[CP2K-user] [CP2K:19144] Crash in combining D3_EXCLUDE_KIND and .xyz reading

['Niccolò Bancone' via cp2k]

Dear Jürg,

Thank you for your answer.
I generate the cif files with VESTA 3.5.7, I don't know if it can help.

I have performed a couple of other tests on a system with 230 atoms in the 
unit cell.
With the cif format, the D3_EXCLUDE_KIND works with any number between 1 
and 230, that is, with any number equal or smaller than the total number of 
atoms. When I write a number equal or higher than 231 I get the 
segmentation fault error.

With the xyz format, the D3_EXCLUDE_KIND works with any number between 1 
and 6, that is, equal or smaller than the number of atomic kinds I specify 
in the input I sent two days ago. If the number is 7 or higher, I get again 
the segmentation fault.

So actually it seems right as you wrote, that is, when reading my cif file 
I get a number of atomic kinds equal to the number of atoms.

I have been looking for a print option of the Grimme's parameters of each 
atom to check this hypothesis but I was not able to find it. Is there one?

Thank you again.
Regards,
Niccolò
Il giorno martedì 25 luglio 2023 alle 15:49:38 UTC+2 Jürg Hutter ha scritto:

> Hi
>
> you have
> D3_EXCLUDE_KIND 135..198
> in your input, but only 6 KINDS, so 135-198 is out of range.
>
> Why did it work with a cif file? Probably CP2K generated a different Kind 
> for each atom in the cif file.
> We fixed this behavior for most types of cif files, but you are either 
> using an older version or
> found an new type of cif files.
>
> regards
> JH
>
> ________________________________________
> From: 'Niccolò Bancone' via cp2k <cp... at googlegroups.com>
> Sent: Monday, July 24, 2023 4:50 PM
> To: cp2k
> Subject: [CP2K:19136] Crash in combining D3_EXCLUDE_KIND and .xyz reading
>
> Dear all,
>
> I am facing problems in performing calculations when I try to read a .xyz 
> file while the D3_EXCLUDE_KIND keyword is active.
> I get a segmentation fault error every time I try to combine the two 
> conditions listed above.
>
> I have tested the calculations ENERGY, GEO_OPT, CELL_OPT and BAND on two 
> different machines.
> I also tried both the .popt and .psmp and different cp2k versions, namely 
> 8.2, 9.1, 2022.2.
> The structures I have been testing are 3D and 2D periodic systems of 
> different extensions (118 to 294 atoms in the unit cell), involving both 
> ionic and molecular crystals.
>
> In all my attempts I got the same error.
>
> What confuses me the most is that if I perform exactly the same 
> calculation reading a .cif file instead of the .xyz the calculations work 
> perfectly when the D3_EXCLUDE_KIND keyword is active.
>
> I am really out of ideas and i am starting to wonder if there is a bug 
> related the the D3_EXCLUDE_KIND keyword.
>
> Has anybody ever faced such a situation?
>
> Best,
> Niccolò
>
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