def _set_force_constants(phonon, force_constants_filename, force_sets_filename,
use_alm):
natom = phonon.supercell.get_number_of_atoms()
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(natom=natom,
filename=force_sets_filename)
if force_sets:
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants(
calculate_full_force_constants=False, use_alm=use_alm)
elif os.path.isfile("FORCE_SETS"):
force_sets = parse_FORCE_SETS(natom=natom)
if force_sets:
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants(
calculate_full_force_constants=False, use_alm=use_alm)
def _compute_force_constants(phonon,
dataset=None,
force_constants_filename=None,
force_sets_filename=None,
calculator=None,
fc_calculator=None):
natom = phonon.supercell.get_number_of_atoms()
_dataset = None
if dataset is not None:
_dataset = dataset
elif force_constants_filename is not None:
dot_split = force_constants_filename.split('.')
p2s_map = phonon.primitive.p2s_map
if len(dot_split) > 1 and dot_split[-1] == 'hdf5':
fc = load_helper.read_force_constants_from_hdf5(
filename=force_constants_filename,
p2s_map=p2s_map,
calculator=calculator)
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:
_dataset = parse_FORCE_SETS(natom=natom, filename=force_sets_filename)
elif os.path.isfile("FORCE_SETS"):
_dataset = parse_FORCE_SETS(natom=natom)
if _dataset is not None:
phonon.dataset = _dataset
_produce_force_constants(phonon, fc_calculator)
def set_dataset_and_force_constants(
phonon,
dataset,
fc, # From phonopy_yaml
force_constants_filename=None,
force_sets_filename=None,
fc_calculator=None,
fc_calculator_options=None,
produce_fc=True,
symmetrize_fc=True,
is_compact_fc=True,
log_level=0):
natom = len(phonon.supercell)
# dataset and fc are those obtained from phonopy_yaml unless None.
if dataset is not None:
phonon.dataset = dataset
if fc is not None:
phonon.force_constants = fc
_fc = None
_dataset = None
if force_constants_filename is not None:
_fc = _read_force_constants_file(phonon, force_constants_filename)
_force_constants_filename = force_constants_filename
elif force_sets_filename is not None:
_dataset = parse_FORCE_SETS(natom=natom, filename=force_sets_filename)
_force_sets_filename = force_sets_filename
elif phonon.forces is None and phonon.force_constants is None:
# unless provided these from phonopy_yaml.
if os.path.isfile("FORCE_CONSTANTS"):
_fc = _read_force_constants_file(phonon, "FORCE_CONSTANTS")
_force_constants_filename = "FORCE_CONSTANTS"
elif os.path.isfile("force_constants.hdf5"):
_fc = _read_force_constants_file(phonon, "force_constants.hdf5")
_force_constants_filename = "force_constants.hdf5"
elif os.path.isfile("FORCE_SETS"):
_dataset = parse_FORCE_SETS(natom=natom)
_force_sets_filename = "FORCE_SETS"
if _fc is not None:
phonon.force_constants = _fc
if log_level:
print("Force constants were read from \"%s\"." %
_force_constants_filename)
if phonon.force_constants is None:
# Overwrite dataset
if _dataset is not None:
phonon.dataset = _dataset
if log_level:
print("Force sets were read from \"%s\"." %
_force_sets_filename)
if produce_fc:
_produce_force_constants(phonon, fc_calculator,
fc_calculator_options, symmetrize_fc,
is_compact_fc, log_level)
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()
born_elems = {'Na': [[1.08703, 0, 0],
[0, 1.08703, 0],
[0, 0, 1.08703]],
'Cl': [[-1.08672, 0, 0],
[0, -1.08672, 0],
[0, 0, -1.08672]]}
born = [born_elems[s] for s in ['Na', 'Cl']]
epsilon = [[2.43533967, 0, 0],
[0, 2.43533967, 0],
[0, 0, 2.43533967]]
factors = 14.400
phonon.set_nac_params({'born': born,
'factor': factors,
'dielectric': epsilon})
return phonon
def setup(self):
phonon = Phonopy(self._bulk,
