Merge branch 'main' of https://github.com/CliMA/CloudMicrophysics.jl into al/immer_hom_parcel

Author: amylu00

.buildkite/JuliaProject.toml

@@ -0,0 +1,5 @@
+[extras]
+CUDA_Runtime_jll = "76a88914-d11a-5bdc-97e0-2f5a05c973a2"
+
+[preferences.CUDA_Runtime_jll]
+version = "local"

.buildkite/pipeline.yml

@@ -1,56 +1,43 @@
+agents:
+  queue: central
+  slurm_mem: 8G
+  modules: julia/1.9.3 cuda/11.8 ucx/1.14.1_cuda-11.8 openmpi/4.1.5_cuda-11.8 hdf5/1.12.2-ompi415 nsight-systems/2023.2.1
+
 env:
-  JULIA_VERSION: "1.9.2"
-  OPENMPI_VERSION: "4.0.4"
+  JULIA_LOAD_PATH: "${JULIA_LOAD_PATH}:${BUILDKITE_BUILD_CHECKOUT_PATH}/.buildkite"
   OPENBLAS_NUM_THREADS: 1
+  JULIA_NVTX_CALLBACKS: gc
+  OMPI_MCA_opal_warn_on_missing_libcuda: 0
+  JULIA_CPU_TARGET: 'broadwell;skylake'
 
 steps:
-  - label: "init :computer:"
-    key: "init_cpu_env"
+  - label: "initialize"
+    key: "initialize"
     command:
-      - "julia --project -e 'using Pkg; Pkg.instantiate(;verbose=true)'"
-      - "julia --project -e 'using Pkg; Pkg.precompile(;strict=true)'"
-      - "julia --project -e 'using Pkg; Pkg.status()'"
-    agents:
-      config: cpu
-      queue: central
-      slurm_ntasks: 1
+      - echo "--- Instantiate project"
+      - julia --project -e 'using Pkg; Pkg.instantiate(;verbose=true); Pkg.precompile(;strict=true)'
 
-  - label: "init :flower_playing_cards:"
-    key: "init_gpu_env"
-    command:
-      - "julia --project -e 'using Pkg; Pkg.instantiate(;verbose=true)'"
-      - "julia --project -e 'using Pkg; Pkg.precompile()'"
+      - echo "--- Instantiate test"
+      - julia --project=test -e 'using Pkg; Pkg.develop(path="."); Pkg.instantiate(;verbose=true); Pkg.precompile(;strict=true)'
 
-      # force the initialization of the CUDA runtime as it is lazily loaded by default
-      - "julia --project=test -e 'using Pkg; Pkg.develop(path=\".\"); Pkg.instantiate(;verbose=true); Pkg.precompile(;strict=true)'"
-      - "julia --project=test -e 'using CUDA; CUDA.versioninfo()'"
-      - "julia --project=test -e 'using CUDA; CUDA.precompile_runtime()'"
-      - "julia --project=test -e 'using Pkg; Pkg.status()'"
+      - julia --project=test -e 'using CUDA; CUDA.precompile_runtime()'
+      - julia --project=test -e 'using Pkg; Pkg.status()'
     agents:
-      config: gpu
-      queue: central
-      slurm_ntasks: 1
-      slurm_gres: "gpu:1"
+      slurm_gpus: 1
+      slurm_cpus_per_task: 8
+    env:
+      JULIA_NUM_PRECOMPILE_TASKS: 8
 
   - wait
 
   - label: ":computer: unit tests"
     key: "cpu_unittests"
     command:
-      - "julia --project=test -e 'using Pkg; Pkg.develop(path=\".\"); Pkg.instantiate(;verbose=true); Pkg.precompile(;strict=true)'"
       - "julia --project=test --color=yes test/runtests.jl"
-    agents:
-      config: cpu
-      queue: central
-      slurm_ntasks: 1
 
-  - label: ":flower_playing_cards: unit tests"
+  - label: ":flower_playing_cards: GPU unit tests"
     key: "gpu_unittests"
     command:
-      - "julia --project=test -e 'using Pkg; Pkg.develop(path=\".\"); Pkg.instantiate(;verbose=true); Pkg.precompile(;strict=true)'"
       - "julia --project=test --color=yes test/gpu_tests.jl"
     agents:
-      config: gpu
-      queue: central
-      slurm_ntasks: 1
-      slurm_gres: "gpu:1"
+      slurm_gpus: 1

