def test_GridPoints_NaCl_with_rotations_fit_BZ(ph_nacl):
rec_lat = np.linalg.inv(ph_nacl.primitive.cell)
rotations = ph_nacl.primitive_symmetry.get_pointgroup_operations()
mesh = [5, 5, 5]
gpf = GridPoints(mesh, rec_lat, rotations=rotations,
fit_in_BZ=False)
gpt = GridPoints(mesh, rec_lat, rotations=rotations,
fit_in_BZ=True)
np.testing.assert_allclose(
gpf.qpoints,
[[0.0, 0.0, 0.0],
[0.2, 0.0, 0.0],
[0.4, 0.0, 0.0],
[0.2, 0.2, 0.0],
[0.4, 0.2, 0.0],
[-0.4, 0.2, 0.0],
[-0.2, 0.2, 0.0],
[0.4, 0.4, 0.0],
[-0.4, 0.4, 0.0],
[-0.4, 0.4, 0.2]], atol=1e-8)
np.testing.assert_allclose(
gpt.qpoints,
[[0.0, 0.0, 0.0],
[0.2, 0.0, 0.0],
[0.4, 0.0, 0.0],
[0.2, 0.2, 0.0],
[0.4, 0.2, 0.0],
[-0.4, 0.2, 0.0],
[-0.2, 0.2, 0.0],
[0.4, 0.4, 0.0],
[-0.4, -0.6, 0.0],
[0.6, 0.4, 0.2]], atol=1e-8)
def __init__(
self,
dynamical_matrix,
mesh,
shift=None,
is_time_reversal=True,
is_mesh_symmetry=True,
with_eigenvectors=False,
is_gamma_center=False,
rotations=None, # Point group operations in real space
factor=VaspToTHz):
self._mesh = np.array(mesh, dtype='intc')
self._with_eigenvectors = with_eigenvectors
self._factor = factor
self._cell = dynamical_matrix.get_primitive()
self._dynamical_matrix = dynamical_matrix
self._gp = GridPoints(self._mesh,
np.linalg.inv(self._cell.get_cell()),
q_mesh_shift=shift,
is_gamma_center=is_gamma_center,
is_time_reversal=(is_time_reversal
and is_mesh_symmetry),
rotations=rotations,
is_mesh_symmetry=is_mesh_symmetry)
self._qpoints = self._gp.qpoints
self._weights = self._gp.weights
self._frequencies = None
self._eigenvectors = None
self._q_count = 0
def test_GridPoints_NaCl_with_rotations(ph_nacl):
rec_lat = np.linalg.inv(ph_nacl.primitive.cell)
rotations = ph_nacl.primitive_symmetry.get_pointgroup_operations()
gp = GridPoints([4, 4, 4], rec_lat, rotations=rotations)
np.testing.assert_array_equal(
gp.ir_grid_points, [0, 1, 2, 5, 6, 7, 10, 27])
np.testing.assert_array_equal(gp.weights, [1, 8, 4, 6, 24, 12, 3, 6])
np.testing.assert_array_equal(
gp.grid_mapping_table,
[0, 1, 2, 1, 1, 5, 6, 7, 2, 6,
10, 6, 1, 7, 6, 5, 1, 5, 6, 7,
5, 1, 7, 6, 6, 7, 6, 27, 7, 6,
27, 6, 2, 6, 10, 6, 6, 7, 6, 27,
10, 6, 2, 6, 6, 27, 6, 7, 1, 7,
6, 5, 7, 6, 27, 6, 6, 27, 6, 7,
5, 6, 7, 1])
np.testing.assert_allclose(
gp.qpoints,
[[0.0, 0.0, 0.0],
[0.25, 0.0, 0.0],
[0.5, 0.0, 0.0],
[0.25, 0.25, 0.0],
[0.5, 0.25, 0.0],
[-0.25, 0.25, 0.0],
[0.5, 0.5, 0.0],
[-0.25, 0.5, 0.25]], atol=1e-8)
def test_GridPoints_SnO2_with_rotations_MP(ph_sno2):
rec_lat = np.linalg.inv(ph_sno2.primitive.cell)
rotations = ph_sno2.primitive_symmetry.get_pointgroup_operations()
gp = GridPoints([4, 4, 4], rec_lat, rotations=rotations,
is_gamma_center=False)
np.testing.assert_array_equal(
gp.ir_grid_points, [0, 1, 5, 16, 17, 21])
np.testing.assert_array_equal(gp.weights, [8, 16, 8, 8, 16, 8])