supercell_matrix=[[6, 0, 0], [0, 6, 0], [0, 0, 6]])
self._phonon = phonon
self._symmetry = self._phonon.get_symmetry()
self._force_sets = parse_FORCE_SETS()
phonon.get_displacement_dataset()
def _get_phonon(self, spgtype, dim, pmat):
cell = read_vasp("POSCAR_%s" % spgtype)
phonon = Phonopy(cell, np.diag(dim), primitive_matrix=pmat)
force_sets = parse_FORCE_SETS(filename="FORCE_SETS_%s" % spgtype)
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
return phonon
def get_data_from_dir(directory, i_volume):
data_sets = file_IO.parse_FORCE_SETS(
filename=directory + '/phonon-{0:02d}/FORCE_SETS'.format(i_volume))
yaml_file = open(
directory + '/phonon-{0:02d}/phonon.yaml'.format(i_volume), 'r')
data = yaml.load_all(yaml_file).next()
unit_cell = PhonopyAtoms(
symbols=[item['symbol'] for item in data['points']],
scaled_positions=[item['coordinates'] for item in data['points']],
cell=data['lattice'])
phonon = Phonopy(unit_cell, data['supercell_matrix'])
phonon.set_displacement_dataset(data_sets)
phonon.produce_force_constants()
force_constants = phonon.get_force_constants()
supercell = phonon.get_supercell()
volume = unit_cell.get_volume()
energy = data['electric_total_energy']
return supercell, volume, energy, force_constants, data['supercell_matrix']
def get_phonons(self):
"""
Calculate the phonon bandstructures along a path
"""
phonon = self.phonon
#get forces
force_sets = file_IO.parse_FORCE_SETS(filename='%s/FORCE_SETS' %
self.material_id)
phonon.set_displacement_dataset(force_sets)
#get force constants
phonon.produce_force_constants()
phonon.symmetrize_force_constants_by_space_group()
#get NAC
nac_params = file_IO.parse_BORN(phonon.get_primitive(),
filename="%s/BORN" % self.material_id)
nac_factor = Hartree * Bohr
if nac_params['factor'] == None:
nac_params['factor'] = nac_factor
phonon.set_nac_params(nac_params)
#get band-structure
phonon.set_band_structure(self.bands,
is_eigenvectors=True,
is_band_connection=True)
phonon.get_band_structure()
def _get_phonon(self, cell):
phonon = Phonopy(cell, np.diag([1, 1, 1]))
force_sets = parse_FORCE_SETS(
filename=os.path.join(data_dir, "FORCE_SETS"))
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
return phonon
def _get_phonon(self, cell):
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]])
force_sets = parse_FORCE_SETS(filename="FORCE_SETS_moment")
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
supercell = phonon.get_supercell()
born_elems = {'Na': [[1.08703, 0, 0],
[0, 1.08703, 0],
[0, 0, 1.08703]],
'Cl': [[-1.08672, 0, 0],
[0, -1.08672, 0],
[0, 0, -1.08672]]}
born = [born_elems[s] for s in ['Na', 'Cl']]
epsilon = [[2.43533967, 0, 0],
[0, 2.43533967, 0],
[0, 0, 2.43533967]]
factors = 14.400
phonon.set_nac_params({'born': born,
'factor': factors,
'dielectric': epsilon})
return phonon
def _get_phonon(self, cell):
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]])
force_sets = parse_FORCE_SETS(filename=os.path.join(data_dir,"FORCE_SETS_moment"))
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
supercell = phonon.get_supercell()
born_elems = {'Na': [[1.08703, 0, 0],
[0, 1.08703, 0],
[0, 0, 1.08703]],
'Cl': [[-1.08672, 0, 0],
[0, -1.08672, 0],
[0, 0, -1.08672]]}
born = [born_elems[s] for s in ['Na', 'Cl']]
epsilon = [[2.43533967, 0, 0],
[0, 2.43533967, 0],
[0, 0, 2.43533967]]
factors = 14.400
phonon.set_nac_params({'born': born,
'factor': factors,
'dielectric': epsilon})
return phonon
def read_phonopy(sposcar='SPOSCAR',
sc_mat=np.eye(3),
force_constants=None,
disp_yaml=None,
force_sets=None):
if force_constants is None and (disp_yaml is None or force_sets is None):
raise ValueError(
"Either FORCE_CONSTANTS or (disp.yaml&FORCE_SETS) file should be provided."
