Version 0.8.3. Now uses F_int rather than T_int for internal flux. Updated docs and paper. New notebooks

nichollsh · nichollsh · commit 5f92e1fbcd1c · 2024-09-20T10:46:11.000+01:00
diff --git a/CITATION.cff b/CITATION.cff
@@ -5,7 +5,7 @@ authors:
   given-names: "Harrison"
   orcid: "https://orcid.org/0000-0002-8368-4641"
 title: "AGNI"
-version: 0.8.2
+version: 0.8.3
 doi: 10.xx/xx.xx
-date-released: 2024-09-13
+date-released: 2024-09-20
 url: "https://github.com/nichollsh/AGNI"
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "AGNI"
 uuid = "ede838c1-9ec3-4ebe-8ae8-da4091b3f21c"
 authors = ["Harrison Nicholls <harrison.nicholls@physics.ox.ac.uk>"]
-version = "0.8.2"
+version = "0.8.3"
 
 [deps]
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
diff --git a/README.md b/README.md
@@ -18,7 +18,7 @@
 </p>
 
 <p align="center">
-  <b>A radiative-convective atmosphere model designed for interior coupling.</b>
+  <b>A radiative-convective model for lava planet atmospheres.</b>
 </p>
 
 
diff --git a/codemeta.json b/codemeta.json
@@ -15,9 +15,9 @@
   "datePublished": "2024-09-13",
   "dateModified": "2024-09-13",
   "dateCreated": "2024-09-13",
-  "description": "A radiative-convective model for the atmospheres of rocky planets",
+  "description": "A radiative-convective model for lava planet atmospheres.",
   "keywords": "physics, radiative transfer, exoplanets, astronomy, convection, radiation, planets, atmospheres",
   "license": "GPL v3.0",
   "title": "AGNI",
-  "version": "0.8.2"
+  "version": "0.8.3"
 }
diff --git a/docs/paper/paper.md b/docs/paper/paper.md
@@ -1,5 +1,5 @@
 ---
-title: 'AGNI: A radiative-convective model for the atmospheres of rocky planets'
+title: 'AGNI: A radiative-convective model for lava planet atmospheres.'
 tags:
   - astronomy
   - physics,
@@ -24,7 +24,7 @@ affiliations:
    index: 1
  - name: Kapteyn Astronomical Institute, University of Groningen, P.O. Box 800, 9700 AV Groningen, The Netherlands
    index: 2
-date: 16 September 2024
+date: 20 September 2024
 bibliography: paper.bib
 
 ---
diff --git a/docs/src/usage.md b/docs/src/usage.md
@@ -50,7 +50,7 @@ Some parameters:
 * `execution.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_int = sigma * tmp_int^4`
+     - 3 : the net flux (up minus down) at each layer is equal to `flux_int`
 
 * `execution.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
diff --git a/misc/L98-59d.ipynb b/misc/L98-59d.ipynb
diff --git a/res/config/55cnce_chem.toml b/res/config/55cnce_chem.toml
@@ -10,7 +10,7 @@ title = "Roughly 55 Cancri e @ fO2=IW"
     surface_material= "res/surface_albedos/basalt_tuff.dat"
     radius          = 1.1959e7
     gravity         = 22.304
-    tmp_int         = 0.0
+    flux_int        = 0.0
     turb_coeff      = 0.001
     wind_speed      = 2.0
 
diff --git a/res/config/L-98-59d.toml b/res/config/L-98-59d.toml
@@ -10,7 +10,7 @@ title = "L 98-59 d"
     surface_material= "res/surface_albedos/lunar_marebasalt.dat"
     radius          = 6.59051e6
     gravity         = 16.73
-    tmp_int         = 0.0
+    flux_int        = 0.0
     turb_coeff      = 0.001
     wind_speed      = 2.0
 
diff --git a/res/config/condense.toml b/res/config/condense.toml
@@ -11,7 +11,7 @@ title = "Condensation test"
     albedo_s        = 0.2
     radius          = 6.37e6
     gravity         = 9.81
-    tmp_int         = 0.0
+    flux_int        = 0.0
     turb_coeff      = 1.0e-4
     wind_speed      = 10.0
     skin_k          = 2.0
diff --git a/res/config/default.toml b/res/config/default.toml
@@ -17,7 +17,7 @@ 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_int         = 0.0               # Planet's effective interior temperature [K]. Used when sol_type=3.
+    flux_int        = 0.0               # Planet's internal flux [W m-2]. 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].
 
diff --git a/res/config/hotdry.toml b/res/config/hotdry.toml
@@ -11,7 +11,7 @@ title = "Hot and dry"
     albedo_s        = 0.0
     radius          = 6.37e6
     gravity         = 9.81
-    tmp_int         = 0.0
+    flux_int        = 0.0
     turb_coeff      = 1.0e-2
     wind_speed      = 10.0
 
diff --git a/src/AGNI.jl b/src/AGNI.jl
@@ -32,7 +32,7 @@ module AGNI
     import .plotting
     import .energy
     import .solver
-    import .realgas 
+    import .realgas
 
