Add implicit diffusion solver

CliMA · Nov 29, 2023 · b41603f · b41603f
1 parent 48d6f4f
commit b41603f
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Showing 13 changed files with 282 additions and 89 deletions.
diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml
@@ -266,6 +266,20 @@ steps:
           --nc_dir sphere_baroclinic_wave_rhoe_equilmoist_expvdiff
           --fig_dir sphere_baroclinic_wave_rhoe_equilmoist_expvdiff --case_name aquaplanet
         artifact_paths: "sphere_baroclinic_wave_rhoe_equilmoist_expvdiff/*"
+
+      - label: ":computer: no lim ARS baroclinic wave (ρe) equilmoist implicit vertdiff"
+        command: >
+          julia --color=yes --project=examples examples/hybrid/driver.jl
+          --config_file $CONFIG_PATH/sphere_baroclinic_wave_rhoe_equilmoist_impvdiff.yml
+
+          julia --color=yes --project=examples post_processing/remap/remap_pipeline.jl
+          --data_dir sphere_baroclinic_wave_rhoe_equilmoist_impvdiff
+          --out_dir sphere_baroclinic_wave_rhoe_equilmoist_impvdiff
+
+          julia --color=yes --project=examples post_processing/plot/plot_pipeline.jl
+          --nc_dir sphere_baroclinic_wave_rhoe_equilmoist_impvdiff
+          --fig_dir sphere_baroclinic_wave_rhoe_equilmoist_impvdiff --case_name aquaplanet
+        artifact_paths: "sphere_baroclinic_wave_rhoe_equilmoist_impvdiff/*"
 
       # Add this back when we figure out what to do with SSP and zalesak
       # - label: ":computer: SSP zalesak tracer & energy upwind baroclinic wave (ρe_tot) equilmoist"

diff --git a/Project.toml b/Project.toml
@@ -50,7 +50,7 @@ Artifacts = "1"
 AtmosphericProfilesLibrary = "0.1"
 CLIMAParameters = "0.7.25"
 ClimaComms = "0.5.6"
-ClimaCore = "0.11.0"
+ClimaCore = "0.11.1"
 ClimaTimeSteppers = "0.7.14"
 CloudMicrophysics = "0.15.0"
 Colors = "0.12"

diff --git a/config/default_configs/default_config.yml b/config/default_configs/default_config.yml
@@ -243,6 +243,15 @@ prognostic_tke:
 prognostic_surface:
   help: "Determines if surface temperature is prognostic [`false` (default), , `true`, `PrognosticSurfaceTemperature`, `PrescribedSurfaceTemperature`]"
   value: "false"
+implicit_diffusion:
+  help: "Whether the implicit tendency should include vertical diffusion  [`false`, `true` (default)]"
+  value: true
+use_diffusion_derivative:
+  help: "Whether the Jacobian should include the derivative of vertical diffusion with respect to the quantities being diffused [`false` (default), `true`]"
+  value: false
+use_enthalpy_derivative:
+  help: "Whether the Jacobian should include the derivative of total enthalpy with respect to vertical velocity [`false` (default), `true`]"
+  value: false
 override_τ_precip:
   help: "If true, sets τ_precip to dt. Otherwise, τ_precip is set to the value in the toml dictionary"
   value: true

diff --git a/config/model_configs/sphere_baroclinic_wave_rhoe_equilmoist_expvdiff.yml b/config/model_configs/sphere_baroclinic_wave_rhoe_equilmoist_expvdiff.yml
@@ -4,7 +4,8 @@ z_elem: 20
 dz_bottom: 100
 dt_save_to_disk: "12hours"
 initial_condition: "MoistBaroclinicWave"
-dt: "40secs"
+implicit_diffusion: false
+dt: "20secs"
 t_end: "12hours"
 job_id: "sphere_baroclinic_wave_rhoe_equilmoist_expvdiff"
 moist: "equil"

diff --git a/config/model_configs/sphere_baroclinic_wave_rhoe_equilmoist_impvdiff.yml b/config/model_configs/sphere_baroclinic_wave_rhoe_equilmoist_impvdiff.yml
@@ -0,0 +1,13 @@
+precip_model: "0M"
+vert_diff: "true"
+z_elem: 20
+dz_bottom: 100
+dt_save_to_disk: "12hours"
+initial_condition: "MoistBaroclinicWave"
+use_diffusion_derivative: true
+max_newton_iters_ode: 3
+dt: "400secs"
+t_end: "6days"
+job_id: "sphere_baroclinic_wave_rhoe_equilmoist_impvdiff"
+moist: "equil"
+toml: [toml/sphere_baroclinic_wave_rhoe_equilmoist_expvdiff.toml]
diff --git a/docs/Manifest.toml b/docs/Manifest.toml
@@ -269,10 +269,14 @@ uuid = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d"
 version = "0.5.6"
 
