[CP2K-user] [CP2K:17060] Re: Rhombohedral structure optimization (CELL_OPT)

[Matt Watkins]

Mystery solved. 
Thanks, Matthias.

On Friday, 27 May 2022 at 09:31:22 UTC+1 Matthias Krack wrote:

> Hi 
>
>  
>
> the interatomic distance check for systems with less than 2000 atoms is a 
> default task only since CP2K version 9.1. For earlier versions, you have to 
> request that check explicitly using this keyword 
> <https://manual.cp2k.org/cp2k-9_1-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/PRINT/INTERATOMIC_DISTANCES.html#CHECK_INTERATOMIC_DISTANCES>
> .
>
>  
>
> Best
>
>  
>
> Matthias
>
>  
>
> *From: *"cp... at googlegroups.com" <cp... at googlegroups.com> on behalf of 
> Matt Watkins <mattwa... at gmail.com>
> *Reply to: *"cp... at googlegroups.com" <cp... at googlegroups.com>
> *Date: *Friday, 27 May 2022 at 10:18
> *To: *"cp... at googlegroups.com" <cp... at googlegroups.com>
> *Subject: *[CP2K:17056] Re: Rhombohedral structure optimization (CELL_OPT)
>
>  
>
> Hello, odd you don't see the same message.
>
> I am using the dev version (10.0)
>
> You could also ask cp2k to dump coordinates + cell to pdb or similar 
> format and see if they are what you expect.
>
> Matt
>
>  
>
>
> Dear Matthew, 
>
>  
>
> Thank you very much for your prompt reply.
>
> Unusually, I did not observe any such warnings, in fact there were none in 
> the output file...
>
> The version of CP2K I am using is 8.1.0, could that issue have perhaps 
> been due to a version difference?
>
> In the meantime, I will give it a try with a cubic conventional cell and 
> update you.
>
>  
>
> Kind regards,
>
> Tomoki
>
> On Thursday, 26 May 2022 at 10:00:10 UTC+1 Matt Watkins wrote:
>
> Hello, 
>
> I think your structure / periodic boundaries are incorrect. When I run 
> your input I see
>
> "
>
>  *** WARNING in particle_methods.F:684 :: The distance between the atoms 
>  ***
>  *** 78 and 89 is only 0.224 angstrom and thus smaller than the threshold 
> ***
>  *** of 0.500 angstrom
>
> "
> this is going to lead to massive force and explosions.
>
> Making your structure into a cubic conventional cell might make life 
> easier.
>
> Matt
>
>  
>
> On Thursday, 26 May 2022 at 02:49:51 UTC+1 Tomoki Ogata wrote:
>
> Hi there everyone, 
>
>  
>
> First time posting here, thank you in advance! 
>
> I am trying to do a structural optimization of FAU zeolite, which has a 
> rhombohedral unit cell (a = b = c = 17.9 A, alpha = beta = gamma = 60 
> degrees). 
>
>  
>
> I tried running the input file attached, but unfortunately, the 
> crystallinity of the structure collapsed. 
>
>  
>
>  
>
> I believe that the reason is related to the line in my input file 
> "SYMMETRY RHOMBOHEDRAL", since the structure is preserved if this line is 
> excluded. However, without SYMMETRY RHOMBOHEDRAL, the a, b and c parameters 
> of the cell deviate from 17.9 A. I looked through the CP2K manual, but was 
> unfortunately unable to find any information which might help solve the 
> problem.
>
>  
>
> A part of my input file which is attached:
>
> &CELL
>
>     &CELL_REF
>
>       A 12.6592017 12.6592017 0.0000000 
>
>       B 12.6592017 0.0000000 12.6592017 
>
>       C 0.0000000 12.6592017 12.6592017
>
>       MULTIPLE_UNIT_CELL 1 1 1
>
>       ALPHA_BETA_GAMMA 60 60 60
>
>       SYMMETRY RHOMBOHEDRAL
>
>     &END CELL_REF
>
>     A 12.6592017 12.6592017 0.0000000 
>
>     B 12.6592017 0.0000000 12.6592017 
>
>     C 0.0000000 12.6592017 12.6592017
>
>     MULTIPLE_UNIT_CELL 1 1 1
>
>     ALPHA_BETA_GAMMA 60 60 60
>
>     SYMMETRY RHOMBOHEDRAL
>
> &END CELL
>
>  
>
> Would anyone happen to know of a way to do a structural optimisation for a 
> rhombohedral system while preserving the a, b and c parameters and without 
> the structure falling apart?
>
>  
>
> Thank you in advance,
>
> Tomoki
>
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>

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