def test_concentrations_w_options(self):
actual = parse_args([
"c",
"--energies",
"a",
"--unitcell",
"b",
"--filtering",
"c",
"--frac_mag_to_one",
"--verbose",
"--temperature",
"1.1",
"--quenched_temperature",
"2.1",
])
expected = Namespace(
energies="a",
unitcell="b",
filtering="c",
frac_mag_to_one=True,
verbose=True,
temperature=1.1,
quenched_temperature=2.1,
func=actual.func,
)
self.assertEqual(expected, actual)
def test_initial_setting_w_options(self):
actual = parse_args([
"is", "--poscar", "a", "--matrix", "10", "--criterion", "0.1",
"--min_num_atoms", "1", "--max_num_atoms", "2", "-cb", "F",
"--most_isotropic", "--rhombohedral_angle", "3.1",
"--supercell_set", "--dopants", "Ga", "In", "--antisite", "F",
"--en_diff", "4.1", "--included", "b", "--excluded", "c",
"--displacement_distance", "5.1", "--interstitial_sites", "i1",
"i2", "--complex_defect_names", "d", "e", "--print_dopant", "Cs",
"--symprec", "6.1", "--angle_tolerance", "7.1"
])
expected = Namespace(
poscar="a",
matrix=[10],
isotropy_criterion=0.1,
min_num_atoms=1,
max_num_atoms=2,
conventional_base=False,
most_isotropic=True,
rhombohedral_angle=3.1,
supercell_set=True,
dopants=["Ga", "In"],
antisite=False,
en_diff=4.1,
included=["b"],
excluded=["c"],
displacement_distance=5.1,
interstitials=["i1", "i2"],
complex_defect_names=["d", "e"],
print_dopant="Cs",
symprec=6.1,
angle_tolerance=7.1,
func=actual.func,
)
self.assertEqual(expected, actual)
def test_defect_entry_w_options(self):
actual = parse_args([
"de",
"--print",
"--make_defect_entry",
"--yaml",
"a",
"--json",
"b",
"--perfect_poscar",
"c",
"--defect_poscar",
"d",
"--displacement_distance",
"0.1",
"--defect_name",
"e",
])
expected = Namespace(
print=True,
make_defect_entry=True,
yaml="a",
json="b",
perfect_poscar="c",
defect_poscar="d",
displacement_distance=0.1,
defect_name="e",
func=actual.func,
)
self.assertEqual(expected, actual)
def test_defect_w_options(self):
actual = parse_args([
"d",
"--defect_dirs",
"a",
"b",
"--diagnose",
"--json",
"c",
"--perfect",
"d",
"--defect_entry",
"e",
"--correction",
"f",
"--dft_results",
"g",
"--band_edge",
"h",
"i",
])
expected = Namespace(
defect_dirs=["a", "b"],
diagnose=True,
json="c",
perfect="d",
defect_entry="e",
correction="f",
dft_results="g",
band_edge=["h", "i"],
func=actual.func,
)
self.assertEqual(expected, actual)
def test_vasp_parchg_set_w_options(self):
actual = parse_args([
"vps",
"--read_dir",
"a",
"--write_dir",
"b",
"--band_indices",
"1",
"2",
"3",
"--kpoint_indices",
"4",
"5",
"6",
"--contcar",
"c",
])
expected = Namespace(
read_dir="a",
write_dir="b",
band_indices=[1, 2, 3],
kpoint_indices=[4, 5, 6],
contcar="c",
func=actual.func,
)
self.assertEqual(expected, actual)
def test_initial_setting_wo_options(self):
actual = parse_args(["is"])
d = get_default_args(DefectInitialSetting.from_basic_settings)
d.update(get_default_args(Supercells))
