Thank you Lorenzo and Paolo for troubleshooting the input file error. Now the code is running smoothly. Suraj Research student, IIT Kharagpur
----- Original Message ----- From: users-requ...@lists.quantum-espresso.org To: "users" <users@lists.quantum-espresso.org> Sent: Monday, July 15, 2024 3:30:01 PM Subject: users Digest, Vol 204, Issue 12 Send users mailing list submissions to users@lists.quantum-espresso.org 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 users-requ...@lists.quantum-espresso.org You can reach the person managing the list at users-ow...@lists.quantum-espresso.org When replying, please edit your Subject line so it is more specific than "Re: Contents of users digest..." Today's Topics: 1. Re: dipole correction with assume isolated ESM (Minoru Otani) 2. MPI error (Suraj P) 3. Re: MPI error (Paolo Giannozzi) 4. Re: MPI error (Lorenzo Paulatto) 5. Re: MPI error (Lorenzo Paulatto) 6. Re: dipole correction with assume isolated ESM (Lucian D. Filip) ---------------------------------------------------------------------- Message: 1 Date: Mon, 15 Jul 2024 10:59:05 +0900 From: Minoru Otani <ot...@ccs.tsukuba.ac.jp> To: Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org> Subject: Re: [QE-users] dipole correction with assume isolated ESM Message-ID: <4c175fd1-0cd7-485c-8acc-b28da0ca5...@ccs.tsukuba.ac.jp> Content-Type: text/plain; charset=us-ascii Dear Lucian, By using esm_bc=bc1, you can obtain the desired results. In this case, dipole correction is not necessary. If you are calculating a system with no net dipole, the electrostatic potential on both sides will be flat and at the same level. On the other hand, if the system has a net dipole, the electrostatic potential on both sides will be flat, but the height of these flat regions will differ. This difference in height is related to the total dipole moment of the system. The former can be correctly calculated even with conventional periodic boundary conditions, while the latter can be naturally calculated using ESM (esm_bc=bc1). Best regards, Minoru ------------------------------------------------------------------------------------------------------- Minoru Otani, Ph.D., Professor Center for Computational Sciences and Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan E-mail: ot...@ccs.tsukuba.ac.jp Web: https://www2.ccs.tsukuba.ac.jp/public/otani/ -------------------------------------------------------------------------------------------------------- > On Jul 12, 2024, at 18:47, Lucian D. Filip <lucian.fi...@infim.ro> wrote: > > Hello all, > > Is it possible to use the " assume_isolated='esm' ", with the " esm_bc='bc2' > " flag for a slab geometry and perform the dipole correction? I have tried > with 'esm_field=0' but it doesn't seem to enforce the 0 field in vacuum. > Rather it just performs a regular scf calculation with no applied field. > > I know about the '2D' option but that adds other complications because if I > increase the slab thickness, the vacuum region becomes really big in order to > ensure that the Coulombian cutoff is not too close to the slab to influence > the slab. > > Is there a way to enforce a zero field in the vacuum region with ESM? > > > Regards, > > > Lucian > > -- > Dr. Lucian Dragos Filip > National Institute of Materials Physics > Atomistilor str. 405A, PO Box MG. 7 > Magurele, 077125 > Bucharest, Romania > E-mail: lucian.fi...@infim.ro > Website: https://lucianfilip.wordpress.com/ > > _______________________________________________ > 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@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users ------------------------------ Message: 2 Date: Mon, 15 Jul 2024 11:35:05 +0530 (IST) From: Suraj P <sur...@iitkgp.ac.in> To: users@lists.quantum-espresso.org Subject: [QE-users] MPI error Message-ID: <658935827.2695548.1721023505157.javamail.zim...@iitkgp.ac.in> Content-Type: text/plain; charset="utf-8" Dear QE users, Im trying to do a relaxation calculation of a Copper unit cell doped with Nickel. 