Marcus D. Hanwell's Blog

What a hectic week. I never got chance to record our first all American weekend on the long weekend. We started off on Saturday morning shopping in the sales and found a great BBQ at Wal-Mart. It is nearly twice the size of the one we had back in the UK with a great labour saving ash collector at the bottom. We then loaded up on meat and other BBQ essentials.

Had lots of friends over on Saturday evening and then exposed our American friends to the Eurovision song contest! It was very hard to explain this phenomenon to them but it was as amusing as ever with expert commentary by Terry Wogan

Then on Sunday we went along to our first ever baseball game and saw the Pittsburgh Pirates beat the Chicago Cubs. It was a really fun day out, beautiful sunny weekend and then we had another BBQ when we got back. I have always loved BBQs and our new one works great.

This weekend we are heading out on a road trip with a few friends from work. I haven't really taken any photos for about a year now so I am really hoping we can see a little of the country around us and get some photos I can show off. I would love more time for hacking on code too, may be Sunday evening when we get back. I have been seriously neglecting my new game too - GTA IV.

I thought I should post a few thoughts on the development of Avogadro and OpenBabel as there seems to be some confusion in replies to some of my posts. Ever since Avogadro began development it has used OpenBabel as its chemical library. OpenBabel provides Avogadro's internal representation of molecules, atoms, bonds, cube data etc.

Avogadro has driven the development of some new features in OpenBabel. In return we have been able to leverage many of the existing library functions to rapidly implement new features in Avogadro. OpenBabel isn't just a library for loading and saving chemical file formats. It provides information on the atoms, bond typing, force fields such as UFF to do geometry optimisation and lots of other very useful features. Many of the recent releases of Avogadro (which is still in beta) have been accompanied by a new beta release of OpenBabel due to each project driving the development of the other. I now work on both (but still mainly on Avogadro) as there were bugs I needed to fix in OpenBabel and Geoff got sick of me sending him patches!

As Kalzium uses Avogadro to do all of its molecular editing and visualisation this also means that the optional molecular editor depends on new releases of the OpenBabel library. I hope this makes it clearer why Avogadro and Kalzium generally rely upon the latest version of OpenBabel - many times we have implemented new features in OpenBabel for Avogadro but they should also be useful outside of Avogadro. As always I am open to suggestions and feedback on the way we do our development but I would love to hear more feedback on the software I am writing rather than the packaging issues. As a Gentoo developer I do appreciate that packaging is extremely important and so am doing what I can to make packaging as easy as possible too.

Some of you with long memories may recall that I worked on the Kalzium molecular editor for my Google Summer of Code (TM) project last summer. The observant among you may have also noticed that Kalzium in KDE 4.0 featured a molecular viewer. Well the freeze meant that much of my work didn't make it into KDE 4.0. This is the case with many of our current GSoC students (Naomi among them) who are just starting to code as KDE 4.1 is being frozen and released.

Since last summer life has been really hectic, the shipment of my household possessions from the UK to the US was delayed significantly by an incompetent shipping company which also proceeded to break many things... This led to me having no Linux system to develop on for quite some time, and then less time to develop due to having to deal with the fallout of a botched delivery. Still, I am very pleased to be able to show off some of my latest work which made it into KDE 4.1 and will be in KDE 4.1 beta1 (due out in a few days).

I was able to expose some of the extra display types I added along with support for drawing and editing molecules. You can also measure distances and angles of the molecule you are looking at and do some geometry optimisation. Given a little more time I would have liked to expose some of the manipulation features but this new six month cycle was so short and my time was constrained anyway. It will make it into 4.2 at least.

I am looking forward to seeing the animation support Naomi is working on now and am very happy to be able to mentor her over the summer. I think high quality, open source educatonal programs are very important and hope that this editor will be useful in that role. The Avogadro library and application should hopefully be able to satisfy college students and researchers. With the scripting support and open source nature of the two projects I think they interact very well and complement one another.

As always I would love to hear your feedback on the Kalzium changes and the other work we are doing.

On Monday we officially released Avogadro 0.8.0. I think this is a great release with many improvements over 0.6.1. We have been working really hard on improving the stability of Avogadro and I hope this shows in this release. There have also been some very nice improvements in speed and lots of new features.

The screen shot above shows an imported Gaussian formatted checkpoint file displaying the HOMO molecular orbital. The import of output from quantum codes and subsequent calculation of MOs is at a very early stage but you should take a look at it in the extensions menu if you are interested. It currently only calculates s, p and d orbitals and can only parse formatted checkpoint files from Gaussian. The goal is to add at least f orbitals and many more quantum codes.

I don't think I ever talked about the new periodic table QGraphicsView that I am very proud of. It allows you to select elements that are not listed in the combobox, shows the colour they will have on screen and is about as compact as I can make it. I have already packaged Avogadro 0.8.0 for Gentoo, we have binaries (Windows, Mac) and source available for download and should hopefully have packages available for Debian and Ubuntu very soon.

There were a few features that didn't make it in and a few bug fixes we found just after release. Once we have ironed out a few more bugs and received more feedback we will make a bug fix release. I was amazed to see that Avogadro is currently shooting up the Categories: Avogadro, Chemistry, Gentoo, GSoC, KDE | 4 Comments