Single Site System Generator

Custom Site and SpinSystem parameters can be passed to the single_site_system_generator() method to create a list of uncoupled spin systems. Each SpinSystem in the returned list holds a single Site object since the backend simulation is more efficient for single site spin systems. Import the method as below

from mrsimulator.utils.collection import single_site_system_generator

The arguments passed to the function, defined in Table 5, can either be a scalar quantity (float or str, where applicable) or a list/np.array of those quantities. All lists passed must have the same length, otherwise an error will be thrown. For example,

single_site_system_generator(
    isotope=["1H", "1H", "13C", "17O"],
    isotropic_chemical_shift=[1.3, 3.7, 65.0],
)

Out:

Traceback (most recent call last):
...
ValueError: An array or list was either too short or too long. All arguments must be the
same size. If one attribute is a type list of length n, then all attributes with list types
must also be of length n, and all remaining attributes must be scalar (singular float, int,
or str).

The attributes of each returned spin system at a certain index correspond to the attribute passed at that index. For example,

single_site_system_generator(
    isotope=["1H", "1H", "13C"],
    isotropic_chemical_shift=[1.3, 3.7, 65.0],
)

returns a list of 3 spin systems. The first two spin systems represent proton sites with isotropic chemical shifts of 1.3 ppm and 3.7 ppm, respectively. The third spin system is a \(^{13}\text{C}\) site with a chemical shift of 65.0 ppm.

Broadcasting Length of List

Arguments passed as a single value will be broadcast to a list of that value with the same length as other lists passed. For example

single_site_system_generator(
    isotope=["1H", "1H", "1H"],
    isotropic_chemical_shift=2.0,
)

is equivalent to calling

single_site_system_generator(
    isotope=["1H", "1H", "1H"],
    isotropic_chemical_shift=[2.0, 2.0, 2.0],
)

Passing lists of Tensor Parameters

Tensor parameters for sites are passed as dictionaries where the keywords represent the tensor attribute and the values are single values or a list/np.array of values. Again, these lists must have the same length of all other lists passed. Single values will be broadcast to a list of that value with the same length as other lists passed. For example

single_site_system_generator(
    isotope="13C",
    shielding_symmetric={
        "zeta": [5, 10, 15, 20, 25],
        "eta": 0.3,
    },
)

returns a list of five \(^{13}\text{C}\) spin systems with different shielding_symmetric.zeta values but the same shielding_symmetric.eta value.

If you need to intermix sites with and without tensor parameters, simply put None at the index of the site without the tensor parameter.

single_site_system_generator(
    isotope=["1H", "17O"],
    quadrupolar={
        "Cq": [None, 3.2e6],
        "eta": [None, 0.5],
    },
)

Examples using single_site_system_generator()

Amorphous material, ²⁹Si (I=1/2)

Amorphous material, ²⁹Si (I=1/2)

Amorphous material, ²⁹Si (I=1/2)
Amorphous material, ²⁷Al (I=5/2)

Amorphous material, ²⁷Al (I=5/2)

Amorphous material, ²⁷Al (I=5/2)
Czjzek distribution (Shielding and Quadrupolar)

Czjzek distribution (Shielding and Quadrupolar)

Czjzek distribution (Shielding and Quadrupolar)
Extended Czjzek distribution (Shielding and Quadrupolar)

Extended Czjzek distribution (Shielding and Quadrupolar)

Extended Czjzek distribution (Shielding and Quadrupolar)
Simulating site disorder (crystalline)

Simulating site disorder (crystalline)

Simulating site disorder (crystalline)
Czjzek distribution, ²⁷Al (I=5/2) 3QMAS

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

Czjzek distribution, ²⁷Al (I=5/2) 3QMAS
¹³C 2D MAT NMR of L-Histidine

¹³C 2D MAT NMR of L-Histidine

¹³C 2D MAT NMR of L-Histidine
¹⁷O 2D DAS NMR of Coesite

¹⁷O 2D DAS NMR of Coesite

¹⁷O 2D DAS NMR of Coesite
⁸⁷Rb 2D 3QMAS NMR of RbNO₃

⁸⁷Rb 2D 3QMAS NMR of RbNO₃

⁸⁷Rb 2D 3QMAS NMR of RbNO₃

Table 5 Arguments for single_site_system_generator

Name

Type

Description

isotope

str or list of str

A required string or list of strings representing the label of the isotope attribute of the Site (e.g. "1H" or ["29Si", "17O"]).

isotropic_chemical_shift

float, list of float, or numpy array

An optional number or list of numbers representing the isotropic_chemical_shift attribute of the Site (e.g. 17.3 or [2.4, 19.5]) in ppm. The default value is 0.

shielding_symmetric

dict

An optional dictionary representing the shielding_symmetric attribute of the Site where the keys are valid SymmetricTensor attributes and the values are floats or lists/numpy arrays of floats. The default is None.

shielding_antisymmetric

dict

An optional dictionary representing the shielding_antisymmetric attribute of the Site where the keys are valid AntisymmetricTensor attributes and the values are floats or lists/numpy arrays of floats. The default is None.

quadrupolar

dict

An optional dictionary representing the quadrupolar attribute of the Site where the keys are valid SymmetricTensor attributes and the values are floats or lists/numpy arrays of floats. The default is None.

abundance

float, list of float, or numpy array

An optional number or list of numbers representing the abundance attribute of the SpinSystem (e.g. 0.182 or [85, 7.3]. By default, the abundance of each spin system will be set to 1 / n_sys where n_sys is the number of spin systems generated.

site_name

str or list of str

An optional string or list of strings representing the name attribute of each Site. By default, each Site will take the default name of None

site_label

str or list of str

An optional string or list of strings representing the label attribute of each Site. By default, each Site will take the default label of None

site_description

str or list of str

An optional string or list of strings representing the description attribute of each Site. By default, each Site will take the default description of None