def HS_and_eigen(self, kpts=None, convention=2):
if kpts is not None:
self.calc.set(kpts=kpts)
self.atoms.calc=self.calc
self.atoms.get_total_energy()
self.calc.set(symmetry='off', fixdensity=True)
self.atoms.get_total_energy()
#self.kpt_u = self.wfs.kpt_u
H, S= get_lcao_hamiltonian(self.calc)
np.save('kpts.npy', kpts)
np.save('H.npy', H)
np.save('S.npy', S)
nspin, nkpt, norb, _ = H.shape
nbasis=nspin*norb
evals=np.zeros((nkpt, nbasis), dtype=float)
evecs=np.zeros((nkpt, nbasis, nbasis),dtype=complex)
if self.calc.get_spin_polarized():
H2=np.zeros((nkpt, nbasis, nbasis),dtype=complex)
# spin up
H2[:, :nbasis, :nbasis]=H[0]
# spin down
H2[:, nbasis:, nbasis:]=H[1]
S2=np.zeros((nkpt, nbasis, nbasis),dtype=complex)
S2[:, :norb, :orb]=S
S2[:, norb:, norb:]=S
for ikpt, k in enumerate(self.calc.get_ibz_k_points()):
evals0, evecs0 = eigh(H[0, ikpt,:,:], S[ikpt,:,:])
evals1, evecs1 = eigh(H[1, ikpt,:,:], S[ikpt,:,:])
evals[ikpt, :nbasis]=evals0
evals[ikpt, nbasis:]=evals1
evecs[ikpt, :nbasis, :nbasis]=evecs0
evecs[ikpt, nbasis:, nbasis:]=evecs1
else:
H2=H[0]
for ikpt, k in self.kpt_u:
evals[ikpt], evecs[ikpt]= eigh(H[0, ikpt], S[ikpt])
np.save('kpts.npy', kpts)
np.save('H2.npy', H2)
np.save('S2.npy', S2)
np.save('evals.npy', evals)
np.save('evecs.npy', evecs)
return H2, S2, evals, evecs
def __init__(self, calc, spin=0):
assert calc.wfs.gd.comm.size == 1
assert calc.wfs.kd.comm.size == 1
assert calc.wfs.bd.comm.size == 1
from gpaw.lcao.tools import get_lcao_hamiltonian
H_skMM, S_kMM = get_lcao_hamiltonian(calc)
self.calc = calc
self.dtype = calc.wfs.dtype
self.spin = spin
self.H_qww = H_skMM[spin]
self.S_qww = S_kMM
self.P_aqwi = calc.wfs.P_aqMi
self.Nw = self.S_qww.shape[-1]
for S in self.S_qww:
print('Condition number: %0.1e' % condition_number(S))
def __init__(self, calc, spin=0):
assert calc.wfs.gd.comm.size == 1
assert calc.wfs.kd.comm.size == 1
assert calc.wfs.band_comm.size == 1
from gpaw.lcao.tools import get_lcao_hamiltonian
H_skMM, S_kMM = get_lcao_hamiltonian(calc)
self.calc = calc
self.dtype = calc.wfs.dtype
self.spin = spin
self.H_qww = H_skMM[spin]
self.S_qww = S_kMM
self.P_aqwi = calc.wfs.P_aqMi
self.Nw = self.S_qww.shape[-1]
for S in self.S_qww:
print('Condition number: %0.1e' % condition_number(S))
def get_h_and_s(calc, direction='x'):
'''
The function below performs
1. tri2full
2. *= Hartree
'''
h_skmm, s_kmm = get_lcao_hamiltonian(calc)
'''
The code below performs
1. remove_pbc
2. align_fermi
'''
d = 'xyz'.index(direction)
nspins, nkpts = h_skmm.shape[:2]
for s in range(nspins):
for k in range(nkpts):
if s == 0:
remove_pbc(atoms, h_skmm[s, k], s_kmm[k], d)
else:
remove_pbc(atoms, h_skmm[s, k], None, d)
h_skmm[s, k] -= s_kmm[k] * calc.occupations.get_fermi_level()
return h_skmm, s_kmm
basis='szp(dzp)',
occupations=FermiDirac(width=0.1),
kpts=(1, 1, 1),
mode='lcao',
txt='pt_h2_lcao_scat.txt',
mixer=Mixer(0.1, 5, weight=100.0),
symmetry={
'point_group': False,
'time_reversal': False
})
atoms.set_calculator(calc)
atoms.get_potential_energy() # Converge everything!
Ef = atoms.calc.get_fermi_level()
H_skMM, S_kMM = get_lcao_hamiltonian(calc)
# Only use first kpt, spin, as there are no more
H, S = H_skMM[0, 0], S_kMM[0]
H -= Ef * S
remove_pbc(atoms, H, S, 0)
# Dump the Hamiltonian and Scattering matrix to a pickle file
pickle.dump((H, S), open('scat_hs.pickle', 'wb'), 2)
########################
# Left principal layer #
########################
# Use four Pt atoms in the lead, so only take those from before
atoms = atoms[:4].copy()
atoms.set_cell([4 * a, L, L])
if world.rank == 0:
basis = BasisMaker('Li', 'szp').generate(1, 1)
basis.write_xml()
world.barrier()
if setup_paths[0] != '.':
setup_paths.insert(0, '.')
if 1:
a = 2.7
bulk = Atoms('Li', pbc=True, cell=[a, a, a])
calc = GPAW(gpts=(8, 8, 8), kpts=(4, 4, 4), mode='lcao', basis='szp')
bulk.set_calculator(calc)
e = bulk.get_potential_energy()
niter = calc.get_number_of_iterations()
calc.write('temp.gpw')
atoms, calc = restart('temp.gpw')
H_skMM, S_kMM = get_lcao_hamiltonian(calc)
eigs = calc.get_eigenvalues(kpt=2)
if world.rank == 0:
eigs2 = np.linalg.eigvals(np.linalg.solve(S_kMM[2], H_skMM[0, 2])).real
eigs2.sort()
assert abs(sum(eigs - eigs2)) < 1e-8
energy_tolerance = 0.00003
niter_tolerance = 0
equal(e, -1.82847, energy_tolerance)
equal(niter, 5, niter_tolerance)