Module docstrings. Fixed tests. Moved calc_layer_props back to atmosphere module. Moved colours to style module. Add header to all files

Author: nichollsh

src/AGNI.jl

@@ -1,3 +1,4 @@
+# This file is part of AGNI. License is GPL-3.0: https://www.gnu.org/licenses
 # Core file containing functions for running the model
 
 # Not for direct execution
@@ -26,8 +27,8 @@ module AGNI
     include("energy/spectrum.jl"); import .spectrum; export spectrum
     include("state/atmosphere.jl"); import .atmosphere; export atmosphere
     include("state/diagnostics.jl"); import .diagnostics; export diagnostics
-    include("state/layers.jl"); import .layers; export layers
     include("compose/ocean.jl"); import .ocean; export ocean
+    include("compose/fastchem.jl"); import .fastchem; export fastchem
     include("compose/chemistry.jl"); import .chemistry; export chemistry
     include("energy/rfm.jl"); import .rfm; export rfm
     include("interface/setpt.jl"); import .setpt; export setpt

src/compose/chemistry.jl

@@ -1,4 +1,4 @@
-# Contains things relating to atmospheric chemistry
+# This file is part of AGNI. License is GPL-3.0: https://www.gnu.org/licenses
 
 """
 This module handles chemistry, condensation, and evaporation.
@@ -17,10 +17,9 @@ module chemistry
     # Local files
     import ..phys
     import ..atmosphere
-    import ..layers
     import ..species
     import ..ocean
-    include("fastchem.jl"); import .fastchem
+    import ..fastchem
 
     # Constants
     const SMALL_FLOAT::Float64  = 1e-20     # small number for numerical stability
@@ -96,7 +95,7 @@ module chemistry
         atmosphere.generate_pgrid!(atmos)
 
         # Layer properties
-        layers.calc_layer_props!(atmos)
+        atmosphere.calc_layer_props!(atmos)
     end
 
 
@@ -143,7 +142,7 @@ module chemistry
                 # rainout completely, and skip condensation
                 dp = -p_gas[c]
                 atmos.p_boa += dp
-                @debug @sprintf("            %s de-mixed, partial pressure += %+.3f bar", c, dp/1e5)
+                @debug @sprintf("            %s de-mixed, partial pressure += %+.3e bar", c, dp/1e5)
                 any_changed = true
 
             # If supercritical, do nothing
@@ -163,13 +162,13 @@ module chemistry
 
                 # Super-saturated at the surface...
                 elseif dp < 0
-                    @debug @sprintf("            %s super-saturated, partial pressure += %+.3f bar", c, dp/1e5)
+                    @debug @sprintf("            %s super-saturated, partial pressure += %+.3e bar", c, dp/1e5)
 
                 # Sub-saturated at the surface...
                 #     work out change in partial pressure based on initial reservoir amount
                 else
                     dp = min(dp, atmos.ocean_ini[c] * atmos.grav_surf / (atmos.gas_dat[c].mmw/atmos.layer_μ[end]))
-                    @debug @sprintf("            %s sub-saturated, partial pressure += %+.3f bar", c, dp/1e5)
+                    @debug @sprintf("            %s sub-saturated, partial pressure += %+.3e bar", c, dp/1e5)
                 end
 
                 # Record that at least one component has as changed
@@ -207,7 +206,7 @@ module chemistry
         atmosphere.generate_pgrid!(atmos)
 
         # Calculate new values for layer properties
-        layers.calc_layer_props!(atmos)
+        atmosphere.calc_layer_props!(atmos)
 
         return any_changed
     end
@@ -301,7 +300,7 @@ module chemistry
                 end # end saturation check
 
                 # recalculate layer properties after raining-out this species
-                layers.calc_layer_props!(atmos)
+                atmosphere.calc_layer_props!(atmos)
 
             end # end condensate
 
@@ -395,15 +394,15 @@ module chemistry
             end # go to next j level (below)
 
             # Layer properties
-            layers.calc_layer_props!(atmos)
+            atmosphere.calc_layer_props!(atmos)
 
         end # end loop over condensates
 
         # Layer properties
         for i in 1:atmos.nlev_c
             normalise_vmrs!(atmos, i)
         end
-        layers.calc_layer_props!(atmos)
+        atmosphere.calc_layer_props!(atmos)
 
