Renamed F_eff to F_int. Requires julia>=1.9 explicitly. Fixes to note…

…books.:

Project.toml

@@ -22,3 +22,6 @@ Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 TOML = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
+
+[compat]
+julia = ">= 1.9"

docs/src/model/index.md

@@ -131,4 +131,4 @@ using a 1D golden-section search method on $\alpha$. This means that the model i
 AGNI can calculate emission spectra, provided with T(p) and the volume mixing ratios of the gases. This is performed using the same RT as the RCE calculations, so is limited in resolution by the choice of correlated-k bands. Similarly, the longwave contribution function can also be calculated.
 
 ## Julia and Fortran
-AGNI is primarily written in Julia, while SOCRATES itself is written in Fortran. Julia was chosen because it allows the SOCRATES binaries to be included in the precompiled code, which significantly improves performance.
+AGNI is primarily written in Julia, while SOCRATES itself is written in Fortran. Julia was chosen because it allows the SOCRATES binaries to be included in the precompiled code, which significantly improves performance. In theory, it is possible to call AGNI from a Python program via [PythonCall.jl](https://github.com/JuliaPy/PythonCall.jl).

docs/src/usage.md

@@ -34,7 +34,7 @@ Some `execution` parameters:
 * `solution_type` tells the model which state to solve for. The allowed values (integers) are...
      - 1 : zero flux divergence at fixed `tmp_surf`
      - 2 : zero flux divergence, with `tmp_surf` set such that the conductive skin (CBL) conserves energy flux
-     - 3 : the net upward flux at each layer is equal to `flux_eff = sigma * tmp_eff^4`
+     - 3 : the net upward flux at each layer is equal to `flux_int = sigma * tmp_int^4`
 
 * `solvers` tells the model which solvers to use. This is a list of strings, so multiple solvers can be applied sequentially. An empty string is always appended to the end of this list. Allowed solvers are...
      - [empty string] : no solving takes place, so the model just calculates fluxes using the initial state

res/config/chemistry.toml

@@ -14,7 +14,7 @@ title = "Equilibrium chemistry demo"                    # Name for this configur
     p_top           = 1e-5              # Total top-of-atmosphere pressure [bar]
     vmr             = { H2O = 0.6, CO2=0.1, N2=0.1, SO2=0.1, O2=0.05, Fe=0.05}     # Volatile volume mixing ratios
     condensates     = []
-    tmp_eff         = 0.0               # Effective temperature
+    tmp_int         = 0.0               # Effective temperature
 
 [files]
     clean_output    = true

res/config/cloud.toml

@@ -14,7 +14,7 @@ title = "Test clouds w/ prescribed T(p)"
     p_top           = 1e-6         
     vmr             = { H2O = 1.0 }
     condensates     = ["H2O"]
-    tmp_eff         = 0.0          
+    tmp_int         = 0.0          
 
 [files]
     clean_output    = true

res/config/condense.toml

@@ -14,7 +14,7 @@ title = "Condensation test"                    # Name for this configuration fil
     p_top           = 1e-5            
     vmr             = { H2O=0.8, CO2=0.1, CH4=0.08, H2=0.02}    
     condensates     = ["H2O", "CO2"]
-    tmp_eff         = 0.0            
+    tmp_int         = 0.0            
     turb_coeff      = 1.0e-4
     wind_speed      = 10.0
     skin_k          = 2.0

res/config/default.toml

@@ -18,7 +18,7 @@ title = "Default"                       # Name for this configuration file
     skin_d          = 0.01              # Conductive skin thickness [m]. Used when sol_type=2.
     skin_k          = 2.0               # Conductive skin conductivity [W m-1 K-1]. Used when sol_type=2.
     tmp_magma       = 3000.0            # Magma temperature [K]. Used when sol_type=2.
-    tmp_eff         = 0.0               # Planet's effective interior temperature [K]. Used when sol_type=3.
+    tmp_int         = 0.0               # Planet's effective interior temperature [K]. Used when sol_type=3.
     turb_coeff      = 0.001             # Turbulent exchange coefficient for sensible heat.
     wind_speed      = 2.0               # Effective wind speed for sensible heat [m s-1].
 

