def test_coord_shift(self):
benzene = Geometry(TestGeometry.benzene)
mol = Geometry(TestGeometry.benzene)
# shift all atoms
vector = np.array([0, 3.2, -1.0])
for a in benzene.atoms:
a.coords += vector
mol.coord_shift([0, 3.2, -1.0])
self.assertTrue(np.linalg.norm(benzene.coords() - mol.coords()) == 0)
# shift some atoms
vector = np.array([0, -3.2, 1.0])
for a in benzene.atoms[0:5]:
a.coords += vector
mol.coord_shift([0, -3.2, 1.0], [str(i) for i in range(1, 6)])
self.assertTrue(np.linalg.norm(benzene.coords() - mol.coords()) == 0)
if args.reverse:
x_factor *= -1
dX += x_factor * G_AAron_file.other['frequency'].data[combo].vector
if args.animate is not None:
#animate by setting up 3 geometries: -, 0, and +
#then create a Pathway to interpolate between these
#if roundtrip, - -> 0 -> + -> 0 -> -
#if not roundtrip, - -> 0 -> +
w = width(args.animate[0])
fmt = "%0" + "%i" % w + "i"
Gf = G.copy()
Gf.update_geometry(G.coords() + dX)
Gr = G.copy()
Gr.update_geometry(G.coords() - dX)
#make a scales(t) function so we can see the animation progress in the XYZ file comment
if args.roundtrip:
S = Pathway([Gf, G, Gr, G, Gf])
ev = [
Pathway.get_splines_vector([-x, 0, x, 0, -x]) for x in scale[i]
]
m = Pathway.get_splines_mat(5)
else:
S = Pathway([Gf, G, Gr])
ev = [Pathway.get_splines_vector([-x, 0, x]) for x in scale[i]]
m = Pathway.get_splines_mat(3)
