Tidy up configuration files. Add TOI561b. Fix doc links? Update tests

Author: nichollsh

test/runtests.jl

@@ -10,11 +10,11 @@ Pkg.activate(ROOT_DIR)
 
 # Include libraries
 using LoggingExtras
+using NCDatasets
 using AGNI
 
 @info "Begin AGNI tests"
 
-
 # Prepare
 RES_DIR         = joinpath(ROOT_DIR,"res/")
 OUT_DIR         = joinpath(ROOT_DIR,"out/")
@@ -642,7 +642,7 @@ if suite > 9
         @info "Pass"
     else
         @warn "Fail"
-        display(atmos.flux_u_lw)
+        show(atmos.flux_u_lw)
         failed += 1
     end
     total += 1
@@ -665,19 +665,18 @@ if suite > 9
             @info "Pass"
         else
             @warn "Fail"
-            display(atmos.flux_tot)
+            show(atmos.flux_tot)
             failed += 1
         end
         total += 1
-        atmosphere.deallocate!(atmos)
         @info "--------------------------"
     end
 end
 
-# -------------
-# Run example TOML config file
-# -------------
 if suite > 15
+    # -------------
+    # Run example TOML config file (writes to output folder)
+    # -------------
     @info " "
     @info "Testing model with energy-conserving TP solver"
     cfg = AGNI.open_config(joinpath(TEST_DIR, "test.toml"))
@@ -691,10 +690,83 @@ if suite > 15
         failed += 1
     end
     total += 1
-    atmosphere.deallocate!(atmos)
+    @info "--------------------------"
+
+    # -------------
+    # Compare result from NetCDF
+    # -------------
+    @info " "
+    @info "Testing values from model solution"
+
+    # Read result
+    @debug "ALL DEBUG SUPPRESSED"
+    with_logger(MinLevelLogger(current_logger(), Logging.Info-200)) do
+
+        # open netcdf
+        ds = Dataset(joinpath(OUT_DIR,"atm.nc"),"r")
+
+        # read profiles from netCDF file
+        arr_o_tmp::Array{Float64,1} = ds["tmpl"][:]
+        arr_o_flN::Array{Float64,1} = ds["fl_N"][:]
+        arr_o_flC::Array{Float64,1} = ds["fl_cnvct"][:]
+        arr_o_Kzz::Array{Float64,1} = ds["Kzz"][:]
+
+        # close netcdf
+        close(ds)
+    end
+    @debug "ALL DEBUG RESTORED"
+
+    # temperature profile
+    @info "Temperature..."
+    arr_e[:] .= [160.5675648884, 171.994064313637, 177.938575310175, 179.113900851404,  179.801478507666, 179.167818376284, 179.40614826252, 181.556769798685,  183.007095076024, 182.624208591575, 183.399201292413, 186.261911326026,  190.412634382101, 195.47048174129, 201.251679339825, 207.654691790094,  214.451046157178, 221.848979602947, 231.737439525989, 246.412351141343,  263.513451113498, 288.073705588398, 320.936573630417, 355.668949498865,  393.166000909574, 430.332142915339, 461.765909449321, 488.839407157943,  516.896086763742, 545.950964338871, 573.226076102865, 596.498543067942,  613.203600564291, 622.65575000879, 627.239385241944, 629.635777119968,  631.102258523775, 631.936413339924, 632.289738849541, 632.396879253831,  632.422477552567, 632.428125540173, 632.429337440917, 632.429439784017,  632.429440335934]
+    if maximum((arr_e[:] .- arr_o_tmp[:]) ./ arr_e[:]) < rtol + 0.2
+        @info "Pass"
+    else
+        @warn "Fail"
+        show(arr_o_tmp)
+        failed += 1
+    end
+    total += 1
+
+    # radiative flux
+    @info "Radiative flux..."