)
atoms = read(sposcar)
#vesta_view(atoms)
primitive_matrix = inv(sc_mat)
bulk = PhonopyAtoms(symbols=atoms.get_chemical_symbols(),
scaled_positions=atoms.get_scaled_positions(),
cell=atoms.get_cell())
phonon = Phonopy(
bulk,
supercell_matrix=np.eye(3),
primitive_matrix=primitive_matrix,
#factor=factor,
#symprec=symprec
)
if disp_yaml is not None:
disp = parse_disp_yaml(filename=disp_yaml)
phonon.set_displacement_dataset(disp)
if force_sets is not None:
fc = parse_FORCE_SETS(filename=force_sets)
phonon.set_forces(fc)
fc = parse_FORCE_CONSTANTS(force_constants)
phonon.set_force_constants(fc)
return phonon
def _get_phonon(self, cell):
phonon = Phonopy(cell,
np.diag([1, 1, 1]),
is_auto_displacements=False)
force_sets = parse_FORCE_SETS()
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
return phonon
def get_force_sets_from_file(file_name='FORCE_SETS', fs_supercell=None):
# Just a wrapper to phonopy function
force_sets = ForceSets(parse_FORCE_SETS(filename=file_name))
if fs_supercell is not None:
force_sets.set_supercell(fs_supercell)
return force_sets
def _get_phonon(spgtype, dim, pmat):
cell = read_vasp(os.path.join(data_dir, "POSCAR_%s" % spgtype))
phonon = Phonopy(cell, np.diag(dim), primitive_matrix=pmat)
force_sets = parse_FORCE_SETS(
filename=os.path.join(data_dir, "FORCE_SETS_%s" % spgtype))
phonon.dataset = force_sets
phonon.produce_force_constants()
return phonon
def __set_ForcesSets(self, filename, phonon):
"""
sets forces
"""
force_sets = parse_FORCE_SETS(filename=filename)
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
def _get_phonon(self, spgtype, dim, pmat):
cell = read_vasp(os.path.join(data_dir, "POSCAR_%s" % spgtype))
phonon = Phonopy(cell, np.diag(dim), primitive_matrix=pmat)
filename = os.path.join(data_dir, "FORCE_SETS_%s" % spgtype)
force_sets = parse_FORCE_SETS(filename=filename)
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
print(phonon.get_symmetry().get_pointgroup())
return phonon
def _get_phonon(self, spgtype, dim, pmat):
cell = read_vasp(os.path.join(data_dir,"POSCAR_%s" % spgtype))
phonon = Phonopy(cell,
np.diag(dim),
primitive_matrix=pmat)
force_sets = parse_FORCE_SETS(filename=os.path.join(data_dir,"FORCE_SETS_%s" % spgtype))
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
return phonon
def get_frequency(poscar_filename, force_sets_filename):
bulk = read_vasp(poscar_filename)
volume = bulk.get_volume()
phonon = Phonopy(bulk, [[2, 0, 0], [0, 2, 0], [0, 0, 2]],
is_auto_displacements=False)
force_sets = parse_FORCE_SETS(filename=force_sets_filename)
phonon.set_force_sets(force_sets)
phonon.set_post_process([[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]])
return phonon.get_frequencies([0.5, 0.5, 0]), volume
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_frequency(poscar_filename, force_sets_filename):
bulk = read_vasp(poscar_filename)
volume = bulk.get_volume()
phonon = Phonopy(bulk, [[2, 0, 0], [0, 2, 0], [0, 0, 2]],
is_auto_displacements=False)
force_sets = parse_FORCE_SETS(filename=force_sets_filename)
phonon.set_force_sets(force_sets)
phonon.set_post_process([[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]])
return phonon.get_frequencies([0.5, 0.5, 0]), volume
def get_frequency(poscar_filename, force_sets_filename):
unitcell = read_vasp(poscar_filename)
volume = unitcell.get_volume()
phonon = Phonopy(unitcell, [[2, 0, 0], [0, 2, 0], [0, 0, 2]],
primitive_matrix=[[0, 0.5, 0.5], [0.5, 0, 0.5],
[0.5, 0.5, 0]])
force_sets = parse_FORCE_SETS(filename=force_sets_filename)
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
return phonon.get_frequencies([0.5, 0.5, 0]), volume
def get_force_sets_from_file(file_name='FORCE_SETS', fs_supercell=None):
# Just a wrapper to phonopy function
force_sets = ForceSets(parse_FORCE_SETS(filename=file_name))
if fs_supercell is not None:
force_sets.set_supercell(fs_supercell)
else:
print('No force sets supercell defined, set to identity')
force_sets.set_supercell(np.identity(3))
return force_sets
def _get_dynmatrix(self):
"""Extracts the force constants from `FORCE_SETS` and constructs the
dynamical matrix for the calculation.
