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_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]))
