.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "examples/2D_simulation(crystalline)/plot_0_MQMAS_RbNO3.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code .. rst-class:: sphx-glr-example-title .. _sphx_glr_examples_2D_simulation(crystalline)_plot_0_MQMAS_RbNO3.py: RbNO₃, ⁸⁷Rb (I=3/2) 3QMAS ^^^^^^^^^^^^^^^^^^^^^^^^^ ⁸⁷Rb (I=3/2) triple-quantum magic-angle spinning (3Q-MAS) simulation. .. GENERATED FROM PYTHON SOURCE LINES 9-13 The following is an example of the 3QMAS simulation of :math:`\text{RbNO}_3`, which has three distinct :math:`^{87}\text{Rb}` sites. The :math:`^{87}\text{Rb}` tensor parameters were obtained from Massiot `et al.` [#f1]_. In this simulation, a Gaussian broadening is applied to the spectrum as a post-simulation step. .. GENERATED FROM PYTHON SOURCE LINES 13-22 .. code-block:: Python import matplotlib.pyplot as plt from mrsimulator import Simulator, SpinSystem, Site from mrsimulator.method.lib import ThreeQ_VAS from mrsimulator import signal_processor as sp from mrsimulator.spin_system.tensors import SymmetricTensor from mrsimulator.method import SpectralDimension .. GENERATED FROM PYTHON SOURCE LINES 24-25 Generate the site and spin system objects. .. GENERATED FROM PYTHON SOURCE LINES 25-44 .. code-block:: Python Rb87_1 = Site( isotope="87Rb", isotropic_chemical_shift=-27.4, # in ppm quadrupolar=SymmetricTensor(Cq=1.68e6, eta=0.2), # Cq is in Hz ) Rb87_2 = Site( isotope="87Rb", isotropic_chemical_shift=-28.5, # in ppm quadrupolar=SymmetricTensor(Cq=1.94e6, eta=1.0), # Cq is in Hz ) Rb87_3 = Site( isotope="87Rb", isotropic_chemical_shift=-31.3, # in ppm quadrupolar=SymmetricTensor(Cq=1.72e6, eta=0.5), # Cq is in Hz ) sites = [Rb87_1, Rb87_2, Rb87_3] # all sites spin_systems = [SpinSystem(sites=[s]) for s in sites] .. GENERATED FROM PYTHON SOURCE LINES 45-47 Select a Triple Quantum variable-angle spinning method. You may optionally provide a `rotor_angle` to the method. The default `rotor_angle` is the magic-angle. .. GENERATED FROM PYTHON SOURCE LINES 47-71 .. code-block:: Python method = ThreeQ_VAS( channels=["87Rb"], magnetic_flux_density=9.4, # in T spectral_dimensions=[ SpectralDimension( count=128, spectral_width=7e3, # in Hz reference_offset=-7e3, # in Hz label="Isotropic dimension", ), SpectralDimension( count=256, spectral_width=1e4, # in Hz reference_offset=-4e3, # in Hz label="MAS dimension", ), ], ) # A graphical representation of the method object. plt.figure(figsize=(5, 2.5)) method.plot() plt.show() .. image-sg:: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_0_MQMAS_RbNO3_001.png :alt: ThreeQ_VAS :srcset: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_0_MQMAS_RbNO3_001.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 72-74 Create the Simulator object, add the method and spin system objects, and run the simulation. .. GENERATED FROM PYTHON SOURCE LINES 74-77 .. code-block:: Python sim = Simulator(spin_systems=spin_systems, methods=[method]) sim.run() .. GENERATED FROM PYTHON SOURCE LINES 78-79 The plot of the simulation. .. GENERATED FROM PYTHON SOURCE LINES 79-90 .. 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_0_MQMAS_RbNO3_002.png :alt: plot 0 MQMAS RbNO3 :srcset: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_0_MQMAS_RbNO3_002.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 91-92 Add post-simulation signal processing. .. GENERATED FROM PYTHON SOURCE LINES 92-104 .. code-block:: Python processor = sp.SignalProcessor( operations=[ # Gaussian convolution along both dimensions. sp.IFFT(dim_index=(0, 1)), sp.apodization.Gaussian(FWHM="0.08 kHz", dim_index=0), sp.apodization.Gaussian(FWHM="0.22 kHz", dim_index=1), sp.FFT(dim_index=(0, 1)), ] ) processed_dataset = processor.apply_operations(dataset=sim.methods[0].simulation) processed_dataset /= processed_dataset.max() .. GENERATED FROM PYTHON SOURCE LINES 105-106 The plot of the simulation after signal processing. .. GENERATED FROM PYTHON SOURCE LINES 106-115 .. 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.set_ylim(-40, -70) ax.set_xlim(-20, -60) plt.tight_layout() plt.show() .. image-sg:: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_0_MQMAS_RbNO3_003.png :alt: plot 0 MQMAS RbNO3 :srcset: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_0_MQMAS_RbNO3_003.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 116-125 .. [#f1] Massiot, D., Touzoa, B., Trumeaua, D., Coutures, J.P., Virlet, J., Florian, P., Grandinetti, P.J. Two-dimensional magic-angle spinning isotropic reconstruction sequences for quadrupolar nuclei, ssnmr, (1996), **6**, *1*, 73-83. `DOI: 10.1016/0926-2040(95)01210-9 `_ .. seealso:: :ref:`sphx_glr_examples_2D_simulation(macro_amorphous)_plot_0_crystalline_disorder.py` for RbNO3. .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 0.969 seconds) .. _sphx_glr_download_examples_2D_simulation(crystalline)_plot_0_MQMAS_RbNO3.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_0_MQMAS_RbNO3.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_0_MQMAS_RbNO3.py ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_