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 test_nacl(ph_nacl: Phonopy):
"""Test displacements of NaCl 2x2x2."""
dataset = deepcopy(ph_nacl.dataset)
disp_ref = [[0, 0.01, 0.0, 0.0], [32, 0.01, 0.0, 0.0]]
np.testing.assert_allclose(ph_nacl.displacements, disp_ref, atol=1e-8)
ph_nacl.generate_displacements()
np.testing.assert_allclose(ph_nacl.displacements, disp_ref, atol=1e-8)
ph_nacl.dataset = dataset
def test_si(ph_si: Phonopy):
"""Test displacements of Si."""
dataset = deepcopy(ph_si.dataset)
disp_ref = [[0, 0.0, 0.0070710678118655, 0.0070710678118655]]
np.testing.assert_allclose(ph_si.displacements, disp_ref, atol=1e-8)
ph_si.generate_displacements()
np.testing.assert_allclose(ph_si.displacements, disp_ref, atol=1e-8)
ph_si.dataset = dataset
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(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 test_tipn3(ph_tipn3: Phonopy):
"""Test displacements of Zr3N4."""
dataset = deepcopy(ph_tipn3.dataset)
disp_ref = [
[0, 0.01, 0.0, 0.0],
[0, 0.0, 0.01, 0.0],
[0, 0.0, 0.0, 0.01],
[0, 0.0, 0.0, -0.01],
[16, 0.01, 0.0, 0.0],
[16, 0.0, 0.01, 0.0],
[16, 0.0, 0.0, 0.01],
[16, 0.0, 0.0, -0.01],
[32, 0.01, 0.0, 0.0],
[32, 0.0, 0.01, 0.0],
[32, 0.0, -0.01, 0.0],
[32, 0.0, 0.0, 0.01],
[32, 0.0, 0.0, -0.01],
[40, 0.01, 0.0, 0.0],
[40, 0.0, 0.01, 0.0],
[40, 0.0, 0.0, 0.01],
[40, 0.0, 0.0, -0.01],
]
np.testing.assert_allclose(ph_tipn3.displacements, disp_ref, atol=1e-8)
ph_tipn3.generate_displacements()
disp_gen = [
[0, 0.006370194270018462, 0.006021020526083804, 0.00481330829956917],
[
0, -0.006370194270018462, -0.006021020526083804,
-0.00481330829956917
],
[16, 0.006370194270018462, 0.006021020526083804, 0.00481330829956917],
[
16, -0.006370194270018462, -0.006021020526083804,
-0.00481330829956917
],
[32, 0.007267439570389398, 0.0068690845162028965, 0.0],
[32, -0.007267439570389398, -0.0068690845162028965, 0.0],
[32, 0.0, 0.0, 0.01],
[32, 0.0, 0.0, -0.01],
[40, 0.006370194270018462, 0.006021020526083804, 0.00481330829956917],
[
40, -0.006370194270018462, -0.006021020526083804,
-0.00481330829956917
],
]
np.testing.assert_allclose(ph_tipn3.displacements, disp_gen, atol=1e-8)
ph_tipn3.dataset = dataset
def test_sno2(ph_sno2: Phonopy):
"""Test displacements of SnO2."""
dataset = deepcopy(ph_sno2.dataset)
disp_ref = [
[0, 0.01, 0.0, 0.0],
[0, -0.01, 0.0, 0.0],
[0, 0.0, 0.0, 0.01],
[48, 0.01, 0.0, 0.0],
[48, 0.0, 0.0, 0.01],
]
np.testing.assert_allclose(ph_sno2.displacements, disp_ref, atol=1e-8)
ph_sno2.generate_displacements()
disp_gen = [
[0, 0.007032660602415084, 0.0, 0.007109267532681459],
[0, -0.007032660602415084, 0.0, -0.007109267532681459],
[48, 0.007032660602415084, 0.0, 0.007109267532681459],
]
np.testing.assert_allclose(ph_sno2.displacements, disp_gen, atol=1e-8)
ph_sno2.dataset = dataset
def get_phonon_from_phonolammps(phonolammps) -> Phonopy:
"""
Get Phonopy class object from PhonoLammps.
Args:
phonolammps: Phonlammps class object.
