<div dir="ltr"><div dir="ltr"><div>Hello Pietro,</div><div>I'm sorry that was not clear in my question because i'm totally new to QE.</div><div>Yes, the structural relaxation</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, May 31, 2019 at 5:00 AM <<a href="mailto:users-request@lists.quantum-espresso.org">users-request@lists.quantum-espresso.org</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Send users mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. Oxygen PAW Pseudopotentials have 3d core electrons. (Amreen Bano)<br>
2. parallelization of pw.x (Michal Krompiec)<br>
3. Re: parallelization of pw.x (Giuseppe Mattioli)<br>
4. Re: parallelization of pw.x (Pietro Delugas)<br>
5. Re: parallelization of pw.x (Michal Krompiec)<br>
6. Re: Output files for ph.x (Appleton, Robert J)<br>
7. Re: Output files for ph.x (Paolo Giannozzi)<br>
8. Re: higher total energy in the last stage of vc-relax (Kevin May)<br>
9. Core wavefunction (emin klc)<br>
10. Re: Oxygen PAW Pseudopotentials have 3d core electrons.<br>
(Paolo Giannozzi)<br>
11. Large input problem (???)<br>
12. Relaxation of CaCO3 (Hassan Ahmed Mohammed)<br>
13. Re: Relaxation of CaCO3 (Pietro Davide Delugas)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 30 May 2019 08:53:55 -0500<br>
From: Amreen Bano <<a href="mailto:banoamreen.7@gmail.com" target="_blank">banoamreen.7@gmail.com</a>><br>
To: <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
Subject: [QE-users] Oxygen PAW Pseudopotentials have 3d core<br>
electrons.<br>
Message-ID:<br>
<CA+VtDcNJCri3s9f=TJk=<a href="mailto:e0rQK-XPA3WsovVsOEqAyepCYLYO0Q@mail.gmail.com" target="_blank">e0rQK-XPA3WsovVsOEqAyepCYLYO0Q@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear all,<br>
<br>
I am working Oxygen based clusters. After performing the Pdos calculation i<br>
found that O-3d states are also present. Why this is so? Is this an error<br>
in the PP file or something else. Kindly suggest me the if there is any<br>
problem with this PP.<br>
<br>
Thanks in advance.<br>
Amreen.<br>
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Message: 2<br>
Date: Thu, 30 May 2019 15:42:18 +0100<br>
From: Michal Krompiec <<a href="mailto:michal.krompiec@gmail.com" target="_blank">michal.krompiec@gmail.com</a>><br>
To: Quantum Espresso users Forum <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
Subject: [QE-users] parallelization of pw.x<br>
Message-ID:<br>
<<a href="mailto:CAOWoSSPpcqz4nTJirQi30hM5KQNyQRr5e-40U_2ropO2nQXuLw@mail.gmail.com" target="_blank">CAOWoSSPpcqz4nTJirQi30hM5KQNyQRr5e-40U_2ropO2nQXuLw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hello,<br>
I am trying to run a calculation on a 2D slab with a bit of adsorbate (119<br>
atoms in total), and I would like to parallelize it as much as possible. I<br>
am using a 3 3 1 Monkhorst-Pack grid (so I have 5 k-points).<br>
I tried using -npool 5 -nt 4 using 20 MPI processes and 5 threads per<br>
process but, as it seems, the speedup was just 3.7x:<br>
PWSCF : 1d 4h27m CPU 7h43m WALL<br>
What could have gone wrong, is there anything "obvious" I can do to<br>
diagnose the problem? I am using QE 6.4rc, compiled with gcc and OpenMPI,<br>
without ELPA.<br>
<br>
Best regards,<br>
<br>
Michal Krompiec<br>
<br>
Merck KGaA and University of Southampton<br>
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Message: 3<br>
Date: Thu, 30 May 2019 17:14:44 +0200<br>
From: Giuseppe Mattioli <<a href="mailto:giuseppe.mattioli@ism.cnr.it" target="_blank">giuseppe.mattioli@ism.cnr.it</a>><br>
To: Quantum ESPRESSO users Forum <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
Subject: Re: [QE-users] parallelization of pw.x<br>
Message-ID:<br>
