def test_single_pseudo_from_dict_deprecated():
"""Check that from_dict still works as intented"""
with (TEST_DIR / "inputs" / "GTH_POTENTIALS.Cl").open() as fhandle:
pseudo = PseudopotentialData.from_lines([line for line in fhandle])
asdict = pseudo.dict()
with pytest.deprecated_call():
reloaded = PseudopotentialData.from_dict(asdict)
assert reloaded == pseudo
def test_single_pseudo_parse_obj_nlcc_empty_default():
"""Check that for local/non_local data we can also use the abbrev 'coeffs' for loading"""
with (TEST_DIR / "inputs" / "GTH_POTENTIALS.Cl").open() as fhandle:
pseudo = PseudopotentialData.from_lines([line for line in fhandle])
assert pseudo.nlcc is not None
asdict = pseudo.dict()
asdict.pop("nlcc")
reloaded = PseudopotentialData.parse_obj(asdict)
assert reloaded.nlcc == []
def test_single_pseudo_parse_obj_aliased():
"""Check that for local/non_local data we can also use the abbrev 'coeffs' for loading"""
with (TEST_DIR / "inputs" / "GTH_POTENTIALS.Cl").open() as fhandle:
pseudo = PseudopotentialData.from_lines([line for line in fhandle])
assert pseudo.local.coefficients
asdict = pseudo.dict()
asdict["local"]["coeffs"] = asdict["local"].pop("coefficients")
reloaded = PseudopotentialData.parse_obj(asdict)
assert reloaded == pseudo
def _dict2pseudodata(data: Dict[str, Any]) -> PseudopotentialData:
obj = {
k: v
for k, v in data.items() if k not in ("name", "tags", "version")
}
obj["identifiers"] = obj.pop("aliases")
return PseudopotentialData.parse_obj(obj)
def _pseudodata2dict(data: PseudopotentialData) -> Dict[str, Any]:
"""
Convert a PseudopotentialData to a compatible dict with:
* Decimals replaced by strings
* the required attrs set on the root
* the key "coefficients" replaced with "coeffs"
"""
pseudo_dict = data.dict(by_alias=True)
stack = [pseudo_dict]
while stack:
current = stack.pop()
for key, val in current.items():
if isinstance(val, dict):
stack.append(val)
elif isinstance(val, Decimal):
current[key] = str(val)
elif isinstance(val, list) and val and isinstance(val[0], dict):
stack += val
elif isinstance(val, list) and val and isinstance(val[0], Decimal):
current[key] = [str(v) for v in val]
pseudo_dict["aliases"] = sorted(pseudo_dict.pop("identifiers"),
key=lambda i: -len(i))
pseudo_dict["name"] = pseudo_dict["aliases"][0]
pseudo_dict["tags"] = pseudo_dict["name"].split("-")
return pseudo_dict
def test_single_pseudo_from_dict_type_map_deprecated():
"""Check that from_dict still works as intented with the type_map and its likely only use case"""
with (TEST_DIR / "inputs" / "GTH_POTENTIALS.Cl").open() as fhandle:
pseudo = PseudopotentialData.from_lines([line for line in fhandle])
asdict = pseudo.dict()
asdict["local"]["coeffs"] = asdict["local"].pop("coefficients")
def rename(data):
data["coefficients"] = data.pop("coeffs")
return data
with pytest.deprecated_call():
reloaded = PseudopotentialData.from_dict(asdict, type_hooks={PseudopotentialDataLocal: rename})
assert reloaded == pseudo
def test_single_pseudo_import():
with (TEST_DIR / "inputs" / "GTH_POTENTIALS.Cl").open() as fhandle:
pseudo = PseudopotentialData.from_lines([line for line in fhandle])
assert pseudo.element == "Cl"
assert pseudo.n_el == [2, 5]
assert len(pseudo.local.coefficients) == 1
assert len(pseudo.non_local) == 2
assert pseudo.non_local[0].nproj == 2
assert pseudo.non_local[1].nproj == 1
def from_cp2k(cls,
fhandle,
filters=None,
duplicate_handling="ignore",
ignore_invalid=False):
"""
Constructs a list with pseudopotential objects from a Pseudopotential in CP2K format
:param fhandle: open file handle
:param filters: a dict with attribute filter functions
:param duplicate_handling: how to handle duplicates ("ignore", "error", "new" (version))
:param ignore_invalid: whether to ignore invalid entries silently
:rtype: list
"""
from cp2k_input_tools.pseudopotentials import PseudopotentialData
if not filters:
filters = {}
def matches_criteria(pseudo):
return all(
fspec(pseudo[field]) for field, fspec in filters.items())
def exists(pseudo):
try:
cls.get(pseudo["element"], pseudo["name"], match_aliases=False)
except NotExistent:
return False
return True
pseudos = [
p for p in (_pseudodata2dict(p)
for p in PseudopotentialData.datafile_iter(
fhandle, keep_going=ignore_invalid))
if matches_criteria(p)
]
if duplicate_handling == "ignore": # simply filter duplicates
pseudos = [p for p in pseudos if not exists(p)]
elif duplicate_handling == "error":
for pseudo in pseudos:
try:
latest = cls.get(pseudo["element"],
pseudo["name"],
match_aliases=False)
except NotExistent:
pass
else:
raise UniquenessError(
f"Gaussian Pseudopotential already exists for"
f" element={pseudo['element']}, name={pseudo['name']}: {latest.uuid}"
)
elif duplicate_handling == "new":
for pseudo in pseudos:
try:
latest = cls.get(pseudo["element"],
pseudo["name"],
match_aliases=False)
except NotExistent:
pass
else:
pseudo["version"] = latest.version + 1
else:
raise ValueError(
f"Specified duplicate handling strategy not recognized: '{duplicate_handling}'"
)
return [cls(**p) for p in pseudos]
def test_single_pseudo_roundtrip():
with (TEST_DIR / "inputs" / "GTH_POTENTIALS.Cl").open() as fhandle:
lines = [line.rstrip() for line in fhandle]
pseudo = PseudopotentialData.from_lines(lines)
assert list(pseudo.cp2k_format_line_iter()) == lines