def get_equivalent_smallest_vectors(atom_number_supercell,
atom_number_primitive, supercell,
primitive_lattice, symprec):
distances = []
differences = []
reduced_bases = get_reduced_bases(supercell.get_cell(), symprec)
positions = np.dot(supercell.get_positions(), np.linalg.inv(reduced_bases))
# Atomic positions are confined into the lattice made of reduced bases.
for pos in positions:
pos -= np.rint(pos)
p_pos = positions[atom_number_primitive]
s_pos = positions[atom_number_supercell]
for i in (-1, 0, 1):
for j in (-1, 0, 1):
for k in (-1, 0, 1):
# The vector arrow is from the atom in primitive to
# the atom in supercell cell plus a supercell lattice
# point. This is related to determine the phase
# convension when building dynamical matrix.
diff = s_pos + [i, j, k] - p_pos
differences.append(diff)
vec = np.dot(diff, reduced_bases)
distances.append(np.linalg.norm(vec))
minimum = min(distances)
smallest_vectors = []
for i in range(27):
if abs(minimum - distances[i]) < symprec:
relative_scale = np.dot(reduced_bases,
np.linalg.inv(primitive_lattice))
smallest_vectors.append(np.dot(differences[i], relative_scale))
return smallest_vectors
def get_equivalent_smallest_vectors(
atom_number_supercell, atom_number_primitive, supercell, primitive_lattice, symprec
):
distances = []
differences = []
reduced_bases = get_reduced_bases(supercell.get_cell(), symprec)
positions = np.dot(supercell.get_positions(), np.linalg.inv(reduced_bases))
# Atomic positions are confined into the lattice made of reduced bases.
for pos in positions:
pos -= np.rint(pos)
p_pos = positions[atom_number_primitive]
s_pos = positions[atom_number_supercell]
for i in (-1, 0, 1):
for j in (-1, 0, 1):
for k in (-1, 0, 1):
# The vector arrow is from the atom in primitive to
# the atom in supercell cell plus a supercell lattice
# point. This is related to determine the phase
# convension when building dynamical matrix.
diff = s_pos + [i, j, k] - p_pos
differences.append(diff)
vec = np.dot(diff, reduced_bases)
distances.append(np.linalg.norm(vec))
minimum = min(distances)
smallest_vectors = []
for i in range(27):
if abs(minimum - distances[i]) < symprec:
relative_scale = np.dot(reduced_bases, np.linalg.inv(primitive_lattice))
smallest_vectors.append(np.dot(differences[i], relative_scale))
return smallest_vectors
def __init__(self, primitive_vectors):
self._primitive_vectors = primitive_vectors # column vectors
self._tolerance = min(np.sum(primitive_vectors ** 2, axis=0)) * 0.01
self._reduced_bases = get_reduced_bases(primitive_vectors.T)
self._tmat = np.dot(np.linalg.inv(self._primitive_vectors), self._reduced_bases)
self._tmat_inv = np.linalg.inv(self._tmat)
self._shortest_qpoints = None
def get_equivalent_smallest_vectors_np(atom_number_supercell,
atom_number_primitive, supercell,
primitive_lattice, symprec):
distances = []
differences = []
reduced_bases = get_reduced_bases(supercell.get_cell(), symprec)
positions = np.dot(supercell.get_positions(), np.linalg.inv(reduced_bases))
# Atomic positions are confined into the lattice made of reduced bases.
positions -= np.rint(positions)
p_pos = positions[atom_number_primitive]
s_pos = positions[atom_number_supercell]
sc_range_1 = np.array([-1, 0, 1])[:, None] * np.array([1, 0, 0])[None, :]
sc_range_2 = np.array([-1, 0, 1])[:, None] * np.array([0, 1, 0])[None, :]
sc_range_3 = np.array([-1, 0, 1])[:, None] * np.array([0, 0, 1])[None, :]
