown", "Random"]
@@ -648,9 +648,9 @@ 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 = "cac4f28778a22404724ba667368f071047b513c1"
+git-tree-sha1 = "cddb567fbab1c40b22914e24ad2fe917ff00d8c9"
 uuid = "9e8cae18-63c1-5223-a75c-80ca9d6e9a09"
-version = "0.92.0"
+version = "0.93.1"
 
     [deps.Oceananigans.extensions]
     OceananigansEnzymeExt = "Enzyme"
@@ -833,9 +833,9 @@ version = "0.3.5"
 
 [[deps.SentinelArrays]]
 deps = ["Dates", "Random"]
-git-tree-sha1 = "ff11acffdb082493657550959d4feb4b6149e73a"
+git-tree-sha1 = "305becf8af67eae1dbc912ee9097f00aeeabb8d5"
 uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c"
-version = "1.4.5"
+version = "1.4.6"
 
 [[deps.Serialization]]
 uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
@@ -856,9 +856,9 @@ version = "1.10.0"
 
 [[deps.StaticArrays]]
 deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"]
-git-tree-sha1 = "eeafab08ae20c62c44c8399ccb9354a04b80db50"
+git-tree-sha1 = "777657803913ffc7e8cc20f0fd04b634f871af8f"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "1.9.7"
+version = "1.9.8"
 
     [deps.StaticArrays.extensions]
     StaticArraysChainRulesCoreExt = "ChainRulesCore"
@@ -932,20 +932,16 @@ version = "1.10.0"
 
 [[deps.TaylorSeries]]
 deps = ["LinearAlgebra", "Markdown", "Requires", "SparseArrays"]
-git-tree-sha1 = "90c9bc500f4c5cdd235c81503ec91b2048f06423"
+git-tree-sha1 = "abc13c4d3cccd1703335ba03abdaf0dc8ecc97e2"
 uuid = "6aa5eb33-94cf-58f4-a9d0-e4b2c4fc25ea"
-version = "0.17.8"
+version = "0.17.3"
 
     [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]]
@@ -954,14 +950,14 @@ uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [[deps.TimerOutputs]]
 deps = ["ExprTools", "Printf"]
-git-tree-sha1 = "5a13ae8a41237cff5ecf34f73eb1b8f42fff6531"
+git-tree-sha1 = "3a6f063d690135f5c1ba351412c82bae4d1402bf"
 uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
-version = "0.5.24"
+version = "0.5.25"
 
 [[deps.TranscodingStreams]]
-git-tree-sha1 = "e84b3a11b9bece70d14cce63406bbc79ed3464d2"
+git-tree-sha1 = "0c45878dcfdcfa8480052b6ab162cdd138781742"
 uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
-version = "0.11.2"
+version = "0.11.3"
 
 [[deps.UUIDs]]
 deps = ["Random", "SHA"]
@@ -983,15 +979,15 @@ version = "0.2.1"
 
 [[deps.XML2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"]
-git-tree-sha1 = "1165b0443d0eca63ac1e32b8c0eb69ed2f4f8127"
+git-tree-sha1 = "6a451c6f33a176150f315726eba8b92fbfdb9ae7"
 uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a"
-version = "2.13.3+0"
+version = "2.13.4+0"
 
 [[deps.XZ_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "ac88fb95ae6447c8dda6a5503f3bafd496ae8632"
+git-tree-sha1 = "15e637a697345f6743674f1322beefbc5dcd5cfc"
 uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800"
-version = "5.4.6+0"
+version = "5.6.3+0"
 
 [[deps.Zlib_jll]]
 deps = ["Libdl"]
@@ -1019,13 +1015,13 @@ version = "1.1.2+0"
 [[deps.libblastrampoline_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
-version = "5.8.0+1"
+version = "5.11.0+0"
 
 [[deps.libzip_jll]]
 deps = ["Artifacts", "Bzip2_jll", "GnuTLS_jll", "JLLWrappers", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"]
-git-tree-sha1 = "3282b7d16ae7ac3e57ec2f3fa8fafb564d8f9f7f"
+git-tree-sha1 = "668ac0297e6bd8f4d53dfdcd3ace71f2e00f4a35"
 uuid = "337d8026-41b4-5cde-a456-74a10e5b31d1"
-version = "1.10.1+0"
+version = "1.11.1+0"
 
 [[deps.nghttp2_jll]]
 deps = ["Artifacts", "Libdl"]

Project.toml

@@ -1,7 +1,7 @@
 name = "OceanBioME"
 uuid = "a49af516-9db8-4be4-be45-1dad61c5a376"
 authors = ["Jago Strong-Wright <[email protected]> and contributors"]
-version = "0.13.0"
+version = "0.13.2"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
@@ -24,7 +24,7 @@ EnsembleKalmanProcesses = "1"
 GibbsSeaWater = "0.1"
 JLD2 = "0.4, 0.5"
 KernelAbstractions = "0.9"
-Oceananigans = "0.91.9, 0.92"
+Oceananigans = "^0.92.1, ^0.93.0"
 OffsetArrays = "1.14"
 Roots = "2"
 SeawaterPolynomials = "0.3"

