def collect_lead_data(self, obj):
data = {}
data['bzk_kc'] = obj.wfs.kd.bzk_kc
#data['bzk_qc'] = obj.wfs.bzk_qc
data['ibzk_kc'] = obj.wfs.kd.ibzk_kc
data['ibzk_qc'] = obj.wfs.kd.ibzk_qc
#data['setups'] = obj.wfs.setups
data['cell_cv'] = obj.gd.cell_cv
data['parsize_c'] = obj.gd.parsize_c
data['pbc_c'] = obj.gd.pbc_c
data['N_c'] = obj.gd.N_c
data['nao'] = obj.wfs.setups.nao
data['fine_N_c'] = obj.finegd.N_c
data['nspins'] = obj.wfs.nspins
data['fermi'] = obj.get_fermi_level()
den, ham = obj.density, obj.hamiltonian
gd = obj.gd
vt_sG = gd.collect(ham.vt_sG)
nt_sG = gd.collect(den.nt_sG)
data['vt_sG'] = vt_sG
data['nt_sG'] = nt_sG
finegd = obj.finegd
vt_sg = finegd.collect(ham.vt_sg)
nt_sg = finegd.collect(den.nt_sg)
vHt_g = finegd.collect(ham.vHt_g)
rhot_g = finegd.collect(den.rhot_g)
data['vt_sg'] = vt_sg
data['nt_sg'] = nt_sg
data['vHt_g'] = vHt_g
data['rhot_g'] = rhot_g
D_asp = collect_atomic_matrices(den.D_asp, den.setups,
den.nspins, den.gd.comm,
den.rank_a)
dH_asp = collect_atomic_matrices(ham.dH_asp, ham.setups,
ham.nspins, ham.gd.comm,
ham.rank_a)
data['D_asp'] = D_asp
data['dH_asp'] = dH_asp
return data
def collect_lead_data(self, obj):
data = {}
data['bzk_kc'] = obj.wfs.kd.bzk_kc
#data['bzk_qc'] = obj.wfs.bzk_qc
data['ibzk_kc'] = obj.wfs.kd.ibzk_kc
data['ibzk_qc'] = obj.wfs.kd.ibzk_qc
#data['setups'] = obj.wfs.setups
data['cell_cv'] = obj.gd.cell_cv
data['parsize_c'] = obj.gd.parsize_c
data['pbc_c'] = obj.gd.pbc_c
data['N_c'] = obj.gd.N_c
data['nao'] = obj.wfs.setups.nao
data['fine_N_c'] = obj.finegd.N_c
data['nspins'] = obj.wfs.nspins
data['fermi'] = obj.get_fermi_level()
den, ham = obj.density, obj.hamiltonian
gd = obj.gd
vt_sG = gd.collect(ham.vt_sG)
nt_sG = gd.collect(den.nt_sG)
data['vt_sG'] = vt_sG
data['nt_sG'] = nt_sG
finegd = obj.finegd
vt_sg = finegd.collect(ham.vt_sg)
nt_sg = finegd.collect(den.nt_sg)
vHt_g = finegd.collect(ham.vHt_g)
rhot_g = finegd.collect(den.rhot_g)
data['vt_sg'] = vt_sg
data['nt_sg'] = nt_sg
data['vHt_g'] = vHt_g
data['rhot_g'] = rhot_g
D_asp = collect_atomic_matrices(den.D_asp, den.setups, den.nspins,
den.gd.comm, den.rank_a)
dH_asp = collect_atomic_matrices(ham.dH_asp, ham.setups, ham.nspins,
ham.gd.comm, ham.rank_a)
data['D_asp'] = D_asp
data['dH_asp'] = dH_asp
return data
def abstract_boundary(self):
#abtract the effective potential, hartree potential, and average density
#out from the electrode calculation.
