Shells

class MagInt.Shells.shells(general_par, filename=None, interacting_types=None, interact_sites=None, interact_basis=None, max_n_shells=3, print_vecs='Translation', R_arr=None, R_arr_site=None, R_arr_origin=None, run_only=False, calc_all_sites=False)

Initialize the class for analyzing interacting shells in various DFT software outputs.

__init__(general_par, filename=None, interacting_types=None, interact_sites=None, interact_basis=None, max_n_shells=3, print_vecs='Translation', R_arr=None, R_arr_site=None, R_arr_origin=None, run_only=False, calc_all_sites=False)

Initialize the class for analyzing interacting shells in various DFT software outputs.

Parameters:

general_pardict

General parameters dictionary containing:

• ‘dft_exec’ (str): Specifies the DFT software (‘Wien2k’, ‘Vasp’, etc.).

• ‘verbosity’ (int): Specifies the verbosity level.

• ‘tol_shells’ (int): tollerance N for vectors length difference 10^(-N)

  in sorting them between coordination shells

filenamestr, optional

File name for the data. Defaults to None.

interacting_typeslist, optional

List of two atom types that are interacting. Defaults to None.

interact_siteslist, optional

List of interacting sites. Defaults to None.

interact_basislist, optional

Basis for the interaction. Defaults to None.

max_n_shellsint, optional

Maximum number of shells to consider. Defaults to 3.

R_arrlist, optional

Custom array of interaction vectors. Defaults to None.

R_arr_sitelist, optional

Sites associated with R_arr. Defaults to None.

R_arr_originlist, optional

Origin points for R_arr. Defaults to None.

calc_all_sitesbool

True: lattice vectors connecting all sites of given types are calculated False : only lattice vectors connecting the representative sites with all other sites are calculated

Notes:

This method initializes the class based on the DFT software specified in general_par[‘dft_exec’]. Currently supported DFT software are ‘Wien2k’ and ‘Vasp’. Support for ‘QuantumEspresso’ may be added in the future.

calc_d_origin(verbosity=1)

Computes the minimal connecting vectors between the interaction sites of two atoms.

Parameters:

verbosity (int, optional) – Determines the amount of output information. Higher values produce more verbose output. Default value is 1.

Returns:

d_origin – A dictionary storing minimal connecting vectors between interaction sites for the specified atom pairs. Keys are tuples in the form (atom_type1, site1, atom_type2, site2), and the corresponding values are the minimal connecting vectors. This dictionary is also set as an attribute of the object.

Return type:

dict

Notes

The function uses R_arr_set to determine if lattice vectors have been read from an output file. If not, R_origins are assumed to be [0,0,0]. The function also uses the method __shift_vec_ to correct for vectors crossing periodic boundaries.

find_nn(max_n_shells, direct, tol)

Finds the nearest neighbors, next nearest neighbors, and so on from the POSCAR file in VASP or case.outputnn in Wien2k. It also initializes the structural data necessary for MagInt.

Parameters:

• max_n_shells (int) – Maximum number of shells to be considered when finding neighbors.

• direct (bool) – If True, returns the basis vector. If False, returns the dot product of the a_brav.T matrix and the basis vector.

Returns:

• nshells (int) – Number of shells found.

• R_shell (list of floats) – Sorted list of unique distances, indicating the radial distances for each shell.

• R_vec (dict) – Dictionary mapping each shell and coordinate number to the corresponding vector. The keys are strings in the format “nshell_coorNum”.

• R_site (dict) – Dictionary similar to R_vec, but the values are initialized to 0.

• coor_num (list of ints) – A list indicating the coordination number for each shell.

Notes

The function uses the atom_list attribute to determine if only one atom type is present. It employs a brute-force approach, computing distances for all possible shell combinations up to max_n_shells, and then sorts and filters the results to extract the relevant shells and coordination numbers.