def test_make_defect_entry(defect_entry):
relaxed_coords = \
[[0.25, 0.0, 0.0], [0.5, 0.5, 0.0], [0.5, 0.0, 0.5], [0.0, 0.5, 0.5],
[0.0, 0.0, 0.51], [0.0, 0.51, 0.0], [0.5, 0.0, 0.0], [0.5, 0.5, 0.5]]
relaxed_defect = IStructure(
Lattice.cubic(10.0), ["Li"] + ["H"] * 3 + ["He"] * 4, relaxed_coords)
unrelaxed_coords = \
[[0.25, 0.0, 0.0], [0.5, 0.5, 0.0], [0.5, 0.0, 0.5], [0.0, 0.5, 0.5],
[0.0, 0.0, 0.5], [0.0, 0.5, 0.0], [0.5, 0.0, 0.0], [0.5, 0.5, 0.5]]
unrelaxed_defect = IStructure(
Lattice.cubic(10.0), ["Li"] + ["H"] * 3 + ["He"] * 4, unrelaxed_coords)
actual = make_defect_entry(name="Va_O1",
charge=1,
perfect_structure=perfect,
defect_structure=relaxed_defect)
expected = DefectEntry(name="Va_O1",
charge=1,
structure=unrelaxed_defect,
perturbed_structure=None,
site_symmetry="4mm",
defect_center=(0.125, 0.0, 0.0))
assert actual == expected
def test_make_defect_energy_info(mocker):
defect_entry = mocker.Mock(DefectEntry, autospec=True)
defect_entry.name = "Va_Mg1"
defect_entry.charge = -1
calc_results = mocker.Mock(CalcResults, autospec=True)
calc_results.structure = IStructure(Lattice.cubic(1.0), ["O"], [[0.0] * 3])
calc_results.energy = 10.0
calc_results.electronic_conv = False
correction = mocker.Mock(Correction, autospec=True)
correction.correction_dict = {"a": 10.0}
p_calc_results = mocker.Mock(CalcResults, autospec=True)
p_calc_results.structure = IStructure(Lattice.cubic(1.0), ["Mg", "O"],
[[0.0] * 3] * 2)
p_calc_results.energy = 1.0
standard_energies = StandardEnergies({"Mg": 10.0, "O": 20.0})
unitcell = mocker.Mock()
unitcell.vbm = 100.0
actual = make_defect_energy_info(defect_entry, calc_results, correction,
p_calc_results, standard_energies,
unitcell)
energy = DefectEnergy(formation_energy=10.0 - 1.0 + 10 - 100.0,
energy_corrections={"a": 10.0},
is_shallow=None)
expected = DefectEnergyInfo(name="Va_Mg1",
charge=-1,
atom_io={"Mg": -1},
defect_energy=energy)
assert actual == expected
def test_make_calc_summary(mocker):
defect_entry = mocker.Mock(spec=DefectEntry, autospec=True)
defect_entry.name = "Va_O1"
defect_entry.charge = 1
defect_entry.full_name = "Va_O1_1"
calc_results = mocker.Mock(spec=CalcResults, autospec=True)
calc_results.structure = \
IStructure(Lattice.cubic(1.0), ["Mg"], [[0.0]*3])
calc_results.energy = 10.0 + defaults.abs_strange_energy - 0.1
structure_info = mocker.Mock(spec=DefectStructureInfo, autospec=True)
p_calc_results = mocker.Mock(spec=CalcResults, autospec=True)
p_calc_results.structure = \
IStructure(Lattice.cubic(1.0), ["Mg", "O"], [[0.0]*3]*2)
p_calc_results.energy = 10.0
actual = make_calc_summary(calc_set=[(calc_results, defect_entry,
