Advanced Examples

This section provides advanced examples demonstrating specialized features of gauNEGF.

Spin Transport

Example of spin-dependent transport:

import numpy as np
from gauNEGF.scf import NEGF
from gauNEGF.transport import calculate_transmission, SigmaCalculator

har_to_eV = 27.211386

# Initialize with unrestricted calculation
negf = NEGF(
    fn='molecule',
    spin='u'  # Unrestricted calculation
)

# Orbital indices of the contact atoms; for spin='u' the alpha orbitals
# come first, then the beta orbitals
lInd, rInd = negf.setContacts([1], [2])
nL, nR = len(lInd)//2, len(rInd)//2

# Spin-dependent contacts: one diagonal matrix per contact
sig1 = np.diag([-0.1j]*nL + [-0.05j]*nL)    # left: up -0.1j, down -0.05j
sig2 = np.diag([-0.05j]*nR + [-0.1j]*nR)    # right: up -0.05j, down -0.1j
negf.setSigma(lContact=[1], rContact=[2], sig=sig1, sig2=sig2)

# Run at equilibrium
negf.setVoltage(0.0)
negf.SCF(1e-3, 0.01)

# Calculate spin-resolved transmission (F is stored in hartree)
sigma1, sigma2 = negf.getSigma()
Elist = np.linspace(-5, 5, 1000)
T, Tspin = calculate_transmission(
    negf.F*har_to_eV, negf.S, SigmaCalculator(sigma1, sigma2),
    Elist + negf.fermi, spin='u'
)

Temperature Effects

Finite temperature can be set globally through gauNEGF.config, before the other gauNEGF modules are imported (they bind the default at import time):

from gauNEGF import config
config.TEMPERATURE = 300

from gauNEGF.scfE import NEGFE  # import after changing the default

Or locally on an NEGFE object by setting the temperature argument (NEGFE overrides setSigma/setContactBethe/setContact1D to accept the T keyword; the base NEGF class does not):

from gauNEGF.scfE import NEGFE

negf = NEGFE('molecule', basis='lanl2dz')

# Set basic temperature-dependent contact
negf.setSigma(
    lContact=[1], rContact=[2],
    sig=-0.05j,
    T=300     # Temperature in Kelvin
)

# Set up temperature-dependent Bethe Lattice contacts
negf.setContactBethe(
    contactList=[[1,2,3], [4,5,6]],
    latFile='Au',
    T=300  # Temperature in Kelvin
)

Energy-Dependent Contacts

Using realistic contact models (NEGFE provides setContactBethe and setContact1D; both are NEGFE-only methods):

from gauNEGF.scfE import NEGFE

negf = NEGFE('molContacts', basis='lanl2dz')

# Either: Bethe lattice contacts at atoms {1,2,3} and {6,7,8}
negf.setContactBethe(
    contactList=[[1,2,3], [6,7,8]],
    latFile='Au', # Slater-Koster parameters defined in Au.bethe
    eta=1e-6      # Broadening term (eV)
)

# Or: 1D chain contacts auto-extracted from the device Fock block
# (a second contact call replaces the first).
# See /guides/contacts_1d for the explicit-matrix and tau-list patterns.
negf.setContact1D(
    contactList=[[1], [6]],
    symmetrize_contacts=True,
    eta=1e-3
)

Custom Analysis

Advanced analysis tools:

import numpy as np
import matplotlib.pyplot as plt
from gauNEGF.transport import calculate_dos, calculate_transmission, SigmaCalculator

#... run energy dependent NEGFE() calculation

# Calculate DOS and transmission (F is stored in hartree; pass eV)
har_to_eV = 27.211386
F_eV = negf.F*har_to_eV
E = np.linspace(-5, 5, 1000) + negf.fermi
dos, dos_list = calculate_dos(F_eV, negf.S, SigmaCalculator(negf.g), E)
T = calculate_transmission(F_eV, negf.S, SigmaCalculator(negf.g), E)

# Plot correlation
plt.figure(figsize=(10, 5))
plt.subplot(121)
plt.plot(E, dos)
plt.xlabel('Energy (eV)')
plt.ylabel('DOS')

plt.subplot(122)
plt.semilogy(E, T)
plt.xlabel('Energy (eV)')
plt.ylabel('Transmission')

plt.tight_layout()
plt.show()

See Also