Submitted by lev_lafayette on Thu, 01/14/2010 - 04:25
LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is used to model atoms or as a parallel particle simulator at the atomic, meso, or continuum scale. It has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems.
I'm surprised I haven't documented this in the past, because I've installed it plenty of times. Nevertheless here's how it goes.
Submitted by lev_lafayette on Thu, 12/10/2009 - 00:41
For a variety of reasons, you may wish to upgrade your Debian/Ubuntu or similar system without going through the normal process of a distribution update. Perhaps you are, for example, moving to entirely new hardware. Obviously you want to keep the data in your home directory; but you may also wish to keep the various packages you have previously downloaded. The following is some simple steps to make your life easier.
Submitted by lev_lafayette on Thu, 11/12/2009 - 04:50
A user visited with what at first appeared to be a minor problem. Previously we had installed Fluent CFD on their Macintosh system running Ubuntu but they particularly wanted to run Gambit as well, which does primarily the design modelling and meshing transition. Licenses had been received and from this point on it would seem to be a fairly trivial task.
Submitted by lev_lafayette on Tue, 11/10/2009 - 23:36
Dilbert's "Salary Theorem" states that "Engineers and scientists can never earn as much as business executives and sales people."
This theorem can now be supported by a mathematical equation based on the following two postulates:
Postulate 1: Knowledge is Power.
Postulate 2: Time is money.
As every engineer knows: Power = Work / Time
Since Knowledge = Power and Time = Money, therefore Knowledge = Work / Money
Solving this equation for Money, we get: Money = Work / Knowledge
Submitted by lev_lafayette on Fri, 10/09/2009 - 04:34
"FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).", so says the website. FFTW stands for "Fastest Fourier Transform in the West." *sigh*
Submitted by lev_lafayette on Thu, 09/24/2009 - 04:53
CPMD, Car-Parrinello Molecular Dynamics, is an ab initio Electronic Structure and Molecular Dynamics Program and is copyrighted jointly by IBM Corp and by Max Planck Institute, Stuttgart, but distributed free of charge (with source) to non-profit organizations.
Submitted by lev_lafayette on Fri, 09/18/2009 - 01:17
Dreamwidth is an alternative to Livejournal that uses much of the same code-base. However they is certain additional features that make this a more worthwhile product to develop even if it currently is in a beta-stage.
Submitted by lev_lafayette on Thu, 09/17/2009 - 05:29
Different Wikis are suitable for different things. TWiki has the best features, but really needs some crafting in terms of appearance. MediaWiki is easily to deploy, is attractive, but is not structured. If you need a structured Wiki with workspaces you'll might want Confluence. If you want community development in an unstructured manner, you want MediaWiki. If you want separate webs, structure, but also community development, go for TWiki - and then reskin it.
Submitted by lev_lafayette on Mon, 08/31/2009 - 04:38
EMBOSS is "The European Molecular Biology Open Software Suite", a free and open source analysis package specially developed for the molecular biology community, by allowing the retrieval of sequence data in a variety of formats as well as providing extensive libraries.
Submitted by lev_lafayette on Fri, 07/31/2009 - 03:49
UltraScan "attempts to be a comprehensive data analysis tool for the hydrodynamic studies of macromolecules and macromolecular assemblies with analytical ultracentrifugation experiments."
Sounds like fun. Let's install it. Get the tarball, ignore the part of the site which uses frames and extract in a sensible place, such as /usr/local/src/ULTRASCAN (
tar xvf ultrascan-9.9-888-qt-3.3.8-ix86-linux.tar.gz).