def test_val_0D_ind(self): """Values without PBC""" masses = np.array([1.] * 4) ric = RIC() ric.add_lin_bend([1, 2, 3], 4) ric.setup(masses) for coords, ref in [ ([[-1, 0, 0], [0, 0, 0], [1, 0, 0], [0, 1, 0]], [0, 0]), # x-y ([[-1, 0, 0], [0, 0, 0], [1, 0, 0], [0, 0, 1]], [0, 0]), # x-z ([[-1, 0, 0], [0, 0, 0], [1, 0, 0], [0, 1, 1]], [0, 0]), # x-yz ([[-1, 0, 0], [0, 0, 0], [1, 0, 0], [1, 1, 1]], [0, 0]), # x-xyz ([[0, -1, 0], [0, 0, 0], [0, 1, 0], [2, 0, 0]], [0, 0]), # y-x ([[0, -1, 0], [0, 0, 0], [0, 1, 0], [0, 0, 2]], [0, 0]), # y-z ([[0, -1, 0], [0, 0, 0], [0, 1, 0], [0, 2, 2]], [0, 0]), # y-yz ([[0, -1, 0], [0, 0, 0], [0, 1, 0], [2, 2, 2]], [0, 0]), # y-xyz ([[0, 0, -1], [0, 0, 0], [0, 0, 1], [3, 0, 0]], [0, 0]), # z-x ([[0, 0, -1], [0, 0, 0], [0, 0, 1], [0, 3, 0]], [0, 0]), # z-y ([[0, 0, -1], [0, 0, 0], [0, 0, 1], [3, 3, 0]], [0, 0]), # z-xy ([[0, 0, -1], [0, 0, 0], [0, 0, 1], [3, 3, 3]], [0, 0]), # z-xyz ]: ric.construct_b_matrix(None, np.array(coords, dtype=np.float64)) res = ric.get_val_lin_bends() #print coords #print ref #print res self.assertAlmostEqual(res[0], np.radians(ref[0])) self.assertAlmostEqual(res[1], np.radians(ref[1]))
def test_grad_0D_ind_rand(self): masses = np.array([1.] * 4) ric = RIC() ric.add_lin_bend([1, 2, 3], 4) ric.setup(masses) def func(x): ric.construct_b_matrix(None, np.reshape(x, (-1, 3))) res = np.copy(ric.get_val_lin_bends()) return res jac = nd.Jacobian(func, step_nom=[0.01] * 12) # This is buggy! def func0(x): ric.construct_b_matrix(None, np.reshape(x, (-1, 3))) res = np.copy(ric.get_val_lin_bends()) return res[0] def func1(x): ric.construct_b_matrix(None, np.reshape(x, (-1, 3))) res = np.copy(ric.get_val_lin_bends()) return res[1] grad0 = nd.Gradient(func0, step_nom=[0.01] * 12) grad1 = nd.Gradient(func1, step_nom=[0.01] * 12) for coords in 2 * np.random.random((10, 4, 3)) - 1: coords = np.array(coords, dtype=np.float64) res = ric.construct_b_matrix(None, coords) vals = np.degrees(ric.get_val_lin_bends()) #if np.any(np.abs(vals) > 45): continue # HACK: disable the axes updates _inds = np.copy(ric._ric.ric_lin_bend_inds) ric._ric.ric_lin_bend_inds[:] = 0 #ref = jac(coords.flatten()) ref0 = grad0(coords.flatten()) ref1 = grad1(coords.flatten()) # HACK: enbale the axes updates ric._ric.ric_lin_bend_inds = _inds #print coords #print vals #print ref #print ref0 #print ref1 #print res #self.assertLess(np.max(np.abs(ref-res)),1.e-8) self.assertLess(np.max(np.abs(ref0 - res[0])), 1.e-8) self.assertLess(np.max(np.abs(ref1 - res[1])), 1.e-8)
