LAMMPS website

Pre/Post Processing Tools for use with LAMMPS

This page gives pointers to various software tools and data repositories which can be used in conjunction with LAMMPS. Some tools are listed in multiple categories below.

Speaking for the LAMMPS developers, we think these kinds of tools, whether free-ware or commercial software, can be very useful. They extend the scope of problems that LAMMPS can model and its ease of use. We are happy to "advertise" such tools here, so that people can try them out. Send us an email if you want to add your software or tools that you use to the list.

GUI and Analysis Software - commercial and free software that wraps LAMMPS

Molecular Builders - free software to build molecular inputs for LAMMPS

Data Sites - WWW sites with data useable as LAMMPS input or that archive LAMMPS output



GUI and Analysis Software that wraps LAMMPS

This section describes both commercial and free software that wraps LAMMPS to provide a user-friendly environment for developing models, running simulations, and analyzing the results.


Materials Design, Inc.

Materials Design, Inc. develops MedeA®, an atomistic simulation and modeling environment that provides productivity, model building and analysis tools for use with LAMMPS. MedeA® simplifies LAMMPS simulations with flowcharts that allow you to assemble complex simulation protocols using simple discrete LAMMPS stages. The resulting LAMMPS simulations are easily shared among colleagues, edited for future reuse, and can be customized by LAMMPS experts.

With MedeA®, atomistic models may be constructed using a variety of methods for crystalline systems, and with the MedeA® Amorphous and Thermoset builders, which are tools to create input for LAMMPS. They also provide validated methods for the prediction of mechanical properties, including elastic constants, diffusivity, transport properties and cohesive energies based on LAMMPS simulations. MedeA® also facilitates the management of forcefields for the simulation of organic, inorganic, and metallic systems; the Materials Design team has an established track record in the development of accurate forcefields for organic and metallic systems.


Scienomics

The company Scienomics has developed an interface to LAMMPS as part of their Materials and Processes Simulations (MAPS) platform, which allows both novice LAMMPS users and experts to quickly and efficiently create LAMMPS input files - for both atomistic and DPD simulations. Scienomics provides full phone and email support for LAMMPS users. The LAMMPS Plugins within MAPS also allow users to create input files for LAMMPS, visualize and perform analysis on the output from LAMMPS simulations. MAPS also has a number of forcefields to choose from (for atomistic modeling and coarse grain modeling) with LAMMPS. They also have a tool called Amorphous Builder and Crosslink Builder which can be used to create input geometries for LAMMPS plus tools to analyze the results of ReaxFF simulations and other powerful functionalities for calculating key properties such as elastic properties, structural properties, transport properties, etc.

MAPS is a comprehensive software platform incorporating the workflow of Build-Simulate-Analyze. This empowers users with an efficient and seamless way to model complex materials systems, to choose from an array of simulation engines including LAMMPS to model processes, and to analyze output to extract a number of properties such as mechanical, thermal, transport, rheological, etc. See the Scienomics web page for more details on all these tools and services.


Scifes Inc

The company Scifes Inc. has launched a software product called "Lammpsfe", which stands for LAMMPS frontend, which is a user interface specifically created for LAMMPS. Lammpsfe consists of a GUI for creating LAMMPS input scripts and an MDViewer for LAMMPS output visualization. It runs on Linux,Mac,Windows. The MDViewer, which is based on the latest OpenGL-technology, includes such capabilities as viewing several millions of atoms as well as looking at LAMMPS trajectories with changing numbers of atoms/molecules.


XenoView

Developed by Sergei Shenogin (Rensselaer Nanotechnology Center), shenos3 at rpi.edu. This software is free for non-commercial users. XenoView is Windows-based software for molecular dynamics simulation. Its interface provides extensive tools for building the structure from the scratch. Also, you can import structure from many formats (e.g. PDB format). Bonds can be automatically defined and force fields can be automatically assigned. XenoView can export data files and input scripts that can be used in LAMMPS for large-scale simulations. See the XenoView home page for more details.


Atomman

The atomman tool is open-source (free) software developed by Lucas Hale at NIST. It is a Python package for interacting with large-scale atomic systems. It allows the user to prepare, run, and analyze MD simulations entirely from Python.


Virtual NanoLab

Virtual NanoLab (VNL) is an ideal tool for constructing structures and analyzing simulation results for use with LAMMPS. The VNL builder has a database with an extensive range of atomistic structures. Moreover, all common structure file formats are supported.

