WWW Site - Documentation - Tools Documentation

Version info:

The "version" is the date when it was released, such as 1 May 2010. is updated continuously. Whenever we fix a bug or add a feature, we release it immediately, and post a notice on this page of the WWW site. Each dated copy of contains all the features and bug-fixes up to and including that version date. The version date is printed to the screen and logfile every time you run It is also in the file src/version.h and in the directory name created when you unpack a tarball. is a loosely integrated collection of tools written in Python, many of which provide pre- and post-processing capability for the LAMMPS molecular dynamics, ChemCell cell simulator, and SPARTA Direcct Simulation Monte Carlo (DSMC) packages. There are tools to create input files, convert between file formats, process log and dump files, create plots, and visualize and animate simulation snapshots.

The name is meant to evoke the aroma of a collection of "toppings" that the user can combine in different ways on a "crust" of basic functionality, with Python as the "cheese" that glues everything together.

The maintainer of is Steve Plimpton at Sandia National Laboratories, a US Department of Energy (DOE) laboratory. Many of the tools were written by Matt Jones, a BYU student who spent a summer at Sandia. The WWW Site at has more information about and its uses.

The documentation is organized into the following sections. If you find errors or omissions in this manual or have suggestions for useful information to add, please send an email to so we can improve the documentation.

PDF file of the entire manual, generated by htmldoc

  1. Introduction
  2. Installing
  3. Basics of using
  4. Tools within
  5. Example scripts
  6. Extending

List of tools in Animate a series of image files Read LAMMPS dump local files with bond info Read, write, manipulate ChemCell data files Create bead-spring chains for LAMMPS input Convert LAMMPS snapshots to CFG format Read, write, manipulate LAMMPS data files Read, write, manipulate dump files and particle attributes Convert LAMMPS snapshots to Ensight format 3d interactive visualization via OpenGL Create plots via GnuPlot plotting program Particle density histogram from a dump View and manipulate images Read LAMMPS dump files with line info Read LAMMPS log files and extract thermodynamic data Create plots via MatLab numerical analysis program Read, write, manipulate mesh dump files Read other log files (ChemCell, SPPARKS, SPARTA) and extract time-series data Compute LAMMPS pairwise energies Create patchy Lennard-Jones particles for LAMMPS input Read, write PDB files in combo with LAMMPS snapshots Plot multiple vectors from a data set 3d visualization via RasMol program 3d visualization via Raster3d program Read, write, manipulate SPARTA surface files 3d visualization via SVG files Read LAMMPS dump files with triangle info VCR-style GUI for 3d interactive OpenGL visualization Create numeric vectors from columns in file or list of vecs Convert LAMMPS snapshots to VTK format Wrapper on VMD visualization package Convert LAMMPS snapshots to XYZ format