LAMMPS

Large-scale Atomic/Molecular Massively Parallel Simulator

Original author(s)| Steve Plimpton, Aidan Thompson, Stan Moore, Axel Kohlmeyer, Richard Berger
Developer(s)| Sandia National Laboratories
Temple University
Initial release| 1995; 29 years ago (1995)
Stable release|

2August2023 / August 2, 2023; 6 months ago (2023-08-02)

Repository| github.com/lammps/lammps
Written in| C++
Operating system| Cross-platform: Linux, macOS, Windows, FreeBSD, Solaris
Platform| x86, x86-64, ARM, POWER9
Size| 534 MB
Available in| English
Type| Molecular dynamics
License| GNU General Public License
Website| www.lammps.org

Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a molecular dynamics program from Sandia National Laboratories.[1] LAMMPS makes use of Message Passing Interface (MPI) for parallel communication and is free and open-source software, distributed under the terms of the GNU General Public License.[1]

LAMMPS was originally developed under a Cooperative Research and Development Agreement between two laboratories from United States Department of Energy and three other laboratories from private sector firms.[1] (As of 2016), it is maintained and distributed by researchers at the Sandia National Laboratories and Temple University.[1]

## Contents

* 1 Features
* 2 See also
* 3 References
* 4 External links

## Features

For computing efficiency, LAMMPS uses neighbor lists (Verlet lists) to keep track of nearby particles. The lists are optimized for systems with particles that repel at short distances, so that the local density of particles never grows too large.[2]

On parallel computers, 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 subdomain. LAMMPS is most efficient (in a parallel computing sense) for systems whose particles fill a 3D rectangular box with approximately uniform density. Lots of accelerators are supported by LAMMPS, for example, GPU (CUDA, OpenCL, HIP, SYCL), Intel Xeon Phi, and OpenMP support for many code features.

LAMMPS also allows for coupled spin and molecular dynamics in an accelerated fashion.[3]

LAMMPS is coupled to many analysis tools and engines as well.[4][5][6] LAMMPS also can be coupled with free energy calculators, such as PLUMED and Colvar[7][8]

## See also

* Parallel computing
* Comparison of software for molecular mechanics modeling
* Molecular design software
* List of free and open-source software packages

## References

1. ↑ 1.0 1.1 1.2 1.3 "LAMMPS Molecular Dynamics Simulator". Sandia National Laboratories. https://www.lammps.org/. Retrieved 2022-07-13.
2. ↑ Plimpton, S. (1993-05-01). Fast parallel algorithms for short-range molecular dynamics. doi:10.2172/10176421. https://digital.library.unt.edu/ark:/67531/metadc1389173/.
3. ↑ Tranchida, Julien Guy; Wood, Mitchell; Moore, Stan Gerald (2018-09-01). Coupled Magnetic Spin Dynamics and Molecular Dynamics in a Massively Parallel Framework: LDRD Final Report.. doi:10.2172/1493836. https://www.osti.gov/biblio/1493836.
4. ↑ Stukowski, Alexander (2009-12-15). "Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool". Modelling and Simulation in Materials Science and Engineering 18 (1): 015012. doi:10.1088/0965-0393/18/1/015012. ISSN 0965-0393. https://iopscience.iop.org/article/10.1088/0965-0393/18/1/015012.
5. ↑ Goswami, Rohit; Goswami, Amrita; Singh, Jayant K. (2019). "dSEAMS: Deferred Structural Elucidation Analysis for Molecular Simulations". Journal of Chemical Information and Modeling. doi:10.1021/acs.jcim.0c00031.s001.
6. ↑ McGibbon, Robert T; Beauchamp, Kyle A; Schwantes, Christian R; Wang, Lee-Ping; Hernández, Carlos X; Harrigan, Matthew P; Lane, Thomas J; Swails, Jason M et al. (2014-09-09). "MDTraj: a modern, open library for the analysis of molecular dynamics trajectories". Biophysical Journal 109 (8): 1528–32. doi:10.1016/j.bpj.2015.08.015. PMID 26488642.
7. ↑ Tribello, Gareth A.; Bonomi, Massimiliano; Branduardi, Davide; Camilloni, Carlo; Bussi, Giovanni (2014-02-01). "PLUMED 2: New feathers for an old bird". Computer Physics Communications 185 (2): 604–613. doi:10.1016/j.cpc.2013.09.018. ISSN 0010-4655. https://www.sciencedirect.com/science/article/pii/S0010465513003196.
8. ↑ Fiorin, Giacomo; Klein, Michael L.; Hénin, Jérôme (December 2013). "Using collective variables to drive molecular dynamics simulations" (in en). Molecular Physics 111 (22–23): 3345–3362. doi:10.1080/00268976.2013.813594. ISSN 0026-8976.