structure_info)],
p_calc_results=p_calc_results)
single_summary = SingleCalcSummary(
charge=1,
atom_io={"O": -1},
electronic_conv=calc_results.electronic_conv,
ionic_conv=calc_results.ionic_conv,
is_energy_strange=False,
same_config_from_init=structure_info.same_config_from_init,
defect_type=structure_info.defect_type,
symm_relation=structure_info.symm_relation)
expected = CalcSummary({"Va_O1_1": single_summary})
assert actual == expected
def structure_analyzer():
cu2o_perfect = IStructure(
Lattice.cubic(5),
species=["Cu"] * 4 + ["O"] * 2,
coords=[
[0.25, 0.25, 0.25], # removed
[0.25, 0.74, 0.74], # removed
[0.75, 0.75, 0.25],
[0.75, 0.25, 0.75],
[0, 0, 0],
[0.5, 0.5, 0.5]
])
# add [0.1, -0.1, 0]
# 3rd -- 6th
# [0.85, 0.65, 0.25] - [0.76, 0.73, 0.24] = [0.09, -0.08, 0.01]
# [0.85, 0.15, 0.75] - [0.75, 0.25, 0.73] = [0.10, -0.10, 0.02]
# [0.1, -0.1, 0] -[0.1, -0.1, 0] = [0, 0, 0]
# [0.6, 0.4, 0.5] - [0.5, 0.5, 0.5] = [0.1, -0.1, 0]
cu2o_defect = IStructure(
Lattice.cubic(5),
species=["Cu"] * 3 + ["O"] * 2 + ["H"],
coords=[
[0.25, 0.5, 0.5], # defect
[0.76, 0.73, 0.24],
[0.75, 0.25, 0.73],
[0.05, 0.95, 0],
[0.5, 0.5, 0.5],
[0.25] * 3
]) # defect
return DefectStructureComparator(defect_structure=cu2o_defect,
perfect_structure=cu2o_perfect)
def test_make_single_defect_energy(mocker):
perfect = mocker.Mock(CalcResults, autospec=True)
perfect.energy = 1.0
perfect.structure = IStructure(Lattice.cubic(1), ["H"] * 2, [[0] * 3] * 2)
defect = mocker.Mock(CalcResults, autospec=True)
defect.energy = 3.0
defect.structure = IStructure(Lattice.cubic(1), ["H"], [[0] * 3])
name, charge = "Va_H1", 5
defect_entry = mocker.Mock(DefectEntry, autospec=True)
defect_entry.name = name
defect_entry.charge = charge
single_defect_energy = \
make_single_defect_energy(perfect=perfect,
defect=defect,
defect_entry=defect_entry,
abs_chem_pot={Element.H: 100},
correction=ManualCorrection(7.0))
energy = 3.0 - 1.0 + 100
assert isinstance(single_defect_energy, SingleDefectEnergy)
assert single_defect_energy == SingleDefectEnergy(name, charge, energy,
7.0)
def complex_monoclinic():
lattice = Lattice.monoclinic(3, 4, 5, 100)
coords = [[0.0, 0.0, 0.0], [0.1, 0.0, 0.0], [0.9, 0.0, 0.0],
[0.2, 0.0, 0.0], [0.8, 0.0, 0.0]]
return IStructure(lattice=lattice,
species=["H", "He", "He", "He", "He"],
coords=coords)
def structure_analyzer_periodic_issue():
cu2o_perfect = IStructure(Lattice.cubic(5),
species=["Cu"] * 4 + ["O"] * 2,
coords=[[0.25, 0.25, 0.25], [0.25, 0.75, 0.75],
[0.75, 0.75, 0.25], [0.75, 0.25, 0.75],
[0, 0, 0], [0.5, 0.5, 0.5]])
# defect center is ([1.0, 1.0, 1.0] + [0.99, 0.99, 0.99]) / 2 = [0.995]*3
cu2o_defect = IStructure(Lattice.cubic(5),
