[CP2K-user] [CP2K:20809] Re: Gallium + CO2 lack of convergence

[Michela Benazzi]

Hi Marcella and everyone,

I wanted to follow up on your advice. I used an equilibrated structure of 
64 Ga atoms, eliminated ~8 central Ga atoms and added the CO2 molecule. The 
MD steps converged until step #14, then the SCF loop did not converge. I 
wanted to update anyone who may be looking at this thread for guidance: I 
will be sizing up my cell dimensions.

Thank you,

Michela

On Thursday, October 3, 2024 at 1:22:48 PM UTC-4 Marcella Iannuzzi wrote:

> Hi
> If you have a good equilibrated Ga liquid box (right density and low 
> stress tensor) I wouldn't run GEO_OPT
> Obviously introducing CO2 is going to change the conditions, but I would 
> anyway start with a NVT run for a first equilibration and then run NPT to 
> re-equilibrate the volume. I would add the CO2 molecule and remove all the 
> Ga atoms within a certain radius from the center of mass of the molecule, 
> and then run the equilibrations as described above. 
> The only way to lower the concentration is to increase the amount of Ga, 
> i.e., increase the box. 
> Regards
> Marcella 
>
> On Thursday, October 3, 2024 at 5:02:46 PM UTC+2 bnzmi... at gmail.com wrote:
>
>> Hi Marcella,
>>
>> Thank you again!
>>
>> 1) should I run GEO_OPT on the pure Ga liquid, then add CO2?
>> 2) How should I form a cavity artificially without disrupting the newly 
>> equilibrated Ga structure?
>> 3) I only have one molecule of CO2 in there - How should I go about 
>> lowering the concentration? Should I just increase my #Ga atoms and add 1 
>> CO2 molecule?
>>
>> Best,
>>
>> Michela
>> On Thursday, October 3, 2024 at 10:20:25 AM UTC-4 Marcella Iannuzzi wrote:
>>
>>>
>>> Dear Michela, 
>>>
>>> The procedure you describe  does not sound very appropriate to me. 
>>> You should first obtain a liquid system, without solute. 
>>> I suppose you should check for density and other properties and have a 
>>> sufficiently large box. 
>>> Then you can create a cavity in the equilibrated liquid and insert the 
>>> solute, still with the right C-O bond length.
>>> If the SCF does not converge anymore after a few steps it is probably 
>>> because of the coordinates. 
>>> The concentration of CO2 seems rather high. 
>>>
>>> You can use GAPW. It is more commonly used for all electron 
>>> calculations. With PP, GPW is as accurate.
>>>
>>> Regards
>>> Marcella
>>>
>>>
>>>
>>> On Thursday, October 3, 2024 at 3:02:10 PM UTC+2 bnzmi... at gmail.com 
>>> wrote:
>>>
>>>> Hi Marcella,
>>>>
>>>> thank you for your kind response and your time.
>>>>
>>>> 1) I just switched to double zeta quality a few hours ago, but my MD 
>>>> just crashed because, weirdly, it converged for the first few SCF loops, 
>>>> but then it stopped converging (attached the output file here to explain).
>>>>
>>>> 2) I am using GAPW because I found that augmented plane waves method 
>>>> worked really well with my liquid Al systems before. that method is also 
>>>> reported in DFT literature for liquid Ga. Rationalizing it, I think it 
>>>> works because it samples regions of space with different charge densities 
>>>> with more accuracy. Do you think I should consider something else?
>>>>
>>>> 3) I used a cell size to represent the density of liquid Ga with the # 
>>>> of atoms I have. I prepared my coordinates with a Python script, then 
>>>> relaxed the geometry in Avogadro2 software and inserted CO2 such that it 
>>>> was a distance of min 2.5 A to minimize initial repulsion with Ga atoms. Do 
>>>> you have any suggestions to prepare a structure? I am leaving 1-2 A on all 
>>>> sides from the unit cell boundaries because I have been worried about Ga 
>>>> atoms being too close to neighbors across periodic boundaries.
>>>>
>>>> Michela
>>>> On Thursday, October 3, 2024 at 8:23:26 AM UTC-4 Marcella Iannuzzi 
>>>> wrote:
>>>>
>>>>> Dear Michela, 
>>>>>
>>>>> The basis set you are using is of poor quality. 
>>>>> The coordinates you sent show a rather strange C-O bond length
>>>>> The cell is very small, but still there is vacuum space among the 
>>>>> replicas in all directions, it is a rather weird choice of coordinates. 
>>>>>
>>>>> Is there a reason why you are using GAPW?
>>>>>
>>>>> Regards
>>>>> Marcella
>>>>> On Wednesday, October 2, 2024 at 7:27:59 PM UTC+2 bnzmi... at gmail.com 
>>>>> wrote:
>>>>>
>>>>>> Good morning dear CP2K community,
>>>>>>
>>>>>> how are you? You may know me from previous posts on liquid Al (+CO2) 
>>>>>> MD troubleshooting. All of your responses have been super helpful so far, 
>>>>>> and I am coming here again for a different liquid metal.
>>>>>>
>>>>>> My simulations with pure liquid Gallium have been less troublesome 
>>>>>> than all of my liquid Al simulations, but the MD with 1 CO2 molecule won't 
>>>>>> converge. Can I please get some help troubleshooting?
>>>>>>
>>>>>> Thank you,
>>>>>>
>>>>>> Michela
>>>>>>
>>>>>

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