From divyasrivastava at jncasr.ac.in Thu Mar 1 07:38:57 2012 From: divyasrivastava at jncasr.ac.in (Divya Srivastava) Date: Thu, 01 Mar 2012 12:08:57 +0530 Subject: [Pw_forum] (no subject) Message-ID: <1330583937.4f4f1981da078@mercury.jncasr.ac.in> Hi I want to do phonon calculation for Nickel with 6 6 6 nq's point. Can any body suggest me how many nodes I should take to run ph.x in parallel environment. Divya Srivastava Research Associate TSU, JNCASR Jakkur, Bangalore-64 Tel: 080-2208-2834 From giacsport at libero.it Thu Mar 1 07:55:07 2012 From: giacsport at libero.it (giacsport at libero.it) Date: Thu, 1 Mar 2012 07:55:07 +0100 (CET) Subject: [Pw_forum] "vc_relax" + "nscf" calculation Message-ID: <7419024.4571951330584907945.JavaMail.defaultUser@defaultHost> Dear all, I performed some calculations with the version of the code installed in the Cineca Supercomputer Center (4.1). I did "vc_relax" calculations for the optimization of ZB, RS, and WZ-ZnO and I got reasonable results. Then I would like to do "nscf" calculation for the bands. Anyway, once I restart the "nscf" calculation (where I increase the k-point sampling and the number of Bands) I get this error message that is related to the incompatibility of the FFT between the "vc_relax" and the "nscf" calculation. .......................... G cutoff = 596.5241 ( 16071 G-vectors) FFT grid: ( 36, 36, 42) Largest allocated arrays est. size (Mb) dimensions Kohn-Sham Wavefunctions 0.40 Mb ( 174, 150) NL pseudopotentials 0.07 Mb ( 174, 26) Each V/rho on FFT grid 0.16 Mb ( 5184, 2) Each G-vector array 0.01 Mb ( 1339) G-vector shells 0.01 Mb ( 1021) Largest temporary arrays est. size (Mb) dimensions Auxiliary wavefunctions 1.59 Mb ( 174, 600) Each subspace H/S matrix 5.49 Mb ( 600, 600) Each matrix 0.06 Mb ( 26, 150) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_rho_xml : error # 1 dimensions do not match %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... How to fix it? Thanks in advance!Giacomo This is the input file for the "nscf" calculation. ( The "vc-relax" went fine, so I do not report the input) &control calculation = 'nscf' restart_mode = 'restart' prefix='ZnO_RS', tprnfor = .true., tstress = .true., wf_collect=.true., pseudo_dir='./', outdir='./', / &system ibrav= 2, celldm(1) =8.088027231 nat= 2, ntyp= 2, ecutwfc =90., nbnd = 150, nspin=2, tot_magnetization=0, occupations='smearing', degauss=0.01,smearing='gaussian', starting_magnetization(1)=1, force_symmorphic=.true. / &electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES Zn 65.38 Zn-GGA-pbe.fhi.UPF O 15.9994 O-GGA-pbe.fhi.UPF ATOMIC_POSITIONS (crystal) Zn 0.00000 0.00000 0.00000 O 0.00000 0.00000 0.50000 K_POINTS automatic 8 8 8 0 0 0 -- *************************************** Giacomo Giorgi, Ph.D. Yamashita & Ushiyama Laboratory, Department of Chemical System Engineering, Faculty of Engineering, The University of Tokyo. tel&fax: +81-3-5841-7286 email: giacomo at tcl.t.u-tokyo.ac.jp HP: http://www.tcl.t.u-tokyo.ac.jp/ *************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120301/399ac751/attachment.htm From giacsport at libero.it Thu Mar 1 08:22:56 2012 From: giacsport at libero.it (giacsport at libero.it) Date: Thu, 1 Mar 2012 08:22:56 +0100 (CET) Subject: [Pw_forum] R: Re: "vc_relax" + "nscf" calculation Message-ID: <16042325.4578011330586576198.JavaMail.defaultUser@defaultHost> Well, I did but the "scf" restarted calculation (from the .save dir) leads to a different (higher) value of the final enthalpy.... and this makes me suspicious about such procedure.... thanks in any case, G ----Messaggio originale---- Da: nkxirainbow at gmail.com Data: 01/03/2012 8.01 A: "giacsport at libero.it" Ogg: Re: [Pw_forum] "vc_relax" + "nscf" calculation Dear Giacomo Giorgi? Try to do an additional scf calculation before "nscf". Maybe it works:) On Thu, Mar 1, 2012 at 2:55 PM, giacsport at libero.it wrote: Dear all, I performed some calculations with the version of the code installed in the Cineca Supercomputer Center (4.1). I did "vc_relax" calculations for the optimization of ZB, RS, and WZ-ZnO and I got reasonable results. Then I would like to do "nscf" calculation for the bands. Anyway, once I restart the "nscf" calculation (where I increase the k-point sampling and the number of Bands) I get this error message that is related to the incompatibility of the FFT between the "vc_relax" and the "nscf" calculation. .......................... G cutoff = 596.5241 ( 16071 G-vectors) FFT grid: ( 36, 36, 42) Largest allocated arrays est. size (Mb) dimensions Kohn-Sham Wavefunctions 0.40 Mb ( 174, 150) NL pseudopotentials 0.07 Mb ( 174, 26) Each V/rho on FFT grid 0.16 Mb ( 5184, 2) Each G-vector array 0.01 Mb ( 1339) G-vector shells 0.01 Mb ( 1021) Largest temporary arrays est. size (Mb) dimensions Auxiliary wavefunctions 1.59 Mb ( 174, 600) Each subspace H/S matrix 5.49 Mb ( 600, 600) Each matrix 0.06 Mb ( 26, 150) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_rho_xml : error # 1 dimensions do not match %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... How to fix it? Thanks in advance!Giacomo This is the input file for the "nscf" calculation. ( The "vc-relax" went fine, so I do not report the input) &control calculation = 'nscf' restart_mode = 'restart' prefix='ZnO_RS', tprnfor = .true., tstress = .true., wf_collect=.true., pseudo_dir='./', outdir='./', / &system ibrav= 2, celldm(1) =8.088027231 nat= 2, ntyp= 2, ecutwfc =90., nbnd = 150, nspin=2, tot_magnetization=0, occupations='smearing', degauss=0.01,smearing='gaussian', starting_magnetization(1)=1, force_symmorphic=.true. / &electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES Zn 65.38 Zn-GGA-pbe.fhi.UPF O 15.9994 O-GGA-pbe.fhi.UPF ATOMIC_POSITIONS (crystal) Zn 0.00000 0.00000 0.00000 O 0.00000 0.00000 0.50000 K_POINTS automatic 8 8 8 0 0 0 -- *************************************** Giacomo Giorgi, Ph.D. Yamashita & Ushiyama Laboratory, Department of Chemical System Engineering, Faculty of Engineering, The University of Tokyo. tel&fax: +81-3-5841-7286 email: giacomo at tcl.t.u-tokyo.ac.jp HP: http://www.tcl.t.u-tokyo.ac.jp/ *************************************** _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- ____________________________________ Hui Wang School of physics, Fudan University, Shanghai, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120301/4eb2686a/attachment-0001.htm From giannozz at democritos.it Thu Mar 1 08:39:40 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 1 Mar 2012 08:39:40 +0100 Subject: [Pw_forum] "vc_relax" + "nscf" calculation In-Reply-To: <16042325.4578011330586576198.JavaMail.defaultUser@defaultHost> References: <16042325.4578011330586576198.JavaMail.defaultUser@defaultHost> Message-ID: On Mar 1, 2012, at 8:22 , giacsport at libero.it wrote: > I did but the "scf" restarted calculation (from the .save dir) > leads to a different (higher) value of the final enthalpy.... > and this makes me suspicious about such procedure.... ...and this makes me suspicious about the correctness of what you are doing P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giacsport at libero.it Thu Mar 1 08:52:59 2012 From: giacsport at libero.it (giacsport at libero.it) Date: Thu, 1 Mar 2012 08:52:59 +0100 (CET) Subject: [Pw_forum] R: Re: "vc_relax" + "nscf" calculation Message-ID: <970303.4701271330588379462.JavaMail.defaultUser@defaultHost> Good morning Paolo, well, if I do a "nscf" after the "vc-relax" as far as I know the geometry taken into account should be that from the previous optimization.... but maybe I am wrong.... Thanks and excuse me, G >----Messaggio originale---- >Da: giannozz at democritos.it >Data: 01/03/2012 8.39 >A: >Cc: >Ogg: Re: [Pw_forum] "vc_relax" + "nscf" calculation > > >On Mar 1, 2012, at 8:22 , giacsport at libero.it wrote: > >> I did but the "scf" restarted calculation (from the .save dir) >> leads to a different (higher) value of the final enthalpy.... >> and this makes me suspicious about such procedure.... > >...and this makes me suspicious about the correctness >of what you are doing > >P. >--- >Paolo Giannozzi, Dept of Chemistry&Physics&Environment, >Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >Phone +39-0432-558216, fax +39-0432-558222 > > > > > From somayehfotohi at yahoo.com Thu Mar 1 09:40:10 2012 From: somayehfotohi at yahoo.com (somayeh fotohi) Date: Thu, 1 Mar 2012 00:40:10 -0800 (PST) Subject: [Pw_forum] scf calculations Message-ID: <1330591210.15616.YahooMailClassic@web161402.mail.bf1.yahoo.com> Dear all, ? I performe?scf calculations but running the program is stopped with erorr " too many bands are not converged".I chane the below parameter in the input scf but?the error remains . ? - reduce mixing beta from 0.7 to 0.5 and 0.3. - increase energy cut off to from 60 to 70 Ry Also, I alter?C.pz-vbc.UPF to C.pz-rrkjus.UPF but this failure appears?" diagonalization (ZHEGV*) failed " ? ?Can anyone help me? ? Somayeh Fotoohi ? ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120301/9d4f2b5c/attachment.htm From giacsport at libero.it Thu Mar 1 10:11:05 2012 From: giacsport at libero.it (giacsport at libero.it) Date: Thu, 1 Mar 2012 10:11:05 +0100 (CET) Subject: [Pw_forum] R: Re: "vc_relax" + "nscf" calculation Message-ID: <8747375.4750571330593065338.JavaMail.defaultUser@defaultHost> Dear Paolo, I think I figured it out. After the "vc-relax" (ibrav=2) calculation, an "scf" calculation with ibrav=0 and starting from the optimized cell parameter (alat) from the "vc-relax" calculation. Then on top of it the "nscf" one. Best regards, Giacomo >----Messaggio originale---- >Da: giannozz at democritos.it >Data: 01/03/2012 8.39 >A: >Cc: >Ogg: Re: [Pw_forum] "vc_relax" + "nscf" calculation > > >On Mar 1, 2012, at 8:22 , giacsport at libero.it wrote: > >> I did but the "scf" restarted calculation (from the .save dir) >> leads to a different (higher) value of the final enthalpy.... >> and this makes me suspicious about such procedure.... > >...and this makes me suspicious about the correctness >of what you are doing > >P. >--- >Paolo Giannozzi, Dept of Chemistry&Physics&Environment, >Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >Phone +39-0432-558216, fax +39-0432-558222 > > > > > From habdslam at yahoo.fr Thu Mar 1 10:30:02 2012 From: habdslam at yahoo.fr (Abdeslam Houari) Date: Thu, 1 Mar 2012 09:30:02 +0000 (GMT) Subject: [Pw_forum] Re : scf calculations In-Reply-To: <1330591210.15616.YahooMailClassic@web161402.mail.bf1.yahoo.com> Message-ID: <1330594202.48876.YahooMailClassic@web27405.mail.ukl.yahoo.com> Dear Somayeh; Since you have reduced the beta-mixing and increased the cut-off without success, try to change the type of diagonalization (for the two kind of PP)...it will may be work.? Good luck ======================================= Abdesalem HOUARI ------------------------------------------------------------------------------------------- Department of physics, Theoretical Physics Laboratory University of Bejaia-06000. Algeria. E-mail:?abdeslam.houari at univ-bejaia.dz & habdslam at yahoo.fr https://sites.google.com/site/houariabdeslam/homepage ======================================== --- En date de?: Jeu 1.3.12, somayeh fotohi a ?crit?: De: somayeh fotohi Objet: [Pw_forum] scf calculations ?: Pw_forum at pwscf.org Date: Jeudi 1 mars 2012, 9h40 Dear all, ? I performe?scf calculations but running the program is stopped with erorr " too many bands are not converged".I chane the below parameter in the input scf but?the error remains . ? - reduce mixing beta from 0.7 to 0.5 and 0.3. - increase energy cut off to from 60 to 70 Ry Also, I alter?C.pz-vbc.UPF to C.pz-rrkjus.UPF but this failure appears?" diagonalization (ZHEGV*) failed " ? ?Can anyone help me? ? Somayeh Fotoohi ? ? -----La pi?ce jointe associ?e suit----- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120301/72f2f90c/attachment.htm From giannozz at democritos.it Thu Mar 1 10:37:15 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 01 Mar 2012 10:37:15 +0100 Subject: [Pw_forum] R: Re: "vc_relax" + "nscf" calculation In-Reply-To: <8747375.4750571330593065338.JavaMail.defaultUser@defaultHost> References: <8747375.4750571330593065338.JavaMail.defaultUser@defaultHost> Message-ID: <1330594635.20858.34.camel@fe12lx.fisica.uniud.it> On Thu, 2012-03-01 at 10:11 +0100, giacsport at libero.it wrote: > After the "vc-relax" (ibrav=2) calculation, an "scf" calculation > with ibrav=0 and starting from the optimized cell parameter (alat) > from the "vc-relax" calculation. Then on top of it the "nscf" one. I don't think it is no longer needed to perform an intermediate scf calculation. Just get the final optimized cell parameters and positions (the latter will be read from data file anyway, but the input cell parameters determine the real- and reciprocal space grid). You should have the same FFT grid parameters (nr1, nr1s etc.: they are reprinted on output) that in the final scf run of the vc-relax calculation (may differ from those in the initial run). Works properly only on recent releases (4.3.2 and later) P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From m.abbasnejad at gmail.com Thu Mar 1 13:23:36 2012 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Thu, 1 Mar 2012 15:53:36 +0330 Subject: [Pw_forum] (010) surface of Anatase Message-ID: Dear all, I am focusing on simulation of (1 0 1) surface of Anatase TiO2. I have derived the orthogonal vectors for this surface as : a' = c-a, b' = b, c' = 4c + 25 a (a, b, c are related to the conventional unit cell) However, I am not sure about my procedure, since it leads to the volume 29 times of the conventional bulk structure. which it means that I have to consider 29*12 atoms for constructing. I will appreciate it if you would help me about the atomic position and normal vectors in this surface. Thanks in advance. Yours, Mohaddeseh --------------------------------------------------------- Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran, North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 Cellphone: +98 917 731 7514 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir --------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120301/f28d7001/attachment.htm From bdslipun at gmail.com Thu Mar 1 13:34:15 2012 From: bdslipun at gmail.com (bhabya sahoo) Date: Thu, 1 Mar 2012 18:04:15 +0530 Subject: [Pw_forum] thermal conductivity In-Reply-To: References: Message-ID: On Tue, Feb 28, 2012 at 12:30 PM, bhabya sahoo wrote: > how one can calculate the thermal conductivity by the use of boltzmann > transport theory > using quantum espresso code bcause i have seen some journal papers about > this > what should be path to get this > > > references and suggetions are highly appricieted > > > > > > > > Bd SAHOO RESERCH SCHOLAR > > MUMBAI > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120301/eaf1898c/attachment.htm From yunpengwang at live.com Thu Mar 1 16:39:33 2012 From: yunpengwang at live.com (Peter Wang) Date: Thu, 1 Mar 2012 23:39:33 +0800 Subject: [Pw_forum] surface embedding method to simulate semi-infinite system Message-ID: Hi PW developers and users: Recently I found the ?surface embedding method? propused by Inglesfield and Ishida is interesting and maybe powerful. In this method, surfaces are simulated by infinite system instead of slabs with finite number of layers. I found that this method seems to be implemented in LAPW basis. My question is has this method been implemented by PWSCF? Or is there any other free software implementing this method? best wishes, Yun-Peng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120301/ec4d0351/attachment.htm From cwandtj at gmail.com Thu Mar 1 20:56:46 2012 From: cwandtj at gmail.com (Chan-Woo Lee) Date: Thu, 1 Mar 2012 14:56:46 -0500 Subject: [Pw_forum] [LDA+U] elements in occupation matrix are real number? Message-ID: <000901ccf7e5$70303240$509096c0$@gmail.com> Dear QE developers and users, I have a question in understanding occupation matrix from LDA+U output file. 1) Definition of occupation matrix, n is: n= \sum{f}, where psi is KS eigenstates, phi_i is atomic orbital of i orbital, f is scaling factor. As i and j from phi_i and phi_j don't have to be identical, I think it's not guaranteed that elements in n matrix are always real. However, in the QE output, they are all shown as real numbers. In new_ns.f90, I can find that n (nr and ns) are defined as real numbers but I can't find any restrictions other than this. 2) While elements in the matrix are real, some of them are "negative". How can I understand this? I found one paper about multiconfigurational character of wave functions (http://jcp.aip.org/resource/1/jcpsa6/v110/i9/p4199_s1 ) but it's beyond my scope. Did I miss something? Any suggestions and advices will truly be appreciated. Sincerely, Chan-Woo ------- Chan-Woo Lee, Ph.D. Postdoctoral Research Associate Department of Chemistry University of Pennsylvania 231 South 34th Street Philadelphia, PA 19104-6323 Phone: 1-215-898-3564 (Office) Email: leechanw at sas.upenn.edu / cwandtj at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120301/b6d62b1d/attachment-0001.htm From cwandtj at gmail.com Fri Mar 2 04:08:12 2012 From: cwandtj at gmail.com (Chan-Woo Lee) Date: Thu, 1 Mar 2012 22:08:12 -0500 Subject: [Pw_forum] Error in using bands_FS.x to get Fermi surface, Message-ID: <000f01ccf821$b57a6b90$206f42b0$@gmail.com> Dear QE developers and users, I am trying to get Fermi surface using kvecs_FS.x and bands_FS.x. I have followed example08 and have succeeded to get K-points using kvecs_FS.x. However, I got following error message when I execute bands_FS.x: At line 230 of file bands_FS.f90 Fortran runtime error: Bad real number in item 13 of list input Line 230 of bands_FS.f90 is about reading spin-up energies.. But I have no idea why the code is not working. FYI, I added my input files for kvecs_FS.x and bands_FS.x: kvecs_FS.in: 0.317093 0.00 0.00 0.00 0.317093 0.00 0.00 0.00 0.317093 12 12 12 CWrium input_FS.in: 10 14 22.8158 CWrium 12 12 12 0.317093 0.00 0.00 0.00 0.317093 0.00 0.00 0.00 0.317093 Here, 10 14 are min. and max. band no. (no. of bands for my SCF calc. is 20), and 22.8158 is Fermi energy. Again, your help will truly be appreciated. I cc'ed Dr. Eyvaz Isaev who is the author of the two codes. Sincerely, Chan-Woo ------- Chan-Woo Lee, Ph.D. Postdoctoral Research Associate Department of Chemistry University of Pennsylvania 231 South 34th Street Philadelphia, PA 19104-6323 Phone: 1-215-898-3564 (Office) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120301/20d8ad7e/attachment.htm From flux_ray12 at 163.com Fri Mar 2 06:02:12 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Fri, 2 Mar 2012 13:02:12 +0800 (CST) Subject: [Pw_forum] Error in using bands_FS.x to get Fermi surface, In-Reply-To: <000f01ccf821$b57a6b90$206f42b0$@gmail.com> References: <000f01ccf821$b57a6b90$206f42b0$@gmail.com> Message-ID: <437a2cf1.1af57.135d1c969fe.Coremail.flux_ray12@163.com> I checked the code of bands_FS.f90, and found like this: open(12,file='input_FS') read(12,*) n_start, n_last read(12,*) E_fermi read(12,*) sysname read(12,*) na,nb, nc read(12,*) x(1),x(2),x(3) read(12,*) y(1),y(2),y(3) read(12,*) z(1),z(2),z(3) So I am just wondering whether it can work well, if you change your input file name as "input_FS", and run only by the command bands_FS.x < CWrium.fs.in > CWrium.fs.out, where CWrium.fs.in is a nscf calculation input file with the K_Points obtained by kvec_FS.x. The more ditailed process is in example 08. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-03-02 11:08:12,"Chan-Woo Lee" wrote: Dear QE developers and users, I am trying to get Fermi surface using kvecs_FS.x and bands_FS.x. I have followed example08 and have succeeded to get K-points using kvecs_FS.x. However, I got following error message when I execute bands_FS.x: At line 230 of file bands_FS.f90 Fortran runtime error: Bad real number in item 13 of list input Line 230 of bands_FS.f90 is about reading spin-up energies?. But I have no idea why the code is not working. FYI, I added my input files for kvecs_FS.x and bands_FS.x: kvecs_FS.in: 0.317093 0.00 0.00 0.00 0.317093 0.00 0.00 0.00 0.317093 12 12 12 CWrium input_FS.in: 10 14 22.8158 CWrium 12 12 12 0.317093 0.00 0.00 0.00 0.317093 0.00 0.00 0.00 0.317093 Here, 10 14 are min. and max. band no. (no. of bands for my SCF calc. is 20), and 22.8158 is Fermi energy. Again, your help will truly be appreciated. I cc?ed Dr. Eyvaz Isaev who is the author of the two codes. Sincerely, Chan-Woo ------- Chan-Woo Lee, Ph.D. Postdoctoral Research Associate Department of Chemistry University of Pennsylvania 231 South 34th Street Philadelphia, PA 19104-6323 Phone: 1-215-898-3564 (Office) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120302/ddc3f215/attachment.htm From giannozz at democritos.it Fri Mar 2 08:44:11 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 02 Mar 2012 08:44:11 +0100 Subject: [Pw_forum] Eyvaz Isaev Message-ID: <1330674251.26056.5.camel@fe12lx.fisica.uniud.it> I have the regret to announce that Prof. Dr. Eyvaz Isaev, author of QHA and PlotPhon packages, passed away on Sept.11, 2011 P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From hashemifar at cc.iut.ac.ir Fri Mar 2 09:36:27 2012 From: hashemifar at cc.iut.ac.ir (Seyed Javad Hashemifar) Date: Fri, 2 Mar 2012 12:06:27 +0330 Subject: [Pw_forum] Hartree calculations for small molecules In-Reply-To: <1330536641.19716.17.camel@fe12lx.fisica.uniud.it> References: <1330536641.19716.17.camel@fe12lx.fisica.uniud.it> Message-ID: Dear Giuseppe and Paolo Thank you very much for your kind answers. I will use the classroom codes of Paolo to provide some Hartree calculations on Helium atom. Kind regards SJ Hashemifar ====================================== Seyed Javad Hashemifar Department of Physics, Isfahan University of Technology 84156-83111 Isfahan, Iran Tel: +98 311 391 2375 Fax:+98 311 3912376 Email: hashemifar at cc.iut.ac.ir Group Homepage: http://cmsgroup.iut.ac.ir Personal Homepage: http://hashemifar.iut.ac.ir --------------------------------------------------------------------------- On Wed, Feb 29, 2012 at 9:00 PM, Paolo Giannozzi wrote: > On Wed, 2012-02-29 at 17:26 +0330, Seyed Javad Hashemifar wrote: > > > For educational purpose, I am looking for some Hartree calculations > > on small molecules such as H2. > > not sure QE is the right tool for such a simple problem. Here some > simpler tools: > http://www.fisica.uniud.it/~giannozz/Corsi/MQ/mq.html > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120302/1912aa69/attachment.htm From asmogunov at gmail.com Fri Mar 2 09:46:05 2012 From: asmogunov at gmail.com (Alex Smogunov) Date: Fri, 2 Mar 2012 09:46:05 +0100 Subject: [Pw_forum] [LDA+U] elements in occupation matrix are real number? In-Reply-To: <000901ccf7e5$70303240$509096c0$@gmail.com> References: <000901ccf7e5$70303240$509096c0$@gmail.com> Message-ID: Dear Chan-Woo. The n matrix is always hermitian, it is clear from definition. In the case of collinear LSDA there is always psi_sigma --> psi_sigma* symmetry, due to hermicity of Hamiltonians for each spin, which can be considered as the time-reversal operation. This is why you always have k --> -k symmetry even if you do not have inversion operation. Because of this time-reversal symmetry one can readily see that the n matrix should be real. It is not anymore the case in general noncollinear calculation where the occupation matrix is in general complex (and hermitian). Concerning negative eigenvalues, I think they are just small numbers, probably due to computational errors, which should be thought of as 0. regards, Alexander Le 1 mars 2012 20:56, Chan-Woo Lee a ?crit : > Dear QE developers and users,**** > > ** ** > > I have a question in understanding occupation matrix from LDA+U output > file.**** > > ** ** > > 1) Definition of occupation matrix, n is:**** > > ** ** > > n= \sum{f}, where psi is KS eigenstates, phi_i is > atomic orbital of i orbital, f is scaling factor. As i and j from phi_i and > phi_j don?t have to be identical, I think it?s not guaranteed that elements > in n matrix are always real? However, in the QE output, they are all shown > as real numbers. In new_ns.f90, I can find that n (nr and ns) are defined > as real numbers but I can?t find any restrictions other than this. **** > > ** ** > > 2) While elements in the matrix are real, some of them are ?negative?. How > can I understand this? I found one paper about multiconfigurational > character of wave functions ( > http://jcp.aip.org/resource/1/jcpsa6/v110/i9/p4199_s1 ) but it?s beyond > my scope. **** > > ** ** > > Did I miss something? Any suggestions and advices will truly be > appreciated?**** > > ** ** > > Sincerely,**** > > ** ** > > Chan-Woo**** > > ** ** > > ** ** > > *------- > Chan-Woo Lee, Ph.D.* > > *Postdoctoral Research Associate* > > * * > > *Department of Chemistry > University of Pennsylvania > 231 South 34th Street > Philadelphia, PA 19104-6323 > Phone: 1-215-898-3564 (Office) > *Email: leechanw at sas.upenn.edu / cwandtj at gmail.com**** > > ** ** > > ** ** > > ** ** > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120302/90853a47/attachment.htm From zafartariq2003 at yahoo.com Fri Mar 2 12:18:56 2012 From: zafartariq2003 at yahoo.com (zafar rasheed) Date: Fri, 2 Mar 2012 03:18:56 -0800 (PST) Subject: [Pw_forum] Dr. Eyvaz Isaev In-Reply-To: Message-ID: <1330687136.65942.YahooMailClassic@web65414.mail.ac4.yahoo.com> Oh God .......... So Sad on the death of Dr. Eyvaz Isaev. Muhammad Zafar PhD Scholar Department of Physics The Islamia University of Bahawalpur,Pakistan --- On Fri, 3/2/12, pw_forum-request at pwscf.org wrote: From: pw_forum-request at pwscf.org Subject: Pw_forum Digest, Vol 57, Issue 4 To: pw_forum at pwscf.org Date: Friday, March 2, 2012, 1:42 PM Send Pw_forum mailing list submissions to ??? pw_forum at pwscf.org To subscribe or unsubscribe via the World Wide Web, visit ??? http://www.democritos.it/mailman/listinfo/pw_forum or, via email, send a message with subject or body 'help' to ??? pw_forum-request at pwscf.org You can reach the person managing the list at ??? pw_forum-owner at pwscf.org When replying, please edit your Subject line so it is more specific than "Re: Contents of Pw_forum digest..." Today's Topics: ???1. Error in using bands_FS.x to get Fermi surface, (Chan-Woo Lee) ???2. Re: Error in using bands_FS.x to get Fermi surface, (GAO Zhe) ???3. Eyvaz Isaev (Paolo Giannozzi) ???4. Re: Hartree calculations for small molecules ? ? ? (Seyed Javad Hashemifar) ---------------------------------------------------------------------- Message: 1 Date: Thu, 1 Mar 2012 22:08:12 -0500 From: "Chan-Woo Lee" Subject: [Pw_forum] Error in using bands_FS.x to get Fermi surface, To: Message-ID: <000f01ccf821$b57a6b90$206f42b0$@gmail.com> Content-Type: text/plain; charset="us-ascii" Dear QE developers and users, I am trying to get Fermi surface using kvecs_FS.x and bands_FS.x. I have followed example08 and have succeeded to get K-points using kvecs_FS.x. However, I got following error message when I execute bands_FS.x: At line 230 of file bands_FS.f90 Fortran runtime error: Bad real number in item 13 of list input Line 230 of bands_FS.f90 is about reading spin-up energies.. But I have no idea why the code is not working. FYI, I added my input files for kvecs_FS.x and bands_FS.x: kvecs_FS.in: 0.317093? 0.00? 0.00 0.00? 0.317093? 0.00 0.00? 0.00? 0.317093 12? 12? 12 CWrium input_FS.in: 10 14 22.8158 CWrium 12 12 12 0.317093? 0.00? 0.00 0.00? 0.317093? 0.00 0.00? 0.00? 0.317093 Here, 10 14 are min. and max. band no. (no. of bands for my SCF calc. is 20), and 22.8158 is Fermi energy. Again, your help will truly be appreciated. I cc'ed Dr. Eyvaz Isaev who is the author of the two codes. Sincerely, Chan-Woo ------- Chan-Woo Lee, Ph.D. Postdoctoral Research Associate Department of Chemistry University of Pennsylvania 231 South 34th Street Philadelphia, PA 19104-6323 Phone: 1-215-898-3564 (Office) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120301/20d8ad7e/attachment.html ------------------------------ Message: 2 Date: Fri, 2 Mar 2012 13:02:12 +0800 (CST) From: "GAO Zhe" Subject: Re: [Pw_forum] Error in using bands_FS.x to get Fermi ??? surface, To: pw_forum at pwscf.org Message-ID: <437a2cf1.1af57.135d1c969fe.Coremail.flux_ray12 at 163.com> Content-Type: text/plain; charset="gbk" I checked the code of bands_FS.f90, and found like this: ? ? ? ? open(12,file='input_FS') ? ? ? ? read(12,*) n_start, n_last ? ? ? ? read(12,*) E_fermi ? ? ? ? read(12,*) sysname ? ? ? ? read(12,*) na,nb, nc ? ? ? ? read(12,*) x(1),x(2),x(3) ? ? ? ? read(12,*) y(1),y(2),y(3) ? ? ? ? read(12,*) z(1),z(2),z(3) So I am just wondering whether it can work well, if you change your input file name as "input_FS", and run only by the command bands_FS.x < CWrium.fs.in > CWrium.fs.out, where CWrium.fs.in is a nscf calculation input file with the K_Points obtained by kvec_FS.x. The more ditailed process is in example 08. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-03-02 11:08:12,"Chan-Woo Lee" wrote: Dear QE developers and users, I am trying to get Fermi surface using kvecs_FS.x and bands_FS.x. I have followed example08 and have succeeded to get K-points using kvecs_FS.x. However, I got following error message when I execute bands_FS.x: At line 230 of file bands_FS.f90 Fortran runtime error: Bad real number in item 13 of list input Line 230 of bands_FS.f90 is about reading spin-up energies?. But I have no idea why the code is not working. FYI, I added my input files for kvecs_FS.x and bands_FS.x: kvecs_FS.in: 0.317093? 0.00? 0.00 0.00? 0.317093? 0.00 0.00? 0.00? 0.317093 12? 12? 12 CWrium input_FS.in: 10 14 22.8158 CWrium 12 12 12 0.317093? 0.00? 0.00 0.00? 0.317093? 0.00 0.00? 0.00? 0.317093 Here, 10 14 are min. and max. band no. (no. of bands for my SCF calc. is 20), and 22.8158 is Fermi energy. Again, your help will truly be appreciated. I cc?ed Dr. Eyvaz Isaev who is the author of the two codes. Sincerely, Chan-Woo ------- Chan-Woo Lee, Ph.D. Postdoctoral Research Associate Department of Chemistry University of Pennsylvania 231 South 34th Street Philadelphia, PA 19104-6323 Phone: 1-215-898-3564 (Office) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120302/ddc3f215/attachment-0001.htm ------------------------------ Message: 3 Date: Fri, 02 Mar 2012 08:44:11 +0100 From: Paolo Giannozzi Subject: [Pw_forum] Eyvaz Isaev To: PWSCF Forum Message-ID: <1330674251.26056.5.camel at fe12lx.fisica.uniud.it> Content-Type: text/plain I have the regret to announce that Prof. Dr. Eyvaz Isaev, author of QHA and PlotPhon packages, passed away on Sept.11, 2011 P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy ------------------------------ Message: 4 Date: Fri, 2 Mar 2012 12:06:27 +0330 From: Seyed Javad Hashemifar Subject: Re: [Pw_forum] Hartree calculations for small molecules To: PWSCF Forum Message-ID: ??? Content-Type: text/plain; charset="iso-8859-1" Dear Giuseppe and Paolo Thank you very much for your kind answers. I will use the classroom codes of Paolo to provide some Hartree calculations on Helium atom. Kind regards SJ Hashemifar ====================================== Seyed Javad? Hashemifar Department of Physics, Isfahan University of Technology 84156-83111 Isfahan, Iran Tel: +98 311 391 2375? ???Fax:+98 311 3912376 Email:? hashemifar at cc.iut.ac.ir Group Homepage:? ? ? http://cmsgroup.iut.ac.ir Personal Homepage:? http://hashemifar.iut.ac.ir --------------------------------------------------------------------------- On Wed, Feb 29, 2012 at 9:00 PM, Paolo Giannozzi wrote: > On Wed, 2012-02-29 at 17:26 +0330, Seyed Javad Hashemifar wrote: > > > For educational purpose, I am looking for some Hartree calculations > > on small molecules such as H2. > > not sure QE is the right tool for such a simple problem. Here some > simpler tools: >???http://www.fisica.uniud.it/~giannozz/Corsi/MQ/mq.html > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120302/1912aa69/attachment-0001.htm ------------------------------ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum End of Pw_forum Digest, Vol 57, Issue 4 *************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120302/67c75d0e/attachment-0001.htm From elie.moujaes at hotmail.co.uk Fri Mar 2 15:14:59 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Fri, 2 Mar 2012 14:14:59 +0000 Subject: [Pw_forum] errors while executing ph.x in parallel computing mode Message-ID: Dear all, I am running ph.x on the parallel computing version (on two nodes) and after 15 seconds I get the following errors: from create_directory: error: # 29/home_cluster/fis718/eliemouj/..../GB42_phresults/_ph0 : non existent or non writable from create_directory: error: # 29/home_cluster/fis718/eliemouj/..../GB42_phresults/_ph0 : non existent or non writable Since I got the same error twice, it might be related to nodes. I am doing phonon calculations so I ran a rather dense k gried for the scf calculations then I ran ph.x and I got this error....is it a parallel computing problem or might be due to an error in the input? Thanks Elie HoujaesUniversity of NottinghamNG7 2RDUK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120302/8b240860/attachment.htm From stewart at cnf.cornell.edu Fri Mar 2 16:31:57 2012 From: stewart at cnf.cornell.edu (Derek Stewart) Date: Fri, 02 Mar 2012 10:31:57 -0500 Subject: [Pw_forum] Eyvaz Isaev In-Reply-To: <1330674251.26056.5.camel@fe12lx.fisica.uniud.it> References: <1330674251.26056.5.camel@fe12lx.fisica.uniud.it> Message-ID: <4F50E7ED.8050902@cnf.cornell.edu> Hi everyone, I was very saddened to hear that Eyvaz passed away. Although I never had a chance to meet him in person, we exchanged emails on several research topics and I feel lucky to have met him through this forum. He was always ready to provide advice and encouragement to anyone working with Quantum Espresso. For my own research, his contributions to QE on phonon properties and Fermi surface visualization have been extremely helpful. He will definitely be missed. Derek ################################ Derek Stewart, Ph. D. Senior Research Associate http://sites.google.com/site/dft4nano/ 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 On 3/2/2012 2:44 AM, Paolo Giannozzi wrote: > I have the regret to announce that Prof. Dr. Eyvaz Isaev, > author of QHA and PlotPhon packages, passed away on Sept.11, 2011 > > P. From giannozz at democritos.it Fri Mar 2 18:05:53 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 02 Mar 2012 18:05:53 +0100 Subject: [Pw_forum] errors while executing ph.x in parallel computing mode In-Reply-To: References: Message-ID: <1330707953.29456.1.camel@fe12lx.fisica.uniud.it> On Fri, 2012-03-02 at 14:14 +0000, Elie M wrote: > is it a parallel computing problem or might be due to an error in the > input? likely, none of the above, but some weird problem with the file system. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From ksaha at physics.udel.edu Fri Mar 2 18:07:47 2012 From: ksaha at physics.udel.edu (ksaha at physics.udel.edu) Date: Fri, 2 Mar 2012 12:07:47 -0500 (EST) Subject: [Pw_forum] Convergene of Magnetic moment is very slow Message-ID: <56309.10.7.69.26.1330708067.squirrel@wiki.physics.udel.edu> Dear Users, I am running scf-iterations of a ferrimagnetic yttrium iron garnet (bcc primitive cell with 80 atoms) system and find that the convergence of magnetic moment is very slow. Can you any suggest me how to accelerate the overall convergence? Please see the last a few steps of magmom of the 100-scf steps: total magnetization = 78.61 Bohr mag/cell total magnetization = 78.79 Bohr mag/cell total magnetization = 78.78 Bohr mag/cell total magnetization = 78.91 Bohr mag/cell total magnetization = 79.25 Bohr mag/cell total magnetization = 79.17 Bohr mag/cell total magnetization = 79.22 Bohr mag/cell total magnetization = 79.06 Bohr mag/cell total magnetization = 79.08 Bohr mag/cell total magnetization = 79.10 Bohr mag/cell total magnetization = 79.12 Bohr mag/cell total magnetization = 79.09 Bohr mag/cell total magnetization = 79.15 Bohr mag/cell total magnetization = 79.23 Bohr mag/cell total magnetization = 79.17 Bohr mag/cell total magnetization = 79.47 Bohr mag/cell total magnetization = 79.45 Bohr mag/cell total magnetization = 79.15 Bohr mag/cell total magnetization = 81.33 Bohr mag/cell total magnetization = 82.16 Bohr mag/cell total magnetization = 82.24 Bohr mag/cell total magnetization = 82.32 Bohr mag/cell total magnetization = 82.53 Bohr mag/cell total magnetization = 84.89 Bohr mag/cell total magnetization = 82.93 Bohr mag/cell total magnetization = 78.05 Bohr mag/cell total magnetization = 84.82 Bohr mag/cell total magnetization = 84.32 Bohr mag/cell total magnetization = 84.69 Bohr mag/cell total magnetization = 85.38 Bohr mag/cell total magnetization = 87.34 Bohr mag/cell Also, here is the part of the script which you may want to look at: &system ibrav = 3, celldm(1) = 23.24362966, ! = a, in Bohr nat= 80, ntyp= 3, nspin=2, starting_magnetization(1)=0.0, starting_magnetization(2)=2.60, starting_magnetization(3)=0.0, occupations='smearing', smearing='mp', degauss=0.02, ecutwfc =30, ecutrho =240 / &electrons electron_maxstep = 400, diagonalization='david', conv_thr = 1.0e-6, mixing_beta = 0.05, !mixing_ndim = 6 mixing_ndim = 10 / ATOMIC_SPECIES Y 88.90585 Y.pbe-nsp-van.UPF Fe 55.84500 Fe.pbe-sp-van_mit.UPF O 15.99940 O.pbe-van_ak.UPF . . . K_POINTS automatic 5 5 5 1 1 1 Many thanks for your comments and suggestions, Regards, Kamal ========================================================== Kamal K. Saha Department of Physics and Astronomy University of Delaware Newark, DE 19716-2570 Phone: (302) 831-8519, Fax: (302) 831-1637 http://web.physics.udel.edu/about/directory/postdoc/kamal-k-saha ========================================================== From faccin.giovani at gmail.com Fri Mar 2 18:53:20 2012 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Fri, 2 Mar 2012 13:53:20 -0400 Subject: [Pw_forum] Convergene of Magnetic moment is very slow In-Reply-To: <56309.10.7.69.26.1330708067.squirrel@wiki.physics.udel.edu> References: <56309.10.7.69.26.1330708067.squirrel@wiki.physics.udel.edu> Message-ID: Kamal, The scf will try to optimize the total energy. Once the energy is optimized, the magnetic moment should stop oscillating. Each step the program prints this line: "estimated scf accuracy: XXXXX". If XXXXX is becoming smaller over time, the calculation is converging. If not, then you can try other beta values, as discussed here: http://www.quantum-espresso.org/user_guide/node64.html#SECTION000137020000000000000 Just looking at the magnetization before the system gets self-consistent is pointless, since all kind of values will show up. A little idea that might help: be sure that you have enough kpoints. 5x5x5 can be too few for many purposes. I'd give it a try with, say, 11x11x11 to see if the final magnetization (after the scf is concluded) changes. Best regards, Giovani M. Faccin CPPP / UFMS - Brazil 2012/3/2 > Dear Users, > > I am running scf-iterations of a ferrimagnetic yttrium iron garnet (bcc > primitive cell with 80 atoms) system and find that the convergence of > magnetic moment is very slow. Can you any suggest me how to accelerate the > overall convergence? Please see the last a few steps of magmom of the > 100-scf steps: > > total magnetization = 78.61 Bohr mag/cell > total magnetization = 78.79 Bohr mag/cell > total magnetization = 78.78 Bohr mag/cell > total magnetization = 78.91 Bohr mag/cell > total magnetization = 79.25 Bohr mag/cell > total magnetization = 79.17 Bohr mag/cell > total magnetization = 79.22 Bohr mag/cell > total magnetization = 79.06 Bohr mag/cell > total magnetization = 79.08 Bohr mag/cell > total magnetization = 79.10 Bohr mag/cell > total magnetization = 79.12 Bohr mag/cell > total magnetization = 79.09 Bohr mag/cell > total magnetization = 79.15 Bohr mag/cell > total magnetization = 79.23 Bohr mag/cell > total magnetization = 79.17 Bohr mag/cell > total magnetization = 79.47 Bohr mag/cell > total magnetization = 79.45 Bohr mag/cell > total magnetization = 79.15 Bohr mag/cell > total magnetization = 81.33 Bohr mag/cell > total magnetization = 82.16 Bohr mag/cell > total magnetization = 82.24 Bohr mag/cell > total magnetization = 82.32 Bohr mag/cell > total magnetization = 82.53 Bohr mag/cell > total magnetization = 84.89 Bohr mag/cell > total magnetization = 82.93 Bohr mag/cell > total magnetization = 78.05 Bohr mag/cell > total magnetization = 84.82 Bohr mag/cell > total magnetization = 84.32 Bohr mag/cell > total magnetization = 84.69 Bohr mag/cell > total magnetization = 85.38 Bohr mag/cell > total magnetization = 87.34 Bohr mag/cell > > Also, here is the part of the script which you may want to look at: > > &system > ibrav = 3, > celldm(1) = 23.24362966, ! = a, in Bohr > nat= 80, > ntyp= 3, > nspin=2, > starting_magnetization(1)=0.0, > starting_magnetization(2)=2.60, > starting_magnetization(3)=0.0, > occupations='smearing', > smearing='mp', > degauss=0.02, > ecutwfc =30, > ecutrho =240 > / > &electrons > electron_maxstep = 400, > diagonalization='david', > conv_thr = 1.0e-6, > mixing_beta = 0.05, > !mixing_ndim = 6 > mixing_ndim = 10 > / > ATOMIC_SPECIES > Y 88.90585 Y.pbe-nsp-van.UPF > Fe 55.84500 Fe.pbe-sp-van_mit.UPF > O 15.99940 O.pbe-van_ak.UPF > . > . > . > K_POINTS automatic > 5 5 5 1 1 1 > > Many thanks for your comments and suggestions, > > Regards, > Kamal > > ========================================================== > Kamal K. Saha > Department of Physics and Astronomy > University of Delaware > Newark, DE 19716-2570 > Phone: (302) 831-8519, Fax: (302) 831-1637 > > http://web.physics.udel.edu/about/directory/postdoc/kamal-k-saha > ========================================================== > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120302/9e98cd7b/attachment.htm From somayehfotohi at yahoo.com Fri Mar 2 20:19:29 2012 From: somayehfotohi at yahoo.com (somayeh fotohi) Date: Fri, 2 Mar 2012 11:19:29 -0800 (PST) Subject: [Pw_forum] scf cslculation Message-ID: <1330715969.52852.YahooMailClassic@web161402.mail.bf1.yahoo.com> Dear all, I performed scf cslculation but? end of the output file of scf appears this massage: End of self-consistent calculation convergence NOT achieved after 100 iterations: stopping . . . JOB DONE. what do I change in input file? for obtaining correct answer? Many thanks for your comments and suggestions, Regards, Somayeh Fotoohi ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120302/6c2df899/attachment.htm From elie.moujaes at hotmail.co.uk Fri Mar 2 22:41:37 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Fri, 2 Mar 2012 21:41:37 +0000 Subject: [Pw_forum] errors while executing ph.x in parallel computing mode In-Reply-To: <1330707953.29456.1.camel@fe12lx.fisica.uniud.it> References: , <1330707953.29456.1.camel@fe12lx.fisica.uniud.it> Message-ID: Professor Giannozzi, Thanks for the reply. I have figured it out. Elie > Subject: Re: [Pw_forum] errors while executing ph.x in parallel computing mode > From: giannozz at democritos.it > To: elie.moujaes at hotmail.co.uk > CC: pw_forum at pwscf.org > Date: Fri, 2 Mar 2012 18:05:53 +0100 > > On Fri, 2012-03-02 at 14:14 +0000, Elie M wrote: > > > is it a parallel computing problem or might be due to an error in the > > input? > > likely, none of the above, but some weird problem with the file > system. > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120302/b05e0b40/attachment-0001.htm From rahen29 at yahoo.com Sat Mar 3 04:03:32 2012 From: rahen29 at yahoo.com (Rahen Badsha) Date: Fri, 2 Mar 2012 19:03:32 -0800 (PST) Subject: [Pw_forum] Spin polarization of Graphene In-Reply-To: <1330698059.78316.YahooMailNeo@web44710.mail.sp1.yahoo.com> References: <1330698059.78316.YahooMailNeo@web44710.mail.sp1.yahoo.com> Message-ID: <1330743812.18016.YahooMailNeo@web44709.mail.sp1.yahoo.com> Dear QE users, I am a researcher on graphene. I want to calculate the spin polarization of graphene. What will be the input code(i.e. scf, nscf, band, plotband and dos) of graphene as a spintronic material? How can I progress? What is the amount of percent of spin polarization of graphene? Please help me. Regards- Rahen Badsha (Raihan) A post graduate thesis student University of Rajshahi, Bangladesh. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120302/c8b5ee43/attachment.htm From rahen29 at yahoo.com Sat Mar 3 04:03:32 2012 From: rahen29 at yahoo.com (Rahen Badsha) Date: Fri, 2 Mar 2012 19:03:32 -0800 (PST) Subject: [Pw_forum] Spin polarization of Graphene In-Reply-To: <1330698059.78316.YahooMailNeo@web44710.mail.sp1.yahoo.com> References: <1330698059.78316.YahooMailNeo@web44710.mail.sp1.yahoo.com> Message-ID: <1330743812.18016.YahooMailNeo@web44709.mail.sp1.yahoo.com> Dear QE users, I am a researcher on graphene. I want to calculate the spin polarization of graphene. What will be the input code(i.e. scf, nscf, band, plotband and dos) of graphene as a spintronic material? How can I progress? What is the amount of percent of spin polarization of graphene? Please help me. Regards- Rahen Badsha (Raihan) A post graduate thesis student University of Rajshahi, Bangladesh. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120302/c8b5ee43/attachment-0001.htm From rahen29 at yahoo.com Sat Mar 3 04:04:43 2012 From: rahen29 at yahoo.com (Rahen Badsha) Date: Fri, 2 Mar 2012 19:04:43 -0800 (PST) Subject: [Pw_forum] Explanation of plotband program In-Reply-To: <1330692801.28406.YahooMailNeo@web44701.mail.sp1.yahoo.com> References: <1330692801.28406.YahooMailNeo@web44701.mail.sp1.yahoo.com> Message-ID: <1330743883.89515.YahooMailNeo@web44714.mail.sp1.yahoo.com> Dear QE PWscf Users, I calculated the electronic structure of graphene. So I run scf, nscf, bands,plotband and dos program and got the output. But I could not understand the input code of plotband program and the output band structure. Have any person who will explain ? Please Please....... help me. Best Wishes- Rahen Badsha (Raihan) A post graduate thesis student University of Rajshahi, Bangladesh. Mobile:+8801710550252 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120302/b1dc1251/attachment.htm From rahen29 at yahoo.com Sat Mar 3 04:04:43 2012 From: rahen29 at yahoo.com (Rahen Badsha) Date: Fri, 2 Mar 2012 19:04:43 -0800 (PST) Subject: [Pw_forum] Explanation of plotband program In-Reply-To: <1330692801.28406.YahooMailNeo@web44701.mail.sp1.yahoo.com> References: <1330692801.28406.YahooMailNeo@web44701.mail.sp1.yahoo.com> Message-ID: <1330743883.89515.YahooMailNeo@web44714.mail.sp1.yahoo.com> Dear QE PWscf Users, I calculated the electronic structure of graphene. So I run scf, nscf, bands,plotband and dos program and got the output. But I could not understand the input code of plotband program and the output band structure. Have any person who will explain ? Please Please....... help me. Best Wishes- Rahen Badsha (Raihan) A post graduate thesis student University of Rajshahi, Bangladesh. Mobile:+8801710550252 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120302/b1dc1251/attachment-0001.htm From rahen29 at yahoo.com Sat Mar 3 04:06:47 2012 From: rahen29 at yahoo.com (Rahen Badsha) Date: Fri, 2 Mar 2012 19:06:47 -0800 (PST) Subject: [Pw_forum] Electronic structure calculation of graphene as a spintronic material using espresso-4.2) In-Reply-To: <1330582327.11293.YahooMailNeo@web44714.mail.sp1.yahoo.com> References: <1330582327.11293.YahooMailNeo@web44714.mail.sp1.yahoo.com> Message-ID: <1330744007.47298.YahooMailNeo@web44708.mail.sp1.yahoo.com> Dear QE PWscf users, I calculated scf, nscf,bands,plotband , dos and spin polarization of Graphene as a spintronic material. The band structure that I got is not desired as a semimetal(i.e. graphene) and the spin polarization is not desired(high %). I am appreciate for any suggestion and comments. "Please tell me where I was wrong or which detail I ignored." I used the following PWscf code: 1. SCF code: ?&control ? calculation = 'scf' ? restart_mode='from_scratch' ? prefix='graphene' ? tstress=.true. ? tprnfor=.true. ? pseudo_dir = '/home/live/Desktop/pseudo/', ? outdir = '/home/live/Desktop/testgraphene/' ? / ? &system ? ibrav=4 ? celldm(1)=4.7243 ? celldm(3)=3.92 ? nat=2 ? ntyp=1 ? nspin=2 ? starting_magnetization(1)=0.6 ? ecutwfc=15.0 ? ecutrho=350.0 ? occupations='smearing' ? smearing='gaussian' ? nbnd = 8 ? degauss=0.01 ? / ? &electrons ? diagonalization='david' ? electron_maxstep = 100 ? mixing_mode='plain' ? mixing_beta=0.1 ? conv_thr = 1.0e-8 ? / ? ATOMIC_SPECIES ? C 12.011 C.pz-rrkjus.UPF ? ? ? ATOMIC_POSITIONS (angstrom) ? C 0.000000000 0.000000000 0.000000000 ? C 1.232850116 0.706423116 0.000000000 ? K_POINTS {automatic} ? 16 16 1 0 0 0 2. NSCF code: ?&control ? calculation = 'nscf' ? restart_mode='from_scratch' ? prefix='graphene' ? tstress=.true. ? tprnfor=.true. ? pseudo_dir = '/home/live/Desktop/pseudo/', ? outdir = '/home/live/Desktop/testgraphene/' ? / ? &system ? ibrav=4 ? celldm(1)=4.7243 ? celldm(3)=3.92 ? nat=2 ? ntyp=1 ? nspin=2 ? starting_magnetization(1)=0.6 ? ecutwfc=15.0 ? ecutrho=350.0 ? occupations='smearing' ? smearing='gaussian' ? nbnd = 8 ? degauss=0.01 ? / ? &electrons ? diagonalization='david' ? electron_maxstep = 100 ? mixing_mode='plain' ? mixing_beta=0.1 ? conv_thr = 1.0e-8 ? / ? ATOMIC_SPECIES ? C 12.011 C.pz-rrkjus.UPF ? ? ? ATOMIC_POSITIONS (angstrom) ? C 0.000000000 0.000000000 0.000000000 ? C 1.232850116 0.706423116 0.000000000 ? K_POINTS {automatic} ? 