class SymmetryFinder:
accuracy = 1e-04 # recommended accuracy value = 0.0001
def __init__(self, accuracy=None):
self.error = None
self.accuracy=accuracy if accuracy else SymmetryFinder.accuracy
self.angle_tolerance=4
def get_spacegroup(self, tilde_obj):
try:
symmetry = spg.get_spacegroup(tilde_obj['structures'][-1], symprec=self.accuracy, angle_tolerance=self.angle_tolerance)
except Exception as ex:
self.error = 'Symmetry finder error: %s' % ex
else:
symmetry = symmetry.split()
self.i = symmetry[0]
try: self.n = int( symmetry[1].replace("(", "").replace(")", "") )
except (ValueError, IndexError): self.n = 0
if self.n == 0:
self.error = 'Symmetry finder error (probably, coinciding atoms)'
def refine_cell(self, tilde_obj):
'''
NB only used for perovskite_tilting app
'''
try: lattice, positions, numbers = spg.refine_cell(tilde_obj['structures'][-1], symprec=self.accuracy, angle_tolerance=self.angle_tolerance)
except Exception as ex:
self.error = 'Symmetry finder error: %s' % ex
else:
self.refinedcell = Atoms(numbers=numbers, cell=lattice, scaled_positions=positions, pbc=tilde_obj['structures'][-1].get_pbc())
self.refinedcell.periodicity = sum(self.refinedcell.get_pbc())
self.refinedcell.dims = abs(det(tilde_obj['structures'][-1].cell))
def crystalAtoms(self,
start_layer=0,
end_layer=1,
coordinates='orth_surface',
sub_layers=False,
minimal=True,
):
atoms = self.crystal().atoms()
if sub_layers:
in_equal_layers = self.inequivalentLayers()
repeats = int(np.ceil(end_layer/float(in_equal_layers)))
atoms = atoms.repeat((1, 1, repeats + 1))
atoms.positions -= self.crystal().unitCell()*(repeats)
start_layer += in_equal_layers -1
end_layer += in_equal_layers -1
atoms = orderAtoms(atoms, (2, 1, 0))
sl = slice(start_layer, end_layer)
groups = groupAtoms(atoms)[::-1][sl]
if len(groups) == 0:
atoms = Atoms([], cell=atoms.get_cell(), pbc=atoms.get_pbc())
else:
atoms, indices = groups[0]
for group, indices in groups[1:]:
atoms += group
else:
cell = atoms.unitCell()
atoms = atoms.repeat((1, 1, end_layer-start_layer))
atoms.positions += cell*start_layer
return atoms
class SymmetryFinder:
accuracy = 1e-04 # recommended accuracy value = 0.0001
def __init__(self, accuracy=None):
self.error = None
self.accuracy = accuracy if accuracy else SymmetryFinder.accuracy
self.angle_tolerance = 4
def get_spacegroup(self, tilde_obj):
try:
symmetry = spg.get_spacegroup(tilde_obj['structures'][-1],
symprec=self.accuracy,
angle_tolerance=self.angle_tolerance)
except Exception as ex:
self.error = 'Symmetry finder error: %s' % ex
else:
symmetry = symmetry.split()
self.i = symmetry[0]
try:
self.n = int(symmetry[1].replace("(", "").replace(")", ""))
except (ValueError, IndexError):
self.n = 0
if self.n == 0:
self.error = 'Symmetry finder error (probably, coinciding atoms)'
def refine_cell(self, tilde_obj):
'''
NB only used for perovskite_tilting app
'''
try:
lattice, positions, numbers = spg.refine_cell(
tilde_obj['structures'][-1],
symprec=self.accuracy,
angle_tolerance=self.angle_tolerance)
except Exception as ex:
self.error = 'Symmetry finder error: %s' % ex
else:
self.refinedcell = Atoms(numbers=numbers,
cell=lattice,
scaled_positions=positions,
pbc=tilde_obj['structures'][-1].get_pbc())
self.refinedcell.periodicity = sum(self.refinedcell.get_pbc())
self.refinedcell.dims = abs(det(tilde_obj['structures'][-1].cell))
def __init__(self, geometry=None, **kwargs) -> None:
if geometry == None:
atoms = Atoms(**kwargs)
elif type(geometry) == ase.atoms.Atoms:
atoms = geometry.copy()
elif Path(geometry).is_file():
if str(Path(geometry).parts[-1]) == "geometry.in.next_step":
atoms = ase.io.read(geometry, format="aims")
else:
try:
atoms = ase.io.read(geometry)
except Exception as excpt:
logger.error(str(excpt))
raise Exception(
"ASE was not able to recognize the file format, e.g., a non-standard cif-format."
)
elif Path(geometry).is_dir():
raise Exception(
"You specified a directory as input. The geometry must be a file."
)
else:
atoms = None
assert type(atoms) == ase.atoms.Atoms, "Atoms not read correctly."
# Get data from another Atoms object:
numbers = atoms.get_atomic_numbers()
positions = atoms.get_positions()
cell = atoms.get_cell()
celldisp = atoms.get_celldisp()
pbc = atoms.get_pbc()
constraint = [c.copy() for c in atoms.constraints]
masses = atoms.get_masses()
magmoms = None
charges = None
momenta = None
if atoms.has("initial_magmoms"):
magmoms = atoms.get_initial_magnetic_moments()
if atoms.has("initial_charges"):
charges = atoms.get_initial_charges()
if atoms.has("momenta"):
momenta = atoms.get_momenta()
self.arrays = {}
super().__init__(
numbers=numbers,
positions=positions,
cell=cell,
celldisp=celldisp,
pbc=pbc,
constraint=constraint,
masses=masses,
magmoms=magmoms,
charges=charges,
momenta=momenta,
)
self._is_1d = None
self._is_2d = None
self._is_3d = None
self._periodic_axes = None
self._check_lattice_vectors()
try:
self.sg = ase.spacegroup.get_spacegroup(self, symprec=1e-2)
except:
self.sg = ase.spacegroup.Spacegroup(1)
self.lattice = self.cell.get_bravais_lattice().crystal_family
def get_displacement(self, atoms: Atoms):
if not all(atoms.get_pbc()):
return space.free()
return space.periodic_general(self.box, fractional_coordinates=False)
