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Hi Bingxin,
<div class=""><br class="">
</div>
<div class="">Thanks for the clarifications. I am still confused on your last statement. If you have problems with running a simulation you should try to explain what did not work and give actual explanations on what you did and what you got. The statement
that the parabolic correction method cannot do the dipole correction automatically makes no sense to me, since for a neutral system the parabolic correction is the dipole correction. </div>
<div class=""><br class="">
</div>
<div class="">Here I am trying to figure out without any indication what may have gone wrong. My best bet is that you did not see the expected behavior in the electrostatic potential. If this is the case and you are plotting the electrostatic potential using
PP, I can confirm you that you will not see the contributions of Environ in the PP output. You need to exploit the output of Environ to plot the potential (namely set verbosity > 2 in Environ and analyze the *.cube files). </div>
<div class=""><br class="">
</div>
<div class="">You are clearly fine with doing Environ simulations with PBC, but if you do have problems with the electrostatic corrections it would be better to sort them out now, before later. </div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class=""><br class="">
</div>
<div class="">Oliviero</div>
<div class=""><br class="">
<div class="">
<div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
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Oliviero Andreussi<br class="">
--<br class="">
Assistant Professor<br class="">
Department of Physics<br class="">
University of North Texas<br class="">
<a href="mailto:oliviero.andreussi@unt.edu" class="">Email: oliviero.andreussi@unt.edu</a> </div>
<div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">
Phone: +1-(940)-369-5316<br class="">
Skype: olivieroandreussi<br class="">
Web: <a href="https://sites.google.com/site/olivieroandreussi" class="">https://sites.google.com/site/olivieroandreussi</a></div>
</div>
</div>
</div>
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Feb 27, 2020, at 5:20 AM, Li, Bingxin <<a href="mailto:bingxin.li18@imperial.ac.uk" class="">bingxin.li18@imperial.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="">Dear Oliviero,<br class="">
<br class="">
Thanks for your reply. Sorry for the confusing statements in my last e-mail. Actually, the calculated system is a neutral Mg slab with some neutral hydroxyl groups on one side of it. Basically, the system does not have any extra charges but has an extra dipole
along the direction vertical to the slab. Due to this extra dipole, the vacuum potential in different sides of the slab is different, which means it is necessary to do the dipole correction to ensure the vacuum potential is horizontal rather than with slope.
<br class="">
<br class="">
Actually, I have done the calculation with parabolic correction method and found it cannot do the dipole correction automatically. According to your suggestions, I feel it is better to close the parabolic correction for a neutral slab calculation. <br class="">
<br class="">
Best Regards,<br class="">
BIngxin<br class="">
<br class="">
On 27/02/2020, 11:03, "users on behalf of <a href="mailto:users-request@lists.quantum-espresso.org" class="">
users-request@lists.quantum-espresso.org</a>" <<a href="mailto:users-bounces@lists.quantum-espresso.org" class="">users-bounces@lists.quantum-espresso.org</a> on behalf of
<a href="mailto:users-request@lists.quantum-espresso.org" class="">users-request@lists.quantum-espresso.org</a>> wrote:<br class="">
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Today's Topics:<br class="">
<br class="">
1. Question about parabolic correction method in Environ<br class="">
(Li, Bingxin)<br class="">
