def test_mp_query(mocker):
mock = mocker.patch("pydefect.util.mp_tools.MPRester")
expected = [{
'full_formula': 'Mg9'
}, {
'full_formula': 'Mg1O1'
}, {
'full_formula': 'O8'
}, {
'full_formula': 'O2'
}, {
'full_formula': 'O2'
}, {
'full_formula': 'O8'
}]
mock.return_value.__enter__.return_value.query.return_value = expected
element_list = ["Mg", "O"]
excluded = list(set(elements) - set(element_list))
mp_query = MpQuery(element_list=element_list, properties=["full_formula"])
mock.return_value.__enter__.return_value.query.assert_called_with(
criteria={
"elements": {
"$in": element_list,
"$nin": excluded
},
"e_above_hull": {
"$lte": 1e-5
}
},
properties=["full_formula"])
assert mp_query.materials == expected
def make_chem_pot_diag_from_mp(target: Union[Composition, str],
additional_elements: List[str] = None,
vertex_elements: List[str] = None,
atom_energy_yaml: Optional[str] = None):
"""Obtain the energies from Materials Project."""
properties = ["task_id", "full_formula", "final_energy"]
target = target if isinstance(target, Composition) else Composition(target)
elements = target.chemical_system.split("-")
vertex_elements = vertex_elements or elements
vertex_elements = [Element(e) for e in vertex_elements]
if additional_elements:
elements.extend(additional_elements)
query = MpQuery(elements, properties=properties)
comp_es = []
if atom_energy_yaml:
if ".yaml" in atom_energy_yaml:
energies = loadfn(atom_energy_yaml)
else:
logger.info(f"Atom energy set for {atom_energy_yaml} is used.")
energies = AtomEnergyType.from_string(atom_energy_yaml).energies
diff = {e: energies[e] - mp_energies[e] for e in elements}
else:
diff = None
for m in query.materials:
energy = m["final_energy"]
if diff:
for k, v in Composition(m["full_formula"]).as_dict().items():
energy += diff[k] * v
comp_es.append(
CompositionEnergy(Composition(m["full_formula"]), energy,
m["task_id"]))
comp_es = remove_higher_energy_comp(comp_es)
return ChemPotDiag(comp_es, target, vertex_elements)
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 make_competing_phase_dirs(args):
query = MpQuery(element_list=args.elements, e_above_hull=args.e_above_hull)
make_poscars_from_query(materials_query=query.materials, path=Path.cwd())
def test_mp_actual_query():
element_list = ["Mg", "O"]
mp_query = MpQuery(element_list=element_list,
properties=["full_formula", "structure"])
print(mp_query.materials)