Comments from copilot review. Safe imports and fix syntax. Type checking for symbols. Copy arrays for globe

Author: nichollsh

src/compose/fastchem.jl

@@ -170,9 +170,9 @@ module fastchem
         end # end write metallicities
 
         # Work out which indices are visited by fc
-        fc_levels::Array{Int,1} = Float64[atmos.nlev_c]
+        fc_levels::Array{Int64,1} = Int64[atmos.nlev_c]
         if !atmos.fastchem_wellmixed
-            fc_levels = collect(Float64,1:atmos.nlev_c)
+            fc_levels = collect(Int64,1:atmos.nlev_c)
         end
 
         # Write PT profile every time

src/interface/paths.jl

@@ -15,8 +15,16 @@ module paths
     const FWL_DATA::String = joinpath(get(ENV, "FWL_DATA", RES_DIR))
     export FWL_DATA
 
-    # Get path to other data dirs (can be overridden)
-    function get_dir(name::String)::String
+    """
+    **Get path to other data dirs (can be overridden)**
+
+    Arguments:
+    - `name::String` name of the directory to get
+
+    Returns:
+    - `String` path to the requested directory, or `nothing` if the name is unknown.
+    """
+    function get_dir(name::String)::Union{String, Nothing}
 
         if name == "thermodynamics"
             return joinpath(RES_DIR, "thermodynamics")

src/solver/globe.jl

@@ -3,8 +3,9 @@ module solve_globe
     using Printf
     using LoggingExtras
 
-    import ..multicol
     import ..atmosphere
+    import ..multicol
+    include("energy.jl"); import .solve_energy: solve_energy!
 
     """
     **Solve multi-column problem for radiative-convective equilibrium across the globe**
@@ -64,13 +65,14 @@ module solve_globe
             conv = succ
 
             #   Determine a reasonable target value
-            conv_val = median([atmos.flux_tot[end] for atmos in globe.atmos_arr])
+            conv_val = median([atmos.flux_tot[1] for atmos in globe.atmos_arr])
             @info @sprintf("    Convergence target = %+.2e W m-2", conv_val)
 
             #    Check all columns
             for (iatmos,atmos) in enumerate(globe.atmos_arr)
-                resid_val = atmos.flux_tot[end]-conv_val
-                conv &= (abs(resid_val) < globe_atol + globe_rtol * conv_val)
+                resid_val = atmos.flux_tot[1]-conv_val
+                conv_val  = globe_atol + globe_rtol * abs(conv_val)
+                conv &= (abs(resid_val) < conv_val)
                 @info @sprintf("    Column %d: resid = %+.2e W m-2 (%+.2f%%)",
                                 iatmos, resid_val, resid_val/conv_val*100
                                 )

src/solver/transparent.jl

@@ -5,6 +5,7 @@ module solve_transparent
 
     import ..atmosphere
     import ..energy
+    import ..golden: gs_search
 
     """
     **Solve for energy balance with a transparent atmosphere.**
@@ -62,7 +63,7 @@ module solve_transparent
 
                 # Residual = radiative flux minus skin flux
                 energy.calc_fluxes!(atmos, radiative=true)
-                return (atmos.flux_tot[end-1] - energy.skin_flux(atmos))^2
+                return (atmos.flux_tot[1] - energy.skin_flux(atmos))^2
             end
 
             # Find solution for T_surf
@@ -84,7 +85,7 @@ module solve_transparent
 
                 # Residual = radiative flux minus desired flux
                 energy.calc_fluxes!(atmos, radiative=true)
-                return (atmos.flux_tot[end-1] - atmos.flux_int)^2
+                return (atmos.flux_tot[1] - atmos.flux_int)^2
             end
 
             # Find solution for T_surf
@@ -106,7 +107,7 @@ module solve_transparent
 
                 # Residual = radiative flux minus desired flux
                 energy.calc_fluxes!(atmos, radiative=true)
-                return (atmos.flux_u_lw[end-1] - atmos.target_olr)^2
+                return (atmos.flux_u_lw[1] - atmos.target_olr)^2
             end
 
             # Find solution for T_surf

src/state/layers.jl

@@ -207,10 +207,11 @@ module layers
             else
                 if HYDROGRAV_selfg
                     # gravity changes with mass and radius
-                    return phys.grav_accel(mj, rj)
+                    # approximate mass as constant for this part of the integration
+                    return phys.grav_accel(mj, r)
                 else
                     # gravity changes with radius only
-                    return g0 * (r0/rj)^2
+                    return g0 * (r0/r)^2
                 end
             end
         end
@@ -243,7 +244,7 @@ module layers
             rj += dp/6 * (k1 + 2*k2 + 2*k3 + k4)
 
             # Integrate mass enclosed ...
-            mj += 4 * pi * rj^2 * (-1 * dp) / gj
+            mj += 4 * pi * rj^2 * (-1 * dp) / _accel(rj) 
 