"""
unitcell = phonolammps.get_unitcell()
force_constants = phonolammps.get_force_constants()
supercell_matrix = phonolammps.get_supercell_matrix()
primitive_matrix = phonolammps.get_primitve_matrix()
phonon = Phonopy(unitcell=unitcell,
primitive_matrix=primitive_matrix,
supercell_matrix=supercell_matrix)
dataset = phonolammps.get_force_constants(include_data_set=True)[1]
phonon.dataset = dataset
phonon.produce_force_constants()
return phonon
def test_zr3n4(ph_zr3n4: Phonopy):
"""Test displacements of Zr3N4."""
dataset = deepcopy(ph_zr3n4.dataset)
disp_ref = [
[0, 0.01, 0.0, 0.0],
[0, -0.01, 0.0, 0.0],
[16, 0.01, 0.0, 0.0],
[16, 0.0, 0.01, 0.0],
]
np.testing.assert_allclose(ph_zr3n4.displacements, disp_ref, atol=1e-8)
ph_zr3n4.generate_displacements()
disp_gen = [
[0, 0.01, 0.0, 0.0],
[0, -0.01, 0.0, 0.0],
[16, 0.007071067811865475, 0.007071067811865475, 0.0],
[16, -0.007071067811865475, -0.007071067811865475, 0.0],
]
np.testing.assert_allclose(ph_zr3n4.displacements, disp_gen, atol=1e-8)
ph_zr3n4.dataset = dataset
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
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 get_random_displacements(structure,
number_of_snapshots,
temperature,
phonon_setting_info,
dataset_for_fc,
random_seed=None):
"""Generate supercells with random displacemens
The random displacements are generated from phonons and harmonic
oscillator distribution function of canonical ensemble. The input
phonons are calculated from force constants calculated from
forces and displacemens of the supercell snapshots in previous
phonon calculation steps.
Returns
-------
dataset : Dict
Displacement datasets to run force calculations.
"""
# Calculate force constants by fitting using ALM
smat = phonon_setting_info['supercell_matrix']
ph = Phonopy(phonopy_atoms_from_structure(structure),
supercell_matrix=smat,
primitive_matrix='auto')
d = dataset_for_fc.get_array('displacements')
f = dataset_for_fc.get_array('forces')
ph.dataset = {'displacements': d, 'forces': f}
ph.produce_force_constants(fc_calculator='alm')
if random_seed is not None:
_random_seed = random_seed.value
else:
_random_seed = None
dataset = _generate_random_displacements(ph,
number_of_snapshots.value,
temperature.value,
random_seed=_random_seed)
return Dict(dict=dataset)
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)
def get_frequency(poscar_filename, force_sets):
"""Calculate phonons and return frequencies."""
unitcell = read_vasp(poscar_filename)
volume = unitcell.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]],
)
disps = np.zeros_like(force_sets)
disps[0] = [0.01, 0, 0]
phonon.dataset = {
"natom":
len(force_sets),
"first_atoms": [{
"number": 0,
"displacement": [0.01, 0, 0],
"forces": force_sets
}],
}
phonon.produce_force_constants()
return phonon.get_frequencies([0.5, 0.5, 0]), volume
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
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()
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 test_tio2(ph_tio2: Phonopy):
"""Test displacements of TiO2."""
dataset = deepcopy(ph_tio2.dataset)
disp_ref = [
[0, 0.01, 0.0, 0.0],
[0, 0.0, 0.01, 0.0],
[0, 0.0, 0.0, 0.01],
[0, 0.0, 0.0, -0.01],
[72, 0.01, 0.0, 0.0],
[72, 0.0, 0.0, 0.01],
]
np.testing.assert_allclose(ph_tio2.displacements, disp_ref, atol=1e-8)
ph_tio2.generate_displacements()
disp_gen = [
[0, 0.0060687317141537135, 0.0060687317141537135, 0.0051323474905008],
[
0, -0.0060687317141537135, -0.0060687317141537135,
-0.0051323474905008
],
[72, 0.007635558297727332, 0.0, 0.006457418174627326],
[72, -0.007635558297727332, 0.0, -0.006457418174627326],
]
np.testing.assert_allclose(ph_tio2.displacements, disp_gen, atol=1e-8)
ph_tio2.dataset = dataset
# [0.5, 0, 0.5],
# [0.5, 0.5, 0],
# [0.5, 0.5, 0.5],
# [0.5, 0, 0],
# [0, 0.5, 0],
# [0, 0, 0.5]])
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]])
symmetry = phonon.get_symmetry()
print("Space group: %s" % symmetry.get_international_table())
force_sets = parse_FORCE_SETS()
phonon.dataset = force_sets
phonon.produce_force_constants()
