Cia
===
.. code-block:: python
    :name: Cia
    :linenos:

    """
    
    This file will showcase how you can load collision-induced absorption (CIA)
    data from arts-cat-data into the workspace and do the required setups to
    perform a simple forward calculations using this data
    
    Note that this example presumes that you have set the environment variable
    ARTS_DATA_PATH to contain a path to a local copy of both arts-cat-data and
    arts-xml-data before you import pyarts.  Please check that this is the case
    if the example does not work for you.  You can easily check if this path is
    set by adding the following two lines at the top of this pyarts-controlfile:
    
    ```
    import os
    print(os.environ.get("ARTS_DATA_PATH"))
    ```
    
    """
    
    import pyarts
    import numpy as np
    import matplotlib.pyplot as plt
    
    # Initialize ARTS
    ws = pyarts.workspace.Workspace()
    
    """
    
    Set ws.abs_species to the species tags that you wish to use.  CIA tags are
    structured so that the main and secondary species are separated by the word
    "CIA"
    
    This example sets up self CIA by molecular oxygen
    
    CIA is not just self-induced but can occur between two different molecules.  In
    this case you can change the tag to read something like "O2-CIA-N2", though
    you must ensure that there also exists another N2 species in your ws.abs_species
    as this is the only way to pass the volume mixing ratio of the atmosphere into
    ARTS
    
    """
    ws.absorption_speciesSet(species=["O2-CIA-O2"])
    
    """
    
    Loads all CIA data from a given folder.  This command expects the file
    "cia/O2-CIA-O2.xml" to be found either by relative local path or in the
    user-defined search paths.
    
    """
    ws.absorption_cia_dataReadSpeciesSplitCatalog(basename="cia/")
    
    
    """
    
    This example does not deal with line-by-line absorption at all.  We must still
    ensure that the line-by-line catalog has the correct size and that it has been
    set so that our automatic agenda routine can do its work
    
    """
    ws.absorption_bands = {}
    
    """
    
    You should generally always call this after you are done setting up your
    ws.abs_species and ws.abs_lines_per_species.  It will deal with the internal
    ARTS setup for you.  Note that the flag use_abs_lookup=1 can be passed to this
    method call to set up the agenda for USING the the lookup-table.  Without the
    flag, ARTS should be configured correctly to either COMPUTE the lookup-table
    or to compute the absorption on-the-fly
    
    In this case, it turns out that the temparature extrapolation is not enough
    for a tropical atmosphere scenario below, so we extend it a small bit.  Play
    with this "T_extrapolfac" value to see the relevant error message
    
    """
    ws.propagation_matrix_agendaAuto(T_extrapolfac=1)
    
    """
    
    Compute absorption
    
    Now we can use the propagation_matrix_agenda to compute the absorption of O2-66.
    We can also use this agenda in more complicated setups that might require
    absorption calculations, but that is for other examples
    
    To just execute the agenda we need to still define its both its inputs and the
    inputs required to initialize the propagation matrix
    
    """
    
    ws.jacobian_targets = pyarts.arts.JacobianTargets()
    ws.frequency_grid = pyarts.arts.convert.wavelen2freq(np.linspace(6900e-9, 5900e-9, 1001))
    ws.atmospheric_point.temperature = 295  # At room temperature
    ws.atmospheric_point.pressure = 1e5  # At 1 bar
    ws.atmospheric_point["O2"] = 0.21  # At 21% atmospheric Oxygen
    ws.ray_path_point # No particular POSLOS
    
    # Call the agenda with inputs above
    ws.propagation_matrix_agendaExecute()
    
    # Plot the absorption of this example
    plt.figure(1)
    plt.clf()
    plt.plot(
        1e9 * pyarts.arts.convert.freq2wavelen(ws.frequency_grid.value),
        ws.propagation_matrix[:, 0],
    )
    plt.xlabel("Wavelength [nm]")
    plt.ylabel("Absorption [1/m]")
    plt.title("O2-CIA-O2 absorption from examples/arts-cat-data/cia/cia.py")
    
    """
    That's it!  You are done and have reached the end of this example.  Everything
    below here is just to ensure that ARTS does not break in the future.  It can
    be safely ignored
    
    """
    # Save test results
    # ws.propagation_matrix.savexml("cia_test_result.xml", type="ascii")
    
    # test that we are still OK
    propagation_matrix_agenda = \
        pyarts.arts.PropmatVector.fromxml("cia_test_result.xml")
    assert np.allclose(
        propagation_matrix_agenda, ws.propagation_matrix
    ), "O2 Absorption has changed"