def angles(self):
angles = []
for triplet in self.psf.angles:
c_atom = triplet.atom2
a_1 = triplet.atom1
a_2 = triplet.atom3
v1 = np.array(self.positions[a_1]) - np.array(
self.positions[c_atom])
v2 = np.array(self.positions[a_2]) - np.array(
self.positions[c_atom])
prod = np.dot(v1, v2)
if prod == 0:
angle = np.pi / 2
else:
prod /= (np.linalg.norm(v1) * np.linalg.norm(v2))
prod = np.clip(prod, -1, 1)
angle = np.arccos(prod)
angles.append([(a_1.type, c_atom.type, a_2.type),
np.degrees(angle)])
return angles
def dihedrals(self):
d_angles = []
for quad in self.psf.dihedrals:
a_1, a_2, a_3, a_4 = quad.atom1, quad.atom2, quad.atom3, quad.atom4
v1 = np.array(self.positions[a_2]) - np.array(self.positions[a_1])
v2 = np.array(self.positions[a_3]) - np.array(self.positions[a_1])
n1 = np.cross(v1, v2)
v3 = np.array(self.positions[a_4]) - np.array(self.positions[a_3])
v4 = -v2
n2 = np.cross(v3, v4)
prod = np.dot(n1, n2)
if prod == 0:
angle = 0
else:
prod /= (np.linalg.norm(n1) * np.linalg.norm(n2))
prod = np.clip(prod, -1, 1)
angle = np.arccos(prod)
d_angles.append([(a_1.type, a_2.type, a_3.type, a_4.type),
np.degrees(angle)])
return d_angles
def TE_angle(self):
# Returns the trailing edge angle of the airfoil, in degrees
upper_TE_vec = self.coordinates[0, :] - self.coordinates[1, :]
lower_TE_vec = self.coordinates[-1, :] - self.coordinates[-2, :]
return np.degrees(np.arctan2(
upper_TE_vec[0] * lower_TE_vec[1] - upper_TE_vec[1] * lower_TE_vec[0],
upper_TE_vec[0] * lower_TE_vec[0] + upper_TE_vec[1] * upper_TE_vec[1]
))
def impropers(self):
i_angles = []
for quad in self.psf.impropers: # a_1 bonded to a_2, a_1 is central atom
a_1, a_2, a_3, a_4 = quad.atom1, quad.atom2, quad.atom3, quad.atom4
v1 = np.array(self.positions[a_3]) - np.array(self.positions[a_1])
v2 = np.array(self.positions[a_4]) - np.array(self.positions[a_1])
n = np.cross(v1, v2)
v3 = np.array(self.positions[a_2]) - np.array(self.positions[a_1])
prod = np.dot(n, v3)
if prod == 0:
angle = np.pi / 2
else:
prod /= (np.linalg.norm(n) * np.linalg.norm(v3))
prod = np.clip(prod, -1, 1)
angle = np.pi / 2 - np.arccos(prod)
i_angles.append([(a_1.type, a_2.type, a_3.type, a_4.type),
np.degrees(angle)])
return i_angles
def test_degrees():
fun = lambda x : 3.0 * np.degrees(x)
d_fun = grad(fun)
check_grads(fun, 10.0*npr.rand())
check_grads(d_fun, 10.0*npr.rand())
def test_degrees():
fun = lambda x : 3.0 * np.degrees(x)
d_fun = grad(fun)
check_grads(fun, 10.0*npr.rand())
check_grads(d_fun, 10.0*npr.rand())
def test_degrees(): unary_ufunc_check(lambda x : np.degrees(x)/50.0, test_complex=False) def test_exp(): unary_ufunc_check(np.exp)
def test_degrees():
unary_ufunc_check(lambda x: np.degrees(x) / 50.0, test_complex=False)
def test_degrees():
fun = lambda x: 3.0 * np.degrees(x)
check_grads(fun)(10.0 * npr.rand())
def deduce_state(self, s):
rpy = np.degrees(rowan.to_euler(rowan.normalize(s[6:10]), 'xyz'))
return rpy
def test_degrees():
fun = lambda x : 3.0 * np.degrees(x)
check_grads(fun)(10.0*npr.rand())
