From b44f9e74f2ee0ce2328bd3fbac2898b20936200f Mon Sep 17 00:00:00 2001
From: nefrathenrici <nat.henrici@gmail.com>
Date: Fri, 25 Aug 2023 11:45:22 -0700
Subject: [PATCH 1/3] Remove params from config, add TOMLs for overrides

---
 .dev/Manifest.toml                            | 32 +++++++++++--------
 .github/workflows/julia_formatter.yml         |  2 +-
 config/default_configs/default_config.yml     | 19 -----------
 ...y_highres_hightop_rayleigh35e3_float64.yml |  3 +-
 .../longrun_compressible_edmf_trmm.yml        |  5 ++-
 .../longrun_hs_rhoe_dry_nz63_55km_rs35km.yml  |  2 +-
 ...hs_rhoe_equilmoist_nz63_0M_55km_rs35km.yml |  3 +-
 config/model_configs/bomex_box_rhoe.yml       |  2 +-
 config/model_configs/edmf_trmm.yml            |  2 +-
 config/model_configs/edmfx_bomex_box_v1.yml   |  2 +-
 config/model_configs/edmfx_bomex_box_v2.yml   |  2 +-
 .../plane_agnesi_mountain_test_stretched.yml  |  2 +-
 .../plane_agnesi_mountain_test_uniform.yml    |  2 +-
 .../plane_schar_mountain_test_stretched.yml   |  2 +-
 .../plane_schar_mountain_test_uniform.yml     |  2 +-
 ...lmoist_allsky_gw_raw_zonallyasymmetric.yml |  2 +-
 ...uaplanet_rhoe_equilmoist_allsky_gw_res.yml |  2 +-
 ..._suarez_rhoe_equilmoist_hightop_sponge.yml |  3 +-
 config/perf_configs/flame/perf_gw.yml         |  2 +-
 src/parameters/Parameters.jl                  | 18 ++++++++++-
 src/parameters/create_parameters.jl           | 13 +++++++-
 src/solver/model_getters.jl                   | 29 ++++++++++-------
 src/solver/type_getters.jl                    | 20 +++++++++---
 toml/bomex_box_rhoe.toml                      |  5 +++
 toml/edmf_trmm.toml                           |  5 +++
 toml/edmfx_bomex_box_v1.toml                  |  5 +++
 toml/edmfx_bomex_box_v2.toml                  |  5 +++
 toml/flame_perf_gw.toml                       |  4 +++
 ..._highres_hightop_rayleigh35e3_float64.toml | 10 ++++++
 toml/longrun_compressible_edmf_trmm.toml      |  5 +++
 .../longrun_hs_rhoe_dry_nz63_55km_rs35km.toml |  5 +++
 ...uilmoist_highres_hightop_rayleigh30e3.toml | 10 ++++++
 ...s_rhoe_equilmoist_nz63_0M_55km_rs35km.toml | 10 ++++++
 .../plane_agnesi_mountain_test_stretched.toml |  5 +++
 toml/plane_agnesi_mountain_test_uniform.toml  |  5 +++
 toml/plane_schar_mountain_test_stretched.toml |  5 +++
 toml/plane_schar_mountain_test_uniform.toml   |  5 +++
 ...moist_allsky_gw_raw_zonallyasymmetric.toml |  5 +++
 ...aplanet_rhoe_equilmoist_allsky_gw_res.toml |  5 +++
 ...suarez_rhoe_equilmoist_hightop_sponge.toml | 10 ++++++
 ...suarez_rhoe_equilmoist_hightop_sponge.toml | 10 ++++++
 41 files changed, 211 insertions(+), 74 deletions(-)
 create mode 100644 toml/bomex_box_rhoe.toml
 create mode 100644 toml/edmf_trmm.toml
 create mode 100644 toml/edmfx_bomex_box_v1.toml
 create mode 100644 toml/edmfx_bomex_box_v2.toml
 create mode 100644 toml/flame_perf_gw.toml
 create mode 100644 toml/longrun_aquaplanet_rhoe_equil_clearsky_highres_hightop_rayleigh35e3_float64.toml
 create mode 100644 toml/longrun_compressible_edmf_trmm.toml
 create mode 100644 toml/longrun_hs_rhoe_dry_nz63_55km_rs35km.toml
 create mode 100644 toml/longrun_hs_rhoe_equilmoist_highres_hightop_rayleigh30e3.toml
 create mode 100644 toml/longrun_hs_rhoe_equilmoist_nz63_0M_55km_rs35km.toml
 create mode 100644 toml/plane_agnesi_mountain_test_stretched.toml
 create mode 100644 toml/plane_agnesi_mountain_test_uniform.toml
 create mode 100644 toml/plane_schar_mountain_test_stretched.toml
 create mode 100644 toml/plane_schar_mountain_test_uniform.toml
 create mode 100644 toml/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_raw_zonallyasymmetric.toml
 create mode 100644 toml/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_res.toml
 create mode 100644 toml/sphere_held_suarez_rhoe_equilmoist_hightop_sponge.toml
 create mode 100644 toml/sphere_ssp_first_tracer_energy_upwind_held_suarez_rhoe_equilmoist_hightop_sponge.toml

