[CP2K-user] [CP2K:14471] Re: Generate "Radius of gyration" from CP2K output files

[HB H]

Hi  Vladimir,

Thank you very much!

Wish you best luck with your work!

Cheers,
Haibei



Vladimir Rybkin <rybk... at gmail.com> 于2021年1月4日周一 下午10:28写道：

> Dear Haibei,
>
> please find attached.
>
> Usage (here I center around atom # 42):
>   ./cubecruncher.x -center 42 -i  "spin_"$i".cube" -o
> "spin_center_"$i".cube"
>    ./cubecruncher.x -dcent -i  "spin_center_"$i".cube" -o
> "spin_center_"$i".cube"
>
> It will produce distr_param.dat file.
>
> Yours,
>
> Vladimir
>
>
> 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
>>>>
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