def _testBrillouinZone(self, direct_lat, mesh, is_shift):
_, grid_address = get_stabilized_reciprocal_mesh(mesh,
rotations=[
np.eye(
3,
dtype='intc'),
],
is_shift=is_shift)
rec_lat = np.linalg.inv(direct_lat)
bz_grid_address, bz_map = relocate_BZ_grid_address(grid_address,
mesh,
rec_lat,
is_shift=is_shift)
qpoints = (grid_address + np.array(is_shift) / 2.0) / mesh
bz = BrillouinZone(rec_lat)
bz.run(qpoints)
sv_all = bz.shortest_qpoints # including BZ boundary duplicates
sv = [v[0] for v in sv_all]
bz_qpoints = (bz_grid_address + np.array(is_shift) / 2.0) / mesh
d2_this = (np.dot(sv, rec_lat.T)**2).sum(axis=1)
d2_spglib = (np.dot(bz_qpoints[:np.prod(mesh)],
rec_lat.T)**2).sum(axis=1)
diff = d2_this - d2_spglib
diff -= np.rint(diff)
# Following both of two tests are necessary.
# Check equivalence of vectors by lattice translation
np.testing.assert_allclose(diff, 0, atol=1e-8)
# Check being in same (hopefull first) Brillouin zone by their lengths
np.testing.assert_allclose(d2_this, d2_spglib, atol=1e-8)
def get_ir_grid_points(mesh, rotations, mesh_shifts=[False, False, False]):
grid_mapping_table, grid_address = spg.get_stabilized_reciprocal_mesh(
mesh, rotations, is_shift=np.where(mesh_shifts, 1, 0))
(ir_grid_points,
ir_grid_weights) = extract_ir_grid_points(grid_mapping_table)
return ir_grid_points, ir_grid_weights, grid_address
def _set_ir_qpoints(self,
rotations,
is_time_reversal=True):
grid_mapping_table, grid_address = get_stabilized_reciprocal_mesh(
self._mesh,
rotations,
is_shift=self._is_shift,
is_time_reversal=is_time_reversal)
shift = np.array(self._is_shift, dtype='intc') * 0.5
if self._fit_in_BZ:
self._grid_address = relocate_BZ_grid_address(
grid_address,
self._mesh,
self._rec_lat,
is_shift=self._is_shift)[0][:np.prod(self._mesh)]
else:
self._grid_address = grid_address
(self._ir_grid_points,
self._ir_weights) = extract_ir_grid_points(grid_mapping_table)
self._ir_qpoints = (self._grid_address[self._ir_grid_points] +
shift) / self._mesh
self._grid_mapping_table = grid_mapping_table
def get_grid_address(mesh):
grid_mapping_table, grid_address = spg.get_stabilized_reciprocal_mesh(
mesh,
[[[1, 0, 0], [0, 1, 0], [0, 0, 1]]],
is_time_reversal=False)
return grid_address
def _set_ir_qpoints(self,
rotations,
is_time_reversal=True):
grid_mapping_table, grid_address = get_stabilized_reciprocal_mesh(
self._mesh,
rotations,
is_shift=self._is_shift,
is_time_reversal=is_time_reversal)
shift = np.array(self._is_shift, dtype='intc') * 0.5
if self._fit_in_BZ:
self._grid_address = relocate_BZ_grid_address(
grid_address,
self._mesh,
self._rec_lat,
is_shift=self._is_shift)[0][:np.prod(self._mesh)]
else:
self._grid_address = grid_address
(self._ir_grid_points,
self._ir_weights) = extract_ir_grid_points(grid_mapping_table)
self._ir_qpoints = np.array(
(self._grid_address[self._ir_grid_points] + shift) / self._mesh,
dtype='double', order='C')
self._grid_mapping_table = grid_mapping_table
def get_grid_address(mesh):
grid_mapping_table, grid_address = spg.get_stabilized_reciprocal_mesh(
mesh,
[[[1, 0, 0], [0, 1, 0], [0, 0, 1]]],
is_time_reversal=False)
return grid_address
def _testBrillouinZone(self, direct_lat, mesh, is_shift):
_, grid_address = get_stabilized_reciprocal_mesh(
mesh,
rotations=[np.eye(3, dtype='intc'), ],
is_shift=is_shift)
rec_lat = np.linalg.inv(direct_lat)
bz_grid_address, bz_map = relocate_BZ_grid_address(
grid_address,
mesh,
rec_lat,
is_shift=is_shift)
qpoints = (grid_address + np.array(is_shift) / 2.0) / mesh
bz = BrillouinZone(rec_lat)
bz.run(qpoints)
sv_all = bz.shortest_qpoints # including BZ boundary duplicates
sv = [v[0] for v in sv_all]
bz_qpoints = (bz_grid_address + np.array(is_shift) / 2.0) / mesh
d2_this = (np.dot(sv, rec_lat.T) ** 2).sum(axis=1)
d2_spglib = (np.dot(bz_qpoints[:np.prod(mesh)],
rec_lat.T) ** 2).sum(axis=1)
diff = d2_this - d2_spglib
diff -= np.rint(diff)