diff --git a/.dev/Manifest.toml b/.dev/Manifest.toml
index 55e29357911..1bd47e53105 100644
--- 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
index 706dd84f501..2dae8be05d3 100644
--- 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
index d41abfafe31..68a29152405 100644
--- 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/config/longrun_configs/longrun_aquaplanet_rhoe_equil_clearsky_highres_hightop_rayleigh35e3_float64.yml b/config/longrun_configs/longrun_aquaplanet_rhoe_equil_clearsky_highres_hightop_rayleigh35e3_float64.yml
index 5d22c995683..7e74f8c3fdf 100644
--- a/config/longrun_configs/longrun_aquaplanet_rhoe_equil_clearsky_highres_hightop_rayleigh35e3_float64.yml
+++ b/config/longrun_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
index 0d858773ee4..7fcaac0c345 100644
--- 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"
\ No newline at end of file
+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
index 7fc5a161e19..2b855133eb8 100644
--- 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
index 96107aabe91..0be31066aaf 100644
--- 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
index cd522c6bc27..ede4276567d 100644
--- 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
index ac278104c44..8e0d1eaa028 100644
--- 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
index a00528c85ae..b6f76f61aef 100644
--- 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
index fababeec1c8..b812875c63a 100644
--- 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
index 6f908628c4b..55bfc259776 100644
--- 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
index bb6e0ff5044..8c888b62090 100644
--- 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
index 1e6890b6f45..32491e9a528 100644
--- 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
index f627e30234e..c87b9641354 100644
--- 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
index 2ac2bb11bfe..120abb0af9f 100644
--- 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
index d1a07a1db0a..5e546d00705 100644
--- 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
index 5c8defe7925..466b9944dfb 100644
--- 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
index ccfe571f298..9016c0b16b2 100644
--- 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/src/parameters/Parameters.jl b/src/parameters/Parameters.jl
index 26b5234410b..022bffe3331 100644
--- 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
diff --git a/src/parameters/create_parameters.jl b/src/parameters/create_parameters.jl
index 79331f6f40f..74625c36436 100644
--- a/src/parameters/create_parameters.jl
+++ b/src/parameters/create_parameters.jl
@@ -98,7 +98,15 @@ function create_climaatmos_parameter_set(
 