Project.toml

@@ -16,7 +16,7 @@ Thermodynamics = "b60c26fb-14c3-4610-9d3e-2d17fe7ff00c"
 CLIMAParameters = "0.7.15"
 DocStringExtensions = "0.8, 0.9"
 ForwardDiff = "0.10"
-KernelAbstractions = "0.8, 0.9"
+KernelAbstractions = "0.9"
 RootSolvers = "0.3, 0.4"
 SpecialFunctions = "1, 2"
 Thermodynamics = "0.9, 0.10, 0.11"

docs/Project.toml

@@ -7,6 +7,7 @@ DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 RootSolvers = "7181ea78-2dcb-4de3-ab41-2b8ab5a31e74"
+SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 Thermodynamics = "b60c26fb-14c3-4610-9d3e-2d17fe7ff00c"
 
 [compat]

docs/make.jl

@@ -15,7 +15,6 @@ pages = Any[
     "Non-equilibrium cloud formation" => "MicrophysicsNonEq.md",
     "Smooth transition at thresholds" => "ThresholdsTransition.md",
     "Aerosol activation" => "AerosolActivation.md",
-    "ARG2000 activation example" => "ARG2000_example.md",
     "Water Activity" => "WaterActivity.md",
     "Ice Nucleation" => "IceNucleation.md",
     "Aerosol Nucleation" => "AerosolNucleation.md",

docs/src/API.md

@@ -8,6 +8,7 @@ CurrentModule = CloudMicrophysics
 ```@docs
 Parameters.CloudMicrophysicsParameters0M
 Parameters.CloudMicrophysicsParametersP3
+Parameters.H2SO4SolutionParameters
 ```
 
 # Non-equilibrium cloud formation

docs/src/ARG2000_example.md

@@ -346,7 +346,7 @@ end
 
 # data read from Fig 1 in Abdul-Razzak and Ghan 2000
 # using https://automeris.io/WebPlotDigitizer/
-include("ARGdata.jl")
+include("plots/ARGdata.jl")
 
 PL.plot(N_2_range * 1e-6, N_act_frac_B, label="CliMA-B", xlabel="Mode 2 aerosol number concentration [1/cm3]", ylabel="Mode 1 number fraction activated")
 PL.scatter!(Fig1_x_obs, Fig1_y_obs, markercolor = :black, label="paper observations")
@@ -355,3 +355,20 @@ PL.plot!(Fig1_x_param, Fig1_y_param, linecolor = :black, label="paper parameteri
 PL.savefig("Abdul-Razzak_and_Ghan_fig_1.svg")
 ```
 ![](Abdul-Razzak_and_Ghan_fig_1.svg)
+
+## Example of Aerosol Activation from ARG2000
+
+The figures below have been reproduced from [Abdul-RazzakandGhan2000](@cite)
+using the aerosol activation parameterization implemented in this project.
+
+```@example
+include("plots/ARGplots.jl")
+make_ARG_figX(2)
+make_ARG_figX(3)
+make_ARG_figX(4)
+make_ARG_figX(5)
+```
+![](Abdul-Razzak_and_Ghan_fig_2.svg)
+![](Abdul-Razzak_and_Ghan_fig_3.svg)
+![](Abdul-Razzak_and_Ghan_fig_4.svg)
+![](Abdul-Razzak_and_Ghan_fig_5.svg)

docs/src/AerosolActivation.md

@@ -60,7 +60,7 @@ The values of free parameters ``p``, ``u``, ``v``, ``w``, and ``a`` are defined
 Below figure reproduces results from [Dunne2016](@cite) without negative ion concentrations.
 
 ```@example
-include("nucleation_plotting/CLOUD_Nucleation_Plots.jl")
+include("plots/CLOUD_Nucleation_Plots.jl")
 ```
 ![](CLOUD_nucleation.svg)
 
@@ -71,7 +71,7 @@ Below we show a comparison between the Vehkamaki et al 2002 parameterization
   and the Dunne et al 2016 parameterization for two relative humidities.
 
