diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml index f399ec8e78..cdef5a3ed4 100644 --- a/.buildkite/pipeline.yml +++ b/.buildkite/pipeline.yml @@ -184,7 +184,6 @@ steps: slurm_mem: 16G slurm_gpus: 1 soft_fail: true - - group: "Plane Examples" steps: - label: ":computer: Agnesi linear hydrostatic mountain experiment (uniform)" diff --git a/.gitignore b/.gitignore index 4cf65a220c..ed7ca00073 100644 --- a/.gitignore +++ b/.gitignore @@ -32,6 +32,8 @@ docs/src/config.md test/Manifest*.toml calibration/test/Manifest*.toml +Artifacts.toml + # ignore vscode artifacts *.vscode *.DS diff --git a/config/default_configs/default_config.yml b/config/default_configs/default_config.yml index 708cdf0801..b372fbf76e 100644 --- a/config/default_configs/default_config.yml +++ b/config/default_configs/default_config.yml @@ -145,6 +145,14 @@ vert_diff: hyperdiff: help: "Hyperdiffusion [`ClimaHyperdiffusion` (or `true`; default), `none` (or `false`)]" value: "CAM_SE" +smagorinsky_lilly: + value: false +c_smag: + help: "Smagorinsky coefficient" + value: 0.2 +prandtl_turbulent_neutral: + help: "Turbulent Prandtl number for neutral stratification" + value: 0.333 bubble: help: "Enable bubble correction for more accurate surface areas" value: true diff --git a/config/model_configs/box_density_current_test.yml b/config/model_configs/box_density_current_test.yml index 0c3e346d21..cd45b2adab 100644 --- a/config/model_configs/box_density_current_test.yml +++ b/config/model_configs/box_density_current_test.yml @@ -1,16 +1,21 @@ -dt_save_state_to_disk: "10secs" initial_condition: "DryDensityCurrentProfile" +config: "box" +smagorinsky_lilly: true +c_smag: 0.25 +discrete_hydrostatic_balance: true +hyperdiff: "false" x_max: 51200.0 +y_max: 51200.0 +z_max: 6400.0 +x_elem: 45 +y_elem: 45 z_elem: 45 -dt: "0.1secs" -t_end: "10.0secs" -discrete_hydrostatic_balance: true -y_max: 6400.0 -y_elem: 15 z_stretch: false -x_elem: 45 -config: "box" -z_max: 6400.0 +dt: "0.25secs" +t_end: "20secs" +prandtl_turbulent_neutral: 0.333 +dt_save_state_to_disk: "5secs" +netcdf_interpolation_num_points: [40, 40, 80] diagnostics: - - short_name: thetaa - period: 10secs + - short_name: [thetaa, wa, ua, ta, va, hfes, rhoa, rv, ha] + period: 5secs diff --git a/config/model_configs/les_isdac_box.yml b/config/model_configs/les_isdac_box.yml index 06bdbf55a9..5d424ebe72 100644 --- a/config/model_configs/les_isdac_box.yml +++ b/config/model_configs/les_isdac_box.yml @@ -15,6 +15,7 @@ hyperdiff: "false" apply_limiter: false smagorinsky_lilly: true c_smag: 0.20 +prandtl_turbulent_neutral: 0.333 # time- and spatial discretization x_elem: 10 x_max: 3.2e3 @@ -24,11 +25,13 @@ z_elem: 15 z_max: 2.5e3 z_stretch: false rayleigh_sponge: true -toml: [toml/isdac_box.toml] # sponge height +toml: [toml/les_isdac.toml] # sponge height ode_algo: "SSPKnoth" dt: "0.05secs" t_end: "2mins" dt_cloud_fraction: "10mins" +restart_file: "/groups/esm/hervik/climaatmos-les-artifacts/les_isdac_day0.0.hdf5" +# diagnostics dt_save_state_to_disk: "1mins" netcdf_interpolation_num_points: [30, 30, 150] diagnostics: diff --git a/examples/Manifest-v1.11.toml b/examples/Manifest-v1.11.toml new file mode 100644 index 0000000000..4c5779a60f --- /dev/null +++ b/examples/Manifest-v1.11.toml @@ -0,0 +1,2704 @@ +# This file is machine-generated - editing it directly is not advised + +julia_version = "1.11.1" +manifest_format = "2.0" +project_hash = "acdac96270a93ae35f3e35c16b314df5a99f63c8" + +[[deps.ADTypes]] +git-tree-sha1 = "eea5d80188827b35333801ef97a40c2ed653b081" +uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" +version = "1.9.0" +weakdeps = ["ChainRulesCore", "EnzymeCore"] + + [deps.ADTypes.extensions] + ADTypesChainRulesCoreExt = "ChainRulesCore" + ADTypesEnzymeCoreExt = "EnzymeCore" + +[[deps.AbstractFFTs]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef" +uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" +version = "1.5.0" +weakdeps = ["ChainRulesCore", "Test"] + + 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a/examples/Manifest.toml b/examples/Manifest.toml index 909a799dcd..ea65caba91 100644 --- a/examples/Manifest.toml +++ b/examples/Manifest.toml @@ -290,10 +290,10 @@ uuid = "159f3aea-2a34-519c-b102-8c37f9878175" version = "1.1.1" [[deps.CairoMakie]] -deps = ["CRC32c", "Cairo", "Colors", "FileIO", "FreeType", "GeometryBasics", "LinearAlgebra", "Makie", "PrecompileTools"] -git-tree-sha1 = "d69c7593fe9d7d617973adcbe4762028c6899b2c" +deps = ["CRC32c", "Cairo", "Cairo_jll", "Colors", "FileIO", "FreeType", "GeometryBasics", "LinearAlgebra", "Makie", "PrecompileTools"] +git-tree-sha1 = "7947d2b61995eda7d5ca50c697b12bb578b918e5" uuid = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" -version = "0.11.11" +version = "0.12.14" [[deps.Cairo_jll]] deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] @@ -312,14 +312,14 @@ weakdeps = ["SparseArrays"] ChainRulesCoreSparseArraysExt = "SparseArrays" [[deps.ClimaAnalysis]] -deps = ["Dates", "Interpolations", "NCDatasets", "NaNStatistics", "OrderedCollections", "Reexport", "Statistics"] -git-tree-sha1 = "e13d742cd5a5ad287cf72ab22cb0927780cfe596" +deps = ["Dates", "Interpolations", "NCDatasets", "NaNStatistics", "OrderedCollections", "Reexport", "Statistics", "Unitful"] +git-tree-sha1 = "1f6c4859eafc66f1b6df4932bd7040747581d816" uuid = "29b5916a-a76c-4e73-9657-3c8fd22e65e6" -version = "0.5.7" +version = "0.5.10" [deps.ClimaAnalysis.extensions] - GeoMakieExt = "GeoMakie" - MakieExt = "Makie" + ClimaAnalysisGeoMakieExt = "GeoMakie" + ClimaAnalysisMakieExt = "Makie" [deps.ClimaAnalysis.weakdeps] GeoMakie = "db073c08-6b98-4ee5-b6a4-5efafb3259c6" @@ -992,9 +992,9 @@ version = "1.3.14+0" [[deps.GridLayoutBase]] deps = ["GeometryBasics", "InteractiveUtils", "Observables"] -git-tree-sha1 = "6f93a83ca11346771a93bbde2bdad2f65b61498f" +git-tree-sha1 = "fc713f007cff99ff9e50accba6373624ddd33588" uuid = "3955a311-db13-416c-9275-1d80ed98e5e9" -version = "0.10.2" +version = "0.11.0" [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" @@ -1130,13 +1130,11 @@ deps = ["Adapt", "AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArr git-tree-sha1 = "88a101217d7cb38a7b481ccd50d21876e1d1b0e0" uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" version = "0.15.1" +weakdeps = ["Unitful"] [deps.Interpolations.extensions] InterpolationsUnitfulExt = "Unitful" - [deps.Interpolations.weakdeps] - Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" - [[deps.IntervalArithmetic]] deps = ["CRlibm", "FastRounding", "LinearAlgebra", "Markdown", "Random", "RecipesBase", "RoundingEmulator", "SetRounding", "StaticArrays"] git-tree-sha1 = "5ab7744289be503d76a944784bac3f2df7b809af" @@ -1542,16 +1540,16 @@ uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" version = "0.5.13" [[deps.Makie]] -deps = ["Animations", "Base64", "CRC32c", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "DelaunayTriangulation", "Distributions", "DocStringExtensions", "Downloads", "FFMPEG_jll", "FileIO", "FilePaths", "FixedPointNumbers", "Format", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageIO", "InteractiveUtils", "IntervalSets", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MacroTools", "MakieCore", "Markdown", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "PrecompileTools", "Printf", "REPL", "Random", "RelocatableFolders", "Scratch", "ShaderAbstractions", "Showoff", "SignedDistanceFields", "SparseArrays", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "TriplotBase", "UnicodeFun"] -git-tree-sha1 = "4d49c9ee830eec99d3e8de2425ff433ece7cc1bc" +deps = ["Animations", "Base64", "CRC32c", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "Dates", "DelaunayTriangulation", "Distributions", "DocStringExtensions", "Downloads", "FFMPEG_jll", "FileIO", "FilePaths", "FixedPointNumbers", "Format", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageBase", "ImageIO", "InteractiveUtils", "Interpolations", "IntervalSets", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MacroTools", "MakieCore", "Markdown", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "PrecompileTools", "Printf", "REPL", "Random", "RelocatableFolders", "Scratch", "ShaderAbstractions", "Showoff", "SignedDistanceFields", "SparseArrays", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "TriplotBase", "UnicodeFun", "Unitful"] +git-tree-sha1 = "3df66da15ba7b37b34f6557b7e1c95a3ff5c670b" uuid = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" -version = "0.20.10" +version = "0.21.14" [[deps.MakieCore]] -deps = ["Observables", "REPL"] -git-tree-sha1 = "248b7a4be0f92b497f7a331aed02c1e9a878f46b" +deps = ["ColorTypes", "GeometryBasics", "IntervalSets", "Observables"] +git-tree-sha1 = "4604f03e5b057e8e62a95a44929cafc9585b0fe9" uuid = "20f20a25-4f0e-4fdf-b5d1-57303727442b" -version = "0.7.3" +version = "0.8.9" [[deps.ManualMemory]] git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd" @@ -1569,9 +1567,9 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" [[deps.MathTeXEngine]] deps = ["AbstractTrees", "Automa", "DataStructures", "FreeTypeAbstraction", "GeometryBasics", "LaTeXStrings", "REPL", "RelocatableFolders", "UnicodeFun"] -git-tree-sha1 = "96ca8a313eb6437db5ffe946c457a401bbb8ce1d" +git-tree-sha1 = "e1641f32ae592e415e3dbae7f4a188b5316d4b62" uuid = "0a4f8689-d25c-4efe-a92b-7142dfc1aa53" -version = "0.5.7" +version = "0.6.1" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] @@ -2457,6 +2455,17 @@ git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf" uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" version = "0.4.1" +[[deps.Unitful]] +deps = ["Dates", "LinearAlgebra", "Random"] +git-tree-sha1 = "d95fe458f26209c66a187b1114df96fd70839efd" +uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" +version = "1.21.0" +weakdeps = ["ConstructionBase", "InverseFunctions"] + + [deps.Unitful.extensions] + ConstructionBaseUnitfulExt = "ConstructionBase" + InverseFunctionsUnitfulExt = "InverseFunctions" + [[deps.Unrolled]] deps = ["MacroTools"] git-tree-sha1 = "6cc9d682755680e0f0be87c56392b7651efc2c7b" diff --git a/post_processing/ci_plots.jl b/post_processing/ci_plots.jl index df2c26072e..2f652cb8cd 100644 --- a/post_processing/ci_plots.jl +++ b/post_processing/ci_plots.jl @@ -42,7 +42,7 @@ import CairoMakie import CairoMakie.Makie import ClimaAnalysis import ClimaAnalysis: Visualize as viz -import ClimaAnalysis: SimDir, slice, read_var, average_xy +import ClimaAnalysis: SimDir, slice, read_var, average_xy, window, average_time import ClimaAnalysis.Utils: kwargs as ca_kwargs import ClimaCoreSpectra: power_spectrum_2d @@ -577,6 +577,7 @@ end function make_plots( ::Val{:box_density_current_test}, + ::Val{:box_rising_thermal_test}, output_paths::Vector{<:AbstractString}, ) simdirs = SimDir.(output_paths) @@ -1065,6 +1066,118 @@ function make_plots(::Aquaplanet1MPlots, output_paths::Vector{<:AbstractString}) ) end +LESBoxPlots = Union{ + Val{:les_rico_box}, + Val{:les_dycoms_box}, + Val{:les_bomex_box}, + Val{:les_gabls_box}, +} + +""" + plot_les_vert_profile!(grid_loc, var_group) + +Helper function for `make_plots_generic`. Takes a list of variables and plots +them on the same axis. +""" +function plot_les_vert_profile!