# func is a pointer so need to point the same address.
expected = Namespace(poscar="POSCAR",
matrix=None,
isotropy_criterion=d["criterion"],
min_num_atoms=d["min_num_atoms"],
max_num_atoms=d["max_num_atoms"],
conventional_base=True,
most_isotropic=False,
rhombohedral_angle=d["rhombohedral_angle"],
supercell_set=False,
dopants=d["dopants"],
antisite=True,
en_diff=d["en_diff"],
included=d["included"],
excluded=d["excluded"],
displacement_distance=d["displacement_distance"],
interstitials=d["interstitial_sites"],
complex_defect_names=d["complex_defect_names"],
print_dopant=None,
func=actual.func,
**symprec_args)
self.assertEqual(expected, actual)
def test_vertical_transition_energy_w_options(self):
actual = parse_args([
"vte",
"--unitcell_json",
"a",
"--initial_dir",
"b",
"--dir",
"c",
"--print",
"--y_range",
"0.1",
"0.2",
"--json",
"d",
"--show",
])
expected = Namespace(
unitcell_json="a",
initial_dir="b",
dir="c",
print=True,
y_range=[0.1, 0.2],
json="d",
show=True,
func=actual.func,
)
self.assertEqual(expected, actual)
def test_vertical_transition_input_maker_wo_options(self):
actual = parse_args(["vtim"])
expected = Namespace(
additional_charge=None,
initial_dir_name=None,
contcar="CONTCAR",
func=actual.func,
)
self.assertEqual(expected, actual)
def test_supercell_calc_results_w_options(self):
actual = parse_args([
"efc",
"--nocorr",
"--manual",
"0.1",
"--unitcell_json",
"a",
"--perfect_json",
"b",
"--ewald_json",
"c",
"--ewald_initial_param",
"0.2",
"--ewald_convergence",
"0.3",
"--ewald_accuracy",
"0.4",
"--dirs",
"d",
"e",
"--dir_all",
"--force_overwrite",
"--center",
"0.5",
"0.6",
"0.7",
"--json_file",
"f",
"--print",
"--plot_potential",
"--y_range",
"0.8",
"0.9",
])
expected = Namespace(
nocorr=True,
manual=0.1,
unitcell_json="a",
perfect_json="b",
ewald_json="c",
ewald_initial_param=0.2,
ewald_convergence=0.3,
ewald_accuracy=0.4,
dirs=["d", "e"],
dir_all=True,
force_overwrite=True,
defect_center=[0.5, 0.6, 0.7],
json_file="f",
print=True,
plot_potential=True,
y_range=[0.8, 0.9],
func=actual.func,
)
self.assertEqual(expected, actual)
def test_plot_energy_w_options(self):
actual = parse_args([
"pe",
"--name",
"a",
"--x_range",
"0.1",
"0.2",
"--y_range",
"0.3",
"0.4",
"--save_file",
"b",
"--energies",
"c",
"--unitcell",
"d",
"--perfect",
"e",
"--defect_dirs",
"g",
"h",
"--chem_pot_json",
"i",
"--chem_pot_label",
"j",
"--filtering",
"k",
"--concentration",
"--show_transition_level",
"--show_all",
"--reload_defects",
"--print",
])
expected = Namespace(
name="a",
x_range=[0.1, 0.2],
y_range=[0.3, 0.4],
save_file="b",
energies="c",
unitcell="d",
perfect="e",
defect_dirs=["g", "h"],
chem_pot_json="i",
chem_pot_label="j",
filtering="k",
concentration=True,
show_transition_level=True,
show_all=True,
reload_defects=True,
print=True,
func=actual.func,
)
self.assertEqual(expected, actual)
def test_parse_eigenvalues_wo_options(self):
actual = parse_args(["eig"])
expected = Namespace(
title="",
y_range=None,
save_file=None,
unitcell="../unitcell/unitcell.json",
defect_dir=None,
func=actual.func,
)
self.assertEqual(expected, actual)
def test_local_structure_wo_options(self):
actual = parse_args(["ls"])
d = get_default_args(defect_structure_matcher)
expected = Namespace(
show_all=False,
compare_structure=False,
site_tolerance=d["site_tolerance"],
defect_dirs=None,
func=actual.func,
)
self.assertEqual(expected, actual)
def test_vertical_transition_energy_wo_options(self):
actual = parse_args(["vte"])
expected = Namespace(
unitcell_json="../unitcell/unitcell.json",
initial_dir=None,
dir=None,
print=False,
y_range=None,
json="vte_correction.json",
show=False,
func=actual.func,
)
self.assertEqual(expected, actual)
def test_local_structure_w_options(self):
actual = parse_args([
"ls", "--show_all", "--compare_structure", "--site_tolerance",
"0.1", "--defect_dirs", "b", "c"
])
expected = Namespace(
show_all=True,
compare_structure=True,
site_tolerance=0.1,
defect_dirs=["b", "c"],
func=actual.func,
)
self.assertEqual(expected, actual)
def test_concentrations_wo_options(self):
actual = parse_args(["c"])
expected = Namespace(
energies="defect_energies.json",
unitcell="../unitcell/unitcell.json",
filtering=None,
frac_mag_to_one=False,
verbose=False,
temperature=None,
quenched_temperature=298,
func=actual.func,
)
self.assertEqual(expected, actual)
def test_defect_wo_options(self):
actual = parse_args(["d"])
expected = Namespace(
defect_dirs=None,
diagnose=False,
json="defect.json",
perfect="perfect/dft_results.json",
defect_entry="defect_entry.json",
correction="correction.json",
dft_results="dft_results.json",
band_edge=None,
func=actual.func,
)
self.assertEqual(expected, actual)
def test_defect_entry_wo_options(self):
actual = parse_args(["de"])
d = get_default_args(DefectEntry.from_defect_structure)
expected = Namespace(
print=False,
make_defect_entry=False,
yaml=None,
json="defect_entry.json",
perfect_poscar="../perfect/POSCAR",
defect_poscar="POSCAR",
displacement_distance=d["displacement_distance"],
defect_name=d["defect_name"],
func=actual.func,
)
self.assertEqual(expected, actual)
def test_unitcell_calc_results_wo_options(self):
actual = parse_args(["ur"])
