.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples_generated/03-tutorials/phonons.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

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

        :ref:`Go to the end <sphx_glr_download_examples_generated_03-tutorials_phonons.py>`
        to download the full example code.

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

.. _sphx_glr_examples_generated_03-tutorials_phonons.py:

.. _phonons:

===================================================
Phonon calculations with small displacement method
===================================================

Simple example showing how to calculate the phonon dispersion for bulk aluminum
using a 5x5x5 supercell within effective medium theory:

.. GENERATED FROM PYTHON SOURCE LINES 12-19

.. code-block:: Python

    import matplotlib.pyplot as plt
    import numpy as np

    from ase.build import bulk
    from ase.calculators.emt import EMT
    from ase.phonons import Phonons








.. GENERATED FROM PYTHON SOURCE LINES 20-21

Setup Al crystal

.. GENERATED FROM PYTHON SOURCE LINES 21-23

.. code-block:: Python

    atoms = bulk('Al', 'fcc', a=4.05)








.. GENERATED FROM PYTHON SOURCE LINES 24-25

Setup phonon calculation with EMT calculator

.. GENERATED FROM PYTHON SOURCE LINES 25-35

.. code-block:: Python

    N = 5
    ph = Phonons(
        atoms,
        EMT(),
        supercell=(N, N, N),
        use_mean_minimum_images=True,
        minimum_image_tol=1e-6,
    )
    ph.run()








.. GENERATED FROM PYTHON SOURCE LINES 36-37

Read forces and assemble the dynamical matrix

.. GENERATED FROM PYTHON SOURCE LINES 37-40

.. code-block:: Python

    ph.read()
    ph.clean()





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

 .. code-block:: none


    7



.. GENERATED FROM PYTHON SOURCE LINES 41-42

Set and plot phonon band-structure along specific path

.. GENERATED FROM PYTHON SOURCE LINES 42-72

.. code-block:: Python

    path = atoms.cell.bandpath('GXULGK', npoints=100)
    bs = ph.get_band_structure(path)

    # Get phonon DoS
    dos = ph.get_dos(kpts=(20, 20, 20)).sample_grid(npts=100, width=1e-3)
    fig = plt.figure(figsize=(7, 4))
    ax = fig.add_axes([0.12, 0.07, 0.67, 0.85])

    # Plot phonon band structure and DoS
    emax = 0.035
    bs.plot(ax=ax, emin=0.0, emax=emax)

    dosax = fig.add_axes([0.8, 0.07, 0.17, 0.85])
    dosax.fill_between(
        dos.get_weights(),
        dos.get_energies(),
        y2=0,
        color='grey',
        edgecolor='k',
        lw=1,
    )

    dosax.set_ylim(0, emax)
    dosax.set_yticks([])
    dosax.set_xticks([])
    dosax.set_xlabel('DoS', fontsize=18)
    plt.show()

    # fig.savefig('Al_phonon.png')




.. image-sg:: /examples_generated/03-tutorials/images/sphx_glr_phonons_001.png
   :alt: phonons
   :srcset: /examples_generated/03-tutorials/images/sphx_glr_phonons_001.png
   :class: sphx-glr-single-img


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

 .. code-block:: none

    WARNING, 1 imaginary frequencies at q = ( 0.00,  0.00,  0.00) ; (omega_q = 5.742e-09*i)
    WARNING, 1 imaginary frequencies at q = ( 0.00,  0.00,  0.00) ; (omega_q = 5.742e-09*i)




.. GENERATED FROM PYTHON SOURCE LINES 73-74

You can visualize the modes with the following script:

.. GENERATED FROM PYTHON SOURCE LINES 74-94

.. code-block:: Python


    # Write modes for specific q-vector to trajectory file
    L = np.array(path.special_points['L'])
    ph.write_modes(
        L / 2.0,
        branches=[2],
        repeat=(8, 8, 8),
        kT=3e-4,
        center=True,
    )

    # Optionally, generate gif animation

    # from ase.io.trajectory import Trajectory
    # from ase.io import write

    # Temporarily disabled due to matplotlib writer compatibility issue.
    # with Trajectory('phonon.mode.2.traj', 'r') as traj:
    #    write('Al_mode.gif', traj, interval=50,
    #           rotation='-36x,26.5y,-25z')








.. _sphx_glr_download_examples_generated_03-tutorials_phonons.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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