def get_BORN_lines(unitcell,
borns,
epsilon,
factor=None,
primitive_matrix=None,
supercell_matrix=None,
symprec=1e-5):
borns, epsilon, atom_indices = elaborate_borns_and_epsilon(
unitcell,
borns,
epsilon,
symmetrize_tensors=True,
primitive_matrix=primitive_matrix,
supercell_matrix=supercell_matrix,
symprec=symprec)
text = "# epsilon and Z* of atoms "
text += ' '.join(["%d" % n for n in atom_indices + 1])
lines = [
text,
]
lines.append(("%13.8f " * 9) % tuple(epsilon.flatten()))
for z in borns:
lines.append(("%13.8f " * 9) % tuple(z.flatten()))
return lines
def get_born_OUTCAR(poscar_filename="POSCAR",
outcar_filename=None,
primitive_matrix=None,
supercell_matrix=None,
is_symmetry=True,
symmetrize_tensors=False,
symprec=1e-5):
if outcar_filename is None:
filename = "OUTCAR"
else:
filename = outcar_filename
ucell = read_vasp(poscar_filename)
borns, epsilon = _read_born_and_epsilon_from_OUTCAR(filename)
if len(borns) == 0 or len(epsilon) == 0:
return None
else:
return elaborate_borns_and_epsilon(
ucell,
borns,
epsilon,
primitive_matrix=primitive_matrix,
supercell_matrix=supercell_matrix,
is_symmetry=is_symmetry,
symmetrize_tensors=symmetrize_tensors,
symprec=symprec)
def get_born_vasprunxml(filename="vasprun.xml",
primitive_matrix=None,
supercell_matrix=None,
is_symmetry=True,
symmetrize_tensors=False,
symprec=1e-5):
import io
borns = []
epsilon = []
with io.open(filename, "rb") as f:
vasprun = VasprunxmlExpat(f)
if vasprun.parse():
epsilon = vasprun.get_epsilon()
borns = vasprun.get_born()
lattice = vasprun.get_lattice()[-1]
points = vasprun.get_points()[-1]
symbols = vasprun.get_symbols()
ucell = Atoms(symbols=symbols,
scaled_positions=points,
cell=lattice)
else:
return None
return elaborate_borns_and_epsilon(ucell,
borns,
epsilon,
primitive_matrix=primitive_matrix,
supercell_matrix=supercell_matrix,
is_symmetry=is_symmetry,
symmetrize_tensors=symmetrize_tensors,
symprec=symprec)
def get_BORN_lines(unitcell,
borns,
epsilon,
factor=None,
primitive_matrix=None,
supercell_matrix=None,
symprec=1e-5,
symmetrize_tensors=False):
"""
Helper function imported from phonopy.file_IO that exposes the
option of not symmetrizing the tensor.
"""
from phonopy.structure.symmetry import elaborate_borns_and_epsilon
borns, epsilon, atom_indices = elaborate_borns_and_epsilon(
unitcell,
borns,
epsilon,
symmetrize_tensors=symmetrize_tensors,
primitive_matrix=primitive_matrix,
supercell_matrix=supercell_matrix,
symprec=symprec)
text = "# epsilon and Z* of atoms "
text += ' '.join(["%d" % n for n in atom_indices + 1])
lines = [
text,
]
lines.append(("%13.8f " * 9) % tuple(epsilon.flatten()))
for z in borns:
lines.append(("%13.8f " * 9) % tuple(z.flatten()))
return lines
def get_born_OUTCAR(poscar_filename="POSCAR",
outcar_filename=None,
primitive_matrix=None,
supercell_matrix=None,
is_symmetry=True,
symmetrize_tensors=False,
symprec=1e-5):
if outcar_filename is None:
filename = "OUTCAR"
else:
filename = outcar_filename
ucell = read_vasp(poscar_filename)
borns, epsilon = _read_born_and_epsilon_from_OUTCAR(filename)
if len(borns) == 0 or len(epsilon) == 0:
return None
else:
return elaborate_borns_and_epsilon(
ucell,
borns,
epsilon,
primitive_matrix=primitive_matrix,
supercell_matrix=supercell_matrix,
is_symmetry=is_symmetry,
symmetrize_tensors=symmetrize_tensors,
symprec=symprec)
def get_born_vasprunxml(filename="vasprun.xml",
primitive_matrix=None,
supercell_matrix=None,
is_symmetry=True,
symmetrize_tensors=False,
symprec=1e-5):
with io.open(filename, "rb") as f:
vasprun = VasprunxmlExpat(f)
try:
vasprun.parse()
except xml.parsers.expat.ExpatError:
raise xml.parsers.expat.ExpatError(
"Could not parse \"%s\". Please check the content." % filename)
except ValueError:
raise ValueError(
"Could not parse \"%s\". Please check the content." % filename)
return elaborate_borns_and_epsilon(vasprun.cell,
vasprun.born,
vasprun.epsilon,
primitive_matrix=primitive_matrix,
supercell_matrix=supercell_matrix,
is_symmetry=is_symmetry,
symmetrize_tensors=symmetrize_tensors,
symprec=symprec)
def get_born_vasprunxml(filename="vasprun.xml",
primitive_matrix=None,
supercell_matrix=None,
is_symmetry=True,
symmetrize_tensors=False,
symprec=1e-5):
import io
borns = []
epsilon = []
with io.open(filename, "rb") as f:
vasprun = VasprunxmlExpat(f)
if vasprun.parse():
epsilon = vasprun.get_epsilon()
