def write_force_constants(self, fc_format='hdf5'):
if self.fc is not None:
if fc_format == 'hdf5':
p2s_map = self.primitive.get_primitive_to_supercell_map()
write_force_constants_to_hdf5(self.fc, p2s_map=p2s_map)
else:
write_FORCE_CONSTANTS(self.fc)
def create_FORCE_CONSTANTS(filename, options, log_level):
fc_and_atom_types = read_force_constant_vasprun_xml(filename)
if not fc_and_atom_types:
print('')
print("\'%s\' dones not contain necessary information." % filename)
return 1
force_constants, atom_types = fc_and_atom_types
if options.is_hdf5:
try:
import h5py
except ImportError:
print('')
print("You need to install python-h5py.")
return 1
write_force_constants_to_hdf5(force_constants)
if log_level > 0:
print("force_constants.hdf5 has been created from vasprun.xml.")
else:
write_FORCE_CONSTANTS(force_constants)
if log_level > 0:
print("FORCE_CONSTANTS has been created from vasprun.xml.")
if log_level > 0:
print("Atom types: %s" % (" ".join(atom_types)))
return 0
def create_FORCE_CONSTANTS(filename, options, log_level):
fc_and_atom_types = read_force_constant_vasprun_xml(filename)
if not fc_and_atom_types:
print
print "\'%s\' dones not contain necessary information." % filename
return 1
force_constants, atom_types = fc_and_atom_types
if options.is_hdf5:
try:
import h5py
except ImportError:
print
print "You need to install python-h5py."
return 1
write_force_constants_to_hdf5(force_constants)
if log_level > 0:
print "force_constants.hdf5 has been created from vasprun.xml."
else:
write_FORCE_CONSTANTS(force_constants)
if log_level > 0:
print "FORCE_CONSTANTS has been created from vasprun.xml."
if log_level > 0:
print "Atom types:", atom_types
return 0
def create_FORCE_CONSTANTS(filename, is_hdf5, log_level):
fc_and_atom_types = parse_force_constants(filename)
if not fc_and_atom_types:
print('')
print("\'%s\' dones not contain necessary information." % filename)
return 1
force_constants, atom_types = fc_and_atom_types
if is_hdf5:
try:
import h5py
except ImportError:
print('')
print("You need to install python-h5py.")
return 1
write_force_constants_to_hdf5(force_constants)
if log_level > 0:
print("force_constants.hdf5 has been created from vasprun.xml.")
else:
write_FORCE_CONSTANTS(force_constants)
if log_level > 0:
print("FORCE_CONSTANTS has been created from vasprun.xml.")
if log_level > 0:
print("Atom types: %s" % (" ".join(atom_types)))
return 0
def create_FORCE_CONSTANTS(filename, is_hdf5, log_level):
"""Parse vasprun.xml and write it into force constants file."""
force_constants, atom_types = parse_force_constants(filename)
if force_constants is None:
print("")
print("'%s' dones not contain necessary information." % filename)
return 1
if is_hdf5:
try:
import h5py # noqa F401
except ImportError:
print("")
print("You need to install python-h5py.")
return 1
write_force_constants_to_hdf5(force_constants)
if log_level > 0:
print("force_constants.hdf5 has been created from vasprun.xml.")
else:
write_FORCE_CONSTANTS(force_constants)
if log_level > 0:
print("FORCE_CONSTANTS has been created from vasprun.xml.")
if log_level > 0:
print("Atom types: %s" % (" ".join(atom_types)))
return 0
def write_force_constants(self, fc_format='hdf5'):
if self.fc is not None:
if fc_format == 'hdf5':
p2s_map = self.primitive.get_primitive_to_supercell_map()
write_force_constants_to_hdf5(self.fc, p2s_map=p2s_map)
else:
write_FORCE_CONSTANTS(self.fc)
def write_force_constants(self, fc_format="hdf5"):
"""Write force constatns to file in hdf5."""
if self.fc is not None:
if fc_format == "hdf5":
write_force_constants_to_hdf5(self.fc,
p2s_map=self.primitive.p2s_map)
else:
write_FORCE_CONSTANTS(self.fc)
def write_force_constants(self, filename='FORCE_CONSTANTS', hdf5=False):
"""
Write the force constants in a file in phonopy plain text format
:param filename: Force constants filename
"""
force_constants = self.get_force_constants()
if hdf5:
write_force_constants_to_hdf5(force_constants, filename=filename)
else:
write_FORCE_CONSTANTS(force_constants, filename=filename)
def load_phonopy(filename, structure, dim, symprec=0.01, primitive_matrix=None,
factor=VaspToTHz, symmetrise=True, born=None, write_fc=False):
"""Load phonopy output and return an ``phonopy.Phonopy`` object.