# d = get_default_args(UnitcellCalcResults)
# func is a pointer so need to point the same address.
expected = Namespace(json_file="unitcell.json",
static_diele=None,
ionic_diele=None,
band_edge_dir=None,
static_diele_dir=None,
ionic_diele_dir=None,
total_dos_dir=None,
outcar="OUTCAR",
vasprun="vasprun.xml",
print=False,
func=actual.func)
self.assertEqual(expected, actual)
def test_supercell_calc_results_w_options(self):
actual = parse_args([
"sr",
"--dirs",
"a",
"b",
"--dir_all",
"-v",
"c",
"-c",
"d",
"-o",
"e",
"-p",
"f",
"--center",
"10",
"-de",
"g",
"--json",
"h",
"--cutoff",
"0.1",
"--print",
"--defect_symprec",
"1.1",
"--angle_tolerance",
"2.1",
])
expected = Namespace(
dirs=["a", "b"],
dir_all=True,
vasprun="c",
contcar="d",
outcar="e",
procar="f",
defect_center=[10.0], # be careful
defect_entry_name="g",
json="h",
cutoff=0.1,
print=True,
defect_symprec=1.1,
angle_tolerance=2.1,
func=actual.func,
)
self.assertEqual(expected, actual)
def test_supercell_calc_results_wo_options(self):
actual = parse_args(["sr"])
d = get_default_args(SupercellCalcResults.from_vasp_files)
expected = Namespace(dirs=None,
dir_all=False,
vasprun=d["vasprun"],
contcar=d["contcar"],
outcar=d["outcar"],
procar=d["procar"],
defect_center=None,
defect_entry_name="defect_entry.json",
json="dft_results.json",
cutoff=d["cutoff"],
print=False,
func=actual.func,
**defect_prec_args)
self.assertEqual(expected, actual)
def test_vertical_transition_input_maker_w_options(self):
actual = parse_args([
"vtim",
"--additional_charge",
"1",
"--initial_dir_name",
"a",
"--contcar",
"b",
])
expected = Namespace(
additional_charge=1,
initial_dir_name="a",
contcar="b",
func=actual.func,
)
self.assertEqual(expected, actual)
def test_complex_defects_w_options(self):
actual = parse_args([
"cd",
"--yaml",
"a",
"--dposcar",
"b",
"--defect_in",
"c",
"--removed_atom_indices",
"1",
"--inserted_elements",
"H",
"--inserted_coords",
"0.1",
"0.2",
"--name",
"d",
"--extreme_charge_state",
"100",
"--annotation",
"e",
"--defect_symprec",
"1.1",
"--angle_tolerance",
"2.1",
])
d = get_default_args(ComplexDefects.add_defect)
d.update(get_default_args(ComplexDefects.from_files))
# func is a pointer so need to point the same address.
expected = Namespace(
yaml="a",
dposcar="b",
defect_in="c",
removed_atom_indices=[1],
inserted_elements=["H"],
inserted_coords=[0.1, 0.2],
name="d",
extreme_charge_state=100,
annotation="e",
defect_symprec=1.1,
angle_tolerance=2.1,
func=actual.func,
)
self.assertEqual(expected, actual)
def test_interstitial_wo_options(self):
actual = parse_args(["i"])
d = get_default_args(InterstitialSiteSet.add_sites)
d.update(get_default_args(InterstitialSiteSet.from_files))
d.update(get_default_args(interstitials_from_charge_density))
