def test_cif_parse():
tools.skip_if_pkg_missing('CifFile')
for filename in ['files/cif_struct.cif', 'files/cif_cart_struct.cif']:
p1 = CifFile(filename).get_struct()
assert p1.cell is not None
assert p1.cryst_const is not None
assert p1.symbols is not None
assert p1.coords is not None
assert p1.coords_frac is not None
# test writing
filename = os.path.join(testdir, 'test_write_cif.cif')
io.write_cif(filename, p1)
p2 = CifFile(filename).get_struct()
np.testing.assert_array_almost_equal(p1.coords_frac, p2.coords_frac)
np.testing.assert_array_almost_equal(p1.coords, p2.coords)
np.testing.assert_array_almost_equal(p1.cryst_const, p2.cryst_const)
np.testing.assert_array_almost_equal(p1.cell, p2.cell)
assert p1.symbols == p2.symbols
def test_symmetry():
tools.skip_if_pkg_missing('pyspglib')
st_prim = crys.Structure(coords_frac=np.array([[0] * 3, [.5] * 3]),
cryst_const=np.array([3.5] * 3 + [60] * 3),
symbols=['Al', 'N'])
st_sc = crys.scell(st_prim, (2, 3, 4))
st_prim2 = symmetry.spglib_get_primitive(st_sc, symprec=1e-2)
# irreducible structs
assert symmetry.spglib_get_primitive(st_prim, symprec=1e-2) is None
assert symmetry.spglib_get_primitive(st_prim2, symprec=1e-2) is None
for st in [st_prim, st_sc, st_prim2]:
assert symmetry.spglib_get_spacegroup(st_prim,
symprec=1e-2) == (225, 'Fm-3m')
# this is redundant since we have is_same_struct(), but keep it anyway
tools.assert_dict_with_all_types_almost_equal(
st_prim.__dict__,
st_prim2.__dict__,
keys=['natoms', 'symbols', 'volume', 'cryst_const'])
assert symmetry.is_same_struct(st_prim, st_prim2)
def test_angle():
# CaCl struct, the supercell will have 0 and 180 degrees -> check corner
# cases
tools.skip_if_pkg_missing('CifFile')
st = io.read_cif('files/angle/rs.cif')
st = crys.scell(st, (2, 1, 1))
nang = st.natoms * (st.natoms - 1) * (st.natoms - 2)
mask_val = 999.0
for deg in [True, False]:
for pbc in [True, False]:
agf = crys.angles(st, pbc=pbc, mask_val=mask_val)
agpy, aipy = angles(st, pbc=pbc, mask_val=mask_val)
eps = np.finfo(float).eps * 5
assert np.allclose(agf, agpy)
assert aipy.shape[0] == nang
assert len((agf != mask_val).nonzero()[0]) == nang
angleidx = np.array(list(zip(*(agf != mask_val).nonzero())))
assert (angleidx == aipy).all()
assert not np.isnan(agpy).any(), "python angle nan"
assert not np.isnan(agf).any(), "fortran angle nan"
# do we have 0 and 180 degrees?
assert (agf < eps).any(), "no zero degree cases"
assert (agf - 180.0 < eps).any(), "no 180 degree cases"
assert (agf >= 0.0).all(), "negative angles"
def test_cif2sgroup():
tools.skip_if_pkg_missing('CifFile')
exe = os.path.join(os.path.dirname(__file__), '../../bin/cif2sgroup.py')
cmd = '{e} files/cif_struct.cif > cif2sgroup.log'.format(e=exe)
sp.run(cmd, check=True, shell=True)
def __init__(self):
tools.skip_if_pkg_missing('pyspglib')