This section provides an overview of what LAMMPS can and can't do, describes what it means for LAMMPS to be an open-source code, and acknowledges the funding and people who have contributed to LAMMPS over the years.1.1 What is LAMMPS
LAMMPS is a classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, metallic, granular, and coarse-grained systems using a variety of force fields and boundary conditions.
For examples of LAMMPS simulations, see the Publications page of the LAMMPS WWW Site.
LAMMPS runs efficiently on single-processor desktop or laptop machines, but is designed for parallel computers. It will run on any parallel machine that compiles C++ and supports the MPI message-passing library. This includes distributed- or shared-memory parallel machines and Beowulf-style clusters.
LAMMPS can model systems with only a few particles up to millions or billions. See Section_perf for information on LAMMPS performance and scalability, or the Benchmarks section of the LAMMPS WWW Site.
LAMMPS is a freely-available open-source code, distributed under the terms of the GNU Public License, which means you can use or modify the code however you wish. See this section for a brief discussion of the open-source philosophy.
LAMMPS is designed to be easy to modify or extend with new capabilities, such as new force fields, atom types, boundary conditions, or diagnostics. See Section_modify for more details.
The current version of LAMMPS is written in C++. Earlier versions were written in F77 and F90. See Section_history for more information on different versions. All versions can be downloaded from the LAMMPS WWW Site.
LAMMPS was originally developed under a US Department of Energy CRADA (Cooperative Research and Development Agreement) between two DOE labs and 3 companies. It is distributed by Sandia National Labs. See this section for more information on LAMMPS funding and individuals who have contributed to LAMMPS.
In the most general sense, LAMMPS integrates Newton's equations of motion for collections of atoms, molecules, or macroscopic particles that interact via short- or long-range forces with a variety of initial and/or boundary conditions. For computational efficiency LAMMPS uses neighbor lists to keep track of nearby particles. The lists are optimized for systems with particles that are repulsive at short distances, so that the local density of particles never becomes too large. On parallel machines, LAMMPS uses spatial-decomposition techniques to partition the simulation domain into small 3d sub-domains, one of which is assigned to each processor. Processors communicate and store "ghost" atom information for atoms that border their sub-domain. LAMMPS is most efficient (in a parallel sense) for systems whose particles fill a 3d rectangular box with roughly uniform density. Papers with technical details of the algorithms used in LAMMPS are listed in this section.
This section highlights LAMMPS features, with pointers to specific commands which give more details. If LAMMPS doesn't have your favorite interatomic potential, boundary condition, or atom type, see Section_modify, which describes how you can add it to LAMMPS.
(atom style command)
(pair style, bond style, angle style, dihedral style, improper style, kspace style commands)
(read_data, lattice, create_atoms, delete_atoms, displace_atoms, replicate commands)
(run, run_style, minimize commands)
(dump, restart commands)
nudged elastic band parallel replica dynamics temperature accelerated dynamics parallel tempering
These are LAMMPS capabilities which you may not think of as typical molecular dynamics options:
LAMMPS is designed to efficiently compute Newton's equations of motion for a system of interacting particles. Many of the tools needed to pre- and post-process the data for such simulations are not included in the LAMMPS kernel for several reasons:
Specifically, LAMMPS itself does not:
A few tools for pre- and post-processing tasks are provided as part of the LAMMPS package; they are described in this section. However, many people use other codes or write their own tools for these tasks.
As noted above, our group has also written and released a separate toolkit called Pizza.py which addresses some of the listed bullets. It provides tools for doing setup, analysis, plotting, and visualization for LAMMPS simulations. Pizza.py is written in Python and is available for download from the Pizza.py WWW site.
LAMMPS requires as input a list of initial atom coordinates and types, molecular topology information, and force-field coefficients assigned to all atoms and bonds. LAMMPS will not build molecular systems and assign force-field parameters for you.
For atomic systems LAMMPS provides a create_atoms command which places atoms on solid-state lattices (fcc, bcc, user-defined, etc). Assigning small numbers of force field coefficients can be done via the pair coeff, bond coeff, angle coeff, etc commands. For molecular systems or more complicated simulation geometries, users typically use another code as a builder and convert its output to LAMMPS input format, or write their own code to generate atom coordinate and molecular topology for LAMMPS to read in.