75 % of the atoms are doped with Nickel and the remaining atoms are Copper. During the vc-relax calculation, Im getting an error message as follows, and the calculation gets automatically terminated: ______________________________________________________________________________________________ forrtl: severe (24): end-of-file during read, unit -5, file Internal List-Directed Read Image PC Routine Line Source pw.x 0000000000FE39AB Unknown Unknown Unknown pw.x 00000000010143B2 Unknown Unknown Unknown pw.x 0000000001013138 Unknown Unknown Unknown pw.x 0000000000A03FCC read_cards_module 135 read_cards.f90 pw.x 00000000009230B6 read_input_mp_rea 67 read_input.f90 pw.x 000000000040BF62 MAIN__ 84 pwscf.f90 pw.x 000000000040BDD2 Unknown Unknown Unknown libc-2.17.so 00007F893BB0A555 __libc_start_main Unknown Unknown pw.x 000000000040BCE9 Unknown Unknown Unknown ______________________________________________________________________________ I have attached the input and output files herewith. Kindly help me in troubleshooting this issue. Im using quantum_espresso-6.8 and openmpi-5.0.3 compiler. Thanks regards Suraj Research student,IIT kharagpur -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: inputfile.in URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20240715/5ad993ee/attachment-0002.ksh> -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: outputfile.out URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20240715/5ad993ee/attachment-0003.ksh> ------------------------------ Message: 3 Date: Mon, 15 Jul 2024 08:38:51 +0200 From: Paolo Giannozzi <paolo.gianno...@uniud.it> To: Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org>, Suraj P <sur...@iitkgp.ac.in> Subject: Re: [QE-users] MPI error Message-ID: <ba603840-b5ac-4f98-8962-67740ef8d...@uniud.it> Content-Type: text/plain; charset=UTF-8; format=flowed Dear Suraj, it's not a "MPI error": it is an error reading the input data, notably one of the "cards". There is nothing obviously wrong in your data, but consider that errors can be produced by bad characters, DOS CR-LF characters, missing EOL (end-of-line) in the last line, ... PAolo On 15/07/2024 08:05, Suraj P wrote: > > Dear QE users, > > Im trying to do a relaxation calculation of a Copper unit cell doped with > Nickel. 75 % of the atoms are doped with Nickel and the remaining atoms are > Copper. > During the vc-relax calculation, Im getting an error message as follows, and > the calculation gets automatically terminated: > ______________________________________________________________________________________________ > > forrtl: severe (24): end-of-file during read, unit -5, file Internal > List-Directed Read > Image PC Routine Line Source > pw.x 0000000000FE39AB Unknown Unknown Unknown > pw.x 00000000010143B2 Unknown Unknown Unknown > pw.x 0000000001013138 Unknown Unknown Unknown > pw.x 0000000000A03FCC read_cards_module 135 > read_cards.f90 > pw.x 00000000009230B6 read_input_mp_rea 67 > read_input.f90 > pw.x 000000000040BF62 MAIN__ 84 pwscf.f90 > pw.x 000000000040BDD2 Unknown Unknown Unknown > libc-2.17.so 00007F893BB0A555 __libc_start_main Unknown Unknown > pw.x 000000000040BCE9 Unknown Unknown Unknown > ______________________________________________________________________________ > > > I have attached the input and output files herewith. Kindly help me in > troubleshooting this issue. > Im using quantum_espresso-6.8 and openmpi-5.0.3 compiler. > > Thanks regards > Suraj > Research student,IIT kharagpur > > > _______________________________________________ > 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@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 X SCUOLA ENERGIE RINNOVABILI 16-21/9/2024 - PRE-ISCRIZIONE https://agenda.infn.it/event/39573/ ------------------------------ Message: 4 Date: Mon, 15 Jul 2024 09:49:16 +0200 From: Lorenzo Paulatto <lorenzo.paula...@cnrs.fr> To: <users@lists.quantum-espresso.org> Subject: Re: [QE-users] MPI error Message-ID: <f10fea8f-fad5-4dca-8979-e621bc414...@cnrs.fr> Content-Type: text/plain; charset="utf-8"; Format="flowed" Hello, if I understand correctly, you used the dash character ??? instead of minus sign ?-? in many places all over the file. On 15/07/2024 08:05, Suraj P wrote: > Dear QE users, > > Im trying to do a relaxation calculation of a Copper unit cell doped with > Nickel. 