From 42f8aff83bdc64a4e687a0a6500ffcb4fd4d7843 Mon Sep 17 00:00:00 2001
From: LenkaNovak <lenka@caltech.edu>
Date: Tue, 3 Oct 2023 18:49:41 -0700
Subject: [PATCH] add atmos toml path

---
 config/longrun_configs/dyamond_target.yml     |  2 +-
 experiments/AMIP/modular/cli_options.jl       |  2 ++
 .../components/atmosphere/climaatmos_init.jl  | 20 ++++++++++++-------
 3 files changed, 16 insertions(+), 8 deletions(-)

diff --git a/config/longrun_configs/dyamond_target.yml b/config/longrun_configs/dyamond_target.yml
index 0c8748408e..bd574b1cc0 100644
--- a/config/longrun_configs/dyamond_target.yml
+++ b/config/longrun_configs/dyamond_target.yml
@@ -10,5 +10,5 @@ dt_save_to_sol: "0.5days"
 dt_save_to_disk: "0.5days"
 turb_flux_partition: "CombinedStateFluxes"
 atmos_config_file: "config/longrun_configs/longrun_aquaplanet_dyamond.yml"
+atmos_toml_file: "toml/longrun_aquaplanet_dyamond.toml"
 monthly_checkpoint: false
-
diff --git a/experiments/AMIP/modular/cli_options.jl b/experiments/AMIP/modular/cli_options.jl
index f6b83656ae..bdc66d342c 100644
--- a/experiments/AMIP/modular/cli_options.jl
+++ b/experiments/AMIP/modular/cli_options.jl
@@ -59,6 +59,8 @@ function argparse_settings()
         default = "PrescribedSurface"
         "--atmos_config_file"
         help = "A yaml file used to set the atmospheric model configuration. If nothing is specified, the default configuration is used."
+        "--atmos_toml_file"
+        help = "A toml file used to overwrite the atmospheric model parameters. If nothing is specified, the default parameters are used."
         # ClimaLSM specific
         "--land_albedo_type"
         help = "Access land surface albedo information from data file. [`function`, `map_static`, `map_temporal`]"
diff --git a/experiments/AMIP/modular/components/atmosphere/climaatmos_init.jl b/experiments/AMIP/modular/components/atmosphere/climaatmos_init.jl
index 967176e957..94c119cfd6 100644
--- a/experiments/AMIP/modular/components/atmosphere/climaatmos_init.jl
+++ b/experiments/AMIP/modular/components/atmosphere/climaatmos_init.jl
@@ -28,19 +28,25 @@ Returns the specified atmospheric configuration (`atmos_config_dict`) overwitten
 in the coupler dictionary (`config_dict`).
 """
 function get_atmos_config(coupler_dict)
-    atmos_file = coupler_dict["atmos_config_file"]
+    atmos_config_file = coupler_dict["atmos_config_file"]
     # override default or specified configs with coupler arguments, and set the correct atmos config_file
-    if isnothing(atmos_file)
+    if isnothing(atmos_config_file)
         @info "Using Atmos default configuration"
-        merge(CA.default_config_dict(), coupler_dict, Dict("config_file" => atmos_file))
+        atmos_config = merge(CA.default_config_dict(), coupler_dict, Dict("config_file" => atmos_config_file))
     else
-        @info "Using Atmos configuration from $atmos_file"
-        merge(
-            CA.override_default_config(joinpath(pkgdir(CA), atmos_file)),
+        @info "Using Atmos configuration from $atmos_config_file"
+        atmos_config = merge(
+            CA.override_default_config(joinpath(pkgdir(CA), atmos_config_file)),
             coupler_dict,
-            Dict("config_file" => atmos_file),
+            Dict("config_file" => atmos_config_file),
         )
     end
+    atmos_toml_file = coupler_dict["atmos_toml_file"]
+    if !isnothing(atmos_toml_file)
+        @info "Overwriting Atmos parameters from $atmos_toml_file"
+        atmos_config = merge(atmos_config, Dict("toml" => [joinpath(pkgdir(CA), atmos_toml_file)]))
+    end
+    return atmos_config
 end
 
 function atmos_init(::Type{FT}, atmos_config_dict::Dict) where {FT}