def get_triplets_at_q(grid_point,
mesh,
point_group, # real space point group of space group
primitive_lattice, # column vectors
is_time_reversal=True,
stores_triplets_map=False):
map_triplets, map_q, grid_address = _get_triplets_reciprocal_mesh_at_q(
grid_point,
mesh,
point_group,
is_time_reversal=is_time_reversal)
bz_grid_address, bz_map = spg.relocate_BZ_grid_address(grid_address,
mesh,
primitive_lattice)
triplets_at_q, weights = _get_BZ_triplets_at_q(
grid_point,
bz_grid_address,
bz_map,
map_triplets,
mesh)
assert np.prod(mesh) == weights.sum(), \
"Num grid points %d, sum of weight %d" % (
np.prod(mesh), weights.sum())
# These maps are required for collision matrix calculation.
if not stores_triplets_map:
map_triplets = None
map_q = None
return triplets_at_q, weights, bz_grid_address, bz_map, map_triplets, map_q
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 _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 _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 _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_triplets_at_q(
grid_point,
mesh,
point_group, # real space point group of space group
primitive_lattice, # column vectors
is_time_reversal=True,
stores_triplets_map=False):
map_triplets, map_q, grid_address = spg.get_triplets_reciprocal_mesh_at_q(
grid_point, mesh, point_group, is_time_reversal=is_time_reversal)
bz_grid_address, bz_map = spg.relocate_BZ_grid_address(
grid_address, mesh, primitive_lattice)
triplets_at_q, weights = spg.get_BZ_triplets_at_q(grid_point,
bz_grid_address, bz_map,
map_triplets, mesh)
assert np.prod(mesh) == weights.sum(), \
"Num grid points %d, sum of weight %d" % (
np.prod(mesh), weights.sum())
# These maps are required for collision matrix calculation.
if not stores_triplets_map:
map_triplets = None
map_q = None
return triplets_at_q, weights, bz_grid_address, bz_map, map_triplets, map_q
def get_bz_grid_address(mesh, primitive_lattice, with_boundary=False):
grid_address = get_grid_address(mesh)
bz_grid_address, bz_map = spg.relocate_BZ_grid_address(
grid_address, mesh, primitive_lattice)
if with_boundary:
return bz_grid_address, bz_map
else:
return bz_grid_address[:np.prod(mesh)]
def get_bz_grid_address(mesh, primitive_lattice, with_boundary=False):
grid_address = get_grid_address(mesh)
bz_grid_address, bz_map = spg.relocate_BZ_grid_address(grid_address,
mesh,
primitive_lattice)
if with_boundary:
return bz_grid_address, bz_map
else:
return bz_grid_address[:np.prod(mesh)]
def get_bz_grid_address(mesh, reciprocal_lattice, with_boundary=False):
grid_address = get_grid_address(mesh)
bz_grid_address, bz_map = spg.relocate_BZ_grid_address(grid_address,
mesh,
reciprocal_lattice,
is_dense=True)
if with_boundary:
return bz_grid_address, bz_map
else:
return bz_grid_address[:np.prod(mesh)]
def get_coarse_ir_grid_points(primitive,
mesh,
mesh_divisors,
coarse_mesh_shifts,
is_nosym=False,
symprec=1e-5):
if mesh_divisors is None:
mesh_divs = [1, 1, 1]
else:
mesh_divs = mesh_divisors
mesh = np.array(mesh, dtype='intc')
mesh_divs = np.array(mesh_divs, dtype='intc')
coarse_mesh = mesh / mesh_divs
if coarse_mesh_shifts is None:
coarse_mesh_shifts = [False, False, False]
if is_nosym:
coarse_grid_address = get_grid_address(coarse_mesh)
coarse_grid_points = np.arange(np.prod(coarse_mesh), dtype='intc')
