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 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 read_force_constants_from_hdf5(filename='force_constants.hdf5',
p2s_map=None,
calculator=None):
fc = read_force_constants_hdf5(filename=filename, p2s_map=p2s_map)
fc_unit = read_physical_unit_in_force_constants_hdf5(filename=filename)
if fc_unit is None:
return fc
else:
factor = get_force_constant_conversion_factor(fc_unit, calculator)
return fc * factor
def read_force_constants_from_hdf5(filename='force_constants.hdf5',
p2s_map=None,
calculator=None):
"""Convert force constants physical unit
Each calculator interface has own default force constants physical unit.
This method reads the physical unit of force constants if it exists and
if the read physical unit is different from the default one, the force
constants values are converted to have the default physical units.
Note
----
This method is also used from phonopy script.
"""
fc = read_force_constants_hdf5(filename=filename, p2s_map=p2s_map)
fc_unit = read_physical_unit_in_force_constants_hdf5(filename=filename)
if fc_unit is None:
return fc
else:
factor = get_force_constant_conversion_factor(fc_unit, calculator)
return fc * factor
def read_force_constants_from_hdf5(filename="force_constants.hdf5",
p2s_map=None,
calculator=None):
"""Convert force constants physical unit.
Each calculator interface has own default force constants physical unit.
This method reads 'physical_unit' in force constants hdf5 file and
if this is different from the one for 'calculator', the force constants
are converted to have the physical unit of the calculator.
Note
----
This method is also used from phonopy script.
"""
fc, fc_unit = read_force_constants_hdf5(filename=filename,
p2s_map=p2s_map,
return_physical_unit=True)
if fc_unit is None:
return fc
else:
factor = get_force_constant_conversion_factor(fc_unit, calculator)
return fc * factor
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
def read_fc2_from_hdf5(filename='fc2.hdf5', p2s_map=None):
return read_force_constants_hdf5(filename=filename, p2s_map=p2s_map)
