<div dir="ltr">Hello Omar and Prasenjit,<div><br></div><div>Thank you for the advice! The calculation proceeds fine now when I turn off the dftd3_threebody tag. Another question I had in mind is that are there particular reasons for running D3 with BJ damping or D3M/D3M-BJ instead of the standard "zero damping" D3?</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, May 15, 2024 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>
<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<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>
or, via email, send a message with subject or body 'help' to<br>
<a href="mailto:users-request@lists.quantum-espresso.org" target="_blank">users-request@lists.quantum-espresso.org</a><br>
<br>
You can reach the person managing the list at<br>
<a href="mailto:users-owner@lists.quantum-espresso.org" target="_blank">users-owner@lists.quantum-espresso.org</a><br>
<br>
When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of users digest..."<br>
<br>
<br>
Today's Topics:<br>
<br>
1. Not able to converge Triplet O2 with quantum espresso v 7.2<br>
(AKHILESH SHARMA 22909003)<br>
2. Phonon calculation with DFT-D3 correction (Jing Lian Ng)<br>
3. Re: Phonon calculation with DFT-D3 correction (Omar Ashour)<br>
4. Re: Phonon calculation with DFT-D3 correction (Ghosh, Prasenjit)<br>
5. [SPAM] Inquiry Regarding the libxc (=?ISO-8859-1?B?emhvdWNoYW8=?=)<br>
6. Re: [SPAM] Inquiry Regarding the libxc (Paolo Giannozzi)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 14 May 2024 15:58:23 +0530<br>
From: AKHILESH SHARMA 22909003 <<a href="mailto:akhilesh_s@cy.iitr.ac.in" target="_blank">akhilesh_s@cy.iitr.ac.in</a>><br>
To: <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
Subject: [QE-users] Not able to converge Triplet O2 with quantum<br>
espresso v 7.2<br>
Message-ID:<br>
<CAHw7Tc7uksQ=FzPTe1oX__5k=dAvZC0RLEb0R3ih4=<a href="mailto:AapASSNA@mail.gmail.com" target="_blank">AapASSNA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hello everyone<br>
<br>
I'm currently facing challenges in optimizing the triplet state of an<br>
dioxygen molecule within Quantum espresso version7.2. In order to calculate<br>
the change in energy in my reaction pathway, it requires the energy of a<br>
dioxygen molecule. I've already set up the calculation with the parameters<br>
specified in the input file but at the end it is not converging. Below,<br>
I've provided both the input and output files for your reference and I have<br>
also attached the image of the error. I would greatly appreciate your<br>
assistance in resolving this issue.<br>
[image: image (1).png]<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://lists.quantum-espresso.org/pipermail/users/attachments/20240514/11ab47a1/attachment-0001.html" rel="noreferrer" target="_blank">http://lists.quantum-espresso.org/pipermail/users/attachments/20240514/11ab47a1/attachment-0001.html</a>><br>
-------------- next part --------------<br>
A non-text attachment was scrubbed...<br>
Name: image (1).png<br>
Type: image/png<br>
Size: 45499 bytes<br>
Desc: not available<br>
URL: <<a href="http://lists.quantum-espresso.org/pipermail/users/attachments/20240514/11ab47a1/attachment-0001.png" rel="noreferrer" target="_blank">http://lists.quantum-espresso.org/pipermail/users/attachments/20240514/11ab47a1/attachment-0001.png</a>><br>
-------------- next part --------------<br>
A non-text attachment was scrubbed...<br>
Name: T_O2.in<br>
Type: application/octet-stream<br>
Size: 1035 bytes<br>
Desc: not available<br>
URL: <<a href="http://lists.quantum-espresso.org/pipermail/users/attachments/20240514/11ab47a1/attachment-0002.obj" rel="noreferrer" target="_blank">http://lists.quantum-espresso.org/pipermail/users/attachments/20240514/11ab47a1/attachment-0002.obj</a>><br>
-------------- next part --------------<br>
A non-text attachment was scrubbed...<br>
Name: T_O2.out<br>
Type: application/octet-stream<br>
Size: 39829 bytes<br>
Desc: not available<br>
URL: <<a href="http://lists.quantum-espresso.org/pipermail/users/attachments/20240514/11ab47a1/attachment-0003.obj" rel="noreferrer" target="_blank">http://lists.quantum-espresso.org/pipermail/users/attachments/20240514/11ab47a1/attachment-0003.obj</a>><br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Tue, 14 May 2024 16:50:28 -0500<br>
From: Jing Lian Ng <<a href="mailto:jinglian@utexas.edu" target="_blank">jinglian@utexas.edu</a>><br>
To: <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
