def set_thermal_displacement_matrices(self,
t_step=10,
t_max=1000,
t_min=0,
cutoff_frequency=None):
"""
cutoff_frequency:
phonon modes that have frequencies below cutoff_frequency
are ignored.
direction:
Projection direction in reduced coordinates
"""
self._thermal_displacement_matrices = None
if self._mesh is None:
print("\'set_mesh\' has to finish correctly "
"before \'set_thermal_displacement_matrices\'.")
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
tdm = ThermalDisplacementMatrices(frequencies,
eigvecs,
self._primitive.get_masses(),
cutoff_frequency=cutoff_frequency)
tdm.set_temperature_range(t_min, t_max, t_step)
tdm.run()
self._thermal_displacement_matrices = tdm
return True
def set_thermal_displacement_matrices(self,
t_step=10,
t_max=1000,
t_min=0,
freq_min=None,
freq_max=None,
t_cif=None):
"""Prepare thermal displacement matrices
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_displacement_matrices = None
if self._mesh is not None:
eigvecs = self._mesh.get_eigenvectors()
if eigvecs is None:
print("Warning: Eigenvectors have to be calculated.")
return False
if np.prod(self._mesh.get_mesh_numbers()) != 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_displacement_matrices\'.")
return False
tdm = ThermalDisplacementMatrices(iter_phonons,
self._primitive.get_masses(),
freq_min=freq_min,
freq_max=freq_max,
lattice=self._primitive.get_cell().T)
if t_cif is None:
tdm.set_temperature_range(t_min, t_max, t_step)
else:
tdm.set_temperatures([t_cif])
tdm.run()
self._thermal_displacement_matrices = tdm
return True
def set_thermal_displacement_matrices(self,
t_step=10,
t_max=1000,
t_min=0,
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)
tdm = ThermalDisplacementMatrices(frequencies,
eigvecs,
self._primitive.get_masses(),
cutoff_eigenvalue=cutoff_eigenvalue)
tdm.set_temperature_range(t_min, t_max, t_step)
# tdm.run()
tdm.run_mesh()
self._thermal_displacement_matrices = tdm
def set_thermal_displacement_matrices(self,
t_step=10,
t_max=1000,
t_min=0,
cutoff_frequency=None,
t_cif=None):
"""
cutoff_frequency:
phonon modes that have frequencies below cutoff_frequency
are ignored.
direction:
Projection direction in reduced coordinates
"""
self._thermal_displacement_matrices = None
if self._mesh is not None:
eigvecs = self._mesh.get_eigenvectors()
if eigvecs is None:
print("Warning: Eigenvectors have to be calculated.")
return False
if np.prod(self._mesh.get_mesh_numbers()) != 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_displacement_matrices\'.")
return False
tdm = ThermalDisplacementMatrices(
iter_phonons,
self._primitive.get_masses(),
cutoff_frequency=cutoff_frequency,
lattice=self._primitive.get_cell().T)
if t_cif is None:
tdm.set_temperature_range(t_min, t_max, t_step)
else:
tdm.set_temperatures([t_cif])
tdm.run()
self._thermal_displacement_matrices = tdm
return True
def set_thermal_displacement_matrices(self,
t_step=10,
t_max=1000,
t_min=0,
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)
tdm = ThermalDisplacementMatrices(frequencies,
eigvecs,
self._primitive.get_masses(),
cutoff_eigenvalue=cutoff_eigenvalue)
tdm.set_temperature_range(t_min, t_max, t_step)
# tdm.run()
tdm.run_mesh()
self._thermal_displacement_matrices = tdm