:py:mod:`exo_k.chemistry`
=========================

.. py:module:: exo_k.chemistry

.. autoapi-nested-parse::

   @author: jeremy leconte



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

.. py:class:: EquChemTable(filename=None, remove_zeros=False)


   Bases: :py:obj:`object`

   Class to load and interpolate chemistry data.


   Initializes chemical composition tables from various init files

   :param filename: Name of the input file
   :type filename: :class:`str`

   .. py:method:: read_composition_in(filename=None, remove_zeros=False, skiprows=7)

      Initializes chemical composition tables from composition.in files

      :param filename: Name of the input file
      :type filename: :class:`str`
      :param skiprows: Number of lines to skip in the file
      :type skiprows: :class:`int`, *optional*


   .. py:method:: read_composition_dat(filename=None, remove_zeros=False, skiprows=1)

      Initializes chemical composition tables from composition.in files

      :param filename: Name of the input file
      :type filename: :class:`str`
      :param skiprows: Number of lines to skip in the file
      :type skiprows: :class:`int`, *optional*


   .. py:method:: remove_zeros(deltalog_min_value=30.0)

      Finds zeros in the chem data and set them to (10.^-deltalog_min_value)
      times the minimum positive value
      in the table. This is to be able to work in logspace.


   .. py:method:: setup_interpolation()

      Creates interpolating functions to be called later on.



   .. py:method:: vmr(logP, T, mol)

      Interpolates a single molecule on a logP-T value



   .. py:method:: interpolate_vmr(logp_array=None, t_array=None, mols=None, grid=False)

      Interpolates all molecules in mols on a logP-T grid




.. py:class:: InterpolationChemistry(filename=None, t_min=260)


   Bases: :py:obj:`object`

   Chemistry model interpolating Volume Mixing Ratios based on a datafile
   provided by V. Parmentier.

   :param filename: The path to the datafile.
   :type filename: :class:`str`
   :param t_min: minimal temperature to consider.
                 Cannot be below 260K because not enough data in the file.
   :type t_min: :class:`float`

   .. py:method:: compute_vmr(molecule=None, logp_array=None, t_array=None)

      :param molecule: Name of molecule to deal with
      :type molecule: :class:`str`
      :param logp_array: Array of log10 pressures (Pa)
      :type logp_array: :class:`array`, :class:`np.ndarray`
      :param t_array: Array of temperatures (K)
      :type t_array: :class:`array`, :class:`np.ndarray`


   .. py:method:: compute_vmr_grid(molecule=None, logp_array=None, t_array=None)