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

.. only:: html

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

        Click :ref:`here <sphx_glr_download_gallery_plot_structure.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_structure.py:


Unit cell
=========

This example shows how to display the unit cell with matplotlib.

.. GENERATED FROM PYTHON SOURCE LINES 8-11

.. code-block:: default

    from abipy.abilab import abiopen
    import abipy.data as abidata








.. GENERATED FROM PYTHON SOURCE LINES 12-13

Extract structure from the netcdf file:

.. GENERATED FROM PYTHON SOURCE LINES 13-17

.. code-block:: default


    with abiopen(abidata.ref_file("sio2_kpath_GSR.nc")) as gsr:
        structure = gsr.structure








.. GENERATED FROM PYTHON SOURCE LINES 18-19

To visualize the structure with matplotlib, use:

.. GENERATED FROM PYTHON SOURCE LINES 19-21

.. code-block:: default

    structure.plot(color_scheme="Jmol")




.. image:: /gallery/images/sphx_glr_plot_structure_001.png
    :alt: Si3 O6
    :class: sphx-glr-single-img


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

 Out:

 .. code-block:: none


    <Figure size 640x480 with 1 Axes>



.. GENERATED FROM PYTHON SOURCE LINES 22-23

To wrap sites into first unit cell, use:

.. GENERATED FROM PYTHON SOURCE LINES 23-26

.. code-block:: default


    # sphinx_gallery_thumbnail_number = 2
    structure.plot(to_unit_cell=True)



.. image:: /gallery/images/sphx_glr_plot_structure_002.png
    :alt: Si3 O6
    :class: sphx-glr-single-img


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

 Out:

 .. code-block:: none


    <Figure size 640x480 with 1 Axes>




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

   **Total running time of the script:** ( 0 minutes  0.258 seconds)


.. _sphx_glr_download_gallery_plot_structure.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_structure.ipynb
      :alt: Launch binder
      :width: 150 px


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

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



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

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


.. only:: html

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

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