def set_thermal_displacements(self,
t_step=10,
t_max=1000,
t_min=0,
temperatures=None,
direction=None,
cutoff_frequency=None):
"""
cutoff_frequency:
phonon modes that have frequencies below cutoff_frequency
are ignored.
direction:
Projection direction in reduced coordinates (
"""
self._thermal_displacements = None
if self._mesh is not None:
eigvecs = self._mesh.get_eigenvectors()
mesh_nums = self._mesh.get_mesh_numbers()
if eigvecs is None:
print("Warning: Eigenvectors have to be calculated.")
return False
if np.prod(mesh_nums) != len(eigvecs):
print("Warning: Sampling mesh must not be symmetrized.")
return False
iter_phonons = self._mesh
else:
if self._iter_mesh is not None:
iter_phonons = self._iter_mesh
else:
print("Warning: \'set_mesh\' has to finish correctly "
"before \'set_thermal_displacements\'.")
return False
if direction is not None:
projection_direction = np.dot(direction,
self._primitive.get_cell())
td = ThermalDisplacements(
iter_phonons,
self._primitive.get_masses(),
projection_direction=projection_direction,
cutoff_frequency=cutoff_frequency)
else:
td = ThermalDisplacements(iter_phonons,
self._primitive.get_masses(),
cutoff_frequency=cutoff_frequency)
if temperatures is None:
td.set_temperature_range(t_min, t_max, t_step)
else:
td.set_temperatures(temperatures)
td.run()
self._thermal_displacements = td
return True
def _get_thermal_displacements(self, proj_dir):
td = ThermalDisplacements(
self._mesh_phonon,
projection_direction=proj_dir,
freq_min=self._fmin,
freq_max=self._fmax,
)
td.temperatures = [self._T]
td.run()
return td.temperatures, td.thermal_displacements
def set_thermal_displacements( self,
t_step=10,
t_max=1000,
t_min=0,
projector=None,
cutoff_eigenvalue=None ):
"""
cutoff_eigenvalue:
phonon modes that have frequencies below cutoff_eigenvalue
are ignored.
e.g. 0.1 (THz)
"""
if self.__mesh==None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
if self.__mesh.get_eigenvectors() == None:
print "Eigenvectors have to be calculated."
sys.exit(1)
td = ThermalDisplacements( self.__mesh.get_eigenvalues(),
self.__mesh.get_eigenvectors(),
self.__mesh.get_weights(),
self.primitive.get_masses(),
factor=self.factor,
cutoff_eigenvalue=cutoff_eigenvalue )
td.set_temperature_range( t_min, t_max, t_step )
if not projector==None:
td.project_eigenvectors( projector, self.primitive.get_cell() )
td.set_thermal_displacements()
self.__thermal_displacements = td
def _get_thermal_displacements(self, Q):
td = ThermalDisplacements(self._mesh_phonon,
projection_direction=Q,
freq_min=self._fmin,
freq_max=self._fmax)
td.set_temperatures([self._T])
td.run()
return td.get_thermal_displacements()
def set_thermal_displacements(self,
t_step=10,
t_max=1000,
t_min=0,
temperatures=None,
direction=None,
cutoff_frequency=None):
"""
cutoff_frequency:
phonon modes that have frequencies below cutoff_frequency
are ignored.
direction:
Projection direction in reduced coordinates
"""
self._thermal_displacements = None
if self._mesh is None:
print("Warning: \'set_mesh\' has to finish correctly "
"before \'set_thermal_displacements\'.")
return False
eigvecs = self._mesh.get_eigenvectors()
frequencies = self._mesh.get_frequencies()
mesh_nums = self._mesh.get_mesh_numbers()
if self._mesh.get_eigenvectors() is None:
print("Warning: Eigenvectors have to be calculated.")
return False
if np.prod(mesh_nums) != len(eigvecs):
print("Warning: Sampling mesh must not be symmetrized.")
