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)
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)
#print specified angles
out = ""
for angle in args.measure:
a1 = geom.find(str(angle[0]))[0]
a2 = geom.find(str(angle[1]))[0]
a3 = geom.find(str(angle[2]))[0]
val = geom.angle(a1, a2, a3)
if not args.radians:
val *= 180 / np.pi
out += "%f\n" % val
out = out.rstrip()
if len(args.set_ang) + len(args.change) > 0:
if args.outfile:
outfile = args.outfile
if "$INFILE" in outfile:
outfile = outfile.replace("$INFILE", get_filename(f))
geom.write(append=True, outfile=outfile)
else:
print(geom.write(outfile=False))
def test_angle(self):
mol = Geometry(TestGeometry.benz_NO2_Cl)
angle = mol.angle("13", "12", "14")
self.assertTrue(is_close(np.rad2deg(angle), 124.752, 10**-2))