         # Set water clouds at levels where condensation occurs
         if "H2O" in atmos.condensates
@@ -466,7 +465,7 @@ module chemistry
         end
 
         # recalculate layer properties
-        layers.calc_layer_props!(atmos)
+        atmosphere.calc_layer_props!(atmos)
 
         # Warn on failure
         if state > 0

src/compose/fastchem.jl

@@ -1,3 +1,12 @@
+# This file is part of AGNI. License is GPL-3.0: https://www.gnu.org/licenses
+
+"""
+**Run FastChem to solve gas phase chemistry.**
+
+FastChem is a fast and robust chemical equilibrium solver, designed for use in exoplanet
+and brown dwarf atmospheres. This module writes the necessary input files for FastChem,
+runs the code, and parses the output to update the gas phase composition.
+"""
 module fastchem
 
     # Import packages
@@ -6,8 +15,10 @@ module fastchem
     import DelimitedFiles:readdlm
 
     # Include local modules
-    using ..atmosphere
-    using ..phys
+    import ..atmosphere
+    import ..phys
+    import ..consts
+    import ..formulae
 
     # Constants
     const SMOOTH_SCALE::Float64 = 12.0      # smoothing scale for fastchem floor
@@ -93,7 +104,7 @@ module fastchem
                 @debug "Elements set by user-provided metallicities"
 
                 # copy original to calculated; set elem to zero if it was not provided
-                for e in phys.elems_standard
+                for e in consts.elems_standard
                     atmos.metal_calc[e] = get(atmos.metal_orig, e, 0.0)
                 end
                 atmos.metal_calc["H"] = 1.0
@@ -104,8 +115,8 @@ module fastchem
 
                 # Calculate elemental abundances from surface mixing ratios [molecules/m^3]
                 #   assuming ideal gas: N/V = P*x/(Kb*T) , where x is the VMR
-                N_inp_t = zeros(Float64, length(phys.elems_standard)) # total atoms in all gases
-                N_inp_g = zeros(Float64, length(phys.elems_standard)) # atoms in current gas
+                N_inp_t = zeros(Float64, length(consts.elems_standard)) # total atoms in all gases
+                N_inp_g = zeros(Float64, length(consts.elems_standard)) # atoms in current gas
                 #    loop over gases
                 for gas in atmos.gas_names
                     fill!(N_inp_g, 0.0)
@@ -116,16 +127,16 @@ module fastchem
                     end
 
                     # count atoms in this gas
-                    d = phys.count_atoms(gas)
-                    for (i,e) in enumerate(phys.elems_standard)
+                    d = formulae.count_atoms(gas)
+                    for (i,e) in enumerate(consts.elems_standard)
                         if haskey(d, e)
                             N_inp_g[i] += d[e] # N_inp_g stores num of atoms in this gas
                         end
                     end
 
                     # Get gas abundance from original VMR value
                     #    scale number of atoms by the abundance of the gas (p = Ng kB T)
-                    N_inp_g *= atmos.gas_vmr[gas][end] * atmos.p[end] / (phys.k_B * atmos.tmp[end])
+                    N_inp_g *= atmos.gas_vmr[gas][end] * atmos.p[end] / (consts.k_B * atmos.tmp[end])
 
                     # Add atoms from this gas to total atoms in the mixture
                     N_inp_t += N_inp_g
@@ -138,7 +149,7 @@ module fastchem
                 end
 
                 # Convert elemental abundances to metallicity number ratios, rel to hydrogen
-                for (i,e) in enumerate(phys.elems_standard)
+                for (i,e) in enumerate(consts.elems_standard)
                     atmos.metal_calc[e] = N_inp_t[i]/N_inp_t[1]
                 end
             end
@@ -148,7 +159,7 @@ module fastchem
             #     for each element `e`, value = log10(N_e/N_H) + 12
             open(atmos.fastchem_elem,"w") do f
                 write(f,"# Elemental abundances file written by AGNI \n")
-                for e in phys.elems_standard
+                for e in consts.elems_standard
 
