[QE-users] Ph.x with grimme D3
Dear QE users, I am running phonons calculations using QE 6.4. When I use PBE+D3, everything converges without any warning or error message even if phq_readin.f90 is supposed to complain because of the use of grimme-D3 correction. Am I computing phonons with PBE-D3 or not? Best regards, L. Mariano, Simap laboratory Grenoble (France) ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Ph.x with grimme D3
If you check the output file or error file, you will see a message that grimme-D3 correction is not implemented in ph.x. I use grimme-D2 correction. Regards Bhamu On Tue, Feb 22, 2022, 5:38 PM Lorenzo Mariano < antonio-lorenzo.mari...@grenoble-inp.fr> wrote: > Dear QE users, > > I am running phonons calculations using QE 6.4. When I use PBE+D3, > everything converges without any warning or error message even if > phq_readin.f90 is supposed to complain because of the use of grimme-D3 > correction. Am I computing phonons with PBE-D3 or not? > > Best regards, > > L. Mariano, > Simap laboratory > Grenoble (France) > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] ghost like bands ?
Dear Kazume I think these 'ghost like bands' at 2 eV are irrelevant states and should not appear in the band structure. Or am I wrong? Maybe a stupid question. Are they f-like states of Pr, not present as valence states in the Pr.pbe-spdn-kjpaw_psl.1.0.0.UPF pseudopotential? HTH Giuseppe Quoting Kazume NISHIDATE : Dear all, I have been checking the SSSP pseudopotentials by applying these to my system (Ba2PrBiO6), but I encountered something strange result when I calculate its band structure. I attached the band structure plot along the gamma to X points. I can obtain the left hand side plot when I use the 'legacy' pseudopotentials. Ba 137.327 Ba.pbe-spn-kjpaw_psl.1.0.0.UPF Pr 140.90765 Pr.pbe-spdn-kjpaw_psl.1.0.0.UPF Bi 208.9804 Bi.pbe-dn-kjpaw_psl.1.0.0.UPF O 15.999 O.pbe-n-kjpaw_psl.1.0.0.UPF These are taken from the 'Ready-to-use PP tables'. http://pseudopotentials.quantum-espresso.org/legacy_tables Where the Fermi level was set to zero eV. We can see the two Bi states at 2 eV. The same band structure plot can be obtained by using the another DFT code (VASP) and I think it is a reliable one. However, if I switch the Pr pseudopotential to the SSSP one (Pr.GGA-PBE-paw-v1.0.UPF) suddenly ghost like states appear at the 2 eV (right hand side plot). I know that there are also the SSSP version for Bi and O but these do not alter the band structure plot (all these resulted in the left hand side plot). I think these 'ghost like bands' at 2 eV are irrelevant states and should not appear in the band structure. Or am I wrong? Any information regarding the above points would be greatly appreciated. 敬具 Best regards --- 西館数芽 Kazume NISHIDATE Ph.D Department of Systems Innovation Engineering, Graduate School of Science and Engineering, Iwate University 4-3-5 Ueda, Morioka, Iwate, 020-8551 JAPAN Phone:+81-19-621-6391 kazume.nishid...@gmail.com, nisid...@iwate-u.ac.jp https://sites.google.com/site/nisidatelab/ GIUSEPPE MATTIOLI CNR - ISTITUTO DI STRUTTURA DELLA MATERIA Via Salaria Km 29,300 - C.P. 10 I-00015 - Monterotondo Scalo (RM) Mob (*preferred*) +39 373 7305625 Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Ph.x with grimme D3
In the ph.x output file there are no indications that something went wrong. And the error/output file generated by the cluster system that I use is ok, no messages about the use of Grimme-D3. Regards, Lorenzo - Mail original - De: "Dr. K. C. Bhamu" À: "Antonio Lorenzo Mariano" , "Quantum ESPRESSO users Forum" Envoyé: Mardi 22 Février 2022 09:49:18 Objet: Re: [QE-users] Ph.x with grimme D3 If you check the output file or error file, you will see a message that grimme-D3 correction is not implemented in ph.x. I use grimme-D2 correction. Regards Bhamu On Tue, Feb 22, 2022, 5:38 PM Lorenzo Mariano < antonio-lorenzo.mari...@grenoble-inp.fr> wrote: > Dear QE users, > > I am running phonons calculations using QE 6.4. When I use PBE+D3, > everything converges without any warning or error message even if > phq_readin.f90 is supposed to complain because of the use of grimme-D3 > correction. Am I computing phonons with PBE-D3 or not? > > Best regards, > > L. Mariano, > Simap laboratory > Grenoble (France) > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] ghost like bands ?
