def make_supercell(self, sc_matrix=None, smaker=None):
"""
make supercell
sc_matrix: supercell matrix.
"""
if self.atoms is not None:
natoms = len(self.atoms)
else:
natoms = set(e.site for e in self)
if smaker is None:
smaker = SupercellMaker(sc_matrix)
if self.atoms is not None:
sc_atoms = smaker.sc_atoms(self.atoms)
sc_sites = smaker.sc_index(self.get_sites(), n_ind=natoms)
sc_labels = smaker.sc_trans_invariant(self.get_labels())
sc_spins = smaker.sc_trans_invariant(self.get_spins())
sc_indices = smaker.sc_index(self.get_indices())
sc_bset = BasisSet()
sc_bset.set_atoms(sc_atoms)
for site, label, spin, ind in zip(sc_sites, sc_labels, sc_spins,
sc_indices):
sc_bset.append(Basis(site, label, spin, ind))
sc_bset.set_nspin(self.nspin)
return sc_bset
def make_supercell(self, sc_matrix=None, supercell_maker=None):
if supercell_maker is None:
spm = SupercellMaker(sc_matrix=sc_matrix)
else:
spm = supercell_maker
sc_ref_atoms = spm.sc_atoms(self.ref_atoms)
print("maker supercell for ifc")
sc_ifc = self.total_ifc.make_supercell(scmaker=spm)
return Lattice(ifc=sc_ifc, ref_atoms=sc_ref_atoms)
def make_supercell(self, sc_maker=None, sc_matrix=None):
from minimulti.utils.supercell import SupercellMaker
if sc_maker is None:
sc_maker = SupercellMaker(sc_matrix)
if self.atoms is not None:
sc_atoms = sc_maker.sc_atoms(self.atoms)
#print(self.HwannR.shape)
sc_Rlist, sc_HR = sc_maker.sc_Rlist_HR(self.Rlist,
self.HwannR,
n_basis=self.nwann)
return sc_atoms, sc_Rlist, sc_HR
def lwf_to_atoms(mylwf: LWF, scmat, amplist):
patoms = mylwf.atoms
scmaker = SupercellMaker(scmat)
scatoms = scmaker.sc_atoms(patoms)
positions = scatoms.get_positions()
nR, natom3, nlwf = mylwf.wannR.shape
scnatom = len(scatoms)
print(mylwf.wannR[mylwf.Rdict[(0, 0, 0)], :, 0].real)
displacement = np.zeros_like(positions.flatten())
for (R, iwann, ampwann) in amplist:
for Rwann, iRwann in mylwf.Rdict.items():
for j in range(natom3):
sc_j, sc_R = scmaker.sc_jR_to_scjR(j, Rwann, R, natom3)
#print(f"{mylwf.wannR[iRwann, iwann, j].real: .2f}")
amp = ampwann * mylwf.wannR[iRwann, j, iwann]
#print(f"{amp:.2f}")
displacement[sc_j] += amp.real
sc_pos = positions + displacement.reshape((scnatom, 3))
#print(displacement.reshape((scnatom, 3))[:6])
scatoms.set_positions(sc_pos)
return scatoms