[CP2K-user] [CP2K:14449] Re: Generate "Radius of gyration" from CP2K output files

Vladimir Rybkin rybk... at gmail.com
Mon Jan 4 14:28:55 UTC 2021

Dear Haibei,

please find attached. 

Usage (here I center around atom # 42):
  ./cubecruncher.x -center 42 -i  "spin_"$i".cube" -o 
   ./cubecruncher.x -dcent -i  "spin_center_"$i".cube" -o 

It will produce distr_param.dat file.



среда, 30 декабря 2020 г. в 01:47:04 UTC+1, ha... at gmail.com: 

> Dear  Vladimir,
> I will be appreciated if you could kindly share the code with me, because 
> the "gyration radius" has troubled me quite a lot recently. 
> Also please let me know if there is any copyright protection of the code, 
> or should I make any citation when I use the code.
> Meanwhile, Multiwfn cannot read CP2K generated .wfn files.
> Thanks again, have a nice day!
> Haibei
> Vladimir Rybkin <ry... at gmail.com> 于2020年12月29日周二 下午9:35写道:
>> Dear Haibei,
>> this can't be done using ouputs, but it can be done using spin density 
>> cubes. I was using the locally-modified version of cubecruncher, which I 
>> could share. However, care must be taken since under periodic boundary 
>> conditions gyration radius is strictly speaking not defined: the trick is 
>> to center the spin density in the middle of the cell (also can be done by 
>> cubecruncher) and treat it as non-periodic. 
>> Actually, CP2K generates .wfn files, although I am not sure whether they 
>> are of the format needed for Multiwfn (probably not).
>> Yours sincerely,
>> Vladimir
>> воскресенье, 27 декабря 2020 г. в 09:05:00 UTC+1, ha... at gmail.com: 
>>> Hi everyone,
>>> I have a technical issue regarding with generating the "Radius of 
>>> gyration" of the spin density from maybe cube files of cp2k.
>>> The "Radius of gyration" of one electron basically indicates how much 
>>> this electron is spreading its density in the e.g. cystall. In fact, there 
>>> are a lot of cp2k related studies mentioned such information, yet I just 
>>> donot know where to find and how to calculate it from cp2k output files. 
>>> I konw "Multiwfn software" can do this but it needs files that 
>>> contain Gaussian type functions (GTFs) in the cube files.  
>>> So my question is do I have to write a code, or is there any software 
>>> can do this for me from any of cp2k output files?
>>> Thx in advance,
>>> Haibei
>> -- 
>> You received this message because you are subscribed to a topic in the 
>> Google Groups "cp2k" group.
>> To unsubscribe from this topic, visit 
>> https://groups.google.com/d/topic/cp2k/71e-QDzKLSM/unsubscribe.
>> To unsubscribe from this group and all its topics, send an email to 
>> cp... at googlegroups.com.
>> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/cp2k/1fbeb98e-9bb4-42e8-af00-5659b09992d6n%40googlegroups.com 
>> <https://groups.google.com/d/msgid/cp2k/1fbeb98e-9bb4-42e8-af00-5659b09992d6n%40googlegroups.com?utm_medium=email&utm_source=footer>
>> .
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20210104/2478a5ff/attachment.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: cubecruncher.tar.gz
Type: application/x-gzip
Size: 20836 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20210104/2478a5ff/attachment.bin>

More information about the CP2K-user mailing list