Args:
filename (str): Path to phonopy output. Can be any of ``FORCE_SETS``,
``FORCE_CONSTANTS``, or ``force_constants.hdf5``.
structure (:obj:`~pymatgen.core.structure.Structure`): The unitcell
structure.
dim (list): The supercell size, as a :obj:`list` of :obj:`float`.
symprec (:obj:`float`, optional): The tolerance for determining the
crystal symmetry.
primitive_matrix (:obj:`list` or :obj:`str`, optional): The
transformation matrix from the conventional to primitive cell. Only
required when the conventional cell was used as the starting
structure. Should be provided as a 3x3 :obj:`list` of :obj:`float`.
Alternatively the str 'auto' may be provided.
factor (:obj:`float`, optional): The conversion factor for phonon
frequency. Defaults to :obj:`phonopy.units.VaspToTHz`.
symmetrise (:obj:`bool`, optional): Symmetrise the force constants.
Defaults to ``True``.
born (:obj:`str`, optional): Path to file containing Born effective
charges. Should be in the same format as the file produced by the
``phonopy-vasp-born`` script provided by phonopy.
write_fc (:obj:`bool` or :obj:`str`, optional): Write the force
constants to disk. If ``True``, a ``FORCE_CONSTANTS`` file will be
written. Alternatively, if set to ``"hdf5"``, a
``force_constants.hdf5`` file will be written. Defaults to
``False`` (force constants not written).
"""
unitcell = get_phonopy_structure(structure)
num_atom = unitcell.get_number_of_atoms()
num_satom = determinant(dim) * num_atom
phonon = Phonopy(unitcell, dim, primitive_matrix=primitive_matrix,
factor=factor, symprec=symprec)
if 'FORCE_CONSTANTS' == filename or '.hdf5' in filename:
# if force constants exist, use these to avoid recalculating them
if '.hdf5' in filename:
fc = file_IO.read_force_constants_hdf5(filename)
elif 'FORCE_CONSTANTS' == filename:
fc = file_IO.parse_FORCE_CONSTANTS(filename=filename)
if fc.shape[0] != num_satom:
msg = ("\nNumber of atoms in supercell is not consistent with the "
"matrix shape of\nforce constants read from {}.\nPlease"
"carefully check --dim.")
logging.error(msg.format(filename))
sys.exit()
phonon.set_force_constants(fc)
elif 'FORCE_SETS' == filename:
# load the force sets from file and calculate force constants
fs = file_IO.parse_FORCE_SETS()
if fs['natom'] != num_satom:
msg = ("\nNumber of atoms in supercell is not consistent with the "
"the data in FORCE_SETS\nPlease carefully check --dim.")
logging.error(msg.format(filename))
sys.exit()
phonon.set_displacement_dataset(fs)
logging.info("Calculating force constants...")
phonon.produce_force_constants()
if born:
# load born parameters from a file
nac_params = file_IO.parse_BORN(phonon._primitive,
symprec=symprec,
filename=born)
# set the nac unit conversion factor manual, specific to VASP
nac_params['factor'] = Hartree * Bohr
phonon.set_nac_params(nac_params)
if symmetrise:
phonon.symmetrize_force_constants()
if write_fc == 'hdf5':
file_IO.write_force_constants_to_hdf5(phonon.get_force_constants())
logging.info("Force constants written to force_constants.hdf5.")
elif write_fc:
file_IO.write_FORCE_CONSTANTS(phonon.get_force_constants())
logging.info("Force constants written to FORCE_CONSTANTS.")
return phonon
file_IO.write_FORCE_CONSTANTS(phonon.get_force_constants(),
filename='FORCE_CONSTANTS_SPG')
if log_level > 0:
print(
"Symmetrized force constants are written into "
"FORCE_CONSTANTS_SPG.")
# Imporse translational invariance and index permulation symmetry to
# force constants
if settings.get_fc_symmetry_iteration() > 0:
phonon.symmetrize_force_constants(settings.get_fc_symmetry_iteration())
# Write FORCE_CONSTANTS
if settings.get_is_force_constants() == "write":
if settings.get_is_hdf5():
file_IO.write_force_constants_to_hdf5(phonon.get_force_constants())
if log_level > 0:
print("Force constants are written into force_constants.hdf5.")
else:
file_IO.write_FORCE_CONSTANTS(phonon.get_force_constants())
if log_level > 0:
print("Force constants are written into FORCE_CONSTANTS.")
# Show the rotational invariance condition (just show!)
if settings.get_is_rotational_invariance():
phonon.get_rotational_condition_of_fc()
# Atomic species without mass case
symbols_with_no_mass = []
if primitive.get_masses() is None:
for s in primitive.get_chemical_symbols():
def write_fc2_to_hdf5(force_constants, filename='fc2.hdf5', p2s_map=None):
write_force_constants_to_hdf5(force_constants,
filename=filename,
p2s_map=p2s_map)
