def test_val_0D_1(self):
"""Values without PBC"""
masses = np.array([1.] * 2)
ric = RIC()
ric.add_stretch([1, 2])
ric.setup(masses)
for coords, ref in [([[-1, 0, 0], [1, 0, 0]], 2),
([[0, -1, 0], [0, 1, 0]], 2),
([[0, 0, -1], [0, 0, 1]], 2),
([[1, 1, 1], [-1, -1, -1]], 2 * np.sqrt(3))]:
ric.construct_b_matrix(None, np.array(coords, dtype=np.float64))
res = ric.get_val_stretches()[0]
self.assertAlmostEqual(res, ref)
def test_val_3D_1(self):
"""Values with PBC in an orthogonal box"""
masses = np.array([1.] * 2)
hmat = np.array([[5., 0., 0.], [0., 6., 0.], [0., 0., 7.]])
ric = RIC()
ric.add_stretch([1, 2])
ric.setup(masses)
for coords, ref in [([[-1, 0, 0], [1, 0, 0]], 2),
([[0, -1, 0], [0, 1, 0]], 2),
([[0, 0, -1], [0, 0, 1]], 2),
([[1, 1, 1], [-1, -1, -1]], 2 * np.sqrt(3))]:
ric.construct_b_matrix(hmat, np.array(coords, dtype=np.float64))
res = ric.get_val_stretches()[0]
self.assertAlmostEqual(res, ref)
def test_1(self):
ric = RIC()
ric.add_stretch([1, 2])
ric.add_eckart()
ric.setup(self.masses)
bmat = ric.construct_b_matrix(self.hmat, self.coords)
self.assertEqual(
ric.get_val_stretches()[0],
np.sqrt(np.sum((self.coords[0, :] - self.coords[1, :])**2)))
bmat_inv, rank = ric.invert_b_matrix()
bmat_inv_ = nl.pinv(bmat)
self.assertLess(np.max(np.abs(bmat_inv - bmat_inv_)), 1.e-14)
hess = ric.project_hessian(self.hess)
hess_ = np.dot(bmat_inv.T, np.dot(self.hess, bmat_inv))
self.assertLess(np.max(np.abs(hess - hess_)), 1.e-14)