np.testing.assert_array_equal(
gp.grid_mapping_table,
[0, 1, 1, 0, 1, 5, 5, 1, 1, 5,
5, 1, 0, 1, 1, 0, 16, 17, 17, 16,
17, 21, 21, 17, 17, 21, 21, 17, 16, 17,
17, 16, 16, 17, 17, 16, 17, 21, 21, 17,
17, 21, 21, 17, 16, 17, 17, 16, 0, 1,
1, 0, 1, 5, 5, 1, 1, 5, 5, 1,
0, 1, 1, 0])
np.testing.assert_allclose(
gp.qpoints,
[[0.125, 0.125, 0.125],
[0.375, 0.125, 0.125],
[0.375, 0.375, 0.125],
[0.125, 0.125, 0.375],
[0.375, 0.125, 0.375],
[0.375, 0.375, 0.375]], atol=1e-8)
def testGridPoints(self):
gp = GridPoints([11, 11, 11], [[-1, 1, 1], [1, -1, 1], [1, 1, -1]])
self.assertTrue((gp.grid_address == gp.get_grid_address()).all())
self.assertTrue((gp.ir_grid_points == gp.get_ir_grid_points()).all())
np.testing.assert_allclose(gp.qpoints, gp.get_ir_qpoints())
self.assertTrue((gp.weights == gp.get_ir_grid_weights()).all())
self.assertTrue(
(gp.grid_mapping_table == gp.get_grid_mapping_table()).all())
def test_GridPoints():
"""Test of GridPoints."""
gp = GridPoints([2, 3, 4], [[-1, 1, 1], [1, -1, 1], [1, 1, -1]])
assert gp.ir_grid_points.dtype == np.dtype("int_")
assert gp.weights.dtype == np.dtype("int_")
assert gp.grid_mapping_table.dtype == np.dtype("int_")
assert gp.grid_address.dtype == np.dtype("intc")
assert gp.mesh_numbers.dtype == np.dtype("intc")
assert gp.reciprocal_lattice.dtype == np.dtype("double")
assert gp.qpoints.dtype == np.dtype("double")
np.testing.assert_array_equal(gp.grid_address, ga234)
def __init__(self,
dynamical_matrix,
cell,
mesh,
shift=None,
is_time_reversal=False,
is_mesh_symmetry=True,
is_eigenvectors=False,
is_band_connection=False,
is_gamma_center=False,
group_velocity=None,
factor=VaspToTHz,
symprec=1e-5):
self._mesh = np.array(mesh)
self._is_band_connection=is_band_connection
self._band_order = None
self._is_eigenvectors = is_eigenvectors
self._factor = factor
self._cell = cell
self._dynamical_matrix = dynamical_matrix
# self._qpoints, self._weights = get_qpoints(self._mesh,
# self._cell,
# shift,
# is_gamma_center,
# is_time_reversal,
# symprec,
# is_symmetry)
rotations = Symmetry(self._cell).get_pointgroup_operations()
self._gp = GridPoints(self._mesh,
np.linalg.inv(self._cell.get_cell()),
q_mesh_shift=shift,
is_gamma_center=is_gamma_center,
is_time_reversal=is_time_reversal,
rotations=rotations,
is_mesh_symmetry=is_mesh_symmetry)
self._qpoints = self._gp.get_ir_qpoints()
self._weights = self._gp.get_ir_grid_weights()
self._eigenvalues = None
self._eigenvectors = None
self._set_eigenvalues()
if self._is_band_connection:
self._set_band_connection()
self._group_velocities = None
if group_velocity is not None:
self._set_group_velocities(group_velocity)
def test_GridPoints_NaCl_with_rotations_fit_BZ(ph_nacl: Phonopy, fit_in_BZ):
"""Test of GridPoints with rotations from NaCl and fit_in_BZ."""
