Archive for November, 2005

Density functional repository

29 November, 2005

I stumbled across this site today that acts as a repository for Fortran 77 subroutines that describe density functionals for use in electronic structure programs. The site is associated with the CCLRC so I assume these are the subroutines (or very close to them) that are used in GAMESS-UK.

Looking at the source code it seems that the subroutines have been generated automatically with Maple and the dfauto script that has been described in Comp. Phys. Comm. It may just be the computer/maths geek in me, but something about that seems very cool.

GOTO BLAS libraries make slashdot

28 November, 2005

The GOTO BLAS libraries have been mentioned on slashdot (and on the new york time website). I’ve been using this library for quite a while now and I’ve seen massive improvements in the speed of several codes (including the venerable Gaussian). I can really recommend them to anyone trying to save a little time with code that relies on BLAS or ATLAS.

Glad to see the author is getting some much deserved credit for his good work.

What is an orbital?

22 November, 2005

I thought of this interesting question today – “what is an orbital?”

I asked it to the various PhD students that I share an office with and it made some of them squirm, the answers ranged from the (hopefully) humorous – “they’re a bit like a donut”, to the not bad – “area of space within which there is a certain probability that an electron can be found”. I should probably state that none of these match what my answer would be.

The responses made me wonder if some of the frankly bizarre posts on CCL about how nothing meaningful can be obtained from orbitals (a purely mathematical construct) and only the electron density should be used stem from not properly grasping what an orbital (in ab initio theories) is?? Is this a deficiency in how QC is taught / what’s written in texts?

It would be interesting to get a few comments about how readers would answer “what is an orbital?”


16 November, 2005

I’ve found this great food blog called delicious.days. I know the links between chemistry and cooking aren’t all that great (sorry Heston Blumenthal), but hopefully some people out there will enjoy it! If you don’t like the food articles at least you should be able to admire the brilliant design of the site.

I particually liked the entry on the silver spoon, an Italian cookbook – check it out!!

Intel Powerbooks

14 November, 2005

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

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

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

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….