                     # skip this element if its abundance is too small
                     if atmos.metal_calc[e] < 1.0e-30
@@ -160,7 +171,7 @@ module fastchem
                         write(f, @sprintf("%s    %.3f \n",e,log10(atmos.metal_calc[e]) + 12.0))
                     else
                         @warn "Got non-finite metallicity for $e - adopting solar value"
-                        write(f, @sprintf("%s    %.3f \n",e,phys.consts._solar_metallicity[e]))
+                        write(f, @sprintf("%s    %.3f \n",e,consts.solar_metallicity[e]))
                     end
 
                     count_elem_nonzero += 1
@@ -276,10 +287,10 @@ module fastchem
 
             # not stored => search based on atoms
             if !match
-                d_fc = phys.count_atoms(g_fc)  # get atoms dict from FC name
+                d_fc = formulae.count_atoms(g_fc)  # get atoms dict from FC name
 
                 for g in atmos.gas_names
-                    if phys.same_atoms(d_fc, atmos.gas_dat[g].atoms)
+                    if formulae.same_atoms(d_fc, atmos.gas_dat[g].atoms)
                         match = true
                         g_in = g
                         break

src/compose/ocean.jl

@@ -1,3 +1,4 @@
+# This file is part of AGNI. License is GPL-3.0: https://www.gnu.org/licenses
 # Contains module handling surface oceans
 
 """

src/energy/energy.jl

@@ -1,5 +1,12 @@
-# Contains the energy module, for everything relating to energy transport
+# This file is part of AGNI. License is GPL-3.0: https://www.gnu.org/licenses
 
+
+"""
+**Contains the energy module, for everything relating to energy transport**
+
+Calculates radiative, convective, conductive, etc, flux terms. Combines them together
+self-consistently to update the temperature profile.
+"""
 module energy
 
     # System libraries

src/energy/rfm.jl

@@ -1,5 +1,13 @@
-# Contains module and functions for performing radiative transfer with RFM
+# This file is part of AGNI. License is GPL-3.0: https://www.gnu.org/licenses
 
+
+"""
+**Module and functions for performing radiative transfer with RFM**
+
+The RFM (Reference Forward Model) is a line-by-line radiative transfer code developed
+by Anu Dudhia at Oxford. This module contains writies the required input files, runs it,
+and parses the output to update the radiative fluxes in AGNI for post-processing.
+"""
 module rfm
 
     # Import modules

src/energy/spectrum.jl

@@ -1,6 +1,12 @@
-# Contains the spectrum module, for updating the SOCRATES spectral file at
-# runtime with the solar flux / thermal source function, and scattering.
+# This file is part of AGNI. License is GPL-3.0: https://www.gnu.org/licenses
 
+
+"""
+**Contains the spectrum module, for updating the SOCRATES spectral files**
+
+Specifically for SOCRATES. Inserts solar flux, thermal source function, and scattering
+data into the spectral files using SOCRATES utilities.
+"""
 module spectrum
 
     using LoggingExtras

src/interface/load.jl

@@ -1,9 +1,11 @@
-# Load atmosphere from NetCDF file
+# This file is part of AGNI. License is GPL-3.0: https://www.gnu.org/licenses
 
+"""
+**Module for loading atmospheric states from NetCDF and CSV files.**
+"""
 module load
 
     import ..atmosphere
-    import ..layers: calc_layer_props!
 
     using NCDatasets
     using LoggingExtras

src/interface/paths.jl

@@ -1,3 +1,8 @@
+# This file is part of AGNI. License is GPL-3.0: https://www.gnu.org/licenses
+
+"""
+**Module for handling file paths and directories.**
+"""
 module paths
 
     # Load modules

src/interface/plotting.jl

@@ -1,5 +1,8 @@
-# Contains functions for plotting/diagnosing the atmosphere
+# This file is part of AGNI. License is GPL-3.0: https://www.gnu.org/licenses
 
+"""
+**Contains functions for plotting/diagnosing the atmosphere**
+"""
 module plotting
 
     # Import stuff
@@ -14,22 +17,11 @@ module plotting
     import ..phys
     import ..species
     import ..multicol
-
-    # Allowed plot file extensions
-    const ALLOWED_EXTS::Set{String} = Set(["png", "pdf", "svg"])
+    using ..style
 
     # Axis margins
     TMP_MARGIN::Float64 = 100.0
 
-    # Colors
-    const col_r::String = "#c0c0c0"
-    const col_n::String = "#000000"
-    const col_c::String = "#6495ed"
-    const col_t::String = "#ff4400"
-    const col_o::String = "#66CD00"
-    const col_p::String = "#ecb000"
-    const col_d::String = "#8B008B"
-
     # Default plotting configuration
     const la::Float64 = 0.7
     const lw::Float64 = 1.9