# The vector arrow is from the atom in primitive to
# the atom in supercell cell plus a supercell lattice
# point. This is related to determine the phase
# convension when building dynamical matrix.
differences = (s_pos + sc_range_1[:, None, None] +
sc_range_2[None, :, None] + sc_range_3[None, None, :] -
p_pos)
vecs = np.dot(differences, reduced_bases)
distances = np.linalg.norm(vecs, axis=-1)
relative_scale = np.dot(reduced_bases, np.linalg.inv(primitive_lattice))
minimum = np.min(distances)
indices = np.where(np.abs(minimum - distances) < symprec)
smallest_vectors = np.dot(differences[indices], relative_scale)
smallest_vectors = smallest_vectors.reshape(-1, 3)
return smallest_vectors
def __init__(self, primitive_vectors):
self._primitive_vectors = primitive_vectors # column vectors
self._tolerance = min(np.sum(primitive_vectors ** 2, axis=0)) * 0.01
self._reduced_bases = get_reduced_bases(primitive_vectors.T)
self._tmat = np.dot(np.linalg.inv(self._primitive_vectors),
self._reduced_bases)
self._tmat_inv = np.linalg.inv(self._tmat)
self._shortest_qpoints = None
def cutoff_force_constants(force_constants,
supercell,
cutoff_radius,
symprec=1e-5):
num_atom = supercell.get_number_of_atoms()
reduced_bases = get_reduced_bases(supercell.get_cell(), tolerance=symprec)
positions = np.dot(supercell.get_positions(), np.linalg.inv(reduced_bases))
for i in range(num_atom):
pos_i = positions[i]
for j in range(num_atom):
pos_j = positions[j]
min_distance = _get_shortest_distance_in_PBC(
pos_i, pos_j, reduced_bases)
if min_distance > cutoff_radius:
force_constants[i, j] = 0.0
def cutoff_force_constants(force_constants,
supercell,
cutoff_radius,
symprec=1e-5):
num_atom = supercell.get_number_of_atoms()
reduced_bases = get_reduced_bases(supercell.get_cell(), symprec)
positions = np.dot(supercell.get_positions(),
np.linalg.inv(reduced_bases))
for i in range(num_atom):
pos_i = positions[i]
for j in range(num_atom):
pos_j = positions[j]
min_distance = _get_shortest_distance_in_PBC(pos_i,
pos_j,
reduced_bases)
if min_distance > cutoff_radius:
force_constants[i, j] = 0.0
def __init__(self, reciprocal_lattice, tolerance=0.01):
"""Init method.
Parameters
----------
reciprocal_lattice : array_like
Reciprocal primitive cell basis vectors given in column vectors.
shape=(3,3)
dtype=float
tolerance : float, optional
Default = 0.01
"""
self._reciprocal_lattice = np.array(reciprocal_lattice)
self._tolerance = min(np.sum(reciprocal_lattice**2,
axis=0)) * tolerance
self._reduced_bases = get_reduced_bases(reciprocal_lattice.T)
self._tmat = np.dot(np.linalg.inv(self._reciprocal_lattice),
self._reduced_bases.T)
self._tmat_inv = np.linalg.inv(self._tmat)
self.shortest_qpoints = None
def __init__(self, reciprocal_lattice, tolerance=0.01):
"""
Parameters
----------
reciprocal_lattice : array_like
Reciprocal primitive cell basis vectors given in column vectors.
shape=(3,3)
dtype=float
tolerance : float, optional
Default = 0.01
"""
self._reciprocal_lattice = np.array(reciprocal_lattice)
self._tolerance = min(
np.sum(reciprocal_lattice ** 2, axis=0)) * tolerance
self._reduced_bases = get_reduced_bases(reciprocal_lattice.T)
self._tmat = np.dot(np.linalg.inv(self._reciprocal_lattice),
self._reduced_bases.T)
self._tmat_inv = np.linalg.inv(self._tmat)
self.shortest_qpoints = None
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! ")
if len(symbols_with_no_mass) > 0:
if log_level > 0:
print_end()
sys.exit(1)
phonon.set_dynamical_matrix()
dmat = phonon._dynamical_matrix
# rescale fcmat by THZ**2
fcmat = dmat._force_constants * factor**2 # FORCE_CONSTANTS
smallest_vectors = dmat._smallest_vectors
#mass = dmat._mass
mass = dmat._pcell.get_masses()
multi = dmat._multiplicity
reduced_bases = get_reduced_bases(supercell.get_cell(), options.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 hr
def _relocate_BZ_grid_address(
D_diag,
Q,
reciprocal_lattice, # column vectors
is_shift=None,
store_dense_gp_map=False,
):
"""Grid addresses are relocated to be inside first Brillouin zone.
