def _get_supercell_phonon(self, ph_in):
"""Return Phonopy instance of supercell as the primitive."""
ph = Phonopy(ph_in.supercell,
supercell_matrix=[1, 1, 1],
primitive_matrix="P")
fc_shape = ph_in.force_constants.shape
if fc_shape[0] == fc_shape[1]: # assume full fc
ph.force_constants = ph_in.force_constants.copy()
else:
ph.force_constants = compact_fc_to_full_fc(ph_in,
ph_in.force_constants)
if ph_in.nac_params:
p2p = ph_in.primitive.p2p_map
s2p = ph_in.primitive.s2p_map
s2pp = [p2p[i] for i in s2p]
born_in = ph_in.nac_params["born"]
born = [born_in[i] for i in s2pp]
nac_params = {
"born": np.array(born, dtype="double", order="C"),
"factor": ph_in.nac_params["factor"],
"dielectric": ph_in.nac_params["dielectric"].copy(),
}
ph.nac_params = nac_params
return ph
def _get_supercell_phonon(self, ph_in):
"""Returns Phonopy instance of supercell as the primitive"""
ph = Phonopy(ph_in.supercell,
supercell_matrix=[1, 1, 1],
primitive_matrix='P')
fc_shape = ph_in.force_constants.shape
if fc_shape[0] == fc_shape[1]: # assume full fc
ph.force_constants = ph_in.force_constants.copy()
else:
ph.force_constants = compact_fc_to_full_fc(ph_in,
ph_in.force_constants)
if ph_in.nac_params:
p2p = ph_in.primitive.p2p_map
s2p = ph_in.primitive.s2p_map
s2pp = [p2p[i] for i in s2p]
born_in = ph_in.nac_params['born']
born = [born_in[i] for i in s2pp]
nac_params = {
'born': np.array(born, dtype='double', order='C'),
'factor': ph_in.nac_params['factor'],
'dielectric': ph_in.nac_params['dielectric'].copy()
}
ph.nac_params = nac_params
return ph
def get_phonon(pk, pk_nac):
n = load_node(pk)
unitcell = phonopy_atoms_from_structure(n.inputs.structure)
smat = n.outputs.phonon_setting_info['supercell_matrix']
ph = Phonopy(unitcell, supercell_matrix=smat, primitive_matrix='auto')
force_sets = n.outputs.force_sets.get_array('force_sets')
dataset = n.outputs.phonon_setting_info['displacement_dataset']
ph.dataset = dataset
ph.forces = force_sets
ph.nac_params = get_nac_params(pk_nac)
return ph
def _get_phonon(ph_in):
ph = Phonopy(ph_in.supercell, supercell_matrix=[1, 1, 1])
ph.force_constants = ph_in.force_constants
born_elems = {
s: ph_in.nac_params['born'][i]
for i, s in enumerate(ph_in.primitive.symbols)
}
born = [born_elems[s] for s in ph_in.supercell.symbols]
epsilon = ph_in.nac_params['dielectric']
factors = ph_in.nac_params['factor']
ph.nac_params = {'born': born, 'factor': factors, 'dielectric': epsilon}
return ph
def _phonons_allclose(self, ph, fc333):
ph333 = Phonopy(ph.unitcell,
supercell_matrix=[3, 3, 3],
primitive_matrix=ph.primitive_matrix)
ph333.force_constants = fc333
ph333.nac_params = ph.nac_params
comm_points = self._get_comm_points(ph)
ph.run_qpoints(comm_points)
ph333.run_qpoints(comm_points)
np.testing.assert_allclose(ph.get_qpoints_dict()['frequencies'],
ph333.get_qpoints_dict()['frequencies'],
atol=1e-5)
def _get_phonon(ph_in):
ph = Phonopy(ph_in.supercell, supercell_matrix=[1, 1, 1])
ph.force_constants = ph_in.force_constants
born_elems = {
s: ph_in.nac_params["born"][i]
for i, s in enumerate(ph_in.primitive.symbols)
}
born = [born_elems[s] for s in ph_in.supercell.symbols]
epsilon = ph_in.nac_params["dielectric"]
factors = ph_in.nac_params["factor"]
ph.nac_params = {"born": born, "factor": factors, "dielectric": epsilon}
return ph
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.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.nac_params = nac_params
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.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.nac_params = nac_params
return phonon
def get_phonopy_instance(structure, phonon_settings_dict, params):
from phonopy import Phonopy
phonon = Phonopy(phonopy_atoms_from_structure(structure),
supercell_matrix=phonon_settings_dict['supercell_matrix'],
primitive_matrix='auto',
