def get_dimensionality_gorai(structure, max_hkl=2, el_radius_updates=None, min_slab_size=5, min_vacuum_size=5, standardize=True, bonds=None): """ This method returns whether a structure is 3D, 2D (layered), or 1D (linear chains or molecules) according to the algorithm published in Gorai, P., Toberer, E. & Stevanovic, V. Computational Identification of Promising Thermoelectric Materials Among Known Quasi-2D Binary Compounds. J. Mater. Chem. A 2, 4136 (2016). Note that a 1D structure detection might indicate problems in the bonding algorithm, particularly for ionic crystals (e.g., NaCl) Users can change the behavior of bonds detection by passing either el_radius_updates to update atomic radii for auto-detection of max bond distances, or bonds to explicitly specify max bond distances for atom pairs. Note that if you pass both, el_radius_updates are ignored. Args: structure: (Structure) structure to analyze dimensionality for max_hkl: (int) max index of planes to look for layers el_radius_updates: (dict) symbol->float to update atomic radii min_slab_size: (float) internal surface construction parameter min_vacuum_size: (float) internal surface construction parameter standardize (bool): whether to standardize the structure before analysis. Set to False only if you already have the structure in a convention where layers / chains will be along low <hkl> indexes. bonds ({(specie1, specie2): max_bond_dist}: bonds are specified as a dict of tuples: float of specie1, specie2 and the max bonding distance. For example, PO4 groups may be defined as {("P", "O"): 3}. Returns: (int) the dimensionality of the structure - 1 (molecules/chains), 2 (layered), or 3 (3D) """ if standardize: structure = SpacegroupAnalyzer(structure). \ get_conventional_standard_structure() if not bonds: bonds = get_max_bond_lengths(structure, el_radius_updates) num_surfaces = 0 for h in range(max_hkl): for k in range(max_hkl): for l in range(max_hkl): if max([h, k, l]) > 0 and num_surfaces < 2: sg = SlabGenerator(structure, (h, k, l), min_slab_size=min_slab_size, min_vacuum_size=min_vacuum_size) slabs = sg.get_slabs(bonds) for _ in slabs: num_surfaces += 1 return 3 - min(num_surfaces, 2)
def list_maximum_bond_length(list_struc): return [ get_max_bond_lengths(structure, el_radius_updates=None) for structure in list_struc ]