Removed the now-redundant advective heat flux array, since this is handled by the new deep_heating functionality. Updated configs to remove advect key. Updated plot function

nichollsh · nichollsh · commit 8fb74f721e6d · 2026-02-23T21:27:46.000Z
diff --git a/docs/src/model/assets/model_flowchart.svg b/docs/src/model/assets/model_flowchart.svg
diff --git a/docs/src/usage.md b/docs/src/usage.md
@@ -213,7 +213,6 @@ Parameters that describe how the model should treat the physics.
 | `real_gas      `  | Use real-gas equation(s) of state where possible (true/false) |
 | `thermo_funct  `  | Use temperature-dependent thermodynamic properties (true/false) |
 | `sensible_heat `  | Include turbulent sensible heat transport at the surface (true/false) |
-| `advection `      | Include advective heat transport into each cell (true/false) |
 | `convection    `  | Include vertical heat transport associated with convection (true/false) |
 | `convection_crit` | Criterion for convective stability. Options: (s)chwarzschild, (l)edoux |
 | `latent_heat   `  | Include vertical heat transport from condensation and evaporation (true/false) |
diff --git a/res/config/default.toml b/res/config/default.toml
@@ -66,14 +66,13 @@ title = "Default"                       # Name for this configuration file
     oceans          = false                     # Model ocean formation - check saturation at surface
     rainout         = false                     # Model rainout - phase change impacts gas mixing ratios, not just energy fluxes
     latent_heat     = false                     # Include heat release from phase change
-    advection       = false                     # Include advective heat flux from dynamics
     convection_crit = "s"                       # Stability criterion for convection. Options: (s)chwarzschild or (l)edoux.
     convection      = true                      # Include heat transport by convection
 
     [physics.deep_heating]
-        Pmid            = 1e-3              # Center of Gaussian heating profile [bar]
+        Pmid            = 1.0              # Center of Gaussian heating profile [bar]
         Pwid            = 1.0               # Width of Gaussian in log-Pascal units.
-        power_mode      = "off"             # Power mode for heating (off, rel, abs)
+        power_mode      = "abs"             # Power mode for heating (off, rel, abs)
         norm_method     = "pressure"        # Normalisation coordinate: "pressure" (legacy dF/dP), or "mass" (dm-weighted).
         domain          = "clamp"           # How to handle Pmid outside domain (clamp, boundary_flux)
         flux_rel        = 0.0               # Set flux by fraction of instellation, used for power_mode="rel".
diff --git a/res/config/hotdry.toml b/res/config/hotdry.toml
@@ -54,11 +54,10 @@ title = "Hot and dry"
     sensible_heat   = true
     conduction      = true
     latent_heat     = false
-    advection       = false
     convection      = true
     convection_crit = "l"
     rainout         = false
-    oceans          = false 
+    oceans          = false
     grey_lw         = 5e-3
     grey_sw         = 2e-3
 
