L = 7.00
basis = BasisMaker('Na').generate(1, 1, energysplit=0.3)
atoms = Atoms('Na9', pbc=(0, 0, 1), cell=[L, L, 9 * a])
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)
atoms.set_calculator(t)
t.calculate_iv(0.5, 2)
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)
atoms = Atoms('Na12', pbc=(0, 0, 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=(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),
guess_steps=10,
pl_atoms=[pl_atoms1, pl_atoms2],
pl_cells=[pl_cell1, pl_cell2],
pl_kpts=(1, 1, 15),
non_sc=True,
analysis_data_list=['tc'],
fixed_boundary=False,
edge_atoms=[[0, 3], [0, 11]],
mol_atoms=range(4, 8))
atoms.set_calculator(t)
t.negf_prepare()
t.non_sc_analysis()
magmoms = np.zeros([134])
magmoms[:54]=0.7
magmoms[-54:] = -0.7
system.set_initial_magnetic_moments(magmoms)
t = Transport( h=0.2,
xc='RPBE',
basis={'Ni': 'szp', 'H': 'szp', 'C': 'szp', 'S':'szp'},
kpts=(2, 2, 1),
occupations=FermiDirac(0.2),
mode='lcao',
txt='NiC8.txt',
buffer_guess=True,
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',
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)
xc='LDA',
basis={'Na': basis},
kpts=(1,1,1),
occupations=FermiDirac(0.1),
mode='lcao',
mixer=Mixer(0.1, 5, weight=100.0),
txt='Device.txt'))
Device.get_potential_energy()
from gpaw.transport.tools import save_bias_data_file
save_bias_data_file(Lead1, Lead2, Device)
system = Device.copy()
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',
txt='Na_lcao.txt',
mixer=Mixer(0.1, 5, weight=100.0),
pl_atoms=[range(4), range(5,9)],
pl_cells=[pl_cell1, pl_cell2],
leads=[Lead1,Lead2],
pl_kpts=(1,1,5),
analysis_mode=True)
system.set_calculator(t)
t.analysis(1)
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=(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),
guess_steps=10,
fix_contour=True,
pl_atoms=[pl_atoms1, pl_atoms2],
pl_cells=[pl_cell1, pl_cell2],
pl_kpts=(1,1,16),
fixed_boundary=False,
analysis_data_list=['tc'],
edge_atoms=[[0, 3], [0, 11]],
mol_atoms=range(4, 8))
atoms.set_calculator(t)
t.calculate_to_bias(0.0, 1)
qn=QuasiNewton(atoms, trajectory='transport.traj')
qn.run(fmax=0.05)
pl_cell2 = pl_cell1
pl_cell3 = pl_cell1
t = Transport(h=0.25,
xc='LDA',
basis='sz',
occupations=FermiDirac(0.2),
kpts=(1, 1, 1),
mode='lcao',
poissonsolver=PoissonSolver(nn=2, relax='GS'),
txt='Na_lcao.txt',
mixer=Mixer(0.1, 5, weight=100.0),
guess_steps=10,
LR_leads=False,
bias=[0] * 3,
fixed_boundary=False,
identical_leads=True,
pl_atoms=[pl_atoms1, pl_atoms2, pl_atoms3],
pl_cells=[pl_cell1, pl_cell2, pl_cell3],
pl_kpts=(1, 1, 15),
save_file=True,
use_buffer=True,
neutral=False,
normalize_density=False,
extended_atoms=eatoms,
multi_lead_directions=[[6, 9], [10, 13], [14, 17]],
nleadlayers=[1, 1, 1],
edge_atoms=[[0, 0, 0], [6, 10, 14]],
mol_atoms=range(6) + range(18, 21))
atoms.set_calculator(t)
lp = []
system.set_initial_magnetic_moments(magmoms)
t = Transport(h=0.2,
xc='RPBE',
basis={
'Ni': 'szp',
'H': 'szp',
'C': 'szp',
'S': 'szp'
},
kpts=(2, 2, 1),
occupations=FermiDirac(0.2),
mode='lcao',
txt='NiC8.txt',
buffer_guess=True,
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()
pl_cell2 = pl_cell1
pl_cell3 = pl_cell1
t = Transport(h=0.25,
xc='LDA',
basis='sz',
occupations=FermiDirac(0.2),
kpts=(1,1,1),
mode='lcao',
poissonsolver=PoissonSolver(nn=2, relax='GS'),
txt='Na_lcao.txt',
mixer=Mixer(0.1, 5, weight=100.0),
guess_steps=10,
LR_leads=False,
bias=[0]*3,
fixed_boundary=False,
identical_leads=True,
pl_atoms=[pl_atoms1, pl_atoms2, pl_atoms3],
pl_cells=[pl_cell1, pl_cell2, pl_cell3],
pl_kpts=(1,1,15),
save_file=True,
use_buffer=True,
neutral=False,
normalize_density=False,
extended_atoms=eatoms,
multi_lead_directions=[[6, 9], [10, 13], [14,17]],
nleadlayers=[1,1,1],
edge_atoms=[[0, 0, 0], [6, 10, 14]],
mol_atoms=range(6)+ range(18,21))
atoms.set_calculator(t)
lp = []
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)
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=(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),
guess_steps=10,
pl_atoms=[pl_atoms1, pl_atoms2],
pl_cells=[pl_cell1, pl_cell2],
pl_kpts=(1,1,15),
non_sc=True,
analysis_data_list=['tc'],
fixed_boundary=False,
edge_atoms=[[0, 3], [0, 11]],
mol_atoms=range(4, 8))
atoms.set_calculator(t)
t.negf_prepare()
t.non_sc_analysis()
a = 3.6
L = 7.00
basis = BasisMaker('Na').generate(1, 1, energysplit=0.3)
atoms = Atoms('Na12', pbc=(0, 0, 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=(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=(1,1,16),
non_sc=True)
atoms.set_calculator(t)
t.calculate_iv()
pl_cell2 = pl_cell1 # Cell for the right principal layer
atoms.rotate('x', 'z')
# Attach a GPAW calculator
atoms.set_calculator(
Transport(h=0.3,
xc='PBE',
basis='szp(dzp)',
occupations=FermiDirac(width=0.1),
kpts=(1, 1, 1),
mode='lcao',
save_file=False,
txt='pt_h2_transport.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, 13),
mol_atoms=range(4, 8),
lead_restart=False,
scat_restart=False,
edge_atoms=[[0, 3], [0, 11]],
analysis_data_list=['tc'],
data_file='Pt_H2_nsc.dat',
non_sc=True))
t = atoms.calc
t.set_energies(np.linspace(-5, 3, 201))
t.negf_prepare()
t.non_sc_analysis()
a = 3.6
L = 7.00
basis = BasisMaker('Na').generate(1, 1, energysplit=0.3)
atoms = Atoms('Na12', pbc=(0, 0, 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=(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, 16),
non_sc=True)
atoms.set_calculator(t)
t.calculate_iv()
