.. only:: html

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

        Click :ref:`here <sphx_glr_download_examples_2D_simulation(crystalline)_plot_5_COASTER_Rb2CrO4.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_5_COASTER_Rb2CrO4.py:


Rb2CrO4, 87Rb (I=3/2) COASTER
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

87Rb (I=3/2) Correlation of anisotropies separated through echo refocusing (COASTER)
simulation.

The following is a correlation of anisotropies separated through echo refocusing
(COASTER) simulation of :math:`\text{Rb}_2\text{CrO}_4`. The Rb site with the smaller
quadrupolar interaction is selectively observed and reported by Ash `et. al.` [#f1]_.
The following is the simulation based on the published tensor parameters.


.. 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 Method2D

    # 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="87Rb",
        isotropic_chemical_shift=-9,  # in ppm
        shielding_symmetric={"zeta": 110, "eta": 0},
        quadrupolar={
            "Cq": 3.5e6,  # in Hz
            "eta": 0.36,
            "alpha": 0,  # in rads
            "beta": 70 * 3.14159 / 180,  # in rads
            "gamma": 0,  # in rads
        },
    )
    spin_system = SpinSystem(sites=[site])








Use the generic 2D method, `Method2D`, to simulate a COASTER spectrum by customizing
the method parameters, as shown below. Note, the Method2D method simulates an infinite
spinning speed spectrum.


.. code-block:: python

    coaster = Method2D(
        channels=["87Rb"],
        magnetic_flux_density=9.4,  # in T
        rotor_angle=70.12 * 3.14159 / 180,  # in rads
        spectral_dimensions=[
            {
                "count": 256,
                "spectral_width": 4e4,  # in Hz
                "reference_offset": -8e3,  # in Hz
                "label": "3Q dimension",
                "events": [{"transition_query": {"P": [3], "D": [0]}}],
            },
            # The last spectral dimension block is the direct-dimension
            {
                "count": 256,
                "spectral_width": 2e4,  # in Hz
                "reference_offset": -3e3,  # in Hz
                "label": "70.12 dimension",
                "events": [{"transition_query": {"P": [-1], "D": [0]}}],
            },
        ],
    )








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


.. code-block:: python

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

    # configure the simulator object. For non-coincidental tensors, set the value of the
    # `integration_volume` attribute to `hemisphere`.
    sim.config.integration_volume = "hemisphere"
    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_5_COASTER_Rb2CrO4_001.png
    :alt: plot 5 COASTER Rb2CrO4
    :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="0.3 kHz", dim_index=0),
            apo.Gaussian(FWHM="0.3 kHz", dim_index=1),
            sp.FFT(dim_index=(0, 1)),
        ]
    )
    processed_data = processor.apply_operations(data=data)
    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.invert_xaxis()
    ax.invert_yaxis()
    plt.tight_layout()
    plt.show()




.. image:: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_5_COASTER_Rb2CrO4_002.png
    :alt: plot 5 COASTER Rb2CrO4
    :class: sphx-glr-single-img





.. [#f1] Jason T. Ash, Nicole M. Trease, and Philip J. Grandinetti. Separating
      Chemical Shift and Quadrupolar Anisotropies via Multiple-Quantum NMR
      Spectroscopy, J. Am. Chem. Soc. (2008) **130**, 10858-10859.
      `DOI: 10.1021/ja802865x <https://doi.org/10.1021/ja802865x>`_


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

   **Total running time of the script:** ( 0 minutes  0.595 seconds)


.. _sphx_glr_download_examples_2D_simulation(crystalline)_plot_5_COASTER_Rb2CrO4.py:


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