def test_convert_atom_to_voxel(self):
# 20 points with coords between -5 and 5, centered at 0
coords_range = 10
xyz = (np.random.rand(20, 3) - 0.5) * coords_range
for idx in np.random.choice(20, 6):
for box_width in (10, 20, 40):
for voxel_width in (0.5, 1, 2):
voxel = rgf.convert_atom_to_voxel(xyz, idx, box_width, voxel_width)
self.assertIsInstance(voxel, list)
self.assertEqual(len(voxel), 1)
self.assertIsInstance(voxel[0], np.ndarray)
self.assertEqual(voxel[0].shape, (3,))
self.assertIs(voxel[0].dtype, np.dtype('int'))
# indices are positive
self.assertTrue((voxel[0] >= 0).all())
# coordinates were properly translated and scaled
self.assertTrue(
(voxel[0] < (box_width + coords_range) / 2.0 / voxel_width).all())
self.assertTrue(
np.allclose(voxel[0],
np.floor((xyz[idx] + box_width / 2.0) / voxel_width)))
# for coordinates outside of the box function should properly transform them
# to indices and warn the user
for args in ((np.array([[0, 1, 6]]), 0, 10, 1.0), (np.array([[0, 4, -6]]),
0, 10, 1.0)):
# TODO check if function warns. There is assertWarns method in unittest,
# but it is not implemented in 2.7 and buggy in 3.5 (issue 29620)
voxel = rgf.convert_atom_to_voxel(*args)
self.assertTrue(
np.allclose(voxel[0], np.floor((args[0] + args[2] / 2.0) / args[3])))
def test_convert_atom_to_voxel(self):
# 20 points with coords between -5 and 5, centered at 0
coords_range = 10
xyz = (np.random.rand(20, 3) - 0.5) * coords_range
for idx in np.random.choice(20, 6):
for box_width in (10, 20, 40):
for voxel_width in (0.5, 1, 2):
voxel = rgf.convert_atom_to_voxel(xyz, idx, box_width, voxel_width)
self.assertIsInstance(voxel, list)
self.assertEqual(len(voxel), 1)
self.assertIsInstance(voxel[0], np.ndarray)
self.assertEqual(voxel[0].shape, (3,))
self.assertIs(voxel[0].dtype, np.dtype('int'))
# indices are positive
self.assertTrue((voxel[0] >= 0).all())
# coordinates were properly translated and scaled
self.assertTrue(
(voxel[0] < (box_width + coords_range) / 2.0 / voxel_width).all())
self.assertTrue(
np.allclose(voxel[0],
np.floor((xyz[idx] + box_width / 2.0) / voxel_width)))
# for coordinates outside of the box function should properly transform them
# to indices and warn the user
for args in ((np.array([[0, 1, 6]]), 0, 10, 1.0), (np.array([[0, 4, -6]]),
0, 10, 1.0)):
# TODO check if function warns. There is assertWarns method in unittest,
# but it is not implemented in 2.7 and buggy in 3.5 (issue 29620)
voxel = rgf.convert_atom_to_voxel(*args)
self.assertTrue(
np.allclose(voxel[0], np.floor((args[0] + args[2] / 2.0) / args[3])))
def test_convert_atom_pair_to_voxel(self):
# 20 points with coords between -5 and 5, centered at 0
coords_range = 10
xyz1 = (np.random.rand(20, 3) - 0.5) * coords_range
xyz2 = (np.random.rand(20, 3) - 0.5) * coords_range
# 3 pairs of indices
for idx1, idx2 in np.random.choice(20, (3, 2)):
for box_width in (10, 20, 40):
for voxel_width in (0.5, 1, 2):
v1 = rgf.convert_atom_to_voxel(xyz1, idx1, box_width, voxel_width)
v2 = rgf.convert_atom_to_voxel(xyz2, idx2, box_width, voxel_width)
v_pair = rgf.convert_atom_pair_to_voxel((xyz1, xyz2), (idx1, idx2),
box_width, voxel_width)
self.assertEqual(len(v_pair), 2)
self.assertTrue((v1 == v_pair[0]).all())
self.assertTrue((v2 == v_pair[1]).all())
def test_convert_atom_pair_to_voxel(self):
# 20 points with coords between -5 and 5, centered at 0
coords_range = 10
xyz1 = (np.random.rand(20, 3) - 0.5) * coords_range
xyz2 = (np.random.rand(20, 3) - 0.5) * coords_range
# 3 pairs of indices
for idx1, idx2 in np.random.choice(20, (3, 2)):
for box_width in (10, 20, 40):
for voxel_width in (0.5, 1, 2):
v1 = rgf.convert_atom_to_voxel(xyz1, idx1, box_width, voxel_width)
v2 = rgf.convert_atom_to_voxel(xyz2, idx2, box_width, voxel_width)
v_pair = rgf.convert_atom_pair_to_voxel((xyz1, xyz2), (idx1, idx2),
box_width, voxel_width)
self.assertEqual(len(v_pair), 2)
self.assertTrue((v1 == v_pair[0]).all())
self.assertTrue((v2 == v_pair[1]).all())