zeus21.T21coefficients
======================

.. py:module:: zeus21.T21coefficients

.. autoapi-nested-parse::

   Bulk of the Zeus21 calculation:
       - Determines Lyman-alpha and X-ray fluxes,
       - Evolves the cosmic-dawn IGM state (WF coupling and heating),
       - Computes the 21-cm global signal and the effective biases gammaR to determine the 21-cm power spectrum.

   Authors: zeus21 v2 collaboration - June 2026
       Emily Bregou ;
       Hector Afonso G. Cruz ;
       Sarah Libanore ;
       Julian B. Muñoz ;
       Yonny Sklansky ;
       Emilie Thélie ;
       Alessandra Venditti
   arXiv:2302.08506, arXiv:2306.09403, arXiv:2407.18294, Sklansky et al. (in prep)



Classes
-------

.. autoapisummary::

   zeus21.T21coefficients.LyAlpha_class
   zeus21.T21coefficients.Xrays_class
   zeus21.T21coefficients.get_T21_coefficients


Module Contents
---------------

.. py:class:: LyAlpha_class(UserParams, CosmoParams, AstroParams, HMFinterp, z_Init=None, SFRD_Init=None)

   Determines Lyman-alpha properties and fluxes.

   :param UserParams:
   :type UserParams: UserParams class
   :param CosmoParams:
   :type CosmoParams: CosmoParams class
   :param AstroParams:
   :type AstroParams: AstroParams class
   :param HMFinterp:
   :type HMFinterp: HMFinterp class
   :param z_Init: Initial redshift matrices for the calculation (see sfrd.py for details).
                  Default is None.
   :type z_Init: Z_init class, optional
   :param SFRD_Init: Initial star formation rate density for the calculation (see sfrd.py for details).
                     Default is None.
   :type SFRD_Init: SFRD_class class, optional

   .. attribute:: coeff1LyAzp

      Redshift-dependent coefficient in the J_alpha flux computation, see Eq. 29 in arXiv:2302.08506.

      :type: array

   .. attribute:: coeff2LyAzpRR_II

      Coefficient that multiplies the SFRD in the integral for J_alpha for Pop II stars, see Eq. 30 of arXiv:2302.08506.

      :type: array

   .. attribute:: coeff2LyAzpRR_III

      Coefficient that multiplies the SFRD in the integral for J_alpha for Pop III stars.

      :type: array


   .. py:attribute:: coeff1LyAzp


   .. py:attribute:: coeff2LyAzpRR_II


.. py:class:: Xrays_class(UserParams, CosmoParams, AstroParams, HMFinterp, z_Init=None, SFRD_Init=None)

   Determines X-ray properties and fluxes.

   :param UserParams:
   :type UserParams: UserParams class
   :param CosmoParams:
   :type CosmoParams: CosmoParams class
   :param AstroParams:
   :type AstroParams: AstroParams class
   :param HMFinterp:
   :type HMFinterp: HMFinterp class
   :param z_Init: Initial redshift matrices for the calculation (see sfrd.py for details).
                  Default is None.
   :type z_Init: Z_init class, optional
   :param SFRD_Init: Initial star formation rate density for the calculation (see sfrd.py for details).
                     Default is None.
   :type SFRD_Init: SFRD_class class, optional

   .. attribute:: atomfractions

      Fraction of baryons in HI and HeI, assumed to just be the avg cosmic. Used to compute X-ray absorption.

      :type: array

   .. attribute:: atomEnIon

      Threshold energies for HI and HeI, in eV.

      :type: array

   .. attribute:: TAUMAX

      Maximum optical depth, cut to 0 after to avoid overflows.

      :type: float

   .. attribute:: coeff1Xzp

      Redshift-dependent coefficient in the X-ray flux computation, with extra factors to account for adiabatic cooling and the fact that we compute the integral in redshift instead of time.