def test_grad_0D_yz(self): masses = np.array([1.] * 3) ric = RIC() ric.add_lin_bend([1, 2, 3], 'yz') ric.setup(masses) def func(x): assert x.dtype == np.float64 ric.construct_b_matrix(None, np.reshape(x, (-1, 3))) res = np.copy(ric.get_val_lin_bends()) assert res.dtype == np.float64 return res jac = nd.Jacobian(func, step_nom=[0.01] * 9) # This is buggy! def func0(x): ric.construct_b_matrix(None, np.reshape(x, (-1, 3))) res = np.copy(ric.get_val_lin_bends()) return res[0] def func1(x): ric.construct_b_matrix(None, np.reshape(x, (-1, 3))) res = np.copy(ric.get_val_lin_bends()) return res[1] grad0 = nd.Gradient(func0, step_nom=[0.01] * 9) grad1 = nd.Gradient(func1, step_nom=[0.01] * 9) for coords in [ [[-1, 0, 0], [0, 0, 0], [1, 0, 0]], # Ref [[-1, -1, -1], [0, 0, 0], [1, 1, 1]], # Diagonal [[0, 0, 0], [1, 1, 1], [2, 2, 2]], # Offset [[-3, 0, 0], [0, 0, 0], [5, 0, 0]], # Longer [[-1, 0, 0], [0, 0, 0], [1, -1, 0]], # -y [[-1, 0, 0], [0, 0, 0], [1, 1, 0]], # +y [[-1, 0, 0], [0, 0, 0], [1, 0, -1]], # -z [[-1, 0, 0], [0, 0, 0], [1, 0, 1]], # +z ]: coords = np.array(coords, dtype=np.float64) #ref = jac(coords.flatten()) ref0 = grad0(coords.flatten()) ref1 = grad1(coords.flatten()) res = ric.construct_b_matrix(None, coords) #print coords #print ref #print ref0 #print ref1 #print res #self.assertLess(np.max(np.abs(ref-res)),1.e-8) self.assertLess(np.max(np.abs(ref0 - res[0])), 1.e-8) self.assertLess(np.max(np.abs(ref1 - res[1])), 1.e-8)
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_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_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)
def test_val_0D_yz(self): """Values without PBC""" masses = np.array([1.] * 3) ric = RIC() ric.add_lin_bend([1, 2, 3], 'yz') ric.setup(masses) for coords, ref in [ ([[-1, 0, 0], [0, 0, 0], [1, 0, 0]], [0, 0]), # Ref ([[-1, -1, -1], [0, 0, 0], [1, 1, 1]], [0, 0]), # Diagonal ([[0, 0, 0], [1, 1, 1], [2, 2, 2]], [0, 0]), # Offset ([[-3, 0, 0], [0, 0, 0], [5, 0, 0]], [0, 0]), # Longer ([[-1, 0, 0], [0, 0, 0], [1, -1, 0]], [0, 45]), # -y ([[-1, 0, 0], [0, 0, 0], [1, 1, 0]], [0, -45]), # +y ([[-1, 0, 0], [0, 0, 0], [1, 0, -1]], [-45, 0]), # -z ([[-1, 0, 0], [0, 0, 0], [1, 0, 1]], [45, 0]), # +z ]: ric.construct_b_matrix(None, np.array(coords, dtype=np.float64)) res = ric.get_val_lin_bends() self.assertAlmostEqual(res[0], np.radians(ref[0])) self.assertAlmostEqual(res[1], np.radians(ref[1]))
def test_5(self): masses = np.array(range(1, 14), dtype=np.float64) ric = RIC() ric.add_lin_bend([1, 2, 3], 'xy') ric.add_lin_bend([4, 5, 6], 'xz') ric.add_lin_bend([7, 8, 9], 'yz') ric.add_lin_bend([10, 11, 12], 13) ric.setup(masses) self.assertListEqual(list(ric._ric.ric_def_lin_bends[:, 0]), [1, 2, 3]) self.assertListEqual(list(ric._ric.ric_def_lin_bends[:, 1]), [1, 2, 3]) self.assertListEqual(list(ric._ric.ric_def_lin_bends[:, 2]), [4, 5, 6]) self.assertListEqual(list(ric._ric.ric_def_lin_bends[:, 3]), [4, 5, 6]) self.assertListEqual(list(ric._ric.ric_def_lin_bends[:, 4]), [7, 8, 9]) self.assertListEqual(list(ric._ric.ric_def_lin_bends[:, 5]), [7, 8, 9]) self.assertListEqual(list(ric._ric.ric_def_lin_bends[:, 6]), [10, 11, 12]) self.assertListEqual(list(ric._ric.ric_def_lin_bends[:, 7]), [10, 11, 