Here are the instructions:
http://theossrv1.epfl.ch/Main/OxidationStates Sent from a tiny keyboard... Contact info: http://theossrv1.epfl.ch/Main/Contact On 27 Feb 2019, at 07:17, Małgorzata Wawrzyniak-Adamczewska <[email protected]<mailto:[email protected]>> wrote: Dear Quantum Espresso Users and Developers, I have a question regarding a constrained DFT with the PAW/US-PAW. Is it possible to perform calculations in the constrained scheme with QE package. I would like to calculate possible charge transfer in a system. Regards, Malgorzata Wawrzyniak W dniu 2019-02-26 12:00, [email protected]<mailto:[email protected]> napisał(a): Send users mailing list submissions to [email protected]<mailto:[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]<mailto:[email protected]> You can reach the person managing the list at [email protected]<mailto:[email protected]> When replying, please edit your Subject line so it is more specific than "Re: Contents of users digest..." Today's Topics: 1. Phonons with images (Malte Sachs) 2. Re: The virtual.x problems (Pietro Delugas) 3. Re: Phonons with images (Paolo Giannozzi) 4. Re: The virtual.x problems (Fabio Costa) 5. Re: The virtual.x problems (Pietro Delugas) 6. Phonon Calculation erroneous (Offermans Willem) 7. Re: Phonon Calculation erroneous (Lorenzo Paulatto) ---------------------------------------------------------------------- Message: 1 Date: Mon, 25 Feb 2019 13:53:06 +0100 From: Malte Sachs <[email protected]<mailto:[email protected]>> To: Quantum Espresso users Forum <[email protected]<mailto:[email protected]>> Subject: [QE-users] Phonons with images Message-ID: <[email protected]<mailto:[email protected]>> Content-Type: text/plain; charset="utf-8"; Format="flowed" Dear all, I have tested the image-example for phonon calculations using QuantumEspresso 6.3. In the case I am using these commands: mpirun -np 4 pw.x < ... mpirun -np 4 ph.x -ni 2 < ... mpirun -np 4 ph.x < .... everything works fine. However, using this: mpirun -np 2 pw.x < ... mpirun -np 4 ph.x -ni 2 < ... mpirun -np 2 ph.x < .... yields an error in the last step: "pw.x run with a different number of processors. Use wf_collect=.true."? However, I have the same number of processors in pw.x and ph.x and the wf_collect option is activated by default. So I don't know what is going on. Best regards, Malte Sachs -- Malte Sachs Anorganische Chemie, Fluorchemie Philipps-Universit?t Marburg Hans-Meerwein-Stra?e 4 35032 Marburg (Paketpost: 35043 Marburg) Tel.: +49 (0)6421 28 - 25 68 0 http://www.uni-marburg.de/fb15/ag-kraus/ -------------- next part -------------- A non-text attachment was scrubbed... Name: malte_sachs.vcf Type: text/x-vcard Size: 379 bytes Desc: not available URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20190225/f24d4115/attachment-0001.vcf> -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 5303 bytes Desc: S/MIME Cryptographic Signature URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20190225/f24d4115/attachment-0001.p7s> ------------------------------ Message: 2 Date: Mon, 25 Feb 2019 15:46:17 +0100 From: Pietro Delugas <[email protected]<mailto:[email protected]>> To: [email protected]<mailto:[email protected]> Subject: Re: [QE-users] The virtual.x problems Message-ID: <[email protected]<mailto:[email protected]>> Content-Type: text/plain; charset="windows-1252"; Format="flowed" Hi Fabio Pseudos from pseudo-dojo are perfect, they are norm-conserving and they are in upf format. ?You have to keep in mind that VCA has sense? for isovalent atoms e. g C? with Si. Ga.? and In. Also pseudos would better? be built with the same number of projectors. Mixing pseudos with a different number of valence electrons like B and Si is most likely not going to work. I checked B with Si though,? and disappointingly the program produces an upf file.? I think that it would be useful at least to print out a very evident? warning about the usability of such? file. Pietro The problem is the On 25/02/19 11:58, Fabio Costa wrote: Thanks for the quick reply To perform this task, I downloaded the full table of PP?from pseudo dojo, with the following settings: Type:NC SR (ONCVPSP v0.4) XC: PBE Accuracy: standard Format: upf My attempts so far were to mix B-C and Si-Al, both unsuccessful. Maybe my mistake is in the choice of these PP files, and if so, where can I get the adequate ones to work with the virtual.x? Thank you all for the assistance F?bio Costa ------------------------------------------------------------------------ *De:* users <[email protected]<mailto:[email protected]>> em nome de Pietro Delugas <[email protected]<mailto:[email protected]>> *Enviado:* segunda-feira, 25 de fevereiro de 2019 09:05 *Para:* [email protected]<mailto:[email protected]> *Assunto:* Re: [QE-users] The virtual.x problems Hi Fabio I just tried current version with Al-Ga Ga-In Al-In C-Si Si-Ge P-As, which are more or less all of pairs which come to my mind where virtual can be used, and apart from Al-Ga where it doesn't work because Ga pseudo has usually d semicores every seems to work fine. Please le me have the 2 pseudos you are trying to mix. Pietro On 24/02/19 23:41, Fabio Costa wrote: Hello everybody Sorry for reopening this post, but Im currently struggling to work with this virtual.x tool. I?m working with QE v.6.3, and tried to do the task with both the updated and original version of virtual.x. After inputting the PP to mix together, the program generates the output file, but ends with the message: At line 215 of file write_upf_v2.f90 Fortran runtime error: End of file Also, when I open the output PP, NewPseudo.UPF, it contains the following text: <?xml version ?1.0? encoding=?UTF-8??> <UPF version=?2.0.1?> Thank you all for any assistance Cheers F?bio Costa _______________________________________________ users mailing list [email protected]<mailto:[email protected]> <mailto:[email protected]<mailto:[email protected]>> https://lists.quantum-espresso.org/mailman/listinfo/users _______________________________________________ users mailing list [email protected]<mailto:[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/20190225/4dee66aa/attachment-0001.html> ------------------------------ Message: 3 Date: Mon, 25 Feb 2019 15:59:50 +0100 From: Paolo Giannozzi <[email protected]<mailto:[email protected]>> To: Quantum Espresso users Forum <[email protected]<mailto:[email protected]>> Subject: Re: [QE-users] Phonons with images Message-ID: <capmgbcvp3+-7j6haed9hxq83otkhzolj8gs+-17+8wo5twu...@mail.gmail.com<mailto:capmgbcvp3+-7j6haed9hxq83otkhzolj8gs+-17+8wo5twu...@mail.gmail.com>> Content-Type: text/plain; charset="utf-8" I recently removed many such checks that had become obsolete. Try commenting out the check. Paolo On Mon, Feb 25, 2019 at 1:53 PM Malte Sachs < [email protected]<mailto:[email protected]>> wrote: Dear all, I have tested the image-example for phonon calculations using QuantumEspresso 6.3. In the case I am using these commands: mpirun -np 4 pw.x < ... mpirun -np 4 ph.x -ni 2 < ... mpirun -np 4 ph.x < .... everything works fine. However, using this: mpirun -np 2 pw.x < ... mpirun -np 4 ph.x -ni 2 < ... mpirun -np 2 ph.x < .... yields an error in the last step: "pw.x run with a different number of processors. Use wf_collect=.true." However, I have the same number of processors in pw.x and ph.x and the wf_collect option is activated by default. So I don't know what is going on. Best regards, Malte Sachs -- Malte Sachs Anorganische Chemie, Fluorchemie Philipps-Universit?t Marburg Hans-Meerwein-Stra?e 4 35032 Marburg (Paketpost: 35043 Marburg) Tel.: +49 (0)6421 28 - 25 68 0 http://www.uni-marburg.de/fb15/ag-kraus/ _______________________________________________ users mailing list [email protected]<mailto:[email protected]> https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20190225/06876d25/attachment-0001.html> ------------------------------ Message: 4 Date: Mon, 25 Feb 2019 19:14:42 +0000 From: Fabio Costa <[email protected]<mailto:[email protected]>> To: Quantum Espresso users Forum <[email protected]<mailto:[email protected]>> Subject: Re: [QE-users] The virtual.x problems Message-ID: <ro1pr80mb3660456258da73d35f7a73bff2...@ro1pr80mb3660.lamprd80.prod.outlook.com<mailto:ro1pr80mb3660456258da73d35f7a73bff2...@ro1pr80mb3660.lamprd80.prod.outlook.com>> Content-Type: text/plain; charset="windows-1252" Thanks for the assistance Pietro I understood the point of mixing elements with different valence electrons. But even when I try to mix together isoelectronic species (such as Si and C), the generated output file NewPseudo.UPF has no information. At first I tried to use the virtual.x that comes within QE 6.3, and also tried with this updated version , after making a new virtual.x, based on these instructions: https://www.mail-archive.com/[email protected]/msg33969.html The outcome is always the same: the program ends with this fortran runtime error, and the output file comes with two lines of text: <?xml version="1.0" encoding="UTF-8"?