def test_add_periodicities(self):
for counter in xrange(100):
#print counter
uc = UnitCell()
uc.cell = numpy.random.uniform(-1, 1, (3, 3))
uc.cell_active[:] = False
uc.add_cell_vector(numpy.random.uniform(-2,2,3))
uc.add_cell_vector(numpy.random.uniform(-2,2,3))
uc.add_cell_vector(numpy.random.uniform(-2,2,3))
def test_add_periodicities(self):
for counter in xrange(100):
#print counter
uc = UnitCell()
uc.cell = numpy.random.uniform(-1, 1, (3, 3))
uc.cell_active[:] = False
uc.add_cell_vector(numpy.random.uniform(-2, 2, 3))
uc.add_cell_vector(numpy.random.uniform(-2, 2, 3))
uc.add_cell_vector(numpy.random.uniform(-2, 2, 3))
def create_pattern():
"Read the atom positions and transform them to the flat coordinates"
active, inactive = universe.get_active_inactive()
tmp_cell = UnitCell()
tmp_cell.add_cell_vector(universe.cell[:,active[0]])
tmp_cell.add_cell_vector(universe.cell[:,active[1]])
r = tmp_cell.calc_align_rotation_matrix()
return [
(atom.number, numpy.dot(r, atom.get_absolute_frame().t))
for atom in yield_atoms([universe])
]