coarse_grid_weights = np.ones(len(coarse_grid_points), dtype='intc')
else:
symmetry = Symmetry(primitive, symprec)
(coarse_grid_points,
coarse_grid_weights,
coarse_grid_address) = get_ir_grid_points(
coarse_mesh,
symmetry.get_pointgroup_operations(),
mesh_shifts=coarse_mesh_shifts)
grid_points = from_coarse_to_dense_grid_points(
mesh,
mesh_divs,
coarse_grid_points,
coarse_grid_address,
coarse_mesh_shifts=coarse_mesh_shifts)
grid_address = get_grid_address(mesh)
primitive_lattice = np.linalg.inv(primitive.get_cell())
spg.relocate_BZ_grid_address(grid_address,
mesh,
primitive_lattice)
return grid_points, coarse_grid_weights, grid_address
def get_coarse_ir_grid_points(primitive,
mesh,
mesh_divisors,
coarse_mesh_shifts,
is_kappa_star=True,
symprec=1e-5):
mesh = np.array(mesh, dtype='intc')
symmetry = Symmetry(primitive, symprec)
point_group = symmetry.get_pointgroup_operations()
if mesh_divisors is None:
(ir_grid_points,
ir_grid_weights,
grid_address,
grid_mapping_table) = get_ir_grid_points(mesh, point_group)
else:
mesh_divs = np.array(mesh_divisors, dtype='intc')
coarse_mesh = mesh // mesh_divs
if coarse_mesh_shifts is None:
coarse_mesh_shifts = [False, False, False]
if not is_kappa_star:
coarse_grid_address = get_grid_address(coarse_mesh)
coarse_grid_points = np.arange(np.prod(coarse_mesh), dtype='uintp')
else:
(coarse_ir_grid_points,
coarse_ir_grid_weights,
coarse_grid_address,
coarse_grid_mapping_table) = get_ir_grid_points(
coarse_mesh,
point_group,
mesh_shifts=coarse_mesh_shifts)
ir_grid_points = from_coarse_to_dense_grid_points(
mesh,
mesh_divs,
coarse_grid_points,
coarse_grid_address,
coarse_mesh_shifts=coarse_mesh_shifts)
grid_address = get_grid_address(mesh)
ir_grid_weights = ir_grid_weights
reciprocal_lattice = np.linalg.inv(primitive.get_cell())
bz_grid_address, bz_map = spg.relocate_BZ_grid_address(grid_address,
mesh,
reciprocal_lattice,
is_dense=True)
return (ir_grid_points,
ir_grid_weights,
bz_grid_address,
grid_mapping_table)
def get_coarse_ir_grid_points(primitive,
mesh,
mesh_divisors,
coarse_mesh_shifts,
is_kappa_star=True,
symprec=1e-5):
mesh = np.array(mesh, dtype='intc')
symmetry = Symmetry(primitive, symprec)
point_group = symmetry.get_pointgroup_operations()
if mesh_divisors is None:
(ir_grid_points,
ir_grid_weights,
grid_address,
grid_mapping_table) = get_ir_grid_points(mesh, point_group)
else:
mesh_divs = np.array(mesh_divisors, dtype='intc')
coarse_mesh = mesh // mesh_divs
if coarse_mesh_shifts is None:
coarse_mesh_shifts = [False, False, False]
if not is_kappa_star:
coarse_grid_address = get_grid_address(coarse_mesh)
coarse_grid_points = np.arange(np.prod(coarse_mesh), dtype='intc')
coarse_grid_weights = np.ones(len(coarse_grid_points), dtype='intc')
else:
(coarse_ir_grid_points,
coarse_ir_grid_weights,
coarse_grid_address,
coarse_grid_mapping_table) = get_ir_grid_points(
coarse_mesh,
point_group,
mesh_shifts=coarse_mesh_shifts)
ir_grid_points = from_coarse_to_dense_grid_points(
mesh,
mesh_divs,
coarse_grid_points,
coarse_grid_address,
coarse_mesh_shifts=coarse_mesh_shifts)
grid_address = get_grid_address(mesh)
ir_grid_weights = ir_grid_weights
primitive_lattice = np.linalg.inv(primitive.get_cell())
bz_grid_address, bz_map = spg.relocate_BZ_grid_address(grid_address,
mesh,
primitive_lattice)