     # Export
     # export atmosphere
@@ -328,9 +328,9 @@ module AGNI
             tmp_magma   = cfg["planet"]["tmp_magma"]
         end
         #     effective temperature case
-        tmp_int::Float64 = 0.0
+        flux_int::Float64 = 0.0
         if sol_type == 3
-            tmp_int = cfg["planet"]["tmp_int"]
+            flux_int = cfg["planet"]["flux_int"]
         end
         #     target OLR case
         target_olr::Float64 = 0.0
@@ -358,7 +358,7 @@ module AGNI
                                 overlap_method=overlap,
                                 skin_d=skin_d, skin_k=skin_k, tmp_magma=tmp_magma,
                                 target_olr=target_olr,
-                                tmp_int=tmp_int,
+                                flux_int=flux_int,
                                 surface_material=surface_mat,
                                 albedo_s=albedo_s,
                                 thermo_functions=thermo_funct,
diff --git a/src/atmosphere.jl b/src/atmosphere.jl
@@ -70,7 +70,6 @@ module atmosphere
         surf_e_arr::Array{Float64,1}    # Spectral surface emissivity
 
         tmp_surf::Float64               # Surface brightness temperature [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
 
@@ -269,7 +268,7 @@ 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_int::Float64`                planet's effective (or internal) brightness temperature [K] for sol_type==3.
+    - `flux_int::Float64`               planet's internal flux 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?
@@ -302,7 +301,7 @@ module atmosphere
                     skin_k::Float64 =           2.0,
                     overlap_method::Int =       4,
                     target_olr::Float64 =       0.0,
-                    tmp_int::Float64 =          0.0,
+                    flux_int::Float64 =         0.0,
                     all_channels::Bool  =       true,
                     flag_rayleigh::Bool =       false,
                     flag_gcontinuum::Bool =     false,
@@ -319,7 +318,7 @@ module atmosphere
         end
 
         # Code versions
-        atmos.AGNI_VERSION = "0.8.2"
+        atmos.AGNI_VERSION = "0.8.3"
         atmos.SOCRATES_VERSION = readchomp(joinpath(ENV["RAD_DIR"],"version"))
         @debug "AGNI VERSION = $(atmos.AGNI_VERSION)"
         @debug "Using SOCRATES at $(ENV["RAD_DIR"])"
@@ -356,7 +355,6 @@ 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_int =         tmp_int
         atmos.grav_surf =       max(1.0e-7, gravity)
         atmos.zenith_degrees =  max(min(zenith_degrees,89.8), 0.2)
         atmos.surface_material= surface_material
@@ -367,7 +365,7 @@ module atmosphere
         atmos.toa_heating =     atmos.instellation * (1.0 - atmos.albedo_b) *
                                     s0_fact * cosd(atmos.zenith_degrees)
 
-        atmos.flux_int =        phys.sigma * (atmos.tmp_int)^4.0
+        atmos.flux_int =        flux_int
         atmos.target_olr =      max(1.0e-20,target_olr)
 
         atmos.C_d =             max(0,C_d)
@@ -425,8 +423,8 @@ module atmosphere
         atmos.cloud_arr_f   = zeros(Float64, atmos.nlev_c)
 
         # Phase change timescales [seconds]
-        atmos.phs_tau_mix = 1.0e4   # mixed composition case
-        atmos.phs_tau_sgl = 1.0e4   # single gas case
+        atmos.phs_tau_mix = 1.0e5   # mixed composition case
+        atmos.phs_tau_sgl = 1.0e5   # single gas case
 
         # Hardcoded cloud properties
         atmos.cond_alpha    = 0.0     # 0% of condensate is retained (i.e. complete rainout)
diff --git a/src/dump.jl b/src/dump.jl
@@ -126,7 +126,7 @@ module dump
             # Scalar quantities
             #    Create variables
             var_tmp_surf =  defVar(ds, "tmp_surf",      Float64, (), attrib = OrderedDict("units" => "K"))      # Surface brightness temperature [K]
-            var_tmp_int =   defVar(ds, "tmp_int",       Float64, (), attrib = OrderedDict("units" => "K"))      # Effective temperature [K]
+            var_flux_int =  defVar(ds, "flux_int",      Float64, (), attrib = OrderedDict("units" => "W m-2"))  # Internal flux [W m-2]
             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_int[1] =    atmos.tmp_int
+            var_flux_int[1] =   atmos.flux_int
             var_inst[1] =       atmos.instellation
             var_s0fact[1] =     atmos.s0_fact
             var_albbond[1] =    atmos.albedo_b
diff --git a/src/load.jl b/src/load.jl
@@ -59,7 +59,7 @@ module load
             # ----------------------
             # Load scalar quantities
             atmos.tmp_surf =        ds["tmp_surf"][]        # Surface brightness temperature [K]
-            atmos.tmp_int  =        ds["tmp_int"][]         # Effective temperature [K]
+            atmos.flux_int  =       ds["flux_int"][]        # Internal flux [W m-2]
             atmos.instellation =    ds["instellation"][]    # Solar flux
             atmos.s0_fact =         ds["inst_factor"][]     # Scale factor applied to instellation
             atmos.albedo_b =        ds["bond_albedo"][]     # Bond albedo used to scale-down instellation
diff --git a/src/solver.jl b/src/solver.jl
@@ -73,7 +73,7 @@ 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_int | 4: tgt_olr
+    - `sol_type::Int`                   solution type, 1: tmp_surf | 2: skin | 3: flux_int | 4: tgt_olr
     - `chem_type::Int`                  chemistry type (see wiki)
     - `convect::Bool`                   include convection
     - `sens_heat::Bool`                 include sensible heating
@@ -263,7 +263,6 @@ 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_int^4
                 resid[1] = atmos.flux_tot[1] - atmos.flux_int
 
             elseif (sol_type == 4)
@@ -401,8 +400,7 @@ 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_int  = %.2f K",     atmos.tmp_int)
-            @info @sprintf("    f_int    = %.2f W m-2", atmos.flux_int)
+            @info @sprintf("    flux_int = %.2f W m-2", atmos.flux_int)
         elseif (sol_type == 4)
             @info @sprintf("    tgt_olr  = %.2f W m-2", atmos.target_olr)
         end
