Methods Library

For convenience, mrsimulator offers the following pre-built methods -

• Bloch Decay Spectrum

• Bloch Decay Central Transition

• Multi-Quantum VAS

• Satellite-Transition VAS

• SSB2D

An example of the syntax that all library methods follows is shown below.

from mrsimulator.method import SpectralDimension
from mrsimulator.method.lib import BlochDecaySpectrum

lib_method = BlochDecaySpectrum(
    channels=["29Si"],  # list of isotopes
    magnetic_flux_density=4.7,  # T
    rotor_angle=57.735 * 3.1415 / 180,  # rad
    rotor_frequency=10000,  # Hz
    spectral_dimensions=[
        SpectralDimension(count=512, spectral_width=5e4, reference_offset=10),
    ],
)

where BlochDecaySpectrum can be replaced with another library method class. Each method has the channels attribute, which is a list of isotopes probed by the method as well as the magnetic_flux_density, rotor_angle, and rotor_frequency attributes which define the global experiment parameters. See Table 6 for more details.

The method object also has the spectral_dimensions attribute, which contains a list of SpectralDimension objects defining the spectral grid. A 2D method will have two spectral dimensions in this list, whereas a 1D method will only have one. See Table 7 for the attributes of a SpectralDimension object.

Bloch Decay Spectrum

The BlochDecaySpectrum class simulates the Bloch decay spectrum.

from mrsimulator.method.lib import BlochDecaySpectrum
from mrsimulator.method import SpectralDimension

method = BlochDecaySpectrum(
    channels=["1H"],
    rotor_frequency=12500,  # in Hz
    rotor_angle=54.735 * 3.14159 / 180,  # in rad
    magnetic_flux_density=9.4,  # in tesla
    spectral_dimensions=[
        SpectralDimension(
            count=1024,
            spectral_width=25e3,  # in Hz
            reference_offset=-4e3,  # in Hz
        )
    ],
)

Examples

Figure 31 Wollastonite, ²⁹Si (I=1/2)

Figure 32 Coupled spin-1/2 (Static dipolar spectrum)

Figure 33 Coupled spin-1/2 (CSA + heteronuclear dipolar + J-couplings)

Figure 34 Protein GB1, ¹³C and ¹⁵N (I=1/2)

Figure 35 Amorphous material, ²⁹Si (I=1/2)

Figure 36 Czjzek distribution (Shielding and Quadrupolar)

Figure 37 Extended Czjzek distribution (Shielding and Quadrupolar)

Figure 38 ³¹P MAS NMR of crystalline Na2PO4 (CSA)

Figure 39 ³¹P static NMR of crystalline Na2PO4 (CSA)

Figure 40 ¹³C MAS NMR of Glycine (CSA) [960 Hz]

Figure 41 ¹³C MAS NMR of Glycine (CSA) multi-spectra fit

Figure 42 1D PASS/MAT sideband order cross-section

Figure 43 ²⁷Al MAS NMR of YAG (1st and 2nd order Quad)

Figure 44 ²H MAS NMR of Methionine

Figure 45 ¹¹⁹Sn MAS NMR of SnO

Bloch Decay Central Transition

The BlochDecayCTSpectrum class simulates the Bloch decay central transition selective spectrum.

from mrsimulator.method.lib import BlochDecayCTSpectrum
from mrsimulator.method import SpectralDimension

method = BlochDecayCTSpectrum(
    channels=["87Rb"],
    rotor_frequency=12500,  # in Hz
    rotor_angle=54.735 * 3.14159 / 180,  # in rad
    magnetic_flux_density=9.4,  # in tesla
    spectral_dimensions=[
        SpectralDimension(
            count=1024,
            spectral_width=25e3,  # in Hz
            reference_offset=-4e3,  # in Hz
        )
    ],
)

Examples

Figure 46 Potassium Sulfate, ³³S (I=3/2)

Figure 47 Coesite, ¹⁷O (I=5/2)

Figure 48 Non-coincidental Quad and CSA, ¹⁷O (I=5/2)

Figure 49 Amorphous material, ²⁷Al (I=5/2)

Figure 50 Czjzek distribution (Shielding and Quadrupolar)

Figure 51 Extended Czjzek distribution (Shielding and Quadrupolar)

Figure 52 ¹⁷O MAS NMR of crystalline Na₂SiO₃ (2nd order quad)

Figure 53 ¹¹B MAS NMR of Lithium orthoborate crystal

Multi-Quantum VAS

The ThreeQ_VAS, FiveQ_VAS, and SevenQ_VAS classes all simulate a multiple quantum VAS spectrum. The spinning speed for all three methods is fixed at infinite speed. The spectrum is also sheared such that the correlated dimensions are the isotropic dimension and the VAS dimension.

