def gen_impurity(symbol='H', tetrahedral=True, sup_cell=[5, 5, 5]):
"""
Add an element of type symbol to a supercell defined by the size sup_cell.
If tetrahedral is true the element is initially placed in a tetrahedral position
otherwise it is placed in an octahedral position.
"""
#Molybdenum is 42!!!
alat = 2.82893
atomic_number_dict = {'H': 1, 'B': 5, 'C': 6, 'P': 15, 'Mn': 25, 'Mo': 42}
tetra_pos = alat * np.array([0.5, 0.0, 0.75])
octa_pos = alat * np.array([0.5, 0.5, 0.0])
#Structures
ats = BodyCenteredCubic(directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
size=(sup_cell[0], sup_cell[1], sup_cell[2]),
symbol='Fe',
pbc=(1, 1, 1),
latticeconstant=alat)
mid_point = 0.5 * (np.diag(ats.get_cell()))
mid_point = [((sup_cell[0] - 1) / 2.) * alat for sp in sup_cell]
if tetrahedral:
tetra_pos += mid_point
ats.append(Atom(position=tetra_pos, symbol=symbol))
else:
octa_pos += mid_point
ats.append(Atom(position=octa_pos, symbol=symbol))
return ats
