Merge branch 'main' into sk/dyamond_summer_ics

.dev/Manifest.toml

@@ -1,6 +1,6 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.10.6"
+julia_version = "1.10.7"
 manifest_format = "2.0"
 project_hash = "b280bcf3b481823c97fa1a62c1b5e65114b8fa18"
 
@@ -67,9 +67,9 @@ deps = ["Base64"]
 uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 
 [[deps.OrderedCollections]]
-git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5"
+git-tree-sha1 = "12f1439c4f986bb868acda6ea33ebc78e19b95ad"
 uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
-version = "1.6.3"
+version = "1.7.0"
 
 [[deps.PrecompileTools]]
 deps = ["Preferences"]

.github/workflows/ci.yml

@@ -38,7 +38,7 @@ jobs:
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         with:
           file: lcov.info
           token: ${{secrets.CODECOV_TOKEN}}

.gitignore

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

NEWS.md

@@ -3,7 +3,13 @@ ClimaAtmos.jl Release Notes
 
 Main
 -------
+### Features
+
+### Write diagnostics to text files
 
+Added functionality to write diagnostics in DictWriter to text files.
+This is useful for outputing scalar diagnostics, such as total mass of
+the atmosphere. PR [3476](https://github.com/CliMA/ClimaAtmos.jl/pull/3476)
 
 v0.27.9
 -------

config/default_configs/default_config.yml

@@ -145,6 +145,9 @@ 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
 bubble:
   help: "Enable bubble correction for more accurate surface areas"
   value: true
@@ -256,7 +259,7 @@ implicit_diffusion:
 approximate_linear_solve_iters:
   help: "Number of iterations for the approximate linear solve (used when `implicit_diffusion` is true)"
   value: 1
-override_τ_precip:
+override_precip_timescale:
   help: "If true, sets τ_precip to dt. Otherwise, τ_precip is set to the value in the toml dictionary"
   value: true
 output_default_diagnostics:

config/longrun_configs/amip_target_diagedmf.yml

@@ -9,7 +9,7 @@ dt_save_state_to_disk: "20days"
 moist: "equil"
 cloud_model: "quadrature_sgs"
 precip_model: "0M"
-override_τ_precip: false
+override_precip_timescale: false
 rad: "allskywithclear"
 dt_rad: "1hours"
 dt_cloud_fraction: "1hours"

config/longrun_configs/longrun_aquaplanet_allsky_diagedmf_0M.yml

@@ -25,5 +25,5 @@ edmfx_nh_pressure: true
 edmfx_sgs_mass_flux: true
 edmfx_sgs_diffusive_flux: true
 precip_model: "0M"
-override_τ_precip: false
+override_precip_timescale: false
 toml: [toml/longrun_aquaplanet_diagedmf.toml]

config/longrun_configs/longrun_aquaplanet_allsky_progedmf_diffonly_0M.yml

@@ -27,5 +27,5 @@ edmfx_filter: true
 edmfx_sgs_mass_flux: false
 edmfx_sgs_diffusive_flux: true
 precip_model: "0M"
-override_τ_precip: false
+override_precip_timescale: false
 toml: [toml/longrun_aquaplanet_progedmf.toml]

config/model_configs/box_density_current_test.yml

@@ -1,16 +1,20 @@
-dt_save_state_to_disk: "10secs"
+reference_job_id: "les_box"
 initial_condition: "DryDensityCurrentProfile"
+config: "box"
+smagorinsky_lilly: true
+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"
+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/diagnostic_edmfx_trmm_box_0M.yml

