def get_h_and_s(calc, spin=0, kpt=0):
calc.atoms.set_calculator(calc)
if calc.wfs.S_qMM is None:
calc.wfs.set_positions(calc.spos_ac)
tkpts_kc, tweights_k, H_skMM, S_kMM = get_lead_lcao_hamiltonian(
calc, direction='x')
fermi = calc.get_fermi_level()
s = S_kMM[kpt]
h = H_skMM[spin, kpt] - fermi * s
remove_pbc(calc.atoms, h, s, d=0)
return h, s
def get_hs(natoms, nkpts):
calc = GPAW(h=0.25, mode='lcao', basis='sz', width=0.2, kpts=nkpts,
mixer=Mixer(0.1, 5, weight=80.0), usesymm=False)
atoms = Atoms('Na', pbc=True, cell=(L, L, L)).repeat(natoms)
atoms.set_calculator(calc)
atoms.get_potential_energy()
fermi = calc.get_fermi_level()
ibz, w, h, s = get_lead_lcao_hamiltonian(calc, direction=direction)
h = h[0] - fermi * s
for h1, s1 in zip(h, s):
remove_pbc(atoms, h1, s1, d=dir)
return ibz, w, h, s
def get_h_and_s(calc, kpt=0):
calc.atoms.set_calculator(calc)
if calc.wfs.S_qMM is None:
calc.wfs.set_positions(calc.spos_ac)
h = calc.wfs.eigensolver.calculate_hamiltonian_matrix(
hamiltonian=calc.hamiltonian, wfs=calc.wfs, kpt=calc.wfs.kpt_u[kpt])
s = calc.wfs.S_qMM[kpt]
tri2full(h)
tri2full(s)
h *= Hartree
h -= calc.get_fermi_level() * s
remove_pbc(atoms=calc.atoms, h=h, s=s)
return h, s
def get_hs(natoms, nkpts):
calc = GPAW(h=0.25,
mode='lcao',
basis='sz',
width=0.2,
kpts=nkpts,
mixer=Mixer(0.1, 5, weight=80.0),
usesymm=False)
atoms = Atoms('Na', pbc=True, cell=(L, L, L)).repeat(natoms)
atoms.set_calculator(calc)
atoms.get_potential_energy()
fermi = calc.get_fermi_level()
ibz, w, h, s = get_lead_lcao_hamiltonian(calc, direction=direction)
h = h[0] - fermi * s
for h1, s1 in zip(h, s):
remove_pbc(atoms, h1, s1, d=dir)
return ibz, w, h, 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
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])
# Attach a GPAW calculator
calc = GPAW(
h=0.3,
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])
# Attach a GPAW calculator
calc = GPAW(h=0.3,
xc='PBE',