75 % of the atoms are doped with Nickel and the remaining atoms are > Copper. > During the vc-relax calculation, Im getting an error message as follows, and > the calculation gets automatically terminated: > ______________________________________________________________________________________________ > > forrtl: severe (24): end-of-file during read, unit -5, file Internal > List-Directed Read > Image PC Routine Line Source > pw.x 0000000000FE39AB Unknown Unknown Unknown > pw.x 00000000010143B2 Unknown Unknown Unknown > pw.x 0000000001013138 Unknown Unknown Unknown > pw.x 0000000000A03FCC read_cards_module 135 > read_cards.f90 > pw.x 00000000009230B6 read_input_mp_rea 67 > read_input.f90 > pw.x 000000000040BF62 MAIN__ 84 pwscf.f90 > pw.x 000000000040BDD2 Unknown Unknown Unknown > libc-2.17.so 00007F893BB0A555 __libc_start_main Unknown Unknown > pw.x 000000000040BCE9 Unknown Unknown Unknown > ______________________________________________________________________________ > > > I have attached the input and output files herewith. Kindly help me in > troubleshooting this issue. > Im using quantum_espresso-6.8 and openmpi-5.0.3 compiler. > > Thanks regards > Suraj > Research student,IIT kharagpur > > _______________________________________________ > 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 listus...@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Dr. Lorenzo Paulatto IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Universit? phone: +33 (0)1 442 79822 / skype: paulatz http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/ 23-24/423 B115, 4 place Jussieu 75252 Paris CX 05 -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20240715/6a3a9a14/attachment-0001.html> ------------------------------ Message: 5 Date: Mon, 15 Jul 2024 09:53:38 +0200 From: Lorenzo Paulatto <lorenzo.paula...@cnrs.fr> To: <users@lists.quantum-espresso.org> Subject: Re: [QE-users] MPI error Message-ID: <7eff1ec7-d390-4ed4-b0f0-79766b263...@cnrs.fr> Content-Type: text/plain; charset="utf-8"; Format="flowed" Nevermind, my monitor was playing tricks on me. The actual problem is the line just before "ATOMIC_POSITIONS" which is not empty, but contains several TAB characters. Remove it and the input will work hth On 15/07/2024 09:49, Lorenzo Paulatto wrote: > > Hello, > > if I understand correctly, you used the dash character ??? instead of > minus sign ?-? in many places all over the file. > > On 15/07/2024 08:05, Suraj P wrote: >> Dear QE users, >> >> Im trying to do a relaxation calculation of a Copper unit cell doped with >> Nickel. 75 % of the atoms are doped with Nickel and the remaining atoms are >> Copper. >> During the vc-relax calculation, Im getting an error message as follows, and >> the calculation gets automatically terminated: >> ______________________________________________________________________________________________ >> >> forrtl: severe (24): end-of-file during read, unit -5, file Internal >> List-Directed Read >> Image PC Routine Line Source >> pw.x 0000000000FE39AB Unknown Unknown Unknown >> pw.x 00000000010143B2 Unknown Unknown Unknown >> pw.x 0000000001013138 Unknown Unknown Unknown >> pw.x 0000000000A03FCC read_cards_module 135 >> read_cards.f90 >> pw.x 00000000009230B6 read_input_mp_rea 67 >> read_input.f90 >> pw.x 000000000040BF62 MAIN__ 84 pwscf.f90 >> pw.x 000000000040BDD2 Unknown Unknown Unknown >> libc-2.17.so 00007F893BB0A555 __libc_start_main Unknown Unknown >> pw.x 000000000040BCE9 Unknown Unknown Unknown >> ______________________________________________________________________________ >> >> >> I have attached the input and output files herewith. Kindly help me in >> troubleshooting this issue. >> Im using quantum_espresso-6.8 and openmpi-5.0.3 compiler. >> >> Thanks regards >> Suraj >> Research student,IIT kharagpur >> >> _______________________________________________ >> 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 listus...