[CP2K:6526] Re: reading dcd files

Matthias Krack matthia... at psi.ch
Wed May 20 15:13:05 UTC 2015

Hi Steve

the DCD file header is only written once at the beginning of the simulation 
run. Thus no way to guess how many frames will be dumped during the run 
eventually. The time for a frame could be retrieved from the print interval 
and the initial time step which are both dumped, but this works only for a 
constant time step interval (no variable time step). I am afraid there is 
no official "DCD standard", but.the CP2K implementation should be quite 
close to the CHARMM/NAMD definition. It is most important that common tools 
like VMD are able to digest the DCD files dumped by CP2K even if one could 
certainly devise a better binary format.

Note, that dumpdcd.f90 has also some nice extra feature like

   - definition of first and last frame dumped
   - stride (i.e. skipping frames regularily)
   - applying PBC (at box centre or at 0,0,0), e.g. useful for movies
   - tracing of atoms which leave the original cell


OK thanks, that was helpful. So you just read until the end of the file 
> and cp2k doesn't store the number of steps (frames) in the header. And 
> cp2k seems to store the angles directly [a,gamma,b,beta,alpha,c], while 
> lammps stores their cosines [a,cos(gamma),b,cos(beta),cos(alpha),c] and 
> both do this in the same somewhat unusual ordering. Well, this dcd 
> business is really something. Is there an official specification of the 
> format(s)? Anyway, thank you very much for this tool and the fast 
> response. 
> best, 
> Steve 
> -- 
> Steve Schmerler 
> Institut für Theoretische Physik 
> TU Freiberg, Germany 
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