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

.. only:: html

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

        Click :ref:`here <sphx_glr_download_flow_gallery_run_gkq.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_gkq.py:


Flow to compute e-ph matrix elements along a q-path
===================================================

This example shows how to compute the e-ph matrix elements in AlAs along a q-path with AbiPy flows.
The final results are stored in the GKQ.nc file (one file for q-point) in the outdata of each task.

.. GENERATED FROM PYTHON SOURCE LINES 9-89

.. code-block:: default

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

    from abipy import flowtk


    def make_scf_input(ngkpt):
        """
        This function constructs the input file for the GS calculation:
        """
        structure = abidata.structure_from_ucell("AlAs")
        pseudos = abidata.pseudos("13al.981214.fhi", "33as.pspnc")
        gs_inp = abilab.AbinitInput(structure, pseudos=pseudos)

        gs_inp.set_vars(
            nband=6,
            ecut=6.0,
            ngkpt=ngkpt,
            nshiftk=1,
            shiftk=[0, 0, 0],
            tolvrs=1.0e-10,
        )

        return gs_inp


    def build_flow(options):
        """
        Create a `Flow` for the computation of e-ph matrix elements
        """
        # 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_")

        # Use 2x2x2 both for k-mesh.
        # Build input for GS calculation
        scf_input = make_scf_input(ngkpt=(2, 2, 2))

        # corresponding to a [2, 2, 2] q-mesh.
        ngqpt = (2, 2, 2)

        # Create flow to compute all the independent atomic perturbations
        # Use ndivsm = 0 to pass an explicit list of q-points.
        # If ndivsm > 0, qpath_list is interpreted as a list of boundaries for the q-path
        qpath_list = [[0.0, 0.0, 0.0], [0.01, 0, 0], [0.1, 0, 0],
                      [0.24, 0, 0], [0.3, 0, 0], [0.45, 0, 0], [0.5, 0.0, 0.0]]

        from abipy.flowtk.eph_flows import GkqPathFlow
        flow = GkqPathFlow.from_scf_input(options.workdir, scf_input,
                                          ngqpt, qpath_list, ndivsm=0, with_becs=True,
                                          ddk_tolerance={"tolwfr": 1e-8})

        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_gkq_001.png
    :alt: run gkq
    :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 90-97

Run the script with:

    run_gkq.py -s

then use:

   abirun.py flow_phonons history


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

   **Total running time of the script:** ( 0 minutes  2.809 seconds)


.. _sphx_glr_download_flow_gallery_run_gkq.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_gkq.ipynb
      :alt: Launch binder
      :width: 150 px


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

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



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

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


.. only:: html

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

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