def test_plot_defect_formation_energy(mocker):
mock_summary = mocker.Mock(spec=DefectEnergySummary, autospec=True)
def side_effect(filename):
if filename == "defect_energy_summary.json":
return mock_summary
else:
raise ValueError
mocker.patch("pydefect.cli.main.loadfn", side_effect=side_effect)
parsed_args = parse_args_main([
"pe", "-d", "defect_energy_summary.json", "-l", "A", "-y", "-5", "5",
"--allow_shallow", "--no_corrections", "--no_label_line",
"--no_add_charges"])
expected = Namespace(
defect_energy_summary=mock_summary,
label="A",
y_range=[-5, 5],
allow_shallow=True,
with_corrections=False,
label_line=False,
add_charges=False,
func=parsed_args.func)
assert parsed_args == expected
def test_plot_cpd_options(mocker):
mock_loadfn = mocker.patch("pydefect.cli.main.loadfn")
parsed_args = parse_args_main(["pc"])
expected = Namespace(
chem_pot_diag=mock_loadfn.return_value,
func=parsed_args.func)
assert parsed_args == expected
def test_defect_structure_info(mocker):
mock_supercell_info = mocker.Mock(spec=SupercellInfo, autospec=True)
def side_effect(filename):
if filename == "supercell_info.json":
return mock_supercell_info
else:
raise ValueError
mock_loadfn = mocker.patch("pydefect.cli.main.loadfn",
side_effect=side_effect)
parsed_args = parse_args_main(["dsi",
"-s", "supercell_info.json",
"-d", "Va_O1_0",
"-nccr",
"-dt", "1.0",
"--symprec", "2.0"])
expected = Namespace(
supercell_info=mock_supercell_info,
check_calc_results=False,
dirs=[Path("Va_O1_0")],
dist_tolerance=1.0,
symprec=2.0,
verbose=False,
func=parsed_args.func)
assert parsed_args == expected
def test_defect_energy_summary(mocker):
mock_pbes = mocker.Mock(spec=PerfectBandEdgeState, autospec=True)
mock_unitcell = mocker.patch("pydefect.cli.main.Unitcell")
def side_effect(filename):
if filename == "perfect/calc_results.json":
return mock_pbes
else:
print(filename)
raise ValueError
mocker.patch("pydefect.cli.main.loadfn", side_effect=side_effect)
parsed_args = parse_args_main(["des",
"-d", "Va_O1_0", "Va_O1_1",
"-p", "perfect/calc_results.json",
"-u", "unitcell.json",
"-t", "target_vertices.yaml"])
expected = Namespace(
dirs=[Path("Va_O1_0"), Path("Va_O1_1")],
p_state=mock_pbes,
unitcell=mock_unitcell.from_yaml.return_value,
target_vertices_yaml="target_vertices.yaml",
verbose=False,
func=parsed_args.func)
assert parsed_args == expected
def test_defect_set_wo_options():
parsed_args = parse_args_main(["ds"])
expected = Namespace(oxi_states=None,
dopants=None,
kwargs=None,
func=parsed_args.func)
assert parsed_args == expected
def test_make_cpd_and_vertices_options():
parsed_args = parse_args_main(["cv", "-t", "MgO", "-e", "Mg", "O", "Al"])
expected = Namespace(rel_energy_yaml="relative_energies.yaml",
target="MgO",
elements=["Mg", "O", "Al"],
func=parsed_args.func)
assert parsed_args == expected
def test_defect_set_w_options():
parsed_args = parse_args_main(
["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_make_supercell_wo_options(mocker):
mock = mocker.patch("pydefect.cli.main.IStructure")
parsed_args = parse_args_main(["s", "-p", "POSCAR-tmp"])
# 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
def test_pop_interstitial(mocker):
mock_loadfn = mocker.patch("pydefect.cli.main.loadfn")
mock_supercell_info = mocker.Mock(spec=SupercellInfo, autospec=True)