README.md

@@ -40,8 +40,8 @@ biogeochemistry = NutrientPhytoplanktonZooplanktonDetritus(; grid)
 
 model = NonhydrostaticModel(; grid, biogeochemistry,
                               advection = WENO(; grid),
-			                  closure = AnisotropicMinimumDissipation(),
-			                  buoyancy = SeawaterBuoyancy(constant_salinity = true))
+                              closure = AnisotropicMinimumDissipation(),
+			      buoyancy = SeawaterBuoyancy(constant_salinity = true))
 
 @inline front(x, z, μ, δ) = μ + δ * tanh((x - 7000 + 4 * z) / 500)
 

docs/Project.toml

@@ -16,11 +16,11 @@ Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [compat]
-CairoMakie = "0.11"
+CairoMakie = "0.11, 0.12"
 Documenter = "1"
 DocumenterCitations = "1"
 EnsembleKalmanProcesses = "1"
 JLD2 = "0.4"
 Literate = "≥2.9.0"
-Oceananigans = "0.91"
+Oceananigans = "^0.92.1"
 julia = "1.10"

docs/src/index.md

@@ -43,8 +43,8 @@ biogeochemistry = NutrientPhytoplanktonZooplanktonDetritus(; grid)
 
 model = NonhydrostaticModel(; grid, biogeochemistry,
                               advection = WENO(; grid),
-			                  closure = AnisotropicMinimumDissipation(),
-			                  buoyancy = SeawaterBuoyancy(constant_salinity = true))
+			      closure = AnisotropicMinimumDissipation(),
+                              buoyancy = SeawaterBuoyancy(constant_salinity = true))
 
 @inline front(x, z, μ, δ) = μ + δ * tanh((x - 7000 + 4 * z) / 500)
 
@@ -158,7 +158,6 @@ If you use OceanBioME as part of your research, teaching, or other activities, w
 }
 ```
 
-
 ## Funding
 
 OceanBioME.jl is supported through grants from the [Center for Climate Repair at Cambridge](https://www.climaterepair.cam.ac.uk/) and the [Gordon and Betty Moore Foundation](https://www.moore.org/).

src/Models/Sediments/Sediments.jl

@@ -9,7 +9,7 @@ using OceanBioME: DiscreteBiogeochemistry, ContinuousBiogeochemistry, BoxModelGr
 using Oceananigans
 using Oceananigans.Architectures: device, architecture, on_architecture
 using Oceananigans.Utils: launch!
-using Oceananigans.Advection: advective_tracer_flux_z, TracerAdvection
+using Oceananigans.Advection: advective_tracer_flux_z, FluxFormAdvection
 using Oceananigans.Units: day
 using Oceananigans.Fields: ConstantField
 using Oceananigans.Biogeochemistry: biogeochemical_drift_velocity
@@ -38,13 +38,13 @@ function update_tendencies!(bgc, sediment::FlatSediment, model)
 
     launch!(arch, model.grid, :xy,
             calculate_sediment_tendencies!,
-            sediment, biogeochemistry, model.grid, 
-            sinking_advection(biogeochemistry, model.advection), 
-            required_tracers(sediment, biogeochemistry, model.tracers), 
-            required_tendencies(sediment, biogeochemistry, model.timestepper.Gⁿ), 
+            sediment, biogeochemistry, model.grid,
+            sinking_advection(biogeochemistry, model.advection),
+            required_tracers(sediment, biogeochemistry, model.tracers),
+            required_tendencies(sediment, biogeochemistry, model.timestepper.Gⁿ),
             sediment.tendencies.Gⁿ,
             model.clock.time)
-            
+
     return nothing
 end
 
@@ -72,9 +72,9 @@ end
 
 @inline advection_scheme(advection, val_tracer) = advection
 @inline advection_scheme(advection::NamedTuple, val_tracer::Val{T}) where T = advection_scheme(advection[T], val_tracer)
-@inline advection_scheme(advection::TracerAdvection, val_tracer) = advection.z
+@inline advection_scheme(advection::FluxFormAdvection, val_tracer) = advection.z
 
-@inline function sinking_flux(i, j, k, grid, advection, val_tracer::Val{T}, bgc, tracers) where T 
+@inline function sinking_flux(i, j, k, grid, advection, val_tracer::Val{T}, bgc, tracers) where T
     return - advective_tracer_flux_z(i, j, k, grid, advection_scheme(advection, val_tracer), biogeochemical_drift_velocity(bgc, val_tracer).w, tracers[T]) /
       volume(i, j, k, grid, Center(), Center(), Center())
 end