return (ir_grid_points,
ir_grid_weights,
bz_grid_address,
grid_mapping_table)
def get_BZ_triplets_at_q(grid_point, mesh, reciprocal_lattice, grid_address,
map_q):
bz_grid_address, bz_map = spg.relocate_BZ_grid_address(
grid_address, mesh, reciprocal_lattice)
triplets_at_q, weights = spg.get_BZ_triplets_at_q(grid_point,
bz_grid_address, bz_map,
map_q, mesh)
assert np.prod(mesh) == weights.sum(), \
"Num grid points %d, sum of weight %d" % (
np.prod(mesh), weights.sum())
return triplets_at_q, weights, bz_grid_address, bz_map
def get_coarse_ir_grid_points(primitive,
mesh,
mesh_divisors,
coarse_mesh_shifts,
is_nosym=False,
symprec=1e-5):
if mesh_divisors is None:
mesh_divs = [1, 1, 1]
else:
mesh_divs = mesh_divisors
mesh = np.array(mesh, dtype='intc')
mesh_divs = np.array(mesh_divs, dtype='intc')
coarse_mesh = mesh / mesh_divs
if coarse_mesh_shifts is None:
coarse_mesh_shifts = [False, False, False]
if is_nosym:
coarse_grid_address = get_grid_address(coarse_mesh)
coarse_grid_points = np.arange(np.prod(coarse_mesh), dtype='intc')
coarse_grid_weights = np.ones(len(coarse_grid_points), dtype='intc')
else:
symmetry = Symmetry(primitive, symprec)
(coarse_grid_points, coarse_grid_weights,
coarse_grid_address) = get_ir_grid_points(
coarse_mesh,
symmetry.get_pointgroup_operations(),
mesh_shifts=coarse_mesh_shifts)
grid_points = from_coarse_to_dense_grid_points(
mesh,
mesh_divs,
coarse_grid_points,
coarse_grid_address,
coarse_mesh_shifts=coarse_mesh_shifts)
grid_address = get_grid_address(mesh)
primitive_lattice = np.linalg.inv(primitive.get_cell())
spg.relocate_BZ_grid_address(grid_address, mesh, primitive_lattice)
return grid_points, coarse_grid_weights, grid_address
def get_bz_grid_address(mesh, primitive_lattice, with_boundary=False, is_bz_map_to_pp=False):
"is_bz_map_to_pp: Brillouine zone mapping to the original parallelpipe"
grid_address = get_grid_address(mesh)
bz_grid_address, bz_map, bz_to_pp_map = spg.relocate_BZ_grid_address(grid_address,
mesh,
primitive_lattice,
is_bz_map_to_orig=is_bz_map_to_pp)
if with_boundary:
if is_bz_map_to_pp:
return bz_grid_address, bz_map, bz_to_pp_map
else:
return bz_grid_address, bz_map
else:
return bz_grid_address[:np.prod(mesh)]
def get_nosym_triplets_at_q(grid_point,
mesh,
primitive_lattice,
stores_triplets_map=False):
grid_address = get_grid_address(mesh)
map_q = np.arange(len(grid_address), dtype='intc')
bz_grid_address, bz_map = spg.relocate_BZ_grid_address(
grid_address, mesh, primitive_lattice)
triplets_at_q, weights = spg.get_BZ_triplets_at_q(grid_point,
bz_grid_address, bz_map,
map_q, mesh)
if not stores_triplets_map:
map_q = None
return triplets_at_q, weights, bz_grid_address, bz_map, map_q
def get_nosym_triplets_at_q(grid_point,
mesh,
reciprocal_lattice,
stores_triplets_map=False):
grid_address = get_grid_address(mesh)
map_triplets = np.arange(len(grid_address), dtype='intc')
bz_grid_address, bz_map = spg.relocate_BZ_grid_address(
grid_address, mesh, reciprocal_lattice)
triplets_at_q, weights = _get_BZ_triplets_at_q(grid_point, bz_grid_address,
bz_map, map_triplets, mesh)
if not stores_triplets_map:
map_triplets = None
map_q = None
else:
map_q = map_triplets.copy()
return triplets_at_q, weights, bz_grid_address, bz_map, map_triplets, map_q
def get_bz_grid_address(mesh,