2. Re: [EXT] Question about parabolic correction method in<br class="">
Environ (Andreussi, Oliviero)<br class="">
3. Parallelizing QE/SternheimerGW Germanium (grayj6)<br class="">
4. Re: Parallelizing QE/SternheimerGW Germanium (Paolo Giannozzi)<br class="">
5. Re: Parallelizing QE/SternheimerGW Germanium (grayj6)<br class="">
6. How to plot the fat bands (Abhijeet Jaysingrao Kale (P18PH001))<br class="">
<br class="">
<br class="">
----------------------------------------------------------------------<br class="">
<br class="">
Message: 1<br class="">
Date: Wed, 26 Feb 2020 16:46:42 +0000<br class="">
From: "Li, Bingxin" <bingxin.li18@imperial.ac.uk><br class="">
To: "users@lists.quantum-espresso.org"<br class="">
<span class="Apple-tab-span" style="white-space:pre"> </span><users@lists.quantum-espresso.org><br class="">
Subject: [QE-users] Question about parabolic correction method in<br class="">
<span class="Apple-tab-span" style="white-space:pre"> </span>Environ<br class="">
Message-ID: <E5A065D4-B0E3-4F32-8BAB-71CF3D9D4DE2@ic.ac.uk><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Dear all,<br class="">
<br class="">
Recently I am using Environ + QE to calculate the work function of Mg(0001) surface based on slab model. I have calculate the work function of slab model in vacuum. Now I want to calculate that in water (implicit solvent). But I have add some hydroxyl groups
on the surface, which means it is necessary to do the dipole correction to obtain accurate vacuum potential. There is a parabolic correction method in Environ, which can treat the charged slab in vacuum/solvent. However, I find this method cannot do the dipole
correction for the neutral slab. Can I closed PBC term in the environment input file and do the dipole correction in the QE input? Is this parameter (Pbc: parabolic) necessary to do the implicit solvent calculation?<br class="">
<br class="">
Could anyone understand this and help me?<br class="">
<br class="">
Best Regards,<br class="">
Bingxin<br class="">
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<br class="">
------------------------------<br class="">
<br class="">
Message: 2<br class="">
Date: Wed, 26 Feb 2020 17:00:49 +0000<br class="">
From: "Andreussi, Oliviero" <Oliviero.Andreussi@unt.edu><br class="">
To: Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org><br class="">
Subject: Re: [QE-users] [EXT] Question about parabolic correction<br class="">
<span class="Apple-tab-span" style="white-space:pre"> </span>method in Environ<br class="">
Message-ID: <2CDA66A8-0168-4538-9AFE-03ECA291525F@unt.edu><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Hi Bingxin,<br class="">
<br class="">
The pbc_correction = parabolic option in Environ is not necessary, you should be able to perform the implicit solvent calculation even with pbc. However, it is highly recommended that you remove pbc artifacts if you are studying slabs systems, in particular
if they have a finite dipole moment in the direction perpendicular to the slab.<br class="">
<br class="">
Having said this, there are a couple of statements in your email that I find confusing. Is your system neutral or charged? When you say that the parabolic correction cannot do the dipole correction for the neutral slab, you mean a slab without a dipole or
a slab without a charge?<br class="">
<br class="">
If you are studying charge neutral slabs, then you should be able to apply the parabolic correction to both the slab without the hydroxyl and the slab with the hydroxyl, both in vacuum and in solution. All these simulations should work reasonably smoothly
in Environ. Note that if you want to only perform the parabolic correction on a slab without the implicit solvent, in environ you need to specify env_electrostatic = .true.. Otherwise, if there is no dielectric and no diffuse layer, Environ will skip the electrostatic
corrections.<br class="">
<br class="">
