Hello Omar and Prasenjit, 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?
On Wed, May 15, 2024 at 5:00 AM <[email protected]> wrote: > 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. Not able to converge Triplet O2 with quantum espresso v 7.2 > (AKHILESH SHARMA 22909003) > 2. Phonon calculation with DFT-D3 correction (Jing Lian Ng) > 3. Re: Phonon calculation with DFT-D3 correction (Omar Ashour) > 4. Re: Phonon calculation with DFT-D3 correction (Ghosh, Prasenjit) > 5. [SPAM] Inquiry Regarding the libxc (=?ISO-8859-1?B?emhvdWNoYW8=?=) > 6. Re: [SPAM] Inquiry Regarding the libxc (Paolo Giannozzi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 14 May 2024 15:58:23 +0530 > From: AKHILESH SHARMA 22909003 <[email protected]> > To: [email protected] > Subject: [QE-users] Not able to converge Triplet O2 with quantum > espresso v 7.2 > Message-ID: > <CAHw7Tc7uksQ=FzPTe1oX__5k=dAvZC0RLEb0R3ih4= > [email protected]> > Content-Type: text/plain; charset="utf-8" > > Hello everyone > > I'm currently facing challenges in optimizing the triplet state of an > dioxygen molecule within Quantum espresso version7.2. In order to calculate > the change in energy in my reaction pathway, it requires the energy of a > dioxygen molecule. I've already set up the calculation with the parameters > specified in the input file but at the end it is not converging. Below, > I've provided both the input and output files for your reference and I have > also attached the image of the error. I would greatly appreciate your > assistance in resolving this issue. > [image: image (1).png] > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.quantum-espresso.org/pipermail/users/attachments/20240514/11ab47a1/attachment-0001.html > > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: image (1).png > Type: image/png > Size: 45499 bytes > Desc: not available > URL: < > http://lists.quantum-espresso.org/pipermail/users/attachments/20240514/11ab47a1/attachment-0001.png > > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: T_O2.in > Type: application/octet-stream > Size: 1035 bytes > Desc: not available > URL: < > http://lists.quantum-espresso.org/pipermail/users/attachments/20240514/11ab47a1/attachment-0002.obj > > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: T_O2.out > Type: application/octet-stream > Size: 39829 bytes > Desc: not available > URL: < > http://lists.quantum-espresso.org/pipermail/users/attachments/20240514/11ab47a1/attachment-0003.obj > > > > ------------------------------ > > Message: 2 > Date: Tue, 14 May 2024 16:50:28 -0500 > From: Jing Lian Ng <[email protected]> > To: [email protected] > Subject: [QE-users] Phonon calculation with DFT-D3 correction > Message-ID: > <CAB+GxZkCtNTFZLnPrCrXOULV1tUa_5rWZGf145TTfnA= > [email protected]> > Content-Type: text/plain; charset="utf-8" > > Hello all, > > 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: > > 1. Relax / Scf calculation > 2. run d3hess.x > 3. run ph.x > > However, I encounter an error on step2, with the error message being: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > task # 28 > from pbcgdisp : error # 1 > Atom displacement not implemented with the threebody term > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > My input file for scf is as follows: > > ########################################################################## > / > &SYSTEM > ntyp = 1 > nat = 2 > ibrav = 0 > ecutwfc = 100 > ecutrho = 400 > vdw_corr = 'DFT-D3' > / > &ELECTRONS > mixing_mode = 'plain' > mixing_beta = 0.3 > / > &IONS > / > &CELL > / > ATOMIC_SPECIES > H 1.008 H.upf > > CELL_PARAMETERS angstrom > 5.21657500000000 0.00000000000000 0.00000000000000 > 0.00000000000000 6.04926000000000 0.00000000000000 > -6.40884630521040 0.00000000000000 36.38325638013446 > ########################################################################## > > Can someone advise on what could be the possible error? Thanks! > -- > Best regards, > *Jing Lian Ng*, PhD Student > Wang Material Group > The University of Texas at Austin | McKetta Department of Chemical > Engineering <http://che.utexas.edu> | Wang Materials Group > <https://wangmaterialsgroup.com/> > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.quantum-espresso.org/pipermail/users/attachments/20240514/5df9d648/attachment-0001.html > > > > ------------------------------ > > Message: 3 > Date: Tue, 14 May 2024 15:19:18 -0700 > From: Omar Ashour <[email protected]> > To: Quantum ESPRESSO users Forum <[email protected]> > Subject: Re: [QE-users] Phonon calculation with DFT-D3 correction > Message-ID: <[email protected]> > Content-Type: text/plain; charset="us-ascii" > > An HTML attachment was scrubbed... > URL: < > http://lists.quantum-espresso.org/pipermail/users/attachments/20240514/f7031963/attachment-0001.html > > > > ------------------------------ > > Message: 4 > Date: Wed, 15 May 2024 09:18:04 +0530 (IST) > From: "Ghosh, Prasenjit" <[email protected]> > To: Omar Ashour <[email protected]>, users > <[email protected]> > Subject: Re: [QE-users] Phonon calculation with DFT-D3 correction > Message-ID: > <[email protected]> > Content-Type: text/plain; charset="utf-8" > > Alternatively, you can calculate using the frozen phonon method. > > Prasenjit > IISER Pune > > > From: "users" <[email protected]> > To: "users" <[email protected]> > Sent: Wednesday, May 15, 2024 3:49:18 AM > Subject: Re: [QE-users] Phonon calculation with DFT-D3 correction > > 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. > > 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). > > 