def test_methods():
tr = crys.Trajectory(coords=rand(100, 10, 3),
cell=rand(100, 3, 3),
symbols=['H'] * 10)
st = crys.Structure(coords=rand(10, 3),
cell=rand(3, 3),
symbols=['H'] * 10)
for obj, indices in [(st, [0, 1, 2]), (tr, [0, 0, 1, 2])]:
if obj.is_traj:
v0 = obj.coords[indices[0], indices[1], ...]
v1 = obj.coords[indices[0], indices[2], ...]
v2 = obj.coords[indices[0], indices[3], ...]
else:
v0 = obj.coords[indices[0], ...]
v1 = obj.coords[indices[1], ...]
v2 = obj.coords[indices[2], ...]
# use eps=0 since the new system is not orthogonal, only test API
o1 = crys.align_cart(obj, x=v1 - v0, y=v2 - v0, eps=0)
o2 = crys.align_cart(obj, vecs=np.array([v0, v1, v2]), eps=0)
o3 = crys.align_cart(obj, indices=indices, eps=0)
tools.assert_dict_with_all_types_almost_equal(o1.__dict__,
o2.__dict__,
keys=o1.attr_lst)
tools.assert_dict_with_all_types_almost_equal(o1.__dict__,
o3.__dict__,
keys=o1.attr_lst)
def test_methods():
tr = crys.Trajectory(coords=rand(100,10,3),
cell=rand(100,3,3),
symbols=['H']*10)
st = crys.Structure(coords=rand(10,3),
cell=rand(3,3),
symbols=['H']*10)
for obj,indices in [(st, [0,1,2]), (tr, [0,0,1,2])]:
if obj.is_traj:
v0 = obj.coords[indices[0],indices[1],...]
v1 = obj.coords[indices[0],indices[2],...]
v2 = obj.coords[indices[0],indices[3],...]
else:
v0 = obj.coords[indices[0],...]
v1 = obj.coords[indices[1],...]
v2 = obj.coords[indices[2],...]
# use eps=0 since the new system is not orthogonal, only test API
o1 = crys.align_cart(obj, x=v1-v0, y=v2-v0, eps=0)
o2 = crys.align_cart(obj, vecs=np.array([v0,v1,v2]), eps=0)
o3 = crys.align_cart(obj, indices=indices, eps=0)
tools.assert_dict_with_all_types_almost_equal(o1.__dict__,
o2.__dict__,
keys=o1.attr_lst)
tools.assert_dict_with_all_types_almost_equal(o1.__dict__,
o3.__dict__,
keys=o1.attr_lst)
def test_correct():
coords = rand(20, 3)
cell = rand(3, 3)
st = crys.Structure(coords=coords, cell=cell, symbols=['H'])
# new cartesian coord sys, created by rotating the old E=identity(3) by 3
# random angles
angles = [rand() * 360, rand() * 180, rand() * 360]
rmat = euler_rotation(*tuple(angles))
newcoords = np.array([np.dot(rmat, x) for x in st.coords])
newcell = np.array([np.dot(rmat, x) for x in st.cell])
st2 = crys.align_cart(st, cart=rmat, eps=1e-3)
assert np.allclose(newcoords, np.dot(st.coords, rmat.T))
assert np.allclose(
newcoords, crys.coord_trans(st.coords, old=np.identity(3), new=rmat))
assert np.allclose(newcell, np.dot(st.cell, rmat.T))
assert np.allclose(newcell,
crys.coord_trans(st.cell, old=np.identity(3), new=rmat))
assert np.allclose(st2.coords, newcoords)
def test_correct():
coords = rand(20,3)
cell = rand(3,3)
st = crys.Structure(coords=coords,
cell=cell,
symbols=['H'])
# new cartesian coord sys, created by rotating the old E=identity(3) by 3
# random angles
angles = [rand()*360, rand()*180, rand()*360]
rmat = euler_rotation(*tuple(angles))
newcoords = np.array([np.dot(rmat, x) for x in st.coords])
newcell = np.array([np.dot(rmat, x) for x in st.cell])
st2 = crys.align_cart(st, cart=rmat, eps=1e-3)
assert np.allclose(newcoords, np.dot(st.coords, rmat.T))
assert np.allclose(newcoords, crys.coord_trans(st.coords,
old=np.identity(3),
new=rmat))
assert np.allclose(newcell, np.dot(st.cell, rmat.T))
assert np.allclose(newcell, crys.coord_trans(st.cell,
old=np.identity(3),
new=rmat))
assert np.allclose(st2.coords, newcoords)