<<a href="mailto:20190530171444.Horde.LA-Caab3_EJI1ko_PWRE3_7@webmail.sic.rm.cnr.it" target="_blank">20190530171444.Horde.LA-Caab3_EJI1ko_PWRE3_7@webmail.sic.rm.cnr.it</a>><br>
Content-Type: text/plain; charset=utf-8; format=flowed; DelSp=Yes<br>
<br>
<br>
Dear Michal<br>
Speed-up wrt what?<br>
<br>
> PWSCF : 1d 4h27m CPU 7h43m WALL<br>
<br>
AFAIK, the sensible quantity is WALL...<br>
HTH<br>
Giuseppe<br>
<br>
Quoting Michal Krompiec <<a href="mailto:michal.krompiec@gmail.com" target="_blank">michal.krompiec@gmail.com</a>>:<br>
<br>
> Hello,<br>
> I am trying to run a calculation on a 2D slab with a bit of adsorbate (119<br>
> atoms in total), and I would like to parallelize it as much as possible. I<br>
> am using a 3 3 1 Monkhorst-Pack grid (so I have 5 k-points).<br>
> I tried using -npool 5 -nt 4 using 20 MPI processes and 5 threads per<br>
> process but, as it seems, the speedup was just 3.7x:<br>
> PWSCF : 1d 4h27m CPU 7h43m WALL<br>
> What could have gone wrong, is there anything "obvious" I can do to<br>
> diagnose the problem? I am using QE 6.4rc, compiled with gcc and OpenMPI,<br>
> without ELPA.<br>
><br>
> Best regards,<br>
><br>
> Michal Krompiec<br>
><br>
> Merck KGaA and University of Southampton<br>
<br>
<br>
<br>
GIUSEPPE MATTIOLI<br>
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA<br>
Via Salaria Km 29,300 - C.P. 10<br>
I-00015 - Monterotondo Scalo (RM)<br>
Mob (*preferred*) +39 373 7305625<br>
Tel + 39 06 90672342 - Fax +39 06 90672316<br>
E-mail: <<a href="mailto:giuseppe.mattioli@ism.cnr.it" target="_blank">giuseppe.mattioli@ism.cnr.it</a>><br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Thu, 30 May 2019 17:18:46 +0200<br>
From: Pietro Delugas <<a href="mailto:pdelugas@sissa.it" target="_blank">pdelugas@sissa.it</a>><br>
To: <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
Subject: Re: [QE-users] parallelization of pw.x<br>
Message-ID: <<a href="mailto:23e09611-c434-c23f-7353-66a3f528c6dc@sissa.it" target="_blank">23e09611-c434-c23f-7353-66a3f528c6dc@sissa.it</a>><br>
Content-Type: text/plain; charset="utf-8"; Format="flowed"<br>
<br>
Dear Michal<br>
<br>
3.7x with respect to what ?<br>
<br>
your cut and paste refers to the wall time and the total cpu time per <br>
mpi task, they differ because you are using thread parallelism.<br>
<br>
if you don't have memory issues I would try to increase the number of <br>
mpi processes decreasing the number of thread and usually when the <br>
number on MPI tasks is smaller than the dimesions of the fft grid it is <br>
better to avoid using nt.<br>
<br>
Hope it helps<br>
<br>
regards<br>
<br>
Pietro<br>
<br>
On 30/05/19 16:42, Michal Krompiec wrote:<br>
> Hello,<br>
> I am trying to run a calculation on a 2D slab with a bit of adsorbate <br>
> (119 atoms in total), and I would like to parallelize it as much as <br>
> possible. I am using a 3 3 1 Monkhorst-Pack grid (so I have 5 k-points).<br>
> I tried using -npool 5 -nt 4 using 20 MPI processes and 5 threads per <br>
> process but, as it seems, the speedup was just 3.7x:<br>
> ? ?PWSCF ? ? ? ?: ? 1d 4h27m CPU ? ? ?7h43m WALL<br>
> What could have gone?wrong, is there anything "obvious" I can do to <br>
> diagnose the problem? I am using QE 6.4rc, compiled with gcc and <br>
> OpenMPI, without ELPA.<br>
><br>
> Best regards,<br>
><br>
> Michal Krompiec<br>
><br>
> Merck KGaA and University of Southampton<br>
><br>
> _______________________________________________<br>
> Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso" rel="noreferrer" target="_blank">www.max-centre.eu/quantum-espresso</a>)<br>
> users mailing list <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
> <a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br>