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). > > Omar A. Ashour > UC Berkeley > > > > On May 14, 2024, at 2:51 PM, Jing Lian Ng <[email protected]> wrote: > > > > > > BQ_BEGIN > > Hello all, > 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: > > > 1. Relax / Scf calculation > 2. run d3hess.x > 3. run ph.x > > However, I encounter an error on step2, with the error message being: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > task # 28 > from pbcgdisp : error # 1 > Atom displacement not implemented with the threebody term > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > My input file for scf is as follows: > > ########################################################################## > / > &SYSTEM > ntyp = 1 > nat = 2 > ibrav = 0 > ecutwfc = 100 > ecutrho = 400 > vdw_corr = 'DFT-D3' > / > &ELECTRONS > mixing_mode = 'plain' > mixing_beta = 0.3 > / > &IONS > / > &CELL > / > ATOMIC_SPECIES > H 1.008 H.upf > > CELL_PARAMETERS angstrom > 5.21657500000000 0.00000000000000 0.00000000000000 > 0.00000000000000 6.04926000000000 0.00000000000000 > -6.40884630521040 0.00000000000000 36.38325638013446 > ########################################################################## > > Can someone advise on what could be the possible error? Thanks! > -- > Best regards, > Jing Lian Ng , PhD Student > Wang Material Group > The University of Texas at Austin | [ http://che.utexas.edu/ | McKetta > Department of Chemical Engineering ] | [ https://wangmaterialsgroup.com/ > | Wang Materials Group ] > _______________________________________________ > The Quantum ESPRESSO community stands by the Ukrainian > people and expresses its concerns about the devastating > effects that the Russian military offensive has on their > country and on the free and peaceful scientific, cultural, > and economic cooperation amongst peoples > _______________________________________________ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list [email protected] > https://lists.quantum-espresso.org/mailman/listinfo/users > > BQ_END > > > _______________________________________________ > The Quantum ESPRESSO community stands by the Ukrainian > people and expresses its concerns about the devastating > effects that the Russian military offensive has on their > country and on the free and peaceful scientific, cultural, > and economic cooperation amongst peoples > _______________________________________________ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list [email protected] > https://lists.quantum-espresso.org/mailman/listinfo/users > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.quantum-espresso.org/pipermail/users/attachments/20240515/caeb620f/attachment-0001.html > > > > ------------------------------ > > Message: 5 > Date: Wed, 15 May 2024 15:00:38 +0800 > From: "=?ISO-8859-1?B?emhvdWNoYW8=?=" <[email protected]> > To: "=?ISO-8859-1?B?dXNlcnM=?=" <[email protected]> > Subject: [QE-users] [SPAM] Inquiry Regarding the libxc > Message-ID: <[email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > 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 > > > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.quantum-espresso.org/pipermail/users/attachments/20240515/6be37c79/attachment-0001.html > > > > ------------------------------ > > Message: 6 > Date: Wed, 15 May 2024 10:20:22 +0200 > From: Paolo Giannozzi <[email protected]> > To: zhouchao <[email protected]>, Quantum ESPRESSO users Forum > <[email protected]> > Subject: Re: [QE-users] [SPAM] Inquiry Regarding the libxc > Message-ID: <[email protected]> > Content-Type: text/plain; charset=UTF-8; format=flowed > > You need to compile QE for libxc in order to use it. Please read here: > https://www.quantum-espresso.org/Doc/user_guide/node13.html > Paolo > > On 15/05/2024 09:00, zhouchao via users wrote: > > 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 > > > > 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 > > > > > > _______________________________________________ > > The Quantum ESPRESSO community stands by the Ukrainian > > people and expresses its concerns about the devastating > > effects that the Russian military offensive has on their > > country and on the free and peaceful scientific, cultural, > > and economic cooperation amongst peoples > > _______________________________________________ > > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > > 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 206, 33100 Udine Italy, +39-0432-558216 > AVAILABLE POSITION: > https://physicslab.uniud.it/persone/paolo-giannozzi/prin2022 > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > > The Quantum ESPRESSO community stands by the Ukrainian > people and expresses its concerns about the devastating > effects that the Russian military offensive has on their > country and on the free and peaceful scientific, cultural, > and economic cooperation amongst peoples. > _______________________________________________ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list [email protected] > https://lists.quantum-espresso.org/mailman/listinfo/users > > ------------------------------ > > End of users Digest, Vol 202, Issue 12 > ************************************** >
_______________________________________________ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples _______________________________________________ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list [email protected] https://lists.quantum-espresso.org/mailman/listinfo/users
