def test_cell_wrap(self):
"""Test that coordinates are correctly wrapped inside the cell.
"""
system = System(
scaled_positions=[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]],
symbols=["H", "H"],
cell=[
[1, 0, 0],
[0, 1, 0],
[0, 0, 1]
],
pbc = [True, True, True],
)
#orig = np.array([[2, 1.45, -4.8]])
orig = np.array([[0.5, 0.5, 1.5]])
scal = system.to_scaled(orig, wrap = True)
cart = system.to_cartesian(scal)
self.assertFalse(np.allclose(orig, cart))
scal2 = system.to_scaled(orig)
cart2 = system.to_cartesian(scal2, wrap = True)
self.assertFalse(np.allclose(orig, cart2))
scal3 = system.to_scaled(orig, True)
cart3 = system.to_cartesian(scal3, wrap = True)
self.assertFalse(np.allclose(orig, cart3))
scal4 = system.to_scaled(orig)
cart4 = system.to_cartesian(scal4)
self.assertTrue(np.allclose(orig, cart4))
self.assertTrue(np.allclose(cart2, cart3))
def test_transformations(self):
"""Test that coordinates are correctly transformed from scaled to
cartesian and back again.
"""
system = System(
scaled_positions=[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]],
symbols=["H", "H"],
cell=[[5, 5, 0], [0, -5, -5], [5, 0, 5]],
)
orig = np.array([[2, 1.45, -4.8]])
scal = system.to_scaled(orig)
cart = system.to_cartesian(scal)
self.assertTrue(np.allclose(orig, cart))