"""
with chdir(self.folder):
force_sets = file_IO.parse_FORCE_SETS()
self.phonopy.set_displacement_dataset(force_sets)
self.phonopy.produce_force_constants(
calculate_full_force_constants=True,
computation_algorithm="svd")
self.phonopy._set_dynamical_matrix()
def get_force_sets_from_file(file_name='FORCE_SETS', fs_supercell=None):
# Just a wrapper to phonopy function
force_sets = ForceSets(parse_FORCE_SETS(filename=file_name))
if fs_supercell is not None:
force_sets.set_supercell(fs_supercell)
else:
print('No force sets supercell defined, set to identity')
force_sets.set_supercell(np.identity(3))
return force_sets
def test_parse_vasprun_xml(self):
filename_vasprun = os.path.join(data_dir, "vasprun.xml.tar.bz2")
self._tar = tarfile.open(filename_vasprun)
filename = os.path.join(data_dir, "FORCE_SETS_NaCl")
dataset = parse_FORCE_SETS(filename=filename)
for i, member in enumerate(self._tar.getmembers()):
vr = Vasprun(self._tar.extractfile(member), use_expat=True)
# for force in vr.read_forces():
# print("% 15.8f % 15.8f % 15.8f" % tuple(force))
# print("")
ref = dataset['first_atoms'][i]['forces']
np.testing.assert_allclose(ref, vr.read_forces(), atol=1e-8)
def create_FORCES_FC2_from_FORCE_SETS_then_exit(log_level):
filename = 'FORCE_SETS'
file_exists(filename, log_level)
disp_dataset = parse_FORCE_SETS(filename=filename)
write_FORCES_FC2(disp_dataset)
write_disp_fc2_yaml(disp_dataset, None)
if log_level:
print("FORCES_FC2 and disp_fc2.yaml have been created from "
"FORCE_SETS.")
print_end()
sys.exit(0)
def test_parse_vasprun_xml(self):
filename_vasprun = os.path.join(data_dir, "vasprun.xml.tar.bz2")
self._tar = tarfile.open(filename_vasprun)
filename = os.path.join(data_dir, "FORCE_SETS_NaCl")
dataset = parse_FORCE_SETS(filename=filename)
for i, member in enumerate(self._tar.getmembers()):
vr = Vasprun(self._tar.extractfile(member), use_expat=True)
# for force in vr.read_forces():
# print("% 15.8f % 15.8f % 15.8f" % tuple(force))
# print("")
ref = dataset['first_atoms'][i]['forces']
np.testing.assert_allclose(ref, vr.read_forces(), atol=1e-8)
def read_from_phonopy_file(self, filename):
"""
Read the force constants from a phonopy FORCE_SETS file
:param filename: FORCE_SETS file name
"""
from phonopy.file_IO import parse_FORCE_SETS
data_sets = parse_FORCE_SETS(filename=filename)
self.set_data_sets(data_sets)
self.set_forces([displacement['forces'] for displacement in data_sets['first_atoms']])
def set_force_constants(
phonon,
dataset=None,
force_constants_filename=None,
force_sets_filename=None,
calculator=None,
use_alm=False):
natom = phonon.supercell.get_number_of_atoms()
_dataset = None
if dataset is not None:
_dataset = dataset
elif 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_from_hdf5(
filename=force_constants_filename,
p2s_map=p2s_map,
calculator=calculator)
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:
_dataset = parse_FORCE_SETS(natom=natom,
filename=force_sets_filename)
elif os.path.isfile("FORCE_SETS"):
_dataset = parse_FORCE_SETS(natom=natom)
if _dataset:
phonon.set_displacement_dataset(_dataset)
try:
phonon.produce_force_constants(
calculate_full_force_constants=False,
use_alm=use_alm)
except RuntimeError:
pass
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()
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_NaCl(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()
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(self, cell):
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()
filename_born = os.path.join(data_dir, "../BORN_NaCl")
nac_params = parse_BORN(phonon.get_primitive(), filename=filename_born)
nac_params['method'] = 'wang'
phonon.set_nac_params(nac_params)
return phonon
def test_properties(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()
dynmat = phonon.dynamical_matrix
dynmat.set_dynamical_matrix([0, 0, 0])
self.assertTrue(id(dynmat.primitive) == id(dynmat.get_primitive()))
self.assertTrue(id(dynmat.supercell) == id(dynmat.get_supercell()))
np.testing.assert_allclose(dynmat.dynamical_matrix,
dynmat.get_dynamical_matrix())
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()
supercell = phonon.get_supercell()
born_elems = {
"Na": [[1.08703, 0, 0], [0, 1.08703, 0], [0, 0, 1.08703]],
"Cl": [[-1.08672, 0, 0], [0, -1.08672, 0], [0, 0, -1.08672]],