borns = vasprun.get_born()
lattice = vasprun.get_lattice()[-1]
points = vasprun.get_points()[-1]
symbols = vasprun.get_symbols()
ucell = Atoms(symbols=symbols,
scaled_positions=points,
cell=lattice)
else:
return None
return elaborate_borns_and_epsilon(
ucell,
borns,
epsilon,
primitive_matrix=primitive_matrix,
supercell_matrix=supercell_matrix,
is_symmetry=is_symmetry,
symmetrize_tensors=symmetrize_tensors,
symprec=symprec)
def get_born_vasprunxml(filename="vasprun.xml",
primitive_matrix=None,
supercell_matrix=None,
is_symmetry=True,
symmetrize_tensors=False,
symprec=1e-5):
import io
with io.open(filename, "rb") as f:
vasprun = VasprunxmlExpat(f)
if vasprun.parse():
epsilon = vasprun.epsilon
borns = vasprun.born
ucell = vasprun.cell
else:
return None
return elaborate_borns_and_epsilon(
ucell,
borns,
epsilon,
primitive_matrix=primitive_matrix,
supercell_matrix=supercell_matrix,
is_symmetry=is_symmetry,
symmetrize_tensors=symmetrize_tensors,
symprec=symprec)
def get_born_vasprunxml(filename="vasprun.xml",
primitive_matrix=None,
supercell_matrix=None,
is_symmetry=True,
symmetrize_tensors=False,
symprec=1e-5):
import io
with io.open(filename, "rb") as f:
vasprun = VasprunxmlExpat(f)
if vasprun.parse():
epsilon = vasprun.epsilon
borns = vasprun.born
ucell = vasprun.cell
else:
return None
return elaborate_borns_and_epsilon(
ucell,
borns,
epsilon,
primitive_matrix=primitive_matrix,
supercell_matrix=supercell_matrix,
is_symmetry=is_symmetry,
symmetrize_tensors=symmetrize_tensors,
symprec=symprec)
def get_BORN_lines(unitcell, borns, epsilon,
factor=None,
primitive_matrix=None,
supercell_matrix=None,
symprec=1e-5):
from phonopy.structure.symmetry import elaborate_borns_and_epsilon
borns, epsilon, atom_indices = elaborate_borns_and_epsilon(
unitcell, borns, epsilon, symmetrize_tensors=True,
primitive_matrix=primitive_matrix,
supercell_matrix=supercell_matrix,
symprec=symprec)
text = "# epsilon and Z* of atoms "
text += ' '.join(["%d" % n for n in atom_indices + 1])
lines = [text, ]
lines.append(("%13.8f " * 9) % tuple(epsilon.flatten()))
for z in borns:
lines.append(("%13.8f " * 9) % tuple(z.flatten()))
return lines
def get_born_vasprunxml(
filename="vasprun.xml",
primitive_matrix=None,
supercell_matrix=None,
is_symmetry=True,
symmetrize_tensors=False,
symprec=1e-5,
):
"""Parse vasprun.xml to get NAC parameters.
In phonopy, primitive cell is created through the path of
unit cell -> supercell -> primitive cell. To trace this path exactly,
`primitive_matrix` and `supercell_matrix` can be given, but these are
optional.
Returns
-------
See elaborate_borns_and_epsilon.
"""
with open(filename, "rb") as f:
vasprun = VasprunxmlExpat(f)
try:
vasprun.parse()
except xml.parsers.expat.ExpatError:
raise xml.parsers.expat.ExpatError(
'Could not parse "%s". Please check the content.' % filename)
except ValueError:
raise ValueError(
'Could not parse "%s". Please check the content.' % filename)
return elaborate_borns_and_epsilon(
vasprun.cell,
vasprun.born,
vasprun.epsilon,
primitive_matrix=primitive_matrix,
supercell_matrix=supercell_matrix,
is_symmetry=is_symmetry,
symmetrize_tensors=symmetrize_tensors,
symprec=symprec,
)
def get_BORN_txt(nac_data, symprec=1.e-5, parameters=None, structure=None):
from phonopy.structure.atoms import PhonopyAtoms
try:
from phonopy.structure.symmetry import elaborate_borns_and_epsilon
except ImportError:
# Old version of phonopy
from phonopy.interface.vasp import _get_indep_borns as elaborate_borns_and_epsilon
born_charges = nac_data.get_array('born_charges')
epsilon = nac_data.get_array('epsilon')
structure_born = nac_data.get_structure()
ucell = PhonopyAtoms(
symbols=[site.kind_name for site in structure_born.sites],
positions=[site.position for site in structure_born.sites],
cell=structure_born.cell)
reduced_borns, epsilon, atom_indices = elaborate_borns_and_epsilon(
ucell,
born_charges,
epsilon,
primitive_matrix=None,
supercell_matrix=None,
is_symmetry=True,
symmetrize_tensors=False,
symprec=1.e-5)
born_txt = "# epsilon and Z* of atoms "
born_txt += ' '.join(["%d" % n for n in atom_indices + 1]) + '\n'
for num in epsilon.flatten():
born_txt += ('{0:4.8f} '.format(num))
born_txt += ('\n')
for atom in reduced_borns:
for num in atom.flatten():
born_txt += ('{0:4.8f} '.format(num))
born_txt += ('\n')
return born_txt
