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

[Hasan Al-Mahayni]

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 <anirud... at gmail.com>
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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