      :type: array

   .. attribute:: coeff2XzpRR_II

      Coefficient that multiplies the SFRD in the integral for the X-ray flux for Pop II stars

      :type: array

   .. attribute:: coeff2XzpRR_III

      Coefficient that multiplies the SFRD in the integral for the X-ray flux for Pop III stars

      :type: array

   .. attribute:: _GammaXray_II

      X-ray ionization rate for Pop II stars, in s^-1, see Eq. 37 in arXiv:2302.08506

      :type: array

   .. attribute:: _GammaXray_III

      X-ray ionization rate for Pop III stars, in s^-1

      :type: array

   .. attribute:: coeff_Gammah_Tx_II

      Coefficient that multiplies the X-ray ionization rate to get the X-ray heating rate for Pop II stars, in K/s, see Eq. 41 in arXiv:2302.08506.

      :type: array

   .. attribute:: coeff_Gammah_Tx_III

      Coefficient that multiplies the X-ray ionization rate to get the X-ray heating rate for Pop III stars, in K/s

      :type: array

   .. attribute:: Gammaion_II

      X-ray ionization rate for Pop II stars, in s^-1

      :type: array

   .. attribute:: Gammaion_III

      X-ray ionization rate for Pop III stars, in s^-1

      :type: array

   .. attribute:: _xe_avg_ad

      Average ionization fraction of the IGM from adiabatic cooling and recombinations

      :type: array

   .. attribute:: _xe_avg

      Average ionization fraction of the IGM, including both the contribution from UV photons and the partial ionization from X-rays

      :type: array

   .. attribute:: _fheat

      Fraction of X-ray energy that goes into heating, as opposed to ionization

      :type: array

   .. attribute:: Gammaheat_II

      X-ray heating rate for Pop II stars, in K/s

      :type: array

   .. attribute:: Gammaheat_III

      X-ray heating rate for Pop III stars, in K/s

      :type: array

   .. attribute:: Tk_xray

      Average kinetic temperature of the IGM from X-ray heating, in K

      :type: array

   .. attribute:: Tk_ad

      Average kinetic temperature of the IGM from adiabatic cooling only, in K

      :type: array

   .. attribute:: Tk_avg

      Average kinetic temperature of the IGM, including both adiabatic cooling and X-ray heating, in K

      :type: array

   .. attribute:: sigma_HI

      Cross section for X-ray absorption by HI, as a function of energy in eV, in cm^2

      :type: function

   .. attribute:: sigma_HeI

      Cross section for X-ray absorption by HeI, as a function of energy in eV, in cm^2

      :type: function


   .. py:attribute:: atomfractions


   .. py:attribute:: atomEnIon


   .. py:attribute:: TAUMAX
      :value: 100.0



   .. py:attribute:: coeff1Xzp


   .. py:attribute:: coeff2XzpRR_II


   .. py:attribute:: coeff_Gammah_Tx_II


   .. py:attribute:: coeff_Gammah_Tx_III


   .. py:attribute:: Gammaion_II


   .. py:attribute:: Gammaion_III


   .. py:attribute:: xe_avg_ad


   .. py:attribute:: xe_avg


   .. py:attribute:: Gammaheat_II


   .. py:attribute:: Gammaheat_III


   .. py:attribute:: Tk_xray


   .. py:attribute:: Tk_ad


   .. py:attribute:: Tk_avg


   .. py:method:: sigma_HI(Energyin)

      Cross section for Xray absorption for neutral HI, from astro-ph/9601009

      :param Energyin: Energy in eV
      :type Energyin: float

      :returns: Cross section in cm^2.
      :rtype: float



   .. py:method:: sigma_HeI(Energyin)

      Cross section for Xray absorption for neutral HI

      :param Energyin: Energy in eV
      :type Energyin: float

      :returns: Cross section in cm^2.
      :rtype: float



.. py:class:: get_T21_coefficients(UserParams, CosmoParams, AstroParams, HMFinterp, z_Init=None, SFRD_Init=None)

   Loops through SFRD integrals and accounts for LyA coupling and Xray heating to obtain the average T21 and the coefficients for its power spectrum

   :param UserParams: User-defined parameters
   :type UserParams: object
   :param CosmoParams: Cosmological parameters
   :type CosmoParams: object
   :param AstroParams: Astrophysical parameters
   :type AstroParams: object
   :param HMFinterp: Halo mass function interpolator
   :type HMFinterp: object