Subject: [QE-users] Phonon calculation with DFT-D3 correction<br>
Message-ID:<br>
<CAB+GxZkCtNTFZLnPrCrXOULV1tUa_5rWZGf145TTfnA=<a href="mailto:xEkQ5Q@mail.gmail.com" target="_blank">xEkQ5Q@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hello all,<br>
<br>
I am currently trying to perform phonon calculation with DFT-D3 correction.<br>
Based on what I read from d3hess.x documentation, I believe I can include<br>
dispersion effects on vibrational frequencies by:<br>
<br>
1. Relax / Scf calculation<br>
2. run d3hess.x<br>
3. run ph.x<br>
<br>
However, I encounter an error on step2, with the error message being:<br>
<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
task # 28<br>
from pbcgdisp : error # 1<br>
Atom displacement not implemented with the threebody term<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
<br>
My input file for scf is as follows:<br>
<br>
##########################################################################<br>
/<br>
&SYSTEM<br>
ntyp = 1<br>
nat = 2<br>
ibrav = 0<br>
ecutwfc = 100<br>
ecutrho = 400<br>
vdw_corr = 'DFT-D3'<br>
/<br>
&ELECTRONS<br>
mixing_mode = 'plain'<br>
mixing_beta = 0.3<br>
/<br>
&IONS<br>
/<br>
&CELL<br>
/<br>
ATOMIC_SPECIES<br>
H 1.008 H.upf<br>
<br>
CELL_PARAMETERS angstrom<br>
5.21657500000000 0.00000000000000 0.00000000000000<br>
0.00000000000000 6.04926000000000 0.00000000000000<br>
-6.40884630521040 0.00000000000000 36.38325638013446<br>
##########################################################################<br>
<br>
Can someone advise on what could be the possible error? Thanks!<br>
-- <br>
Best regards,<br>
*Jing Lian Ng*, PhD Student<br>
Wang Material Group<br>
The University of Texas at Austin | McKetta Department of Chemical<br>
Engineering <<a href="http://che.utexas.edu" rel="noreferrer" target="_blank">http://che.utexas.edu</a>> | Wang Materials Group<br>
<<a href="https://wangmaterialsgroup.com/" rel="noreferrer" target="_blank">https://wangmaterialsgroup.com/</a>><br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://lists.quantum-espresso.org/pipermail/users/attachments/20240514/5df9d648/attachment-0001.html" rel="noreferrer" target="_blank">http://lists.quantum-espresso.org/pipermail/users/attachments/20240514/5df9d648/attachment-0001.html</a>><br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Tue, 14 May 2024 15:19:18 -0700<br>
From: Omar Ashour <<a href="mailto:ashour@berkeley.edu" target="_blank">ashour@berkeley.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] Phonon calculation with DFT-D3 correction<br>
Message-ID: <<a href="mailto:26F0CF8B-B1C1-4964-8678-7E57907216C0@berkeley.edu" target="_blank">26F0CF8B-B1C1-4964-8678-7E57907216C0@berkeley.edu</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://lists.quantum-espresso.org/pipermail/users/attachments/20240514/f7031963/attachment-0001.html" rel="noreferrer" target="_blank">http://lists.quantum-espresso.org/pipermail/users/attachments/20240514/f7031963/attachment-0001.html</a>><br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Wed, 15 May 2024 09:18:04 +0530 (IST)<br>
From: "Ghosh, Prasenjit" <<a href="mailto:pghosh@iiserpune.ac.in" target="_blank">pghosh@iiserpune.ac.in</a>><br>
To: Omar Ashour <<a href="mailto:ashour@berkeley.edu" target="_blank">ashour@berkeley.edu</a>>, users<br>
<<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
Subject: Re: [QE-users] Phonon calculation with DFT-D3 correction<br>
Message-ID:<br>
<<a href="mailto:289716418.23401380.1715744884109.JavaMail.zimbra@iiserpune.ac.in" target="_blank">289716418.23401380.1715744884109.JavaMail.zimbra@iiserpune.ac.in</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Alternatively, you can calculate using the frozen phonon method. <br>
<br>
Prasenjit <br>
IISER Pune <br>
<br>
<br>
From: "users" <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>> <br>
To: "users" <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>> <br>
Sent: Wednesday, May 15, 2024 3:49:18 AM <br>
Subject: Re: [QE-users] Phonon calculation with DFT-D3 correction <br>
<br>
ph.x currently does not support the three-body terms with the D3 dispersion correction. You can turn it off with the dftd3_threebody tag in pw.x, and follow the three step procedure you outlined in your email. If you want to include the three-body terms, you can use the supercell approach (e.g., phonopy) instead of DFPT with ph.x. <br>
<br>
