def get_phonon_tb(
# phonopy_atoms=[],
atoms=[],
fc=[],
out_file="phonopyTB_hr.dat",
distance_to_A=1.0,
scell=np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]),
factor=VaspToTHz,
symprec=1e-05,
displacement_distance=0.01,
):
"""Generate phonon TB Hamiltonia, along with WannierHamn."""
# Forked from Wannier-tools
unitcell = atoms.phonopy_converter()
# unitcell = phonopy_atoms
prim_mat = np.array(PhonopyInputs(atoms).prim_axis().split("=")[1].split(),
dtype="float").reshape(3, 3)
# print("cell", unitcell.cell)
num_atom = unitcell.get_number_of_atoms()
num_satom = determinant(scell) * num_atom
if fc.shape[0] != num_satom:
print("Check Force constant matrix.")
phonon = Phonopy(
unitcell,
scell,
primitive_matrix=prim_mat,
factor=factor,
dynamical_matrix_decimals=None,
force_constants_decimals=None,
symprec=symprec,
is_symmetry=True,
use_lapack_solver=False,
log_level=1,
)
supercell = phonon.get_supercell()
primitive = phonon.get_primitive()
# Set force constants
phonon.set_force_constants(fc)
phonon._set_dynamical_matrix()
dmat = phonon._dynamical_matrix
# rescale fcmat by THZ**2
fcmat = dmat._force_constants * factor**2 # FORCE_CONSTANTS
# fcmat = dmat._force_constants * factor ** 2 # FORCE_CONSTANTS
smallest_vectors = dmat._smallest_vectors
# mass = dmat._mass
mass = dmat._pcell.get_masses()
print("mass=", mass)
multi = dmat._multiplicity
reduced_bases = get_reduced_bases(supercell.get_cell(), symprec)
positions = np.dot(supercell.get_positions(), np.linalg.inv(reduced_bases))
# for pos in positions: pos -= np.rint(pos)
relative_scale = np.dot(reduced_bases, np.linalg.inv(primitive.get_cell()))
super_pos = np.zeros((num_satom, 3), dtype=np.float64)
for i in range(num_satom):
super_pos[i] = np.dot(positions[i], relative_scale)
p2s_map = dmat._p2s_map = primitive.get_primitive_to_supercell_map()
s2p_map = dmat._s2p_map = primitive.get_supercell_to_primitive_map()
num_satom = supercell.get_number_of_atoms()
num_patom = primitive.get_number_of_atoms()
get_phonon_hr(
fcmat,
smallest_vectors,
mass,
multi,
super_pos,
p2s_map,
s2p_map,
num_satom,
num_patom,
out_file,
)
print("phonopy_TB.dat generated! ")
