.. _doc_overview:

Overview of the modules
==============================

COLIBRÌ consists of simple Python files. One, named ``constants.py`` is just a collection of physical constants, useful numbers and conversion factors between different units of measurement. A second one, ``useful_functions.py`` contains some routines of everyday life for a cosmologist. The file ``fourier.py`` contains routines to perform Fourier and Hankel transforms. The remaining ones each contain one or more Python classes. Moreover two folders cotaining tests and Python notebooks are provided with the code.

In the following sections we briefly present the codes.
The documentation for both classes and built-in methods is inside the code as well as on `ReadTheDocs <https://colibri-cosmology.readthedocs.io/en/latest/>`_ .

.. _cosmology_overview:

`cosmology` module
----------------------------

The main file of COLIBRÌ is without doubt the ``cosmology.py`` file.
This file contains one Python class, named :func:`colibri.cosmology.cosmo()`, in whose initialization the cosmological parameters must be provided (otherwise the default values will be loaded).
This class has all the routines necessary to compute distances, ages, density parameters, halo mass functions, void size functions and power spectra.
For the latter, both Boltzmann solvers **CAMB** and **Class** can be used, provided their Python wrapper is correclty compiled (see :ref:`prerequisites`), as well as the Eisenstein-Hu formula (see `arXiv:9710252 <https://arxiv.org/abs/astro-ph/9710252>`_).

`nonlinear` module
----------------------------

Included here are several different ways to compute the non-linear matter power spectrum from a linear one.
These methods include ``HMcode2016`` by Mead `et al.` (see `arXiv:1505.07833 <https://arxiv.org/abs/1505.07833>`_ ),  ``HMcode2020`` by Mead `et al.` (see `arXiv:2009.01858 <https://arxiv.org/abs/2009.01858>`_ ) ``Takahashi`` and  ``Bird`` following the prescription by Takahashi et al. for the former (see `arXiv:1208.2701 <https://arxiv.org/abs/1208.2701>`_ ) and the correction for the presence of massive neutrinos by Bird et al. for the latter (see `arXiv:1109.4416 <https://arxiv.org/abs/1109.4416>`_ ).

`limber` module
----------------------------

The :func:`colibri.limber.limber` class inside this file is finalized to compute angular power spectra and correlation functions in the flat sky and Limber's approximations. In this file are provided the routines to compute example functions for galaxy distributions (although different ones can be defined by the user outside the class) and window functions.

`halo`, `galaxy`, `RSD`
----------------------------

This three files are linked with each other. The basis is ``halo.py`` : it contains the class :func:`colibri.halo.halo` which computes the non-linear matter power spectrum according to the pure halo model (see for instance `arXiv:0206508 <https://arxiv.org/abs/astro-ph/0206508>`_).
While this is known to return a poor description of the matter clustering, the class has routines able to compute properly halo mass functions and halo biases.
In the file ``galaxy.py`` the class :func:`colibri.galaxy.galaxy` is implemented, which uses the Halo Occupation Distribution (see e.g. `arXiv:0408564 <https://arxiv.org/pdf/astro-ph/0408564.pdf>`_) prescription to predict the galaxy power spectrum in real space.
Conversely, the redshift-space power spectrum is provided by the class :func:`colibri.RSD.RSD` in the file ``RSD.py``: currently the dispersion model is implemented (with both Gaussian and Lorentzian dampings) as well as a halo model based prescription.

`fourier` module
----------------------------

This file contains routines to compute Fourier and Hankel Transforms. They employ the NumPy FFT libraries as well as FFTlog in some cases. They return sorted frequencies for an immediate interpretation of the outcomes.
In particular, these routines can be useful to compute two-point correlation functions starting from a power spectrum.


`constants` module
----------------------------

This file is just a compilation of physical constants and does not contain any class or method. While typing ``help(constants)`` will provide the list of quantities, it will not be documented. To obtain a full description of the quantities, type in a Python session or program::


    import constants
    constants.explanatory()


`useful_functions` module
----------------------------

The file contains (as is obvious) useful functions such as extrapolation of arrays and top-hat window functions.


Tests
----------------------------

Together with the files, two folders containing some useful and explanatory tests and Python example notebooks are provided. Each of them is adequately commented, so check them out and run them!

Otherwise, you may want to go the :ref:`cosmology_test` section.