(grid_loc, var_group) + z = var_group[1].dims["z"] + units = var_group[1].attributes["units"] + ax = CairoMakie.Axis( + grid_loc[1, 1], + ylabel = "z [$(var_group[1].dim_attributes["z"]["units"])]", + xlabel = "$(short_name(var_group[1])) [$units]", + title = parse_var_attributes(var_group[1]), + ) + + for var in var_group + CairoMakie.lines!(ax, var.data, z, label = short_name(var)) + end + length(var_group) > 1 && Makie.axislegend(ax) +end + +function make_plots( + sim_type::Union{LESBoxPlots}, + output_paths::Vector{<:AbstractString}, +) + simdirs = SimDir.(output_paths) + + reduction = "inst" + short_names = [ + "wa", + "ua", + "va", + "ta", + "thetaa", + "ha", + "hus", + "hur", + "cl", + "clw", + "cli", + ] + available_periods = ClimaAnalysis.available_periods( + simdirs[1]; + short_name = short_names[1], + reduction, + ) + # if "5m" in available_periods + # period = "5m" + # elseif "10m" in available_periods + # period = "10m" + # elseif "30m" in available_periods + # period = "30m" + # elseif "1h" in available_periods + # period = "1h" + # end + + # Window average from instantaneous snapshots? + function horizontal_average(var) + return average_xy(var) + end + function windowed_reduction(var) + hours = 3600.0 + window_end = last(var.dims["time"]) + window_start = window_end - 2hours + var_window = ClimaAnalysis.window( + var, + "time"; + left = window_start, + right = window_end, + ) + var_reduced = horizontal_average(average_time(var_window)) + return var_reduced + end + + var_groups_xyt_reduced = + map_comparison(simdirs, short_names) do simdir, short_name + return [get(simdir; short_name, reduction) |> windowed_reduction] + end + + var_groups_xy_reduced = + map_comparison(simdirs, short_names) do simdir, short_name + return [get(simdir; short_name, reduction) |> horizontal_average] + end + + tmp_file = make_plots_generic( + output_paths, + var_groups_xyt_reduced, + output_name = "tmp"; + plot_fn = plot_les_vert_profile!, + MAX_NUM_COLS = 2, + MAX_NUM_ROWS = 4, + ) + + make_plots_generic( + output_paths, + vcat(var_groups_xy_reduced...), + plot_fn = plot_parsed_attribute_title!, + summary_files = [tmp_file], + MAX_NUM_COLS = 2, + MAX_NUM_ROWS = 4, + ) +end + + EDMFBoxPlots = Union{ Val{:diagnostic_edmfx_gabls_box}, Val{:diagnostic_edmfx_bomex_box}, @@ -1097,7 +1210,6 @@ EDMFBoxPlotsWithPrecip = Union{ Val{:diagnostic_edmfx_trmm_stretched_box}, } - """ plot_edmf_vert_profile!(grid_loc, var_group) diff --git a/src/ClimaAtmos.jl b/src/ClimaAtmos.jl index d09a10bddc..bc760a56bc 100644 --- a/src/ClimaAtmos.jl +++ b/src/ClimaAtmos.jl @@ -110,6 +110,13 @@ include( ) include(joinpath("parameterized_tendencies", "sponge", "rayleigh_sponge.jl")) include(joinpath("parameterized_tendencies", "sponge", "viscous_sponge.jl")) +include( + joinpath( + "parameterized_tendencies", + "les_sgs_models", + "smagorinsky_lilly.jl", + ), +) include(joinpath("prognostic_equations", "advection.jl")) include(joinpath("cache", "temporary_quantities.jl")) diff --git a/src/cache/precomputed_quantities.jl b/src/cache/precomputed_quantities.jl index 5d41912fd4..6acf4fa2ad 100644 --- a/src/cache/precomputed_quantities.jl +++ b/src/cache/precomputed_quantities.jl @@ -156,6 +156,19 @@ function precomputed_quantities(Y, atmos) ᶜqᵣ = similar(Y.c, FT), ᶜqₛ = similar(Y.c, FT), ) : (;) + smagorinsky_lilly_quantities = + if atmos.smagorinsky_lilly isa SmagorinskyLilly + uvw_vec = UVW(FT(0), FT(0), FT(0)) + (; + ᶜτ_smag = similar(Y.c, typeof(uvw_vec * uvw_vec')), + ᶠτ_smag = similar(Y.f, typeof(uvw_vec * uvw_vec')), + ᶜD_smag = similar(Y.c, FT), + ᶠD_smag = similar(Y.f, FT), + ) + else + (;) + end + return (; gs_quantities..., sgs_quantities..., @@ -164,6 +177,7 @@ function precomputed_quantities(Y, atmos) vert_diff_quantities..., precipitation_quantities..., cloud_diagnostics_tuple, + smagorinsky_lilly_quantities..., ) end @@ -633,6 +647,10 @@ NVTX.