siesta-transmission-pathway

TBtrans Pathways 2D (siesta-transmission-pathway) A Python program to visualize 2D transmission/current pathways from SIESTA/TranSIESTA TBtrans bond-resolved outputs (bond transmission / bond current). TBtrans provides bond-current and related post-processing capabilities for transport analysis. This tool produces publication-ready pathway plots with cell clipping and periodic-bond skeleton rendering. Conceptual equivalence: It visualizes local bond contributions T_ij similarly to QuantumATK’s “TransmissionPathways” analysis (splitting total transmission into bond contributions). Key features (implemented in this script):- 2D projection planes: yz / xz / xy, with 4-view support via viewdir (+ / -).- Arrow direction determined by sign of bond value; arrow color determined by projection onto a chosen global transport axis.- Optional element coloring & bond skeleton from an auxiliary structure file (recommended: out.xyz/extxyz) using ASE neighbor lists.- Periodic-bond handling and cell-projection clipping for clean plots. Input:- TBtrans NetCDF output (e.g., *.TBT.nc or *.TBT.AV.nc)- Optional: out.xyz/extxyz (recommended for reliable species/bond perception) Dependencies:- Python 3- numpy, matplotlib- sisl (for reading TBtrans-related data)- ase (optional; used when --xyz is provided) Suggested citation:Bai, Z. siesta-transmission-pathway (Software). Zenodo. DOI: 10.5281/zenodo.11896224 Access / rights:The record metadata is public for citation. Files are restricted; source code access is granted only upon explicit permission by the author.