 [[deps.ClimaCore]]
-deps = ["Adapt", "BandedMatrices", "BlockArrays", "CUDA", "ClimaComms", "CubedSphere", "DataStructures", "DocStringExtensions", "ForwardDiff", "GaussQuadrature", "GilbertCurves", "HDF5", "InteractiveUtils", "IntervalSets", "LinearAlgebra", "Memoize", "PkgVersion", "RecursiveArrayTools", "Requires", "RootSolvers", "SparseArrays", "Static", "StaticArrays", "Statistics", "WeakValueDicts"]
-git-tree-sha1 = "5c3809c5da88a3b01b8fe18558f50470fd3c33ed"
+deps = ["Adapt", "BandedMatrices", "BlockArrays", "CUDA", "ClimaComms", "CubedSphere", "DataStructures", "DocStringExtensions", "ForwardDiff", "GaussQuadrature", "GilbertCurves", "HDF5", "InteractiveUtils", "IntervalSets", "KrylovKit", "LinearAlgebra", "Memoize", "PkgVersion", "RecursiveArrayTools", "RootSolvers", "SparseArrays", "Static", "StaticArrays", "Statistics", "WeakValueDicts"]
+git-tree-sha1 = "3d6cd2e89f0d99664b23549da9081ade4e7d8fdb"
 uuid = "d414da3d-4745-48bb-8d80-42e94e092884"
-version = "0.11.0"
+version = "0.11.1"
+weakdeps = ["Krylov"]
+
+    [deps.ClimaCore.extensions]
+    KrylovExt = "Krylov"
 
 [[deps.ClimaTimeSteppers]]
 deps = ["CUDA", "ClimaComms", "Colors", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "KernelAbstractions", "Krylov", "LinearAlgebra", "LinearOperators", "NVTX", "SciMLBase", "StaticArrays"]
@@ -856,6 +860,12 @@ git-tree-sha1 = "17e462054b42dcdda73e9a9ba0c67754170c88ae"
 uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7"
 version = "0.9.4"
 
+[[deps.KrylovKit]]
+deps = ["ChainRulesCore", "GPUArraysCore", "LinearAlgebra", "Printf"]
+git-tree-sha1 = "1a5e1d9941c783b0119897d29f2eb665d876ecf3"
+uuid = "0b1a1467-8014-51b9-945f-bf0ae24f4b77"
+version = "0.6.0"
+
 [[deps.LDLFactorizations]]
 deps = ["AMD", "LinearAlgebra", "SparseArrays", "Test"]
 git-tree-sha1 = "70f582b446a1c3ad82cf87e62b878668beef9d13"

diff --git a/examples/Manifest.toml b/examples/Manifest.toml
@@ -314,10 +314,14 @@ uuid = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d"
 version = "0.5.6"
 
 [[deps.ClimaCore]]
-deps = ["Adapt", "BandedMatrices", "BlockArrays", "CUDA", "ClimaComms", "CubedSphere", "DataStructures", "DocStringExtensions", "ForwardDiff", "GaussQuadrature", "GilbertCurves", "HDF5", "InteractiveUtils", "IntervalSets", "LinearAlgebra", "Memoize", "PkgVersion", "RecursiveArrayTools", "Requires", "RootSolvers", "SparseArrays", "Static", "StaticArrays", "Statistics", "WeakValueDicts"]
-git-tree-sha1 = "5c3809c5da88a3b01b8fe18558f50470fd3c33ed"
+deps = ["Adapt", "BandedMatrices", "BlockArrays", "CUDA", "ClimaComms", "CubedSphere", "DataStructures", "DocStringExtensions", "ForwardDiff", "GaussQuadrature", "GilbertCurves", "HDF5", "InteractiveUtils", "IntervalSets", "KrylovKit", "LinearAlgebra", "Memoize", "PkgVersion", "RecursiveArrayTools", "RootSolvers", "SparseArrays", "Static", "StaticArrays", "Statistics", "WeakValueDicts"]
+git-tree-sha1 = "3d6cd2e89f0d99664b23549da9081ade4e7d8fdb"
 uuid = "d414da3d-4745-48bb-8d80-42e94e092884"
-version = "0.11.0"
+version = "0.11.1"
+weakdeps = ["Krylov"]
+
+    [deps.ClimaCore.extensions]
+    KrylovExt = "Krylov"
 