mock_loadfn.return_value = mock_supercell_info
parsed_args = parse_args_main(
["pi", "-s", "supercell_info.json", "-i", "1000", "--pop_all"])
expected = Namespace(supercell_info=mock_supercell_info,
index=1000,
pop_all=True,
func=parsed_args.func)
assert parsed_args == expected
def test_band_edge_states(mocker):
mock = mocker.patch("pydefect.cli.main.loadfn")
parsed_args = parse_args_main([
"bes", "-d", "Va_O1_0", "Va_O1_1", "-nccr", "-p",
"perfect/perfect_band_edge_state.json"
])
expected = Namespace(dirs=[Path("Va_O1_0"),
Path("Va_O1_1")],
check_calc_results=False,
p_state=mock.return_value,
func=parsed_args.func)
assert parsed_args == expected
mock.assert_any_call("perfect/perfect_band_edge_state.json")
def test_make_supercell_w_options(mocker):
mock = mocker.patch("pydefect.cli.main.IStructure")
parsed_args = parse_args_main([
"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_append_interstitial(mocker):
mock_loadfn = mocker.patch("pydefect.cli.main.loadfn")
mock_supercell_info = mocker.Mock(spec=SupercellInfo, autospec=True)
mock_loadfn.return_value = mock_supercell_info
mock_structure = mocker.patch("pydefect.cli.main.Structure")
parsed_args = parse_args_main([
"ai", "-s", "supercell_info.json", "-p", "POSCAR", "-c", "0.1", "0.2",
"0.3", "-i", "info"
])
expected = Namespace(supercell_info=mock_supercell_info,
base_structure=mock_structure.from_file.return_value,
frac_coords=[0.1, 0.2, 0.3],
info="info",
func=parsed_args.func)
assert parsed_args == expected
def test_defect_energy_infos(mocker):
mock_unitcell = mocker.patch("pydefect.cli.main.Unitcell")
mock_loadfn = mocker.patch("pydefect.cli.main.loadfn")
mock_std_energy = mocker.patch("pydefect.cli.main.StandardEnergies")
parsed_args = parse_args_main([
"dei", "-d", "Va_O1_0", "Va_O1_1", "-nccr", "-u", "unitcell.json",
"-p", "perfect/perfect_band_edge_state.json", "-s",
"standard_energies.yaml"
])
expected = Namespace(dirs=[Path("Va_O1_0"),
Path("Va_O1_1")],
check_calc_results=False,
unitcell=mock_unitcell.from_yaml.return_value,
perfect_calc_results=mock_loadfn.return_value,
std_energies=mock_std_energy.from_yaml.return_value,
func=parsed_args.func)
assert parsed_args == expected
mock_loadfn.assert_called_once_with("perfect/perfect_band_edge_state.json")
mock_std_energy.from_yaml.assert_called_once_with("standard_energies.yaml")
def test_efnv_correction(mocker):
mock_calc_results = mocker.Mock(spec=CalcResults, autospec=True)
mock_unitcell = mocker.patch("pydefect.cli.main.Unitcell")
def side_effect(filename):
if filename == "perfect/calc_results.json":
return mock_calc_results
else:
raise ValueError
mocker.patch("pydefect.cli.main.loadfn", side_effect=side_effect)
parsed_args = parse_args_main([
"efnv", "-d", "Va_O1_0", "Va_O1_1", "-nccr", "-pcr",
"perfect/calc_results.json", "-u", "unitcell.json"
])
expected = Namespace(dirs=[Path("Va_O1_0"),
Path("Va_O1_1")],
check_calc_results=False,
perfect_calc_results=mock_calc_results,
unitcell=mock_unitcell.from_yaml.return_value,
func=parsed_args.func)
assert parsed_args == expected
def test_make_standard_and_relative_energies_options():
parsed_args = parse_args_main(["sre"])
expected = Namespace(
composition_energies_yaml="composition_energies.yaml",
func=parsed_args.func)
assert parsed_args == expected