Three-body terms tend to have a pretty small effect in my experience, but that's system-dependent, in principle, and you might want to test it. Refer to the original D3 papers for a discussion. Three-body terms are not used at all in VASP, for reference (but they're hidden in the source code). <br>
<br>
I also generally recommend using D3 with BJ damping or D3M/D3M-BJ instead of the standard "zero damping" D3. (dftd3_version flag in pw.x). <br>
<br>
Omar A. Ashour <br>
UC Berkeley <br>
<br>
<br>
<br>
On May 14, 2024, at 2:51 PM, Jing Lian Ng <<a href="mailto:jinglian@utexas.edu" target="_blank">jinglian@utexas.edu</a>> wrote: <br>
<br>
<br>
<br>
<br>
<br>
BQ_BEGIN<br>
<br>
Hello all, <br>
I am currently trying to perform phonon calculation with DFT-D3 correction. Based on what I read from d3hess.x documentation, I believe I can include dispersion effects on vibrational frequencies by: <br>
<br>
<br>
1. Relax / Scf calculation <br>
2. run d3hess.x <br>
3. run ph.x <br>
<br>
However, I encounter an error on step2, with the error message being: <br>
<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% <br>
task # 28 <br>
from pbcgdisp : error # 1 <br>
Atom displacement not implemented with the threebody term <br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% <br>
<br>
My input file for scf is as follows: <br>
<br>
########################################################################## <br>
/ <br>
&SYSTEM <br>
ntyp = 1 <br>
nat = 2 <br>
ibrav = 0 <br>
ecutwfc = 100 <br>
ecutrho = 400 <br>
vdw_corr = 'DFT-D3' <br>
/ <br>
&ELECTRONS <br>
mixing_mode = 'plain' <br>
mixing_beta = 0.3 <br>
/ <br>
&IONS <br>
/ <br>
&CELL <br>
/ <br>
ATOMIC_SPECIES <br>
H 1.008 H.upf <br>
<br>
CELL_PARAMETERS angstrom <br>
5.21657500000000 0.00000000000000 0.00000000000000 <br>
0.00000000000000 6.04926000000000 0.00000000000000 <br>
-6.40884630521040 0.00000000000000 36.38325638013446 <br>
########################################################################## <br>
<br>
Can someone advise on what could be the possible error? Thanks! <br>
-- <br>
Best regards, <br>
Jing Lian Ng , PhD Student <br>
Wang Material Group <br>
The University of Texas at Austin | [ <a href="http://che.utexas.edu/" rel="noreferrer" target="_blank">http://che.utexas.edu/</a> | McKetta Department of Chemical Engineering ] | [ <a href="https://wangmaterialsgroup.com/" rel="noreferrer" target="_blank">https://wangmaterialsgroup.com/</a> | Wang Materials Group ] <br>
_______________________________________________ <br>
The Quantum ESPRESSO community stands by the Ukrainian <br>
people and expresses its concerns about the devastating <br>
effects that the Russian military offensive has on their <br>
country and on the free and peaceful scientific, cultural, <br>
and economic cooperation amongst peoples <br>
_______________________________________________ <br>
Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu" rel="noreferrer" target="_blank">www.max-centre.eu</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>
BQ_END<br>
<br>
<br>
_______________________________________________ <br>
The Quantum ESPRESSO community stands by the Ukrainian <br>
people and expresses its concerns about the devastating <br>
effects that the Russian military offensive has on their <br>
country and on the free and peaceful scientific, cultural, <br>
and economic cooperation amongst peoples <br>
_______________________________________________ <br>
Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu" rel="noreferrer" target="_blank">www.max-centre.eu</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>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://lists.quantum-espresso.org/pipermail/users/attachments/20240515/caeb620f/attachment-0001.html" rel="noreferrer" target="_blank">http://lists.quantum-espresso.org/pipermail/users/attachments/20240515/caeb620f/attachment-0001.html</a>><br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Wed, 15 May 2024 15:00:38 +0800<br>
From: "=?ISO-8859-1?B?emhvdWNoYW8=?=" <<a href="mailto:994646659@qq.com" target="_blank">994646659@qq.com</a>><br>
To: "=?ISO-8859-1?B?dXNlcnM=?=" <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
Subject: [QE-users] [SPAM] Inquiry Regarding the libxc<br>
Message-ID: <<a href="mailto:tencent_C5BB28FD94FA858BAE9EC1D92542E9B5A205@qq.com" target="_blank">tencent_C5BB28FD94FA858BAE9EC1D92542E9B5A205@qq.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear Quantum ESPRESSO Community, I am currently working with Quantum ESPRESSO version 7.0 and Libxc version 6.0.0. The functional I am using is specified as Input_dft='XC-000I-000I-000L-130L-707L-000I'. For the Meta-GGA exchange, I have selected the TASK exchange functional with id=707. However, I encountered the following error: Error in routine matching_shortIDs (1): libxc needed for this functional, but it is not linked <br>
