This page is for downloading software packages that I distribute. Sandia's molecular dynamics code LAMMPS has its own download page.
Follow the info links below for more information on the individual packages.
After clicking a download link below, your browser should prompt you to download gzipped tar file. Unpack it with the following commands, and look for a README to get you started.
gunzip file.tar.gz tar xvf file.tar
Some of these packages will unpack into a directory like pizza-16Mar09, which is the version date for the current version.
Some of this software is distributed freely; some is copyrighted open-source software distributed under the terms of the GNU Public license or modified BSD license.
There have been ~56,000 downloads from this page and another ~387,000 from the LAMMPS download page from Sept 2004 thru Dec 2020.
Molecular dynamics codes:
|LAMMPS||download||general materials modeling MD code||GPL/LGPL||100+ MB|
|ParaDyn||download||embedded atom method (EAM) code||-||390 KB|
|Lennard-Jones||download||LJ codes with 3 parallel algorithms||-||47 KB|
|SPARTA||download||Direct Simulation Monte Carlo (DSMC) simulator||GPL||4.4 MB|
|SPPARKS||download||Kinetic and Metropolis Monte Carlo simulator||GPL||3.5 MB|
|ChemCell||download||particle-based biological cell simulator||GPL||1.3 MB|
|Mapreduce-MPI||download||MapReduce-MPI library||BSD||1.8 MB|
|PHISH||download||PHISH streaming library||BSD||1.3 MB|
|CSlib||download||client/server messaging library||BSD||1.0 MB|
|fftMPI||download||parallel 3d/2d complex FFT library||BSD||0.9 MB|
|Pizza.py Toolkit||download||analysis/plotting/viz for LAMMPS, SPARTA, SPPARKS, ChemCell||GPL||1.6 MB|
|HPCC RandomAccess||download||algorithm for HPCC GUPS benchmark||-||22 KB|
|Parallel GeneHunter||download||parallel genetic linkage analysis||-||740 KB|
|txt2html||download||text file to HTML converter for webpages and documentation||-||19 KB|
ParaDyn is a parallel F77 code that implements all the features of the popular serial EAM code for metals and metal alloys known as DYNAMO. DYNAMO was written by two of the EAM originators, Stephen Foiles and Murray Daw. ParaDyn's parallelism is based on the atom- and force-decomposition algorithms discussed on this page and in the 1993 MRS paper listed below.
Nearly all of ParaDyn's functionality is now in LAMMPS, which runs 2-4x faster than ParaDyn both on a single processor and in parallel. This is due to force computations and neighbor list building being implemented in a different way. So only download ParaDyn if you're sure it's what you want.ParaDyn overview
Parallel Molecular Dynamics With the Embedded Atom Method, S. J. Plimpton and B. A. Hendrickson, in Materials Theory and Modelling, edited by J. Broughton, P. Bristowe, and J. Newsam, MRS Proceedings 291, Pittsburgh, PA, 1993, p 37. (abstract)
These are 3 parallel Lennard-Jones codes discussed in the 1995 J Comp Phys paper listed below. Each code performs the same computations, but implements either a atom-, force-, or spatial-decomposition algorithm. The algorithms are discussed briefly on this page and fully in the paper. These codes were written before MPI was around, so the codes have their own message-passing libraries with a wrapper on a vanilla MPI send and receive that was added later.Documentation for LJ codes
Fast Parallel Algorithms for Short-Range Molecular Dynamics, S. J. Plimpton, J Comp Phys, 117, 1-19 (1995). (abstract)
I wrote an optimized version of this HPCC benchmark using a synchronous hypercube-style all2all algorithm. It enables scalable GUPS performance on large numbers of processors. The tar file includes files for a simple stand-alone code for quick testing, as well as modules that can be incorporated into the HPCC harness for running an official benchmark test.
The algorithm is described briefly on this page and fully in this paper:
A Simple Synchronous Distributed-Memory Algorithm for the HPCC RandomAccess Benchmark, S. J. Plimpton, R. Brightwell, C. Vaughan, K. Underwood, M. Davis, Proc of Cluster 2006 - IEEE International Conf on Cluster Computing, Sept 2006. (abstract) (pdf)Download menu (top of this page)
I worked with a UNM biology student, Gavin Conant, to parallelize the MIT WhiteHead Institue linkage analysis code GeneHunter. This page gives all the details as does the paper below. Gavin did the bulk of this work and supports the modified code.Download menu (top of this page)
Parallel Genehunter: Implementation of a Linkage Analysis Package for Distributed-Memory Architectures, G. C. Conant, S. J. Plimpton, W. Old, A. Wagner, P. R. Fain, T. R. Pacheco, and G. Heffelfinger, Journal of Parallel and Distributed Computing, 63, 674-682 (2003). (abstract)
This is a small C++ program (one file) that converts text files into HTML files. The text files can contain simple a few simple formatting and markup commands that get converted into appropriate HTML syntax.
I wrote this tool because I am more productive using a text editor (emacs) to write vanilla text than trying to write HTML or use a browser's WYSIWYG composer tool with an editor I don't like. Anna Reese wrote the table capabilities in txt2html.
All the WWW pages on my site and the LAMMPS website were converted to HTML via txt2html. As you view any of those pages, you can see what the underlying text file looks like, by changing the .html suffix of the URL you are browsing to .txt (not the same as viewing the source of the HTML file). An example is given below.
Curiously, looking at the .txt version of the page you are currently on (download.html), or the doc and example files for the txt2html itself, are not great examples of the simple syntax of .txt files that the tool recognizes. This is because they have to contain a lot of native HTML to fool a browser into displaying HTML itself or displaying the download form up above.Documentation for txt2html