.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/gcbc_example.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_auto_examples_gcbc_example.py>`
        to download the full example code

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_gcbc_example.py:


GEOS-Chem Benchmark LBC for CMAQ
================================

This example shows how to use aqmbc with GEOS-Chem's publicly available
benchmark outputs.

* Dowload from Harvard (if not previously downloaded).
* Define translations.
* Extract, translate, and create time-independent files.
* Display figures and statistics.

Time-independence allows files to be used in CMAQ with multiple dates in the
same month, or as a climatology for other years.

.. GENERATED FROM PYTHON SOURCE LINES 15-22

.. code-block:: default


    from os.path import basename, exists
    import aqmbc
    import matplotlib.pyplot as plt
    import requests
    import tarfile


.. GENERATED FROM PYTHON SOURCE LINES 23-25

Download from Harvard
---------------------

.. GENERATED FROM PYTHON SOURCE LINES 25-53

.. code-block:: default


    inpaths = [
        'OutputDir/GEOSChem.SpeciesConc.20190401_0000z.nc4',
        'OutputDir/GEOSChem.SpeciesConc.20190701_0000z.nc4',
    ]
    if any([not exists(p) for p in inpaths]):
        # Download 7G tar file
        rurl = 'http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/'
        url = f'{rurl}/14.0.0-rc.0/GCClassic/FullChem/OutputDir.tar.gz'
        dest = basename(url)
        if not exists(dest):
            with requests.get(url, stream=True) as r:
                r.raise_for_status()
                with open(dest, 'wb') as f:
                    for chunk in r.iter_content(chunk_size=1024*1024):
                        f.write(chunk)
        else:
            print('Using cached OutputDir.tar.gz')

        # Unzip only files that will be used.
        tf = tarfile.open(dest)
        for memb in tf.getmembers():
            if memb.path in inpaths:
                if not exists(memb.path):
                    tf.extract(memb)
                else:
                    print('Using cached', memb.path)


.. GENERATED FROM PYTHON SOURCE LINES 54-59

Define Chemical Translation
---------------------------

Using gc14_o3so4.expr, which only uses ozone and sulfate aerosols.


.. GENERATED FROM PYTHON SOURCE LINES 59-69

.. code-block:: default


    print(aqmbc.exprlib.avail('gc'))  # Show all possible expressions
    exprpaths = aqmbc.exprlib.exprpaths([                      # for a full run,
        'gcnc_airmolden.expr',                                 # keep this
        'gc14_o3so4.expr',                                     # Comment this
        # 'gc14_to_cb6r5.expr', 'gc14_to_cb6mp.expr',          # Uncomment this
        # 'gc14_soas_to_ae7.expr'                              # uncomment this
    ], prefix='gc')



.. GENERATED FROM PYTHON SOURCE LINES 70-72

Tranlate Files and Make Time-independent
----------------------------------------

.. GENERATED FROM PYTHON SOURCE LINES 72-97

.. code-block:: default


    gdnam = '12US1'
    gcdims = aqmbc.options.dims['gc']
    suffix = f'_{gdnam}_BCON.nc'
    metaf = aqmbc.options.getmetaf(bctype='bcon', gdnam=gdnam, vgnam='EPA_35L')

    # For "real" VGLVLS use
    # METBDY3D_PATH = '...'
    # METCRO3D_PATH = '...'
    # metaf = pnc.pncopen(METBDY3D_PATH, format='ioapi').subset(['PRES'])
    # pnc.conventions.ioapi.add_cf_from_ioapi(metaf)

    bcpaths = []
    for inpath in inpaths:
        print(inpath, flush=True)
        outpath = basename(inpath).replace('.nc4', suffix)
        history = f'From {outpath}'
        outf = aqmbc.bc(
            inpath, outpath, metaf, vmethod='linear', exprpaths=exprpaths,
            dimkeys=gcdims, format_kw={'format': 'gcbench'}, history=history,
            clobber=True, verbose=0, timeindependent=True
        )

        bcpaths.append(outpath)


.. GENERATED FROM PYTHON SOURCE LINES 98-100

Figures and Statistics
----------------------

.. GENERATED FROM PYTHON SOURCE LINES 100-105

.. code-block:: default


    vprof = aqmbc.report.get_vertprof(bcpaths)
    statdf = aqmbc.report.getstats(bcpaths)
    statdf.to_csv('gcbc_summary.csv')


.. GENERATED FROM PYTHON SOURCE LINES 106-108

Plot Vertical Profiles
~~~~~~~~~~~~~~~~~~~~~~

.. GENERATED FROM PYTHON SOURCE LINES 108-113

.. code-block:: default


    fig = aqmbc.report.plot_2spc_vprof(vprof)
    fig.suptitle('GEOS-Chem v14 Boundary Conditions for CMAQ')
    fig.savefig('gcbc_profiles.png')


.. GENERATED FROM PYTHON SOURCE LINES 114-116

Plot Normalized Means
~~~~~~~~~~~~~~~~~~~~~

.. GENERATED FROM PYTHON SOURCE LINES 116-119

.. code-block:: default


    fig = aqmbc.report.plot_gaspm_bars(statdf)
    fig.savefig('gcbc_bar.png')


.. rst-class:: sphx-glr-timing

   **Total running time of the script:** ( 0 minutes  0.000 seconds)


.. _sphx_glr_download_auto_examples_gcbc_example.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example




    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: gcbc_example.py <gcbc_example.py>`

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: gcbc_example.ipynb <gcbc_example.ipynb>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_