def __init__(self,
dynamical_matrix,
dimension,
phonon_modes,
delta_q=None,
derivative_order=None,
nac_q_direction=None,
factor=VaspToTHz):
"""Class describe atomic modulations
Atomic modulations corresponding to phonon modes are created.
"""
self._dm = dynamical_matrix
self._primitive = dynamical_matrix.get_primitive()
self._phonon_modes = phonon_modes
self._dimension = dimension
self._delta_q = delta_q # 1st/2nd order perturbation direction
self._nac_q_direction = nac_q_direction
self._ddm = DerivativeOfDynamicalMatrix(dynamical_matrix)
self._derivative_order = derivative_order
self._factor = factor
self._u = []
self._eigvecs = []
self._eigvals = []
self._supercell = None
dim = self._get_dimension_3x3()
self._supercell = get_supercell(self._primitive, dim)
def __init__(self,
dynamical_matrix,
q_length=None,
symmetry=None,
frequency_factor_to_THz=VaspToTHz,
cutoff_frequency=1e-4):
"""
q_points is a list of sets of q-point and q-direction:
[[q-point, q-direction], [q-point, q-direction], ...]
q_length is used such as D(q + q_length) - D(q - q_length).
"""
self._dynmat = dynamical_matrix
primitive = dynamical_matrix.get_primitive()
self._reciprocal_lattice_inv = primitive.get_cell()
self._reciprocal_lattice = np.linalg.inv(self._reciprocal_lattice_inv)
self._q_length = q_length
if q_length is None:
self._ddm = DerivativeOfDynamicalMatrix(dynamical_matrix)
else:
self._ddm = None
self._symmetry = symmetry
self._factor = frequency_factor_to_THz
self._cutoff_frequency = cutoff_frequency
self._directions = np.array(
[[1, 2, 3], [1, 0, 0], [0, 1, 0], [0, 0, 1]], dtype='double')
self._directions[0] /= np.linalg.norm(self._directions[0])
self._q_points = None
self._group_velocity = None
self._perturbation = None
def __init__(
self,
dynamical_matrix: Union[DynamicalMatrix, DynamicalMatrixNAC],
dimension,
phonon_modes,
delta_q=None,
derivative_order=None,
nac_q_direction=None,
factor=VaspToTHz,
):
"""Init method."""
self._dm = dynamical_matrix
self._primitive = dynamical_matrix.primitive
self._phonon_modes = phonon_modes
self._dimension = np.array(dimension).ravel()
self._delta_q = delta_q # 1st/2nd order perturbation direction
self._nac_q_direction = nac_q_direction
self._ddm = DerivativeOfDynamicalMatrix(dynamical_matrix)
self._derivative_order = derivative_order
self._factor = factor
dim = self._get_dimension_3x3()
self._supercell = get_supercell(self._primitive, dim)
complex_dtype = "c%d" % (np.dtype("double").itemsize * 2)
self._u = np.zeros(
(len(self._phonon_modes), len(self._supercell), 3),
dtype=complex_dtype,
order="C",
)
self._eigvals = np.zeros(len(self._phonon_modes), dtype="double")
self._eigvecs = np.zeros(
(len(self._phonon_modes), len(self._primitive) * 3), dtype=complex_dtype
)
def _assert(ph: Phonopy, ref_vals, show=False):
dynmat = ph.dynamical_matrix
ddynmat = DerivativeOfDynamicalMatrix(dynmat)
ddynmat.run([0, 0.1, 0.1])
ddm = ddynmat.d_dynamical_matrix
condition = np.abs(ddm) > 1e-8
vals = np.extract(condition, ddm).real
if show:
_show(vals)
np.testing.assert_allclose(vals, ref_vals, rtol=0, atol=1e-7)
def __init__(
self,
dynamical_matrix: Union[DynamicalMatrix, DynamicalMatrixNAC],
q_length=None,
symmetry: Optional[Symmetry] = None,
frequency_factor_to_THz=VaspToTHz,
cutoff_frequency=1e-4,
):
"""Init method.
dynamical_matrix : DynamicalMatrix or DynamicalMatrixNAC
Dynamical matrix class instance.
q_length : float
This is used such as D(q + q_length) - D(q - q_length) for
calculating finite difference of dynamical matrix.
Default is None, which gives 1e-5.
symmetry : Symmetry
This is used to symmetrize group velocity at each q-points.
Default is None, which means no symmetrization.
frequency_factor_to_THz : float
Unit conversion factor to convert to THz. Default is VaspToTHz.
cutoff_frequency : float
Group velocity is set zero if phonon frequency is below this value.
"""
self._dynmat = dynamical_matrix
primitive = dynamical_matrix.primitive
self._reciprocal_lattice_inv = primitive.cell
self._reciprocal_lattice = np.linalg.inv(self._reciprocal_lattice_inv)
self._q_length = q_length
if self._dynmat.is_nac() and self._dynmat.nac_method == "gonze":
if self._q_length is None:
self._q_length = self.Default_q_length
self._ddm: Optional[DerivativeOfDynamicalMatrix]
if self._q_length is None:
self._ddm = DerivativeOfDynamicalMatrix(dynamical_matrix)
else:
self._ddm = None
self._symmetry = symmetry
self._factor = frequency_factor_to_THz
self._cutoff_frequency = cutoff_frequency
self._directions = np.array(
[[1, 2, 3], [1, 0, 0], [0, 1, 0], [0, 0, 1]], dtype="double"
)
self._directions[0] /= np.linalg.norm(self._directions[0])
self._q_points = None
self._group_velocities = None
self._perturbation = None
def __init__(self,
dynamical_matrix,
q_length=None,
symmetry=None,
frequency_factor_to_THz=VaspToTHz,
cutoff_frequency=1e-4,
log_level=0):
"""
q_points is a list of sets of q-point and q-direction:
[[q-point, q-direction], [q-point, q-direction], ...]
q_length is used such as D(q + q_length) - D(q - q_length).
"""
self._dynmat = dynamical_matrix
primitive = dynamical_matrix.get_primitive()
self._reciprocal_lattice_inv = primitive.get_cell()
self._reciprocal_lattice = np.linalg.inv(self._reciprocal_lattice_inv)
self._q_length = q_length
if self._dynmat.is_nac() and self._dynmat.get_nac_method() == 'gonze':
if self._q_length is None:
self._q_length = 1e-5
if log_level:
print("Group velocity calculation:")
text = ("Analytical derivative of dynamical matrix is not "
"implemented for NAC by Gonze et al. Instead "
"numerical derivative of it is used with dq=1e-5 "
"for group velocity calculation.")
print(textwrap.fill(text,
initial_indent=" ",
subsequent_indent=" ",
width=70))
if self._q_length is None:
self._ddm = DerivativeOfDynamicalMatrix(dynamical_matrix)
else:
self._ddm = None
self._symmetry = symmetry
self._factor = frequency_factor_to_THz
self._cutoff_frequency = cutoff_frequency
self._directions = np.array([[1, 2, 3],
[1, 0, 0],
[0, 1, 0],
[0, 0, 1]], dtype='double')
self._directions[0] /= np.linalg.norm(self._directions[0])
self._q_points = None
self._group_velocity = None
self._perturbation = None
def __init__(self,
dynamical_matrix,
q,
is_little_cogroup=False,
nac_q_direction=None,
factor=VaspToTHz,
symprec=1e-5,
degeneracy_tolerance=1e-5,
log_level=0):
self._is_little_cogroup = is_little_cogroup
self._nac_q_direction = nac_q_direction
self._factor = factor
self._log_level = log_level
self._q = np.array(q)
self._degeneracy_tolerance = degeneracy_tolerance
self._symprec = symprec
self._primitive = dynamical_matrix.get_primitive()
self._dynamical_matrix = dynamical_matrix
self._ddm = DerivativeOfDynamicalMatrix(dynamical_matrix)
def __init__(
self,
dynamical_matrix: Union[DynamicalMatrix, DynamicalMatrixNAC],
q,
is_little_cogroup=False,
nac_q_direction=None,
factor=VaspToTHz,
symprec=1e-5,
degeneracy_tolerance=None,
log_level=0,
):
"""Init method."""
self._is_little_cogroup = is_little_cogroup
self._nac_q_direction = nac_q_direction
self._factor = factor
self._log_level = log_level
self._q = np.array(q)
if degeneracy_tolerance is None:
self._degeneracy_tolerance = 1e-5
else:
self._degeneracy_tolerance = degeneracy_tolerance
self._symprec = symprec
self._primitive = dynamical_matrix.primitive
self._dynamical_matrix = dynamical_matrix
self._ddm = DerivativeOfDynamicalMatrix(dynamical_matrix)
self._character_table = None
self._symmetry_dataset = Symmetry(
self._primitive, symprec=self._symprec
).dataset
if not is_primitive_cell(self._symmetry_dataset["rotations"]):
raise RuntimeError(
"Non-primitve cell is used. Your unit cell may be transformed to "
"a primitive cell by PRIMITIVE_AXIS tag."
)
