[CP2K-user] [CP2K:13952] Re: gas phase calculations

[Pierre Cazade]

Hi Matt,

Thanks for your answer. I will try the analytic Poisson solver.

Regards,
Pierre

On 22/09/2020 16:22, Matt W wrote:
> There are no timings for the gas phase run but it looks like the pw 
> operations are dominating - they don't really care how many atoms are 
> involved just the box size (you have nearly 8x more grid points). With 
> the wavelet poisson solver you only need around 5A space around the 
> system to be OK but having to be cubic means you are limited by the 
> largest dimension of your molecule. If it is very much bigger in one 
> direction you might be better with analytic poisson solver and a 
> non-cubic box.
>
> Matt
>
> On Tuesday, September 22, 2020 at 3:14:58 PM UTC+1 
> pier... at gmail.com wrote:
>
>     Dear Marcella,
>
>     Please find as attached document two output files. The first
>     aco-mo.inp contains the results for a crystal made of 78 atoms.
>     This is a normal condensed phase calculation. The second opt.out
>     is for the gas phase system made of 75 atoms. The systems have
>     nothing in common.
>
>     I would like to attract your attention that the grid cutoffs of
>     aco-mo.inp are much larger than those of opt.inp, and yet
>     aco-mo.inp is much faster than opt.inp.
>
>     I am also running the gas phase system on a single node of a
>     cluster with 40 MPI tasks. The calculation is obviously faster
>     than on my workstation but still frustratingly slow.
>
>     Regards,
>     Pierre
>
>
>     On 22/09/2020 14:00, Marcella Iannuzzi wrote:
>>     Dear Pierre,
>>
>>     from the timings in the output you should be able to determine
>>     where the calculation is spending most of the time and compare to
>>     the condensed matter calculation. Most probably OMP is not the
>>     most efficient in this case to parallelise. Have you tried with 8
>>     tasks instead.
>>     Regards
>>     Marcella
>>
>>
>>     On Tuesday, September 22, 2020 at 1:53:36 PM UTC+2
>>     pier... at gmail.com wrote:
>>
>>         Hi Marcella,
>>
>>         I am trying to run the calculation on my workstation with
>>         just OMP (8 threads). This usually works for condensed phase
>>         with a two hundred atoms so I thought it would be fine for
>>         just 75 atoms. Anyway, I reduced the cutoffs and it seems to
>>         be helping a lot but it is still slow and require a lot of
>>         memory. Please find as attached document the input file I am
>>         using.
>>
>>         Regards,
>>         Pierre
>>
>>
>>         On 22/09/2020 11:06, Marcella Iannuzzi wrote:
>>>         Dear Pierre,
>>>
>>>         Without additional information, like input, output, scaling
>>>         with the number of processors ...,
>>>         it is not possible fo provide any help.
>>>         Regards
>>>         Marcella
>>>
>>>
>>>         On Monday, September 21, 2020 at 1:09:03 PM UTC+2
>>>         pier... at gmail.com wrote:
>>>
>>>             Dear CP2K users,
>>>
>>>             I would like to know how to perform a gas phase
>>>             calculation with CP2K. I tried to follow some of the
>>>             examples available in the tutorials but they lead to
>>>             very slow and heavy calculations for a system with only
>>>             75 atoms.
>>>
>>>             I used wavelet for the Poisson solver, I set periodic
>>>             none for both the solver and the cell. The cell is cubic
>>>             with a size of 26.250 A. I am using DFT (PBE) with OT.
>>>             Should the number of grid be changed compared to a
>>>             condensed phase? What about the cutoffs?
>>>
>>>             Alternatively, I tried the periodic approach with a
>>>             larger cell so that the molecule "does not interact"
>>>             with its periodic image .Yet again, the calculation is
>>>             extremely demanding in terms of memory which makes the
>>>             OS kill the job.
>>>
>>>             Is there a solution to these problems?
>>>
>>>             Regards,
>>>             Pierre
>>>
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>>
>>         -- 
>>         Dr Pierre Cazade, PhD
>>         AD3-023, Bernal Institute,
>>         University of Limerick,
>>         Plassey Park Road,
>>         Castletroy, co. Limerick,
>>         Ireland
>>
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>
>     -- 
>     Dr Pierre Cazade, PhD
>     AD3-023, Bernal Institute,
>     University of Limerick,
>     Plassey Park Road,
>     Castletroy, co. Limerick,
>     Ireland
>
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-- 
Dr Pierre Cazade, PhD
AD3-023, Bernal Institute,
University of Limerick,
Plassey Park Road,
Castletroy, co. Limerick,
Ireland

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