Software Resources

Software tools to make your research life easier (with an emphasis on open-source packages)

Particularly useful resources are marked with a **.

The library: sometimes (old) textbooks are the way to go!
Google scholar: the power of Google search but for journal articles, patents, and reviews
RSS feeds: get notified about the latest publications via email; most journals have an RSS feed as does Google Scholar
**Starting off with a review. Reviews are typically more pedagogical and can help you get the bigger picture understanding. Some common revew journals in our field:
- Review of Modern Physics
- Chemical Reviews
- Accounts of Chemical Research
Seminal Papers in the field. See Reading List for a few.
Fun way of finding related papers: https://www.connectedpapers.com/

Zotero: collect, organize, annotate, cite, and share research. Wennie recommends add-ons like Zotfile for pdf managment and Better BibTeX for better integration with LaTeX. Zotero also comes with a browser plug-in for directly importing a reference from the browser to your library!
Mendeley (not open-source but free to use)
EndNote (commercial): licenses sold at discount price for UT Austin affiliates

VASP (licensed): plane-wave DFT based on PAW pseudopotentials
QuantumESPRESSO: integrated suite of open-source codes based on plane-wave DFT and pseudopotentials
Abinit: software suite for plane-wave DFT; usually has very user friendly documentation- useful for a highlight of the theory and how it is implemented in code
PySCF: quantum chemistry package implemented using Python/C combined
Yambo: many-body perturbation theory methods (GW and BSE) and TD-DFT; frequently interfaced with QuantumESPRESSO and Abinit
Wannier90: generation and analysis of maximally-localized Wannier functions
FHI aims: all-electron code based on numeric atom-centered orbitals
Wien2k: all-electron code based on full-potential (linearized) augmented plane-wave + local orbitals [(L)APW] method
Gaussian: quantum chemistry code that uses a Gaussian basis set
ORCA: DFT and semi-empirical SCF-MO package

Pymatgen: open-source Python library for materials analysis, most support for analysing VASP calculations
atomate: creating computational workflows; particularly useful for use with VASP
Materials Project: web-based access to materials database of crystalline systems
Atomic Simulation Environment (ASE): Python library for materials analysis, including lots of support for QuantumESPRESSO calculations
Mathematica
MATLAB (or its open source counterpart, Octave)

Gnuplot: portable, command-line graphing utility; great for quick visualization
Xmgrace: also a command-line graphing utility
VESTA: visualize 3D rendered crystal structures
Xcrysden: visualize and analyze crystal structures (more diret compatbility with QuantumESPRESSO file format)
TRAVIS: visualize and analyze trajectories from MD simulations
VMD: also a visualizer for MD trajectories
Ovito (Basic edition is free): general visualization for atomistic and other particle-based models

**Vim, emacs (emacs org), nano: terminal-based text editors
**LaTeX: a document preparation system with high-quality typesetting.
LibreOffice Write (and the rest of the office suite): word processor
Lyx: WYSIWYG document processor for LaTeX documents; useful for digitized homeworks!
Pandoc: near universal document format converter
Joplin: take multimedia notes with markdown (images, videos, audio, pdfs, links)
Sublime: Text editor with syntax highlighting; handles LaTeX and various coding languages
Pycharm: IDE for python
Gitbook: publish documentation; integration with Github

Git: version control system; Github: platform for building, scaling, and delivering software packages
Insync: sync a file system between computers including Google Drive, OneDrive, and Dropbox
i3: tile windows automatically in Linux and BSD operating systems

Last updated 1 year ago