def __init__(self, gcell, zoom=1):
self.lattice = gcell.lattice
self.positions = gcell.positions
self.numbers = gcell.numbers
self.atoms_name_list = list(
map(lambda x: Specie.to_name(x), list(self.numbers)))
self.zoom = zoom
def comment(self):
from collections import Counter, OrderedDict
atoms_name_list = list(
map(lambda x: Specie.to_name(x), list(self.numbers)))
d = Counter(atoms_name_list)
ordered_atoms = OrderedDict(
sorted(d.items(), key=lambda x: Specie(x[0]).Z))
if 'G' in ordered_atoms:
del ordered_atoms['G']
comment = ''.join(
['{}{}'.format(k, v) for k, v in ordered_atoms.items()])
return comment
def __init__(self, gcell):
self.lattice = np.around(gcell.lattice, decimals=6)
self.positions = np.around(gcell.positions, decimals=6)
self.numbers = gcell.numbers
atoms_name_list = list(
map(lambda x: Specie.to_name(x), list(self.numbers)))
d = Counter(atoms_name_list)
ordered_atoms = OrderedDict(
sorted(d.items(), key=lambda x: Specie(x[0]).Z))
# remove Ghostatoms
if 'G' in ordered_atoms:
del ordered_atoms['G']
self.comment = ''.join(
['{}{}'.format(k, v) for k, v in ordered_atoms.items()])