If you are studying a charged slab, i.e. you are adding negative hydroxyls to your slab, the parabolic correction alone will not be a physically sound model. Charged periodic 2D systems have infinite energy, in reality the charge on the slab should be compensated
by the electrolyte in solution. Thus, even though the parabolic correction will work, the energy you will get will depend on the size of the cell (growing linearly as you increase the direction perpendicular to the slab). For a realistic model you would need
to include a diffuse layer, which can still be done with Environ. The easiest option is to use pbc_correction = ?gcs?, but you would need to specify a couple of other details. If this is what you are trying to do, let me know and I will try to help.<br class="">
<br class="">
Hope this helps.<br class="">
<br class="">
Best,<br class="">
<br class="">
Oliviero<br class="">
<br class="">
Oliviero Andreussi<br class="">
--<br class="">
Assistant Professor<br class="">
Department of Physics<br class="">
University of North Texas<br class="">
Email: oliviero.andreussi@unt.edu<mailto:oliviero.andreussi@unt.edu><br class="">
Phone: +1-(940)-369-5316<br class="">
Skype: olivieroandreussi<br class="">
Web: https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsites.google.com%2Fsite%2Folivieroandreussi&data=02%7C01%7Coliviero.andreussi%40unt.edu%7C7fed9c55a4d2471afdc108d7bb772050%7C70de199207c6480fa318a1afcba03983%7C0%7C1%7C637183992650023619&sdata=5BcCiKaj6zVIp%2FGCpPp0%2FZUhxoTVKrtXopYJ31mqLqw%3D&reserved=0<br class="">
<br class="">
On Feb 26, 2020, at 10:46 AM, Li, Bingxin <bingxin.li18@imperial.ac.uk<mailto:bingxin.li18@imperial.ac.uk>> wrote:<br class="">
<br class="">
Dear all,<br class="">
<br class="">
Recently I am using Environ + QE to calculate the work function of Mg(0001) surface based on slab model. I have calculate the work function of slab model in vacuum. Now I want to calculate that in water (implicit solvent). But I have add some hydroxyl groups
on the surface, which means it is necessary to do the dipole correction to obtain accurate vacuum potential. There is a parabolic correction method in Environ, which can treat the charged slab in vacuum/solvent. However, I find this method cannot do the dipole
correction for the neutral slab. Can I closed PBC term in the environment input file and do the dipole correction in the QE input? Is this parameter (Pbc: parabolic) necessary to do the implicit solvent calculation?<br class="">
<br class="">
Could anyone understand this and help me?<br class="">
<br class="">
Best Regards,<br class="">
Bingxin<br class="">
_______________________________________________<br class="">
Quantum ESPRESSO is supported by MaX (https://nam04.safelinks.protection.outlook.com/?url=www.max-centre.eu%2Fquantum-espresso&data=02%7C01%7Coliviero.andreussi%40unt.edu%7C7fed9c55a4d2471afdc108d7bb772050%7C70de199207c6480fa318a1afcba03983%7C0%7C1%7C637183992650023619&sdata=u2A1TNeMHdCwMmtVyV7ztcSVw3b9Ygit9Q2UOjw%2B8c4%3D&reserved=0)<br class="">
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------------------------------<br class="">
<br class="">
Message: 3<br class="">
Date: Wed, 26 Feb 2020 13:30:56 -0500<br class="">
From: grayj6 <grayj6@rpi.edu><br class="">
To: users@lists.quantum-espresso.org<br class="">
Subject: [QE-users] Parallelizing QE/SternheimerGW Germanium<br class="">
Message-ID: <ded55414f8be34ee008ed4137f827888@rpi.edu><br class="">
Content-Type: text/plain; charset=UTF-8; format=flowed<br class="">
<br class="">
Hello,<br class="">
<br class="">
I have a calculation of Germanium that I would like to run, but I am <br class="">
uncertain as to how to parallelize it. I have a kpt_grid of 4, 4, 4 and <br class="">
a qpt_grid of 4, 4, 4. The number of bands, num_band is 18. I did the <br class="">
scf calculation on a kpoint grid of 8 8 8 0 0 0.<br class="">
<br class="">