}
born = [born_elems[s] for s in ["Na", "Cl"]]
epsilon = [[2.43533967, 0, 0], [0, 2.43533967, 0], [0, 0, 2.43533967]]
factors = 14.400
phonon.set_nac_params({"born": born, "factor": factors, "dielectric": epsilon})
return phonon
def get_phonons(self):
# calculate the phonon dispersion
folder = '%s/gruneisen-00' % material_id
ph_yaml = phonopyYaml('%s/phonon.yaml' % folder)
atoms = ph_yaml.get_atoms()
supercell_matrix = ph_yaml._data['supercell_matrix']
self.phonon = Phonopy(atoms, supercell_matrix)
phonon = self.phonon
force_sets = file_IO.parse_FORCE_SETS(filename='%s/FORCE_SETS' %
folder)
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
phonon.symmetrize_force_constants_by_space_group()
phonon.set_band_structure(self.bands,
is_eigenvectors=True,
is_band_connection=True)
phonon.get_band_structure()
def test_properties(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()
dynmat = phonon.dynamical_matrix
dynmat.set_dynamical_matrix([0, 0, 0])
self.assertTrue(id(dynmat.primitive)
== id(dynmat.get_primitive()))
self.assertTrue(id(dynmat.supercell)
== id(dynmat.get_supercell()))
np.testing.assert_allclose(dynmat.dynamical_matrix,
dynmat.get_dynamical_matrix())
def create_FORCES_FC2_from_FORCE_SETS_then_exit(log_level):
"""Convert FORCE_SETS to FORCES_FC2."""
filename = "FORCE_SETS"
file_exists(filename, log_level)
disp_dataset = parse_FORCE_SETS(filename=filename)
write_FORCES_FC2(disp_dataset)
if log_level:
print("")
print("FORCES_FC2 has been created from FORCE_SETS.")
print("The following yaml lines should replace respective part of")
print("phono3py_disp.yaml made with --dim-fc2=dim_of_FORCE_SETS.")
print("")
print("\n".join(displacements_yaml_lines_type1(disp_dataset)))
if log_level:
print_end()
sys.exit(0)
def _get_phonon(self, cell):
phonon = Phonopy(cell, np.diag([1, 1, 1]))
force_sets = parse_FORCE_SETS(
filename=os.path.join(data_dir, "FORCE_SETS"))
phonon.dataset = force_sets
phonon.produce_force_constants()
supercell = phonon.get_supercell()
born_elems = {'Na': [[1.08703, 0, 0],
[0, 1.08703, 0],
[0, 0, 1.08703]],
'Cl': [[-1.08672, 0, 0],
[0, -1.08672, 0],
[0, 0, -1.08672]]}
born = [born_elems[s]
for s in supercell.get_chemical_symbols()]
epsilon = [[2.43533967, 0, 0],
[0, 2.43533967, 0],
[0, 0, 2.43533967]]
factors = 14.400
phonon.set_nac_params({'born': born,
'factor': factors,
'dielectric': epsilon})
return phonon
#!/usr/bin/env python
import numpy as np
import phonopy.file_IO as file_IO
import dynaphopy.interface.iofile as reading
import dynaphopy.classes.controller as controller
################################## STRUCTURE FILES #######################################
# 1. Set the directory in where the FORCE_SETS and structure OUTCAR are placed
# FORCE_SETS : force set file obtained from PHONOPY calculation
# OUTCAR : Single Point calculation of the unit cell structure used in PHONOPY calculation
directory ='/home/abel/VASP/Si-phonon/4x4x4B/'
structure = reading.read_from_file_structure_poscar(directory+'POSCAR')
structure.set_force_set(file_IO.parse_FORCE_SETS(filename=directory+'FORCE_SETS'))
############################### PHONOPY CELL INFORMATION ####################################
# 2. Set primitive matrix, this matrix fulfills that:
# Primitive_cell = Unit_cell x Primitive_matrix
# This matrix is the same needed for PHONOPY calculation
structure.set_primitive_matrix([[0.5, 0.0, 0.0],
[0.0, 0.5, 0.0],
[0.0, 0.0, 0.5]])
# 3. Set super cell phonon, this matrix denotes the super cell used in PHONOPY for creating
# the finite displacements
def _get_phonon(self, cell):
phonon = Phonopy(cell, np.diag([1, 1, 1]))
force_sets = parse_FORCE_SETS(filename=os.path.join(data_dir, "FORCE_SETS"))
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
return phonon
from phonopy import Phonopy
from phonopy.interface.vasp import read_vasp
from phonopy.file_IO import parse_FORCE_SETS, parse_BORN
import numpy as np
cell = read_vasp("POSCAR")
# Initialize phonon. Supercell matrix has to have the shape of (3, 3)
phonon = Phonopy(cell, np.diag([2, 2, 1]))
symmetry = phonon.get_symmetry()
print "Space group:", symmetry.get_international_table()
# Read and convert forces and displacements
force_sets = parse_FORCE_SETS(cell.get_number_of_atoms() * 4)
