Consistently use @warn for most problems, and @error for immediately critical problems. Update tests to only print @error calls, hiding @warn to avoid spam. Functions return success/failure more consistently.

Author: nichollsh

.zenodo.json

@@ -22,7 +22,7 @@
         }
     ],
     "title": "AGNI: An open-source model for extreme atmospheres on rocky exoplanets",
-    "version": "1.9.3",
+    "version": "1.9.4",
     "access_right": "open",
     "related_identifiers": [
         {

CITATION.cff

@@ -10,7 +10,7 @@ title: "AGNI: An open-source model for extreme atmospheres on rocky exoplanets"
 doi: 10.21105/joss.07726
 date-released: 2025-11-20
 
-version: 1.9.3
+version: 1.9.4
 url: "https://github.com/nichollsh/AGNI"
 type: software
 license: "GPL-3.0"

Project.toml

@@ -1,7 +1,7 @@
 name = "AGNI"
 uuid = "ede838c1-9ec3-4ebe-8ae8-da4091b3f21c"
 authors = ["Harrison Nicholls <contact@h-nicholls.space>"]
-version = "1.9.3"
+version = "1.9.4"
 
 [deps]
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"

codemeta.json

@@ -19,5 +19,5 @@
   "keywords": "exoplanets, radiation, astronomy, atmosphere, optimization, julia, fortran, convection, chemistry, magma, planetary, physics",
   "license": "GPL-3.0",
   "title": "AGNI",
-  "version": "1.9.3"
+  "version": "1.9.4"
 }

docs/src/tutorials/getting_started.md

@@ -16,21 +16,28 @@ GNU/Linux and MacOS (including ARM) are supported.
     Do not install Julia using your system package manager. Install only from julialang.org as below.
 
 ## Installation
-Follow the steps below in order to setup the code.
-1. Install Julia's package manager: `curl -fsSL https://install.julialang.org | sh`
-2. Switch to Julia 1.11: `juliaup add 1.11 && juliaup default 1.11`
-3. Download AGNI: `git clone https://github.com/nichollsh/AGNI.git`
+Follow the ordered steps below
+1. Install Julia's package manager
+    - `curl -fsSL https://install.julialang.org | sh`
+2. Switch to Julia 1.11
+    - `juliaup add 1.11 && juliaup default 1.11`
+3. Download AGNI
+    - `git clone https://github.com/nichollsh/AGNI.git`
 4. Change directory: `cd AGNI`
 5. Setup SOCRATES by doing either **ONE** of the following...
-    - Follow the instructions on the [SOCRATES GitHub](https://github.com/FormingWorlds/SOCRATES) page
-    - Run `./src/get_socrates.sh`
-6. Finally, install AGNI: `./src/get_agni.sh`
-AGNI is now installed as a package into the Julia environment of the AGNI
-directory. This will also have downloaded some basic input data and run the tests.
+    a. Follow the instructions on the [SOCRATES GitHub](https://github.com/FormingWorlds/SOCRATES) page
+    b. **OR**, run `./src/get_socrates.sh`
+6. Setup FastChem
+    - `./src/get_fastchem.sh`
+7. Add `RAD_DIR` and `FC_DIR` to your environment and bashrc file
+8. Finally, install AGNI
+    - `./src/get_agni.sh`
+
+AGNI is now installed as a package of the Julia environment in the `AGNI/`
+directory. These steps will have downloaded some basic input data.
 
 !!! warning
-    The `RAD_DIR` environment variable must be set to your SOCRATES path whenever AGNI is being used.
-    This is so that AGNI can locate the SOCRATES libraries.
+    The `RAD_DIR` environment variable must be set to your SOCRATES path whenever AGNI is being used. This is so that AGNI can locate the SOCRATES libraries.
 