For complicated molecular systems (e.g. a protein), a multitude of topology information and hundreds of force-field coefficients must typically be specified. We suggest you use a program like CHARMM or AMBER or other molecular builders to setup such problems and dump its information to a file. You can then reformat the file as LAMMPS input. Some of the tools in this section can assist in this process.
Similarly, LAMMPS creates output files in a simple format. Most users post-process these files with their own analysis tools or re-format them for input into other programs, including visualization packages. If you are convinced you need to compute something on-the-fly as LAMMPS runs, see Section_modify for a discussion of how you can use the dump and compute and fix commands to print out data of your choosing. Keep in mind that complicated computations can slow down the molecular dynamics timestepping, particularly if the computations are not parallel, so it is often better to leave such analysis to post-processing codes.
A very simple (yet fast) visualizer is provided with the LAMMPS package - see the xmovie tool in this section. It creates xyz projection views of atomic coordinates and animates them. We find it very useful for debugging purposes. For high-quality visualization we recommend the following packages:
Other features that LAMMPS does not yet (and may never) support are discussed in Section_history.
Finally, these are freely-available molecular dynamics codes, most of them parallel, which may be well-suited to the problems you want to model. They can also be used in conjunction with LAMMPS to perform complementary modeling tasks.
CHARMM, AMBER, NAMD, NWCHEM, and Tinker are designed primarily for modeling biological molecules. CHARMM and AMBER use atom-decomposition (replicated-data) strategies for parallelism; NAMD and NWCHEM use spatial-decomposition approaches, similar to LAMMPS. Tinker is a serial code. DL_POLY includes potentials for a variety of biological and non-biological materials; both a replicated-data and spatial-decomposition version exist.
LAMMPS comes with no warranty of any kind. As each source file states in its header, it is a copyrighted code that is distributed free-of- charge, under the terms of the GNU Public License (GPL). This is often referred to as open-source distribution - see www.gnu.org or www.opensource.org for more details. The legal text of the GPL is in the LICENSE file that is included in the LAMMPS distribution.
Here is a summary of what the GPL means for LAMMPS users:
(1) Anyone is free to use, modify, or extend LAMMPS in any way they choose, including for commercial purposes.
(2) If you distribute a modified version of LAMMPS, it must remain open-source, meaning you distribute it under the terms of the GPL. You should clearly annotate such a code as a derivative version of LAMMPS.
(3) If you release any code that includes LAMMPS source code, then it must also be open-sourced, meaning you distribute it under the terms of the GPL.
(4) If you give LAMMPS files to someone else, the GPL LICENSE file and source file headers (including the copyright and GPL notices) should remain part of the code.
In the spirit of an open-source code, these are various ways you can contribute to making LAMMPS better. You can send email to the developers on any of these items.
LAMMPS development has been funded by the US Department of Energy (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life programs and its OASCR and OBER offices.
Specifically, work on the latest version was funded in part by the US Department of Energy's Genomics:GTL program (www.doegenomestolife.org) under the project, "Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling".
The following paper describe the basic parallel algorithms used in LAMMPS. If you use LAMMPS results in your published work, please cite this paper and include a pointer to the LAMMPS WWW Site (http://lammps.sandia.gov):
S. J. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995).
Other papers describing specific algorithms used in LAMMPS are listed under the Citing LAMMPS link of the LAMMPS WWW page.
The Publications link on the LAMMPS WWW page lists papers that have cited LAMMPS. If your paper is not listed there for some reason, feel free to send us the info. If the simulations in your paper produced cool pictures or animations, we'll be pleased to add them to the Pictures or Movies pages of the LAMMPS WWW site.
The core group of LAMMPS developers is at Sandia National Labs:
The following folks are responsible for significant contributions to the code, or other aspects of the LAMMPS development effort. Many of the packages they have written are somewhat unique to LAMMPS and the code would not be as general-purpose as it is without their expertise and efforts.
As discussed in Section_history, LAMMPS originated as a cooperative project between DOE labs and industrial partners. Folks involved in the design and testing of the original version of LAMMPS were the following: