def test_grad_0D(self): masses = np.array([1.]*4) ric = RIC() ric.add_out_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_out_bends()) return res grad = nd.Gradient(func,step_nom=[0.01]*12) for coords in [ [[ 0 ,0, 0],[0,1, 0],[-1,-1,0],[1,-1,0]], [[ 0 ,0, 0],[0,1, 0],[-2,-2,0],[1,-1,0]], [[ 0 ,0, 0],[0,1, 1],[-1,-1,0],[1,-1,0]], [[ 0 ,0, 0],[0,1, 0],[-1,-1,0],[1,-1,1]], [[ 0 ,0, 0],[0,1, 1],[-2,-2,1],[2,-2,1]], [[.1,.1,.9],[0,1, 0],[-1,-1,0],[1,-1,0]], ]: 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_grad_0D_rand(self): masses = np.array([1.]*4) ric = RIC() ric.add_out_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_out_bends()) return res grad = nd.Gradient(func,step_nom=[0.01]*12) for coords in 2*np.random.random((10,4,3))-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-9)
def test_values_1(self): masses = np.array([1.]*4) hmat = np.array([[0.,0.,0.]]*3) for coords, ref in [ ([[0,0,0],[0,0, 1],[-1,-1,0],[1,-1,0]], 0), ([[0,0,0],[0,1, 1],[-1,-1,0],[1,-1,0]], 45), ([[0,0,0],[0,1, 0],[-1,-1,0],[1,-1,0]], 90), ([[0,0,0],[0,1,-1],[-1,-1,0],[1,-1,0]], 135), ([[0,0,0],[0,0,-1],[-1,-1,0],[1,-1,0]], 180), ]: ric = RIC() ric.add_out_bend([1,2,3,4]) ric.setup(masses) ric.construct_b_matrix(hmat,np.array(coords,dtype=np.float64)) res = ric.get_val_out_bends()[0] self.assertAlmostEqual(res,np.radians(ref)) del ric
def test_4(self): masses = np.array(range(1, 7), dtype=np.float64) ric = RIC() ric.add_out_bend([1, 2, 3, 4]) ric.add_out_bend([3, 4, 5, 6]) ric.setup(masses) self.assertListEqual(list(ric._ric.ric_def_out_bends[:, 0]), [1, 2, 3, 4]) self.assertListEqual(list(ric._ric.ric_def_out_bends[:, 1]), [3, 4, 5, 6]) self.assertListEqual(list(ric._ric.ric_ibr_out_bends), [1, 2]) self.assertEqual(ric.num_ric, 2) self.assertEqual(ric.num_stretch, 0) self.assertEqual(ric.num_in_bend, 0) self.assertEqual(ric.num_out_bend, 2) self.assertEqual(ric.num_lin_bend, 0) self.assertEqual(ric.num_torsion, 0) self.assertEqual(ric.num_eckart, 0)
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)