calc = self.atoms.calc
gd = calc.gd
finegd = calc.finegd
nn = finegd.N_c[2]
ns = calc.wfs.nspins
dim = gd.N_c
d1 = dim[0] // 2
d2 = dim[1] // 2
vHt_g = finegd.collect(calc.hamiltonian.vHt_g)
vt_sg = finegd.collect(calc.hamiltonian.vt_sg)
nt_sg = finegd.collect(calc.density.nt_sg)
rhot_g = finegd.collect(calc.density.rhot_g)
vt_sG = gd.collect(calc.hamiltonian.vt_sG)
nt_sG = gd.collect(calc.density.nt_sG)
self.boundary_vHt_g = None
self.boundary_vHt_g1 = None
self.boundary_vt_sg_line = None
self.boundary_nt_sg = None
self.boundary_rhot_g_line = None
self.boundary_vt_sG = None
self.boundary_nt_sG = None
if gd.comm.rank == 0:
self.boundary_vHt_g = self.slice(nn, vHt_g)
self.boundary_nt_sg = self.slice(nn, nt_sg)
if self.direction == '-':
other_direction= '+'
else:
other_direction= '-'
h = self.h_cz / 2.0
b_vHt_g0 = self.boundary_vHt_g.copy()
b_vHt_g1 = self.boundary_vHt_g.copy()
self.boundary_vHt_g = interpolate_array(b_vHt_g0,
finegd, h, self.direction)
self.boundary_vHt_g1 = interpolate_array(b_vHt_g1,
finegd, h, other_direction)
vt_sg = interpolate_array(vt_sg, finegd, h, self.direction)
self.boundary_vt_sg_line = aa1d(vt_sg)
self.boundary_nt_sg = interpolate_array(self.boundary_nt_sg,
finegd, h, self.direction)
rhot_g = interpolate_array(rhot_g, finegd, h, self.direction)
self.boundary_rhot_g_line = aa1d(rhot_g)
nn /= 2
h *= 2
self.boundary_vt_sG = self.slice(nn, vt_sG)
self.boundary_nt_sG = self.slice(nn, nt_sG)
self.boundary_vt_sG = interpolate_array(self.boundary_vt_sG,
gd, h, self.direction)
self.boundary_nt_sG = interpolate_array(self.boundary_nt_sG,
gd, h, self.direction)
den, ham = calc.density, calc.hamiltonian
self.D_asp = collect_atomic_matrices(den.D_asp, den.setups,
den.nspins, den.gd.comm,
den.rank_a)
self.dH_asp = collect_atomic_matrices(ham.dH_asp, ham.setups,
ham.nspins, ham.gd.comm,
ham.rank_a)
del self.atoms
def abstract_boundary(self):
#abtract the effective potential, hartree potential, and average density
#out from the electrode calculation.
calc = self.atoms.calc
gd = calc.gd
finegd = calc.finegd
nn = finegd.N_c[2]
ns = calc.wfs.nspins
dim = gd.N_c
d1 = dim[0] // 2
d2 = dim[1] // 2
vHt_g = finegd.collect(calc.hamiltonian.vHt_g)
vt_sg = finegd.collect(calc.hamiltonian.vt_sg)
nt_sg = finegd.collect(calc.density.nt_sg)
rhot_g = finegd.collect(calc.density.rhot_g)
vt_sG = gd.collect(calc.hamiltonian.vt_sG)
nt_sG = gd.collect(calc.density.nt_sG)
self.boundary_vHt_g = None
self.boundary_vHt_g1 = None
self.boundary_vt_sg_line = None
self.boundary_nt_sg = None
self.boundary_rhot_g_line = None
self.boundary_vt_sG = None
self.boundary_nt_sG = None
if gd.comm.rank == 0:
self.boundary_vHt_g = self.slice(nn, vHt_g)
self.boundary_nt_sg = self.slice(nn, nt_sg)
if self.direction == '-':
other_direction = '+'
else:
other_direction = '-'
h = self.h_cz / 2.0
b_vHt_g0 = self.boundary_vHt_g.copy()
b_vHt_g1 = self.boundary_vHt_g.copy()
self.boundary_vHt_g = interpolate_array(b_vHt_g0, finegd, h,
self.direction)
self.boundary_vHt_g1 = interpolate_array(b_vHt_g1, finegd, h,
other_direction)
vt_sg = interpolate_array(vt_sg, finegd, h, self.direction)
self.boundary_vt_sg_line = aa1d(vt_sg)
self.boundary_nt_sg = interpolate_array(self.boundary_nt_sg,
finegd, h, self.direction)
rhot_g = interpolate_array(rhot_g, finegd, h, self.direction)
self.boundary_rhot_g_line = aa1d(rhot_g)
nn /= 2
h *= 2
self.boundary_vt_sG = self.slice(nn, vt_sG)
self.boundary_nt_sG = self.slice(nn, nt_sG)
self.boundary_vt_sG = interpolate_array(self.boundary_vt_sG, gd, h,
self.direction)
self.boundary_nt_sG = interpolate_array(self.boundary_nt_sG, gd, h,
self.direction)
den, ham = calc.density, calc.hamiltonian
self.D_asp = collect_atomic_matrices(den.D_asp, den.setups, den.nspins,
den.gd.comm, den.rank_a)
self.dH_asp = collect_atomic_matrices(ham.dH_asp, ham.setups,
ham.nspins, ham.gd.comm,
ham.rank_a)
del self.atoms