<br>
<br>
I am unsure of the cause of this error. Could you provide guidance on what might be causing this issue? Additionally, since the TASK functional only provides an exchange functional, I am uncertain about which correlation functional to select. Could you explain the logic behind choosing an appropriate correlation functional in this context? Thank you for your assistance. Best regards, zhouchao<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://lists.quantum-espresso.org/pipermail/users/attachments/20240515/6be37c79/attachment-0001.html" rel="noreferrer" target="_blank">http://lists.quantum-espresso.org/pipermail/users/attachments/20240515/6be37c79/attachment-0001.html</a>><br>
<br>
------------------------------<br>
<br>
Message: 6<br>
Date: Wed, 15 May 2024 10:20:22 +0200<br>
From: Paolo Giannozzi <<a href="mailto:paolo.giannozzi@uniud.it" target="_blank">paolo.giannozzi@uniud.it</a>><br>
To: zhouchao <<a href="mailto:994646659@qq.com" target="_blank">994646659@qq.com</a>>, Quantum ESPRESSO users Forum<br>
<<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
Subject: Re: [QE-users] [SPAM] Inquiry Regarding the libxc<br>
Message-ID: <<a href="mailto:6bc809ea-033a-44d9-97fb-fb5c4a4dc88a@uniud.it" target="_blank">6bc809ea-033a-44d9-97fb-fb5c4a4dc88a@uniud.it</a>><br>
Content-Type: text/plain; charset=UTF-8; format=flowed<br>
<br>
You need to compile QE for libxc in order to use it. Please read here:<br>
<a href="https://www.quantum-espresso.org/Doc/user_guide/node13.html" rel="noreferrer" target="_blank">https://www.quantum-espresso.org/Doc/user_guide/node13.html</a><br>
Paolo<br>
<br>
On 15/05/2024 09:00, zhouchao via users wrote:<br>
> Dear Quantum ESPRESSO Community, I am currently working with Quantum <br>
> ESPRESSO version 7.0 and Libxc version 6.0.0. The functional I am using <br>
> is specified as Input_dft='XC-000I-000I-000L-130L-707L-000I'. For the <br>
> Meta-GGA exchange, I have selected the TASK exchange functional with <br>
> id=707. However, I encountered the following error: Error in routine <br>
> matching_shortIDs (1): libxc needed for this functional, but it is not <br>
> linked<br>
> <br>
> I am unsure of the cause of this error. Could you provide guidance on <br>
> what might be causing this issue? Additionally, since the TASK <br>
> functional only provides an exchange functional, I am uncertain about <br>
> which correlation functional to select. Could you explain the logic <br>
> behind choosing an appropriate correlation functional in this context? <br>
> Thank you for your assistance. Best regards, zhouchao<br>
> <br>
> <br>
> _______________________________________________<br>
> The Quantum ESPRESSO community stands by the Ukrainian<br>
> people and expresses its concerns about the devastating<br>
> effects that the Russian military offensive has on their<br>
> country and on the free and peaceful scientific, cultural,<br>
> and economic cooperation amongst peoples<br>
> _______________________________________________<br>
> Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu" rel="noreferrer" target="_blank">www.max-centre.eu</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>
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>
Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216<br>
AVAILABLE POSITION: <br>
<a href="https://physicslab.uniud.it/persone/paolo-giannozzi/prin2022" rel="noreferrer" target="_blank">https://physicslab.uniud.it/persone/paolo-giannozzi/prin2022</a><br>
<br>
<br>
------------------------------<br>
<br>
Subject: Digest Footer<br>
<br>
_______________________________________________<br>
<br>
The Quantum ESPRESSO community stands by the Ukrainian<br>
people and expresses its concerns about the devastating<br>
effects that the Russian military offensive has on their<br>
country and on the free and peaceful scientific, cultural,<br>
and economic cooperation amongst peoples.<br>
_______________________________________________<br>
Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu" rel="noreferrer" target="_blank">www.max-centre.eu</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>
End of users Digest, Vol 202, Issue 12<br>
**************************************<br>
</blockquote></div>