16 16 1 0 0 0 3.pw.x band code: ?&control ? calculation = 'bands' ? restart_mode='from_scratch' ? prefix='graphene' ? tstress=.true. ? tprnfor=.true. ? pseudo_dir = '/home/live/Desktop/pseudo/', ? outdir = '/home/live/Desktop/testgraphene/' ? / ? &system ? ibrav=4 ? celldm(1)=4.7243 ? celldm(3)=3.92 ? nat=2 ? ntyp=1 ? nspin=2 ? starting_magnetization(1)=0.6 ? ecutwfc=15.0 ? ecutrho=350.0 ? occupations='smearing' ? smearing='gaussian' ? nbnd = 8 ? degauss=0.01 ? / ? &electrons ? diagonalization='david' ? electron_maxstep = 100 ? mixing_mode='plain' ? mixing_beta=0.1 ? conv_thr = 1.0e-8 ? / ? ATOMIC_SPECIES ? C 12.011 C.pz-rrkjus.UPF ? ? ? ATOMIC_POSITIONS (angstrom) ? C 0.000000000 0.000000000 0.000000000 ? C 1.232850116 0.706423116 0.000000000 ? K_POINTS {automatic} ? 16 16 1 0 0 0 4.band.x code: &inputpp ?? prefix='graphene', ?? outdir='/home/live/Desktop/testgraphene/' ?? !filband='graphene.bands' ?? / 5.plotband.x code: bands.out -10.0 20.0 graphene.xmgr graphene.ps 1.000 2.0 1.00 EOF 6. dos.x code: ?&inputpp ? prefix='graphene' ? outdir=/home/live/Desktop/Graphenenbnd8/' ? fildos='graphene.dos', ? Emin=-25.0, Emax=20.0, DeltaE=0.1 Regards- Rahen Badsha (Raihan) A post graduate Thesis student University of Rajshahi, Bangladesh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120302/67dfbd0e/attachment-0002.htm From rahen29 at yahoo.com Sat Mar 3 04:06:47 2012 From: rahen29 at yahoo.com (Rahen Badsha) Date: Fri, 2 Mar 2012 19:06:47 -0800 (PST) Subject: [Pw_forum] Electronic structure calculation of graphene as a spintronic material using espresso-4.2) In-Reply-To: <1330582327.11293.YahooMailNeo@web44714.mail.sp1.yahoo.com> References: <1330582327.11293.YahooMailNeo@web44714.mail.sp1.yahoo.com> Message-ID: <1330744007.47298.YahooMailNeo@web44708.mail.sp1.yahoo.com> Dear QE PWscf users, I calculated scf, nscf,bands,plotband , dos and spin polarization of Graphene as a spintronic material. The band structure that I got is not desired as a semimetal(i.e. graphene) and the spin polarization is not desired(high %). I am appreciate for any suggestion and comments. "Please tell me where I was wrong or which detail I ignored." I used the following PWscf code: 1. SCF code: ?&control ? calculation = 'scf' ? restart_mode='from_scratch' ? prefix='graphene' ? tstress=.true. ? tprnfor=.true. ? pseudo_dir = '/home/live/Desktop/pseudo/', ? outdir = '/home/live/Desktop/testgraphene/' ? / ? &system ? ibrav=4 ? celldm(1)=4.7243 ? celldm(3)=3.92 ? nat=2 ? ntyp=1 ? nspin=2 ? starting_magnetization(1)=0.6 ? ecutwfc=15.0 ? ecutrho=350.0 ? occupations='smearing' ? smearing='gaussian' ? nbnd = 8 ? degauss=0.01 ? / ? &electrons ? diagonalization='david' ? electron_maxstep = 100 ? mixing_mode='plain' ? mixing_beta=0.1 ? conv_thr = 1.0e-8 ? / ? ATOMIC_SPECIES ? C 12.011 C.pz-rrkjus.UPF ? ? ? ATOMIC_POSITIONS (angstrom) ? C 0.000000000 0.000000000 0.000000000 ? C 1.232850116 0.706423116 0.000000000 ? K_POINTS {automatic} ? 16 16 1 0 0 0 2. NSCF code: ?&control ? calculation = 'nscf' ? restart_mode='from_scratch' ? prefix='graphene' ? tstress=.true. ? tprnfor=.true. ? pseudo_dir = '/home/live/Desktop/pseudo/', ? outdir = '/home/live/Desktop/testgraphene/' ? / ? &system ? ibrav=4 ? celldm(1)=4.7243 ? celldm(3)=3.92 ? nat=2 ? ntyp=1 ? nspin=2 ? starting_magnetization(1)=0.6 ? ecutwfc=15.0 ? ecutrho=350.0 ? occupations='smearing' ? smearing='gaussian' ? nbnd = 8 ? degauss=0.01 ? / ? &electrons ? diagonalization='david' ? electron_maxstep = 100 ? mixing_mode='plain' ? mixing_beta=0.1 ? conv_thr = 1.0e-8 ? / ? ATOMIC_SPECIES ? C 12.011 C.pz-rrkjus.UPF ? ? ? ATOMIC_POSITIONS (angstrom) ? C 0.000000000 0.000000000 0.000000000 ? C 1.232850116 0.706423116 0.000000000 ? K_POINTS {automatic} ? 16 16 1 0 0 0 3.pw.x band code: ?&control ? calculation = 'bands' ? restart_mode='from_scratch' ? prefix='graphene' ? tstress=.true. ? tprnfor=.true. ? pseudo_dir = '/home/live/Desktop/pseudo/', ? outdir = '/home/live/Desktop/testgraphene/' ? / ? &system ? ibrav=4 ? celldm(1)=4.7243 ? celldm(3)=3.92 ? nat=2 ? ntyp=1 ? nspin=2 ? starting_magnetization(1)=0.6 ? ecutwfc=15.0 ? ecutrho=350.0 ? occupations='smearing' ? smearing='gaussian' ? nbnd = 8 ? degauss=0.01 ? / ? &electrons ? diagonalization='david' ? electron_maxstep = 100 ? mixing_mode='plain' ? mixing_beta=0.1 ? conv_thr = 1.0e-8 ? / ? ATOMIC_SPECIES ? C 12.011 C.pz-rrkjus.UPF ? ? ? ATOMIC_POSITIONS (angstrom) ? C 0.000000000 0.000000000 0.000000000 ? C 1.232850116 0.706423116 0.000000000 ? K_POINTS {automatic} ? 16 16 1 0 0 0 4.band.x code: &inputpp ?? prefix='graphene', ?? outdir='/home/live/Desktop/testgraphene/' ?? !filband='graphene.bands' ?? / 5.plotband.x code: bands.out -10.0 20.0 graphene.xmgr graphene.ps 1.000 2.0 1.00 EOF 6. dos.x code: ?&inputpp ? prefix='graphene' ? outdir=/home/live/Desktop/Graphenenbnd8/' ? fildos='graphene.dos', ? Emin=-25.0, Emax=20.0, DeltaE=0.1 Regards- Rahen Badsha (Raihan) A post graduate Thesis student University of Rajshahi, Bangladesh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120302/67dfbd0e/attachment-0003.htm From flux_ray12 at 163.com Sat Mar 3 04:25:48 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Sat, 3 Mar 2012 11:25:48 +0800 (CST) Subject: [Pw_forum] Eyvaz Isaev In-Reply-To: <1330674251.26056.5.camel@fe12lx.fisica.uniud.it> References: <1330674251.26056.5.camel@fe12lx.fisica.uniud.it> Message-ID: <467943e.3686.135d697832b.Coremail.flux_ray12@163.com> I am so sad to hear such a bad news. Without Prof. Isaev's kind help, I might not overcome the difficulty in calculations by PWscf and write my papers. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-03-02 15:44:11,"Paolo Giannozzi" wrote: >I have the regret to announce that Prof. Dr. Eyvaz Isaev, >author of QHA and PlotPhon packages, passed away on Sept.11, 2011 > >P. >-- >Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120303/6f564f2f/attachment.htm From samadzare at gmail.com Sat Mar 3 05:53:23 2012 From: samadzare at gmail.com (samad zare) Date: Sat, 3 Mar 2012 08:23:23 +0330 Subject: [Pw_forum] run pwgui Message-ID: hello i install pwgui successful but when i want run a example of pwscf i see this error couldn't execute "pw.x": no such file or directory couldn't execute "pw.x": no such file or directory while executing "open [concat | $args] r" (procedure "::tclu::nonblocking" line 28) invoked from within "::tclu::nonblocking exec 1 pw.x < /home/linux/espresso-4.3.1/sample.pw.in2> /home/linux/espresso-4.3.1/sample.pw.err" ("eval" body line 1) invoked from within "eval ::tclu::nonblocking exec $execID $runCmd < $run(inpFile,$moduleObj) 2> $run(errFile,$moduleObj)" (procedure "::pwscf::run::run" line 95) invoked from within "::pwscf::run::run ::gUI0" invoked from within ".gui0.shellchildsite.menubar.menubar.run.menu invoke active" ("uplevel" body line 1) invoked from within "uplevel #0 [list $w invoke active]" (procedure "tk::MenuInvoke" line 50) invoked from within "tk::MenuInvoke .gui0.shellchildsite.menubar.menubar.run.menu 1" (command bound to event) thank -- With Best Regards SAMAD ZARE, phD Student UTM university Nanotechnology Research Alliance APSI, UTM 81310, Skudai,Johor Bahru, Malaysia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120303/58732162/attachment.htm From tone.kokalj at ijs.si Sat Mar 3 10:22:35 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Sat, 03 Mar 2012 10:22:35 +0100 Subject: [Pw_forum] run pwgui In-Reply-To: References: Message-ID: <1330766555.3857.12.camel@catalyst.ijs.si> On Sat, 2012-03-03 at 08:23 +0330, samad zare wrote: > hello > i install pwgui successful but when i want run a example of pwscf i > see this error > > couldn't execute "pw.x": no such file or directory > couldn't execute "pw.x": no such file or directory which means you did not setup the pwgui, i.e., you didn't specify where are your executables. To do so, click the Edit-->Settings menu and provide the needed data. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From sengere at webmail.co.za Sat Mar 3 11:32:10 2012 From: sengere at webmail.co.za (MAPASHA REFILWE) Date: Sat, 03 Mar 2012 12:32:10 +0200 Subject: [Pw_forum] coutour plot Message-ID: <3950497d2e2e1256501321ee3f76fc9c@www.webmail.co.za> Dear QE users, I am a researcher on graphene and bilayer graphene I want to plot the contour plot of charge densities between molecular hydrogen and bilayer graphene. I M failing to find the plot correct. I have gone through the QE doc and example 05 of silicon but it does not materialise. Here is my charge density input file (pp_rho.in) &inputpp prefix = 'graphite' filplot = 'graphitecharge' outdir = 'tmp' plot_num= 0 / &plot nfile = 1 filepp(1) = 'graphitecharge' weight(1) = 2.0 iflag = 2 output_format = 2 fileout = 'graphite.rho.dat' e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0, e2(1) =0.0, e2(2)=0.75, e2(3) = 0.0, x0(1)=0.00, x0(2)=0.00, x0(3)=0.00, nx=100, ny=100 / Please help me. Regards- Edwin Mapasha PhD student University of pretoria, South Africa. ____________________________________________________________ South Africas premier free email service - www.webmail.co.za For super low premiums, click here. http://www.dialdirect.co.za/?vdn=15828 From lfhuang at theory.issp.ac.cn Sat Mar 3 12:07:47 2012 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?TGlhbmcgRmVuZyBIdWFuZw==?=) Date: Sat, 03 Mar 2012 19:07:47 +0800 Subject: [Pw_forum] =?utf-8?q?Eyvaz_Isaev?= Message-ID: <20120303110747.18287.qmail@ms.hfcas.ac.cn> Prof. Eyvaz Isaey has helped so many PWSCF users (including me) a lot on this forum. The computational skills and physical understanding that he has taught others are very invaluable to these people's academic career. He is a so kind hearted person. If leaving this world is a new beginning of the journey to another one, I believe he will go to the best one. > At 2012-03-02 15:44:11,"Paolo Giannozzi" wrote: > I have the regret to announce that Prof. Dr. Eyvaz Isaev, > author of QHA and PlotPhon packages, passed away on Sept.11, 2011 > > P. > > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy ------ ====================================================================== L.F.Huang ?????, Electronic Structure and Phonon Physics ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591440(office) Fax: 86-551-5591434 ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120303/3fbe45db/attachment.htm From mpayami at aeoi.org.ir Sat Mar 3 12:24:20 2012 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Sat, 3 Mar 2012 14:54:20 +0330 Subject: [Pw_forum] Eyvaz Isaev References: <20120303110747.18287.qmail@ms.hfcas.ac.cn> Message-ID: <6E5ADA0B99CE4852BB91BCB82EF83AC0@b> In my memory, Prof. Eyvaz Isaev is a scientist that was so kind and loved helping. In a few correspondences with him, he helped me so much. I feel so sad today. mahmoud payami > At 2012-03-02 15:44:11,"Paolo Giannozzi" wrote: > I have the regret to announce that Prof. Dr. Eyvaz Isaev, > author of QHA and PlotPhon packages, passed away on Sept.11, 2011 > > P. > > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120303/5e127134/attachment.htm From mdulski at us.edu.pl Sat Mar 3 13:44:08 2012 From: mdulski at us.edu.pl (mateusz dulski) Date: Sat, 3 Mar 2012 13:44:08 +0100 Subject: [Pw_forum] visualization Message-ID: <000601ccf93b$53e75d00$6501a8c0@polpress88ef18> Dear all, How can I visualize phonon calculation in XcrysDen? I used dynmat.x software to create filmxsf=*.axsf but unfortunatelly I cannot open this file in XCrysden. Do I have to make something else for example use one more software to create some file "*.out" based on previous "*.axsf" file? Thank You in advance for help Sincerely, Mateusz -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120303/74c37e49/attachment.htm From giannozz at democritos.it Sat Mar 3 16:00:56 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 3 Mar 2012 16:00:56 +0100 Subject: [Pw_forum] Eyvaz Isaev In-Reply-To: <6E5ADA0B99CE4852BB91BCB82EF83AC0@b> References: <20120303110747.18287.qmail@ms.hfcas.ac.cn> <6E5ADA0B99CE4852BB91BCB82EF83AC0@b> Message-ID: <355B0EC0-20F1-43AB-89C6-26DF440E7B33@democritos.it> I have received a message from Leyla Isaeva, the daughter of Eyvaz, who would like to thank everybody for the kind words. Eyvaz would have been 53 years old today. Paolo --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From gkucukdalyan at gmail.com Sun Mar 4 02:29:02 2012 From: gkucukdalyan at gmail.com (Gulcin Kucukdalyan) Date: Sat, 3 Mar 2012 20:29:02 -0500 Subject: [Pw_forum] Minimization of Energy by fixing lattice parameters and relaxing lattice parameters Message-ID: Hi Everyone, I would like to minimize the energy of graphene lithium system by fixing lattice parameters and relaxing lattice parameters. How should i do so? Thanks, Gulcin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120303/50b32e7d/attachment.htm From akohlmey at gmail.com Sun Mar 4 02:36:32 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Sat, 3 Mar 2012 20:36:32 -0500 Subject: [Pw_forum] Minimization of Energy by fixing lattice parameters and relaxing lattice parameters In-Reply-To: References: Message-ID: On Sat, Mar 3, 2012 at 8:29 PM, Gulcin Kucukdalyan wrote: > Hi Everyone, > > I would like to minimize the energy of graphene lithium system by fixing > lattice parameters and relaxing lattice parameters. How should i do so? hmmm... you want to *fix* and *relax* at the same time? there must be something missing here. please clarify. cheers, axel. > Thanks, > > Gulcin > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com ?http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA. From m.abbasnejad at gmail.com Sun Mar 4 07:01:06 2012 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Sun, 4 Mar 2012 09:31:06 +0330 Subject: [Pw_forum] (101) surface of Anatase Message-ID: Dear all, I am focusing on simulation of (1 0 1) surface of Anatase TiO2. I have derived the orthogonal vectors for this surface as : a' = b, b' = c-a, c' = 4c + 25 a (a, b, c are related to the conventional unit cell) However, I am not sure about my procedure, since it leads to the volume 29 times of the conventional bulk structure. which it means that I have to consider 29*12 atoms for constructing. I will appreciate it if you would help me about the atomic position and normal vectors in this surface. Thanks in advance. Yours, Mohaddeseh --------------------------------------------------------- Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran, North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 Cellphone: +98 917 731 7514 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir --------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120304/6025a866/attachment-0001.htm From baroni at sissa.it Sun Mar 4 10:14:40 2012 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 4 Mar 2012 10:14:40 +0100 Subject: [Pw_forum] Eyvaz Isaev In-Reply-To: <355B0EC0-20F1-43AB-89C6-26DF440E7B33@democritos.it> References: <20120303110747.18287.qmail@ms.hfcas.ac.cn> <6E5ADA0B99CE4852BB91BCB82EF83AC0@b> <355B0EC0-20F1-43AB-89C6-26DF440E7B33@democritos.it> Message-ID: Let me just add that I wish I could know him in person. Eyvaz was one of the first to believe in the Quantum Espresso project and to join this lively community. We have co-authored a paper together (http://arxiv.org/abs/1112.4977). I enjoyed immensely collaborating with him through the internet, but, sadly, never had the chance to meet him in person. I knew from him that this would not probably have been possible, and I regret this very much. Stefano Baroni On Mar 3, 2012, at 4:00 PM, Paolo Giannozzi wrote: > I have received a message from Leyla Isaeva, the daughter > of Eyvaz, who would like to thank everybody for the kind > words. Eyvaz would have been 53 years old today. > > Paolo > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120304/a3c5e1cd/attachment.htm From giannozz at democritos.it Sun Mar 4 10:21:15 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 4 Mar 2012 10:21:15 +0100 Subject: [Pw_forum] visualization In-Reply-To: <000601ccf93b$53e75d00$6501a8c0@polpress88ef18> References: <000601ccf93b$53e75d00$6501a8c0@polpress88ef18> Message-ID: On Mar 3, 2012, at 13:44 , mateusz dulski wrote: > How can I visualize phonon calculation in XcrysDen? > I used dynmat.x software to create filmxsf=*.axsf but > unfortunatelly I cannot open this file in XCrysden. you should be able to visualize that file with XCrysDen. Nothing has changed in that part of the code. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From mpayami at aeoi.org.ir Sun Mar 4 10:45:34 2012 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Sun, 4 Mar 2012 14:15:34 +0430 Subject: [Pw_forum] (101) surface of Anatase References: Message-ID: <0CBE78B98C534E12907FA70F92A36CF1@b> Dear Mohaddeseh, You just need to find two non-colinear base vectors on the (101) surface, and the third one is the vector that connects two adjacent surfaces. Using these three basis vectors, you are able to construct your favorite supercell. HTH. mahmoud payami Dear all, I am focusing on simulation of (1 0 1) surface of Anatase TiO2. I have derived the orthogonal vectors for this surface as : a' = b, b' = c-a, c' = 4c + 25 a (a, b, c are related to the conventional unit cell) However, I am not sure about my procedure, since it leads to the volume 29 times of the conventional bulk structure. which it means that I have to consider 29*12 atoms for constructing. I will appreciate it if you would help me about the atomic position and normal vectors in this surface. Thanks in advance. Yours, Mohaddeseh --------------------------------------------------------- Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran, North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 Cellphone: +98 917 731 7514 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir --------------------------------------------------------- ------------------------------------------------------------------------------ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120304/693f62c4/attachment.htm From giannozz at democritos.it Sun Mar 4 10:51:02 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 4 Mar 2012 10:51:02 +0100 Subject: [Pw_forum] coutour plot In-Reply-To: <3950497d2e2e1256501321ee3f76fc9c@www.webmail.co.za> References: <3950497d2e2e1256501321ee3f76fc9c@www.webmail.co.za> Message-ID: <5202EC72-7F95-41A3-9EB3-2FDF797E09A4@democritos.it> On Mar 3, 2012, at 11:32 , MAPASHA REFILWE wrote: > e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0, > e2(1) =0.0, e2(2)=0.75, e2(3) = 0.0, you are plotting the xy plane. Is this what you want? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From abdeslam.houari at gmail.com Sun Mar 4 10:53:07 2012 From: abdeslam.houari at gmail.com (Abdeslam HOUARI) Date: Sun, 4 Mar 2012 10:53:07 +0100 Subject: [Pw_forum] scf cslculation In-Reply-To: <1330715969.52852.YahooMailClassic@web161402.mail.bf1.yahoo.com> References: <1330715969.52852.YahooMailClassic@web161402.mail.bf1.yahoo.com> Message-ID: 2012/3/2 somayeh fotohi > Dear all, > I performed scf cslculation but end of the output file of scf appears > this massage: > > End of self-consistent calculation > convergence NOT achieved after 100 iterations: stopping > . > . > . > JOB DONE. > > what do I change in input file for obtaining correct answer? > > Many thanks for your comments and suggestions, > > Regards, > > Somayeh Fotoohi > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > Dear Somaya; Try to increase the maximum number of iteration in the SCF cycle (electron_maxstep) in NAMELIST:&ELECTRONS... or equivalently try to monitor the convergence threshold (conv_thr). Good luck -- ============================================== Dr. Abdesalem HOUARI ------------------------------------------------------------------------------------------- Department of physics, Theoretical Physics Laboratory University of Bejaia-06000. Algeria. E-mail: abdeslam.houari at univ-bejaia.dz& habdeslam at gmail.com https://sites.google.com/site/houariabdeslam/homepage =============================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120304/1fb04f9e/attachment.htm From giannozz at democritos.it Sun Mar 4 10:59:35 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 4 Mar 2012 10:59:35 +0100 Subject: [Pw_forum] Electronic structure calculation of graphene as a spintronic material using espresso-4.2) In-Reply-To: <1330744007.47298.YahooMailNeo@web44708.mail.sp1.yahoo.com> References: <1330582327.11293.YahooMailNeo@web44714.mail.sp1.yahoo.com> <1330744007.47298.YahooMailNeo@web44708.mail.sp1.yahoo.com> Message-ID: <9D61590A-6C26-4A32-A933-0C0FB8478BCC@democritos.it> On Mar 3, 2012, at 4:06 , Rahen Badsha wrote: > nspin=2 > starting_magnetization(1)=0.6 graphene is nonmagnetic, and it will not turn magnetic by just imposing a starting magnetization P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sun Mar 4 11:01:31 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 4 Mar 2012 11:01:31 +0100 Subject: [Pw_forum] scf cslculation In-Reply-To: References: <1330715969.52852.YahooMailClassic@web161402.mail.bf1.yahoo.com> Message-ID: <66F2B0C7-F938-4EB5-8447-9C3D930B7114@democritos.it> On Mar 4, 2012, at 10:53 , Abdeslam HOUARI wrote: > what do I change in input file for obtaining correct answer? what about having a look at what the user guide says about this case? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giuseppe.mattioli at ism.cnr.it Sun Mar 4 13:13:56 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Sun, 4 Mar 2012 13:13:56 +0100 Subject: [Pw_forum] visualization In-Reply-To: References: <000601ccf93b$53e75d00$6501a8c0@polpress88ef18> Message-ID: <20120304131356.84isd85lm7go08sc@webmail.sic.rm.cnr.it> Dear Mateusz You may find something useful here http://people.sissa.it/~degironc/QE-Tutorial/tutorial_phon.htm HTH Giuseppe Giuseppe Mattioli ISM-CNR Italy Quoting Paolo Giannozzi : > > On Mar 3, 2012, at 13:44 , mateusz dulski wrote: > >> How can I visualize phonon calculation in XcrysDen? >> I used dynmat.x software to create filmxsf=*.axsf but >> unfortunatelly I cannot open this file in XCrysden. > > you should be able to visualize that file with XCrysDen. > Nothing has changed in that part of the code. > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From hashemifar at cc.iut.ac.ir Sun Mar 4 13:28:32 2012 From: hashemifar at cc.iut.ac.ir (Seyed Javad Hashemifar) Date: Sun, 4 Mar 2012 15:58:32 +0330 Subject: [Pw_forum] Eyvaz Isaev In-Reply-To: References: <20120303110747.18287.qmail@ms.hfcas.ac.cn> <6E5ADA0B99CE4852BB91BCB82EF83AC0@b> <355B0EC0-20F1-43AB-89C6-26DF440E7B33@democritos.it> Message-ID: I also express my deep condolence for the death of Prof. Eyvaz Isaev. I hope god forgives him and wish him a blissful afterlife. S. Javad Hashemifar > ====================================== > Seyed Javad Hashemifar > Department of Physics, Isfahan University of Technology > 84156-83111 Isfahan, Iran > Tel: +98 311 391 2375 Fax:+98 311 3912376 > Email: hashemifar at cc.iut.ac.ir > Group Homepage: http://cmsgroup.iut.ac.ir > Personal Homepage: http://hashemifar.iut.ac.ir > --------------------------------------------------------------------------- > > > > On Sat, Mar 3, 2012 at 6:30 PM, Paolo Giannozzi wrote: > >> I have received a message from Leyla Isaeva, the daughter >> of Eyvaz, who would like to thank everybody for the kind >> words. Eyvaz would have been 53 years old today. >> >> Paolo >> --- >> Paolo Giannozzi, Dept of Chemistry&Physics&Environment, >> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >> Phone +39-0432-558216, fax +39-0432-558222 >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120304/d28412b1/attachment.htm From faccin.giovani at gmail.com Mon Mar 5 00:13:14 2012 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Sun, 4 Mar 2012 19:13:14 -0400 Subject: [Pw_forum] About k-points Message-ID: Dear QE-Users, Could: K_POINTS{gamma} be somehow made equivalent to: K_POINTS {automatic} nk1 nk2 nk3 sk1 sk2 sk3 ? If so, how should one set the nk and sk values above to have the calculation performed at gamma only (or if not possible, at least including gamma), while using the second syntax? Thank you! Giovani Faccin CPPP / UFMS - Brazil -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120304/943d0751/attachment.htm From Lorenzo.Paulatto at impmc.upmc.fr Mon Mar 5 00:30:15 2012 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Mon, 05 Mar 2012 00:30:15 +0100 Subject: [Pw_forum] About k-points In-Reply-To: References: Message-ID: On Mon, 05 Mar 2012 00:13:14 +0100, Giovani Faccin wrote: > Dear QE-Users, > > Could: > > K_POINTS{gamma} > > be somehow made equivalent to: > > K_POINTS {automatic} > nk1 nk2 nk3 sk1 sk2 sk3 > > ? If so, how should one set the nk and sk values above to have the > calculation performed at gamma only (or if not possible, at least > including gamma), while using the second syntax? The followng syntax performs a calculation with Gamma point sampling: K_POINTS automatic 1 1 1 0 0 0 it is however not equivalent to K_POINTS gamma The latter uses the fact that wavefunctions at Gamma are (can be set) real to save a lot of memory and cpu time. In order to do so it uses several tricks that are not compatible with all the post-processing and additional codes. Notably, the phonon code does not work with the gamma-only sampling tricks. bests P.S. note that all the curly braces are not necessary, they also do not hurt -- Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www.impmc.upmc.fr/~paulatto/ mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From faccin.giovani at gmail.com Mon Mar 5 00:37:59 2012 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Sun, 4 Mar 2012 19:37:59 -0400 Subject: [Pw_forum] About k-points In-Reply-To: References: Message-ID: Thank you very much Lorenzo! Giovani 2012/3/4 Lorenzo Paulatto > On Mon, 05 Mar 2012 00:13:14 +0100, Giovani Faccin > wrote: > > > Dear QE-Users, > > > > Could: > > > > K_POINTS{gamma} > > > > be somehow made equivalent to: > > > > K_POINTS {automatic} > > nk1 nk2 nk3 sk1 sk2 sk3 > > > > ? If so, how should one set the nk and sk values above to have the > > calculation performed at gamma only (or if not possible, at least > > including gamma), while using the second syntax? > > > The followng syntax performs a calculation with Gamma point sampling: > K_POINTS automatic > 1 1 1 0 0 0 > > it is however not equivalent to > K_POINTS gamma > > The latter uses the fact that wavefunctions at Gamma are (can be set) real > to save a lot of memory and cpu time. In order to do so it uses several > tricks that are not compatible with all the post-processing and additional > codes. Notably, the phonon code does not work with the gamma-only sampling > tricks. > > bests > > P.S. note that all the curly braces are not necessary, they also do not > hurt > > > -- > Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6 > phone: +33 (0)1 44275 084 / skype: paulatz > www: http://www.impmc.upmc.fr/~paulatto/ > mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120304/c4dc6474/attachment.htm From pankajsahota at gmail.com Mon Mar 5 06:46:03 2012 From: pankajsahota at gmail.com (pankaj sahota) Date: Mon, 5 Mar 2012 11:16:03 +0530 Subject: [Pw_forum] about the pwcond.x calculation Message-ID: Hi, I am new to transport calculation. I am calculating the the quantum conductance of wires. There is one tag "iofspin" whose default value is one. I would like to know that if I do not give the iofspin tag then will it be a non spin polarized calculation of it will calculate the transmission for up spin and setting iofspin=2 will calculate the down spin. Waiting for your reply. Thanks and regards. Pankaj. -- Pankaj Kumar DST Project Fellow(Ph.D.) Department of Physics The LNM IIT Jaipur Mob. No. +91 9736694726 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120305/8132fcf7/attachment.htm From asmogunov at gmail.com Mon Mar 5 10:01:55 2012 From: asmogunov at gmail.com (Alex Smogunov) Date: Mon, 5 Mar 2012 10:01:55 +0100 Subject: [Pw_forum] about the pwcond.x calculation In-Reply-To: References: Message-ID: Dear Pankaj. All depends on scf calculation which you perform first before pwcond. If it was non spin-polarized - you should specify iofspin = 1 or nothing (iofspin = 2 will probably crash ...), if it was spin-polarized you specify 1 (2) for up (down) spin as you have said. regards, Alexander Le 5 mars 2012 06:46, pankaj sahota a ?crit : > Hi, > > I am new to transport calculation. I am calculating the the quantum > conductance of wires. There is one tag "iofspin" whose default value is > one. I would like to know that if I do not give the iofspin tag then will > it be a non spin polarized calculation of it will calculate the > transmission for up spin and setting iofspin=2 will calculate the down spin. > > Waiting for your reply. > Thanks and regards. > Pankaj. > > -- > Pankaj Kumar > DST Project Fellow(Ph.D.) > Department of Physics > The LNM IIT Jaipur > Mob. No. +91 9736694726 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120305/4b431326/attachment.htm From eariel99 at gmail.com Mon Mar 5 12:21:54 2012 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Mon, 5 Mar 2012 12:21:54 +0100 Subject: [Pw_forum] Eyvaz Isaev Message-ID: I wish to express my sadness from Prof. Eyvaz Isaev departure. At the beginning I was reluctant to use the forum byte allowance to express my private condolence and thought that the obituary by Paolo was enough. Although I did not have much interaction with him, I appreciated him as one of the most helpful and kind guys of this community. He belonged plenty to this community of persons that sacrifice a non-neglgible amount of time and productivity to help the fellows and make science a delightful activity. -- Eduardo Menendez Proupin Departamento de Qu?mica Fisica Aplicada Facultad de Ciencias Universidad Aut?noma de Madrid 28049 Madrid, Spain Phone: +34 91 497 6706 "...man never knows for who he suffers and waits. He suffers and waits and works for peoples he will never meet, and who at the same time will suffer and wait and work for others who will also not be happy, as man always desires a happiness that is beyond the lot that he is given. But the greatness of man is precisely in wanting to improve what he is. In assigning himself Tasks. In the Kingdom of Heaven there is no greatness to conquer, for everything there is an established hierarchy, the unknown is unobscured, existence is without end, sacrifice, rest, and delight are impossibilities. Therefore, overwhelmed with hardships and Tasks, beautiful within his misery, capable of loving in the middle of calamity, man can only find his greatness, his full self-realization, in the Kingdom of this World." - Alejo Carpentier- The kingdom of this world -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120305/94552c0b/attachment.htm From chen_shao_hua197 at yahoo.com.tw Tue Mar 6 08:04:24 2012 From: chen_shao_hua197 at yahoo.com.tw (=?big5?B?s68gpNa12A==?=) Date: Tue, 6 Mar 2012 15:04:24 +0800 (CST) Subject: [Pw_forum] FW: Eyvaz Isaev In-Reply-To: <1330674251.26056.5.camel@fe12lx.fisica.uniud.it> References: <1330674251.26056.5.camel@fe12lx.fisica.uniud.it> Message-ID: <1331017464.84116.YahooMailNeo@web74205.mail.tp2.yahoo.com> I regret his death. He help me a lot in e-ph calculations four years ago. May him rest in peace. max ----- ???? ---- ???? Paolo Giannozzi ???? PWSCF Forum ????? 2012/3/2 (??) 3:44 PM ??? [Pw_forum] Eyvaz Isaev I have the regret to announce that Prof. Dr. Eyvaz Isaev, author of QHA and PlotPhon packages, passed away on Sept.11, 2011 P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120306/749e7d3c/attachment.htm From farzad_c81 at yahoo.com Tue Mar 6 09:53:21 2012 From: farzad_c81 at yahoo.com (Farzad Molani) Date: Tue, 6 Mar 2012 00:53:21 -0800 (PST) Subject: [Pw_forum] Dos & PDOS Message-ID: <1331024001.48973.YahooMailClassic@web125905.mail.ne1.yahoo.com> Hi QE users, I want to get band gap for my system which consist fo carbons and Ti. I used dos.x for getting dos plot?and projwfc.x for pdos plot, but when I want to compare pdos plot with dos plot?I get?difference band gap from?both of them. why band gap from dos and pdos is different? please help me.? Farzad Molani, Ph.D Student, Department of Theoretical Physical Chemistry, K. N. Toosi University of Technology, Tehran, Iran. Tel.: 009891 4442 3308 Tel.: 009821 2306 4280 Fax: 009821 2285 3650 Web: http://www.chem.kntu.ac.ir/~sjalili:/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120306/41c601a8/attachment.htm From giacsport at libero.it Tue Mar 6 10:01:19 2012 From: giacsport at libero.it (giacsport at libero.it) Date: Tue, 6 Mar 2012 10:01:19 +0100 (CET) Subject: [Pw_forum] HSE from PBE in an atomic system Message-ID: <23950076.71031331024479765.JavaMail.defaultUser@defaultHost> Dear all, I am doing some HSE calculations on top of PBE ones. I wanted to calculate the energy of the atom of Oxygen. I am using the development version of PWscf. The same input gave reasnable results at PBE, but when I add the HSE part, I get this error: ZHEEVX : 2538-2156 No eigenvalues were computed since the Gershgorin interval initially used was incorrect. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from c_bands : error # 1 too many bands are not converged %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... And I honestly did not find anything in the forum regarding the Gershgorin interval. Could you kindly tell me where I am wrong? I attach you the HSE input file Thanks in advance for any possible hint. Best regards,Giacomo &CONTROL calculation = "scf" pseudo_dir = './' outdir='./', prefix='O_atom', tprnfor = .true., tstress = .true., wf_collect=.true., / &SYSTEM ibrav= 1, celldm(1) = 18.897259886 nat= 1, ntyp= 1, ecutwfc =90.0, nbnd = 20, nspin=2, tot_magnetization=2, occupations='smearing', degauss=0.01,smearing='gaussian' force_symmorphic=.true., starting_magnetization(1)=1, input_dft='hse', nqx1=1, nqx2=1, nqx3=1, x_gamma_extrapolation = .TRUE. / &ELECTRONS diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES O 15.9994 O-GGA-pbe.fhi.UPF ATOMIC_POSITIONS (crystal) O 0.5 0.5 0.5 K_POINTS (automatic) 1 1 1 0 0 0 -- *************************************** Giacomo Giorgi, Ph.D. Yamashita & Ushiyama Laboratory, Department of Chemical System Engineering, Faculty of Engineering, The University of Tokyo. tel&fax: +81-3-5841-7286 email: giacomo at tcl.t.u-tokyo.ac.jp HP: http://www.tcl.t.u-tokyo.ac.jp/ *************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120306/8efb8f7e/attachment.htm From giannozz at democritos.it Tue Mar 6 10:14:37 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 06 Mar 2012 10:14:37 +0100 Subject: [Pw_forum] HSE from PBE in an atomic system In-Reply-To: <23950076.71031331024479765.JavaMail.defaultUser@defaultHost> References: <23950076.71031331024479765.JavaMail.defaultUser@defaultHost> Message-ID: <1331025277.5261.34.camel@fe12lx.fisica.uniud.it> On Tue, 2012-03-06 at 10:01 +0100, giacsport at libero.it wrote: > No eigenvalues were computed since the Gershgorin interval > initially used was incorrect. nice error message: best of the year until now. My guess is that HSE is still producing NaN's under some circumstances. Try to enable floating-point checks. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giacsport at libero.it Tue Mar 6 12:42:57 2012 From: giacsport at libero.it (giacsport at libero.it) Date: Tue, 6 Mar 2012 12:42:57 +0100 (CET) Subject: [Pw_forum] R: Re: HSE from PBE in an atomic system Message-ID: <28604245.192341331034177405.JavaMail.defaultUser@defaultHost> Thanks Paolo. I will. Best, Giacomo >----Messaggio originale---- >Da: giannozz at democritos.it >Data: 06/03/2012 10.14 >A: "giacsport at libero.it" >Cc: >Ogg: Re: [Pw_forum] HSE from PBE in an atomic system > >On Tue, 2012-03-06 at 10:01 +0100, giacsport at libero.it wrote: > >> No eigenvalues were computed since the Gershgorin interval >> initially used was incorrect. > >nice error message: best of the year until now. > >My guess is that HSE is still producing NaN's under some >circumstances. Try to enable floating-point checks. > >P. >-- >Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > From giannozz at democritos.it Tue Mar 6 12:48:09 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 06 Mar 2012 12:48:09 +0100 Subject: [Pw_forum] Dos & PDOS In-Reply-To: <1331024001.48973.YahooMailClassic@web125905.mail.ne1.yahoo.com> References: <1331024001.48973.YahooMailClassic@web125905.mail.ne1.yahoo.com> Message-ID: <1331034489.6736.3.camel@fe12lx.fisica.uniud.it> On Tue, 2012-03-06 at 00:53 -0800, Farzad Molani wrote: > I want to compare pdos plot with dos plot I get difference > band gap from both of them. why band gap from dos and pdos > is different? it isn't. You used different gaussian broadenings or different algorithms (tetrahedra vs broadening) P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From amiri_physics at yahoo.com Tue Mar 6 16:40:46 2012 From: amiri_physics at yahoo.com (peyman amiri) Date: Tue, 6 Mar 2012 07:40:46 -0800 (PST) Subject: [Pw_forum] regret from death of Prof. Eyvaz Isaev In-Reply-To: <1331048250.20018.YahooMailNeo@web161702.mail.bf1.yahoo.com> References: <1330674251.26056.5.camel@fe12lx.fisica.uniud.it> <1331017464.84116.YahooMailNeo@web74205.mail.tp2.yahoo.com> <1331021123.94345.YahooMailNeo@web161703.mail.bf1.yahoo.com> <1331048250.20018.YahooMailNeo@web161702.mail.bf1.yahoo.com> Message-ID: <1331048446.33855.YahooMailNeo@web161705.mail.bf1.yahoo.com> ?Dear Paolo Giannozzi ? Please accept my condolence message?for the death of Prof. Eyvaz Isaev. He was one?of the kind scientists in all the world. God bless him and?give patience to his family. Peiman ====================================== Peiman Amiri Computational Condensed Matter Research Lab Physics Department, Isfahan University of Technology, Iran Tel lab: +98 311 391 3733 Fax Office: +98311 391 3746 ------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120306/c9de3f2c/attachment.htm From makhyoun2 at yahoo.com Wed Mar 7 01:02:54 2012 From: makhyoun2 at yahoo.com (mohamed makhyoun) Date: Tue, 6 Mar 2012 16:02:54 -0800 (PST) Subject: [Pw_forum] error in running pw.x in scf mode. Message-ID: <1331078574.57007.YahooMailClassic@web126005.mail.ne1.yahoo.com> Dear all: I am trying to do phonon calculation on some silver complex in solid. As a first step the the use of pw.x in the scf mode gave the following error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ???? from? card_kpoints? : error #???????? 2 ????? two occurrences %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% The input is included below. I appreciate any help or suggestions. Best regard Mohamed &CONTROL ???????????????? calculation = 'scf' , ??????????????? restart_mode = 'from_scratch' , ????????????????? outdir = '$TMP_DIR' , ????????????????? pseudo_dir = '/home/mohamed/espresso/exec/pseudo' , ???????????????????? disk_io = 'low' , ?????????????????? verbosity = 'default' , ?????????????????? nstep=100 , ?????????????????? tprnfor=.true. , ?????????????? / ?&SYSTEM ?????????????????????????? ibrav=14? ?????????????????????????? A = 8.1664 , ?????????????????????????? B = 8.4103 , ?????????????????????????? C = 10.4848 , ?????????????????????? cosAB = .48285 , ?????????????????????? cosAC = .23670 , ?????????????????????? cosBC = .33604 , ???????????????????????? nat = 58, ??????????????????????? ntyp = 5, ???????????????????? ecutwfc = 50. , ???????????????????? nbnd= 106 , ?/ ?&ELECTRONS ????????????? conv_thr=1.0D-8 , ?/ ATOMIC_SPECIES ?? Ag? 107.86800? Ag.pbe-d-rrkjus.UPF ??? N?? 14.00700? N.pbe-rrkjus.UPF ??? O?? 15.99900? O.pbe-rrkjus.UPF ??? C?? 12.01100? C.pbe-rrkjus.UPF ??? H??? 1.00800? H.pbe-rrkjus.UPF ATOMIC_POSITIONS {crystal} Ag????? -0.112709927?? 0.087193977?? 0.200542078 Ag?????? 0.112709927? -0.087193977? -0.200542078 N??????? 0.038970214? -0.113394975?? 0.373873350 N?????? -0.038970214?? 0.113394975? -0.373873350 N?????? -0.210836888?? 0.320473795?? 0.024629773 N??????? 0.210836888? -0.320473795? -0.024629773 N?????? -0.346566812? -0.141338901?? 0.194634935 N??????? 0.346566812?? 0.141338901? -0.194634935 O??????? 0.465894055? -0.234016565? -0.490005525 O?????? -0.465894055?? 0.234016565?? 0.490005525 O?????? -0.260556713? -0.200738581? -0.116145710 O??????? 0.260556713?? 0.200738581?? 0.116145710 O?????? -0.435204501? -0.227554058?? 0.194452751 O??????? 0.435204501?? 0.227554058? -0.194452751 O?????? -0.227980395? -0.117943277?? 0.095287701 O??????? 0.227980395?? 0.117943277? -0.095287701 O?????? -0.370301880? -0.075383782?? 0.294502189 O??????? 0.370301880?? 0.075383782? -0.294502189 C??????? 0.307812645? -0.236172715?? 0.495562045 C?????? -0.307812645?? 0.236172715? -0.495562045 C?????? -0.262184111? -0.364985975? -0.102413562 C??????? 0.262184111?? 0.364985975?? 0.102413562 C??????? 0.197520149? -0.112042887?? 0.387418343 C?????? -0.197520149?? 0.112042887? -0.387418343 C?????? -0.018470426? -0.236520568?? 0.466885975 C??????? 0.018470426?? 0.236520568? -0.466885975 C?????? -0.321122130? -0.385355915? -0.208406542 C??????? 0.321122130?? 0.385355915?? 0.208406542 C?????? -0.206159440?? 0.482723105?? 0.012393688 C??????? 0.206159440? -0.482723105? -0.012393688 C??????? 0.248213648? -0.363603164? -0.408021893 C?????? -0.248213648?? 0.363603164?? 0.408021893 C?????? -0.323408790?? 0.446418433? -0.194833337 C??????? 0.323408790? -0.446418433?? 0.194833337 C?????? -0.268773432?? 0.301829349? -0.077007224 C??????? 0.268773432? -0.301829349?? 0.077007224 C??????? 0.083853381? -0.363193581? -0.423485237 C?????? -0.083853381?? 0.363193581?? 0.423485237 H??????? 0.238545808? -0.010482339?? 0.309906844 H?????? -0.238545808?? 0.010482339? -0.309906844 H?????? -0.148089076? -0.230591681?? 0.451069134 H??????? 0.148089076?? 0.230591681? -0.451069134 H?????? -0.369133736? -0.268357583? -0.297827765 H??????? 0.369133736?? 0.268357583?? 0.297827765 H?????? -0.159479698?? 0.492875537?? 0.096833996 H??????? 0.159479698? -0.492875537? -0.096833996 H??????? 0.332539226? -0.463733893? -0.324420815 H?????? -0.332539226?? 0.463733893?? 0.324420815 H?????? -0.369559127?? 0.426943641? -0.275068705 H??????? 0.369559127? -0.426943641?? 0.275068705 H?????? -0.273325896?? 0.169744869? -0.061624293 H??????? 0.273325896? -0.169744869?? 0.061624293 H??????? 0.033773777? -0.461122219? -0.350682505 H?????? -0.033773777?? 0.461122219?? 0.350682505 H?????? -0.243391058? -0.186728030? -0.028835874 H??????? 0.243391058?? 0.186728030?? 0.028835874 H?????? -0.487685811? -0.161797721?? 0.423823038 H??????? 0.487685811?? 0.161797721? -0.423823038 K_POINTS automatic ?1 1 1 0 0 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120306/30446913/attachment-0001.htm From gm030212 at gmail.com Wed Mar 7 03:15:46 2012 From: gm030212 at gmail.com (Fen Hong) Date: Wed, 7 Mar 2012 11:15:46 +0900 Subject: [Pw_forum] Raman intensity unit Message-ID: Dear All, Does A^4/amu in dynmat.out mean Ang^4/amu for Raman cross sections? Is the meaning of Raman and IR cross sections same with Raman and IR intensity? Thanks. Best Wishes Takai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120307/fb2b8d3b/attachment.htm From giannozz at democritos.it Wed Mar 7 08:28:50 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 7 Mar 2012 08:28:50 +0100 Subject: [Pw_forum] Raman intensity unit In-Reply-To: References: Message-ID: On Mar 7, 2012, at 3:15 , Fen Hong wrote: > Does A^4/amu in dynmat.out mean Ang^4/amu for Raman cross sections? > Is the meaning of Raman and IR cross sections same with Raman and > IR intensity? yes and yes P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed Mar 7 08:29:48 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 7 Mar 2012 08:29:48 +0100 Subject: [Pw_forum] error in running pw.x in scf mode. In-Reply-To: <1331078574.57007.YahooMailClassic@web126005.mail.ne1.yahoo.com> References: <1331078574.57007.YahooMailClassic@web126005.mail.ne1.yahoo.com> Message-ID: <79F64F7F-0B03-4D25-B79F-521B1370821A@democritos.it> On Mar 7, 2012, at 1:02 , mohamed makhyoun wrote: > from card_kpoints : error # 2 > two occurrences there are two cards K_POINTS P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From Lorenzo.Paulatto at impmc.upmc.fr Wed Mar 7 11:40:16 2012 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Wed, 07 Mar 2012 11:40:16 +0100 Subject: [Pw_forum] error in running pw.x in scf mode. In-Reply-To: <1331078574.57007.YahooMailClassic@web126005.mail.ne1.yahoo.com> References: <1331078574.57007.YahooMailClassic@web126005.mail.ne1.yahoo.com> Message-ID: On Wed, 07 Mar 2012 01:02:54 +0100, mohamed makhyoun wrote: > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from card_kpoints : error # 2 > two occurrences > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Dear Mohamed, this happens if (an only if) your input file includes 2 or more lines like: K_POINTS ... please double check that this is not the case. If you are sure it is not, provide more information, like compiler version, code version, a tar.gz of all your input. kind regards -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From amit99266 at rediffmail.com Wed Mar 7 15:44:24 2012 From: amit99266 at rediffmail.com (Amit Harode) Date: 7 Mar 2012 14:44:24 -0000 Subject: [Pw_forum] =?utf-8?q?Eyvaz_Isaev?