Sunday, April 7, 2013

Building the OpenChemistry Packages on Ubuntu 12.04

Inspired by the latest Google+ posts by several of the developers of Avogadro (+Marcus Hanwell, +David Lonie, +Open Chemistry) I decided to install what is now known as Avogadro2 along with several other Open Chemistry packages.

The first step was to get hold of the sources which proved to be easy.

Second step was to compile which was also quite easy because the new cmake scripts downloads the correct packages you need (clever!). However, on my Ubuntu 12.04 I had to install the following extra packages to get rolling - my approach was to just see what failed and install what was missing.

sudo apt-get install libxt-dev
sudo apt-get install libqt4-opengl-dev
sudo apt-get install libbz2-1.0 libbz2-dev libbz2-ocaml libbz2-ocaml-dev
sudo apt-get install libqt4-dev qt4-dev-tools libqt4-webkit libqt4-core libqtwebkit-dev qt4-designer

Now, I haven't run the make install part of the whole shebang yet, but I have been able to run the new Avogadro application directly from the build directory so at least everything seems to compile fine. I was very inspired by the post on python input generators by David Lonie. Maybe I'll cook something up some day.

For now, it seems that Avogadro2 is a step back in terms of what you can actually do, but it also appears the developers are hard at work actually getting the application up to speed and ready for a beta-release very soon. I know I am excited.


  1. If you want to get your hands dirty (and since I see from the Dalton commit e-mails, that you are now working on the mother ship), I know there is a bug in app. version 1.1.0 (git revision: c1fcc5b) of Avogadro, which gives the wrong number for 'Atomtypes' in generated Dalton Input (the .mol-file). The overall input is correct, but the 'Atomtypes' number equals the total number of atoms in the molecule at hand, which it should not... It should equal the number of different atoms (different Z) in the molecule.

  2. Oh yes. the mother ship. :) I notified Magnus on that bug. Maybe he'll fix it.

  3. Glad you were able to get things up and running so quickly. I just got a new laptop with Ubuntu 12.04, we should find a place to help get up and running on common distros. As you note we don't have all the features from Avogadro 1 yet, but we are working on that and have some great new features. The first release will be to seek early feedback as we co ntinue to build out features, and we intend to "release early, release often". Thanks for giving it a try, and writing about your experiences.

    1. Hey Marcus,

      yeah. It was quite easy actually, but I really was missing a great deal of features. I'll be sure to keep doing git pull to get the latest updates and blog about what I find. Avogadro is still the tool of choice for doing modeling and preparing structures so its very interested to follow.

      As a user, I do hope that most things from Avogadro 1 will make it (of course in time, but rather sooner than later).