.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples/2D_simulation(crystalline)/plot_1_MQMAS_albite.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

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

        :ref:`Go to the end <sphx_glr_download_examples_2D_simulation(crystalline)_plot_1_MQMAS_albite.py>`
        to download the full example code

.. 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.

.. GENERATED FROM PYTHON SOURCE LINES 9-12

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]_.

.. GENERATED FROM PYTHON SOURCE LINES 12-21

.. code-block:: Python

    import matplotlib.pyplot as plt

    from mrsimulator import Simulator, SpinSystem, Site
    from mrsimulator.method.lib import ThreeQ_VAS
    from mrsimulator import signal_processor as sp
    from mrsimulator.spin_system.tensors import SymmetricTensor
    from mrsimulator.method import SpectralDimension









.. GENERATED FROM PYTHON SOURCE LINES 23-24

Generate the site and spin system objects.

.. GENERATED FROM PYTHON SOURCE LINES 24-32

.. code-block:: Python

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

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








.. GENERATED FROM PYTHON SOURCE LINES 33-35

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.

.. GENERATED FROM PYTHON SOURCE LINES 35-54

.. code-block:: Python

    method = ThreeQ_VAS(
        channels=["27Al"],
        magnetic_flux_density=7,  # in T
        spectral_dimensions=[
            SpectralDimension(
                count=256,
                spectral_width=1e4,  # in Hz
                reference_offset=-3e3,  # in Hz
                label="Isotropic dimension",
            ),
            SpectralDimension(
                count=512,
                spectral_width=1e4,  # in Hz
                reference_offset=4e3,  # in Hz
                label="MAS dimension",
            ),
        ],
    )








.. GENERATED FROM PYTHON SOURCE LINES 55-57

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

.. GENERATED FROM PYTHON SOURCE LINES 57-60

.. code-block:: Python

    sim = Simulator(spin_systems=spin_systems, methods=[method])
    sim.run()








.. GENERATED FROM PYTHON SOURCE LINES 61-62

The plot of the simulation.

.. GENERATED FROM PYTHON SOURCE LINES 62-73

.. code-block:: Python

    dataset = sim.methods[0].simulation

    plt.figure(figsize=(4.25, 3.0))
    ax = plt.subplot(projection="csdm")
    cb = ax.imshow(dataset.real / dataset.real.max(), aspect="auto", cmap="gist_ncar_r")
    plt.colorbar(cb)
    ax.invert_xaxis()
    ax.invert_yaxis()
    plt.tight_layout()
    plt.show()




.. image-sg:: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_1_MQMAS_albite_001.png
   :alt: plot 1 MQMAS albite
   :srcset: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_1_MQMAS_albite_001.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 74-75

Add post-simulation signal processing.

.. GENERATED FROM PYTHON SOURCE LINES 75-87

.. code-block:: Python

    processor = sp.SignalProcessor(
        operations=[
            # Gaussian convolution along both dimensions.
            sp.IFFT(dim_index=(0, 1)),
            sp.apodization.Gaussian(FWHM="0.2 kHz", dim_index=0),
            sp.apodization.Gaussian(FWHM="0.2 kHz", dim_index=1),
            sp.FFT(dim_index=(0, 1)),
        ]
    )
    processed_dataset = processor.apply_operations(dataset=sim.methods[0].simulation)
    processed_dataset /= processed_dataset.max()








.. GENERATED FROM PYTHON SOURCE LINES 88-89

The plot of the simulation after signal processing.

.. GENERATED FROM PYTHON SOURCE LINES 89-98

.. code-block:: Python

    plt.figure(figsize=(4.25, 3.0))
    ax = plt.subplot(projection="csdm")
    cb = ax.imshow(processed_dataset.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-sg:: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_1_MQMAS_albite_002.png
   :alt: plot 1 MQMAS albite
   :srcset: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_1_MQMAS_albite_002.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 99-104

.. [#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 0.877 seconds)


.. _sphx_glr_download_examples_2D_simulation(crystalline)_plot_1_MQMAS_albite.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

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

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

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

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


.. only:: html

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

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