     pairs = CP.get_parameter_values!(
         toml_dict,
-        ["Omega", "planet_radius", "astro_unit", "ΔT_y_dry", "ΔT_y_wet"],
+        ["alpha_rayleigh_w", "alpha_rayleigh_uh", "zd_viscous", "zd_rayleigh", "kappa_2_sponge"],
+        )
+    pairs = (; pairs...) # convert to NamedTuple
+    pairs = override_climaatmos_defaults((; pairs...), overrides)
+    sponge_params = CAP.SpongeParameters(; pairs...)
+
+    pairs = CP.get_parameter_values!(
+        toml_dict,
+        ["Omega", "planet_radius", "astro_unit", "ΔT_y_dry", "ΔT_y_wet", "C_E"],
         "ClimaAtmos",
     )
     pairs = (; pairs...) # convert to NamedTuple
@@ -123,6 +131,8 @@ function create_climaatmos_parameter_set(
         detr_coeff = FTD(parsed_args["detr_coeff"]),
         ΔT_y_dry = FTD(pairs.ΔT_y_dry),
         ΔT_y_wet = FTD(pairs.ΔT_y_wet),
+        C_E = FTD(pairs.C_E),
+        sponge_params
     )
     # logfilepath = joinpath(@__DIR__, "logfilepath_$FT.toml")
     # CP.log_parameter_information(toml_dict, logfilepath)
@@ -134,6 +144,7 @@ function create_parameter_set(config::AtmosConfig)
     (; toml_dict, parsed_args) = config
     FT = eltype(config)
     dt = FT(CA.time_to_seconds(parsed_args["dt"]))
+
     return if CA.is_column_edmf(parsed_args)
         overrides = (; MSLP = 100000.0, τ_precip = dt)
         create_climaatmos_parameter_set(toml_dict, parsed_args, overrides)
diff --git a/src/solver/model_getters.jl b/src/solver/model_getters.jl
index 20d4449d8cf..ef72dc28816 100644
--- a/src/solver/model_getters.jl
+++ b/src/solver/model_getters.jl
@@ -50,14 +50,14 @@ end
 function get_vertical_diffusion_model(
     diffuse_momentum,
     parsed_args,
+    params,
     ::Type{FT},
 ) where {FT}
     vert_diff_name = parsed_args["vert_diff"]
     return if vert_diff_name in ("false", false, "none")
         nothing
     elseif vert_diff_name in ("true", true, "VerticalDiffusion")
-        C_E = FT(parsed_args["C_E"])
-        VerticalDiffusion{diffuse_momentum, FT}(; C_E)
+        VerticalDiffusion{diffuse_momentum, FT}(; C_E = params.C_E)
     else
         error("Uncaught diffusion model `$vert_diff_name`.")
     end
@@ -76,30 +76,35 @@ function get_surface_model(parsed_args)
     end
 end
 
-function get_viscous_sponge_model(parsed_args, ::Type{FT}) where {FT}
+function get_viscous_sponge_model(
+    parsed_args,
+    sponge_params,
+    ::Type{FT},
+) where {FT}
     vs_name = parsed_args["viscous_sponge"]
     return if vs_name in ("false", false, "none")
         nothing
     elseif vs_name in ("true", true, "ViscousSponge")
-        zd = parsed_args["zd_viscous"]
-        κ₂ = parsed_args["kappa_2_sponge"]
+        zd = sponge_params.zd_viscous
+        κ₂ = sponge_params.kappa_2_sponge
         ViscousSponge{FT}(; zd, κ₂)
     else
         error("Uncaught viscous sponge model `$vs_name`.")
     end
 end
 
-function get_rayleigh_sponge_model(parsed_args, ::Type{FT}) where {FT}
+function get_rayleigh_sponge_model(
+    parsed_args,
+    sponge_params,
+    ::Type{FT},
+) where {FT}
     rs_name = parsed_args["rayleigh_sponge"]
     return if rs_name in ("false", false)
         nothing
     elseif rs_name in ("true", true, "RayleighSponge")
-        zd = parsed_args["zd_rayleigh"]
-        α_uₕ = parsed_args["alpha_rayleigh_uh"]
-        α_w = parsed_args["alpha_rayleigh_w"]
-        isnothing(zd) && (zd = FT(15e3))
-        isnothing(α_uₕ) && (α_uₕ = FT(1e-4))
-        isnothing(α_w) && (α_w = FT(1))
+        zd = sponge_params.zd_rayleigh
+        α_uₕ = sponge_params.alpha_rayleigh_uh
+        α_w = sponge_params.alpha_rayleigh_w
         RayleighSponge{FT}(; zd, α_uₕ, α_w)
     else
         error("Uncaught rayleigh sponge model `$rs_name`.")
diff --git a/src/solver/type_getters.jl b/src/solver/type_getters.jl
index 459dfc57589..bd1cb42bb3a 100644
--- a/src/solver/type_getters.jl
+++ b/src/solver/type_getters.jl
@@ -13,7 +13,8 @@ import OrdinaryDiffEq as ODE
 import ClimaTimeSteppers as CTS
 import DiffEqCallbacks as DEQ
 
