The following CPC paper is the canonical reference to use for citing LAMMPS. It gives an overview of the code including its parallel algorithms, design features, performance, and brief highlights of many of its materials modeling capabilities. If you wish, you can also mention the URL of the LAMMPS website in your paper, namely https://www.lammps.org.
LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales, A. P. Thompson, H. M. Aktulga, R. Berger, D. S. Bolintineanu, W. M. Brown, P. S. Crozier, P. J. in 't Veld, A. Kohlmeyer, S. G. Moore, T. D. Nguyen, R. Shan, M. J. Stevens, J. Tranchida, C. Trott, S. J. Plimpton, Comp Phys Comm, 271 (2022) 10817.
Here is the DOI which has a link to the PDF: https://doi.org/10.1016/j.cpc.2021.108171. And here is a BibTeX entry for the paper.
This earlier JCP paper was the original citation for LAMMPS. You can cite it if you want to refer to the parallel spatial-decomposition strategy LAMMPS still uses:
Fast Parallel Algorithms for Short-Range Molecular Dynamics, S. Plimpton, J Comp Phys, 117, 1-19 (1995). (abstract)
Many capabilities within LAMMPS were implemented by folks who also wrote papers about their work. If you use their feature in your simulations and write your own paper, we highly recommend you cite their work specifically.
When you run LAMMPS and use a citeable feature, a message is printed to the screen and logfile. A "log.cite" file is also output, which gives a BibTeX form of the corresponding citation.