.. only:: html

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

        Click :ref:`here <sphx_glr_download_examples_2D_simulation(crystalline)_plot_1_STMAS_RbNO3.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_1_STMAS_RbNO3.py:


RbNO3, 87Rb (I=3/2) STMAS
^^^^^^^^^^^^^^^^^^^^^^^^^

87Rb (I=3/2) staellite-transition off magic-angle spinning simulation.

The following is an example of the STMAS simulation of :math:`\text{RbNO}_3`. The
:math:`^{87}\text{Rb}` tensor parameters were obtained from Massiot `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 ST1_VAS

    # global plot configuration
    font = {"size": 9}
    mpl.rc("font", **font)
    mpl.rcParams["figure.figsize"] = [4.25, 3.0]








Generate the site and spin system objects.


.. code-block:: python

    Rb87_1 = Site(
        isotope="87Rb",
        isotropic_chemical_shift=-27.4,  # in ppm
        quadrupolar={"Cq": 1.68e6, "eta": 0.2},  # Cq is in Hz
    )
    Rb87_2 = Site(
        isotope="87Rb",
        isotropic_chemical_shift=-28.5,  # in ppm
        quadrupolar={"Cq": 1.94e6, "eta": 1.0},  # Cq is in Hz
    )
    Rb87_3 = Site(
        isotope="87Rb",
        isotropic_chemical_shift=-31.3,  # in ppm
        quadrupolar={"Cq": 1.72e6, "eta": 0.5},  # Cq is in Hz
    )

    sites = [Rb87_1, Rb87_2, Rb87_3]  # all sites
    spin_systems = [SpinSystem(sites=[s]) for s in sites]








**Step 2:** Select a satellite-transition variable-angle spinning method. The
following `ST1_VAS` method correlates the frequencies from the two inner-satellite
transitions to the central transition. Note, STMAS measurements are highly suspectable
to rotor angle mismatch. In the following, we show two methods, first set to
magic-angle and the second deliberately miss-sets by approximately 0.0059 degrees.


.. code-block:: python


    angles = [54.7359, 54.73]
    method = []
    for angle in angles:
        method.append(
            ST1_VAS(
                channels=["87Rb"],
                magnetic_flux_density=7,  # in T
                rotor_angle=angle * 3.14159 / 180,  # in rad (magic angle)
                spectral_dimensions=[
                    {
                        "count": 256,
                        "spectral_width": 3e3,  # in Hz
                        "reference_offset": -2.4e3,  # in Hz
                        "label": "Isotropic dimension",
                    },
                    {
                        "count": 512,
                        "spectral_width": 5e3,  # in Hz
                        "reference_offset": -4e3,  # in Hz
                        "label": "MAS dimension",
                    },
                ],
            )
        )








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 = method  # add the methods.
    sim.run()








The plot of the simulation.


.. code-block:: python

    data = [sim.methods[0].simulation, sim.methods[1].simulation]
    fig, ax = plt.subplots(1, 2, figsize=(8.5, 3), subplot_kw={"projection": "csdm"})

    titles = ["STVAS @ magic-angle", "STVAS @ 0.0059 deg off magic-angle"]
    for i, item in enumerate(data):
        cb1 = ax[i].imshow(item / item.max(), aspect="auto", cmap="gist_ncar_r")
        ax[i].set_title(titles[i])
        plt.colorbar(cb1, ax=ax[i])
        ax[i].invert_xaxis()
        ax[i].invert_yaxis()
    plt.tight_layout()
    plt.show()




.. image:: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_1_STMAS_RbNO3_001.png
    :alt: STVAS @ magic-angle, STVAS @ 0.0059 deg off magic-angle
    :class: sphx-glr-single-img





Add post-simulation signal processing.


.. code-block:: python

    processor = sp.SignalProcessor(
        operations=[
            # Gaussian convolution along both dimensions.
            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 = []
    for item in data:
        processed_data.append(processor.apply_operations(data=item))
        processed_data[-1] /= processed_data[-1].max()








The plot of the simulation after signal processing.


.. code-block:: python

    ax = plt.subplot(projection="csdm")
    cb = ax.imshow(processed_data[1].real, cmap="gist_ncar_r", aspect="auto")
    plt.colorbar(cb)
    ax.invert_xaxis()
    ax.invert_yaxis()
    plt.tight_layout()
    plt.show()




.. image:: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_1_STMAS_RbNO3_002.png
    :alt: plot 1 STMAS RbNO3
    :class: sphx-glr-single-img





.. [#f1] Massiot, D., Touzoa, B., Trumeaua, D., Coutures, J.P., Virlet, J., Florian,
      P., Grandinetti, P.J. Two-dimensional magic-angle spinning isotropic
      reconstruction sequences for quadrupolar nuclei, ssnmr, (1996), **6**, *1*,
      73-83. `DOI: 10.1016/0926-2040(95)01210-9
      <https://doi.org/10.1016/0926-2040(95)01210-9>`_


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

   **Total running time of the script:** ( 0 minutes  0.913 seconds)


.. _sphx_glr_download_examples_2D_simulation(crystalline)_plot_1_STMAS_RbNO3.py:


.. only :: html

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