.. only:: html

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    .. _sphx_glr_examples_1D_simulation(crystalline)_plot_3_quad_csa.py:


Non-coincidental Quad and CSA, 17O (I=5/2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

17O (I=5/2) quadrupolar static spectrum simulation.

The following example illustrates the simulation of NMR spectra arising from
non-coincidental quadrupolar and shielding tensors. The tensor parameter values for
the simulation are obtained from Yamada `et. al.` [#f1]_, for the
:math:`^{17}\text{O}` site in benzanilide.

.. warning::
    The Euler angles representation using by Yamada `et. al` is different from the
    representation used in mrsimulator. The resulting simulation might not resemble
    the published spectrum.


.. code-block:: python

    import matplotlib as mpl
    import matplotlib.pyplot as plt
    from mrsimulator import Simulator, SpinSystem, Site
    from mrsimulator.methods import BlochDecayCentralTransitionSpectrum
    import numpy as np

    # global plot configuration
    mpl.rcParams["figure.figsize"] = [4.5, 3.0]








**Step 1:** Create the spin system.


.. code-block:: python

    site = Site(
        isotope="17O",
        isotropic_chemical_shift=320,  # in ppm
        shielding_symmetric={"zeta": 376.667, "eta": 0.345},
        quadrupolar={
            "Cq": 8.97e6,  # in Hz
            "eta": 0.15,
            "alpha": 5 * np.pi / 180,
            "beta": np.pi / 2,
            "gamma": 70 * np.pi / 180,
        },
    )
    spin_system = SpinSystem(sites=[site])








**Step 2:** Create a central transition selective Bloch decay spectrum method.


.. code-block:: python

    method = BlochDecayCentralTransitionSpectrum(
        channels=["17O"],
        magnetic_flux_density=11.74,  # in T
        rotor_frequency=0,  # in Hz
        spectral_dimensions=[
            {
                "count": 1024,
                "spectral_width": 1e5,  # in Hz
                "reference_offset": 22500,  # in Hz
                "label": r"$^{17}$O resonances",
            }
        ],
    )








**Step 3:** Create the Simulator object and add method and spin system objects.


.. code-block:: python

    sim = Simulator()
    sim.spin_systems = [spin_system]  # add the spin system
    sim.methods = [method]  # add the method

    # Since the spin system have non-zero Euler angles, set the integration_volume to
    # hemisphere.
    sim.config.integration_volume = "hemisphere"








**Step 4:** Simulate the spectrum.


.. code-block:: python

    sim.run()

    # The plot of the simulation before signal processing.
    ax = plt.subplot(projection="csdm")
    ax.plot(sim.methods[0].simulation.real, color="black", linewidth=1)
    ax.invert_xaxis()
    plt.tight_layout()
    plt.show()





.. image:: /examples/1D_simulation(crystalline)/images/sphx_glr_plot_3_quad_csa_001.png
    :alt: plot 3 quad csa
    :class: sphx-glr-single-img





.. [#f1] Yamada, K., Dong, S., Wu, G., Solid-State 17O NMR Investigation of the
      Carbonyl Oxygen Electric-Field-Gradient Tensor and Chemical Shielding Tensor in
      Amides, J. Am. Chem. Soc. 2000, **122**, 11602-11609.
      `DOI: 10.1021/ja0008315 <https://doi.org/10.1021/ja0008315>`_


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

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