Running the model

First, follow the Getting started instructions. Only read-on once you have confirmed that the code is working.

Input data files

The minimal input data required to run the model will have been downloaded automatically. If you require more data, such as additional stellar spectra or opacities, then these can also be easily obtained using the get_data script in the AGNI root directory. To see how to use this script, run it without arguments like so:

./src/get_data.sh

Tutorials

There are Jupyter notebooks containing tutorials in the tutorials/ directory 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. The best way to do this is to add RAD_DIR=path/to/socrates/folder/ to your shell rc file (e.g. ~/.bashrc).

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. There are examples in res/config/. The default configuration file contains comments explaining the purpose of each parameter, although some are explained in greater detail below. Take care to format the variables in the TOML file correctly. There are no 'default values'. Not all parameters are required in all cases, but the model will return an error naming any parameters which are both necessary and absent.

Broadly, the configuration files are broken up into four sections:

• [planet] - general characteristics of the planet
• [files] - input/output files and other paths
• [composition] - atmospheric composition and chemistry
• [execution] - what the model should do
• [plots] - which plots should be produced

Some parameters:

• files.input_sf is the file path to the "spectral file" containing opacity data. Several spectral files are packged with AGNI, but you can find more online via the Open Science Framework.

• 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 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
  • newton : the Newton-Raphson algorithm is used
  • gauss : the Gauss-Newton algorithm is used
  • levenberg : the Levenberg–Marquardt algorithm is used

• execution.initial_state describes the initial temperature profile applied to the atmosphere. This is a list of strings which are applied in the given order, which allows the user to describe a specific state as required. The descriptors are listed below, some of which take a single argument that needs to immediately follow the descriptor in the list order.

  • dry : integrate the dry adiabatic lapse rate from the surface upwards
  • str, arg : apply an isothermal stratosphere at arg kelvin
  • iso, arg : set the whole atmosphere to be isothermal at arg kelvin
  • csv, arg : set the temperature profile using the CSV file at the file path arg
  • sat, arg : apply Clausius-Clapeyron saturation curve for the gas arg
  • ncdf, arg : load profile from the NetCDF file located at arg
  • loglin, arg : log-linear profile between tmp_surf at the bottom and arg at the top

  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, 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)
  • 3 : Equilibrium, with condensation (condensates rained out)

Outputs

Results are optionally plotted and animated, and data will be saved as NetCDF or CSV files.

Python

It is possible to interact with the model using Python. This is best done with the juliacall package from PythonCall.jl, and is implemented this way in the PROTEUS framework.