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

July 2018 tutorial and symposium on Modeling Supra-molecular Structures with LAMMPS will be held at Temple University.

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.

• (3/18) New stable release, 16Mar18 version.
• (9/17) Wrapper on the LATTE DFTB (density-functional tight-binding) quantum code via the fix latte command. See details here.
• (9/17) USER-MESO package from the Karniadakis group at Brown University, with various dissipative particle dynamics (DPD) models, including eDPD, mDPD, tDPD. See details here.
• (8/17) New stable release, 11Aug17 version.
• Biennial LAMMPS Workshop and Symposium in ABQ, NM. PDFs of talks and posters and the tutorial sessions are available at the workshop link.
• (3/17) New stable release, 31Mar17 version.
• (1/17) Added a fix mscg command to enable building of multi-scale coarse-graining (MSCG) models via the Voth group's (U Chicago) MS-CG library.
• (12/16) Significant features added to LAMMPS in the fourth quarter of 2016 include these new commands: compute global/atom global_atom.html, temper/grem and fix grem, pair tersoff/mod/c, pair agni, pair born/coul/dsf and pair_style born/coul/dsf/cs, dump nc and dump nc/mpiio, fix halt, fix dpd/energy, dump_modify thresh LAST option, and fix wall/gran/region. See authors here and details here.
• (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) Significant features added to LAMMPS in the third quarter of 2016 include these new commands: allow for multiple procs per replica with the neb command, options for weighted load balancing via the balance and fix balance commands, fix cmap for CHARMM ff 5-body crossterms, pair_style vashishta/table, Kokkos support for kspace_style pppm, fix flow/gauss, fix controller, wildcard syntax for specifying multiple vector values or multiple array columns, for input to other commands (compute, fix, dump, thermo output), and dihedral_style spherical. See authors here and details here.
• (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) Significant features added to LAMMPS in the second quarter of 2016 include these new commands: Kokkos version of pair_style reax/c, timeout option for timer command, fix orient/bcc, compute rigid/local, fix spring/chunk, fix ehex, reactive models for the USER-DPD package, USER-MANIFOLD package, restructuring of doc dir with new tools for building the doc pages, write_coeff, pair morse/soft, and compute dipole/chunk. See authors here and details here.
• (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.
• (3/16) Significant features added to LAMMPS in the first quarter of 2016 include these new commands: pair airebo/morse, compute bond, compute angle, compute dihedral, compute improper, vector-style variables, dump custom/vtk, fix nvt/body, fix npt/body, fix nph/body, compute temp/body, USER-DPD package, variety of new styles added to the USER-INTEL package, and dump image options for line, triangle, body particles. See authors here and details here.
• (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.
• 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)