wulfric.crystal#

Basic manipulations#

`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)).
`ensure_000`(atoms)	Ensures that all atoms are from (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.

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

standardize(cell, atoms[, S_matrix, ...])

Standardize cell with respect to the Bravais lattice type as defined in [R5a16871852d6-1] and update atom's relative coordinates.