= In-Reply-To: <1330674251.26056.5.camel@fe12lx.fisica.uniud.it> Message-ID: <1330674299.S.2235.11100.H.TlBhb2xvIEdpYW5ub3p6aQBbUHdfZm9ydW1dIEV5dmF6IElzYWV2.RU.rfs216, rfs216, 1003, 340.f4-234-88.1331131464.20527@webmail.rediffmail.com> I am very sorry to know this loss of PW forum and package. He helped me a lot in QHA calculations. The QHA package contributed by Prof Eyvaz Isaev is excellently automated. PW forum is going to miss him. May his soul rest in peace ... Warm Regards Amit N Harode CR Labs INDIA On Fri, 02 Mar 2012 13:14:59 +0530 wrote >I have the regret to announce that Prof. Dr. Eyvaz Isaev, author of QHA and PlotPhon packages, passed away on Sept.11, 2011 P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120307/7bdbd994/attachment.htm From suza.rri at gmail.com Wed Mar 7 18:35:09 2012 From: suza.rri at gmail.com (Suza W) Date: Wed, 7 Mar 2012 18:35:09 +0100 Subject: [Pw_forum] PBESOL Message-ID: Hello All, Does any of you have a PBESOL USPP for Zr ? Thanks and Regards, Suza W From payam.norouzzadeh at gmail.com Wed Mar 7 23:41:36 2012 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Wed, 7 Mar 2012 16:41:36 -0600 Subject: [Pw_forum] relaxation with vc-relax Message-ID: Dear QE users My system has 54 atoms with a BCC structure. Its primitive unit cell includes 27 atoms. I am trying to find its lattice constant by using vc-relax. After running it several times and for more than 3 weeks still the convergence thresholds are not satisfied. The forces don't like to get smaller than a specific value (around 0.02). Is something wrong with my input file? Please let me know your comments. Best regards,Payam Norouzzadeh &CONTROL title = Eight, calculation = "vc-relax", restart_mode = 'from_scratch' , prefix = "Eight", pseudo_dir = "/...", wfcdir = '...' , outdir = '/...', nstep = 100 , etot_conv_thr = 1.0E-9 , forc_conv_thr = 5.0D-5 , max_seconds = 172800 , dt = 100 , / &SYSTEM ibrav = 3, celldm(1)=19.622, nat = 27, ntyp = 3, ecutwfc = 70.D0, ecutrho = 700.D0, occupations='smearing', smearing='gaussian', degauss=0.02, / &ELECTRONS diagonalization = 'cg', conv_thr = 1.D-9, mixing_beta = 0.5D0, / &IONS ion_dynamics = 'damp' , / &CELL cell_dynamics = 'damp-w', / ATOMIC_SPECIES Al 26.98154 Al.pw91-n-van.UPF Si 28.0855 Si.pw91-n-van.UPF Ba 137.327 Ba.pw91-nsp-van.UPF ATOMIC_POSITIONS crystal Al 0.216201457 0.378180997 0.237078143 Al 0.034697037 0.023737131 0.761262755 Al 0.547173316 0.281036341 0.747383956 Al 0.499243974 0.592176706 0.241711510 Al 0.079436185 0.571961647 0.770077147 Al 0.696760320 0.247074460 0.186155320 Al 0.763858042 0.534829188 0.108400015 Si -0.084375501 0.661831874 -0.052015722 Si 0.768579606 0.003812573 0.065138231 Si 0.015665804 -0.146726664 0.029763195 Si 0.219167074 0.647981279 0.510896217 Si 0.688206047 0.299356062 0.551238353 Si 0.813578233 0.574824765 0.373099840 Si 0.455287149 0.559729400 0.815079368 Si 0.236709112 0.370770979 0.535759218 Si -0.101920499 0.795055135 0.400098065 Si 0.540358072 0.119760142 0.526376973 Si 0.817782198 0.005623765 0.511008919 Si 0.260966498 0.808368895 0.269851937 Si 0.611991634 -0.079635051 0.839306911 Si 0.368449934 0.463356223 0.046445257 Si 0.051075029 0.331552898 0.665912314 Si 0.416741872 0.793935246 -0.103728118 Ba 0.635745128 0.714712066 0.579828902 Ba 0.158096139 0.054209356 0.465675155 Ba -0.077117796 0.267386792 -0.044545628 Ba 0.416141346 0.060760806 0.081304511 K_POINTS automatic 6 6 6 0 0 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120307/41a9acbc/attachment.htm From csatya11 at gmail.com Thu Mar 8 04:15:35 2012 From: csatya11 at gmail.com (satyananda chab) Date: Thu, 8 Mar 2012 08:45:35 +0530 Subject: [Pw_forum] submission Message-ID: Dear Sir, I am using Quantum Espresso codes for materials modelling. So, I want to be in your mailing list. Yours truly, Satyananda Research Scholar Gauhati University email:csatya11 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120308/fdb58916/attachment.htm From payam.norouzzadeh at gmail.com Thu Mar 8 04:45:27 2012 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Thu, 8 Mar 2012 07:15:27 +0330 Subject: [Pw_forum] relaxation with vc-relax In-Reply-To: References: Message-ID: Dear Sonu Kumar Thank you for your guidelines. I will test them. Best regards,Payam Norouzzadeh On Thu, Mar 8, 2012 at 7:11 AM, Sonu Kumar <1009ukumar at gmail.com> wrote: > On Thu, Mar 8, 2012 at 4:11 AM, Payam Norouzzadeh < > payam.norouzzadeh at gmail.com> wrote: > >> Dear QE users >> >> My system has 54 atoms with a BCC structure. Its primitive unit cell >> includes 27 atoms. >> I am trying to find its lattice constant by using vc-relax. >> After running it several times and for more than 3 weeks still the >> convergence thresholds are not satisfied. >> The forces don't like to get smaller than a specific value (around 0.02). >> Is something wrong with my input file? Please let me know your comments. >> >> Best regards,Payam Norouzzadeh >> >> >> &CONTROL >> title = Eight, >> calculation = "vc-relax", >> restart_mode = 'from_scratch' , >> prefix = "Eight", >> pseudo_dir = "/...", >> wfcdir = '...' , >> outdir = '/...', >> nstep = 100 , >> etot_conv_thr = 1.0E-9 , >> forc_conv_thr = 5.0D-5 , >> max_seconds = 172800 , >> dt = 100 , >> / >> > > force and energy threshold seems to very high, especially > the latter. reduce them. > > >> &SYSTEM >> ibrav = 3, >> celldm(1)=19.622, >> nat = 27, >> ntyp = 3, >> ecutwfc = 70.D0, >> ecutrho = 700.D0, >> occupations='smearing', >> smearing='gaussian', >> degauss=0.02, >> / >> &ELECTRONS >> diagonalization = 'cg', >> conv_thr = 1.D-9, >> mixing_beta = 0.5D0, >> / >> > > use diagonalization= david > > >> &IONS >> ion_dynamics = 'damp' , >> / >> > > use default bfgs algorithm for dynamics > > >> &CELL >> cell_dynamics = 'damp-w', >> / >> > > similarly, use default bfgs. > >> >> > GOOD LUCK !! > > SKumar > IITD > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120308/8112f4bc/attachment.htm From mpayami at aeoi.org.ir Thu Mar 8 04:55:55 2012 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Thu, 8 Mar 2012 08:25:55 +0430 Subject: [Pw_forum] submission References: Message-ID: <5E04ED6E996342E49AAF1E092DF54042@b> Dear Satyananda, Please refer to: http://www.democritos.it/mailman/listinfo/pw_forum Bests, mahmoud -------------------------------- Mahmoud Payami Physics Group Atomic Energy Organization of Iran Tehran-Iran Email: mpayami at aeoi.org.ir Phone: +98 (0) 21 82064393 ---------------------------------------------- Dear Sir, I am using Quantum Espresso codes for materials modelling. So, I want to be in your mailing list. Yours truly, Satyananda Research Scholar Gauhati University email:csatya11 at gmail.com ------------------------------------------------------------------------------ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120308/4c1cc91e/attachment-0001.htm From giannozz at democritos.it Thu Mar 8 08:20:40 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 8 Mar 2012 08:20:40 +0100 Subject: [Pw_forum] relaxation with vc-relax In-Reply-To: References: Message-ID: On Mar 7, 2012, at 23:41 , Payam Norouzzadeh wrote: > &IONS > ion_dynamics = 'damp' , > / > &CELL > cell_dynamics = 'damp-w', > / if you use cell_dynamics = 'damp-w', I think shouldn't specify ions_dynamics. You should also choose a suitable value for "wmass": not sure how good the default value is P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From f.anis45 at yahoo.com Thu Mar 8 09:32:04 2012 From: f.anis45 at yahoo.com (F Anis) Date: Thu, 8 Mar 2012 00:32:04 -0800 (PST) Subject: [Pw_forum] mathematical method for computing in quantm espresso Message-ID: <1331195524.23019.YahooMailClassic@web120304.mail.ne1.yahoo.com> Hi, What?mathematical?method?for?computing the?optical properties and self consist cycle in the?quantum?espresso?is used. thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120308/92ad3ecb/attachment.htm From abdeslam.houari at gmail.com Thu Mar 8 11:39:45 2012 From: abdeslam.houari at gmail.com (Abdeslam HOUARI) Date: Thu, 8 Mar 2012 11:39:45 +0100 Subject: [Pw_forum] mathematical method for computing in quantm espresso In-Reply-To: <1331195524.23019.YahooMailClassic@web120304.mail.ne1.yahoo.com> References: <1331195524.23019.YahooMailClassic@web120304.mail.ne1.yahoo.com> Message-ID: You know, it's seems so hard (at least for me) to give a satisfactory answer !!! ???? could you please give a bit clarification about what you need !! 2012/3/8 F Anis > Hi, > What mathematical method for computing the optical properties and self > consist cycle in the quantum espresso is used. > thanks. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > ============================================== Dr. Abdesalem HOUARI ------------------------------------------------------------------------------------------- Department of physics, Theoretical Physics Laboratory University of Bejaia-06000. Algeria. E-mail: abdeslam.houari at univ-bejaia.dz& habdeslam at gmail.com https://sites.google.com/site/houariabdeslam/homepage =============================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120308/2437b042/attachment.htm From eariel99 at gmail.com Thu Mar 8 11:53:16 2012 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Thu, 8 Mar 2012 11:53:16 +0100 Subject: [Pw_forum] mathematical method for computing in quantm espresso Message-ID: Read this espresso-4.3.2/TDDFPT/Doc/turboTDDFT-CPC.pdf or Comput. Phys. Commun. 182 (2011) 1744-1754. and the user guide at www.quantum-espresso.org For the optical properties there is also a less sophisticated approach implemented in the epsilon.x code, the manual is in the file espresso-4.3.2/Doc/eps_man.pdf Enjoy, Eduardo Menendez Proupin Departamento de Qu?mica Fisica Aplicada Facultad de Ciencias Universidad Aut?noma de Madrid 28049 Madrid, Spain Phone: +34 91 497 6706 ---------- Mensaje reenviado ---------- > From: F Anis > To: pw_forum at pwscf.org > Cc: > Date: Thu, 8 Mar 2012 00:32:04 -0800 (PST) > Subject: [Pw_forum] mathematical method for computing in quantm espresso > Hi, > What mathematical method for computing the optical properties and self > consist cycle in the quantum espresso is used. > thanks. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120308/3c042b18/attachment.htm From sohailphysics at yahoo.co.in Thu Mar 8 12:30:39 2012 From: sohailphysics at yahoo.co.in (Sohail Ahmad) Date: Thu, 8 Mar 2012 19:30:39 +0800 (SGT) Subject: [Pw_forum] GUI Message-ID: <1331206239.86101.YahooMailClassic@web192201.mail.sg3.yahoo.com> Dear PW User ? Is there any option of GUI in QE as it is available in WIEN2K/Gaussian ? Sohail King Khalid University Saudi Arabia -------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120308/fb8f11de/attachment.htm From payam.norouzzadeh at gmail.com Thu Mar 8 15:50:49 2012 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Thu, 8 Mar 2012 18:20:49 +0330 Subject: [Pw_forum] relaxation with vc-relax In-Reply-To: References: Message-ID: Dear Prof.Giannozzi Thank you for your comment. Best regards,Payam Norouzzadeh On Thu, Mar 8, 2012 at 10:50 AM, Paolo Giannozzi wrote: > > On Mar 7, 2012, at 23:41 , Payam Norouzzadeh wrote: > > &IONS >> ion_dynamics = 'damp' , >> / >> &CELL >> cell_dynamics = 'damp-w', >> / >> > > if you use cell_dynamics = 'damp-w', I think shouldn't > specify ions_dynamics. You should also choose a suitable > value for "wmass": not sure how good the default value is > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > 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://www.democritos.it/pipermail/pw_forum/attachments/20120308/ba7e5150/attachment.htm From rahen29 at yahoo.com Thu Mar 8 18:40:38 2012 From: rahen29 at yahoo.com (Rahen Badsha) Date: Thu, 8 Mar 2012 09:40:38 -0800 (PST) Subject: [Pw_forum] High symmetry points In-Reply-To: <1330743883.89515.YahooMailNeo@web44714.mail.sp1.yahoo.com> References: <1330692801.28406.YahooMailNeo@web44701.mail.sp1.yahoo.com> <1330743883.89515.YahooMailNeo@web44714.mail.sp1.yahoo.com> Message-ID: <1331228438.22391.YahooMailNeo@web44713.mail.sp1.yahoo.com> Dear QE Users,I am facing some problems for electronic structure calculation of graphene.For showing high symmetry points in band structure of graphene(i.e. It is an HCP two dimensional structure). In which program I define the high symmetry points .? Have any one who help me about? this? Best Wishes- Rahen Badsha (Raihan) A post graduate thesis student University of Rajshahi, Bangladesh. Mobile:+8801710550252 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120308/07b3f4a9/attachment.htm From rahen29 at yahoo.com Thu Mar 8 18:40:38 2012 From: rahen29 at yahoo.com (Rahen Badsha) Date: Thu, 8 Mar 2012 09:40:38 -0800 (PST) Subject: [Pw_forum] High symmetry points In-Reply-To: <1330743883.89515.YahooMailNeo@web44714.mail.sp1.yahoo.com> References: <1330692801.28406.YahooMailNeo@web44701.mail.sp1.yahoo.com> <1330743883.89515.YahooMailNeo@web44714.mail.sp1.yahoo.com> Message-ID: <1331228438.22391.YahooMailNeo@web44713.mail.sp1.yahoo.com> Dear QE Users,I am facing some problems for electronic structure calculation of graphene.For showing high symmetry points in band structure of graphene(i.e. It is an HCP two dimensional structure). In which program I define the high symmetry points .? Have any one who help me about? this? Best Wishes- Rahen Badsha (Raihan) A post graduate thesis student University of Rajshahi, Bangladesh. Mobile:+8801710550252 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120308/07b3f4a9/attachment-0001.htm From makhyoun2 at yahoo.com Fri Mar 9 03:06:35 2012 From: makhyoun2 at yahoo.com (mohamed makhyoun) Date: Thu, 8 Mar 2012 18:06:35 -0800 (PST) Subject: [Pw_forum] error in running pw.x in scf mode. In-Reply-To: Message-ID: <1331258795.60983.YahooMailClassic@web126005.mail.ne1.yahoo.com> Dear Sir: I am sorry I discovered a forgotten second K_POINTS card at the bottom of the input file. Thank you for the tip. Best regard Mohamed --- On Wed, 3/7/12, Lorenzo Paulatto wrote: From: Lorenzo Paulatto Subject: Re: [Pw_forum] error in running pw.x in scf mode. To: pw_forum at pwscf.org Date: Wednesday, March 7, 2012, 12:40 PM On Wed, 07 Mar 2012 01:02:54 +0100, mohamed makhyoun ? wrote: > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >? ? ? from? card_kpoints? : error #? ? ? ???2 >? ? ???two occurrences > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Dear Mohamed, this happens if (an only if) your input file includes 2 or more lines like: K_POINTS ... please double check that this is not the case. If you are sure it is not,? provide more information, like compiler version, code version, a tar.gz of? all your input. kind regards -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www:???http://www-int.impmc.upmc.fr/~paulatto/ mail:? 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120308/ac970d4f/attachment-0001.htm From yccheng.nju at gmail.com Fri Mar 9 14:09:36 2012 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Fri, 9 Mar 2012 16:09:36 +0300 Subject: [Pw_forum] GUI In-Reply-To: <1331206239.86101.YahooMailClassic@web192201.mail.sg3.yahoo.com> References: <1331206239.86101.YahooMailClassic@web192201.mail.sg3.yahoo.com> Message-ID: pwgui 2012/3/8 Sohail Ahmad > Dear PW User > > Is there any option of GUI in QE as it is available in WIEN2K/Gaussian > > Sohail > King Khalid University > Saudi Arabia > > -------------------------------------------------------------------- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120309/bd3f26aa/attachment.htm From bdslipun at gmail.com Fri Mar 9 18:48:31 2012 From: bdslipun at gmail.com (bhabya sahoo) Date: Fri, 9 Mar 2012 23:18:31 +0530 Subject: [Pw_forum] band structure Message-ID: how to change the colour of bands in electronic band structure in quantum espresso b d sahoo reserch scholar mumbai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120309/d7f0ffc6/attachment.htm From farzad_c81 at yahoo.com Sat Mar 10 16:03:54 2012 From: farzad_c81 at yahoo.com (Farzad Molani) Date: Sat, 10 Mar 2012 07:03:54 -0800 (PST) Subject: [Pw_forum] Dos & PDOS In-Reply-To: <1331034489.6736.3.camel@fe12lx.fisica.uniud.it> Message-ID: <1331391834.16012.YahooMailClassic@web125903.mail.ne1.yahoo.com> Hello, Thanks for your comment, How can I choose the best value for degauss. my systems probebly is semiconductor. thank you. Farzad Molani, Ph.D Student, Department of Theoretical Physical Chemistry, K. N. Toosi University of Technology, Tehran, Iran. Tel.: 009891 4442 3308 Tel.: 009821 2306 4280 Fax: 009821 2285 3650 Web: http://www.chem.kntu.ac.ir/~sjalili:/ --- On Tue, 3/6/12, Paolo Giannozzi wrote: From: Paolo Giannozzi Subject: Re: [Pw_forum] Dos & PDOS To: "Farzad Molani" Cc: "pwscf" Date: Tuesday, March 6, 2012, 3:18 PM On Tue, 2012-03-06 at 00:53 -0800, Farzad Molani wrote: > I want to compare pdos plot with dos plot I get difference > band gap from both of them. why band gap from dos and pdos > is different? it isn't. You used different gaussian broadenings or different algorithms (tetrahedra vs broadening) P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120310/ae50436a/attachment.htm From henod2001 at yahoo.com Sun Mar 11 13:23:07 2012 From: henod2001 at yahoo.com (henry odhiambo) Date: Sun, 11 Mar 2012 05:23:07 -0700 (PDT) Subject: [Pw_forum] Charge Density Message-ID: <1331468587.58694.YahooMailClassic@web121004.mail.ne1.yahoo.com> Hello, ? I want to extract the charge density for a hexagonal cell.?Is it possible with the four-index system (hkil)? ? Henry Otunga Dept. of Physics Maseno Univ Kenya? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120311/d496bd4c/attachment.htm From giannozz at democritos.it Sun Mar 11 18:15:23 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 11 Mar 2012 18:15:23 +0100 Subject: [Pw_forum] Charge Density In-Reply-To: <1331468587.58694.YahooMailClassic@web121004.mail.ne1.yahoo.com> References: <1331468587.58694.YahooMailClassic@web121004.mail.ne1.yahoo.com> Message-ID: On Mar 11, 2012, at 13:23 , henry odhiambo wrote: > I want to extract the charge density for a hexagonal cell. > Is it possible with the four-index system (hkil)? tha charge density can be easily extracted either in real space, rho(r), on a grid, or in reciprocal space, rho(G). Making the connection between these and the four-index system is your task P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From makhyoun2 at yahoo.com Sun Mar 11 20:22:57 2012 From: makhyoun2 at yahoo.com (mohamed makhyoun) Date: Sun, 11 Mar 2012 12:22:57 -0700 (PDT) Subject: [Pw_forum] read_pseudo_gipaw : error # 1 Message-ID: <1331493777.91282.YahooMailClassic@web126001.mail.ne1.yahoo.com> Dear all : Running pw.x for the benzene example found in ./qe-gipaw-4.3.2/examples/benzene-USPP/benzene-scf.in? I got the following error : %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ???? from read_pseudo_gipaw : error #???????? 1 ???? Reading pseudo file ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Since I am interested to do nmr calculations on some complexes containing? C, H I appreciate any help. Best regard Mohamed ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120311/8f4a6d7a/attachment.htm From bahadira at buffalo.edu Sun Mar 11 23:43:56 2012 From: bahadira at buffalo.edu (bahadir) Date: Sun, 11 Mar 2012 18:43:56 -0400 Subject: [Pw_forum] tmp/_ph0/{PREFIX}_qxx directories, safe to remove? Message-ID: <4F5D2AAC.5020506@buffalo.edu> Hi, i wonder if it is safe to remove tmp/_ph0/{PREFIX}_qxx directories after the calculation on xx q-point and obtaining elph files for correcponding q-point? i have 64 q-point and 35 of them are completed, tmp files are 123gb and increasing. i want to have some space by removing these directories. thanks -- Dr.Bahadir Altintas * Dept. of Chemistry SUNY Buffalo NY,USA * Abant Izzet Baysal University Dept. of Computer Education Bolu,Turkey From davide.ceresoli at istm.cnr.it Mon Mar 12 10:00:43 2012 From: davide.ceresoli at istm.cnr.it (Davide Ceresoli) Date: Mon, 12 Mar 2012 10:00:43 +0100 Subject: [Pw_forum] read_pseudo_gipaw : error # 1 In-Reply-To: <1331493777.91282.YahooMailClassic@web126001.mail.ne1.yahoo.com> References: <1331493777.91282.YahooMailClassic@web126001.mail.ne1.yahoo.com> Message-ID: <4F5DBB3B.6060901@istm.cnr.it> Dear Mohamed, if QE issues an error while reading GIPAW pseudopotentials, edit the UPF file, search for the and tags and change the version from '0.1' to '1'. HTH Davide On 01/-10/-28163 08:59 PM, mohamed makhyoun wrote: > Dear all : > > Running pw.x for the benzene example found in > ./qe-gipaw-4.3.2/examples/benzene-USPP/benzene-scf.in I got the following error : > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_pseudo_gipaw : error # 1 > Reading pseudo file > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > Since I am interested to do nmr calculations on some complexes containing C, H > > I appreciate any help. > > Best regard > Mohamed > From flux_ray12 at 163.com Mon Mar 12 12:21:30 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Mon, 12 Mar 2012 19:21:30 +0800 (CST) Subject: [Pw_forum] LDA+U or GGA+U? Message-ID: <127a2912.1de02.13606a445e7.Coremail.flux_ray12@163.com> Dear QE developer and users: I just began to try LDA+U method in QE, by adding lda_plus_u = .true. and Hubbard_U(i) parameters to scf input file, where the U value was determined by following M.Cococcioni's thesis and Prof. Marzari's paper (PRL, 97, 103001). However, when I check other code about this area, I found these days they are using GGA+U as well. Such like in VASP, I saw they mentioned in forum that LDA or GGA is just depends on XC in pseudo-potential. And in the case of Abinit, the official example is calculated by PBE-PAW pseudo-potential. Therefore, I am wondering that, if I setted lda_plus_u = .true. and used GGA pseudo-potential, may I say I am using GGA+U method? Since when I tried in that way, I saw the output is as: LDA+U calculation, Hubbard_lmax = 2 atomic species L Hubbard U Hubbard alpha Any suggestion is welcome. Thanks. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120312/b685b995/attachment.htm From Lorenzo.Paulatto at impmc.upmc.fr Mon Mar 12 12:29:34 2012 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Mon, 12 Mar 2012 12:29:34 +0100 Subject: [Pw_forum] LDA+U or GGA+U? In-Reply-To: <127a2912.1de02.13606a445e7.Coremail.flux_ray12@163.com> References: <127a2912.1de02.13606a445e7.Coremail.flux_ray12@163.com> Message-ID: On Mon, 12 Mar 2012 12:21:30 +0100, GAO Zhe wrote: > Therefore, I am wondering that, if I setted lda_plus_u = .true. and used > GGA pseudo-potential, may I say I am using GGA+U method? Yes, you may. The +U correction can be applied to any kind of functional. The "lda" in "lda+U" is just a name, it does not imply that the functional has to be strictly local. best regards -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From abdeslam.houari at gmail.com Mon Mar 12 17:16:42 2012 From: abdeslam.houari at gmail.com (Abdeslam HOUARI) Date: Mon, 12 Mar 2012 17:16:42 +0100 Subject: [Pw_forum] LDA+U or GGA+U? In-Reply-To: <127a2912.1de02.13606a445e7.Coremail.flux_ray12@163.com> References: <127a2912.1de02.13606a445e7.Coremail.flux_ray12@163.com> Message-ID: Dear GAO Zhe; As told by Lorenzo Paulatto, I think that LDA+U is just a name and all the important thing is how to include the Hubbard "U" term. However, in may opinion, this still being true only for DFT (LDA or GGA) XC functional, and one should take care if the XC functional is a Hybrid-type one (HF like exchange, EXX ...etc).. I hope I'm right about this !!! ============================================== Abdesalem HOUARI ------------------------------------------------------------------------------------------- Department of physics, Theoretical Physics Laboratory University of Bejaia-06000. Algeria. E-mail: abdeslam.houari at univ-bejaia.dz& habdeslam at gmail.com https://sites.google.com/site/houariabdeslam/homepage =============================================== 2012/3/12 GAO Zhe > Dear QE developer and users: > I just began to try LDA+U method in QE, by adding lda_plus_u = .true. and > Hubbard_U(i) parameters to scf input file, where the U value was determined > by following M.Cococcioni's thesis and Prof. Marzari's paper (PRL, 97, > 103001). > However, when I check other code about this area, I found these days they > are using GGA+U as well. Such like in VASP, I saw they mentioned in forum > that LDA or GGA is just depends on XC in pseudo-potential. And in the case > of Abinit, the official example is calculated by PBE-PAW pseudo-potential. > Therefore, I am wondering that, if I setted lda_plus_u = .true. and used > GGA pseudo-potential, may I say I am using GGA+U method? Since when I tried > in that way, I saw the output is as: > LDA+U calculation, Hubbard_lmax = 2 > atomic species L Hubbard U Hubbard alpha > Any suggestion is welcome. Thanks. > -- > GAO Zhe > CMC Lab, Materials Science & Engineering Department, > Seoul National University, South Korea > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120312/543a8c89/attachment.htm From trambui at u.boisestate.edu Mon Mar 12 22:49:01 2012 From: trambui at u.boisestate.edu (Tram Bui) Date: Mon, 12 Mar 2012 15:49:01 -0600 Subject: [Pw_forum] Average potential calculation and Cs ultra soft pseudo-potential Message-ID: Dear All QE users, I have a quick question regarding the average potential and hope someone would have time to help me out. And that is would it possible to calculate the average potential over a region in QE? If so, would you please give me some direction on what is needed for the input file? Also, besides the one and only in QE pseudo library, does anyone have an ultra soft PP for Cs that gerenated using PBE exchange correlation? would you please share it with me? I am trying to compare results of defect formation energy by using different PP of Cs. Best regards, Tram Bui M.S. Materials Science & Engineering trambui at u.boisestate.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120312/174bf736/attachment.htm From giannozz at democritos.it Tue Mar 13 12:19:51 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 13 Mar 2012 12:19:51 +0100 Subject: [Pw_forum] Average potential calculation and Cs ultra soft pseudo-potential In-Reply-To: References: Message-ID: <1331637591.32748.6.camel@fe12lx.fisica.uniud.it> On Mon, 2012-03-12 at 15:49 -0600, Tram Bui wrote: > would it possible to calculate the average potential over a region in QE? have a look at the utility code PP/average.f90 P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Tue Mar 13 12:41:33 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 13 Mar 2012 12:41:33 +0100 Subject: [Pw_forum] tmp/_ph0/{PREFIX}_qxx directories, safe to remove? In-Reply-To: <4F5D2AAC.5020506@buffalo.edu> References: <4F5D2AAC.5020506@buffalo.edu> Message-ID: <1331638893.734.8.camel@fe12lx.fisica.uniud.it> On Sun, 2012-03-11 at 18:43 -0400, bahadir wrote: > i wonder if it is safe to remove tmp/_ph0/{PREFIX}_qxx directories after > the calculation on xx q-point and obtaining elph files for correcponding > q-point? you mean: while the code is still running? Hard to say. You may want to try this for a simple case first, initially removing only large files (some of them can for sure be removed once the calculation for a given wave-vector is done). P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From bahadira at buffalo.edu Tue Mar 13 18:13:26 2012 From: bahadira at buffalo.edu (bahadir) Date: Tue, 13 Mar 2012 13:13:26 -0400 Subject: [Pw_forum] tmp/_ph0/{PREFIX}_qxx directories, safe to remove? In-Reply-To: <1331638893.734.8.camel@fe12lx.fisica.uniud.it> References: <4F5D2AAC.5020506@buffalo.edu> <1331638893.734.8.camel@fe12lx.fisica.uniud.it> Message-ID: <4F5F8036.5010200@buffalo.edu> i just removed the directories of completed q_points and code seems working well. dyn and elph files are producing without any problem. thank you On 03/13/2012 07:41 AM, Paolo Giannozzi wrote: > On Sun, 2012-03-11 at 18:43 -0400, bahadir wrote: > >> i wonder if it is safe to remove tmp/_ph0/{PREFIX}_qxx directories after >> the calculation on xx q-point and obtaining elph files for correcponding >> q-point? > you mean: while the code is still running? Hard to say. You may want to > try this for a simple case first, initially removing only large files > (some of them can for sure be removed once the calculation for a given > wave-vector is done). > > P. -- Dr.Bahadir Altintas * Dept. of Chemistry SUNY Buffalo NY,USA * Abant Izzet Baysal University Dept. of Computer Education Bolu,Turkey From makhyoun2 at yahoo.com Tue Mar 13 23:15:49 2012 From: makhyoun2 at yahoo.com (mohamed makhyoun) Date: Tue, 13 Mar 2012 15:15:49 -0700 (PDT) Subject: [Pw_forum] error during testing gipaw.x Message-ID: <1331676949.84735.YahooMailClassic@web126003.mail.ne1.yahoo.com> Dear all: By running the examples of quartz and benzene found in ( ./qe-gipaw-4.3.2 /examples) using gipaw.x I got the following error in both cases: ??? mpi-abort But I couldn't open the help file: ??? /home/mohamed/ompi-lib-1.4.4/share/openmpi/help-mpi-api.txt: No such file or directory.? Sorry! -------------------------------------------------------------------------- ???????????? 0.0336???????? -1.6847???????? -0.0244 ??????????? -0.0025???????? -0.0245???????? -1.7006 ???? Paramagnetic US L_R Q_R contribution in ppm: ???? Atom? 1? Si? pos: (? 0.470100 -0.814241? 0.733333)? sigma:??????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ???? Atom? 2? Si? pos: (? 0.470100? 0.814241? 1.466667)? sigma:??????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ???? Atom? 3? Si? pos: ( -0.940200? 0.000000? 0.000000)? sigma:??????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ???? Atom? 4? O?? pos: (? 0.681300 -0.253747? 0.471680)? sigma:??????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ???? Atom? 5? O?? pos: ( -0.120900? 0.716899? 1.205013)? sigma:??????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ???? Atom? 6? O?? pos: ( -0.560400 -0.463152? 1.938347)? sigma:??????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ???? Atom? 7? O?? pos: (? 0.681300? 0.253747 -0.471680)? sigma:??????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ???? Atom? 8? O?? pos: ( -0.120900 -0.716899? 0.994987)? sigma:??????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ???? Atom? 9? O?? pos: ( -0.560400? 0.463152? 0.261653)? sigma:??????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ??????????????? NaN???????????? NaN???????????? NaN ???? Total NMR chemical shifts in ppm: --------------------------------------- ???? Atom? 1? Si? pos: (? 0.470100 -0.814241? 0.733333)? sigma:??????????? NaN ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ???? from cdiagh : error #???????? 2 ???? diagonalization (ZHEEV) failed ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I appreciate any help. Best Regard Mohamed -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120313/3233f160/attachment.htm From jptrinastic at phys.ufl.edu Wed Mar 14 13:00:48 2012 From: jptrinastic at phys.ufl.edu (Jonathan Trinastic) Date: Wed, 14 Mar 2012 08:00:48 -0400 Subject: [Pw_forum] Error while using Mg PAW potential given on website Message-ID: <4F608870.3050103@phys.ufl.edu> Dear All, I'm wondering if anyone has had problems using the Mg PAW potential (Mg.pbe-nsp-bpaw.UPF) listed on the QE website? When I use it, I receive the error from read_ncpp: error # 1 Wrong nlc or nnl I understand this has to do with the number of channels being read, however I'm in the process of learning how to generate potentials and don't yet know how to fix it. In the meantime, does anyone know a quick fix for this potential. Its formatting is a little different compared to other potentials in UPF format on the website. Thanks much for your help, Jonathan -- Jonathan Trinastic, M.S. Graduate Student Department of Physics University of Florida -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120314/729adb0a/attachment.htm From giannozz at democritos.it Wed Mar 14 19:25:25 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 14 Mar 2012 19:25:25 +0100 Subject: [Pw_forum] Error while using Mg PAW potential given on website In-Reply-To: <4F608870.3050103@phys.ufl.edu> References: <4F608870.3050103@phys.ufl.edu> Message-ID: <5A3261D5-B2FE-4E35-9103-7584D04871CC@democritos.it> On Mar 14, 2012, at 13:00 , Jonathan Trinastic wrote: > I'm wondering if anyone has had problems using the Mg PAW potential > (Mg.pbe-nsp-bpaw.UPF) listed on the QE website? When I use it, I > receive the error > > from read_ncpp: error # 1 > Wrong nlc or nnl It works for me. "read_ncpp" is the routine that reads the (obsolete) norm-conserving pseudopotential format and should not be called in this case. You should first of all understand why it is called (routine "read_pp" in "Modules/ read_pseudo.f90") P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From torstein.fjermestad at kjemi.uio.no Wed Mar 14 21:18:52 2012 From: torstein.fjermestad at kjemi.uio.no (Torstein Fjermestad) Date: Wed, 14 Mar 2012 21:18:52 +0100 Subject: [Pw_forum] problem with neb calculations / openmpi Message-ID: <7cc5a1dba0f79b23e01b110892cd1aea@ulrik.uio.no> Dear all, I recently installed quantum espresso v4.3.2 in my home directory at an external supercomputer cluster. The way I did this was to execute the following commands: ./configure make all after first having loaded the the mpi environment, the fortran and C compiler with the following commands: module load openmpi module load g95/093 module load gcc ./configure was successful and make seemed to finish normally (at least I did not get any error message). So far I have only been using the pw.x and neb.x executables. In a file named "slurm-jobID.out" that is generated by the queuing system, I get the following message when running both pw.x and neb.x: mca: base: component_find: unable to open /site/VERSIONS/openmpi-1.3.3.gnu/lib/openmpi/mca_mtl_psm: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored) This message seems rather clear, but I am not sure how relevant it is because pw.x runs without problem on 64 processors (I have compared the output with that generated on another machine). neb.x on the other hand works when running on a single processor, but fails when running in parallel (yes, I have used the -inp option). The output of the neb calculation is only 13 lines and the last three lines are Parallel version (MPI), running on 16 processors path-images division: nimage = 10 R & G space division: proc/pool = 16 In the output files out.n_0 where n={1,9} the error message Message from routine read_line : read error is repeated several thousand times. I have a feeling that there is something I have got wrong with the parallel environment. If I (accidentally) compiled QE for a different openmpi version than 1.3.3.gnu, It would be interesting to know which one. Does anyone have an idea on how I can check this? In case the cause of the problem is a different one, it would be nice if someone had any suggestions on how to solve it. Thank you very much in advance. Yours sincerely, Torstein Fjermestad University of Oslo, Norway From akohlmey at gmail.com Wed Mar 14 21:36:15 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Wed, 14 Mar 2012 16:36:15 -0400 Subject: [Pw_forum] problem with neb calculations / openmpi In-Reply-To: <7cc5a1dba0f79b23e01b110892cd1aea@ulrik.uio.no> References: <7cc5a1dba0f79b23e01b110892cd1aea@ulrik.uio.no> Message-ID: On Wed, Mar 14, 2012 at 4:18 PM, Torstein Fjermestad wrote: > ?Dear all, > > ?I recently installed quantum espresso v4.3.2 in my home directory at an > ?external supercomputer cluster. > ?The way I did this was to execute the following commands: > > ?./configure > ?make all > > ?after first having loaded the the mpi environment, the fortran and C > ?compiler with the following commands: > ?module load openmpi > ?module load g95/093 > ?module load gcc > > ?./configure was successful and make seemed to finish normally (at least > ?I did not get any error message). > > ?So far I have only been using the pw.x and neb.x executables. > ?In a file named "slurm-jobID.out" that is generated by the queuing > ?system, I get the following message when running both pw.x and neb.x: > > ?mca: base: component_find: unable to open > ?/site/VERSIONS/openmpi-1.3.3.gnu/lib/openmpi/mca_mtl_psm: perhaps a > ?missing symbol, or compiled for a different version of Open MPI? > ?(ignored) > > ?This message seems rather clear, but I am not sure how relevant it is > ?because pw.x runs without problem on 64 processors (I have compared the > ?output with that generated on another machine). neb.x on the other hand > ?works when running on a single processor, but fails when running in > ?parallel (yes, I have used the -inp option). > > ?The output of the neb calculation is only 13 lines and the last three > ?lines are > > ? ? ?Parallel version (MPI), running on ? ?16 processors > ? ? ?path-images division: ?nimage ? ?= ? 10 > ? ? ?R & G space division: ?proc/pool = ? 16 > > > ?In the output files out.n_0 where n={1,9} the error message > > ? ? ?Message from routine ?read_line : > ? ? ?read error > > ?is repeated several thousand times. > > > ?I have a feeling that there is something I have got wrong with the > ?parallel environment. If I (accidentally) compiled QE for a different > ?openmpi version than 1.3.3.gnu, It would be interesting to know which > ?one. Does anyone have an idea on how I can check this? > > ?In case the cause of the problem is a different one, it would be nice > ?if someone had any suggestions on how to solve it. this sounds a lot like one of the nodes that you are using has a network problem and you are trying to read from an NFS exported directory, but only i/o errors. the OpenMPI based error supports this. at least, i have only seen this kind of error when one of the nodes in a parallel job had to be rebooted hard because of a an obscure and rarely triggered bug in the ethernet driver. you should see, if this happens always or only if there is one specific node that is assigned to your job. i would also talk to the sysadmin of the machine. HTH, axel. > > ?Thank you very much in advance. > > ?Yours sincerely, > > ?Torstein Fjermestad > ?University of Oslo, > ?Norway > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com ?http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA. From giannozz at democritos.it Wed Mar 14 21:50:12 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 14 Mar 2012 21:50:12 +0100 Subject: [Pw_forum] Error while using Mg PAW potential given on website In-Reply-To: <4F608870.3050103@phys.ufl.edu> References: <4F608870.3050103@phys.ufl.edu> Message-ID: <924540EE-0133-4E2B-89AE-E4DDC3DABBBB@democritos.it> On Mar 14, 2012, at 13:00 , Jonathan Trinastic wrote: > In the meantime, does anyone know a quick fix for this potential. > Its formatting is a little different compared to other potentials in > UPF format on the website. there is nothing to fix: its format is a most recent version. However you may want to check whether "UTF-8 Unicode" (whatever it means) characters in file are a source of problem (I don't see why, but I also don't see why CR-LF characters should be a source of problem: they are on AIX machines). Just edit the file, replace the line Author="..." with something not containing non-ASCII character, save P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From jptrinastic at phys.ufl.edu Thu Mar 15 00:07:57 2012 From: jptrinastic at phys.ufl.edu (Jonathan Trinastic) Date: Wed, 14 Mar 2012 19:07:57 -0400 Subject: [Pw_forum] Error while using Mg PAW potential given on website In-Reply-To: <924540EE-0133-4E2B-89AE-E4DDC3DABBBB@democritos.it> References: <4F608870.3050103@phys.ufl.edu> <924540EE-0133-4E2B-89AE-E4DDC3DABBBB@democritos.it> Message-ID: <4F6124CD.9050406@phys.ufl.edu> Thanks for the help! I've got it working now. On 3/14/2012 4:50 PM, Paolo Giannozzi wrote: > > On Mar 14, 2012, at 13:00 , Jonathan Trinastic wrote: > >> In the meantime, does anyone know a quick fix for this potential. >> Its formatting is a little different compared to other potentials in >> UPF format on the website. > > there is nothing to fix: its format is a most recent version. > However you may want to check whether "UTF-8 Unicode" > (whatever it means) characters in file are a source of problem > (I don't see why, but I also don't see why CR-LF characters > should be a source of problem: they are on AIX machines). > Just edit the file, replace the line Author="..." with something > not containing non-ASCII character, save > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > -- Jonathan Trinastic, M.S. Graduate Student Department of Physics University of Florida From giannozz at democritos.it Thu Mar 15 07:40:59 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 15 Mar 2012 07:40:59 +0100 Subject: [Pw_forum] Error while using Mg PAW potential given on website In-Reply-To: <4F6124CD.9050406@phys.ufl.edu> References: <4F608870.3050103@phys.ufl.edu> <924540EE-0133-4E2B-89AE-E4DDC3DABBBB@democritos.it> <4F6124CD.9050406@phys.ufl.edu> Message-ID: <591662D8-B8BB-4DFF-ADAC-BA3D1F47DFDA@democritos.it> On Mar 15, 2012, at 24:07 , Jonathan Trinastic wrote: > Thanks for the help! I've got it working now. you've got it workin now...how? what was the problem? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From t_nissie at yahoo.co.jp Thu Mar 15 14:44:19 2012 From: t_nissie at yahoo.co.jp (Takeshi NISHIMATSU) Date: Thu, 15 Mar 2012 22:44:19 +0900 (JST) Subject: [Pw_forum] Correct phonon branch connection patch to espresso-4.3.1/PH/matdyn.f90 Message-ID: <870086.71868.qm@web100718.mail.kks.yahoo.co.jp> Dear QUANTUM ESPRESSO developers and users, I fixed espresso-4.3.1/PH/matdyn.f90 for correct phonon branch connection in the same manner described in http://forum.abinit.org/viewtopic.php?f=12&t=483#p1503 . It uses absolute values of "similarity of eigenvectors". New matdyn.f90, matdym.patch (also applicable to the svn HEAD file), si.before.pdf, si.after.pdf, and zzz.gp (quick plot script in gnuplot) are attached to this email. I checked it with the example of silicon in http://people.sissa.it/~degironc/QE-Tutorial/tutorial_disp.htm . But I have not checked it with ionic crystals with LO-TO splitting. Please check it with your systems, -- love && peace && free_software Takeshi Nishimatsu @ IMR, Tohoku University http://loto.sourceforge.net/feram/ Fast MD program for perovskite-type ferroelectrics -------------- next part -------------- A non-text attachment was scrubbed... Name: matdyn.patch Type: application/octet-stream Size: 2189 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120315/dbf10c6c/attachment-0003.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: matdyn.f90 Type: application/octet-stream Size: 75472 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120315/dbf10c6c/attachment-0004.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: si.after.pdf Type: application/pdf Size: 5000 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120315/dbf10c6c/attachment-0002.pdf -------------- next part -------------- A non-text attachment was scrubbed... Name: si.before.pdf Type: application/pdf Size: 5000 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120315/dbf10c6c/attachment-0003.pdf -------------- next part -------------- A non-text attachment was scrubbed... Name: zzz.gp Type: application/octet-stream Size: 532 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120315/dbf10c6c/attachment-0005.obj From payam.norouzzadeh at gmail.com Thu Mar 15 16:25:06 2012 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Thu, 15 Mar 2012 10:25:06 -0500 Subject: [Pw_forum] A question about Total force Message-ID: Dear QE users I usually look at total force to check if my structure is being relaxed or not.Most of times it reduces to a certain level (~0.003) continuously and then starts to fluctuate. I mean it reverses the trend of reducing total force.Simply total force begins to grow and sometimes never gets smaller. The question is that how can I push QE to reduce total force continuously when I am trying to relax a structure?Why total force fluctuates? Best regards,Payam Norouzzadeh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120315/b1a3ed9a/attachment.htm From jptrinastic at phys.ufl.edu Thu Mar 15 16:25:41 2012 From: jptrinastic at phys.ufl.edu (Jonathan Trinastic) Date: Thu, 15 Mar 2012 11:25:41 -0400 Subject: [Pw_forum] Error while using Mg PAW potential given on website In-Reply-To: <591662D8-B8BB-4DFF-ADAC-BA3D1F47DFDA@democritos.it> References: <4F608870.3050103@phys.ufl.edu> <924540EE-0133-4E2B-89AE-E4DDC3DABBBB@democritos.it> <4F6124CD.9050406@phys.ufl.edu> <591662D8-B8BB-4DFF-ADAC-BA3D1F47DFDA@democritos.it> Message-ID: <4F6209F5.1080201@phys.ufl.edu> The version that Savas had attached worked correctly for me. His version included the exact same content in its body but also had some header info not present in the version online (PP_HEADER and PP_MESH). As an experiment, I tried adding this header information to the version I had that didn't work, and after this it worked properly. I'm still working on learning how to build pseudopotentials myself. On 3/15/2012 2:40 AM, Paolo Giannozzi wrote: > > On Mar 15, 2012, at 24:07 , Jonathan Trinastic wrote: > >> Thanks for the help! I've got it working now. > > you've got it workin now...how? what was the problem? > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > -- Jonathan Trinastic, M.S. Graduate Student Department of Physics University of Florida From sagduk82 at hotmail.com Thu Mar 15 16:49:28 2012 From: sagduk82 at hotmail.com (=?windows-1254?B?c2F2Yf4gYfBkdWs=?=) Date: Thu, 15 Mar 2012 17:49:28 +0200 Subject: [Pw_forum] Error while using Mg PAW potential given on website In-Reply-To: <4F6209F5.1080201@phys.ufl.edu> References: <4F608870.3050103@phys.ufl.edu>, <924540EE-0133-4E2B-89AE-E4DDC3DABBBB@democritos.it>, <4F6124CD.9050406@phys.ufl.edu>, <591662D8-B8BB-4DFF-ADAC-BA3D1F47DFDA@democritos.it>, <4F6209F5.1080201@phys.ufl.edu> Message-ID: Dear Jonathan, My message bounced by pw_forum because of file size limitation. Sorry for this. I'm not sure about the source of your problem. The attached files in the mail I sent yesterday show that online version of Mg paw data properly works on gcc-4.4.5 compiled QE-4.3.2 . Sava? A?DUKKarabuk UniversityPhysics Department > Date: Thu, 15 Mar 2012 11:25:41 -0400 > From: jptrinastic at phys.ufl.edu > To: giannozz at democritos.it > CC: pw_forum at pwscf.org > Subject: Re: [Pw_forum] Error while using Mg PAW potential given on website > > The version that Savas had attached worked correctly for me. His > version included the exact same content in its body but also had some > header info not present in the version online (PP_HEADER and PP_MESH). > As an experiment, I tried adding this header information to the version > I had that didn't work, and after this it worked properly. > > I'm still working on learning how to build pseudopotentials myself. > > On 3/15/2012 2:40 AM, Paolo Giannozzi wrote: > > > > On Mar 15, 2012, at 24:07 , Jonathan Trinastic wrote: > > > >> Thanks for the help! I've got it working now. > > > > you've got it workin now...how? what was the problem? > > > > P. > > --- > > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > > > > > -- > Jonathan Trinastic, M.S. > Graduate Student > Department of Physics > University of Florida > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120315/5e6fac88/attachment.htm From torstein.fjermestad at kjemi.uio.no Thu Mar 15 20:48:18 2012 From: torstein.fjermestad at kjemi.uio.no (Torstein Fjermestad) Date: Thu, 15 Mar 2012 20:48:18 +0100 Subject: [Pw_forum] =?utf-8?q?problem_with_neb_calculations_/_openmpi?= In-Reply-To: References: <7cc5a1dba0f79b23e01b110892cd1aea@ulrik.uio.no> Message-ID: <6544c6636af26d34452cb5e76a47f325@ulrik.uio.no> Dear Dr. Kohlmeyer, Thank you for your suggestion. Since yesterday I have made some progress, and I know think I see a more systematic behavior. What I did was first to recompile pw.x and neb.x with a newer version of openmpi (openmpi/1.4.3.gnu). Apparently this made the openmpi error message disappear. pw.x now works without problem, but neb.x only works when one node (with 8 processors) is requested. I have run two tests requesting two nodes (16 processors) and in both cases I see the same erroneous behavior: The output file is only 13 lines long and the last three lines are as follows: Parallel version (MPI), running on 2 processors path-images division: nimage = 8 R & G space division: proc/pool = 2 In the working directory of the calculations the files of type out.5_0 contain several million repetitions of the error message Message from routine read_line : read error I think this behavior is general because it is rather unlikely that both calculations accidentally are submitted to a defect node. To me it seems like there is some kind of failure in the communication between the nodes. I should certainly contact the sysadmin of the machine, but in order to make their work easier, I would like to make sure whether the erroneous behavior is caused by the machine or by the compilation/installation of quantum espresso. If anyone has had similar experiences before, it would be nice if you could share ideas on possible causes. Thanks in advance. Yours sincerely, Torstein Fjermestad University of Oslo, Norway On Wed, 14 Mar 2012 16:36:15 -0400, Axel Kohlmeyer wrote: > On Wed, Mar 14, 2012 at 4:18 PM, Torstein Fjermestad > wrote: >> ?Dear all, >> >> ?I recently installed quantum espresso v4.3.2 in my home directory >> at an >> ?external supercomputer cluster. >> ?The way I did this was to execute the following commands: >> >> ?./configure >> ?make all >> >> ?after first having loaded the the mpi environment, the fortran and >> C >> ?compiler with the following commands: >> ?module load openmpi >> ?module load g95/093 >> ?module load gcc >> >> ?./configure was successful and make seemed to finish normally (at >> least >> ?I did not get any error message). >> >> ?So far I have only been using the pw.x and neb.x executables. >> ?In a file named "slurm-jobID.out" that is generated by the queuing >> ?system, I get the following message when running both pw.x and >> neb.x: >> >> ?mca: base: component_find: unable to open >> ?/site/VERSIONS/openmpi-1.3.3.gnu/lib/openmpi/mca_mtl_psm: perhaps a >> ?missing symbol, or compiled for a different version of Open MPI? >> ?(ignored) >> >> ?This message seems rather clear, but I am not sure how relevant it >> is >> ?because pw.x runs without problem on 64 processors (I have compared >> the >> ?output with that generated on another machine). neb.x on the other >> hand >> ?works when running on a single processor, but fails when running in >> ?parallel (yes, I have used the -inp option). >> >> ?The output of the neb calculation is only 13 lines and the last >> three >> ?lines are >> >> ? ? ?Parallel version (MPI), running on ? ?16 processors >> ? ? ?path-images division: ?nimage ? ?= ? 10 >> ? ? ?R & G space division: ?proc/pool = ? 16 >> >> >> ?In the output files out.n_0 where n={1,9} the error message >> >> ? ? ?Message from routine ?read_line : >> ? ? ?read error >> >> ?is repeated several thousand times. >> >> >> ?I have a feeling that there is something I have got wrong with the >> ?parallel environment. If I (accidentally) compiled QE for a >> different >> ?openmpi version than 1.3.3.gnu, It would be interesting to know >> which >> ?one. Does anyone have an idea on how I can check this? >> >> ?In case the cause of the problem is a different one, it would be >> nice >> ?if someone had any suggestions on how to solve it. > > this sounds a lot like one of the nodes that you are using > has a network problem and you are trying to read from > an NFS exported directory, but only i/o errors. the OpenMPI > based error supports this. at least, i have only seen this > kind of error when one of the nodes in a parallel job had > to be rebooted hard because of a an obscure and rarely > triggered bug in the ethernet driver. > > you should see, if this happens always or only if there > is one specific node that is assigned to your job. > i would also talk to the sysadmin of the machine. > > HTH, > axel. > > >> >> ?Thank you very much in advance. >> >> ?Yours sincerely, >> >> ?Torstein Fjermestad >> ?University of Oslo, >> ?Norway >> >> >> >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum From akohlmey at gmail.com Thu Mar 15 21:00:36 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Thu, 15 Mar 2012 16:00:36 -0400 Subject: [Pw_forum] problem with neb calculations / openmpi In-Reply-To: <6544c6636af26d34452cb5e76a47f325@ulrik.uio.no> References: <7cc5a1dba0f79b23e01b110892cd1aea@ulrik.uio.no> <6544c6636af26d34452cb5e76a47f325@ulrik.uio.no> Message-ID: On Thu, Mar 15, 2012 at 3:48 PM, Torstein Fjermestad wrote: > Dear Dr. Kohlmeyer, > > Thank you for your suggestion. Since yesterday I have made some progress, > and I know think I see a more systematic behavior. What I did was first to > recompile pw.x and neb.x with a newer version of openmpi > (openmpi/1.4.3.gnu). Apparently this made the openmpi error message > disappear. > pw.x now works without problem, but neb.x only works when one node (with 8 > processors) is requested. I have run two tests requesting two nodes (16 > processors) and in both cases I see the same erroneous behavior: > > The output file is only 13 lines long and the last three lines are as > follows: > > ? ? Parallel version (MPI), running on ? ? 