[Kalzium] [Open Babel] OBUnitCell, some question, code contribution

[Jean Bréfort]

Le dimanche 18 juin 2006 à 10:08 +0200, Carsten Niehaus a écrit :
> Guten Morgen

Hi Carsten,

I have projects for some of the issues you raise. Just I'm missing time
at the moment to do any work on that because of serious personal issues.
My goal is to import CIF files and support symmetry operations,
including space and point groups. You'll find more details in this list
archives (around begining of last month).

Cheers,
Jean

> I am starting to write a crystal-cell viewer for Kalzium. For that I need some 
> information about the cell:
> 
> - The x/y/z-pos of all atoms in it
> - The type of the Atoms (for example in NaCl if a certain atom is Na or Cl)
> - The position of all Tetraederlücken (sorry, I couldn't find the english word 
> for it, not even in Wikepedia. The german article is in [1])
> - The position of all Oktaederlücken. (again, no translation found. The german 
> article is in [2], a nice picture which says it all is in [3])
> - The crystalsystem or (even better) the Bravis-lattice of the unitcell.
> - the length of the vectors a,b,c
> - the angles alpha, beta, gamma
> 
> Ok, some of this is in OBUnitCell, some is not. Of course, the position of 
> the "holes" (Tetraeder- and Oktaderlücken) can be calculated, if I know the 
> Bravis-lattice I can calculate the xyz of all atoms and so on.
> 
> Still, I am missing some things and would like to discuss this. Perhaps it is 
> already somewhere and I just didn't find it our perhaps I am stupid ;-)
> 
> What I am missing:
> 
> == 1 ==
>  - an enum of the crystalsystem. Currently I am working around this like this 
> in my own code:
> 
>         enum LATTICE
>         {
>             TRICLINIC,
>             MONOCLINIC,
>             ORTHORHOMBIC,
>             TETRAGONAL,
>             RHOMBOHEDRAL,
>             HEXAGONAL,
>             CUBIC
>         };
> 
>   I think this could find a nice place in OpenBabel as well as those seven 
> types won't ever change. Currently there is
> 	std::string GetSpaceGroup( )
>   As there is no API-documentation at all about it I guess these represent the 
> 230 spacegroups we all know? If so there should/could be something like
>             LATTICE bravisLattice( std::string spacegroup )
>   as each spacegroup is in one of the 14 bravislattice... Same for the 
> pointgroups. Why not adding a pointgroup2crystalgroup method?
> 
> == 2 ==
>  - An algo which computes the volume of a OBUnitCell. Well, do not longer 
> care, just commit the attached code ;-) I ported from my own code. Any free 
> licences (GPL, FreeBSD ...) is fine with me. Any chance to get this in OB2.1?
> 
> == 3 ==
> - I still have not figured out how to use OBUnitCell. Of course I can store 
> the vectors and angles. Fine. But that give me the information which atoms 
> are where. I googled for codeuses of this class but found no matches.
> For example, if I want to draw Lithium niobate (Spacegroup R3m, pointgroup 3m, 
> crystalsystem trigonal) I have three atomtypes (Li, Nb, O). (Picture in [4]). 
> I cannot put all that information into OBUnitCell. Same for NaCl (picture in 
> [5]).
> So what am I supposed to do? Do I create an OBMol from the information in the 
> OBUnitCell to store the information of the atoms? That doesn't make real 
> sense, neither code-wise nor chemically...
> 
> Gruß, 
>   Carsten
> 
> [1] http://de.wikipedia.org/wiki/Tetraederlücke
> [2] http://de.wikipedia.org/wiki/Oktaederlücke
> [3] http://de.wikipedia.org/wiki/Bild:Kfz_oktaederluecke.png
> [4] 
> http://upload.wikimedia.org/wikipedia/commons/thumb/f/f5/Linbo3_Unit_Cell.png/300px-Linbo3_Unit_Cell.png
> [5] 
> http://upload.wikimedia.org/wikipedia/commons/d/db/NaCl-estructura_cristalina.svg
> 
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