res/config/hotdry.toml

@@ -14,7 +14,7 @@ title = "Hot and dry"
     p_top           = 1e-5              # Total top-of-atmosphere pressure [bar]
     vmr             = { H2O = 1.0 }     # Volatile volume mixing ratios
     condensates     = []                
-    tmp_eff         = 0.0               # Effective temperature
+    tmp_int         = 0.0               # Effective temperature
     turb_coeff      = 1.0e-4
     wind_speed      = 10.0
 

res/config/k2-18b.toml

@@ -14,7 +14,7 @@ title = "Roughly K2-18b @ IW-4"
     p_top           = 1e-5           
     vmr             = { H2O=0.0085, N2=0.0009, H2=0.7931, CO=0.0111, CH4=0.1864  }    
     condensates     = ["H2O","CH4","CO"]               
-    tmp_eff         = 0.0
+    tmp_int         = 100.0
     turb_coeff      = 0.001           
     wind_speed      = 2.0             
 

res/config/proteus.toml

@@ -15,7 +15,7 @@ title = "PROTEUS configured"
     skin_k          = 2.0
     skin_d          = 0.01
     tmp_magma       = 1950.1074604027003
-    # tmp_eff         = 1000.0
+    # tmp_int         = 1000.0
     turb_coeff      = 1.0e-3
     wind_speed      = 10.0
     condensates     = []

res/config/selsis.toml

@@ -14,7 +14,7 @@ title = "Comparison with Selsis+23"
     p_top           = 1e-5           
     vmr             = { H2O = 1.0 }  
     condensates     = ["H2O"]        
-    tmp_eff         = 0.0            
+    tmp_int         = 0.0            
     turb_coeff      = 1.0e-4
     wind_speed      = 10.0
 

res/literature_data/profile/readme.txt

@@ -17,5 +17,5 @@ This can be achieved by setting the following parameters in AGNI:
 
 To solve for these profiles, we need to set the net flux boundary condition such
 that the same OLR is achieved. This may be done via:
-    F_eff = sigma (T_eff)^4 = OTR + F_UP_SW - F_DN_SW 
+    F_int = sigma (T_int)^4 = OTR + F_UP_SW - F_DN_SW 
 

src/AGNI.jl

@@ -275,9 +275,9 @@ module AGNI
             tmp_magma   = cfg["planet"]["tmp_magma"]
         end 
         #     effective temperature case 
-        tmp_eff::Float64 = 0.0
+        tmp_int::Float64 = 0.0
         if sol_type == 3
-            tmp_eff = cfg["planet"]["tmp_eff"]
+            tmp_int = cfg["planet"]["tmp_int"]
         end 
         #     target OLR case 
         target_olr::Float64 = 0.0
@@ -311,7 +311,7 @@ module AGNI
                                 overlap_method=overlap,
                                 skin_d=skin_d, skin_k=skin_k, tmp_magma=tmp_magma,
                                 target_olr=target_olr,
-                                tmp_eff=tmp_eff, albedo_s=albedo_s,
+                                tmp_int=tmp_int, albedo_s=albedo_s,
                                 thermo_functions=thermo_funct,
                                 C_d=turb_coeff, U=wind_speed,
                                 fastchem_path=fastchem_path

src/atmosphere.jl

@@ -26,7 +26,7 @@ module atmosphere
     SOL_TYPES::Array{String, 1} = [
         "steadystate_ext",  # zero divergence at fixed tmp_surf, extrapolated tmpl[end]
         "cond_skin",        # set tmp_surf such that conductive skin conserves energy flux
-        "flux_eff",         # total flux at each level equal to flux_eff
+        "flux_int",         # total flux at each level equal to flux_int
         "target_olr",       # OLR is equal to target_olr
     ]
 
@@ -71,7 +71,7 @@ module atmosphere
         instellation::Float64           # Solar flux at top of atmopshere [W m-2]
         s0_fact::Float64                # Scale factor to instellation (cronin+14)
         tmp_surf::Float64               # Surface brightness temperature [K]
-        tmp_eff::Float64                # Effective temperature of the planet [K]
+        tmp_int::Float64                # Effective temperature of the planet [K]
         grav_surf::Float64              # Surface gravity [m s-2]
         overlap_method::Int             # Absorber overlap method to be used
 
@@ -128,7 +128,7 @@ module atmosphere
         layer_mass::Array{Float64,1}        # mass per unit area [kg m-2]
 
         # Calculated bolometric radiative fluxes (W m-2)
-        flux_eff::Float64                   # Effective flux  [W m-2] for sol_type=3
+        flux_int::Float64                   # Effective flux  [W m-2] for sol_type=3
         target_olr::Float64                 # Target olr [W m-2] for sol_type=4
 