 ```@example
-include("nucleation_plotting/compare_vehkamaki_CLOUD_nucleation.jl")
+include("plots/compare_vehkamaki_CLOUD_nucleation.jl")
 ```
 ![](CLOUD_Vehk_comparison_236.svg)
 ![](CLOUD_Vehk_comparison_298.svg)
@@ -114,7 +114,7 @@ k_{MT,OH} = 1.2 \; 10^{-11} \; exp(444/T)
 ### Example plots
 
 ```@example
-include("nucleation_plotting/Kirkby_organic_nucleation_plots.jl")
+include("plots/Kirkby_organic_nucleation_plots.jl")
 ```
 ![](Kirkby_organic_nucleation.svg)
 ## Nucleation of organics with sulfuric acid
@@ -139,7 +139,7 @@ An empirical derivation is given by:
 
 Below is a plot reproducing the results from [Riccobono2014](@cite), with a constant `H_2SO_4` concentration of `2.6e6 cm\^{-3}.
 ```@example
-include("nucleation_plotting/Riccobono_mixed_nucleation_plots.jl")
+include("plots/Riccobono_mixed_nucleation_plots.jl")
 ```
 ![](Riccobono_nucleation.svg)
 
@@ -173,7 +173,7 @@ m = \frac{log(CG(d_x) / CG(d_1))}{(log(d_x / d_1)}
 ### Example plots
 
 ```@example
-include("nucleation_plotting/lehtinen_apparent_nucleation_rate.jl")
+include("plots/lehtinen_apparent_nucleation_rate.jl")
 ```
 ![](apparent_nucleation.svg)
 

docs/src/AerosolNucleation.md

@@ -92,14 +92,14 @@ The following plot shows ``J`` as a function of ``\Delta a_w`` as compared to
   of ``\Delta a_w``, with no implications of whether ``\Delta a_w`` is properly
   parameterized. For more on water activity, please see above section.
 ```@example
-include("ice_nucleation_plots/KnopfAlpert2013_fig1.jl")
+include("plots/KnopfAlpert2013_fig1.jl")
 ```
 ![](Knopf_Alpert_fig_1.svg)
 
 The following plot shows J as a function of temperature as compared to figure 5a in Knopf & Alpert 2013.
 
 ```@example
-include("ice_nucleation_plots/KnopfAlpert2013_fig5.jl")
+include("plots/KnopfAlpert2013_fig5.jl")
 ```
 ![](KnopfAlpert2013_fig5.svg)
 Note that water activity of the droplet was assumed equal to relative humidity so that:
@@ -144,7 +144,7 @@ Here is a comparison of our parameterization of ``J_{hom}`` compared to Koop 200
   Koop 2000 uses the difference in chemical potential.
 
 ```@example
-include("ice_nucleation_plots/HomFreezingPlots.jl")
+include("plots/HomFreezingPlots.jl")
 ```
 ![](HomFreezingPlots.svg)
 

docs/src/IceNucleation.md

@@ -166,7 +166,7 @@ Here we plot the terminal velocity formulae from the current default 1-moment sc
 We also show the aspect ratio of snow particles.
 
