The following JCP paper is the canoncial reference to use for citing LAMMPS. It describes the parallel spatial-decomposition, neighbor-finding, and communcation algorithms used in the code. Please also give the URL of the LAMMPS WWW Site in your paper, namely lammps.sandia.gov.
S. J. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995). (abstract) (postscript) (ps.gz) (tar file of figures if they don't display correctly in the PS file)
If you send us the relevant info (citation, abstract) about your publication that uses LAMMPS results, we'll be pleased to add it to the Publications page of the LAMMPS WWW Site. Ditto for a picture or movie for the Pictures or Movies pages. See the authors page for contact information.
Below are other papers that describe specific algorithms used within LAMMPS.
This paper describes the ellipsoidal Gay-Berne potential in LAMMPS and its application to mixture systems.
Liquid crystal nanodroplets in solution, W. M. Brown, M. K. Petersen, S. J. Plimpton, and G. S. Grest, J Chem Phys, 130, 044901 (2009). (abstract)
This paper describes the coupling of LAMMPS to the POEMS multi-body dynamics solver, available in LAMMPS via the fix poems command.
Substructured molecular dynamics using multibody dynamics algorithms, R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson, Intl J of Non-Linear Mechanics, 43, 1045-1055 (2008). (abstract)
This paper describes the implementation of Peridynamics in LAMMPS, which is a particle-based model of continuum mechanics, suitable for modeling materials at the mesoscale and macroscale.
Implementing peridynamics within a molecular dynamics code, M. L. Parks, R. B. Lehoucq, S. J. Plimpton, S. A. Silling, Comp Phys Comm, 179, 777-783 (2008). (abstract)
This paper describes the neighboring and communication algorithms developed for efficient simulation of mixtures with particles of widely varying size as implemented in the neighbor multi and communicate multi commands:
Accurate and Efficient Methods for Modeling Colloidal Mixtures in an Explicit Solvent using Molecular Dynamics, P. J. in 't Veld, S. J. Plimpton, G. S. Grest, Comp Phys Comm, 179, 320-329 (2008). (abstract)
This paper describes the grain boundary driving force methodology that allows more rapid computation of grain boundary mobility, as implemented in the fix orient/fcc command:
Computing the Mobility of Grain Boundaries, K. G. F. Janssens, D. Olmsted, E.A. Holm, S. M. Foiles, S. J. Plimpton, and P. M. Derlet, Nature Materials, 5, 124-127 (2006). (abstract)
This paper discusses the Monte Carlo bond-swapping algorithm used in LAMMPS as implemented in the fix bond/swap command:
Equilibration of long chain polymer melts in computer simulations, R. Auhl, R. Everaers, G. S. Grest, K. Kremer, S. J. Plimpton,J Chem Phys, 119, 12718-12728 (2003). (abstract)
This paper discusses the implementation of the PPPM solver (variant of PME) and rRESPA within LAMMPS, including a discussion of how the parallel FFTs work.
S. J. Plimpton, R. Pollock, M. Stevens, Particle-Mesh Ewald and rRESPA for Parallel Molecular Dynamics Simulations, in Proc of the Eighth SIAM Conference on Parallel Processing for Scientific Computing, Minneapolis, MN (March 1997). (abstract) (postscript) (ps.gz)