CIV_forest

Codes to model the enrichment of the IGM, generate skewers of the CIV forest with Nyx and Cloudy simulations, analyze their auto-correlation, model and mask CGM absorbers, and perform forecasting on the model parameters with MCMC.

Main scripts:

1. cloudy_run/cloudy_grid*.in - scripts to run Cloudy models
   
2. cloudy_run/cloudy_utils.py - functions to automatically generate cloudy scripts, read in cloudy outputs, and compute the ionization fraction of a metal ion
   
3. halos_skewers.py - extract the halo catalogs from Nyx simulation and create models of the metal distribution
   
4. metal_frac_skewers.py - create skewers of ionic fraction by interpolating Cloudy outputs on Nyx skewers
   
5. prodrun_create_tau_skewers.py - create the metal-line forest skewers for the uniform enrichment model
   
6. prodrun_metal_skewers.enrichment.py - create the metal-line forest skewers for the inhomogeneous enrichment model
   
7. metal_corrfunc.py - compute the CIV correlation function
   
8. civ_cgm.py - modeling the abundance of CGM absorbers based on existing observations
   
9. civ_find_new.py - automated detection and masking of CGM absorbers
   
10. compute_model_grid_civ_new.py - generate mock datasets and compute their covariances for all models (note: this code lives at https://github.com/enigma-igm/enigma/enigma/reion_forest/)
    
11. mcmc_inference.py - performing inference using MCMC sampler
    
12. misc.py - various convenience functions