-function get_atmos(config::AtmosConfig, turbconv_params)
+function get_atmos(config::AtmosConfig, params)
+    (; turbconv_params, sponge_params) = params
     (; parsed_args) = config
     FT = eltype(config)
     moisture_model = get_moisture_model(parsed_args)
@@ -36,7 +37,8 @@ function get_atmos(config::AtmosConfig, turbconv_params)
     @assert edmfx_nh_pressure in (false, true)
 
     model_config = get_model_config(parsed_args)
-    vert_diff = get_vertical_diffusion_model(diffuse_momentum, parsed_args, FT)
+    vert_diff =
+        get_vertical_diffusion_model(diffuse_momentum, parsed_args, params, FT)
     atmos = AtmosModel(;
         moisture_model,
         model_config,
@@ -70,8 +72,16 @@ function get_atmos(config::AtmosConfig, turbconv_params)
         ),
         hyperdiff = get_hyperdiffusion_model(parsed_args, FT),
         vert_diff,
-        viscous_sponge = get_viscous_sponge_model(parsed_args, FT),
-        rayleigh_sponge = get_rayleigh_sponge_model(parsed_args, FT),
+        viscous_sponge = get_viscous_sponge_model(
+            parsed_args,
+            sponge_params,
+            FT,
+        ),
+        rayleigh_sponge = get_rayleigh_sponge_model(
+            parsed_args,
+            sponge_params,
+            FT,
+        ),
         sfc_temperature = get_sfc_temperature_form(parsed_args),
         surface_model = get_surface_model(parsed_args),
     )
@@ -688,7 +698,7 @@ end
 function get_integrator(config::AtmosConfig)
     params = create_parameter_set(config)
 