species=["Cu"] * 4 + ["O"] + ["H"],
coords=[[0.25, 0.25, 0.25], [0.25, 0.75, 0.75],
[0.75, 0.75, 0.25], [0.75, 0.25, 0.75],
[0.5, 0.5, 0.5], [0.99, 0.99, 0.99]])
return DefectStructureComparator(defect_structure=cu2o_defect,
perfect_structure=cu2o_perfect)
def simple_cubic_2x2x2():
lattice = Lattice.cubic(2.0)
coords = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.0], [0.5, 0.0,
0.5], [0.0, 0.5, 0.5],
[0.0, 0.0, 0.5], [0.0, 0.5, 0.0], [0.5, 0.0, 0.0],
[0.5, 0.5, 0.5]]
return IStructure(lattice=lattice, species=["H"] * 8, coords=coords)
def make_defect_entry(name: str, charge: int, perfect_structure: IStructure,
defect_structure: IStructure):
analyzer = DefectStructureAnalyzer(perfect_structure, defect_structure)
species = []
frac_coords = []
for d, p in enumerate(analyzer.p_to_d):
if p is None:
site = defect_structure[d]
else:
site = perfect_structure[p]
species.append(site.specie)
frac_coords.append(site.frac_coords)
initial_structure = IStructure(perfect_structure.lattice, species,
frac_coords)
symmetrizer = StructureSymmetrizer(initial_structure)
return DefectEntry(name,
charge,
initial_structure,
None,
site_symmetry=symmetrizer.point_group,
defect_center=tuple(analyzer.defect_center_coord))
def calc_results():
return CalcResults(structure=IStructure(Lattice.cubic(1.0), ["H"],
[[0.0] * 3]),
energy=1.0,
magnetization=0.0,
potentials=[0.0],
electronic_conv=False,
ionic_conv=False)
def make_defect_entry_from_poscars(dirname, perf_poscar, defect_poscar):
names = dirname.split("_")
try:
name = "_".join(names[:-1])
charge = int(names[-1])
except ValueError:
logger.warning(f"Directory name {dirname} is invalid.")
raise
perfect = IStructure.from_file(perf_poscar)
defect = IStructure.from_file(defect_poscar)
defect_entry = make_defect_entry(name=name,
charge=charge,
perfect_structure=perfect,
defect_structure=defect)
defect_entry.to_json_file()
def test_make_recommended_supercell(simple_cubic, simple_cubic_2x2x2, tmpdir):
args = Namespace(unitcell=simple_cubic, matrix=None, min_num_atoms=8, max_num_atoms=8)
tmpdir.chdir()
make_supercell(args)
info = loadfn("supercell_info.json")
assert IStructure.from_file("SPOSCAR") == simple_cubic_2x2x2
assert info.structure == simple_cubic_2x2x2
assert info.transformation_matrix == [[2, 0, 0], [0, 2, 0], [0, 0, 2]]
def test_make_supercell_from_matrix(simple_cubic, simple_cubic_2x1x1, tmpdir):
matrix = [2, 1, 1]
args = Namespace(unitcell=simple_cubic, matrix=matrix, min_num_atoms=None, max_num_atoms=None)
tmpdir.chdir()
make_supercell(args)
info = loadfn("supercell_info.json")