primitive_lattice,
with_boundary=False,
is_bz_map_to_pp=False):
"is_bz_map_to_pp: Brillouine zone mapping to the original parallelpipe"
grid_address = get_grid_address(mesh)
bz_grid_address, bz_map, bz_to_pp_map = spg.relocate_BZ_grid_address(
grid_address,
mesh,
primitive_lattice,
is_bz_map_to_orig=is_bz_map_to_pp)
if with_boundary:
if is_bz_map_to_pp:
return bz_grid_address, bz_map, bz_to_pp_map
else:
return bz_grid_address, bz_map
else:
return bz_grid_address[:np.prod(mesh)]
def get_BZ_triplets_at_q(grid_point,
mesh,
reciprocal_lattice,
grid_address,
map_q):
bz_grid_address, bz_map = spg.relocate_BZ_grid_address(grid_address,
mesh,
reciprocal_lattice)
triplets_at_q, weights = spg.get_BZ_triplets_at_q(
grid_point,
bz_grid_address,
bz_map,
map_q,
mesh)
assert np.prod(mesh) == weights.sum(), \
"Num grid points %d, sum of weight %d" % (
np.prod(mesh), weights.sum())
return triplets_at_q, weights, bz_grid_address, bz_map
def get_nosym_triplets_at_q(grid_point,
mesh,
primitive_lattice,
stores_triplets_map=False):
grid_address = get_grid_address(mesh)
map_q = np.arange(len(grid_address), dtype='intc')
bz_grid_address, bz_map = spg.relocate_BZ_grid_address(grid_address,
mesh,
primitive_lattice)
triplets_at_q, weights = spg.get_BZ_triplets_at_q(
grid_point,
bz_grid_address,
bz_map,
map_q,
mesh)
if not stores_triplets_map:
map_q = None
return triplets_at_q, weights, bz_grid_address, bz_map, map_q
from phonopy.structure.spglib import get_ir_reciprocal_mesh, relocate_BZ_grid_address
import sys
cell = read_vasp(sys.argv[1])
symmetry = Symmetry(cell)
mesh = [4, 4, 4]
is_shift = np.array([0, 0, 0], dtype='intc')
mapping_table, grid_address = get_ir_reciprocal_mesh(
mesh,
cell,
is_shift=is_shift)
ir_grid_points = np.unique(mapping_table)
primitive_vectors = np.linalg.inv(cell.get_cell())
bz_grid_address, bz_map = relocate_BZ_grid_address(
grid_address,
mesh,
np.linalg.inv(cell.get_cell()),
is_shift=is_shift)
bz_points = np.extract(bz_map > -1, bz_map)
qpoints = (grid_address + is_shift / 2.0) / mesh
qpoints -= (qpoints > 0.5001) * 1
bz = BrillouinZone(primitive_vectors)
bz.run(qpoints)
sv = bz.get_shortest_qpoints()
print("%d %d" % (len(bz_points), np.sum(len(x) for x in sv)))
for q, vs in zip(qpoints, sv):
if np.allclose(q, vs[0]):
print(q)
else:
def _set_grid_address(self):
grid_address = get_grid_address(self._mesh)
self._grid_address, self._bz_map = spg.relocate_BZ_grid_address(
grid_address,
self._mesh,
np.linalg.inv(self._primitive.get_cell()))
def set_bz_grid_points(self):
self._bz_grid_address, self._bz_map , self._bz_to_pp_map= \
relocate_BZ_grid_address(self._grid_address,
self._mesh,
np.linalg.inv(self._primitive.get_cell()),
is_bz_map_to_orig=True)
def _set_grid_address(self):
grid_address = get_grid_address(self._mesh)
self._grid_address, self._bz_map = spg.relocate_BZ_grid_address(
grid_address, self._mesh,
np.linalg.inv(self._primitive.get_cell()))
from phonopy.structure.spglib import get_ir_reciprocal_mesh, relocate_BZ_grid_address
import sys
cell = read_vasp(sys.argv[1])
symmetry = Symmetry(cell)
mesh = [4, 4, 4]
is_shift = np.array([0, 0, 0], dtype='intc')
mapping_table, grid_address = get_ir_reciprocal_mesh(
mesh,
cell,
is_shift=is_shift)
ir_grid_points = np.unique(mapping_table)
primitive_vectors = np.linalg.inv(cell.get_cell())