2 processors > ? ? path-images division: ?nimage ? ?= ? ?8 > ? ? R & G space division: ?proc/pool = ? ?2 > > In the working directory of the calculations the files of type out.5_0 > contain several million repetitions of the error message > > > ? ? ?Message from routine ?read_line : > ? ? ?read error > > I think this behavior is general because it is rather unlikely that both > calculations accidentally are submitted to a defect node. To me it seems > like there is some kind of failure in the communication between the nodes. > > I should certainly contact the sysadmin of the machine, but in order to make > their work easier, I would like to make sure whether the erroneous behavior > is caused by the machine or by the compilation/installation of quantum > espresso. more likely in this respect would be that you specify, create, and/or try to access a temporary directory that is only available on the first node of a group of nodes. this also can happen, if the various nodes in the cluster don't share your home directory, but that has become very unlikely with the way that most clusters are set up these days. whether any of this applies can be seen from your input, job submission script, and information about how the cluster itself is being set up. cheers, axel. > > If anyone has had similar experiences before, it would be nice if you could > share ideas on possible causes. > > Thanks in advance. > > > Yours sincerely, > > Torstein Fjermestad > University of Oslo, > Norway > > > On Wed, 14 Mar 2012 16:36:15 -0400, Axel Kohlmeyer > wrote: >> >> On Wed, Mar 14, 2012 at 4:18 PM, Torstein Fjermestad >> wrote: >>> >>> ?Dear all, >>> >>> ?I recently installed quantum espresso v4.3.2 in my home directory at an >>> ?external supercomputer cluster. >>> ?The way I did this was to execute the following commands: >>> >>> ?./configure >>> ?make all >>> >>> ?after first having loaded the the mpi environment, the fortran and C >>> ?compiler with the following commands: >>> ?module load openmpi >>> ?module load g95/093 >>> ?module load gcc >>> >>> ?./configure was successful and make seemed to finish normally (at least >>> ?I did not get any error message). >>> >>> ?So far I have only been using the pw.x and neb.x executables. >>> ?In a file named "slurm-jobID.out" that is generated by the queuing >>> ?system, I get the following message when running both pw.x and neb.x: >>> >>> ?mca: base: component_find: unable to open >>> ?/site/VERSIONS/openmpi-1.3.3.gnu/lib/openmpi/mca_mtl_psm: perhaps a >>> ?missing symbol, or compiled for a different version of Open MPI? >>> ?(ignored) >>> >>> ?This message seems rather clear, but I am not sure how relevant it is >>> ?because pw.x runs without problem on 64 processors (I have compared the >>> ?output with that generated on another machine). neb.x on the other hand >>> ?works when running on a single processor, but fails when running in >>> ?parallel (yes, I have used the -inp option). >>> >>> ?The output of the neb calculation is only 13 lines and the last three >>> ?lines are >>> >>> ? ? ?Parallel version (MPI), running on ? ?16 processors >>> ? ? ?path-images division: ?nimage ? ?= ? 10 >>> ? ? ?R & G space division: ?proc/pool = ? 16 >>> >>> >>> ?In the output files out.n_0 where n={1,9} the error message >>> >>> ? ? ?Message from routine ?read_line : >>> ? ? ?read error >>> >>> ?is repeated several thousand times. >>> >>> >>> ?I have a feeling that there is something I have got wrong with the >>> ?parallel environment. If I (accidentally) compiled QE for a different >>> ?openmpi version than 1.3.3.gnu, It would be interesting to know which >>> ?one. Does anyone have an idea on how I can check this? >>> >>> ?In case the cause of the problem is a different one, it would be nice >>> ?if someone had any suggestions on how to solve it. >> >> >> this sounds a lot like one of the nodes that you are using >> has a network problem and you are trying to read from >> an NFS exported directory, but only i/o errors. the OpenMPI >> based error supports this. at least, i have only seen this >> kind of error when one of the nodes in a parallel job had >> to be rebooted hard because of a an obscure and rarely >> triggered bug in the ethernet driver. >> >> you should see, if this happens always or only if there >> is one specific node that is assigned to your job. >> i would also talk to the sysadmin of the machine. >> >> HTH, >> ? ?axel. >> >> >>> >>> ?Thank you very much in advance. >>> >>> ?Yours sincerely, >>> >>> ?Torstein Fjermestad >>> ?University of Oslo, >>> ?Norway >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum > > -- Dr. Axel Kohlmeyer akohlmey at gmail.com ?http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA. From giannozz at democritos.it Thu Mar 15 22:26:22 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 15 Mar 2012 22:26:22 +0100 Subject: [Pw_forum] problem with neb calculations / openmpi In-Reply-To: <6544c6636af26d34452cb5e76a47f325@ulrik.uio.no> References: <7cc5a1dba0f79b23e01b110892cd1aea@ulrik.uio.no> <6544c6636af26d34452cb5e76a47f325@ulrik.uio.no> Message-ID: <9BB14D18-F7CE-4C6B-A8E6-330B2F20FBC7@democritos.it> On Mar 15, 2012, at 20:48 , Torstein Fjermestad wrote: > pw.x now works without problem, but neb.x only works when one node > (with 8 processors) is requested. I have run two tests requesting two > nodes (16 processors) and in both cases I see the same erroneous > behavior: with "image" parallelization in both cases? can you run neb.x with 1 image and 16 processors? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From alex.kutana at gmail.com Fri Mar 16 00:09:31 2012 From: alex.kutana at gmail.com (Alex Kutana) Date: Thu, 15 Mar 2012 19:09:31 -0400 Subject: [Pw_forum] Definition of the electron-phonon coupling matrix element Message-ID: Dear PW forum users: Does anyone here know the exact definition of the electron-phonon coupling matrix element in Quantum Espresso (array el_ph_mat in the file elphon.f90)? It almost seems like every author is using their own definition of g, but which one is actually calculated? In particular, is g divided by the square root of frequency? Thank you. Alex -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120315/109bbaf1/attachment-0001.htm From fratesi at mater.unimib.it Fri Mar 16 09:51:23 2012 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Fri, 16 Mar 2012 09:51:23 +0100 Subject: [Pw_forum] A question about Total force In-Reply-To: References: Message-ID: <4F62FF0B.4090201@mater.unimib.it> Dear Payam, what you report is consistent with a too high threshold for the self-consistency loop (ie forces are not computed accurately enough): try reducing conv_thr (say to 1d-8) or use upscale. Also have a look to the total energy: is that decreasing, while forces are fluctuating? Then, the system is still relaxing towards its minimum even though forces are small. HTH, Guido PS Notice that it occurs sometimes that the system relaxes in one direction, reducing the force quite rapidly. Then the algorithm finds new possibilities to further reduce the total energy, yet the forces are small. An example of that might be when you put a strongly deformed molecule close to a surface, above an adsorption site which is not the optimal one. First, the molecule relaxes more or less where you placed it, then it finds its way towards another adsorption site (if symmetry allows it to do so). Il 03/15/2012 04:25 PM, Payam Norouzzadeh ha scritto: > Dear QE users > > I usually look at total force to check if my structure is being relaxed > or not.Most of times it reduces to a certain level (~0.003) continuously > and > then starts to fluctuate. I mean it reverses the trend of reducing total > force.Simply total force begins to grow and sometimes never gets smaller. > The question is that how can I push QE to reduce total force > continuously when I am trying to relax a structure?Why total force > fluctuates? > > Best regards,Payam Norouzzadeh > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca via Cozzi 53, 20125 Milano, Italy From d.tiana at bath.ac.uk Fri Mar 16 11:35:21 2012 From: d.tiana at bath.ac.uk (Davide Tiana) Date: Fri, 16 Mar 2012 10:35:21 +0000 Subject: [Pw_forum] bands calculation crash Message-ID: <20120316103521.Horde.4TTebVLxr25PYxdp8U8jT1A@webmail.bath.ac.uk> Dear all, I am running some calculations on coordination polymers. I made calculations on other 8 molecules and everything was ok. Making calculation on this new molecule bands crash pushing out this error: " chpc-aw7:mol_i davidetiana$ [chpc-aw7:00467] *** Process received signal *** [chpc-aw7:00467] Signal: Segmentation fault: 11 (11) [chpc-aw7:00467] Signal code: Address not mapped (1) [chpc-aw7:00467] Failing at address: 0x26ddb6df8 [chpc-aw7:00467] [ 0] 2 libsystem_c.dylib 0x00007fff904b4cfa _sigtramp + 26 [chpc-aw7:00467] [ 1] 3 libsystem_c.dylib 0x00007fff904501f0 gettimeofday + 43 [chpc-aw7:00467] [ 2] 4 bands.x 0x0000000107d453c9 cgracsc_ + 121 [chpc-aw7:00467] *** End of error message *** " I can't see any problem in the pw.x band output file : " Writing output data file mol_g.save init_run : 39.73s CPU 41.63s WALL ( 1 calls) electrons : 684.36s CPU 699.78s WALL ( 1 calls) Called by init_run: wfcinit : 0.00s CPU 0.00s WALL ( 1 calls) potinit : 3.10s CPU 3.30s WALL ( 1 calls) Called by electrons: c_bands : 684.36s CPU 699.78s WALL ( 1 calls) v_of_rho : 2.44s CPU 2.57s WALL ( 1 calls) newd : 13.11s CPU 14.51s WALL ( 1 calls) Called by c_bands: init_us_2 : 0.43s CPU 0.50s WALL ( 11 calls) cegterg : 608.19s CPU 621.12s WALL ( 22 calls) Called by *egterg: h_psi : 546.45s CPU 562.23s WALL ( 385 calls) s_psi : 23.37s CPU 22.46s WALL ( 385 calls) g_psi : 1.05s CPU 1.33s WALL ( 352 calls) cdiaghg : 6.79s CPU 6.93s WALL ( 363 calls) Called by h_psi: add_vuspsi : 23.84s CPU 27.38s WALL ( 385 calls) General routines calbec : 25.01s CPU 25.23s WALL ( 385 calls) fft : 2.26s CPU 2.36s WALL ( 13 calls) ffts : 0.04s CPU 0.04s WALL ( 1 calls) fftw : 381.94s CPU 390.76s WALL ( 17028 calls) interpolate : 0.22s CPU 0.24s WALL ( 1 calls) davcio : 0.00s CPU 0.17s WALL ( 22 calls) Parallel routines fft_scatter : 86.85s CPU 89.38s WALL ( 17042 calls) PWSCF : 12m 9.06s CPU 12m29.92s WALL This run was terminated on: 21:26:28 15Mar2012 =------------------------------------------------------------------------------= JOB DONE. =------------------------------------------------------------------------------= " So I am lost and I am not able to manage such error. Any help, tips or suggestion? Thank a lot From elie.moujaes at hotmail.co.uk Fri Mar 16 19:14:39 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Fri, 16 Mar 2012 18:14:39 +0000 Subject: [Pw_forum] parallel computation too slow Message-ID: Dear all, I am running phonon calculations for a supercell of 60 atoms at the gamma point. I am running the calculation at the gamma point only. First I tried running it on two nodes but then I realised it is going too slow (I have got 180 IRRs representations). I then changed to 3 nodes but still , things are slow. The threshold tr2_ph was set to 10^(-17) as higher values produced negative (frequency)^2 modes. What could the possible causes of this slowness be? Is it something to do with the nodes or with phonon calculations in general? Is there a way to check? Regards Elie MUniversity of NottsNG7 2RDUK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120316/c74910e2/attachment.htm From giannozz at democritos.it Fri Mar 16 21:48:15 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 16 Mar 2012 21:48:15 +0100 Subject: [Pw_forum] parallel computation too slow In-Reply-To: References: Message-ID: <3B7C8BBB-2790-4177-8285-8DF287684F89@democritos.it> On Mar 16, 2012, at 19:14 , Elie M wrote: > I am running phonon calculations for a supercell of 60 atoms at the > gamma point [...] > What could the possible causes of this slowness be? Is it something > to do with the > nodes or with phonon calculations in general? Is there a way to check? > a phonon calculation for N atoms requires a CPU time of the order of 3N the time of the correspoding scf calculation. Does yours? if it does, there is nothing that can be done. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Fri Mar 16 21:54:35 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 16 Mar 2012 21:54:35 +0100 Subject: [Pw_forum] bands calculation crash In-Reply-To: <20120316103521.Horde.4TTebVLxr25PYxdp8U8jT1A@webmail.bath.ac.uk> References: <20120316103521.Horde.4TTebVLxr25PYxdp8U8jT1A@webmail.bath.ac.uk> Message-ID: On Mar 16, 2012, at 11:35 , Davide Tiana wrote: > I am running some calculations on coordination polymers. I made > calculations on other 8 molecules and everything was ok. Making > calculation on this new molecule bands crash pushing out this error: the error is for the bands.x executable. You should first of all understand under which circumstances it crashes (serial, parallel, always, random...) P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Fri Mar 16 22:00:38 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 16 Mar 2012 22:00:38 +0100 Subject: [Pw_forum] Definition of the electron-phonon coupling matrix element In-Reply-To: References: Message-ID: <5AF207A9-1C2B-4662-97F3-BBE12FE35F42@democritos.it> On Mar 16, 2012, at 24:09 , Alex Kutana wrote: > Does anyone here know the exact definition of the electron-phonon > coupling matrix element in Quantum Espresso (array el_ph_mat in > the file elphon.f90)? once again (and for the last time: I am putting this in the documentation): -------------- next part -------------- A non-text attachment was scrubbed... Name: e-ph.pdf Type: application/pdf Size: 45083 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120316/6a1b26c7/attachment-0001.pdf -------------- next part -------------- P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From rahen29 at yahoo.com Sat Mar 17 05:28:57 2012 From: rahen29 at yahoo.com (Rahen Badsha) Date: Fri, 16 Mar 2012 21:28:57 -0700 (PDT) Subject: [Pw_forum] Fw: High symmetry points In-Reply-To: <1331228438.22391.YahooMailNeo@web44713.mail.sp1.yahoo.com> References: <1330692801.28406.YahooMailNeo@web44701.mail.sp1.yahoo.com> <1330743883.89515.YahooMailNeo@web44714.mail.sp1.yahoo.com> <1331228438.22391.YahooMailNeo@web44713.mail.sp1.yahoo.com> Message-ID: <1331958537.27859.YahooMailNeo@web44716.mail.sp1.yahoo.com> Dear QE Users,How I can show the high symmetry points on band structure of Graphene? Have any one who help me about? this? Best Wishes- Rahen Badsha (Raihan) A post graduate thesis student University of Rajshahi, Bangladesh. Mobile:+8801710550252 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120316/70a39a14/attachment.htm From rahen29 at yahoo.com Sat Mar 17 05:28:57 2012 From: rahen29 at yahoo.com (Rahen Badsha) Date: Fri, 16 Mar 2012 21:28:57 -0700 (PDT) Subject: [Pw_forum] Fw: High symmetry points In-Reply-To: <1331228438.22391.YahooMailNeo@web44713.mail.sp1.yahoo.com> References: <1330692801.28406.YahooMailNeo@web44701.mail.sp1.yahoo.com> <1330743883.89515.YahooMailNeo@web44714.mail.sp1.yahoo.com> <1331228438.22391.YahooMailNeo@web44713.mail.sp1.yahoo.com> Message-ID: <1331958537.27859.YahooMailNeo@web44716.mail.sp1.yahoo.com> Dear QE Users,How I can show the high symmetry points on band structure of Graphene? Have any one who help me about? this? Best Wishes- Rahen Badsha (Raihan) A post graduate thesis student University of Rajshahi, Bangladesh. Mobile:+8801710550252 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120316/70a39a14/attachment-0001.htm From ramzialaya at hotmail.fr Sat Mar 17 09:45:11 2012 From: ramzialaya at hotmail.fr (ramzi alaya) Date: Sat, 17 Mar 2012 09:45:11 +0100 Subject: [Pw_forum] (no subject) Message-ID: Dear all, How can the spin?orbit coupling take into account in calculations? do exist any parameter in input file. This is the input file for the "scf" calculation&control calculation = 'scf' restart_mode = 'from_scratch' tstress = .true., tprnfor = .true., prefix='810-28', pseudo_dir='./', outdir='./',/&system ibrav= 2, celldm(1) =11.850000 nat= 2, ntyp= 2, ecutwfc =100.0, ecutrho=400.0, /&electrons diagonalization='david' mixing_beta = 0.7 conv_thr = 1.0d-7/ATOMIC_SPECIES al 26.9815 al_pz.upf bi 208.980 bi_pz.upf ATOMIC_POSITIONS al 0.00000 0.00000 0.00000 bi 0.25000 0.25000 0.25000 K_POINTS automatic8 8 8 0 0 0 This is the input file for the "nscf" calculation&control calculation = 'nscf' restart_mode = 'from_scratch' tstress = .true., tprnfor = .true., prefix='810-28', pseudo_dir='./', outdir='./',/&system ibrav= 2, celldm(1) =11.850000 nat= 2, ntyp= 2, nbnd = 8, ecutwfc =100.0, ecutrho=400.0, /&electrons diagonalization='david' mixing_beta = 0.7 conv_thr = 1.0d-7/ATOMIC_SPECIES al 26.9815 al_pz.upf bi 208.980 bi_pz.upf ATOMIC_POSITIONS al 0.00000 0.00000 0.00000 bi 0.25000 0.25000 0.25000 K_POINTS 210.0000 0.5000 1.00000.1000 0.5000 0.90000.2000 0.5000 0.80000.3000 0.5000 0.70000.4000 0.5000 0.60000.5000 0.5000 0.50000.4000 0.4000 0.40000.3000 0.3000 0.30000.2000 0.2000 0.20000.1000 0.1000 0.10000.0000 0.0000 0.00000.0000 0.0000 0.10000.0000 0.0000 0.20000.0000 0.0000 0.30000.0000 0.0000 0.40000.0000 0.0000 0.50000.0000 0.0000 0.60000.0000 0.0000 0.70000.0000 0.0000 0.80000.0000 0.0000 0.90000.0000 0.0000 1.0000 *********************************************************** Ramzi Alaya E-mail : ramzialaya at hotmail.fr Facult? des Sciences de Gab?s, Cit? Erriadh 6072 Gab?s- Tunisie Unit? de Recherche sur les H?t?ro-Epitaxies et Applications -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120317/e6982a5c/attachment.htm From payam.norouzzadeh at gmail.com Sat Mar 17 15:34:15 2012 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Sat, 17 Mar 2012 18:04:15 +0330 Subject: [Pw_forum] Thank you (a question about total force) Message-ID: Dear Guido Thank you very much for your informative response. Best regards,Payam Norouzzadeh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120317/8176cebe/attachment.htm From d.tiana at bath.ac.uk Sat Mar 17 20:37:44 2012 From: d.tiana at bath.ac.uk (Davide Tiana) Date: Sat, 17 Mar 2012 19:37:44 +0000 Subject: [Pw_forum] bands calculation crash In-Reply-To: References: <20120316103521.Horde.4TTebVLxr25PYxdp8U8jT1A@webmail.bath.ac.uk> Message-ID: <20120317193744.Horde.KU38AFLxr25PZOgIt4_BNoA@webmail.bath.ac.uk> >> I am running some calculations on coordination polymers. I made >> calculations on other 8 molecules and everything was ok. Making >> calculation on this new molecule bands crash pushing out this error: > > the error is for the bands.x executable. You should first of all understand > under which circumstances it crashes (serial, parallel, always, random...) > > P. > --- It crashes always both running serial and parallel Davide From giannozz at democritos.it Sat Mar 17 20:50:06 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 17 Mar 2012 20:50:06 +0100 Subject: [Pw_forum] bands calculation crash In-Reply-To: <20120317193744.Horde.KU38AFLxr25PZOgIt4_BNoA@webmail.bath.ac.uk> References: <20120316103521.Horde.4TTebVLxr25PYxdp8U8jT1A@webmail.bath.ac.uk> <20120317193744.Horde.KU38AFLxr25PZOgIt4_BNoA@webmail.bath.ac.uk> Message-ID: On Mar 17, 2012, at 20:37 , Davide Tiana wrote: > It crashes always both running serial and parallel in all cases? only for a specific set of data? also for the provided examples? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From payam.norouzzadeh at gmail.com Sun Mar 18 00:51:31 2012 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Sun, 18 Mar 2012 04:21:31 +0430 Subject: [Pw_forum] Relaxed atomic positions Message-ID: Dear Q.E users I've relaxed a structure by using variable cell method (vc-relax). Now I want to do scf and nscf calculations so I need to have the lattice constant (which is derivable from unit cell volume) and relaxed atomic positions but the lattice vectors have been changed during relaxation. They are not equal to what I had in the beginning of relaxation process. How can I derive the relaxed atomic positions? Is the last reported atomic position in output file the one I should use or I have to scale them by last reported lattice vectors in output file? What is the standard procedure? Best regards, Payam Norouzzadeh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120318/f53e3730/attachment-0001.htm From deluquetoro at gmail.com Sun Mar 18 03:38:08 2012 From: deluquetoro at gmail.com (crispulo enrique deluque toro) Date: Sat, 17 Mar 2012 23:38:08 -0300 Subject: [Pw_forum] vc-relax "insulators" Message-ID: Dear all I want to do a calculation vc_relax for a perovskite antiferromagnetic insulating properties, but unfortunately I can not get that converges Sending data file. I appreciate any cooperation you can give me. &control calculation = 'vc-relax', restart_mode = 'from_scratch' prefix ='afm01', tstress = .true., tprnfor = .true., pseudo_dir = '/home/deluque/espresso-4.3.2/pseudo/', outdir=$SCRATCH / &system ibrav= 1, celldm(1) = 15.035622339, nat= 40, ntyp= 7, nspin = 2, starting_magnetization(1)= 0.5, starting_magnetization(2)= 0.5, !! Sr - Zr starting_magnetization(3)= 0.7, starting_magnetization(4)=-0.7, !! Mn1 - Mn2 starting_magnetization(5)=-0.7, starting_magnetization(7)= 0.7, !! Mn3 - Mn4 starting_magnetization(7)= 0.5, !! O ecutwfc = 60, ecutrho = 720.0, occupations='smearing', degauss=0.02, / &electrons diagonalization = 'david', mixing_mode = 'plain', conv_thr = 1.0d-7 mixing_beta = 0.3 / &IONS bfgs_ndim = 1, / &CELL cell_dynamics = 'bfgs' cell_dofree = 'all' / ATOMIC_SPECIES Sr 87.620 Sr.pbe-sp-van.UPF Zr 91.224 Zr.pbe-nsp-van.UPF Mn1 54.93805 Mn.pbe-sp-van_mit.UPF Mn2 54.93805 Mn.pbe-sp-van_mit.UPF Mn3 54.93805 Mn.pbe-sp-van_mit.UPF Mn4 54.93805 Mn.pbe-sp-van_mit.UPF O 15.9994 O.pbe-van_ak.UPF ATOMIC_POSITIONS crystal Sr 0.250000000 0.250000000 0.250000000 Sr 0.750000000 0.250000000 0.250000000 Sr 0.750000000 0.750000000 0.250000000 Sr 0.250000000 0.750000000 0.250000000 Sr 0.250000000 0.750000000 0.750000000 Sr 0.250000000 0.250000000 0.750000000 Sr 0.750000000 0.250000000 0.750000000 Sr 0.750000000 0.750000000 0.750000000 Zr 0.000000000 0.500000000 0.500000000 Zr 0.500000000 0.000000000 0.500000000 Zr 0.500000000 0.500000000 0.000000000 Zr 0.000000000 0.000000000 0.000000000 Mn1 0.500000000 0.000000000 0.000000000 Mn2 0.000000000 0.500000000 0.000000000 Mn3 0.000000000 0.000000000 0.500000000 Mn4 0.500000000 0.500000000 0.500000000 O 0.260000000 0.000000000 0.000000000 O 0.000000000 0.260000000 0.000000000 O 0.740000000 0.000000000 0.000000000 O 0.000000000 0.740000000 0.000000000 O 0.000000000 0.000000000 0.740000000 O 0.000000000 0.000000000 0.260000000 O 0.260000000 0.500000000 0.500000000 O 0.000000000 0.760000000 0.500000000 O 0.740000000 0.500000000 0.500000000 O 0.000000000 0.240000000 0.500000000 O 0.000000000 0.500000000 0.240000000 O 0.000000000 0.500000000 0.760000000 O 0.760000000 0.000000000 0.500000000 O 0.500000000 0.260000000 0.500000000 O 0.240000000 0.000000000 0.500000000 O 0.500000000 0.740000000 0.500000000 O 0.500000000 0.000000000 0.240000000 O 0.500000000 0.000000000 0.760000000 O 0.760000000 0.500000000 0.000000000 O 0.500000000 0.760000000 0.000000000 O 0.240000000 0.500000000 0.000000000 O 0.500000000 0.240000000 0.000000000 O 0.500000000 0.500000000 0.740000000 O 0.500000000 0.500000000 0.260000000 K_POINTS automatic 5 5 5 0 0 0 -- *Crispulo E. Deluque Toro* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120317/4eaaf9da/attachment.htm From rahen29 at yahoo.com Sun Mar 18 05:06:56 2012 From: rahen29 at yahoo.com (Rahen Badsha) Date: Sat, 17 Mar 2012 21:06:56 -0700 (PDT) Subject: [Pw_forum] Fermi energy In-Reply-To: <1331958537.27859.YahooMailNeo@web44716.mail.sp1.yahoo.com> References: <1330692801.28406.YahooMailNeo@web44701.mail.sp1.yahoo.com> <1330743883.89515.YahooMailNeo@web44714.mail.sp1.yahoo.com> <1331228438.22391.YahooMailNeo@web44713.mail.sp1.yahoo.com> <1331958537.27859.YahooMailNeo@web44716.mail.sp1.yahoo.com> Message-ID: <1332043616.8813.YahooMailNeo@web44712.mail.sp1.yahoo.com> Dear QE Users,I am calculating the Electronic structure of Nickel and Graphene(using QE-4.2). But I am facing a problem in plotband program those I submitted below: 1.Nickel: bands.out -20.0? 20.0 ni.xmgr ni.ps 1.000------------------------->In this program what should be the value of Fermi Energy for Nickel? 2.0 1.000 EOF 2. Graphene: bands.out -20.0 20.0 graphene.xmgr graphene.ps 1.000-------------------->In this line what should be the value of Fermi Energy for Graphene? 2.0 1.000 EOF PLEASE HELP ME .................. Best Wishes- Rahen Badsha (Raihan) A post graduate thesis student University of Rajshahi, Bangladesh. Mobile:+8801710550252 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120317/615cd27b/attachment.htm From rahen29 at yahoo.com Sun Mar 18 05:06:56 2012 From: rahen29 at yahoo.com (Rahen Badsha) Date: Sat, 17 Mar 2012 21:06:56 -0700 (PDT) Subject: [Pw_forum] Fermi energy In-Reply-To: <1331958537.27859.YahooMailNeo@web44716.mail.sp1.yahoo.com> References: <1330692801.28406.YahooMailNeo@web44701.mail.sp1.yahoo.com> <1330743883.89515.YahooMailNeo@web44714.mail.sp1.yahoo.com> <1331228438.22391.YahooMailNeo@web44713.mail.sp1.yahoo.com> <1331958537.27859.YahooMailNeo@web44716.mail.sp1.yahoo.com> Message-ID: <1332043616.8813.YahooMailNeo@web44712.mail.sp1.yahoo.com> Dear QE Users,I am calculating the Electronic structure of Nickel and Graphene(using QE-4.2). But I am facing a problem in plotband program those I submitted below: 1.Nickel: bands.out -20.0? 20.0 ni.xmgr ni.ps 1.000------------------------->In this program what should be the value of Fermi Energy for Nickel? 2.0 1.000 EOF 2. Graphene: bands.out -20.0 20.0 graphene.xmgr graphene.ps 1.000-------------------->In this line what should be the value of Fermi Energy for Graphene? 2.0 1.000 EOF PLEASE HELP ME .................. Best Wishes- Rahen Badsha (Raihan) A post graduate thesis student University of Rajshahi, Bangladesh. Mobile:+8801710550252 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120317/615cd27b/attachment-0001.htm From zafartariq2003 at yahoo.com Sun Mar 18 07:36:58 2012 From: zafartariq2003 at yahoo.com (zafar rasheed) Date: Sat, 17 Mar 2012 23:36:58 -0700 (PDT) Subject: [Pw_forum] Phonon calculation takes much time................... Message-ID: <1332052618.92630.YahooMailClassic@web65408.mail.ac4.yahoo.com> Dear Paolo Giannaozzi I am calculating phonon calculation for ZnS using 8 atoms. But it take a long time nearly 7 days to compleet calculation. I have dual core 1.866 GHz laptop with 2 Gb RAM. Am I putting some wrong parameter due to which this calculation is too slow. For 2 atoms calculation it take 6 to 7 hours. Muhammad Zafar PhD Scholar Department of Physics The Islamia University of Bahawalpur,Pakistan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120317/3e61b6b3/attachment.htm From abdeslam.houari at gmail.com Sun Mar 18 14:06:04 2012 From: abdeslam.houari at gmail.com (Abdeslam HOUARI) Date: Sun, 18 Mar 2012 14:06:04 +0100 Subject: [Pw_forum] (no subject) In-Reply-To: References: Message-ID: Please, have a look to the documentation: QE/Doc/INPUT_PW.txt, you will certainly find it. (lspinorb = .true) Good luck 2012/3/17 ramzi alaya > Dear all,****** > > How can the spin?orbit coupling take into account in calculations? do > exist any parameter in input file.**** > > This is the input file for the "scf" calculation**** > > &control**** > > ** ** > > ** ** > > calculation = 'scf'**** > > restart_mode = 'from_scratch'**** > > tstress = .true., **** > > tprnfor = .true.,**** > > prefix='810-28',**** > > pseudo_dir='./',**** > > outdir='./',**** > > /**** > > &system**** > > ** ** > > ** ** > > ibrav= 2, celldm(1) =11.850000**** > > nat= 2, ntyp= 2,**** > > ecutwfc =100.0, ecutrho=400.0,**** > > ** ** > > /**** > > &electrons**** > > ** ** > > ** ** > > diagonalization='david'**** > > mixing_beta = 0.7**** > > conv_thr = 1.0d-7**** > > /**** > > ATOMIC_SPECIES**** > > ** ** > > al 26.9815 al_pz.upf**** > > bi 208.980 bi_pz.upf**** > > ** ** > > ** ** > > ATOMIC_POSITIONS **** > > ** ** > > al 0.00000 0.00000 0.00000**** > > bi 0.25000 0.25000 0.25000**** > > ** ** > > K_POINTS automatic**** > > 8 8 8 0 0 0**** > > ** ** > > This is the input file for the "nscf" calculation**** > > &control**** > > ** ** > > ** ** > > calculation = 'nscf'**** > > restart_mode = 'from_scratch'**** > > tstress = .true., **** > > tprnfor = .true.,**** > > prefix='810-28',**** > > pseudo_dir='./',**** > > outdir='./',**** > > /**** > > &system**** > > ** ** > > ** ** > > ibrav= 2, celldm(1) =11.850000**** > > nat= 2, ntyp= 2, nbnd = 8, **** > > ecutwfc =100.0, ecutrho=400.0,**** > > ** ** > > /**** > > &electrons**** > > ** ** > > ** ** > > diagonalization='david'**** > > mixing_beta = 0.7**** > > conv_thr = 1.0d-7**** > > /**** > > ATOMIC_SPECIES**** > > ** ** > > al 26.9815 al_pz.upf**** > > bi 208.980 bi_pz.upf > > ** ** > > ** ** > > ATOMIC_POSITIONS > > ** ** > > al 0.00000 0.00000 0.00000 > > bi 0.25000 0.25000 0.25000 > > ** ** > > K_POINTS > > 21 > > 0.0000 0.5000 1.0000 > > 0.1000 0.5000 0.9000 > > 0.2000 0.5000 0.8000 > > 0.3000 0.5000 0.7000 > > 0.4000 0.5000 0.6000 > > 0.5000 0.5000 0.5000 > > 0.4000 0.4000 0.4000 > > 0.3000 0.3000 0.3000 > > 0.2000 0.2000 0.2000 > > 0.1000 0.1000 0.1000 > > 0.0000 0.0000 0.0000 > > 0.0000 0.0000 0.1000 > > 0.0000 0.0000 0.2000 > > 0.0000 0.0000 0.3000 > > 0.0000 0.0000 0.4000 > > 0.0000 0.0000 0.5000 > > 0.0000 0.0000 0.6000 > > 0.0000 0.0000 0.7000 > > 0.0000 0.0000 0.8000 > > 0.0000 0.0000 0.9000 > > 0.0000 0.0000 1.0000 > > ** ** > > *********************************************************** > Ramzi Alaya**** > > E-mail : ramzialaya at hotmail.fr > Facult? des Sciences de Gab?s, Cit? Erriadh 6072 Gab?s- Tunisie > Unit? de Recherche sur les H?t?ro-Epitaxies et Applications**** > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ============================================== Abdesalem HOUARI ------------------------------------------------------------------------------------------- Department of physics, Theoretical Physics Laboratory University of Bejaia-06000. Algeria. E-mail: abdeslam.houari at univ-bejaia.dz& habdeslam at gmail.com https://sites.google.com/site/houariabdeslam/homepage =============================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120318/989a70f6/attachment.htm From avallabh at purdue.edu Sun Mar 18 20:31:13 2012 From: avallabh at purdue.edu (Ajit Vallabhaneni) Date: Sun, 18 Mar 2012 15:31:13 -0400 (EDT) Subject: [Pw_forum] e-p calculation on customised K-mesh In-Reply-To: <1434562725.32144.1332098843861.JavaMail.root@mailhub016.itcs.purdue.edu> Message-ID: <1777748669.32150.1332099073450.JavaMail.root@mailhub016.itcs.purdue.edu> Dear Users, I want to know if it is possible to perform e-ph calculations on a system whose K-mesh is asymmetric and not specified by Monkhorst-pack. All the e-ph examples i have come across used M-P grid of some size. I want to do some e-ph calculations on graphite where i want the K-mesh to be dense around some K-points in the BZ. I tried to develop K-points outside QE and ran the scf calculations which run perfectly ok. But when i ran an e-ph calculation with q=(0,0,0) , it was terminated with the message: stopping ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from lint : error # 1 cannot remap grid on k-point list Since q=0, the program does not need the energies at new k-states other than my initial K-points. I am confused about this remapping of grid. Can someone help me with this? Thanks Ajit From torstein.fjermestad at kjemi.uio.no Mon Mar 19 11:12:13 2012 From: torstein.fjermestad at kjemi.uio.no (Torstein Fjermestad) Date: Mon, 19 Mar 2012 11:12:13 +0100 Subject: [Pw_forum] =?utf-8?q?problem_with_neb_calculations_/_openmpi?= In-Reply-To: <9BB14D18-F7CE-4C6B-A8E6-330B2F20FBC7@democritos.it> References: <7cc5a1dba0f79b23e01b110892cd1aea@ulrik.uio.no> <6544c6636af26d34452cb5e76a47f325@ulrik.uio.no> <9BB14D18-F7CE-4C6B-A8E6-330B2F20FBC7@democritos.it> Message-ID: Dear Prof. Giannozzi, Thanks for the suggestion. The two tests I referred to were both run with image parallelization (16 processors and 8 images). The tests were run with the same input file and submit script. The command line was as follows: mpirun -np 16 -npernode 8 neb.x -nimage 8 -inp input.inp > output.out In this case the job is submitted and is labelled as "running". It stays like this until the end of the requested time, but it produces no output. At the end of the file slurm-.out the following message is printed: slurmd[compute-14-6]: *** JOB 9146164 CANCELLED AT 2012-03-15T23:20:09 DUE TO TIME LIMIT *** mpirun: killing job... Job 9146164 ("neb_11") completed on compute-14-[6-7] at Thu Mar 15 23:20:09 CET 2012 -------------------------------------------------------------------------- mpirun noticed that process rank 0 with PID 523 on node compute-14-6.local exited on signal 0 (Unknown signal 0). -------------------------------------------------------------------------- [compute-14-6.local:00516] [[31454,0],0]-[[31454,0],1] mca_oob_tcp_msg_recv: readv failed: Connection reset by peer (104) mpirun: clean termination accomplished When removing the image parallelization by either setting -nimage 1 or removing the option altogether (but still running on 16 processors), the job only runs for a few seconds. At the end of the file slurm-.out the following message is printed: from test_input_xml: Empty input file .. stopping -------------------------------------------------------------------------- mpirun has exited due to process rank 11 with PID 32678 on node compute-14-13 exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -------------------------------------------------------------------------- Job 9163874 ("neb_13") completed on compute-14-[12-13] at Sat Mar 17 19:55:23 CET 2012 I found in particular the line "from test_input_xml: Empty input file .. stopping" interesting. The program stops because it thinks a file is empty. Although I did not get much closer to having a running program, I thought that this change in behavior was interesting. Maybe it can give you (or someone else) a hint on what is going on. Of cause this erroneous behavior may have other causes, such as a machine related issue, the openmpi environment, the installation procedure, etc. However, before contacting to the sysadmin, I would like to rule out (to the extent possible) any issues related to quantum espresso itself. Thanks in advance. Yours sincerely, Torstein Fjermestad University of Oslo, Norway On Thu, 15 Mar 2012 22:26:22 +0100, Paolo Giannozzi wrote: > On Mar 15, 2012, at 20:48 , Torstein Fjermestad wrote: > >> pw.x now works without problem, but neb.x only works when one node >> (with 8 processors) is requested. I have run two tests requesting >> two >> nodes (16 processors) and in both cases I see the same erroneous >> behavior: > > with "image" parallelization in both cases? can you run neb.x with 1 > image > and 16 processors? > > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 From elie.moujaes at hotmail.co.uk Mon Mar 19 14:45:09 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Mon, 19 Mar 2012 13:45:09 +0000 Subject: [Pw_forum] parallel computation too slow In-Reply-To: <3B7C8BBB-2790-4177-8285-8DF287684F89@democritos.it> References: , <3B7C8BBB-2790-4177-8285-8DF287684F89@democritos.it> Message-ID: Professor Giannozzi, Thanks for the reply. The CPU time is 1 hr 26 min (2hrs 2 min normal time) for the scf calculation on the nodes (3 of them). If I have 42 atoms then this is equivalent to almost 8 days CPU time or 10 days normal time. Four days have passed and I am still in representation 6 out of 126 which i guess is not the normal situation...Can anything be done (or checked) in this case? Regards Elie > CC: pw_forum at pwscf.org > From: giannozz at democritos.it > Subject: Re: [Pw_forum] parallel computation too slow > Date: Fri, 16 Mar 2012 21:48:15 +0100 > To: elie.moujaes at hotmail.co.uk > > > On Mar 16, 2012, at 19:14 , Elie M wrote: > > > I am running phonon calculations for a supercell of 60 atoms at the > > gamma point [...] > > What could the possible causes of this slowness be? Is it something > > to do with the > > nodes or with phonon calculations in general? Is there a way to check? > > > > > a phonon calculation for N atoms requires a CPU time of the order of > 3N the time of > the correspoding scf calculation. Does yours? if it does, there is > nothing that can be > done. > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > 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://www.democritos.it/pipermail/pw_forum/attachments/20120319/f179b699/attachment.htm From lmartinsamos at gmail.com Mon Mar 19 14:53:29 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Mon, 19 Mar 2012 14:53:29 +0100 Subject: [Pw_forum] problem with neb calculations / openmpi In-Reply-To: References: <7cc5a1dba0f79b23e01b110892cd1aea@ulrik.uio.no> <6544c6636af26d34452cb5e76a47f325@ulrik.uio.no> <9BB14D18-F7CE-4C6B-A8E6-330B2F20FBC7@democritos.it> Message-ID: Dear Torstein could you send the file input.inp, just to try to reproduce the error in an other machine? bests Layla 2012/3/19 Torstein Fjermestad > Dear Prof. Giannozzi, > > Thanks for the suggestion. > The two tests I referred to were both run with image parallelization > (16 processors and 8 images). > The tests were run with the same input file and submit script. The > command line was as follows: > > mpirun -np 16 -npernode 8 neb.x -nimage 8 -inp input.inp > output.out > > In this case the job is submitted and is labelled as "running". It > stays like this until the end of the requested time, but it produces no > output. At the end of the file slurm-.out the following message > is printed: > > > > slurmd[compute-14-6]: *** JOB 9146164 CANCELLED AT 2012-03-15T23:20:09 > DUE TO TIME LIMIT *** > mpirun: killing job... > > Job 9146164 ("neb_11") completed on compute-14-[6-7] at Thu Mar 15 > 23:20:09 CET 2012 > -------------------------------------------------------------------------- > mpirun noticed that process rank 0 with PID 523 on node > compute-14-6.local exited on signal 0 (Unknown signal 0). > -------------------------------------------------------------------------- > [compute-14-6.local:00516] [[31454,0],0]-[[31454,0],1] > mca_oob_tcp_msg_recv: readv failed: Connection reset by peer (104) > mpirun: clean termination accomplished > > > > > When removing the image parallelization by either setting -nimage 1 or > removing the option altogether (but still running on 16 processors), the > job only runs for a few seconds. At the end of the file > slurm-.out the following message is printed: > > > > from test_input_xml: Empty input file .. stopping > -------------------------------------------------------------------------- > mpirun has exited due to process rank 11 with PID 32678 on > node compute-14-13 exiting without calling "finalize". This may > have caused other processes in the application to be > terminated by signals sent by mpirun (as reported here). > -------------------------------------------------------------------------- > Job 9163874 ("neb_13") completed on compute-14-[12-13] at Sat Mar 17 > 19:55:23 CET 2012 > > > I found in particular the line "from test_input_xml: Empty input file > .. stopping" interesting. The program stops because it thinks a file is > empty. > > Although I did not get much closer to having a running program, I > thought that this change in behavior was interesting. Maybe it can give > you (or someone else) a hint on what is going on. > > Of cause this erroneous behavior may have other causes, such as a > machine related issue, the openmpi environment, the installation > procedure, etc. However, before contacting to the sysadmin, I would like > to rule out (to the extent possible) any issues related to quantum > espresso itself. > > Thanks in advance. > > Yours sincerely, > Torstein Fjermestad > University of Oslo, > Norway > > > > > > > On Thu, 15 Mar 2012 22:26:22 +0100, Paolo Giannozzi > wrote: > > On Mar 15, 2012, at 20:48 , Torstein Fjermestad wrote: > > > >> pw.x now works without problem, but neb.x only works when one node > >> (with 8 processors) is requested. I have run two tests requesting > >> two > >> nodes (16 processors) and in both cases I see the same erroneous > >> behavior: > > > > with "image" parallelization in both cases? can you run neb.x with 1 > > image > > and 16 processors? > > > > > > P. > > --- > > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > > Phone +39-0432-558216, fax +39-0432-558222 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120319/daf1595d/attachment.htm From akohlmey at gmail.com Mon Mar 19 15:00:37 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Mon, 19 Mar 2012 10:00:37 -0400 Subject: [Pw_forum] parallel computation too slow In-Reply-To: References: <3B7C8BBB-2790-4177-8285-8DF287684F89@democritos.it> Message-ID: On Mon, Mar 19, 2012 at 9:45 AM, Elie M wrote: > Professor Giannozzi, > > Thanks for the reply. The CPU time is 1 hr 26 min (2hrs 2 min normal time) > for the scf calculation on the nodes (3 of them). If I have 42 atoms then > this is equivalent to almost 8 days CPU time or 10 days normal time. Four > days have passed and I am still in representation 6 out of 126 which i guess > is not the normal situation...Can anything be done ?(or checked) in this > case? get a real computer! if you already lose a quarter of the time due to swapping for the scf calculation, you'll be seriously out of memory for anything more advanced. your laptop is obviously not suitable to carry out this kind of calculation. sorry. axel. > > Regards > > > Elie > >> CC: pw_forum at pwscf.org >> From: giannozz at democritos.it >> Subject: Re: [Pw_forum] parallel computation too slow >> Date: Fri, 16 Mar 2012 21:48:15 +0100 >> To: elie.moujaes at hotmail.co.uk > >> >> >> On Mar 16, 2012, at 19:14 , Elie M wrote: >> >> > I am running phonon calculations for a supercell of 60 atoms at the >> > gamma point [...] >> > What could the possible causes of this slowness be? Is it something >> > to do with the >> > nodes or with phonon calculations in general? Is there a way to check? >> >> > >> >> a phonon calculation for N atoms requires a CPU time of the order of >> 3N the time of >> the correspoding scf calculation. Does yours? if it does, there is >> nothing that can be >> done. >> >> P. >> --- >> Paolo Giannozzi, Dept of Chemistry&Physics&Environment, >> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >> Phone +39-0432-558216, fax +39-0432-558222 >> >> >> >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com ?http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA. From fabrizio.gala at uniroma1.it Mon Mar 19 15:19:56 2012 From: fabrizio.gala at uniroma1.it (fabrizio gala) Date: Mon, 19 Mar 2012 15:19:56 +0100 Subject: [Pw_forum] A question about projwfc.x and pseudopotential generation Message-ID: <4F67408C.1030208@uniroma1.it> Dear all, I generated a pseudo-potential for Calcium with the valence configuration 3d^{0} 4s^{2} 4p^{0}, with an energy of +0.05 a.u. for the unbound d and p states (instead of 0.0 a.u, as suggested in INPUT_LD1.txt); however after a scf+projwfc.x run, there are no projections on such states. Can I solve the problem generating a Ca pseudo-potential with a valence configuration of the form: 3d^{\alpha}4s^{2-2\alpha}4p^{\alpha} with \alpha a small fraction of electron charge, or have I to generate the Ca pseudo-potential with a negative pseudo-energy for them? (or am I making a big mistake I do not recognize?) -- Dr. Fabrizio Gala Dipartimento di Scienze di Base e Applicate per l'Ingegneria, Sezione di Fisica. La Sapienza,University of Rome and Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM) via A. Scarpa 14-16 00161 Rome - ITALY phone: +390649766772 fax: +390644240183 From elie.moujaes at hotmail.co.uk Mon Mar 19 16:05:16 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Mon, 19 Mar 2012 15:05:16 +0000 Subject: [Pw_forum] parallel computation too slow In-Reply-To: References: , <3B7C8BBB-2790-4177-8285-8DF287684F89@democritos.it>, , Message-ID: Hello, It is not a computer. It is a cluster and I am doing parallel computing on 3 nodes each with 8 processors which is a total of 24 processors; this is why I am surprised that the calculation is slow . I tried performing the calculations on different nodes but in vain. N.B: I did calculations on one server with only 8 processors for the Gamma point and the calculations finished in three weeks (though with some negative frequencies, this is why I decided to minimize the tr2_ph) But now that server is down. I thought on more nodes things would be faster; apparently not Regards Elie > Date: Mon, 19 Mar 2012 10:00:37 -0400 > Subject: Re: [Pw_forum] parallel computation too slow > From: akohlmey at gmail.com > To: elie.moujaes at hotmail.co.uk > CC: pw_forum at pwscf.org > > On Mon, Mar 19, 2012 at 9:45 AM, Elie M wrote: > > Professor Giannozzi, > > > > Thanks for the reply. The CPU time is 1 hr 26 min (2hrs 2 min normal time) > > for the scf calculation on the nodes (3 of them). If I have 42 atoms then > > this is equivalent to almost 8 days CPU time or 10 days normal time. Four > > days have passed and I am still in representation 6 out of 126 which i guess > > is not the normal situation...Can anything be done (or checked) in this > > case? > > get a real computer! if you already lose a quarter of the time due to > swapping for the scf calculation, you'll be seriously out of memory > for anything more advanced. your laptop is obviously not suitable > to carry out this kind of calculation. sorry. > > axel. > > > > > Regards > > > > > > Elie > > > >> CC: pw_forum at pwscf.org > >> From: giannozz at democritos.it > >> Subject: Re: [Pw_forum] parallel computation too slow > >> Date: Fri, 16 Mar 2012 21:48:15 +0100 > >> To: elie.moujaes at hotmail.co.uk > > > >> > >> > >> On Mar 16, 2012, at 19:14 , Elie M wrote: > >> > >> > I am running phonon calculations for a supercell of 60 atoms at the > >> > gamma point [...] > >> > What could the possible causes of this slowness be? Is it something > >> > to do with the > >> > nodes or with phonon calculations in general? Is there a way to check? > >> > >> > > >> > >> a phonon calculation for N atoms requires a CPU time of the order of > >> 3N the time of > >> the correspoding scf calculation. Does yours? if it does, there is > >> nothing that can be > >> done. > >> > >> P. > >> --- > >> Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > >> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > >> Phone +39-0432-558216, fax +39-0432-558222 > >> > >> > >> > >> > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > Dr. Axel Kohlmeyer > akohlmey at gmail.com http://goo.gl/1wk0 > > College of Science and Technology > Temple University, Philadelphia PA, USA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120319/f965267d/attachment-0001.htm From giannozz at democritos.it Mon Mar 19 18:30:32 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 19 Mar 2012 18:30:32 +0100 Subject: [Pw_forum] A question about projwfc.x and pseudopotential generation In-Reply-To: <4F67408C.1030208@uniroma1.it> References: <4F67408C.1030208@uniroma1.it> Message-ID: <1332178232.14869.15.camel@fe12lx.fisica.uniud.it> On Mon, 2012-03-19 at 15:19 +0100, fabrizio gala wrote: > I generated a pseudo-potential for Calcium with the valence > configuration 3d^{0} 4s^{2} 4p^{0}, with an energy of +0.05 a.u. > for the unbound d and p states (...); however after a scf+projwfc.x > run, there are no projections on such states. projections are calculated only for bound atomic states. I think that unbound states are not even saved to the UPF files in the PP_PSWFC section. Not sure that projecting over unbound states makes any sense. > Can I solve the problem generating a Ca pseudo-potential with a valence > configuration of the form: > 3d^{\alpha}4s^{2-2\alpha}4p^{\alpha} with \alpha a small fraction of > electron charge, or have I to generate the Ca pseudo-potential with a > negative pseudo-energy for them? you have to produce in a way or another bound 3d and 4p states. This can be done by changing the reference electron configuration. You may need to use an ionic configuration, though. Another option is to keep you PP but generate bound 3d and 4p states from an ionic configuration, replace the atomic orbitals of the PP_PSWFC section (they are not used in actual calculations, except to generate starting wavefunctions and projections over atomic states, which are ill-defined anyway). PG -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Mon Mar 19 18:38:38 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 19 Mar 2012 18:38:38 +0100 Subject: [Pw_forum] parallel computation too slow In-Reply-To: References: , <3B7C8BBB-2790-4177-8285-8DF287684F89@democritos.it> , , Message-ID: <1332178718.14869.23.camel@fe12lx.fisica.uniud.it> On Mon, 2012-03-19 at 15:05 +0000, Elie M wrote: > I am doing parallel computing on 3 nodes each with 8 processors > which is a total of 24 processors; this is why I am surprised > that the calculation is slow there are two different aspects here: - how fast the algorithm is, and - how effective the parallelization is. What are we talking about? P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From akohlmey at gmail.com Mon Mar 19 18:57:50 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Mon, 19 Mar 2012 13:57:50 -0400 Subject: [Pw_forum] parallel computation too slow In-Reply-To: <1332178718.14869.23.camel@fe12lx.fisica.uniud.it> References: <3B7C8BBB-2790-4177-8285-8DF287684F89@democritos.it> <1332178718.14869.23.camel@fe12lx.fisica.uniud.it> Message-ID: On Mon, Mar 19, 2012 at 1:38 PM, Paolo Giannozzi wrote: > On Mon, 2012-03-19 at 15:05 +0000, Elie M wrote: > >> I am doing parallel computing on 3 nodes each with 8 processors >> which is a total of 24 processors; this is why I am surprised >> ?that the calculation is slow > > there are two different aspects here: > - how fast the algorithm is, and > - how effective the parallelization is. you forgot. how well can the available hardware handle the calculation (RAM, network speed, I/O speed, load from other users). axel. > What are we talking about? > > P. > > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com ?http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA. From giannozz at democritos.it Mon Mar 19 19:00:28 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 19 Mar 2012 19:00:28 +0100 Subject: [Pw_forum] problem with neb calculations / openmpi In-Reply-To: References: <7cc5a1dba0f79b23e01b110892cd1aea@ulrik.uio.no> <6544c6636af26d34452cb5e76a47f325@ulrik.uio.no> <9BB14D18-F7CE-4C6B-A8E6-330B2F20FBC7@democritos.it> Message-ID: <1332180028.14869.42.camel@fe12lx.fisica.uniud.it> On Mon, 2012-03-19 at 11:12 +0100, Torstein Fjermestad wrote: > I found in particular the line "from test_input_xml: Empty input file > .. stopping" interesting. The program stops because it thinks a file is > empty. most likely, the program stops because the file _is_ empty (or not there) Is the input file on a file system that is visible from each processor? I don't remember exactly how NEB reads data now, but it might assume that the input file is readable by all processors. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Mon Mar 19 19:06:57 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 19 Mar 2012 19:06:57 +0100 Subject: [Pw_forum] e-p calculation on customised K-mesh In-Reply-To: <1777748669.32150.1332099073450.JavaMail.root@mailhub016.itcs.purdue.edu> References: <1777748669.32150.1332099073450.JavaMail.root@mailhub016.itcs.purdue.edu> Message-ID: <1332180417.14869.48.camel@fe12lx.fisica.uniud.it> On Sun, 2012-03-18 at 15:31 -0400, Ajit Vallabhaneni wrote: > I want to do some e-ph calculations on graphite where i want > the K-mesh to be dense around some K-points in the BZ. I tried > to develop K-points outside QE and ran the scf calculations which > run perfectly ok. But when i ran an e-ph calculation with q=(0,0,0) I don't think you can use a non-uniform grid with the current ('interpolation') algorithm. It might be feasible with the old 'simple' algorithm, available again in the SVN version (see variable "electron_phonon", replacing "elph") P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Mon Mar 19 19:10:14 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 19 Mar 2012 19:10:14 +0100 Subject: [Pw_forum] vc-relax "insulators" In-Reply-To: References: Message-ID: <1332180614.14869.50.camel@fe12lx.fisica.uniud.it> On Sat, 2012-03-17 at 23:38 -0300, crispulo enrique deluque toro wrote: > I want to do a calculation vc_relax for a perovskite antiferromagnetic > insulating properties, but unfortunately I can not get that converges have you made any preliminary tests on simpler cases? for all pseudopotentials? do they work? P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From torstein.fjermestad at kjemi.uio.no Mon Mar 19 21:47:30 2012 From: torstein.fjermestad at kjemi.uio.no (Torstein Fjermestad) Date: Mon, 19 Mar 2012 21:47:30 +0100 Subject: [Pw_forum] =?utf-8?q?problem_with_neb_calculations_/_openmpi?= In-Reply-To: References: <7cc5a1dba0f79b23e01b110892cd1aea@ulrik.uio.no> <6544c6636af26d34452cb5e76a47f325@ulrik.uio.no> <9BB14D18-F7CE-4C6B-A8E6-330B2F20FBC7@democritos.it> Message-ID: Dear Layla, The file is attached. Thank you very much for your help. Yours sincerely, Torstein Fjermestad On Mon, 19 Mar 2012 14:53:29 +0100, Layla Martin-Samos wrote: > Dear Torstein could you send the file input.inp, just to try to > reproduce the error in an other machine? > > bests > > Layla > -------------- next part -------------- A non-text attachment was scrubbed... Name: neb_12.inp Type: application/octet-stream Size: 9937 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120319/aa33f157/attachment-0001.obj From avallabh at purdue.edu Mon Mar 19 22:21:51 2012 From: avallabh at purdue.edu (Ajit Vallabhaneni) Date: Mon, 19 Mar 2012 17:21:51 -0400 (EDT) Subject: [Pw_forum] e-p calculation on customised K-mesh In-Reply-To: <1332180417.14869.48.camel@fe12lx.fisica.uniud.it> Message-ID: <121501226.35764.1332192111692.JavaMail.root@mailhub016.itcs.purdue.edu> Dr. Paolo, Thanks for your reply. I downloaded the svn version and found the example 03 in the PHonon folder which uses "electron_phonon" for Al. But i am not able to compile it on my cluster on which i had compiled the 4.3.2 version successfully. I executed the "configure" successfully. But when i tried to use "make pw or make ph" , it was terminated with the following message. Are there any extra steps involved in compiling the svn version? Please let me know make[2]: *** [pw.x] Error 1 make[2]: Leaving directory `/scratch/a/Quantumespresso/espresso-4.3.2/TEMP/trunk/espresso/PW/src' make[1]: *** [pw] Error 2 make[1]: Leaving directory `/scratch/a/Quantumespresso/espresso-4.3.2/TEMP/trunk/espresso/PW' make: *** [pw] Error 2 Thanks Ajit From giannozz at democritos.it Mon Mar 19 22:50:16 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 19 Mar 2012 22:50:16 +0100 Subject: [Pw_forum] e-p calculation on customised K-mesh In-Reply-To: <121501226.35764.1332192111692.JavaMail.root@mailhub016.itcs.purdue.edu> References: <121501226.35764.1332192111692.JavaMail.root@mailhub016.itcs.purdue.edu> Message-ID: <7A4B8714-2912-4453-AEC8-D3376A5BBAD1@democritos.it> On Mar 19, 2012, at 22:21 , Ajit Vallabhaneni wrote: > Are there any extra steps involved in compiling the svn version? no > make[2]: *** [pw.x] Error 1 there must be an error before this one P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From avallabh at purdue.edu Tue Mar 20 00:54:58 2012 From: avallabh at purdue.edu (Ajit Vallabhaneni) Date: Mon, 19 Mar 2012 19:54:58 -0400 (EDT) Subject: [Pw_forum] e-p calculation on customised K-mesh In-Reply-To: <7A4B8714-2912-4453-AEC8-D3376A5BBAD1@democritos.it> Message-ID: <1981361664.36192.1332201298141.JavaMail.root@mailhub016.itcs.purdue.edu> Dr. Paolo, I thought so. But i could not figure out what the error is. I am attaching the log file. Please take a look and let me know what the problem is. Thanks Ajit -------------- next part -------------- A non-text attachment was scrubbed... Name: log.out Type: application/octet-stream Size: 101476 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120319/ff9431a8/attachment-0001.obj From akohlmey at gmail.com Tue Mar 20 01:19:08 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Mon, 19 Mar 2012 20:19:08 -0400 Subject: [Pw_forum] e-p calculation on customised K-mesh In-Reply-To: <1981361664.36192.1332201298141.JavaMail.root@mailhub016.itcs.purdue.edu> References: <7A4B8714-2912-4453-AEC8-D3376A5BBAD1@democritos.it> <1981361664.36192.1332201298141.JavaMail.root@mailhub016.itcs.purdue.edu> Message-ID: On Mon, Mar 19, 2012 at 7:54 PM, Ajit Vallabhaneni wrote: > Dr. Paolo, > > ? ? ? ? ? ?I thought so. But i could not figure out what the error is. I am attaching the log file. Please take a look and let me know what the problem is. trivial. you are trying to use a scalapack that has been compiled against OpenMPI as MPI library, but apparently your MPI library is different. see all the undefined references? axel. > > > Thanks > Ajit > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com ?http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA. From henod2001 at yahoo.com Tue Mar 20 07:23:23 2012 From: henod2001 at yahoo.com (henry odhiambo) Date: Mon, 19 Mar 2012 23:23:23 -0700 (PDT) Subject: [Pw_forum] Calculation of dynamical matrices Message-ID: <1332224603.58064.YahooMailClassic@web121005.mail.ne1.yahoo.com> Hello every one, ? I am trying to calculate dynamical matrices using the code ph.x for?the input file bellow ? phonons of gst ?&inputph ?tr2_ph=1.0d-14 ?ldisp=.true., ?nq1=4, nq2=4, nq3=4, ?amass (1)=72.61, ?amass (2)=121.76, ?amass (3)=127.60, ?prefix='gst', ?outdir='./', ?fildyn='dyn' ? I only get the dynamical matrices?dyn1 and?dyn2 whereas in the QE examples,?they should be from dyn1 to dyn 8. Morover, when I try calculating IFC's in real space using the code q2r.x, I dont get any output. What could be the problem?? ? Henry Otunga Dept. of Physics Maseno University Kenya ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120319/3e0bd5f1/attachment.htm From lmartinsamos at gmail.com Tue Mar 20 08:47:11 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Tue, 20 Mar 2012 08:47:11 +0100 Subject: [Pw_forum] problem with neb calculations / openmpi In-Reply-To: References: <7cc5a1dba0f79b23e01b110892cd1aea@ulrik.uio.no> <6544c6636af26d34452cb5e76a47f325@ulrik.uio.no> <9BB14D18-F7CE-4C6B-A8E6-330B2F20FBC7@democritos.it> Message-ID: Dear Torstein, I dont see anything strange in the input file. What could happen is that all the cpu do not see the same "HOME" or/and "SCRATCH". NEB assumes that the input are in ./ and that every cpu knows what is ./ and have the same ./ . First control that the code has generated correctly the files neb.dat and pw_i.in, pw_2.in in your running directory. If yes, you can overcome the problem with the file system changing inside the file neb.f90 ( espresso/NEB/src) : open(unit=stdinpath,file="neb.dat",status="old") with open(unit=stdinpath,file="PATH_TO_YOUR_RUNNING_DIR/neb.dat",status="old") and change the two occurrence of OPEN(unit_tmp, file=trim(engine_prefix)//"1.in") with OPEN(unit_tmp, file="PATH_TO_YOUR_RUNNING_DIR"//"trim(engine_prefix)//"1.in ") and recompile. cheers Layla 2012/3/19 Torstein Fjermestad > Dear Layla, > > The file is attached. > Thank you very much for your help. > > Yours sincerely, > > Torstein Fjermestad > > > > > > On Mon, 19 Mar 2012 14:53:29 +0100, Layla Martin-Samos < > lmartinsamos at gmail.com> wrote: > >> Dear Torstein could you send the file input.inp, just to try to >> reproduce the error in an other machine? >> >> bests >> >> Layla >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120320/ea2bac27/attachment.htm From d.tiana at bath.ac.uk Tue Mar 20 10:10:23 2012 From: d.tiana at bath.ac.uk (Davide Tiana) Date: Tue, 20 Mar 2012 09:10:23 +0000 Subject: [Pw_forum] bands calculation crash In-Reply-To: References: <20120316103521.Horde.4TTebVLxr25PYxdp8U8jT1A@webmail.bath.ac.uk> <20120317193744.Horde.KU38AFLxr25PZOgIt4_BNoA@webmail.bath.ac.uk> Message-ID: <20120320091023.Horde.y-HwbVLxr25PaEl-7uggU5A@webmail.bath.ac.uk> I run all the examples and tried on other systems. I can conclude it crashes always. Thus, Although during the compilation I didn't have any problems, warnings or errors, I guess it is a compilation problem. My workstation is a MacOS Lion, I compiled with mpi and mkl. Quoting Paolo Giannozzi : > > in all cases? only for a specific set of data? also for the > provided examples? > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Tue Mar 20 11:20:58 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 20 Mar 2012 11:20:58 +0100 Subject: [Pw_forum] bands calculation crash In-Reply-To: <20120320091023.Horde.y-HwbVLxr25PaEl-7uggU5A@webmail.bath.ac.uk> References: <20120316103521.Horde.4TTebVLxr25PYxdp8U8jT1A@webmail.bath.ac.uk> <20120317193744.Horde.KU38AFLxr25PZOgIt4_BNoA@webmail.bath.ac.uk> <20120320091023.Horde.y-HwbVLxr25PaEl-7uggU5A@webmail.bath.ac.uk> Message-ID: <1332238858.17013.25.camel@fe12lx.fisica.uniud.it> On Tue, 2012-03-20 at 09:10 +0000, Davide Tiana wrote: > I guess it is a compilation problem. > My workstation is a MacOS Lion, I compiled with mpi and mkl. if it works on a different machine (or even on the same machine with a different compiler), it is likely a compilation problem. If not, please file a bug report on qe-forge P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Tue Mar 20 11:29:38 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 20 Mar 2012 11:29:38 +0100 Subject: [Pw_forum] Calculation of dynamical matrices In-Reply-To: <1332224603.58064.YahooMailClassic@web121005.mail.ne1.yahoo.com> References: <1332224603.58064.YahooMailClassic@web121005.mail.ne1.yahoo.com> Message-ID: <1332239378.17013.36.camel@fe12lx.fisica.uniud.it> On Mon, 2012-03-19 at 23:23 -0700, henry odhiambo wrote: > I only get the dynamical matrices dyn1 and dyn2 whereas > in the QE examples, they should be from dyn1 to dyn8 > > no, they should be from dyn1 to dynN, where N is the number > of wavevectors (q) that are inequivalent by symmetry. no, they should be from dyn1 to dynN, where N is the number of wavevectors (q) that are inequivalent by symmetry. You should look into the output file to understand why the code has stopped P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From bdslipun at gmail.com Tue Mar 20 13:56:35 2012 From: bdslipun at gmail.com (bhabya sahoo) Date: Tue, 20 Mar 2012 18:26:35 +0530 Subject: [Pw_forum] phonon dos Message-ID: i am calculating vibrational properties using QHA of espresso code i have the fcc structure having 2 atoms in unit cell i get the static energy -147.245069 Ry at zero pressure after that i calculted vibrational properties at zero pressure which is given below my question the out put f_vibrational energy is Ry/Cell so i have to add the f_vibrational energy to the energy at T=0k so whether i add the f_vibr or i have to divide anything in the vibrational energy which will be added to cold energy for my system having NaCl structure SAHOO B D RESERCH SCHOLAR MUMBAI -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120320/7fc061fe/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: cd43.QHA.out Type: application/octet-stream Size: 27749 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120320/7fc061fe/attachment-0001.obj From bdslipun at gmail.com Tue Mar 20 16:08:15 2012 From: bdslipun at gmail.com (bhabya sahoo) Date: Tue, 20 Mar 2012 20:38:15 +0530 Subject: [Pw_forum] Fwd: phonon dos In-Reply-To: References: Message-ID: ---------- Forwarded message ---------- From: bhabya sahoo Date: Tue, Mar 20, 2012 at 6:26 PM Subject: phonon dos To: PWSCF Forum , giannozz at democritos.it, Axel Kohlmeyer i am calculating vibrational properties using QHA of espresso code i have the fcc structure having 2 atoms in unit cell i get the static energy -147.245069 Ry at zero pressure after that i calculted vibrational properties at zero pressure which is given below my question the out put f_vibrational energy is Ry/Cell so i have to add the f_vibrational energy to the energy at T=0k so whether i add the f_vibr or i have to divide anything in the vibrational energy which will be added to cold energy for my system having NaCl structure SAHOO B D RESERCH SCHOLAR MUMBAI -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120320/84b98107/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: cd43.QHA.out Type: application/octet-stream Size: 27749 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120320/84b98107/attachment-0001.obj From jptrinastic at phys.ufl.edu Tue Mar 20 16:15:09 2012 From: jptrinastic at phys.ufl.edu (Jonathan Trinastic) Date: Tue, 20 Mar 2012 11:15:09 -0400 Subject: [Pw_forum] Problem with scf convergence Message-ID: <4F689EFD.6010905@phys.ufl.edu> Hi, I'm having an issue getting a Co-MgO interface to converge properly. Basically, the setup includes 8 layers of bcc Co interfaced with 8 layers of MgO, periodic in x and y and a vacuum between interfaces in the z direction. I'm trying to find the Co-O distance that gives the energy minimum, so I'm trying to relax structures with varying distances - I'm using a 2.17 A distance to start based on experimental values. I've been able to relax the Co and MgO parts separately without a problem, but when I combine them they won't converge. I've included my pw.x input below, however I have also tried adjust many of the parameters based on feedback in other posts and the QE User guide, such as: increasing degauss or adding bands to account for metallic nature of Co, decreasing mixing beta, increasing the energy cutoff value, however all these end up having the same convergence problems where the estimated scf accuracy hovers around 1-10. Does anyone see potential issues with the input I'm using that I'm missing? I've chosen my energy and charge density cutoffs based on the recommended choices for the oxygen PAW potential, which is higher than for Co or Mg. Thanks, Jonathan &control calculation='scf', restart_mode='from_scratch', pseudo_dir = '/scratch/hpc/jptrinas/espresso-4.3.2/pseudo/', outdir='./tmp/' prefix='bcc.co.mgo' tstress = .true. tprnfor = .true. / &system ibrav = 6, celldm(1) =5.32, celldm(3) = 19.52, nat= 24, ntyp= 3 starting_magnetization(1)=0.7, nspin=2 ecutwfc = 38.0, ecutrho = 151.0 occupations='smearing', smearing='gaussian', degauss=0.02 / &electrons diagonalization='cg' conv_thr = 1.0e-6 mixing_beta = 0.3 / ATOMIC_SPECIES Co 58.93 Co.pbe-p-paw.UPF Mg 24.31 Mg.pbe-nsp-bpaw.UPF O 15.99 O.pbe-kjpaw.UPF ATOMIC_POSITIONS (alat) Co 0.0 0.0 5.000 Co 0.5 0.5 5.500 Co 0.0 0.0 6.000 Co 0.5 0.5 6.500 Co 0.0 0.0 7.000 Co 0.5 0.5 7.500 Co 0.0 0.0 8.000 Co 0.5 0.5 8.500 O 0.5 0.5 9.270 Mg 0.0 0.0 9.270 O 0.0 0.0 10.02 Mg 0.5 0.5 10.02 O 0.5 0.5 10.77 Mg 0.0 0.0 10.77 O 0.0 0.0 11.52 Mg 0.5 0.5 11.52 O 0.5 0.5 12.27 Mg 0.0 0.0 12.27 O 0.0 0.0 13.02 Mg 0.5 0.5 13.02 O 0.5 0.5 13.77 Mg 0.0 0.0 13.77 O 0.0 0.0 14.52 Mg 0.5 0.5 14.52 K_POINTS (automatic) 6 6 1 0 0 0 Typical scf accuracy estimates by end of run: estimated scf accuracy < 16.36480484 Ry estimated scf accuracy < 8.36686889 Ry estimated scf accuracy < 2.33384573 Ry estimated scf accuracy < 6.92471882 Ry estimated scf accuracy < 13.18681083 Ry estimated scf accuracy < 11.95347196 Ry estimated scf accuracy < 11.49117957 Ry estimated scf accuracy < 12.65621865 Ry estimated scf accuracy < 8.53355241 Ry estimated scf accuracy < 6.20738100 Ry estimated scf accuracy < 7.91117866 Ry estimated scf accuracy < 17.89939870 Ry estimated scf accuracy < 4.29389382 Ry estimated scf accuracy < 8.11074063 Ry estimated scf accuracy < 3.91904239 Ry estimated scf accuracy < 2.99042194 Ry estimated scf accuracy < 2.47072016 Ry estimated scf accuracy < 5.16323880 Ry estimated scf accuracy < 4.17983416 Ry estimated scf accuracy < 16.77910831 Ry estimated scf accuracy < 8.52666365 Ry estimated scf accuracy < 4.02303973 Ry estimated scf accuracy < 11.00391780 Ry estimated scf accuracy < 4.89255713 Ry -- Jonathan Trinastic, M.S. Graduate Student Department of Physics University of Florida From sbinnie at sissa.it Tue Mar 20 16:22:26 2012 From: sbinnie at sissa.it (Simon Binnie) Date: Tue, 20 Mar 2012 16:22:26 +0100 Subject: [Pw_forum] Problem with scf convergence In-Reply-To: <4F689EFD.6010905@phys.ufl.edu> References: <4F689EFD.6010905@phys.ufl.edu> Message-ID: On Tue, 20 Mar 2012 16:15:09 +0100, Jonathan Trinastic wrote: > Hi, > > I'm having an issue getting a Co-MgO interface to converge properly. > Basically, the setup includes 8 layers of bcc Co interfaced with 8 > layers of MgO, periodic in x and y and a vacuum between interfaces in > the z direction. I'm trying to find the Co-O distance that gives the > energy minimum, so I'm trying to relax structures with varying distances > - I'm using a 2.17 A distance to start based on experimental values. > I've been able to relax the Co and MgO parts separately without a > problem, but when I combine them they won't converge. > Have you tried experimenting with the mixing_mode parameter? I think I've bypassed similar problems with slabs in the past using the 'local-TF' mode. Best regards, Simon -- Simon Binnie | Post Doc, Condensed Matter Sector Scuola Internazionale di Studi Avanzati (SISSA) Via Bonomea 256 | 34100 Trieste | sbinnie at sissa.it From renpj at dicp.ac.cn Tue Mar 20 16:40:03 2012 From: renpj at dicp.ac.cn (PJ Ren) Date: Tue, 20 Mar 2012 23:40:03 +0800 Subject: [Pw_forum] Starting charge for hydrogen using different PP Message-ID: <4F68A4D3.6050006@dicp.ac.cn> Dear all, I have tested some hydrogen PP by calculating the hydrogen molecule. I found that for some PPs the starting charge was not very close to two as I respected. The results: H.pbe-rrkjus.UPF : starting charge 1.80759 H.pz-rrkjus.UPF : starting charge 1.81576 H.pbe-tm-gipaw.UPF: starting charge 0.20000 But all the case were renormalised to 2.00000. I don't know whether it is right or wrong. The last PP was copy from GIPAW example. Thanks. PJ Ren From elbuesta at icqmail.com Tue Mar 20 18:36:40 2012 From: elbuesta at icqmail.com (elbuesta at icqmail.com) Date: Tue, 20 Mar 2012 13:36:40 -0400 (EDT) Subject: [Pw_forum] Problem with scf convergence In-Reply-To: <4F689EFD.6010905@phys.ufl.edu> References: <4F689EFD.6010905@phys.ufl.edu> Message-ID: <8CED4D724A488DA-AB4-190AB@webmail-m099.sysops.aol.com> Dear Jonathan, I am not sure if you tried, but the local-density-dependent TF screening is very important when the cell is large, like in your case. I did not find the PPs you are using in the quantum espresso webpage, so I downloaded the usual USPP and repeated the calculation. Here it is the input and the output that I obtained. It took a significant number of scf cycles to converge (more than 100, I had to restart the calculation), so probably a better optimization of the smearing/charge cutoff/etc... parameters can still be done. But considering it is Co-MgO we are talking about, I would say that it's ok. I hope it helps! All best! Fabio Negreiros Ribeiro, Post-Doc, IPCF - Consiglio Nazionalle delle Ricerche, Pisa, Italy -----Original Message----- From: Jonathan Trinastic To: pw_forum Sent: Tue, Mar 20, 2012 4:15 pm Subject: [Pw_forum] Problem with scf convergence Hi, I'm having an issue getting a Co-MgO interface to converge properly. Basically, the setup includes 8 layers of bcc Co interfaced with 8 layers of MgO, periodic in x and y and a vacuum between interfaces in the z direction. I'm trying to find the Co-O distance that gives the energy minimum, so I'm trying to relax structures with varying distances - I'm using a 2.17 A distance to start based on experimental values. I've been able to relax the Co and MgO parts separately without a problem, but when I combine them they won't converge. I've included my pw.x input below, however I have also tried adjust many of the parameters based on feedback in other posts and the QE User guide, such as: increasing degauss or adding bands to account for metallic nature of Co, decreasing mixing beta, increasing the energy cutoff value, however all these end up having the same convergence problems where the estimated scf accuracy hovers around 1-10. Does anyone see potential issues with the input I'm using that I'm missing? I've chosen my energy and charge density cutoffs based on the recommended choices for the oxygen PAW potential, which is higher than for Co or Mg. Thanks, Jonathan &control calculation='scf', restart_mode='from_scratch', pseudo_dir = '/scratch/hpc/jptrinas/espresso-4.3.2/pseudo/', outdir='./tmp/' prefix='bcc.co.mgo' tstress = .true. tprnfor = .true. / &system ibrav = 6, celldm(1) =5.32, celldm(3) = 19.52, nat= 24, ntyp= 3 starting_magnetization(1)=0.7, nspin=2 ecutwfc = 38.0, ecutrho = 151.0 occupations='smearing', smearing='gaussian', degauss=0.02 / &electrons diagonalization='cg' conv_thr = 1.0e-6 mixing_beta = 0.3 / ATOMIC_SPECIES Co 58.93 Co.pbe-p-paw.UPF Mg 24.31 Mg.pbe-nsp-bpaw.UPF O 15.99 O.pbe-kjpaw.UPF ATOMIC_POSITIONS (alat) Co 0.0 0.0 5.000 Co 0.5 0.5 5.500 Co 0.0 0.0 6.000 Co 0.5 0.5 6.500 Co 0.0 0.0 7.000 Co 0.5 0.5 7.500 Co 0.0 0.0 8.000 Co 0.5 0.5 8.500 O 0.5 0.5 9.270 Mg 0.0 0.0 9.270 O 0.0 0.0 10.02 Mg 0.5 0.5 10.02 O 0.5 0.5 10.77 Mg 0.0 0.0 10.77 O 0.0 0.0 11.52 Mg 0.5 0.5 11.52 O 0.5 0.5 12.27 Mg 0.0 0.0 12.27 O 0.0 0.0 13.02 Mg 0.5 0.5 13.02 O 0.5 0.5 13.77 Mg 0.0 0.0 13.77 O 0.0 0.0 14.52 Mg 0.5 0.5 14.52 K_POINTS (automatic) 6 6 1 0 0 0 Typical scf accuracy estimates by end of run: estimated scf accuracy < 16.36480484 Ry estimated scf accuracy < 8.36686889 Ry estimated scf accuracy < 2.33384573 Ry estimated scf accuracy < 6.92471882 Ry estimated scf accuracy < 13.18681083 Ry estimated scf accuracy < 11.95347196 Ry estimated scf accuracy < 11.49117957 Ry estimated scf accuracy < 12.65621865 Ry estimated scf accuracy < 8.53355241 Ry estimated scf accuracy < 6.20738100 Ry estimated scf accuracy < 7.91117866 Ry estimated scf accuracy < 17.89939870 Ry estimated scf accuracy < 4.29389382 Ry estimated scf accuracy < 8.11074063 Ry estimated scf accuracy < 3.91904239 Ry estimated scf accuracy < 2.99042194 Ry estimated scf accuracy < 2.47072016 Ry estimated scf accuracy < 5.16323880 Ry estimated scf accuracy < 4.17983416 Ry estimated scf accuracy < 16.77910831 Ry estimated scf accuracy < 8.52666365 Ry estimated scf accuracy < 4.02303973 Ry estimated scf accuracy < 11.00391780 Ry estimated scf accuracy < 4.89255713 Ry -- Jonathan Trinastic, M.S. Graduate Student Department of Physics University of Florida _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120320/7503c053/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: input.in Type: application/octet-stream Size: 1241 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120320/7503c053/attachment-0002.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: input.out Type: application/octet-stream Size: 98324 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120320/7503c053/attachment-0003.obj From avallabh at purdue.edu Tue Mar 20 20:40:02 2012 From: avallabh at purdue.edu (Ajit Vallabhaneni) Date: Tue, 20 Mar 2012 15:40:02 -0400 (EDT) Subject: [Pw_forum] e-p calculation on customised K-mesh In-Reply-To: <1332230619.17013.1.camel@fe12lx.fisica.uniud.it> Message-ID: <981530123.38975.1332272402901.JavaMail.root@mailhub016.itcs.purdue.edu> Dr.Paolo, Thanks again. I compiled it and ran e-ph calculation (after scf) with "electron_phonon=interpolated" (like in ex 03) for q=(0,0,0). But it terminated with the same message. stopping ... from lint : error # 1 cannot remap grid on k-point list %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... Thanks Ajit From deluquetoro at gmail.com Tue Mar 20 21:19:34 2012 From: deluquetoro at gmail.com (crispulo enrique deluque toro) Date: Tue, 20 Mar 2012 17:19:34 -0300 Subject: [Pw_forum] vc-relax "insulators" In-Reply-To: <1332180614.14869.50.camel@fe12lx.fisica.uniud.it> References: <1332180614.14869.50.camel@fe12lx.fisica.uniud.it> Message-ID: Dear Paolo Giannozzi Thanks for answering my query, the problem is solved with the mixing_beta = 0.1, regards El 19 de marzo de 2012 15:10, Paolo Giannozzi escribi?: > On Sat, 2012-03-17 at 23:38 -0300, crispulo enrique deluque toro wrote: > > > I want to do a calculation vc_relax for a perovskite antiferromagnetic > > insulating properties, but unfortunately I can not get that converges > > have you made any preliminary tests on simpler cases? for all > pseudopotentials? do they work? > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > -- *Crispulo Enrique Deluque Toro* Becario Posgrado - Universidad Nacional del Comahue, Argentina. Doctorando en Instituto Sabato - Universidad Nacional de San Mart?n, Argentina. Mag?ster en Ciencias F?sica - Universidad Nacional de Colombia Lic. F?sico-Matem?tico - Universidad del Magdalena, Colombia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120320/aca8abcd/attachment.htm From giannozz at democritos.it Tue Mar 20 21:52:13 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 20 Mar 2012 21:52:13 +0100 Subject: [Pw_forum] e-p calculation on customised K-mesh In-Reply-To: <981530123.38975.1332272402901.JavaMail.root@mailhub016.itcs.purdue.edu> References: <981530123.38975.1332272402901.JavaMail.root@mailhub016.itcs.purdue.edu> Message-ID: <8698CB67-791D-4288-8ABA-022421DE270E@democritos.it> On Mar 20, 2012, at 20:40 , Ajit Vallabhaneni wrote: > Thanks again. I compiled it and ran e-ph calculation (after scf) > with "electron_phonon=interpolated" (like in ex 03) for q=(0,0,0). > But it > terminated with the same message. of course, since it does exactly the same thing. You should try "electron_phonon='simple'". Disclaimer: I know nothing about this option. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From makhyoun2 at yahoo.com Tue Mar 20 22:50:33 2012 From: makhyoun2 at yahoo.com (mohamed makhyoun) Date: Tue, 20 Mar 2012 14:50:33 -0700 (PDT) Subject: [Pw_forum] pseudo-PP suitable for gipaw calculation Message-ID: <1332280233.3171.YahooMailClassic@web126001.mail.ne1.yahoo.com> Dear all : Can any body provide me with? example of an input file ( any element ) to be used in the ?production of? PP ( e.g xx.pbe-tm-gipaw.UPF) suitable for the? gipaw calculations. The documents for the ld1.x code is not clear enough to me. ?Best Regard Makhyoun -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120320/0f8a70f2/attachment.htm From tfcao at theory.issp.ac.cn Wed Mar 21 03:23:28 2012 From: tfcao at theory.issp.ac.cn (=?utf-8?B?Q2FvIFRG?=) Date: Wed, 21 Mar 2012 10:23:28 +0800 Subject: [Pw_forum] =?utf-8?q?vc-relax?= Message-ID: <20120321022328.11571.qmail@ms.hfcas.ac.cn> Dear QE users: I want to do the 'vc-relax' calculation of bilayer structure of graphene and BN. And only the lattice constant a, b are allowed to change in the relaxation. So I set cell_dofree = 'xy' , but when the calculation finished, the distance of of the vacuum between different by layers also changed. The vacuum is set 10 A, it changed to 5.76 A in the end. What can be the reasons ? Any suggestions will be greatly appreciated. cell_dofree CHARACTER Default: 'all' Select which of the cell parameters should be moved: all = all axis and angles are moved x = only the x axis is moved y = only the y axis is moved z = only the z axis is moved xy = only the x and y axis are moved, angles are unchanged xz = only the x and z axis are moved, angles are unchanged yz = only the y and z axis are moved, angles are unchanged xyz = x, y and z axis are moved, angles are unchanged shape = all axis and angles, keeping the volume fixed Research Laboratory for Computational Materials Sciences, Institute of Solid State Physics, Chinese Academy of Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120321/dc779323/attachment.htm From giannozz at democritos.it Wed Mar 21 09:16:31 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 21 Mar 2012 09:16:31 +0100 Subject: [Pw_forum] vc-relax In-Reply-To: <20120321022328.11571.qmail@ms.hfcas.ac.cn> References: <20120321022328.11571.qmail@ms.hfcas.ac.cn> Message-ID: <1332317791.26247.6.camel@fe12lx.fisica.uniud.it> On Wed, 2012-03-21 at 10:23 +0800, Cao TF wrote: > I want to do the 'vc-relax' calculation of bilayer structure of graphene and BN. And only the lattice constant a, b are allowed to change in the relaxation. So I set cell_dofree = 'xy' , but when the calculation finished, the distance of of the vacuum between different by layers also changed. I am not sure that the constraints are implemented for all minimization algorithms. Could you please provide an input and the corresponding output? P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From guntram.schmidt at chemie.uni-halle.de Wed Mar 21 14:21:02 2012 From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt) Date: Wed, 21 Mar 2012 14:21:02 +0100 Subject: [Pw_forum] Rydberg to KJ/mole In-Reply-To: <1332317791.26247.6.camel@fe12lx.fisica.uniud.it> References: <20120321022328.11571.qmail@ms.hfcas.ac.cn> <1332317791.26247.6.camel@fe12lx.fisica.uniud.it> Message-ID: <4F69D5BE.50106@chemie.uni-halle.de> Hello together, I'm sure, this question has been already asked - but lacking a search function for the pw_forum and not having found something using google, I'm urged to ask this question to the list: How do I convert the output of pwscf (which is in Ry) to kJ per mole? Conversion to Joules seems to be not a question, using pen&pencil or some tools (e.g., http://www.chemie.fu-berlin.de/chemistry/general/units_en.html). Do I have to multiply the outcome with the avogadro number to get KJ/mol? If so, I'm wondering about the outcome of my calculations. I have two sets of two polymorphic molecular crystals. The have energy differences of 0.09492046 Ry and 0.21669732 Ry, resp. . This would correspond to ca. 120 and 280 kJ/mole! This would exceed the expected energy differences of polymorphs (10-25 kJ/mole) by one order of magnitude! Did I miss something? Has there some other normalisation to be made? Thanks a lot for help, Guntram From tone.kokalj at ijs.si Wed Mar 21 14:29:52 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 21 Mar 2012 14:29:52 +0100 Subject: [Pw_forum] Rydberg to KJ/mole In-Reply-To: <4F69D5BE.50106@chemie.uni-halle.de> References: <20120321022328.11571.qmail@ms.hfcas.ac.cn> <1332317791.26247.6.camel@fe12lx.fisica.uniud.it> <4F69D5BE.50106@chemie.uni-halle.de> Message-ID: <1332336592.15551.39.camel@catalyst.ijs.si> On Wed, 2012-03-21 at 14:21 +0100, Guntram Schmidt wrote: > Hello together, > > I'm sure, this question has been already asked - but lacking a search > function for the pw_forum and not having found something using google, > I'm urged to ask this question to the list: > > How do I convert the output of pwscf (which is in Ry) to kJ per mole? ? -- 1.0 ry = = 0.5 hartree = 1.0 ry = 13.605691930242388 eV = 1312.7496997450642 kJ/mol = 313.75470835207074 kcal/mol = 2.17987197e-21 kJ = 5.21001904875717e-22 kcal = 2.1798719700000002e-11 erg As a convenience you may use the "unitconv" utility of xcrysden (attached). Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- A non-text attachment was scrubbed... Name: unitconv Type: application/x-shellscript Size: 2488 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120321/c286fe31/attachment.bin From guntram.schmidt at chemie.uni-halle.de Wed Mar 21 14:53:33 2012 From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt) Date: Wed, 21 Mar 2012 14:53:33 +0100 Subject: [Pw_forum] Rydberg to KJ/mole - polymorphs In-Reply-To: <1332336592.15551.39.camel@catalyst.ijs.si> References: <20120321022328.11571.qmail@ms.hfcas.ac.cn> <1332317791.26247.6.camel@fe12lx.fisica.uniud.it> <4F69D5BE.50106@chemie.uni-halle.de> <1332336592.15551.39.camel@catalyst.ijs.si> Message-ID: <4F69DD5D.6090507@chemie.uni-halle.de> Thanks for the fast reply! This leaves me to the problem of the interpretation of the results. Has anyone experience with the calculation of polymorphic molecular crystals? My energy differences of 120 and 240 kJ/mole are far too high for polymorphs (see ?ref [1]). Am I mistaken to equalize the "total energy" of pwscf-output with the "lattice energy" (former "structure energy")? I'm aware of the missing Entropy - but it is told to be negligible small... I do use nc pseudopotentials and my system is composed of triphenylphosphine moities with aminobenzoic acids connected. I'll attach the input lines [2]. Thanks a lot for further assistance, Guntram [1] Gavezzotti, A., & Filippini, G. (1995). Polymorphic Forms of Organic Crystals at Room Conditions: Thermodynamic and Structural Implications. Journal of the American Chemical Society, 117(49), 12299-12305. doi:10.1021/ja00154a032 [2] &control calculation = 'scf', restart_mode='from_scratch', prefix='i2t0491.xyz.50.200', tstress = .true., tprnfor = .true., pseudo_dir = '/pseudo/', outdir='/tmp/i2t0491.xyz.50.200/', verbosity = 'high', / &system ibrav = 14, A = 14.8387, B = 14.8390, C = 18.0441, cosAB = 0, cosAC = 0, cosBC = 0, nat = 392, ntyp = 5, occupations = 'fixed', ecutwfc = 50, ecutrho = 200, input_dft = 'vdW-DF', / &electrons conv_thr = 1.0d-8, electron_maxstep= 1000, / ATOMIC_SPECIES P 1.0 P.rpb-nc.UPF O 1.0 O.rpb-nc.UPF N 1.0 N.rpb-nc.UPF H 1.0 H.rpb-nc.UPF C 1.0 C.rpb-nc.UPF ATOMIC_POSITIONS angstrom C 2.883901 5.973588 10.295242 . . . K_POINTS automatic 1 1 1 0 0 0 Am 21.03.2012 14:29, schrieb Tone Kokalj: > On Wed, 2012-03-21 at 14:21 +0100, Guntram Schmidt wrote: >> Hello together, >> >> I'm sure, this question has been already asked - but lacking a search >> function for the pw_forum and not having found something using google, >> I'm urged to ask this question to the list: >> >> How do I convert the output of pwscf (which is in Ry) to kJ per mole? > > ? > -- > > 1.0 ry = > = 0.5 hartree > = 1.0 ry > = 13.605691930242388 eV > = 1312.7496997450642 kJ/mol > = 313.75470835207074 kcal/mol > = 2.17987197e-21 kJ > = 5.21001904875717e-22 kcal > = 2.1798719700000002e-11 erg > > As a convenience you may use the "unitconv" utility of xcrysden > (attached). > > Regards, Tone > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From alex.kutana at gmail.com Wed Mar 21 17:05:41 2012 From: alex.kutana at gmail.com (Alex Kutana) Date: Wed, 21 Mar 2012 12:05:41 -0400 Subject: [Pw_forum] Rydberg to KJ/mole In-Reply-To: <4F69D5BE.50106@chemie.uni-halle.de> References: <20120321022328.11571.qmail@ms.hfcas.ac.cn> <1332317791.26247.6.camel@fe12lx.fisica.uniud.it> <4F69D5BE.50106@chemie.uni-halle.de> Message-ID: On Wed, Mar 21, 2012 at 9:21 AM, Guntram Schmidt < guntram.schmidt at chemie.uni-halle.de> wrote: > Hello together, > > I'm sure, this question has been already asked - but lacking a search > function for the pw_forum > There is a search function for the pw_forum, although It's well hidden. Here is the URL: http://www.google.com/cse/home?cx=000217952118062629757:xew9tb5yarq Alex -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120321/6f98d051/attachment.htm From bdslipun at gmail.com Wed Mar 21 17:45:14 2012 From: bdslipun at gmail.com (bhabya sahoo) Date: Wed, 21 Mar 2012 22:15:14 +0530 Subject: [Pw_forum] Fwd: phonon dos In-Reply-To: References: Message-ID: ---------- Forwarded message ---------- From: bhabya sahoo Date: Tue, Mar 20, 2012 at 6:26 PM Subject: phonon dos To: PWSCF Forum , giannozz at democritos.it, Axel Kohlmeyer i am calculating vibrational properties using QHA of espresso code i have the fcc structure having 2 atoms in unit cell i get the static energy -147.245069 Ry at zero pressure after that i calculted vibrational properties at zero pressure which is given below my question the out put f_vibrational energy is Ry/Cell so i have to add the f_vibrational energy to the energy at T=0k so whether i add the f_vibr or i have to divide anything in the vibrational energy which will be added to cold energy for my system having NaCl structure SAHOO B D RESERCH SCHOLAR MUMBAI -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120321/b04b3272/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: cd43.QHA.out Type: application/octet-stream Size: 27749 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120321/b04b3272/attachment-0001.obj From giannozz at democritos.it Wed Mar 21 19:14:34 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 21 Mar 2012 19:14:34 +0100 Subject: [Pw_forum] Rydberg to KJ/mole In-Reply-To: References: <20120321022328.11571.qmail@ms.hfcas.ac.cn> <1332317791.26247.6.camel@fe12lx.fisica.uniud.it> <4F69D5BE.50106@chemie.uni-halle.de> Message-ID: On Mar 21, 2012, at 17:05 , Alex Kutana wrote: > There is a search function for the pw_forum, although It's well hidden there are two search functions, both linked and well visible in the "Contacts" page of the QE web site. About the original qeustion: QE calculates total energies per unit cell, in Ry. The absolute value of the energy depends upon the specific set of pseudoppotential and has no physical meaning; energy differences have physical meaning P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed Mar 21 22:41:35 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 21 Mar 2012 22:41:35 +0100 Subject: [Pw_forum] vc-relax In-Reply-To: <4F69B20F.10106@theory.issp.ac.cn> References: <20120321022328.11571.qmail@ms.hfcas.ac.cn> <1332317791.26247.6.camel@fe12lx.fisica.uniud.it> <4F6994A1.1090106@theory.issp.ac.cn> <1332320305.26247.18.camel@fe12lx.fisica.uniud.it> <4F69B20F.10106@theory.issp.ac.cn> Message-ID: <341AF71E-32DA-4E2E-A56A-1F0BE982833C@democritos.it> On Mar 21, 2012, at 11:48 , tfcao at theory.issp.ac.cn wrote: > Thank you very much, I will try in it again in the recent version. >> You are using a rather old version of the code (4.1.1). I am >> not sure if the implementation of constraints was correct >> at that time actually it does not work with the latest version as well, but at least the documentation is correct: var cell_dofree -type CHARACTER { default { 'all' } info { Select which of the cell parameters should be moved: all = all axis and angles are moved x = only the x component of axis 1 (v1_x) is moved y = only the y component of axis 2 (v2_y) is moved z = only the z component of axis 3 (v3_z) is moved xy = only v1_x and v_2y are moved xz = only v1_x and v_3z are moved yz = only v2_x and v_3z are moved xyz = only v1_x, v2_x, v_3z are moved shape = all axis and angles, keeping the volume fixed Beware: if axis are not orthogonal, some of the above options will break symmetry In fact, for hexagonal lattices, symmetry will be broken and the code will stop after the first step. This behavior can be easily changed, though: just edit file Modules/cell_base.f90, locate lines CASE ('xy') iforceh = 0 iforceh(1,1) = 1 iforceh(2,1) = 1 add lines iforceh(1,2) = 1 iforceh(2,1) = 1 P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From spmmal at gmail.com Wed Mar 21 23:35:09 2012 From: spmmal at gmail.com (Caloma Trumica) Date: Wed, 21 Mar 2012 18:35:09 -0400 Subject: [Pw_forum] About DFPT Message-ID: Dear All, When reading the lecture notes about DFPT, I met following similar terms: "star of q", " q star", I was wondering what are they referred to. Do they mean "q*"? Thank you. Andy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120321/8f2ec076/attachment.htm From elie.moujaes at hotmail.co.uk Thu Mar 22 03:36:36 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Thu, 22 Mar 2012 02:36:36 +0000 Subject: [Pw_forum] Fortran compilation error Message-ID: Dear all, Maybe this is a very basic question and might have been asked several times. I am installing QE on yet another server and when I try to configure using ./configure I get the following error: checking build system type... i686-pc-linux-gnuchecking architecture... ia32checking for ifort... nochecking for pgf90... nochecking for pathf95... nochecking for sunf95... nochecking for openf95... nochecking for gfortran... nochecking for g95... nochecking for f90... nochecking for Fortran compiler default output file name...configure: error: Fortran compiler cannot create executablesSee `config.log' for more details. Obviously QE cannot find any of the fortran compilers. I have got gcc but i tried to use options with configure such as ./configure CC=gcc but in vain..I also looked at the config.log file. which is attached to this e-mail but still could not find what is wrong. Any help or guidance is highly appreciated. Elie MoukaesUNiversity of NottsNG7 2RDuk -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120322/6f8cd766/attachment.htm -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: config.log Url: http://www.democritos.it/pipermail/pw_forum/attachments/20120322/6f8cd766/attachment.txt From akohlmey at gmail.com Thu Mar 22 04:02:17 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Wed, 21 Mar 2012 23:02:17 -0400 Subject: [Pw_forum] Fortran compilation error In-Reply-To: References: Message-ID: On Wed, Mar 21, 2012 at 10:36 PM, Elie M wrote: > Dear all, > > Maybe this is a very basic question and might have been asked several times. > I am installing QE on yet another server and when I try to configure using > ./configure I get the following error: > > checking build system type... i686-pc-linux-gnu > checking architecture... ia32 > checking for ifort... no > checking for pgf90... no > checking for pathf95... no > checking for sunf95... no > checking for openf95... no > checking for gfortran... no > checking for g95... no > checking for f90... no > checking for Fortran compiler default output file name... > configure: error: Fortran compiler cannot create executables > See `config.log' for more details. > > > Obviously QE cannot find any of the fortran compilers. I have got gcc but i > tried to use options with configure such as ./configure CC=gcc but in > vain..I also looked at the config.log file. which is attached to this e-mail > but still could not find what is wrong. Any help or guidance is highly > appreciated. that fact that you have gcc doesn't mean that you have to have gfortran or some other fortran compiler installed. you should probably talk to the system manager to get to know if/where a fortran compiler is installed. axel. > Elie Moukaes > UNiversity of Notts > NG7 2RD > uk > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com ?http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA. From guntram.schmidt at chemie.uni-halle.de Thu Mar 22 09:25:22 2012 From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt) Date: Thu, 22 Mar 2012 09:25:22 +0100 Subject: [Pw_forum] Rydberg to KJ/mole In-Reply-To: References: <20120321022328.11571.qmail@ms.hfcas.ac.cn> <1332317791.26247.6.camel@fe12lx.fisica.uniud.it> <4F69D5BE.50106@chemie.uni-halle.de> Message-ID: <4F6AE1F2.3020209@chemie.uni-halle.de> Dear Paolo, that's why, I only quoted and argued on energy differences. However, they seem to be too far away from expectation (10-fold). Is there any normalisation to be made? Dividing by the number of molecules per unit cell (if there is one per asymmetric unit, this would refer to 8 for an orthorombic case, e.g.)? I'm not sure, what the "reference" of the calculated Rydberg value is - if it would be the whole cell, I would get doubled energy values and differences when I calculate a 2x1x1 supercell... The other way round: what does "per mole" really mean in a conversion of "some amount" to "a mole" (e.g.: Joule to Joule/mol)... Thanks for helping me! Am 21.03.2012 19:14, schrieb Paolo Giannozzi: > > On Mar 21, 2012, at 17:05 , Alex Kutana wrote: > >> There is a search function for the pw_forum, although It's well hidden > > there are two search functions, both linked and well visible in the > "Contacts" page of the QE web site. > > About the original qeustion: QE calculates total energies per unit cell, > in Ry. The absolute value of the energy depends upon the specific > set of pseudoppotential and has no physical meaning; energy differences > have physical meaning > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > From Lorenzo.Paulatto at impmc.upmc.fr Thu Mar 22 10:26:13 2012 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Thu, 22 Mar 2012 10:26:13 +0100 Subject: [Pw_forum] Rydberg to KJ/mole - polymorphs In-Reply-To: <4F69DD5D.6090507@chemie.uni-halle.de> References: <20120321022328.11571.qmail@ms.hfcas.ac.cn> <1332317791.26247.6.camel@fe12lx.fisica.uniud.it> <4F69D5BE.50106@chemie.uni-halle.de> <1332336592.15551.39.camel@catalyst.ijs.si> <4F69DD5D.6090507@chemie.uni-halle.de> Message-ID: > My energy differences of 120 and 240 kJ/mole are far too high for > polymorphs (see ?ref [1]). > Am I mistaken to equalize the "total energy" of pwscf-output with the > "lattice energy" (former "structure energy")? > I'm aware of the missing Entropy - but it is told to be negligible > small... I'm not entirely sure I understand your problem; I just want to remind that total energy periodic system does not have any absolute meaning: only energy differences count. So, with what are you comparing the energy of your crystal? As your reference is in kJ/mol your reference could be the homo-atomic molecular phase of the constituents, i.e. O2, N2, H2, and in whetever form C and P are normally bought by a chemistry lab. Another possibility is to compare with isolated atoms, this gives you the binding energy of the crystal. I suspect the details are somewhere in [1]. > I do use nc pseudopotentials and my system is composed of > triphenylphosphine moities with aminobenzoic acids connected. In any case, you MUST use the same pseudopotential and cutoffs when doing the reference calculation for the comparison to be useful. bests -- Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www.impmc.upmc.fr/~paulatto/ mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From giannozz at democritos.it Thu Mar 22 10:37:59 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 22 Mar 2012 10:37:59 +0100 Subject: [Pw_forum] Rydberg to KJ/mole In-Reply-To: <4F6AE1F2.3020209@chemie.uni-halle.de> References: <20120321022328.11571.qmail@ms.hfcas.ac.cn> <1332317791.26247.6.camel@fe12lx.fisica.uniud.it> <4F69D5BE.50106@chemie.uni-halle.de> <4F6AE1F2.3020209@chemie.uni-halle.de> Message-ID: <8F4F4EBD-AEDB-42CA-83F1-5696845ED19A@democritos.it> On Mar 22, 2012, at 9:25 , Guntram Schmidt wrote: > Is there any normalisation to be made? energies are given per unit cell. > if it would be the whole cell, I would get doubled energy > values and differences when I calculate a 2x1x1 supercell... you get doubled energy values. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Thu Mar 22 10:44:02 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 22 Mar 2012 10:44:02 +0100 Subject: [Pw_forum] About DFPT In-Reply-To: References: Message-ID: <370C530E-FC4E-4F2D-B7A5-2737BDFB2248@democritos.it> On Mar 21, 2012, at 23:35 , Caloma Trumica wrote: > "star of q", " q star", > I was wondering what are they referred to. Do they mean "q*"? they mean "the set of q-vectors that are generated by applying all symmetry operations to a given q-vector". It is a basic concept in group theory applied to crystals. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From abdeslam.houari at gmail.com Thu Mar 22 11:13:21 2012 From: abdeslam.houari at gmail.com (Abdeslam HOUARI) Date: Thu, 22 Mar 2012 11:13:21 +0100 Subject: [Pw_forum] Fortran compilation error In-Reply-To: References: Message-ID: Dear Elie; As said by Axel, you must have a 90(95)-FORTRAN compiler installed in your machine to configure and install any (the most of) ab initio code. The configure script tells you that !! However, even though you one FORTRAN compiler installed, you may still encounter the error message "Fortran compiler cannot create executables". In this case, try to modify the configure script in QE/install sub-directory by the specifying the right one somewhere in the file. Good luck Best regards ============================================== Dr. Abdesalem HOUARI ------------------------------------------------------------------------------------------- Department of physics, Theoretical Physics Laboratory University of Bejaia-06000. Algeria. E-mail: abdeslam.houari at univ-bejaia.dz& habdeslam at gmail.com https://sites.google.com/site/houariabdeslam/homepage =============================================== 2012/3/22 Elie M > Dear all, > > Maybe this is a very basic question and might have been asked several > times. I am installing QE on yet another server and when I try to configure > using ./configure I get the following error: > > checking build system type... i686-pc-linux-gnu > checking architecture... ia32 > checking for ifort... no > checking for pgf90... no > checking for pathf95... no > checking for sunf95... no > checking for openf95... no > checking for gfortran... no > checking for g95... no > checking for f90... no > checking for Fortran compiler default output file name... > configure: error: Fortran compiler cannot create executables > See `config.log' for more details. > > > Obviously QE cannot find any of the fortran compilers. I have got gcc but > i tried to use options with configure such as ./configure CC=gcc but in > vain..I also looked at the config.log file. which is attached to this > e-mail but still could not find what is wrong. Any help or guidance is > highly appreciated. > > Elie Moukaes > UNiversity of Notts > NG7 2RD > uk > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120322/74646e83/attachment.htm From eariel99 at gmail.com Thu Mar 22 13:45:51 2012 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Thu, 22 Mar 2012 13:45:51 +0100 Subject: [Pw_forum] Rydberg to kJ/mole Message-ID: >Is there any normalisation to be made? Dividing by the number of molecules per unit cell (if there is one per >asymmetric unit, this would refer to 8 for an orthorombic case, e.g.)? QE gives the energy of the cell defined in the input. >I'm not sure, what the "reference" of the calculated Rydberg value is - if it would be the whole cell, I would get >doubled energy values and differences when I calculate a 2x1x1 supercell... Yes. Yo can make the test. there my be a few details. If you double the cell in X direction, divide by 2 the number of k-points in the first direction. If the number of electron is odd, it may be necessary to do a spin polarised calculation. >The other way round: what does "per mole" really mean in a conversion of "some amount" to "a mole" (e.g.: >Joule to Joule/mol)... Take the energy in Ry, multiply by the number of Avogadro, and convert to kJ. My only doubt is per mole o what ? Moles of supercells, molecules or atoms? I do not know. -- Eduardo Menendez Proupin Departamento de Qu?mica Fisica Aplicada Facultad de Ciencias Universidad Aut?noma de Madrid 28049 Madrid, Spain Phone: +34 91 497 6706 On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de Chile URL: http://fisica.ciencias.uchile.cl/~emenendez -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120322/091af3e1/attachment.htm From kissi at uni-mainz.de Thu Mar 22 14:25:17 2012 From: kissi at uni-mainz.de (Kiss, Ioan) Date: Thu, 22 Mar 2012 13:25:17 +0000 Subject: [Pw_forum] Is variable-cell metadynamics implemented in PWSCF or Plumed? Message-ID: Dear PWSCF community, I have a simple question whether the variable-cell metadynamics is implemented in the PWSCF code. I have head a look on the manual and on the mailing list, and all what I found was that now metadynamics is handled by the external routines of the Plumed package. It would be helpful if you could point me towards a manual or any kind of description regarding how one can perform variable cell metadynamics simulations either with stand-alone PWSCF or with PWSCF combined with Plumed or some similar open-source metaMD driver. By looking at the manual of Plumed I am afraid that such thing is not possible because there are no collective variables implemented for this purpose. Any hints/comments are welcome. Best regards, Janos Kiss. ========================================== Dr. Janos Kiss e-mail: kissi at uni-mainz.de Johannes Gutenberg-Universitaet Institut f. Anorg. u. Analyt. Chemie AK Prof. Dr. Claudia Felser Staudinger Weg 9 / Raum 01-230 55128 Mainz/ Germany Phone: +49-(0)6131-39-22703 Fax: +49-(0)6131-39-26267 Web: http://www.superconductivity.de/ ========================================= From akohlmey at gmail.com Thu Mar 22 14:32:57 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Thu, 22 Mar 2012 09:32:57 -0400 Subject: [Pw_forum] Is variable-cell metadynamics implemented in PWSCF or Plumed? In-Reply-To: References: Message-ID: On Thu, Mar 22, 2012 at 9:25 AM, Kiss, Ioan wrote: > Dear PWSCF community, > > I have a simple question whether the variable-cell metadynamics > is implemented in the PWSCF code. I have head a look on the manual > and on the ?mailing list, and all what I found was that now metadynamics > is handled by the external routines of the Plumed package. > > It would be helpful if you could point me towards a manual or any kind > of description regarding how one can perform variable cell metadynamics > simulations either with stand-alone PWSCF or with PWSCF combined with > Plumed or some similar open-source metaMD driver. > By looking at the manual of Plumed I am afraid that such thing is not possible > because there are no collective variables implemented for this purpose. hi janos, i guess you're stuck with CPMD and finding a big machine so you can afford norm-conserving pseudo potentials and converged stress tensor... cheers, axel. > > Any hints/comments are welcome. > > Best regards, > Janos Kiss. > > ========================================== > ?Dr. Janos Kiss ? ? ?e-mail: kissi at uni-mainz.de > ?Johannes Gutenberg-Universitaet > ?Institut f. Anorg. u. Analyt. Chemie > ?AK Prof. Dr. Claudia Felser > ?Staudinger Weg 9 / Raum 01-230 > ?55128 Mainz/ Germany > ?Phone: +49-(0)6131-39-22703 > ?Fax: ? ? +49-(0)6131-39-26267 > ?Web: ? ? http://www.superconductivity.de/ > ?========================================= > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com ?http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA. From pandey.bramha at gmail.com Thu Mar 22 14:38:56 2012 From: pandey.bramha at gmail.com (bramha pandey) Date: Thu, 22 Mar 2012 19:08:56 +0530 Subject: [Pw_forum] Small value of stress at equilibrium (T=0,P=0) Message-ID: Dear all, I am using AlN with zincblede structure using USPP (PBE xc). After completing convergence test of ecut and k-point, i calculated the equilibrium lattice constant(at T=0, P=0). But i wondered if i put this equilibrium lattice constant in calculation i got, small value of stress(-7.36kbar). i know this is Pulay stress and think it may be zero (may be i am wrong if so please correct me) at equilibrium but here it is not the case. i want to know whether this will affect the other property like bulk modulus, lattice constant calculation etc at different pressure and temperature. How can i fix it. Your valuable comment is highly aappriciable. -- Thanks and Regards Bramha Prasad Pandey GLA University, Mathura. INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120322/1f71483e/attachment-0001.htm From eariel99 at gmail.com Thu Mar 22 14:49:35 2012 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Thu, 22 Mar 2012 14:49:35 +0100 Subject: [Pw_forum] Small value of stress at equilibrium (T=0,P=0) Message-ID: Relax again from the last structure and you should get smaller residual stress. Otherwise, increase the cutoffs. Please, read this http://www.quantum-espresso.org/wiki/index.php/Methodological_Background#Stress Stress smaller than 10 kbar in a solid generally have little effect. Eduardo Menendez Proupin Departamento de Qu?mica Fisica Aplicada Facultad de Ciencias Universidad Aut?noma de Madrid 28049 Madrid, Spain Phone: +34 91 497 6706 ---------- Mensaje reenviado ---------- From: bramha pandey To: PWSCF Forum Cc: Date: Thu, 22 Mar 2012 19:08:56 +0530 Subject: [Pw_forum] Small value of stress at equilibrium (T=0,P=0) Dear all, I am using AlN with zincblede structure using USPP (PBE xc). After completing convergence test of ecut and k-point, i calculated the equilibrium lattice constant(at T=0, P=0). But i wondered if i put this equilibrium lattice constant in calculation i got, small value of stress(-7.36kbar). i know this is Pulay stress and think it may be zero (may be i am wrong if so please correct me) at equilibrium but here it is not the case. i want to know whether this will affect the other property like bulk modulus, lattice constant calculation etc at different pressure and temperature. How can i fix it. Your valuable comment is highly aappriciable. -- Thanks and Regards Bramha Prasad Pandey GLA University, Mathura. INDIA. -- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120322/30ace243/attachment.htm From elie.moujaes at hotmail.co.uk Thu Mar 22 15:03:05 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Thu, 22 Mar 2012 14:03:05 +0000 Subject: [Pw_forum] Fortran compilation error In-Reply-To: References: , Message-ID: Thank you all for your help. Problem sorted. Elie Date: Thu, 22 Mar 2012 11:13:21 +0100 Subject: Re: [Pw_forum] Fortran compilation error From: abdeslam.houari at gmail.com To: elie.moujaes at hotmail.co.uk CC: pw_forum at pwscf.org Dear Elie; As said by Axel, you must have a 90(95)-FORTRAN compiler installed in your machine to configure and install any (the most of) ab initio code. The configure script tells you that !! However, even though you one FORTRAN compiler installed, you may still encounter the error message "Fortran compiler cannot create executables". In this case, try to modify the configure script in QE/install sub-directory by the specifying the right one somewhere in the file. Good luckBest regards ============================================== Dr. Abdesalem HOUARI------------------------------------------------------------------------------------------- Department of physics, Theoretical Physics LaboratoryUniversity of Bejaia-06000. Algeria. E-mail: abdeslam.houari at univ-bejaia.dz & habdeslam at gmail.com https://sites.google.com/site/houariabdeslam/homepage=============================================== 2012/3/22 Elie M Dear all, Maybe this is a very basic question and might have been asked several times. I am installing QE on yet another server and when I try to configure using ./configure I get the following error: checking build system type... i686-pc-linux-gnuchecking architecture... ia32checking for ifort... nochecking for pgf90... nochecking for pathf95... no checking for sunf95... nochecking for openf95... nochecking for gfortran... nochecking for g95... nochecking for f90... nochecking for Fortran compiler default output file name... configure: error: Fortran compiler cannot create executablesSee `config.log' for more details. Obviously QE cannot find any of the fortran compilers. I have got gcc but i tried to use options with configure such as ./configure CC=gcc but in vain..I also looked at the config.log file. which is attached to this e-mail but still could not find what is wrong. Any help or guidance is highly appreciated. Elie MoukaesUNiversity of NottsNG7 2RDuk _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120322/55546881/attachment.htm From elie.moujaes at hotmail.co.uk Thu Mar 22 15:07:38 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Thu, 22 Mar 2012 14:07:38 +0000 Subject: [Pw_forum] error in reading namelist system Message-ID: Dear all, I am trying to run an scf calculation but the code complains: " from read_namelists : error # 19 reading namelist system" I have checked into my &system but could not find anything wrong. "&control prefix='elphmono', calculation='scf', restart_mode='from_scratch', verbosity='high', tprnfor=.true., pseudo_dir = '/home_cluster/fis718/eliemouj/espresso-4.3.2/pseudo', outdir='/home_cluster/fis718/eliemouj/espresso-4.3.2/monographene/MONODIR', / &system ibrav= 4, celldm(1) =4.608737, celldm(3)=4.53666, nat=2, ntyp= 1, ecutwfc =32, occupations='smearing', smearing='methfessel-paxton', degauss=0.01, la2F=.true. / &electrons conv_thr=1.D-9, mixing_beta=0.1D0, / ATOMIC_SPECIES C 12.0107 C.pbe-rrkjus.UPF ATOMIC_POSITIONS crystalC 0.000000 0.000000 0.000000C 0.333333 -0.333333 0.000000 K_POINTS {automatic}50 50 1 0 0 0 "Can anyone spot anything wrong with it. Thank you all Elie MoukaesUniversity of NottinghamNG7 2RDUK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120322/425eda36/attachment.htm From renpj at dicp.ac.cn Thu Mar 22 15:23:06 2012 From: renpj at dicp.ac.cn (PJ Ren) Date: Thu, 22 Mar 2012 22:23:06 +0800 Subject: [Pw_forum] Starting charge for hydrogen using different PP In-Reply-To: <4F68A4D3.6050006@dicp.ac.cn> References: <4F68A4D3.6050006@dicp.ac.cn> Message-ID: <4F6B35CA.2090006@dicp.ac.cn> Could anyone tell me whether these PPs of Hydrogen is right or wrong? On 03/20/2012 11:40 PM, PJ Ren wrote: > Dear all, > > I have tested some hydrogen PP by calculating the hydrogen molecule. I > found that for some PPs the starting charge was not very close to two as > I respected. The results: > H.pbe-rrkjus.UPF : starting charge 1.80759 > H.pz-rrkjus.UPF : starting charge 1.81576 > H.pbe-tm-gipaw.UPF: starting charge 0.20000 > But all the case were renormalised to 2.00000. I don't know whether it > is right or wrong. > > The last PP was copy from GIPAW example. > > Thanks. > > PJ Ren > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From akohlmey at gmail.com Thu Mar 22 15:25:22 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Thu, 22 Mar 2012 10:25:22 -0400 Subject: [Pw_forum] Starting charge for hydrogen using different PP In-Reply-To: <4F6B35CA.2090006@dicp.ac.cn> References: <4F68A4D3.6050006@dicp.ac.cn> <4F6B35CA.2090006@dicp.ac.cn> Message-ID: On Thu, Mar 22, 2012 at 10:23 AM, PJ Ren wrote: > Could anyone tell me whether these PPs of Hydrogen is right or wrong? the value of the starting charge has no relation to the correctness of the potential. axel. > > On 03/20/2012 11:40 PM, PJ Ren wrote: >> Dear all, >> >> I have tested some hydrogen PP by calculating the hydrogen molecule. I >> found that for some PPs the starting charge was not very close to two as >> I respected. The results: >> H.pbe-rrkjus.UPF : ? ? ? ? ?starting charge ? ?1.80759 >> H.pz-rrkjus.UPF : ? ? ? ? ? ? starting charge ? ?1.81576 >> H.pbe-tm-gipaw.UPF: ? ? starting charge ? ?0.20000 >> But all the case were renormalised to 2.00000. I don't know whether it >> is right or wrong. >> >> The last PP was copy from GIPAW example. >> >> Thanks. >> >> PJ Ren >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com ?http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA. From avallabh at purdue.edu Thu Mar 22 15:25:38 2012 From: avallabh at purdue.edu (Ajit Vallabhaneni) Date: Thu, 22 Mar 2012 10:25:38 -0400 (EDT) Subject: [Pw_forum] error in reading namelist system In-Reply-To: Message-ID: <14534768.45339.1332426338397.JavaMail.root@mailhub016.itcs.purdue.edu> Elie, I am able to run your script with out any errors. Please check the names of pseudo_dir and out_dir in your file. Thanks Ajit From elie.moujaes at hotmail.co.uk Thu Mar 22 16:17:54 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Thu, 22 Mar 2012 15:17:54 +0000 Subject: [Pw_forum] error in reading namelist system In-Reply-To: <14534768.45339.1332426338397.JavaMail.root@mailhub016.itcs.purdue.edu> References: , <14534768.45339.1332426338397.JavaMail.root@mailhub016.itcs.purdue.edu> Message-ID: There is nothing wrong with the pseudo_dir or outdir otherwise it would have complained that the directory does not exist. This is really weird. I cannot find any errors in the &system part Elie > Date: Thu, 22 Mar 2012 10:25:38 -0400 > From: avallabh at purdue.edu > To: elie.moujaes at hotmail.co.uk > CC: pw_forum at pwscf.org > Subject: Re: [Pw_forum] error in reading namelist system > > Elie, > > I am able to run your script with out any errors. Please check the names of pseudo_dir and out_dir in your file. > > Thanks > Ajit -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120322/6023a95b/attachment-0001.htm From gabriele.sclauzero at epfl.ch Thu Mar 22 17:54:04 2012 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Thu, 22 Mar 2012 17:54:04 +0100 Subject: [Pw_forum] error in reading namelist system In-Reply-To: References: Message-ID: <29F38135-EE75-490D-8C43-B02D915F2768@epfl.ch> Dear Elie, are you sure that this la2F keyword is part of the pw.x &system namelist? Anyway, it's always good practice to specify which version of QE you are using as well as the compiler. If you are using version 4.3.2 with some versions of the Intel 12.x.x compiler, there could be some problems with the new handling of the input files. Indeed, what I have observed is that lines longer than 80 characters are split when the original input is copied to the input_tmp.in file. This can possibly lead to a wrong interpretation of your input. Is this the case for you? HTH GS Il giorno 22/mar/2012, alle ore 15.07, Elie M ha scritto: > Dear all, > > I am trying to run an scf calculation but the code complains: > > " from read_namelists : error # 19 > reading namelist system" > > I have checked into my &system but could not find anything wrong. > > "&control > prefix='elphmono', > calculation='scf', > restart_mode='from_scratch', > verbosity='high', > tprnfor=.true., > pseudo_dir = '/home_cluster/fis718/eliemouj/espresso-4.3.2/pseudo', > outdir='/home_cluster/fis718/eliemouj/espresso-4.3.2/monographene/MONODIR', > > / > &system > ibrav= 4, celldm(1) =4.608737, celldm(3)=4.53666, nat=2, ntyp= 1, ecutwfc =32, occupations='smearing', smearing='methfessel-paxton', degauss=0.01, la2F=.true. > > / > &electrons > conv_thr=1.D-9, > mixing_beta=0.1D0, > > / > > ATOMIC_SPECIES > C 12.0107 C.pbe-rrkjus.UPF > > ATOMIC_POSITIONS crystal > C 0.000000 0.000000 0.000000 > C 0.333333 -0.333333 0.000000 > > K_POINTS {automatic} > 50 50 1 0 0 0 " > Can anyone spot anything wrong with it. Thank you all > > Elie Moukaes > University of Nottingham > NG7 2RD > UK > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120322/bfda29f2/attachment.htm From pandey.bramha at gmail.com Thu Mar 22 18:39:57 2012 From: pandey.bramha at gmail.com (bramha pandey) Date: Thu, 22 Mar 2012 23:09:57 +0530 Subject: [Pw_forum] Small value of stress at equilibrium (T=0,P=0) In-Reply-To: References: Message-ID: Thank you Eduardo Menendez Proupin Sir.. i have fixed it with meaningful results with your help. thanks once again to you and all pw users. On Thu, Mar 22, 2012 at 7:19 PM, Eduardo Ariel Menendez Proupin < eariel99 at gmail.com> wrote: > Relax again from the last structure and you should get smaller residual > stress. Otherwise, increase the cutoffs. > Please, read this > > http://www.quantum-espresso.org/wiki/index.php/Methodological_Background#Stress > > Stress smaller than 10 kbar in a solid generally have little effect. > > Eduardo Menendez Proupin > Departamento de Qu?mica Fisica Aplicada > Facultad de Ciencias > Universidad Aut?noma de Madrid > 28049 Madrid, Spain > Phone: +34 91 497 6706 > > > > ---------- Mensaje reenviado ---------- > From: bramha pandey > To: PWSCF Forum > Cc: > Date: Thu, 22 Mar 2012 19:08:56 +0530 > Subject: [Pw_forum] Small value of stress at equilibrium (T=0,P=0) > > Dear all, > I am using AlN with zincblede structure using USPP (PBE xc). > After completing convergence test of ecut and k-point, i calculated the > equilibrium lattice constant(at T=0, P=0). > But i wondered if i put this equilibrium lattice constant in calculation i > got, small value of stress(-7.36kbar). > i know this is Pulay stress and think it may be zero (may be i am wrong if > so please correct me) at equilibrium but here it is not the case. > i want to know whether this will affect the other property like bulk > modulus, lattice constant calculation etc at different pressure and > temperature. > How can i fix it. > Your valuable comment is highly aappriciable. > > -- > Thanks and Regards > Bramha Prasad Pandey > GLA University, Mathura. > INDIA. > > -- > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Thanks and Regards Bramha Prasad Pandey GLA University, Mathura. INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120322/ad4c1bdd/attachment.htm From csatya11 at gmail.com Fri Mar 23 04:27:29 2012 From: csatya11 at gmail.com (satyananda chab) Date: Fri, 23 Mar 2012 08:57:29 +0530 Subject: [Pw_forum] segmentation fault Message-ID: Dear all, When I tried to run the Ecut convergence test for Co2NiGa system , I got segmentation errors like this: writing the input file doing calculation for Ecut = 50 running pw.x ./run_varyEcut: line 38: 2299 Segmentation fault pw.x < input/Co2NiGa$Ecut.in > output/Co2NiGa_$Ecut.out pw.x ends and my input file line numbber 38 is: for $Ecut in 35 40 45 50 55 60 If someone in this forum can give me some solutions, I will be thankfull to you. Satyananda Chabungbam Gauhati University India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120323/c2c6ae60/attachment.htm From giannozz at democritos.it Fri Mar 23 09:18:58 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 23 Mar 2012 09:18:58 +0100 Subject: [Pw_forum] segmentation fault In-Reply-To: References: Message-ID: <1332490738.16181.3.camel@fe12lx.fisica.uniud.it> On Fri, 2012-03-23 at 08:57 +0530, satyananda chab wrote: > I got segmentation errors http://www.quantum-espresso.org/user_guide/node52.html#SECTION000121090000000000000 > If someone in this forum can give me some solutions, nobody can P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From eariel99 at gmail.com Fri Mar 23 18:10:10 2012 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Fri, 23 Mar 2012 18:10:10 +0100 Subject: [Pw_forum] runtime error for GWW in example01-benzene Message-ID: Hi, I have found runtime errors running pw4gww.x in the example01 (benzene) when the code is compiled with gfortran, either serially or parallel. Using Intel compiler and OpenMPI bilt with Intel compilers, the problem is solved. I report this error because of my system is quite extended, I guess, and allows the easiest installation. Before this problem, in the same machine, I had used the phonon, TDDFT, and epsilon programs without any problem. Follows the stdout and stderr output ........ 114 10.578069863696490 115 10.626629777342377 FUNCTION WFC_REAL IBND: 1 lbound and ubound of psic: 1 884736 before after *** glibc detected *** ../../../../bin/pw4gww.x: malloc(): memory corruption: 0x00000000024614d0 *** ======= Backtrace: ========= /lib/x86_64-linux-gnu/libc.so.6(+0x7a87a)[0x7fc65433487a] /lib/x86_64-linux-gnu/libc.so.6(__libc_malloc+0x6e)[0x7fc654336e1e] /usr/lib/x86_64-linux-gnu/libgfortran.so.3(+0x167c9)[0x7fc654b007c9] /usr/lib/x86_64-linux-gnu/libgfortran.so.3(+0xa3a90)[0x7fc654b8da90] /usr/lib/x86_64-linux-gnu/libgfortran.so.3(+0xb0800)[0x7fc654b9a800] ../../../../bin/pw4gww.x[0x582b3e] ../../../../bin/pw4gww.x[0x5974a7] ../../../../bin/pw4gww.x[0x43c0ce] ../../../../bin/pw4gww.x[0x411e63] ../../../../bin/pw4gww.x[0x404ad6] ..........(enough, I guess) My system is Ubuntu 11.04 Linux version 2.6.38-13-generic (buildd at yellow) (gcc version 4.5.2 (Ubuntu/Linaro 4.5.2-8ubuntu4) ) #56-Ubuntu SMP Tue Feb 14 12:39:59 UTC 2012 gcc version 4.5.2 I hope it helps -- Eduardo Menendez Proupin Departamento de Qu?mica Fisica Aplicada Facultad de Ciencias Universidad Aut?noma de Madrid 28049 Madrid, Spain Phone: +34 91 497 6706 On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de Chile URL: http://fisica.ciencias.uchile.cl/~emenendez "*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices, pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n que le es otorgada. Pero la grandeza del hombre est? precisamente en querer mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay grandeza que conquistar, puesto que all? todo es jerarqu?a establecida, inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio, reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar su grandeza, su m?xima medida en el Reino de este Mundo*". Alejo Carpentier, El reino de este mundo, (1949). "...man never knows for who he suffers and waits. He suffers and waits and works for peoples he will never meet, and who at the same time will suffer and wait and work for others who will also not be happy, as man always desires a happiness that is beyond the lot that he is given. But the greatness of man is precisely in wanting to improve what he is. In assigning himself Tasks. In the Kingdom of Heaven there is no greatness to conquer, for everything there is an established hierarchy, the unknown is unobscured, existence is without end, sacrifice, rest, and delight are impossibilities. Therefore, overwhelmed with hardships and Tasks, beautiful within his misery, capable of loving in the middle of calamity, man can only find his greatness, his full self-realization, in the Kingdom of this World." - Alejo Carpentier -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120323/719f14f3/attachment.htm From trambui at u.boisestate.edu Sat Mar 24 00:20:59 2012 From: trambui at u.boisestate.edu (Tram Bui) Date: Fri, 23 Mar 2012 17:20:59 -0600 Subject: [Pw_forum] problems with band structure calculations for SiC between ibrav 2 and ibrav 0 Message-ID: Dear QE users, I did a band structure calculation for bulk 3C-SiC (zincblend structure) using ibrav=2, and using high K_points of FCC's BZ including :K, gamma, X, L, U and W. I got a good band structure with indirect band gap from gamma to X point (which agree well with literature). However, I did the same calculation process using ibrav=0 to confirm my band structure, now I used k-point path of simple cubic BZ including : X,M,R, and gamma points. But my band structure do not seem to be correct. I have attached the input files and the plots of band structure for two cases here for your review. Please let me know what I did wrong. If you need more information, please also let me know. I really look forward for any suggestion you can give me. Best regards, Tram Bui M.S. Materials Science & Engineering trambui at u.boisestate.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120323/b56aec17/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: band.in Type: application/octet-stream Size: 1112 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120323/b56aec17/attachment-0002.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: bands.ps Type: application/postscript Size: 20528 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120323/b56aec17/attachment-0002.ps -------------- next part -------------- A non-text attachment was scrubbed... Name: newband.in Type: application/octet-stream Size: 1176 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120323/b56aec17/attachment-0003.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: newbands.ps Type: application/postscript Size: 42480 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120323/b56aec17/attachment-0003.ps From pandey.bramha at gmail.com Sat Mar 24 05:35:08 2012 From: pandey.bramha at gmail.com (bramha pandey) Date: Sat, 24 Mar 2012 10:05:08 +0530 Subject: [Pw_forum] Consideration of Temperature in equilibrium system(T=0, P=0) Message-ID: Dear All, I want to incorporate the temperature effect in my calculation. As i know for this purpose firstly i have to compute the free energy and then this free energy is added to the ground state total energy(T=0,P=0). then by the equation of state we have to find out the lattice parameter. But i am wonder if i am trying to fit eos, it will give the equilibrium lattice parameter not the temperature dependent lattice parameter. Please let me know whether i am proceeding wrong way if so then how can i obtained my lattice parameter which is dependent upon temperature? Any type of help is highly appreciable . -- Thanks and Regards Bramha Prasad Pandey GLA University, Mathura. INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120324/cd8a3716/attachment.htm From nicola.marzari at epfl.ch Sat Mar 24 11:32:55 2012 From: nicola.marzari at epfl.ch (Nicola Marzari) Date: Sat, 24 Mar 2012 11:32:55 +0100 Subject: [Pw_forum] Consideration of Temperature in equilibrium system(T=0, P=0) In-Reply-To: References: Message-ID: <4F6DA2D7.4020206@epfl.ch> Here it is: http://arxiv.org/abs/1112.4977v1 Thermal properties of materials from ab-initio quasi-harmonic phonons Stefano Baroni, Paolo Giannozzi, Eyvaz Isaev nicola On 24/03/2012 05:35, bramha pandey wrote: > Dear All, > I want to incorporate the temperature effect in my calculation. As i > know for this purpose firstly i have to compute the free energy and then > this free energy is added to the ground state total energy(T=0,P=0). > then by the equation of state we have to find out the lattice parameter. > But i am wonder if i am trying to fit eos, it will give the equilibrium > lattice parameter not the temperature dependent lattice parameter. > Please let me know whether i am proceeding wrong way if so then how can > i obtained my lattice parameter which is dependent upon temperature? > Any type of help is highly appreciable . > > -- > Thanks and Regards > Bramha Prasad Pandey > GLA University, Mathura. > INDIA. > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ---------------------------------------------------------------------- Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL From victormengwa at gmail.com Sat Mar 24 13:28:34 2012 From: victormengwa at gmail.com (Victor Meng'wa) Date: Sat, 24 Mar 2012 15:28:34 +0300 Subject: [Pw_forum] problem with relax convergence in SnO2(110) surface calculation Message-ID: Dear QE users, am trying to relax 3 layer SnO2 (110) surface supercell of 52 atoms but the calculation does not converge .i've tried this for the last 3 weeks but unsuccesful. varied several parameters in the input file but the problem persists. i experienced an error from checkallsym : error # 1 some of the original symmetry operations not satisfied but included nosym=.true. the problem didn't recur but still no convergence The bottom atoms are fixed. my kpoints and ecut are reduced to ensure fast convergence, once the problem is fixed i will adjust them. here is the input file please welcome any assistance on this. &CONTROL restart_mode='from_scratch', calculation='relax', outdir='./', pseudo_dir='/home/mikeat/Applications/espresso-4.3.2/pseudo/', prefix = 'SnOru_exc1', tstress = .t., tprnfor = .t., etot_conv_thr = 1.d-5, forc_conv_thr = 1.d-4 verbosity = 'high' / &SYSTEM ibrav=6, celldm(1)=44.7607, celldm(3)=0.5084, nat= 52, ntyp= 2, ecutwfc =10,ecutrho = 120, occupations='smearing', smearing='marzari-vanderbilt', degauss=0.07 nosym = .true. / &ELECTRONS diagonalization = 'david' mixing_mode = 'local-TF', mixing_beta = 0.3, conv_thr = 1.0e-8, / &IONS / ATOMIC_SPECIES Sn 50.011 Sn.pw91-n-van.UPF O 15.9994 O.pw91- van_ak.UPF ATOMIC_POSITIONS {bohr} Sn 8.952203138 26.85642044 -0.000000000 Sn 8.952203138 26.85642044 6.021425723 Sn 17.90421730 26.85642044 -0.000000000 Sn 17.90421730 26.85642044 6.021425723 Sn 13.42821022 22.38041336 3.010712862 Sn 13.42821022 22.38041336 9.032138585 Sn 8.952203138 35.80862358 -0.000000000 Sn 8.952203138 35.80862358 6.021425723 Sn 17.90421730 35.80862358 -0.000000000 0 0 0 Sn 17.90421730 35.80862358 6.021425723 0 0 0 Sn 4.476007083 31.33242752 3.010712862 Sn 4.476007083 31.33242752 9.032138585 Sn 13.42821022 31.33242752 3.010712862 Sn 13.42821022 31.33242752 9.032138585 Sn 22.38041336 31.33242752 3.010712862 0 0 0 Sn 22.38041336 31.33242752 9.032138585 0 0 0 Sn 13.42821022 40.28463066 3.010712862 0 0 0 Sn 13.42821022 40.28463066 9.032138585 0 0 0 O 11.70043294 29.60483921 -0.000000000 O 11.70043294 29.60483921 6.021425723 O 20.65263607 29.60483921 -0.000000000 0 0 0 O 15.155987510 24.10819064 -0.000000000 0 0 0 O 20.65263607 29.60483921 6.021425723 0 0 0 O 15.155987510 24.10819064 6.021425723 0 0 0 O 10.67998042 25.12864316 3.010712862 O 7.224425854 28.58419773 3.010712862 O 7.224425854 28.58419773 9.032138585 O 10.67998042 25.12864316 9.032138585 O 16.17644002 28.58419773 3.010712862 O 16.17644002 28.58419773 9.032138585 O 11.70043294 38.55685338 -0.000000000 O 6.203784367 33.06020481 -0.000000000 O 11.70043294 38.55685338 6.021425723 O 6.203784367 33.06020481 6.021425723 O 15.155987510 33.06020481 -0.000000000 O 15.155987510 33.06020481 6.021425723 O 10.679980420 34.0808463 3.010712862 O 10.679980420 34.0808463 9.032138585 O 19.631994590 34.0808463 3.010712862 O 19.631994590 34.0808463 9.032138585 O 16.176440020 37.53640086 3.010712862 O 16.176440020 37.53640086 9.032138585 Sn 8.952203138 26.85642044 12.04285145 Sn 17.90421730 26.85642044 12.04285145 Sn 8.952203138 35.80862358 12.04285145 Sn 17.90421730 35.80862358 12.04285145 0 0 0 O 11.70043294 29.60483921 12.04285145 O 20.65263607 29.60483921 12.04285145 0 0 0 O 15.15598751 24.10819064 12.04285145 0 0 0 O 11.70043294 38.55685338 12.04285145 O 6.203784367 33.06020481 12.04285145 O 15.15598751 33.06020481 12.04285145 K_POINTS {automatic} 2 2 3 0 0 0 VICTOR KIRUI MENG'WA,MSC STUDENT CHEPKOILEL UNIVERSITY COLLEGE, COMPUTATIONAL PHYSICS GROUP, ELDORET, KENYA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120324/54cf6f85/attachment.htm From pandey.bramha at gmail.com Sat Mar 24 19:49:38 2012 From: pandey.bramha at gmail.com (bramha pandey) Date: Sun, 25 Mar 2012 00:19:38 +0530 Subject: [Pw_forum] Consideration of Temperature in equilibrium system(T=0, P=0) In-Reply-To: <4F6DA2D7.4020206@epfl.ch> References: <4F6DA2D7.4020206@epfl.ch> Message-ID: Dear Dr. Stefano and Dr. Nicola Marzari thanks for your quick reply. Actualy i have calculated the Helmholtz free energy (F) which is given as F(V, T) = E0(V) + Fvib (V, T). The Fvib(V, T) is calculated by PH/fqha.x utility and E0(V) is the equilibrium ground state energy which is calculated by pw.x. it is stated in a research paper>>>>For a given T and V, the equilibrium state of the crystal is determined by minimising F with respect to all possible degrees of freedom. The equation of state (pressure (P) versus V) of the system is obtained by equating P to minus the derivative of F with respect to V at constant T, or P = ? (?F/?V)T <<<<<< Sir i was tried for QHA package in QE as given paper http://arxiv.org/abs/1112.4977v1 , it is using the QHA pakage which is not well understood by me and also this was giving wrong result but it was ok with PH/fqha.x. Please show me the ray of light regarding Helmholtz free energy (F) which is the base root of all thermodynamics property describe by one paper http://iopscience.iop.org/0953-8984/24/3/035401 for your kind reference. Any comment in any form is appreciable. 2012/3/24 Nicola Marzari > > Here it is: > > http://arxiv.org/abs/1112.**4977v1 > Thermal properties of materials from ab-initio quasi-harmonic phonons > Stefano Baroni, Paolo Giannozzi, Eyvaz Isaev > > nicola > > > > On 24/03/2012 05:35, bramha pandey wrote: > >> Dear All, >> I want to incorporate the temperature effect in my calculation. As i >> know for this purpose firstly i have to compute the free energy and then >> this free energy is added to the ground state total energy(T=0,P=0). >> then by the equation of state we have to find out the lattice parameter. >> But i am wonder if i am trying to fit eos, it will give the equilibrium >> lattice parameter not the temperature dependent lattice parameter. >> Please let me know whether i am proceeding wrong way if so then how can >> i obtained my lattice parameter which is dependent upon temperature? >> Any type of help is highly appreciable . >> >> -- >> Thanks and Regards >> Bramha Prasad Pandey >> GLA University, Mathura. >> INDIA. >> >> >> >> ______________________________**_________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/**mailman/listinfo/pw_forum >> > > > -- > > ------------------------------**------------------------------**---------- > Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL > -- Thanks and Regards Bramha Prasad Pandey GLA University, Mathura. INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120325/535c17f4/attachment.htm From giannozz at democritos.it Sat Mar 24 22:09:34 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 24 Mar 2012 22:09:34 +0100 Subject: [Pw_forum] problem with relax convergence in SnO2(110) surface calculation In-Reply-To: References: Message-ID: On Mar 24, 2012, at 13:28 , Victor Meng'wa wrote: > ecutwfc =10, ecutrho = 120, too small > from checkallsym : error # 1 > some of the original symmetry operations not satisfied > [...] > Sn 17.90421730 35.80862358 -0.000000000 0 0 0 > Sn 17.90421730 35.80862358 6.021425723 0 0 0 > [...] constraining atoms may break the symmetry. If so, the code will complain after the first force calculation P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From flux_ray12 at 163.com Sun Mar 25 06:15:26 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Sun, 25 Mar 2012 12:15:26 +0800 (CST) Subject: [Pw_forum] error in reading namelist system In-Reply-To: <29F38135-EE75-490D-8C43-B02D915F2768@epfl.ch> References: <29F38135-EE75-490D-8C43-B02D915F2768@epfl.ch> Message-ID: <3883bf2a.2902.1364810db50.Coremail.flux_ray12@163.com> Dear Gabriele: I am afraid it has to be if one wanted to calculate electron-phonon interactions, although la2F is not mentioned in INPUT_PW and PWgui. This parameter helps to form a la2F data file in outdir from SCF and will be used by ph.x once setting elph = .true. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-03-23 00:54:04,"Gabriele Sclauzero" wrote: Dear Elie, are you sure that this la2F keyword is part of the pw.x &system namelist? Anyway, it's always good practice to specify which version of QE you are using as well as the compiler. If you are using version 4.3.2 with some versions of the Intel 12.x.x compiler, there could be some problems with the new handling of the input files. Indeed, what I have observed is that lines longer than 80 characters are split when the original input is copied to the input_tmp.in file. This can possibly lead to a wrong interpretation of your input. Is this the case for you? HTH GS Il giorno 22/mar/2012, alle ore 15.07, Elie M ha scritto: Dear all, I am trying to run an scf calculation but the code complains: " from read_namelists : error # 19 reading namelist system" I have checked into my &system but could not find anything wrong. "&control prefix='elphmono', calculation='scf', restart_mode='from_scratch', verbosity='high', tprnfor=.true., pseudo_dir = '/home_cluster/fis718/eliemouj/espresso-4.3.2/pseudo', outdir='/home_cluster/fis718/eliemouj/espresso-4.3.2/monographene/MONODIR', / &system ibrav= 4, celldm(1) =4.608737, celldm(3)=4.53666, nat=2, ntyp= 1, ecutwfc =32, occupations='smearing', smearing='methfessel-paxton', degauss=0.01, la2F=.true. / &electrons conv_thr=1.D-9, mixing_beta=0.1D0, / ATOMIC_SPECIES C 12.0107 C.pbe-rrkjus.UPF ATOMIC_POSITIONS crystal C 0.000000 0.000000 0.000000 C 0.333333 -0.333333 0.000000 K_POINTS {automatic} 50 50 1 0 0 0 " Can anyone spot anything wrong with it. Thank you all Elie Moukaes University of Nottingham NG7 2RD UK _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120325/6096e0d8/attachment-0001.htm From flux_ray12 at 163.com Sun Mar 25 06:09:39 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Sun, 25 Mar 2012 12:09:39 +0800 (CST) Subject: [Pw_forum] error in reading namelist system In-Reply-To: References: , <14534768.45339.1332426338397.JavaMail.root@mailhub016.itcs.purdue.edu> Message-ID: <25941b3.2870.136480b9277.Coremail.flux_ray12@163.com> How about adding a "," after la2F = .true. as: &system ... la2F = .true. , / -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-03-22 23:17:54,"Elie M" wrote: There is nothing wrong with the pseudo_dir or outdir otherwise it would have complained that the directory does not exist. This is really weird. I cannot find any errors in the &system part Elie > Date: Thu, 22 Mar 2012 10:25:38 -0400 > From: avallabh at purdue.edu > To: elie.moujaes at hotmail.co.uk > CC: pw_forum at pwscf.org > Subject: Re: [Pw_forum] error in reading namelist system > > Elie, > > I am able to run your script with out any errors. Please check the names of pseudo_dir and out_dir in your file. > > Thanks > Ajit -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120325/9ef7e8f1/attachment.htm From giannozz at democritos.it Sun Mar 25 11:11:22 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 25 Mar 2012 11:11:22 +0200 Subject: [Pw_forum] error in reading namelist system In-Reply-To: <25941b3.2870.136480b9277.Coremail.flux_ray12@163.com> References: , <14534768.45339.1332426338397.JavaMail.root@mailhub016.itcs.purdue.edu> <25941b3.2870.136480b9277.Coremail.flux_ray12@163.com> Message-ID: On Mar 25, 2012, at 6:09 , GAO Zhe wrote: > How about adding a "," after la2F = .true. it will have no effect P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From ihsanas at yahoo.com Sun Mar 25 15:16:06 2012 From: ihsanas at yahoo.com (Ihsan Erikat) Date: Sun, 25 Mar 2012 06:16:06 -0700 (PDT) Subject: [Pw_forum] neb error Message-ID: <1332681366.23060.YahooMailClassic@web130202.mail.mud.yahoo.com> Dear all ?we??run neb calculation???by using?espresso 4.3.1 on??parallization machine openmpi we have this error forrtl: No such file or directory forrtl: severe (28): CLOSE error, unit 16, file "Unknown" Image????????????? PC??????????????? Routine??????????? Line??????? Source???????????? neb.x????????????? 00000000009408CA? Unknown?????????????? Unknown? Unknown neb.x????????????? 000000000093F445? Unknown?????????????? Unknown? Unknown neb.x????????????? 00000000008DDF96? Unknown?????????????? Unknown? Unknown neb.x????????????? 0000000000878C45? Unknown?????????????? Unknown? Unknown neb.x????????????? 0000000000878401? Unknown?????????????? Unknown? Unknown neb.x????????????? 000000000086FCBD? Unknown?????????????? Unknown? Unknown neb.x????????????? 0000000000446386? close_files_?????????????? 42? close_files.f90 neb.x????????????? 0000000000408888? compute_scf_IP_do???????? 407? compute_scf.f90 neb.x????????????? 0000000000406682? compute_scf_????????????? 150? compute_scf.f90 neb.x????????????? 00000000004139BF? path_base_mp_sear???????? 879? path_base.f90 ? The output file is ? ?? Program NEB v.4.3.1??????? starts on 24Mar2012 at 16:26:48 ???? This program is part of the open-source Quantum ESPRESSO suite ???? for quantum simulation of materials; please cite ???????? "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); ????????? URL http://www.quantum-espresso.org", ???? in publications or presentations arising from this work. More details at ???? http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO ? ?parsing_file_name: neb2 Warning: card? &IONS ignored Warning: card?? POT_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card??? WFC_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card?? / ignored ???? Program NEB v.4.3.1??????? starts on 24Mar2012 at 16:26:48 ???? This program is part of the open-source Quantum ESPRESSO suite ???? for quantum simulation of materials; please cite ???????? "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); ????????? URL http://www.quantum-espresso.org", ???? in publications or presentations arising from this work. More details at ???? http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO ? ?parsing_file_name: neb2 ???? Program NEB v.4.3.1??????? starts on 24Mar2012 at 16:26:48 ???? This program is part of the open-source Quantum ESPRESSO suite ???? for quantum simulation of materials; please cite ???????? "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); ????????? URL http://www.quantum-espresso.org", ???? in publications or presentations arising from this work. More details at ???? http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO ? ?parsing_file_name: neb2 ???? Program NEB v.4.3.1??????? starts on 24Mar2012 at 16:26:48 ???? This program is part of the open-source Quantum ESPRESSO suite ???? for quantum simulation of materials; please cite ???????? "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); ????????? URL http://www.quantum-espresso.org", ???? in publications or presentations arising from this work. More details at ???? http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO ? ?parsing_file_name: neb2 ???? Program NEB v.4.3.1??????? starts on 24Mar2012 at 16:26:48 ???? This program is part of the open-source Quantum ESPRESSO suite ???? for quantum simulation of materials; please cite ???????? "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); ????????? URL http://www.quantum-espresso.org", ???? in publications or presentations arising from this work. More details at ???? http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO ? ?parsing_file_name: neb2 ???? Program NEB v.4.3.1??????? starts on 24Mar2012 at 16:26:48 ???? This program is part of the open-source Quantum ESPRESSO suite ???? for quantum simulation of materials; please cite ???????? "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); ????????? URL http://www.quantum-espresso.org", ???? in publications or presentations arising from this work. More details at ???? http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO ? ?parsing_file_name: neb2 ???? Program NEB v.4.3.1??????? starts on 24Mar2012 at 16:26:48 ???? This program is part of the open-source Quantum ESPRESSO suite ???? for quantum simulation of materials; please cite ???????? "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); ????????? URL http://www.quantum-espresso.org", ???? in publications or presentations arising from this work. More details at ???? http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO ? ?parsing_file_name: neb2 Warning: card? &IONS ignored Warning: card?? POT_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card??? WFC_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card?? / ignored Warning: card? &IONS ignored Warning: card?? POT_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card??? WFC_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card?? / ignored Warning: card? &IONS ignored Warning: card? &IONS ignored Warning: card? &IONS ignored Warning: card?? POT_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card??? WFC_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card?? / ignored Warning: card? &IONS ignored Warning: card?? POT_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card??? WFC_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card?? / ignored Warning: card?? POT_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card?? POT_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card??? WFC_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card?? / ignored Warning: card??? WFC_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card?? / ignored ???? file N.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? file N.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? file N.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? file N.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? file N.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? file N.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? file N.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? file O.