primitive = phonon.primitive
# Born effective charges and dielectric constants are read from BORN file.
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]]
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
def phonopy_to_abinit(unit_cell,
supercell_matrix,
out_ddb_path,
ngqpt=None,
qpt_list=None,
force_constants=None,
force_sets=None,
born=None,
primitive_matrix="auto",
symprec=1e-5,
tolsym=None,
supercell=None,
calculator=None,
manager=None,
workdir=None,
pseudos=None,
verbose=False):
"""
Converts the data from phonopy to an abinit DDB file. The data can be provided
in form of arrays or paths to the phonopy files that should be parsed.
The minimal input should contains the FORCE_CONSTANTS or FORCE_SETS.
If BORN is present the Born effective charges (BEC) and dielectric
tensor will also be added to the DDB.
The best agreement is obtained with supercell_matrix and ngqpt being
equivalent (i.e. supercell_matrix a diagonal matrix with ngqpt as diagonal
elements). Non diagonal supercell_matrix are allowed as well, but the information
encoded in the DDB will be the result of an interpolation done through phonopy.
Phonopy is used to convert the IFC to the dynamical matrix. However, in order to
determine the list of q-points in the irreducible Brillouin zone and to prepare the
base for the final DDB file, abinit will be called for a very short and inexpensive run.
Performs a check to verify if the two codes identify the same symmetries and it gives a
warning in case of failure. Mismatching symmetries may lead to incorrect conversions.
Args:
unit_cell: a |Structure| object that identifies the unit cell used for the phonopy
calculation.
supercell_matrix: a 3x3 array representing the supercell matrix used to generated the
forces with phonopy.
out_ddb_path: a full path to the file where the new DDB will be written
ngqpt: a list of 3 elements indicating the grid of q points that will be used in the DDB.
qpt_list: alternatively to ngqpt an explicit list of q-points can be provided here.
At least one among ngqpt and qpt_list should be defined.
force_constants: an array with shape (num atoms unit cell, num atoms supercell, 3, 3)
containing the force constants. Alternatively a string with the path to the
FORCE_CONSTANTS file. This or force_set should be defined. If both given this
has precedence.
force_sets: a dictionary obtained from the force sets generated with phonopy.
Alternatively a string with the path to the FORCE_SETS file. This or force_constants
should be defined.
born: a dictionary with "dielectric" and "born" keywords as obtained from the nac_params
in phonopy. Alternatively a string with the path to the BORN file. Notice that
the "factor" attribute is not taken into account, so the values should be in
default phonopy units.
primitive_matrix: a 3x3 array with the primitive matrix passed to Phonopy. "auto" will
use spglib to try to determine it automatically. If the DDB file should contain the
actual unit cell this should be the identity matrix.
symprec: distance tolerance in Cartesian coordinates to find crystal symmetry in phonopy.
It might be that the value should be tuned so that it leads to the the same symmetries
as in the abinit calculation.
tolsym: Gives the tolerance to identify symmetries in abinit. See abinit documentation for
more details.
supercell: if given it should represent the supercell used to get the force constants,
without any perturbation. It will be used to match it to the phonopy supercell
and sort the IFC in the correct order.
calculator: a string with the name of the calculator. Will be used to set the conversion
factor for the force constants coming from phonopy.
manager: |TaskManager| object. If None, the object is initialized from the configuration file
pseudos: List of filenames or list of |Pseudo| objects or |PseudoTable| object. It will be
used by abinit to generate the base DDB file. If None the abipy.data.hgh_pseudos.HGH_TABLE
table will be used.
verbose: verbosity level. Set it to a value > 0 to get more information
workdir: path to the directory where the abinit calculation will be executed.
Returns:
a DdbFile instance of the file written in out_ddb_path.