Dear Giuseppe, Thank you for your reply. I'll check the PDOS to see its components and post the result (and the input file for the scf) in the next email. 敬具 Best regards --- 西館数芽 Kazume NISHIDATE Ph.D Department of Systems Innovation Engineering, Graduate School of Science and Engineering, Iwate University 4-3-5 Ueda, Morioka, Iwate, 020-8551 JAPAN Phone:+81-19-621-6391 kazume.nishid...@gmail.com, nisid...@iwate-u.ac.jp https://sites.google.com/site/nisidatelab/ 2022年2月22日 17:51 +0900、Giuseppe Mattioli のメール: > > Dear Kazume > > > I think these 'ghost like bands' at 2 eV are irrelevant states > > and should not appear in the band structure. > > Or am I wrong? > > Maybe a stupid question. Are they f-like states of Pr, not present as > valence states in the Pr.pbe-spdn-kjpaw_psl.1.0.0.UPF pseudopotential? > HTH > Giuseppe > ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Ph.x with grimme D3
On Tue, Feb 22, 2022 at 9:38 AM Lorenzo Mariano < antonio-lorenzo.mari...@grenoble-inp.fr> wrote: I am running phonons calculations using QE 6.4. When I use PBE+D3, > everything converges without any warning or error message even if > phq_readin.f90 is supposed to complain because of the use of grimme-D3 > correction. Am I computing phonons with PBE-D3 or not? > no, for two reasons: - your scf calculation was not done with DFT-D3, and - it is not implemented anyway. Demostration: $ grep -A1 dftd3 qe-6.4/PHonon/PH/*f90 [...] qe-6.4/PHonon/PH/phq_readin.f90: IF (ldftd3) CALL errore('phq_readin',& qe-6.4/PHonon/PH/phq_readin.f90- 'The phonon code with Grimme''s DFT-D3 is not yet available',1) Paolo > Best regards, > > L. Mariano, > Simap laboratory > Grenoble (France) > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@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 Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] ghost like bands ?
You may also look into the pseudopotential file and see if it contains an l=3 channel among valence electrons. If I'm reading everything correctly, Pr.pbe-spdn-kjpaw_psl.1.0.0.UPF does not contain f electrons Generated using "atomic" code by A. Dal Corso v.6.2.2 Author: ADC Generation date: 4May2018 Pseudopotential type: PAW Element: Pr Functional: SLA PW PBX PBC Suggested minimum cutoff for wavefunctions: 41. Ry Suggested minimum cutoff for charge density: 309. Ry The Pseudo was generated with a Scalar-Relativistic Calculation Local Potential by smoothing AE potential with Bessel fncs, cutoff radius: 2. Pseudopotential contains additional information for GIPAW reconstruction. Valence configuration: nl pn l occ RcutRcut US E pseu 5S 1 0 2.00 1.300 1.600-3.142979 6S 2 0 1.50 1.300 1.600-0.304450 5P 2 1 6.00 1.400 1.800-1.805127 6P 3 1 0.50 1.400 1.800-0.119192 5D 3 2 1.00 1.100 1.700-0.255308 Generation configuration: 5S 1 0 2.00 1.300 1.600-3.143013 6S 2 0 1.50 1.300 1.600-0.304456 5P 2 1 6.00 1.400 1.800-1.805149 6P 3 1 0.50 1.400 1.800-0.119194 5D 3 2 1.00 1.100 1.700-0.255322 5D 3 2 0.00 1.100 1.700 2.00 Pseudization used: troullier-martins unlike Pr.GGA-PBE-paw-v1.0.UPF that seems to have the f shell in valence l_max="3" <-- I cannot read the atompaw input, but this should be enough... l_max_rho="6" mesh_size=" 1103" number_of_wfc=" 8" number_of_proj=" 8" /> HTH Giuseppe Quoting Kazume NISHIDATE : Dear Giuseppe, Thank you for your reply. I'll check the PDOS to see its components and post the result (and the input file for the scf) in the next email. 敬具 Best regards --- 西館数芽 Kazume NISHIDATE Ph.D Department of Systems Innovation Engineering, Graduate School of Science and Engineering, Iwate University 4-3-5 Ueda, Morioka, Iwate, 020-8551 JAPAN Phone:+81-19-621-6391 kazume.nishid...@gmail.com, nisid...