def test_values_2(self):
masses = np.array([1.]*11)
hmat = np.array([[0.,0.,0.]]*3)
coords = np.array([[ 1., 0., 0.], # 1: 0
[ 1., 1.,-1.], # 2: 45
[ 0., 1.,-2.], # 3: 90
[-1., 1.,-3.], # 4: 135
[-1., 0.,-4.], # 5: 180
[ 0., 0., 0.], # central
[ 0., 0., 1.], # central
[ 1., 0., 1.], # 1: 0
[ 1.,-1., 2.], # 2: -45
[ 0.,-1., 3.], # 3: -90
[-1.,-1., 4.]]) # 4: -135
for ivals, ref in [([1,1], 0),([1,2], 45),([1,3], 90),([1,4], 135),
([2,1], 45),([2,2], 90),([2,3], 135),([2,4], 180),
([3,1], 90),([3,2], 135),([3,3], 180),([3,4],-135),
([4,1], 135),([4,2], 180),([4,3],-135),([4,4], -90),
([5,1], 180),([5,2],-135),([5,3], -90),([5,4], -45)]:
ric = RIC()
ric.add_torsion([1,2,3,4,5,6,7,8,9,10,11,0],ivals=ivals)
ric.setup(masses)
ric.construct_b_matrix(hmat,coords)
res = ric.get_val_torsions()[0]
self.assertAlmostEqual(res,np.radians(ref))
del ric
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_values_1(self):
masses = np.array([1.]*4)
hmat = np.array([[0.,0.,0.]]*3)
for coords, ref in [([[ 0,-1, 0],[0,0,0],[0,0,1],[1,0,1]], -90),
([[ 1,-1, 0],[0,0,0],[0,0,1],[1,0,1]], -45),
([[ 1, 0, 0],[0,0,0],[0,0,1],[1,0,1]], 0),
([[ 1, 0,-1],[0,0,0],[0,0,1],[1,0,2]], 0),
([[ 1, 1, 0],[0,0,0],[0,0,1],[1,0,1]], 45),
([[ 2, 2, 0],[0,0,0],[0,0,1],[3,0,1]], 45),
([[ 0, 1, 0],[0,0,0],[0,0,1],[1,0,1]], 90),
([[-1, 0, 0],[0,0,0],[0,0,1],[1,0,1]], 180)]:
ric = RIC()
ric.add_torsion([1,2,3,4])
ric.setup(masses)
ric.construct_b_matrix(hmat,np.array(coords,dtype=np.float64))
res = ric.get_val_torsions()[0]
self.assertAlmostEqual(res,np.radians(ref))
del ric
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_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_6(self):
masses = np.array(range(1, 10), dtype=np.float64)
ric = RIC()
ric.add_torsion([1, 0, 0, 0, 0, 2, 3, 4, 0, 0, 0, 0])
ric.add_torsion([3, 4, 0, 0, 0, 5, 6, 7, 8, 9, 0, 0], ivals=[2, 3])
ric.setup(masses)
self.assertListEqual(list(ric._ric.ric_def_torsions[:, 0]),
[1, 0, 0, 0, 0, 2, 3, 4, 0, 0, 0, 0])
self.assertListEqual(list(ric._ric.ric_def_torsions[:, 1]),
[3, 4, 0, 0, 0, 5, 6, 7, 8, 9, 0, 0])
self.assertListEqual(list(ric._ric.ric_torsion_ivals[:, 0]), [1, 1])
self.assertListEqual(list(ric._ric.ric_torsion_ivals[:, 1]), [2, 3])
self.assertListEqual(list(ric._ric.ric_ibr_torsions), [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, 0)
self.assertEqual(ric.num_lin_bend, 0)
self.assertEqual(ric.num_torsion, 2)
self.assertEqual(ric.num_eckart, 0)