 [[deps.ClimaCoreMakie]]
 deps = ["ClimaCore", "Makie"]
@@ -1236,6 +1240,12 @@ git-tree-sha1 = "17e462054b42dcdda73e9a9ba0c67754170c88ae"
 uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7"
 version = "0.9.4"
 
+[[deps.KrylovKit]]
+deps = ["ChainRulesCore", "GPUArraysCore", "LinearAlgebra", "Printf"]
+git-tree-sha1 = "1a5e1d9941c783b0119897d29f2eb665d876ecf3"
+uuid = "0b1a1467-8014-51b9-945f-bf0ae24f4b77"
+version = "0.6.0"
+
 [[deps.LAME_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c"
@@ -1421,9 +1431,9 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
 [[deps.LinearAlgebraX]]
 deps = ["LinearAlgebra", "Mods", "Permutations", "Primes", "SimplePolynomials"]
-git-tree-sha1 = "3d93e38b11993bbdbfac967a46dcb36dd9dd733f"
+git-tree-sha1 = "8889b8aa6821c0ee73828a2139314b4d596e7dbc"
 uuid = "9b3f67b0-2d00-526e-9884-9e4938f8fb88"
-version = "0.2.1"
+version = "0.2.2"
 
 [[deps.LinearOperators]]
 deps = ["FastClosures", "LDLFactorizations", "LinearAlgebra", "Printf", "SparseArrays", "TimerOutputs"]
@@ -1757,9 +1767,9 @@ version = "0.11.30"
 
 [[deps.PNGFiles]]
 deps = ["Base64", "CEnum", "ImageCore", "IndirectArrays", "OffsetArrays", "libpng_jll"]
-git-tree-sha1 = "5ded86ccaf0647349231ed6c0822c10886d4a1ee"
+git-tree-sha1 = "eed372b0fa15624273a9cdb188b1b88476e6a233"
 uuid = "f57f5aa1-a3ce-4bc8-8ab9-96f992907883"
-version = "0.4.1"
+version = "0.4.2"
 
 [[deps.Packing]]
 deps = ["GeometryBasics"]
@@ -2228,9 +2238,9 @@ version = "0.3.1"
 
 [[deps.SimplePolynomials]]
 deps = ["Mods", "Multisets", "Polynomials", "Primes"]
-git-tree-sha1 = "d537c31cf9995236166e3e9afc424a5a1c59ff9d"
+git-tree-sha1 = "e14e1a7063179a90c2981faf3c8cbf12aacccdaf"
 uuid = "cc47b68c-3164-5771-a705-2bc0097375a0"
-version = "0.2.14"
+version = "0.2.16"
 
 [[deps.SimpleRandom]]
 deps = ["Distributions", "LinearAlgebra", "Random"]
@@ -2531,9 +2541,9 @@ version = "0.4.1"
 
 [[deps.Unitful]]
 deps = ["Dates", "LinearAlgebra", "Random"]
-git-tree-sha1 = "242982d62ff0d1671e9029b52743062739255c7e"
+git-tree-sha1 = "3c793be6df9dd77a0cf49d80984ef9ff996948fa"
 uuid = "1986cc42-f94f-5a68-af5c-568840ba703d"
-version = "1.18.0"
+version = "1.19.0"
 weakdeps = ["ConstructionBase", "InverseFunctions"]
 
     [deps.Unitful.extensions]

diff --git a/perf/Manifest.toml b/perf/Manifest.toml
@@ -325,10 +325,14 @@ uuid = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d"
 version = "0.5.6"
 
