[CP2K-user] [CP2K:17056] Re: Rhombohedral structure optimization (CELL_OPT)

[Matt Watkins]

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. 
>>
>> [image: structure_collapse.png]
>>
>> 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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