:orphan:



.. _sphx_glr_examples:

.. _example_gallery:

===================
Simulation Examples
===================

In this section, we use the ``mrsimulator`` tools to create spin systems and
simulate spectrum with practical/experimental applications. The examples illustrate

- building spin systems,
- building NMR methods,
- simulating spectrum, and
- processing spectrum (e.g. adding line-broadening).

For mrsimulator applications related to least-squares fitting, see the
:ref:`fitting_examples`.


.. raw:: html

    <div class="sphx-glr-clear"></div>



.. _sphx_glr_examples_1D_simulation(crystalline):


1D NMR simulation (crystalline solids)
--------------------------------------

The following examples are the NMR spectrum simulation of crystalline solids for the
following methods:

- Bloch decay method (:class:`~mrsimulator.methods.BlochDecaySpectrum`),
- Central transition selective Bloch decay method (:class:`~mrsimulator.methods.BlochDecayCentralTransitionSpectrum`).
- Generic one-dimensional method (:class:`~mrsimulator.methods.Method1D`).



.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="29Si (I=1/2) spinning sideband simulation.">

.. only:: html

 .. figure:: /examples/1D_simulation(crystalline)/images/thumb/sphx_glr_plot_0_Wollastonite_thumb.png
     :alt: Wollastonite, 29Si (I=1/2)

     :ref:`sphx_glr_examples_1D_simulation(crystalline)_plot_0_Wollastonite.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/1D_simulation(crystalline)/plot_0_Wollastonite

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="33S (I=3/2) quadrupolar spectrum simulation.">

.. only:: html

 .. figure:: /examples/1D_simulation(crystalline)/images/thumb/sphx_glr_plot_1_PotassiumSulfate_thumb.png
     :alt: Potassium Sulfate, 33S (I=3/2)

     :ref:`sphx_glr_examples_1D_simulation(crystalline)_plot_1_PotassiumSulfate.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/1D_simulation(crystalline)/plot_1_PotassiumSulfate

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="17O (I=5/2) quadrupolar spectrum simulation.">

.. only:: html

 .. figure:: /examples/1D_simulation(crystalline)/images/thumb/sphx_glr_plot_2_Coesite_thumb.png
     :alt: Coesite, 17O (I=5/2)

     :ref:`sphx_glr_examples_1D_simulation(crystalline)_plot_2_Coesite.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/1D_simulation(crystalline)/plot_2_Coesite

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="17O (I=5/2) quadrupolar static spectrum simulation.">

.. only:: html

 .. figure:: /examples/1D_simulation(crystalline)/images/thumb/sphx_glr_plot_3_quad_csa_thumb.png
     :alt: Non-coincidental Quad and CSA, 17O (I=5/2)

     :ref:`sphx_glr_examples_1D_simulation(crystalline)_plot_3_quad_csa.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/1D_simulation(crystalline)/plot_3_quad_csa

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="27Al (I=5/2) quadrupolar spectrum simulation.">

.. only:: html

 .. figure:: /examples/1D_simulation(crystalline)/images/thumb/sphx_glr_plot_3_satellite_transition_sim_thumb.png
     :alt: Simulate arbitrary transitions (single-quantum)

     :ref:`sphx_glr_examples_1D_simulation(crystalline)_plot_3_satellite_transition_sim.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/1D_simulation(crystalline)/plot_3_satellite_transition_sim

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="33S (I=5/2) quadrupolar spectrum simulation.">

.. only:: html

 .. figure:: /examples/1D_simulation(crystalline)/images/thumb/sphx_glr_plot_4_multi-quantum_spectrum_thumb.png
     :alt: Simulate arbitrary transitions (multi-quantum)

     :ref:`sphx_glr_examples_1D_simulation(crystalline)_plot_4_multi-quantum_spectrum.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/1D_simulation(crystalline)/plot_4_multi-quantum_spectrum
.. raw:: html

    <div class="sphx-glr-clear"></div>



.. _sphx_glr_examples_1D_simulation(macro_amorphous):


1D NMR simulation (macromolecules/amorphous solids)
---------------------------------------------------

The following examples are the NMR spectrum simulation of macromolecules and amorphous
materials for the following methods:

- Bloch decay method (:class:`~mrsimulator.methods.BlochDecaySpectrum`),
- Central transition selective Bloch decay method (:class:`~mrsimulator.methods.BlochDecayCentralTransitionSpectrum`).

For NMR simulation of amorphous solids, we also show examples of simulating spectrum
using user-deined model or using commonly accepted models such as Czjzek or extended
Czjzek distribution.