             # Integrate pressure (negative change )
             pj += dp

src/state/multicol.jl

@@ -26,7 +26,7 @@ module multicol
     SHARED_TYPES     = Union{AbstractArray, AbstractVector, Number, AbstractDict, AbstractString}
     PROTECTED_FIELDS = Symbol[:num_rt_eval, :tim_rt_eval]
     shared_fields = Symbol[]
-    for (field,type) in zip(fieldnames(atmosphere.Atmos_t), atmosphere.Atmos_t.types)
+    for (field,type) in zip(fieldnames(atmosphere.Atmos_t), fieldtypes(atmosphere.Atmos_t))
         if (type <: SHARED_TYPES) && !(field in PROTECTED_FIELDS)
             push!(shared_fields, field)
         end
@@ -204,7 +204,11 @@ module multicol
     """
     function copy_atmos_fields!(dst::atmosphere.Atmos_t, src::atmosphere.Atmos_t)::Bool
         for field in shared_fields
-            setfield!(dst, field, getfield(src, field))
+            if isa(getfield(src, field), AbstractArray)
+                copyto!(getfield(dst, field), getfield(src, field))
+            else
+                setfield!(dst, field, getfield(src, field))
+            end
         end
         return true
     end

src/util/style.jl

@@ -52,7 +52,7 @@ module style
         out::String = ""
         for c in gas
             if isnumeric(c)
-                d = parse(Int, c)
+                d = parse(Int, string(c))
                 out *= Char(parse(Int,"208$d", base=16))
             else
                 out *= c

test/test_consts.jl

@@ -50,25 +50,25 @@ using AGNI
         ("Fe",  5.584500e-02),
     ]
     for (elem, expected) in element_mmw_cases
-        @test isapprox(AGNI.phys.formulae._lookup_mmw[elem], expected; rtol=1e-6)
+        @test isapprox(AGNI.formulae._lookup_mmw[elem], expected; rtol=1e-6)
     end
 
     # All MMW values should be positive
-    for (species, mmw) in AGNI.phys.formulae._lookup_mmw
+    for (species, mmw) in AGNI.formulae._lookup_mmw
         @test mmw > 0.0  # MMW for all species should be positive
     end
 
     # -------------
     # Atom counts for key molecules
     # -------------
-    @test AGNI.phys.formulae._lookup_count_atoms["H2O"]["H"] == 2
-    @test AGNI.phys.formulae._lookup_count_atoms["H2O"]["O"] == 1
-    @test AGNI.phys.formulae._lookup_count_atoms["CO2"]["C"] == 1
-    @test AGNI.phys.formulae._lookup_count_atoms["CO2"]["O"] == 2
-    @test AGNI.phys.formulae._lookup_count_atoms["S8"]["S"] == 8
+    @test AGNI.formulae._lookup_count_atoms["H2O"]["H"] == 2
+    @test AGNI.formulae._lookup_count_atoms["H2O"]["O"] == 1
+    @test AGNI.formulae._lookup_count_atoms["CO2"]["C"] == 1
+    @test AGNI.formulae._lookup_count_atoms["CO2"]["O"] == 2
+    @test AGNI.formulae._lookup_count_atoms["S8"]["S"] == 8
 
     # All atom counts should be positive integers
-    for (molecule, atoms) in AGNI.phys.formulae._lookup_count_atoms
+    for (molecule, atoms) in AGNI.formulae._lookup_count_atoms
         for (element, count) in atoms
             @test count > 0  # Atom counts should be positive
             @test count == floor(count)  # Atom counts should be integers
@@ -79,10 +79,10 @@ using AGNI
     # Plotting colours: known gases and key elements must be present
     # -------------
     for gas in ["H2O", "CO2", "H2"]
-        @test haskey(lookup_colour, gas)
+        @test haskey(AGNI.style._lookup_colour, gas)
     end
     for elem in ["H", "C", "O", "N", "S", "Fe", "Si"]
-        @test haskey(lookup_colour, elem)
+        @test haskey(AGNI.style._lookup_colour, elem)
     end
 
     # -------------
@@ -100,10 +100,10 @@ using AGNI
     # For all molecules with defined atom counts, ensure constituent
     # elements are in elems_standard and have assigned colors
     # -------------
-    for (molecule, atoms_dict) in lookup_count_atoms
+    for (molecule, atoms_dict) in AGNI.formulae._lookup_count_atoms
         for element in keys(atoms_dict)
             @test element in AGNI.consts.elems_standard
-            @test haskey(lookup_colour, element)
+            @test haskey(AGNI.style._lookup_colour, element)
         end
     end
 
@@ -113,7 +113,7 @@ using AGNI
         # Check if it's a single element (1-2 character string, starts with uppercase)
         if length(species) <= 2 && occursin(r"^[A-Z][a-z]?$", species)
             @test species in AGNI.consts.elems_standard
-            @test haskey(lookup_colour, species)
+            @test haskey(AGNI.style._lookup_colour, species)
         end
     end
 
@@ -145,18 +145,18 @@ using AGNI
     # -------------
     # Liquid densities for ocean module
     # -------------
-    @test isapprox(lookup_liquid_rho["H2O"], 958.37; rtol=1e-5)
-    @test lookup_liquid_rho["CO2"] > lookup_liquid_rho["H2O"]
+    @test isapprox(AGNI.phys.density._lookup_liquid_rho["H2O"], 958.37; rtol=1e-5)
+    @test AGNI.phys.density._lookup_liquid_rho["CO2"] > AGNI.phys.density._lookup_liquid_rho["H2O"]
 
     # All liquid densities should be positive
-    for (species, rho) in lookup_liquid_rho
+    for (species, rho) in AGNI.phys.density._lookup_liquid_rho
         @test rho > 0.0  # All liquid densities should be positive
     end
 
     # -------------
     # Color assignments: all colors should be valid hex codes
     # -------------
-    for (species, color) in AGNI.phys.species.style._lookup_colour
+    for (species, color) in AGNI.style._lookup_colour
         @test occursin(r"^#[0-9A-Fa-f]{6}$", color)  # Valid hex color format
     end
 
@@ -165,7 +165,7 @@ using AGNI
     # -------------
     # Species with MMW should include key atmospheric gases
     for gas in ["H2O", "CO2", "H2", "N2", "CH4", "O2"]
-        @test haskey(AGNI.phys.formulae._lookup_mmw, gas)
+        @test haskey(AGNI.formulae._lookup_mmw, gas)
     end
 
     # gases_standard should contain most species without significant duplication