Merge pull request #70 from nichollsh/hn/slim

Moved themodynamic data

.gitignore

@@ -28,6 +28,7 @@ res/spectral_files/*
 res/stellar_spectra/*
 res/surface_albedos/*
 res/realgas/*
+res/thermodynamics/*.nc
 !res/*/_readme.txt
 
 # Output files

CITATION.cff

@@ -5,7 +5,7 @@ authors:
   given-names: "Harrison"
   orcid: "https://orcid.org/0000-0002-8368-4641"
 title: "AGNI"
-version: 0.9.0
+version: 0.10.0
 doi: 10.xx/xx.xx
 date-released: 2024-09-20
 url: "https://github.com/nichollsh/AGNI"

Project.toml

@@ -1,7 +1,7 @@
 name = "AGNI"
 uuid = "ede838c1-9ec3-4ebe-8ae8-da4091b3f21c"
 authors = ["Harrison Nicholls <harrison.nicholls@physics.ox.ac.uk>"]
-version = "0.9.0"
+version = "0.10.0"
 
 [deps]
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"

README.md

@@ -40,9 +40,6 @@ See the [Getting Started](https://nichollsh.github.io/AGNI/dev/setup/) page in t
 ## Repository structure
 * `agni.jl`         - The main AGNI executable
 * `LICENSE.txt`     - License for use and re-use
-* `get_fastchem.sh` - Download and setup FastChem
-* `get_socrates.sh` - Download and setup SOCRATES
-* `get_data.sh`     - Download input data files
 * `deps/`           - Package build scripts
 * `docs/`           - Documentation source files
 * `misc/`           - Miscellaneous files

codemeta.json

@@ -19,5 +19,5 @@
   "keywords": "physics, radiative transfer, exoplanets, astronomy, convection, radiation, planets, atmospheres",
   "license": "GPL v3.0",
   "title": "AGNI",
-  "version": "0.9.0"
+  "version": "0.10.0"
 }

deps/build.jl

@@ -19,7 +19,7 @@ end
 
 # Download basic data
 println("Get data")
-get_data = joinpath(ROOT_DIR,"get_data.sh")
+get_data = joinpath(ROOT_DIR,"src/get_data.sh")
 run(`bash $get_data basic`)
 
 println("Build completed")

docs/src/setup.md

@@ -25,7 +25,7 @@ directory. This will also have downloaded some basic input data.
 You should run the tests next.
 
 !!! tip
-    The `get_socrates.sh` script automatically adds the radiation code to your
+    The `src/get_socrates.sh` script automatically adds the radiation code to your
     environment with the variable `RAD_DIR`, which points to the SOCRATES installation.
     This variable must be set whenever AGNI is being used.
 

docs/src/troubleshooting.md

@@ -1,18 +1,18 @@
 # Troubleshooting
-This page may be useful if you are having problems. However, I would suggest that 
+This page may be useful if you are having problems. However, I would suggest that
 you also double check the [Getting started](@ref) instructions.
 
 ## Julia errors on start, potentially referencing the CURL library
-It is important that the shell environment variable `LD_LIBRARY_PATH` is 
-not set when running AGNI. This will cause Julia to use the wrong libraries, 
+It is important that the shell environment variable `LD_LIBRARY_PATH` is
+not set when running AGNI. This will cause Julia to use the wrong libraries,
 which will causes problems. You can unset this variable or reset using either of the
-following commands 
+following commands
 ```bash
 unset LD_LIBRARY_PATH
 export LD_LIBRARY_PATH=""
 ```
 If this does not help, it's possible that you are using a Julia distribution provided by
-your system package manager. It's important that you only use Julia distributed from the 
+your system package manager. It's important that you only use Julia distributed from the
 official website.
 
 
@@ -24,15 +24,15 @@ or you haven't added it to your `PATH`.
 
