def test_gyration_tensor_no_coords(self):
a = np.array([])
g_tensor = ftmd.gyration_tensor(a, diagonalize=True)
self.assertTrue(
all(
math.isnan(g_tensor[i, j])
for i, j in it.product(range(3), repeat=2)))
def test_gyration_tensor_vs_rog(self):
a1 = np.array([[1., 1., 1.], [0., 0., 0.], [-1., -1., -1.],
[-2, -2, -2]])
rog = ftmd.radius_of_gyration(a1)
g_tensor = ftmd.gyration_tensor(a1, diagonalize=True)
print(rog, g_tensor)
#the first invariant is the rog
self.assertAlmostEqual(
g_tensor[0, 0] + g_tensor[1, 1] + g_tensor[2, 2], rog**2)
def test_gyration_tensor_vs_rog(self):
a1 = np.array([[1., 1., 1.], [0., 0., 0.],
[-1., -1., -1.], [-2, -2, -2]])
rog = ftmd.radius_of_gyration(a1)
g_tensor = ftmd.gyration_tensor(a1, diagonalize=True)
print(rog, g_tensor)
# the first invariant is the rog
self.assertAlmostEqual(
g_tensor[0, 0] + g_tensor[1, 1] + g_tensor[2, 2], rog**2)
def test_gyration_tensor_diagonalize(self):
a1 = np.array([[1., 1., 1.], [0., 0., 0.], [-1., -1., -1.],
[-2, -2, -2]])
a2 = np.array([[1., 2., 1.], [0., 0., 0.], [-1., -1., -2.],
[-12, -2, -25]])
for a in [a1, a2]:
g_tensor = ftmd.gyration_tensor(a1, diagonalize=True)
self.assertEqual(g_tensor[0, 1], 0)
self.assertEqual(g_tensor[0, 2], 0)
self.assertEqual(g_tensor[1, 2], 0)
self.assertEqual(g_tensor[1, 0], 0)
self.assertEqual(g_tensor[2, 0], 0)
self.assertEqual(g_tensor[2, 1], 0)
self.assertGreaterEqual(g_tensor[0, 0], g_tensor[1, 1])
self.assertGreaterEqual(g_tensor[1, 1], g_tensor[2, 2])
def test_gyration_tensor_diagonalize(self):
a1 = np.array([[1., 1., 1.], [0., 0., 0.],
[-1., -1., -1.], [-2, -2, -2]])
a2 = np.array([[1., 2., 1.], [0., 0., 0.],
[-1., -1., -2.], [-12, -2, -25]])
for a in [a1, a2]:
g_tensor = ftmd.gyration_tensor(a1, diagonalize=True)
self.assertEqual(g_tensor[0, 1], 0)
self.assertEqual(g_tensor[0, 2], 0)
self.assertEqual(g_tensor[1, 2], 0)
self.assertEqual(g_tensor[1, 0], 0)
self.assertEqual(g_tensor[2, 0], 0)
self.assertEqual(g_tensor[2, 1], 0)
self.assertGreaterEqual(g_tensor[0, 0], g_tensor[1, 1])
self.assertGreaterEqual(g_tensor[1, 1], g_tensor[2, 2])
def test_gyration_tensor_no_coords(self):
a = np.array([])
g_tensor = ftmd.gyration_tensor(a, diagonalize=True)
self.assertTrue(
all(math.isnan(g_tensor[i, j]) for i, j in it.product(range(3), repeat=2)))