@@ -15,7 +15,7 @@ moist: equil
 cloud_model: "quadrature_sgs"
 call_cloud_diagnostics_per_stage: true
 precip_model: "0M"
-override_τ_precip: false
+override_precip_timescale: false
 config: box
 x_max: 1e8
 y_max: 1e8

config/model_configs/diagnostic_edmfx_trmm_stretched_box.yml

@@ -16,7 +16,7 @@ moist: equil
 cloud_model: "quadrature_sgs"
 call_cloud_diagnostics_per_stage: true
 precip_model: "1M"
-override_τ_precip: false
+override_precip_timescale: false
 config: box
 x_max: 1e8
 y_max: 1e8

config/model_configs/gpu_aquaplanet_dyamond.yml

@@ -24,3 +24,7 @@ prescribed_aerosols: ["CB1", "CB2", "DST01", "DST02", "DST03", "DST04", "OC1", "
 prescribe_clouds_in_radiation: true
 radiation_reset_rng_seed: true
 toml: [toml/longrun_aquaplanet.toml]
+diagnostics:
+  - short_name: [massa, energya]
+    period: 1hours
+    writer: dict

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"
@@ -14,7 +15,6 @@ approximate_linear_solve_iters: 2
 hyperdiff: "false" 
 apply_limiter: false
 smagorinsky_lilly: true
-c_smag: 0.20
 # time- and spatial discretization
 x_elem: 10
 x_max: 3.2e3
@@ -24,11 +24,13 @@ 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:

config/model_configs/prognostic_edmfx_simpleplume_column.yml

@@ -1,14 +1,13 @@
 initial_condition: "SimplePlume"
 surface_setup: "SimplePlume"
 turbconv: "prognostic_edmfx"
-implicit_diffusion: true
-implicit_sgs_advection: true
+implicit_diffusion: false
+implicit_sgs_advection: false
 approximate_linear_solve_iters: 2
 max_newton_iters_ode: 3
-zero_tendency: "grid_scale"
 edmfx_upwinding: first_order
 edmfx_entr_model: "Generalized"
-edmfx_detr_model: "Generalized"
+edmfx_detr_model: "SmoothArea"
 edmfx_sgs_mass_flux: false
 edmfx_sgs_diffusive_flux: false
 edmfx_nh_pressure: true
@@ -19,10 +18,10 @@ cloud_model: "quadrature_sgs"
 call_cloud_diagnostics_per_stage: true
 config: "column"
 z_max: 4e3
-z_elem: 80
+z_elem: 40
 z_stretch: false
 perturb_initstate: false
-dt: 20secs"
+dt: 30secs"
 t_end: "12hours"
 dt_save_state_to_disk: "10mins"
 toml: [toml/prognostic_edmfx_simpleplume.toml]

config/model_configs/rcemipii_box_diagnostic_edmfx.yml

@@ -16,7 +16,7 @@ edmfx_sgs_diffusive_flux: true
 rayleigh_sponge: true
 moist: equil
 precip_model: 0M
-override_τ_precip: false
+override_precip_timescale: false
 dt: 30secs
 t_end: 3600secs
 dt_save_state_to_disk: 12hours

config/model_configs/rcemipii_sphere_diagnostic_edmfx.yml

@@ -15,7 +15,7 @@ edmfx_sgs_diffusive_flux: true
 rayleigh_sponge: true
 moist: equil
 precip_model: 0M
-override_τ_precip: false
+override_precip_timescale: false
 dt: 100secs
 t_end: 12hours
 dt_save_state_to_disk: 12hours

config/model_configs/sphere_baroclinic_wave_conservation.yml

@@ -4,3 +4,7 @@ t_end: "5days"
 moist: "equil"
 dt_save_state_to_disk: "5days"
 check_conservation: true
+diagnostics:
+  - short_name: [massa, energya]
+    period: 1days
+    writer: dict

config/model_configs/sphere_baroclinic_wave_conservation_ft64.yml

@@ -5,3 +5,7 @@ t_end: "5days"
 moist: "equil"
 dt_save_state_to_disk: "5days"
 check_conservation: true
+diagnostics:
+  - short_name: [massa, energya]
+    period: 1days
+    writer: dict

config/model_configs/sphere_baroclinic_wave_conservation_source.yml

@@ -9,3 +9,7 @@ precip_model: "0M"
 vert_diff: true
 dt_save_state_to_disk: "5days"
 check_conservation: true
+diagnostics:
+  - short_name: [massa, energya, watera, energyo, watero]
+    period: 1days
+    writer: dict