FastChem accessed via FC_DIR env variable, rather than through cfg. C…

…onsistent with SOCRATES RAD_DIR
nichollsh · Jul 4, 2024 · 45012c2 · 45012c2
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diff --git a/.gitignore b/.gitignore
@@ -5,6 +5,10 @@ radiation_code.lock
 socrates 
 SOCRATES 
 
+# FastChem folder 
+fastchem
+FastChem 
+
 # Package 
 deps/*.log
 test/out/

diff --git a/docs/src/usage.md b/docs/src/usage.md
@@ -9,12 +9,16 @@ of the repository.
 ## General execution
 The environment variable `RAD_DIR` must point to the SOCRATES installation 
 directory. This is required for AGNI to find the SOCRATES libraries, and can be 
-done by running `source path/to/set_rad_env` in your terminal.       
+done by running `source path/to/socrates/set_rad_env` in your terminal.       
 
 Then to use the model, simply run `./agni.jl [cfg]` where `[cfg]` is the path 
 to the required configuration file. If `[cfg]` is not passed, then the default 
 configuration will be used.
 
+To calculate equilibrium chemistry self-consistently with the climate, FastChem
+is coupled to AGNI. For AGNI to find FastChem, the environment variable `FC_DIR`
+must point to the FastChem installation directory.
+
 ## Configuration 
 AGNI configuration files are formatted using [TOML](https://toml.io/en/). There 
 are examples in `res/config/`. The default configuration file contains comments 
@@ -53,7 +57,7 @@ Some parameters:
 
     For example, setting `initial_state = ["dry", "sat", "H2O", "str", "180"]` will set T(p) to follow the dry adiabat from the surface, the water condensation curve above that, and then to be isothermal at 180 K until the top of the model.
 
-* `composition.chem_type` describes the type of chemistry to implement within the model. This is handled externally by FastChem. You must also provide the path to the FastChem installation directory `fastchem_path` in the `[files]` section. The allowed values (integers) are...
+* `composition.chem_type` describes the type of chemistry to implement within the model. This is handled externally by FastChem, so you must set the environment variable `FC_DIR` to point to the FastChem directory. The allowed values (integers) are...
      - 0 : Disabled 
      - 1 : Equilibrium, gas phase only
      - 2 : Equilibrium, with condensation (condensates retained)

diff --git a/get_fastchem.sh b/get_fastchem.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+
+# Download via HTTPS only
+fcpath="fastchem"
+rm -rf "$fcpath"
+
+git clone https://github.com/NewStrangeWorlds/FastChem.git "$fcpath"
+
+# Compile FastChem
+cd "$fcpath"
+mkdir build
+cd build 
+
+cmake ".."
+make
+
+cd ..
+export FC_DIR="$(realpath $fcpath)"
diff --git a/res/config/55cnce_chem.toml b/res/config/55cnce_chem.toml
@@ -18,7 +18,6 @@ title = "Roughly 55 Cancri e @ fO2=IW"
     input_sf        = "res/spectral_files/nogit/Dayspring/256/Dayspring.sf"   
     input_star      = "res/stellar_spectra/hd97658.txt"                       
     output_dir      = "out/"       
-    fastchem_path   = "/Users/nichollsh/Projects/FastChem/"
 
 [composition]
     p_top           = 1e-7    

diff --git a/res/literature_data/profile/readme.txt b/res/literature_data/profile/readme.txt
@@ -12,10 +12,5 @@ Their Seff = 1 corresponds to a value of 341.5 Wm−2, which comes from:
 This can be achieved by setting the following parameters in AGNI:
  - s0_fact = 0.6652   
  - zenith_angle = 60.0
- - albedo_b = 0.18
+ - albedo_b = 0.0, but rayleigh scattering enabled
  - instellation = 1366 * S_eff
-
-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_int = sigma (T_int)^4 = OTR + F_UP_SW - F_DN_SW 
-
diff --git a/res/literature_data/runaway/readme.txt → res/literature_data/readme.txt b/res/literature_data/runaway/readme.txt → res/literature_data/readme.txt
diff --git a/src/AGNI.jl b/src/AGNI.jl
@@ -196,7 +196,7 @@ module AGNI
         # Hello
         @info "Hello"
 