@lists.quantum-espresso.org >> https://lists.quantum-espresso.org/mailman/listinfo/users > -- > Dr. Lorenzo Paulatto > IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Universit? > phone: +33 (0)1 442 79822 / skype: paulatz > http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/ > 23-24/423 B115, 4 place Jussieu 75252 Paris CX 05 -- Dr. Lorenzo Paulatto IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Universit? phone: +33 (0)1 442 79822 / skype: paulatz http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/ 23-24/423 B115, 4 place Jussieu 75252 Paris CX 05 -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20240715/e7d6d01f/attachment-0001.html> ------------------------------ Message: 6 Date: Mon, 15 Jul 2024 12:09:47 +0300 From: "Lucian D. Filip" <lucian.fi...@infim.ro> To: users@lists.quantum-espresso.org Subject: Re: [QE-users] dipole correction with assume isolated ESM Message-ID: <61fe331f-678f-4c97-81a0-d83a1a4d1...@infim.ro> Content-Type: text/plain; charset=UTF-8; format=flowed Dear Minoru, Thank you very much for this clarification! I finally understand it now! I have now tested my example and saw that there is no difference between a 10 angstrom vacuum region and a 20 vacuum region on either side of my slab. This is good news for me for my future calculations! Best regards, Lucian On 15-Jul-24 4:59 AM, Minoru Otani wrote: > Dear Lucian, > > By using esm_bc=bc1, you can obtain the desired results. In this case, dipole > correction is not necessary. > > If you are calculating a system with no net dipole, the electrostatic > potential on both sides will be flat and at the same level. On the other > hand, if the system has a net dipole, the electrostatic potential on both > sides will be flat, but the height of these flat regions will differ. This > difference in height is related to the total dipole moment of the system. > > The former can be correctly calculated even with conventional periodic > boundary conditions, while the latter can be naturally calculated using ESM > (esm_bc=bc1). > > Best regards, > Minoru > ------------------------------------------------------------------------------------------------------- > Minoru Otani, Ph.D., Professor > Center for Computational Sciences and Faculty of Pure and Applied Sciences, > University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan > E-mail: ot...@ccs.tsukuba.ac.jp > Web: https://www2.ccs.tsukuba.ac.jp/public/otani/ > -------------------------------------------------------------------------------------------------------- > >> On Jul 12, 2024, at 18:47, Lucian D. Filip <lucian.fi...@infim.ro> wrote: >> >> Hello all, >> >> Is it possible to use the " assume_isolated='esm' ", with the " esm_bc='bc2' >> " flag for a slab geometry and perform the dipole correction? I have tried >> with 'esm_field=0' but it doesn't seem to enforce the 0 field in vacuum. >> Rather it just performs a regular scf calculation with no applied field. >> >> I know about the '2D' option but that adds other complications because if I >> increase the slab thickness, the vacuum region becomes really big in order >> to ensure that the Coulombian cutoff is not too close to the slab to >> influence the slab. >> >> Is there a way to enforce a zero field in the vacuum region with ESM? >> >> >> Regards, >> >> >> Lucian >> >> -- >> Dr. Lucian Dragos Filip >> National Institute of Materials Physics >> Atomistilor str. 405A, PO Box MG. 7 >> Magurele, 077125 >> Bucharest, Romania >> E-mail: lucian.fi...@infim.ro >> Website: https://lucianfilip.wordpress.com/ >> >> _______________________________________________ >> 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@lists.quantum-espresso.org >> https://lists.quantum-espresso.org/mailman/listinfo/users > _______________________________________________ > 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@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Dr. Lucian Dragos Filip National Institute of Materials Physics Atomistilor str. 405A, PO Box MG. 7 Magurele, 077125 Bucharest, Romania E-mail: lucian.fi...@infim.ro Website: https://lucianfilip.wordpress.com/ ------------------------------ 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@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users ------------------------------ End of users Digest, Vol 204, 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 users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users