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

.. only:: html

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

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

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

.. _sphx_glr_gallery_plot_den.py:


Density File
============

This example shows how to analyze the electronic density
stored in the DEN.nc file.

.. GENERATED FROM PYTHON SOURCE LINES 9-18

.. code-block:: Python

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

    # Open the DEN.nc file
    ncfile = abiopen(abidata.ref_file("si_DEN.nc"))

    # The DEN file has a `Density`, a `Structure` and an `ElectronBands` object
    print(ncfile.structure)





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

 .. code-block:: none

    Full Formula (Si2)
    Reduced Formula: Si
    abc   :   3.866975   3.866975   3.866975
    angles:  60.000000  60.000000  60.000000
    pbc   :       True       True       True
    Sites (2)
      #  SP       a     b     c
    ---  ----  ----  ----  ----
      0  Si    0     0     0
      1  Si    0.25  0.25  0.25

    Abinit Spacegroup: spgid: 227, num_spatial_symmetries: 48, has_timerev: True, symmorphic: True




.. GENERATED FROM PYTHON SOURCE LINES 19-20

To plot the KS eigenvalues.

.. GENERATED FROM PYTHON SOURCE LINES 20-28

.. code-block:: Python

    ncfile.ebands.plot()

    density = ncfile.density
    print(density)

    # To visualize the total charge wih vesta
    #visu = density.visualize("vesta"); visu()




.. image-sg:: /gallery/images/sphx_glr_plot_den_001.png
   :alt: plot den
   :srcset: /gallery/images/sphx_glr_plot_den_001.png
   :class: sphx-glr-single-img


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

 .. code-block:: none

    Density: nspinor: 1, nsppol: 1, nspden: 1
    Mesh3D: nx=18, ny=18, nz=18




.. GENERATED FROM PYTHON SOURCE LINES 29-31

To plot the density along the line connecting
the first and the second in the structure:

.. GENERATED FROM PYTHON SOURCE LINES 31-33

.. code-block:: Python

    density.plot_line(point1=0, point2=1)




.. image-sg:: /gallery/images/sphx_glr_plot_den_002.png
   :alt: plot den
   :srcset: /gallery/images/sphx_glr_plot_den_002.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 34-36

alternatively, one can define the line in terms of two points
in fractional coordinates:

.. GENERATED FROM PYTHON SOURCE LINES 36-38

.. code-block:: Python

    density.plot_line(point1=[0, 0, 0], point2=[2.25, 2.25, 2.25], num=300)




.. image-sg:: /gallery/images/sphx_glr_plot_den_003.png
   :alt: plot den
   :srcset: /gallery/images/sphx_glr_plot_den_003.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 39-41

To plot the density along the lines connect the firt atom in the structure
and all the neighbors within a sphere of radius 3 Angstrom:

.. GENERATED FROM PYTHON SOURCE LINES 41-42

.. code-block:: Python

    density.plot_line_neighbors(site_index=0, radius=3)



.. image-sg:: /gallery/images/sphx_glr_plot_den_004.png
   :alt: Si, [ 0.25  0.25 -0.75], dist=2.368 A, Si, [0.25 0.25 0.25], dist=2.368 A, Si, [-0.75  0.25  0.25], dist=2.368 A, Si, [ 0.25 -0.75  0.25], dist=2.368 A
   :srcset: /gallery/images/sphx_glr_plot_den_004.png
   :class: sphx-glr-single-img






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

   **Total running time of the script:** (0 minutes 0.479 seconds)


.. _sphx_glr_download_gallery_plot_den.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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