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Too busy to update this page...
Posted: Apr 15, 2008
I've been so busy with other things, that I never have any time to update this page. It will be redesigned (again) sometime soon, maybe then I'll keep it up more up to date.
As such, the information this webpage has on HOOMD has been inaccurate for a while, now. An initial version of HOOMD has already been made available for download at www.ameslab.gov/hoomd. Anyone interested in molecular dynamics simulations accelerated CUDA capable graphics cards should check it out. I'm hard at work on the next version of the software which will include many new features and performance enchancements.
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HOOMD demonstrated at SC07
Posted: Nov 13, 2007
NVIDIA will be have a live demo of HOOMD running in their booth at Supercomputing 2007. If you are going to be there, it is worth checking out.
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HOOMD coming soon...
Posted: Oct 23, 2007
HOOMD stands for Highly Optimized Object-oriented Molecular Dynamics, and is the software developed for the paper: General Purpose Molecular Dynamics Simulations Fully Implemented on Graphics Processing Units. The paper has been submitted and is currently under review. HOOMD will be released under an open source license. Work is currently being done to add the features needed to make HOOMD useful for performing production runs, and a beta version will be ready soon.
Using a single 8800 GTX GPU, HOOMD reaches a level of performance previously only accessible with a cluster. Here is a teaser figure from the paper, where a system of coarse-grained polymers (see my publications) was used as a benchmark to compare HOOMD to LAMMPS running on Lightning. Click on the figure to access a much more readable pdf.
Check back for updates...
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jsMath up and running
Posted: Oct 7, 2007
Lots of websites exist out there with (attempted) formatted equations on them. LaTeX is, arguably, the best tool for producing beautiful equations for print, postscript, and pdf files. Transforming a perfectly good vector representation of an equation to the web is usually done by a horrible looking rasterization to ugly low resolution gifs. They look bad, and it requires webpage writers to put lots of img tags everywhere in the document.
Enter jsMath. It is a tool that allows web developers to add LaTeX equations directly to the web page content easily: Simply put <div class="math">M = \frac{1}{b-a}\int_a^b f(x)dx </div> in the page source and get:
M = \frac{1}{b-a}\int_a^b f(x)dxPretty, isn't it? If you don't believe me, check the page source. Best of all, this still allows xhtml compliant pages. jsMath does cheat a little and use image based fonts, which may or may not take you a while to download on first use. Do yourself a favor and go to the jsMath web page and download the fonts from there. It will reduce page load times and make the resulting equations look just that much better.
Another neat feature I just discovered of jsMath is that you can double click on the equation and get the LaTeX source code for easy copy and paste elswhere, how cool is that? Anyways, if it isn't already obvious, I have jsMath installed on this page, and plan on using it to make writing future content easier.
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Welcome!
Posted: Oct 7, 2007
This site has had it's design modified a bit. This is going to be the new layout. Not much has changed visually yet, but the back end for the site now uses some fun scripting that is going to make it easier for me to add new content. I have a lot of ideas of some (hopefully useful) things to add, so stay tuned.