@iwate-u.ac.jp https://sites.google.com/site/nisidatelab/ 2022年2月22日 17:51 +0900、Giuseppe Mattioli のメール: Dear Kazume > I think these 'ghost like bands' at 2 eV are irrelevant states > and should not appear in the band structure. > Or am I wrong? Maybe a stupid question. Are they f-like states of Pr, not present as valence states in the Pr.pbe-spdn-kjpaw_psl.1.0.0.UPF pseudopotential? HTH Giuseppe GIUSEPPE MATTIOLI CNR - ISTITUTO DI STRUTTURA DELLA MATERIA Via Salaria Km 29,300 - C.P. 10 I-00015 - Monterotondo Scalo (RM) Mob (*preferred*) +39 373 7305625 Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Ph.x with grimme D3
Dear Paolo, thanks for the replay. I verified and in QE 7.0 the error is printed correctly and the calculation stops. This is not the case for the 6.4.1 version (just a warning for the other users). Best regards, Lorenzo - Mail original - De: "Paolo Giannozzi" À: "Antonio Lorenzo Mariano" , "Quantum ESPRESSO users Forum" Envoyé: Mardi 22 Février 2022 13:15:37 Objet: Re: [QE-users] Ph.x with grimme D3 On Tue, Feb 22, 2022 at 9:38 AM Lorenzo Mariano < antonio-lorenzo.mari...@grenoble-inp.fr> wrote: I am running phonons calculations using QE 6.4. When I use PBE+D3, > everything converges without any warning or error message even if > phq_readin.f90 is supposed to complain because of the use of grimme-D3 > correction. Am I computing phonons with PBE-D3 or not? > no, for two reasons: - your scf calculation was not done with DFT-D3, and - it is not implemented anyway. Demostration: $ grep -A1 dftd3 qe-6.4/PHonon/PH/*f90 [...] qe-6.4/PHonon/PH/phq_readin.f90: IF (ldftd3) CALL errore('phq_readin',& qe-6.4/PHonon/PH/phq_readin.f90- 'The phonon code with Grimme''s DFT-D3 is not yet available',1) Paolo > Best regards, > > L. Mariano, > Simap laboratory > Grenoble (France) > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@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 Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Ph.x with grimme D3
The error check is there also for v.6.4.1. What might have happened is that the flag "ldftd3" was not written to the data file, though Paolo On Tue, Feb 22, 2022 at 6:52 PM Lorenzo Mariano < antonio-lorenzo.mari...@grenoble-inp.fr> wrote: > Dear Paolo, > > thanks for the replay. I verified and in QE 7.0 the error is printed > correctly and the calculation stops. This is not the case for the 6.4.1 > version (just a warning for the other users). > > Best regards, > > Lorenzo > > - Mail original - > De: "Paolo Giannozzi" > À: "Antonio Lorenzo Mariano" , > "Quantum ESPRESSO users Forum" > Envoyé: Mardi 22 Février 2022 13:15:37 > Objet: Re: [QE-users] Ph.x with grimme D3 > > On Tue, Feb 22, 2022 at 9:38 AM Lorenzo Mariano < > antonio-lorenzo.mari...@grenoble-inp.fr> wrote: > > I am running phonons calculations using QE 6.4. When I use PBE+D3, > > everything converges without any warning or error message even if > > phq_readin.f90 is supposed to complain because of the use of grimme-D3 > > correction. Am I computing phonons with PBE-D3 or not? > > > > no, for two reasons: > - your scf calculation was not done with DFT-D3, and > - it is not implemented anyway. > > Demostration: > > $ grep -A1 dftd3 qe-6.4/PHonon/PH/*f90 > [...] > qe-6.4/PHonon/PH/phq_readin.f90: IF (ldftd3) CALL errore('phq_readin',& > qe-6.4/PHonon/PH/phq_readin.f90- 'The phonon code with Grimme''s DFT-D3 > is not yet available',1) > > Paolo > > > > Best regards, > > > > L. Mariano, > > Simap laboratory > > Grenoble (France) > > ___ > > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > > users mailing list users@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 > Phone +39-0432-558216, fax +39-0432-558222 > -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 206, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users