This is a code that uses the pymultinest package (Feroz et al. 2009; Buchner et al. 2014) to calculate and fit Lyman-alpha (Lyα) damping-wing absorption, both from the IGM and local damped-Lyα absorbing (DLA) systems. The main functionality is described in D'Eugenio et al. (2023) and Hainline et al. (2024). Below, its usage is illustrated with examples.
First, obtain and install the latest version of the code, which can be done via pip. You can clone the repository by navigating to your desired installation folder and using
git clone https://github.com/joriswitstok/lymana_absorption.git
Running the code requires the following Python packages:
numpyscipyastropympi4pypymultinestspectrescornermatplotlibseabornmock
Most of these modules are easily installed via the file lya3.yml provided in the main folder, which can be used to create an conda environment in Python 3 that contains all the required packages (see the conda documentation on environments for more details). However, the lymana_absorption code and several MPI-related packages (mpi4py and pymultinest) should be installed via pip to ensure properly linking to a local MPI installation (if using MPI functionality).
If you have conda installed and set up as a python distribution, creating an environment can be achieved with:
conda env create -f lya3.yml
Before running the code, the environment needs to be activated using
conda activate lya3
By default, the terminal will indicate the environment is active by showing a prompt similar to:
(lya3) $
After navigating into the installation folder (see Cloning), the lymana_absorption code is then installed into your python distribution via pip (pip3). NB: the pip executable related to the conda environment (or any other python distribution) should be used here - to verify which pip executable is active, use which pip. For example:
(lya3) $ which pip3
pip3 is /Users/Joris/anaconda3/envs/lya3/bin/pip3
(lya3) $ cd lymana_absorption
(lya3) $ ls
LICENSE lya3.yml setup.py
README.md lymana_absorption
build lymana_absorption.egg-info
(lya3) $ pip3 install .
This section goes through an example usage case of lymana_absorption by running the file example_plots.py (located in the examples folder). The first step is to activate the environment as explained in the previous section. So, starting from the main folder, the script would be run as follows:
$ conda activate lya3
(lya3) $ cd lymana_absorption/examples/
(lya3) $ python example_plots.py
If it has finished successfully, several figures illustrating IGM and DLA transmission curves will have been saved in the examples folder. For instance, it will plot a comparison between various IGM and DLA transmission curves for a source at z = 9:
A more advanced example usage case is illustrated by running the file example_fit.py (again located in the examples folder). This script performs a fitting routine to the observed spectrum of GS-z13 (as in Hainline et al. 2024), given a resolution curve and an intrinsic model spectrum.