[CP2K-user] [CP2K:13720] Re: Running CP2K calc with ASE

[Sun Geng]

Dear Aniruddha,

Sometimes ago, I have encountered a similar problem,
I think the reason is that the python code communicates positions/forces 
with the mpi cp2k_shell.popt. 
There is a problem when MPI code read the pipe: the MPI code will only read 
truncated data  (such as positions) from the pipe, not all of them.
So CP2K_shell.popt is still waiting for more coordinates and gets stuck.

Best,
Geng



在2020年8月13日星期四 UTC-7 下午1:20:17<ani... at gmail.com> 写道：

> 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
>>>
>>> -- 
>>> You received this message because you are subscribed to the Google 
>>> Groups "cp2k" group.
>>>
>> To unsubscribe from this group and stop receiving emails from it, send an 
>>> email to c... at googlegroups.com.
>>
>>
>>> To view this discussion on the web visit 
>>> https://groups.google.com/d/msgid/cp2k/df050a2d-1161-4e2c-98c9-0463adcb4c3do%40googlegroups.com 
>>> <https://groups.google.com/d/msgid/cp2k/df050a2d-1161-4e2c-98c9-0463adcb4c3do%40googlegroups.com?utm_medium=email&utm_source=footer>
>>> .
>>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20200817/bccdfa37/attachment.htm>