.. only:: html

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

        Click :ref:`here <sphx_glr_download_examples_2D_simulation(crystalline)_plot_0_MQMAS_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_0_MQMAS_RbNO3.py:


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

87Rb (I=3/2) triple-quantum magic-angle spinning (3Q-MAS) simulation.

The following is an example of the 3QMAS simulation of :math:`\text{RbNO}_3`, which
has three distinct :math:`^{87}\text{Rb}` sites. The :math:`^{87}\text{Rb}` tensor
parameters were obtained from Massiot `et. al.` [#f1]_. In this simulation, a Gaussian
broadening is applied to the spectrum as a post-simulation step.


.. 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 ThreeQ_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]








Select a Triple Quantum variable-angle spinning method. You may optionally
provide a `rotor_angle` to the method. The default `rotor_angle` is the magic-angle.


.. code-block:: python

    method = ThreeQ_VAS(
        channels=["87Rb"],
        magnetic_flux_density=9.4,  # in T
        spectral_dimensions=[
            {
                "count": 128,
                "spectral_width": 7e3,  # in Hz
                "reference_offset": -7e3,  # in Hz
                "label": "Isotropic dimension",
            },
            {
                "count": 256,
                "spectral_width": 1e4,  # 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 method.
    sim.run()








The plot of the simulation.


.. code-block:: python

    data = sim.methods[0].simulation
    ax = plt.gca(projection="csdm")
    cb = ax.imshow(data / data.max(), 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_0_MQMAS_RbNO3_001.png
    :alt: plot 0 MQMAS RbNO3
    :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="0.08 kHz", dim_index=0),
            apo.Gaussian(FWHM="0.22 kHz", dim_index=1),
            sp.FFT(dim_index=(0, 1)),
        ]
    )
    processed_data = processor.apply_operations(data=sim.methods[0].simulation)
    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.real, cmap="gist_ncar_r", aspect="auto")
    plt.colorbar(cb)
    ax.set_ylim(-40, -70)
    ax.set_xlim(-20, -60)
    plt.tight_layout()
    plt.show()




.. image:: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_0_MQMAS_RbNO3_002.png
    :alt: plot 0 MQMAS 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>`_

.. seealso::
  :ref:`sphx_glr_examples_2D_simulation(macro_amorphous)_plot_0_crystalline_disorder.py`
  for RbNO3.


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

   **Total running time of the script:** ( 0 minutes  0.522 seconds)


.. _sphx_glr_download_examples_2D_simulation(crystalline)_plot_0_MQMAS_RbNO3.py:


.. only :: html

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