 !!! tip
     Visit the [Troubleshooting](@ref) page if you encounter any problems. This page can

src/AGNI.jl

@@ -503,7 +503,7 @@ module AGNI
 
         # Setup atmosphere
         @debug "Setup atmosphere "
-        atmosphere.setup!(atmos, ROOT_DIR,output_dir,
+        if !atmosphere.setup!(atmos, ROOT_DIR,output_dir,
                                 String(cfg["files" ]["input_sf"]),
                                 Float64(cfg["planet"]["instellation"]),
                                 Float64(cfg["planet"]["s0_fact"]),
@@ -537,10 +537,16 @@ module AGNI
                                 rfm_parfile=rfm_parfile,
                                 κ_grey_lw=κ_grey_lw,
                                 κ_grey_sw=κ_grey_sw
-                        ) || return false
+                        )
+            @error "Could not setup atmosphere object"
+            return false
+        end
 
         # Allocate atmosphere
-        atmosphere.allocate!(atmos,star_file; stellar_Teff=star_Teff) || return false
+        if !atmosphere.allocate!(atmos,star_file; stellar_Teff=star_Teff)
+            @error "Could not allocate atmosphere object"
+            return false
+        end
 
         # Configure deep atmospheric heating
         if haskey(cfg["physics"],"deep_heating")
@@ -571,14 +577,21 @@ module AGNI
         else
             # Set T(p) by looping over requests in the config.
             #     Each request may be a command, or an argument following a command
-            setpt.request!(atmos, cfg["execution"]["initial_state"]) || return false
+            if !setpt.request!(atmos, cfg["execution"]["initial_state"])
+                @error "Could not set initial temperature profile"
+                return false
+            end
         end
 
         # Write initial state
         save.write_profile(atmos, joinpath(atmos.OUT_DIR,"prof_initial.csv"))
 
         # Run chemistry in the first instance
-        chemistry.calc_composition!(atmos, oceans, chem, rainout)
+        chem_state = chemistry.calc_composition!(atmos, oceans, chem, rainout)
+        if chem_state == 1
+            @error "Chemistry failed!"
+            return false
+        end
 
         # Frame dir
         if plt_ani
@@ -588,7 +601,6 @@ module AGNI
         end
 
         # Loop over requested solvers
-        solver_success::Bool = true
         return_success::Bool = true
         allowed_solvers::Array{String,1} = ["newton", "gauss", "levenberg", "jacobinewton"]
         sol = strip(lowercase(cfg["execution"]["solver"]))
@@ -599,15 +611,15 @@ module AGNI
 
         # No solve - just calc fluxes at the end
         if sol == "none"
-            energy.calc_fluxes!(atmos, radiative=true, latent_heat=incl_latent,
+            return_success &= energy.calc_fluxes!(atmos, radiative=true, latent_heat=incl_latent,
                                 convective=incl_convect, sens_heat=incl_sens,
                                 conductive=incl_conduct,
                                 deep=incl_deep,
                                 calc_cf=Bool(cfg["plots"]["contribution"]))
 
         # Transparent atmosphere solver
         elseif sol == "transparent"
-            solver_success = solver.solve_transparent!(atmos, sol_type=sol_type,
+            return_success &= solver.solve_transparent!(atmos, sol_type=sol_type,
                                 conv_atol=conv_atol,
                                 conv_rtol=conv_rtol,
                                 max_steps=Int(cfg["execution"]["max_steps"]))
@@ -619,7 +631,7 @@ module AGNI
                 modplot = 1
             end
             method_idx = findfirst(==(sol), allowed_solvers)
-            solver_success = solver.solve_energy!(atmos, sol_type=sol_type,
+            return_success &= solver.solve_energy!(atmos, sol_type=sol_type,
                                 conduct=incl_conduct, chem=chem,
                                 convect=incl_convect, latent=incl_latent,
                                 sens_heat=incl_sens, deep=incl_deep,
@@ -642,18 +654,17 @@ module AGNI
 
         # Invalid selection
         else
-            @error "Invalid solver '$sol'"
+            @warn "Invalid solver '$sol'"
             return_success = false
         end
 
-        return_success &= solver_success
         @info "    done"
         @info "Total radiative transfer evaluations: $(atmos.num_rt_eval)"
 
