def test_remove_higher_energy_comp():
comp_es = CompositionEnergies(
{Composition('Mg1'): CompositionEnergy(-1.9, "mp-2"),
Composition('Mg2'): CompositionEnergy(-4.0, "mp-3"),
Composition('O2'): CompositionEnergy(-4.0, "mp-4")})
actual = remove_higher_energy_comp(comp_es)
expected = CompositionEnergies(
{Composition('Mg2'): CompositionEnergy(-4.0, "mp-3"),
Composition('O2'): CompositionEnergy(-4.0, "mp-4"),})
assert actual == expected
def make_composition_energies(args):
if args.yaml_file:
composition_energies = CompositionEnergies.from_yaml(args.yaml_file)
else:
composition_energies = CompositionEnergies()
for d in args.dirs:
vasprun = Vasprun(d / defaults.vasprun)
composition = vasprun.final_structure.composition
energy = float(vasprun.final_energy) # original type is FloatWithUnit
composition_energies[composition] = CompositionEnergy(energy, "local")
composition_energies.to_yaml_file()
def make_composition_energies(args):
if args.yaml_file:
composition_energies = CompositionEnergies.from_yaml(args.yaml_file)
else:
composition_energies = CompositionEnergies()
for d in args.dirs:
outcar = Outcar(d / defaults.outcar)
composition = Structure.from_file(d / defaults.contcar).composition
energy = float(outcar.final_energy) # original type is FloatWithUnit
composition_energies[composition] = CompositionEnergy(energy, "local")
composition_energies.to_yaml_file()
def make_composition_energies_from_mp(
elements: List[str],
atom_energy_yaml: Optional[str] = None,
) -> CompositionEnergies:
"""Obtain the energies from Materials Project.
When the atom_energy_yaml is provided, the total energies are aligned
via atom energies.
"""
properties = ["task_id", "full_formula", "final_energy"]
query = MpQuery(elements, properties=properties)
comp_es = {}
if atom_energy_yaml:
energies = loadfn(atom_energy_yaml)
diff = {e: energies[e] - mp_energies[e] for e in elements}
else:
diff = {e: 0.0 for e in elements}
for m in query.materials:
key = Composition(m["full_formula"])
energy = m["final_energy"]
for k, v in key.as_dict().items():
energy += diff[k] * v
comp_es[key] = CompositionEnergy(energy, m["task_id"])
print(comp_es)
comp_es = remove_higher_energy_comp(comp_es)
print(comp_es)
return CompositionEnergies(comp_es)
def comp_energies_corr():
return CompositionEnergies({
Composition('O8'):
CompositionEnergy(-39.58364375 + diff["O"] * 8, "mp-1"),
Composition('Mg3'):
CompositionEnergy(-4.79068775 + diff["Mg"] * 3, "mp-2"),
Composition('Mg1O1'):
CompositionEnergy(-11.96742144 + diff["Mg"] + diff["O"], "mp-3")
})
def comp_energies():
return CompositionEnergies({
Composition('O8'):
CompositionEnergy(-39.58364375, "mp-1"),
Composition('Mg3'):
CompositionEnergy(-4.79068775, "mp-2"),
Composition('Mg1O1'):
CompositionEnergy(-11.96742144, "mp-3")
})
def composition_energies():
return CompositionEnergies({
Composition("H"):
CompositionEnergy(0.0, "a"),
Composition("H4O2"):
CompositionEnergy(-4.0, "c"),
Composition("O"):
CompositionEnergy(1.0, "b"),
Composition("Cl"):
CompositionEnergy(12.0, "f"),
Composition("O2Cl"):
CompositionEnergy(3.0, "e"),
Composition("O2Cl2"):
CompositionEnergy(6.0, "d")
})
def test_composition_energies_from_mp(mocker, tmpdir):
tmpdir.chdir()
args = Namespace(elements=["H"], atom_energy_yaml="a.yaml")
mock = mocker.patch(
"pydefect.cli.main_util_functions.make_composition_energies_from_mp")
mock.return_value = CompositionEnergies(
{Composition("H"): CompositionEnergy(1.0, "mp-1")})
composition_energies_from_mp(args)
mock.assert_called_once_with(elements=["H"], atom_energy_yaml="a.yaml")
actual = Path("composition_energies.yaml").read_text()
expected = """H1:
energy: 1.0
source: mp-1
"""
assert actual == expected
def test_make_standard_and_relative_energies(mocker, tmpdir):
tmpdir.chdir()
args = Namespace(composition_energies_yaml="a.yaml")
mock = mocker.patch("pydefect.cli.main_functions.CompositionEnergies")
mock.from_yaml.return_value = CompositionEnergies({
Composition("H"):
CompositionEnergy(-1.0),
Composition("He"):
CompositionEnergy(-2.0),
Composition("HHe"):
CompositionEnergy(-5.0)
})
make_standard_and_relative_energies(args)
mock.from_yaml.assert_called_once_with("a.yaml")
actual = Path("standard_energies.yaml").read_text()
expected = """H: -1.0
He: -2.0
"""
assert actual == expected
actual = Path("relative_energies.yaml").read_text()
expected = """HHe: -1.0
"""
assert actual == expected
def make_composition_energies_from_mp(elements: List[str],
atom_energy_yaml: Optional[str] = None,
) -> CompositionEnergies:
"""Obtain the energies from Materials Project.
When the atom_energy_yaml is provided, the total energies are aligned
via atom energies.
"""
entries: List[ComputedEntry] = MpEntries(elements).materials
comp_es = {}
if atom_energy_yaml:
energies = loadfn(atom_energy_yaml)
diff = {e: energies[e] - mp_energies[e] for e in elements}
else:
diff = {e: 0.0 for e in elements}
for e in entries:
key = e.composition
energy = e.energy
for k, v in key.as_dict().items():
energy += diff[k] * v
comp_es[key] = CompositionEnergy(energy, e.entry_id)
comp_es = remove_higher_energy_comp(comp_es)
return CompositionEnergies(comp_es)
def make_standard_and_relative_energies(args):
comp_energies = CompositionEnergies.from_yaml(
args.composition_energies_yaml)
std_energies, rel_energies = comp_energies.std_rel_energies
std_energies.to_yaml_file()
rel_energies.to_yaml_file()
def test_composition_energies_from_dict():
actual = CompositionEnergies.from_dict({"Mg": -1.0})
expected = CompositionEnergies(
{Composition("Mg"): CompositionEnergy(-1.0)})
assert actual == expected
actual = actual.std_rel_energies