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized Warning: card? &IONS ignored Warning: card?? POT_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card??? WFC_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card?? / ignored ???? file O.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized Warning: card? &IONS ignored Warning: card?? POT_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card??? WFC_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card?? / ignored ???? file O.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? file O.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized Warning: card? &IONS ignored ???? file O.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized Warning: card?? POT_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card??? WFC_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card?? / ignored Warning: card? &IONS ignored Warning: card?? POT_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card??? WFC_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card?? / ignored Warning: card? &IONS ignored Warning: card?? POT_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card??? WFC_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card?? / ignored ???? file O.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? file O.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized Warning: card? &IONS ignored Warning: card? &IONS ignored Warning: card?? POT_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card??? WFC_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card?? / ignored Warning: card?? POT_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card??? WFC_EXTRAPOLATION = "SECOND_ORDER", ignored Warning: card?? / ignored ???? file N.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? file N.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? file N.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? file N.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? file N.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? file N.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? file N.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? file O.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? initial path length?????????? = 36.4958 bohr ???? initial inter-image distance? =? 6.0826 bohr ? ???? string_method???????????????? =? neb ???? restart_mode????????????????? =? from_scratch ???? opt_scheme??????????????????? =? broyden ???? num_of_images???????????????? =? 7 ???? nstep_path??????????????????? =? 100 ???? CI_scheme???????????????????? =? auto ???? first_last_opt??????????????? =? F ???? use_freezing????????????????? =? F ???? ds??????????????????????????? =? 1.0000 a.u. ???? k_max???????????????????????? =? 0.3000 a.u. ???? k_min???????????????????????? =? 0.2000 a.u. ???? suggested k_max?????????????? =? 0.6169 a.u. ???? suggested k_min?????????????? =? 0.4112 a.u. ???? path_thr????????????????????? =? 0.1000 eV / A ???? file O.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? ------------------------------ iteration?? 1 ------------------------------ ???? tcpu =????? 0.2??? self-consistency for image?? 1 ???? file O.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? file O.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? file O.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? file O.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? file O.pbe-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? initial path length?????????? = 36.4958 bohr ???? initial inter-image distance? =? 6.0826 bohr ? ???? string_method???????????????? =? neb ???? restart_mode????????????????? =? from_scratch ???? opt_scheme??????????????????? =? broyden ???? num_of_images???????????????? =? 7 ???? nstep_path??????????????????? =? 100 ???? CI_scheme???????????????????? =? auto ???? first_last_opt??????????????? =? F ???? use_freezing????????????????? =? F ???? ds??????????????????????????? =? 1.0000 a.u. ???? k_max???????????????????????? =? 0.3000 a.u. ???? k_min???????????????????????? =? 0.2000 a.u. ???? suggested k_max?????????????? =? 0.6169 a.u. ???? suggested k_min?????????????? =? 0.4112 a.u. ???? path_thr????????????????????? =? 0.1000 eV / A ???? initial path length?????????? = 36.4958 bohr ???? initial inter-image distance? =? 6.0826 bohr ? ???? string_method???????????????? =? neb ???? restart_mode????????????????? =? from_scratch ???? opt_scheme??????????????????? =? broyden ???? num_of_images???????????????? =? 7 ???? nstep_path??????????????????? =? 100 ???? CI_scheme???????????????????? =? auto ???? first_last_opt??????????????? =? F ???? use_freezing????????????????? =? F ???? ds??????????????????????????? =? 1.0000 a.u. ???? k_max???????????????????????? =? 0.3000 a.u. ???? initial path length?????????? = 36.4958 bohr ???? initial inter-image distance? =? 6.0826 bohr ? ???? string_method???????????????? =? neb ???? restart_mode????????????????? =? from_scratch ???? k_min???????????????????????? =? 0.2000 a.u. ???? opt_scheme??????????????????? =? broyden ???? num_of_images???????????????? =? 7 ???? nstep_path??????????????????? =? 100 ???? CI_scheme???????????????????? =? auto ???? first_last_opt??????????????? =? F ???? use_freezing????????????????? =? F ???? ds??????????????????????????? =? 1.0000 a.u. ???? k_max???????????????????????? =? 0.3000 a.u. ???? k_min???????????????????????? =? 0.2000 a.u. ???? suggested k_max?????????????? =? 0.6169 a.u. ???? suggested k_min?????????????? =? 0.4112 a.u. ???? path_thr????????????????????? =? 0.1000 eV / A ???? suggested k_max?????????????? =? 0.6169 a.u. ???? suggested k_min?????????????? =? 0.4112 a.u. ???? path_thr????????????????????? =? 0.1000 eV / A ???? initial path length?????????? = 36.4958 bohr ???? initial inter-image distance? =? 6.0826 bohr ? ???? string_method???????????????? =? neb ???? restart_mode????????????????? =? from_scratch ???? opt_scheme??????????????????? =? broyden ???? num_of_images???????????????? =? 7 ???? nstep_path??????????????????? =? 100 ???? CI_scheme???????????????????? =? auto ???? first_last_opt??????????????? =? F ???? use_freezing????????????????? =? F ???? ds??????????????????????????? =? 1.0000 a.u. ???? k_max???????????????????????? =? 0.3000 a.u. ???? k_min???????????????????????? =? 0.2000 a.u. ???? suggested k_max?????????????? =? 0.6169 a.u. ???? suggested k_min?????????????? =? 0.4112 a.u. ???? path_thr????????????????????? =? 0.1000 eV / A ???? initial path length?????????? = 36.4958 bohr ???? initial inter-image distance? =? 6.0826 bohr ? ???? string_method???????????????? =? neb ???? restart_mode????????????????? =? from_scratch ???? opt_scheme??????????????????? =? broyden ???? num_of_images???????????????? =? 7 ???? nstep_path??????????????????? =? 100 ???? CI_scheme???????????????????? =? auto ???? first_last_opt??????????????? =? F ???? use_freezing????????????????? =? F ???? ds??????????????????????????? =? 1.0000 a.u. ???? k_max???????????????????????? =? 0.3000 a.u. ???? initial path length?????????? = 36.4958 bohr ???? initial inter-image distance? =? 6.0826 bohr ? ???? string_method???????????????? =? neb ???? restart_mode????????????????? =? from_scratch ???? opt_scheme??????????????????? =? broyden ???? num_of_images???????????????? =? 7 ???? nstep_path??????????????????? =? 100 ???? CI_scheme???????????????????? =? auto ???? first_last_opt??????????????? =? F ???? use_freezing????????????????? =? F ???? ds??????????????????????????? =? 1.0000 a.u. ???? k_max???????????????????????? =? 0.3000 a.u. ???? k_min???????????????????????? =? 0.2000 a.u. ???? suggested k_max?????????????? =? 0.6169 a.u. ???? suggested k_min?????????????? =? 0.4112 a.u. ???? path_thr????????????????????? =? 0.1000 eV / A ???? k_min???????????????????????? =? 0.2000 a.u. ???? suggested k_max?????????????? =? 0.6169 a.u. ???? suggested k_min?????????????? =? 0.4112 a.u. ???? path_thr????????????????????? =? 0.1000 eV / A ???? ------------------------------ iteration?? 1 ------------------------------ ???? tcpu =????? 0.2??? self-consistency for image?? 1 ???? ------------------------------ iteration?? 1 ------------------------------ ???? tcpu =????? 0.2??? self-consistency for image?? 1 ???? ------------------------------ iteration?? 1 ------------------------------ ???? tcpu =????? 0.2??? self-consistency for image?? 1 ???? ------------------------------ iteration?? 1 ------------------------------ ???? tcpu =????? 0.2??? self-consistency for image?? 1 ???? ------------------------------ iteration?? 1 ------------------------------ ???? ------------------------------ iteration?? 1 ------------------------------ ???? tcpu =????? 0.2??? self-consistency for image?? 1 ???? tcpu =????? 0.2??? self-consistency for image?? 1 ???? tcpu =? 30544.0??? self-consistency for image?? 2 forrtl: No such file or directory forrtl: severe (28): CLOSE error, unit 16, file "Unknown" Image????????????? PC??????????????? Routine??????????? Line??????? Source???????????? neb.x????????????? 00000000009408CA? Unknown?????????????? Unknown? Unknown neb.x????????????? 000000000093F445? Unknown?????????????? Unknown? Unknown neb.x????????????? 00000000008DDF96? Unknown?????????????? Unknown? Unknown neb.x????????????? 0000000000878C45? Unknown?????????????? Unknown? Unknown neb.x????????????? 0000000000878401? Unknown?????????????? Unknown? Unknown neb.x????????????? 000000000086FCBD? Unknown?????????????? Unknown? Unknown neb.x????????????? 0000000000446386? close_files_?????????????? 42? close_files.f90 neb.x????????????? 0000000000408888? compute_scf_IP_do???????? 407? compute_scf.f90 neb.x????????????? 0000000000406682? compute_scf_????????????? 150? compute_scf.f90 neb.x????????????? 00000000004139BF? path_base_mp_sear???????? 879? path_base.f90 neb.x????????????? 00000000004060D0? MAIN__??????????????????? 186? neb.f90 neb.x????????????? 00000000004054BC? Unknown?????????????? Unknown? Unknown libc.so.6????????? 0000003A38C1D994? Unknown?????????????? Unknown? Unknown neb.x????????????? 00000000004053C9? Unknown?????????????? Unknown? Unknown forrtl: No such file or directory forrtl: severe (28): CLOSE error, unit 16, file "Unknown" Image????????????? PC??????????????? Routine??????????? Line??????? Source???????????? neb.x????????????? 00000000009408CA? Unknown?????????????? Unknown? Unknown neb.x????????????? 000000000093F445? Unknown?????????????? Unknown? Unknown neb.x????????????? 00000000008DDF96? Unknown?????????????? Unknown? Unknown neb.x????????????? 0000000000878C45? Unknown?????????????? Unknown? Unknown neb.x????????????? 0000000000878401? Unknown?????????????? Unknown? Unknown neb.x????????????? 000000000086FCBD? Unknown?????????????? Unknown? Unknown neb.x????????????? 0000000000446386? close_files_?????????????? 42? close_files.f90 neb.x????????????? 0000000000408888? compute_scf_IP_do???????? 407? compute_scf.f90 neb.x????????????? 0000000000406682? compute_scf_????????????? 150? compute_scf.f90 neb.x????????????? 00000000004139BF? path_base_mp_sear???????? 879? path_base.f90 neb.x????????????? 00000000004060D0? MAIN__??????????????????? 186? neb.f90 neb.x????????????? 00000000004054BC? Unknown?????????????? Unknown? Unknown libc.so.6????????? 0000003A38C1D994? Unknown?????????????? Unknown? Unknown neb.x????????????? 00000000004053C9? Unknown?????????????? Unknown? Unknown forrtl: No such file or directory forrtl: severe (28): CLOSE error, unit 16, file "Unknown" Image????????????? PC??????????????? Routine??????????? Line??????? Source???????????? neb.x????????????? 00000000009408CA? Unknown?????????????? Unknown? Unknown neb.x????????????? 000000000093F445? Unknown?????????????? Unknown? Unknown neb.x????????????? 00000000008DDF96? Unknown?????????????? Unknown? Unknown neb.x????????????? 0000000000878C45? Unknown?????????????? Unknown? Unknown neb.x????????????? 0000000000878401? Unknown?????????????? Unknown? Unknown neb.x????????????? 000000000086FCBD? Unknown?????????????? Unknown? Unknown neb.x????????????? 0000000000446386? close_files_?????????????? 42? close_files.f90 neb.x????????????? 0000000000408888? compute_scf_IP_do???????? 407? compute_scf.f90 neb.x????????????? 0000000000406682? compute_scf_????????????? 150? compute_scf.f90 neb.x????????????? 00000000004139BF? path_base_mp_sear???????? 879? path_base.f90 neb.x????????????? 00000000004060D0? MAIN__??????????????????? 186? neb.f90 neb.x????????????? 00000000004054BC? Unknown?????????????? Unknown? Unknown libc.so.6????????? 0000003A38C1D994? Unknown?????????????? Unknown? Unknown neb.x????????????? 00000000004053C9? Unknown?????????????? Unknown? Unknown forrtl: No such file or directory forrtl: severe (28): CLOSE error, unit 16, file "Unknown" Image????????????? PC??????????????? Routine??????????? Line??????? Source???????????? neb.x????????????? 00000000009408CA? Unknown?????????????? Unknown? Unknown neb.x????????????? 000000000093F445? Unknown?????????????? Unknown? Unknown neb.x????????????? 00000000008DDF96? Unknown?????????????? Unknown? Unknown neb.x????????????? 0000000000878C45? Unknown?????????????? Unknown? Unknown neb.x????????????? 0000000000878401? Unknown?????????????? Unknown? Unknown neb.x????????????? 000000000086FCBD? Unknown?????????????? Unknown? Unknown neb.x????????????? 0000000000446386? close_files_?????????????? 42? close_files.f90 neb.x????????????? 0000000000408888? compute_scf_IP_do???????? 407? compute_scf.f90 neb.x????????????? 0000000000406682? compute_scf_????????????? 150? compute_scf.f90 neb.x????????????? 00000000004139BF? path_base_mp_sear???????? 879? path_base.f90 neb.x????????????? 00000000004060D0? MAIN__??????????????????? 186? neb.f90 neb.x????????????? 00000000004054BC? Unknown?????????????? Unknown? Unknown libc.so.6????????? 0000003A38C1D994? Unknown?????????????? Unknown? Unknown neb.x????????????? 00000000004053C9? Unknown?????????????? Unknown? Unknown forrtl: No such file or directory forrtl: severe (28): CLOSE error, unit 16, file "Unknown" Image????????????? PC??????????????? Routine??????????? Line??????? Source???????????? neb.x????????????? 00000000009408CA? Unknown?????????????? Unknown? Unknown neb.x????????????? 000000000093F445? Unknown?????????????? Unknown? Unknown neb.x????????????? 00000000008DDF96? Unknown?????????????? Unknown? Unknown neb.x????????????? 0000000000878C45? Unknown?????????????? Unknown? Unknown neb.x????????????? 0000000000878401? Unknown?????????????? Unknown? Unknown neb.x????????????? 000000000086FCBD? Unknown?????????????? Unknown? Unknown neb.x????????????? 0000000000446386? close_files_?????????????? 42? close_files.f90 neb.x????????????? 0000000000408888? compute_scf_IP_do???????? 407? compute_scf.f90 neb.x????????????? 0000000000406682? compute_scf_????????????? 150? compute_scf.f90 neb.x????????????? 00000000004139BF? path_base_mp_sear???????? 879? path_base.f90 neb.x????????????? 00000000004060D0? MAIN__??????????????????? 186? neb.f90 neb.x????????????? 00000000004054BC? Unknown?????????????? Unknown? Unknown libc.so.6????????? 0000003A38C1D994? Unknown?????????????? Unknown? Unknown neb.x????????????? 00000000004053C9? Unknown?????????????? Unknown? Unknown forrtl: No such file or directory forrtl: severe (28): CLOSE error, unit 16, file "Unknown" Image????????????? PC??????????????? Routine??????????? Line??????? Source???????????? neb.x????????????? 00000000009408CA? Unknown?????????????? Unknown? Unknown neb.x????????????? 000000000093F445? Unknown?????????????? Unknown? Unknown neb.x????????????? 00000000008DDF96? Unknown?????????????? Unknown? Unknown neb.x????????????? 0000000000878C45? Unknown?????????????? Unknown? Unknown neb.x????????????? 0000000000878401? Unknown?????????????? Unknown? Unknown neb.x????????????? 000000000086FCBD? Unknown?????????????? Unknown? Unknown neb.x????????????? 0000000000446386? close_files_?????????????? 42? close_files.f90 neb.x????????????? 0000000000408888? compute_scf_IP_do???????? 407? compute_scf.f90 neb.x????????????? 0000000000406682? compute_scf_????????????? 150? compute_scf.f90 neb.x????????????? 00000000004139BF? path_base_mp_sear???????? 879? path_base.f90 neb.x????????????? 00000000004060D0? MAIN__??????????????????? 186? neb.f90 neb.x????????????? 00000000004054BC? Unknown?????????????? Unknown? Unknown libc.so.6????????? 0000003A38C1D994? Unknown?????????????? Unknown? Unknown neb.x????????????? 00000000004053C9? Unknown?????????????? Unknown? Unknown ???? tcpu =? 63774.0??? self-consistency for image?? 3 (END)? ?Does anyone know what might cause this behavior? Dr.Ihsan Erikat Jerash University-Jordan ?????????????????????????? ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120325/fb02cdb5/attachment-0001.htm From giannozz at democritos.it Sun Mar 25 15:34:15 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 25 Mar 2012 15:34:15 +0200 Subject: [Pw_forum] neb error In-Reply-To: <1332681366.23060.YahooMailClassic@web130202.mail.mud.yahoo.com> References: <1332681366.23060.YahooMailClassic@web130202.mail.mud.yahoo.com> Message-ID: On Mar 25, 2012, at 15:16 , Ihsan Erikat wrote: > Does anyone know what might cause this behavior? you are running in parallel a code compiled for serial execution P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From avallabh at purdue.edu Sun Mar 25 15:44:20 2012 From: avallabh at purdue.edu (Ajit Vallabhaneni) Date: Sun, 25 Mar 2012 09:44:20 -0400 (EDT) Subject: [Pw_forum] Problem with QE4.0.3 In-Reply-To: <520455869.51252.1332683019357.JavaMail.root@mailhub016.itcs.purdue.edu> Message-ID: <974760405.51254.1332683060800.JavaMail.root@mailhub016.itcs.purdue.edu> Dear users, I am trying to install QE V4.0.3 for some purpose although i installed V4.3.2 before. I followed the same procedure as 4.3.2 (./configure-> make PW,PH) after loading the same modules. I am able to generate the pw.x and ph.x files but they are not working properly. [avallabh at hansen-fe00 bin]$ ./pw.x ./pw.x: error while loading shared libraries: libmkl_lapack.so: cannot open shared object file: No such file or directory Please let me know how should i fix this. I didnot have this problem with V4.3.2. Thanks Ajit From flux_ray12 at 163.com Sun Mar 25 15:53:47 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Sun, 25 Mar 2012 21:53:47 +0800 (CST) Subject: [Pw_forum] Problem with QE4.0.3 In-Reply-To: <974760405.51254.1332683060800.JavaMail.root@mailhub016.itcs.purdue.edu> References: <974760405.51254.1332683060800.JavaMail.root@mailhub016.itcs.purdue.edu> Message-ID: <22f7d5ff.76e2.1364a225b7f.Coremail.flux_ray12@163.com> If you have installed ifort and MKL, then you can add ifort into environment variables. For example, the 64bit ifort installed in /opt/intel, by writing source /opt/intel/bin/compilervars.sh intel64 into your ${HOME}/.bashrc software will find MKL automaticly. BTW, lmkl_lapack.so is looked from an old version of ifort or mkl. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-03-25 21:44:20,"Ajit Vallabhaneni" wrote: >Dear users, > > I am trying to install QE V4.0.3 for some purpose although i installed V4.3.2 before. I followed the same procedure as 4.3.2 (./configure-> make PW,PH) after loading the same modules. I am able to generate the pw.x and ph.x files but they are not working properly. > > >[avallabh at hansen-fe00 bin]$ ./pw.x >./pw.x: error while loading shared libraries: libmkl_lapack.so: cannot open shared object file: No such file or directory > > > Please let me know how should i fix this. I didnot have this problem with V4.3.2. > > >Thanks >Ajit >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120325/17caa790/attachment.htm From ihsanas at yahoo.com Sun Mar 25 17:41:42 2012 From: ihsanas at yahoo.com (Ihsan Erikat) Date: Sun, 25 Mar 2012 08:41:42 -0700 (PDT) Subject: [Pw_forum] neb error In-Reply-To: Message-ID: <1332690102.4033.YahooMailClassic@web130204.mail.mud.yahoo.com> Dear Paolo We run several parallel jobs by using pw.x , and they work well. Why it does not work well for neb.x. ? PS: we use the following command: ? mpirun -np 7 ./neb.x -inp? neb2 > neb2.out & ? Thanks in advance ? Ihsan Erikat ? Jerash University, Jordan ? ? --- On Sun, 3/25/12, Paolo Giannozzi wrote: From: Paolo Giannozzi Subject: Re: [Pw_forum] neb error To: "Ihsan Erikat" Cc: "PWSCF Forum" Date: Sunday, March 25, 2012, 9:34 AM On Mar 25, 2012, at 15:16 , Ihsan Erikat wrote: > Does anyone know what might cause this behavior? you are running in parallel a code compiled for serial execution P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, 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://www.democritos.it/pipermail/pw_forum/attachments/20120325/c2f55214/attachment.htm From giannozz at democritos.it Sun Mar 25 17:45:49 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 25 Mar 2012 17:45:49 +0200 Subject: [Pw_forum] neb error In-Reply-To: <1332690102.4033.YahooMailClassic@web130204.mail.mud.yahoo.com> References: <1332690102.4033.YahooMailClassic@web130204.mail.mud.yahoo.com> Message-ID: On Mar 25, 2012, at 17:41 , Ihsan Erikat wrote: > We run several parallel jobs by using pw.x , and they work well. > Why it does not work well for neb.x. I cannot know why, I didn't compile the code on your machine. What I know for sure is that your output exhibits the typical behaviour of the serial code run in parallel (no initial message stating the number of processes, multiple copies of output) P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From avallabh at purdue.edu Sun Mar 25 21:35:57 2012 From: avallabh at purdue.edu (Ajit Vallabhaneni) Date: Sun, 25 Mar 2012 15:35:57 -0400 (EDT) Subject: [Pw_forum] Problem with QE4.0.3 In-Reply-To: <22f7d5ff.76e2.1364a225b7f.Coremail.flux_ray12@163.com> Message-ID: <496405997.51690.1332704157301.JavaMail.root@mailhub016.itcs.purdue.edu> Dr. Zhe, I am getting a new error now which i think is associated with lapack. (It's not showing any errors while compiling, only during run time, it is showing errors). Please let me know how to fix it. [avallabh at steele-fe02 bin]$ ./pw.x < scf.in Program PWSCF v.4.0.3 starts ... Today is 25Mar2012 at 15:31:13 Parallel version (MPI) Number of processors in use: 1 For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW Current dimensions of program pwscf are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 ./pw.x: symbol lookup error: ./pw.x: undefined symbol: dgetrf_ Thanks Ajit From spiga.filippo at gmail.com Sun Mar 25 22:14:55 2012 From: spiga.filippo at gmail.com (Filippo Spiga) Date: Sun, 25 Mar 2012 21:14:55 +0100 Subject: [Pw_forum] New version of Quantum ESPRESSO (v0.6, r8825) has been released Message-ID: Dear all, a new version of Quantum ESPRESSO (v0.6, r8825) has been released! The new tar.gz is here: http://qe-forge.org/frs/shownotes.php?release_id=113 Even if this release is marked as a beta, we are working really hard to consolidate the package and deliver new functionalities. We reinforced some fall-back strategies (like switch to CPU-only computation if CPU-GPU fails or cannot run) and we improved other CUDA parts. Moreover this is the last version compatible with Quantum ESPRESSO v4.3.2 because the new Quantum ESPRESSO v5.0 is expected to be released soon! Me and Ivan Girotto would thank all the people that directly or indirectly helped us by providing several input files that we used to validate the GPU code and discover/solve bugs. Some people asked when also the Car-Parrinello package will be GPU accelerated. If everything will go smooth in the next months, a first version will be available no later than September. Feedbacks and suggestions are always welcome (-: Regards, Filippo -- Filippo SPIGA ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120325/9a2d64a0/attachment.htm From giannozz at democritos.it Sun Mar 25 22:29:28 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 25 Mar 2012 22:29:28 +0200 Subject: [Pw_forum] Problem with QE4.0.3 In-Reply-To: <496405997.51690.1332704157301.JavaMail.root@mailhub016.itcs.purdue.edu> References: <496405997.51690.1332704157301.JavaMail.root@mailhub016.itcs.purdue.edu> Message-ID: On Mar 25, 2012, at 21:35 , Ajit Vallabhaneni wrote: > I am getting a new error now which i think is associated with lapack look into the make.sys that works: it should be sufficient to copy a few variables, like BLAS_LIBS and LAPACK_LIBS, into the make.sys that doesn't work. Yours is a problem with MKL, not with the code itself. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From avallabh at purdue.edu Sun Mar 25 23:06:00 2012 From: avallabh at purdue.edu (Ajit Vallabhaneni) Date: Sun, 25 Mar 2012 17:06:00 -0400 (EDT) Subject: [Pw_forum] Problem with QE4.0.3 In-Reply-To: Message-ID: <1095627742.51860.1332709560124.JavaMail.root@mailhub016.itcs.purdue.edu> Dr. paolo, Thanks a lot. It worked finally. Thanks Ajit From elie.moujaes at hotmail.co.uk Mon Mar 26 03:05:51 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Mon, 26 Mar 2012 02:05:51 +0100 Subject: [Pw_forum] error in reading namelist system In-Reply-To: References: , , <14534768.45339.1332426338397.JavaMail.root@mailhub016.itcs.purdue.edu>, , <25941b3.2870.136480b9277.Coremail.flux_ray12@163.com>, Message-ID: Hello, Thanks everyone for your help. I found the error: it was in "system" namelist I wrote ecutwfc=32.D0. i have corrected it Regards > From: giannozz at democritos.it > Date: Sun, 25 Mar 2012 11:11:22 +0200 > To: flux_ray12 at 163.com > CC: pw_forum at pwscf.org > Subject: Re: [Pw_forum] error in reading namelist system > > > On Mar 25, 2012, at 6:09 , GAO Zhe wrote: > > > How about adding a "," after la2F = .true. > > it will have no effect > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120326/fdca6ab7/attachment-0001.htm From elie.moujaes at hotmail.co.uk Mon Mar 26 03:10:22 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Mon, 26 Mar 2012 02:10:22 +0100 Subject: [Pw_forum] Input for lambda.x execution for el-ph coupling Message-ID: Dear all, I want to use the lambda.x executable (within the el-ph interaction package) to calculate the el-ph coefficient lambda and also Tc. I have read the input in example07 but have not quite understood how to produce the points in the input file (it states using kpoints.x) but still a bit vague for me..Any clarification regarding this issue would be appreciated. Thanks Regards Elie MoudaesUniversity of NottimghamNG7 2RDUK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120326/4230e88b/attachment.htm From bahadira at buffalo.edu Mon Mar 26 06:37:24 2012 From: bahadira at buffalo.edu (bahadir) Date: Mon, 26 Mar 2012 00:37:24 -0400 Subject: [Pw_forum] Input for lambda.x execution for el-ph coupling In-Reply-To: References: Message-ID: <4F6FF284.7080803@buffalo.edu> if you know the q-grid that you used in elphon calculation, you can just use kpoint.x and give the information about system as follow: bravais lattice >> {your bravis lattice no 1...14} filout [mesh_k] >> {just hit enter} then it will asks for some info (depends on your lattice), just enter them . . . mesh: n1 n2 n3 >> {enter your q-grid in X X X format "example: 8 8 8"} mesh: k1 k2 k3 (0 no shift, 1 shifted) >> enter 0 0 0 (no shift for all direction) write all k? [f] >> {just hit enter} then read the file that code creates named mesh_k hope it works bahadir On 03/25/2012 09:10 PM, Elie M wrote: > Dear all, > > I want to use the lambda.x executable (within the el-ph interaction > package) to calculate the el-ph coefficient lambda and also Tc. I have > read the input in example07 but have not quite understood how to > produce the points in the input file (it states using kpoints.x) but > still a bit vague for me..Any clarification regarding this issue would > be appreciated. Thanks > > > Regards > > Elie Moudaes > University of Nottimgham > NG7 2RD > UK > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Dr.Bahadir Altintas * Dept. of Chemistry SUNY Buffalo NY,USA * Abant Izzet Baysal University Dept. of Computer Education Bolu,Turkey -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120326/7f1fd79b/attachment.htm From giannozz at democritos.it Mon Mar 26 07:07:32 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 26 Mar 2012 07:07:32 +0200 Subject: [Pw_forum] error in reading namelist system In-Reply-To: References: , , <14534768.45339.1332426338397.JavaMail.root@mailhub016.itcs.purdue.edu>, , <25941b3.2870.136480b9277.Coremail.flux_ray12@163.com>, Message-ID: <07D15FD2-AE30-4008-8CF9-4A61AB493D06@democritos.it> On Mar 26, 2012, at 3:05 , Elie M wrote: > I found the error: it was in "system" namelist I wrote ecutwfc=32.D0. "ecutwfc=32.D0" is a perfectly legal syntax. Anyway the file you sent contained "ecutwfc=32", also a legal syntax (although not a ice one). P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From abhinavsrivastava at in.ibm.com Mon Mar 26 14:48:56 2012 From: abhinavsrivastava at in.ibm.com (Abhinav 122) Date: Mon, 26 Mar 2012 18:18:56 +0530 Subject: [Pw_forum] Problems in running check-pw.x.j Message-ID: Hi, I received the following error during check-pw.x.j. Please suggest the required steps to remove the following errors. [root at bluehorse14 tests]# ./check-pw.x.j Checking atom...passed Checking atom-lsda...passed Checking atom-pbe...discrepancy in number of scf iterations detected Reference: 7, You got: 5 discrepancy in pressure detected Reference: -14.46, You got: -14.50 Checking atom-sigmapbe...discrepancy in number of scf iterations detected Reference: 11, You got: 14 Checking berry...passed Checking berry, step 2 ...######################################################################################################################## # FROM IOTK LIBRARY, VERSION 1.2.0 # UNRECOVERABLE ERROR (ierr=1) # ERROR IN: iotk_scan_end (iotk_scan.f90:241) # CVS Revision: 1.23 # foundl # ERROR IN: iotk_close_read (iotk_files.f90:746) # CVS Revision: 1.20 ########################################################################################################################application called MPI_Abort(MPI_COMM_WORLD, 1) - prcess 0 Thanks & Regards, Abhinav Srivastava Software Engineer High Performance Analytic Group Next Generation systems IBM Research Laboratory New Delhi - 110070 India From giannozz at democritos.it Mon Mar 26 18:42:04 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 26 Mar 2012 18:42:04 +0200 Subject: [Pw_forum] Problems in running check-pw.x.j In-Reply-To: References: Message-ID: <1332780124.10829.6.camel@fe12lx.fisica.uniud.it> On Mon, 2012-03-26 at 18:18 +0530, Abhinav 122 wrote: > I received the following error during check-pw.x.j. > Please suggest the required steps to remove the following errors. most likely, your compiler is buggy. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From chengyu.young at gmail.com Mon Mar 26 21:29:18 2012 From: chengyu.young at gmail.com (chengyu yang) Date: Mon, 26 Mar 2012 15:29:18 -0400 Subject: [Pw_forum] [xcrysden]:how to get the output structure file as xyz format Message-ID: Dear Everyone, I have a very simple question: I set up a structure and repeat it in Xcrysden, and then I want to get the structure file for the whole periodic structure as xyz file. How could I do that? I can only find .xsf format and other formats. Can you help me out? Thank you. Regards. Chengyu Yang MMAE,University of Central Florida -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120326/5faf9bc4/attachment.htm From chengyu.young at gmail.com Mon Mar 26 22:01:04 2012 From: chengyu.young at gmail.com (chengyu yang) Date: Mon, 26 Mar 2012 16:01:04 -0400 Subject: [Pw_forum] Fwd: [xcrysden]:how to get the output structure file as xyz format In-Reply-To: References: Message-ID: Can some one else help please? Thanks. Chengyu Yang MMAE, UCF > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120326/0affd085/attachment.htm From makhyoun2 at yahoo.com Tue Mar 27 00:33:35 2012 From: makhyoun2 at yahoo.com (mohamed makhyoun) Date: Mon, 26 Mar 2012 15:33:35 -0700 (PDT) Subject: [Pw_forum] error two atoms overlap Message-ID: <1332801215.47749.YahooMailClassic@web126001.mail.ne1.yahoo.com> Dear All: By running the given input file for pw.x I get the error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ???? from check_atoms : error #???????? 1 ???? atoms #?? 1 and #?? 2 overlap! %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Although I checked the input by XCRYSDEN visualization program and nothing is wrong. ?I appreciate any help. Best Regard Mohamed ################################################################### &CONTROL ???????????????? calculation = 'scf' , ???????????????? prefix='cu3nbs4' ??????????????? restart_mode = 'from_scratch' , ????????????????? outdir = '$TMP_DIR/' , ????????????????? pseudo_dir = '/home/mohamed/espresso/exec/pseudo' , ????????????????? verbosity = 'default' , ?/ ?&SYSTEM ?????????????????????????? ibrav=1 ?????????????????????????? celldm(1)= 10.397 , ?????????????????????????? nat = 20, ??????????????????????? ntyp = 3, ???????????????????? ecutwfc = 60. , ???????????????????? nbnd=90, ?/ ?&ELECTRONS ????????????? conv_thr=1.0D-8 , ?/ ATOMIC_SPECIES ?? Nb? 92.9064?? Nb.pbe-sR-sc-us.UPF ?? Cu? 63.546??? Cu.pbe-sR-us.UPF ??? S?? 32.06???? S.pbe-van-bm.UPF ?ATOMIC_POSITIONS crystal Nb?????? 0.000000000????? 0.000000000????? 0.000000000 Nb????? -1.000000000????? 0.000000000????? 0.000000000 Nb?????? 0.000000000????? 0.000000000???? -1.000000000 Nb?????? 1.000000000????? 0.000000000????? 0.000000000 Cu?????? 0.500000000????? 0.000000000????? 0.000000000 Cu?????? 0.000000000????? 0.000000000???? -0.500000000 Cu????? -0.500000000????? 0.000000000????? 0.000000000 Cu?????? 0.000000000???? -0.500000000????? 0.000000000 Cu?????? 0.000000000????? 0.500000000????? 0.000000000 Cu?????? 0.000000000????? 0.000000000????? 0.500000000 S??????? 0.242599953????? 0.242599953????? 0.242599953 S??????? 0.242599953???? -0.242599953???? -0.242599953 S?????? -0.242599953????? 0.242599953???? -0.242599953 S?????? -0.242599953???? -0.242599953????? 0.242599953 S?????? -0.757400047????? 0.242599953????? 0.242599953 S??????? 0.242599953????? 0.242599953???? -0.757400047 S?????? -0.757400047???? -0.242599953???? -0.242599953 S??????? 0.757400047????? 0.242599953???? -0.242599953 S?????? -0.242599953???? -0.242599953???? -0.757400047 S??????? 0.757400047???? -0.242599953????? 0.242599953 K_POINTS gamma -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120326/4d6e688e/attachment.htm From akohlmey at gmail.com Tue Mar 27 00:39:43 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Mon, 26 Mar 2012 18:39:43 -0400 Subject: [Pw_forum] error two atoms overlap In-Reply-To: <1332801215.47749.YahooMailClassic@web126001.mail.ne1.yahoo.com> References: <1332801215.47749.YahooMailClassic@web126001.mail.ne1.yahoo.com> Message-ID: On Mon, Mar 26, 2012 at 6:33 PM, mohamed makhyoun wrote: > Dear All: > > By running the given input file for pw.x I get the error: > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from check_atoms : error # 1 > atoms # 1 and # 2 overlap! > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > Although I checked the input by XCRYSDEN visualization program and nothing > is wrong. > I appreciate any help. > there is a lot wrong. on a crystal lattice positions 0.0 0.0 0.0 and -1.0 0.0 0.0 are indeed the same, just shifted by an entire cell. your structure should have only one Nb atom. axel. > > Best Regard > > Mohamed > ################################################################### > > &CONTROL > calculation = 'scf' , > prefix='cu3nbs4' > restart_mode = 'from_scratch' , > outdir = '$TMP_DIR/' , > pseudo_dir = '/home/mohamed/espresso/exec/pseudo' , > verbosity = 'default' , > > / > &SYSTEM > ibrav=1 > celldm(1)= 10.397 , > nat = 20, > ntyp = 3, > ecutwfc = 60. , > nbnd=90, > / > &ELECTRONS > conv_thr=1.0D-8 , > / > ATOMIC_SPECIES > Nb 92.9064 Nb.pbe-sR-sc-us.UPF > Cu 63.546 Cu.pbe-sR-us.UPF > S 32.06 S.pbe-van-bm.UPF > ATOMIC_POSITIONS crystal > Nb 0.000000000 0.000000000 0.000000000 > Nb -1.000000000 0.000000000 0.000000000 > Nb 0.000000000 0.000000000 -1.000000000 > Nb 1.000000000 0.000000000 0.000000000 > Cu 0.500000000 0.000000000 0.000000000 > Cu 0.000000000 0.000000000 -0.500000000 > Cu -0.500000000 0.000000000 0.000000000 > Cu 0.000000000 -0.500000000 0.000000000 > Cu 0.000000000 0.500000000 0.000000000 > Cu 0.000000000 0.000000000 0.500000000 > S 0.242599953 0.242599953 0.242599953 > S 0.242599953 -0.242599953 -0.242599953 > S -0.242599953 0.242599953 -0.242599953 > S -0.242599953 -0.242599953 0.242599953 > S -0.757400047 0.242599953 0.242599953 > S 0.242599953 0.242599953 -0.757400047 > S -0.757400047 -0.242599953 -0.242599953 > S 0.757400047 0.242599953 -0.242599953 > S -0.242599953 -0.242599953 -0.757400047 > S 0.757400047 -0.242599953 0.242599953 > K_POINTS gamma > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120326/e590c3fc/attachment-0001.htm From flux_ray12 at 163.com Tue Mar 27 04:23:12 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Tue, 27 Mar 2012 10:23:12 +0800 (CST) Subject: [Pw_forum] error two atoms overlap In-Reply-To: <1332801215.47749.YahooMailClassic@web126001.mail.ne1.yahoo.com> References: <1332801215.47749.YahooMailClassic@web126001.mail.ne1.yahoo.com> Message-ID: <36a5107d.46bd.13651f6d3e7.Coremail.flux_ray12@163.com> Since your system is simple cubic, and your first and second atoms position are (0,0,0) and (-1,0,0), which are both at the vertex position of a cubic, thus the 1st and 2nd atoms at exactly same position (please think about the translation in crystal). Actually, in you input file, atom 1~4 aimed the same position. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-03-27 06:33:35,"mohamed makhyoun" wrote: | Dear All: By running the given input file for pw.x I get the error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from check_atoms : error # 1 atoms # 1 and # 2 overlap! %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Although I checked the input by XCRYSDEN visualization program and nothing is wrong. I appreciate any help. Best Regard Mohamed ################################################################### &CONTROL calculation = 'scf' , prefix='cu3nbs4' restart_mode = 'from_scratch' , outdir = '$TMP_DIR/' , pseudo_dir = '/home/mohamed/espresso/exec/pseudo' , verbosity = 'default' , / &SYSTEM ibrav=1 celldm(1)= 10.397 , nat = 20, ntyp = 3, ecutwfc = 60. , nbnd=90, / &ELECTRONS conv_thr=1.0D-8 , / ATOMIC_SPECIES Nb 92.9064 Nb.pbe-sR-sc-us.UPF Cu 63.546 Cu.pbe-sR-us.UPF S 32.06 S.pbe-van-bm.UPF ATOMIC_POSITIONS crystal Nb 0.000000000 0.000000000 0.000000000 Nb -1.000000000 0.000000000 0.000000000 Nb 0.000000000 0.000000000 -1.000000000 Nb 1.000000000 0.000000000 0.000000000 Cu 0.500000000 0.000000000 0.000000000 Cu 0.000000000 0.000000000 -0.500000000 Cu -0.500000000 0.000000000 0.000000000 Cu 0.000000000 -0.500000000 0.000000000 Cu 0.000000000 0.500000000 0.000000000 Cu 0.000000000 0.000000000 0.500000000 S 0.242599953 0.242599953 0.242599953 S 0.242599953 -0.242599953 -0.242599953 S -0.242599953 0.242599953 -0.242599953 S -0.242599953 -0.242599953 0.242599953 S -0.757400047 0.242599953 0.242599953 S 0.242599953 0.242599953 -0.757400047 S -0.757400047 -0.242599953 -0.242599953 S 0.757400047 0.242599953 -0.242599953 S -0.242599953 -0.242599953 -0.757400047 S 0.757400047 -0.242599953 0.242599953 K_POINTS gamma | -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120327/e0400c5c/attachment.htm From carlo.nervi at unito.it Tue Mar 27 10:41:46 2012 From: carlo.nervi at unito.it (Carlo Nervi) Date: Tue, 27 Mar 2012 10:41:46 +0200 Subject: [Pw_forum] Problems in running check-pw.x.j In-Reply-To: <1332780124.10829.6.camel@fe12lx.fisica.uniud.it> References: <1332780124.10829.6.camel@fe12lx.fisica.uniud.it> Message-ID: <4F717D4A.4080802@unito.it> Hi Paolo, hello community... your experience could be of great help: I also tried to use check-pw.x.j on QE 4.3.2. First I did not use mpirun: it passed with 1-2 not significant numerical discrepancy. By using "mpirun -n 2" more discrepancies appears (sometimes very different number of iterations, i.e. 86 instead of 57 in lda+U_gamma test). By using "mpirun -n 48" it crash at dipole calculation. Too fast for 48 cores? Up to now I used pw.x "apparently" without problems, but...should I be worried? QE was compiled with gfortran 4.6.1 and acml 5.0.0 (libacml.a and libacml_mv.a) and with amdlibm 3.0.1 Thanks, Carlo Il 26/03/2012 18.42, Paolo Giannozzi ha scritto: > On Mon, 2012-03-26 at 18:18 +0530, Abhinav 122 wrote: > >> I received the following error during check-pw.x.j. >> Please suggest the required steps to remove the following errors. > > most likely, your compiler is buggy. > > P. -- ------------------------------------------------------------ Prof. Carlo Nervi carlo.nervi at unito.it Tel:+39 0116707507/8 Fax: +39 0116707855 - Dipartimento di Chimica, via P. Giuria 7, 10125 Torino, Italy. http://lem.ch.unito.it/ From Lorenzo.Paulatto at impmc.upmc.fr Tue Mar 27 10:54:58 2012 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Tue, 27 Mar 2012 10:54:58 +0200 Subject: [Pw_forum] Problems in running check-pw.x.j In-Reply-To: <4F717D4A.4080802@unito.it> References: <1332780124.10829.6.camel@fe12lx.fisica.uniud.it> <4F717D4A.4080802@unito.it> Message-ID: On Tue, 27 Mar 2012 10:41:46 +0200, Carlo Nervi wrote: > By using "mpirun -n 48" it crash at dipole calculation. Too fast for 48 > cores? Some test are too mall to be run with so many processors. I.e. most tests only have one or a few k-points, so they can only be run with one or a few pools. In particular, the dipole test a FFT grid with only 38 points along the Z axis, hence it cannot parallelized on more then 38 processors per pool (without using bands, taskground or openmp). You can see it at the beginning: sticks: dense smooth PW G-vecs: dense smooth PW Min 7 7 1 728 728 22 Max 8 8 2 816 816 146 Sum 303 303 75 29755 29755 3661 Tot 152 152 38 You see that the "tot" value for PW says 38. You can also notice that dimension constraints of the DFFT algorithm make you waste a lot of cpu time (every cpu doubles the size of its FFT grid along z!). Running with 39 cpus you do actually get this error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 38 from n_plane_waves : error # 1 No plane waves found: running on too many processors? %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% for some reason this message does not get printed to stdout, but you can get it from the CRASH file. bests -- Lorenzo Paulatto IdR CNRS @ IMPMC/UPMC - Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www.impmc.upmc.fr/~paulatto/ mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From giannozz at democritos.it Tue Mar 27 11:02:05 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 27 Mar 2012 11:02:05 +0200 Subject: [Pw_forum] Problems in running check-pw.x.j In-Reply-To: <4F717D4A.4080802@unito.it> References: <1332780124.10829.6.camel@fe12lx.fisica.uniud.it> <4F717D4A.4080802@unito.it> Message-ID: <1332838925.12449.6.camel@fe12lx.fisica.uniud.it> On Tue, 2012-03-27 at 10:41 +0200, Carlo Nervi wrote: > By using "mpirun -n 2" more discrepancies appears (sometimes very > different number of iterations, i.e. 86 instead of 57 in lda+U_gamma test). the lda+U test is especially sensitive to small numerical differences, and the Gamma-only one seems to be the most sensitive of all. I suspect that the origin of such numerical differences between is mainly in mathematical libraries, blas and lapack. If so, there isn't much that can be done P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Tue Mar 27 11:04:39 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 27 Mar 2012 11:04:39 +0200 Subject: [Pw_forum] problems with band structure calculations for SiC between ibrav 2 and ibrav 0 In-Reply-To: References: Message-ID: <1332839079.12449.8.camel@fe12lx.fisica.uniud.it> On Fri, 2012-03-23 at 17:20 -0600, Tram Bui wrote: > However, I did the same calculation process using ibrav=0 to > confirm my band structure, now I used k-point path of simple > cubic BZ including : X,M,R, and gamma points. But my band > structure do not seem to be correct. why? P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giuseppe.mattioli at ism.cnr.it Tue Mar 27 11:53:28 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Tue, 27 Mar 2012 11:53:28 +0200 Subject: [Pw_forum] Fwd: [xcrysden]:how to get the output structure file as xyz format In-Reply-To: References: Message-ID: <201203271153.28321.giuseppe.mattioli@ism.cnr.it> The xsf file (standard xcrysden output) contains cartesian coordinates in angstrom. If you substitute by hand Z (numbers) with appropriate atom names you will obtain a xyz file HTH Giuseppe On Monday 26 March 2012 22:01:04 chengyu yang wrote: > Can some one else help please? > Thanks. > > > Chengyu Yang > MMAE, UCF -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: From siyouber at yahoo.fr Tue Mar 27 12:16:03 2012 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Tue, 27 Mar 2012 11:16:03 +0100 (BST) Subject: [Pw_forum] Fwd: [xcrysden]:how to get the output structure file as xyz format In-Reply-To: <1332843276.72400.YahooMailNeo@web171203.mail.ir2.yahoo.com> References: <201203271153.28321.giuseppe.mattioli@ism.cnr.it> <1332843276.72400.YahooMailNeo@web171203.mail.ir2.yahoo.com> Message-ID: <1332843363.75201.YahooMailNeo@web171204.mail.ir2.yahoo.com> Exatly, As Giuseppe said, the cartesian coordinates of the atoms are written under the heading ATOMS in the xsf file in angstrom. Therefore it willbe necessary in your new QE input to change ATOMIC_POSITIONS{crystal} to ATOMIC_POSITIONS{angstrom}.? Note also that the followings parameters should be modified accordingly: nat, celldm(1) or CELL_PARAMETERS. Bertrand ********************** Bertrand SITAMTZE YOUMBI Laboratory of Material Sciences University of Yaound? I-Cameroon ________________________________ De?: Giuseppe Mattioli ??: pw_forum at pwscf.org Envoy? le : Mardi 27 mars 2012 11h53 Objet?: Re: [Pw_forum] Fwd: [xcrysden]:how to get the output structure file as xyz format The xsf file (standard xcrysden output) contains cartesian coordinates in angstrom. If you substitute by hand Z (numbers) with appropriate atom names you will obtain a xyz file HTH Giuseppe On Monday 26 March 2012 22:01:04 chengyu yang wrote: > Can some one else help please? > Thanks. > > > Chengyu Yang > MMAE, UCF -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? Giuseppe Mattioli? ? ? ? ? ? ? ? ? ? ? ? ? ? ? CNR - ISTITUTO DI STRUTTURA DELLA MATERIA? ? v. Salaria Km 29,300 - C.P. 10? ? ? ? ? ? ? ? ? I 00015 - Monterotondo Stazione (RM)? ? ? ? ? ? Tel + 39 06 90672836 - Fax +39 06 90672316? ? ? E-mail: _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120327/082142da/attachment.htm From ramzialaya at hotmail.fr Tue Mar 27 12:38:56 2012 From: ramzialaya at hotmail.fr (ramzi alaya) Date: Tue, 27 Mar 2012 11:38:56 +0100 Subject: [Pw_forum] xcrysden Message-ID: Dear all, I have a file input structure Zinc blenbe relaxed, do I draw this structure with xcrysden? Can you help me out? Thank you. Regards. ********************************************************************************** Ramzi Alaya E-mail : ramzialaya at hotmail.fr Facult? des Sciences de Gab?s, Cit? Erriadh 6072 Gab?s- Tunisie Unit? de Recherche sur les H?t?ro-Epitaxies et Applications -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120327/d89188f3/attachment-0001.htm From elie.moujaes at hotmail.co.uk Tue Mar 27 19:35:40 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Tue, 27 Mar 2012 18:35:40 +0100 Subject: [Pw_forum] Input for lambda.x execution for el-ph coupling In-Reply-To: <4F6FF284.7080803@buffalo.edu> References: , <4F6FF284.7080803@buffalo.edu> Message-ID: Thanks very much for your response. So if I understood correctly, the points used for the el-ph calculations (obtained from ph.x) in my case 10 x 10x 1 (14 q points) are the ones to be used in the lambda.in file right? what about the weight of each point? do we need to give them in the input and how to calculate them? Thanks again Date: Mon, 26 Mar 2012 00:37:24 -0400 From: bahadira at buffalo.edu To: pw_forum at pwscf.org Subject: Re: [Pw_forum] Input for lambda.x execution for el-ph coupling if you know the q-grid that you used in elphon calculation, you can just use kpoint.x and give the information about system as follow: bravais lattice >> {your bravis lattice no 1...14} filout [mesh_k] >> {just hit enter} then it will asks for some info (depends on your lattice), just enter them . . . mesh: n1 n2 n3 >> {enter your q-grid in X X X format "example: 8 8 8"} mesh: k1 k2 k3 (0 no shift, 1 shifted) >> enter 0 0 0 (no shift for all direction) write all k? [f] >> {just hit enter} then read the file that code creates named mesh_k hope it works bahadir On 03/25/2012 09:10 PM, Elie M wrote: Dear all, I want to use the lambda.x executable (within the el-ph interaction package) to calculate the el-ph coefficient lambda and also Tc. I have read the input in example07 but have not quite understood how to produce the points in the input file (it states using kpoints.x) but still a bit vague for me..Any clarification regarding this issue would be appreciated. Thanks Regards Elie Moudaes University of Nottimgham NG7 2RD UK _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr.Bahadir Altintas * Dept. of Chemistry SUNY Buffalo NY,USA * Abant Izzet Baysal University Dept. of Computer