.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples/1D_simulation(crystalline)/plot_91_custom_isotope_general.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

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

        :ref:`Go to the end <sphx_glr_download_examples_1D_simulation(crystalline)_plot_91_custom_isotope_general.py>`
        to download the full example code.

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

.. _sphx_glr_examples_1D_simulation(crystalline)_plot_91_custom_isotope_general.py:


Using Custom Isotopes
^^^^^^^^^^^^^^^^^^^^^

Simulating spectra of custom isotopes.

.. GENERATED FROM PYTHON SOURCE LINES 9-12

Mrsimulator includes the capability for simulating isotopes with user-defined
attributes. In this example, we show how to define a custom isotopes and simulate
spectra using custom isotopes.

.. GENERATED FROM PYTHON SOURCE LINES 12-20

.. code-block:: Python

    from mrsimulator.spin_system.isotope import Isotope
    from mrsimulator import Site, SpinSystem, Simulator
    from mrsimulator.method import SpectralDimension
    from mrsimulator.method.lib import BlochDecayCTSpectrum

    import matplotlib.pyplot as plt









.. GENERATED FROM PYTHON SOURCE LINES 22-26

First, we register a new isotope symbol with custom attributes using the
:py:meth:`~mrsimulator.spin_system.isotope.Isotope.register` method. The new symbol
cannot match any real isotope symbols, and re-calling register on a custom symbol will
update the stored attributes of that isotope.

.. GENERATED FROM PYTHON SOURCE LINES 26-33

.. code-block:: Python

    Isotope.register(
        symbol="custom",
        spin_multiplicity=4,  # Spin of I=3/2
        gyromagnetic_ratio=12.3,
        quadrupole_moment=0.045,
    )








.. GENERATED FROM PYTHON SOURCE LINES 34-37

Create :py:class:`~mrsimulator.spin_system.Site` and
:py:class:`~mrsimulator.method.Method` objects using the new isotope symbol. The
syntax is the same as any other isotope.

.. GENERATED FROM PYTHON SOURCE LINES 37-51

.. code-block:: Python

    site = Site(
        isotope="custom",
        isotropic_chemical_shift=-30,
        quadrupolar={"Cq": 1.3e6, "eta": 0.5},
    )
    sys = SpinSystem(sites=[site])

    mth = BlochDecayCTSpectrum(
        channels=["custom"],
        spectral_dimensions=[
            SpectralDimension(spectral_width=12e3, reference_offset=-3000)
        ],
    )








.. GENERATED FROM PYTHON SOURCE LINES 52-60

.. code-block:: Python

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

    plt.figure(figsize=(4.25, 3))
    plt.subplot(projection="csdm")
    plt.plot(sim.methods[0].simulation.real, color="black", linewidth=1)
    plt.tight_layout()
    plt.show()



.. image-sg:: /examples/1D_simulation(crystalline)/images/sphx_glr_plot_91_custom_isotope_general_001.png
   :alt: plot 91 custom isotope general
   :srcset: /examples/1D_simulation(crystalline)/images/sphx_glr_plot_91_custom_isotope_general_001.png
   :class: sphx-glr-single-img






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

   **Total running time of the script:** (0 minutes 0.203 seconds)


.. _sphx_glr_download_examples_1D_simulation(crystalline)_plot_91_custom_isotope_general.py:

.. only:: html

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

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

      :download:`Download Jupyter notebook: plot_91_custom_isotope_general.ipynb <plot_91_custom_isotope_general.ipynb>`

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

      :download:`Download Python source code: plot_91_custom_isotope_general.py <plot_91_custom_isotope_general.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: plot_91_custom_isotope_general.zip <plot_91_custom_isotope_general.zip>`


.. only:: html

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

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