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<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Thu, 30 May 2019 16:59:15 +0100<br>
From: Michal Krompiec <<a href="mailto:michal.krompiec@gmail.com" target="_blank">michal.krompiec@gmail.com</a>><br>
To: Quantum ESPRESSO users Forum <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
Subject: Re: [QE-users] parallelization of pw.x<br>
Message-ID:<br>
<<a href="mailto:CAOWoSSMC-dHeHSemUcojbQFeKyYzve0e7NXL-%2BdBhXCVtRP%2BOA@mail.gmail.com" target="_blank">CAOWoSSMC-dHeHSemUcojbQFeKyYzve0e7NXL-+dBhXCVtRP+OA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Pietro, dear Giuseppe,<br>
Thanks, indeed my comment on speedup was hasty and didn?t make sense.<br>
Thanks for the suggestions regarding increasing number of mpi processes and<br>
not using nt.<br>
Best,<br>
Michal<br>
<br>
On Thu, 30 May 2019 at 16:18, Pietro Delugas <<a href="mailto:pdelugas@sissa.it" target="_blank">pdelugas@sissa.it</a>> wrote:<br>
<br>
> Dear Michal<br>
><br>
> 3.7x with respect to what ?<br>
><br>
> your cut and paste refers to the wall time and the total cpu time per mpi<br>
> task, they differ because you are using thread parallelism.<br>
><br>
> if you don't have memory issues I would try to increase the number of mpi<br>
> processes decreasing the number of thread and usually when the number on<br>
> MPI tasks is smaller than the dimesions of the fft grid it is better to<br>
> avoid using nt.<br>
><br>
> Hope it helps<br>
><br>
> regards<br>
><br>
> Pietro<br>
> On 30/05/19 16:42, Michal Krompiec wrote:<br>
><br>
> Hello,<br>
> I am trying to run a calculation on a 2D slab with a bit of adsorbate (119<br>
> atoms in total), and I would like to parallelize it as much as possible. I<br>
> am using a 3 3 1 Monkhorst-Pack grid (so I have 5 k-points).<br>
> I tried using -npool 5 -nt 4 using 20 MPI processes and 5 threads per<br>
> process but, as it seems, the speedup was just 3.7x:<br>
> PWSCF : 1d 4h27m CPU 7h43m WALL<br>
> What could have gone wrong, is there anything "obvious" I can do to<br>
> diagnose the problem? I am using QE 6.4rc, compiled with gcc and OpenMPI,<br>
> without ELPA.<br>
><br>
> Best regards,<br>
><br>
> Michal Krompiec<br>
><br>
> Merck KGaA and University of Southampton<br>
><br>
> _______________________________________________<br>
> Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso" rel="noreferrer" target="_blank">www.max-centre.eu/quantum-espresso</a>)<br>
> users mailing list users@lists.quantum-espresso.orghttps://<a href="http://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer" target="_blank">lists.quantum-espresso.org/mailman/listinfo/users</a><br>
><br>
> _______________________________________________<br>
> Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso" rel="noreferrer" target="_blank">www.max-centre.eu/quantum-espresso</a>)<br>
> users mailing list <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
> <a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br>
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<br>
Message: 6<br>
Date: Thu, 30 May 2019 18:13:18 +0000<br>
From: "Appleton, Robert J" <<a href="mailto:rapplet@calstatela.edu" target="_blank">rapplet@calstatela.edu</a>><br>
To: Quantum ESPRESSO users Forum <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
Subject: Re: [QE-users] Output files for ph.x<br>
Message-ID:<br>
<<a href="mailto:BN8PR06MB624280A0F519C8D2AD13DA48DA180@BN8PR06MB6242.namprd06.prod.outlook.com" target="_blank">BN8PR06MB624280A0F519C8D2AD13DA48DA180@BN8PR06MB6242.namprd06.prod.outlook.com</a>><br>
<br>
Content-Type: text/plain; charset="windows-1252"<br>
<br>
