[QE-users] Bond population calculation

[Akhil g.nair via users]

Dear QE community,
I am writing to seek guidance on calculating the "mean bond population" using 
Quantum Espresso tools. I have come across a paper 
(https://doi.org/10.1016/j.ceramint.2022.06.028) where the authors performed a 
similar calculation using CASTEP, but I am interested in replicating it using 
Quantum Espresso.

I would appreciate it if anyone could provide assistance or share relevant 
information regarding this calculation.
Thank you for your time and consideration.
Best regards,
Akhil NairResearch scholar,HBNI, INDIA___
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Re: [QE-users] Requested some guidelines in First-principles molecular dynamics

[Lorenzo Paulatto]

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 
 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
 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
 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


___
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 listus...@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users
-- 
Dr. Lorenzo Paulatto

IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Univers

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

[Lorenzo Paulatto]

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 
 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
 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


___
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 listus...@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
___
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@lists.quantum-espresso.org
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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-