LAMMPS WWW Site

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.

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 - 3rd-party commercial software that wraps LAMMPS

Molecular Builders - free software to build molecular inputs for LAMMPS

Data Sites - WWW sites with data useable as LAMMPS input



GUI and Analysis Software that wraps LAMMPS

This section describes commercial software that wraps LAMMPS to provide a user-friendly environment for developing simulations 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 created an interface to LAMMPS as part of their Materials and Processes Simulations (MAPS) platform. It can be used to visualize and perform analysis on the output of LAMMPS simulations. They also have a tool called Amorphous Builder which can be used to create input geometries for LAMMPS, plus tools to predict elastic properties and analyze the results of ReaxFF simulations. See the Scienomics WWW page for more details on all the tools.


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.



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 or MacOS 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.

Need to add some pictures.


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.



Data Sites

This section lists WWW sites that provide data, such as atomic configurations, that can be used to initialize models for LAMMPS simulations.


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.