.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples/2D_simulation(crystalline)/plot_2_STMAS_quad_coupling_cross.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_2_STMAS_quad_coupling_cross.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_examples_2D_simulation(crystalline)_plot_2_STMAS_quad_coupling_cross.py:


Co59 (I=7/2) STMAS
^^^^^^^^^^^^^^^^^^

Co59 (I=7/2) satellite-transition magic-angle spinning simulation.
(Quad-coupling cross terms)

.. GENERATED FROM PYTHON SOURCE LINES 11-20

.. code-block:: Python

    import matplotlib.pyplot as plt

    from mrsimulator import Simulator, SpinSystem, Site, Coupling
    from mrsimulator.method.lib import ST1_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 22-23

Generate the site and spin system objects.

.. GENERATED FROM PYTHON SOURCE LINES 23-36

.. code-block:: Python

    Co_sites = [
        Site(
            isotope="59Co",  # 59Co
            isotropic_chemical_shift=0,  # in ppm
            # shielding_symmetric=SymmetricTensor(zeta=-1750, eta=0),
            quadrupolar=SymmetricTensor(Cq=3.1e6, eta=0.2),  # Cq is in Hz
        ),
        Site(isotope="1H", isotropic_chemical_shift=0),
    ]

    coupling = [Coupling(site_index=[0, 1], dipolar={"D": 50000})]
    spin_systems = [SpinSystem(sites=Co_sites, couplings=coupling)]








.. GENERATED FROM PYTHON SOURCE LINES 37-40

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.

.. GENERATED FROM PYTHON SOURCE LINES 40-66

.. code-block:: Python


    method = ST1_VAS(
        channels=["59Co"],
        magnetic_flux_density=4.684,  # in T
        rotor_angle=54.7359 * 3.14159 / 180,  # in rad (magic angle)
        spectral_dimensions=[
            SpectralDimension(
                count=256,
                spectral_width=1e3,  # in Hz
                # reference_offset=-1e3,  # in Hz
                label="Isotropic dimension",
            ),
            SpectralDimension(
                count=512,
                spectral_width=3e3,  # in Hz
                reference_offset=-1e3,  # in Hz
                label="MAS dimension",
            ),
        ],
    )

    # A graphical representation of the method object.
    plt.figure(figsize=(5, 2.5))
    method.plot()
    plt.show()




.. image-sg:: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_2_STMAS_quad_coupling_cross_001.png
   :alt: ST1_VAS
   :srcset: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_2_STMAS_quad_coupling_cross_001.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 67-69

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

.. GENERATED FROM PYTHON SOURCE LINES 69-73

.. code-block:: Python

    sim = Simulator(spin_systems=spin_systems, methods=[method])
    sim.config.decompose_spectrum = "spin_system"
    sim.run()








.. GENERATED FROM PYTHON SOURCE LINES 74-75

Add post-simulation signal processing.

.. GENERATED FROM PYTHON SOURCE LINES 75-88

.. code-block:: Python

    dataset = sim.methods[0].simulation
    processor = sp.SignalProcessor(
        operations=[
            # Gaussian convolution along both dimensions.
            sp.IFFT(dim_index=(0, 1)),
            sp.apodization.Gaussian(FWHM="20 Hz", dim_index=0),
            sp.apodization.Gaussian(FWHM="20 Hz", dim_index=1),
            sp.FFT(dim_index=(0, 1)),
        ]
    )

    processed_dataset = processor.apply_operations(dataset=dataset)








.. GENERATED FROM PYTHON SOURCE LINES 89-90

The plot of the simulation.

.. GENERATED FROM PYTHON SOURCE LINES 90-100

.. code-block:: Python

    _ = [item.to("kHz", "nmr_frequency_ratio") for item in processed_dataset.x]

    processed_dataset = processed_dataset.split()
    plt.figure(figsize=(4.25, 3.0))
    ax = plt.subplot(projection="csdm")
    ax.imshow(processed_dataset[0].real, cmap="gist_ncar_r", aspect="auto")
    ax.invert_xaxis()
    ax.invert_yaxis()
    plt.tight_layout()
    plt.show()



.. image-sg:: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_2_STMAS_quad_coupling_cross_002.png
   :alt: spin system 0
   :srcset: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_2_STMAS_quad_coupling_cross_002.png
   :class: sphx-glr-single-img






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

   **Total running time of the script:** (0 minutes 0.600 seconds)


.. _sphx_glr_download_examples_2D_simulation(crystalline)_plot_2_STMAS_quad_coupling_cross.py:

.. only:: html

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

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

      :download:`Download Jupyter notebook: plot_2_STMAS_quad_coupling_cross.ipynb <plot_2_STMAS_quad_coupling_cross.ipynb>`

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

      :download:`Download Python source code: plot_2_STMAS_quad_coupling_cross.py <plot_2_STMAS_quad_coupling_cross.py>`


.. only:: html

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

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