Merge #2021

2021: Remove parameters from config r=nefrathenrici a=nefrathenrici ## Content - Removes the following config options: `C_E`, `alpha_rayleigh_w`, `alpha_rayleigh_uh`, `zd_viscous`, `zd_rayleigh`, `kappa_2_sponge` - Instead of being set via config, these values are added to ClimaAtmosParameters via a SpongeParameters struct, except for `C_E`, which is at the top-level - Add TOMLs for CI cases that need to change the values above. One file per case. - Updates .dev manifest to 1.9.2 - Update juliaformatter to 1.9 Co-authored-by: nefrathenrici <nat.henrici@gmail.com>
CliMA · Aug 31, 2023 · 8a8621f · 8a8621f
2 parents 934ca7b + bfb2a02
commit 8a8621f
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diff --git a/.dev/Manifest.toml b/.dev/Manifest.toml
@@ -1,6 +1,6 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.8.5"
+julia_version = "1.9.2"
 manifest_format = "2.0"
 project_hash = "b280bcf3b481823c97fa1a62c1b5e65114b8fa18"
 
@@ -27,15 +27,19 @@ uuid = "a80b9123-70ca-4bc0-993e-6e3bcb318db6"
 version = "0.8.12"
 
 [[deps.Compat]]
-deps = ["Dates", "LinearAlgebra", "UUIDs"]
+deps = ["UUIDs"]
 git-tree-sha1 = "e460f044ca8b99be31d35fe54fc33a5c33dd8ed7"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
 version = "4.9.0"
+weakdeps = ["Dates", "LinearAlgebra"]
+
+    [deps.Compat.extensions]
+    CompatLinearAlgebraExt = "LinearAlgebra"
 
 [[deps.CompilerSupportLibraries_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
-version = "1.0.1+0"
+version = "1.0.5+0"
 
 [[deps.Crayons]]
 git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15"
@@ -104,7 +108,7 @@ version = "1.10.2+0"
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 
 [[deps.LinearAlgebra]]
-deps = ["Libdl", "libblastrampoline_jll"]
+deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"]
 uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
 [[deps.Logging]]
@@ -117,14 +121,14 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 [[deps.MbedTLS_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
-version = "2.28.0+0"
+version = "2.28.2+0"
 
 [[deps.Mmap]]
 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
 
 [[deps.MozillaCACerts_jll]]
 uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
-version = "2022.2.1"
+version = "2022.10.11"
 
 [[deps.NetworkOptions]]
 uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
@@ -133,7 +137,7 @@ version = "1.2.0"
 [[deps.OpenBLAS_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
 uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"
-version = "0.3.20+0"
+version = "0.3.21+4"
 
 [[deps.OrderedCollections]]
 git-tree-sha1 = "2e73fe17cac3c62ad1aebe70d44c963c3cfdc3e3"
@@ -147,9 +151,9 @@ uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
 version = "2.7.2"
 
 [[deps.Pkg]]
-deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
+deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
 uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
-version = "1.8.0"
+version = "1.9.2"
 
 [[deps.PrecompileTools]]
 deps = ["Preferences"]
@@ -188,12 +192,12 @@ uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
 [[deps.TOML]]
 deps = ["Dates"]
 uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
-version = "1.0.0"
+version = "1.0.3"
 
 [[deps.Tar]]
 deps = ["ArgTools", "SHA"]
 uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
-version = "1.10.1"
+version = "1.10.0"
 
 [[deps.Tokenize]]
 git-tree-sha1 = "90538bf898832b6ebd900fa40f223e695970e3a5"
@@ -215,12 +219,12 @@ uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 [[deps.Zlib_jll]]
 deps = ["Libdl"]
 uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
-version = "1.2.12+3"
+version = "1.2.13+0"
 
 [[deps.libblastrampoline_jll]]
-deps = ["Artifacts", "Libdl", "OpenBLAS_jll"]
+deps = ["Artifacts", "Libdl"]
 uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
-version = "5.1.1+0"
+version = "5.8.0+0"
 
 [[deps.nghttp2_jll]]
 deps = ["Artifacts", "Libdl"]

diff --git a/.github/workflows/julia_formatter.yml b/.github/workflows/julia_formatter.yml
@@ -31,7 +31,7 @@ jobs:
     - uses: julia-actions/setup-julia@latest
       if: steps.filter.outputs.julia_file_change == 'true'
       with:
-        version: '1.8'
+        version: '1.9'
 
