Atomistic Small Bearing: dynamics performed in NanoEngineer-1, visualized in Blender

The astute viewer will notice two things first:
1-I still can not frame a shot for shit.
2-The back side of the rotor is missing a hydrogen atom

Well, these are still more or less movies where I am more concerned with getting different things to work than I am with cinematography and such. Maybe next time I'll throw in some long parallel walls to frame the action. Also any long time readers of this site will know that I have had my problems with hydrogen in the past, but, all in all, things have come a long way from the last time I posted anything about the famous small bearing first proposed by K. Eric Drexler back in 94, I believe.

A little about how I did it:

NE1 will save simulations in two ways, either as a binary file (which I can't do much with right now expect turn into gibberish) and a series of POV-Ray files, one for each time step. So you are probably thinking "why not just stitch the povs together, adjust the lighting, camera, materials, whatever and call it a day?" I know POV-Ray is great, and I'm pretty sure it is all Pixar uses, but I'm just a gui type of guy I guess. So I have written a Frankenstein's Monster of a script that will read in a series of povs and create atom trajectory files, one for each atom. Normally it would then just be a matter of using Miron Cuperman's import_ipo_script to connect the atom trajectory files with a PDB model which NE1 exports and Miron has also provided a very fast importer for.

The only problem here is NE1 writes the atoms in a different order in povs and PDBs. It is very important that the right trajectory matches up with the right atom. So I added another section (subroutine?) to my script that will read in the first pov ray file and create a bona fide .xyz chemical format file. I went with the .xyz because it is the simplest format I know of. Then all you have to do is run it through Open Babel to convert it into a PDB file that has the same atom order as the pov files and can be imported into Blender. That's all there is to it.

I fully intend to clean it up, rewrite parts so they're not embarrassing (even for me) but if you can't wait, you can get a copy of my ne12blendXXX.py script. The XXX stands for a couple of things. Guess!

C60 and C240 collision at 300eV

Related:

C60 and C240 collision at 10eV

C60 and C240 collision at 10eV

Something a little more than just jiggling

This would not have been possible without the help of Miron Cuperman and his coding skills. Miron has written a nice python script to automate the process of importing csv data in Blender to animate objects. You can get a copy here

I will be the first to admit I am far from a Blender pro, but I hope to be able to show off some of the features that other visualizers don't have or do in a way I find cumbersome. This episode: Camera Tracking

More interesting stuff is on the way too.

MTF

fullerene capsule: molecular dynamics performed in GROMACS, visualized in Blender

and one more, why not?

Can you put it in a wine glass?

Sure

C60 fullerene- molecular dynamics performed in GROMACS, visualization done in Blender

visualizing GROMACS simulations with Blender (teaser)

This was a proof of concept test, so I'm not going into the details of how to do it right now. There are also a couple of steps I still need to automate to make this a practical solution; that's why there is only five atoms in this one. However I'm optimistic those can be worked out easy enough. After that I'll upload a turn-key script of sorts that will give you the features and flexibility of Blender to render GROMACS molecular dynamics simulations.

Related:
Atom Trajectories from GROMACS
Carbon Nanotube Animated in Blender
Molecular Rotor Animated in Blender

MTF