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Avogadro Videos: Transparent Molecules, Rotation and Geometry Optimisation

Posted by Marcus D. Hanwell on

I already wrote this post once, but the bit bucket ate it when my browser crashed... Carsten and I were talking on IRC yesterday about the last post I made and progress with my project in general. He asked if I would try making a few videos demonstrating new features as his system has trouble capturing videos without dropping frames. I am new to the whole video capture scene and have always found screen shots to be enough in the past. He told me about xvidcap and so I emerged it. What else do people use for this kind of thing?

After some trial and error (I found xdamage prevented the OpenGL window from being recorded properly) I recorded a video. The above video is my first successful one, as uploaded to YouTube by Carsten. I don't know about you but I find flash very unreliable on my 64 bit system in my 64 bit browser as there is still no decent 64 bit flash plugin. You can get the original video here (~17MB) and my second attempt here (~14MB) which I think is a little better personally.

I made a new video this morning that is shown above and also available for download here (~5MB) showing some recent changes in Avogadro implemented by Donald - geometry optimisation now takes place in a separate thread. This was on my list of features to implement and I had done some reading and initial code (nothing that worked right). It is a great feature to have implemented as geometry optimisation can take quite some time. My research, reading and coding haven't been in vain either - I learned a lot about how Avogadro, OpenBabel and Qt interact as well as learning quite a bit about threads (never used them before). There are other things that will benefit from threading too, so I hope I will be able to do some coding with threads soon :-)

I would love to hear what you think about the videos, if they are useful demonstrations of new features in Avogadro. Most of this stuff is actually in libavogadro which is used by Avogadro. Kalzium uses a snapshot of libavogadro right now, in KDE 4.1 it should be possible to switch to the system copy of libavogadro. It is a great demonstration of how easy it is to add molecular visualisation capabilities to a program by using libavogadro. I am still learning lots of new stuff and thankfully the development team don't mind me asking questions, even when some of the questions are really stupid... I am still having a great time working on the code pushing the boundaries of what we can accomplish and hope that you find these posts informative.

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Egon Willighagen on :

Egon WillighagenGood work on the force field minimization! If you want to do it the fancy way, you make it a sculpt mode, where you automatically add hydrogens and automatically run a cheap and fast energy minimization. (Hydrogen counts need updating when any bond is added or deleted). Should not be too difficult, but very cool.

Marcus D. Hanwell on :

Marcus D. HanwellThat could be quite a cool feature to add at some point. Threading does add complexity but it is also great for maintaining interactivity if you can get it right.

Geoff Hutchison on :

Geoff HutchisonEgon, please add this as a feature request to the tracker. :-)

We definitely talked about having a more interactive draw tool as well for drawing carbon chains.

I've also talked about (but not coded) an "insert from file" command and tool for adding from a library of molecule templates. This would go a long way towards a build mode like Spartan where you click to add new pieces already in a minimized geometry.

There will also shortly be an extension for converting hydrogens to methyl groups.

liquidat on :

liquidatLooks awesome - what exactly do I need to set this up on my system given that I already have a KDE 4 svn version installed for a loal user?

Btw., many people also use recordMyDesktop for creating screen casts. It comes along with a gtk interface but in the newest version also with an Alpha qt interface.

Benoit Jacob on :

Benoit JacobNormally this should be explained here:

http://avogadro.sourceforge.net/wiki/Compiling

Don't hesitate to ask our avogadro-devel mailing list if you have problems.

liquidat on :

liquidatThanks, I was just too stupid to search for myself :/

Marcus D. Hanwell on :

Marcus D. HanwellIf you use Gentoo you can simply type 'emerge avogadro' and get the 0.1 release - although it doesn't have a lot of the new stuff that has gone in over the past few weeks. Benoit pointed out the instructions for building from the latest sources.

Oded on :

OdedI used Istanbul successfully to record my desktop. I have no idea how it behaves with openGL windows, though.

infopipe on :

infopipevery cool. i'm really impressed :-)

Aaron Seigo on :

Aaron Seigowow.. those videos are terrific. keep 'em coming!

it looks like we're going to have some amazingly great chem tools in kde4 =))

as for screen cap, i use recordMyDesktop with the PyQt front end. works wonderfully, including audio.

Marcus D. Hanwell on :

Marcus D. HanwellGlad you liked the videos. They are a great way to demonstrate some of the progress we are making with certain aspects of the avogadro library. I think we are going to have an awesome set of chemistry tools.

I can't wait for aKademy next week. I will check out recordmydesktop, it would possibly be good to narrate some videos. It would be good to have a tool that can select a window area to record rather than having to draw it. Not sure if I need to tweak the encoding for better file size and ease of use for people wanting to watch it.

Thanks.

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