def generate_selfenergy_database(atoms,
ntk,
filename,
direction=0,
kt=0.1,
bias=[-3, 3],
depth=3,
comm=None):
from gpaw.transport.sparse_matrix import Banded_Sparse_HSD, CP_Sparse_HSD, Se_Sparse_Matrix
from gpaw.transport.selfenergy import LeadSelfEnergy
from gpaw.transport.contour import Contour
hl_skmm, sl_kmm = get_hs(atoms)
dl_skmm = get_lcao_density_matrix(atoms.calc)
fermi = atoms.calc.get_fermi_level()
wfs = atoms.calc.wfs
hl_spkmm, sl_pkmm, dl_spkmm, \
hl_spkcmm, sl_pkcmm, dl_spkcmm = get_pk_hsd(2, ntk,
wfs.ibzk_qc,
hl_skmm, sl_kmm, dl_skmm,
None, wfs.dtype,
direction=direction)
my_npk = len(wfs.ibzk_qc) / ntk
my_nspins = len(wfs.kpt_u) / (my_npk * ntk)
lead_hsd = Banded_Sparse_HSD(wfs.dtype, my_nspins, my_npk)
lead_couple_hsd = CP_Sparse_HSD(wfs.dtype, my_nspins, my_npk)
for pk in range(my_npk):
lead_hsd.reset(0, pk, sl_pkmm[pk], 'S', init=True)
lead_couple_hsd.reset(0, pk, sl_pkcmm[pk], 'S', init=True)
for s in range(my_nspins):
lead_hsd.reset(s, pk, hl_spkmm[s, pk], 'H', init=True)
lead_hsd.reset(s, pk, dl_spkmm[s, pk], 'D', init=True)
lead_couple_hsd.reset(s, pk, hl_spkcmm[s, pk], 'H', init=True)
lead_couple_hsd.reset(s, pk, dl_spkcmm[s, pk], 'D', init=True)
lead_se = LeadSelfEnergy(lead_hsd, lead_couple_hsd)
contour = Contour(kt, [fermi] * 2, bias, depth, comm=comm)
path = contour.get_plot_path(ex=True)
for nid, energy in zip(path.my_nids, path.my_energies):
for kpt in wfs.kpt_u:
if kpt.q % ntk == 0:
flag = str(kpt.k // ntk) + '_' + str(nid)
lead_se.s = kpt.s
lead_se.pk = kpt.q // ntk
data = lead_se(energy)
fd = file(flag, 'w')
cPickle.dump(data, fd, 2)
fd.close()
def generate_selfenergy_database(atoms, ntk, filename, direction=0, kt=0.1,
bias=[-3,3], depth=3, comm=None):
from gpaw.transport.sparse_matrix import Banded_Sparse_HSD, CP_Sparse_HSD, Se_Sparse_Matrix
from gpaw.transport.selfenergy import LeadSelfEnergy
from gpaw.transport.contour import Contour
hl_skmm, sl_kmm = get_hs(atoms)
dl_skmm = get_lcao_density_matrix(atoms.calc)
fermi = atoms.calc.get_fermi_level()
wfs = atoms.calc.wfs
hl_spkmm, sl_pkmm, dl_spkmm, \
hl_spkcmm, sl_pkcmm, dl_spkcmm = get_pk_hsd(2, ntk,
wfs.kd.ibzk_qc,
hl_skmm, sl_kmm, dl_skmm,
None, wfs.dtype,
direction=direction)
my_npk = len(wfs.kd.ibzk_qc) / ntk
my_nspins = len(wfs.kpt_u) / ( my_npk * ntk)
lead_hsd = Banded_Sparse_HSD(wfs.dtype, my_nspins, my_npk)
lead_couple_hsd = CP_Sparse_HSD(wfs.dtype, my_nspins, my_npk)
for pk in range(my_npk):
lead_hsd.reset(0, pk, sl_pkmm[pk], 'S', init=True)
lead_couple_hsd.reset(0, pk, sl_pkcmm[pk], 'S', init=True)
for s in range(my_nspins):
lead_hsd.reset(s, pk, hl_spkmm[s, pk], 'H', init=True)
lead_hsd.reset(s, pk, dl_spkmm[s, pk], 'D', init=True)
lead_couple_hsd.reset(s, pk, hl_spkcmm[s, pk], 'H', init=True)
lead_couple_hsd.reset(s, pk, dl_spkcmm[s, pk], 'D', init=True)
lead_se = LeadSelfEnergy(lead_hsd, lead_couple_hsd)
contour = Contour(kt, [fermi] * 2, bias, depth, comm=comm)
path = contour.get_plot_path(ex=True)
for nid, energy in zip(path.my_nids, path.my_energies):
for kpt in wfs.kpt_u:
if kpt.q % ntk == 0:
flag = str(kpt.k // ntk) + '_' + str(nid)
lead_se.s = kpt.s
lead_se.pk = kpt.q // ntk
data = lead_se(energy)
fd = file(flag, 'w')
cPickle.dump(data, fd, 2)
fd.close()
