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 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:

@software{site_analysis,
  author = {Morgan, Benjamin J.},
  title = {site-analysis: Python module for analysing molecular dynamics simulations of ion transport},
  url = {https://github.com/bjmorgan/site-analysis},
  version = {1.5.0},
  year = {2026}
}

Publications Using the Python site-analysis Package

  • Rotational Stacking Faults in the Ionic Conductor Li3ScCl6 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

  • Enabling ionic transport in Li3AlP2: 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

  • 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

  • Dynamic Lone Pairs and Fluoride-Ion Disorder in Cubic-BaSnF4
    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

  • Mechanistic Origin of Superionic Lithium Diffusion in Anion-Disordered Li6PS5X Argyrodites
    Morgan, B.J.
    Chemistry of Materials, 33, 2004-2018 (2021)
    DOI: 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 Li7La3Zr2O12
    Burbano, M., Carlier, D., Boucher, F., Morgan, B.J., and Salanne, M.
    Physical Review Letters, 116, 135901 (2016)
    DOI: 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

  • 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

  • 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

  • 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

Publications Using Earlier Implementations

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

  • Cation composition effects on oxide conductivity in the Zr2Y2O7-Y3NbO7 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

  • Fluoride ion disorder and clustering in superionic PbF2
    Castiglione, M.J. and Madden, P.A.
    Journal of Physics: Condensed Matter, 13, 9963 (2001)
    DOI: 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