Installation

Prerequisites

  • A working Python installation, including the numpy package.
  • A Fortran compiler (e.g. “gfortran”)

Download Code

Download petitRADTRANS from Gitlab, or clone it from GitLab via

git clone git@gitlab.com:mauricemolli/petitRADTRANS.git

Note

We are working on making petitRADTRANS available via pip install and anaconda, and providing as setup script. In the meantime, please carry out the (few) steps below.

Download opacity data

Download the opacity and input data (4.3 GB), unzip them, and put the “input_data” folder into the “petitRADTRANS” folder (i.e. the same folder where the source is, if you clone from gitlab, this should be the petitRADTRANS folder in the petitRADTRANS folder). This contains the necessary files to run petitRADTRANS, and the low resolution (\(\lambda/\Delta\lambda=1000\)) opacity files. The high resolution (\(\lambda/\Delta\lambda=10^6\)) opacity data (about 240 GB if you want to get all species) can be accessed and downloaded via Dropbox here. To install them, create a folder called “line_by_line” in the “input_data/opacities/lines” folder. Then put the folder of the absorber species you downloaded in there.

Installation

  • In the terminal, enter the petitRADTRANS folder containing the source (.py and .f90 files) (cd petitRADTRANS).
  • Type the following in the terminal chmod +x make.sh, and press Enter.
  • Type the following in the terminal ./make.sh, and press Enter. A lot of text will appear while the Fortran subroutines are being built. If you use Anaconda, see the first installation tip below before carrying out this step.
  • Type ls in the terminal and press Enter. If everything has worked you should see three files with the “.so” extension in the folder. If you are experiencing problems see the installation tips below.
  • Open the “.bash_profile” or “.bashrc” file (depending on your operating system) in your home directory. Add the following as a new line to the file (you may have to use sudo for modifying this file).
export PYTHONPATH=Path of the folder containing the petitRADTRANS source/:$PYTHONPATH

Attention

Don’t forget to adapt the path in the line above :) ! If you clone petitRADTRANS from gitlab, this should be the path of the top-level petitRADTRANS folder containing the petitRADTRANS source folder. If you are uncertain what the absolute path of the folder containing the petitRADTRANS source folder is, then switch to that folder in the terminal, type “pwd”, and press Enter. You can then just copy-paste that path. Don’t forget to put a dash “/“ at the end of the path. Close and reopen the terminal such that it will set the Python path correctly.

Installation tips

  • When running “make.sh”, the shell script will call a program named “f2py”. f2py will compile the Fortran subroutines used by petitRADTRANS, and wrap them for use in Python. f2py is part of the Python numpy package. If you are running Anaconda and use different Python environments, it is important that you activate the Python environment that you want to run petitRADTRANS in before running “make.sh”. Only then will the Fortran subroutines be build with the correct f2py version (using the Python and numpy version valid within the Anaconda environment).
  • If you put the petitRADTRANS folder in a protected area of your file system (like “/Applications” on Mac OS) you may have to carry out all installation steps with the “sudo” command preceding the actual terminal commands chmod and ./make.sh, otherwise you may run into “Permission denied” errors. You will have to enter your password when doing this.
  • Sometimes ./make.sh will not work. In this case copy the lines contained within “make.sh” individually to the clipboard, paste them to the terminal, and press Enter.

Testing the installation

Open a new terminal window (this will source the PYTHONPATH). Then open python and type

from petitRADTRANS import Radtrans
atmosphere = Radtrans(line_species = ['H2O'])

This should produce the following output:

 Read line opacities of H2O...
Done.