implement smagorinsky lilly closure

.gitignore

@@ -32,6 +32,8 @@ docs/src/config.md
 test/Manifest*.toml
 calibration/test/Manifest*.toml
 
+Artifacts.toml
+
 # ignore vscode artifacts
 *.vscode
 *.DS

config/default_configs/default_config.yml

@@ -145,6 +145,15 @@ vert_diff:
 hyperdiff:
   help: "Hyperdiffusion [`ClimaHyperdiffusion` (or `true`; default), `none` (or `false`)]"
   value: "CAM_SE"
+smagorinsky_lilly:
+  help: "Smagorinsky-Lilly diffusive closure [`false` (default), `true`]"
+  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

config/model_configs/box_density_current_test.yml

@@ -1,16 +1,22 @@
-dt_save_state_to_disk: "10secs"
+reference_job_id: "les_box"
 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: [wa, ua, va, ta, thetaa, ha]
+    period: 5secs 

config/model_configs/les_isdac_box.yml

@@ -1,4 +1,5 @@
 # ISDAC config
+reference_job_id: "les_box"  # for plotting
 initial_condition: "ISDAC" 
 subsidence: "ISDAC" 
 surface_setup: "ISDAC"
@@ -15,6 +16,7 @@ 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 +26,13 @@ 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: