Update to new ClimaParams, CloudMicrophysics and Thermodynamics (#140)

* Update to new ClimaParams, CloudMicrophysics, Thermodynamics, ClimaCore and NCdatasets Co-authored-by: Sajjad Azimi <[email protected]>
CliMA · Apr 22, 2024 · 0b23aa0 · 0b23aa0 · sajjadazimi · Apr 22, 2024
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diff --git a/.github/workflows/JuliaFormatter.yml b/.github/workflows/JuliaFormatter.yml
@@ -31,7 +31,7 @@ jobs:
     - uses: julia-actions/setup-julia@latest
       if: steps.filter.outputs.julia_file_change == 'true'
       with:
-        version: 1.8.1
+        version: '1.10'
 
     - name: Apply JuliaFormatter
       if: steps.filter.outputs.julia_file_change == 'true'

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -16,7 +16,7 @@ jobs:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@latest
         with:
-          version: 1.8.1
+          version: '1.10'
       - name: Install dependencies
         run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
       - name: Build and deploy

diff --git a/Project.toml b/Project.toml
@@ -1,14 +1,16 @@
 name = "Kinematic1D"
 uuid = "a8a3bb05-6cc5-4342-abf6-5cc636bd2b35"
 authors = ["Climate Modeling Alliance"]
-version = "0.6.1"
+version = "0.7.0"
 
 [deps]
 ClimaCore = "d414da3d-4745-48bb-8d80-42e94e092884"
 ClimaCorePlots = "cf7c7e5a-b407-4c48-9047-11a94a308626"
+ClimaParams = "5c42b081-d73a-476f-9059-fd94b934656c"
 CloudMicrophysics = "6a9e3e04-43cd-43ba-94b9-e8782df3c71b"
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 EnsembleKalmanProcesses = "aa8a2aa5-91d8-4396-bcef-d4f2ec43552d"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
@@ -26,25 +28,26 @@ Thermodynamics = "b60c26fb-14c3-4610-9d3e-2d17fe7ff00c"
 UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
 
 [compat]
-ClimaCore = "0.11"
+ClimaCore = "0.13"
 ClimaCorePlots = "0.2"
-CloudMicrophysics = "0.15"
+ClimaParams = "0.10.5"
+CloudMicrophysics = "0.18.0"
 DiffEqBase = "6.75"
 Distributions = "0.25"
 EnsembleKalmanProcesses = "1.1"
 Interpolations = "0.15"
 JLD2 = "0.4"
 LinearAlgebra = "1"
 Logging = "1"
-NCDatasets = "0.12"
+NCDatasets = "0.14"
 Optim = "1.7"
 OrdinaryDiffEq = "6.29"
 Plots = "1.29"
 ProgressLogging = "0.1"
 Random = "1"
 SpecialFunctions = "2.3"
 TerminalLoggers = "0.1"
-Thermodynamics = "0.11"
+Thermodynamics = "0.12.6"
 UnPack = "1.0"
 julia = "1.8"
 

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,7 +1,6 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
-Kinematic1D = "a8a3bb05-6cc5-4342-abf6-5cc636bd2b35"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 
 [compat]

diff --git a/src/CalibrateCMP/DistributionUtils.jl b/src/CalibrateCMP/DistributionUtils.jl
@@ -4,15 +4,18 @@ function initial_parameter_ensemble(priors, N_ensemble; rng_seed = 10)
     return initial_ensemble
 end
 
-function construct_priors(params::Dict)
+function construct_priors(
+    params::Dict{String, @NamedTuple{mean::FT, var::FT, lbound::FT, ubound::FT}},
+) where {FT <: Real}
     u_names = collect(keys(params))
     u_values = collect(values(params))
-    u_means = collect([v.mean for v in u_values])
-    u_vars = collect([v.var for v in u_values])
-    u_lbounds = collect([v.lbound for v in u_values])
-    u_ubounds = collect([v.ubound for v in u_values])
+    n_params = length(u_names)
 
     # All vars are approximated as Gaussian in unconstrained space
-    marginal_priors = constrained_gaussian.(u_names, u_means, u_vars, u_lbounds, u_ubounds)
+    marginal_priors = Vector{ParameterDistribution}(undef, n_params)
+    for i in 1:n_params
+        marginal_priors[i] =
+            constrained_gaussian(u_names[i], u_values[i].mean, u_values[i].var, u_values[i].lbound, u_values[i].ubound)
+    end
     return combine_distributions(marginal_priors)
 end
diff --git a/src/CalibrateCMP/IOUtils.jl b/src/CalibrateCMP/IOUtils.jl
@@ -160,7 +160,7 @@ function read_pysdm_data(file)
     # iterate over all variables
     vars = Dict()
     for (varname, var) in ds
-        vars[varname] = var[:]
+        vars[varname] = reshape(var[:], size(var))
     end
 
     close(ds)

diff --git a/src/CalibrateCMP/KiDUtils.jl b/src/CalibrateCMP/KiDUtils.jl
@@ -72,9 +72,8 @@ function run_KiD(u::Array{FT, 1}, u_names::Array{String, 1}, model_settings::Dic
         κ = model_settings["κ"],
     )
 
-    moisture = CO.get_moisture_type(FT, model_settings["moisture_choice"], model_settings["toml_dict"])
+    moisture = CO.get_moisture_type(model_settings["moisture_choice"], model_settings["toml_dict"])
     precip = CO.get_precipitation_type(
-        FT,
         model_settings["precipitation_choice"],
         model_settings["toml_dict"];
         rain_formation_choice = model_settings["rain_formation_choice"],
@@ -152,18 +151,16 @@ function run_KiD_col_sed(u::Array{FT, 1}, u_names::Array{String, 1}, model_setti
 
     update_parameters!(model_settings, u, u_names)
     apply_param_dependency!(model_settings)
-    model_settings["toml_dict"]["νc_SB2006"]["value"] = model_settings["k"]
+    model_settings["toml_dict"]["SB2006_cloud_gamma_distribution_parameter"]["value"] = model_settings["k"]
     common_params = create_common_parameters(
-        FT,
         precip_sources = model_settings["precip_sources"],
         precip_sinks = model_settings["precip_sinks"],
         Nd = model_settings["Nd"],
     )
     kid_params = create_kid_parameters(FT)
 
-    moisture = CO.get_moisture_type(FT, "NonEquilibriumMoisture", model_settings["toml_dict"])
+    moisture = CO.get_moisture_type("NonEquilibriumMoisture", model_settings["toml_dict"])
     precip = CO.get_precipitation_type(
-        FT,
         model_settings["precipitation_choice"],
         model_settings["toml_dict"];
         rain_formation_choice = model_settings["rain_formation_choice"],

diff --git a/src/Common/helper_functions.jl b/src/Common/helper_functions.jl
@@ -1,11 +1,11 @@
 """
     Returns moisture type
 """
-function get_moisture_type(FT, moisture_choice::String, toml_dict)
+function get_moisture_type(moisture_choice::String, toml_dict)
     if moisture_choice == "EquilibriumMoisture"
         moisture = EquilibriumMoisture_ρdTq()
     elseif moisture_choice == "NonEquilibriumMoisture"
-        moisture = NonEquilibriumMoisture_ρdTq(CMP.CloudLiquid(FT, toml_dict), CMP.CloudIce(FT, toml_dict))
+        moisture = NonEquilibriumMoisture_ρdTq(CMP.CloudLiquid(toml_dict), CMP.CloudIce(toml_dict))
     else
         error("Invalid moisture choice: $moisture_choice")
     end
@@ -16,7 +16,6 @@ end
     Returns precipitation type
 """
 function get_precipitation_type(
-    FT,
     precipitation_choice::String,
     toml_dict;
     rain_formation_choice::Union{Nothing, String} = nothing,
@@ -25,50 +24,50 @@ function get_precipitation_type(
     if precipitation_choice == "NoPrecipitation"
         precip = NoPrecipitation()
     elseif precipitation_choice == "Precipitation0M"
-        precip = Precipitation0M(CMP.Parameters0M(FT, toml_dict))
+        precip = Precipitation0M(CMP.Parameters0M(toml_dict))
     elseif precipitation_choice == "Precipitation1M"
         if sedimentation_choice == "CliMA_1M" || sedimentation_choice === nothing
-            st = CMP.Blk1MVelType(FT, toml_dict)
+            st = CMP.Blk1MVelType(toml_dict)
         elseif sedimentation_choice == "Chen2022"
-            st = CMP.Chen2022VelType(FT, toml_dict)
+            st = CMP.Chen2022VelType(toml_dict)
         else
             error("Invalid sedimentation choice: $sedimentation_choice")
         end
         if rain_formation_choice == "CliMA_1M" || rain_formation_choice === nothing
-            rain_params = CMP.Rain(FT, toml_dict)
+            rain_params = CMP.Rain(toml_dict)
             rf = rain_params.acnv1M
         elseif rain_formation_choice == "KK2000"
-            rf = CMP.KK2000(FT, toml_dict)
+            rf = CMP.KK2000(toml_dict)
         elseif rain_formation_choice == "B1994"
-            rf = CMP.B1994(FT, toml_dict)
+            rf = CMP.B1994(toml_dict)
         elseif rain_formation_choice == "TC1980"
-            rf = CMP.TC1980(FT, toml_dict)
+            rf = CMP.TC1980(toml_dict)
         elseif rain_formation_choice == "LD2004"
-            rf = CMP.LD2004(FT, toml_dict)
+            rf = CMP.LD2004(toml_dict)
         elseif rain_formation_choice == "VarTimeScaleAcnv"
-            rf = CMP.VarTimescaleAcnv(FT, toml_dict)
+            rf = CMP.VarTimescaleAcnv(toml_dict)
         else
             error("Invalid rain formation choice: $rain_formation_choice")
         end
         precip = Precipitation1M(
-            CMP.CloudLiquid(FT, toml_dict),
-            CMP.CloudIce(FT, toml_dict),
-            CMP.Rain(FT, toml_dict),
-            CMP.Snow(FT, toml_dict),
-            CMP.CollisionEff(FT, toml_dict),
+            CMP.CloudLiquid(toml_dict),
+            CMP.CloudIce(toml_dict),
+            CMP.Rain(toml_dict),
+            CMP.Snow(toml_dict),
+            CMP.CollisionEff(toml_dict),
             rf,
             st,
         )
     elseif precipitation_choice == "Precipitation2M"
         if sedimentation_choice == "SB2006" || sedimentation_choice === nothing
-            st = CMP.SB2006VelType(FT, toml_dict)
+            st = CMP.SB2006VelType(toml_dict)
         elseif sedimentation_choice == "Chen2022"
-            st = CMP.Chen2022VelTypeRain(FT, toml_dict)
+            st = CMP.Chen2022VelTypeRain(toml_dict)
         else
             error("Invalid sedimentation choice: $sedimentation_choice")
         end
         if rain_formation_choice == "SB2006" || rain_formation_choice === nothing
-            precip = Precipitation2M(CMP.SB2006(FT, toml_dict), st)
+            precip = Precipitation2M(CMP.SB2006(toml_dict), st)
         else
             error("Invalid rain formation choice: $rain_formation_choice")
         end

diff --git a/src/Common/parameters.jl b/src/Common/parameters.jl
@@ -1,21 +1,39 @@
-"""
-    Create common model parameters.
-
-    (Overwriting the default values happens in the driver file.
-    Here we are just creating the CommonParameters struct)
-"""
 module Parameters
 
+using DocStringExtensions
+import ClimaParams as CP
+
 abstract type AbstractCommonParameters end
 const ACP = AbstractCommonParameters
 
-# Define KiD parameters
+"""
+    CommonParameters{FT}
+
+    Common parameters for the kinematic driver simulations
+
+    #Fields
+    $(DocStringExtensions.FIELDS)
+"""
 Base.@kwdef struct CommonParameters{FT} <: ACP
-    precip_sources::Int
-    precip_sinks::Int
+    "Switch to include precipitation formation terms"
+    precip_sources::Bool
+    "Switch to include precipitation sink terms"
+    precip_sinks::Bool
+    "Prescribed number concentration of cloud droplets (needed for some schemes) [1/m3]"
     prescribed_Nd::FT
 end
 
+function CommonParameters(td::CP.AbstractTOMLDict)
+    name_map = (;
+        :precipitation_sources_flag => :precip_sources,
+        :precipitation_sinks_flag => :precip_sinks,
+        :prescribed_Nd => :prescribed_Nd,
+    )
+    parameters = CP.get_parameter_values(td, name_map, "Common")
+    FT = CP.float_type(td)
+    return CommonParameters{FT}(; parameters...)
+end
+
 precip_sources(ps::ACP) = ps.precip_sources
 precip_sinks(ps::ACP) = ps.precip_sinks
 prescribed_Nd(ps::ACP) = ps.prescribed_Nd

diff --git a/src/Common/tendency.jl b/src/Common/tendency.jl
@@ -181,11 +181,11 @@ end
         # autoconversion liquid to rain and ice to snow
         # TODO - can we do it in a more elegant way?
         if rf isa CMP.Acnv1M{FT}
-            tmp = CM1.conv_q_liq_to_q_rai(rf, q.liq, smooth_transition = true)
+            tmp = CM1.conv_q_liq_to_q_rai(rf, q.liq, true)
         elseif typeof(rf) in [CMP.LD2004{FT}, CMP.VarTimescaleAcnv{FT}]
-            tmp = CM2.conv_q_liq_to_q_rai(rf, q.liq, ρ; N_d = common_params.prescribed_Nd)
+            tmp = CM2.conv_q_liq_to_q_rai(rf, q.liq, ρ, common_params.prescribed_Nd)
         elseif typeof(rf.acnv) in [CMP.AcnvKK2000{FT}, CMP.AcnvB1994{FT}, CMP.AcnvTC1980{FT}]
-            tmp = CM2.conv_q_liq_to_q_rai(rf, q.liq, ρ; N_d = common_params.prescribed_Nd)
+            tmp = CM2.conv_q_liq_to_q_rai(rf, q.liq, ρ, common_params.prescribed_Nd)
         else
             error("Unrecognized rain formation scheme")
         end

diff --git a/src/K1DModel/ode_utils.jl b/src/K1DModel/ode_utils.jl
@@ -10,7 +10,7 @@ function make_function_space(FT, z_min, z_max, n_elem)
     domain = CC.Domains.IntervalDomain(
         CC.Geometry.ZPoint{FT}(z_min),
         CC.Geometry.ZPoint{FT}(z_max),
-        boundary_tags = (:bottom, :top),
+        boundary_names = (:bottom, :top),
     )
     mesh = CC.Meshes.IntervalMesh(domain, nelems = n_elem)
 
@@ -22,8 +22,8 @@ end
 
 """
    Interface to ODE solver. Returns the function needed to compute the
-   right hand side of the solved ODE for advection, condensation, 
-   collision, sedimentation and evaporation processes. The rhs is 
+   right hand side of the solved ODE for advection, condensation,
+   collision, sedimentation and evaporation processes. The rhs is
    assembled via dispatch based on the moisture and precipitation types.
 """
 function make_rhs_function(ms::CO.AbstractMoistureStyle, ps::CO.AbstractPrecipitationStyle)
@@ -50,7 +50,7 @@ end
 
 """
    Interface to ODE solver. Returns the function needed to compute the
-   right hand side of the solved ODE for collision and sedimentation 
+   right hand side of the solved ODE for collision and sedimentation
    processes. The rhs is assembled via dispatch based on precipitation type.
 """
 function make_rhs_function_col_sed(ms::CO.AbstractMoistureStyle, ps::CO.AbstractPrecipitationStyle)

diff --git a/src/K1DModel/parameters.jl b/src/K1DModel/parameters.jl
@@ -1,25 +1,51 @@
-"""
-    Create Kinematic1D model parameters.
-
-    (Overwriting the default values happens in the driver file.
-    Here we are just creating the Kinematic1DParameters struct)
-"""
 module Parameters
 
+using DocStringExtensions
+import ClimaParams as CP
+
 abstract type AbstractKinematicParameters end
 const AKP = AbstractKinematicParameters
 
-# Define KiD parameters
+"""
+    Kinematic1DParameters{FT}
+
+    Free parameters for the kinematic 1-dimensional simulation
+
+    #Fields
+    $(DocStringExtensions.FIELDS)
+"""
 Base.@kwdef struct Kinematic1DParameters{FT} <: AKP
+    "Maximum updraft momentum flux m/s kg/m3"
     w1::FT
+    "Time when the updraft is switched off [s]"
     t1::FT
+    "Surface pressure [Pa]"
     p0::FT
+    "Switch to include flux correction for moisture transport"
     qtot_flux_correction::Int
+    "Assumed aerosol dry radius [m]"
     r_dry::FT
+    "Assumed aerosol standard deviation [-]"
     std_dry::FT
+    "Assumed aerosol hygroscopicity"
     κ::FT
 end
 
+function Kinematic1DParameters(td::CP.AbstractTOMLDict)
+    name_map = (;
+        :prescribed_flow_w1 => :w1,
+        :prescribed_flow_t1 => :t1,
+        :surface_pressure => :p0,
+        :qtot_flux_correction_flag => :qtot_flux_correction,
+        :r_dry => :r_dry,
+        :std_dry => :std_dry,
+        :kappa => :κ,
+    )
+    parameters = CP.get_parameter_values(td, name_map, "Kinematic1D")
+    FT = CP.float_type(td)
+    return Kinematic1DParameters{FT}(; parameters...)
+end
+
 w1(ps::AKP) = ps.w1
 t1(ps::AKP) = ps.t1
 p0(ps::AKP) = ps.p0