[CP2K-user] [CP2K:11576] How to remove repeated entries in -pos-1.xyz file from MetaD simulation?

[Tiziano Müller]

Hi Raghav,

In my cp2k-tools Python package [1] there is a `xyz_restart_cleaner.py` 
[2] which does exactly that. The script is also able to handle large 
files efficiently (tested with up to 4GB).

Best regards,
Tiziano

[1] https://pypi.org/project/cp2k-tools/
[2] 
https://github.com/dev-zero/cp2k-tools/blob/develop/cp2k_tools/parser/xyz_cli.py

On 17.04.19 20:20, Raghav wrote:
> Dear all,
> 
> I'm running a *Metadynamics* simulation and I *restarted* my 
> calculations many times, as a result I have a lot of *repeated* entries 
> in my -pos-1.xyz file.  For e.g steps 21 to 29 are repeated in the 
> attached file as a result of restarting.
> 
> I have to perform analysis on the trajectory but for that I need to 
> remove the *repeated *entries. Does anyone know how to do this?
> 
> My system is very large and the trajectory as well, hence doing this 
> manually is a daunting task.*
> *
> *
> *
> Thanks and Regards,
> Raghav*
> *
> 
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-- 
Tiziano Müller
University of Zurich
Department of Chemistry
Winterthurerstrasse 190
CH-8057 Zürich

Tel: +41 44 63 54234
www.chem.uzh.ch
tiziano... at chem.uzh.ch