def test_read_stru_znse():
from javelin.io import read_stru, read_stru_to_ase
filename = os.path.join(os.path.dirname(__file__), 'data', 'znse.cell')
znse_javelin = read_stru(filename)
znse_ase = read_stru_to_ase(filename)
assert len(znse_ase) == 2
assert_array_almost_equal(
znse_ase.get_cell(),
[[3.997, 0, 0], [-1.9985, 3.461504, 0], [0, 0, 6.501]])
assert_array_equal(
znse_ase.get_scaled_positions(),
[[0.3333333, 0.6666667, 0.3671], [0.3333333, 0.6666667, 0.]])
assert znse_ase.get_chemical_formula() == 'SeZn'
# unitcell
assert_array_almost_equal(znse_javelin.unitcell.cell,
ase.geometry.cell_to_cellpar(znse_ase.cell))
# get_atomic_numbers
assert_array_equal(znse_javelin.get_atomic_numbers(),
znse_ase.get_atomic_numbers())
# get_positions
# assert_array_almost_equal(znse_javelin.get_positions(),
# znse_ase.get_positions())
# get_scaled_positions
assert_array_almost_equal(znse_javelin.get_scaled_positions(),
znse_ase.get_scaled_positions())
def test_read_stru_znse():
from javelin.io import read_stru, read_stru_to_ase
filename = os.path.join(os.path.dirname(__file__), 'data', 'znse.cell')
znse_javelin = read_stru(filename)
znse_ase = read_stru_to_ase(filename)
assert len(znse_ase) == 2
assert_array_almost_equal(znse_ase.get_cell(), [[3.997, 0, 0],
[-1.9985, 3.461504, 0],
[0, 0, 6.501]])
assert_array_equal(znse_ase.get_scaled_positions(),
[[0.3333333, 0.6666667, 0.3671],
[0.3333333, 0.6666667, 0.]])
assert znse_ase.get_chemical_formula() == 'SeZn'
# unitcell
assert_array_almost_equal(znse_javelin.unitcell.cell,
ase.geometry.cell_to_cellpar(znse_ase.cell))
# get_atomic_numbers
assert_array_equal(znse_javelin.get_atomic_numbers(),
znse_ase.get_atomic_numbers())
# get_positions
# assert_array_almost_equal(znse_javelin.get_positions(),
# znse_ase.get_positions())
# get_scaled_positions
assert_array_almost_equal(znse_javelin.get_scaled_positions(),
znse_ase.get_scaled_positions())
def test_read_stru_pzn():
from javelin.io import read_stru, read_stru_to_ase
filename = os.path.join(os.path.dirname(__file__), 'data', 'pzn.stru')
pzn_javelin = read_stru(filename, starting_cell=(0, 0, 0))
pzn_ase = read_stru_to_ase(filename)
assert len(pzn_ase) == 15
assert_array_almost_equal(pzn_ase.get_cell(),
[[4.06, 0, 0], [0, 4.06, 0], [0, 0, 4.06]])
assert pzn_ase.get_chemical_formula() == 'Nb2O9Pb3Zn'
# unitcell
assert_array_equal(pzn_javelin.unitcell.cell,
ase.geometry.cell_to_cellpar(pzn_ase.cell))
# get_atomic_numbers
assert_array_equal(pzn_javelin.get_atomic_numbers(),
pzn_ase.get_atomic_numbers())
# get_positions
assert_array_almost_equal(pzn_javelin.get_positions(),
pzn_ase.get_positions())
# get_scaled_positions
assert_array_almost_equal(pzn_javelin.get_scaled_positions(),
pzn_ase.get_scaled_positions())
def test_read_stru_missing_cell():
from javelin.io import read_stru, read_stru_to_ase
filename = os.path.join(os.path.dirname(__file__), 'data',
'missing_cell.cell')
c_javelin = read_stru(filename)
c_ase = read_stru_to_ase(filename)
assert len(c_ase) == 1
assert_array_equal(c_ase.get_cell(), [[1, 0, 0], [0, 1, 0], [0, 0, 1]])
assert_array_equal(c_ase.get_scaled_positions(), [[0.5, 0., 0.25]])
assert c_ase.get_chemical_formula() == 'C'
# unitcell
assert_array_equal(c_javelin.unitcell.cell,
ase.geometry.cell_to_cellpar(c_ase.cell))
# get_atomic_numbers
assert_array_equal(c_javelin.get_atomic_numbers(),
c_ase.get_atomic_numbers())
# get_positions
assert_array_almost_equal(c_javelin.get_positions(), c_ase.get_positions())
# get_scaled_positions
assert_array_almost_equal(c_javelin.get_scaled_positions(),
c_ase.get_scaled_positions())
def test_read_stru_pzn():
from javelin.io import read_stru, read_stru_to_ase
filename = os.path.join(os.path.dirname(__file__), 'data', 'pzn.stru')
pzn_javelin = read_stru(filename, starting_cell=(0, 0, 0))
pzn_ase = read_stru_to_ase(filename)
assert len(pzn_ase) == 15
assert_array_almost_equal(pzn_ase.get_cell(), [[4.06, 0, 0],
[0, 4.06, 0],
[0, 0, 4.06]])
assert pzn_ase.get_chemical_formula() == 'Nb2O9Pb3Zn'
# unitcell
assert_array_equal(pzn_javelin.unitcell.cell,
ase.geometry.cell_to_cellpar(pzn_ase.cell))
# get_atomic_numbers
assert_array_equal(pzn_javelin.get_atomic_numbers(),
pzn_ase.get_atomic_numbers())
# get_positions
assert_array_almost_equal(pzn_javelin.get_positions(),
pzn_ase.get_positions())
# get_scaled_positions
assert_array_almost_equal(pzn_javelin.get_scaled_positions(),
pzn_ase.get_scaled_positions())
def test_read_stru_missing_cell():
from javelin.io import read_stru, read_stru_to_ase
filename = os.path.join(os.path.dirname(__file__), 'data', 'missing_cell.cell')
c_javelin = read_stru(filename)
c_ase = read_stru_to_ase(filename)
assert len(c_ase) == 1
assert_array_equal(c_ase.get_cell(), [[1, 0, 0],
[0, 1, 0],
[0, 0, 1]])
assert_array_equal(c_ase.get_scaled_positions(), [[0.5, 0., 0.25]])
assert c_ase.get_chemical_formula() == 'C'
# unitcell
assert_array_equal(c_javelin.unitcell.cell,
ase.geometry.cell_to_cellpar(c_ase.cell))
# get_atomic_numbers
assert_array_equal(c_javelin.get_atomic_numbers(),
c_ase.get_atomic_numbers())
# get_positions
assert_array_almost_equal(c_javelin.get_positions(),
c_ase.get_positions())
# get_scaled_positions
assert_array_almost_equal(c_javelin.get_scaled_positions(),
c_ase.get_scaled_positions())
