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

.. only:: html

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

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

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

.. _sphx_glr_flow_gallery_run_atdep.py:


Temperature-dependent phonons with aTDEP
========================================

This example shows how to build a flow that computes the temperature-dependent
interatomic force constants of MgO with aTDEP, starting from an AIMD trajectory (HIST.nc file).
The DDB file produced by aTDEP is then passed to anaddb to compute the phonon band structure and DOS.

.. GENERATED FROM PYTHON SOURCE LINES 10-96



.. image-sg:: /flow_gallery/images/sphx_glr_run_atdep_001.png
   :alt: run atdep
   :srcset: /flow_gallery/images/sphx_glr_run_atdep_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


    import os
    import sys

    import abipy.data as abidata
    from abipy import flowtk
    from abipy.abio.inputs import AnaddbInput, AtdepInput


    def make_atdep_input(structure):
        """Build the input file for aTDEP."""
        inp = AtdepInput(structure)
        inp.set_vars(
            multiplicity=[[-2, 2, 2], [2, -2, 2], [2, 2, -2]],
            nstep_max=20,
            nstep_min=1,
            temperature=300,
            rcut=7.0,
            ngqpt1=[2, 2, 2],
            ngqpt2=[1, 1, 1],
        )

        return inp


    def make_anaddb_input(structure):
        """Build the anaddb input file to compute phonon bands and DOS from the aTDEP DDB."""
        inp = AnaddbInput.phbands_and_dos(
            structure, ngqpt=[2, 2, 2], ndivsm=40, line_density=None,
            nqsmall=10, qppa=None, q1shft=(0, 0, 0), qptbounds=None,
            asr=2, chneut=1, dipdip=1, dipquad=0, quadquad=0,
            dos_method="tetra", lo_to_splitting="automatic",
            with_ifc=True, anaddb_kwargs={}, spell_check=False,
        )

        return inp


    def build_flow(options):
        # Set 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_")

        structure = abidata.structure_from_mpid("mp-1265")  # MgO
        ddb_file = abidata.ref_file("MgO_dfpt_aimd/MgO_DDB.nc")
        hist_file = abidata.ref_file("MgO_dfpt_aimd/MgO_HIST.nc")

        atdep_inp = make_atdep_input(structure)
        anaddb_inp = make_anaddb_input(structure)
        anaddb_inp.set_vars(
            ngqpt=atdep_inp["ngqpt1"],
            rifcsph=atdep_inp["rcut"],
        )

        atdep_task = flowtk.AtdepTask(atdep_inp, hist_node=hist_file, ddb_node=ddb_file)
        anaddb_task = flowtk.AnaddbTask(anaddb_inp, ddb_node=atdep_task)

        flow = flowtk.Flow(workdir=options.workdir, manager=options.manager)
        flow.register_task(atdep_task)
        flow.register_task(anaddb_task, deps={atdep_task: "DDB"})

        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())


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

   **Total running time of the script:** (0 minutes 0.356 seconds)


.. _sphx_glr_download_flow_gallery_run_atdep.py:

.. only:: html

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

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

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

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

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

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: run_atdep.zip <run_atdep.zip>`


.. only:: html

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

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