.. _sphx_glr_gallery_plot_isf.py:


Calculating the ISF of Water
=======================================================

In this example the ISF of water oxygens is calculated for a bulk simulation.
Additionally a KWW function is fitted to the results.




.. image:: /gallery/images/sphx_glr_plot_isf_001.png
    :align: center


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

 Out::

    Loading topology: /data/niels/sim/water/bulk/260K/topol.tpr
    Loading trajectory: /data/niels/sim/water/bulk/260K/out/traj_full_water1000bulk260.xtc




|


.. code-block:: python

    from functools import partial
    import matplotlib.pyplot as plt
    from scipy.optimize import curve_fit
    import mdevaluate as md
    import tudplot

    OW = md.open('/data/niels/sim/water/bulk/260K', trajectory='out/*.xtc').subset(atom_name='OW')
    t, S = md.correlation.shifted_correlation(
        partial(md.correlation.isf, q=22.7),
        OW,
        average=True
    )
    # Only include data-points of the alpha-relaxation for the fit
    mask = t > 3e-1
    fit, cov = curve_fit(md.functions.kww, t[mask], S[mask])
    tau = md.functions.kww_1e(*fit)

    tudplot.activate()
    plt.figure()
    plt.plot(t, S, '.', label='ISF of Bulk Water')
    plt.plot(t, md.functions.kww(t, *fit), '-', label=r'KWW, $\tau$={:.2f}ps'.format(tau))
    plt.xscale('log')
    plt.legend()

**Total running time of the script:**
(0 minutes 0.906 seconds)



.. container:: sphx-glr-download

    **Download Python source code:** :download:`plot_isf.py <plot_isf.py>`


.. container:: sphx-glr-download

    **Download IPython notebook:** :download:`plot_isf.ipynb <plot_isf.ipynb>`

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

    `Generated by Sphinx-Gallery <http://sphinx-gallery.readthedocs.io>`_