def create_subsys(self, structure: Union[Structure, Molecule]):
"""
Create the structure for the input
"""
subsys = Subsys()
if isinstance(structure, Structure):
subsys.insert(Cell(structure.lattice))
# Decide what basis sets/pseudopotentials to use
basis_and_potential = get_basis_and_potential(
[str(s) for s in structure.species], self.potential_and_basis
)
# Insert atom kinds by identifying the unique sites (unique element and site properties)
unique_kinds = get_unique_site_indices(structure)
for k in unique_kinds.keys():
kind = k.split("_")[0]
kwargs = {}
if "magmom" in self.structure.site_properties:
kwargs["magnetization"] = self.structure.site_properties["magmom"][
unique_kinds[k][0]
]
if "ghost" in self.structure.site_properties:
kwargs["ghost"] = self.structure.site_properties["ghost"][
unique_kinds[k][0]
]
if "basis_set" in self.structure.site_properties:
basis_set = self.structure.site_properties["basis_set"][
unique_kinds[k][0]
]
else:
basis_set = basis_and_potential[kind]["basis"]
if "potential" in self.structure.site_properties:
potential = self.structure.site_properties["potential"][
unique_kinds[k][0]
]
else:
potential = basis_and_potential[kind]["potential"]
if "aux_basis" in self.structure.site_properties:
kwargs["aux_basis"] = self.structure.site_properties["aux_basis"][
unique_kinds[k][0]
]
subsys.insert(
Kind(kind, alias=k, basis_set=basis_set, potential=potential, **kwargs)
)
coord = Coord(structure, aliases=unique_kinds)
subsys.insert(coord)
self["FORCE_EVAL"].insert(subsys)
self.basis_set_file_names = basis_and_potential["basis_filenames"]
self.potential_file_name = basis_and_potential["potential_filename"]
def activate_nonperiodic(self):
"""
Activates a calculation with non-periodic calculations by turning of PBC and
changing the poisson solver. Still requires a CELL to put the atoms
"""
kwds = {
"POISSON_SOLVER": Keyword("POISSON_SOLVER", "MT"),
"PERIODIC": Keyword("PERIODIC", "NONE"),
}
self["FORCE_EVAL"]["DFT"].insert(Section("POISSON", subsections={}, keywords=kwds))
if not self.check("FORCE_EVAL/SUBSYS/CELL"):
x = max(s.coords[0] for s in self.structure.sites)
y = max(s.coords[1] for s in self.structure.sites)
z = max(s.coords[2] for s in self.structure.sites)
self["FORCE_EVAL"]["SUBSYS"].insert(Cell(lattice=Lattice([[x, 0, 0], [0, y, 0], [0, 0, z]])))
self["FORCE_EVAL"]["SUBSYS"]["CELL"].add(Keyword("PERIODIC", "NONE"))