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

.. only:: html

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

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

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

.. _sphx_glr_auto_examples_plot_rdf.py:

.. _rdf:

Calculating the radial distribution function
********************************************

In this tutorial we will learn how to analyse (ab-initio) molecular dynamics trajectories.
We will use the tool MDAnalysis to read our simulation data files and calculate the radial distribution 
function.

`Wikipedia page on RDF: <https://en.wikipedia.org/wiki/Radial_distribution_function>`_
`MDAnalysis documentation on RDF: <https://docs.mdanalysis.org/stable/documentation_pages/analysis/rdf.html>`_

We first import our python modules

.. GENERATED FROM PYTHON SOURCE LINES 17-25

.. code-block:: Python


    import numpy as np
    import matplotlib.pyplot as plt
    from pathlib import Path

    import MDAnalysis as mda
    from MDAnalysis.analysis.rdf import InterRDF








.. GENERATED FROM PYTHON SOURCE LINES 26-27

Then we define our project path. Replace the path with your own project path

.. GENERATED FROM PYTHON SOURCE LINES 27-30

.. code-block:: Python


    PROJECT_PATH=Path("../../../solutions/")








.. GENERATED FROM PYTHON SOURCE LINES 31-32

Next, we load our simulation output.

.. GENERATED FROM PYTHON SOURCE LINES 32-35

.. code-block:: Python


    universe = mda.Universe(PROJECT_PATH / "dft"/ "Argon_Simulation-pos-1.xyz")








.. GENERATED FROM PYTHON SOURCE LINES 36-38

# The Universe object contains the atomic positions for each timestep. 
# Note that the xyz file does not contain any information on the dimensions

.. GENERATED FROM PYTHON SOURCE LINES 38-41

.. code-block:: Python


    print(f"dimensions from xyz file {universe.dimensions}")





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

 .. code-block:: none

    dimensions from xyz file None




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So we must set the dimensions ourself to 

.. GENERATED FROM PYTHON SOURCE LINES 43-47

.. code-block:: Python


    box_l = 17.0742
    universe.dimensions = [box_l, box_l, box_l, 90, 90, 90]








.. GENERATED FROM PYTHON SOURCE LINES 48-49

Let's also check how many frames we've loaded with

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.. code-block:: Python


    print(f"loaded {len(universe.trajectory)} frames")





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

 .. code-block:: none

    loaded 10001 frames




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We now want to run an radial distribution analysis using InterRDF

.. GENERATED FROM PYTHON SOURCE LINES 54-60

.. code-block:: Python


    rdf = InterRDF(universe.atoms, universe.atoms, 
                   n_bins = 100,
                   range = (1.0, box_l / 2)
                   )








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We then run the analysis with

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.. code-block:: Python


    rdf.run()





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

 .. code-block:: none

    /fibus/fs3/0b/ckf7015/.local/lib/python3.11/site-packages/MDAnalysis/analysis/base.py:522: UserWarning: Reader has no dt information, set to 1.0 ps
      self.times[idx] = ts.time

    <MDAnalysis.analysis.rdf.InterRDF object at 0x7fee45ffb490>



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Next, we plot our results

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.. code-block:: Python


    plt.plot(rdf.results.bins, rdf.results.rdf)
    plt.xlabel("$r$ in A")
    plt.ylabel("g(r)")




.. image-sg:: /auto_examples/images/sphx_glr_plot_rdf_001.png
   :alt: plot rdf
   :srcset: /auto_examples/images/sphx_glr_plot_rdf_001.png
   :class: sphx-glr-single-img


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

 .. code-block:: none


    Text(42.597222222222214, 0.5, 'g(r)')



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and save our figure

.. GENERATED FROM PYTHON SOURCE LINES 74-77

.. code-block:: Python


    plt.savefig(PROJECT_PATH / "lammps" / "rdf.png", dpi=300)




.. image-sg:: /auto_examples/images/sphx_glr_plot_rdf_002.png
   :alt: plot rdf
   :srcset: /auto_examples/images/sphx_glr_plot_rdf_002.png
   :class: sphx-glr-single-img






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

   **Total running time of the script:** (0 minutes 7.606 seconds)


.. _sphx_glr_download_auto_examples_plot_rdf.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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