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

.. only:: html

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

        Click :ref:`here <sphx_glr_download_gallery_plot_phonons_msqd.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_gallery_plot_phonons_msqd.py:


Debye-Waller and generalized phonon DOS
=======================================

This example shows how to plot the generalized phonon DOS with the mean square
displacement tensor in cartesian coords and how to calculate Debye Waller factors
as a function of temperature.

See :cite:`Lee1995` for the further details about the internal implementation and
:cite:`Trueblood1996` for the different conventions used by crystallographers.

.. GENERATED FROM PYTHON SOURCE LINES 13-55



.. rst-class:: sphx-glr-horizontal


    *

      .. image:: /gallery/images/sphx_glr_plot_phonons_msqd_001.png
          :alt: Si0 (3b), O3 (6c)
          :class: sphx-glr-multi-img

    *

      .. image:: /gallery/images/sphx_glr_plot_phonons_msqd_002.png
          :alt: plot phonons msqd
          :class: sphx-glr-multi-img

    *

      .. image:: /gallery/images/sphx_glr_plot_phonons_msqd_003.png
          :alt: plot phonons msqd
          :class: sphx-glr-multi-img


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

 Out:

 .. code-block:: none

    Creating temporary file: /var/folders/nc/k69spyd12qv2tk3stk2xrxg40000gr/T/tmppv_2pfu8mp-7000_DDB






|

.. code-block:: default

    import os
    import abipy.data as abidata

    from abipy import abilab

    # Open DDB file for alpha-SiO2 taken from https://materialsproject.org/materials/mp-7000/
    filepath = os.path.join(abidata.dirpath, "refs", "mp-7000_DDB.bz2")
    ddb = abilab.abiopen(filepath)

    # Invoke anaddb to compute phonon bands and dos.
    #dos_method = "gaussian"
    dos_method = "tetra"
    phbst_file, phdos_file = ddb.anaget_phbst_and_phdos_files(nqsmall=4, dos_method=dos_method,
                                                              ndivsm=1, mpi_procs=2)

    # Extract msqd_dos
    msqd_dos = phdos_file.msqd_dos
    #print(msqd_dos)

    #for fmt in ("cartesian", "cif", "ustar", "beta", "B"):
    for fmt in ("cartesian", "cif"):
        df = msqd_dos.get_dataframe(temp=300, view="all", fmt=fmt)
        abilab.print_dataframe(df, title="Format: %s" % fmt)

    # Plot generalized phonon DOS for each inequivalent atom in the unit cell.
    msqd_dos.plot()

    # Plot tensor(T) for each inequivalent atom.
    msqd_dos.plot_tensor()

    msqd_dos.plot_uiso()

    # To save the structure and the U tensor at T=300K in CIF format, use:
    #msqd_dos.write_cif_file("DW.cif", temp=300)

    # To visualize the thermal ellipsoids with Vesta, use:
    #msqd_dos.vesta_open(temp=300)

    # Remember to close the files.
    phbst_file.close()
    phdos_file.close()
    ddb.close()


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

   **Total running time of the script:** ( 0 minutes  6.181 seconds)


.. _sphx_glr_download_gallery_plot_phonons_msqd.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/gallery/plot_phonons_msqd.ipynb
      :alt: Launch binder
      :width: 150 px


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

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



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

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


.. only:: html

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

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