def test_distances(self):
"""Tests that the periodicity is taken into account when calculating
distances.
"""
scaled_positions = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]]
system = System(
scaled_positions=scaled_positions,
symbols=["H", "H"],
cell=[
[5, 5, 0],
[0, -5, -5],
[5, 0, 5]
],
)
disp = system.get_displacement_tensor()
# For a non-periodic system, periodicity should not be taken into
# account even if cell is defined.
pos = system.get_positions()
assumed = np.array([
[pos[0] - pos[0], pos[1] - pos[0]],
[pos[0] - pos[1], pos[1] - pos[1]],
])
self.assertTrue(np.allclose(assumed, disp))
# For a periodic system, the nearest copy should be considered when
# comparing distances to neighbors or to self
system.set_pbc([True, True, True])
disp = system.get_displacement_tensor()
assumed = np.array([
[[5.0, 5.0, 0.0], [5, 0, 0]],
[[-5, 0, 0], [5.0, 5.0, 0.0]]])
self.assertTrue(np.allclose(assumed, disp))
# Tests that the displacement tensor is found correctly even for highly
# non-orthorhombic systems.
positions = np.array([
[1.56909, 2.71871, 6.45326],
[3.9248, 4.07536, 6.45326]
])
cell = np.array([
[4.7077, -2.718, 0.],
[0., 8.15225, 0.],
[0., 0., 50.]
])
system = System(
positions=positions,
symbols=["H", "H"],
cell=cell,
pbc=True,
)
# Fully periodic with minimum image convention
dist_mat = system.get_distance_matrix()
distance = dist_mat[0, 1]
# The minimum image should be within the same cell
expected = np.linalg.norm(positions[0, :] - positions[1, :])
self.assertTrue(np.allclose(distance, expected))
def test_set_positions(self):
"""Test the method set_positions() of the System class
"""
scaled_positions = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]]
system = System(
scaled_positions=scaled_positions,
symbols=["H", "H"],
cell=[
[5, 5, 0],
[0, -5, -5],
[5, 0, 5]
],
)
pos = system.get_positions()
new_pos = pos * 2
system.set_positions(new_pos)
new_pos = system.get_positions()
self.assertTrue(np.allclose(pos * 2, new_pos))
self.assertFalse(np.allclose(pos, new_pos))