diff --git a/res/config/physics/chemcond.toml b/res/config/physics/chemcond.toml
@@ -56,7 +56,6 @@ title = "Chemistry and condensation together"
     real_gas        = false
     thermo_funct    = true
     sensible_heat   = true
-    advection       = false
     conduction      = true
     convection      = true
     convection_crit = "s"
diff --git a/res/config/physics/chemistry.toml b/res/config/physics/chemistry.toml
@@ -55,7 +55,6 @@ title = "Chemistry by metallicity"
     thermo_funct    = true
     sensible_heat   = false
     conduction      = true
-    advection       = false
     latent_heat     = false
     convection      = true
     convection_crit = "l"
diff --git a/res/config/physics/cloud.toml b/res/config/physics/cloud.toml
@@ -52,7 +52,6 @@ title = "Cloud radiative properties test"
     sensible_heat   = false
     conduction      = true
     latent_heat     = false
-    advection       = false
     convection      = true
     convection_crit = "s"
     rainout         = true
diff --git a/res/config/physics/greygas.toml b/res/config/physics/greygas.toml
@@ -57,7 +57,6 @@ title = "Grey gas"
     thermo_funct    = true
     sensible_heat   = false
     conduction      = false
-    advection       = false
     latent_heat     = false
     convection      = true
     convection_crit = "s"
diff --git a/res/config/physics/lbl_validation.toml b/res/config/physics/lbl_validation.toml
@@ -55,7 +55,6 @@ title = "Line-by-line validation tests"
     real_gas        = false
     thermo_funct    = true
     sensible_heat   = false
-    advection       = false
     conduction      = true
     latent_heat     = false
     convection      = false
diff --git a/res/config/physics/ocean.toml b/res/config/physics/ocean.toml
@@ -56,7 +56,6 @@ title = "Ocean formation test"
     real_gas        = false
     thermo_funct    = true
     sensible_heat   = true
-    advection       = false
     conduction      = true
     latent_heat     = true
     convection      = true
diff --git a/res/config/planets/55cnce_chem.toml b/res/config/planets/55cnce_chem.toml
@@ -51,7 +51,6 @@ title = "Roughly 55 Cancri e @ fO2=IW"
     thermo_funct    = true
     sensible_heat   = false
     conduction      = true
-    advection       = false
     latent_heat     = false
     convection      = true
     convection_crit = "l"
diff --git a/res/config/planets/k218b.toml b/res/config/planets/k218b.toml
@@ -52,7 +52,6 @@ title = "K2-18 b, mixed"
     real_gas        = false
     thermo_funct    = true
     sensible_heat   = true
-    advection       = false
     conduction      = true
     latent_heat     = false
     convection      = true
diff --git a/res/config/planets/l9859d.toml b/res/config/planets/l9859d.toml
@@ -53,7 +53,6 @@ title = "L 98-59 d"
     real_gas        = true
     thermo_funct    = true
     sensible_heat   = true
-    advection       = false
     conduction      = true
     latent_heat     = false
     convection      = true
diff --git a/res/config/planets/toi561b.toml b/res/config/planets/toi561b.toml
@@ -52,7 +52,6 @@ title = "TOI-561 b"
     thermo_funct    = true
     sensible_heat   = false
     conduction      = true
-    advection       = false
     latent_heat     = false
     convection      = true
     convection_crit = "l"
diff --git a/res/config/planets/trappist1b.toml b/res/config/planets/trappist1b.toml
@@ -52,7 +52,6 @@ title = "TRAPPIST-1 b"
     real_gas        = true
     thermo_funct    = true
     sensible_heat   = true
-    advection       = false
     conduction      = true
     latent_heat     = false
     convection      = true
diff --git a/res/config/struct_grid.toml b/res/config/struct_grid.toml
@@ -59,7 +59,6 @@ title = "Base config for structure calcs"
     thermo_funct    = true
     sensible_heat   = false
     conduction      = false
-    advection       = false
     latent_heat     = false
     convection      = true
     convection_crit = "s"
diff --git a/res/config/transparent.toml b/res/config/transparent.toml
@@ -52,7 +52,6 @@ title = "Transparent atmosphere"
     thermo_funct    = false
     sensible_heat   = false
     conduction      = true
-    advection       = false
     latent_heat     = false
     convection      = false
     convection_crit = "s"
diff --git a/src/AGNI.jl b/src/AGNI.jl
@@ -413,7 +413,6 @@ module AGNI
         #    solver stuff
         incl_convect::Bool     = cfg["physics"]["convection"]
         incl_conduct::Bool     = cfg["physics"]["conduction"]
-        incl_advect::Bool      = cfg["physics"]["advection"]
         incl_sens::Bool        = cfg["physics"]["sensible_heat"]
         incl_latent::Bool      = cfg["physics"]["latent_heat"]
         sol_type::Int          = cfg["execution"]["solution_type"]
@@ -589,7 +588,7 @@ module AGNI
         if sol == "none"
             energy.calc_fluxes!(atmos, radiative=true, latent_heat=incl_latent,
                                 convective=incl_convect, sens_heat=incl_sens,
-                                conductive=incl_conduct, advective=incl_advect,
+                                conductive=incl_conduct,
                                 deep=incl_deep,
                                 calc_cf=Bool(cfg["plots"]["contribution"]))
 