@annotate function set_precomputed_quantities!(Y, p, t) set_cloud_fraction!(Y, p, moisture_model, cloud_model) end + if p.atmos.smagorinsky_lilly isa SmagorinskyLilly + set_smagorinsky_lilly_precomputed_quantities!(Y, p) + end + return nothing end diff --git a/src/cache/temporary_quantities.jl b/src/cache/temporary_quantities.jl index 4482e86147..cee88bc51d 100644 --- a/src/cache/temporary_quantities.jl +++ b/src/cache/temporary_quantities.jl @@ -10,6 +10,7 @@ function temporary_quantities(Y, atmos) FT = Spaces.undertype(center_space) CTh = CTh_vector_type(Y.c) + uvw_vec = UVW(FT(0), FT(0), FT(0)) return (; ᶠtemp_scalar = Fields.Field(FT, face_space), # ᶠp, ᶠρK_E ᶜtemp_scalar = Fields.Field(FT, center_space), # ᶜ1 @@ -45,14 +46,12 @@ function temporary_quantities(Y, atmos) face_space, ), # ᶠω¹²ʲs ᶠtemp_C123 = Fields.Field(C123{FT}, face_space), # χ₁₂₃ - ᶜtemp_UVWxUVW = Fields.Field( - typeof(UVW(FT(0), FT(0), FT(0)) * UVW(FT(0), FT(0), FT(0))'), - center_space, - ), # ᶜstrain_rate - ᶠtemp_UVWxUVW = Fields.Field( - typeof(UVW(FT(0), FT(0), FT(0)) * UVW(FT(0), FT(0), FT(0))'), - face_space, - ), # ᶠstrain_rate + ᶜtemp_UVW = Fields.Field(typeof(uvw_vec), center_space), # UVW(ᶜu) + ᶠtemp_UVW = Fields.Field(typeof(uvw_vec), face_space), # UVW(ᶠu³) + ᶜtemp_UVWxUVW = Fields.Field(typeof(uvw_vec * uvw_vec'), center_space), # ᶜstrain_rate + ᶠtemp_UVWxUVW = Fields.Field(typeof(uvw_vec * uvw_vec'), face_space), # ᶠstrain_rate + ᶜtemp_strain = Fields.Field(typeof(uvw_vec * uvw_vec'), center_space), # ᶜstrain_rate + ᶠtemp_strain = Fields.Field(typeof(uvw_vec * uvw_vec'), face_space), # ᶠstrain_rate # TODO: Remove this hack sfc_temp_C3 = Fields.Field(C3{FT}, Spaces.level(face_space, half)), # ρ_flux_χ # Implicit solver cache: diff --git a/src/parameterized_tendencies/les_sgs_models/smagorinsky_lilly.jl b/src/parameterized_tendencies/les_sgs_models/smagorinsky_lilly.jl new file mode 100644 index 0000000000..fb63815d12 --- /dev/null +++ b/src/parameterized_tendencies/les_sgs_models/smagorinsky_lilly.jl @@ -0,0 +1,174 @@ +##### +##### Smagorinsky Lilly Diffusion +##### + +import ClimaCore.Fields as Fields +import ClimaCore.Operators as Operators +import ClimaCore: Geometry + +""" + set_smagorinsky_lilly_precomputed_quantities!(Y, p) + +Compute the Smagorinsky-Lilly diffusivity tensors, `ᶜτ_smag`, `ᶠτ_smag`, `ᶜD_smag`, and `ᶠD_smag`. +Store in the precomputed quantities `p.precomputed`. + +The subgrid-scale momentum flux tensor is defined by `τ = -2 νₜ ∘ S`, where `νₜ` is the Smagorinsky-Lilly eddy viscosity +and `S` is the strain rate tensor. + +The turbulent diffusivity is defined as `D = νₜ / Pr_t`, where `Pr_t` is the turbulent Prandtl number for neutral +stratification. + +These quantities are computed for both cell centers and faces, with prefixes `ᶜ` and `ᶠ`, respectively. + + +# Arguments +- `Y`: The model state. +- `p`: The model parameters, e.g. `AtmosCache`. +""" +function set_smagorinsky_lilly_precomputed_quantities!(Y, p) + + (; atmos, precomputed, scratch, params) = p + (; Cs, Pr_t) = atmos.smagorinsky_lilly + (; ᶜu, ᶠu³, ᶜts, ᶜτ_smag, ᶠτ_smag, ᶜD_smag, ᶠD_smag) = precomputed + FT = eltype(Y) + grav = CAP.grav(params) + thermo_params = CAP.thermodynamics_params(params) + (; ᶜtemp_UVWxUVW, ᶠtemp_UVWxUVW, ᶜtemp_strain, ᶠtemp_strain) = scratch + (; ᶜtemp_scalar, ᶜtemp_scalar_2, ᶠtemp_scalar, ᶜtemp_UVW, ᶠtemp_UVW) = + scratch + + ∇ᵥuvw_boundary = Geometry.outer(Geometry.WVector(0), UVW(0, 0, 0)) + ᶠgradᵥ_uvw = Operators.GradientC2F( + bottom = Operators.SetGradient(∇ᵥuvw_boundary), + top = Operators.SetGradient(∇ᵥuvw_boundary), + ) + axis_uvw = (Geometry.UVWAxis(),) + + # Compute UVW velocities + ᶜu_uvw = @. ᶜtemp_UVW = UVW(ᶜu) + ᶠu_uvw = @. ᶠtemp_UVW = UVW(ᶠinterp(Y.c.uₕ)) + UVW(ᶠu³) + + # Gradients + ## cell centers + ∇ᶜu_uvw = @. ᶜtemp_UVWxUVW = Geometry.project(axis_uvw, ᶜgradᵥ(ᶠu_uvw)) # vertical component + @. ∇ᶜu_uvw += Geometry.project(axis_uvw, gradₕ(ᶜu_uvw)) # horizontal component + ## cell faces + ∇ᶠu_uvw = @. ᶠtemp_UVWxUVW = Geometry.project(axis_uvw, ᶠgradᵥ_uvw(ᶜu_uvw)) # vertical component + @. ∇ᶠu_uvw += Geometry.project(axis_uvw, gradₕ(ᶠu_uvw)) # horizontal component + + # Strain rate tensor + ᶜS = @. ᶜtemp_strain = (∇ᶜu_uvw + adjoint(∇ᶜu_uvw)) / 2 + ᶠS = @. ᶠtemp_strain = (∇ᶠu_uvw + adjoint(∇ᶠu_uvw)) / 2 + + # Stratification correction + ᶜθ_v = @. ᶜtemp_scalar = TD.virtual_pottemp(thermo_params, ᶜts) + ᶜ∇ᵥθ = @. ᶜtemp_scalar_2 = + Geometry.WVector(ᶜgradᵥ(ᶠinterp(ᶜθ_v))).components.data.:1 + ᶜN² = @. ᶜtemp_scalar = grav / ᶜθ_v * ᶜ∇ᵥθ + ᶜS_norm = @. ᶜtemp_scalar_2 = √(2 * CA.norm_sqr(ᶜS)) + + ᶜRi = @. ᶜtemp_scalar = ᶜN² / (ᶜS_norm^2 + eps(FT)) # Ri = N² / |S|² + ᶜfb = @. ᶜtemp_scalar = ifelse(ᶜRi ≤ 0, 1, max(0, 1 - ᶜRi / Pr_t)^(1 / 4)) + + # filter scale + h_space = Spaces.horizontal_space(axes(Y.c)) + Δ_xy = Spaces.node_horizontal_length_scale(h_space)^2 # Δ_x * Δ_y + ᶜΔ_z = Fields.Δz_field(Y.c) + ᶜΔ = @. ᶜtemp_scalar = ∛(Δ_xy * ᶜΔ_z) * ᶜfb + + # Smagorinsky-Lilly eddy viscosity + ᶜνₜ = @. ᶜtemp_scalar = Cs^2 * ᶜΔ^2 * ᶜS_norm + ᶠνₜ = @. ᶠtemp_scalar = ᶠinterp(ᶜνₜ) + + # Subgrid-scale momentum flux tensor, `τ = -2 νₜ ∘ S` + @. ᶜτ_smag = -2 * ᶜνₜ * ᶜS + @. ᶠτ_smag = -2 * ᶠνₜ * ᶠS + + # Turbulent diffusivity + @. ᶜD_smag = ᶜνₜ / Pr_t + @. ᶠD_smag = ᶠνₜ / Pr_t + + nothing +end + +horizontal_smagorinsky_lilly_tendency!(Yₜ, Y, p, t, ::Nothing) = nothing +vertical_smagorinsky_lilly_tendency!(Yₜ, Y, p, t, ::Nothing) = nothing + +function horizontal_smagorinsky_lilly_tendency!(Yₜ, Y, p, t, ::SmagorinskyLilly) + (; ᶜτ_smag, ᶠτ_smag, ᶜD_smag, ᶜspecific, ᶜh_tot) = p.precomputed + + ## Momentum tendencies + ᶠρ = @. p.scratch.ᶠtemp_scalar = ᶠinterp(Y.c.ρ) + @. Yₜ.c.uₕ -= C12(wdivₕ(Y.c.ρ * ᶜτ_smag) / Y.c.ρ) + @. Yₜ.f.u₃ -= C3(wdivₕ(ᶠρ * ᶠτ_smag) / ᶠρ) + + ## Total energy tendency + @. Yₜ.c.ρe_tot += wdivₕ(Y.c.ρ * ᶜD_smag * gradₕ(ᶜh_tot)) + + ## Tracer diffusion and associated mass changes + for (ᶜρχₜ, ᶜχ, χ_name) in CA.matching_subfields(Yₜ.c, ᶜspecific) + χ_name == :e_tot && continue + ᶜρχₜ_diffusion = + @. p.scratch.ᶜtemp_scalar = wdivₕ(Y.c.ρ * ᶜD_smag * gradₕ(ᶜχ)) + @. ᶜρχₜ += ᶜρχₜ_diffusion + # Rain and snow does not affect the mass + if χ_name ∉ (:q_rai, :q_sno) + @. Yₜ.c.ρ += ᶜρχₜ_diffusion + end + end + +end + +function vertical_smagorinsky_lilly_tendency!(Yₜ, Y, p, t, ::SmagorinskyLilly) + FT = eltype(Y) + (; sfc_temp_C3, ᶠtemp_scalar, ᶜtemp_scalar) = p.scratch + (; ᶜτ_smag, ᶠτ_smag, ᶠD_smag, ᶜspecific, ᶜh_tot, sfc_conditions) = + p.precomputed + (; ρ_flux_uₕ, ρ_flux_h_tot) = sfc_conditions + + # Define operators + ᶠgradᵥ = Operators.GradientC2F() # apply BCs to ᶜdivᵥ, which wraps ᶠgradᵥ + ᶜdivᵥ_uₕ = Operators.DivergenceF2C( + top = Operators.SetValue(C3(FT(0)) ⊗ C12(FT(0), FT(0))), + bottom = Operators.SetValue(ρ_flux_uₕ), + ) + ᶠdivᵥ = Operators.DivergenceC2F( + bottom = Operators.SetDivergence(FT(0)), + top = Operators.SetDivergence(FT(0)), + ) + top = Operators.SetValue(C3(FT(0))) + ᶜdivᵥ_ρe_tot = Operators.DivergenceF2C(; + top, + bottom = Operators.SetValue(ρ_flux_h_tot), + ) + + # Apply to tendencies + ## Horizontal momentum tendency + ᶠρ = @. ᶠtemp_scalar = ᶠinterp(Y.c.ρ) + @. Yₜ.c.uₕ -= C12(ᶜdivᵥ(ᶠρ * ᶠτ_smag) / Y.c.ρ) + ## Apply boundary condition for momentum flux + @. Yₜ.c.uₕ -= ᶜdivᵥ_uₕ(-(FT(0) * ᶠgradᵥ(Y.c.uₕ))) / Y.c.