         # RFM calculation?
         if atmos.flag_rfm
             @info "Running RFM line-by-line radiative transfer..."
-            rfm.run_rfm(atmos, rfm_wn_min, rfm_wn_max)
+            return_success &= rfm.run_rfm(atmos, rfm_wn_min, rfm_wn_max)
             @info "    done"
         end
 

src/atmosphere.jl

@@ -33,7 +33,7 @@ module atmosphere
     import ..spectrum
 
     # Code versions
-    const AGNI_VERSION::String     = "1.9.3"  # current agni version
+    const AGNI_VERSION::String     = "1.9.4"  # current agni version
     const SOCVER_minimum::Float64  = 2407.2    # minimum required socrates version
 
     # Hydrostatic+gravity+mass calculation (constants and limits)

src/chemistry.jl

@@ -520,7 +520,7 @@ module chemistry
 
                 # Check that we have some hydrogen...
                 if N_inp_t[1] < 1e-30
-                    @error "Cannot calculate metallicity of hydrogen-free mixture!"
+                    @warn "Cannot calculate metallicity of hydrogen-free mixture!"
                     state = 1
                 end
 
@@ -546,7 +546,7 @@ module chemistry
                     if isfinite(atmos.metal_calc[e])
                         write(f, @sprintf("%s    %.3f \n",e,log10(atmos.metal_calc[e]) + 12.0))
                     else
-                        @error "Got non-finite metallicity for $e - adopting solar value"
+                        @warn "Got non-finite metallicity for $e - adopting solar value"
                         write(f, @sprintf("%s    %.3f \n",e,phys.consts._solar_metallicity[e]))
                     end
 
@@ -625,7 +625,7 @@ module chemistry
 
         # Get gas chemistry output
         if !isfile(atmos.fastchem_chem)
-            @error "Could not find fastchem output"
+            @warn "Could not find FastChem output file '$(atmos.fastchem_chem)'"
             return 1
         end
         (data,head) = readdlm(atmos.fastchem_chem, '\t', Float64, header=true)

src/energy.jl

@@ -258,17 +258,17 @@ module energy
         # Check finite
         if !all(isfinite, atmos.radout.flux_down)
             if lw
-                @error "Non-finite value in LW DN flux array"
+                @warn "Non-finite value in LW DN flux array"
             else
-                @error "Non-finite value in SW DN flux array"
+                @warn "Non-finite value in SW DN flux array"
             end
             make_finite!(atmos.radout.flux_down, FILL_FINITE_FLUX)
         end
         if !all(isfinite, atmos.radout.flux_up)
             if lw
-                @error "Non-finite value in LW UP flux array"
+                @warn "Non-finite value in LW UP flux array"
             else
-                @error "Non-finite value in SW UP flux array"
+                @warn "Non-finite value in SW UP flux array"
             end
             make_finite!(atmos.radout.flux_up, FILL_FINITE_FLUX)
         end

src/get_agni.sh

@@ -5,7 +5,7 @@ set -e
 
 # User arguments
 if [ -z "$1" ]; then
-    testsuite="all" # default
+    testsuite="fast" # default
 else
     testsuite="$1" # requested test suite
 fi
@@ -21,12 +21,21 @@ if [ -n "$RAD_DIR" ]; then
     echo "Found SOCRATES path: yes"
 else
     echo "Found SOCRATES path: no"
-    echo "You need to install SOCRATES and set the RAD_DIR environment variable"
-    echo "This requires modifying your shell rc file to export RAD_DIR"
-    echo "Check the docs: https://www.h-nicholls.space/AGNI/"
+    echo "    You need to install SOCRATES and set the RAD_DIR environment variable"
+    echo "    This requires modifying your shell rc file to export RAD_DIR"
+    echo "    Check the docs: https://www.h-nicholls.space/AGNI/"
     exit 1
 fi
 
+# FastChem?
+if [ -n "$FC_DIR" ]; then
+    echo "Found FastChem path: yes"
+else
+    echo "Found FastChem path: no"
+    echo "    It is highly recommended that you install FastChem and set the FC_DIR environment variable"
+    echo "    Check the docs: https://www.h-nicholls.space/AGNI/"
+fi
+
 # Install
 echo "Installing AGNI..."
 rm -f Manifest.toml