basis = BasisMaker('Na').generate(1, 1, energysplit=0.3)
atoms = Atoms('Na12', pbc=(1, 1, 1), cell=[L, L, 12 * a])
atoms.positions[:12, 2] = [i * a for i in range(12)]
atoms.positions[:, :2] = L / 2.
atoms.center()
pl_atoms1 = range(4)
pl_atoms2 = range(8, 12)
pl_cell1 = (L, L, 4 * a)
pl_cell2 = pl_cell1
t = Transport(h=0.3,
xc='LDA',
basis={'Na': basis},
kpts=(2, 2, 1),
occupations=FermiDirac(0.1),
mode='lcao',
poissonsolver=PoissonSolver(nn=2, relax='GS'),
txt='Na_lcao.txt',
mixer=Mixer(0.1, 5, weight=100.0),
guess_steps=10,
pl_atoms=[pl_atoms1, pl_atoms2],
pl_cells=[pl_cell1, pl_cell2],
pl_kpts=(2, 2, 15),
analysis_data_list=['tc'],
edge_atoms=[[0, 3], [0, 11]],
mol_atoms=range(4, 8))
atoms.set_calculator(t)
t.calculate_iv(0.5, 2)
lead_guess=True,
spinpol=True,
guess_steps=80,
beta_guess=0.003,
alpha=0.1,
poissonsolver=PoissonSolver(nn=2),
mixer=MixerSum(0.005, 5, weight=100.0),
extra_density=True,
pl_atoms=[pl_atoms1, pl_atoms2],
pl_cells=[pl_cell1, pl_cell2],
pl_kpts=[2 , 2 , 15],
edge_atoms=[[ 0, 35],[0 , 133]],
mol_atoms=range(36, 98),
nleadlayers=[1,1])
system.set_calculator(t)
t.calculate_iv()
t = Transport( h=0.2,
xc='RPBE',
basis={'Ni': 'szp', 'H': 'szp', 'C': 'szp', 'S':'szp'},
kpts=(12, 12, 1),
occupations=FermiDirac(0.2),
parallel={'domain':(1,1,1)},
mode='lcao',
txt='NiC8.txt',
buffer_guess=True,
lead_guess=True,
spinpol=True,
guess_steps=80,
beta_guess=0.003,
alpha=0.1,
lead_guess=True,
spinpol=True,
guess_steps=80,
beta_guess=0.003,
alpha=0.1,
poissonsolver=PoissonSolver(nn=2),
mixer=MixerSum(0.005, 5, weight=100.0),
extra_density=True,
pl_atoms=[pl_atoms1, pl_atoms2],
pl_cells=[pl_cell1, pl_cell2],
pl_kpts=[2, 2, 15],
edge_atoms=[[0, 35], [0, 133]],
mol_atoms=range(36, 98),
nleadlayers=[1, 1])
system.set_calculator(t)
t.calculate_iv()
t = Transport(h=0.2,
xc='RPBE',
basis={
'Ni': 'szp',
'H': 'szp',
'C': 'szp',
'S': 'szp'
},
kpts=(12, 12, 1),
occupations=FermiDirac(0.2),
parallel={'domain': (1, 1, 1)},
mode='lcao',
txt='NiC8.txt',
buffer_guess=True,
atoms.positions[:9, 2] = [i * a for i in range(9)]
atoms.positions[:, :2] = L / 2.
atoms.center()
pl_atoms1 = range(4)
pl_atoms2 = range(5, 9)
pl_cell1 = (L, L, 4 * a)
pl_cell2 = pl_cell1
t = Transport(h=0.3,
xc='LDA',
basis={'Na': basis},
kpts=(1,1,1),
occupations=FermiDirac(0.1),
mode='lcao',
poissonsolver=PoissonSolver(nn=2, relax='GS'),
txt='Na_lcao.txt',
mixer=Mixer(0.1, 5, weight=100.0),
pl_atoms=[pl_atoms1, pl_atoms2],
pl_cells=[pl_cell1, pl_cell2],
pl_kpts=(1,1,5),
edge_atoms=[[0, 3], [0, 8]],
mol_atoms=[4],
guess_steps=1,
fixed_boundary=False,
foot_print=False)
atoms.set_calculator(t)
t.calculate_iv(0.5, 2)
import numpy as np
from ase.io import read
from gpaw import FermiDirac, PoissonSolver, Mixer
from gpaw.transport.calculator import Transport
system = read('BDT.traj', -1)
pl_atoms1 = range(36)
pl_atoms2 = range(72, 108)
pl_cell1 = np.diag(system.cell)
pl_cell1[2] = 7.067
pl_cell2 = pl_cell1
t = Transport(h=0.2,
xc='PBE',
basis={'Au': 'sz(dzp)', 'H': 'dzp', 'C': 'dzp', 'S':'dzp'},
kpts=(1, 1, 1),
occupations=FermiDirac(0.1),
mode='lcao',
txt='ABA.txt',
poissonsolver=PoissonSolver(nn=2),
mixer=Mixer(0.1, 5, weight=100.0),
pl_atoms=[pl_atoms1, pl_atoms2],
pl_cells=[pl_cell1, pl_cell2],
pl_kpts=[1, 1, 15],
extra_density=True,
analysis_data_list=['tc'],
edge_atoms=[[ 0, 35],[0 , 107]],
mol_atoms=range(36, 72))
system.set_calculator(t)
t.calculate_iv(3.0, 2)
