Marcus D. Hanwell's Blog

Earlier today we released Avogadro 0.6. This release is quite overdue and we had originally planned to make a release around the new year. This release has many, many new features that have been implemented since the last release.

I am especially proud of the new support for displaying surfaces. This initially led to the surface engine that displays a Van der Waals surface. Tim added the ability to map the electostatic surface potential onto that. I then began work on adding support for displaying orbitals. This led to me getting commit access to OpenBabel and making quite a few commits as I got Gaussian cube loading working. While I was there I couldn't resist improving the Grid classes (still a little more I would like to add in).

Another new feature I am really pleased with is the QGraphicsView based periodic table. I think it works very nicely and I am hoping to add this code to Kalzium. I think the Avogadro library is in great shape for me to begin porting Kalzium to use it. Tim and Geoff have been doing some amazing work in OpenBabel on improving the force fields used for geometry optimisations.

We have also been doing a lot of work to improve Avogadro's performance when rendering large systems. We have added quickRender functions and OpenGL display lists to improve interactivity as well as threading calculations where this made sense. We have a cool little colour widget Geoff coded too that allows colours to be displayed and picked easily, improved default layout and one of my personal favourites - persistent settings in most of Avogadro.

There are certainly some bugs remaining. I would like to get to the bottom of as many as I can and hope to make one or two bug fix releases in the 0.6 branch. We would love to get feedback from people. We have already made a source release and a Mac binary. I will be adding Gentoo ebuilds shortly and we will hopefully get a Windows binary out by early next week.

Hope you enjoy this release. I think we are getting close to a stable API that we can call 1.0 and have most of the core features I was hoping to get into Avogadro. Our framework is extremely modular and extensible and I hope that we will be able to build up a community around Avogadro. It was also great to be able to make this release on 29 February - we have so few of them

So over the weekend I spent quite a lot of time hacking away at OpenBabel working on the Gaussian cube format support I needed to get working in order to be able to visualise electronic orbitals. The initial support was taken from Molekel but contained no error checking and it was not reading in the example cube file I had.

Thankfully a colleague pointed out a page with details on the Gaussian cube format and I used this as a basis to get it working in OpenBabel with better error checking and a more resilient tokenisation of the cube points. I made my first few commits to OpenBabel over the weekend and got at least simple Gaussian cube files loading that only contain one cube. More will follow I am sure.

After I got the file loading sorted a few more changes to Avogadro got me my first ever orbitals in Avogadro - the benzene HOMO! I believe the cube file came from the JMol test files. Geoff informed me that chemists for some reason see positive as blue and negative as red. That seemed very strange to me and I had initially put it the other way around. Growing up playing with electronics it seemed to me that positive should be red just as the wires in a circuit have a red positive... Other than that orbitals seemed to be working well and I was very pleased.

Next I started to load up some other cube files I had been given as examples. I thought the above image of the electrostatic potential of CH₃Cl looked very nice. When I showed Geoff he also liked it and we wondered if it had been visualised in this way before. I know normally the cube would be mapped onto the Van der Waals surface of a molecule.

Anyway I was pleased and also felt more productive as I now have my laptop back up and running and am developing on Gentoo again. It would be great to hear what other people think of this new support. I am already working on various improvements to the code and getting ready for another release of Avogadro!

I am pleased to announce that we now have working surface support in Avogadro. We originally began working on support for surfaces around November time when Geoff improved the support in OpenBabel for grids and added some initial code to the Avogadro repository. Quite quickly it became evident that this algorithm did not deal well with data sets containing discrete objects that you wanted to polygonise.

I began a search of the available algorithms and came across a very nice guide to the marching cube algorithm with example code. I had a brief look for a C++ implementation and didn't find anything initially, began implementing what was on his page and then came across Zhu3d which is a Qt 4 based program that actually uses an implementation of the algorithms described in the guide and references them. As it is GPL licenced code I imported the relevant class into our repository and began the task of adapting it to fit into our framework.

With some code from Geoff, more pointers from Geoff, some reading and quite a bit of help from Tim (not sure if he has a web page/blog) we got it working. Since then Tim has actually fixed a big bug in OpenBabel that was causing crashes and done more work on the IsoGen class. The screenshots above show the results of our early work where initially we got points and then lines working. I was very pleased at this stage as it adds a feature that had been missing for quite some time to the Avogadro framework.

I then got filled triangles added with transparency support, allowing us to visualise the underlying structure of the molecule and map other parameters onto the surface. Tim then added electrostatic charge mapping to the colour of the surface which I hope you agree is already looking very good.

There is still quite a bit left to do. I need to move the class into libavogadro and out of the engines, integrate it into our Painter API, implement caching and am thinking of using the Qt Concurrent framework to do intelligent multithreading once Qt 4.4 is released as surface generation is quite slow for big molecules. I also need to link the mesh size to the global quality level and see what other optimisations might be possible. Another big one is adding support for visualising molecular orbitals. Geoff has already done a lot of work on the back end in OpenBabel for this and so hopefully it will not take me long to get it added in.

Lots to do but some great progress already. I would love to know what you think. Once we have been able to polish this new feature a little I hope we can get a release out of the door so that more people can test out these new features and let us know what they think, point out bugs and shower us with compliments Until then I hope you enjoy the screenshots!

Note: For some reason the exported graphics shown in this post were not antialiased. They are on screen and I need to look into why they are not when I export graphics in this way.