def get_phonon(structure, NAC=False):
force_atoms_file = structure.get_force_set()['natom']
force_atoms_input = np.product(np.diagonal(structure.get_super_cell_phonon()))*structure.get_number_of_atoms()
if force_atoms_file != force_atoms_input:
print("Error: FORCE_SETS file does not match with SUPERCELL MATRIX")
exit()
#Preparing the bulk type object
bulk = PhonopyAtoms(symbols=structure.get_atomic_types(),
scaled_positions=structure.get_scaled_positions(),
cell=structure.get_cell().T)
phonon = Phonopy(bulk, structure.get_super_cell_phonon(),
primitive_matrix=structure.get_primitive_matrix(),
is_auto_displacements=False)
#Non Analytical Corrections (NAC) from Phonopy [Frequencies only, eigenvectors no affected by this option]
if NAC:
print("Phonopy warning: Using Non Analytical Corrections")
get_is_symmetry = True #from phonopy: settings.get_is_symmetry()
primitive = phonon.get_primitive()
nac_params = parse_BORN(primitive, get_is_symmetry)
phonon.set_nac_params(nac_params=nac_params)
phonon.set_displacement_dataset(structure.get_force_set())
phonon.produce_force_constants(computation_algorithm="svd")
return phonon
def get_phonon(structure, NAC=False, setup_forces=True, custom_supercell=None):
super_cell_phonon = structure.get_supercell_phonon()
if not(isinstance(custom_supercell, type(None))):
super_cell_phonon = custom_supercell
#Preparing the bulk type object
bulk = PhonopyAtoms(symbols=structure.get_atomic_types(),
scaled_positions=structure.get_scaled_positions(),
cell=structure.get_cell().T)
phonon = Phonopy(bulk, super_cell_phonon,
primitive_matrix=structure.get_primitive_matrix())
# Non Analytical Corrections (NAC) from Phonopy [Frequencies only, eigenvectors no affected by this option]
if NAC:
print("Phonopy warning: Using Non Analytical Corrections")
get_is_symmetry = True #from phonopy: settings.get_is_symmetry()
primitive = phonon.get_primitive()
nac_params = parse_BORN(primitive, get_is_symmetry)
phonon.set_nac_params(nac_params=nac_params)
if setup_forces:
if not structure.forces_available():
# if not np.array(structure.get_force_constants()).any() and not np.array(structure.get_force_sets()).any():
print('No force sets/constants available!')
exit()
if np.array(structure.get_force_constants()).any():
phonon.set_force_constants(structure.get_force_constants())
else:
phonon.set_displacement_dataset(structure.get_force_sets())
phonon.produce_force_constants(computation_algorithm="svd")
return phonon
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 load(supercell_matrix,
primitive_matrix=None,
nac_params=None,
unitcell=None,
calculator="vasp",
unitcell_filename=None,
born_filename=None,
force_sets_filename=None,
force_constants_filename=None,
factor=VaspToTHz,
frequency_scale_factor=None,
symprec=1e-5,
is_symmetry=True,
log_level=0):
if unitcell is None:
_unitcell, _ = read_crystal_structure(filename=unitcell_filename,
interface_mode=calculator)
else:
_unitcell = unitcell
# units keywords: factor, nac_factor, distance_to_A
units = get_default_physical_units(calculator)
phonon = Phonopy(_unitcell,
supercell_matrix,
primitive_matrix=primitive_matrix,
factor=units['factor'])
if nac_params is None:
if born_filename is None:
_nac_params = None
else:
_nac_params = parse_BORN(phonon.primitive, filename=born_filename)
else:
_nac_params = nac_params
if _nac_params is not None:
if _nac_params['factor'] is None:
_nac_params['factor'] = units['nac_factor']
phonon.set_nac_params(_nac_params)
if force_constants_filename is not None:
dot_split = force_constants_filename.split('.')
p2s_map = phonon.primitive.get_primitive_to_supercell_map()
if len(dot_split) > 1 and dot_split[-1] == 'hdf5':
fc = read_force_constants_hdf5(filename=force_constants_filename,
p2s_map=p2s_map)
else:
fc = parse_FORCE_CONSTANTS(filename=force_constants_filename,
p2s_map=p2s_map)
phonon.set_force_constants(fc)
elif force_sets_filename is not None:
force_sets = parse_FORCE_SETS(filename=force_sets_filename)
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
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(self):
cell = read_vasp(os.path.join(data_dir, "..", "POSCAR_NaCl"))
phonon = Phonopy(cell,
np.diag([2, 2, 2]),
primitive_matrix=[[0, 0.5, 0.5], [0.5, 0, 0.5],
[0.5, 0.5, 0]])
filename = os.path.join(data_dir, "..", "FORCE_SETS_NaCl")
force_sets = parse_FORCE_SETS(filename=filename)
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
phonon.symmetrize_force_constants()
filename_born = os.path.join(data_dir, "..", "BORN_NaCl")
nac_params = parse_BORN(phonon.get_primitive(), filename=filename_born)
phonon.set_nac_params(nac_params)
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