runs test

add physical diags

format

add more comments

.buildkite/pipeline.yml

@@ -188,6 +188,13 @@ steps:
         agents:
           slurm_mem: 20GB
 
+      - label: "Slabplanet: extra atmos diagnostics"
+        key: "slabplanet_atmos_diags"
+        command: "julia --color=yes --project=experiments/AMIP/ experiments/AMIP/coupler_driver.jl --config_file $CONFIG_PATH/slabplanet_atmos_diags.yml"
+        artifact_paths: "experiments/AMIP/output/slabplanet/slabplanet_atmos_diags_artifacts/*"
+        agents:
+          slurm_mem: 20GB
+
       # AMIP
 
       # ...

Project.toml

@@ -34,7 +34,7 @@ Dates = "1"
 DocStringExtensions = "0.8, 0.9"
 Insolation = "0.9"
 JLD2 = "0.4"
-NCDatasets = "0.11, 0.12, 0.13, 0.14"
+NCDatasets = "0.11, 0.12, 0.13, =0.14.1"
 Plots = "1.39.0"
 SciMLBase = "1, 2"
 StaticArrays = "1"

config/model_configs/slabplanet_atmos_diags.yml

@@ -0,0 +1,19 @@
+anim: true
+apply_limiter: false
+dt: "200secs"
+dt_cpl: 200
+dt_save_to_sol: "9days"
+energy_check: true
+h_elem: 4
+job_id: "slabplanet_atmos_diags"
+mode_name: "slabplanet"
+moist: "equil"
+mono_surface: true
+precip_model: "0M"
+rad: "gray"
+run_name: "slabplanet_atmos_diags"
+t_end: "10days"
+vert_diff: "true"
+diagnostics:
+  - short_name: [mse, lr, ediff]
+    period: 1days

experiments/AMIP/components/atmosphere/climaatmos_extra_diags.jl

@@ -0,0 +1,83 @@
+# these extensions add extra diagnostics to the atmos model output
+import ClimaAtmos.Diagnostics as CAD
+
+import ClimaAtmos.Diagnostics: add_diagnostic_variable!
+
+"""
+    add_diagnostic_variable!(short_name::String, long_name::String, standard_name::String, units::String, comments::String, compute!::Function)
+
+This is an extension of the `add_diagnostic_variable!` function from ClimaAtmos.Diagnostics, and it adds the specified variable
+to the ClimaAtmos.Diagnostics.ALL_DIAGNOSTICS dictionary of possible diagnostic variables.
+The `compute!` function is called at every atmos time step to compute the diagnostic variable.
+
+To output these variables, short_name needs to be specified under diagnostics in the required yml file.
+"""
+add_diagnostic_variable!(
+    short_name = "mse",
+    long_name = "Moist static energy",
+    standard_name = "moist_static_energy",
+    units = "J/kg",
+    comments = "Moist static energy",
+    compute! = (out, state, cache, time) -> begin
+        (; params) = cache
+        (; ᶜts) = cache.precomputed
+        c_space = axes(state.c)
+        thermo_params = CAP.thermodynamics_params(params)
+        e_pot = CAP.grav(params) .* Fields.coordinate_field(c_space).z
+        if isnothing(out)
+            return TD.moist_static_energy.(thermo_params, ᶜts, e_pot)
+        else
+            out .= TD.moist_static_energy.(thermo_params, ᶜts, e_pot)
+        end
+    end,
+)
+
+add_diagnostic_variable!(
+    short_name = "lr",
+    long_name = "Lapse rate",
+    standard_name = "lapse_rate",
+    units = "K/m",
+    comments = "Lapse rate",
+    compute! = (out, state, cache, time) -> begin
+        (; params) = cache
+        (; ᶜts) = cache.precomputed
+        thermo_params = CAP.thermodynamics_params(params)
+        ᶜT = @. TD.air_temperature(thermo_params, ᶜts)
+        if isnothing(out)
+            return ClimaCore.Geometry.WVector.(CAD.ᶜgradᵥ.(CAD.ᶠinterp.(ᶜT))).components.data.:1
+        else
+            out .= ClimaCore.Geometry.WVector.(CAD.ᶜgradᵥ.(CAD.ᶠinterp.(ᶜT))).components.data.:1
+        end
+
+    end,
+)
+
+add_diagnostic_variable!(
+    short_name = "ediff",
+    long_name = "Eddy diffusivity",
+    standard_name = "eddy_diffusivity",
+    units = "m2/s",
+    comments = "Eddy diffusivity consistent with the VerticalDiffusion scheme in ClimaAtmos",
+    compute! = (out, state, cache, time) -> begin
+        (; ᶜp) = cache.precomputed
+        (; C_E) = cache.atmos.vert_diff
+        interior_uₕ = Fields.level(state.c.uₕ, 1)
+        ᶠp = ᶠK_E = cache.scratch.ᶠtemp_scalar
+        Fields.bycolumn(axes(ᶜp)) do colidx
+            @. ᶠp[colidx] = CAD.ᶠinterp(ᶜp[colidx])
+            ᶜΔz_surface = Fields.Δz_field(interior_uₕ)
+            @. ᶠK_E[colidx] = CA.eddy_diffusivity_coefficient(
+                C_E,
+                CA.norm(interior_uₕ[colidx]),
+                ᶜΔz_surface[colidx] / 2,
+                ᶠp[colidx],
+            )
+        end
+        if isnothing(out)
+            return CAD.ᶜinterp.(ᶠK_E)
+        else
+            out .= CAD.ᶜinterp.(ᶠK_E)
+        end
+
+    end,
+)

experiments/AMIP/components/atmosphere/climaatmos_init.jl

@@ -14,6 +14,8 @@ import ClimaCoupler.Interfacer: get_field, update_field!, name
 import ClimaCoupler.Checkpointer: get_model_state_vector
 using StaticArrays
 
+include("climaatmos_extra_diags.jl")
+
 # the clima atmos `integrator` is now defined
 struct ClimaAtmosSimulation{P, Y, D, I} <: AtmosModelSimulation
     params::P