 ```@example
-include("TerminalVelocityComparisons.jl")
+include("plots/TerminalVelocityComparisons.jl")
 ```
 ![](1M_individual_terminal_velocity_comparisons.svg)
 
@@ -772,7 +772,7 @@ const param_set = cloud_microphysics_parameters(toml_dict)
 thermo_params = CMP.thermodynamics_params(param_set)
 
 const air_props = CMT.AirProperties(FT)
-const liquid = CMT.LiquidType()
+const liquid = CMT.LiquidType(FT)
 const ice = CMT.IceType(FT)
 const rain = CMT.RainType(FT)
 const snow = CMT.SnowType(FT)

docs/src/Microphysics1M.md

@@ -355,6 +355,16 @@ The default free parameter values are:
 |``\alpha_r``                | ``159 \, m \cdot s^{-1} \cdot kg^{-\beta_r}``   |
 |``\alpha_r``                | ``0.266``                                       |
 
+!!! note
+    In our implementation we approximate the incomplete gamma function in order to get good
+    performance on the GPU. Below we show the evaporation rates for the number concnetration
+    and mass using both the exact and approximated gamma function
+
+```@example
+include("plots/RainEvapoartionSB2006.jl")
+```
+![](SB2006_rain_evaporation.svg)
+
 ## Additional 2-moment microphysics options
 
 ### Terminal Velocity
@@ -404,7 +414,7 @@ We also compare bulk number weighted [ND] and mass weighted [MD]
 terminal velocities for both formulas integrated over the size distribution from [SeifertBeheng2006](@cite).
 We also show the mass weighted terminal velocity from the 1-moment scheme.
 ```@example
-include("TerminalVelocityComparisons.jl")
+include("plots/TerminalVelocityComparisons.jl")
 ```
 ![](2M_terminal_velocity_comparisons.svg)
 
@@ -643,20 +653,20 @@ toml_dict = CP.create_toml_dict(FT; dict_type = "alias")
 const param_set = cloud_microphysics_parameters(toml_dict)
 thermo_params = CMP.thermodynamics_params(param_set)
 
-const liquid = CMT.LiquidType()
+const liquid = CMT.LiquidType(FT)
 const rain = CMT.RainType(FT)
 
 const KK2000 = CMT.KK2000Type()
 const B1994  = CMT.B1994Type()
 const TC1980 = CMT.TC1980Type()
 const LD2004 = CMT.LD2004Type()
-const VarTimeScaleAcnv = CMT.VarTimeScaleAcnvType()
 const SB2006 = CMT.SB2006Type()
 const acnv_SB2006 = CMT.AutoconversionSB2006(FT)
 const acnv_KK2000 = CMT.AutoconversionKK2000(FT)
 const acnv_B1994 = CMT.AutoconversionB1994(FT)
 const acnv_TC1980 = CMT.AutoconversionTC1980(FT)
 const acnv_LD2004 = CMT.AutoconversionLD2004(FT)
+const acnv_TSc = CMT.AutoconversionVarTimescale(FT)
 const rain_acnv_1m = CMT.Autoconversion1M(FT, rain)
 const accretion_KK2000 = CMT.AccretionKK2000(FT)
 const accretion_B1994 = CMT.AccretionB1994(FT)
@@ -665,7 +675,7 @@ const accretion_SB2006 = CMT.AccretionSB2006(FT)
 const ce = CMT.CollisionEfficiency(FT)
 
 
-include(joinpath(pkgdir(CloudMicrophysics), "docs", "src", "Wooddata.jl"))
+include(joinpath(pkgdir(CloudMicrophysics), "docs", "src", "plots", "Wooddata.jl"))
 
 # Example values
 q_liq_range = range(1e-8, stop=1e-3, length=1000)
@@ -679,15 +689,15 @@ q_liq_KK2000 = [CM2.conv_q_liq_to_q_rai(acnv_KK2000, q_liq, ρ_air, N_d = 1e8) f
 q_liq_B1994 = [CM2.conv_q_liq_to_q_rai(acnv_B1994, q_liq, ρ_air, N_d = 1e8) for q_liq in q_liq_range]
 q_liq_TC1980 = [CM2.conv_q_liq_to_q_rai(acnv_TC1980, q_liq, ρ_air, N_d = 1e8) for q_liq in q_liq_range]
 q_liq_LD2004 = [CM2.conv_q_liq_to_q_rai(acnv_LD2004, q_liq, ρ_air, N_d = 1e8) for q_liq in q_liq_range]
-q_liq_VarTimeScaleAcnv = [CM2.conv_q_liq_to_q_rai(param_set, VarTimeScaleAcnv, q_liq, ρ_air, N_d = 1e8) for q_liq in q_liq_range]
+q_liq_VarTimeScaleAcnv = [CM2.conv_q_liq_to_q_rai(acnv_TSc, q_liq, ρ_air, N_d = 1e8) for q_liq in q_liq_range]
 q_liq_SB2006 = [CM2.autoconversion(acnv_SB2006, q_liq, q_rai, ρ_air, 1e8).dq_rai_dt for q_liq in q_liq_range]
 q_liq_K1969 = [CM1.conv_q_liq_to_q_rai(rain_acnv_1m, q_liq) for q_liq in q_liq_range]
 
 N_d_KK2000 = [CM2.conv_q_liq_to_q_rai(acnv_KK2000, 5e-4, ρ_air, N_d = N_d) for N_d in N_d_range]
 N_d_B1994 = [CM2.conv_q_liq_to_q_rai(acnv_B1994, 5e-4, ρ_air, N_d = N_d) for N_d in N_d_range]
 N_d_TC1980 = [CM2.conv_q_liq_to_q_rai(acnv_TC1980, 5e-4, ρ_air, N_d = N_d) for N_d in N_d_range]
 N_d_LD2004 = [CM2.conv_q_liq_to_q_rai(acnv_LD2004, 5e-4, ρ_air, N_d = N_d) for N_d in N_d_range]
-N_d_VarTimeScaleAcnv = [CM2.conv_q_liq_to_q_rai(param_set, VarTimeScaleAcnv, 5e-4, ρ_air, N_d = N_d) for N_d in N_d_range]
+N_d_VarTimeScaleAcnv = [CM2.conv_q_liq_to_q_rai(acnv_TSc, 5e-4, ρ_air, N_d = N_d) for N_d in N_d_range]
 N_d_SB2006 = [CM2.autoconversion(acnv_SB2006, q_liq, q_rai, ρ_air, N_d).dq_rai_dt for N_d in N_d_range]
 
 accKK2000_q_liq = [CM2.accretion(accretion_KK2000, q_liq, q_rai, ρ_air) for q_liq in q_liq_range]

docs/src/Microphysics2M.md

@@ -123,7 +123,7 @@ where all variables from the m(D) regime are as defined above, and:
 Below we show the m(D) regime, replicating Figures 1 (a) and (b) from [MorrisonMilbrandt2015](@cite).
 We also show a(D).
 ```@example
-include("P3SchemePlots.jl")
+include("plots/P3SchemePlots.jl")
 ```
 ![](MorrisonandMilbrandtFig1a.svg)
 ![](MorrisonandMilbrandtFig1b.svg)

docs/src/P3Scheme.md

@@ -26,6 +26,6 @@ Where $R$ is the set of all process rates that contribute to precipitation produ
 Example reproducing Fig. 2 From [Glassmeier2016](@cite):
 