 [[deps.ClimaCore]]
-deps = ["Adapt", "BandedMatrices", "BlockArrays", "CUDA", "ClimaComms", "CubedSphere", "DataStructures", "DocStringExtensions", "ForwardDiff", "GaussQuadrature", "GilbertCurves", "HDF5", "InteractiveUtils", "IntervalSets", "LinearAlgebra", "Memoize", "PkgVersion", "RecursiveArrayTools", "Requires", "RootSolvers", "SparseArrays", "Static", "StaticArrays", "Statistics", "WeakValueDicts"]
-git-tree-sha1 = "5c3809c5da88a3b01b8fe18558f50470fd3c33ed"
+deps = ["Adapt", "BandedMatrices", "BlockArrays", "CUDA", "ClimaComms", "CubedSphere", "DataStructures", "DocStringExtensions", "ForwardDiff", "GaussQuadrature", "GilbertCurves", "HDF5", "InteractiveUtils", "IntervalSets", "KrylovKit", "LinearAlgebra", "Memoize", "PkgVersion", "RecursiveArrayTools", "RootSolvers", "SparseArrays", "Static", "StaticArrays", "Statistics", "WeakValueDicts"]
+git-tree-sha1 = "3d6cd2e89f0d99664b23549da9081ade4e7d8fdb"
 uuid = "d414da3d-4745-48bb-8d80-42e94e092884"
-version = "0.11.0"
+version = "0.11.1"
+weakdeps = ["Krylov"]
+
+    [deps.ClimaCore.extensions]
+    KrylovExt = "Krylov"
 
 [[deps.ClimaCoreMakie]]
 deps = ["ClimaCore", "Makie"]
@@ -1288,6 +1292,12 @@ git-tree-sha1 = "17e462054b42dcdda73e9a9ba0c67754170c88ae"
 uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7"
 version = "0.9.4"
 
+[[deps.KrylovKit]]
+deps = ["ChainRulesCore", "GPUArraysCore", "LinearAlgebra", "Printf"]
+git-tree-sha1 = "1a5e1d9941c783b0119897d29f2eb665d876ecf3"
+uuid = "0b1a1467-8014-51b9-945f-bf0ae24f4b77"
+version = "0.6.0"
+
 [[deps.LAME_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c"
@@ -1479,9 +1489,9 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
 [[deps.LinearAlgebraX]]
 deps = ["LinearAlgebra", "Mods", "Permutations", "Primes", "SimplePolynomials"]
-git-tree-sha1 = "3d93e38b11993bbdbfac967a46dcb36dd9dd733f"
+git-tree-sha1 = "8889b8aa6821c0ee73828a2139314b4d596e7dbc"
 uuid = "9b3f67b0-2d00-526e-9884-9e4938f8fb88"
-version = "0.2.1"
+version = "0.2.2"
 
 [[deps.LinearOperators]]
 deps = ["FastClosures", "LDLFactorizations", "LinearAlgebra", "Printf", "SparseArrays", "TimerOutputs"]
@@ -1809,9 +1819,9 @@ version = "0.11.30"
 
 [[deps.PNGFiles]]
 deps = ["Base64", "CEnum", "ImageCore", "IndirectArrays", "OffsetArrays", "libpng_jll"]
-git-tree-sha1 = "5ded86ccaf0647349231ed6c0822c10886d4a1ee"
+git-tree-sha1 = "eed372b0fa15624273a9cdb188b1b88476e6a233"
 uuid = "f57f5aa1-a3ce-4bc8-8ab9-96f992907883"
-version = "0.4.1"
+version = "0.4.2"
 
 [[deps.PProf]]
 deps = ["AbstractTrees", "EnumX", "FlameGraphs", "Libdl", "OrderedCollections", "Profile", "ProgressMeter", "ProtoBuf", "pprof_jll"]
@@ -2304,9 +2314,9 @@ version = "0.3.1"
 
 [[deps.SimplePolynomials]]
 deps = ["Mods", "Multisets", "Polynomials", "Primes"]
-git-tree-sha1 = "d537c31cf9995236166e3e9afc424a5a1c59ff9d"
+git-tree-sha1 = "e14e1a7063179a90c2981faf3c8cbf12aacccdaf"
 uuid = "cc47b68c-3164-5771-a705-2bc0097375a0"
-version = "0.2.14"
+version = "0.2.16"
 
 [[deps.SimpleRandom]]
 deps = ["Distributions", "LinearAlgebra", "Random"]
@@ -2625,9 +2635,9 @@ version = "0.4.1"
 
 [[deps.Unitful]]
 deps = ["Dates", "LinearAlgebra", "Random"]
-git-tree-sha1 = "242982d62ff0d1671e9029b52743062739255c7e"
+git-tree-sha1 = "3c793be6df9dd77a0cf49d80984ef9ff996948fa"
 uuid = "1986cc42-f94f-5a68-af5c-568840ba703d"
-version = "1.18.0"
+version = "1.19.0"
 weakdeps = ["ConstructionBase", "InverseFunctions"]
 
     [deps.Unitful.extensions]