[QE-users] [EXT] Question about parabolic correction method in Environ (Andreussi, Oliviero)
Li, Bingxin
bingxin.li18 at imperial.ac.uk
Thu Feb 27 12:20:17 CET 2020
Dear Oliviero,
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.
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.
Best Regards,
BIngxin
On 27/02/2020, 11:03, "users on behalf of users-request at lists.quantum-espresso.org" <users-bounces at lists.quantum-espresso.org on behalf of users-request at lists.quantum-espresso.org> wrote:
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Today's Topics:
1. Question about parabolic correction method in Environ
(Li, Bingxin)
2. Re: [EXT] Question about parabolic correction method in
Environ (Andreussi, Oliviero)
3. Parallelizing QE/SternheimerGW Germanium (grayj6)
4. Re: Parallelizing QE/SternheimerGW Germanium (Paolo Giannozzi)
5. Re: Parallelizing QE/SternheimerGW Germanium (grayj6)
6. How to plot the fat bands (Abhijeet Jaysingrao Kale (P18PH001))
----------------------------------------------------------------------
Message: 1
Date: Wed, 26 Feb 2020 16:46:42 +0000
From: "Li, Bingxin" <bingxin.li18 at imperial.ac.uk>
To: "users at lists.quantum-espresso.org"
<users at lists.quantum-espresso.org>
Subject: [QE-users] Question about parabolic correction method in
Environ
Message-ID: <E5A065D4-B0E3-4F32-8BAB-71CF3D9D4DE2 at ic.ac.uk>
Content-Type: text/plain; charset="utf-8"
Dear all,
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?
Could anyone understand this and help me?
Best Regards,
Bingxin
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Message: 2
Date: Wed, 26 Feb 2020 17:00:49 +0000
From: "Andreussi, Oliviero" <Oliviero.Andreussi at unt.edu>
To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
Subject: Re: [QE-users] [EXT] Question about parabolic correction
method in Environ
Message-ID: <2CDA66A8-0168-4538-9AFE-03ECA291525F at unt.edu>
Content-Type: text/plain; charset="utf-8"
Hi Bingxin,
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.
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?
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.
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.
Hope this helps.
Best,
Oliviero
Oliviero Andreussi
--
Assistant Professor
Department of Physics
University of North Texas
Email: oliviero.andreussi at unt.edu<mailto:oliviero.andreussi at unt.edu>
Phone: +1-(940)-369-5316
Skype: olivieroandreussi
Web: https://sites.google.com/site/olivieroandreussi
On Feb 26, 2020, at 10:46 AM, Li, Bingxin <bingxin.li18 at imperial.ac.uk<mailto:bingxin.li18 at imperial.ac.uk>> wrote:
Dear all,
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?
Could anyone understand this and help me?
Best Regards,
Bingxin
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Message: 3
Date: Wed, 26 Feb 2020 13:30:56 -0500
From: grayj6 <grayj6 at rpi.edu>
To: users at lists.quantum-espresso.org
Subject: [QE-users] Parallelizing QE/SternheimerGW Germanium
Message-ID: <ded55414f8be34ee008ed4137f827888 at rpi.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed
Hello,
I have a calculation of Germanium that I would like to run, but I am
uncertain as to how to parallelize it. I have a kpt_grid of 4, 4, 4 and
a qpt_grid of 4, 4, 4. The number of bands, num_band is 18. I did the
scf calculation on a kpoint grid of 8 8 8 0 0 0.
My current submit command is:
mpirun -np 4 /home/grayj6/data/q-e-qe-6.3/SternheimerGW/main/bin/gw.x
-npool 4 < gw.in >gw.out
... but I do not observe any noticeable speed ups when I add in nbgrp or
ntask parallelization.
Thank you!
------------------------------
Message: 4
Date: Wed, 26 Feb 2020 19:43:51 +0100
From: Paolo Giannozzi <p.giannozzi at gmail.com>
To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
Subject: Re: [QE-users] Parallelizing QE/SternheimerGW Germanium
Message-ID:
<CAPMgbCs_qmrGK0XAJw0vOkSdk1uXokPA9YA_VsmxSyAY9iVaMA at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Parallelization levels do not appear spontaneously: they have to be
implemented, sometimes with a lot of effort. Somewhere in the documentation
of SternheimerGW it must be stated which parallelization levels are
available: presumably, k-point and/or plane-wave parallelization. The two
parallelization levels you mention are implemented only in a subset of QE
codes.