 ## Spectral file does not exist
 Check the path in the configuration file. Download additional spectral files using the
-`get_data` script in the AGNI root directory. For example, for additional pure-steam 
+`get_data` script in the AGNI root directory. For example, for additional pure-steam
 spectral files you would run
-```bash 
-./get_data.sh steam
+```bash
+./src/get_data.sh steam
 ```
 
 
 ## Finally...
-If you are still stuck, or feel that there is a problem with the code, then 
+If you are still stuck, or feel that there is a problem with the code, then
 you can contact the authors using the information on the main page.
 
 

src/atmosphere.jl

@@ -324,7 +324,7 @@ module atmosphere
         end
 
         # Code versions
-        atmos.AGNI_VERSION = "0.9.0"
+        atmos.AGNI_VERSION = "0.10.0"
         atmos.SOCRATES_VERSION = readchomp(joinpath(ENV["RAD_DIR"],"version"))
         @debug "AGNI VERSION = $(atmos.AGNI_VERSION)"
         @debug "Using SOCRATES at $(ENV["RAD_DIR"])"

get_data.sh → src/get_data.sh

@@ -13,18 +13,21 @@ fi
 
 # Root and resources folders
 root=$(dirname $(realpath $0))
-res="$root/res/"
+root=$(realpath "$root/..")
+res="$root/res"
 spfiles=$res/spectral_files
 stellar=$res/stellar_spectra
 surface=$res/surface_albedos
 realgas=$res/realgas
+thermo=$res/thermodynamics
 
 # Make basic data folders
 mkdir -p $res
 mkdir -p $spfiles
 mkdir -p $stellar
 mkdir -p $surface
 mkdir -p $realgas
+mkdir -p $thermo
 
 # Help strings
 help_basic="Get the basic data required to run the model"
@@ -33,6 +36,7 @@ help_steam="Get pure-steam spectral files"
 help_stellar="Get a collection of stellar spectra"
 help_surfaces="Get a collection of surface single-scattering albedos"
 help_realgas="Get a real-gas EOS coefficients and lookup tables"
+help_thermo="Get lookup data for thermodynamics (heat capacities, etc.)"
 help="\
 Helper script used to download and unpack data used to run the model.
 
@@ -52,6 +56,8 @@ Where [TARGET] can be any of the following:
         $help_surfaces
     realgas
         $help_realgas
+    thermodynamics
+        $help_thermo
 "
 
 # Generic OSF downloader function
@@ -77,6 +83,17 @@ function osf {
     return 0
 }
 
+# Get zip file
+function get_zip {
+    # $1 = OSF identifier
+    # $2 = target folder
+
+    zipfile=".temp.zip"
+    osf $1 $2 $zipfile
+    unzip -oq $2/$zipfile -d $2
+    rm $2/$zipfile
+}
+
 # Handle request for downloading a group of data
 function handle_request {
     case $1 in
@@ -92,7 +109,9 @@ function handle_request {
             osf b5gsh $spfiles/Dayspring/256/ Dayspring.sf
             osf dn6wh $spfiles/Dayspring/256/ Dayspring.sf_k
 
-            osf 2qdu8 $res/stellar_spectra sun.txt
+            osf 2qdu8 $stellar sun.txt
+
+            get_zip 4m5x8 $thermo
             ;;
 
         "highres")
@@ -153,10 +172,15 @@ function handle_request {
             echo $help_realgas
 
             # AQUA PT lookup
-            zipfile=".aqua_temp.zip"
-            osf uqrdx $realgas $zipfile
-            unzip -oq $realgas/$zipfile -d $realgas
-            rm $realgas/$zipfile
+            get_zip uqrdx $realgas
+
+            ;;
+
+        "thermodynamics")
+            echo $help_thermo
+
+            # NetCDF files from OSF
+            get_zip 4m5x8 $thermo
 
             ;;
 

get_fastchem.sh → src/get_fastchem.sh

@@ -1,8 +1,11 @@
 #!/bin/bash
 # Download and compile fastchem
 
+root=$(dirname $(realpath $0))
+root=$(realpath "$root/..")
+
 # Download via HTTPS only
-fcpath="fastchem"
+fcpath=$(realpath "$root/fastchem")
 rm -rf "$fcpath"
 
 git clone https://github.com/NewStrangeWorlds/FastChem.git "$fcpath"

get_socrates.sh → src/get_socrates.sh

@@ -5,7 +5,9 @@
 if [ -n "$RAD_DIR" ]; then
     echo "WARNING: You already have SOCRATES installed"
     echo "         RAD_DIR=$RAD_DIR"
-    exit 1
+    echo "Continuing..."
+    echo ""
+    sleep 5
 fi
 
 # Check SSH access to GitHub
@@ -17,7 +19,9 @@ else
 fi
 
 # Download (using SSH if possible)
-socpath="$(realpath .)/socrates"
+root=$(dirname $(realpath $0))
+root=$(realpath "$root/..")
+socpath=$(realpath "$root/socrates")
 rm -rf "$socpath"
 if [ "$use_ssh" = true ]; then
     git clone git@github.com:nichollsh/SOCRATES.git "$socpath"