symprec=phonon_settings_dict['symmetry_tolerance'])
if 'nac_params' in params:
from phonopy.interface.calculator import get_default_physical_units
units = get_default_physical_units('vasp')
factor = units['nac_factor']
nac_params = {
'born': params['nac_params'].get_array('born_charges'),
'dielectric': params['nac_params'].get_array('epsilon'),
'factor': factor
}
phonon.nac_params = nac_params
return phonon
def bunch_phonons(pks,
pk_nac,
max_items=None,
include_ratio=None,
linear_decay=True):
nodes = [load_node(pk) for pk in pks]
displacements, forces, energies = _extract_dataset_from_db(
[n.outputs.force_sets for n in nodes],
[n.outputs.phonon_setting_info for n in nodes])
d, f, e, idx = _create_dataset(displacements,
forces,
energies,
max_items,
include_ratio,
linear_decay=linear_decay)
unitcell = phonopy_atoms_from_structure(nodes[0].inputs.structure)
smat = nodes[0].outputs.phonon_setting_info['supercell_matrix']
ph = Phonopy(unitcell, supercell_matrix=smat, primitive_matrix='auto')
ph.dataset = {'displacements': d, 'forces': f}
ph.nac_params = get_nac_params(pk_nac)
return ph
def dump_phonopy(pk):
n = load_node(pk)
unitcell = phonopy_atoms_from_structure(n.inputs.structure)
smat = n.outputs.phonon_setting_info['supercell_matrix']
ph = Phonopy(unitcell, smat, primitive_matrix='auto')
force_sets = n.outputs.force_sets.get_array('force_sets')
dataset = n.outputs.phonon_setting_info['displacement_dataset']
ph.dataset = dataset
ph.forces = force_sets
if 'nac_params' in n.outputs:
borns = n.outputs.nac_params.get_array('born_charges')
epsilon = n.outputs.nac_params.get_array('epsilon')
nac_params = {
'born': borns,
'factor': 14.399652,
'dielectric': epsilon
}
ph.nac_params = nac_params
# phonopy-params.yaml is written out.
ph.save()
print("phonopy_params.yaml was made for PK=%d" % pk)
nac_params = parse_BORN(primitive, filename="BORN")
# Or it can be of course given by hand as follows:
# born = [[[1.08703, 0, 0],
# [0, 1.08703, 0],
# [0, 0, 1.08703]],
# [[-1.08672, 0, 0],
# [0, -1.08672, 0],
# [0, 0, -1.08672]]]
# epsilon = [[2.43533967, 0, 0],
# [0, 2.43533967, 0],
# [0, 0, 2.43533967]]
# factors = 14.400
# nac_params = {'born': born,
# 'factor': factors,
# 'dielectric': epsilon}
phonon.nac_params = nac_params
# BAND = 0.0 0.0 0.0 0.5 0.0 0.0 0.5 0.5 0.0 0.0 0.0 0.0 0.5 0.5 0.5
bands = []
append_band(bands, [0.0, 0.0, 0.0], [0.5, 0.0, 0.0])
append_band(bands, [0.5, 0.0, 0.0], [0.5, 0.5, 0.0])
append_band(bands, [0.5, 0.5, 0.0], [0.0, 0.0, 0.0])
append_band(bands, [0.0, 0.0, 0.0], [0.5, 0.5, 0.5])
phonon.set_band_structure(bands)
band_dict = phonon.get_band_structure_dict()
q_points = band_dict['qpoints']
distances = band_dict['distances']
frequencies = band_dict['frequencies']
eigvecs = band_dict['eigenvectors']
for q_path, d_path, freq_path in zip(q_points, distances, frequencies):
for q, d, freq in zip(q_path, d_path, freq_path):
def load_phonopy(
filename,
structure,
dim,
symprec=1e-5,
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" in 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" in 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.force_constants = fc
elif "FORCE_SETS" in filename:
# load the force sets from file and calculate force constants
fs = file_IO.parse_FORCE_SETS(filename=filename)
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.dataset = fs
logging.info("Calculating force constants...")
phonon.produce_force_constants()
if symmetrise:
phonon.symmetrize_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.nac_params = nac_params
if write_fc == "hdf5":
file_IO.write_force_constants_to_hdf5(phonon.force_constants)
logging.info("Force constants written to force_constants.hdf5.")
elif write_fc:
file_IO.write_FORCE_CONSTANTS(phonon.force_constants)
logging.info("Force constants written to FORCE_CONSTANTS.")
return phonon
