def test_gkfo_correction(mocker):
mock_i_correction = mocker.Mock(spec=ExtendedFnvCorrection, autospec=True)
mock_i_calc_results = mocker.Mock(spec=CalcResults, autospec=True)
mock_f_calc_results = mocker.Mock(spec=CalcResults, autospec=True)
mock_unitcell = mocker.Mock(spec=Unitcell, autospec=True)
def side_effect(filename):
if filename == "a/correction.json":
return mock_i_correction
elif filename == "a/calc_results.json":
return mock_i_calc_results
elif filename == "a/absorption/calc_results.json":
return mock_f_calc_results
elif filename == "unitcell.json":
return mock_unitcell
else:
raise ValueError
mocker.patch("pydefect.cli.vasp.main.loadfn", side_effect=side_effect)
parsed_args = parse_args([
"gkfo", "-iefnv", "a/correction.json", "-cd", "1", "-icr",
"a/calc_results.json", "-fcr", "a/absorption/calc_results.json", "-u",
"unitcell.json"
])
expected = Namespace(initial_efnv_correction=mock_i_correction,
initial_calc_results=mock_i_calc_results,
final_calc_results=mock_f_calc_results,
charge_diff=1,
unitcell=mock_unitcell,
func=parsed_args.func)
assert parsed_args == expected
def test_plot_cpd_options():
parsed_args = parse_args(["pcpd",
"-y", "a.yaml"])
expected = Namespace(
yaml="a.yaml",
func=parsed_args.func)
assert parsed_args == expected
def test_defect_formation_energy(mocker):
mock_calc_results = mocker.Mock(spec=CalcResults, autospec=True)
mock_unitcell = mocker.Mock(spec=Unitcell, autospec=True)
mock_chem_pot_diag = mocker.Mock(spec=ChemPotDiag, autospec=True)
def side_effect(filename):
if filename == "perfect/calc_results.json":
return mock_calc_results
elif filename == "unitcell.json":
return mock_unitcell
else:
raise ValueError
mocker.patch("pydefect.cli.vasp.main.loadfn", side_effect=side_effect)
parsed_args = parse_args([
"e", "-d", "Va_O1_0", "Va_O1_1", "-pcr", "perfect/calc_results.json",
"-u", "unitcell.json", "-c", "cpd.yaml", "-l", "A", "-y", "-5", "5",
"-s", "-p"
])
expected = Namespace(dirs=[Path("Va_O1_0"),
Path("Va_O1_1")],
perfect_calc_results=mock_calc_results,
unitcell=mock_unitcell,
cpd_yaml="cpd.yaml",
label="A",
y_range=[-5, 5],
skip_shallow=True,
print=True,
func=parsed_args.func)
assert parsed_args == expected
def test_calc_results():
parsed_args = parse_args(["cr", "-d", "Va_O1_0", "Va_O1_1"])
expected = Namespace(
dirs=[Path("Va_O1_0"), Path("Va_O1_1")],
func=parsed_args.func,
)
assert parsed_args == expected
def test_make_poscars_wo_options():
parsed_args = parse_args(["mp",
"-e", "Mg", "O"])
expected = Namespace(
elements=["Mg", "O"],
e_above_hull=defaults.e_above_hull,
func=parsed_args.func)
assert parsed_args == expected
def test_defect_set_wo_options():
parsed_args = parse_args(["ds"])
expected = Namespace(
oxi_states=None,
dopants=None,
kwargs=None,
func=parsed_args.func,
)
assert parsed_args == expected
def test_make_cpd_options():
parsed_args = parse_args(["mcpd", "-d", "Mg", "O", "-t", "MgO"])
expected = Namespace(dirs=[Path("Mg"), Path("O")],
target=Composition("MgO"),
elements=None,
atom_energy_yaml=None,
yaml="cpd.yaml",
update=False,
func=parsed_args.func)
assert parsed_args == expected
def test_defect_set_w_options():
parsed_args = parse_args(
["ds", "-o", "He", "1", "-d", "Li", "-k", "Li_H1", "Va_H1_0"])
expected = Namespace(
oxi_states=["He", 1],
dopants=["Li"],
kwargs=["Li_H1", "Va_H1_0"],
func=parsed_args.func,
)
assert parsed_args == expected
def test_band_edge_states(mocker):
mock = mocker.patch("pydefect.cli.vasp.main.loadfn")
parsed_args = parse_args([
"es", "-d", "Va_O1_0", "Va_O1_1", "-p", "perfect/edge_characters.json"
])
expected = Namespace(dirs=[Path("Va_O1_0"),
Path("Va_O1_1")],
perfect_edge_characters=mock.return_value,
func=parsed_args.func)
assert parsed_args == expected
mock.assert_any_call("perfect/edge_characters.json")
def test_pop_interstitial(mocker):
mock_loadfn = mocker.patch("pydefect.cli.vasp.main.loadfn")
mock_supercell_info = mocker.Mock(spec=SupercellInfo, autospec=True)
mock_loadfn.return_value = mock_supercell_info
parsed_args = parse_args(["pi", "-s", "supercell_info.json", "-i", "1000"])
expected = Namespace(
supercell_info=mock_supercell_info,
index=1000,
func=parsed_args.func,
)
assert parsed_args == expected
def test_make_supercell_wo_options(mocker):
mock = mocker.patch("pydefect.cli.vasp.main.IStructure")
parsed_args = parse_args(["s"])
