LaCE

Lyman-alpha Cosmology Emulator. This code is a Gaussian process emulator for the 1D flux power spectrum of the Lyman-alpha forest, and was used to generate the results shown in https://arxiv.org/abs/2011.15127. Please cite this article if you use this emulator in your research.

Installation

(Last update Oct 27)

To install on NERSC, you first need to load python module with module load python. This is not necessary for personal computers.
Create a new conda environment. It is usually better to follow python version one or two behind. In October 2023, latest is 3.11, so we recommend 3.10.

conda create -n lace python=3.10
conda activate lace

If you are not a developer, simply pip install. The following command will take care of the dependencies.

pip install git@github.com:igmhub/LaCE.git

If you are a developer, first clone the repo into your machine and perform an editable installation:

git clone git@github.com:igmhub/LaCE.git
cd LacE
pip install -e .

If you want to use notebooks via JupyterHub, you'll also need to download ipykernel:

pip install ipykernel
python -m ipykernel install --user --name lace --display-name lace

Nyx users:

You may need to add the Nyx path as an enviroment variable in your notebook kernel. The first is done writting in the kernel.json file:

 "env": {
  "NYX_PATH":"path_to_Nyx"
 }

For convenience, you could also add the Nyx path as an environment variable.

To improve the reading time, you can precompute all cosmological information needed using CAMB. This is done by running the script

python src/lace/scripts/compute_nyx_emu_cosmo.py

Note that you may need to update it as explained inside the file.

Emulator parameters:

These are the parameters that describe each individual P1D(k) power spectrum. We have detached these from redshift and traditional cosmology parameters.

Cosmological parameters:

Delta2_p is the amplitude of the (dimensionless) linear spectrum at k_p = 0.7 1/Mpc

n_p is the slope of the linear power spectrum at k_p

alpha_p is the running of the linear power spectrum at k_p

f_p is the (scale-independent) logarithmic growth rate

The current version of the emulator, relased in this repo, does not emulate alpha_p and f_p. However, these parameters are stored in the P1D archive.

IGM parameters:

mF is the mean transmitted flux fraction in the box (mean flux)

sigT_Mpc is the thermal broadening scale in comoving units, computed from T_0 in the temperature-density relation

gamma is the slope of the temperature-density relation

kF_Mpc is the filtering length (or pressure smoothing scale) in inverse comoving units

Tutorials:

In the Notebooks folder, there are several tutorials one can run to learn how to use the emulators and archives. The Durham2023_LaCETutorial is the more complete one that shows how to get the different archives and run them with the available emulator options.