def test_val_0D_1(self):
"""Values without PBC"""
masses = np.array([1.] * 3)
ric = RIC()
ric.add_in_bend([1, 2, 3])
ric.setup(masses)
for coords, ref in [([[1, 0, 0], [0, 0, 0], [1, 0, 0]], 0),
([[1, 0, 0], [0, 0, 0], [1, 1, 0]], 45),
([[1, 0, 0], [0, 0, 0], [0, 1, 0]], 90),
([[1, 0, 0], [0, 0, 0], [-1, 1, 0]], 135),
([[1, 0, 0], [0, 0, 0], [-1, 0, 0]], 180),
([[1, 1, 1], [0, 0, 0], [-1, -1, -1]], 180)]:
ric.construct_b_matrix(None, np.array(coords, dtype=np.float64))
res = ric.get_val_in_bends()[0]
self.assertAlmostEqual(res, np.radians(ref))
def test_2(self):
"""Multiple repeated calls"""
ric = RIC()
ric.add_stretch([1, 2])
ric.add_stretch([2, 3])
ric.add_stretch([3, 4])
ric.add_in_bend([1, 2, 3])
ric.add_in_bend([2, 3, 4])
ric.add_torsion([1, 0, 0, 0, 0, 2, 3, 4, 0, 0, 0, 0])
ric.add_eckart()
ric.setup(self.masses)
bmat = ric.construct_b_matrix(None, self.coords)
b1 = np.copy(bmat)
bmat = ric.construct_b_matrix(None, self.coords)
b2 = np.copy(bmat)
self.assertEqual(np.max(np.abs(b1 - b2)), 0)
bmat_inv, rank = ric.invert_b_matrix()
i1 = np.copy(bmat_inv)
bmat = ric.construct_b_matrix(None, self.coords)
b3 = np.copy(bmat)
bmat_inv, rank = ric.invert_b_matrix()
i2 = np.copy(bmat_inv)
self.assertEqual(np.max(np.abs(b1 - b3)), 0)
self.assertEqual(np.max(np.abs(i1 - i2)), 0)
hess = ric.project_hessian(self.hess)
h1 = np.copy(hess)
bmat = ric.construct_b_matrix(None, self.coords)
b4 = np.copy(bmat)
bmat_inv, rank = ric.invert_b_matrix()
i3 = np.copy(bmat_inv)
hess = ric.project_hessian(self.hess)
h2 = np.copy(hess)
hess = ric.get_ric_hessian()
h3 = np.copy(hess)
self.assertEqual(np.max(np.abs(b1 - b4)), 0)
self.assertEqual(np.max(np.abs(i1 - i3)), 0)
self.assertEqual(np.max(np.abs(h1 - h2)), 0)
self.assertEqual(np.max(np.abs(h1 - h3)), 0)
def test_grad_0D_rand(self):
masses = np.array([1.] * 3)
ric = RIC()
ric.add_in_bend([1, 2, 3])
ric.setup(masses)
def func(x):
ric.construct_b_matrix(None, np.reshape(x, (-1, 3)))
res = np.copy(ric.get_val_in_bends())
return res
grad = nd.Gradient(func, step_nom=[0.01] * 9)
for coords in 2 * np.random.random((10, 3, 3)) - 1:
coords = np.array(coords, dtype=np.float64)
ref = grad(coords.flatten())
res = ric.construct_b_matrix(None, coords)[0, :]
self.assertLess(np.max(np.abs(ref - res)), 1.e-10)
def test_3(self):
masses = np.array(range(1, 6), dtype=np.float64)
ric = RIC()
ric.add_in_bend([1, 2, 3])
ric.add_in_bend([3, 4, 5])
ric.setup(masses)
self.assertListEqual(list(ric._ric.ric_def_in_bends[:, 0]), [1, 2, 3])
self.assertListEqual(list(ric._ric.ric_def_in_bends[:, 1]), [3, 4, 5])
self.assertListEqual(list(ric._ric.ric_ibr_in_bends), [1, 2])
self.assertEqual(ric.num_ric, 2)
self.assertEqual(ric.num_stretch, 0)
self.assertEqual(ric.num_in_bend, 2)
self.assertEqual(ric.num_out_bend, 0)
self.assertEqual(ric.num_lin_bend, 0)
self.assertEqual(ric.num_torsion, 0)
self.assertEqual(ric.num_eckart, 0)
def test_1(self):
ric = RIC()
ric.add_stretch([1, 2])
ric.add_stretch([2, 3])
ric.add_stretch([3, 4])
ric.add_in_bend([1, 2, 3])
ric.add_in_bend([2, 3, 4])
ric.add_torsion([1, 0, 0, 0, 0, 2, 3, 4, 0, 0, 0, 0])
ric.add_eckart()
ric.setup(self.masses)
bmat = ric.construct_b_matrix(None, self.coords)
bmat_inv, rank = ric.invert_b_matrix()
bmat_inv_ = nl.pinv(bmat)
self.assertLess(np.max(np.abs(bmat_inv - bmat_inv_)), 7.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_)), 3.e-13)
def test_1(self):
ric = RIC()
ric.add_stretch([1, 2])
ric.add_stretch([2, 3])
ric.add_in_bend([2, 1, 3])
