Simulator

The Simulator object is the core of the mrsimulator library. Each Simulator object holds a list of SpinSystem objects and a list of Method objects. A simulator object also holds a ConfigSimulator object, which can be modified to change aspects of the simulation as discussed below.

Set Up

Setting up a simulator object and running a simulation is simple. Below we add some arbitrary spin systems and methods to a simulator object.

from mrsimulator import Site, Simulator, SpinSystem
from mrsimulator.method.lib import BlochDecaySpectrum

# Setup the spin system and method objects
system1 = SpinSystem(sites=[Site(isotope="1H")])  # Proton spin system
system2 = SpinSystem(sites=[Site(isotope="17O")])  # Oxygen spin system
system3 = SpinSystem(sites=[Site(isotope="29Si")])  # Silicon spin system
method1 = BlochDecaySpectrum(channels=["1H"])
method2 = BlochDecaySpectrum(channels=["29Si"])

# Create the Simulator object
sim = Simulator()
sim.spin_systems = [system1, system2, system3]  # Add list of spin systems
sim.methods = [method1, method2]  # add list of methods

sim is a Simulator object which holds three spin systems and two methods. See Spin System and Method documentation for more information on the respective classes.

Running a Simulation

To simulate the NMR spectrum of the given spin systems using each method, call the simulator class method run().

sim.run()

The simulated spectrum is stored as a CSDM object in each method object under the simulation attribute. For more information on the Core Scientific Data Model (CSDM), see the csdmpy documentation. Below we put the simulated spectra of the method at index 0 into the variable dataset_0

dataset_0 = sim.methods[0].simulation
# dataset_n = sim.methods[n].simulation (for multiple methods)

Configuring the Simulator Object

Until now, we have used the simulator object with the default settings. In mrsimulator, we choose the default settings such that it applies to a wide range of simulations, including static, magic angle spinning (MAS), and variable angle spinning (VAS) spectra. In certain situations, however, the default settings are insufficient to represent the spectrum accurately.

The following code is used to create the plots in this section.

import matplotlib.pyplot as plt
import matplotlib as mpl

mpl.rcParams["figure.figsize"] = (6, 3.5)
mpl.rcParams["font.size"] = 11

# function to render figures.
def plot(csdm_object):
    ax = plt.subplot(projection="csdm")
    ax.plot(csdm_object.real, linewidth=1.5)
    ax.invert_xaxis()
    plt.tight_layout()
    plt.show()

Number of Sidebands

The number of sidebands simulated is determined by the attribute number_of_sidebands where sim is a simulator object. The default value is 64 and is sufficient for most cases.

In certain circumstances, especially when the anisotropy is large or the rotor spin frequency is low, 64 sidebands might not be sufficient.

from mrsimulator import Simulator, SpinSystem, Site
from mrsimulator.method.lib import BlochDecaySpectrum
from mrsimulator.method import SpectralDimension
from mrsimulator.spin_system.tensors import SymmetricTensor

# create a site with a large anisotropy of 100 ppm
Si29_site = Site(isotope="29Si", shielding_symmetric=SymmetricTensor(zeta=100, eta=0.2))
Si29_sys = SpinSystem(sites=[Si29_site])

# create a method with a low rotor frequency of 200 Hz
method = BlochDecaySpectrum(
    channels=["29Si"],
    rotor_frequency=200,
    spectral_dimensions=[SpectralDimension(count=1024, spectral_width=25000)],
)

sim = Simulator(spin_systems=[Si29_sys], methods=[method])
sim.run()

# plot the dataset using the method defined above
plot(sim.methods[0].simulation)

(png, hires.png, pdf)

../../_images/simulator-5.png

Figure 65 Inaccurate simulation resulting from computing low number of sidebands.

Looking at the spinning sideband patterns, we see an abrupt termination of the sideband amplitudes at the edges. This inaccurate simulation arises from evaluating a small number of sidebands relative to the given anisotropy. Increasing the number of sidebands to 90 should resolve the issue.

# sim already holds our spin systems and methods; no need to reconstruct
# set number of sidebands to 90
sim.config.number_of_sidebands = 90
sim.run()
plot(sim.methods[0].simulation)

(png, hires.png, pdf)

../../_images/simulator-6.png

Figure 67 Accurate simulation after increasing number of sidebands computed.

Conversely, 64 sidebands might be redundant, so the number of sidebands can be reduced. Reducing the number of sidebands will significantly improve performance, which might save computation time when used in iterative algorithms, such as least-squares minimization.

Integration Volume

The attribute integration_volume is an enumeration with two string literals, octant and hemisphere. The integration volume refers to the volume of the sphere over which the NMR frequencies are integrated. The default value is octant, i.e., the spectrum is comprised of integrated frequencies arising from the positive octant of the sphere. mrsimulator can exploit the problem’s orientational symmetry, thus optimizing the simulation by performing a partial integration.