## External links

* v
* t
* e

Computational chemistry software

Cheminformatics|

| Open-source|

* Avalon Cheminformatics Toolkit
* Bioclipse
* Blue Obelisk
* Chemistry Development Kit
* ECCE
* JOELib
* OELib
* Open Babel
* RDKit

|

Proprietary|

* Canvas
* Chemicalize
* Discovery Studio

Chemical kinetics|

| Open-source|

* APBS
* Cantera
* KPP

|

Proprietary|

* Autochem
* Chemical WorkBench
* CHEMKIN
* COSILAB
* DelPhi
* Khimera

Molecular modelling and visualization|

List of molecular graphics systems

| Open-source|

* Ascalaph Designer
* Avogadro
* BALL
* Biskit
* CPMD
* Gabedit
* Ghemical
* Jmol
* Molekel
* PyMOL
* QuteMol
* RasMol

|

Proprietary|

* Abalone
* ACD/ChemSketch
* Atomistix ToolKit
* ChemDraw
* EzMol
* Gaussian
* Maestro
* MarvinSketch
* MarvinView
* MODELLER
* Molecular Operating Environment
* Spartan
* UCSF Chimera
* VMD

Molecular docking|

List of protein-ligand docking software

| Open-source|

* AutoDock
* AutoDock Vina
* FlexAID
* rDock

|

Proprietary|

* Glide
* Molecular Operating Environment

Molecular dynamics|

| Open-source|

* GROMACS
* LAMMPS
* OpenMM
* PLUMED

|

Proprietary|

* Abalone
* AMBER
* CHARMM
* Desmond
* GROMOS
* NAMD

Quantum chemistry|

List of quantum chemistry and solid-state physics software

| Open-source|

* ABINIT
* ACES (CFOUR)
* AIMAll
* BigDFT
* CP2K
* DACAPO
* Dalton
* DP code
* FreeON
* HORTON
* MADNESS
* MPQC
* NWChem
* Octopus
* PSI
* PyQuante
* PySCF
* Quantum ESPRESSO (PWscf)
* RMG
* SAMSON
* SIESTA
* VB2000
* YAMBO code

|

Proprietary|

* ADF
* AMPAC
* DMol3
* CADPAC
* CASINO
* CASTEP
* COLUMBUS
* CONQUEST
* CPMD
* CRUNCH
* CRYSTAL
* DIRAC
* Firefly
* GAMESS (UK)
* GAMESS (US)
* Gaussian
* Jaguar
* MOLCAS
* MOLPRO
* MOPAC
* ONETEP
* OpenAtom
* ORCA
* PARSEC
* PLATO
* PQS
* Q-Chem
* Quantemol
* Scigress
* Spartan
* TeraChem
* TURBOMOLE
* VASP
* WIEN2k
* XMVB

Skeletal structure drawing|

| Open-source|

* BKChem
* JChemPaint
* JME Molecule Editor
* Molsketch
* XDrawChem

|

Proprietary|

* ACD/ChemSketch
* ChemDoodle
* ChemDraw
* MarvinSketch

Others|

* Aqion
* Eulim
* EXC code
* GenX
* GSim
* ICM (ICM-Browser)
* Materials Studio
* Molden
* OpenChrom
* RubyChem
* SASHIMI

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