[QE-users] Requested some guidelines in First-principles molecular dynamics

[Md. Jahid Hasan Sagor]

Hi Dr. Paulatto,

Thank you for your advice. I also like your idea about epsilon.x. But the
dielectric function we get using epsilon.x (QE), Isn't it for only 0 K? How
can I extend it to another temperature?

Best
Md Jahid

On Thu, Jan 11, 2024 at 2:36 PM Lorenzo Paulatto <lorenzo.paulatto at cnrs.fr>
wrote:

>
> On 11/01/2024 20:06, Md. Jahid Hasan Sagor wrote:
>
> Hi Dr. Paulatto,
>
> Thank you so much for your suggestions. I was going in the wrong
> direction. So if I use your recommended code (
> https://anharmonic.github.io/thermal2/#d3_r2qx-code), would I be able to
> generate the following figure for Bulk GaAs?
>
> No. The anharmonic code is about vibrational properties.
>
>
> Actually my main goal is to calculate dielectric function at different
> temperatures (not 0 K).
>
> You can try to do like in the paper. Or you can try a different approach,
> i.e. replacing the sampling via molecular dynamics with a stochastic
> sampling, like the one provided by the SSCHA code http://sscha.eu/, which
> is also compatible with QE. Anyway, the supercell they use is tiny (8
> atoms, which is just the simple-cubic form of GaAs), you should be able to
> use the epsilon.x code that comes with QE (check the manual in
> PP/Doc/man_eps.pdf). I would say, start with just epsilon as a function of
> the volume, test convergence and see if you can afford it,.
>
> kind regards
>
>
>
> Thanks
> Md Jahid Hasan
>
> On Thu, Jan 11, 2024 at 9:19 AM Lorenzo Paulatto <lorenzo.paulatto at cnrs.fr>
> wrote:
>
>> Hello Jahid,
>>
>> I have read the article very quickly, but I do not think they use the RMS
>> to compute epsilon. All they do is compute epsilon for a few sample atomic
>> potisions reached during the MD run, then they average it. The "Theoretical
>> Method" section does not have any logic, but it is explained in the
>> "Conclusions". The RMS seems to be only used to ascertain the validity of
>> the simulation.
>> hth
>>
>> On 1/11/24 04:42, Md. Jahid Hasan Sagor wrote:
>>
>> Hi Dr. Paulatto,
>>
>> Thank you so much for your comments.
>>
>> Actually, The paper (attached) extracted the temperature of each
>> configuration from the mean square displacement per atom of the
>> configuration (GaAs). In the harmonic approximation, they determined the
>> relationship between  mean square displacement and temperature T from the
>> phonon density of states of bulk GaAs calculated by Giannozzi et al. The
>> equation as follows:
>>
>> [image: image.png]
>> Here is the figure they generated
>> [image: image.png]
>>
>> So, now If I can find out the RMS of GaAs using CPMD, I will try to
>> observe the corresponding configuration of GaAs atoms. Finally, the atomic
>> positions will be the input of Quantum Espresso pw.x etc ( I mean normally
>> how do we calculate dielectric constant in QE).
>>
>> Can I use  it ( https://anharmonic.github.io/thermal2/#d3_r2qx-code) for
>> the same purpose?
>>
>> Best
>> Hasan
>>
>>
>> On Wed, Jan 10, 2024 at 3:13 PM Lorenzo Paulatto <
>> lorenzo.paulatto at cnrs.fr> wrote:
>>
>>> I would guess that you calculate the static dielectric constant at the
>>> temperature-dependent volume (experimental, or quasi-harmonic) and you are
>>> 90% of the way there. Do you have a specific reason to believe that it
>>> would be proportional to the RMS ?
>>>
>>> Btw, the code d3_r2q.x included with the "anharmonic" package can
>>> compute the RMS from an inexpensive phonon calculation, maybe have a look
>>> at it before doing a large supercell MD.
>>>
>>> https://anharmonic.github.io/thermal2/#d3_r2qx-code
>>> cheers
>>>
>>> On 10/01/2024 19:35, Md. Jahid Hasan Sagor wrote:
>>>
>>> Actually, I have to calculate Dielectric constant for GaAs for different
>>> temperatures (not 0 k). To do that, I need to extract atomic positions for
>>> different RMS using CPMD. If anyone know someone/ or give some guidelines,
>>> it would be great help for me.
>>>
>>> Thank you.
>>>
>>> On Tue, Jan 9, 2024, 2:09 PM Md. Jahid Hasan Sagor <md.sagor at maine.edu>
>>> wrote:
>>>
>>>> Dear QE community,
>>>>
>>>> I want to calculate the mean square displacement of GaAs using CPMD.
>>>> From the mean square displacement, I want to extract the configuration of
>>>> atoms (e.g atomic position of Ga and As). Could anyone please give me some
>>>> guidelines on how I can perform it? Should I use only the cp.x package or
>>>> by other means? Your time and suggestions would be a great help for me.
>>>>
>>>> Best Regards
>>>> Md Jahid Hasan
>>>> PhD Student, Mechanical Engineering
>>>> University of Maine
>>>>
>>>
>>> _______________________________________________
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>>>
>>> --
>>> Dr. Lorenzo Paulatto
>>> IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université
>>> phone: +33 (0)1 442 79822 / skype: paulatz
>>> http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
>>> 23-24/423 B115, 4 place Jussieu 75252 Paris CX 05
>>> _______________________________________________
>>> 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
>>
>> --
>> Dr. Lorenzo Paulatto
>> IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université
>> phone: +33 (0)1 442 79822 / skype: paulatz
>> http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
>> 23-24/423 B115, 4 place Jussieu 75252 Paris CX 05
>>
> --
> Dr. Lorenzo Paulatto
> IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université
> phone: +33 (0)1 442 79822 / skype: paulatz
> http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
> 23-24/423 B115, 4 place Jussieu 75252 Paris CX 05
>
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