# func is a pointer so need to point the same address.
expected = Namespace(yaml=d["yaml_filename"],
uposcar=d["uposcar"],
defect_in="defect.in",
interstitial_coords=None,
site_name=None,
radius=d["vicinage_radius"],
interstitial_symprec=d["interstitial_symprec"],
method=d["method"],
chgcar=None,
func=actual.func,
**defect_prec_args)
self.assertEqual(expected, actual)
def test_interstitial_w_options(self):
actual = parse_args([
"i",
"--yaml",
"a",
"--uposcar",
"b",
"--defect_in",
"c",
"-c",
"0.1",
"0.2",
"0.3",
"--name",
"d",
"--radius",
"1.1",
"--interstitial_symprec",
"2.1",
"--method",
"e",
"--chgcar",
"f",
"--defect_symprec",
"3.1",
"--angle_tolerance",
"4.1",
])
expected = Namespace(
yaml="a",
uposcar="b",
defect_in="c",
interstitial_coords=[0.1, 0.2, 0.3],
site_name="d",
radius=1.1,
interstitial_symprec=2.1,
method="e",
chgcar="f",
defect_symprec=3.1,
angle_tolerance=4.1,
func=actual.func,
)
self.assertEqual(expected, actual)
def test_complex_defects_wo_options(self):
actual = parse_args(["cd"])
d = get_default_args(ComplexDefects.add_defect)
d.update(get_default_args(ComplexDefects.from_files))
# func is a pointer so need to point the same address.
expected = Namespace(
yaml=d["yaml_filename"],
dposcar=d["dposcar"],
defect_in="defect.in",
removed_atom_indices=None,
inserted_elements=None,
inserted_coords=None,
name=None,
extreme_charge_state=None,
annotation=None,
func=actual.func,
**defect_prec_args,
)
self.assertEqual(expected, actual)
def test_defect_vasp_set_maker_wo_options(self):
actual = parse_args(["dvs"])
# default set used in the vise unittest
from vise.cli.tests.test_main import default_vasp_args
default_vasp_args.pop("charge")
default_vasp_args.pop("task")
expected = Namespace(
spin_polarize=True,
defect_in="defect.in",
dposcar="DPOSCAR",
keywords=None,
specified_defects=None,
force_overwrite=False,
kpt_density=DEFECT_KPT_DENSITY,
wavecar=True,
func=actual.func,
**default_vasp_args,
)
self.assertEqual(expected, actual)
def test_vasp_parchg_set_wo_options(self):
actual = parse_args([
"vps",
"--read_dir",
"a",
"--band_indices",
"1",
"2",
"3",
])
expected = Namespace(
read_dir="a",
write_dir=".",
band_indices=[1, 2, 3],
kpoint_indices=None,
contcar="CONTCAR",
func=actual.func,
)
self.assertEqual(expected, actual)
def test_unitcell_calc_results_w_options(self):
actual = parse_args([
"ur", "--json_file", "a", "--static_diele", "0.0", "0.1", "0.2",
"--ionic_diele", "0.3", "0.4", "0.5", "--band_edge_dir", "b-dir",
"--static_diele_dir", "s-dir", "--ionic_diele_dir", "i-dir",
"--total_dos_dir", "d-dir", "--outcar", "c", "--vasprun", "d",
"--print"
])
expected = Namespace(json_file="a",
static_diele=[0.0, 0.1, 0.2],
ionic_diele=[0.3, 0.4, 0.5],
band_edge_dir="b-dir",
static_diele_dir="s-dir",
ionic_diele_dir="i-dir",
total_dos_dir="d-dir",
outcar="c",
vasprun="d",
print=True,
func=actual.func)
self.assertEqual(expected, actual)
def test_plot_energy_wo_options(self):
actual = parse_args(["pe"])
expected = Namespace(
name=None,
x_range=None,
y_range=None,
save_file=None,
energies="defect_energies.json",
unitcell="../unitcell/unitcell.json",
perfect="perfect/dft_results.json",
defect_dirs=None,
chem_pot_json="../competing_phases/cpd.json",
chem_pot_label="A",
filtering=None,
concentration=False,
show_transition_level=False,
show_all=False,
reload_defects=False,
print=False,
func=actual.func,
)
self.assertEqual(expected, actual)
def test_supercell_calc_results_wo_options(self):
actual = parse_args(["efc"])
d = get_default_args(Ewald.from_optimization)
expected = Namespace(
nocorr=False,
manual=0.0,
unitcell_json="../unitcell/unitcell.json",
perfect_json="perfect/dft_results.json",
ewald_json="ewald.json",
ewald_initial_param=d["initial_ewald_param"],
ewald_convergence=d["convergence"],
ewald_accuracy=d["prod_cutoff_fwhm"],
dirs=None,
dir_all=False,
force_overwrite=False,
defect_center=None,
json_file="correction.json",
print=False,
plot_potential=False,
y_range=None,
func=actual.func,
)
self.assertEqual(expected, actual)
