[Jmol-developers] Crystal's in Jmol-HEAD

[E.L. W. (Egon) <eg...@sc...>]

Hi Fabian, Miguel,

Today, I've uploaded two patches that might interest you. Both deal with 
crystal support in Jmol-HEAD.

The first is in jmol.adapters.CdkJmolModelAdapter (1.22->1.23) which 
interfaces CDK with Jmol's rendering engine... I've implemented the 
getCrystalCellIterator() method, hopefully correct... but looks ok.

It uses a CrystalCellIterator to loop over the unit cell axis, a,b and c.

Miguel, the result is that it only shows these three axis... how should I make
it complete the full unit cell box?

The second patch is in cdk.io.VASPReader, which was yet unimplemented...
Fabian, some time ago you asked about ABINIT in CDK... I hope this VASP reader 
could help you get an idea of how that would look like in CDK...
I've basically copied the VASP code in Jmol, so it should be straight forward 
to see what changes I had to make...
Note that is has not been fully succesful yet... if you open the VASP file in 
Jmol-HEAD you'll see that there is something wrong with the coordinates... 
Haven't figured out yet why it is so... I've tried to interpret the 
coordinates in the VASP as fractional... and tried to use both cartesian 
*and* fractional in the CDK objects... both with the same result...

Have to figure out why this is so...

Also, it is not yet possible to store symmetry operations for a spacegroup, 
neither is it possible to define the crystal box yet in Jmol-HEAD... I'll 
work on this later... But I think it would be best to keep the crystal box 
stuff on the Jmol side... I think this bit as part of the rendering 
process... but the space group symmetry operations (-x, y+0.5, z etc) should 
go into CDK's Crystal class...

I need also to make to helper class that converts the Crystal into a P1 
crystal, thus applying the given symmetry operations... As Peter noted, this
should take into account symmetry operations that lead to atoms at the same 
coordinates... and I was thinking to use the Bspt code for this,

Miguel, can the Bspt code be used in a dynamic process? I.e. can I add atoms 
to the tree while using it at the same time?

Ok, enough for now.

Egon

Egon

-- 
PhD Molecular Representation in Chemometrics
Laboratory of Analytical Chemistry
http://www-cac.sci.kun.nl/people/egonw.html