def path_selfenergy(atoms, ntk, filename, begin, end, num= 257, direction=0):
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)
begin += fermi
end += fermi
ee = np.linspace(begin, end, num)
se = []
for e in ee:
se.append(lead_se(e).recover())
se = np.array(se)
fd = file(filename + '_' + str(world.rank), 'w')
cPickle.dump((se, ee), 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()
def test_selfenergy_interpolation(atoms, ntk, filename, begin, end, base, scale, direction=0):
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)
begin += fermi
end += fermi
ee = np.linspace(begin, end, base)
cmp_ee = np.linspace(begin, end, base * scale)
se = []
cmp_se = []
from scipy import interpolate
for e in ee:
se.append(lead_se(e).recover())
se = np.array(se)
ne, ny, nz= se.shape
nie = len(cmp_ee)
data = np.zeros([nie, ny, nz], se.dtype)
for yy in range(ny):
for zz in range(nz):
ydata = se[:, yy, zz]
f = interpolate.interp1d(ee, ydata)
data[:, yy, zz] = f(cmp_ee)
inter_se_linear = data
for e in cmp_ee:
cmp_se.append(lead_se(e).recover())
fd = file(filename, 'w')
cPickle.dump((cmp_se, inter_se_linear, ee, cmp_ee), fd, 2)
fd.close()
for i,e in enumerate(cmp_ee):
print(e, np.max(abs(cmp_se[i] - inter_se_linear[i])), 'linear', np.max(abs(cmp_se[i])))
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 path_selfenergy(atoms, ntk, filename, begin, end, num=257, direction=0):
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)
begin += fermi
end += fermi
ee = np.linspace(begin, end, num)
se = []
for e in ee:
se.append(lead_se(e).recover())
se = np.array(se)
fd = file(filename + '_' + str(world.rank), 'w')
cPickle.dump((se, ee), fd, 2)
fd.close()
