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 http://lammps.sandia.gov.
S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995). (abstract) (pdf) (tar file of figures if they don't display correctly in the PDF file)
Below are other papers that describe specific algorithms used within LAMMPS.
This paper describes the per-atom stress calculation that can now be used in LAMMPS with the long-range PPPM solver.
Characteristics of thermal conductivity in classical water models, T. W. Sirk, S. Moore, E. F. Brown, J Chem Phys, 138, 064505 (2013). (abstract)
This paper gives an overview of the many-body potentials available in LAMMPS.
Computational Aspects of Many-body Potentials, S. J. Plimpton and A. P. Thompson, MRS Bulletin, 37, 513-521 (2012). (abstract)
This paper describes work by Metin Aktulga (now at LBNL) and collaborators at Purdue to implement the ReaxFF force field in LAMMPS, available as the pair_style reax/c command.
Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques, H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, Parallel Computing, 38, 245-259 (2012). (abstract)
This paper describes how the fix phonon command in LAMMPS works to compute dynamical matrices and phonon dispersion relations:
Phonon dispersion measured directly from molecular dynamics simulations, L. T. Kong, Comp Phys Comm, 182, 2201-2207 (2011). (abstract)
This paper describes work by Andres Jaramillo-Botero and collaborators at Caltech to implement their electron force field (eFF) in LAMMPS as the USER-EFF package.
Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments, A. Jaramillo-Botero, J. Su, A. Qi, W. A. Goddard III, J Comp Chem, 32, 497-512 (2011). (abstract)
These papers describe work by Mike Brown (ORNL) to adapt several of the LAMMPS kernels (force calculation, neighbor list construction) for "hybrid" processors, meaning ones that hvae both multicore CPUs and GPUs.
Implementing Molecular Dynamics on Hybrid High Performance Computers - Short Range Forces, W. M. Brown, P. Wang, S. J. Plimpton, A. N. Tharrington, Comp Phys Comm, 182, 898-911, (2011). (abstract)
Implementing Molecular Dynamics on Hybrid High Performance Computers - Particle-Particle Particle-Mesh, W. M. Brown, A. Kohlmeyer, S. J. Plimpton, A. N. Tharrington, Comp Phys Comm, 183, 449-459 (2012). (abstract)
This paper describes the stochastic rotation dynamics (SRD) model as implemented in LAMMPS for use as a coarse-grained cheap solvent. This is for a pure SRD fluid model; a paper describing mixture systems (coarse-grained solute particles in SRD fluid) will be forthcoming.
Mesoscale Hydrodynamics via Stochastic Rotation Dynamics: Comparison with Lennard-Jones Fluid, M. K. Petersen, J. B. Lechman, S. J. Plimpton, G. S. Grest, P. J. in't Veld, P. R. Schunk, J Chem Phys, 132, 174106 (2010). (abstract)
This paper describes different ways of formulating per-atom and global virial and stress calculations, including how it is done in LAMMPS.
General formulation of pressure and stress tensor for arbitrary many-body interaction potentials under periodic boundary conditions, A. P. Thompson, S. J. Plimpton, W. Mattson, J Chem Phys, 131, 154107 (2009). (abstract)
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.
Particle-Mesh Ewald and rRESPA for Parallel Molecular Dynamics Simulations, S. J. Plimpton, R. Pollock, M. Stevens, in Proc of the Eighth SIAM Conference on Parallel Processing for Scientific Computing, Minneapolis, MN (March 1997). (abstract) (postscript) (ps.gz)