.. only:: html

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

        Click :ref:`here <sphx_glr_download_examples_1D_simulation(crystalline)_plot_2_Coesite.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_examples_1D_simulation(crystalline)_plot_2_Coesite.py:


Coesite, 17O (I=5/2)
^^^^^^^^^^^^^^^^^^^^

17O (I=5/2) quadrupolar spectrum simulation.

Coesite is a high-pressure (2-3 GPa) and high-temperature (700°C) polymorph of silicon
dioxide :math:`\text{SiO}_2`. Coesite has five crystallographic :math:`^{17}\text{O}`
sites. In the following, we use the :math:`^{17}\text{O}` EFG tensor information from
Grandinetti `et. al.` [#f1]_


.. code-block:: python

    import matplotlib as mpl
    import matplotlib.pyplot as plt
    import mrsimulator.signal_processing as sp
    import mrsimulator.signal_processing.apodization as apo
    from mrsimulator import Simulator, SpinSystem, Site
    from mrsimulator.methods import BlochDecayCentralTransitionSpectrum

    # global plot configuration
    mpl.rcParams["figure.figsize"] = [4.5, 3.0]








**Step 1:** Create the sites.


.. code-block:: python


    # default unit of isotropic_chemical_shift is ppm and Cq is Hz.
    O17_1 = Site(
        isotope="17O", isotropic_chemical_shift=29, quadrupolar={"Cq": 6.05e6, "eta": 0.000}
    )
    O17_2 = Site(
        isotope="17O", isotropic_chemical_shift=41, quadrupolar={"Cq": 5.43e6, "eta": 0.166}
    )
    O17_3 = Site(
        isotope="17O", isotropic_chemical_shift=57, quadrupolar={"Cq": 5.45e6, "eta": 0.168}
    )
    O17_4 = Site(
        isotope="17O", isotropic_chemical_shift=53, quadrupolar={"Cq": 5.52e6, "eta": 0.169}
    )
    O17_5 = Site(
        isotope="17O", isotropic_chemical_shift=58, quadrupolar={"Cq": 5.16e6, "eta": 0.292}
    )

    # all five sites.
    sites = [O17_1, O17_2, O17_3, O17_4, O17_5]








**Step 2:** Create the spin systems from these sites. For optimum performance, we
create five single-site spin systems instead of a single five-site spin system. The
abundance of each spin system is taken from above reference.


.. code-block:: python

    abundance = [0.83, 1.05, 2.16, 2.05, 1.90]
    spin_systems = [SpinSystem(sites=[s], abundance=a) for s, a in zip(sites, abundance)]








**Step 3:** Create a central transition selective Bloch decay spectrum method.


.. code-block:: python

    method = BlochDecayCentralTransitionSpectrum(
        channels=["17O"],
        rotor_frequency=14000,  # in Hz
        spectral_dimensions=[
            {
                "count": 2048,
                "spectral_width": 50000,  # in Hz
                "label": r"$^{17}$O resonances",
            }
        ],
    )








The above method is set up to record the :math:`^{17}\text{O}` resonances at the
magic angle, spinning at 14 kHz and 9.4 T (default, if the value is not provided)
external magnetic flux density. The resonances are recorded over 50 kHz spectral
width using 2048 points.

**Step 4:** Create the Simulator object and add the method and spin system objects.


.. code-block:: python

    sim = Simulator()
    sim.spin_systems = spin_systems  # add the spin systems
    sim.methods = [method]  # add the method








**Step 5:** Simulate the spectrum.


.. code-block:: python

    sim.run()

    # The plot of the simulation before signal processing.
    ax = plt.subplot(projection="csdm")
    ax.plot(sim.methods[0].simulation.real, color="black", linewidth=1)
    ax.invert_xaxis()
    plt.tight_layout()
    plt.show()




.. image:: /examples/1D_simulation(crystalline)/images/sphx_glr_plot_2_Coesite_001.png
    :alt: plot 2 Coesite
    :class: sphx-glr-single-img





**Step 6:** Add post-simulation signal processing.


.. code-block:: python

    processor = sp.SignalProcessor(
        operations=[
            sp.IFFT(),
            apo.Exponential(FWHM="30 Hz"),
            apo.Gaussian(FWHM="145 Hz"),
            sp.FFT(),
        ]
    )
    processed_data = processor.apply_operations(data=sim.methods[0].simulation)

    # The plot of the simulation after signal processing.
    ax = plt.subplot(projection="csdm")
    ax.plot(processed_data.real, color="black", linewidth=1)
    ax.invert_xaxis()
    plt.tight_layout()
    plt.show()




.. image:: /examples/1D_simulation(crystalline)/images/sphx_glr_plot_2_Coesite_002.png
    :alt: plot 2 Coesite
    :class: sphx-glr-single-img





.. [#f1] Grandinetti, P. J., Baltisberger, J. H., Farnan, I., Stebbins, J. F.,
      Werner, U. and Pines, A.
      Solid-State :math:`^{17}\text{O}` Magic-Angle and Dynamic-Angle Spinning NMR
      Study of the :math:`\text{SiO}_2` Polymorph Coesite, J. Phys. Chem. 1995,
      **99**, *32*, 12341-12348.
      `DOI: 10.1021/j100032a045 <https://doi.org/10.1021/j100032a045>`_


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

   **Total running time of the script:** ( 0 minutes  0.446 seconds)


.. _sphx_glr_download_examples_1D_simulation(crystalline)_plot_2_Coesite.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/DeepanshS/mrsimulator/master?urlpath=lab/tree/docs/_build/html/../../notebooks/examples/1D_simulation(crystalline)/plot_2_Coesite.ipynb
      :alt: Launch binder
      :width: 150 px


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

     :download:`Download Python source code: plot_2_Coesite.py <plot_2_Coesite.py>`



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

     :download:`Download Jupyter notebook: plot_2_Coesite.ipynb <plot_2_Coesite.ipynb>`


.. only:: html

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

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