-    atmos = get_atmos(config, params.turbconv_params)
+    atmos = get_atmos(config, params)
     numerics = get_numerics(config.parsed_args)
     simulation = get_simulation(config, config.comms_ctx)
     initial_condition = get_initial_condition(config.parsed_args)
diff --git a/toml/bomex_box_rhoe.toml b/toml/bomex_box_rhoe.toml
new file mode 100644
index 00000000000..3da20f5a66b
--- /dev/null
+++ b/toml/bomex_box_rhoe.toml
@@ -0,0 +1,5 @@
+[C_E]
+alias = "C_E"
+value = 0.044
+type = "float"
+
diff --git a/toml/edmf_trmm.toml b/toml/edmf_trmm.toml
new file mode 100644
index 00000000000..a941cbf18ea
--- /dev/null
+++ b/toml/edmf_trmm.toml
@@ -0,0 +1,5 @@
+[alpha_rayleigh_uh]
+alias = "alpha_rayleigh_uh"
+value = 0.0001
+type = "float"
+
diff --git a/toml/edmfx_bomex_box_v1.toml b/toml/edmfx_bomex_box_v1.toml
new file mode 100644
index 00000000000..3da20f5a66b
--- /dev/null
+++ b/toml/edmfx_bomex_box_v1.toml
@@ -0,0 +1,5 @@
+[C_E]
+alias = "C_E"
+value = 0.044
+type = "float"
+
diff --git a/toml/edmfx_bomex_box_v2.toml b/toml/edmfx_bomex_box_v2.toml
new file mode 100644
index 00000000000..3da20f5a66b
--- /dev/null
+++ b/toml/edmfx_bomex_box_v2.toml
@@ -0,0 +1,5 @@
+[C_E]
+alias = "C_E"
+value = 0.044
+type = "float"
+
diff --git a/toml/flame_perf_gw.toml b/toml/flame_perf_gw.toml
new file mode 100644
index 00000000000..c8fdd94c22b
--- /dev/null
+++ b/toml/flame_perf_gw.toml
@@ -0,0 +1,4 @@
+[zd_rayleigh]
+alias = "zd_rayleigh"
+value = 30000.0
+type = "float"
diff --git a/toml/longrun_aquaplanet_rhoe_equil_clearsky_highres_hightop_rayleigh35e3_float64.toml b/toml/longrun_aquaplanet_rhoe_equil_clearsky_highres_hightop_rayleigh35e3_float64.toml
new file mode 100644
index 00000000000..9a4640c8616
--- /dev/null
+++ b/toml/longrun_aquaplanet_rhoe_equil_clearsky_highres_hightop_rayleigh35e3_float64.toml
@@ -0,0 +1,10 @@
+[alpha_rayleigh_w]
+alias = "alpha_rayleigh_w"
+value = 10.0
+type = "float"
+
+[zd_rayleigh]
+alias = "zd_rayleigh"
+value = 35000.0
+type = "float"
+
diff --git a/toml/longrun_compressible_edmf_trmm.toml b/toml/longrun_compressible_edmf_trmm.toml
new file mode 100644
index 00000000000..3d25ee688ee
--- /dev/null
+++ b/toml/longrun_compressible_edmf_trmm.toml
@@ -0,0 +1,5 @@
+[zd_rayleigh]
+alias = "zd_rayleigh"
+value = 15000
+type = "float"
+
diff --git a/toml/longrun_hs_rhoe_dry_nz63_55km_rs35km.toml b/toml/longrun_hs_rhoe_dry_nz63_55km_rs35km.toml
new file mode 100644
index 00000000000..466f90f978c
--- /dev/null
+++ b/toml/longrun_hs_rhoe_dry_nz63_55km_rs35km.toml
@@ -0,0 +1,5 @@
+[zd_rayleigh]
+alias = "zd_rayleigh"
+value = 35000.0
+type = "float"
+
diff --git a/toml/longrun_hs_rhoe_equilmoist_highres_hightop_rayleigh30e3.toml b/toml/longrun_hs_rhoe_equilmoist_highres_hightop_rayleigh30e3.toml
new file mode 100644
index 00000000000..c7741e67f93
--- /dev/null
+++ b/toml/longrun_hs_rhoe_equilmoist_highres_hightop_rayleigh30e3.toml
@@ -0,0 +1,10 @@
+[alpha_rayleigh_w]
+alias = "alpha_rayleigh_w"
+value = 10.0
+type = "float"
+
+[zd_rayleigh]
+alias = "zd_rayleigh"
+value = 30000.0
+type = "float"
+
diff --git a/toml/longrun_hs_rhoe_equilmoist_nz63_0M_55km_rs35km.toml b/toml/longrun_hs_rhoe_equilmoist_nz63_0M_55km_rs35km.toml
new file mode 100644
index 00000000000..9a4640c8616
--- /dev/null
+++ b/toml/longrun_hs_rhoe_equilmoist_nz63_0M_55km_rs35km.toml
@@ -0,0 +1,10 @@
+[alpha_rayleigh_w]
+alias = "alpha_rayleigh_w"
+value = 10.0
+type = "float"
+
+[zd_rayleigh]
+alias = "zd_rayleigh"
+value = 35000.0
+type = "float"
+
diff --git a/toml/plane_agnesi_mountain_test_stretched.toml b/toml/plane_agnesi_mountain_test_stretched.toml
new file mode 100644
index 00000000000..aae1913cb60
--- /dev/null
+++ b/toml/plane_agnesi_mountain_test_stretched.toml
