wulfric.crystal

Atom's modification

ensure_000(atoms)	Ensures that all atoms are within (0,0,0) unit cell.
shift_atoms(atoms[, gravity_point, cell, ...])	Shifts all atoms with the same vector in a way that the gravity_point is located in the middle between minimum and maximum relative coordinates of the atoms, individually for each lattice vector.
cure_negative(atoms)	Shifts all atoms with the same vector in a way that all relative coordinates becomes non-negative.

Atom's properties

get_atom_species(name[, raise_on_fail])	Attempts to identify atom's species based on its name (i.e. Cr1 -> Cr, ...).
get_atoms_species(atoms[, raise_on_fail])	Attempts to identify atoms species based on their names (i.e. Cr1 -> Cr, ...).
get_unique_names(atoms[, strategy])	Ensures that atoms have unique "names".

Crystal's properties

get_vector(cell, atoms, atom1, atom2[, R, ...])	Computes a vector from atom1 (from (0,0,0)) to atom2 (from (i,j,k)).
get_distance(cell, atoms, atom1, atom2[, R])	Computes distance between atom1 (from (0,0,0)) and atom2 (from (i,j,k)).

Validation of the data

validate_atoms(atoms[, required_keys, ...])

Validate keys and values of the atoms dictionary.

Choice of the cell

get_conventional(cell, atoms[, convention, ...])	Return conventional cell and atoms associated with the given cell and atoms.
get_primitive(cell, atoms[, convention, ...])	Return primitive cell and atoms associated with the given cell and atoms.

HPKOT [1] convention

hpkot_get_example(extended_bl_symbol[, ...])	Returns an example of the crystal structure for each of the given extended Bravais lattice symbol as defined in [R3255d3b36b54-1].
hpkot_get_extended_bl_symbol(cell, atoms[, ...])	Returns extended bravais lattice symbol as defined in the paper by Hinuma, Pizzi, Kumagai, Oba, and Tanaka [Reac59ab78e89-1].

SC convention [2]

sc_get_variation(cell, atoms[, spglib_data])

Return variation of the lattice as defined in the paper by Setyawan and Curtarolo [R6d38e3fe5dda-1].

References

[1]

Hinuma, Y., Pizzi, G., Kumagai, Y., Oba, F. and Tanaka, I., 2017. Band structure diagram paths based on crystallography. Computational Materials Science, 128, pp.140-184.

[2]

Setyawan, W. and Curtarolo, S., 2010. High-throughput electronic band structure calculations: Challenges and tools. Computational materials science, 49(2), pp. 299-312.