def lat_in_to_sqs(atat_lattice_in, rename=True):
"""
Convert a string-like ATAT-style lattice.in to an abstract SQS.
Parameters
----------
atat_lattice_in : str
String-like of a lattice.in in the ATAT format.
rename : bool
If True, SQS format element names will be renamed, e.g. `a_B` -> `Xab`. Default is True.
Returns
-------
SQS
Abstract SQS.
"""
# TODO: handle numeric species, e.g. 'g1'. Fixed
# Problems: parser has trouble with matching next line and we have to rename it so pymatgen
# doesn't think it's a charge.
# parse the data
parsed_data = _parse_atat_lattice(atat_lattice_in)
atat_coord_system = parsed_data[0]
atat_lattice = parsed_data[1]
atat_atoms = parsed_data[2]
# create the lattice
if len(atat_coord_system) == 3:
# we have a coordinate system matrix
coord_system = Lattice(atat_coord_system.asList()).matrix
else:
# we have length and angles
#coord_system = Lattice.from_lengths_and_angles(list(atat_coord_system[0]), list(atat_coord_system[1])).matrix
(lat_a, lat_b, lat_c) = list(atat_coord_system[0])
(lat_alpha, lat_beta, lat_gamma) = list(atat_coord_system[1])
coord_system = Lattice.from_parameters(lat_a, lat_b, lat_c, lat_alpha,
lat_beta, lat_gamma).matrix
direct_lattice = Lattice(atat_lattice.asList())
lattice = coord_system.dot(direct_lattice.matrix)
# create the list of atoms, converted to the right coordinate system
species_list = []
species_positions = []
subl_model = {
} # format {'subl_name': 'atoms_found_in_subl, e.g. "aaabbbb"'}
for position, atoms in atat_atoms:
# atoms can be a list of atoms, e.g. for not abstract SQS
if len(atoms) > 1:
raise NotImplementedError(
'Cannot parse atom list {} because the sublattice is unclear.\nParsed data: {}'
.format(atoms, atat_atoms))
atom = atoms[0]
if rename:
# change from `a_B` style to `Xab`
atom = atom.lower().split('_')
else:
raise NotImplementedError(
'Cannot rename because the atom name and sublattice name may be ambigous.'
)
# add the abstract atom to the sublattice model
subl = atom[0]
#Replace the digital by alphas, 1->a, 2->b, 3->c, ...
rep_items = re.findall(r"\d+", subl)
for rep_item in rep_items:
subl = subl.replace(rep_item, chr(96 + int(rep_item)))
subl_atom = atom[1]
subl_model[subl] = subl_model.get(subl, set()).union({subl_atom})
# add the species and position to the lists
species_list.append('X' + subl + subl_atom)
species_positions.append(list(position))
# create the structure
sublattice_model = [[e for e in sorted(list(set(subl_model[s])))]
for s in sorted(subl_model.keys())]
sublattice_names = [s for s in sorted(subl_model.keys())]
sqs = AbstractSQS(direct_lattice,
species_list,
species_positions,
coords_are_cartesian=True,
sublattice_model=sublattice_model,
sublattice_names=sublattice_names)
sqs.lattice = Lattice(lattice)
#sqs.modify_lattice(Lattice(lattice)) #This will be deprecated in v2020
return sqs