from mrsimulator.method.lib import ThreeQ_VAS
from mrsimulator.method import SpectralDimension

method = ThreeQ_VAS(
    channels=["87Rb"],
    magnetic_flux_density=7,  # in T
    spectral_dimensions=[
        SpectralDimension(
            count=128,
            spectral_width=3e3,  # in Hz
            reference_offset=-2e3,  # in Hz
            label="Isotropic dimension",
        ),
        SpectralDimension(
            count=512,
            spectral_width=1e4,  # in Hz
            reference_offset=-5e3,  # in Hz
            label="MAS dimension",
        ),
    ],
)

The other methods, employing five and seven quantum transitions, can be imported as follows:

from mrsimulator.method.lib import FiveQ_VAS
from mrsimulator.method.lib import SevenQ_VAS

Examples

Figure 54 RbNO₃, ⁸⁷Rb (I=3/2) 3QMAS

Figure 55 Albite, ²⁷Al (I=5/2) 3QMAS

Figure 56 Coesite, ¹⁷O (I=5/2) 3QMAS

Figure 57 Simulating site disorder (crystalline)

Figure 58 Czjzek distribution, ²⁷Al (I=5/2) 3QMAS

Figure 59 ⁸⁷Rb 2D 3QMAS NMR of RbNO₃

Satellite-Transition VAS

The ST1_VAS and ST2_VAS classes simulate a sheared and scaled satellite and central transition correlation spectrum. The spinning speed for these methods is fixed at infinite speed.

from mrsimulator.method.lib import ST1_VAS
from mrsimulator.method import SpectralDimension

method = ST1_VAS(
    channels=["87Rb"],
    magnetic_flux_density=9.4,  # in T
    spectral_dimensions=[
        SpectralDimension(
            count=128,
            spectral_width=1e3,  # in Hz
            reference_offset=-5e3,  # in Hz
            label="Isotropic dimension",
        ),
        SpectralDimension(
            count=256,
            spectral_width=1e4,  # in Hz
            reference_offset=-3e3,  # in Hz
            label="MAS dimension",
        ),
    ],
)

Examples

Figure 60 RbNO₃, ⁸⁷Rb (I=3/2) STMAS

SSB2D

The SSB2D class simulates a sheared 2D finite to infinite speed MAS correlation spectrum. The spinning speed for the second spectral dimension is fixed at infinite spinning speed

from mrsimulator.method.lib import SSB2D
from mrsimulator.method import SpectralDimension

method = SSB2D(
    channels=["13C"],
    magnetic_flux_density=7,  # in T
    rotor_frequency=1500,  # in Hz
    spectral_dimensions=[
        SpectralDimension(
            count=16,
            spectral_width=16 * 1500,  # in Hz (= count * rotor_frequency)
            reference_offset=-5e3,  # in Hz
            label="Sideband dimension",
        ),
        SpectralDimension(
            count=512,
            spectral_width=1e4,  # in Hz
            reference_offset=-4e3,  # in Hz
            label="Isotropic dimension",
        ),
    ],
)

Examples

Figure 61 Itraconazole, ¹³C (I=1/2) PASS

Figure 62 Rb₂SO₄, ⁸⁷Rb (I=3/2) QMAT

Figure 63 ¹³C 2D MAT NMR of L-Histidine

Figure 64 ⁸⁷Rb 2D QMAT NMR of Rb₂SO₄

Attribute Summaries

Table 6 Attribute description for generic library methods.

Attribute Name	Type	Description
channels	list	A required list of isotopes given as strings over which the given method applies. For example, ["1H"].
magnetic_flux_density	float	An optional float describing the macroscopic magnetic flux density of the applied external magnetic field in tesla. For example, 18.8 tesla. The default value is 9.4 tesla.
rotor_frequency	float	An optional float describing the sample rotation frequency in Hz. For example, 2000 Hz. The default value is 0 Hz.
rotor_angle	float	An optional float describing the angle between the sample rotation axis and the external magnetic field in radians. The default value is the magic angle, 54.735 * 3.14159 / 180 = 0.955305 radians.
spectral_dimensions	list	A list of SpectralDimension objects describing the spectral dimensions for the method.
simulation	CSDM object	A CSDM object representing the spectrum simulated by the method. By default, the value is None. A value is assigned to this attribute when you run the simulation using the run() method.
experiment	CSDM object	An optional CSDM object holding an experimental measurement of the method. The default value is None

Table 7 Spectral dimension attributes for use with library methods.

Attribute Name	Type	Description
count	int	An optional integer representing the number of points, \(N\), along the spectroscopic dimension. For example, 4096. The default value is 1024.
spectral_width	float	An optional float representing the width, \(\Delta x\), of the spectroscopic dimension in Hz. For example, 10e3 for 10 kHz. The default value is 25000 Hz.
reference_offset	float	An optional float representing the reference offset, \(x_0\), of the spectroscopic dimension in Hz. For example, -8000 Hz. The default value is 0.
origin_offset	float	An optional float representing the origin offset, or Larmor frequency, along the spectroscopic dimension in units of Hz. The default value is None and the origin offset is set to the Larmor frequency of isotope from the channels attribute of the method containing the spectral dimension.