[QE-users] Requested some guidelines in First-principles molecular dynamics
Lorenzo Paulatto
lorenzo.paulatto at cnrs.fr
Thu Jan 11 20:36:01 CET 2024
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.png
>> Here is the figure they generated
>> 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
>> <http://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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