.. only:: html

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

        Click :ref:`here <sphx_glr_download_auto_examples_plot_overlap_population_plot_overlap_population.py>`     to download the full example code
    .. rst-class:: sphx-glr-example-title

    .. _sphx_glr_auto_examples_plot_overlap_population_plot_overlap_population.py:


=================================================================
Plotting cyrstal orbital overlap population obtained from lobster
=================================================================

This example shows how to plot overlap population data
See http://www.cohp.de/ for details


.. code-block:: default


    import os
    import numpy as np
    import matplotlib.pyplot as plt
    from pdos_overlap.overlap_population import get_example_data
    from pdos_overlap.overlap_population import OVERLAP_POPULATION
    from pdos_overlap.plotting_tools import set_figure_settings








Load COOPCAR file
-----------------

First we will, get the example data, load a COOPCAR file and use it to
instantiate an OVERLAP_POPULATION object


.. code-block:: default


    set_figure_settings('paper')
    example_path = get_example_data()
    COOPCAR = os.path.join(example_path, 'C2H4/COOPCAR.lobster')

    POP = OVERLAP_POPULATION(COOPCAR)








Identify bonding interactions and check for spin
------------------------------------------------



.. code-block:: default

    print(POP.interactions)
    print(POP.is_spin)






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

 Out:

 .. code-block:: none

    ['No.1:C1->C2(1.3399356553485977)', 'No.2:C1->H3(1.0931450325373071)', 'No.3:C1->H4(1.0932440535076346)', 'No.4:C2->H5(1.093162987441443)', 'No.5:C2->H6(1.0932085731970578)']
    True




Obtain projected overlap
------------------------

We projected orbital overlap for the C-C bond and C-H bonds in C2H4
We group the CH bonds and ensure to sum for spins as all electrons are paired


.. code-block:: default


    CC_overlap = POP.get_pcoop(interactions=[0], sum_pcoop=False, sum_spin=True)
    CH_overlap = POP.get_pcoop(interactions=[1,2,3,4], sum_pcoop=True, sum_spin=True)








Plot the bonding populaiton with respect to the CC and CH bonds
---------------------------------------------------------------

A positive value on the x-axis indicates are greater proportion of states in
in the bond than outside of the bond


.. code-block:: default


    plt.figure(figsize=(3,5))
    plt.plot(CC_overlap, POP.get_energies(), zorder=3)
    plt.plot(CH_overlap, POP.get_energies(), zorder=2)
    plt.plot([np.min([CC_overlap, CH_overlap]), np.max([CC_overlap, CH_overlap])]\
             ,[POP.e_fermi, POP.e_fermi],'k--', zorder=1, linewidth=5)
    plt.legend(['C-C overlap population','C-H overlap population','fermi level'],loc='best')
    plt.xlabel('Orbital overlap')
    plt.ylabel('Energy [eV]')
    plt.show()



.. image:: /auto_examples/plot_overlap_population/images/sphx_glr_plot_overlap_population_001.png
    :class: sphx-glr-single-img


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

 Out:

 .. code-block:: none

    C:\Users\lansf\Box Sync\Synced_Files\Coding\Python\Github\pDOS_overlap\examples\plot_overlap_population\plot_overlap_population.py:63: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.
      plt.show()





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

   **Total running time of the script:** ( 0 minutes  0.294 seconds)


.. _sphx_glr_download_auto_examples_plot_overlap_population_plot_overlap_population.py:


.. only :: html

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



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

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



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

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


.. only:: html

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

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