Has anyone had this experience where one of the dynamical matrices produced by ph.x was an empty file? I tried adding trans=.true. to the <a href="http://ph.in" rel="noreferrer" target="_blank">ph.in</a> file but this is the default and should of been already included. I executed the ph.x command but I am afraid I will have the same results and the process takes very long so I don?t want to keep running it if it is incorrect. Let me know if you have any suggestions.<br>
<br>
Robert<br>
<br>
Get Outlook for iOS<<a href="https://aka.ms/o0ukef" rel="noreferrer" target="_blank">https://aka.ms/o0ukef</a>><br>
________________________________<br>
From: users <<a href="mailto:users-bounces@lists.quantum-espresso.org" target="_blank">users-bounces@lists.quantum-espresso.org</a>> on behalf of Appleton, Robert J <<a href="mailto:rapplet@calstatela.edu" target="_blank">rapplet@calstatela.edu</a>><br>
Sent: Tuesday, May 28, 2019 2:50:34 PM<br>
To: <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
Subject: [QE-users] Output files for ph.x<br>
<br>
Hello,<br>
<br>
After running vc-relax and scf calculations on a material BaZrS3 I tried to run the ph.x command. The ph.out file was created along with 2 files containing the dynamical matrices. The bazrs.dyn0 file was fine but the bazrs.dyn1 file was completely empty. This meant I could not run q2r.x to calculate the IFC?s. Can someone explain why the file did not contain the dynamical matrix? Also I expected more then just the 2 files because an example I am following that someone did previously for a different structure they had .dyn0-13 while I only got .dyn0 and .dyn1 with .dyn1 being empty.<br>
<br>
I am still new to quantum espresso and any information could help.<br>
<br>
Thanks.<br>
<br>
Robert<br>
<br>
Get Outlook for iOS<<a href="https://aka.ms/o0ukef" rel="noreferrer" target="_blank">https://aka.ms/o0ukef</a>><br>
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<br>
Message: 7<br>
Date: Thu, 30 May 2019 21:56:39 +0200<br>
From: Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com" target="_blank">p.giannozzi@gmail.com</a>><br>
To: Quantum ESPRESSO users Forum <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
Subject: Re: [QE-users] Output files for ph.x<br>
Message-ID:<br>
<CAPMgbCsgD9mEcdorWer2a_zNHRp3U=<a href="mailto:vfx_cMSVgs8AGAVNy-cA@mail.gmail.com" target="_blank">vfx_cMSVgs8AGAVNy-cA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
On Thu, May 30, 2019 at 8:14 PM Appleton, Robert J <<a href="mailto:rapplet@calstatela.edu" target="_blank">rapplet@calstatela.edu</a>><br>
wrote:<br>
<br>
> Has anyone had this experience where one of the dynamical matrices<br>
> produced by ph.x was an empty file?<br>
><br>
<br>
yes, when the code crashes. Have a look at the output.<br>
<br>
Paolo<br>
<br>
I tried adding trans=.true. to the <a href="http://ph.in" rel="noreferrer" target="_blank">ph.in</a> file but this is the default and<br>
> should of been already included. I executed the ph.x command but I am<br>
> afraid I will have the same results and the process takes very long so I<br>
> don?t want to keep running it if it is incorrect. Let me know if you have<br>
> any suggestions.<br>
><br>
> Robert<br>
><br>
> Get Outlook for iOS <<a href="https://aka.ms/o0ukef" rel="noreferrer" target="_blank">https://aka.ms/o0ukef</a>><br>
> ------------------------------<br>
> *From:* users <<a href="mailto:users-bounces@lists.quantum-espresso.org" target="_blank">users-bounces@lists.quantum-espresso.org</a>> on behalf of<br>
> Appleton, Robert J <<a href="mailto:rapplet@calstatela.edu" target="_blank">rapplet@calstatela.edu</a>><br>
> *Sent:* Tuesday, May 28, 2019 2:50:34 PM<br>
> *To:* <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
> *Subject:* [QE-users] Output files for ph.x<br>
