.. only:: html

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

        Click :ref:`here <sphx_glr_download_examples_2D_simulation(crystalline)_plot_8_MAF.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_2D_simulation(crystalline)_plot_8_MAF.py:


Wollastonite, 29Si (I=1/2), MAF
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

29Si (I=1/2) magic angle flipping.

Wollastonite is a high-temperature calcium-silicate,
:math:`\beta−\text{Ca}_3\text{Si}_3\text{O}_9`, with three distinct
:math:`^{29}\text{Si}` sites. The :math:`^{29}\text{Si}` tensor parameters
were obtained from Hansen `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 Method2D

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








Create the sites and spin systems


.. code-block:: python

    sites = [
        Site(
            isotope="29Si",
            isotropic_chemical_shift=-89.0,  # in ppm
            shielding_symmetric={"zeta": 59.8, "eta": 0.62},  # zeta in ppm
        ),
        Site(
            isotope="29Si",
            isotropic_chemical_shift=-89.5,  # in ppm
            shielding_symmetric={"zeta": 52.1, "eta": 0.68},  # zeta in ppm
        ),
        Site(
            isotope="29Si",
            isotropic_chemical_shift=-87.8,  # in ppm
            shielding_symmetric={"zeta": 69.4, "eta": 0.60},  # zeta in ppm
        ),
    ]

    spin_systems = [SpinSystem(sites=[s]) for s in sites]








Use the generic 2D method, `Method2D`, to simulate a MAF spectrum by customizing the
method parameters, as shown below. Note, the Method2D method simulates an infinite
spinning speed spectrum.


.. code-block:: python

    maf = Method2D(
        channels=["29Si"],
        magnetic_flux_density=14.1,  # in T
        spectral_dimensions=[
            {
                "count": 128,
                "spectral_width": 2e4,  # in Hz
                "label": "Anisotropic dimension",
                "events": [{"rotor_angle": 90 * 3.14159 / 180}],
            },
            {
                "count": 128,
                "spectral_width": 3e3,  # in Hz
                "reference_offset": -1.05e4,  # in Hz
                "label": "Isotropic dimension",
                "events": [{"rotor_angle": 54.735 * 3.14159 / 180}],
            },
        ],
        affine_matrix=[[1, -1], [0, 1]],
    )








Create the Simulator object, add the method and spin system objects, and run the
simulation.


.. code-block:: python

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








Add post-simulation signal processing.


.. code-block:: python

    csdm_data = sim.methods[0].simulation
    processor = sp.SignalProcessor(
        operations=[
            sp.IFFT(dim_index=(0, 1)),
            apo.Gaussian(FWHM="50 Hz", dim_index=0),
            apo.Gaussian(FWHM="50 Hz", dim_index=1),
            sp.FFT(dim_index=(0, 1)),
        ]
    )
    processed_data = processor.apply_operations(data=csdm_data).real
    processed_data /= processed_data.max()








The plot of the simulation after signal processing.


.. code-block:: python

    ax = plt.subplot(projection="csdm")
    cb = ax.imshow(processed_data.T, aspect="auto", cmap="gist_ncar_r")
    plt.colorbar(cb)
    ax.invert_xaxis()
    ax.invert_yaxis()
    plt.tight_layout()
    plt.show()




.. image:: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_8_MAF_001.png
    :alt: plot 8 MAF
    :class: sphx-glr-single-img





.. [#f1] Hansen, M. R., Jakobsen, H. J., Skibsted, J., :math:`^{29}\text{Si}`
      Chemical Shift Anisotropies in Calcium Silicates from High-Field
      :math:`^{29}\text{Si}` MAS NMR Spectroscopy, Inorg. Chem. 2003,
      **42**, *7*, 2368-2377.
      `DOI: 10.1021/ic020647f <https://doi.org/10.1021/ic020647f>`_


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

   **Total running time of the script:** ( 0 minutes  0.289 seconds)


.. _sphx_glr_download_examples_2D_simulation(crystalline)_plot_8_MAF.py:


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