ρ + ## Vertical momentum tendency + @. Yₜ.f.u₃ -= C3(ᶠdivᵥ(Y.c.ρ * ᶜτ_smag) / ᶠρ) + + ## Total energy tendency + @. Yₜ.c.ρe_tot -= ᶜdivᵥ_ρe_tot(-(ᶠρ * ᶠD_smag * ᶠgradᵥ(ᶜh_tot))) + + ## Tracer diffusion and associated mass changes + sfc_zero = @. sfc_temp_C3 = C3(FT(0)) + for (ᶜρχₜ, ᶜχ, χ_name) in CA.matching_subfields(Yₜ.c, ᶜspecific) + χ_name == :e_tot && continue + + bottom = Operators.SetValue( + χ_name == :q_tot ? sfc_conditions.ρ_flux_q_tot : sfc_zero, + ) + ᶜdivᵥ_ρχ = Operators.DivergenceF2C(; top, bottom) + + ᶜ∇ᵥρD∇χₜ = @. ᶜtemp_scalar = ᶜdivᵥ_ρχ(-(ᶠρ * ᶠD_smag * ᶠgradᵥ(ᶜχ))) + @. ᶜρχₜ -= ᶜ∇ᵥρD∇χₜ + # Rain and snow does not affect the mass + if χ_name ∉ (:q_rai, :q_sno) + @. Yₜ.c.ρ -= ᶜ∇ᵥρD∇χₜ + end + end +end diff --git a/src/parameterized_tendencies/radiation/radiation.jl b/src/parameterized_tendencies/radiation/radiation.jl index 019f593077..8804243bc0 100644 --- a/src/parameterized_tendencies/radiation/radiation.jl +++ b/src/parameterized_tendencies/radiation/radiation.jl @@ -365,9 +365,11 @@ function radiation_tendency!(Yₜ, Y, p, t, radiation_mode::RadiationDYCOMS) # Find the values of (z, ρ, q_tot) at the q_tot = 0.008 isoline, i.e., at # the level whose value of q_tot is closest to 0.008. + q_tot_isoline = FT(0.008) Operators.column_reduce!( (nt1, nt2) -> - abs(nt1.q_tot - FT(0.008)) < abs(nt2.q_tot - FT(0.008)) ? nt1 : nt2, + abs(nt1.q_tot - q_tot_isoline) < abs(nt2.q_tot - q_tot_isoline) ? + nt1 : nt2, isoline_z_ρ_q, Base.broadcasted(NT ∘ tuple, ᶜz, Y.c.ρ, ᶜspecific.q_tot), ) diff --git a/src/prognostic_equations/remaining_tendency.jl b/src/prognostic_equations/remaining_tendency.jl index d56ece72f8..b806e0b99d 100644 --- a/src/prognostic_equations/remaining_tendency.jl +++ b/src/prognostic_equations/remaining_tendency.jl @@ -86,8 +86,13 @@ NVTX.@annotate function additional_tendency!(Yₜ, Y, p, t) # NOTE: All ρa tendencies should be applied before calling this function pressure_work_tendency!(Yₜ, Y, p, t, p.atmos.turbconv_model) + sl = p.atmos.smagorinsky_lilly + horizontal_smagorinsky_lilly_tendency!(Yₜ, Y, p, t, sl) + vertical_smagorinsky_lilly_tendency!(Yₜ, Y, p, t, sl) + # NOTE: This will zero out all momentum tendencies in the edmfx advection test # please DO NOT add additional velocity tendencies after this function + # Other SGS tendencies zero_velocity_tendency!(Yₜ, Y, p, t) # TODO: make bycolumn-able diff --git a/src/solver/model_getters.jl b/src/solver/model_getters.jl index e0a6c87f64..115f045476 100644 --- a/src/solver/model_getters.jl +++ b/src/solver/model_getters.jl @@ -156,6 +156,18 @@ function get_viscous_sponge_model(parsed_args, params, ::Type{FT}) where {FT} end end +function get_smagorinsky_lilly_model(parsed_args, params, ::Type{FT}) where {FT} + is_model_active = parsed_args["smagorinsky_lilly"] + Cs = parsed_args["c_smag"] + Pr_t = parsed_args["prandtl_turbulent_neutral"] # Turbulent Prandtl number for neutral stratification + @assert is_model_active in (true, false) + return if is_model_active == true + SmagorinskyLilly{FT}(; Cs, Pr_t) + else + nothing + end +end + function get_rayleigh_sponge_model(parsed_args, params, ::Type{FT}) where {FT} rs_name = parsed_args["rayleigh_sponge"] return if rs_name in ("false", false) diff --git a/src/solver/type_getters.jl b/src/solver/type_getters.jl index ba3faf9c3b..f0d664fd45 100644 --- a/src/solver/type_getters.jl +++ b/src/solver/type_getters.jl @@ -85,6 +85,11 @@ function get_atmos(config::AtmosConfig, params) diff_mode = implicit_diffusion ? Implicit() : Explicit(), sgs_adv_mode = implicit_sgs_advection ? Implicit() : Explicit(), viscous_sponge = get_viscous_sponge_model(parsed_args, params, FT), + smagorinsky_lilly = get_smagorinsky_lilly_model( + parsed_args, + params, + FT, + ), rayleigh_sponge = get_rayleigh_sponge_model(parsed_args, params, FT), sfc_temperature = get_sfc_temperature_form(parsed_args), insolation = get_insolation_form(parsed_args), diff --git a/src/solver/types.jl b/src/solver/types.jl index 1021215aee..916984379c 100644 --- a/src/solver/types.jl +++ b/src/solver/types.jl @@ -125,6 +125,12 @@ Base.