def test_Amm2():
"""Test of DOS calculation using TetrahedronMesh for Amm2 crystal."""
data = np.loadtxt(StringIO(dos_str))
phonon = _get_phonon("Amm2", [3, 2, 2],
[[1, 0, 0], [0, 0.5, -0.5], [0, 0.5, 0.5]])
mesh = [11, 11, 11]
primitive = phonon.primitive
phonon.run_mesh([11, 11, 11])
weights = phonon.mesh.weights
frequencies = phonon.mesh.frequencies
grid_address = phonon.mesh.grid_address
ir_grid_points = phonon.mesh.ir_grid_points
grid_mapping_table = phonon.mesh.grid_mapping_table
thm = TetrahedronMesh(
primitive,
frequencies,
mesh,
np.array(grid_address, dtype="int_"),
np.array(grid_mapping_table, dtype="int_"),
ir_grid_points,
)
thm.set(value="I", division_number=40)
freq_points = thm.get_frequency_points()
dos = np.zeros_like(freq_points)
for i, iw in enumerate(thm):
dos += np.sum(iw * weights[i], axis=1)
dos_comp = np.transpose([freq_points, dos]).reshape(10, 8)
np.testing.assert_allclose(dos_comp, data, atol=1e-5)
def test_Amm2(self):
data = np.loadtxt(StringIO(dos_str))
phonon = self._get_phonon("Amm2",
[3, 2, 2],
[[1, 0, 0],
[0, 0.5, -0.5],
[0, 0.5, 0.5]])
mesh = [11, 11, 11]
primitive = phonon.get_primitive()
phonon.run_mesh([11, 11, 11])
qpoints = phonon.mesh.qpoints
weights = phonon.mesh.weights
frequencies = phonon.mesh.frequencies
grid_address = phonon.mesh.grid_address
ir_grid_points = phonon.mesh.ir_grid_points
grid_mapping_table = phonon.mesh.grid_mapping_table
thm = TetrahedronMesh(primitive,
frequencies,
mesh,
grid_address,
grid_mapping_table,
ir_grid_points)
thm.set(value='I', division_number=40)
freq_points = thm.get_frequency_points()
dos = np.zeros_like(freq_points)
for i, iw in enumerate(thm):
dos += np.sum(iw * weights[i], axis=1)
dos_comp = np.transpose([freq_points, dos]).reshape(10, 8)
self.assertTrue(np.abs(dos_comp - data).all() < 1e-5)
def test_Amm2(self):
data = np.loadtxt(StringIO(dos_str))
phonon = self._get_phonon("Amm2",
[3, 2, 2],
[[1, 0, 0],
[0, 0.5, -0.5],
[0, 0.5, 0.5]])
mesh = [11, 11, 11]
primitive = phonon.get_primitive()
phonon.set_mesh([11, 11, 11])
qpoints, weights, frequencies, _ = phonon.get_mesh()
(grid_address,
ir_grid_points,
grid_mapping_table) = phonon.get_mesh_grid_info()
thm = TetrahedronMesh(primitive,
frequencies,
mesh,
grid_address,
grid_mapping_table,
ir_grid_points)
thm.set(value='I', division_number=40)
freq_points = thm.get_frequency_points()
dos = np.zeros_like(freq_points)
for i, iw in enumerate(thm):
dos += np.sum(iw * weights[i], axis=1)
dos_comp = np.transpose([freq_points, dos]).reshape(10, 8)
self.assertTrue(np.abs(dos_comp - data).all() < 1e-5)
def __init__(self, mesh_object, sigma=None, use_tetrahedron_method=False):
self._mesh_object = mesh_object
self._frequencies = mesh_object.frequencies
self._weights = mesh_object.weights
if use_tetrahedron_method and sigma is None:
self._tetrahedron_mesh = TetrahedronMesh(
mesh_object.dynamical_matrix.primitive, self._frequencies,
mesh_object.mesh_numbers, mesh_object.grid_address,
mesh_object.grid_mapping_table, mesh_object.ir_grid_points)
else:
self._tetrahedron_mesh = None
self._frequency_points = None
self._sigma = sigma
self.set_draw_area()
self.set_smearing_function('Normal')
def __init__(self, mesh_object, sigma=None, tetrahedron_method=False):
self._mesh_object = mesh_object
self._frequencies = mesh_object.get_frequencies()
self._weights = mesh_object.get_weights()
if tetrahedron_method:
self._tetrahedron_mesh = TetrahedronMesh(
mesh_object.get_dynamical_matrix().get_primitive(),
self._frequencies, mesh_object.get_mesh_numbers(),
mesh_object.get_grid_address(),
mesh_object.get_grid_mapping_table())
else:
self._tetrahedron_mesh = None
self._frequency_points = None
self._sigma = sigma
self.set_draw_area()
self.set_smearing_function('Normal')
def __init__(self, mesh_object: Mesh, sigma=None, use_tetrahedron_method=False):
"""Init method."""
