[CP2K-user] [CP2K:17287] Re: WARNING in particle_methods.F:684 :: The distance between the atoms *** *** 10 and 405 is only 0.496 angstrom and thus smaller than the threshold *** *** of 0.500 angstrom

[Marcella Iannuzzi]

You have specified the CELL parameters

    &CELL

      ABC   8.1300   5.1320   3.1302

      ALPHA_BETA_GAMMA  90 90 90

    &END CELL

What you have not done is to set also for the CELL 
PERIODIC NONE, since the default is XYZ

   - PERIODIC 
   <https://manual.cp2k.org/cp2k-9_1-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/CELL.html#list_PERIODIC>

This  is a problem

The CELL parameters are always needed also in the case of PERIODIC NONE
in particular, enough vacuum space around the molecular system is required 
such that the selected Poisson solver for non periodic conditions works 
correctly

Regards
Marcella

On Thursday, July 7, 2022 at 12:06:40 PM UTC+2 wangch... at gmail.com wrote:

> Thank you very much for the advice.
>
> I am using POISSON since it is an isolated cluster and a non-periodic 
> system.
> I did not specify any cell parameters in the input file since it is a 
> cluster. I don't think there is any reason to specify a cell, and I believe 
> the cp2k manual indicates that the program defaults to considering the 
> project an isolated system if there are no cell parameters. Does this make 
> sense to you? 
> It is true that cp2k terminates the program by itself if there are no cell 
> parameters for MD, but for Geo, cp2k just keeps running without any error 
> message.
>
>
> On Thursday, July 7, 2022 at 5:55:36 PM UTC+8 Marcella Iannuzzi wrote:
>
>> Hi
>>
>> The simulation CELL is most probably far too small for the system.
>> Using 
>>     &POISSON
>>       PERIODIC NONE
>>        POISSON_SOLVER MT
>>         &MT
>>           ALPHA 7.0
>>           REL_CUTOFF 1.2
>>         &END MT
>>     &END POISSON 
>> a CELL that is approximately twice the size of the system in all 
>> direction is recommended. 
>>
>> Regards
>> Marcella
>>
>> On Thursday, July 7, 2022 at 11:22:07 AM UTC+2 wangch... at gmail.com wrote:
>>
>>> Dear all,
>>>
>>> I am new to cp2k and am performing a test geometry optimization.
>>>   
>>> The initial geometry is actually the result of Gaussian's geometry 
>>> optimization. So the initial input of the structure should be reasonable 
>>> enough for cp2k to run and converge in a short time. 
>>>
>>> But it displays "WARNING in particle_methods.F:684 :: The distance 
>>> between the atoms *** *** 10 and 405 is only 0.496 angstrom  smaller than 
>>> the threshold *** *** of 0.500 angstrom " a lot. And the program seems to 
>>> be stuck in a weird corner and not updating anything in the output, but it 
>>> keeps running on the server. I here attached the inp and out file here.[image: 
>>> WechatIMG224.jpeg]
>>>
>>> I'm appreciate it if you can help me with this or provide any 
>>> information refers to the problem.
>>>
>>> Thank you !!
>>>
>>

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