> <UPF version="2.0.1"> I already tried to reinstall the whole QE, but nothing has changed. F?bio Costa ________________________________ De: users <[email protected]<mailto:[email protected]>> em nome de Pietro Delugas <[email protected]<mailto:[email protected]>> Enviado: segunda-feira, 25 de fevereiro de 2019 14:46 Para: [email protected]<mailto:[email protected]> Assunto: Re: [QE-users] The virtual.x problems Hi Fabio Pseudos from pseudo-dojo are perfect, they are norm-conserving and they are in upf format. You have to keep in mind that VCA has sense for isovalent atoms e. g C with Si. Ga. and In. Also pseudos would better be built with the same number of projectors. Mixing pseudos with a different number of valence electrons like B and Si is most likely not going to work. I checked B with Si though, and disappointingly the program produces an upf file. I think that it would be useful at least to print out a very evident warning about the usability of such file. Pietro The problem is the On 25/02/19 11:58, Fabio Costa wrote: Thanks for the quick reply To perform this task, I downloaded the full table of PP from pseudo dojo, with the following settings: Type:NC SR (ONCVPSP v0.4) XC: PBE Accuracy: standard Format: upf My attempts so far were to mix B-C and Si-Al, both unsuccessful. Maybe my mistake is in the choice of these PP files, and if so, where can I get the adequate ones to work with the virtual.x? Thank you all for the assistance F?bio Costa ________________________________ De: users <[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>> em nome de Pietro Delugas <[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>> Enviado: segunda-feira, 25 de fevereiro de 2019 09:05 Para: [email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>> Assunto: Re: [QE-users] The virtual.x problems Hi Fabio I just tried current version with Al-Ga Ga-In Al-In C-Si Si-Ge P-As, which are more or less all of pairs which come to my mind where virtual can be used, and apart from Al-Ga where it doesn't work because Ga pseudo has usually d semicores every seems to work fine. Please le me have the 2 pseudos you are trying to mix. Pietro On 24/02/19 23:41, Fabio Costa wrote: Hello everybody Sorry for reopening this post, but Im currently struggling to work with this virtual.x tool. I?m working with QE v.6.3, and tried to do the task with both the updated and original version of virtual.x. After inputting the PP to mix together, the program generates the output file, but ends with the message: At line 215 of file write_upf_v2.f90 Fortran runtime error: End of file Also, when I open the output PP, NewPseudo.UPF, it contains the following text: <?xml version ?1.0? encoding=?UTF-8??> <UPF version=?2.0.1?> Thank you all for any assistance Cheers F?bio Costa _______________________________________________ users mailing list [email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>> https://lists.quantum-espresso.org/mailman/listinfo/users _______________________________________________ users mailing list [email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[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/20190225/211c7156/attachment-0001.html> ------------------------------ Message: 5 Date: Tue, 26 Feb 2019 08:43:14 +0100 From: Pietro Delugas <[email protected]<mailto:[email protected]>> To: [email protected]<mailto:[email protected]> Subject: Re: [QE-users] The virtual.x problems Message-ID: <[email protected]<mailto:[email protected]>> Content-Type: text/plain; charset="windows-1252"; Format="flowed" Hi Fabio can you try to download the 6.3-backports version from here https://gitlab.com/QEF/q-e/tree/qe-6.3-backports ? or better? you can download directly the? development version from gitlab or github. Pietro On 25/02/19 20:14, Fabio Costa wrote: Thanks for the assistance Pietro I understood the point of mixing elements with different valence electrons. But even when I try to mix together isoelectronic species (such as Si and C), the generated output file NewPseudo.UPF has no information. At first I tried to use the virtual.x that comes within QE 6.3, and also tried with this updated version , after making a new virtual.x, based on these instructions: https://www.mail-archive.com/[email protected]/msg33969.html The outcome is always the same: the program ends with this fortran runtime error, and the output file comes with two lines of text: <?xml version="1.0" encoding="UTF-8"?