.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="13C/15N (I=1/2) spinning sideband simulation.">

.. only:: html

 .. figure:: /examples/1D_simulation(macro_amorphous)/images/thumb/sphx_glr_plot_0_protein_GB1_thumb.png
     :alt: Protein GB1, 13C and 15N (I=1/2)

     :ref:`sphx_glr_examples_1D_simulation(macro_amorphous)_plot_0_protein_GB1.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/1D_simulation(macro_amorphous)/plot_0_protein_GB1

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="29Si (I=1/2) simulation of amorphous material.">

.. only:: html

 .. figure:: /examples/1D_simulation(macro_amorphous)/images/thumb/sphx_glr_plot_3_amorphous_like_thumb.png
     :alt: Amorphous material, 29Si (I=1/2)

     :ref:`sphx_glr_examples_1D_simulation(macro_amorphous)_plot_3_amorphous_like.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/1D_simulation(macro_amorphous)/plot_3_amorphous_like

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="27Al (I=5/2) simulation of amorphous material.">

.. only:: html

 .. figure:: /examples/1D_simulation(macro_amorphous)/images/thumb/sphx_glr_plot_4_amorphous_like_quad_thumb.png
     :alt: Amorphous material, 27Al (I=5/2)

     :ref:`sphx_glr_examples_1D_simulation(macro_amorphous)_plot_4_amorphous_like_quad.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/1D_simulation(macro_amorphous)/plot_4_amorphous_like_quad

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="In this example, we illustrate the simulation of spectrum originating from a Czjzek distributio...">

.. only:: html

 .. figure:: /examples/1D_simulation(macro_amorphous)/images/thumb/sphx_glr_plot_5_czjzek_distribution_thumb.png
     :alt: Czjzek distribution (Shielding and Quadrupolar)

     :ref:`sphx_glr_examples_1D_simulation(macro_amorphous)_plot_5_czjzek_distribution.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/1D_simulation(macro_amorphous)/plot_5_czjzek_distribution

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="In this example, we illustrate the simulation of spectrum originating from an extended Czjzek d...">

.. only:: html

 .. figure:: /examples/1D_simulation(macro_amorphous)/images/thumb/sphx_glr_plot_6_extended_czjzek_thumb.png
     :alt: Extended Czjzek distribution (Shielding and Quadrupolar)

     :ref:`sphx_glr_examples_1D_simulation(macro_amorphous)_plot_6_extended_czjzek.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/1D_simulation(macro_amorphous)/plot_6_extended_czjzek
.. raw:: html

    <div class="sphx-glr-clear"></div>



.. _sphx_glr_examples_2D_simulation(crystalline):


2D NMR simulation (Crystalline solids)
--------------------------------------

The following examples are the NMR spectrum simulation for crystalline solids. The
examples include the illustrations for the following methods:

- Triple-quantum variable-angle spinning (3Q-MAS) using the specialized
  :func:`~mrsimulator.methods.ThreeQ_VAS` method.
- Satellite-transition variable-angle spinning (ST-MAS) using the specialized
  :func:`~mrsimulator.methods.ST1_VAS` method.
- Switched angle spinning (SAS) using the generic :func:`~mrsimulator.methods.Method2D` method.
- Double hop Dynamic angle spinning (DAS) using the generic :func:`~mrsimulator.methods.Method2D`
  method.
- Correlation of anisotropies separated through echo refocusing (COASTER) using the generic
  :func:`~mrsimulator.methods.Method2D` method.
- Phase adjusted spinning sidebands (PASS) and Quadrupolar magic-angle turning (QMAT) using the
  specialized :func:`~mrsimulator.methods.SSB2D` method.



.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="87Rb (I=3/2) triple-quantum magic-angle spinning (3Q-MAS) simulation.">

.. only:: html

 .. figure:: /examples/2D_simulation(crystalline)/images/thumb/sphx_glr_plot_0_MQMAS_RbNO3_thumb.png
     :alt: RbNO3, 87Rb (I=3/2) 3QMAS

     :ref:`sphx_glr_examples_2D_simulation(crystalline)_plot_0_MQMAS_RbNO3.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/2D_simulation(crystalline)/plot_0_MQMAS_RbNO3

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="27Al (I=5/2) triple-quantum magic-angle spinning (3Q-MAS) simulation.">

.. only:: html

 .. figure:: /examples/2D_simulation(crystalline)/images/thumb/sphx_glr_plot_1_MQMAS_albite_thumb.png
     :alt: Albite, 27Al (I=5/2) 3QMAS

     :ref:`sphx_glr_examples_2D_simulation(crystalline)_plot_1_MQMAS_albite.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/2D_simulation(crystalline)/plot_1_MQMAS_albite

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="87Rb (I=3/2) staellite-transition off magic-angle spinning simulation.">

.. only:: html

 .. figure:: /examples/2D_simulation(crystalline)/images/thumb/sphx_glr_plot_1_STMAS_RbNO3_thumb.png
     :alt: RbNO3, 87Rb (I=3/2) STMAS

     :ref:`sphx_glr_examples_2D_simulation(crystalline)_plot_1_STMAS_RbNO3.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/2D_simulation(crystalline)/plot_1_STMAS_RbNO3

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="87Rb (I=3/2) Switched-angle spinning (SAS) simulation.">

.. only:: html

 .. figure:: /examples/2D_simulation(crystalline)/images/thumb/sphx_glr_plot_2_SAS_Rb2SO4_thumb.png
     :alt: Rb2SO4, 87Rb (I=3/2) SAS

     :ref:`sphx_glr_examples_2D_simulation(crystalline)_plot_2_SAS_Rb2SO4.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/2D_simulation(crystalline)/plot_2_SAS_Rb2SO4

