update import convention

Project.toml

@@ -4,15 +4,11 @@ authors = ["CliMA Contributors <clima-software@caltech.edu>"]
 version = "0.0.1"
 
 [deps]
-ClimaAtmos = "b2c96348-7fb7-4fe0-8da9-78d88439e717"
 ClimaComms = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d"
 ClimaCore = "d414da3d-4745-48bb-8d80-42e94e092884"
 ClimaCoreTempestRemap = "d934ef94-cdd4-4710-83d6-720549644b70"
-ClimaLand = "08f4d4ce-cf43-44bb-ad95-9d2d5f413532"
-ClimaParams = "5c42b081-d73a-476f-9059-fd94b934656c"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
-Insolation = "e98cc03f-d57e-4e3c-b70c-8d51efe9e0d8"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
@@ -24,15 +20,11 @@ TempestRemap_jll = "8573a8c5-1df0-515e-a024-abad257ee284"
 Thermodynamics = "b60c26fb-14c3-4610-9d3e-2d17fe7ff00c"
 
 [compat]
-ClimaAtmos = "0.22"
 ClimaComms = "0.5.6"
 ClimaCore = "0.13"
 ClimaCoreTempestRemap = "0.3"
-ClimaLand = "0.11"
-ClimaParams = "0.10"
 Dates = "1"
 DocStringExtensions = "0.8, 0.9"
-Insolation = "0.9.2"
 JLD2 = "0.4"
 NCDatasets = "0.11, 0.12, 0.13, 0.14.2"
 Plots = "1.39.0"

experiments/AMIP/Project.toml

@@ -51,13 +51,17 @@ ArgParse = "1.1"
 ArtifactWrappers = "0.2"
 AtmosphericProfilesLibrary = "0.1"
 ClimaAnalysis = "0.5"
+ClimaAtmos = "0.22"
 ClimaCorePlots = "0.2"
+ClimaLand = "0.11"
+ClimaParams = "0.10"
 ClimaTimeSteppers = "0.7"
 Colors = "0.12"
 Dierckx = "0.5"
 ForwardDiff = "0.10"
 Glob = "1"
 HDF5_jll = "1"
+Insolation = "0.9.2"
 IntervalSets = "0.5, 0.6, 0.7"
 JSON = "0.21"
 MPI = "0.20"

experiments/AMIP/components/atmosphere/climaatmos_extra_diags.jl

@@ -1,8 +1,6 @@
 # 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)
 
@@ -13,7 +11,7 @@ The `compute!` function is called at every atmos time step to compute the diagno
 To output these variables, short_name needs to be specified under diagnostics in the required yml file.
 """
 
-add_diagnostic_variable!(
+CAD.add_diagnostic_variable!(
     short_name = "mse",
     long_name = "Moist static energy",
     standard_name = "moist_static_energy",
@@ -24,7 +22,7 @@ add_diagnostic_variable!(
         (; ᶜts) = cache.precomputed
         c_space = axes(state.c)
         thermo_params = CAP.thermodynamics_params(params)
-        e_pot = CAP.grav(params) .* ClimaCore.Fields.coordinate_field(c_space).z
+        e_pot = CAP.grav(params) .* CC.Fields.coordinate_field(c_space).z
         if isnothing(out)
             return TD.moist_static_energy.(thermo_params, ᶜts, e_pot)
         else
@@ -33,7 +31,7 @@ add_diagnostic_variable!(
     end,
 )
 
-add_diagnostic_variable!(
+CAD.add_diagnostic_variable!(
     short_name = "lr",
     long_name = "Lapse rate",
     standard_name = "lapse_rate",
@@ -45,15 +43,15 @@ add_diagnostic_variable!(
         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
+            return CC.Geometry.WVector.(CAD.ᶜgradᵥ.(CAD.ᶠinterp.(ᶜT))).components.data.:1
         else
-            out .= ClimaCore.Geometry.WVector.(CAD.ᶜgradᵥ.(CAD.ᶠinterp.(ᶜT))).components.data.:1
+            out .= CC.Geometry.WVector.(CAD.ᶜgradᵥ.(CAD.ᶠinterp.(ᶜT))).components.data.:1
         end
 
     end,
 )
 
-add_diagnostic_variable!(
+CAD.add_diagnostic_variable!(
     short_name = "ediff",
     long_name = "Eddy diffusivity",
     standard_name = "eddy_diffusivity",
@@ -62,11 +60,11 @@ add_diagnostic_variable!(
     compute! = (out, state, cache, time) -> begin
         (; ᶜp) = cache.precomputed
         (; C_E) = cache.atmos.vert_diff
-        interior_uₕ = ClimaCore.Fields.level(state.c.uₕ, 1)
+        interior_uₕ = CC.Fields.level(state.c.uₕ, 1)
         ᶠp = ᶠK_E = cache.scratch.ᶠtemp_scalar
-        ClimaCore.Fields.bycolumn(axes(ᶜp)) do colidx
+        CC.Fields.bycolumn(axes(ᶜp)) do colidx
             @. ᶠp[colidx] = CAD.ᶠinterp(ᶜp[colidx])
-            ᶜΔz_surface = ClimaCore.Fields.Δz_field(interior_uₕ)
+            ᶜΔz_surface = CC.Fields.Δz_field(interior_uₕ)
             @. ᶠK_E[colidx] = CA.eddy_diffusivity_coefficient(
                 C_E,
                 CA.norm(interior_uₕ[colidx]),