assert IStructure.from_file("SPOSCAR") == simple_cubic_2x1x1
assert info.structure == simple_cubic_2x1x1
assert info.transformation_matrix == [[2, 0, 0], [0, 1, 0], [0, 0, 1]]
def test_make_efnv_correction(mocker):
mock_perfect = mocker.Mock(spec=CalcResults, autospec=True)
mock_defect = mocker.Mock(spec=CalcResults, autospec=True)
mock_perfect.structure = IStructure(Lattice.cubic(10),
species=["H"] + ["He"] * 3 + ["Li"],
coords=[[0, 0, 0], [1 / 2, 1 / 2, 0],
[1 / 2, 0, 1 / 2],
[0, 1 / 2, 1 / 2],
[0, 0, 1 / 2]])
mock_defect.structure = IStructure(Lattice.cubic(10),
species=["He"] * 3 + ["Li"],
coords=[[1 / 2, 1 / 2, 0],
[1 / 2, 0, 1 / 2],
[0, 1 / 2, 1 / 2],
[0, 0, 1 / 2]])
mock_perfect.potentials = [3.0, 4.0, 5.0, 6.0, 7.0]
mock_defect.potentials = [14.0, 25.0, 36.0, 47.0]
mock_ewald = mocker.patch("pydefect.cli.vasp.make_efnv_correction.Ewald")
ewald = mocker.Mock()
ewald.lattice_energy = 1e3
ewald.atomic_site_potential.return_value = 1e4
mock_ewald.return_value = ewald
efnvc = make_efnv_correction(charge=2,
calc_results=mock_defect,
perfect_calc_results=mock_perfect,
dielectric_tensor=np.eye(3))
unit_conversion = 180.95128169876497
assert efnvc.charge == 2
assert efnvc.point_charge_correction == -4e3 * unit_conversion
assert efnvc.defect_region_radius == 5.0
assert efnvc.sites == [
PotentialSite("He", 5 * np.sqrt(2), 10.0, 2e4 * unit_conversion),
PotentialSite("He", 5 * np.sqrt(2), 20.0, 2e4 * unit_conversion),
PotentialSite("He", 5 * np.sqrt(2), 30.0, 2e4 * unit_conversion),
PotentialSite("Li", 5.0, 40.0, None),
]
def ortho_conventional():
lattice = Lattice.orthorhombic(5, 6, 7)
coords = [
[0.0, 0.0, 0.0],
[0.5, 0.5, 0.0],
[0.5, 0.0, 0.5],
[0.0, 0.5, 0.5],
[0.0, 0.0, 0.5],
[0.0, 0.5, 0.0],
[0.5, 0.0, 0.0],
[0.5, 0.5, 0.5],
]
return IStructure(lattice=lattice,
species=["H"] * 4 + ["He"] * 4,
coords=coords)
def setUpClass(cls):
coords = [[0, 0, 0], [0.75, 0.5, 0.75]]
lattice = Lattice([[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]])
cls.struct_si = IStructure(lattice, ["Si"] * 2, coords)
cls.ref_incar = Incar.from_file(
os.path.join(module_dir, "..", "test_files", "setup_test",
"INCAR"))
cls.ref_poscar = Poscar.from_file(
os.path.join(module_dir, "..", "test_files", "setup_test",
"POSCAR"))
cls.ref_potcar = Potcar.from_file(
os.path.join(module_dir, "..", "test_files", "setup_test",
"POTCAR"))
cls.ref_kpoints = Kpoints.from_file(
os.path.join(module_dir, "..", "test_files", "setup_test",
"KPOINTS"))
def setUpClass(cls):
if not SETTINGS.get("VASP_PSP_DIR"):
raise unittest.SkipTest(
'This system is not set up to run VASP jobs. '
'Please set VASP_PSP_DIR variable in your ~/.pmgrc.yaml file.')