@@ -610,7 +609,7 @@ module AGNI
             solver_success = solver.solve_energy!(atmos, sol_type=sol_type,
                                 conduct=incl_conduct, chem=chem,
                                 convect=incl_convect, latent=incl_latent,
-                                sens_heat=incl_sens, advect=incl_advect,
+                                sens_heat=incl_sens, deep=incl_deep,
                                 max_steps=Int(cfg["execution"]["max_steps"]),
                                 max_runtime=Float64(cfg["execution"]["max_runtime"]),
                                 conv_atol=conv_atol,
@@ -683,7 +682,7 @@ module AGNI
             plotting.plot_fluxes(atmos, joinpath(atmos.OUT_DIR,"plot_fluxes.png"),
                                     incl_mlt=incl_convect, incl_eff=(sol_type==3),
                                     incl_cdct=incl_conduct, incl_latent=incl_latent,
-                                    incl_advect=incl_advect, incl_deep=incl_deep)
+                                    incl_deep=incl_deep)
         cfg["plots"]["emission"] && \
             plotting.plot_emission(atmos, joinpath(atmos.OUT_DIR,"plot_emission.png"))
         cfg["plots"]["albedo"] && \
diff --git a/src/atmosphere.jl b/src/atmosphere.jl
@@ -282,9 +282,6 @@ module atmosphere
         cloud_val_l::Float64                #  |-> Default scalar values to above arrays
         cloud_val_f::Float64                # /
 
-        # Cell-internal heating
-        flux_advect::Array{Float64, 1}     # Energy flux advected into each cell [W m-2], treated as entering into its bottom edge
-
         # Deep atmospheric heating
         deepheat_norm_method::Symbol    # Normalisation method for deep heating (:pressure or :mass)
         deepheat_Pmid::Float64          # Deposition pressure centre [Pa]
@@ -2362,8 +2359,6 @@ module atmosphere
         atmos.w_conv =            zeros(Float64, atmos.nlev_l)  # convective velocity [m s-1]
         atmos.λ_conv =            zeros(Float64, atmos.nlev_l)  # mixing length [m]
 
-        atmos.flux_advect =       zeros(Float64, atmos.nlev_l)  # advective heat flux
-
         atmos.flux_tot =          zeros(Float64, atmos.nlev_l)
         atmos.flux_dif =          zeros(Float64, atmos.nlev_c)
         atmos.flux_deep =         zeros(Float64, atmos.nlev_l)  # Deep atmospheric heating flux
diff --git a/src/energy.jl b/src/energy.jl
@@ -958,7 +958,6 @@ module energy
     - `convective::Bool`                include MLT convection flux
     - `sens_heat::Bool`                 include TKE sensible heat flux
     - `conductive::Bool`                include conductive heat flux
-    - `advective::Bool`                 include advective heat flux
     - `deep::Bool`                      include deep heating flux (layer-internal production)
     - `convect_sf::Float64`             scale factor applied to convection fluxes
     - `latent_sf::Float64`              scale factor applied to phase change fluxes
@@ -969,8 +968,7 @@ module energy
     """
     function calc_fluxes!(atmos::atmosphere.Atmos_t;
                           radiative::Bool=false, latent_heat::Bool=false, convective::Bool=false,
-                          sens_heat::Bool=false, conductive::Bool=false, advective::Bool=false,
-                          deep::Bool=false,
+                          sens_heat::Bool=false, conductive::Bool=false, deep::Bool=false,
                           convect_sf::Float64=1.0, latent_sf::Float64=1.0,
                           calc_cf::Bool=false)::Bool
 
@@ -979,7 +977,7 @@ module energy
         ok::Bool = true
 
         # Warn if no flux terms are enabled
-        if !(radiative || latent_heat || convective || sens_heat || conductive || advective || deep)
+        if !(radiative || latent_heat || convective || sens_heat || conductive || deep)
             @warn "No flux terms enabled in call to `calc_fluxes!`"
             ok = false
         end
@@ -1017,11 +1015,6 @@ module energy
             @. atmos.flux_tot += atmos.flux_cdct
         end
 
-        # +Advection
-        if advective
-            @. atmos.flux_tot += atmos.flux_advect
-        end
-
         # +Deep atmospheric heating
         # Note: flux_deep is computed but NOT added to flux_tot.
         # For sol_type>=3, heating is added directly to the solver residual.
diff --git a/src/plotting.jl b/src/plotting.jl
@@ -307,7 +307,7 @@ module plotting
                             size_x::Int=550, size_y::Int=400,
                             incl_eff::Bool=false, incl_mlt::Bool=true,
                             incl_cdct::Bool=true, incl_latent::Bool=true,
-                            incl_deep::Bool=true, incl_advect::Bool=true,
+                            incl_deep::Bool=true, 
                             title::String=""
                         )
 