><br>
> Hello,<br>
><br>
> After running vc-relax and scf calculations on a material BaZrS3 I tried<br>
> to run the ph.x command. The ph.out file was created along with 2 files<br>
> containing the dynamical matrices. The bazrs.dyn0 file was fine but the<br>
> bazrs.dyn1 file was completely empty. This meant I could not run q2r.x to<br>
> calculate the IFC?s. Can someone explain why the file did not contain the<br>
> dynamical matrix? Also I expected more then just the 2 files because an<br>
> example I am following that someone did previously for a different<br>
> structure they had .dyn0-13 while I only got .dyn0 and .dyn1 with .dyn1<br>
> being empty.<br>
><br>
> I am still new to quantum espresso and any information could help.<br>
><br>
> Thanks.<br>
><br>
> Robert<br>
><br>
> Get Outlook for iOS <<a href="https://aka.ms/o0ukef" rel="noreferrer" target="_blank">https://aka.ms/o0ukef</a>><br>
> _______________________________________________<br>
> Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso" rel="noreferrer" target="_blank">www.max-centre.eu/quantum-espresso</a>)<br>
> users mailing list <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
> <a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br>
<br>
<br>
<br>
-- <br>
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br>
Phone +39-0432-558216, fax +39-0432-558222<br>
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<br>
Message: 8<br>
Date: Thu, 30 May 2019 19:54:29 -0400<br>
From: Kevin May <<a href="mailto:kmay@mit.edu" target="_blank">kmay@mit.edu</a>><br>
To: Quantum Espresso users Forum <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
Subject: Re: [QE-users] higher total energy in the last stage of<br>
vc-relax<br>
Message-ID:<br>
<CAE9EMVnnEwQXs--FL1WS_Sn0wAZny2VE_=GcJKuWKawcf8x=<a href="mailto:GA@mail.gmail.com" target="_blank">GA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Mehrdad,<br>
<br>
Just a few more thoughts:<br>
<br>
1) Which reference state are you using for Fe? Jiang et al. use ferromagnetic<br>
BCC Fe in Acta Materialia 56, 3236?3244 (2008). This paper uses constant<br>
volume rather than constant (zero) pressure calculations. I would<br>
definitely do spin polarized calculations. You mentioned your current<br>
pseudopotentials are not recommended for spin polarized calculations--I<br>
would use different ones.<br>
<br>
2) I'm not sure which pseudopotentials you are using exactly, but I have<br>
had good results using those in the Standard Solid State Pseudopotentials<br>
(SSSP) tables, which comes from very useful work of a team at EPFL (<br>
<a href="https://www.materialscloud.org/discover/sssp/" rel="noreferrer" target="_blank">https://www.materialscloud.org/discover/sssp/</a>). In your case, this would be<br>
from PSLibrary 0.3.1 PAW for Fe and PSLibrary 1.0.0 PAW for C. Note the<br>
recommended ecutrho is 12*ecutwfc for Fe. The recommended cutoff there is<br>
90 Ry but you might get away with something smaller if you test it yourself.<br>
<br>
3) A good reference for defect calculations is Rev. Mod. Phys. 86, 253<br>
(2014).<br>
<br>
Best,<br>
<br>
Kevin May, PhD<br>
Postdoctoral Associate<br>
Department of Materials Science and Engineering<br>
Massachusetts Institute of Technology<br>
<br>
<br>
<br>
<br>
On Thu, May 30, 2019 at 3:59 AM mehrdad zamzamian <<br>
<a href="mailto:mehrdad.zamzamian@gmail.com" target="_blank">mehrdad.zamzamian@gmail.com</a>> wrote:<br>
<br>
> Thanks for your attention to my question<br>
> Actually, i defined a supercell (2*2*2), used USPP-PBE.I adjusted the<br>
> cutoff according to what was proposed for it (~70) and for ecut_rho (~400).<br>
> for scf convergence, i set conv=1e-6, ant at here, i set mixing beta~0.04<br>
