Merge pull request #87 from nichollsh/hn/h2

H2 Chabrier EOS, Runge-Kutta hydrostatic integration, self-gravity

.github/workflows/install_and_test.yml

@@ -22,12 +22,15 @@ jobs:
           sudo apt update
           sudo apt-get install libnetcdff-dev netcdf-bin gfortran gcc
 
-      # Setup AGNI
+      # Setup Julia
       - name: Setup Julia
         uses: julia-actions/setup-julia@v2
         with:
           version: '1.11'
 
+      - name: Cache Julia
+        uses: julia-actions/cache@v2
+
       # Setup SOCRATES
       - name: Get SOCRATES
         uses: actions/checkout@v4
@@ -65,6 +68,6 @@ jobs:
         run: |
           export RAD_DIR="/home/runner/work/AGNI/AGNI/SOCRATES"
           export LD_LIBRARY_PATH=""
-          ./test/runtests.jl
+          julia --project=. -e 'using Pkg; Pkg.test()'
 
 

Project.toml

@@ -1,7 +1,7 @@
 name = "AGNI"
 uuid = "ede838c1-9ec3-4ebe-8ae8-da4091b3f21c"
 authors = ["Harrison Nicholls <[email protected]>"]
-version = "1.1.1"
+version = "1.2.0"
 
 [deps]
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
@@ -25,5 +25,4 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 TOML = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
 
 [compat]
-Interpolations = "0.15.1"
 julia = ">= 1.10"

README.md

@@ -20,7 +20,7 @@
 </p>
 
 <p align="center">
-  <b>A radiative-convective atmosphere model for lava planets</b>
+  <b>A radiative-convective model for lava planet atmospheres</b>
 </p>
 
 

agni.jl

@@ -2,21 +2,25 @@
 
 # Don't show plot windows
 ENV["GKSwstype"] = "100"
+AGNI_DIR = dirname(abspath(@__FILE__))
 
 # Check RAD_DIR
 if !("RAD_DIR" in keys(ENV))
     error("Cannot find SOCRATES! Have you set RAD_DIR?")
 end
 
-AGNI_DIR = dirname(abspath(@__FILE__))
+# Check SOCRATES.jl
+SOCjl = joinpath([abspath(ENV["RAD_DIR"]),"julia","src","SOCRATES.jl"])
+if !isfile(SOCjl)
+    error("Cannot find SOCRATES library! Tried: '$SOCjl'")
+end
 
 # Activate environment
 import Pkg
 Pkg.activate(AGNI_DIR)
 
 # Include AGNI
-include(joinpath([AGNI_DIR,"src","AGNI.jl"]))
-import .AGNI
+import AGNI
 
 # Run
 if AGNI.main()

codemeta.json

@@ -19,5 +19,5 @@
   "keywords": "physics, radiative transfer, exoplanets, astronomy, convection, radiation, planets, atmospheres",
   "license": "GPL v3.0",
   "title": "AGNI",
-  "version": "1.1.1"
+  "version": "1.2.0"
 }

docs/src/model/index.md

@@ -17,7 +17,7 @@ Convection is a turbulent process which occurs across more than one spatial dime
 
 MLT directly calculates the energy flux associated with convective heat transport, and thus is the preferred parameterisation within the model. It assumes that parcels of gas are diffused over a characteristic _mixing length_, transporting energy in the process. This requires choosing a scale for this mixing length, but in practice this has very little impact on the results from the model.
 
-The atmosphere is assumed to be hydrostatically supported. Gas densities are combined using Amagat's additive volume law. The densities of each gas are calculated nominally using the Van der Walls equation of state. AQUA can be used as the EOS for water. The model will fallback to the ideal gas EOS if AQUA and VdW data are not available.
+The atmosphere is assumed to be hydrostatically supported. Gas densities are combined using Amagat's additive volume law. The densities of each gas are nominally calculated using the Van der Walls equation of state (EOS). AQUA is implemented as the EOS for water. The Chabrier+2019 EOS is implemented as the EOS for hydrogen. AGNI will fallback to the ideal gas EOS for otherwise unsupported gases.
 
 
 ## Phase change
@@ -37,7 +37,7 @@ AGNI is designed for modelling planetary atmospheres with high surface pressures
 It is necessary to tell AGNI what kind of atmospheric solution to solve for. There are currently a few options available set by the `solution_type` variable in the configuration file.
 * (1) Aim to conserve energy fluxes throughout the column. The surface temperature is fixed.
 * (2) Aim to conserve energy fluxes throughout the column. The surface temperature is set by energy transport through a solid conductive boundary layer of thickness $d$ such that $T_s = T_m - \frac{Fd}{k}$, where $T_m$ is the mantle temperature and $k$ is the thermal conductivity.
-* (3) Solve for a state such that the flux carried at each level is equal to $F_{\text{eff}} = \sigma T_{\text{eff}}^4$, representing the rate at which a planet is losing energy into space.
+* (3) Solve for a state such that the flux carried at each level is equal to $F_{\text{net}} = \sigma T_{\text{net}}^4$, representing the rate at which a planet is losing energy into space.
 
 ### Construction
 The atmosphere is constructed of $N$ levels (cell-centres), corresponding to $N+1$ interfaces (cell-edges). The RT model takes cell-centre temperatures $T_i$, pressures $p_i$, geometric heights, and mixing ratios as input variables at each level $i$. As well as the surface temperature and incoming stellar flux. In return, it provides cell-edges spectral fluxes $F_i$ at all $N+1$ interfaces for LW & SW components and upward & downward streams. Convective fluxes can be estimated using the MLT scheme, condensation fluxes from the condensation scheme, and sensible heat from a simple TKE approximation.

docs/src/setup.md

@@ -19,28 +19,35 @@ Follow the steps below in order to setup the code.
 4. Setup SOCRATES by doing either **ONE** of the following...
     - Follow the instructions on the [SOCRATES GitHub](https://github.com/nichollsh/SOCRATES) page
     - Run `source src/get_socrates.sh`
-5. `julia -e 'using Pkg; Pkg.activate("."); Pkg.build()'`
+5. `bash src/get_agni.sh`
 AGNI is now installed as a package into a Julia environment in the AGNI
-directory. This will also have downloaded some basic input data.
-You should run the tests next.
+directory. This will also have downloaded some basic input data, and have run the tests.
 
 !!! tip
-    The `src/get_socrates.sh` script automatically adds the radiation code to your
+    The `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.
 
 ## Testing
-Now try running the tests in your terminal.
+If you want to run the tests manually, simply use the script in the `test/` folder...
 ```bash
-julia ./test/runtests.jl
+julia test/runtests.jl
 ```
 This will print information on whether tests passed or failed.
 
-## Coupling with FastChem
-This can be enabled using the configuration file parameter `composition.chem_type`. Of
-course, it is first necessary to setup FastChem, which can be done by running
-`source src/get_fastchem.sh` and then setting the `FC_DIR` environment variable.
+## Updating
+It's important that you keep AGNI up to date, especially if you are using as part of
+the [PROTEUS framework](https://github.com/FormingWorlds/PROTEUS). Use this script to
+automatically pull changes from GitHub and download any required data files.
+```bash
+bash src/get_agni.sh
+```
 
 ## Using the code
 See [Running the model](@ref) for information on using the code.
 See [Troubleshooting](@ref) for troubleshooting advice.
+
+## Coupling with FastChem
+This can be enabled using the configuration file parameter `composition.chem_type`. Of
+course, it is first necessary to setup FastChem, which can be done by running
+`source src/get_fastchem.sh` and then setting the `FC_DIR` environment variable.

docs/src/troubleshooting.md

@@ -30,6 +30,7 @@ Check the path in the configuration file. Download additional spectral files usi
 ```bash
 ./src/get_data.sh steam
 ```
+Other spectral files can be downloaded from OSF: https://osf.io/vehxg/.
 
 ## Cannot find FastChem
 You need to install FastChem. This can be done by running the command:

misc/L98-59d.ipynb

@@ -28,18 +28,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "# Import AGNI\n",
     "ROOT_DIR = abspath(joinpath(pwd(),\"../\"))\n",
     "using AGNI\n",
-    "import AGNI.atmosphere as atmosphere\n",
-    "import AGNI.solver as nl\n",
-    "import AGNI.setpt as setpt\n",
-    "import AGNI.dump as dump\n",
-    "import AGNI.plotting as plotting\n",
     "\n",
     "# Disable logging from AGNI module\n",
     "AGNI.setup_logging(\"\",1)"
@@ -140,7 +135,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "solver_success = nl.solve_energy!(atmos,\n",
+    "solver_success = solver.solve_energy!(atmos,\n",
     "                                    sol_type=1,\n",
     "                                    sens_heat=true,\n",
     "                                    latent=true,\n",
@@ -187,7 +182,7 @@
     "    atmosphere.generate_pgrid!(atmos)\n",
     "\n",
     "    # Run model\n",
-    "    solver_success = nl.solve_energy!(atmos,\n",
+    "    solver_success = solver.solve_energy!(atmos,\n",
     "                                    sol_type=3,\n",
     "                                    method=1,\n",
     "                                    dx_max=300.0,\n",
@@ -212,7 +207,7 @@
    "source": [
     "for (i, atm) in enumerate(atm_arr)\n",
     "    @printf(\"Writing index %d \\n\",i)\n",
-    "    dump.write_ncdf(atm, joinpath(atm.OUT_DIR, \"$i.nc\"))\n",
+    "    save.write_ncdf(atm, joinpath(atm.OUT_DIR, \"$i.nc\"))\n",
     "end\n",
     "@printf(\"Done! \\n\")"
    ]