hover to animate -- input script physical analog (start at 3:25) & explanation

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. Many of its models have versions that provide accelerated performance on CPUs, GPUs, and Intel Xeon Phis. The code is designed to be easy to modify or extend with new functionality.

LAMMPS is distributed as an open source code under the terms of the GPL. The current version can be downloaded here. Links are also included to older F90/F77 versions. Periodic releases are also available on SourceForge.

LAMMPS is distributed by Sandia National Laboratories, a US Department of Energy laboratory. The main authors of LAMMPS are listed on this page along with contact info and other contributors. Funding for LAMMPS development has come primarily from DOE (OASCR, OBER, ASCI, LDRD, Genomes-to-Life) and is acknowledged here.

The LAMMPS web site is hosted by Sandia, which has this Privacy and Security statement.

• (11/16) Added temper/grem and fix grem commands to enable tempering via the generalized replica exchange method (gREM) method.
• (10/16) Added a fix wall/gran/region command which allows geometric regions to act as boundaries for granular particles.
• (9/16) Added options for weighted load-balancing to the balance and fix balance commands, which can be useful for better overall performance of heterogeneous simulation models.
• (9/16) Added a fix cmap command for 5-body CMAP crossterms as defined by the CHARMM force field between overlapping dihedrals.
• (9/16) Added Kokkos support (GPU, Phi) for long-range electrostatics via the kspace_style pppm/kk command. (8/16) Added a fix controller command to enable guiding of a simulation to a desired target. If uses a control loop feedback mechanism known as a proportional-integral-derivative (PID) controller.
• (6/16) Added a Kokkos version of the ReaxFF potential, i.e. pair_style reax/c/kk, so it can be run using OpenMP or on GPUs or Intel Phis.
• (6/16) Added reactivity extensions to the USER-DPD package to enable reactive DPD simulations.
• (2/16) Added a dump custom/vtk command that outputs snapshots in VTK format readable by the VTK visualization toolkit or other visualization tools that use it, such as ParaView.
• (2/16) Added a USER-DPD package for performing DPD simulations at constant energy/temperature/pressure/enthalpy with an efficient Shardlow splitting integrator.
• (12/15) Significant features added to LAMMPS in the fourth quarter of 2014 include these new commands: pair_style mgpt, pair_style smtbq, pair_style vashishita, fix ave/correlate/long, compute hexorder/atom, compute orientorder/atom, pair_style lj/mdf, pair_style lennard/mdf, pair_style buck/mdf, improper_style distance, compute chunk/atom bin sphere/cylinder options, and fix qeq/fire. See authors here and details here.
• (10/15) Added two new pair styles: pair_style mgpt for quantum-based model generalized pseudopotential theory (MGPT) multi-ion potentials, and pair_style smtbq for second moment tight binding QEq potentials for ionocovalent bonds in oxides.
• (9/15) Significant features added to LAMMPS in the third quarter of 2014 include a new HTML format for doc pages with a search option, and these new packages and commands: USER-DIFFRACTION package, USER-QTB package, USER-DRUDE package, USER-SMD package, COMPRESS package, USER-TALLY package, dump h5md, read_data for multiple data files, pair_style polymorphic, timer, and a run_style respa hybrid option. See authors here and details here.
• (8/15) Added a dump h5md command which can write HDF5 formatted dump files.
• (7/15) Added a USER-SMD package for performing Smooth Mach Dynamics, which a SPH-related model applicable to solids.
• (7/15) Trying out a new format for the manual doc pages. Thanks to Richard Berger (JKU) for scripting restuctured text (rst) and Sphinx tools to do this.
• (7/15) Added a USER-DRUDE package which implements a thermalized Drude dipole model for polarization effects.
• (7/15) Added a USER-QTB package to enable inclusion of quantum nuclear effects when applicable via 2 commands, fix qtb and fix qbmsst, as an extension to classical MD.
• (7/15) Added a USER-DIFFRACTION package to compute virtual X-ray and electron diffraction patterns.
• (7/15) Extended the read_data command to allow it to be used repeatedly, e.g. to create a complex system from atoms in multiple data files.
• (6/15) Significant features added to LAMMPS in the second quarter of 2014 include a new version of the KOKKOS package and library. See authors here and details here.
• (3/15) Added a PYTHON package with a python command which embeds the Python interpreter in LAMMPS and allows Python code you write to be invoked from a LAMMPS input script, with data passing back and forth between LAMMPS and Python. Section_python gives an overview.
• (3/15) Significant features added to LAMMPS in the first quarter of 2014 include these new packages and commands: PYTHON package with python command to embed Python in input scripts, CORESHELL package, pair_style quip, fix ave/chunk, compute chunk/atom and other per-chunk computes, create_bonds, fix atom/swap, rigid body image flags, fix gcmc enhancments, fix ttm/mod, fix tfmc, pair coul/streitz, fix rattle, and fix temp/csld. See authors here and details here.
• (3/15) Added a CORESHELL package with the capability to run the adiabatic core/shell model for polarization effects. Section_howto 25 gives an overview.
• (2/15) Added an interface to the QUIP/libAtoms MD framework framework and its GAP potentials via a new pair_style quip command.
• (2/15) Added chunks and per-chunk computations to the code, as summarized here.
• (1/15) Added a create_bonds for adding bonds between pairs of atoms based on a distance criterion.
• (1/15) Added a new fix atom/swap command for performing Monte Carlo atom swaps (type and charge) either during a dyanmics run or as a stand-alone MC capability, e.g for surface segregation effects in alloys.
• Old new

Blood flow in capillaries

This is work by Kirill Lykov (kirill.lykov at usi.ch), Xuejin Li et al at the USI, Switzerland and Brown University, USA to develop new Open Boundary Condition (OBC) methods for particle-based methods suitable to simulate flow of deformable bodies in complex computational domains with several inlets and outlets.

The image (left) and movie (right) show the application of the OBCs to red blood cell flow in a straight pipe, bifurcation, and a part of a capillary network. The program Blender was used for the rendering.

This paper has further details.

Inflow/Outflow Boundary Conditions for Particle-Based Blood Flow Simulations: Application to Arterial Bifurcations and Trees, K. Lykov, X. Li, H. Lei, I. V. Pivkin, G. E. Karniadakis, PLoS Computational Biology 11(8): e1004410 (2015). (doi:10.1371/journal.pcbi.1004410) (abstract)