def get_phonon(structure,
NAC=False,
setup_forces=True,
super_cell_phonon=np.identity(3),
primitive_axis=np.identity(3)):
phonon = Phonopy(structure, super_cell_phonon,
primitive_matrix=primitive_axis,
symprec=1e-5)
# Non Analytical Corrections (NAC) from Phonopy [Frequencies only, eigenvectors no affected by this option]
if setup_forces:
if structure.get_force_constants() is not None:
phonon.set_force_constants(structure.get_force_constants().get_array())
elif structure.get_force_sets() is not None:
phonon.set_displacement_dataset(structure.get_force_sets().get_dict())
phonon.produce_force_constants(computation_algorithm="svd")
structure.set_force_constants(ForceConstants(phonon.get_force_constants(),
supercell=structure.get_force_sets().get_supercell()))
else:
print('No force sets/constants available!')
exit()
if NAC:
print("Using non-analytical corrections")
primitive = phonon.get_primitive()
nac_params = parse_BORN(primitive, is_symmetry=True)
phonon.set_nac_params(nac_params=nac_params)
return phonon
def get_phonon(structure,
NAC=False,
setup_forces=True,
super_cell_phonon=np.identity(3),
primitive_matrix=np.identity(3),
symmetrize=True):
"""
Return a phonopy phonon object (instance of the class Phonon)
:param structure: unit cell matrix (lattice vectors in rows)
:param NAC: (Bool) activate/deactivate Non-analytic corrections
:param setup_forces: (Bool) decide if pre-calculate harmonic forces in phonon object
:param super_cell_phonon: 3x3 array containing the supercell to be used to calculate the force constants
:param primitive_matrix: 3x3 array containing the primitive axis (in rows) which define the primitive cell
:param symmetrize: decide if symmetrize the force constants
:return: phonopy phonon object
"""
phonon = Phonopy(structure,
super_cell_phonon,
primitive_matrix=primitive_matrix,
symprec=1e-5,
is_symmetry=symmetrize)
# Non Analytical Corrections (NAC) from Phonopy [Frequencies only, eigenvectors no affected by this option]
if setup_forces:
if structure.get_force_constants() is not None:
phonon.set_force_constants(
structure.get_force_constants().get_array())
elif structure.get_force_sets() is not None:
phonon.set_displacement_dataset(
structure.get_force_sets().get_dict())
phonon.produce_force_constants(computation_algorithm="svd")
structure.set_force_constants(
ForceConstants(
phonon.get_force_constants(),
supercell=structure.get_force_sets().get_supercell()))
else:
print('No force sets/constants available!')
exit()
if NAC:
print("Using non-analytical corrections")
primitive = phonon.get_primitive()
try:
nac_params = parse_BORN(primitive, is_symmetry=True)
phonon.set_nac_params(nac_params=nac_params)
except OSError:
print('Required BORN file not found!')
exit()
return phonon
def get_phonon(structure,
NAC=False,
setup_forces=True,
custom_supercell=None,
symprec=1e-5):
if custom_supercell is None:
super_cell_phonon = structure.get_supercell_phonon()
else:
super_cell_phonon = custom_supercell
# Preparing the bulk type object
bulk = PhonopyAtoms(symbols=structure.get_atomic_elements(),
scaled_positions=structure.get_scaled_positions(),
cell=structure.get_cell())
phonon = Phonopy(bulk,
super_cell_phonon,
primitive_matrix=structure.get_primitive_matrix(),
symprec=symprec)
# Non Analytical Corrections (NAC) from Phonopy [Frequencies only, eigenvectors no affected by this option]
if setup_forces:
if structure.get_force_constants() is not None:
phonon.set_force_constants(
structure.get_force_constants().get_array())
elif structure.get_force_sets() is not None:
phonon.set_displacement_dataset(
structure.get_force_sets().get_dict())
phonon.produce_force_constants()
structure.set_force_constants(
ForceConstants(
phonon.get_force_constants(),
supercell=structure.get_force_sets().get_supercell()))
else:
print('No force sets/constants available!')
exit()
if NAC:
print("Warning: Using Non Analytical Corrections")
primitive = phonon.get_primitive()
nac_params = parse_BORN(primitive, is_symmetry=True)
phonon.set_nac_params(nac_params=nac_params)
return phonon
def get_phonon(structure, NAC=False, setup_forces=True, custom_supercell=None):
if custom_supercell is None:
super_cell_phonon = structure.get_supercell_phonon()
else:
super_cell_phonon = custom_supercell
# Preparing the bulk type object
bulk = PhonopyAtoms(symbols=structure.get_atomic_elements(),
scaled_positions=structure.get_scaled_positions(),
cell=structure.get_cell())
phonon = Phonopy(bulk, super_cell_phonon,
primitive_matrix=structure.get_primitive_matrix(),
symprec=1e-5)
# Non Analytical Corrections (NAC) from Phonopy [Frequencies only, eigenvectors no affected by this option]
if setup_forces:
if structure.get_force_constants() is not None:
phonon.set_force_constants(structure.get_force_constants().get_array())
elif structure.get_force_sets() is not None:
phonon.set_displacement_dataset(structure.get_force_sets().get_dict())
phonon.produce_force_constants()
structure.set_force_constants(ForceConstants(phonon.get_force_constants(),
supercell=structure.get_force_sets().get_supercell()))
else:
print('No force sets/constants available!')
exit()
if NAC:
print("Warning: Using Non Analytical Corrections")
primitive = phonon.get_primitive()
nac_params = parse_BORN(primitive, is_symmetry=True)
phonon.set_nac_params(nac_params=nac_params)
return phonon