coords = [[0, 0, 0], [0.75, 0.5, 0.75]]
lattice = Lattice([[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]])
cls.struct_si = IStructure(lattice, ["Si"] * 2, coords)
cls.ref_incar = Incar.from_file(
os.path.join(module_dir, "reference_files", "setup_test", "INCAR"))
cls.ref_poscar = Poscar.from_file(
os.path.join(module_dir, "reference_files", "setup_test",
"POSCAR"))
cls.ref_potcar = Potcar.from_file(
os.path.join(module_dir, "reference_files", "setup_test",
"POTCAR"))
cls.ref_kpoints = Kpoints.from_file(
os.path.join(module_dir, "reference_files", "setup_test",
"KPOINTS"))
def copy_to_structure(structure: IStructure) -> Structure:
return Structure.from_dict(structure.as_dict())
def simple_cubic_2x1x1():
lattice = Lattice.orthorhombic(2.0, 1.0, 1.0)
coords = [[0.0, 0.0, 0.0], [0.5, 0.0, 0.0]]
return IStructure(lattice=lattice, species=["H", "H"], coords=coords)
def monoclinic():
lattice = Lattice.monoclinic(3, 4, 5, 100)
coords = [[0.0, 0.0, 0.0]]
return IStructure(lattice=lattice, species=["H"], coords=coords)
def elongated_tetragonal():
lattice = Lattice.tetragonal(a=1, c=3 * sqrt(2))
coords = [[0.0, 0.0, 0.0]]
return IStructure(lattice=lattice, species=["H"], coords=coords)
#!/usr/bin/env python # -*- coding: utf-8 -*- import math from pymatgen import Lattice from pymatgen import IStructure a = 4.209 latt = Lattice.cubic(a) structure = IStructure(latt, ["Cs", "Cl"], [[0, 0, 0], [0.5, 0.5, 0.5]]) print(structure.density) print(structure.distance_matrix) print(structure.get_distance)
def test_num_atom_diff():
s1 = IStructure(Lattice.cubic(1), ["H", "He"], [[0] * 3] * 2)
s2 = IStructure(Lattice.cubic(1), ["H", "Li"], [[0] * 3] * 2)
assert num_atom_differences(s1, s2) == {Element.He: 1, Element.Li: -1}
from pydefect.tests.helpers.assertion import assert_json_roundtrip, \
assert_msonable
from pymatgen import Lattice, IStructure
# "H" at [0.0, 0.0, 0.0] is removed here.
perf_coords = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.0], [0.5, 0.0, 0.5], [0.0, 0.5, 0.5],
[0.0, 0.0, 0.5], [0.0, 0.5, 0.0], [0.5, 0.0, 0.0], [0.5, 0.5, 0.5]]
coords = deepcopy(perf_coords)
coords.pop(0)
perturbed_coords = \
[[0.5, 0.5, 0.0], [0.5, 0.0, 0.5], [0.0, 0.5, 0.5],
[0.0, 0.0, 0.501], [0.0, 0.501, 0.0], [0.501, 0.0, 0.0], [0.5, 0.5, 0.5]]
perfect = IStructure(
Lattice.cubic(10.0), ["H"] * 4 + ["He"] * 4, perf_coords)
defect_structure = IStructure(
Lattice.cubic(10.0), ["H"] * 3 + ["He"] * 4, coords)
perturbed_defect = IStructure(
Lattice.cubic(10.0), ["H"] * 3 + ["He"] * 4, perturbed_coords)
@pytest.fixture
def defect_entry():
return DefectEntry(name="Va_O1",
charge=1,
structure=defect_structure,
perturbed_structure=perturbed_defect,
site_symmetry="m-3m",
defect_center=(0, 0, 0))
def bcc():
lattice = Lattice.cubic(1.0)
coords = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]]
return IStructure(lattice=lattice, species=["H"] * 2, coords=coords)
def c_centered_monoclinic():
lattice = Lattice.monoclinic(3, 4, 5, 100)
coords = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.0]]
return IStructure(lattice=lattice, species=["H", "H"], coords=coords)
def a_centered_orthorhombic():
lattice = Lattice([[1, 0, 0], [0, 2, 3], [0, -2, 3]])
coords = [[0.5, 0.8, 0.8], [0.0, 0.3, 0.0], [0.0, 0.0, 0.3]]
return IStructure(lattice=lattice, species=["H"] * 3, coords=coords)
def rhombohedral():
lattice = Lattice.rhombohedral(a=1, alpha=45)
coords = [[0.0, 0.0, 0.0]]
return IStructure(lattice=lattice, species=["H"], coords=coords)
def to_istructure(structure: Structure) -> IStructure:
return IStructure.from_dict(structure.as_dict())
def simple_cubic():
lattice = Lattice.cubic(1.0)
coords = [[0.0, 0.0, 0.0]]
return IStructure(lattice=lattice, species=["H"], coords=coords)