bz_grid_address, bz_map = relocate_BZ_grid_address(
grid_address,
mesh,
np.linalg.inv(cell.get_cell()),
is_shift=is_shift)
bz_points = np.extract(bz_map > -1, bz_map)
qpoints = (grid_address + is_shift / 2.0) / mesh
qpoints -= (qpoints > 0.5001) * 1
bz = BrillouinZone(primitive_vectors)
bz.run(qpoints)
sv = bz.get_shortest_qpoints()
print("%d %d" % (len(bz_points), np.sum(len(x) for x in sv)))
for q, vs in zip(qpoints, sv):
if np.allclose(q, vs[0]):
print(q)
else:
def get_triplets_at_q(grid_point,
mesh,
point_group, # real space point group of space group
reciprocal_lattice, # column vectors
is_time_reversal=True,
swappable=True,
stores_triplets_map=False):
"""Parameters
----------
grid_point : int
A grid point
mesh : array_like
Mesh numbers
shape=(3,), dtype='intc'
point_group : array_like
Rotation matrices in real space. Note that those in reciprocal space
mean these matrices transposed (local terminology).
shape=(n_rot, 3, 3), dtype='intc', order='C'
reciprocal_lattice : array_like
Reciprocal primitive basis vectors given as column vectors
shape=(3, 3), dtype='double', order='C'
is_time_reversal : bool, optional
Inversion symemtry is added if it doesn't exist. Default is True.
swappable : bool, optional
q1 and q2 among (q0, q1, q2) can be swapped. Deafult is True.
Returns
-------
triplets_at_q : ndarray
Symmetry reduced number of triplets are stored as grid point
integer numbers.
shape=(n_triplets, 3), dtype='uintp'
weights : ndarray
Weights of triplets in Brillouin zone
shape=(n_triplets,), dtype='intc'
bz_grid_address : ndarray
Integer grid address of the points in Brillouin zone including
surface. The first prod(mesh) numbers of points are
independent. But the rest of points are
translational-symmetrically equivalent to some other points.
shape=(n_grid_points, 3), dtype='intc', order='C'
bz_map : ndarray
Grid point mapping table containing BZ surface. See more
detail in spglib docstring.
shape=(prod(mesh*2),), dtype='uintp'
map_tripelts : ndarray or None
Returns when stores_triplets_map=True, otherwise None is
returned. Mapping table of all triplets to symmetrically
independent tripelts. More precisely, this gives a list of
index mapping from all q-points to independent q' of
q+q'+q''=G. Considering q' is enough because q is fixed and
q''=G-q-q' where G is automatically determined to choose
smallest |G|.
shape=(prod(mesh),), dtype='uintp'
map_q : ndarray or None
Returns when stores_triplets_map=True, otherwise None is
returned. Irreducible q-points stabilized by q-point of
specified grid_point.
shape=(prod(mesh),), dtype='uintp'
"""
map_triplets, map_q, grid_address = _get_triplets_reciprocal_mesh_at_q(
grid_point,
mesh,
point_group,
is_time_reversal=is_time_reversal,
swappable=swappable)
bz_grid_address, bz_map = spg.relocate_BZ_grid_address(grid_address,
mesh,
reciprocal_lattice,
is_dense=True)
triplets_at_q, weights = _get_BZ_triplets_at_q(
grid_point,
bz_grid_address,
bz_map,
map_triplets,
mesh)
assert np.prod(mesh) == weights.sum(), \
"Num grid points %d, sum of weight %d" % (
np.prod(mesh), weights.sum())
# These maps are required for collision matrix calculation.
if not stores_triplets_map:
map_triplets = None
map_q = None
return triplets_at_q, weights, bz_grid_address, bz_map, map_triplets, map_q