Readme

Folders, codes and readme made by Samuel Mesquita 2025

In this readme I will explain what are the different important files and folders for future usage.
I have made all of those during my 2025 6-month internship.

Validation of structure formation

Here we aim to validate structure formation in Dyablo.
Check folder validation.

The most important codes here are :

my_hmf_cmf.ipynb

Notebook that aimed at making sure I was able to confidently code the HMF (Halo Mass Function) and CMF (Conditional Mass Function).

my_hmf_cmf_lib.py

Python library that contains all the functions that I have coded in the aforementioned notebook and more. Those functions can be use to easily compute values like the fraction of collapsed in a region, or plot the theoretical vs empirical CMF...

hmf_cmf_dyablo_snap.ipynb

Notebook that allows the study of a simulation snapshot from Dyablo.

tri_z_R0_delta_fit.py

Script running PySR (Cranmer, 2023) to try and find a fit to the fraction of collapsed mass in 3D (redshift, radius of the region, density of the region). Its output is fits.txt (python3 tri_z_R0_delta_fit.py > fits.txt).
The 2D fit I found by setting R0 to 1 Mpc seemed correct. I have a harder time finding a 3D fit that works correctly.

NB : Here stylesheet.mplstyle is simply my way to use matplotlib.

The folders here are :

datastageM2

Symbolic link to the data of one simulation that I've studied. It contains snapshots of the simulation at different and also some metadata.

outputs

Folder automatically created by PySR when trying to find a fit. Not very important.

previous_codes

All the scripts and notebooks I have made during my internship. Most of them are not useful and the rest were created for me to able to easily make plots for my internship report/oral.

saved_results

Here you may find images of my results or data that comes from some computation :
saved_results
├── data
│ ├── R_vary - csv files for the computation of the fraction of collapsed mass for different value of the radius of the subregions.
│ └── Particle data - Save of the data I used to my studies (in case the symbolic link breaks).
├── misc - Miscellaneous images that don't belong in z_vary_results.
└── z_vary_results - Images (svg+pdf) for the results of my study of the simulation. There is : the Halo Mass function, the Conditional Mass Function depending on the environment ; the comparison between the empirical et theoretical fraction of collapsed mass.

Improving Dyablo's ionization module

Here we aim to improve Dyablo's ionization module.
Check folder development.

SourceUpdate_Ionization_Chem.cpp

Dyablo file that I've modified with my fit. I've mostly modified lines 71 to 103. Also at the beginning of the function with auxialiary values like redshift, fstar, dnl...

ProbeSnape.ipynb

Allows the study of a simulation, notably the SFR and the evolution of the average ionization fraction and density of ionized gas in the simulation.

cosmo_units.ini

The initial conditions I have used to run my Dyablo simulations.

The important variables here are :

ndot                 = 1.5e48
rho_crit             = 16e-28
write_variables      = xe,rho,zre

ndot is the stellar emissivity which is the number of photons emitted by second by solar mass.

rho_crit was used before but serve no purpose anymore since I have added my code.

write_variables, zre was previously used to store the value of the redshift for the end of reionization. Now the purpose of zre is to store the stellar mass density in each cell.

We also made it so the size of each cell is 1 Mpc to work well with the fit.