TranSIESTA Transport Tutorial

This site is a hands-on tutorial for computing nanoscale quantum transport with SIESTA / TranSIESTA / TBtrans, and for obtaining structural optimization and reference electronic structure with VASP. NEGF transport within VASP itself is not covered. Every chapter follows the sequence theory → input file walkthrough → run → output analysis → exercises.

What You Will Learn

• Practical intuition for the Landauer–Büttiker picture and the NEGF (nonequilibrium Green's function) formalism
• SCF, band, and DOS calculations with SIESTA; structural optimization and reference electronic structure with VASP
• The full TranSIESTA workflow: electrode → device at 0 V → finite-bias chain
• Extracting the transmission $T(E)$ and DOS/PDOS with TBtrans, and post-processing with sisl
• Computing I–V curves via the Landauer integral (and why a symmetric bias window matters)
• Eigenchannel decomposition and visualization, and correcting DFT level errors (level alignment)

Why SIESTA + VASP

Code	Role
SIESTA	Localized-orbital (LCAO) DFT — generates the Hamiltonian for electrodes/device
TranSIESTA	NEGF self-consistent calculation — open boundary conditions, finite bias
TBtrans	Post-processing transport — $T(E)$, DOS, eigenchannels
VASP	Plane-wave DFT — structural optimization, hybrid functional reference

NEGF transport requires a localized-orbital basis, so the SIESTA family handles it, while VASP serves as the reference for structures and energy levels. Moving between the two codes and cross-validating them is the perspective of this tutorial.

Roadmap

1. Setup — Installing the codes (SIESTA/TranSIESTA/TBtrans, sisl, VASP)
2. Fundamentals — Linux/terminal basics, DFT theory (Kohn–Sham, Bloch's theorem and basis sets, BZ sampling), introductions to SIESTA and VASP
3. Tutorial 00–04 — Transport theory basics, SIESTA/VASP fundamentals
4. Tutorial 05–09 — TranSIESTA/TBtrans transport workflow
5. Tutorial 10–12 — Eigenchannels, level alignment, HPC parallelization
6. Advanced — Scattering region convergence, $\eta$ broadening, caveats
7. Beyond 1D — Molecular junctions with metallic (Au) electrodes, bulk/interface transport, IP/EA calculations (ΔSCF)
8. Mini-project — End-to-end calculation of a polyyne–cumulene junction

Prerequisites

• Basic solid-state physics (band structure, Fermi level, Bloch's theorem)
• DFT concepts (exchange-correlation functionals, pseudopotentials, k-point sampling)
• Basics of the Linux shell and Python

note

The input conventions and validation procedures in this tutorial were distilled from real 1D chain and molecular junction calculations. The example systems are simple pedagogical models; before using them for research results, convergence with respect to structure, spin, k-points, and the energy grid must be verified separately for each system.