 ```@example
-include("PrecipitationSusceptibilityPlots.jl")
+include("plots/PrecipitationSusceptibilityPlots.jl")
 ```
 ![](Glassmeier-Lohmann_Fig2.svg)

docs/src/PrecipitationSusceptibility.md

@@ -78,7 +78,7 @@ To verify that our parameterizations for ``p_{i,sat}`` and ``p_{sat}`` from
     implementations of ``p_{i,sat}`` and ``p_{sat}`` (``p_{sat}`` labelled as
     ``p_{liq}`` to emphasize ice vs liquid phase of the pure water).
 ```@example
-include("water_activity_plots/Baumgartner2022_fig5.jl")
+include("plots/Baumgartner2022_fig5.jl")
 ```
 ![](vap_pressure_vs_T.svg)
 
@@ -100,7 +100,7 @@ Another plot to test if our parameterization is reasonable is plotting against o
   droplet is used but setting concentration of H2SO4 to zero. ``using \mu`` refers to the parameterization
   used in [Koop2000](@cite) where water activity is dependent on chemical potential.
 ```@example
-include("water_activity_plots/T_vs_wateractivity.jl")
+include("plots/T_vs_wateractivity.jl")
 ```
 ![](T_vs_wateractivity.svg)
 Taking the difference between any pair of blue and green lines will give a ``\Delta a_w(T)``.

docs/src/WaterActivity.md

@@ -17,7 +17,7 @@ toml_dict = CP.create_toml_dict(FT; dict_type = "alias")
 const param_set = cloud_microphysics_parameters(toml_dict)
 thermo_params = CMP.thermodynamics_params(param_set)
 
-include("ARGdata.jl")
+include("plots/ARGdata.jl")
 
 # Atmospheric conditions
 T = 294.0         # air temperature