     - name: Apply JuliaFormatter
       if: steps.filter.outputs.julia_file_change == 'true'

diff --git a/config/default_configs/default_config.yml b/config/default_configs/default_config.yml
@@ -243,22 +243,3 @@ prognostic_tke:
 prognostic_surface:
   help: "Determines if surface temperature is prognostic [`false` (default), , `true`, `PrognosticSurfaceTemperature`, `PrescribedSurfaceTemperature`]"
   value: "false"
-# Will be moved to ClimaParameters.jl
-C_E:
-  help: "Bulk transfer coefficient"
-  value: 0.0044
-alpha_rayleigh_w:
-  help: "Rayleigh sponge coefficient for vertical velocity"
-  value: 1.0
-alpha_rayleigh_uh:
-  help: "Rayleigh sponge coefficient for horizontal velocity"
-  value: 0.0
-zd_viscous:
-  help: "Viscous sponge height"
-  value: 15000.0
-zd_rayleigh:
-  help: "Rayleigh sponge height"
-  value: 15000.0
-kappa_2_sponge:
-  help: "Viscous sponge coefficient"
-  value: 1.0e6
diff --git a/...n_configs/longrun_aquaplanet_rhoe_equil_clearsky_highres_hightop_rayleigh35e3_float64.yml b/...n_configs/longrun_aquaplanet_rhoe_equil_clearsky_highres_hightop_rayleigh35e3_float64.yml
@@ -1,7 +1,6 @@
 rad: "clearsky"
 dt_save_to_disk: "10days"
 rayleigh_sponge: true
-zd_rayleigh: 35000.0
 z_elem: 50
 dt: "150secs"
 surface_setup: "DefaultMoninObukhov"
@@ -11,9 +10,9 @@ dz_bottom: 30.0
 vert_diff: "true"
 h_elem: 16
 kappa_4: 1.0e16
-alpha_rayleigh_w: 10.0
 FLOAT_TYPE: "Float64"
 z_max: 45000.0
 precip_model: "0M"
 job_id: "longrun_aquaplanet_rhoe_equil_clearsky_highres_hightop_rayleigh35e3_float64"
 moist: "equil"
+toml: [toml/longrun_aquaplanet_rhoe_equil_clearsky_highres_hightop_rayleigh35e3_float64.toml]
diff --git a/config/longrun_configs/longrun_compressible_edmf_trmm.yml b/config/longrun_configs/longrun_compressible_edmf_trmm.yml
@@ -1,4 +1,3 @@
-
 config: "column" 
 FLOAT_TYPE: "Float64" 
 hyperdiff: "false" 
@@ -12,7 +11,7 @@ z_elem: 90
 z_stretch: false 
 z_max: 17000 
 rayleigh_sponge: true 
-zd_rayleigh: 15000 
 job_id: "longrun_compressible_edmf_trmm" 
 dt: "0.2secs" 
-t_end: "3.8hours"
+t_end: "3.8hours"
+toml: [longrun_compressible_edmf_trmm.toml]
diff --git a/config/longrun_configs/longrun_hs_rhoe_dry_nz63_55km_rs35km.yml b/config/longrun_configs/longrun_hs_rhoe_dry_nz63_55km_rs35km.yml
@@ -9,5 +9,5 @@ kappa_4: 1.0e16
 forcing: "held_suarez"
 dt: "300secs"
 rayleigh_sponge: true
-zd_rayleigh: 35000.0
 job_id: "longrun_hs_rhoe_equilmoist_nz63_0M_55km_rs35km"
+toml: [toml/longrun_hs_rhoe_equilmoist_nz63_0M_55km_rs35km.toml]
diff --git a/config/longrun_configs/longrun_hs_rhoe_equilmoist_nz63_0M_55km_rs35km.yml b/config/longrun_configs/longrun_hs_rhoe_equilmoist_nz63_0M_55km_rs35km.yml
@@ -11,7 +11,6 @@ vert_diff: "true"
 moist: "equil"
 precip_model: "0M"
 rayleigh_sponge: true
-alpha_rayleigh_w: 10.0
-zd_rayleigh: 35000.0
 forcing: "held_suarez"
 job_id: "longrun_hs_rhoe_equilmoist_nz63_0M_55km_rs35km"
+toml: [toml/longrun_hs_rhoe_equilmoist_nz63_0M_55km_rs35km.toml]
diff --git a/config/model_configs/bomex_box_rhoe.yml b/config/model_configs/bomex_box_rhoe.yml
@@ -7,7 +7,6 @@ dt: "0.5secs"
 surface_setup: "Bomex"
 perturb_initstate: false
 t_end: "600secs"
-C_E: 0.044
 y_max: 10000.0
 z_stretch: false
 vert_diff: "true"
@@ -17,3 +16,4 @@ z_max: 3000.0
 ls_adv: "Bomex"
 job_id: "bomex_box_rhoe"
 moist: "equil"
+toml: [toml/bomex_box_rhoe.toml]
diff --git a/config/model_configs/edmf_trmm.yml b/config/model_configs/edmf_trmm.yml
@@ -15,7 +15,7 @@ FLOAT_TYPE: "Float64"
 z_max: 16400.0
 precip_model: "1M"
 regression_test: true
-alpha_rayleigh_uh: 0.0001
 dt_save_to_sol: "5mins"
 job_id: "edmf_trmm"
 rad: "TRMM_LBA"
+toml: [toml/edmf_trmm.toml]
diff --git a/config/model_configs/edmfx_bomex_box_v1.yml b/config/model_configs/edmfx_bomex_box_v1.yml
@@ -10,7 +10,6 @@ surface_setup: "Bomex"
 perturb_initstate: false
 edmfx_entr_detr: true
 t_end: "10800secs"
-C_E: 0.044
 y_max: 100000.0
 y_elem: 2
 turbconv: "edmfx"
@@ -24,3 +23,4 @@ z_max: 3000.0
 ls_adv: "Bomex"
 job_id: "edmfx_bomex_box_v1"
 moist: "equil"
+toml: [toml/edmfx_bomex_box_v1.toml]
diff --git a/config/model_configs/edmfx_bomex_box_v2.yml b/config/model_configs/edmfx_bomex_box_v2.yml
@@ -10,7 +10,6 @@ surface_setup: "Bomex"
 perturb_initstate: false
 edmfx_entr_detr: true
 t_end: "10800secs"
-C_E: 0.044
 y_max: 100000.0
 y_elem: 2
 turbconv: "edmfx"
@@ -25,3 +24,4 @@ z_max: 3000.0
 ls_adv: "Bomex"
 job_id: "edmfx_bomex_box_v2"