+    arr_e[:] .= [-1.70936355061713e-05, -0.0001848507873774, -2.19587959691125e-05, -3.68052697012899e-05, -1.17535213348674e-05, -9.21098234130113e-06, -2.99803821803835e-05, -4.89456000991595e-05, -1.5358869575266e-05, -1.09188006263139e-05, -3.93173775137257e-05, -0.000354796292072024, -0.00165987941761614, -0.00528027329954739, -0.0158055913856288, -0.0433923529017761, -0.11140604524968, -0.308141836228856, -1.46423434726591, -9.77401066606802, -37.3100359467623, -38.7488777778792, -39.2155408656643, -23.6328050591985, -7.23626887173242, -0.00023511365176887, -0.000176458639629118, -0.000168000405722069, -0.000180597452342113, -0.000171841531511063, -0.000151788906691763, -0.00011949688596502, -7.29475105316624e-05, -3.52666797951429e-05, -1.70943386361699e-05, -1.02762551650315e-05, -6.48362776556333e-06, -3.05875096534569e-06, -9.87984617728532e-07, -2.40686721166353e-07, -5.31945902250514e-08, -1.16863944068938e-08, -1.6438207365123e-08, 1.3533281159821e-09, -1.25751721498093e-05 ]
+    if maximum((arr_e[:] .- arr_o_flN[:]) ./ arr_e[:]) < rtol + 1e-5
+        @info "Pass"
+    else
+        @warn "Fail"
+        show(arr_o_flN)
+        failed += 1
+    end
+    total += 1
+
+    # convective flux
+    @info "Convective flux..."
+    arr_e[:] .= [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1.70370297292099, 22.4258287268845, 17.7152047690876, 7.20391869209392, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
+    if maximum((arr_e[:] .- arr_o_flC[:]) ./ arr_e[:]) < rtol + 1e-5
+        @info "Pass"
+    else
+        @warn "Fail"
+        show(arr_o_flC)
+        failed += 1
+    end
+
+
+    # eddy diffusion coefficients
+    @info "Kzz..."
+    arr_e[:] .= [343861.803277211, 283750.654425665, 234147.652108032, 193215.846845093, 159439.40985939, 131567.497342447, 108567.927918327, 89588.9578396376, 73927.7383356734, 61004.2869927183, 50340.0092478434, 41539.9745820394, 34278.2910464086, 28286.0364958031, 23341.2995869213, 19260.9617288462, 15893.9156467514, 13115.4694216393, 10822.7287707491, 8930.78656048291, 7369.57843796924, 6081.2881357725, 13638.9561240586, 11895.0041403355, 8254.94954692682, 8254.94954692682, 8254.94954692682, 8254.94954692682, 8254.94954692682, 8254.94954692682, 8254.94954692682, 8254.94954692682, 8254.94954692682, 8254.94954692682, 8254.94954692682, 8254.94954692682, 8254.94954692682, 8254.94954692682, 8254.94954692682, 8254.94954692682, 8254.94954692682, 8254.94954692682, 8254.94954692682, 8254.94954692682, 8254.94954692682]
+    if maximum((arr_e[:] .- arr_o_Kzz[:]) ./ arr_e[:]) < rtol + 1e-2
+        @info "Pass"
+    else
+        @warn "Fail"
+        show(arr_o_Kzz)
+        failed += 1
+    end
+    total += 1
     @info "--------------------------"
 end
 
+
 # -------------
 # Inform at end
 # -------------

test/test.toml

@@ -22,7 +22,7 @@ title = "Unit tests configuration"
 [files]
     input_sf        = "../res/spectral_files/Dayspring/48/Dayspring.sf"
     input_star      = "blackbody"
-    output_dir      = "out/"
+    output_dir      = "../out/"
 
 [composition]
     p_surf          = 7000.0
@@ -62,8 +62,8 @@ title = "Unit tests configuration"
 
 [plots]
     at_runtime      = false
-    temperature     = false
-    fluxes          = false
+    temperature     = true
+    fluxes          = true
     contribution    = false
     emission        = false
     albedo          = false