This page gives pointers to software written and maintained by other groups which can be used with LAMMPS. In some cases, they are LAMMPS add-ons which can be compiled with LAMMPS to extend its capabilities with new commands. In other cases, they are stand-alone tools which perform calculations that generate complex input for LAMMPS, such as force-field fitting. Full documentations for these packages and tools are on their home web sites.
Speaking for the LAMMPS developers, we think this is great, and are happy to "advertise" other group's software here, so that people can try it out. Send us an email if you want to add your package or tool to the list.
Author: Paul Atzberger (UCSB), (atzberg at gmail.com)
SELM stands for Stochastic Eulerian Lagrangian Method. This is a set of numerical methods that utilizes a mixed Eulerian description for hydrodynamic fields coupled to a Lagrangian description of the coarse-grained degrees of freedom. To account for both hydrodynamic flow and thermal fluctuations, fluctuating hydrodynamic equations are introduced and coupled to the coarse-grained degrees of freedom in a manner consistent with statistical mechanics. For implicit-solvent coarse-grained models, the methods can be used to account for momentum transfer through the missing solvent degrees of freedom. The methods provide alternative thermostats to the widely used Langevin thermostat and Dissipative-Particle-Dynamics thermostat.
SELM is provided as a USER-SELM package for LAMMPS, which implements several fluctuating hydrodynamics thermostats for different physical regimes:
A complete list of features, downloads, and tutorials can be found on the package homepage: http://mango-selm.org.
Please feel free to register and download MANGO-SELM from our website. For questions or suggestions, please use the listed MANGO-SELM discussion forums.
Author: Mario Orsi (orsimario at gmail.com)
ELBA-LAMMPS is a toolkit that assists LAMMPS users in simulating the ELBA coarse-grain model, as described in Orsi & Essex, PLoS One 6: e28637 (2011) and illustrated in the following figure. The ELBA-LAMMPS package includes specific installation guidelines, simulation examples, analysis scripts, and tools to enable visualization with VMD.
ELBA coarse-grain model of a DOPC phospholipid (left) and a water molecule (right). Coarse-grain electrostatics are represented by positive ("+" sign) and negative ("-" sign) point charges, and point dipoles (arrows). Click on image to view larger version.
Author: Christoph Kloss (JKU)
LIGGGHTS stands for LAMMPS Improved for General Granular and Granular Heat Transfer Simulations. It is a stand-alone code focused on granular material modeling, which uses LAMMPS intnerally as a particle engine. It implements the following capabilities on top of the LAMMPS "GRANULAR" features:
More features, such as improved handling for non-spherical particle, a 6 degrees of freedom solver for arbitrarily shaped bodies and wall stress analysis, are currently under development. Also, an efficient parallel coupling to the OpenFOAM(R) framework is under development.
LIGGGHTS will stay "backward compatible" to LAMMPS, meaning one can use all powerful LAMMPS features.
For a complete list of features, videos, as well as downloads and tutorials, please refer to the URLs above.
If you are interested in learning more about DEM with LIGGGHTS, there will be 2 classes (each for 3 days) held in the city of Linz, Austria. They are scheduled for June 9-11 and September 22-24. If you are interested in joining one of the classes, please answer to this email.
Feel free to register for free and download LIGGGHTS 1.0 from our website. For any question that may arise, please use the provided discussions forums.
Authors: see PLUMED WWW site
PLUMED is a plugin for free-energy calculations in molecular systems that can be interfaced with some of the most popular molecular dynamics codes using a simple patching procedure.
PLUMED allows one to perform several type of calculations, including:
It has the following features:
Authors: see VOTCA WWW site
VOTCA is a set of tools for creating corase-grained models, as well as simulating charge transport, and has other features as well.
Here is a summary of the methods in the coarse-graining toolkit (VOTCA-CSG):
It has support for processing LAMMPS dump files.
Author: Andres Jaramillo-Botero (Caltech, ajaramil at caltech.edu or ajaramil at gmail.com)
GARFfield is a multi-platform (I have tested it on my Mac OS X and on multiple Linux distributions), multi-objective parallel hybrid genetic algorithm/conjugate-gradient based force field optimization framework. It enables first-principles based force field parameter optimization from quantum mechanical and phenomenological data sets. In principle, the latter allows improved accuracy and transferability over a wider range of molecular compositions, interactions and environmental conditions unexplored by experiments. GARFfield currently supports multiple reactive and non-reactive force fields through LAMMPS. It is particularly well suited to develop adiabatic and non-adiabatic reactive force fields, such as ReaxFF (REAX or USER-REAXC) and eFF-ECP (USER-EFF), respectively allowing relative restraints on bond-order based bonds, angles, torsions, transition states, and also on electron sizes. GARFfield can produce Pareto-optimal parameters, while allowing hill-climbing from local minima solutions, fixed or random weights on training sets, and deterministic conjugate-gradient minimization near a parabolic minima for improved convergence.
New features are currently being developed, including template-based force field support (to avoid syntax dependencies from LAMMPS), heuristic sequencing in parameter optimization, and training set parallelization (in addition to the currently available parallelization at the level of the genetic algorithm string population).
Please refer to the GARFfield User Manual (http://www.wag.caltech.edu/home/ajaramil/GARFFIELDUserManual.pdf) and to the paper by A. Jaramillo-Botero, S. Naserifar., and W.A. Goddard III, "A General Multi-Objective Force Field Optimization Framework, with Application to Reactive Force Fields for Silicon Carbide", Journal of Chemical Theory and Computation, 2014, 10 (4), pp 1426-1439. DOI: 10.1021/ct5001044 for additional information on capabilities and usage.
We are releasing the GARFfield code to promote a community-driven development effort, so If you want to contribute bug fixes, new extensions (e.g. force fields) or features (e.g. GUI) to GARFfield please register, download and compile GARFfield. We ask that once you integrate, validate and test your new extension or feature and submit it back to ajaramil at caltech.edu. Your contribution will then be reviewed and published as part of subsequent code releases.
Jazz is a physics research code used to calculate the lifetimes of vibrational modes in solids. The calculations are implemented as a Python wrapper for LAMMPS, which provides the energies and forces as calculated for any interatomic potential available in that package. The anharmonic character of the normal modes is calculated via the Monte Carlo-based moments approximation as is described in a series of papers by M. Daw and co-workers (D. Dickel, Y. Gao, and H. Wang). It is distributed as open-source software.
LEAD: Prof. Murray Daw (Clemson)
CONTRIBUTORS: Dr. Ted Dickel, Dr. Yang Gao, Mr. Hengjia Wang (were or are physics grad students at Clemson)