cgeniepy.chem
=============

.. py:module:: cgeniepy.chem


Classes
-------

.. autoapisummary::

   cgeniepy.chem.Chemistry
   cgeniepy.chem.ModelCarbon


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

.. py:class:: Chemistry

   .. py:method:: molar_mass(element: str)

      get molar mass (g/mol) of chemistry elements



   .. py:method:: molecular_weight(formula: str)

      Calculate molecular weight using a chemical formula

      :param formula: chemical formula
      :returns: molecular weight

      ---------
      Example
      ----------
      >>> molecular_weight("C6H12O6")
      >>> 180.15588



   .. py:method:: pure_unit(unit: str)

      Get a pure unit string by removing elements in string (e.g., mmol C d-1)

      :param unit: unit string with elements
      :returns: pure unit string

      ---------
      Example
      ----------
      >>> pure_unit("mmol C d-1")
      >>> "mmol d-1"



   .. py:method:: format_base_unit(input_str, latex_format=True)

      Convert the base unit (i.e., no whitespace) to the desired format

      base unit means it is not a compound unit (e.g., m2, m-2, m/s, m s-1),
      which should be handled by the function `format_unit`
              
      :param input_str: a base unit string 
      :return: a formatted string

      ----------
      Example:
      ----------

      >>> convert_a_unit('m2')
      '$m^2$'
      >>> convert_a_unit('m-2')
      '$m^{-2}$'



   .. py:method:: format_unit(input, *args, **kwargs)

      convert a unit in a string seprated by whitespace
      to the desired format, which can be used in plot labels and 
      facilitate the unit calculation

      :param input: a unit string 
      :return: a  formatted string

      ----------
      Example:
      ----------

      >>> format_unit('mol kg-1')
      'mol kg$^{-1}$'
      >>> format_unit('mmol m-2 d-1')
      'mmol m$^{-2}$ d$^{-1}$'



.. py:class:: ModelCarbon(model)

   .. py:attribute:: model


   .. py:method:: get_NPP()

      netprimary production (NPP) in Pg C yr-1



   .. py:method:: get_poc_export(depth=None)

      particulate organic carbon (POC) export at 80 m in Pg C yr-1



   .. py:method:: get_eratio()

      export ratio (ER), calculated as POC export at 80 m divided by NPP



   .. py:method:: get_Teff(zt1=80, zt2=1000)

      transfer efficiency (Teff), default calculated as POC export at 1000 m divided by POC export at 80 m