Number of ir-grid-points inside Brillouin zone is returned.
It is assumed that the following arrays have the shapes of
bz_grid_address : (num_grid_points_in_FBZ, 3)
Note that the shape of grid_address is (prod(mesh), 3) and the
addresses in grid_address are arranged to be in parallelepiped
made of reciprocal basis vectors. The addresses in bz_grid_address
are inside the first Brillouin zone or on its surface. Each
address in grid_address is mapped to one of those in
bz_grid_address by a reciprocal lattice vector (including zero
vector) with keeping element order. For those inside first BZ, the
mapping is one-to-one. For those on the first BZ surface, more
than one addresses in bz_grid_address that are equivalent by the
reciprocal lattice translations are mapped to one address in
grid_address. The bz_grid_address and bz_map are given in the
following format depending on the choice of `store_dense_gp_map`.
store_dense_gp_map = False
--------------------------
Those grid points on the BZ surface except for one of them are
appended to the tail of this array, for which bz_grid_address has
the following data storing:
|------------------array size of bz_grid_address-------------------------|
|--those equivalent to grid_address--|--those on surface except for one--|
|-----array size of grid_address-----|
Number of grid points stored in bz_grid_address is returned.
bz_map is used to recover grid point index expanded to include BZ
surface from grid address. The grid point indices are mapped to
(mesh[0] * 2) x (mesh[1] * 2) x (mesh[2] * 2) space (bz_map).
bz_map[(prod(mesh) * 8):(prod(mesh) * 9 + 1)] contains equivalent
information to bz_map[:] with `store_dense_gp_map=True`.
shape=(prod(mesh * 9) + 1, )
store_dense_gp_map = True
-------------------------
The translationally equivalent grid points corresponding to one grid point
on BZ surface are stored in continuously. If the multiplicity (number of
equivalent grid points) is 1, 2, 1, 4, ... for the grid points,
``bz_map`` stores the multiplicites and the index positions of the first
grid point of the equivalent grid points, i.e.,
bz_map[:] = [0, 1, 3, 4, 8...]
grid_address[0] -> bz_grid_address[0:1]
grid_address[1] -> bz_grid_address[1:3]
grid_address[2] -> bz_grid_address[3:4]
grid_address[3] -> bz_grid_address[4:8]
shape=(prod(mesh) + 1, )
"""
import phono3py._phono3py as phono3c
if is_shift is None:
_is_shift = np.zeros(3, dtype="int_")
else:
_is_shift = np.array(is_shift, dtype="int_")
bz_grid_addresses = np.zeros((np.prod(D_diag) * 8, 3),
dtype="int_",
order="C")
bzg2grg = np.zeros(len(bz_grid_addresses), dtype="int_")
if store_dense_gp_map:
bz_map = np.zeros(np.prod(D_diag) + 1, dtype="int_")
else:
bz_map = np.zeros(np.prod(D_diag) * 9 + 1, dtype="int_")
reclat_T = np.array(reciprocal_lattice.T, dtype="double", order="C")
reduced_basis = get_reduced_bases(reclat_T)
tmat_inv = np.dot(np.linalg.inv(reduced_basis.T), reclat_T.T)
tmat_inv_int = np.rint(tmat_inv).astype("int_")
assert (np.abs(tmat_inv - tmat_inv_int) < 1e-5).all()
num_gp = phono3c.bz_grid_addresses(
bz_grid_addresses,
bz_map,
bzg2grg,
np.array(D_diag, dtype="int_"),
np.array(np.dot(tmat_inv_int, Q), dtype="int_", order="C"),
_is_shift,
np.array(reduced_basis.T, dtype="double", order="C"),
store_dense_gp_map * 1 + 1,
)
bz_grid_addresses = np.array(bz_grid_addresses[:num_gp],
dtype="int_",
order="C")
bzg2grg = np.array(bzg2grg[:num_gp], dtype="int_")
return bz_grid_addresses, bz_map, bzg2grg