Paolo
On Wed, Feb 26, 2020 at 7:31 PM grayj6 <grayj6 at rpi.edu> wrote:
> Hello,
>
> I have a calculation of Germanium that I would like to run, but I am
> uncertain as to how to parallelize it. I have a kpt_grid of 4, 4, 4 and
> a qpt_grid of 4, 4, 4. The number of bands, num_band is 18. I did the
> scf calculation on a kpoint grid of 8 8 8 0 0 0.
>
> My current submit command is:
> mpirun -np 4 /home/grayj6/data/q-e-qe-6.3/SternheimerGW/main/bin/gw.x
> -npool 4 < gw.in >gw.out
>
> ... but I do not observe any noticeable speed ups when I add in nbgrp or
> ntask parallelization.
>
> Thank you!
> _______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
> users mailing list users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
>
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Message: 5
Date: Wed, 26 Feb 2020 14:31:07 -0500
From: grayj6 <grayj6 at rpi.edu>
To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
Subject: Re: [QE-users] Parallelizing QE/SternheimerGW Germanium
Message-ID: <67b100cbbfc65d72402a0012fd8b2f99 at rpi.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed
So it looks like they implement two levels of parallelization; npool and
nimage although nimage seems to be defined differently. Running on Np
processors with Nk x Nk x Nk kpoints and Ni images, there must be a nice
ratio of Ni to Nk and Np which is effecient.
"With the pool parallelization,
we distribute different k or q points to different processors. This
method is very efficient for both G and W,
if the number of these points is a multiple of the number of CPUs. The
image parallelization distributes G
vectors used in the linear response and Fourier transform to different
CPU. For the calculation of W, this
parallelization is very efficient because the solution of
the linear-response equation for each G vector is independent of the
other G vectors." from - Lambert, Henry, and Feliciano Giustino. "Ab
initio Sternheimer-GW method for quasiparticle calculations using plane
waves." Physical Review B 88.7 (2013): 075117.
On 2020-02-26 13:43, Paolo Giannozzi wrote:
> Parallelization levels do not appear spontaneously: they have to be
> implemented, sometimes with a lot of effort. Somewhere in the
> documentation of SternheimerGW it must be stated which parallelization
> levels are available: presumably, k-point and/or plane-wave
> parallelization. The two parallelization levels you mention are
> implemented only in a subset of QE codes.
>
> Paolo
>
> On Wed, Feb 26, 2020 at 7:31 PM grayj6 <grayj6 at rpi.edu> wrote:
>
>> Hello,
>>
>> I have a calculation of Germanium that I would like to run, but I
>> am
>> uncertain as to how to parallelize it. I have a kpt_grid of 4, 4, 4
>> and
>> a qpt_grid of 4, 4, 4. The number of bands, num_band is 18. I did
>> the
>> scf calculation on a kpoint grid of 8 8 8 0 0 0.
>>
>> My current submit command is:
>> mpirun -np 4
>> /home/grayj6/data/q-e-qe-6.3/SternheimerGW/main/bin/gw.x
>> -npool 4 < gw.in [1] >gw.out
>>
>> ... but I do not observe any noticeable speed ups when I add in
>> nbgrp or
>> ntask parallelization.
>>
>> Thank you!
>> _______________________________________________
>> Quantum ESPRESSO is supported by MaX
>> (www.max-centre.eu/quantum-espresso [2])
>> users mailing list users at lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users [3]
>
> --
>
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
> Links:
> ------
> [1] http://gw.in
> [2] http://www.max-centre.eu/quantum-espresso
> [3] https://lists.quantum-espresso.org/mailman/listinfo/users
>
> _______________________________________________
> Quantum ESPRESSO is supported by MaX
> (www.max-centre.eu/quantum-espresso)
> users mailing list users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
------------------------------
Message: 6
Date: Thu, 27 Feb 2020 16:06:24 +0530
From: "Abhijeet Jaysingrao Kale (P18PH001)" <kale.2 at iitj.ac.in>
To: users at lists.quantum-espresso.org
Subject: [QE-users] How to plot the fat bands
Message-ID:
<CAPMT7LgStWqhmGxQjn0j6JERsfW50yWQvafPk1xX=CZS8KfSaw at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear QE users,
I am Abhijeet, from IIT Jodhpur (India) working with the QE-6.0 version. I
would like to plot Fat bands.
After using the *pw.x, bands.x, projwfc.x, *and* plotband.x* executables
respectively, I've got *casebands.dat, caseproj.dat, caseproj.dat.proj*
files along with general output files. I am unable to figure out how to
plot the fat bands using the data in the above files. Please help. Thanks.
regards,
Abhijeet.
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