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

.. only:: html

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

        Click :ref:`here <sphx_glr_download_flow_gallery_run_phonopy_si.py>`
        to download the full example code or to run this example in your browser via Binder

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

.. _sphx_glr_flow_gallery_run_phonopy_si.py:


Phonopy with AbiPy Flow
=======================

This example shows how to compute phonon frequencies with phonopy
(supercells and finite-difference method).

This approach could be useful to obtain vibrational properties with XC functionals
for which DFPT is not yet implemented.

.. warning:

    This example requires the `phonopy package <http://atztogo.github.io/phonopy/examples.html>`_

.. GENERATED FROM PYTHON SOURCE LINES 16-78

.. code-block:: default


    import sys
    import os
    import abipy.abilab as abilab
    import abipy.data as abidata
    import abipy.flowtk as flowtk

    from abipy.flowtk.abiphonopy import PhonopyWork


    def build_flow(options):
        """
        Create a `Flow` for phonon calculations with phonopy:
        """
        # Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
        if not options.workdir:
            options.workdir = os.path.basename(sys.argv[0]).replace(".py", "").replace("run_", "flow_")

        # Initialize structure and pseudos
        structure = abilab.Structure.from_file(abidata.cif_file("si.cif"))
        pseudos = abidata.pseudos("14si.pspnc")

        # Build input for GS calculation.
        gsinp = abilab.AbinitInput(structure, pseudos)
        gsinp.set_vars(ecut=4, nband=4, toldff=1.e-6)

        # This gives ngkpt = 4x4x4 with 4 shifts for the initial unit cell.
        # The k-point sampling will be rescaled when we build the supercell in PhonopyWork.
        gsinp.set_autokmesh(nksmall=4)
        #gsinp.set_vars(ngkpt=[4, 4, 4])

        flow = flowtk.Flow(workdir=options.workdir)

        # Use a 2x2x2 supercell to compute phonons with phonopy
        work = PhonopyWork.from_gs_input(gsinp, scdims=[2, 2, 2])
        flow.register_work(work)

        return flow


    # This block generates the thumbnails in the AbiPy gallery.
    # You can safely REMOVE this part if you are using this script for production runs.
    if os.getenv("READTHEDOCS", False):
        __name__ = None
        import tempfile
        options = flowtk.build_flow_main_parser().parse_args(["-w", tempfile.mkdtemp()])
        build_flow(options).graphviz_imshow()


    @flowtk.flow_main
    def main(options):
        """
        This is our main function that will be invoked by the script.
        flow_main is a decorator implementing the command line interface.
        Command line args are stored in `options`.
        """
        return build_flow(options)


    if __name__ == "__main__":
        sys.exit(main())




.. image:: /flow_gallery/images/sphx_glr_run_phonopy_si_001.png
    :alt: run phonopy si
    :class: sphx-glr-single-img


.. rst-class:: sphx-glr-script-out

 Out:

 .. code-block:: none

    self['nband'] 4 new['nband'] 32
    new ngkpt: [2 2 2]




.. GENERATED FROM PYTHON SOURCE LINES 79-110

Run the script with:

    run_phonopy_si.py -s

the output results are produced in ``flow_phonopy_si/w0/outdata/``
Follow the instructions in the README file:

.. code-block:: md

   To plot bands, use:
           phonopy -p band.conf

   To plot phonon dos, use:
           phonopy -p dos.conf

   To plot bands and dos, use:
           phonopy -p band-dos.conf

   See also:
           http://atztogo.github.io/phonopy/examples.html
           http://atztogo.github.io/phonopy/setting-tags.html#setting-tags

The command:

  phonopy -p band-dos.conf

will produce:

.. image:: https://github.com/abinit/abipy_assets/blob/master/run_phonopy_si.png?raw=true
   :alt: Phonon Band structure computed with phonopy.



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

   **Total running time of the script:** ( 0 minutes  0.398 seconds)


.. _sphx_glr_download_flow_gallery_run_phonopy_si.py:


.. only :: html

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


  .. container:: binder-badge

    .. image:: images/binder_badge_logo.svg
      :target: https://mybinder.org/v2/gh/abinit/abipy/gh-pages?filepath=notebooks/flow_gallery/run_phonopy_si.ipynb
      :alt: Launch binder
      :width: 150 px


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

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



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

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


.. only:: html

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

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