def test_change_angle(self):
def diff(a, b):
return abs(a - b)
mol = Geometry(TestGeometry.benz_NO2_Cl)
# set angle
mol.change_angle("13", "12", "14", np.pi / 2, fix=1)
angle = mol.angle("13", "12", "14")
self.assertTrue(diff(np.rad2deg(angle), 90) < 10**-8)
# change angle
mol.change_angle("13",
"12",
"14",
30,
fix=3,
adjust=True,
radians=False)
angle = mol.angle("13", "12", "14")
self.assertTrue(diff(np.rad2deg(angle), 120) < 10**-8)
mol.change_angle("13", "12", "14", -30, adjust=True, radians=False)
angle = mol.angle("13", "12", "14")
self.assertTrue(diff(np.rad2deg(angle), 90) < 10**-8)
if args.input_format is not None:
infile = FileReader(("from stdin", args.input_format[0], f))
else:
infile = FileReader(("from stdin", "xyz", f))
geom = Geometry(infile)
#set angle to specified value
for angle in args.set_ang:
vals = three_atoms_and_a_float(angle)
a1 = geom.find(str(vals[0]))[0]
a2 = geom.find(str(vals[1]))[0]
a3 = geom.find(str(vals[2]))[0]
geom.change_angle(a1,
a2,
a3,
vals[3],
radians=args.radians,
adjust=False)
#change angle by specified amount
for angle in args.change:
vals = three_atoms_and_a_float(angle)
a1 = geom.find(str(vals[0]))[0]
a2 = geom.find(str(vals[1]))[0]
a3 = geom.find(str(vals[2]))[0]
geom.change_angle(a1,
a2,
a3,
vals[3],
radians=args.radians,
adjust=True)