My current submit command is:<br class="">
mpirun -np 4 /home/grayj6/data/q-e-qe-6.3/SternheimerGW/main/bin/gw.x <br class="">
-npool 4 < gw.in >gw.out<br class="">
<br class="">
... but I do not observe any noticeable speed ups when I add in nbgrp or <br class="">
ntask parallelization.<br class="">
<br class="">
Thank you!<br class="">
<br class="">
<br class="">
------------------------------<br class="">
<br class="">
Message: 4<br class="">
Date: Wed, 26 Feb 2020 19:43:51 +0100<br class="">
From: Paolo Giannozzi <p.giannozzi@gmail.com><br class="">
To: Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org><br class="">
Subject: Re: [QE-users] Parallelizing QE/SternheimerGW Germanium<br class="">
Message-ID:<br class="">
<span class="Apple-tab-span" style="white-space:pre"> </span><CAPMgbCs_qmrGK0XAJw0vOkSdk1uXokPA9YA_VsmxSyAY9iVaMA@mail.gmail.com><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Parallelization levels do not appear spontaneously: they have to be<br class="">
implemented, sometimes with a lot of effort. Somewhere in the documentation<br class="">
of SternheimerGW it must be stated which parallelization levels are<br class="">
available: presumably, k-point and/or plane-wave parallelization. The two<br class="">
parallelization levels you mention are implemented only in a subset of QE<br class="">
codes.<br class="">
<br class="">
Paolo<br class="">
<br class="">
On Wed, Feb 26, 2020 at 7:31 PM grayj6 <grayj6@rpi.edu> wrote:<br class="">
<br class="">
<blockquote type="cite" class="">Hello,<br class="">
<br class="">
I have a calculation of Germanium that I would like to run, but I am<br class="">
uncertain as to how to parallelize it. I have a kpt_grid of 4, 4, 4 and<br class="">
a qpt_grid of 4, 4, 4. The number of bands, num_band is 18. I did the<br class="">
scf calculation on a kpoint grid of 8 8 8 0 0 0.<br class="">
<br class="">
My current submit command is:<br class="">
mpirun -np 4 /home/grayj6/data/q-e-qe-6.3/SternheimerGW/main/bin/gw.x<br class="">
-npool 4 < gw.in >gw.out<br class="">
<br class="">
... but I do not observe any noticeable speed ups when I add in nbgrp or<br class="">
ntask parallelization.<br class="">
<br class="">
Thank you!<br class="">
_______________________________________________<br class="">
Quantum ESPRESSO is supported by MaX (https://nam04.safelinks.protection.outlook.com/?url=www.max-centre.eu%2Fquantum-espresso&data=02%7C01%7Coliviero.andreussi%40unt.edu%7C7fed9c55a4d2471afdc108d7bb772050%7C70de199207c6480fa318a1afcba03983%7C0%7C1%7C637183992650033614&sdata=OsZMKGfOE9ZdQHgJcaLzYfJfYuxny9OfILKA6GM0QGc%3D&reserved=0)<br class="">
users mailing list users@lists.quantum-espresso.org<br class="">
https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.quantum-espresso.org%2Fmailman%2Flistinfo%2Fusers&data=02%7C01%7Coliviero.andreussi%40unt.edu%7C7fed9c55a4d2471afdc108d7bb772050%7C70de199207c6480fa318a1afcba03983%7C0%7C1%7C637183992650033614&sdata=vgy8n1XUh67PRy%2F2CsB6rQlcR3Je5kaLJQyPnz24lqo%3D&reserved=0<br class="">
<br class="">
</blockquote>
<br class="">
<br class="">
-- <br class="">
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br class="">
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br class="">
Phone +39-0432-558216, fax +39-0432-558222<br class="">
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<br class="">
------------------------------<br class="">
<br class="">
Message: 5<br class="">
Date: Wed, 26 Feb 2020 14:31:07 -0500<br class="">
From: grayj6 <grayj6@rpi.edu><br class="">
To: Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org><br class="">
Subject: Re: [QE-users] Parallelizing QE/SternheimerGW Germanium<br class="">
Message-ID: <67b100cbbfc65d72402a0012fd8b2f99@rpi.edu><br class="">
Content-Type: text/plain; charset=UTF-8; format=flowed<br class="">
<br class="">
So it looks like they implement two levels of parallelization; npool and <br class="">