@kwdef struct ViscousSponge{FT} <: AbstractSponge κ₂::FT end +abstract type AbstractEddyViscosityModel end +Base.@kwdef struct SmagorinskyLilly{FT} <: AbstractEddyViscosityModel + Cs::FT = 0.2 + Pr_t::FT = 1 / 3 +end + Base.@kwdef struct RayleighSponge{FT} <: AbstractSponge zd::FT α_uₕ::FT @@ -435,6 +441,7 @@ Base.@kwdef struct AtmosModel{ DM, SAM, VS, + SL, RS, ST, IN, @@ -468,6 +475,7 @@ Base.@kwdef struct AtmosModel{ diff_mode::DM = nothing sgs_adv_mode::SAM = nothing viscous_sponge::VS = nothing + smagorinsky_lilly::SL = nothing rayleigh_sponge::RS = nothing sfc_temperature::ST = nothing insolation::IN = nothing diff --git a/test/parameterized_tendencies/gravity_wave/gw_plotutils.jl b/test/parameterized_tendencies/gravity_wave/gw_plotutils.jl index b7a9b40c62..8ef787dae9 100644 --- a/test/parameterized_tendencies/gravity_wave/gw_plotutils.jl +++ b/test/parameterized_tendencies/gravity_wave/gw_plotutils.jl @@ -40,14 +40,7 @@ function create_plot!( if Z == nothing generic_axis = fig[p_loc[1], p_loc[2]] = GridLayout() axis = Axis(generic_axis[1, 1]; title, xlabel, ylabel, xscale, yscale) - CairoMakie.lines!( - X, - Y; - title, - linewidth, - label = label[1], - linestyle = :solid, - ) + CairoMakie.lines!(X, Y; linewidth, label = label[1], linestyle = :solid) else generic_axis = fig[p_loc[1], p_loc[2]] = GridLayout() # Generic Axis Layout Axis(generic_axis[1, 1]; title, xlabel, ylabel, yscale, yreversed) # Plot specific attributes diff --git a/test/parameterized_tendencies/les_closures/smagorinsky_lilly.jl b/test/parameterized_tendencies/les_closures/smagorinsky_lilly.jl new file mode 100644 index 0000000000..434267f760 --- /dev/null +++ b/test/parameterized_tendencies/les_closures/smagorinsky_lilly.jl @@ -0,0 +1,69 @@ + +using Test +import ClimaAtmos as CA +import ClimaAtmos.Parameters as CAP +import ClimaCore as CC +import Thermodynamics as TD + +### Common Objects ### +@testset begin + "Smagorinsky Lilly function" + ### Boilerplate default integrator objects + config = CA.AtmosConfig( + Dict( + "initial_condition" => "DryDensityCurrentProfile", + "moist" => "dry", + "precip_model" => "0M", + "config" => "box", + "x_max" => π, + "y_max" => π, + "z_max" => 1.0, + "z_stretch" => false, + "output_default_diagnostics" => false, + ), + ) + parsed_args = config.parsed_args + simulation = CA.get_simulation(config) + (; integrator) = simulation + Y = integrator.u + Yₜ = similar(Y) + p = integrator.p + params = p.params + cm_params = CAP.microphysics_params(params) + thermo_params = CAP.thermodynamics_params(params) + + FT = eltype(Y) + ᶜYₜ = Y .* FT(0) + c_xyz = CC.Fields.coordinate_field(Y.c) + f_xyz = CC.Fields.coordinate_field(Y.f) + x = c_xyz.x + y = c_xyz.y + z = f_xyz.z + + u = @. sin(x) * cos(y) + v = @. sin(y) * cos(x) + w = @. Geometry.WVector(z ./ maximum(z)) + + u_x = @. cos(x) * cos(y) + v_x = @. -sin(y) * sin(x) + u_y = @. -sin(x) * sin(y) + v_y = @. cos(y) * cos(x) + w_x = zeros(axes(Y.c)) + w_y = zeros(axes(Y.c)) + + vel = @. CC.Geometry.UVVector(u, v) + + Y.c.ρ .= FT(1) + Y.c.uₕ .= Geometry.Covariant12Vector(vel) + Y.f.u₃ .= Geometry.Covariant3Vector(w) + + horizontal_smagorinsky_lilly_tendency( + Yₜ, + Y, + p, + t, + SmagorinskyLilly(FT(0.2)), + ) + + ### Component test begins here +end diff --git a/toml/isdac_box.toml b/toml/les_isdac.toml similarity index 100% rename from toml/isdac_box.toml rename to toml/les_isdac.toml