         flux_d_lw::Array{Float64,1}         # down component, lw 
@@ -252,7 +252,7 @@ module atmosphere
     - `skin_k::Float64`                 skin thermal conductivity [W m-1 K-1].   
     - `overlap_method::Int`             gaseous overlap scheme (2: rand overlap, 4: equiv extinct, 8: ro+resort+rebin).   
     - `target_olr::Float64`             target OLR [W m-2] for sol_type==4.   
-    - `tmp_eff::Float64`                planet's effective brightness temperature [K] for sol_type==3.   
+    - `tmp_int::Float64`                planet's effective brightness temperature [K] for sol_type==3.   
     - `all_channels::Bool`              use all channels available for RT?   
     - `flag_rayleigh::Bool`             include rayleigh scattering?   
     - `flag_gcontinuum::Bool`           include generalised continuum absorption?   
@@ -284,7 +284,7 @@ module atmosphere
                     skin_k::Float64 =           2.0,
                     overlap_method::Int =       4,
                     target_olr::Float64 =       0.0,
-                    tmp_eff::Float64 =          0.0,
+                    tmp_int::Float64 =          0.0,
                     all_channels::Bool  =       true,
                     flag_rayleigh::Bool =       false,
                     flag_gcontinuum::Bool =     false,
@@ -336,7 +336,7 @@ module atmosphere
         atmos.nlev_c         =  nlev_centre
         atmos.nlev_l         =  atmos.nlev_c + 1
         atmos.tmp_surf =        max(tmp_surf, atmos.tmp_floor)
-        atmos.tmp_eff =         tmp_eff
+        atmos.tmp_int =         tmp_int
         atmos.grav_surf =       max(1.0e-7, gravity)
         atmos.zenith_degrees =  max(min(zenith_degrees,89.8), 0.2)
         atmos.albedo_s =        max(min(albedo_s, 1.0 ), 0.0)
@@ -345,7 +345,7 @@ module atmosphere
         atmos.s0_fact =         max(s0_fact,0.0)
         atmos.toa_heating =     atmos.instellation * (1.0 - atmos.albedo_b) * s0_fact * cosd(atmos.zenith_degrees)
 
-        atmos.flux_eff =        phys.sigma * (atmos.tmp_eff)^4.0  
+        atmos.flux_int =        phys.sigma * (atmos.tmp_int)^4.0  
         atmos.target_olr =      max(1.0e-20,target_olr)
 
         atmos.mask_decay =      15 

src/dump.jl

@@ -125,7 +125,7 @@ module dump
             # Scalar quantities  
             #    Create variables
             var_tmp_surf =  defVar(ds, "tmp_surf",      Float64, (), attrib = OrderedDict("units" => "K"))      # Surface brightness temperature [K]
-            var_tmp_eff =   defVar(ds, "tmp_eff",       Float64, (), attrib = OrderedDict("units" => "K"))      # Effective temperature [K]
+            var_tmp_int =   defVar(ds, "tmp_int",       Float64, (), attrib = OrderedDict("units" => "K"))      # Effective temperature [K]
             var_inst =      defVar(ds, "instellation",  Float64, (), attrib = OrderedDict("units" => "W m-2"))  # Solar flux at TOA
             var_s0fact =    defVar(ds, "inst_factor",   Float64, ())                                            # Scale factor applied to instellation
             var_albbond =   defVar(ds, "bond_albedo",   Float64, ())                                            # Bond albedo used to scale-down instellation
@@ -150,7 +150,7 @@ module dump
 
             #     Store data
             var_tmp_surf[1] =   atmos.tmp_surf 
-            var_tmp_eff[1] =    atmos.tmp_eff 
+            var_tmp_int[1] =    atmos.tmp_int 
             var_inst[1] =       atmos.instellation
             var_s0fact[1] =     atmos.s0_fact
             var_albbond[1] =    atmos.albedo_b

src/energy.jl

@@ -458,47 +458,46 @@ module energy
     """
     function condense_relax!(atmos::atmosphere.Atmos_t)
 
+        # Check if empty
+        if length(atmos.condensates) == 0
+            return nothing 
+        end 
+
         # Get name 
-        c::String = atmos.gas_names[1]
+        c::String = atmos.condensates[1]
 
         # Reset flux and mask 
         fill!(atmos.flux_l, 0.0)
         fill!(atmos.mask_l, 0)
         fill!(atmos.gas_ptran[c], false)
 
-        # Check if empty
-        if length(atmos.condensates) == 0
-            return nothing 
-        end 
-
         # Work variables
         a::Float64 = 1.0 
         pp::Float64 = 0.0
         qsat::Float64 = 0.0
         dif::Array = zeros(Float64, atmos.nlev_c)
 
-
         # Calculate flux (negative) divergence due to latent heat release...
         # For all levels 
         for i in 1:atmos.nlev_c-1
 
+            # Check criticality 
+            if atmos.tmp[i] > atmos.gas_dat[c].T_crit
+                continue 
+            end 
+
             # Get partial pressure 
             pp = atmos.gas_vmr[c][i] * atmos.p[i]
             if pp < 1.0e-10 
                 continue
             end
 
