def test_rand(self):
st1 = rc.get_rand_struct()
st2 = rc.get_rand_struct()
assert not np.allclose(st1.volume, st2.volume)
assert not np.allclose(st1.coords_frac, st2.coords_frac)
assert not np.allclose(st1.cryst_const, st2.cryst_const)
assert not symmetry.is_same_struct(st1, st2)
def test_concatenate():
st = get_rand_struct()
nstep = 5
# cat Structure
tr_cat = crys.concatenate([st] * nstep)
keys = tr_cat.attr_lst
assert tr_cat.nstep == nstep
for x in tr_cat:
assert_dict_with_all_types_equal(x.__dict__, st.__dict__, keys=keys)
none_attrs = ['ekin', 'timestep', 'velocity', 'temperature', 'time']
for attr_name in tr_cat.attrs_nstep:
if attr_name in none_attrs:
assert getattr(tr_cat, attr_name) is None
else:
print("test_concatenate: shape[0] == nstep:", attr_name)
assert getattr(tr_cat, attr_name).shape[0] == nstep
print("test_concatenate: shape[0] == nstep:", attr_name, "...ok")
# cat Trajectory
tr = get_rand_traj()
tr_cat = crys.concatenate([tr] * 3)
assert tr_cat.nstep == 3 * tr.nstep
none_attrs = ['timestep', 'time']
keys = remove_from_lst(tr_cat.attr_lst, none_attrs)
for x in [
tr_cat[0:tr.nstep], tr_cat[tr.nstep:2 * tr.nstep],
tr_cat[2 * tr.nstep:3 * tr.nstep]
]:
assert_dict_with_all_types_equal(x.__dict__, tr.__dict__, keys=keys)
for attr_name in tr_cat.attrs_nstep:
if attr_name in none_attrs:
assert getattr(tr_cat, attr_name) is None
else:
assert getattr(tr_cat, attr_name).shape[0] == 3 * tr.nstep
# cat mixed, Structure is minimal API
st = get_rand_struct()
tr = crys.concatenate([st] * 5)
tr_cat = crys.concatenate([st] * 5 + [tr])
assert tr_cat.nstep == 10
none_attrs = ['ekin', 'timestep', 'velocity', 'temperature', 'time']
keys = remove_from_lst(tr_cat.attr_lst, none_attrs)
for x in tr_cat:
assert_dict_with_all_types_equal(x.__dict__, st.__dict__, keys=keys)
for attr_name in tr_cat.attrs_nstep:
if attr_name in none_attrs:
assert getattr(tr_cat, attr_name) is None
else:
assert getattr(tr_cat, attr_name).shape[0] == 10
def test_same_rotate_cell(self):
st1 = rc.get_rand_struct()
st2 = st1.copy()
st2.cell = None
st2.coords = None
st2.set_all()
assert not np.allclose(st1.coords, st2.coords)
assert not np.allclose(st1.cell, st2.cell)
assert symmetry.is_same_struct(st1, st1)
def test():
# Explicit code duplication even though we could use [...,0,:] which should
# work for (natoms,3) and (nstep,natoms,3) arrays [we use it in
# center_on_atom()], but check if it really does.
st = rc.get_rand_struct()
stc = center_on_atom(st, idx=0, copy=True)
assert (st.coords_frac != stc.coords_frac).all()
assert (st.coords != stc.coords).all()
assert (st.coords_frac[0, :] != np.array([0.5] * 3)).all()
assert (stc.coords_frac[0, :] == np.array([0.5] * 3)).all()
assert (stc.coords_frac[1:, :] != np.array([0.5] * 3)).all()
tr = rc.get_rand_traj()
trc = center_on_atom(tr, idx=0, copy=True)
assert (tr.coords_frac != trc.coords_frac).all()
assert (tr.coords != trc.coords).all()
assert (tr.coords_frac[:, 0, :] != np.array([0.5] * 3)).all()
assert (trc.coords_frac[:, 0, :] == np.array([0.5] * 3)).all()
assert (trc.coords_frac[:, 1:, :] != np.array([0.5] * 3)).all()
def test_api():
tr = get_rand_traj()
st = get_rand_struct()
for name in st.attr_lst:
assert getattr(tr, name) is not None
for name in tr.attrs_only_traj:
assert getattr(st, name) is None
aa = tr[0] # Structure
bb = tr[0:1] # Trajectory
keys = set.difference(set(aa.attr_lst), set(aa.attrs_only_traj))
assert aa.is_struct
assert bb.is_traj
# remove timeaxis before comparing arrays
for name in bb.attrs_nstep:
attr = getattr(bb, name)
if attr.ndim == 1:
setattr(bb, name, attr[0])
else:
setattr(bb, name, attr[0, ...])
assert_dict_with_all_types_equal(aa.__dict__, bb.__dict__, keys=keys)
def test_get_fake_ase_atoms():
st = get_rand_struct()
atoms = st.get_fake_ase_atoms()
assert (st.coords_frac == atoms.get_scaled_positions()).all()
assert (st.cell == atoms.get_cell()).all()
assert (atoms.get_atomic_numbers() == np.array(st.get_znucl())).all()
def test_same(self):
st1 = rc.get_rand_struct()
assert symmetry.is_same_struct(st1, st1)