# Resources

## Software

### Core tools used in this course
- [ASE (Atomic Simulation Environment)](https://wiki.fysik.dtu.dk/ase/) — software framework used throughout
- [GPAW](https://gpaw.readthedocs.io/) — Density functional theory 
- [MACE](https://github.com/acesuit/mace) - Machine-learned interatomic potentials
- [nglview](https://nglviewer.org/nglview/latest/) — interactive 3D molecular viewer for Jupyter

### Useful complementary packages
- [vesta](https://jp-minerals.org/vesta/en/download.html) - visualisation tool
- [pymatgen](https://pymatgen.org/) — materials analysis library; excellent for symmetry analysis
- [phonopy](https://phonopy.github.io/phonopy/) — phonon calculations
- [shakenbreak](https://shakenbreak.readthedocs.io/) — defect geometry exploration
- [materialsproject](https://next-gen.materialsproject.org/api) - the Materials Project API

## Databases
- [Materials Project](https://materialsproject.org) — database for DFT-computed structures and properties
- [Quantum Defect Database (QD²)](https://qd2.materialsproject.org/) — computed properties of defect qubits
- [ICSD](https://icsd.products.fiz-karlsruhe.de/) — inorganic crystal structure database (institutional access)
- [AFLOW](http://aflowlib.org/) — high-throughput computational materials database

## Key Review Articles

### Computational Materials Science

- Spaldin, N. A. *[Fundamental Materials Research and the Course of Human Civilization](https://arxiv.org/pdf/1708.01325)* (2017). — A highly readable account of how materials breakthroughs have shaped civilisation, from the stone age to quantum technologies. 
- Burke, K. and friends. *[The ABC of DFT](https://dft.uci.edu/doc/g1.pdf)* (2007). — Free lecture notes written as an undergraduate text, with exercises.

### Quantum emitters and defect physics

- Aharonovich, I., Englund, D. & Toth, M. *[Solid-state single-photon emitters](https://www.nature.com/articles/nphoton.2016.186)* Nature Photonics (2016). — The standard introductory review of the field, covering NV centres, SiC defects, quantum dots, and 2D materials.
- Freysoldt, C. et al. *[First-principles calculations for point defects in solids](https://link.aps.org/doi/10.1103/RevModPhys.86.253)* Reviews of Modern Physics (2014). — A highly cited computational reference for defect formation energies, charge states, and correction schemes.
- Zhang, G. et al. *[Material platforms for defect qubits and single-photon emitters](https://pubs.aip.org/aip/apr/article/7/3/031308/123998)* Applied Physics Reviews (2020). — A comprehensive review of diamond, SiC, hBN, and silicon platforms, and how first-principles calculations guide the search for new defect qubits.

## Textbooks

- Giustino, F. *Materials Modelling using Density Functional Theory: Properties and Predictions.* Oxford University Press (2014). — Hands-on introduction; works through real material properties without heavy formalism.
- Sholl, D. S. & Steckel, J. A. *Density Functional Theory: A Practical Introduction.* Wiley (2009).
- Martin, R. M. *Electronic Structure: Basic Theory and Practical Methods.* Cambridge University Press (2020).


## Online Courses and Tutorials

- [ASE Workshop tutorials](https://ase-workshop-2023.github.io/tutorial/) — the source for some of this course's core content 
- [GPAW tutorials](https://gpaw.readthedocs.io/tutorialsexercises/) — DFT tutorial exercises
- [The Carpentries — Programming with Python](https://swcarpentry.github.io/python-novice-inflammation/) — Python refresher

## Videos and Talks

- Aron Walsh (Imperial College London): *[New Adventures in Materials Modelling](https://www.youtube.com/watch?v=Bv7n9dEiMuo)* — an accessible overview of modern computational materials science.
- Seán Kavanagh (UCL/Imperial): *[ShakeNBreak: Symmetry-Breaking and Reconstruction at Defects in Solids](https://www.youtube.com/watch?v=aqXlyLofLSU)* — a talk on defect structure searching from the developer of ShakeNBreak. See also his [full YouTube channel](https://www.youtube.com/channel/UCoVGnBeZeWmKzv8_-PzCKCw/about) for further tutorials.
- Materials Project: [YouTube channel](https://www.youtube.com/user/MaterialsProject) — tutorials and seminars on high-throughput materials computation and the Materials Project database.
- Bartomeu Monserrat (University of Cambridge): *[Lattice Dynamics](https://www.youtube.com/watch?v=FrY634Fa5Hc)* and *[Finite Temperature Modelling of Electronic Structure](https://www.youtube.com/watch?v=l65LIlYOpek)* — lectures on phonons and temperature effects on electronic properties from first principles. This isn't covered in this course, but its highly relevant for quantum photonics and many other applications.

## Getting Help or Reporting Issues

For urgent matters it is best to contact the course instructor via email.

- [Materials Science Stack Exchange](https://mattermodeling.stackexchange.com/)
- [Raise an Issue](https://github.com/NU-CEM/Atomistic_Simulation/issues)