> (it helped to reach to convergence fast). and also i set press=0 and its<br>
> threshold to 0.5. I want to calculate the vacancy (lack of Fe) energy. its<br>
> value must be 1.6 eV but i never give the better than 2.2 eV (The<br>
> ridiculous thing is that with molecular dynamics I got a very precise<br>
> amount of 1.6! that of course, its interatomic is more precise than my<br>
> calculation!). according to my PP in this calculation, it is suggested to<br>
> use non-polarized spin. i really do not know what parameter can i changed<br>
> to achieve 1.6 eV.<br>
> In addition, your food for the brain is some hard to be digested!<br>
><br>
> Regards<br>
><br>
> Seyed Mehrdad Zamzamian<br>
> Sharif University of Technology, Tehran, Iran<br>
> Energy engineering department<br>
> E-mail: <a href="mailto:mehrdad.zamzamian@gmail.com" target="_blank">mehrdad.zamzamian@gmail.com</a><br>
><br>
> On Wed, May 29, 2019 at 9:48 PM Kevin May <<a href="mailto:kmay@mit.edu" target="_blank">kmay@mit.edu</a>> wrote:<br>
><br>
>> Hi Mehrdad,<br>
>><br>
>> If you have a large energy difference between the end of the vc-relax<br>
>> algorithm and the final scf step, you may be using a fairly low plane wave<br>
>> cutoff energy for your system, though that may be fine depending on what<br>
>> quantities you are looking at. An important question here is: how are you<br>
>> choosing your convergence criteria? In my experience stresses (vc-relax)<br>
>> require a higher cutoff compared to total energy or forces (just ionic<br>
>> relaxation).<br>
>><br>
>> This all depends of course on what you are trying to get out of your<br>
>> calculation. In my case I was comparing different magnetic ground states<br>
>> that could be very close in energy, where very small changes in geometry<br>
>> can make a difference. For my specific systems I would converge plane wave<br>
>> cutoff, k-points and convergence threshold with respect to unit cell stress<br>
>> using a reference calculation with very high cutoff, low threshold (10^-9<br>
>> Ry), and dense k-point mesh.<br>
>><br>
>> Just some food for thought. I've definitely seen papers in the literature<br>
>> where they claim state A has lower energy than state B. I've reproduced<br>
>> such results using the somewhat lax cutoffs reported, and then found when<br>
>> you actually do CONVERGED calculations, state B is actually lower in energy<br>
>> (whoops!). Convergence is important.<br>
>><br>
>> Best,<br>
>><br>
>> Kevin May, PhD<br>
>> Postdoctoral Associate<br>
>> Department of Materials Science and Engineering<br>
>> Massachusetts Institute of Technology<br>
>><br>
><br>
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<br>
Message: 9<br>
Date: Fri, 31 May 2019 14:34:42 +0900<br>
From: emin klc <<a href="mailto:klcmemin@gmail.com" target="_blank">klcmemin@gmail.com</a>><br>
To: <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
Subject: [QE-users] Core wavefunction<br>
Message-ID:<br>
<CAGkFXWibb818QRgkXnBGCGRG1xu=<a href="mailto:m5SgmwLNg5bL1X3W7x5Quw@mail.gmail.com" target="_blank">m5SgmwLNg5bL1X3W7x5Quw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear QE experts,<br>
<br>
I have tried to generate an Ga Pseudopotentials for theoretical<br>
spectroscopy by ld1.x.<br>
Firstly, I need to have all electron (AE) wave functions including 1s 2s 2p<br>
3s 3p core states and valence states.<br>
I'm having some troubles since the output file (ld1.wfc) only gives 2s 2p<br>
3s 3p as a core states except for 1s, but which is important for K edge<br>
spectroscopy.<br>
I include below my input file for generating all electron wave functions.<br>
<br>
Could you say what is wrong with my input?<br>
