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 [email protected]" <[email protected] on behalf of [email protected]> wrote: ******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Send users mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit https://lists.quantum-espresso.org/mailman/listinfo/users or, via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of users digest..." 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" <[email protected]> To: "[email protected]" <[email protected]> Subject: [QE-users] Question about parabolic correction method in Environ Message-ID: <[email protected]> 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20200226/9aaec621/attachment-0001.html> ------------------------------ Message: 2 Date: Wed, 26 Feb 2020 17:00:49 +0000 From: "Andreussi, Oliviero" <[email protected]> To: Quantum ESPRESSO users Forum <[email protected]> Subject: Re: [QE-users] [EXT] Question about parabolic correction method in Environ Message-ID: <[email protected]> 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: [email protected]<mailto:[email protected]> Phone: +1-(940)-369-5316 Skype: olivieroandreussi Web: https://sites.google.com/site/olivieroandreussi On Feb 26, 2020, at 10:46 AM, Li, Bingxin <[email protected]<mailto:[email protected]>> 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 _______________________________________________ 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%7C818a0dd2d5e14e76402308d7badb90c9%7C70de199207c6480fa318a1afcba03983%7C0%7C0%7C637183324514973413&sdata=J%2FsTe9Z17AhMuTOoABA4E2G1GrxWsAlkxqC6ZryDhmg%3D&reserved=0) users mailing list [email protected]<mailto:[email protected]> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.quantum-espresso.org%2Fmailman%2Flistinfo%2Fusers&data=02%7C01%7Coliviero.andreussi%40unt.edu%7C818a0dd2d5e14e76402308d7badb90c9%7C70de199207c6480fa318a1afcba03983%7C0%7C0%7C637183324514973413&sdata=2jLvz7iSQer99DABHq2obWb%2FgWVbOvVp7n0ECfKwCI4%3D&reserved=0 -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20200226/1bd34770/attachment-0001.html> ------------------------------ Message: 3 Date: Wed, 26 Feb 2020 13:30:56 -0500 From: grayj6 <[email protected]> To: [email protected] Subject: [QE-users] Parallelizing QE/SternheimerGW Germanium Message-ID: <[email protected]> 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 <[email protected]> To: Quantum ESPRESSO users Forum <[email protected]> Subject: Re: [QE-users] Parallelizing QE/SternheimerGW Germanium Message-ID: <capmgbcs_qmrgk0xajw0voksdk1uxokpa9ya_vsmxsyay9iv...@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 <[email protected]> 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 [email protected] > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20200226/8c8d0bcf/attachment-0001.html> ------------------------------ Message: 5 Date: Wed, 26 Feb 2020 14:31:07 -0500 From: grayj6 <[email protected]> To: Quantum ESPRESSO users Forum <[email protected]> Subject: Re: [QE-users] Parallelizing QE/SternheimerGW Germanium Message-ID: <[email protected]> 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 <[email protected]> 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 [email protected] >> 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 [email protected] > https://lists.quantum-espresso.org/mailman/listinfo/users ------------------------------ Message: 6 Date: Thu, 27 Feb 2020 16:06:24 +0530 From: "Abhijeet Jaysingrao Kale (P18PH001)" <[email protected]> To: [email protected] Subject: [QE-users] How to plot the fat bands Message-ID: <CAPMT7LgStWqhmGxQjn0j6JERsfW50yWQvafPk1xX=czs8kf...@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. -------------- next part -------------- An HTML attachment was scrubbed... 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