def find_unique_ions(self):
""" Generate a unique set of the ions, fix duplicates """
ions = dict()
to_remove = set()
for ion1 in self.ions:
if ion1 not in to_remove:
for ion2 in self.ions:
if ion1 != ion2:
dr, _ = self.ions.least_mirror(ion1.position,
ion2.position)
if dr < 0.01:
print ion1, ion2
to_remove.add(ion2)
return AtomsView([atom for atom in self.ions if atom not in to_remove],
self.ions.lattice)
def parse_ions(self):
self.ions_type = None
if 'POSITIONS_ABS' in self.blocks:
self.ions_type = 'POSITIONS_ABS'
self.basis = numpy.array([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0],
[0.0, 0.0, 1.0]])
elif 'POSITIONS_FRAC' in self.blocks:
self.ions_type = 'POSITIONS_FRAC'
self.basis = self.lattice
if self.ions_type is None:
return
convert = False # Dont convert frac to cart
if self.ions_type == 'POSITIONS_FRAC':
convert = True
atoms = []
index_counter = Counter()
self.ions_units = None
for line in self.blocks[self.ions_type]: # Include positions frac
lsplit = line.split()
if len(lsplit) == 4:
s, x, y, z = lsplit
position = (float(x), float(y), float(z))
sl = s.split(":")
species = sl[0]
# Atoms are 1-indexed to match castep.
index_counter[species] += 1
index = index_counter[species]
if len(sl) > 1:
label = sl[1]
else:
label = species
if convert:
position = numpy.dot(self.basis.T, position)
atoms.append(Atom(species, index, position, label))
elif len(lsplit) == 1:
self.ions_units = lsplit[0]
if self.ions_units is None:
self.ions_units = 'ang'
# If we've converted, change the basis
if convert:
self.ions_type = 'POSITIONS_ABS'
self.basis = numpy.array([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0],
[0.0, 0.0, 1.0]])
self.ions = AtomsView(atoms, self.lattice)
