Intel Powerbooks

14 November, 2005 by

Those of you that know me will probably realise I’m a bit of an Apple fan – owning an iMac for almost a year now. Whilst everyone and their dog seems to have had an opinion about Apple’s switch to using Intel x86 based chips from IBM PPC’s I’ve never really sat down and wrote anything about it…

The event that’s prompted me to do this is several rumour sites suggesting that Intel based Powerbooks and iMacs could well be announced/available in January. I’ve been toying with the idea of replacing my Linux/Windows Toshiba laptop for a while now, with a Powerbook being one of the top candidates – moving to Intel just seems to sweeten the deal! Faster processors, possibility of dual booting with windows (for playing the odd game), and the availability of the Intel compilers all make for an attractive platform, especially as Apple laptops generally seem to be well engineered and actually look quite nice!

 From a quantum chemistry point of view the availability of the Intel compilers should mean software such as GAMESS and Gaussian should be quickly available for the platform (although perhaps not supported – hand-editing of the makefiles will probably be necessary).  I wonder how Intel will make the compilers available though, few people in the academic community seem to realise that the current Intel compilers on the “free” non-commercial license are not allowed to be used to research if you recieve a payment for your work.


Open Source QC packages

10 November, 2005 by

As a follow up to my post regarding calls for the Gaussian code to be released (for free) into the community I had a look around for any other OSS QC packages – I’ve found two:

  • MPQC (Massively Parrallel Quantum Chemistry) – it has energies and gradients for HF, DFT and MP2. It claims to have a good geometry optimiser but I haven’t personally tested it.
  • PyQuante – python (with some C for speed) quantum chemistry package. The author aknowledges that the package is slow compared with Gaussian, Gamess etc but claims the advantage that all the routines are easily understood from looking at the source code. Although the program can be used as a single package the main goal is to provide routines that can be incorporated into other codes. Features include HF, LDA DFT and CIS

PyQuante looks promising to me, especially the ability to grab what you need from the codebase and use it in your own applications. Although the author doesn’t ask for any help, a couple of extra people working on this could really take it places.

Thesis handed in

7 November, 2005 by

I handed my PhD thesis in last Friday – I thought I would feel relieved but I don’t really. I guess it’s a strange feeling when you hand over three years of your life and the woman on the other side of the desk (who can’t be bothered to force a smile) gives you a stamped piece of paper in return!

The university should now be refunding me £200 of continuation fees, I’ll be off to find some gadget to spend it on…..

Printing pdf’s

1 November, 2005 by

I thought that using pdf meant that you’d pretty much get the same results on any screen and any printer – I was wrong.

 I’ve got to the point where I’m printing out my PhD thesis when I’ve been bitten by this. Whilst writing my thesis I was using a HP Laserjet 1200 to print out drafts etc, and got all my images to look just the way I wanted them to on it. When I tried to print out a final copy on a HP Laserjet 4000 I found that the fonts within my images were severly messed up. I thought that it was probably my original eps images didn’t have the font embedded and this was casuing the problem. However, whilst I found that embedding the font did change the printed image, it was still far from correct!!

 I’ve now travelled 250 miles to get back to that trusty LJ 1200 and the correct print out – I guess I should reconsider the level of trust I place in PDF documents….

Open Sourcing Gaussian

28 October, 2005 by

There’s been a lot of noise on the CCL (Computational Chemistry List) recently regarding the  gaussian program package. Gaussian is a general quantum chemistry package that allows you to perform many different types of calculations in pretty much a black-box fashion. A couple of people on the list were getting a bit upset about the number of gaussian techincal support questions arising, which should really be handled by Gaussian Inc themselves.

This discussion lead to “arguments” about whether Gaussian and computational chemistry programs in general should be open source, and that as US government funding goes into Gaussian then US taxpayers should be able to use the program for free (Mike Frisch later posted to the list effectively stating that there is very little US taxpayers money going into Gaussian (except via the purchase of licenses of course) and convinced at least me of their current funding situation). What some people failed to realise is that Gaussian is in fact open source (if you purchase the correct license) and they are making a fudamental mistake of confusing free and open source software!

Whilst having free access to the Gaussian source code with submit access to a version control system would be of benefit (at the very least in money terms) to many people working in this field, what benefits are there for Gaussian Inc in doing this? If the FOSS model is such a good idea for a computational chemistry package, why hasn’t there been a collaboration of theoretical chemists across the globe on such a project from scratch? Perhaps we’re too busy deriving and implementing new features (or applying them to new situations) to bother with writing code that needs to do everything (and needs to do it efficiently). Is there enough people out there able to code well enough (and to be interested in technical support, writing documentation, fixing bugs, etc.) for such a project to happen? Would anyone be able to get funding to create such a project?

I see a lot of people moaning about Gaussian, and asking for a GPL or BSD licensed code. What I don’t see is anyone bothering to invest their time and effort into creating such a package, “put your money where your mouth is”.


28 October, 2005 by

I started trialing a new web browser today, it goes by the name of Flock. It’s currently only a developer preview at version 0.5pre, so it’s not for the faint of heart – it is however built on firefox so it’s not a complete mess.

One of the more interesting features is that it uses to store your bookmarks/favourite internet sites on the web. This means that you can access your favourites from anywhere in the world (note. is available without using flock, but flock exclusively uses it for bookmarking). A couple of other items of note are:

  • RSS feed support built into the favourites system
  • Aggregation of your RSS feeds into a single page
  • Built in blog editor (works with wordpress)
  • Many blogging tools
  • Blog about Flickr pictures

I guess your average ma and pa web user probably isn’t going to care about these features (and are they all that different to whats already available as Firefox extensions?), but I’m willing to give it a go…. At least for a short while 😉

Let me know if you try it and what you think.

Beginning of the end

28 October, 2005 by

I’ve finally done it, I’ve started a blog! This is something that I’ve been intending to do for a little while and whilst waiting for a large job to finish on my computer I decided to get on with it!!

Generally I’m going to cover items that are of interest to me (d’uh), so that should probably include Quantum Chemistry, general computer geek topics and some random posts about whatever has my attention at the time.

I should probably get on with writing something interesting then….