@@ -0,0 +1,5 @@
+[alpha_rayleigh_w]
+alias = "alpha_rayleigh_w"
+value = 0.1
+type = "float"
+
diff --git a/toml/plane_agnesi_mountain_test_uniform.toml b/toml/plane_agnesi_mountain_test_uniform.toml
new file mode 100644
index 00000000000..aae1913cb60
--- /dev/null
+++ b/toml/plane_agnesi_mountain_test_uniform.toml
@@ -0,0 +1,5 @@
+[alpha_rayleigh_w]
+alias = "alpha_rayleigh_w"
+value = 0.1
+type = "float"
+
diff --git a/toml/plane_schar_mountain_test_stretched.toml b/toml/plane_schar_mountain_test_stretched.toml
new file mode 100644
index 00000000000..aae1913cb60
--- /dev/null
+++ b/toml/plane_schar_mountain_test_stretched.toml
@@ -0,0 +1,5 @@
+[alpha_rayleigh_w]
+alias = "alpha_rayleigh_w"
+value = 0.1
+type = "float"
+
diff --git a/toml/plane_schar_mountain_test_uniform.toml b/toml/plane_schar_mountain_test_uniform.toml
new file mode 100644
index 00000000000..aae1913cb60
--- /dev/null
+++ b/toml/plane_schar_mountain_test_uniform.toml
@@ -0,0 +1,5 @@
+[alpha_rayleigh_w]
+alias = "alpha_rayleigh_w"
+value = 0.1
+type = "float"
+
diff --git a/toml/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_raw_zonallyasymmetric.toml b/toml/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_raw_zonallyasymmetric.toml
new file mode 100644
index 00000000000..3a4f21f0886
--- /dev/null
+++ b/toml/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_raw_zonallyasymmetric.toml
@@ -0,0 +1,5 @@
+[zd_rayleigh]
+alias = "zd_rayleigh"
+value = 30000.0
+type = "float"
+
diff --git a/toml/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_res.toml b/toml/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_res.toml
new file mode 100644
index 00000000000..3a4f21f0886
--- /dev/null
+++ b/toml/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_res.toml
@@ -0,0 +1,5 @@
+[zd_rayleigh]
+alias = "zd_rayleigh"
+value = 30000.0
+type = "float"
+
diff --git a/toml/sphere_held_suarez_rhoe_equilmoist_hightop_sponge.toml b/toml/sphere_held_suarez_rhoe_equilmoist_hightop_sponge.toml
new file mode 100644
index 00000000000..9196727ee2e
--- /dev/null
+++ b/toml/sphere_held_suarez_rhoe_equilmoist_hightop_sponge.toml
@@ -0,0 +1,10 @@
+[zd_viscous]
+alias = "zd_viscous"
+value = 30000.0
+type = "float"
+
+[zd_rayleigh]
+alias = "zd_rayleigh"
+value = 30000.0
+type = "float"
+
diff --git a/toml/sphere_ssp_first_tracer_energy_upwind_held_suarez_rhoe_equilmoist_hightop_sponge.toml b/toml/sphere_ssp_first_tracer_energy_upwind_held_suarez_rhoe_equilmoist_hightop_sponge.toml
new file mode 100644
index 00000000000..9196727ee2e
--- /dev/null
+++ b/toml/sphere_ssp_first_tracer_energy_upwind_held_suarez_rhoe_equilmoist_hightop_sponge.toml
@@ -0,0 +1,10 @@
+[zd_viscous]
+alias = "zd_viscous"
+value = 30000.0
+type = "float"
+
+[zd_rayleigh]
+alias = "zd_rayleigh"
+value = 30000.0
+type = "float"
+

From d2c69681dfbe960d0a468f40dd85aea679f5cfa1 Mon Sep 17 00:00:00 2001
From: nefrathenrici <nat.henrici@gmail.com>
Date: Thu, 31 Aug 2023 11:57:47 -0700
Subject: [PATCH 2/3] increase alloc limits (edmf, diagnostic edmfx)

---
 perf/flame.jl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/perf/flame.jl b/perf/flame.jl
index 76869960326..38bebad450a 100644
--- 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

From bfb2a02c6d156706e5fcae9c7ee8e2f8216ce90f Mon Sep 17 00:00:00 2001
From: nefrathenrici <nat.henrici@gmail.com>
Date: Thu, 31 Aug 2023 11:58:01 -0700
Subject: [PATCH 3/3] increment ref counter

---
 regression_tests/ref_counter.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/regression_tests/ref_counter.jl b/regression_tests/ref_counter.jl
index 9289ddcee34..9f54fe3133b 100644
--- a/regression_tests/ref_counter.jl
+++ b/regression_tests/ref_counter.jl
@@ -1 +1 @@
-121
+122