VNL is a powerful graphical user interface which can handle millions of atoms. A variety of user-friendly construction tools are implemented as plugins. Cleaving surfaces to a customized orientation, building interfaces between two surfaces, repeating, rotating, mirroring and merging structures, can all be done in the graphics user interface. Other special tools like the Random Alloy, Polycrystal, and Amorphous cell builders are also implemented.

Here are examples of systems built and analyzed with VNL. Click on them for a larger image.

Along with the Movie Tool and the 3D Viewer for the visualization of the LAMMPS result, the MD Analyzer embedded in VNL is designed for analyzing the MD results interactively. It includes a radial/angular distribution function, velocity autocorrelation, local mass density profile, coordination number, mean-square displacement, nearest neighbour number, and neutron scattering factor. Advanced customized analysis is available by python scripting. You can also interface your classical LAMMPS simulations with quantum mechanical calculations by performing a further simulation using the ATK-DFT engine for density functional theory calculations.

VNL is free for academic users, read more on the licensing page of the QuantumWise website.


LOOS = Lightweight Object-Oriented Structure analysis library

LOOS is a package for analyzing molecular dynamics simulations. It is package-agnostic, open source, and runs on all major Linux distributions, as well as OSX. It is distributed with roughly 150 pre-packaged analysis tools, ranging from standard tasks (trajectory manipulation, principal component analysis, etc) to novel tools (assessing simulation convergence, measuring properties of membranes and membrane proteins). Moreover, it is designed for rapid development of new analysis tools, particularly when using the Python wrappers. LOOS is available for download from https://github.com/GrossfieldLab/loos.



Molecular Builders

To simulate molecular systems LAMMPS requires you to input molecular topologies (lists of bonds, angles, dihedrals, etc) as well as force-field coefficients appropriate for your model. Thus the task of building a molecular system is a pre-processing step, and can be a complex task of its own.

This section describes tools that help to automate this process.

Generally speaking, the packages can infer angle, dihedral, and improper interactions from bond topology. They have commands to generate molecular geometry. They can read coordinates from files generated by PACKMOL and other PDB file builders.


Enhanced Monte Carlo (EMC)

Developed and maintained by Pieter J. in 't Veld (BASF), veld at verizon.net.

Enhanced Monte Carlo, or EMC for short, provides an environment for creating and manipulating input structures for particle simulations using COMPASS, CHARMM, OPLS, Martini, DPD, or colloidal force fields. To this end, a scripting language manages access to its functionality. The current version provides manipulation of molecular or coarse-grained structures through SMILES strings, typing these structures - when needed - for selected force fields, and building conformations applying Monte Carlo principles to unoverlap atoms. EMC provides output ports to LAMMPS, PDB, and XYZ formats. A compiled version for Linux, MacOS, or Windows can be found at montecarlo.sourceforge.net

Here are examples of systems built with EMC. Click on them for a larger image.


Moltemplate

Developed and maintained by Andrew Jewett (UCSB), jewett.aij at gmail.com.

This tool is distributed with LAMMPS in the tools/moltemplate directory. See that directory and the moltemplate home page for more details.

Moltemplate was designed for building coarse-grained biomolecular models. Moltemplate can create both: lammps DATA files (containing geometry and topology), and lammps INPUT scripts (containing force-fields, fixes, and groups). Unlike files generated by other conversion tools, moltemplate gives users access to all of the force-fields available in LAMMPS. Users can save molecules in moltemplate's compact, readable template file format (".LT"), and share them with others. Molecules can be used as building blocks for bigger molecules. "Canned" force-fields (such as Dreiding, GAFF, TraPPE, and user creations) can (in principle) also be saved in this format and applied to molecules later.

Molecules can be copied, combined, and linked together to define new molecules. (These can be used to define larger molecules. Unlimited levels of object composition, nesting, and inheritance are supported.) Once built, individual molecules and subunits can be customized (atoms and bonds, and subunits can be moved, deleted and replaced).

Here are examples of systems built with moltemplate. Click on them for a larger image.


VMD TopoTools

Developed and maintained by Axel Kohlmeyer (Temple U), akohlmey at gmail.com.

See the TopoTools home page for more details.

