[QE-users] Clarification on the diffusion coefficient calculation

[Mauro Francesco Sgroi]

Dear  Kazume,
thanks a lot for the reply.
Thanks for the information.
I am not calculating the MSD by myself but just looking at the output of
pw.x at the end of the calculation. I suppose that the value printed by
Quantum Espresso is calculated using a certain number of MD timesteps. So
it should discard the initial part of the trajectory.
Do you know where I can find this information?

Moreover, is there a reference for the selection of raise in MD with
velocity rescaling?

Thanks a lot for your help and best regards,
Mauro.

_______________________

Dr. *Mauro Francesco Sgroi*

Department of Chemistry

University of Turin

Via P. Giuria, 9

I-10125 TORINO (Italy)

Tel.

+39 011-670-8372

+39 011-670-7364

e-mail: maurofrancesco.sgroi at unito.it

Web:

www.met.unito.it

www.chimica.unito.it

Orcid: https://orcid.org/0000-0002-0914-4217


Il giorno ven 24 mar 2023 alle ore 13:00 Kazume NISHIDATE <
nisidate at iwate-u.ac.jp> ha scritto:

> Dear Mauro Francesco Sgroi,
>
> > the diffusion coefficient is calculated using the full trajectory
> >  from the initial step or just using the last part of the trajectory
> >  calculated with the restarted calculation?
>
> This would mean that the diffusion constant evaluated from the "full
> trajectory" was different from the evaluated one only using the "later
> part of the trajectoroy". Right?
>
> In this case, the calculated diffusion cofficient is apparently
> affected by its 'particular' initial configuration and hence it is not
> suitable as a diffusion "constant" because it will vary depending on
> the initial configulation.
>
> The effect of the initial configuration may be weired off after
> several hundred thousand MD time steps, and you should always use the
> later part of the trajectory data to evaluate the diffusion
> "constant".
>
>
> > 2023/03/24 19:49、Mauro Francesco Sgroi <maurofrancesco.sgroi at unito.it
> >のメール:
> >
> > Dear all,
> > I would need a clarification about the calculation of the diffusion
> coefficient.
> > Using the restart function, the diffusion coefficient is calculated
> using the full trajectory from the initial step or just using the last part
> of the trajectory calculated with the restarted calculation?
> >
> > Many thanks in advance and best regards,
> > Mauro Sgroi.
> >  _______________________
> > Dr. Mauro Francesco Sgroi
> > Department of Chemistry University of Turin
> > Via P. Giuria, 9
> > I-10125 TORINO (Italy)
> > Tel.
> > +39 011-670-8372
> > +39 011-670-7364
> > e-mail: maurofrancesco.sgroi at unito.it
> > Web:
> > www.met.unito.it
> > www.chimica.unito.it
> > Orcid: https://orcid.org/0000-0002-0914-4217
> _______________________________________________
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>
>
> 西館数芽
> Kazume NISHIDATE Ph.D
>
> Department of Systems Innovation Engineering,
> Graduate School of Science and Engineering, Iwate University
> 4-3-5 Ueda, Morioka, Iwate, 020-8551 JAPAN
> Phone:+81-19-621-6391
> kazume.nishidate at gmail.com, nisidate at iwate-u.ac.jp
> https://sites.google.com/site/nisidatelab/
>
> _______________________________________________
> The Quantum ESPRESSO community stands by the Ukrainian
> people and expresses its concerns about the devastating
> effects that the Russian military offensive has on their
> country and on the free and peaceful scientific, cultural,
> and economic cooperation amongst peoples
> _______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
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