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)