To learn more about the orientational symmetries, refer to Eden et al. 1

Consider the \(^{29}\text{Si}\) site, Si29_site, from the previous example. This site has a symmetric shielding tensor with zeta and eta as 100 ppm and 0.2, respectively. With only zeta and eta, we can exploit the symmetry of the problem and evaluate the frequency integral over the octant, which is equivalent to the integration over the sphere. By adding the Euler angles to this tensor, we break the symmetry, and the integration over the octant is no longer accurate. Consider the following examples.

# add Euler angles to the previous site Si29 site
Si29_site.shielding_symmetric.alpha = 1.563  # in rad
Si29_site.shielding_symmetric.beta = 1.2131  # in rad
Si29_site.shielding_symmetric.gamma = 2.132  # in rad

# set the method to a static spectrum
sim.methods[0] = BlochDecaySpectrum(
    channels=["29Si"],
    rotor_frequency=0,  # in Hz
    spectral_dimensions=[SpectralDimension(count=1024, spectral_width=25000)],
)

# simulate and plot
sim.run()
plot(sim.methods[0].simulation)

(png, hires.png, pdf)

../../_images/simulator-7.png

Figure 69 Inaccurate simulation resulting from integrating over an octant when the spin system has Euler angles.

To fix this inaccurate spectrum, set the integration volume to hemisphere and re-simulate.

sim.config.integration_volume = "hemisphere"
sim.run()
plot(sim.methods[0].simulation)

(png, hires.png, pdf)

../../_images/simulator-8.png

Figure 71 Accurate CSA spectrum resulting from the frequency contributions evaluated over the top hemisphere.

Integration Density

The attribute integration_density controls the number of orientational points sampled over the given volume. The resulting spectrum is an integration of the NMR resonance frequency evaluated at these orientations. The total number of orientations, \(\Theta_\text{count}\), is given as

(6)\[\Theta_\text{count} = M (n + 1)(n + 2)/2,\]

where \(M\) is the number of octants and \(n\) is value of this attribute. The number of octants is deciphered from the value of the integration_volume attribute. The default value of this attribute, 70, produces 2556 orientations at which the NMR frequency contribution is evaluated.

sim = Simulator()
print(sim.config.integration_density)  # default
# 70
print(sim.config.get_orientations_count())  # 1 * 71 * 72 / 2
# 2556
sim.config.integration_density = 100
print(sim.config.get_orientations_count())  # 1 * 101 * 102 / 2
# 5151

Decreasing the integration density may decrease simulation time for computationally intensive experiments but will also reduce the quality of the spectrum. Similarly, increasing integration density will improve spectrum quality but also increase computation time.

Decompose Spectrum

The attribute decompose_spectrum is an enumeration with two string literals, None and spin_system. The default value is None.

If the value is None (default), the resulting simulation is a single spectrum where the frequency contributions from all the spin systems are co-added. Consider the following example.

# Create two distinct sites
site_A = Site(
    isotope="1H",
    shielding_symmetric=SymmetricTensor(zeta=5, eta=0.1),
)
site_B = Site(
    isotope="1H",
    shielding_symmetric=SymmetricTensor(zeta=-2, eta=0.83),
)

# Create two single site spin systems
sys_A = SpinSystem(sites=[site_A], name="System A")
sys_B = SpinSystem(sites=[site_B], name="System B")

# Create a method representing a simple 1-pulse acquire experiment
method = BlochDecaySpectrum(
    channels=["1H"], spectral_dimensions=[SpectralDimension(count=1024, spectral_width=10000)]
)

# Create simulator object, simulate, and plot
sim = Simulator(spin_systems=[sys_A, sys_B], methods=[method])
sim.run()
plot(sim.methods[0].simulation)

(png, hires.png, pdf)

../../_images/simulator-12.png

Figure 73 The frequency contributions from each individual spin systems are combined into one spectrum.

When decompose_spectrum is set to spin_system, the resulting simulation is a series of spectra each arising from a single spin system. The number of spectra is the same as the number of spin systems within the simulator object. Consider the same system as above, but change the decomposition to spin_system.

# sim already has the two spin systems and method; no need to reconstruct
sim.config.decompose_spectrum = "spin_system"
sim.run()
plot(sim.methods[0].simulation)

(png, hires.png, pdf)

../../_images/simulator-13.png

Figure 75 Each spin system’s frequency contributions are held in separate spectra.

Isotropic interpolation

The attribute isotropic_interpolation is an enumeration with two string literals, linear and gaussian. The default value is linear.

The value specifies the interpolation scheme used in binning isotropic contributions.


1

Edén, M. and Levitt, M. H. Computation of orientational averages in solid-state nmr by gaussian spherical quadrature. J. Mag. Res., 132, 2, 220-239, 1998. doi:10.1006/jmre.1998.1427.