-----------------------<br>
&input<br>
title = 'Ga',<br>
iswitch = 1,<br>
rel = 1,<br>
zed = 31.0,<br>
config = '[Ar] 4s2 4p1 3d10.0',<br>
dft = 'PBE'<br>
------------------------<br>
<br>
Mehmet Emin Kilic, PhD<br>
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<br>
Message: 10<br>
Date: Fri, 31 May 2019 07:44:56 +0200<br>
From: Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com" target="_blank">p.giannozzi@gmail.com</a>><br>
To: Quantum ESPRESSO users Forum <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
Subject: Re: [QE-users] Oxygen PAW Pseudopotentials have 3d core<br>
electrons.<br>
Message-ID:<br>
<<a href="mailto:CAPMgbCs01kZQgRyoZ6JYiUd54opWz1bhj1UQxh2rNx4vEnn77w@mail.gmail.com" target="_blank">CAPMgbCs01kZQgRyoZ6JYiUd54opWz1bhj1UQxh2rNx4vEnn77w@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Which pseudopotential are you referring to? In any case: no, it does not<br>
contain "core" 3d states, for sure.<br>
<br>
Paolo<br>
<br>
On Thu, May 30, 2019 at 3:54 PM Amreen Bano <<a href="mailto:banoamreen.7@gmail.com" target="_blank">banoamreen.7@gmail.com</a>> wrote:<br>
<br>
> Dear all,<br>
><br>
> I am working Oxygen based clusters. After performing the Pdos calculation<br>
> i found that O-3d states are also present. Why this is so? Is this an error<br>
> in the PP file or something else. Kindly suggest me the if there is any<br>
> problem with this PP.<br>
><br>
> Thanks in advance.<br>
> Amreen.<br>
> _______________________________________________<br>
> Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso" rel="noreferrer" target="_blank">www.max-centre.eu/quantum-espresso</a>)<br>
> users mailing list <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
> <a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br>
<br>
<br>
<br>
-- <br>
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br>
Phone +39-0432-558216, fax +39-0432-558222<br>
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<br>
Message: 11<br>
Date: Fri, 31 May 2019 14:46:05 +0800 (GMT+08:00)<br>
From: ??? <<a href="mailto:liuzeshi@ict.ac.cn" target="_blank">liuzeshi@ict.ac.cn</a>><br>
To: <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
Subject: [QE-users] Large input problem<br>
Message-ID: <<a href="mailto:45c31bad.3575d.16b0ca36d50.Coremail.liuzeshi@ict.ac.cn" target="_blank">45c31bad.3575d.16b0ca36d50.Coremail.liuzeshi@ict.ac.cn</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear QE Developers,<br>
<br>
I'm working on accelerating the QM/MM lib (especially the QE part of the lib), and need a large input problem that can generate <br>
tens of GB memory footprint. <br>
<br>
Can you give me a hint on how to generate such a input problem?<br>
Thank you. I appreciate your help.<br>
Zeshi<br>
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<br>
Message: 12<br>
Date: Fri, 31 May 2019 04:17:15 -0500<br>
From: Hassan Ahmed Mohammed <<a href="mailto:ahmedmmedm@gmail.com" target="_blank">ahmedmmedm@gmail.com</a>><br>
To: <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
Subject: [QE-users] Relaxation of CaCO3<br>
Message-ID:<br>
<<a href="mailto:CAKPfy%2BVfRMw%2BSnxhoHx7HSnC7gZ73Y4SNONpSnHi9DSOToDHyw@mail.gmail.com" target="_blank">CAKPfy+VfRMw+SnxhoHx7HSnC7gZ73Y4SNONpSnHi9DSOToDHyw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hello all,<br>
I'm trying to study the adsorption of different compounds on a calcite<br>
slab. I have been trying to do geometry relaxation for the calcite using QE<br>
and used burai to generate the input file. It worked for a long time but it<br>
did not converge. I tried several times with changes such as using kpoints<br>
instead of gamma, using other pseudopotentials but no luck.<br>
