From 9e376b02966dc78bed1a7b41670b6de7bbc642a5 Mon Sep 17 00:00:00 2001
From: Anna Jaruga <ajaruga@caltech.edu>
Date: Mon, 4 Dec 2023 23:03:31 -0800
Subject: [PATCH] more review comments, add CF to new diagnostics

---
 examples/hybrid/driver.jl           |  6 +++---
 src/cache/cloud_fraction.jl         | 12 ++++++------
 src/cache/precomputed_quantities.jl |  2 +-
 src/callbacks/callbacks.jl          |  2 +-
 src/diagnostics/core_diagnostics.jl | 16 ++++++++++++++++
 5 files changed, 27 insertions(+), 11 deletions(-)

diff --git a/examples/hybrid/driver.jl b/examples/hybrid/driver.jl
index 6d7ea394794..14a96e0ddae 100644
--- a/examples/hybrid/driver.jl
+++ b/examples/hybrid/driver.jl
@@ -177,8 +177,8 @@ if config.parsed_args["check_precipitation"]
         )
 
         # cloud fraction diagnostics
-        @assert !any(isnan, sol.prob.p.precomputed.cloud_fraction[colidx])
-        @test minimum(sol.prob.p.precomputed.cloud_fraction[colidx]) >= FT(0)
-        @test maximum(sol.prob.p.precomputed.cloud_fraction[colidx]) <= FT(1)
+        @assert !any(isnan, sol.prob.p.precomputed.ᶜcloud_fraction[colidx])
+        @test minimum(sol.prob.p.precomputed.ᶜcloud_fraction[colidx]) >= FT(0)
+        @test maximum(sol.prob.p.precomputed.ᶜcloud_fraction[colidx]) <= FT(1)
     end
 end
diff --git a/src/cache/cloud_fraction.jl b/src/cache/cloud_fraction.jl
index 57794507935..b455927aba6 100644
--- a/src/cache/cloud_fraction.jl
+++ b/src/cache/cloud_fraction.jl
@@ -3,7 +3,7 @@ import ClimaCore.RecursiveApply: rzero, ⊞, ⊠
 
 # TODO: write a test with scalars that are linear with z
 """
-    Diagnose horizntal covariances based on vertical gradients
+    Diagnose horizontal covariances based on vertical gradients
     (i.e. taking turbulence production as the only term)
 """
 function covariance_from_grad(coeff, ᶜmixing_length, ᶜ∇Φ, ᶜ∇Ψ)
@@ -15,8 +15,8 @@ end
 """
 function set_cloud_fraction!(Y, p, ::DryModel)
     FT = eltype(Y)
-    (; cloud_fraction) = p.precomputed
-    @. cloud_fraction = FT(0)
+    (; ᶜcloud_fraction) = p.precomputed
+    @. ᶜcloud_fraction = FT(0)
 end
 function set_cloud_fraction!(Y, p, ::Union{EquilMoistModel, NonEquilMoistModel})
     (; SG_quad, params) = p
@@ -24,7 +24,7 @@ function set_cloud_fraction!(Y, p, ::Union{EquilMoistModel, NonEquilMoistModel})
     FT = eltype(params)
     thermo_params = CAP.thermodynamics_params(params)
     ᶜdz = Fields.Δz_field(axes(Y.c))
-    (; ᶜts, ᶜp, cloud_fraction) = p.precomputed
+    (; ᶜts, ᶜp, ᶜcloud_fraction) = p.precomputed
 
     ᶜqₜ = p.scratch.ᶜtemp_scalar
     ᶜθ = p.scratch.ᶜtemp_scalar_2
@@ -33,7 +33,7 @@ function set_cloud_fraction!(Y, p, ::Union{EquilMoistModel, NonEquilMoistModel})
 
     coeff = FT(2.1) # TODO - move to parameters
 
-    @. cloud_fraction = quad_loop(
+    @. ᶜcloud_fraction = quad_loop(
         SG_quad,
         ᶜp,
         ᶜqₜ,
@@ -70,7 +70,7 @@ where:
   - qt′qt′, θl′θl′, θl′qt′ are the (co)variances of q_tot and liquid ice potential temperature
   - thermo params are the thermodynamics parameters
 
-The function trnasforms and imposes additional limits on the quadrature points.
+The function transforms and imposes additional limits on the quadrature points.
 It returns cloud fraction computed as a sum over quadrature points.
 """
 function quad_loop(
diff --git a/src/cache/precomputed_quantities.jl b/src/cache/precomputed_quantities.jl
index f81044a5ca9..2d1aa402895 100644
--- a/src/cache/precomputed_quantities.jl
+++ b/src/cache/precomputed_quantities.jl
@@ -54,7 +54,7 @@ function precomputed_quantities(Y, atmos)
         ᶜh_tot = similar(Y.c, FT),
         sfc_conditions = Fields.Field(SCT, Spaces.level(axes(Y.f), half)),
     )
-    cloud_diagnostics = (; cloud_fraction = similar(Y.c, FT),)
+    cloud_diagnostics = (; ᶜcloud_fraction = similar(Y.c, FT),)
     advective_sgs_quantities =
         atmos.turbconv_model isa PrognosticEDMFX ?
         (;
diff --git a/src/callbacks/callbacks.jl b/src/callbacks/callbacks.jl
index 9804c75cb97..b27450e6651 100644
--- a/src/callbacks/callbacks.jl
+++ b/src/callbacks/callbacks.jl
@@ -186,7 +186,7 @@ function common_diagnostics(p, ᶜu, ᶜts)
         specific_enthalpy = TD.specific_enthalpy.(thermo_params, ᶜts),
         buoyancy = CAP.grav(p.params) .* (p.core.ᶜρ_ref .- ᶜρ) ./ ᶜρ,
         density = TD.air_density.(thermo_params, ᶜts),
-        cloud_fraction_gm = p.precomputed.cloud_fraction,
+        cloud_fraction_gm = p.precomputed.ᶜcloud_fraction,
     )
     if !(p.atmos.moisture_model isa DryModel)
         diagnostics = (;
diff --git a/src/diagnostics/core_diagnostics.jl b/src/diagnostics/core_diagnostics.jl
index 007b74da34b..f038e5953e7 100644
--- a/src/diagnostics/core_diagnostics.jl
+++ b/src/diagnostics/core_diagnostics.jl
@@ -210,6 +210,22 @@ add_diagnostic_variable!(
     end,
 )
 
+###
+# Cloud fraction (3d)
+###
+add_diagnostic_variable!(
+    short_name = "cf",
+    long_name = "Cloud fraction",
+    units = "%",
+    compute! = (out, state, cache, time) -> begin
+        FT = eltype(cache.precomputed.ᶜcloud_fraction)
+        if isnothing(out)
+            return copy(cache.precomputed.ᶜcloud_fraction) .* FT(100)
+        else
+            out .= cache.precomputed.ᶜcloud_fraction .* FT(100)
+        end
+    end,
+)
 
 ###
 # Relative humidity (3d)