> <UPF version="2.0.1"> I already tried to reinstall the whole QE, but nothing has changed. F?bio Costa ------------------------------------------------------------------------ *De:* users <[email protected]<mailto:[email protected]>> em nome de Pietro Delugas <[email protected]<mailto:[email protected]>> *Enviado:* segunda-feira, 25 de fevereiro de 2019 14:46 *Para:* [email protected]<mailto:[email protected]> *Assunto:* Re: [QE-users] The virtual.x problems Hi Fabio Pseudos from pseudo-dojo are perfect, they are norm-conserving and they are in upf format. ?You have to keep in mind that VCA has sense for isovalent atoms e. g C? with Si. Ga.? and In. Also pseudos would better? be built with the same number of projectors. Mixing pseudos with a different number of valence electrons like B and Si is most likely not going to work. I checked B with Si though,? and disappointingly the program produces an upf file.? I think that it would be? useful at least to print out a very evident? warning about the usability of such? file. Pietro The problem is the On 25/02/19 11:58, Fabio Costa wrote: Thanks for the quick reply To perform this task, I downloaded the full table of PP?from pseudo dojo, with the following settings: Type:NC SR (ONCVPSP v0.4) XC: PBE Accuracy: standard Format: upf My attempts so far were to mix B-C and Si-Al, both unsuccessful. Maybe my mistake is in the choice of these PP files, and if so, where can I get the adequate ones to work with the virtual.x? Thank you all for the assistance F?bio Costa ------------------------------------------------------------------------ *De:* users <[email protected]<mailto:[email protected]>> <mailto:[email protected]<mailto:[email protected]>> em nome de Pietro Delugas <[email protected]<mailto:[email protected]>> <mailto:[email protected]<mailto:[email protected]>> *Enviado:* segunda-feira, 25 de fevereiro de 2019 09:05 *Para:* [email protected]<mailto:[email protected]> <mailto:[email protected]<mailto:[email protected]>> *Assunto:* Re: [QE-users] The virtual.x problems Hi Fabio I just tried current version with Al-Ga Ga-In Al-In C-Si Si-Ge P-As, which are more or less all of pairs which come to my mind where virtual can be used, and apart from Al-Ga where it doesn't work because Ga pseudo has usually d semicores every seems to work fine. Please le me have the 2 pseudos you are trying to mix. Pietro On 24/02/19 23:41, Fabio Costa wrote: Hello everybody Sorry for reopening this post, but Im currently struggling to work with this virtual.x tool. I?m working with QE v.6.3, and tried to do the task with both the updated and original version of virtual.x. After inputting the PP to mix together, the program generates the output file, but ends with the message: At line 215 of file write_upf_v2.f90 Fortran runtime error: End of file Also, when I open the output PP, NewPseudo.UPF, it contains the following text: <?xml version ?1.0? encoding=?UTF-8??> <UPF version=?2.0.1?> Thank you all for any assistance Cheers F?bio Costa _______________________________________________ users mailing list [email protected]<mailto:[email protected]> <mailto:[email protected]<mailto:[email protected]>> https://lists.quantum-espresso.org/mailman/listinfo/users _______________________________________________ users mailing list [email protected]<mailto:[email protected]> <mailto:[email protected]<mailto:[email protected]>> https://lists.quantum-espresso.org/mailman/listinfo/users _______________________________________________ users mailing list [email protected]<mailto:[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/20190226/98ca1fff/attachment-0001.html> ------------------------------ Message: 6 Date: Tue, 26 Feb 2019 08:05:32 +0000 From: Offermans Willem <[email protected]<mailto:[email protected]>> To: Quantum Espresso users Forum <[email protected]<mailto:[email protected]>> Subject: [QE-users] Phonon Calculation erroneous Message-ID: <[email protected]<mailto:[email protected]>> Content-Type: text/plain; charset="utf-8" Dear Quantum Espresso friends, I?m running a phonon calculation and all seems to run well. But mode 5 cannot converge: <snip> ... Pert. # 1: Fermi energy shift (Ry) = -2.5081E-03 1.6156E-27 iter # 63 total cpu time : 26867.7 secs av.it.: 23.9 thresh= 1.297E-06 alpha_mix = 0.100 |ddv_scf|^2 = 6.099E-11 End of self-consistent calculation Convergence has been achieved Representation # 5 mode # 5 Self-consistent Calculation Pert. # 1: Fermi energy shift (Ry) = -1.7279E-02 0.0000E+00 iter # 1 total cpu time : 26946.8 secs av.it.: 15.7 thresh= 1.000E-02 alpha_mix = 0.100 |ddv_scf|^2 = 3.581E-06 kpoint 1 ibnd 99 solve_linter: root not converged 1.031E-03 Pert. # 1: Fermi energy shift (Ry) = -7.0043E-02 0.0000E+00 iter # 2 total cpu time : 27058.6 secs av.it.: 33.4 thresh= 1.892E-04 alpha_mix = 0.100 |ddv_scf|^2 = 2.379E-04 Pert. # 1: Fermi energy shift (Ry) = -5.5995E-02 0.0000E+00 iter # 3 total cpu time : 27143.0 secs av.it.: 20.6 thresh= 1.542E-03 alpha_mix = 0.100 |ddv_scf|^2 = 3.080E-05 Pert. # 1: Fermi energy shift (Ry) = -1.9838E-03 0.0000E+00 iter # 4 total cpu time : 27233.3 secs av.it.: 23.0 thresh= 5.550E-04 alpha_mix = 0.100 |ddv_scf|^2 = 3.693E-06 kpoint 1 ibnd 99 solve_linter: root not converged 4.283E-04 Pert. # 1: Fermi energy shift (Ry) = 3.4490E-03 0.0000E+00 iter # 5 total cpu time : 27335.3 secs av.it.: 28.2 thresh= 1.922E-04 alpha_mix = 0.100 |ddv_scf|^2 = 2.869E-05 Pert. # 1: Fermi energy shift (Ry) = -1.0061E-02 0.0000E+00 iter # 6 total cpu time : 27426.0 secs av.it.: 23.5 ? Pert. # 1: Fermi energy shift (Ry) = -2.7921E-02 0.0000E+00 iter # 98 total cpu time : 36344.4 secs av.it.: 29.4 thresh= 1.701E-04 alpha_mix = 0.100 |ddv_scf|^2 = 6.016E-06 kpoint 1 ibnd 99 solve_linter: root not converged 9.021E-04 Pert. # 1: Fermi energy shift (Ry) = 2.8328E-03 0.0000E+00 iter # 99 total cpu time : 36444.3 secs av.it.: 27.6 thresh= 2.453E-04 alpha_mix = 0.100 |ddv_scf|^2 = 1.921E-05 Pert. # 1: Fermi energy shift (Ry) = 2.4610E-02 0.0000E+00 iter # 100 total cpu time : 36536.3 secs av.it.: 23.9 thresh= 4.382E-04 alpha_mix = 0.100 |ddv_scf|^2 = 1.317E-05 End of self-consistent calculation No convergence has been achieved </snip> As you might notice, the second value of Fermi energy shift remains 0.0000E+00. What does it mean? On request, I can send you the input files. Met vriendelijke groeten, Mit freundlichen Gr??en, With kind regards, Willem Offermans Researcher Electrocatalysis SCT VITO NV | Boeretang 200 | 2400 Mol Phone:+32(0)14335263 Mobile:+32(0)492182073 [email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>> [cid:[email protected]<mailto:[email protected]>] Indien u VITO Mol bezoekt, hou aub er dan rekening mee dat de hoofdingang voortaan enkel bereikbaar is vanuit de richting Dessel-Retie, niet vanuit richting Mol, zie vito.be/route<http://vito.be/route>.<http://www.vito.be/route> If you plan to visit VITO at Mol, then please note that the main entrance can only be reached coming from Dessel-Retie and no longer coming from Mol, see vito.be/en/contact/locations<http://vito.be/en/contact/locations>.<http://www.vito.be/en/contact/locations> VITO Disclaimer: http://www.vito.be/e-maildisclaimer -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20190226/184aa461/attachment-0001.html> -------------- next part -------------- A non-text attachment was scrubbed... Name: vito.jpg Type: image/jpeg Size: 15232 bytes Desc: vito.jpg URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20190226/184aa461/attachment-0001.jpg> ------------------------------ Message: 7 Date: Tue, 26 Feb 2019 09:11:18 +0100 From: Lorenzo Paulatto <[email protected]<mailto:[email protected]>> To: [email protected]<mailto:[email protected]> Subject: Re: [QE-users] Phonon Calculation erroneous Message-ID: <[email protected]<mailto:[email protected]>> Content-Type: text/plain; charset=utf-8; format=flowed As you might notice, the second value of Fermi energy shift remains ?0.0000E+00. This is normal: if the positions of the atoms are all fixed by symmetry the Fermi shift is zero. Regarding the convergence, it is not converging but it is not exploding either, which may indicate that it is just a question of reducing the alpha_mix of phonon to have it converge, by default it is alpha_mix(1) = 0.7 You can try alpha_mix(1) = 0.3 alpha_mix(2) = 0.1 hth -- Lorenzo Paulatto - Paris ------------------------------ Subject: Digest Footer _______________________________________________ users mailing list [email protected]<mailto:[email protected]> https://lists.quantum-espresso.org/mailman/listinfo/users ------------------------------ End of users Digest, Vol 139, Issue 27 ************************************** _______________________________________________ users mailing list [email protected]<mailto:[email protected]> https://lists.quantum-espresso.org/mailman/listinfo/users
_______________________________________________ users mailing list [email protected] https://lists.quantum-espresso.org/mailman/listinfo/users