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_)), 2.e-13)
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_)), 3.e-14)
def test_8(self):
masses = np.array(range(1, 10), dtype=np.float64)
ric = RIC()
ric.add_stretch([2, 3])
ric.add_in_bend([3, 4, 5])
ric.add_out_bend([4, 5, 6, 7])
ric.add_lin_bend([5, 6, 7], 'xy')
ric.add_torsion([1, 0, 0, 0, 0, 2, 3, 4, 5, 6, 7, 8])
ric.add_torsion([3, 4, 0, 0, 0, 5, 6, 7, 8, 9, 0, 0])
ric.add_eckart(rots=[True, False, True])
ric.setup(masses)
self.assertTrue(np.all(ric._ric.atomic_masses == masses))
self.assertListEqual(list(ric._ric.cart_coords.shape), [3, 9])
self.assertListEqual(list(ric._ric.cart_hessian.shape), [3 * 9, 3 * 9])
self.assertListEqual(list(ric._ric.ric_ibr_stretches), [1])
self.assertListEqual(list(ric._ric.ric_ibr_in_bends), [2])
self.assertListEqual(list(ric._ric.ric_ibr_out_bends), [3])
self.assertListEqual(list(ric._ric.ric_ibr_lin_bends), [4, 5])
self.assertListEqual(list(ric._ric.ric_ibr_torsions), [6, 7])
self.assertListEqual(list(ric._ric.ric_ibr_eckart_trans), [8, 9, 10])
self.assertListEqual(list(ric._ric.ric_ibr_eckart_rots), [11, 12])
self.assertListEqual(list(ric._ric.bmat.shape), [3 * 9, 12])
self.assertEqual(ric._ric.ric_val_stretches.size, 1)
self.assertEqual(ric._ric.ric_val_in_bends.size, 1)
self.assertEqual(ric._ric.ric_val_out_bends.size, 1)
self.assertEqual(ric._ric.ric_val_lin_bends.size, 2)
self.assertListEqual(list(ric._ric.ric_hessian.shape), [12, 12])
self.assertEqual(ric.num_ric, 12)
self.assertEqual(ric.num_stretch, 1)
self.assertEqual(ric.num_in_bend, 1)
self.assertEqual(ric.num_out_bend, 1)
self.assertEqual(ric.num_lin_bend, 2)
self.assertEqual(ric.num_torsion, 2)
self.assertEqual(ric.num_eckart, 5)
def test_2(self):
g1, g2 = Group([1,2,3]), Group([5,6,7])
ric = RIC()
ric.add_stretch([1,3])
ric.add_stretch([2,3])
ric.add_distance([g1,4])
ric.add_distance([4,g2])
ric.add_stretch([5,6])
ric.add_stretch([5,7])
ric.add_in_bend([1,3,2])
ric.add_in_bend([1,3,4])
ric.add_in_bend([2,3,4])
ric.add_in_bend([4,5,6])
ric.add_in_bend([4,5,7])
ric.add_in_bend([6,5,7])
ric.add_lin_bend([3,4,5], 'yz')
ric.add_out_bend([3,1,2,4])
ric.add_out_bend([3,2,4,1])
ric.add_out_bend([3,4,1,2])
ric.add_out_bend([5,4,6,7])
ric.add_out_bend([5,6,7,4])
ric.add_out_bend([5,7,4,6])
ric.add_dihedral([1,2], [g1,g2], [6,7])
ric.add_eckart()
ric.setup(self.masses)
bmat = ric.construct_b_matrix(None, self.coords)
bmat_inv, rank = ric.invert_b_matrix()
bmat_inv_ = nl.pinv(bmat)
self.assertEqual(rank, self.coords.size)
self.assertLess(np.max(np.abs(bmat_inv - bmat_inv_)), 1.e-13)
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-13)
def test_1(self):
ric = RIC()
ric.add_stretch([1,3])
ric.add_stretch([2,3])
ric.add_stretch([3,4])
ric.add_stretch([4,5])
ric.add_stretch([5,6])
ric.add_stretch([5,7])
ric.add_in_bend([1,3,2])
ric.add_in_bend([1,3,4])
ric.add_in_bend([2,3,4])
ric.add_in_bend([4,5,6])
ric.add_in_bend([4,5,7])
ric.add_in_bend([6,5,7])
ric.add_lin_bend([3,4,5], 'yz')
ric.add_out_bend([3,1,2,4])
ric.add_out_bend([3,2,4,1])
ric.add_out_bend([3,4,1,2])
ric.add_out_bend([5,4,6,7])
ric.add_out_bend([5,6,7,4])
ric.add_out_bend([5,7,4,6])
ric.add_torsion([1,2,0,0,0,3,5,6,7,0,0,0])
ric.add_eckart()
ric.setup(self.masses)
bmat = ric.construct_b_matrix(None, self.coords)
bmat_inv, rank = ric.invert_b_matrix()
bmat_inv_ = nl.pinv(bmat)
self.assertEqual(rank, self.coords.size)
self.assertLess(np.max(np.abs(bmat_inv - bmat_inv_)), 7.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_)),3.e-13)