12]) self.assertListEqual(list(ric._ric.ric_ibr_lin_bends), [1, 2, 3, 4, 5, 6, 7, 8]) self.assertListEqual(list(ric._ric.ric_lin_bend_inds), [0, 0, 0, 0, 0, 0, 13, -13]) self.assertListEqual(list(ric._ric.ric_lin_bend_axes[:, 0]), [1, 0, 0]) self.assertListEqual(list(ric._ric.ric_lin_bend_axes[:, 1]), [0, 1, 0]) self.assertListEqual(list(ric._ric.ric_lin_bend_axes[:, 2]), [1, 0, 0]) self.assertListEqual(list(ric._ric.ric_lin_bend_axes[:, 3]), [0, 0, 1]) self.assertListEqual(list(ric._ric.ric_lin_bend_axes[:, 4]), [0, 1, 0]) self.assertListEqual(list(ric._ric.ric_lin_bend_axes[:, 5]), [0, 0, 1]) self.assertListEqual(list(ric._ric.ric_lin_bend_axes[:, 6]), [0, 0, 0]) self.assertListEqual(list(ric._ric.ric_lin_bend_axes[:, 7]), [0, 0, 0]) self.assertEqual(ric.num_ric, 8) self.assertEqual(ric.num_stretch, 0) self.assertEqual(ric.num_in_bend, 0) self.assertEqual(ric.num_out_bend, 0) self.assertEqual(ric.num_lin_bend, 8) self.assertEqual(ric.num_torsion, 0) self.assertEqual(ric.num_eckart, 0)
def test_grad_0D_ind(self): masses = np.array([1.] * 4) ric = RIC() ric.add_lin_bend([1, 2, 3], 4) ric.setup(masses) def func(x): ric.construct_b_matrix(None, np.reshape(x, (-1, 3))) res = np.copy(ric.get_val_lin_bends()) return res jac = nd.Jacobian(func, step_nom=[0.01] * 12) # This is buggy! def func0(x): ric.construct_b_matrix(None, np.reshape(x, (-1, 3))) res = np.copy(ric.get_val_lin_bends()) return res[0] def func1(x): ric.construct_b_matrix(None, np.reshape(x, (-1, 3))) res = np.copy(ric.get_val_lin_bends()) return res[1] grad0 = nd.Gradient(func0, step_nom=[0.01] * 12) grad1 = nd.Gradient(func1, step_nom=[0.01] * 12) for coords in [ [[-1, 0, 0], [.1, 0, 0], [1, 0, 0], [0, 1, 0]], # x-y [[-1, 0, 0], [.1, 0, 0], [1, 0, 0], [0, 0, 1]], # x-z [[-1, 0, 0], [.1, 0, 0], [1, 0, 0], [0, 1, 1]], # x-yz [[-1, 0, 0], [.1, 0, 0], [1, 0, 0], [1, 1, 1]], # x-xyz [[0, -1, 0], [0, .1, 0], [0, 1, 0], [2, 0, 0]], # y-x [[0, -1, 0], [0, .1, 0], [0, 1, 0], [0, 0, 2]], # y-z [[0, -1, 0], [0, .1, 0], [0, 1, 0], [0, 2, 2]], # y-yz [[0, -1, 0], [0, .1, 0], [0, 1, 0], [2, 2, 2]], # y-xyz [[0, 0, -1], [0, 0, .1], [0, 0, 1], [3, 0, 0]], # z-x [[0, 0, -1], [0, 0, .1], [0, 0, 1], [0, 3, 0]], # z-y [[0, 0, -1], [0, 0, .1], [0, 0, 1], [3, 3, 0]], # z-xy [[0, 0, -1], [0, 0, .1], [0, 0, 1], [3, 3, 3]], # z-xyz ]: coords = np.array(coords, dtype=np.float64) res = ric.construct_b_matrix(None, coords) # HACK: disable the axes updates _inds = np.copy(ric._ric.ric_lin_bend_inds) ric._ric.ric_lin_bend_inds[:] = 0 #ref = jac(coords.flatten()) ref0 = grad0(coords.flatten()) ref1 = grad1(coords.flatten()) # HACK: enbale the axes updates ric._ric.ric_lin_bend_inds[:] = _inds #print coords #print ref #print ref0 #print ref1 #print res #self.assertLess(np.max(np.abs(ref-res)),1.e-8) self.assertLess(np.max(np.abs(ref0 - res[0])), 1.e-8) self.assertLess(np.max(np.abs(ref1 - res[1])), 1.e-8)