[QE-users] users Digest, Vol 202, Issue 12
Jing Lian Ng
jinglian at utexas.edu
Thu May 16 20:36:38 CEST 2024
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 <users-request at lists.quantum-espresso.org>
wrote:
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> 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 <akhilesh_s at cy.iitr.ac.in>
> To: users at lists.quantum-espresso.org
> Subject: [QE-users] Not able to converge Triplet O2 with quantum
> espresso v 7.2
> Message-ID:
> <CAHw7Tc7uksQ=FzPTe1oX__5k=dAvZC0RLEb0R3ih4=
> AapASSNA at mail.gmail.com>
> 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]
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>
> ------------------------------
>
> Message: 2
> Date: Tue, 14 May 2024 16:50:28 -0500
> From: Jing Lian Ng <jinglian at utexas.edu>
> To: users at lists.quantum-espresso.org
> Subject: [QE-users] Phonon calculation with DFT-D3 correction
> Message-ID:
> <CAB+GxZkCtNTFZLnPrCrXOULV1tUa_5rWZGf145TTfnA=
> xEkQ5Q at mail.gmail.com>
> 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/>
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>
> ------------------------------
>
> Message: 3
> Date: Tue, 14 May 2024 15:19:18 -0700
> From: Omar Ashour <ashour at berkeley.edu>
> To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] Phonon calculation with DFT-D3 correction
> Message-ID: <26F0CF8B-B1C1-4964-8678-7E57907216C0 at berkeley.edu>
> Content-Type: text/plain; charset="us-ascii"
>
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> ------------------------------
>
> Message: 4
> Date: Wed, 15 May 2024 09:18:04 +0530 (IST)
> From: "Ghosh, Prasenjit" <pghosh at iiserpune.ac.in>
> To: Omar Ashour <ashour at berkeley.edu>, users
> <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] Phonon calculation with DFT-D3 correction
> Message-ID:
> <289716418.23401380.1715744884109.JavaMail.zimbra at iiserpune.ac.in>
> Content-Type: text/plain; charset="utf-8"
>
> Alternatively, you can calculate using the frozen phonon method.
>
> Prasenjit
> IISER Pune
>
>
> From: "users" <users at lists.quantum-espresso.org>
> To: "users" <users at lists.quantum-espresso.org>
> 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 <jinglian at utexas.edu> 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 users at lists.quantum-espresso.org
> 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 users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
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> ------------------------------
>
> Message: 5
> Date: Wed, 15 May 2024 15:00:38 +0800
> From: "=?ISO-8859-1?B?emhvdWNoYW8=?=" <994646659 at qq.com>
> To: "=?ISO-8859-1?B?dXNlcnM=?=" <users at lists.quantum-espresso.org>
> Subject: [QE-users] [SPAM] Inquiry Regarding the libxc
> Message-ID: <tencent_C5BB28FD94FA858BAE9EC1D92542E9B5A205 at qq.com>
> 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
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> ------------------------------
>
> Message: 6
> Date: Wed, 15 May 2024 10:20:22 +0200
> From: Paolo Giannozzi <paolo.giannozzi at uniud.it>
> To: zhouchao <994646659 at qq.com>, Quantum ESPRESSO users Forum
> <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] [SPAM] Inquiry Regarding the libxc
> Message-ID: <6bc809ea-033a-44d9-97fb-fb5c4a4dc88a at uniud.it>
> 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 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 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 users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
>
> ------------------------------
>
> End of users Digest, Vol 202, Issue 12
> **************************************
>
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