[QE-users] Requested some guidelines in First-principles molecular dynamics
Lorenzo Paulatto
lorenzo.paulatto at cnrs.fr
Fri Jan 12 09:00:52 CET 2024
On 1/11/24 20:57, Md. Jahid Hasan Sagor wrote:
> 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?
It is computed with an electronic temperature of 0K, but it is exactly
the same as in the paper you are trying to reproduce. But this is not a
big deal, there is very little direct effect of temperature on
electrons: compare the energy of thermal excitation (k_B T) with the
band gap of GaAs and you will see why. I.e. electron orbitals are far
too rigid to be affected by temperature, especially in insulators. Even
in metal we use fictitious electronic temperature to speed up
integration (aka smearing) that is of the order of 1'000K, and it does
not change the electronic structure much. The effect only come through
the motion of ions, so move the ions and you got finite temperature.
But do not believe me: change the electronic occupation to "smearing"
and set a Fermi-Dirca smearing which is equivalent to the temperature
you want (it is in Ry, i.e. 1 Ry = 157'887 K). Then see how, much the
total energy and band structure change. how many k-points do you need to
have a discernible Fermi surface at the to of valence band, etc.
hth
>
> 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.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
>
--
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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