[CP2K-user] [CP2K:13773] Re: Running CP2K calc with ASE

[Aniruddha Dive]

Thanks Hasan,

I tried using cpus-per-task but I am still getting same results. Would you 
mind sharing your job submission file?

Best Regards,
Aniruddha M Dive

On Monday, August 17, 2020 at 9:56:01 AM UTC-7, Hasan Al-Mahayni wrote:
>
> Hello,
>
> I had a similar problem, however I don't quite understand the submission 
> file as we are in different clusters. For me, i fixed this problem by using 
> cpus-per-task instead of tasks-per-nodes.
>
>
> Hope this helps,
>
> Hasan Al-Mahayni
>
>
> On Thu, Aug 13, 2020 at 4:20 PM Aniruddha Dive <ani... at gmail.com 
> <javascript:>> wrote:
>
>> Thanks Hasan,
>>
>> I was able to get the Cp2K working. However I face another issue. The 
>> simulation runs well for few steps and after that I cannot see my output 
>> file being updated. The simulation shows running however I am not able to 
>> see any output being updated in the cp2k output file as well as the slurm 
>> output file. I have attached my job submission script, python script as 
>> well as the out files for reference. Could this be a memory issue? 
>>
>> Best,
>> Aniruddha M Dive
>>
>> On Tuesday, August 4, 2020 at 10:12:17 AM UTC-7, Hasan Al-Mahayni wrote:
>>>
>>> Hello,
>>>
>>> I had similar problems starting CP2K with ASE earlier this summer. I 
>>> will attach an example of geometric optimization for a slab, I hope it 
>>> helps. You need to copy paste a large portion of your cp2k input file in 
>>> your python script, because ASE does not provide all the input parameters 
>>> you will need to perform geo_opt. Please find an example attached below.
>>>
>>> Cheers,
>>>
>>> Hasan.
>>>
>>> On Tue, Aug 4, 2020 at 1:16 AM Maxime Van den Bossche <
>>> maxi... at gmail.com> wrote:
>>>
>>>> Dear Aniruddha,
>>>>
>>>> Since you haven't provided a minimal example, nor the error message 
>>>> you're getting
>>>> from ASE or CP2K, I haven't looked into debugging the (bulky) example 
>>>> you sent.
>>>>
>>>> But I don't think you can do the geometry optimization in this way. ASE 
>>>> uses the cp2k_shell binary,
>>>> which seems to only perform single-point calculations but not e.g. 
>>>> geometry optimizations.
>>>>
>>>> The idea behind cp2k_shell is that the 'driver' (in this case ASE) is 
>>>> the one moving the atoms
>>>> around, and what CP2K does is e.g. calculating the energy and the 
>>>> gradients for a given geometry.
>>>>
>>>> Here is a minimal example of a geometry optimization, and you can work 
>>>> your way up
>>>> from there:
>>>>
>>>> from ase.build import molecule
>>>> from ase.calculators.cp2k import CP2K
>>>> from ase.optimize import BFGS
>>>>
>>>> atoms = molecule('H2O')
>>>> atoms.center(vacuum=2.0)
>>>>
>>>> calc = CP2K(command='cp2k_shell.sopt')
>>>> atoms.set_calculator(calc)
>>>>
>>>> dyn = BFGS(atoms)
>>>> dyn.run(fmax=0.05)
>>>>
>>>> Best regards,
>>>> Maxime
>>>>
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