clean up tc1

experiments/ClimaCore/tc1_heat-diffusion-with-slab/run.jl

@@ -88,10 +88,8 @@ import ClimaCore: Fields, Domains, Topologies, Meshes, DataLayouts, Operators, G
 import ClimaTimeSteppers as CTS
 
 using Base: show_supertypes
-# using OrdinaryDiffEq: ODEProblem, solve, SSPRK33
 import SciMLBase: step!, ODEProblem, init
 
-
 using Logging: global_logger
 using TerminalLoggers: TerminalLogger
 
@@ -148,22 +146,17 @@ We also use this model to calculate and accumulate the downward surface fluxes,
 """
 function ∑tendencies_atm!(du, u, cache, t)
     parameters, T_sfc = cache
-    T = u.T_atm # u.x = vector of prognostic variables from DifferentialEquations
+    T = u.T_atm
     F_sfc = calculate_flux(T_sfc[1], parent(T)[1], parameters)
     ## set BCs
-    # C3 = Geometry.Covariant3Vector
     C3 = Geometry.WVector
 
 
     bcs_bottom = Operators.SetValue(C3(F_sfc)) # F_sfc is converted to a Cartesian vector in direction 3 (vertical)
     bcs_top = Operators.SetValue(C3(FT(0)))
 
-    ᶠgradᵥ = Operators.GradientC2F()#(top = bcs_top) # Dirichlet BC (center-to-face)
+    ᶠgradᵥ = Operators.GradientC2F() # Dirichlet BC (center-to-face)
     ᶜdivᵥ = Operators.DivergenceF2C(bottom = bcs_bottom, top = bcs_top) # Neumann BC (face-to-center)
-    # divf2c_water = Operators.DivergenceF2C(
-    #     top = Operators.SetValue(Geometry.WVector.(top_flux_bc)),
-    #     bottom = Operators.SetValue(Geometry.WVector.(bot_flux_bc)),
-    # )
 
     ## tendency calculations
     @. du.T_atm = ᶜdivᵥ(parameters.μ * ᶠgradᵥ(T)) # dT/dt
@@ -214,7 +207,6 @@ stepping = (;
     timerange = (0.0, 6.0),
     Δt_coupler = 0.1,
     odesolver = CTS.ExplicitAlgorithm(CTS.RK4()),
-    # odesolver = SSPRK33(),
     nsteps_atm = 8, # number of timesteps of atm per coupling cycle
     nsteps_lnd = 1, # number of timesteps of lnd per coupling cycle
 );
@@ -261,7 +253,7 @@ function coupler_solve!(stepping, ics, parameters)
 
         ## STEP ATMOS
         ## pre_atmos
-        integ_atm.p[2] .= coupler_get_(coupler_T_lnd) # integ_atm.p is the parameter vector of an ODEProblem from DifferentialEquations
+        integ_atm.p[2] .= coupler_get_(coupler_T_lnd) # integ_atm.p is the parameter vector of an ODEProblem from SciMLBase
         integ_atm.u.atm_F_sfc .= 0.0 # surface flux to be accumulated
 
         ## run atmos
@@ -291,12 +283,13 @@ sol_atm, sol_lnd = integ_atm.sol, integ_lnd.sol;
 
 # ## Postprocessing and Visualization
 
-# Each integrator output (`sol_atm`, `sol_lnd`), contains the DifferentialEquations variable `.u` (the name is hard coded).
-# If `ArrayPartition` was used for combining multiple prognostic variables, `u` will include an additional variable `x` (also hard coded)
+# Each integrator output (`sol_atm`, `sol_lnd`), contains the SciMLBase variable `.u` (the name is hard coded).
+# If multiple prognostic variables were solved for, `u` will contain all of those.
 # `parent()` accesses the `Field` values.
-# So, for example, the structure of `u` from Model 1 is:
-#  TODO update comments
-# `parent(sol_atm.u[<time-index>].x[<ArrayPartition-index>])[<z-index>,<variable-index>]`
+# So, for example, the structure of `u` from the atmosphere model is:
+# `parent(sol_atm.u[<time-index>].T_atm)[<z-index>,<variable-index>]`
+# and
+# `parent(sol_atm.u[<time-index>].atm_F_sfc)[<z-index>,<variable-index>]`
 
 ENV["GKSwstype"] = "nul"
 import Plots