 moist: "equil"
+toml: [toml/edmfx_bomex_box_v2.toml]
diff --git a/config/model_configs/plane_agnesi_mountain_test_stretched.yml b/config/model_configs/plane_agnesi_mountain_test_stretched.yml
@@ -11,7 +11,7 @@ dz_bottom: 200.0
 use_reference_state: false
 config: "plane"
 kappa_4: 1.0e6
-alpha_rayleigh_w: 0.1
 z_max: 25000.0
 topography: "Agnesi"
 job_id: "plane_agnesi_mountain_test_stretched"
+toml: [toml/plane_agnesi_mountain_test_stretched.toml]
diff --git a/config/model_configs/plane_agnesi_mountain_test_uniform.yml b/config/model_configs/plane_agnesi_mountain_test_uniform.yml
@@ -10,7 +10,7 @@ x_elem: 80
 use_reference_state: false
 config: "plane"
 kappa_4: 1.0e6
-alpha_rayleigh_w: 0.1
 z_max: 25000.0
 topography: "Agnesi"
 job_id: "plane_agnesi_mountain_test_uniform"
+toml: [toml/plane_agnesi_mountain_test_uniform.toml]
diff --git a/config/model_configs/plane_schar_mountain_test_stretched.yml b/config/model_configs/plane_schar_mountain_test_stretched.yml
@@ -12,7 +12,7 @@ use_reference_state: false
 ode_algo: "SSP33ShuOsher"
 config: "plane"
 kappa_4: 5.0e7
-alpha_rayleigh_w: 0.1
 z_max: 25000.0
 topography: "Schar"
 job_id: "plane_schar_mountain_test_stretched"
+toml: [toml/plane_schar_mountain_test_stretched.toml]
diff --git a/config/model_configs/plane_schar_mountain_test_uniform.yml b/config/model_configs/plane_schar_mountain_test_uniform.yml
@@ -11,7 +11,7 @@ use_reference_state: false
 ode_algo: "SSP33ShuOsher"
 config: "plane"
 kappa_4: 5.0e7
-alpha_rayleigh_w: 0.1
 z_max: 25000.0
 topography: "Schar"
 job_id: "plane_schar_mountain_test_uniform"
+toml: [toml/plane_schar_mountain_test_uniform.toml]
diff --git a/config/model_configs/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_raw_zonallyasymmetric.yml b/config/model_configs/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_raw_zonallyasymmetric.yml
@@ -1,7 +1,6 @@
 rad: "allskywithclear"
 dt_save_to_disk: "18hours"
 rayleigh_sponge: true
-zd_rayleigh: 30000.0
 orographic_gravity_wave: "raw_topo"
 z_elem: 25
 dt: "400secs"
@@ -17,3 +16,4 @@ regression_test: true
 surface_temperature: "ZonallyAsymmetric"
 job_id: "sphere_aquaplanet_rhoe_equilmoist_allsky_gw_raw_zonallyasymmetric"
 moist: "equil"
+toml: [toml/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_raw_zonallyasymmetric.toml]
diff --git a/config/model_configs/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_res.yml b/config/model_configs/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_res.yml
@@ -1,7 +1,6 @@
 rad: "allskywithclear"
 dt_save_to_disk: "18hours"
 rayleigh_sponge: true
-zd_rayleigh: 30000.0
 orographic_gravity_wave: "gfdl_restart"
 z_elem: 25
 dt: "400secs"
@@ -16,3 +15,4 @@ precip_model: "0M"
 regression_test: true
 job_id: "sphere_aquaplanet_rhoe_equilmoist_allsky_gw_res"
 moist: "equil"
+toml: [toml/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_res.toml]
diff --git a/config/model_configs/sphere_held_suarez_rhoe_equilmoist_hightop_sponge.yml b/config/model_configs/sphere_held_suarez_rhoe_equilmoist_hightop_sponge.yml
@@ -1,7 +1,5 @@
 dt_save_to_disk: "4days"
 rayleigh_sponge: true
-zd_rayleigh: 30000.0
-zd_viscous: 30000.0
 dt: "450secs"
 z_elem: 25
 t_end: "4days"
@@ -14,3 +12,4 @@ regression_test: true
 viscous_sponge: true
 job_id: "sphere_held_suarez_rhoe_equilmoist_hightop_sponge"
 moist: "equil"
+toml: [toml/sphere_held_suarez_rhoe_equilmoist_hightop_sponge.toml]
diff --git a/config/perf_configs/flame/perf_gw.yml b/config/perf_configs/flame/perf_gw.yml
@@ -1,6 +1,5 @@
 rad: "allskywithclear"
 rayleigh_sponge: true
-zd_rayleigh: 30000.0
 orographic_gravity_wave: "raw_topo"
 z_elem: 25
 dt: "1secs"
@@ -14,3 +13,4 @@ z_max: 45000.0
 precip_model: "0M"
 job_id: "flame_perf_gw"
 moist: "equil"
+toml: [toml/flame_perf_gw.toml]
diff --git a/perf/flame.jl b/perf/flame.jl
@@ -57,8 +57,8 @@ allocs_limit = Dict()
 allocs_limit["flame_perf_target"] = 4384
 allocs_limit["flame_perf_target_tracers"] = 204016
 allocs_limit["flame_perf_target_edmfx"] = 298688
-allocs_limit["flame_perf_target_diagnostic_edmfx"] = 663952
-allocs_limit["flame_perf_target_edmf"] = 8270517072
+allocs_limit["flame_perf_target_diagnostic_edmfx"] = 664336
+allocs_limit["flame_perf_target_edmf"] = 8282903376
 allocs_limit["flame_perf_target_threaded"] = 6175664
 allocs_limit["flame_perf_target_callbacks"] = 49850536
 allocs_limit["flame_perf_gw"] = 4937136096

