[CP2K-user] [CP2K:19828] Re: Problems in `GEO_OPT` of FeS (Mackinawite) Slab

[Станислав Бачурин]

I think you should give it a try. There's also a rough approach - open the 
coordinate file in an editor, copy it to a spreadsheet program like Excel, 
find the most negative value in each column representing its coordinate, 
and add that value to all the column values. This way, your coordinates 
will shift in a way that allows you to accurately understand the physical 
dimensions of the cell. I did this when I couldn't center it through 
visualization programs.
пятница, 26 января 2024 г. в 22:16:40 UTC+3, 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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