-        # Temp folders
+        # Temp folders for OUTPUT
         dir_fastchem = joinpath(output_dir,"fastchem/")
         dir_frames   = joinpath(output_dir,"frames/")
         rm(dir_fastchem,force=true,recursive=true)
@@ -225,7 +225,6 @@ module AGNI
         mf_dict::Dict{String, Float64}  = Dict{String, Float64}()
         mf_path::String                 = ""
         use_all_gases::Bool             = cfg["composition"]["include_all"]
-        fastchem_path::String           = ""
         if haskey(cfg["composition"],"p_surf")
             # set composition using VMRs + Psurf
             if haskey(cfg["composition"],"vmr_dict")
@@ -259,7 +258,6 @@ module AGNI
                 @error "Misconfiguration: FastChem coupling is incompatible with AGNI condensation scheme"
                 exit(1)
             else
-                fastchem_path = cfg["files"]["fastchem_path"]
                 mkdir(dir_fastchem)
             end 
         end 
@@ -342,7 +340,6 @@ module AGNI
                                 tmp_int=tmp_int, albedo_s=albedo_s,
                                 thermo_functions=thermo_funct,
                                 C_d=turb_coeff, U=wind_speed,
-                                fastchem_path=fastchem_path,
                                 use_all_gases=use_all_gases
                         )
         atmosphere.allocate!(atmos,star_file)

diff --git a/src/atmosphere.jl b/src/atmosphere.jl
@@ -45,9 +45,10 @@ module atmosphere
         is_out_sw::Bool     # Contains data for SW calculation
 
         # Directories
-        ROOT_DIR::String
-        OUT_DIR::String
-        THERMO_DIR::String
+        ROOT_DIR::String        # path to AGNI root folder (containing agni.jl)
+        OUT_DIR::String         # path to output folder 
+        THERMO_DIR::String      # path to thermo data 
+        FC_DIR::String          # path to fastchem exec folder 
 
         # SOCRATES objects
         SOCRATES_VERSION::String
@@ -197,7 +198,6 @@ module atmosphere
 
         # FastChem stuff 
         fastchem_flag::Bool             # Fastchem enabled?
-        fastchem_path::String           # Path to fastchem installation folder (incl. executable)
         fastchem_work::String           # Path to fastchem dir inside AGNI output folder
 
         Atmos_t() = new()
@@ -264,7 +264,6 @@ module atmosphere
     - `flag_aerosol::Bool`              include aersols?   
     - `flag_cloud::Bool`                include clouds?   
     - `thermo_functions::Bool`          use temperature-dependent thermodynamic properties   
-    - `fastchem_path::String`           path to FastChem folder (empty string => disabled)   
     - `use_all_gases::Bool`             store information on all supported gases, incl those not provided in cfg
 
     Returns:
@@ -297,7 +296,6 @@ module atmosphere
                     flag_aerosol::Bool =        false,
                     flag_cloud::Bool =          false,
                     thermo_functions::Bool =    true,
-                    fastchem_path::String =     "",
                     use_all_gases::Bool =       false
                     )
 
@@ -630,23 +628,28 @@ module atmosphere
 
         # Fastchem 
         atmos.fastchem_flag = false 
-        if !isempty(fastchem_path)
+        if ("FC_DIR" in keys(ENV))
+
+            @debug "FastChem env has been set" 
+
             # check folder
-            atmos.fastchem_path = abspath(fastchem_path)
-            if !isdir(fastchem_path)
-                @error "Could not find fastchem folder at '$(fastchem_path)'"
+            atmos.FC_DIR = abspath(ENV["FC_DIR"])
+            if !isdir(atmos.FC_DIR)
+                @error "Could not find fastchem folder at '$(atmos.FC_DIR)'"
                 return 
             end 
-            atmos.fastchem_work = joinpath(atmos.OUT_DIR, "fastchem/")
+            atmos.fastchem_work = joinpath(atmos.OUT_DIR, "fastchem/")  # working directory
 
             # check executable 
-            atmos.fastchem_flag = isfile(joinpath(fastchem_path,"fastchem")) 
+            atmos.fastchem_flag = isfile(joinpath(atmos.FC_DIR,"fastchem")) 
             if !atmos.fastchem_flag 
-                @error "Could not find fastchem executable inside '$(atmos.fastchem_path)' "
+                @error "Could not find fastchem executable inside '$(atmos.FC_DIR)' "
                 return 
             else 
                 @info "Found FastChem executable"
             end 
+        else
+            @debug "FastChem env variable not set" 
         end 
 
         # Record that the parameters are set
@@ -1262,7 +1265,7 @@ module atmosphere
         count_elem_nonzero::Int = 0
 
         # Paths
-        execpath::String = joinpath(atmos.fastchem_path,"fastchem")             # Executable file 
+        execpath::String = joinpath(atmos.FC_DIR,       "fastchem")             # Executable file 
         confpath::String = joinpath(atmos.fastchem_work,"config.input")         # Configuration by AGNI
         chempath::String = joinpath(atmos.fastchem_work,"chemistry.dat")        # Chemistry by FastChem
 
@@ -1293,7 +1296,7 @@ module atmosphere
                 write(f,joinpath(atmos.fastchem_work,"elements.dat")*" \n\n")
 
                 write(f,"#Species data files    \n")
-                logK = joinpath(atmos.fastchem_path,"input/","logK/")
+                logK = joinpath(atmos.FC_DIR, "input/","logK/")
                 write(f,joinpath(logK,"logK.dat")*" "*joinpath(logK,"logK_condensates.dat")*" \n\n")
 
                 write(f,"#Accuracy of chemistry iteration \n")