Ingredients

This is an ingredients list for research, inspired by the personal mathematical roadmap of Julia Wolf. It is an evolving collection of tools, papers, websites and online lectures related to computational energy materials research. It is not exhaustive but highlights what we have found particularly useful.

For online tools we use a pound sign to denote that there is an associated cost and a star to denote open source projects. If you use any of the tools please cite accordingly.

General research toolkit

Paper management and sharing: Zotero^*
Communication: Slack^£ or it’s open source sister Zulip^* (note that both feature built-in video conferencing).
Academic websites: Build it using a static site generator such as Hugo^* or Jekyll^*, and host it using Github.
Presentations: write it in markdown, convert it to html using reveal-md^* and host it using Github.
Notetaking: simplenote^* which syncs with nvALT^* on the Mac.
Text editor: For text with minimal formatting (e.g. abstracts) I write in Markdown using the MacDown^* editor. For larger documents (e.g. funding applications) I write in LaTeX using the Sublime^£ text editor.

Computing (local)

Operating System: I find that using a unix-based system is easiest for code development, and that there are less “why doesn’t this work?” moments with a Mac. (Although I haven’t used a linux OS for almost 10 years; ubuntu^* has most likely improved a lot in that time)
Hardware: For post-processing, writing code and other computationally lightweight tasks I use a MacBook Air with an external monitor, keyboard and curiously shaped ergonomic mouse. I have an iMac in the office which can also do some lightweight DFT.
Back-ups and syncing: For backing up my workstation I use an external drive with Time Machine, for syncing between my laptop and workstation I use a combination of Dropbox^£ and Github.

Computing (high performance)

Computer time: Materials Chemistry Consortium for access to the Tier-1 (national) supercomputer Archer/Archer2, and Prace for access to Tier-0 (European level) HPC.
Storage: Research Data Facility on Archer.

Electronic structure

Density Functional Theory: Vasp^£ and ASE^*
Analysis: vasppy^*, effmass^*, kgrid^* and PolaronMobility^*
Plotting: sumo^*
Visualisation: Vesta
Crystal structures database: ICSD
Property databases: Materials Project (powered by pymatgen^*) and Semiconductors: Data Handbook by Otfried Madelung

Defects

Processing: CPLAP (stable chemical potential range), scfermi (self-consistent Fermi level), CarrierCapture.jl^* (carrier capture rates)
Corrections: sxdefectalign (implements the Freysoldt, Neugebauer and van de Walle scheme)
Review articles: Tutorial: Defects in semiconductors—Combining experiment and theory by Audrius Alkasukas et al, Defects and defect processes by Marshall Stoneham, First-principles calculations for defects and impurities: Applications to III-nitrides by Chris van de Walle, Quick-start guide for first-principles modelling of point defects in crystalline materials by Sunghyun Kim et al.

Phonons

Calculators: phonopy^* (harmonic and quasi-harmonic), phono3py^* (third order phonon-phonon interactions)
Processing: ModeMap^*, JuliaPhonons^*
Visualisation: ASCIIphonons^*, phonon website^*

Photovoltaics

Efficiency tables: NREL, JPhys Energy emerging inorganic

Python

Code editor: Sublime^£
IDE: pycharm^£
Version control: git and the Version Control with Git^* Software carpentry course (available online or in person)
Code repository: Github
Interactive notebook: Jupyter^* and Jupyter Lab^* for interactive code development. The binder^* web app so that others can easily interact with your notebooks.
Python scientific computing stack: matplotlib^* (plotting), pandas^* (data analysis), numpy^* (arrays)
Testing: pytest^*
Continuous integration: Travis CI^* (available as a Github app)
Documentation: Automatically generate and build online documentation using Sphinx^* and ReadTheDocs^*.

Publications

Typesetting: I use LaTeX with the mhchem^* package for formatting chemical equations
Equations: LaTexit
Text editors: I use the Sublime^£ text editor and, for collaborative LaTeX documents, Overleaf
Bibliography: doi2bib
Graphics: Omnigraffle^£ for schematics and matplotlib^* for plotting
Software journals: The Journal of Open Source Software^*

Research funding
(note that this is very much a wish list!)

EPSRC: New investigator award, Fellowship programme
UKRI: Future Leaders Fellowships
Royal Society: Dorothy Hodgkins fellowship

Professional communities

Blogs and group websites

A set of useful links is maintained by the Materials Design Group
Best practices in computational chemistry from Guido von Rudorff
Various tips and tricks for computational chemistry in the appendices of the HackingMaterials handbook
Setting up a mac for computational chemistry from thelostelectron blog

Textbooks

Condensed Matter: Principles of the theory of solids and Electrons and Phonons by John Ziman.
Electronic structure: Electronic structure and the properties of solids by Walter Harrison
Defects: Defects and defect processes in Nonmetallic Solids by Hayes and Stoneham
Phonons: Introduction to Lattice Dynamics by Martin Dove
Photovoltaics: The Physics of Solar Cells by Jenny Nelson
Other: Models of disorder by John Ziman.

Video lectures

Teaching resources

Small Teaching by James M. Lang connects pedagogical theory with some easily implementable ideas for the classroom
Teaching Tech Together by Greg Wilson. Greg Wilson co-founded Software Carpentry and this book expands on the excellent instructor training that is delivered by the organisation.

Miscellaneous

Bird of passage by Rudolf Peierls. This is one of my very favourite books. It is an autobiography from a German born physicist who travelled to the UK and kick-started the Manhattan project with the Frisch-Peierls memorandum. It provides lots of interesting context around the early developments in quantum mechanics and solid state physics.
Motherhood and academia blog Mamaisanacademic
Keith Butler’s Materials Hipster