nimage although nimage seems to be defined differently. Running on Np <br class="">
processors with Nk x Nk x Nk kpoints and Ni images, there must be a nice <br class="">
ratio of Ni to Nk and Np which is effecient.<br class="">
<br class="">
"With the pool parallelization,<br class="">
we distribute different k or q points to different processors. This <br class="">
method is very efficient for both G and W,<br class="">
if the number of these points is a multiple of the number of CPUs. The <br class="">
image parallelization distributes G<br class="">
vectors used in the linear response and Fourier transform to different <br class="">
CPU. For the calculation of W, this<br class="">
parallelization is very efficient because the solution of<br class="">
the linear-response equation for each G vector is independent of the <br class="">
other G vectors." from - Lambert, Henry, and Feliciano Giustino. "Ab <br class="">
initio Sternheimer-GW method for quasiparticle calculations using plane <br class="">
waves." Physical Review B 88.7 (2013): 075117.<br class="">
<br class="">
On 2020-02-26 13:43, Paolo Giannozzi wrote:<br class="">
<blockquote type="cite" class="">Parallelization levels do not appear spontaneously: they have to be<br class="">
implemented, sometimes with a lot of effort. Somewhere in the<br class="">
documentation of SternheimerGW it must be stated which parallelization<br class="">
levels are available: presumably, k-point and/or plane-wave<br class="">
parallelization. The two parallelization levels you mention are<br class="">
implemented only in a subset of QE codes.<br class="">
<br class="">
Paolo<br class="">
<br class="">
On Wed, Feb 26, 2020 at 7:31 PM grayj6 <grayj6@rpi.edu> wrote:<br class="">
<br class="">
<blockquote type="cite" class="">Hello,<br class="">
<br class="">
I have a calculation of Germanium that I would like to run, but I<br class="">
am<br class="">
uncertain as to how to parallelize it. I have a kpt_grid of 4, 4, 4<br class="">
and<br class="">
a qpt_grid of 4, 4, 4. The number of bands, num_band is 18. I did<br class="">
the<br class="">
scf calculation on a kpoint grid of 8 8 8 0 0 0.<br class="">
<br class="">
My current submit command is:<br class="">
mpirun -np 4<br class="">
/home/grayj6/data/q-e-qe-6.3/SternheimerGW/main/bin/gw.x<br class="">
-npool 4 < gw.in [1] >gw.out<br class="">
<br class="">
... but I do not observe any noticeable speed ups when I add in<br class="">
nbgrp or<br class="">
ntask parallelization.<br class="">
<br class="">
Thank you!<br class="">
_______________________________________________<br class="">
Quantum ESPRESSO is supported by MaX<br class="">
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------------------------------<br class="">
<br class="">
Message: 6<br class="">
Date: Thu, 27 Feb 2020 16:06:24 +0530<br class="">
From: "Abhijeet Jaysingrao Kale (P18PH001)" <kale.2@iitj.ac.in><br class="">
To: users@lists.quantum-espresso.org<br class="">
Subject: [QE-users] How to plot the fat bands<br class="">
Message-ID:<br class="">
<span class="Apple-tab-span" style="white-space:pre"> </span><CAPMT7LgStWqhmGxQjn0j6JERsfW50yWQvafPk1xX=CZS8KfSaw@mail.gmail.com><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Dear QE users,<br class="">
<br class="">
I am Abhijeet, from IIT Jodhpur (India) working with the QE-6.0 version. I<br class="">
would like to plot Fat bands.<br class="">
<br class="">
After using the *pw.x, bands.x, projwfc.x, *and* plotband.x* executables<br class="">
respectively, I've got *casebands.dat, caseproj.dat, caseproj.dat.proj*<br class="">
files along with general output files. I am unable to figure out how to<br class="">
plot the fat bands using the data in the above files. Please help. Thanks.<br class="">
<br class="">
regards,<br class="">
Abhijeet.<br class="">
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