.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples/2D_simulation(crystalline)/plot_4_3QMAS_Coesite.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_4_3QMAS_Coesite.py>`
        to download the full example code

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

.. _sphx_glr_examples_2D_simulation(crystalline)_plot_4_3QMAS_Coesite.py:


Coesite, ¹⁷O (I=5/2) 3QMAS
^^^^^^^^^^^^^^^^^^^^^^^^^^

¹⁷O (I=5/2) 3QMAS simulation.

.. GENERATED FROM PYTHON SOURCE LINES 9-12

The following is a triple quantum magic angle spinning (3QMAS) simulation of Coesite.
The NMR EFG tensor parameters for :math:`^{17}\text{O}` sites in coesite is obtained
from Grandinetti `et al.` [#f1]_

.. GENERATED FROM PYTHON SOURCE LINES 12-20

.. code-block:: Python

    import matplotlib.pyplot as plt

    from mrsimulator import Simulator
    from mrsimulator.method.lib import ThreeQ_VAS
    from mrsimulator import signal_processor as sp
    from mrsimulator.method import SpectralDimension









.. GENERATED FROM PYTHON SOURCE LINES 22-23

Create the Simulator object and load the spin systems database or url address.

.. GENERATED FROM PYTHON SOURCE LINES 23-51

.. code-block:: Python

    sim = Simulator()

    # load the spin systems from url.
    filename = "https://ssnmr.org/sites/default/files/mrsimulator/coesite_0.mrsys"
    sim.load_spin_systems(filename)

    method = ThreeQ_VAS(
        channels=["17O"],
        magnetic_flux_density=11.74,  # in T
        spectral_dimensions=[
            SpectralDimension(
                count=256,
                spectral_width=5e3,  # in Hz
                reference_offset=-2.5e3,  # in Hz
                label="Isotropic dimension",
            ),
            # The last spectral dimension block is the direct-dimension
            SpectralDimension(
                count=256,
                spectral_width=2e4,  # in Hz
                reference_offset=0,  # in Hz
                label="MAS dimension",
            ),
        ],
    )
    sim.methods = [method]  # add the method.
    sim.run()  # Run the simulation








.. GENERATED FROM PYTHON SOURCE LINES 52-53

The plot of the simulation.

.. GENERATED FROM PYTHON SOURCE LINES 53-64

.. 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_4_3QMAS_Coesite_001.png
   :alt: plot 4 3QMAS Coesite
   :srcset: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_4_3QMAS_Coesite_001.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 65-66

Add post-simulation signal processing.

.. GENERATED FROM PYTHON SOURCE LINES 66-78

.. code-block:: Python

    processor = sp.SignalProcessor(
        operations=[
            # Gaussian convolution along both dimensions.
            sp.IFFT(dim_index=(0, 1)),
            sp.apodization.Gaussian(FWHM="0.3 kHz", dim_index=0),
            sp.apodization.Gaussian(FWHM="0.15 kHz", dim_index=1),
            sp.FFT(dim_index=(0, 1)),
        ]
    )
    processed_dataset = processor.apply_operations(dataset=dataset)
    processed_dataset /= processed_dataset.max()








.. GENERATED FROM PYTHON SOURCE LINES 79-80

The plot of the simulation after signal processing.

.. GENERATED FROM PYTHON SOURCE LINES 80-89

.. 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.invert_xaxis()
    ax.invert_yaxis()
    plt.tight_layout()
    plt.show()




.. image-sg:: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_4_3QMAS_Coesite_002.png
   :alt: plot 4 3QMAS Coesite
   :srcset: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_4_3QMAS_Coesite_002.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 90-96

.. [#f1] Grandinetti, P. J., Baltisberger, J. H., Farnan, I., Stebbins, J. F.,
      Werner, U. and Pines, A.
      Solid-State :math:`^{17}\text{O}` Magic-Angle and Dynamic-Angle Spinning NMR
      Study of the :math:`\text{SiO}_2` Polymorph Coesite, J. Phys. Chem. 1995,
      **99**, *32*, 12341-12348.
      `DOI: 10.1021/j100032a045 <https://doi.org/10.1021/j100032a045>`_


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

   **Total running time of the script:** (0 minutes 0.915 seconds)


.. _sphx_glr_download_examples_2D_simulation(crystalline)_plot_4_3QMAS_Coesite.py:

.. only:: html

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

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

      :download:`Download Jupyter notebook: plot_4_3QMAS_Coesite.ipynb <plot_4_3QMAS_Coesite.ipynb>`

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

      :download:`Download Python source code: plot_4_3QMAS_Coesite.py <plot_4_3QMAS_Coesite.py>`


.. only:: html

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

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