def test_get_simple_cubic_sublattice(self):
s0 = dd.get_simple_cubic_sublattice()
s0.plot()
s1 = dd.get_simple_cubic_sublattice(image_noise=False)
s1.plot()
s2 = dd.get_simple_cubic_sublattice(image_noise=True)
s2.plot()
def test_many_atoms(self):
sublattice = dd.get_simple_cubic_sublattice(image_noise=True)
atom = sublattice.atom_list[0]
atom.refine_position = False
x_pos_orig = np.array(sublattice.x_position)
y_pos_orig = np.array(sublattice.y_position)
sublattice.find_nearest_neighbors()
sublattice.refine_atom_positions_using_2d_gaussian()
assert atom.pixel_x == x_pos_orig[0]
assert atom.pixel_y == x_pos_orig[1]
assert not (x_pos_orig[1:] == sublattice.x_position[1:]).any()
assert not (y_pos_orig[1:] == sublattice.y_position[1:]).any()
sublattice.refine_atom_positions_using_2d_gaussian()
assert atom.pixel_x == x_pos_orig[0]
assert atom.pixel_y == x_pos_orig[1]
assert not (x_pos_orig[1:] == sublattice.x_position[1:]).any()
assert not (y_pos_orig[1:] == sublattice.y_position[1:]).any()
def setup_method(self):
sublattice = dd.get_simple_cubic_sublattice()
self.x, self.y = sublattice.x_position, sublattice.y_position
self.s = sublattice.get_atom_list_on_image()