def do(self):
total, formula = chemical_formula(iter_atoms(context.application.cache.nodes), True)
if total > 0:
answer = "Chemical formula: %s" % formula
answer += "\nNumber of atoms: %i" % total
else:
answer = "No atoms found."
ok_information(answer, markup=True)
def do(self):
total, formula = chemical_formula(
iter_atoms(context.application.cache.nodes), True)
if total > 0:
answer = "Chemical formula: %s" % formula
answer += "\nNumber of atoms: %i" % total
else:
answer = "No atoms found."
ok_information(answer, markup=True)
def create_pattern():
"Read the atom positions and transform them to the flat coordinates"
active, inactive = universe.cell.active_inactive
a = universe.cell.matrix[:, active[0]]
b = universe.cell.matrix[:, active[1]]
c = numpy.cross(a, b)
tmp_cell = UnitCell(numpy.array([a, b, c]).transpose())
rotation = tmp_cell.alignment_a
return [(atom.number, rotation * atom.get_absolute_frame().t)
for atom in iter_atoms([universe])]
def create_pattern():
"Read the atom positions and transform them to the flat coordinates"
active, inactive = universe.cell.active_inactive
a = universe.cell.matrix[:,active[0]]
b = universe.cell.matrix[:,active[1]]
c = numpy.cross(a,b)
tmp_cell = UnitCell(numpy.array([a,b,c]).transpose())
rotation = tmp_cell.alignment_a
return [
(atom.number, rotation*atom.get_absolute_frame().t)
for atom in iter_atoms([universe])
]