@@ -331,7 +331,7 @@ module plotting
         col_t::String = "#ff4400"
         col_o::String = "#66CD00"
         col_p::String = "#ecb000"
-        col_a::String = "#7700bd"
+        col_d::String = "#8B008B"
 
         alpha = 0.7
         w = 2.0
@@ -386,15 +386,9 @@ module plotting
 
         # Deep heating
         if incl_deep
-            col_d::String = "#8B008B"  # Dark magenta for deep heating
             plot!(plt, _symlog.(atmos.flux_deep), arr_P, label="Deep", lw=w*1.2, lc=col_d, ls=:solid, linealpha=alpha)
         end
 
-        # Advection
-        if incl_advect
-            plot!(plt, _symlog.(atmos.flux_advect), arr_P, label="Advect", lw=w*1.2, lc=col_a, ls=:solid, linealpha=alpha)
-        end
-
         # Sensible heat
         scatter!(plt, [_symlog(atmos.flux_sens)], [arr_P[end]], markershape=:utriangle, markercolor=col_r, label="Sensible")
 
diff --git a/src/solver.jl b/src/solver.jl
@@ -151,7 +151,7 @@ module solver
     - `sens_heat::Bool`                 include sensible heating at the surface
     - `conduct::Bool`                   include conductive heat transport within the atmosphere
     - `latent::Bool`                    include latent heat exchange (condensation/evaporation)
-    - `advect::Bool`                    include advective heat exchange (dynamics)
+    - `deep::Bool`                      include deep heat production (e.g. from dynamics)
     - `rainout::Bool`                   allow rainout (phase change impacts mixing ratios, not just energy fluxes)
     - `oceans::Bool`                    check surface saturation (ocean formation)
 
@@ -184,7 +184,7 @@ module solver
                             sol_type::Int=1,
                             chem::Bool=false,
                             convect::Bool=true, sens_heat::Bool=true,
-                            conduct::Bool=true, latent::Bool=true, advect::Bool=true,
+                            conduct::Bool=true, latent::Bool=true, deep::Bool=true,
                             rainout::Bool=true, oceans::Bool=true,
                             dx_min::Float64=1e-7, dx_max::Float64=400.0,
                             tmp_pad::Float64 = 5.0,
@@ -362,7 +362,7 @@ module solver
             # Calculate fluxes
             step_ok &= energy.calc_fluxes!(atmos, radiative=true,
                                 latent_heat=latent, convective=convect, sens_heat=sens_heat,
-                                conductive=conduct, advective=advect,
+                                conductive=conduct, deep=deep,
                                 convect_sf=easy_sf, latent_sf=easy_sf)
 
             # Calculate residuals subject to the solution type
diff --git a/test/runtests.jl b/test/runtests.jl
@@ -1,6 +1,6 @@
 #!/usr/bin/env -S julia --color=yes --startup-file=no
 # Run this function from inside the `test/` folder
-# e.g. as `julia --project=.. runtests.jl `
+# e.g. as `julia --project=.. runtests.jl`
 
 # Get AGNI root directory
 ROOT_DIR = abspath(joinpath(dirname(abspath(@__FILE__)),"../"))
diff --git a/test/test.toml b/test/test.toml
@@ -57,7 +57,6 @@ title = "Unit tests configuration"
     real_gas        = false
     thermo_funct    = true
     sensible_heat   = true
-    advection       = false
     conduction      = true
     latent_heat     = true
     convection      = true
diff --git a/test/test_integration.jl b/test/test_integration.jl
@@ -286,7 +286,7 @@ TEST_DIR        = joinpath(ROOT_DIR,"test/")
         # -------------
         # Test flux calculation
         # -------------
-        energy.calc_fluxes!(atmos, radiative=true, convective=true, conductive=true, sens_heat=true, latent_heat=true, advective=true)
+        energy.calc_fluxes!(atmos, radiative=true, convective=true, conductive=true, sens_heat=true, latent_heat=true, deep=true)
         val_e = 8518.663363443498  # from previous tests
         val_o = atmos.flux_tot[atmos.nlev_c-10]
         test_pass = isapprox(val_e, val_o; rtol=1e-3)