             # check saturation
-            qsat = phys.get_Psat(atmos.gas_dat[c], atmo.tmp[i])/atmos.p[i]
+            qsat = phys.get_Psat(atmos.gas_dat[c], atmos.tmp[i])/atmos.p[i]
             if (atmos.gas_vmr[c][i] < qsat+1.0e-10)
                 continue 
             end 
 
-            # Check criticality 
-            if atmos.tmp[i] > atmos.gas_dat[c].T_crit
-                continue 
-            end 
-
             # relaxation function
             dif[i] = a*(atmos.gas_vmr[c][i]-qsat)
 

src/plotting.jl

@@ -225,9 +225,9 @@ module plotting
         # Zero line 
         plot!(plt, [0.0, 0.0], [arr_P[1], arr_P[end]], lw=0.4, lc="black", label="")
 
-        # Effective flux
+        # Intrinsic/interior flux
         if incl_eff
-            plot!(plt, [_symlog(atmos.flux_eff)], [arr_P[1], arr_P[end]], ls=:dashdot, lw=0.4, lc="black", label="EFF")
+            plot!(plt, [_symlog(atmos.flux_int)], [arr_P[1], arr_P[end]], ls=:dashdot, lw=0.4, lc="black", label="INT")
         end
 
         # LW component

src/solver.jl

@@ -71,7 +71,7 @@ module solver
 
     Arguments:
     - `atmos::Atmos_t`                  the atmosphere struct instance to be used.
-    - `sol_type::Int`                   solution type, 1: tmp_surf | 2: skin | 3: tmp_eff | 4: tgt_olr
+    - `sol_type::Int`                   solution type, 1: tmp_surf | 2: skin | 3: tmp_int | 4: tgt_olr
     - `chem_type::Int`                  chemistry type (see wiki)
     - `convect::Bool`                   include convection
     - `sens_heat::Bool`                 include sensible heating 
@@ -109,14 +109,17 @@ module solver
                             detect_plateau::Bool=true, perturb_all::Bool=false,
                             modplot::Int=1, save_frames::Bool=true, 
                             modprint::Int=1,
-                            conv_atol::Float64=1.0e-3, conv_rtol::Float64=1.0e-3
+                            conv_atol::Float64=1.0e-2, conv_rtol::Float64=1.0e-3
                             )::Bool
 
         # Validate sol_type
         if (sol_type < 1) || (sol_type > 4)
             @error "Invalid solution type ($sol_type)"
             return false
         end
+        if detect_plateau && !linesearch
+            @warn "Plateau nudging enabled without linesearch - expect instability"
+        end 
 
         # Start timer 
         wct_start::Float64 = time()
@@ -257,8 +260,8 @@ module solver
             elseif (sol_type == 3)
                 # Zero loss
                 resid[2:end] .= atmos.flux_dif[1:end]
-                # Total flux at TOA is equal to sigma*tmp_eff^4
-                resid[1] = atmos.flux_tot[1] - atmos.flux_eff
+                # Total flux at TOA is equal to sigma*tmp_int^4
+                resid[1] = atmos.flux_tot[1] - atmos.flux_int
 
             elseif (sol_type == 4)
                 # Zero loss
@@ -394,8 +397,8 @@ module solver
             @info @sprintf("    skin_d   = %.2f m",         atmos.skin_d)
             @info @sprintf("    skin_k   = %.2f W K-1 m-1", atmos.skin_k)
         elseif (sol_type == 3)
-            @info @sprintf("    tmp_eff  = %.2f K",     atmos.tmp_eff)
-            @info @sprintf("    f_eff    = %.2f W m-2", atmos.flux_eff)
+            @info @sprintf("    tmp_int  = %.2f K",     atmos.tmp_int)
+            @info @sprintf("    f_int    = %.2f W m-2", atmos.flux_int)
         elseif (sol_type == 4)
             @info @sprintf("    tgt_olr  = %.2f W m-2", atmos.target_olr)
         end 
@@ -434,7 +437,9 @@ module solver
             plot_step()
         end
 
-        @info @sprintf("    step  resid_med  resid_2nm  flux_OLR   xvals_med  xvals_max  |dx|_max   flags")
+        if modprint > 0
+            @info @sprintf("    step  resid_med  resid_2nm  flux_OLR   xvals_med  xvals_max  |dx|_max   flags")
+        end 
         info_str::String = ""
         stepflags::String = ""
         while true 
@@ -683,7 +688,7 @@ module solver
         atmos.is_solved = true
         atmos.is_converged = false 
         if code == 0
-            @info "    success"
+            @info "    success in $step steps"
             atmos.is_converged = true
         elseif code == 1
             @error "    failure (maximum iterations)"