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_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_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_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)