From 7fc729905831b8a424c99bd10cc58c47bea62f47 Mon Sep 17 00:00:00 2001
From: Julian Schmitt <jschmitt@caltech.edu>
Date: Tue, 17 Dec 2024 14:16:23 -0500
Subject: [PATCH] rebase and reset ref counter file

Update config/model_configs/prognostic_edmfx_soares_column.yml

Co-authored-by: Zhaoyi Shen <11598433+szy21@users.noreply.github.com>

removes softfail and comment in yml

Update config/model_configs/prognostic_edmfx_soares_column.yml

Co-authored-by: Zhaoyi Shen <11598433+szy21@users.noreply.github.com>
---
 .buildkite/pipeline.yml                       |  9 +++++
 .../prognostic_edmfx_soares_column.yml        | 34 +++++++++++++++++++
 post_processing/ci_plots.jl                   |  1 +
 src/surface_conditions/surface_setups.jl      |  3 +-
 4 files changed, 46 insertions(+), 1 deletion(-)
 create mode 100644 config/model_configs/prognostic_edmfx_soares_column.yml

diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml
index 4c3463378d..6fcfbf0509 100644
--- a/.buildkite/pipeline.yml
+++ b/.buildkite/pipeline.yml
@@ -841,6 +841,15 @@ steps:
         agents:
           slurm_mem: 20GB
 
+      - label: ":genie: Prognostic EDMFX Soares in a column"
+        command: >
+          julia --color=yes --project=examples examples/hybrid/driver.jl
+          --config_file $CONFIG_PATH/prognostic_edmfx_soares_column.yml
+          --job_id prognostic_edmfx_soares_column
+        artifact_paths: "prognostic_edmfx_soares_column/output_active/*"
+        agents:
+          slurm_mem: 20GB
+
   - group: "GPU"
     steps:
 
diff --git a/config/model_configs/prognostic_edmfx_soares_column.yml b/config/model_configs/prognostic_edmfx_soares_column.yml
new file mode 100644
index 0000000000..533f224183
--- /dev/null
+++ b/config/model_configs/prognostic_edmfx_soares_column.yml
@@ -0,0 +1,34 @@
+initial_condition: "Soares"
+surface_setup: "Soares"
+rayleigh_sponge: true
+turbconv: "prognostic_edmfx"
+implicit_diffusion: true
+implicit_sgs_advection: false
+approximate_linear_solve_iters: 2
+edmfx_upwinding: "first_order"
+edmfx_entr_model: "Generalized"
+edmfx_detr_model: "SmoothArea"
+edmfx_sgs_mass_flux: true
+edmfx_sgs_diffusive_flux: true
+edmfx_nh_pressure: true
+edmfx_filter: true
+prognostic_tke: true
+moist: "equil"
+config: "column"
+hyperdiff: false
+z_max: 3750
+z_elem: 75
+z_stretch: false
+perturb_initstate: false
+dt: "5secs"
+t_end: "8hours"
+toml: [toml/prognostic_edmfx.toml]
+netcdf_interpolation_num_points: [2, 2, 100]
+diagnostics:
+  - short_name: [ts, ta, thetaa, ha, pfull, rhoa, ua, va, wa, hur, hus, cl, clw, cli, hussfc, evspsbl, pr]
+    period: 10mins
+  - short_name: [arup, waup, taup, thetaaup, haup, husup, hurup, clwup, cliup, waen, taen, thetaaen, haen, husen, huren, clwen, clien, tke]
+    period: 10mins
+  - short_name: [entr, detr, lmix, bgrad, strain, edt, evu]
+    period: 10mins
+ode_algo: ARS343
diff --git a/post_processing/ci_plots.jl b/post_processing/ci_plots.jl
index 61302f8cef..75d1c4d143 100644
--- a/post_processing/ci_plots.jl
+++ b/post_processing/ci_plots.jl
@@ -1189,6 +1189,7 @@ EDMFBoxPlots = Union{
     Val{:prognostic_edmfx_gcmdriven_column},
     Val{:prognostic_edmfx_bomex_box},
     Val{:rcemipii_box_diagnostic_edmfx},
+    Val{:prognostic_edmfx_soares_column},
 }
 
 EDMFBoxPlotsWithPrecip = Union{
diff --git a/src/surface_conditions/surface_setups.jl b/src/surface_conditions/surface_setups.jl
index 0bb451130b..f335ae42d4 100644
--- a/src/surface_conditions/surface_setups.jl
+++ b/src/surface_conditions/surface_setups.jl
@@ -91,8 +91,9 @@ function (::Soares)(params)
     z0 = FT(0.16) # 0.16 is taken from the Nieuwstadt paper.
     θ_flux = FT(0.06)
     q_flux = FT(2.5e-5)
+    ustar::FT = 0.28 # just to initilize grid mean covariances
     parameterization =
-        MoninObukhov(; z0, fluxes = θAndQFluxes(; θ_flux, q_flux))
+        MoninObukhov(; z0, fluxes = θAndQFluxes(; θ_flux, q_flux), ustar)
     return SurfaceState(; parameterization, T, p, q_vap)
 end