# Sets of forces have to be set before phonon.set_post_process or
# at phonon.set_post_process(..., sets_of_forces=sets_of_forces, ...).
phonon.set_force_sets(force_sets)
# To activate non-analytical term correction.
phonon.set_post_process(primitive_matrix=[[2./3, -1./3, -1./3],
[1./3, 1./3, -2./3],
[1./3, 1./3, 1./3]])
# Parameters for non-analytical term correction can be set
# also after phonon.set_post_process
born = parse_BORN(phonon.get_primitive())
phonon.set_nac_params(born)
# Example to obtain dynamical matrix
dmat = phonon.get_dynamical_matrix_at_q([0,0,0])
curses.endwin()
if x2 == ord('3'):
calculation.set_number_of_mem_coefficients(
int(get_param(screen, "Insert number of coefficients")))
curses.endwin()
curses.endwin()
#Just for testing
if __name__ == 'test_gui.py':
import dynaphopy.classes.controller as controller
import dynaphopy.functions.iofunctions as reading
#Get data from input file
input_parameters = reading.read_parameters_from_input_file(sys.argv[1])
structure = reading.read_from_file_structure_outcar(input_parameters['structure_file_name'])
structure.set_force_set( file_IO.parse_FORCE_SETS(filename=input_parameters['force_constants_file_name']))
structure.set_primitive_matrix(input_parameters['primitive_matrix'])
structure.set_super_cell_phonon(input_parameters['super_cell_matrix'])
trajectory_file_name = sys.argv[2]
trajectory = reading.read_from_file_trajectory(trajectory_file_name,structure,last_steps=5000)
calculation = controller.Calculation(trajectory)
calculation.set_band_ranges(input_parameters['bands'])
def get_force_sets_from_file(file_name='FORCE_SETS'):
#Just a wrapper to phonopy function
force_sets = parse_FORCE_SETS(filename=file_name)
return force_sets
from phonopy import Phonopy
from phonopy.interface.vasp import read_vasp
from phonopy.file_IO import parse_FORCE_SETS
from phonopy.file_IO import parse_FORCE_CONSTANTS, write_FORCE_CONSTANTS
cell = read_vasp("POSCAR")
phonon = Phonopy(cell, [[2, 0, 0], [0, 2, 0], [0, 0, 2]])
force_sets = parse_FORCE_SETS()
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
write_FORCE_CONSTANTS(phonon.get_force_constants(), filename="FORCE_CONSTANTS")
force_constants = parse_FORCE_CONSTANTS()
phonon.set_force_constants(force_constants)
phonon.symmetrize_force_constants(iteration=1)
write_FORCE_CONSTANTS(phonon.get_force_constants(), filename="FORCE_CONSTANTS_NEW")
for i in range(51):
band.append(np.array(q_start) +
(np.array(q_end) - np.array(q_start)) / 50 * i)
bands.append(band)
phonons = {}
for vol in ("orig", "plus", "minus"):
unitcell = read_vasp("%s/POSCAR-unitcell" % vol)
phonon = Phonopy(unitcell,
[[2, 0, 0],
[0, 2, 0],
[0, 0, 2]],
primitive_matrix=[[0, 0.5, 0.5],
[0.5, 0, 0.5],
[0.5, 0.5, 0]])
force_sets = parse_FORCE_SETS(filename="%s/FORCE_SETS" % vol)
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
phonons[vol] = phonon
gruneisen = PhonopyGruneisen(phonons["orig"],
phonons["plus"],
phonons["minus"])
gruneisen.set_mesh([2, 2, 2])
q_points, _, frequencies, _, gammas = gruneisen.get_mesh()
for q, freq, g in zip(q_points, frequencies, gammas):
print(("%5.2f %5.2f %5.2f " + (" %7.3f" * len(freq)))
% ((q[0], q[1], q[2]) + tuple(freq)))
print(((" " * 18) + (" %7.3f" * len(g))) % tuple(g))