self._mesh_object = mesh_object
self._frequencies = mesh_object.frequencies
self._weights = mesh_object.weights
self._tetrahedron_mesh = None
if use_tetrahedron_method and sigma is None:
self._tetrahedron_mesh = TetrahedronMesh(
mesh_object.dynamical_matrix.primitive,
self._frequencies,
mesh_object.mesh_numbers,
np.array(mesh_object.grid_address, dtype="int_"),
np.array(mesh_object.grid_mapping_table, dtype="int_"),
mesh_object.ir_grid_points,
)
self._frequency_points = None
self._sigma = sigma
self.set_draw_area()
self.set_smearing_function("Normal")
def __init__(self, mesh_object, sigma=None, tetrahedron_method=False):
self._frequencies = mesh_object.get_frequencies()
self._weights = mesh_object.get_weights()
if tetrahedron_method:
self._tetrahedron_mesh = TetrahedronMesh(
mesh_object.get_dynamical_matrix().get_primitive(),
self._frequencies, mesh_object.get_mesh_numbers(),
mesh_object.get_grid_address(),
mesh_object.get_grid_mapping_table())
else:
self._tetrahedron_mesh = None
self._omega_pitch = None
if sigma:
self._sigma = sigma
else:
self._sigma = (self._frequencies.max() -
self._frequencies.min()) / 100
self.set_draw_area()
# Default smearing
self.set_smearing_function('Normal')
def __init__(self,
mode_kappa,
cell,
frequencies,
mesh,
grid_address,
grid_mapping_table,
ir_grid_points,
grid_order=None,
num_sampling_points=100):
self._mode_kappa = mode_kappa
self._tetrahedron_mesh = TetrahedronMesh(cell, frequencies, mesh,
grid_address,
grid_mapping_table,
ir_grid_points)
min_freq = min(frequencies.ravel())
max_freq = max(frequencies.ravel()) + epsilon
self._frequency_points = np.linspace(min_freq, max_freq,
num_sampling_points)
self._kdos = np.zeros(
(len(mode_kappa), len(self._frequency_points), 2, 6),
dtype='double')
self._run_tetrahedron_method()
from phonopy.structure.symmetry import Symmetry
from phonopy.interface.vasp import read_vasp
from phonopy.file_IO import parse_FORCE_SETS, parse_BORN
from phonopy.structure.spglib import get_stabilized_reciprocal_mesh
from phonopy.structure.tetrahedron_method import TetrahedronMethod
from phonopy.phonon.tetrahedron_mesh import TetrahedronMesh
cell = read_vasp(sys.argv[1])
phonon = Phonopy(cell, [[2, 0, 0], [0, 2, 0], [0, 0, 2]], is_auto_displacements=False)
force_sets = parse_FORCE_SETS()
phonon.set_force_sets(force_sets)
phonon.set_post_process([[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]])
primitive = phonon.get_primitive()
born = parse_BORN(primitive)
phonon.set_nac_params(born)
symmetry = phonon.get_primitive_symmetry()
mesh = [20, 20, 20]
# phonon.set_mesh(mesh)
# phonon.set_total_DOS(sigma=0.1)
# phonon.plot_total_DOS().show()
rotations = symmetry.get_pointgroup_operations()
thm = TetrahedronMesh(phonon.get_dynamical_matrix(),
mesh,
rotations,
is_gamma_center=True)
thm.run_dos()
for f, iw in zip(thm.get_frequency_points(), thm.get_integration_weights()):
print f, iw