def test_as_dict_and_from_dict(self):
sm = StructureMatcher(ltol=0.1, stol=0.2, angle_tol=2,
primitive_cell=False, scale=False,
comparator=FrameworkComparator())
d = sm.as_dict()
sm2 = StructureMatcher.from_dict(d)
self.assertEqual(sm2.as_dict(), d)
def __init__(
self,
existing_structures,
structure_matcher=StructureMatcher(comparator=ElementComparator()),
symprec=None,
):
"""
Remove existing structures based on the structure matcher
and symmetry (if symprec is given).
Args:
existing_structures: List of existing structures to compare with
structure_matcher: Provides a structure matcher to be used for
structure comparison.
symprec: The precision in the symmetry finder algorithm if None (
default value), no symmetry check is performed and only the
structure matcher is used. A recommended value is 1e-5.
"""
self.symprec = symprec
self.structure_list = []
self.existing_structures = existing_structures
if isinstance(structure_matcher, dict):
self.structure_matcher = StructureMatcher.from_dict(structure_matcher)
else:
self.structure_matcher = structure_matcher
def test_to_dict_and_from_dict(self):
sm = StructureMatcher(ltol=0.1, stol=0.2, angle_tol=2,
primitive_cell=False, scale=False,
comparator=FrameworkComparator())
d = sm.to_dict
sm2 = StructureMatcher.from_dict(d)
self.assertEqual(sm2.to_dict, d)
def __init__(self, structure_matcher=StructureMatcher(
comparator=ElementComparator()), symprec=None):
"""
Remove duplicate structures based on the structure matcher
and symmetry (if symprec is given).
Args:
structure_matcher: Provides a structure matcher to be used for
structure comparison.
symprec: The precision in the symmetry finder algorithm if None (
default value), no symmetry check is performed and only the
structure matcher is used. A recommended value is 1e-5.
"""
self._symprec = symprec
self._structure_list = []
if isinstance(structure_matcher, dict):
self._sm = StructureMatcher.from_dict(structure_matcher)
else:
self._sm = structure_matcher
def run_task(self, fw_spec):
reference_struct = fw_spec.get("base_structure")
results = fw_spec.get("inserted_results", [])
max_inserted_atoms = fw_spec.get("max_inserted_atoms", None)
working_ion = fw_spec.get("working_ion")
sm_dict = fw_spec.get("structure_matcher", SM_DICT)
if not isinstance(sm_dict, dict):
sm_dict = sm_dict.as_dict()
sm_dict["ignored_species"] = [working_ion]
sm = StructureMatcher.from_dict(sm_dict)
if len(results) == 0:
# can happen if all parents fizzled
raise RuntimeError("No insertion calculation completed")
tmp_struct_ = results[0]["structure"] # type: Structure
n_ions = int(tmp_struct_.composition.as_dict()[working_ion])
if max_inserted_atoms is not None and n_ions >= max_inserted_atoms:
return FWAction(defuse_children=True)
best_res = {"energy": math.inf}
n_completed = 0
for ires in results:
n_completed += 1
ires_struct_ = ires["structure"]
if (sm.fit(ires_struct_, reference_struct)
and ires["energy"] < best_res["energy"]):
logger.info("Found new optimal_structure")
best_res = ires
if "structure" not in best_res:
# No matching structure was found in the completed results
if n_completed > 0:
return FWAction(defuse_children=True)
# Get the new structures
return FWAction(
update_spec={"optimal_structure": best_res["structure"]})
def __init__(
self,
structure_matcher=StructureMatcher(comparator=ElementComparator()),
symprec=None):
"""
Remove duplicate structures based on the structure matcher
and symmetry (if symprec is given).
Args:
structure_matcher:
Provides a structure matcher to be used for structure
comparison.
symprec:
The precision in the symmetry finder algorithm
if None (default value), no symmetry check is performed and
only the structure matcher is used. A recommended value is 1e-5
"""
self._symprec = symprec
self._structure_list = []
if isinstance(structure_matcher, dict):
self._sm = StructureMatcher.from_dict(structure_matcher)
else:
self._sm = structure_matcher
