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.. _sphx_glr_examples_2D_simulation(macro_amorphous)_plot_0_crystalline_disorder.py:
Simulating site disorder (crystalline)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
87Rb (I=3/2) 3QMAS simulation with site disorder.
The following example illustrates an NMR simulation of a crystalline solid with site
disorders. We model such disorders with Extended Czjzek distribution. The following
case study shows an :math:`^{87}\text{Rb}` 3QMAS simulation of RbNO3.
.. code-block:: python
import matplotlib as mpl
import numpy as np
from mrsimulator import Simulator
from mrsimulator.methods import ThreeQ_VAS
import matplotlib.pyplot as plt
from mrsimulator.models import ExtCzjzekDistribution
from mrsimulator.utils.collection import single_site_system_generator
from scipy.stats import multivariate_normal
# global plot configuration
mpl.rcParams["figure.figsize"] = [4.5, 3.0]
Generate probability distribution
---------------------------------
Create three extended Czjzek distributions for the three sites in RbNO3 about their
respective mean tensors.
.. code-block:: python
# The range of isotropic chemical shifts, the quadrupolar coupling constant, and
# asymmetry parameters used in generating a 3D grid.
iso_r = np.arange(101) / 6.5 - 35 # in ppm
Cq_r = np.arange(100) / 100 + 1.25 # in MHz
eta_r = np.arange(11) / 10
# The 3D mesh grid over which the distribution amplitudes are evaluated.
iso, Cq, eta = np.meshgrid(iso_r, Cq_r, eta_r, indexing="ij")
def get_prob_dist(iso, Cq, eta, eps, cov):
pdf = 0
for i in range(len(iso)):
# The 2D amplitudes for Cq and eta is sampled from the extended Czjzek model.
avg_tensor = {"Cq": Cq[i], "eta": eta[i]}
_, _, amp = ExtCzjzekDistribution(avg_tensor, eps=eps[i]).pdf(pos=[Cq_r, eta_r])
# The 1D amplitudes for isotropic chemical shifts is sampled as a Gaussian.
iso_amp = multivariate_normal(mean=iso[i], cov=[cov[i]]).pdf(iso_r)
# The 3D amplitude grid is generated as an uncorrelated distribution of the
# above two distribution, which is the product of the two distributions.
pdf_t = np.repeat(amp, iso_r.size).reshape(eta_r.size, Cq_r.size, iso_r.size)
pdf_t *= iso_amp
pdf += pdf_t
return pdf
iso_0 = [-27.4, -28.5, -31.3] # isotropic chemical shifts for the three sites in ppm
Cq_0 = [1.68, 1.94, 1.72] # Cq in MHz for the three sites
eta_0 = [0.2, 1, 0.5] # eta for the three sites
eps_0 = [0.02, 0.02, 0.02] # perturbation fractions for extended Czjzek distribution.
var_0 = [0.1, 0.1, 0.1] # variance for the isotropic chemical shifts in ppm^2.
pdf = get_prob_dist(iso_0, Cq_0, eta_0, eps_0, var_0).T
The two-dimensional projections from this three-dimensional distribution are shown
below.
.. code-block:: python
_, ax = plt.subplots(1, 3, figsize=(9, 3))
# isotropic shift v.s. quadrupolar coupling constant
ax[0].contourf(Cq_r, iso_r, pdf.sum(axis=2))
ax[0].set_xlabel("Cq / MHz")
ax[0].set_ylabel("isotropic chemical shift / ppm")
# isotropic shift v.s. quadrupolar asymmetry
ax[1].contourf(eta_r, iso_r, pdf.sum(axis=1))
ax[1].set_xlabel(r"quadrupolar asymmetry, $\eta$")
ax[1].set_ylabel("isotropic chemical shift / ppm")
# quadrupolar coupling constant v.s. quadrupolar asymmetry
ax[2].contourf(eta_r, Cq_r, pdf.sum(axis=0))
ax[2].set_xlabel(r"quadrupolar asymmetry, $\eta$")
ax[2].set_ylabel("Cq / MHz")
plt.tight_layout()
plt.show()
.. image:: /examples/2D_simulation(macro_amorphous)/images/sphx_glr_plot_0_crystalline_disorder_001.png
:alt: plot 0 crystalline disorder
:class: sphx-glr-single-img
Simulation setup
----------------
Generate spin systems from the above probability distribution.
.. code-block:: python
spin_systems = single_site_system_generator(
isotopes="87Rb",
isotropic_chemical_shifts=iso,
quadrupolar={"Cq": Cq * 1e6, "eta": eta}, # Cq in Hz
abundance=pdf,
)
len(spin_systems)
.. rst-class:: sphx-glr-script-out
Out:
.. code-block:: none
510
Simulate a :math:`^{27}\text{Al}` 3Q-MAS spectrum by using the `ThreeQ_MAS` method.
.. code-block:: python
method = ThreeQ_VAS(
channels=["87Rb"],
magnetic_flux_density=9.4, # in T
rotor_angle=54.735 * np.pi / 180,
spectral_dimensions=[
{
"count": 96,
"spectral_width": 7e3, # in Hz
"reference_offset": -7e3, # in Hz
"label": "Isotropic dimension",
},
{
"count": 256,
"spectral_width": 1e4, # in Hz
"reference_offset": -4e3, # in Hz
"label": "MAS dimension",
},
],
)
Create the simulator object, add the spin systems and method, and run the simulation.
.. code-block:: python
sim = Simulator()
sim.spin_systems = spin_systems # add the spin systems
sim.methods = [method] # add the method
sim.config.number_of_sidebands = 1
sim.run()
data = sim.methods[0].simulation
The plot of the corresponding spectrum.
.. code-block:: python
ax = plt.subplot(projection="csdm")
cb = ax.imshow(data / data.max(), cmap="gist_ncar_r", aspect="auto")
ax.set_ylim(-40, -70)
ax.set_xlim(-20, -60)
plt.colorbar(cb)
plt.tight_layout()
plt.show()
.. image:: /examples/2D_simulation(macro_amorphous)/images/sphx_glr_plot_0_crystalline_disorder_002.png
:alt: plot 0 crystalline disorder
:class: sphx-glr-single-img
.. rst-class:: sphx-glr-timing
**Total running time of the script:** ( 0 minutes 3.338 seconds)
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