"""
if ngqpt is None and qpt_list is None:
raise ValueError(
"at least one among nqgpt and qpt_list should be defined")
if force_sets is None and force_constants is None:
raise ValueError(
"at least one of force_sets and force_constants should be provided"
)
phon_at = get_phonopy_structure(unit_cell)
if isinstance(force_constants, str):
force_constants = parse_FORCE_CONSTANTS(filename=force_constants)
elif force_constants is not None:
force_constants = np.array(force_constants)
force_sets = None
if isinstance(force_sets, str):
force_sets = parse_FORCE_SETS(filename=force_sets)
# no nac_params here, otherwise they will be used for the interpolation
phonon = Phonopy(phon_at,
supercell_matrix,
primitive_matrix=primitive_matrix,
nac_params=None,
symprec=symprec,
calculator=calculator)
primitive = get_pmg_structure(phonon.primitive)
if isinstance(born, str):
born = parse_BORN(phonon.primitive, filename=born)
if supercell is not None:
ph_supercell = get_pmg_structure(phonon.supercell)
if not np.allclose(supercell.lattice.matrix,
ph_supercell.lattice.matrix):
raise RuntimeError("The lattice of the supercells do not match")
sc_mapping = []
for i, site_orig in enumerate(supercell):
for j, site_ph in enumerate(ph_supercell):
d = supercell.lattice.get_distance_and_image(
site_orig.frac_coords, site_ph.frac_coords)[0]
if d < 1e-5:
sc_mapping.append(j)
break
else:
raise RuntimeError(
f"Could not find a match for site {i} with coords "
f"{site_orig.cart_coords} in the supercell.")
# cross check that the same atom was not matched twice
n_matches = len(set(sc_mapping))
if n_matches < len(supercell):
raise RuntimeError(
f"Found matches for {n_matches} different atoms in the supercell: {sc_mapping}"
)
force_constants = force_constants[:, sc_mapping]
if force_constants is not None:
phonon.set_force_constants(force_constants)
else:
phonon.dataset = force_sets
phonon.produce_force_constants()
if calculator:
units = get_default_physical_units(calculator)
fc_factor = get_force_constant_conversion_factor(
units["force_constants_unit"], None)
phonon.set_force_constants(phonon.force_constants * fc_factor)
if pseudos is None:
from abipy.data.hgh_pseudos import HGH_TABLE
pseudos = HGH_TABLE
inp = minimal_scf_input(primitive, pseudos)
# get the qpoints list if not defined
if qpt_list is None:
inp["ngkpt"] = ngqpt
qpt_list = inp.abiget_ibz(verbose=verbose)[0]
dm_list = get_dm(phonon, qpt_list, primitive)
if born is not None:
# for the conversion of the BEC the zion (i.e. the ionic charge of the pseudo)
# it is an additive factor and should be the same that goes in the header of the DDB,
# so take it from the pseudos used to generate it.
zion = inp.valence_electrons_per_atom
born_data = generate_born_deriv(born, zion, primitive)
else:
born_data = None
inp = minimal_scf_input(primitive, pseudos)
if tolsym is not None:
inp["tolsym"] = tolsym
task = inp.run_in_shell(workdir=workdir, manager=manager, verbose=verbose)
# use the output of abinit to check that the spacegroup identified by
# phonopy and abinit are the same.
with GsrFile(task.opath_from_ext("GSR.nc")) as gsr:
abi_spg = gsr.structure.abi_spacegroup.spgid
spglib_spg = phonon.symmetry.dataset["number"]
if abi_spg != spglib_spg:
warnings.warn(
"The space group number obtained based on the DDB symmetries differs "
f"from the one calculated with spglib: {abi_spg} versus "
f"{spglib_spg}. The convertion may be incorrect. Try changing symprec or tolsym."
)
tmp_ddb_path = task.opath_from_ext("DDB")
ddb = DdbFile(tmp_ddb_path)
# remove the blocks generated by the calculation and that are meaningless
ddb.remove_block(dord=0)
ddb.remove_block(dord=1)
add_data_ddb(ddb, dm_list, qpt_list, born_data)
ddb.write(out_ddb_path)
new_ddb = DdbFile(out_ddb_path)
return new_ddb