   .. attribute:: z_Init

      Redshift tables for the calculation (see sfrd.py for details)

      :type: object

   .. attribute:: SFRD_Init

      Initial star formation rate density for the calculation (see sfrd.py for details)

      :type: object

   .. attribute:: USE_POPIII

      Whether to include Pop III stars in the calculation or not, determined by AstroParams

      :type: bool

   .. attribute:: relvel

      Relative velocity between baryons and dark matter, which affects the SFRD and therefore the LyA and X-ray fluxes. Only computed if USE_POPIII is True

      :type: object or None

   .. attribute:: LyA

      Lyman-alpha anisotropies, which depend on the SFRD and the redshift tables; see LyAlpha_class for details

      :type: object

   .. attribute:: Xrays

      X-ray anisotropies, which depend on the SFRD and the redshift tables; see Xrays_class for details

      :type: object

   .. attribute:: ReioGlobal

      Global reionization history, which depends on the SFRD and the redshift tables; see reionization.py for details

      :type: object

   .. attribute:: xHI_avg

      Average neutral hydrogen fraction volume-weighted, computed from the global reionization history

      :type: array

   .. attribute:: T21avg

      Average 21cm brightness temperature

      :type: array

   .. attribute:: tau_reio_val

      Optical depth to reionization, computed from the global reionization history and the average neutral hydrogen fraction

      :type: float

   .. attribute:: __ getattr__

      This method allows us to access the attributes of the classes that we initialized directly from the get_T21_coefficients class, without having to specify which class they come from

      :type: method

   .. attribute:: evolve_T21_fields

      Compute evolution of the LyA flux, LyA coupling coefficient, color temperature and spin temperature

      :type: method

   .. attribute:: Jalpha_avg

      Average LyA flux at all redshifts and radii

      :type: array

   .. attribute:: _coeff_Ja_xa_0

      Normalization of the LyA flux at all redshifts

      :type: array

   .. attribute:: coeff_Ja_xa

      LyA flux corrected with Hirata2006 prescription

      :type: array

   .. attribute:: xa_avg

      LyA coupling coefficient

      :type: array

   .. attribute:: TCMB

      CMB temperature at all redshifts

      :type: array

   .. attribute:: invTcol_avg

      Inverse of the color temperature (equal 1/Tk)

      :type: array

   .. attribute:: _invTs_avg

      Inverse of the spin temperature

      :type: array

   .. attribute:: tau_reio

      Compute the optical depth to reionization

      :type: method

   .. attribute:: Salpha_exp

      Hirata2006 correction to the LyA flux (Eq 55 in astro-ph/0608032)

      :type: method


   .. py:attribute:: USE_POPIII


   .. py:attribute:: LyA


   .. py:attribute:: Xrays


   .. py:attribute:: ReioGlobal


   .. py:attribute:: xHI_avg


   .. py:attribute:: T21avg


   .. py:attribute:: tau_reio_val


   .. py:method:: evolve_T21_fields(UserParams, CosmoParams)

      Compute evolution of the LyA flux, LyA coupling coefficient, color temperature and spin temperature

      :param UserParams: User-defined parameters
      :type UserParams: object
      :param CosmoParams: Cosmological parameters
      :type CosmoParams: object

      :rtype: None



   .. py:method:: tau_reio(CosmoParams, zlist, xHI)

      Compute the optical depth to reionization

      :param CosmoParams: Cosmological parameters
      :type CosmoParams: object
      :param zlist: Redshifts
      :type zlist: list
      :param xHI: Neutral fraction as function of redshift
      :type xHI: array

      :returns: **tau_reio**
      :rtype: list



   .. py:method:: Salpha_exp(z, T, xe)

      Hirata2006 correction to the LyA flux (Eq 55 in astro-ph/0608032). This function is used to initialize the xalpha computation, but then overwritten. Only used if FLAG_WF_ITERATIVE == False

      :param z: Redshifts
      :type z: float
      :param T: Temperature in K
      :type T: float
      :param xe: Free electron fraction with small reionization (xe << 1)
      :type xe: float

      :returns: **Salpha** -- Correction to the LyA flux
      :rtype: float