rec_lat = np.linalg.inv(ph_nacl.primitive.cell)
rotations = ph_nacl.primitive_symmetry.pointgroup_operations
mesh = [5, 5, 5]
gpts = GridPoints(mesh, rec_lat, rotations=rotations, fit_in_BZ=fit_in_BZ)
if fit_in_BZ:
np.testing.assert_allclose(
gpts.qpoints,
[
[0.0, 0.0, 0.0],
[0.2, 0.0, 0.0],
[0.4, 0.0, 0.0],
[0.2, 0.2, 0.0],
[0.4, 0.2, 0.0],
[-0.4, 0.2, 0.0],
[-0.2, 0.2, 0.0],
[0.4, 0.4, 0.0],
[-0.4, -0.6, 0.0],
[0.6, 0.4, 0.2],
],
atol=1e-8,
)
else:
np.testing.assert_allclose(
gpts.qpoints,
[
[0.0, 0.0, 0.0],
[0.2, 0.0, 0.0],
[0.4, 0.0, 0.0],
[0.2, 0.2, 0.0],
[0.4, 0.2, 0.0],
[-0.4, 0.2, 0.0],
[-0.2, 0.2, 0.0],
[0.4, 0.4, 0.0],
[-0.4, 0.4, 0.0],
[-0.4, 0.4, 0.2],
],
atol=1e-8,
)
def __init__(
self,
dynamical_matrix,
mesh,
shift=None,
is_time_reversal=True,
is_mesh_symmetry=True,
is_eigenvectors=False,
is_gamma_center=False,
group_velocity=None,
rotations=None, # Point group operations in real space
factor=VaspToTHz,
use_lapack_solver=False):
self._mesh = np.array(mesh, dtype='intc')
self._is_eigenvectors = is_eigenvectors
self._factor = factor
self._cell = dynamical_matrix.get_primitive()
self._dynamical_matrix = dynamical_matrix
self._use_lapack_solver = use_lapack_solver
self._gp = GridPoints(self._mesh,
np.linalg.inv(self._cell.get_cell()),
q_mesh_shift=shift,
is_gamma_center=is_gamma_center,
is_time_reversal=is_time_reversal,
rotations=rotations,
is_mesh_symmetry=is_mesh_symmetry)
self._qpoints = self._gp.get_ir_qpoints()
self._weights = self._gp.get_ir_grid_weights()
self._frequencies = None
self._eigenvalues = None
self._eigenvectors = None
self._set_phonon()
self._group_velocities = None
if group_velocity is not None:
self._set_group_velocities(group_velocity)
def test_GridPoints_SnO2_with_rotations(ph_sno2):
rec_lat = np.linalg.inv(ph_sno2.primitive.cell)
rotations = ph_sno2.primitive_symmetry.get_pointgroup_operations()
gp = GridPoints([4, 4, 4], rec_lat, rotations=rotations)
np.testing.assert_array_equal(
gp.ir_grid_points,
[0, 1, 2, 5, 6, 10, 16, 17, 18, 21, 22, 26, 32, 33, 34, 37, 38, 42])
np.testing.assert_array_equal(
gp.weights,
[1, 4, 2, 4, 4, 1, 2, 8, 4, 8, 8, 2, 1, 4, 2, 4, 4, 1])
np.testing.assert_array_equal(
gp.grid_mapping_table,
[0, 1, 2, 1, 1, 5, 6, 5, 2, 6,
10, 6, 1, 5, 6, 5, 16, 17, 18, 17,
17, 21, 22, 21, 18, 22, 26, 22, 17, 21,
22, 21, 32, 33, 34, 33, 33, 37, 38, 37,
34, 38, 42, 38, 33, 37, 38, 37, 16, 17,
18, 17, 17, 21, 22, 21, 18, 22, 26, 22,
17, 21, 22, 21])
np.testing.assert_allclose(
gp.qpoints,
[[0.0, 0.0, 0.0],
[0.25, 0.0, 0.0],
[0.5, 0.0, 0.0],
[0.25, 0.25, 0.0],
[0.5, 0.25, 0.0],
[0.5, 0.5, 0.0],
[0.0, 0.0, 0.25],
[0.25, 0.0, 0.25],
[0.5, 0.0, 0.25],
[0.25, 0.25, 0.25],
[0.5, 0.25, 0.25],
[0.5, 0.5, 0.25],
[0.0, 0.0, 0.5],
[0.25, 0.0, 0.5],
[0.5, 0.0, 0.5],
[0.25, 0.25, 0.5],
[0.5, 0.25, 0.5],
