# Publications using site-analysis

This page lists scientific publications that have used the `site_analysis` package and its predecessor implementations. The polyhedral site analysis methodology, particularly the surface normal algorithm, was originally developed as a Fortran code before being reimplemented and expanded in the current Python package.

## Adding Your Publication

**If you have used site-analysis in your research and would like your paper listed here, please raise an issue on the [GitHub repository](https://github.com/bjmorgan/site-analysis) with details of your paper.**

Please include the full citation with DOI.

## Citing site-analysis

**If you use `site_analysis` in your research, please cite the paper published in the [Journal of Open Source Software](https://doi.org/10.21105/joss.09606):**

```bibtex
@article{Morgan2026,
  doi = {10.21105/joss.09606},
  url = {https://doi.org/10.21105/joss.09606},
  year = {2026},
  publisher = {The Open Journal},
  volume = {11},
  number = {122},
  pages = {9606},
  author = {Benjamin J. Morgan},
  title = {site-analysis: A Python package for site-projection analysis of molecular dynamics trajectories},
  journal = {Journal of Open Source Software}
}
```

To cite a specific version of the software, please also cite the archived release on [Zenodo](https://doi.org/10.5281/zenodo.20275363):

```bibtex
@software{site_analysis,
  author = {Morgan, Benjamin J.},
  title = {site-analysis: Python module for analysing molecular dynamics simulations of ion transport},
  doi = {10.5281/zenodo.20275363},
  url = {https://doi.org/10.5281/zenodo.20275363},
  version = {1.5.0},
  year = {2026}
}
```

## Publications Using the Python site-analysis Package

- **Rotational Stacking Faults in the Ionic Conductor Li<sub>3</sub>ScCl<sub>6</sub>**
  Goldmann, B.A., Rosenbach, C., Evans, H.A., Helm, B., Wankmiller, B., Maus, O., Suard, E., Nazar, L.F., Hansen, M.R., Morgan, B.J., Islam, M.S., Zeier, W.G.
  *Chemistry of Materials*, (2025)
  DOI: [10.1021/acs.chemmater.5c02303](https://doi.org/10.1021/acs.chemmater.5c02303) 

- **Enabling ionic transport in Li<sub>3</sub>AlP<sub>2</sub>: the roles of defects and disorder**
  Hu, J., Squires, A.G., Kondek, J., Johnson, M.J., Youd, A.B., Vadhva, P., Paul, P.P., Withers, P.J., Di Michiel, M., Keeble, D.S., Hansen, M.R., Scanlon, D.O., and Rettie, A.J.E.
  *Journal of Materials Chemistry A*, 13, 6427-6439 (2025)
  DOI: [10.1039/D4TA04347B](https://doi.org/10.1039/D4TA04347B)

- **Nature of the Superionic Phase Transition of Lithium Nitride from Machine Learning Force Fields**  
  Krenzer, G., Klarbring, J., Tolborg, K., Rossignol, H., McCluskey, A.R., Morgan, B.J., and Walsh, A.  
  *Chemistry of Materials*, 35, 6133-6140 (2023)  
  DOI: [10.1021/acs.chemmater.3c00874](https://doi.org/10.1021/acs.chemmater.3c00874)

- **Dynamic Lone Pairs and Fluoride-Ion Disorder in Cubic-BaSnF<sub>4</sub>**  
  Mercadier, B., Coles, S.W., Duttine, M., Legein, C., Body, M., Borkiewicz, O.J., Lebedev, O., Morgan, B.J., Masquelier, C., and Dambournet, D.  
  *Journal of the American Chemical Society*, 145, 17700-17714 (2023)  
  DOI: [10.1021/jacs.3c08232](https://doi.org/10.1021/jacs.3c08232)

- **Mechanistic Origin of Superionic Lithium Diffusion in Anion-Disordered Li<sub>6</sub>PS<sub>5</sub>X Argyrodites**  
  Morgan, B.J.  
  *Chemistry of Materials*, 33, 2004-2018 (2021)  
  DOI: [10.1021/acs.chemmater.0c03738](https://doi.org/10.1021/acs.chemmater.0c03738)

## Publications Using the Preceding Fortran Implementation

The following publications used the earlier Fortran implementation of the polyhedral site analysis with the surface normal algorithm, which formed the basis for the current Python `site_analysis` package.

- **Sparse Cyclic Excitations Explain the Low Ionic Conductivity of Stoichiometric Li<sub>7</sub>La<sub>3</sub>Zr<sub>2</sub>O<sub>12</sub>**  
  Burbano, M., Carlier, D., Boucher, F., Morgan, B.J., and Salanne, M.  
  *Physical Review Letters*, 116, 135901 (2016)  
  DOI: [10.1103/PhysRevLett.116.135901](https://doi.org/10.1103/PhysRevLett.116.135901)

- **Relationships between Atomic Diffusion Mechanisms and Ensemble Transport Coefficients in Crystalline Polymorphs**  
  Morgan, B.J. and Madden, P.A.  
  *Physical Review Letters*, 112, 145901 (2014)  
  DOI: [10.1103/PhysRevLett.112.145901](https://doi.org/10.1103/PhysRevLett.112.145901)

- **Molecular dynamics simulation of ionic transport at coherent interfaces in fluorite heterostructures**  
  Morgan, B.J. and Madden, P.A.  
  *Physical Review B*, 89, 054304 (2014)  
  DOI: [10.1103/PhysRevB.89.054304](https://doi.org/10.1103/PhysRevB.89.054304)

- **Absence of a space-charge-derived enhancement of ionic conductivity in β|γ-heterostructured 7H- and 9R-AgI**  
  Morgan, B.J. and Madden, P.A.  
  *Journal of Physics: Condensed Matter*, 24, 275303 (2012)  
  DOI: [10.1088/0953-8984/24/27/275303](https://doi.org/10.1088/0953-8984/24/27/275303)

- **Effects of Lattice Polarity on Interfacial Space Charges and Defect Disorder in Ionically Conducting AgI Heterostructures**  
  Morgan, B.J. and Madden, P.A.  
  *Physical Review Letters*, 107, 206102 (2011)  
  DOI: [10.1103/PhysRevLett.107.206102](https://doi.org/10.1103/PhysRevLett.107.206102)

## Publications Using Earlier Implementations

The following publications used earlier implementations of tetrahedral site projection schemes:

- **Cation composition effects on oxide conductivity in the Zr<sub>2</sub>Y<sub>2</sub>O<sub>7</sub>-Y<sub>3</sub>NbO<sub>7</sub> system**  
  Marrocchelli, D., Madden, P.A., Norberg, S.T. and Hull, S.  
  *Journal of Physics: Condensed Matter*, 21, 405403 (2009)  
  DOI: [10.1088/0953-8984/21/40/405403](https://doi.org/10.1088/0953-8984/21/40/405403)

- **Fluoride ion disorder and clustering in superionic PbF<sub>2</sub>**  
  Castiglione, M.J. and Madden, P.A.  
  *Journal of Physics: Condensed Matter*, 13, 9963 (2001)  
  DOI: [10.1088/0953-8984/13/44/311](https://doi.org/10.1088/0953-8984/13/44/311)

- **Polarization effects in the simulation of lead (II) fluoride**  
  Castiglione, M.J., Wilson, M. and Madden, P.A.  
  *Journal of Physics: Condensed Matter*, 11, 9009-9024 (1999)  
  DOI: [10.1088/0953-8984/11/46/303](https://doi.org/10.1088/0953-8984/11/46/303)