.. only:: html

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

        Click :ref:`here <sphx_glr_download_examples_2D_simulation(crystalline)_plot_1_MQMAS_albite.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_MQMAS_albite.py:


Albite, 27Al (I=5/2) 3QMAS
^^^^^^^^^^^^^^^^^^^^^^^^^^

27Al (I=5/2) triple-quantum magic-angle spinning (3Q-MAS) simulation.

The following is an example of :math:`^{27}\text{Al}` 3QMAS simulation of albite
:math:`\text{NaSi}_3\text{AlO}_8`. The :math:`^{27}\text{Al}` 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 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

    site = Site(
        isotope="27Al",
        isotropic_chemical_shift=64.7,  # in ppm
        quadrupolar={"Cq": 3.25e6, "eta": 0.68},  # Cq is in Hz
    )

    spin_systems = [SpinSystem(sites=[site])]








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=["27Al"],
        magnetic_flux_density=7,  # in T
        spectral_dimensions=[
            {
                "count": 256,
                "spectral_width": 1e4,  # in Hz
                "reference_offset": -3e3,  # in Hz
                "label": "Isotropic dimension",
            },
            {
                "count": 512,
                "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.subplot(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_1_MQMAS_albite_001.png
    :alt: plot 1 MQMAS albite
    :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="0.2 kHz", dim_index=0),
            apo.Gaussian(FWHM="0.2 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_xlim(75, 25)
    ax.set_ylim(-15, -65)
    plt.tight_layout()
    plt.show()




.. image:: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_1_MQMAS_albite_002.png
    :alt: plot 1 MQMAS albite
    :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  0.535 seconds)


.. _sphx_glr_download_examples_2D_simulation(crystalline)_plot_1_MQMAS_albite.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/2D_simulation(crystalline)/plot_1_MQMAS_albite.ipynb
      :alt: Launch binder
      :width: 150 px


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

     :download:`Download Python source code: plot_1_MQMAS_albite.py <plot_1_MQMAS_albite.py>`



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

     :download:`Download Jupyter notebook: plot_1_MQMAS_albite.ipynb <plot_1_MQMAS_albite.ipynb>`


.. only:: html

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

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