Neutral background
=====================

Before the code can be run, the different neutral densities have to be initialised.

.. _neutrals_ini:
Neutral densities
------------------------

The first step is to initialised the neutral densities. This is necessary for two reasons:
- Neutrals are responsible for the absorption of the solar radiation to the D-region altitudes
- Neutrals are the sources of positive ions

:math:`O`, :math:`O_2` and :math:`N_2` are the neutrals which participate the most to the absorption of X-rays and Lyman-alpha radiations. :math:`NO` is the main species ionised to create the D-region in quiet times. In addition to them, :math:`H_2O` vapour participate in some of the chemistry reactions, and need to be initialised. Other species are only involved in the computation of the atmosphere scale-height.

In practice, this is done by calling the :py:meth:`class_definition.neutrals._init_` method. All neutrals except :math:`H_2O` and :math:`NO` are initialised through the MSISE-00 model [picone2002]_ .

.. note::

    The profiles obtained with MSISE are cut at 73 km for :math:`O` and :math:`N`. This causes a problem with :math:`O`, because it is the base on which :math:`NO`, :math:`H_2O` and :math:`O_3` are initialised, and it intervenes in the chemistry reaction rates. :math:`N` doesn't intervene. To mitigate this, we consider that :math:`O` is constant below 73 km, following the profiles given p282 of Brasseur & Solomon for example.

:math:`NO`
^^^^^^^^^^^^^^^^^^^^

The :math:`NO` density is initialised from the densities of :math:`O` and :math:`O_2` following the parametrisation of [mitra1966]_. They are later corrected by a factor :py:obj:`alpha` (see :ref:`ini_ions`).

:math:`H_2O`
^^^^^^^^^^^^^^^^^^^^

The :math:`H_2O` density is computed assuming a mixing ratio of 3 ppm [reid1971]_ . According to this paper, the actual value of the mixing ratio doesn't impact the ion and electron densities much. The results from this technique also matches the 'Wet' curve in Fig. 2(a) of [reid1977]_ .

:math:`O_3`
^^^^^^^^^^^^^^^^^

The :math:`O_3` density is also needed as it plays a part in the reaction between :math:`0_2^-` and :math:`X^-`. To initialise it, we assume that we are in equilibrium conditions, and that a balance is found between the different reactions of :math:`0_3`, following [levine1985]_ (Equation 13, p178)

Results
--------------

For a quiet period in November 2023 over Italy, the initial densities are thus found to be:

.. image:: ../Figures/Initialisation_densities.png