[0.5, 0.5, 0.5]], atol=1e-8)
def __init__(self,
dynamical_matrix,
unitcell_ideal,
primitive_matrix_ideal,
mesh,
shift=None,
is_time_reversal=True,
is_mesh_symmetry=True,
is_eigenvectors=False,
is_gamma_center=False,
star="none",
group_velocity=None,
rotations=None, # Point group operations in real space
factor=VaspToTHz,
use_lapack_solver=False,
mode="eigenvector"):
self._mesh = np.array(mesh, dtype='intc')
self._is_eigenvectors = is_eigenvectors
self._factor = factor
primitive_ideal_wrt_unitcell = (
get_primitive(unitcell_ideal, primitive_matrix_ideal))
self._cell = primitive_ideal_wrt_unitcell
# ._dynamical_matrix must be assigned for calculating DOS
# using the tetrahedron method.
# In the "DOS", this is used to get "primitive".
# In the "TetrahedronMesh", this is used just as the "Atoms".
# Currently, we must not use the tetrahedron method,
# because now we do not give the primitive but the unitcell for the
# self._dynamical_matrix.
self._dynamical_matrix = dynamical_matrix
self._use_lapack_solver = use_lapack_solver
self._gp = GridPoints(self._mesh,
np.linalg.inv(self._cell.get_cell()),
q_mesh_shift=shift,
is_gamma_center=is_gamma_center,
is_time_reversal=is_time_reversal,
rotations=rotations,
is_mesh_symmetry=is_mesh_symmetry)
self._qpoints = self._gp.get_ir_qpoints()
self._weights = self._gp.get_ir_grid_weights()
self._star = star
self._eigenstates_unfolding = Eigenstates(
dynamical_matrix,
unitcell_ideal,
primitive_matrix_ideal,
mode=mode,
star=star,
verbose=False)
self._frequencies = None
self._eigenvalues = None
self._eigenvectors = None
self._set_phonon()
self._group_velocities = None
if group_velocity is not None:
self._set_group_velocities(group_velocity)
def test_GridPoints_SnO2_with_rotations_MP(ph_sno2: Phonopy):
"""Test of GridPoints with non-gamma-centre mesh and rotations from SnO2."""
rec_lat = np.linalg.inv(ph_sno2.primitive.cell)
rotations = ph_sno2.primitive_symmetry.pointgroup_operations
gp = GridPoints([4, 4, 4],
rec_lat,
rotations=rotations,
is_gamma_center=False)
np.testing.assert_array_equal(gp.ir_grid_points, [0, 1, 5, 16, 17, 21])
np.testing.assert_array_equal(gp.weights, [8, 16, 8, 8, 16, 8])
np.testing.assert_array_equal(
gp.grid_mapping_table,
[
0,
1,
1,
0,
1,
5,
5,
1,
1,
5,
5,
1,
0,
1,
1,
0,
16,
17,
17,
16,
17,
21,
21,
17,
17,
21,
21,
17,
16,
17,
17,
16,
16,
17,
17,
16,
17,
21,
21,
17,
17,
21,
21,
17,
16,
17,
17,
16,
0,
1,
1,
0,
1,
5,
5,
1,
1,
5,
5,
1,
0,
1,
1,
0,
],
)
np.testing.assert_allclose(
gp.qpoints,
[
[0.125, 0.125, 0.125],
[0.375, 0.125, 0.125],
[0.375, 0.375, 0.125],
[0.125, 0.125, 0.375],
[0.375, 0.125, 0.375],
[0.375, 0.375, 0.375],
],
atol=1e-8,
)
def test_GridPoints():
gp = GridPoints([2, 3, 4], [[-1, 1, 1], [1, -1, 1], [1, 1, -1]])
np.testing.assert_array_equal(gp.grid_address, ga234)