I appreciate any suggestions or ideas that could lead to my mistake!<br>
Here is my input file<br>
<br>
&CONTROL<br>
calculation = "relax"<br>
forc_conv_thr = 1.00000e-03<br>
max_seconds = 1.72800e+05<br>
nstep = 100<br>
pseudo_dir = "."<br>
tprnfor = .TRUE.<br>
tstress = .TRUE.<br>
/<br>
&SYSTEM<br>
a = 3.30600e+01<br>
b = 1.45800e+01<br>
c = 4.87600e+01<br>
degauss = 1.00000e-02<br>
ecutrho = 2.25000e+02<br>
ecutwfc = 2.50000e+01<br>
ibrav = 8<br>
nat = 480<br>
ntyp = 3<br>
occupations = "smearing"<br>
smearing = "gaussian"<br>
/<br>
&ELECTRONS<br>
conv_thr = 1.00000e-06<br>
electron_maxstep = 200<br>
mixing_beta = 7.00000e-01<br>
startingpot = "atomic"<br>
startingwfc = "atomic+random"<br>
/<br>
&IONS<br>
ion_dynamics = "bfgs"<br>
/<br>
&CELL<br>
/<br>
K_POINTS {gamma}<br>
<br>
ATOMIC_SPECIES<br>
Ca 40.07800 Ca.pbe-nsp-van.UPF<br>
C 12.01070 C.pbe-rrkjus.UPF<br>
O 15.99940 O.pbe-rrkjus.UPF<br>
<br>
ATOMIC_POSITIONS {angstrom}<br>
Ca 25.034002 5.792000 9.889249<br>
.<br>
<br>
.<br>
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<br>
Message: 13<br>
Date: Fri, 31 May 2019 11:43:23 +0200<br>
From: Pietro Davide Delugas <<a href="mailto:pdelugas@sissa.it" target="_blank">pdelugas@sissa.it</a>><br>
To: <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
Subject: Re: [QE-users] Relaxation of CaCO3<br>
Message-ID: <<a href="mailto:29860796-a485-d05e-6155-e34ebeb1ba61@sissa.it" target="_blank">29860796-a485-d05e-6155-e34ebeb1ba61@sissa.it</a>><br>
Content-Type: text/plain; charset="utf-8"; Format="flowed"<br>
<br>
Hello<br>
did not converge what ? the structural relaxation or the self consistency ?<br>
<br>
it is hard to say anything without have more information.<br>
Pietro<br>
<br>
<br>
On 05/31/2019 11:17 AM, Hassan Ahmed Mohammed wrote:<br>
><br>
> Hello all,<br>
> I'm trying to study the adsorption of different compounds on a calcite <br>
> slab. I have been trying to do geometry relaxation for the calcite <br>
> using QE and used burai to generate the input file. It worked for a <br>
> long time but it did not converge. I tried several times with changes <br>
> such as using kpoints instead of gamma, using other pseudopotentials <br>
> but no luck.<br>
> I appreciate any suggestions or ideas that could lead to my mistake!<br>
> Here is my input file<br>
><br>
> &CONTROL<br>
> calculation = "relax"<br>
> forc_conv_thr = 1.00000e-03<br>
> max_seconds = 1.72800e+05<br>
> nstep = 100<br>
> pseudo_dir = "."<br>
> tprnfor = .TRUE.<br>
> tstress = .TRUE.<br>
> /<br>
> &SYSTEM<br>
> a = 3.30600e+01<br>
> b = 1.45800e+01<br>
> c = 4.87600e+01<br>
> degauss = 1.00000e-02<br>
> ecutrho = 2.25000e+02<br>
> ecutwfc = 2.50000e+01<br>
> ibrav = 8<br>
> nat = 480<br>
> ntyp = 3<br>
> occupations = "smearing"<br>
> smearing = "gaussian"<br>
> /<br>
> &ELECTRONS<br>
> conv_thr = 1.00000e-06<br>
> electron_maxstep = 200<br>
> mixing_beta = 7.00000e-01<br>
> startingpot = "atomic"<br>
> startingwfc = "atomic+random"<br>
> /<br>
> &IONS<br>
> ion_dynamics = "bfgs"<br>
> /<br>
> &CELL<br>
> /<br>
> K_POINTS {gamma}<br>
><br>
> ATOMIC_SPECIES<br>
> Ca 40.07800 Ca.pbe-nsp-van.UPF<br>
> C 12.01070 C.pbe-rrkjus.UPF<br>
> O 15.99940 O.pbe-rrkjus.UPF<br>
><br>
> ATOMIC_POSITIONS {angstrom}<br>
> Ca 25.034002 5.792000 9.889249<br>
> .<br>
><br>
> .<br>
><br>
><br>
><br>
><br>
><br>
><br>
> _______________________________________________<br>
> Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso" rel="noreferrer" target="_blank">www.max-centre.eu/quantum-espresso</a>)<br>
> users mailing list <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
> <a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br>
<br>
<br>
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</blockquote></div></div>