# Following both of two tests are necessary.
# Check equivalence of vectors by lattice translation
np.testing.assert_allclose(diff, 0, atol=1e-8)
# Check being in same (hopefull first) Brillouin zone by their lengths
np.testing.assert_allclose(d2_this, d2_spglib, atol=1e-8)
def get_ir_grid_points(mesh, rotations, mesh_shifts=[False, False, False]):
grid_mapping_table, grid_address = spg.get_stabilized_reciprocal_mesh(
mesh,
rotations,
is_shift=np.where(mesh_shifts, 1, 0))
(ir_grid_points,
ir_grid_weights) = extract_ir_grid_points(grid_mapping_table)
return ir_grid_points, ir_grid_weights, grid_address
def get_grid_address(mesh, is_time_reversal=False, is_shift=np.zeros(3, dtype='intc'), is_return_map=False):
grid_mapping_table, grid_address = spg.get_stabilized_reciprocal_mesh(
mesh,
[[[1, 0, 0], [0, 1, 0], [0, 0, 1]]],
is_time_reversal=is_time_reversal,
is_shift=is_shift)
if is_return_map:
return grid_address, grid_mapping_table
else:
return grid_address
def get_ir_grid_points(mesh, rotations, mesh_shifts=[False, False, False]):
grid_mapping_table, grid_address = spg.get_stabilized_reciprocal_mesh(
mesh,
rotations,
is_shift=np.where(mesh_shifts, 1, 0))
ir_grid_points = np.unique(grid_mapping_table)
weights = np.zeros_like(grid_mapping_table)
for g in grid_mapping_table:
weights[g] += 1
ir_grid_weights = weights[ir_grid_points]
return ir_grid_points, ir_grid_weights, grid_address
def get_grid_address(mesh,
is_time_reversal=False,
is_shift=np.zeros(3, dtype='intc'),
is_return_map=False):
grid_mapping_table, grid_address = spg.get_stabilized_reciprocal_mesh(
mesh, [[[1, 0, 0], [0, 1, 0], [0, 0, 1]]],
is_time_reversal=is_time_reversal,
is_shift=is_shift)
if is_return_map:
return grid_address, grid_mapping_table
else:
return grid_address
def set_grid_point(self, grid_point, grid_points2=None, weights2=None):
"The grid_point is numbered using the bz scheme"
self._grid_point = grid_point
if self._grid_address is None:
primitive_lattice = np.linalg.inv(self._primitive.get_cell())
self._grid_address, self._bz_map, self._bz_to_pp_map = get_bz_grid_address(
self._mesh,
primitive_lattice,
with_boundary=True,
is_bz_map_to_pp=True)
if grid_points2 is not None:
self._grid_points2 = grid_points2
self._weights2 = weights2
elif not self._is_nosym:
symmetry = Symmetry(self._primitive, symprec=self._symprec)
qpoint = self._grid_address[grid_point] / np.double(self._mesh)
mapping, grid_points = spg.get_stabilized_reciprocal_mesh(
self._mesh,
symmetry.get_pointgroup_operations(),
is_shift=np.zeros(3, dtype='intc'),
is_time_reversal=True,
qpoints=[qpoint])
grid_points2 = np.unique(mapping)
# weight = np.zeros_like(grid_points2)
# bz_grid_points2 = np.zeros_like(grid_points2)
# for g, grid in enumerate(grid_points2):
# weight[g] = len(np.where(grid == mapping)[0])
# bz_grid_points2[g] = np.where(grid == self._bz_to_pp_map)[0][0]
# self._grid_points2 = bz_grid_points2
weight_temp = np.bincount(mapping)
weight = weight_temp[np.nonzero(weight_temp)]
self._grid_points2 = grid_points2
self._weights2 = weight
else:
self._grid_points2 = np.arange(np.prod(self._mesh))
self._weights2 = np.ones_like(self._grid_points2, dtype="intc")
def set_grid_point(self,
grid_point,
grid_points2=None,
weights2 = None):
"The grid_point is numbered using the bz scheme"
self._grid_point = grid_point
if self._grid_address is None:
primitive_lattice = np.linalg.inv(self._primitive.get_cell())
self._grid_address, self._bz_map, self._bz_to_pp_map = get_bz_grid_address(
self._mesh, primitive_lattice, with_boundary=True, is_bz_map_to_pp=True)
if grid_points2 is not None:
self._grid_points2 = grid_points2
self._weights2 = weights2
elif not self._is_nosym:
symmetry = Symmetry(self._primitive, symprec=self._symprec)
qpoint = self._grid_address[grid_point] / np.double(self._mesh)
mapping, grid_points = spg.get_stabilized_reciprocal_mesh(self._mesh,
symmetry.get_pointgroup_operations(),
is_shift=np.zeros(3, dtype='intc'),
is_time_reversal=True,
qpoints=[qpoint])
grid_points2 = np.unique(mapping)
# weight = np.zeros_like(grid_points2)
# bz_grid_points2 = np.zeros_like(grid_points2)
# for g, grid in enumerate(grid_points2):
# weight[g] = len(np.where(grid == mapping)[0])
# bz_grid_points2[g] = np.where(grid == self._bz_to_pp_map)[0][0]
# self._grid_points2 = bz_grid_points2
weight_temp = np.bincount(mapping)
weight = weight_temp[np.nonzero(weight_temp)]
self._grid_points2 = grid_points2
self._weights2 = weight
else:
self._grid_points2 = np.arange(np.prod(self._mesh))
self._weights2 = np.ones_like(self._grid_points2, dtype="intc")
