def test_1(self):
"""Mutiple instances safeguard"""
ric = RIC()
del ric
ric = RIC()
try:
ric = RIC()
except AssertionError:
pass
del ric
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_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_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_val_0D_1(self):
"""Values without PBC"""
masses = np.array([1., 2., 1.])
ric = RIC()
ric.add_eckart(trans=[True] * 3, rots=[False] * 3)
ric.setup(masses)
for coords, ref in [([[0, 0, 0], [0, 0, 0], [0, 0, 0]], [0, 0, 0]),
([[-1, -1, -1], [0, 0, 0], [1, 1, 1]], [0, 0, 0]),
([[-2, 0, 0], [2, 0, 0], [-2, 0, 0]], [0, 0, 0])]:
ric.construct_b_matrix(None, np.array(coords, dtype=np.float64))
res = ric.get_val_eckarts()
self.assertListEqual(list(res), list(ref))
def test_val_0D_1(self):
"""Values without PBC"""
masses = np.array([1.] * 2)
ric = RIC()
ric.add_stretch([1, 2])
ric.setup(masses)
for coords, ref in [([[-1, 0, 0], [1, 0, 0]], 2),
([[0, -1, 0], [0, 1, 0]], 2),
([[0, 0, -1], [0, 0, 1]], 2),
([[1, 1, 1], [-1, -1, -1]], 2 * np.sqrt(3))]:
ric.construct_b_matrix(None, np.array(coords, dtype=np.float64))
res = ric.get_val_stretches()[0]
self.assertAlmostEqual(res, ref)
def test_7(self):
masses = np.array(range(1, 2), dtype=np.float64)
ric = RIC()
ric.add_eckart(rots=[False, 0, 'a'])
ric.setup(masses)
self.assertListEqual(list(ric._ric.ric_def_eckart_rots), [3])
self.assertListEqual(list(ric._ric.ric_ibr_eckart_rots), [4])
self.assertEqual(ric.num_ric, 4)
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, 0)
self.assertEqual(ric.num_eckart, 4)
def test_val_3D_1(self):
"""Values with PBC in an orthogonal box"""
masses = np.array([1.] * 2)
hmat = np.array([[5., 0., 0.], [0., 6., 0.], [0., 0., 7.]])
ric = RIC()
ric.add_stretch([1, 2])
ric.setup(masses)
for coords, ref in [([[-1, 0, 0], [1, 0, 0]], 2),
([[0, -1, 0], [0, 1, 0]], 2),
([[0, 0, -1], [0, 0, 1]], 2),
([[1, 1, 1], [-1, -1, -1]], 2 * np.sqrt(3))]:
ric.construct_b_matrix(hmat, np.array(coords, dtype=np.float64))
res = ric.get_val_stretches()[0]
self.assertAlmostEqual(res, ref)
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_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_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_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_grad_0D_1(self):
masses = np.array([1.] * 2)
ric = RIC()
ric.add_stretch([1, 2])
ric.setup(masses)
def func(x):
ric.construct_b_matrix(None, np.reshape(x, (2, 3)))
return ric.get_val_stretches()[0]
grad = nd.Gradient(func, step_nom=[0.01] * 6)
for coords in [[[-1, 0, 0], [1, 0, 0]], [[0, -1, 0], [0, 1, 0]],
[[0, 0, -1], [0, 0, 1]], [[2, 2, 2], [-1, -1, -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-12)
def test_1(self):
ric = RIC()
ric.add_stretch([1, 2])
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_)), 1.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_)), 1.e-14)
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_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_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_grad_0D_1(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 [[[1, 0, 0], [0, 0, 0], [1, 1, 0]],
[[1, 0, 0], [0, 0, 0], [0, 1, 0]],
[[1, 0, 0], [0, 0, 0], [-1, 1, 0]],
[[0, 1, 2], [5, 4, 3], [6, 7, 8]]]:
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_1(self):
masses = np.array([1., 2., 1.])
ric = RIC()
ric.add_eckart(trans=[True] * 3, rots=[False] * 3)
ric.setup(masses)
def func(x):
ric.construct_b_matrix(None, np.reshape(x, (3, 3)))
return np.copy(ric.get_val_eckarts())
jac = nd.Jacobian(func, step_nom=[0.01] * 9)
for coords in [[[0, 0, 0], [0, 0, 0], [0, 0, 0]],
[[-1, -1, -1], [0, 0, 0], [1, 1, 1]],
[[-2, 0, 0], [2, 0, 0], [-2, 0, 0]]]:
coords = np.array(coords, dtype=np.float64)
ref = jac(coords.flatten())
res = ric.construct_b_matrix(None, coords)
#print ref
#print res
self.assertLess(np.max(np.abs(ref - res)), 1.e-12)
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_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)
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)
