[CP2K-user] [CP2K:19826] Re: Problems in `GEO_OPT` of FeS (Mackinawite) Slab

[Станислав Бачурин]

Could you check if your system is aligned in the xy plane? Maybe, before 
applying xy periodicity, it needs to be properly oriented.
  Also, it is necessary to set the dimensions along the Z-axis with a 
slight margin in the cell settings until this warning disappears. I 
struggled a lot with calculations under gas-phase conditions. I had exactly 
the same strange behavior - the nuclei almost merged in the organic 
molecule. When I figured out the cell settings and Poisson, everything was 
optimized correctly.
пятница, 26 января 2024 г. в 21:49:57 UTC+3, Ardalan Hayatifar: 

> Thanks for your comment. I have been trying `PERIODIC XYZ` or `PERIODIC 
> XY` and that doesn't fix it either. 
> Having more layers also shows the same behavior.
>
> On Friday, January 26, 2024 at 12:46:41 PM UTC-6 Станислав Бачурин wrote:
>
>> *** WARNING in pw_env_methods.F:738 :: The selected periodicities in the 
>> *** *** sections &CELL and &POISSON do not match *** You set periodicity to 
>> None, but use the periodic Poisson solver. Try wavelet or switch to 
>> Periodic in your Cell's settings.
>> пятница, 26 января 2024 г. в 21:38:47 UTC+3, Ardalan Hayatifar: 
>>
>>> I am using CP2K version 2023.2. I want to perform `GEO_OPT`on FeS layers 
>>> that I have made using Pymatgen. I am using .cif file from published data.
>>>
>>> *Input File:*
>>>
>>> Note: `MAX_SCF` set to 100 results in the same behavior.
>>>
>>> (attached)
>>>
>>> *Problem:*
>>>
>>> This is a convergence problem. Upon visualization I can see that things 
>>> get closer than they should and the system acts crazy.
>>>
>>> *Pictures:*
>>>
>>> Initial:
>>>
>>> [image: Screen Shot 2024-01-26 at 10.46.20 AM.png]
>>>
>>>
>>> After some SCF cycels:
>>>
>>> [image: Screen Shot 2024-01-26 at 10.46.45 AM.png]
>>>
>>> Another representation:
>>>
>>> [image: Screen Shot 2024-01-26 at 10.10.58 AM.png]
>>>
>>> (shown atoms distance ~1A!)
>>>
>>> *What I’ve tried:*
>>>
>>>
>>> - I have changed the slab size in X and Y directions to remove size 
>>> effects. Tried dimensions that are at least 1X1 A and 1.8 X1.8 A dimensions 
>>> - all while having 15 A vacuum in Z
>>>
>>> - I have monitored the input file for close contacts using 
>>> `CHECK_INTERATOMIC_DISTANCES 1`. There are no pair-wise distances below 2.5 
>>> A.
>>>
>>> - PBC effects: I have tried adding 1 A to cell dimensions `ABC` to again 
>>> eliminate possible overlaps, but the behavior persists.
>>>
>>> - I have tried higher cutoff values (e.g. 1200).
>>>
>>> - I have tried writing the input so that it uses a `.xyz` file instead 
>>> of PyCP2K-ASE format and that doesn’t change anything.
>>>
>>> - Centering the solid layer using `&CENTER_COORDINATES` also did not 
>>> help.
>>>
>>>
>>> At this point I’d like to ask for any help or suggestions. It it 
>>> possible that my parameters are wrong?
>>>
>>>
>>> Thanks in advance for your time.
>>>
>>>
>>>
>>>

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