Outputting cell information and fractional coordinates

Matthias Krack matthia... at psi.ch
Wed Dec 11 14:24:07 CET 2013


Hi FX,

I could provide a dumpdcd code for CP2K output files in DCD format. Atomic 
labels are added if a prototype XYZ file is provided. It has also some 
additional features like frame selection (first/last dumped frame, stride), 
an optional application of PBC boundary conditions and a dump of all 
out-of-box atoms. I use often the DCD format, because it allows the 
consideration of the cell information e.g. VMD. I would put the code into 
the cp2k/tools folder in case you are interested.

Matthias


On Wednesday, December 11, 2013 1:27:20 PM UTC+1, fxc... at gmail.com wrote:
>
> Hi all,
>
> I'm running QuickStep MD of triclinic unit cells, and dealing with the 
> trajectory is not effortless, to say the least. I have to piece together 
> the Cartesian coordinates from a .xyz files (MOTION / PRINT / TRAJECTORY) 
> and the cell info (MOTION / PRINT / CELL). Is there any way to print 
> directly fractional coordinates in the trajectory file, with cell 
> information above (like a modified XYZ format). DCD is an option, but 
> impractical since it doesn't contain labels…
>
> Or does someone have an existing post-processing script for this task?
>
> Cheers,
> FX
>
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