# func is a pointer so need to point the same address.
expected = Namespace(
unitcell=mock.from_file.return_value,
matrix=None,
min_num_atoms=50,
max_num_atoms=300,
func=parsed_args.func,
)
assert parsed_args == expected
mock.from_file.assert_called_once_with("POSCAR")
def test_make_supercell_w_options(mocker):
mock = mocker.patch("pydefect.cli.vasp.main.IStructure")
parsed_args = parse_args([
"s", "-p", "POSCAR-tmp", "--matrix", "1", "2", "3", "--min_atoms",
"1000", "--max_atoms", "2000"
])
# func is a pointer so need to point the same address.
expected = Namespace(
unitcell=mock.from_file.return_value,
matrix=[1, 2, 3],
min_num_atoms=1000,
max_num_atoms=2000,
func=parsed_args.func,
)
assert parsed_args == expected
mock.from_file.assert_called_once_with("POSCAR-tmp")
def test_defect_structure(mocker):
mock_perfect_calc_results = mocker.Mock(spec=CalcResults, autospec=True)
def side_effect(filename):
if filename == "perfect/calc_results.json":
return mock_perfect_calc_results
else:
raise ValueError
mock = mocker.patch("pydefect.cli.vasp.main.loadfn",
side_effect=side_effect)
parsed_args = parse_args(
["sds", "-pcr", "perfect/calc_results.json", "-d", "Va_O1_0"])
expected = Namespace(perfect_calc_results=mock_perfect_calc_results,
defect_dir=Path("Va_O1_0"),
func=parsed_args.func)
assert parsed_args == expected
def test_append_interstitial(mocker):
mock_loadfn = mocker.patch("pydefect.cli.vasp.main.loadfn")
mock_supercell_info = mocker.Mock(spec=SupercellInfo, autospec=True)
mock_loadfn.return_value = mock_supercell_info
mock_structure = mocker.patch("pydefect.cli.vasp.main.Structure")
parsed_args = parse_args([
"ai", "-s", "supercell_info.json", "-p", "POSCAR", "-c", "0.1", "0.2",
"0.3"
])
expected = Namespace(
supercell_info=mock_supercell_info,
base_structure=mock_structure.from_file.return_value,
frac_coords=[0.1, 0.2, 0.3],
func=parsed_args.func,
)
assert parsed_args == expected
def test_unitcell(mocker):
mock = mocker.patch("pydefect.cli.vasp.main.Vasprun")
mock_outcar = mocker.patch("pydefect.cli.vasp.main.Outcar")
parsed_args = parse_args([
"u", "-vb", "vasprun.xml", "-ob", "OUTCAR-1", "-odc", "OUTCAR-2",
"-odi", "OUTCAR-3"
])
# func is a pointer so need to point the same address.
expected = Namespace(
vasprun_band=mock.return_value,
outcar_band=mock_outcar.return_value,
outcar_dielectric_clamped=mock_outcar.return_value,
outcar_dielectric_ionic=mock_outcar.return_value,
func=parsed_args.func,
)
assert parsed_args == expected
mock.assert_called_once_with("vasprun.xml")
mock_outcar.assert_any_call("OUTCAR-1")
mock_outcar.assert_any_call("OUTCAR-2")
mock_outcar.assert_called_with("OUTCAR-3")
def test_efnv_correction(mocker):
mock_calc_results = mocker.Mock(spec=CalcResults, autospec=True)
mock_unitcell = mocker.Mock(spec=Unitcell, autospec=True)
def side_effect(filename):
if filename == "perfect/calc_results.json":
return mock_calc_results
elif filename == "unitcell.json":
return mock_unitcell
else:
raise ValueError
mocker.patch("pydefect.cli.vasp.main.loadfn", side_effect=side_effect)
parsed_args = parse_args([
"efnv", "-d", "Va_O1_0", "Va_O1_1", "-pcr",
"perfect/calc_results.json", "-u", "unitcell.json"
])
expected = Namespace(dirs=[Path("Va_O1_0"),
Path("Va_O1_1")],
perfect_calc_results=mock_calc_results,
unitcell=mock_unitcell,
func=parsed_args.func)
assert parsed_args == expected
def test_print(mocker):
mock = mocker.patch("pydefect.cli.vasp.main.loadfn")
parsed_args = parse_args(["p", "-f", "a.json"])
expected = Namespace(obj=mock.return_value, func=parsed_args.func)
assert parsed_args == expected
def test_defect_entries():
parsed_args = parse_args(["de"])
expected = Namespace(func=parsed_args.func, )
assert parsed_args == expected