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="87Rb (I=3/2) Switched-angle spinning (SAS) simulation.">

.. only:: html

 .. figure:: /examples/2D_simulation(crystalline)/images/thumb/sphx_glr_plot_3_SAS_Rb2CrO4_thumb.png
     :alt: Rb2CrO4, 87Rb (I=3/2) SAS

     :ref:`sphx_glr_examples_2D_simulation(crystalline)_plot_3_SAS_Rb2CrO4.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/2D_simulation(crystalline)/plot_3_SAS_Rb2CrO4

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="17O (I=5/2) Dynamic-angle spinning (DAS) simulation.">

.. only:: html

 .. figure:: /examples/2D_simulation(crystalline)/images/thumb/sphx_glr_plot_4_DAS_Coesite_thumb.png
     :alt: Coesite, 17O (I=5/2) DAS

     :ref:`sphx_glr_examples_2D_simulation(crystalline)_plot_4_DAS_Coesite.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/2D_simulation(crystalline)/plot_4_DAS_Coesite

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="87Rb (I=3/2) Correlation of anisotropies separated through echo refocusing (COASTER) simulation...">

.. only:: html

 .. figure:: /examples/2D_simulation(crystalline)/images/thumb/sphx_glr_plot_5_COASTER_Rb2CrO4_thumb.png
     :alt: Rb2CrO4, 87Rb (I=3/2) COASTER

     :ref:`sphx_glr_examples_2D_simulation(crystalline)_plot_5_COASTER_Rb2CrO4.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/2D_simulation(crystalline)/plot_5_COASTER_Rb2CrO4

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="13C (I=1/2) 2D Phase-adjusted spinning sideband (PASS) simulation.">

.. only:: html

 .. figure:: /examples/2D_simulation(crystalline)/images/thumb/sphx_glr_plot_6_PASS_itraconazole_drug_thumb.png
     :alt: Itraconazole, 13C (I=1/2) PASS

     :ref:`sphx_glr_examples_2D_simulation(crystalline)_plot_6_PASS_itraconazole_drug.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/2D_simulation(crystalline)/plot_6_PASS_itraconazole_drug

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="87Rb (I=3/2) Quadrupolar Magic-angle turning (QMAT) simulation.">

.. only:: html

 .. figure:: /examples/2D_simulation(crystalline)/images/thumb/sphx_glr_plot_7_QSSB_Rb2SO4_thumb.png
     :alt: Rb2SO4, 87Rb (I=3/2) QMAT

     :ref:`sphx_glr_examples_2D_simulation(crystalline)_plot_7_QSSB_Rb2SO4.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/2D_simulation(crystalline)/plot_7_QSSB_Rb2SO4

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="29Si (I=1/2) magic angle flipping.">

.. only:: html

 .. figure:: /examples/2D_simulation(crystalline)/images/thumb/sphx_glr_plot_8_MAF_thumb.png
     :alt: Wollastonite, 29Si (I=1/2), MAF

     :ref:`sphx_glr_examples_2D_simulation(crystalline)_plot_8_MAF.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/2D_simulation(crystalline)/plot_8_MAF
.. raw:: html

    <div class="sphx-glr-clear"></div>



.. _sphx_glr_examples_2D_simulation(macro_amorphous):

2D NMR simulation (Disordered/Amorphous solids)
-----------------------------------------------

The following examples are the NMR spectrum simulation for amorphous solids. The
examples include the illustrations for the following methods:

- Triple-quantum variable-angle spinning (:func:`~mrsimulator.methods.ThreeQ_VAS`)

.. - Double hop Dynamic angle spinning (DAS)



.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="87Rb (I=3/2) 3QMAS simulation with site disorder.">

.. only:: html

 .. figure:: /examples/2D_simulation(macro_amorphous)/images/thumb/sphx_glr_plot_0_crystalline_disorder_thumb.png
     :alt: Simulating site disorder (crystalline)

     :ref:`sphx_glr_examples_2D_simulation(macro_amorphous)_plot_0_crystalline_disorder.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/2D_simulation(macro_amorphous)/plot_0_crystalline_disorder

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="27Al (I=5/2) 3QMAS simulation of amorphous material.">

.. only:: html

 .. figure:: /examples/2D_simulation(macro_amorphous)/images/thumb/sphx_glr_plot_1_I=2.5_thumb.png
     :alt: Czjzek distribution, 27Al (I=5/2) 3QMAS

     :ref:`sphx_glr_examples_2D_simulation(macro_amorphous)_plot_1_I=2.5.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/2D_simulation(macro_amorphous)/plot_1_I=2.5
.. raw:: html

    <div class="sphx-glr-clear"></div>



.. only :: html

 .. container:: sphx-glr-footer
    :class: sphx-glr-footer-gallery


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

    :download:`Download all examples in Python source code: examples_python.zip </examples/examples_python.zip>`



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

    :download:`Download all examples in Jupyter notebooks: examples_jupyter.zip </examples/examples_jupyter.zip>`


.. only:: html

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

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