[CP2K-user] [CP2K:19827] Re: Problems in `GEO_OPT` of FeS (Mackinawite) Slab

[Ardalan Hayatifar]

Great catch!
In VMD and using the same exact cell dimensions:
```
pbc set {18.3675 18.3675 20.1312} -all
pbc box
```

[image: Screen Shot 2024-01-26 at 1.11.49 PM.png]
it is off in XY plane.

It seems that in ASE-PyCP2K,
```
structure = read('thickness-1-A_1.cif')
structure.center(axis=2)
```
is not centering anything.

Should I try using `&CENTER_COORDINATES` to center it?

On Friday, January 26, 2024 at 12:59:00 PM UTC-6 Станислав Бачурин wrote:

> 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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