diff --git a/regression_tests/ref_counter.jl b/regression_tests/ref_counter.jl
@@ -1 +1 @@
-121
+122
diff --git a/src/parameters/Parameters.jl b/src/parameters/Parameters.jl
@@ -10,7 +10,8 @@ const ACAP = AbstractClimaAtmosParameters
 
 Base.broadcastable(param_set::ACAP) = tuple(param_set)
 
-Base.@kwdef struct ClimaAtmosParameters{FT, TP, RP, IP, MPP, SFP, TCP} <: ACAP
+Base.@kwdef struct ClimaAtmosParameters{FT, TP, RP, IP, MPP, SFP, TCP, SP} <:
+                   ACAP
     Omega::FT
     f_plane_coriolis_frequency::FT
     planet_radius::FT
@@ -26,11 +27,26 @@ Base.@kwdef struct ClimaAtmosParameters{FT, TP, RP, IP, MPP, SFP, TCP} <: ACAP
     microphysics_params::MPP
     surfacefluxes_params::SFP
     turbconv_params::TCP
+    sponge_params::SP
     entr_coeff::FT = 1
     detr_coeff::FT = 0.001
     # TODO: Figure out a better place for these held-suarez parameters
     ΔT_y_dry::FT
     ΔT_y_wet::FT
+    C_E::FT
+end
+
+"""
+    SpongeParameters{FT}
+
+Parameters for both the viscous and rayleigh sponge.
+"""
+Base.@kwdef struct SpongeParameters{FT}
+    alpha_rayleigh_w::FT
+    alpha_rayleigh_uh::FT
+    zd_viscous::FT
+    zd_rayleigh::FT
+    kappa_2_sponge::FT
 end
 
 Base.eltype(::ClimaAtmosParameters{FT}) where {FT} = FT