return False
td = ThermalDisplacements(frequencies,
eigvecs,
self._primitive.get_masses(),
cutoff_frequency=cutoff_frequency)
if temperatures is None:
td.set_temperature_range(t_min, t_max, t_step)
else:
td.set_temperatures(temperatures)
if direction is not None:
td.project_eigenvectors(direction, self._primitive.get_cell())
td.run()
self._thermal_displacements = td
return True
def _get_thermal_displacements(self, proj_dir):
td = ThermalDisplacements(self._mesh_phonon,
projection_direction=proj_dir,
freq_min=self._fmin,
freq_max=self._fmax)
td.set_temperatures([self._T])
td.run()
return td.get_thermal_displacements()
def set_thermal_displacements(self,
t_step=10,
t_max=1000,
t_min=0,
direction=None,
cutoff_eigenvalue=None):
"""
cutoff_eigenvalue:
phonon modes that have frequencies below cutoff_eigenvalue
are ignored.
e.g. 0.1 (THz^2)
direction:
Projection direction in reduced coordinates
"""
if self._mesh == None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
eigvecs = self._mesh.get_eigenvectors()
frequencies = self._mesh.get_frequencies()
mesh_nums = self._mesh.get_mesh_numbers()
if self._mesh.get_eigenvectors() is None:
print "Eigenvectors have to be calculated."
sys.exit(1)
if np.prod(mesh_nums) != len(eigvecs):
print "Sampling mesh must not be symmetrized."
sys.exit(1)
td = ThermalDisplacements(frequencies,
eigvecs,
self._primitive.get_masses(),
cutoff_eigenvalue=cutoff_eigenvalue)
td.set_temperature_range(t_min, t_max, t_step)
if direction is not None:
td.project_eigenvectors(direction, self._primitive.get_cell())
# td.run()
td.run_mesh()
self._thermal_displacements = td
def set_thermal_displacements(self,
t_step=10,
t_max=1000,
t_min=0,
direction=None,
cutoff_eigenvalue=None):
"""
cutoff_eigenvalue:
phonon modes that have frequencies below cutoff_eigenvalue
are ignored.
e.g. 0.1 (THz^2)
direction:
Projection direction in reduced coordinates
"""
if self._mesh==None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
eigvecs = self._mesh.get_eigenvectors()
frequencies = self._mesh.get_frequencies()
mesh_nums = self._mesh.get_mesh_numbers()
if self._mesh.get_eigenvectors() is None:
print "Eigenvectors have to be calculated."
sys.exit(1)
if np.prod(mesh_nums) != len(eigvecs):
print "Sampling mesh must not be symmetrized."
sys.exit(1)
td = ThermalDisplacements(frequencies,
eigvecs,
self._primitive.get_masses(),
cutoff_eigenvalue=cutoff_eigenvalue)
td.set_temperature_range(t_min, t_max, t_step)
if direction is not None:
td.project_eigenvectors(direction, self._primitive.get_cell())
# td.run()
td.run_mesh()
self._thermal_displacements = td
def set_thermal_displacements(self,
t_step=10,
t_max=1000,
t_min=0,
temperatures=None,
direction=None,
freq_min=None,
freq_max=None):
"""Prepare thermal displacements calculation
Args:
direction:
Projection direction in reduced coordinates.
freq_min: Phonons having frequency larger than this are included.
freq_max: Phonons having frequency smaller than this are included.
"""
self._thermal_displacements = None
if self._mesh is not None:
eigvecs = self._mesh.get_eigenvectors()
mesh_nums = self._mesh.get_mesh_numbers()
if eigvecs is None:
print("Warning: Eigenvectors have to be calculated.")
return False
if np.prod(mesh_nums) != len(eigvecs):
print("Warning: Sampling mesh must not be symmetrized.")
return False
iter_phonons = self._mesh
else:
if self._iter_mesh is not None:
iter_phonons = self._iter_mesh
else:
print("Warning: \'set_mesh\' has to finish correctly "
"before \'set_thermal_displacements\'.")
return False
if direction is not None:
projection_direction = np.dot(direction,
self._primitive.get_cell())
td = ThermalDisplacements(
iter_phonons,
self._primitive.get_masses(),
projection_direction=projection_direction,
freq_min=freq_min,
freq_max=freq_max)
else:
td = ThermalDisplacements(iter_phonons,
self._primitive.get_masses(),
freq_min=freq_min,
freq_max=freq_max)
if temperatures is None:
td.set_temperature_range(t_min, t_max, t_step)
else:
td.set_temperatures(temperatures)
td.run()
self._thermal_displacements = td
return True