Topotools is a molecule builder which leverages the power of VMD and TCL to create lammps DATA files and convert them to and from other formats. Topotools has two components: a middleware script which can extract and manipulate topology information, and several high-level applications built on top of it, which, for example can enable it to read/write data files, replicate and merge systems. Together with VMD, topotools can infer topology from PDB files, PSF files, and atom pair distances, solvate a protein. Additional features for coarse-grained molecules are planned.

Here are examples of systems built with TopoTools. Click on them for a larger image.


Avogadro

Developed and maintained as an open-source project.

See the Avogadro home page for more details.

Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.


Packmol

Developed and maintained as an open-source project.

See the Packmol home page for more details.

Packmol creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short range repulsive interactions do not disrupt the simulations.


Atomsk

Developed and maintained as an open-source project.

See the Atomsk home page for more details.

Atomsk aims at creating, manipulating, and converting atomic systems. It supports many file formats, among which LAMMPS files formats, and also VASP, Quantum Espresso, IMD, DL_POLY, Atomeye CFG format, or xCrySDen XSF format, which makes it easy to convert files for ab initio calculations, classical potential simulations, or visualization. Additionnaly, atomsk can also perform some simple transformations of atomic positions, like rotation, deformation, inserting dislocations.


OCTA and J-OCTA

OCTA is an open source software package which consists of simulation engines (Molecular Dynamics, Rheology simulation, Self Consistent Field Theory, Finite Element Method, etc) and a GUI (visualization, simple molecular builder and analysis tools) for modeling soft matter systems.

OCTA also provides an environment for the collaborative usage of several kinds of simulators, i.e. multi-physics and multi-scale simulations.

A converter program between LAMMPS and COGNAC (MD engine) files is also included. This functionality gives LAMMPS users the ability to use the OCTA GUI and run classical MD simulations in tandem with other theories such as SCFT.

By using the commercial version J-OCTA, complex molecular building for full atomistic and coarse grained MD can also be performed.


Automated Topology Builder (ATB) and Repository - molecular topology building blocks for organic molecules

The ATB project is led by Prof Alan E. Mark (University of Queensland, Australia); the ATB website has a list of the other contributors to the effort.

The ATB provides topology files for organic molecules in formats compatible with LAMMPS and other molecular dynamics packages. The LAMMPS topology files enable the construction of complex systems using the moltemplate tool (distributed with LAMMPS). Moltemplate allows forcefield parameters and molecule template files to be combined to build complex systems, enabling a workflow similar to that used to build system topologies in biomolecular MD simulation packages (e.g. GROMOS, AMBER, CHARMM, etc).

The ATB site provides topologies for a wide variety of molecules (> 20,000 and growing). Molecules can be found using the internal search tools based on name or chemical formula and selecting from the list of results. Once on the page for the molecule of interest, you can select "Molecular Dynamics (MD) Files" and choose "LAMMPS" as the output "Format" If a molecule does not exist in the database, it can be added by submitting a new molecule to be processed (instructions in the site FAQ).



Data Sites

This section lists WWW sites that provide data that can be used with LAMMPS. For example, atomic configurations, that can be used to initialize models for LAMMPS simulations. Or an archive of calculations done with LAMMPS that can be browsed for physical or model insight.


JARVIS database for MD potential calculations on DFT geometries

JARVIS for force-fields (JARVIS-FF) is a high-throughput computational database for LAMMPS calculations on Density functional theory (DFT)-optimized geometric structures with various force-fields/interatomic potentials. The goal of the project is to provide an easy look-up table for evaluation of force-fields through a web-interface and to enhance data-reproducibility. JARVIS-FF is a part of the Materials Genome Initiative (MGI) at the National Institute of Standards and Technology (NIST).

Click for larger image.

See http://www.ctcms.nist.gov/~knc6/periodic.html for details.


Cyberinfrastructure for Atomistic Materials Science (CAMS)

This is an NSF-funded project led by Susan Sinnott and Simon Phillpot at U Florida. The site has a library of atomic-scale structures with atom coordinates of common microstructure features. The hope is that the collection will accelerate future atomistic simulations of material microstructures by allowing users to bypass the common, though often difficult, step associated with building these structures by hand.

See the CAMS home page for more details.


Orsi group at Queen Mary University of London

Mario Orsi's group has a nice collection of LAMMPS input scripts and data files for a variety of water systems (different force fields). They are adding files for protein and lipid membrane systems as well.

See the Orsi group download page for more details.