def get_basis_set(self, atoms, spin=0):
bset = BasisSet()
sdict = symbol_number(atoms.get_chemical_symbols())
for b in self.basis.keys():
sn, label, _, _ = b.split('|')
site = sdict[sn]
bset.append(Basis(site=site, label=label, spin=spin, index=0))
return bset
def __init__(self, sisl_hamiltonian, shift_fermi=None, spin=None):
self.ham = sisl_hamiltonian
self.shift_fermi = shift_fermi
self.spin = spin
self.orbs = []
self.orb_dict = defaultdict(lambda: [])
g = self.ham._geometry
_atoms = self.ham._geometry._atoms
atomic_numbers = []
atom_positions = g.xyz
self.cell = np.array(g.sc.cell)
for ia, a in enumerate(_atoms):
atomic_numbers.append(a.Z)
self.atoms = Atoms(numbers=atomic_numbers,
cell=self.cell,
positions=atom_positions)
xred = self.atoms.get_scaled_positions()
sdict = list(symbol_number(self.atoms).keys())
if self.ham.spin.is_colinear:
if spin is None:
raise ValueError("For colinear spin, spin must be given")
else:
if spin is not None:
raise ValueError(
"For non-colinear spin and unpolarized spin, spin should be None"
)
self.positions = []
if self.ham.spin.is_colinear:
for ia, a in enumerate(_atoms):
symnum = sdict[ia]
orb_names = []
for x in a.orbital:
name = f"{symnum}|{x.name()}|{spin}"
orb_names.append(name)
self.positions.append(xred[ia])
self.orbs += orb_names
self.orb_dict[ia] += orb_names
self.norb = len(self.orbs)
self.nbasis = self.norb
elif self.ham.spin.is_spinorbit:
for spin in ['up', 'down']:
for ia, a in enumerate(_atoms):
symnum = sdict[ia]
orb_names = []
for x in a.orbital:
name = f"{symnum}|{x.name()}|{spin}"
orb_names.append(name)
self.positions.append(xred[ia])
self.orbs += orb_names
self.orb_dict[ia] += orb_names
self.norb = len(self.orbs) / 2
self.nbasis = len(self.orbs)
else:
raise ValueError(
"The hamiltonian should be either spin-orbit or colinear")
self.positions = np.array(self.positions, dtype=float)