Education Bolu,Turkey _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120327/fec41bae/attachment.htm From bahadira at buffalo.edu Tue Mar 27 19:41:29 2012 From: bahadira at buffalo.edu (bahadir) Date: Tue, 27 Mar 2012 13:41:29 -0400 Subject: [Pw_forum] Input for lambda.x execution for el-ph coupling In-Reply-To: References: , <4F6FF284.7080803@buffalo.edu> Message-ID: <4F71FBC9.3080502@buffalo.edu> if you are talking about the q-points in elphon out file(whis are used for naming elph.XXXXXXXXXXXX files), those are not the q-points that should be used in lambda.in file. you have to generate q points by the kpoint.x as i explained in previous reply and obtain mesh_k file as an output of kpoint.x. it will give you the qpoints and their weights(should give same number of q points as in elhon output file, if you say 14q points it should give 14 points in mesh_k file), and yes you must enter the weights in lambda.in file. bahadir On 03/27/2012 01:35 PM, Elie M wrote: > Thanks very much for your response. So if I understood correctly, the > points used for the el-ph calculations (obtained from ph.x) in my case > 10 x 10x 1 (14 q points) are the ones to be used in the lambda.in file > right? what about the weight of each point? do we need to give them in > the input and how to calculate them? > > > Thanks again > > ------------------------------------------------------------------------ > Date: Mon, 26 Mar 2012 00:37:24 -0400 > From: bahadira at buffalo.edu > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] Input for lambda.x execution for el-ph coupling > > > if you know the q-grid that you used in elphon calculation, you can > just use kpoint.x and give the information about system as follow: > > bravais lattice >> {your bravis lattice no 1...14} > filout [mesh_k] >> {just hit enter} > > then it will asks for some info (depends on your lattice), just enter them > . > . > . > mesh: n1 n2 n3 >> {enter your q-grid in X X X format "example: 8 8 8"} > mesh: k1 k2 k3 (0 no shift, 1 shifted) >> enter 0 0 0 (no shift for > all direction) > write all k? [f] >> {just hit enter} > > then read the file that code creates named mesh_k > > hope it works > > > bahadir > > > On 03/25/2012 09:10 PM, Elie M wrote: > > Dear all, > > I want to use the lambda.x executable (within the el-ph > interaction package) to calculate the el-ph coefficient lambda and > also Tc. I have read the input in example07 but have not quite > understood how to produce the points in the input file (it states > using kpoints.x) but still a bit vague for me..Any clarification > regarding this issue would be appreciated. Thanks > > > Regards > > Elie Moudaes > University of Nottimgham > NG7 2RD > UK > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > Dr.Bahadir Altintas > > * Dept. of Chemistry > SUNY Buffalo > NY,USA > > * Abant Izzet Baysal University > Dept. of Computer Education > Bolu,Turkey > > _______________________________________________ Pw_forum mailing list > Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Dr.Bahadir Altintas * Dept. of Chemistry SUNY Buffalo NY,USA * Abant Izzet Baysal University Dept. of Computer Education Bolu,Turkey -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120327/a34d0803/attachment.htm From elie.moujaes at hotmail.co.uk Wed Mar 28 00:00:37 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Tue, 27 Mar 2012 23:00:37 +0100 Subject: [Pw_forum] Input for lambda.x execution for el-ph coupling In-Reply-To: <4F71FBC9.3080502@buffalo.edu> References: , , <4F6FF284.7080803@buffalo.edu>, , <4F71FBC9.3080502@buffalo.edu> Message-ID: Thanks for your help. i have successfully produced the file mesh_k with kpoints.x. One more thing : In the input we have smearing method set to one; mine is methfessel-paxton; does this correspond to smearing method =2? and what about the Coulom coefficient mu at the end of the input file? Is it found in the omega_log file? where is that situated? I ma deling with graphene. Thanks again for your help. Elie Koujaes University of NottsNG7 2RDUK Date: Tue, 27 Mar 2012 13:41:29 -0400 From: bahadira at buffalo.edu To: pw_forum at pwscf.org Subject: Re: [Pw_forum] Input for lambda.x execution for el-ph coupling if you are talking about the q-points in elphon out file(whis are used for naming elph.XXXXXXXXXXXX files), those are not the q-points that should be used in lambda.in file. you have to generate q points by the kpoint.x as i explained in previous reply and obtain mesh_k file as an output of kpoint.x. it will give you the qpoints and their weights(should give same number of q points as in elhon output file, if you say 14q points it should give 14 points in mesh_k file), and yes you must enter the weights in lambda.in file. bahadir On 03/27/2012 01:35 PM, Elie M wrote: Thanks very much for your response. So if I understood correctly, the points used for the el-ph calculations (obtained from ph.x) in my case 10 x 10x 1 (14 q points) are the ones to be used in the lambda.in file right? what about the weight of each point? do we need to give them in the input and how to calculate them? Thanks again Date: Mon, 26 Mar 2012 00:37:24 -0400 From: bahadira at buffalo.edu To: pw_forum at pwscf.org Subject: Re: [Pw_forum] Input for lambda.x execution for el-ph coupling if you know the q-grid that you used in elphon calculation, you can just use kpoint.x and give the information about system as follow: bravais lattice >> {your bravis lattice no 1...14} filout [mesh_k] >> {just hit enter} then it will asks for some info (depends on your lattice), just enter them . . . mesh: n1 n2 n3 >> {enter your q-grid in X X X format "example: 8 8 8"} mesh: k1 k2 k3 (0 no shift, 1 shifted) >> enter 0 0 0 (no shift for all direction) write all k? [f] >> {just hit enter} then read the file that code creates named mesh_k hope it works bahadir On 03/25/2012 09:10 PM, Elie M wrote: Dear all, I want to use the lambda.x executable (within the el-ph interaction package) to calculate the el-ph coefficient lambda and also Tc. I have read the input in example07 but have not quite understood how to produce the points in the input file (it states using kpoints.x) but still a bit vague for me..Any clarification regarding this issue would be appreciated. Thanks Regards Elie Moudaes University of Nottimgham NG7 2RD UK _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr.Bahadir Altintas * Dept. of Chemistry SUNY Buffalo NY,USA * Abant Izzet Baysal University Dept. of Computer Education Bolu,Turkey _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr.Bahadir Altintas * Dept. of Chemistry SUNY Buffalo NY,USA * Abant Izzet Baysal University Dept. of Computer Education Bolu,Turkey _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120327/77e2cbf3/attachment-0001.htm From bahadira at buffalo.edu Wed Mar 28 04:18:44 2012 From: bahadira at buffalo.edu (bahadir) Date: Tue, 27 Mar 2012 22:18:44 -0400 Subject: [Pw_forum] Input for lambda.x execution for el-ph coupling In-Reply-To: References: , , <4F6FF284.7080803@buffalo.edu>, , <4F71FBC9.3080502@buffalo.edu> Message-ID: <4F727504.7050902@buffalo.edu> Dear Elie, as given in lambda.f90 header, smearing method : 0 for simple gaussian, 1 for Methfessel-Paxton you have to decide what mu should be for your system. as i have seen in most articles, intermediate value is ~0.12 but depends on system. it cannot be found in any output file. bahadir On 03/27/2012 06:00 PM, Elie M wrote: > Thanks for your help. i have successfully produced the file mesh_k > with kpoints.x. One more thing : In the input we have smearing method > set to one; mine is methfessel-paxton; does this correspond to > smearing method =2? and what about the Coulom coefficient mu at the > end of the input file? Is it found in the omega_log file? where is > that situated? I ma deling with graphene. Thanks again for your help. > > Elie Koujaes > > University of Notts > NG7 2RD > UK > > ------------------------------------------------------------------------ > Date: Tue, 27 Mar 2012 13:41:29 -0400 > From: bahadira at buffalo.edu > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] Input for lambda.x execution for el-ph coupling > > if you are talking about the q-points in elphon out file(whis are used > for naming elph.XXXXXXXXXXXX files), those are not the q-points that > should be used in lambda.in file. you have to generate q points by the > kpoint.x as i explained in previous reply and obtain mesh_k file as an > output of kpoint.x. it will give you the qpoints and their > weights(should give same number of q points as in elhon output file, > if you say 14q points it should give 14 points in mesh_k file), and > yes you must enter the weights in lambda.in file. > > bahadir > > On 03/27/2012 01:35 PM, Elie M wrote: > > Thanks very much for your response. So if I understood correctly, > the points used for the el-ph calculations (obtained from ph.x) in > my case 10 x 10x 1 (14 q points) are the ones to be used in the > lambda.in file right? what about the weight of each point? do we > need to give them in the input and how to calculate them? > > > Thanks again > > ------------------------------------------------------------------------ > Date: Mon, 26 Mar 2012 00:37:24 -0400 > From: bahadira at buffalo.edu > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] Input for lambda.x execution for el-ph > coupling > > > if you know the q-grid that you used in elphon calculation, you > can just use kpoint.x and give the information about system as follow: > > bravais lattice >> {your bravis lattice no 1...14} > filout [mesh_k] >> {just hit enter} > > then it will asks for some info (depends on your lattice), just > enter them > . > . > . > mesh: n1 n2 n3 >> {enter your q-grid in X X X format "example: 8 > 8 8"} > mesh: k1 k2 k3 (0 no shift, 1 shifted) >> enter 0 0 0 (no shift > for all direction) > write all k? [f] >> {just hit enter} > > then read the file that code creates named mesh_k > > hope it works > > > bahadir > > > On 03/25/2012 09:10 PM, Elie M wrote: > > Dear all, > > I want to use the lambda.x executable (within the el-ph > interaction package) to calculate the el-ph coefficient lambda > and also Tc. I have read the input in example07 but have not > quite understood how to produce the points in the input file > (it states using kpoints.x) but still a bit vague for me..Any > clarification regarding this issue would be appreciated. Thanks > > > Regards > > Elie Moudaes > University of Nottimgham > NG7 2RD > UK > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > Dr.Bahadir Altintas > > * Dept. of Chemistry > SUNY Buffalo > NY,USA > > * Abant Izzet Baysal University > Dept. of Computer Education > Bolu,Turkey > > > _______________________________________________ Pw_forum mailing > list Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > Dr.Bahadir Altintas > > * Dept. of Chemistry > SUNY Buffalo > NY,USA > > * Abant Izzet Baysal University > Dept. of Computer Education > Bolu,Turkey > > _______________________________________________ Pw_forum mailing list > Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Dr.Bahadir Altintas * Dept. of Chemistry SUNY Buffalo NY,USA * Abant Izzet Baysal University Dept. of Computer Education Bolu,Turkey -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120327/7ab4f954/attachment.htm From elie.moujaes at hotmail.co.uk Wed Mar 28 04:52:54 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Wed, 28 Mar 2012 03:52:54 +0100 Subject: [Pw_forum] Input for lambda.x execution for el-ph coupling In-Reply-To: <4F727504.7050902@buffalo.edu> References: , , , <4F6FF284.7080803@buffalo.edu>, , , , <4F71FBC9.3080502@buffalo.edu>, , <4F727504.7050902@buffalo.edu> Message-ID: Thanks again for your help Regards Elie Date: Tue, 27 Mar 2012 22:18:44 -0400 From: bahadira at buffalo.edu To: pw_forum at pwscf.org Subject: Re: [Pw_forum] Input for lambda.x execution for el-ph coupling Dear Elie, as given in lambda.f90 header, smearing method : 0 for simple gaussian, 1 for Methfessel-Paxton you have to decide what mu should be for your system. as i have seen in most articles, intermediate value is ~0.12 but depends on system. it cannot be found in any output file. bahadir On 03/27/2012 06:00 PM, Elie M wrote: Thanks for your help. i have successfully produced the file mesh_k with kpoints.x. One more thing : In the input we have smearing method set to one; mine is methfessel-paxton; does this correspond to smearing method =2? and what about the Coulom coefficient mu at the end of the input file? Is it found in the omega_log file? where is that situated? I ma deling with graphene. Thanks again for your help. Elie Koujaes University of Notts NG7 2RD UK Date: Tue, 27 Mar 2012 13:41:29 -0400 From: bahadira at buffalo.edu To: pw_forum at pwscf.org Subject: Re: [Pw_forum] Input for lambda.x execution for el-ph coupling if you are talking about the q-points in elphon out file(whis are used for naming elph.XXXXXXXXXXXX files), those are not the q-points that should be used in lambda.in file. you have to generate q points by the kpoint.x as i explained in previous reply and obtain mesh_k file as an output of kpoint.x. it will give you the qpoints and their weights(should give same number of q points as in elhon output file, if you say 14q points it should give 14 points in mesh_k file), and yes you must enter the weights in lambda.in file. bahadir On 03/27/2012 01:35 PM, Elie M wrote: Thanks very much for your response. So if I understood correctly, the points used for the el-ph calculations (obtained from ph.x) in my case 10 x 10x 1 (14 q points) are the ones to be used in the lambda.in file right? what about the weight of each point? do we need to give them in the input and how to calculate them? Thanks again Date: Mon, 26 Mar 2012 00:37:24 -0400 From: bahadira at buffalo.edu To: pw_forum at pwscf.org Subject: Re: [Pw_forum] Input for lambda.x execution for el-ph coupling if you know the q-grid that you used in elphon calculation, you can just use kpoint.x and give the information about system as follow: bravais lattice >> {your bravis lattice no 1...14} filout [mesh_k] >> {just hit enter} then it will asks for some info (depends on your lattice), just enter them . . . mesh: n1 n2 n3 >> {enter your q-grid in X X X format "example: 8 8 8"} mesh: k1 k2 k3 (0 no shift, 1 shifted) >> enter 0 0 0 (no shift for all direction) write all k? [f] >> {just hit enter} then read the file that code creates named mesh_k hope it works bahadir On 03/25/2012 09:10 PM, Elie M wrote: Dear all, I want to use the lambda.x executable (within the el-ph interaction package) to calculate the el-ph coefficient lambda and also Tc. I have read the input in example07 but have not quite understood how to produce the points in the input file (it states using kpoints.x) but still a bit vague for me..Any clarification regarding this issue would be appreciated. Thanks Regards Elie Moudaes University of Nottimgham NG7 2RD UK _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr.Bahadir Altintas * Dept. of Chemistry SUNY Buffalo NY,USA * Abant Izzet Baysal University Dept. of Computer Education Bolu,Turkey _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr.Bahadir Altintas * Dept. of Chemistry SUNY Buffalo NY,USA * Abant Izzet Baysal University Dept. of Computer Education Bolu,Turkey _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr.Bahadir Altintas * Dept. of Chemistry SUNY Buffalo NY,USA * Abant Izzet Baysal University Dept. of Computer Education Bolu,Turkey _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120328/d36f7121/attachment-0001.htm From sufeer03 at gmail.com Wed Mar 28 11:25:36 2012 From: sufeer03 at gmail.com (sufyan) Date: Wed, 28 Mar 2012 09:25:36 +0000 Subject: [Pw_forum] Tow question about band gap and occupations= 'smearing or fixed Message-ID: Dear quantum espresso user, i study a case with different constrain and under some constrain this case changes from conductor to semiconductor and vers-versa and I have a question firstly about "occupations= 'smearing or fixed '" what can i do with it ? secondly Does the pw.x give the band gap as numerical results in the out file ? thanks sufyan naji -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120328/495310a0/attachment.htm From nicola.marzari at epfl.ch Wed Mar 28 11:28:30 2012 From: nicola.marzari at epfl.ch (Nicola Marzari) Date: Wed, 28 Mar 2012 11:28:30 +0200 Subject: [Pw_forum] Tow question about band gap and occupations= 'smearing or fixed In-Reply-To: References: Message-ID: <4F72D9BE.4060305@epfl.ch> There is no harm in using smearing in a semiconductor/insulator (only an increased cost in the calculation). To get the band gap you need in any case the empty states - but note that unless you know at which k-point the band gap is, you need to do a close examination of the entire band structure. last, of course the dft band gap is fairly useless. nicola On 28/03/2012 11:25, sufyan wrote: > Dear quantum espresso user, i study a case with different constrain and > under some constrain this case changes from conductor to semiconductor > and vers-versa and I have a question firstly about "occupations= > 'smearing or fixed '" what can i do with it ? secondly Does the pw.x > give the band gap as numerical results in the out file ? thanks sufyan naji > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ---------------------------------------------------------------------- Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL From tone.kokalj at ijs.si Wed Mar 28 11:53:21 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 28 Mar 2012 11:53:21 +0200 Subject: [Pw_forum] xcrysden In-Reply-To: References: Message-ID: <1332928401.14514.12.camel@catalyst.ijs.si> On Tue, 2012-03-27 at 11:38 +0100, ramzi alaya wrote: > Dear all, > > > I have a file input structure Zinc blenbe relaxed, do I draw this > structure with xcrysden? > Can you help me out? You would like to visualize the structure from your pw.x input file or what? If so you may try with: xcrysden --pwi filename Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From pandey.bramha at gmail.com Wed Mar 28 12:20:53 2012 From: pandey.bramha at gmail.com (bramha pandey) Date: Wed, 28 Mar 2012 15:50:53 +0530 Subject: [Pw_forum] Tow question about band gap and occupations= 'smearing or fixed In-Reply-To: <4F72D9BE.4060305@epfl.ch> References: <4F72D9BE.4060305@epfl.ch> Message-ID: 2012/3/28 Nicola Marzari > > > There is no harm in using smearing in a semiconductor/insulator (only > an increased cost in the calculation). > > To get the band gap you need in any case the empty states - but note that > unless you know at which k-point the band gap is, you need to do a close > examination of the entire band structure. > > last, of course the dft band gap is fairly useless. > Dear Sir, so what approch should we take to calculate the band gap of semiconductor structure in QE...Thanks in advanced for your kind response. > > nicola > > > On 28/03/2012 11:25, sufyan wrote: > > Dear quantum espresso user, i study a case with different constrain and > > under some constrain this case changes from conductor to semiconductor > > and vers-versa and I have a question firstly about "occupations= > > 'smearing or fixed '" what can i do with it ? secondly Does the pw.x > > give the band gap as numerical results in the out file ? thanks sufyan > naji > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > -- > > ---------------------------------------------------------------------- > Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Thanks and Regards Bramha Prasad Pandey GLA University, Mathura. INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120328/d562a6cf/attachment.htm From giuseppe.mattioli at ism.cnr.it Wed Mar 28 12:46:41 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Wed, 28 Mar 2012 12:46:41 +0200 Subject: [Pw_forum] Tow question about band gap and occupations= 'smearing or fixed In-Reply-To: References: <4F72D9BE.4060305@epfl.ch> Message-ID: <201203281246.41892.giuseppe.mattioli@ism.cnr.it> Dear Naji (and Nicola) > Dear Sir, so what approch should we take to calculate the band gap of > semiconductor structure in QE... > > last, of course the dft band gap is fairly useless. Very old question, old like DFT... If you cannot afford anything but DFT, then you are stuck to DFT errors (see, for instance, Paula Mori-Sanchez, Aron J. Cohen, and Weitao Yang, PRL 100, 146401 (2008)). But DFT band gaps, if not accurate, may be large enough to perform investigations on semiconductor defects, interfaces, ... If you are working on unit cells and you need more accurate predictions you may consider to perform hybrid exact-exchange calculations, and this is only one of the solutions. If you have to deal with larger supercells, you may try DFT+U corrections. Hard to say without looking at your system. Last but not least, Please remember to sign your posts and to provide your scientific affiliation. HTH Giuseppe On Wednesday 28 March 2012 12:20:53 bramha pandey wrote: > 2012/3/28 Nicola Marzari > > > There is no harm in using smearing in a semiconductor/insulator (only > > an increased cost in the calculation). > > > > To get the band gap you need in any case the empty states - but note that > > unless you know at which k-point the band gap is, you need to do a close > > examination of the entire band structure. > > > > last, of course the dft band gap is fairly useless. > > Dear Sir, so what approch should we take to calculate the band gap of > semiconductor structure in QE...Thanks in advanced for your kind response. > > > nicola > > > > On 28/03/2012 11:25, sufyan wrote: > > > Dear quantum espresso user, i study a case with different constrain and > > > under some constrain this case changes from conductor to semiconductor > > > and vers-versa and I have a question firstly about "occupations= > > > 'smearing or fixed '" what can i do with it ? secondly Does the pw.x > > > give the band gap as numerical results in the out file ? thanks sufyan > > > > naji > > > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > > > > ---------------------------------------------------------------------- > > Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: From vormar at gmail.com Wed Mar 28 13:47:31 2012 From: vormar at gmail.com (Marci) Date: Wed, 28 Mar 2012 13:47:31 +0200 Subject: [Pw_forum] electron-phonon matrix elements for molecules Message-ID: Dear Users and Developers, I would like to calculate electron-phonon matrix elements for molecular systems. As stated in the FAQ/12.8.0.6, electron-phonon calculations are presently implemented for metals only. I think this constraint is due to the integration over the Fermi surface to obtain the electron-phonon coefficients (\lambda). However, I'm not interested in such integration and only the electron-phonon matrix elements are needed. Thus, instead of commenting out the corresponding part of the code I decided to use an artifical small gaussian smearing so that there are no fractional occupations, but still, the code does not complain and calculates everything I need. In order to test whether I get meaningful numbers for a system with only one k-point (gamma) I decided to set up the following test: I compared the electron-phonon matrix elements of a 2x2x2 supercell of silicon (16 atoms), where the BZ is sampled only by the gamma point and primitive cell of silicon (2 atoms), where the BZ is sampled by a 2x2x2 unshifted MP scheme. If all numerical details (cutoff, convergence criteria) are the same then in principle these two calculations should yield exactly the same results within numerical noise. Indeed, total energies/atom are the same, single particle energies can be easily mapped to each other, and also phonon modes are the same, though there are little bit larger than expected deviations (in order of 0.1-1 cm^{-1}) especially for modes whose energy should be zero. Interestingly, when I printed the electron-phonon matrix elements (el_ph_mat in PH/elphon.f90) and compared matrix elements of corresponding non-degenerate bands (so that arbitrary rotations within a degenerate subspace do not matter) I found orders of magnitude differences in some cases. Also, there were non-zero matrix elements even when they should have been zero by symmetry. I expected that by doing the mapping between phonon modes and electronic bands, electron-phonon matrix elements would have been the same. Am I missing something in the comparison? Is there any normalization or any other fundamental/numerical issue of calculating electron-phonon matrix elements for insulators / molecules using only one k-point (gamma)? The espresso version is 4.0.5, since this is the one which is interfaced to a code we are using for post processing. Thanks in advance. Yours sincerely, Marton Voros -- PhD student Department of Atomic Physics Budapest University of Technology and Economics Budafoki ?t 8., H-1111, Budapest, Hungary www.fat.bme.hu/MartonVoros From pandey.bramha at gmail.com Wed Mar 28 15:05:57 2012 From: pandey.bramha at gmail.com (bramha pandey) Date: Wed, 28 Mar 2012 18:35:57 +0530 Subject: [Pw_forum] Tow question about band gap and occupations= 'smearing or fixed In-Reply-To: <201203281246.41892.giuseppe.mattioli@ism.cnr.it> References: <4F72D9BE.4060305@epfl.ch> <201203281246.41892.giuseppe.mattioli@ism.cnr.it> Message-ID: Thank you Dear Giuseppe Mattioli and Nicola for your quick reply to let me the use of hybrid exact-exchange calculations to get some what accurate value of band gap energy in quantum espresso. Thanks and Regards Bramha Prasad Pandey GLA University, Mathura. INDIA. On Wed, Mar 28, 2012 at 4:16 PM, Giuseppe Mattioli < giuseppe.mattioli at ism.cnr.it> wrote: > > Dear Naji (and Nicola) > > > Dear Sir, so what approch should we take to calculate the band gap of > > semiconductor structure in QE... > > > > last, of course the dft band gap is fairly useless. > > Very old question, old like DFT... If you cannot afford anything but DFT, > then you are stuck to DFT > errors (see, for instance, Paula Mori-Sanchez, Aron J. Cohen, and Weitao > Yang, PRL 100, 146401 > (2008)). But DFT band gaps, if not accurate, may be large enough to > perform investigations on > semiconductor defects, interfaces, ... If you are working on unit cells > and you need more accurate > predictions you may consider to perform hybrid exact-exchange > calculations, and this is only one of > the solutions. If you have to deal with larger supercells, you may try > DFT+U corrections. Hard to > say without looking at your system. > > Last but not least, Please remember to sign your posts and to provide your > scientific affiliation. > > HTH > > Giuseppe > > On Wednesday 28 March 2012 12:20:53 bramha pandey wrote: > > 2012/3/28 Nicola Marzari > > > > > There is no harm in using smearing in a semiconductor/insulator (only > > > an increased cost in the calculation). > > > > > > To get the band gap you need in any case the empty states - but note > that > > > unless you know at which k-point the band gap is, you need to do a > close > > > examination of the entire band structure. > > > > > > last, of course the dft band gap is fairly useless. > > > > Dear Sir, so what approch should we take to calculate the band gap of > > semiconductor structure in QE...Thanks in advanced for your kind > response. > > > > > nicola > > > > > > On 28/03/2012 11:25, sufyan wrote: > > > > Dear quantum espresso user, i study a case with different constrain > and > > > > under some constrain this case changes from conductor to > semiconductor > > > > and vers-versa and I have a question firstly about "occupations= > > > > 'smearing or fixed '" what can i do with it ? secondly Does the pw.x > > > > give the band gap as numerical results in the out file ? thanks > sufyan > > > > > > naji > > > > > > > _______________________________________________ > > > > Pw_forum mailing list > > > > Pw_forum at pwscf.org > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > > > > > > ---------------------------------------------------------------------- > > > Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > ******************************************************** > - Article premier - Les hommes naissent et demeurent > libres et ?gaux en droits. Les distinctions sociales > ne peuvent ?tre fond?es que sur l'utilit? commune > - Article 2 - Le but de toute association politique > est la conservation des droits naturels et > imprescriptibles de l'homme. Ces droits sont la libert?, > la propri?t?, la s?ret? et la r?sistance ? l'oppression. > ******************************************************** > > Giuseppe Mattioli > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > v. Salaria Km 29,300 - C.P. 10 > I 00015 - Monterotondo Stazione (RM) > Tel + 39 06 90672836 - Fax +39 06 90672316 > E-mail: > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Thanks and Regards Bramha Prasad Pandey GLA University, Mathura. INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120328/5bdd8235/attachment-0001.htm From tkaloni at gmail.com Wed Mar 28 15:34:13 2012 From: tkaloni at gmail.com (Thaneshwor Kaloni) Date: Wed, 28 Mar 2012 16:34:13 +0300 Subject: [Pw_forum] How to get Fermi energy applying electric field Message-ID: Dear QE_users, I am interested to apply electric field in graphene and want to see the modified band structure. It has been discussed in example31 of the 4.3.1 version. But my point is how to get Fermi energy after applying a finite electric field along z-direction? Thank you in advance. Best, Kaloni PhD Candidate at http://www.kaust.edu.sa/ KAUST, KSA Thuwal -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120328/d4955132/attachment.htm From laiwei at msu.edu Wed Mar 28 15:25:57 2012 From: laiwei at msu.edu (Wei Lai) Date: Wed, 28 Mar 2012 09:25:57 -0400 Subject: [Pw_forum] test case with structure relaxation Message-ID: Dear QE users, I am new to quantum espresso and was playing with a simple test case of variable cell relaxation. I created a virtual tetragonal MgO cell with c/a ratio as 1.4. I was expecting this ratio will become close to 1.4142 (cubic) after relaxation. However, I am getting values that are off this theoretical value. I tried to play with different threshold parameters but didn't see significant improvement. Did I miss an important parameter somewhere? I am pasting the input file. Thanks. Regards, Wei Wei Lai Michigan State University East Lansing, MI 48824 &control calculation = 'vc-relax', restart_mode='from_scratch', prefix='MgO', tstress = .true. tprnfor = .true. pseudo_dir = '/home/espresso-4.3.2/pseudo/', outdir='/home/wl2/tmp/' nstep=100 / &system ibrav= 7, celldm(1) = 5.6298, celldm(3) = 1.4, nat= 2, ntyp= 2, ecutwfc =30, input_dft='pw91' / &electrons mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / &ions ion_dynamics = 'bfgs' trust_radius_ini=1.0d-1 trust_radius_max=1.0d-3 / &cell cell_dynamics='bfgs' / ATOMIC_SPECIES Mg 24.305 Mg.pw91-np-van.UPF O 15.999 O.pw91-van_ak.UPF ATOMIC_POSITIONS Mg 0.00 0.00 0.00 O 0.00 0.00 0.70 K_POINTS (automatic) 3 3 2 0 0 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120328/c639d6cd/attachment.htm From giuseppe.mattioli at ism.cnr.it Wed Mar 28 16:43:51 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Wed, 28 Mar 2012 16:43:51 +0200 Subject: [Pw_forum] test case with structure relaxation In-Reply-To: References: Message-ID: <201203281643.51633.giuseppe.mattioli@ism.cnr.it> Dear Wei > &system > ibrav= 7, celldm(1) = 5.6298, celldm(3) = 1.4, nat= 2, ntyp= 2, > ecutwfc =30, input_dft='pw91' > / > ATOMIC_SPECIES > Mg 24.305 Mg.pw91-np-van.UPF > O 15.999 O.pw91-van_ak.UPF You are using ultrasoft pseudopotentials. You should explicitly assign a value to the ecutrho parameter (&system list). The default value is 4*ecutwfc, and it is a good value for norm conserving PPs. A 6*ecutwfc~10*ecutwfc value is considered as a safe~good one in the case of ultrasoft PPs HTH Giuseppe -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: From victor.bermudez at nrl.navy.mil Wed Mar 28 16:49:39 2012 From: victor.bermudez at nrl.navy.mil (Vic Bermudez) Date: Wed, 28 Mar 2012 10:49:39 -0400 Subject: [Pw_forum] NEB "spring constants" Message-ID: Hello, Can someone please explain the criteria for the proper choice of "k_min" and "k_max" in NEB calculations ? The default choice in QE 4.3.2 is k_min = k_max = 0.2 a.u.. However, when I run NEB job, the start-up information near the beginning of the output file says: suggested k_max = 0.6169 a.u. suggested k_min = 0.6169 a.u. I've been using the suggested values, rather than the defaults, and I'm wondering how sensitive the calculation is to this choice and also how one goes about deciding the best choice. As always, thank you in advance for your assistance ************ Victor M. Bermudez Code 6876 U.S. Naval Research Laboratory 4555 Overlook Ave., S.W. Washington, DC 20375-5347 Phone: 202-767-6728 FAX: 202-767-1165 E-mail: victor.bermudez at nrl.navy.mil From elie.moujaes at hotmail.co.uk Wed Mar 28 17:45:31 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Wed, 28 Mar 2012 16:45:31 +0100 Subject: [Pw_forum] question on electron phonon calculations. Message-ID: Dear all, Sorry to disturb you again with my question on el-phonon coupling. I am a bit confused about things..My input for matdyn.in file is: "&input asr = 'crystal', amass(1) = 12.0107 , flfrc = 'elphmgraph.fc', flfrq = 'elphmgraph.freq', la2F=.true., dos=.true., fldos= 'elphmgraph.dos', nk1=10, nk2=10, nk3=1, ndos=50"(1) Are the (nk1, nk2, nk3) points in q-space along which the DOS will be calculated?(2) what is the meaning of ndos ? My output for the el-phonon lambda coefficient is the following (lambda.x): " lambda = 0.132336 ( 0.000000) = 2442.211K N(Ef)= 0.125375 at degauss=0.005 lambda = 0.060186 ( 0.000000) = 2442.211K N(Ef)= 0.069039 at degauss=0.010 lambda = 0.025467 ( 0.000000) = 2442.211K N(Ef)= 0.084136 at degauss=0.015 lambda = 0.017078 ( 0.000044) = 1854.271K N(Ef)= 0.112212 at degauss=0.020 lambda = 0.015266 ( 0.000282) = 1854.271K N(Ef)= 0.140938 at degauss=0.025 lambda = 0.015856 ( 0.000682) = 1854.271K N(Ef)= 0.170144 at degauss=0.030 lambda = 0.017428 ( 0.001112) = 1854.271K N(Ef)= 0.199989 at degauss=0.035 lambda = 0.019354 ( 0.001435) = 1847.432K N(Ef)= 0.230702 at degauss=0.040 lambda = 0.021508 ( 0.001572) = 1822.899K N(Ef)= 0.262647 at degauss=0.045 lambda = 0.023948 ( 0.001582) = 1662.813K N(Ef)= 0.296316 at degauss=0.050lambda omega_log T_c 0.13234 2442.211 0.000 0.06019 2442.211 ********* 0.02547 2442.211 ********* 0.01708 1854.271 ********* 0.01527 1854.271 ********* 0.01586 1854.271 ********* 0.01743 1854.271 ********* 0.01935 1847.432 ********* 0.02151 1822.899 ********* 0.02395 1662.813 *********" (1) What are the above degauss values? what are they 10 in number?(2) Tc is 0.0 and not being able to be computed for other values of lambda. Is the output normal? or is there something that went wrong in the execution? Thanks a lot again Eie KoujesUniversit of NottsNG7 2RDUK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120328/fef70975/attachment.htm From laiwei at msu.edu Wed Mar 28 18:11:06 2012 From: laiwei at msu.edu (Wei Lai) Date: Wed, 28 Mar 2012 12:11:06 -0400 Subject: [Pw_forum] test case with structure relaxation In-Reply-To: <201203281643.51633.giuseppe.mattioli@ism.cnr.it> References: <201203281643.51633.giuseppe.mattioli@ism.cnr.it> Message-ID: Dear Giuseppe, I tried ecutrho as 8 or 12 times of ecutwfc=30 for ultrasoft PP. Also tried norm conserving PP with ecutwfc=70 and ecutrho=280. The c/a ratio is still far off from the expected 1.4142. Very confused. Regards, Wei Wei Lai Michigan State University East Lansing, MI 48824 On Wed, Mar 28, 2012 at 10:43 AM, Giuseppe Mattioli < giuseppe.mattioli at ism.cnr.it> wrote: > > Dear Wei > > > > &system > > ibrav= 7, celldm(1) = 5.6298, celldm(3) = 1.4, nat= 2, ntyp= 2, > > ecutwfc =30, input_dft='pw91' > > / > > > ATOMIC_SPECIES > > Mg 24.305 Mg.pw91-np-van.UPF > > O 15.999 O.pw91-van_ak.UPF > > You are using ultrasoft pseudopotentials. You should explicitly assign a > value to the ecutrho > parameter (&system list). The default value is 4*ecutwfc, and it is a good > value for norm conserving > PPs. A 6*ecutwfc~10*ecutwfc value is considered as a safe~good one in the > case of ultrasoft PPs > > HTH > > Giuseppe > > -- > ******************************************************** > - Article premier - Les hommes naissent et demeurent > libres et ?gaux en droits. Les distinctions sociales > ne peuvent ?tre fond?es que sur l'utilit? commune > - Article 2 - Le but de toute association politique > est la conservation des droits naturels et > imprescriptibles de l'homme. Ces droits sont la libert?, > la propri?t?, la s?ret? et la r?sistance ? l'oppression. > ******************************************************** > > Giuseppe Mattioli > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > v. Salaria Km 29,300 - C.P. 10 > I 00015 - Monterotondo Stazione (RM) > Tel + 39 06 90672836 - Fax +39 06 90672316 > E-mail: > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120328/66e01065/attachment-0001.htm From arebol2 at uic.edu Wed Mar 28 20:34:54 2012 From: arebol2 at uic.edu (=?iso-8859-1?Q?=22Alejandro_R=E9bola=22?=) Date: Wed, 28 Mar 2012 13:34:54 -0500 Subject: [Pw_forum] How to parallelize phonons Message-ID: Dear all, I'm trying to run phonon calculations using ph.w on a cluster (NERSC), and since I have a big number of atoms I wanted to parallelize it as much and efficiently as possible. I've been reading the documentation, and I've seen the GRID example, I was going to use this but then I saw the following at the end of the INPUT_PH.html file: On parallel machines the q point and the irreps calculations can be split automatically. The procedure is the following: " [...] 1) run pw.x with nproc processors and npools pools. 2) run ph.x with nproc*nimage processors, npools pools and nimage images. 3) run ph.x with the same input and recover=.true. on nproc processors and npools pools and only one image. During the first ph.x run the phonon code split the total amount of work into nimage copies. Each image runs with different q and/or representations. The second run of ph.x is the final run that collects all the data calculated by the images and writes the files with the dynamical matrices." Since I'm not very familiar with the terminology used here (I'm completely lost) I would like to ask some questions: 1) If I'm running on a cluster like NERSC, would I get any advantage from using the GRID method or should I just use the method outlined above? 2) In that case, what does it mean by images for a phonon calculation (I'm just familiar with images for NEB). Where could I find more documentation about this or some example? Thank you in advance, Alejandro R?bola From giannozz at democritos.it Wed Mar 28 21:01:01 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 28 Mar 2012 21:01:01 +0200 Subject: [Pw_forum] test case with structure relaxation In-Reply-To: References: Message-ID: On Mar 28, 2012, at 15:25 , Wei Lai wrote: > I created a virtual tetragonal MgO cell with c/a ratio as 1.4. > I was expecting this ratio will become close to 1.4142 (cubic) > after relaxation. your k-point grid is not symmetric and produces a small symmetry breaking. A denser grid yields a more symmetric final structure P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From payam.norouzzadeh at gmail.com Wed Mar 28 21:05:28 2012 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Wed, 28 Mar 2012 14:05:28 -0500 Subject: [Pw_forum] control of relaxation procedure Message-ID: Hello PWSCF users I used the following flags to control relaxation procedure : etot_conv_thr = 1.0E-9 , forc_conv_thr = 1.0D-4 , but the program reaches to end before satisfying those conditions together .Also nstep was a big number like 2000. What seems to be the problem? Is there any thing else I should care of it? Best regards, Payam Norouzzadeh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120328/195f1445/attachment.htm From arebol2 at uic.edu Wed Mar 28 22:05:38 2012 From: arebol2 at uic.edu (=?iso-8859-1?Q?=22Alejandro_R=E9bola=22?=) Date: Wed, 28 Mar 2012 15:05:38 -0500 Subject: [Pw_forum] How to parallelize phonons In-Reply-To: <348C4E21-9C24-4E10-A46A-D3437F65AF66@anl.gov> References: <348C4E21-9C24-4E10-A46A-D3437F65AF66@anl.gov> Message-ID: <4752da8581fb23abc27a82de340bc3e8.squirrel@webmail.uic.edu> Dear William, Thank you so much for your answer, it was very helpful, Alejandro On Wed, March 28, 2012 2:47 pm, William Parker wrote: > Dear Alejandro, > > The images in phonon calculations are groupings of the irreducible > representations of the phonon modes. Hence, the maximum number of images > is the number of representations. > > There is a speedup as one increases the number of images parallelized > over, but the speedup increases irregularly with image number since > different representations require different amounts of time to calculate. > In my limited experience, the time taken by single representations can > vary at least up to a factor of two. > > The second step does generate all of the right dynamical matrix entries, > but I have been unable to get the recover step to complete successfully > yet, though I am currently working on this (if anyone else on the list has > any comments on this, please speak up). > > Running on parallel with one image but parallelizing over k-points and FFT > grid works properly. I don't have any experience with the GRID method so > perhaps someone else can say something about that. > > I'm not aware of any more documentation beyond what you quoted. > > A simple example I run my tests on is two-atom Si with a 2x1x1 q-mesh (two > q-points, six representations), parallelizing over two images. > With only one CPU per k-point pool, the commands look like: > > mpiexec -n 1 pw.x -npool 1 -inp si.scf.cg.in >& si.scf.cg.out > mpiexec -n 2 ph.x -nimage 2 -npool 1 -inp si.ph.in >& si.ph.out > mpiexec -n 1 ph.x -nimage 1 -npool 1 -inp si.ph_recover.in >& > si.ph_recover.out > > where "diff si.ph.in si.ph_recover.in" returns "recover = .true." > > --William > > On Mar 28, 2012, at 1:34 PM, Alejandro R?bola wrote: > >> Dear all, >> >> I'm trying to run phonon calculations using ph.w on a cluster (NERSC), >> and >> since I have a big number of atoms I wanted to parallelize it as much >> and >> efficiently as possible. I've been reading the documentation, and I've >> seen the GRID example, I was going to use this but then I saw the >> following at the end of the INPUT_PH.html file: >> >> On parallel machines the q point and the irreps calculations can be >> split >> automatically. The procedure is the following: >> >> " [...] >> >> 1) run pw.x with nproc processors and npools pools. >> 2) run ph.x with nproc*nimage processors, npools pools and nimage >> images. >> 3) run ph.x with the same input and recover=.true. on nproc processors >> and npools pools and only one image. >> >> During the first ph.x run the phonon code split the total amount of >> work into nimage copies. Each image runs with different q and/or >> representations. The second run of ph.x is the final run that >> collects all the data calculated by the images and writes the files >> with the dynamical matrices." >> >> Since I'm not very familiar with the terminology used here (I'm >> completely >> lost) I would like to ask some questions: >> 1) If I'm running on a cluster like NERSC, would I get any advantage >> from >> using the GRID method or should I just use the method outlined above? >> 2) In that case, what does it mean by images for a phonon calculation >> (I'm >> just familiar with images for NEB). Where could I find more >> documentation >> about this or some example? >> Thank you in advance, >> >> Alejandro R?bola >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > ********************************************************* > William D. Parker phone: (630) 252-4834 > Computational Postdoctoral Fellow fax: (630) 252-4798 > MSD-212, Rm. C-215 > Argonne National Laboratory > 9700 S. Cass Ave. > Argonne, IL 60439 > ********************************************************* > > > > > > From wparker at anl.gov Wed Mar 28 21:47:27 2012 From: wparker at anl.gov (William Parker) Date: Wed, 28 Mar 2012 14:47:27 -0500 Subject: [Pw_forum] How to parallelize phonons In-Reply-To: References: Message-ID: <348C4E21-9C24-4E10-A46A-D3437F65AF66@anl.gov> Dear Alejandro, The images in phonon calculations are groupings of the irreducible representations of the phonon modes. Hence, the maximum number of images is the number of representations. There is a speedup as one increases the number of images parallelized over, but the speedup increases irregularly with image number since different representations require different amounts of time to calculate. In my limited experience, the time taken by single representations can vary at least up to a factor of two. The second step does generate all of the right dynamical matrix entries, but I have been unable to get the recover step to complete successfully yet, though I am currently working on this (if anyone else on the list has any comments on this, please speak up). Running on parallel with one image but parallelizing over k-points and FFT grid works properly. I don't have any experience with the GRID method so perhaps someone else can say something about that. I'm not aware of any more documentation beyond what you quoted. A simple example I run my tests on is two-atom Si with a 2x1x1 q-mesh (two q-points, six representations), parallelizing over two images. With only one CPU per k-point pool, the commands look like: mpiexec -n 1 pw.x -npool 1 -inp si.scf.cg.in >& si.scf.cg.out mpiexec -n 2 ph.x -nimage 2 -npool 1 -inp si.ph.in >& si.ph.out mpiexec -n 1 ph.x -nimage 1 -npool 1 -inp si.ph_recover.in >& si.ph_recover.out where "diff si.ph.in si.ph_recover.in" returns "recover = .true." --William On Mar 28, 2012, at 1:34 PM, Alejandro R?bola wrote: > Dear all, > > I'm trying to run phonon calculations using ph.w on a cluster (NERSC), and > since I have a big number of atoms I wanted to parallelize it as much and > efficiently as possible. I've been reading the documentation, and I've > seen the GRID example, I was going to use this but then I saw the > following at the end of the INPUT_PH.html file: > > On parallel machines the q point and the irreps calculations can be split > automatically. The procedure is the following: > > " [...] > > 1) run pw.x with nproc processors and npools pools. > 2) run ph.x with nproc*nimage processors, npools pools and nimage images. > 3) run ph.x with the same input and recover=.true. on nproc processors > and npools pools and only one image. > > During the first ph.x run the phonon code split the total amount of > work into nimage copies. Each image runs with different q and/or > representations. The second run of ph.x is the final run that > collects all the data calculated by the images and writes the files > with the dynamical matrices." > > Since I'm not very familiar with the terminology used here (I'm completely > lost) I would like to ask some questions: > 1) If I'm running on a cluster like NERSC, would I get any advantage from > using the GRID method or should I just use the method outlined above? > 2) In that case, what does it mean by images for a phonon calculation (I'm > just familiar with images for NEB). Where could I find more documentation > about this or some example? > Thank you in advance, > > Alejandro R?bola > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ********************************************************* William D. Parker phone: (630) 252-4834 Computational Postdoctoral Fellow fax: (630) 252-4798 MSD-212, Rm. C-215 Argonne National Laboratory 9700 S. Cass Ave. Argonne, IL 60439 ********************************************************* From giannozz at democritos.it Wed Mar 28 23:00:45 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 28 Mar 2012 23:00:45 +0200 Subject: [Pw_forum] How to parallelize phonons In-Reply-To: References: Message-ID: <734CB6B2-1B81-494C-9EDD-739929EC18A0@democritos.it> On Mar 28, 2012, at 20:34 , Alejandro R?bola wrote: > Where could I find more documentation about this there is something in the user guide. The reference paper is unfortunately published in an exotic place: {\it Calculation of Phonon Dispersions on the GRID using Quantum ESPRESSO}, R. di Meo, A. Dal Corso, P. Giannozzi, and S. Cozzini, in {\it Chemistry and Material Science Applications on Grid Infrastructures}, editors: S. Cozzini, A. Lagan\`a, ICTP Lecture Notes Series, Vol. 24, pp.165-183 (2009). You can parallelize over images (irreps and wavevectors) manually (i.e. splitting the complete phonon calculation into smaller pieces, sending them to many different machines, or many different jobs); or automatically, using MPI (in a single run). The latter approach allows running on a large number of processors (something that makes people in large computer facilities happy) but the load balancing is less than ideal, to say the least. A better strategy likely is to write a simple "dynamical" scheduler that submits images when groups of processors are ready, but this requires some work. > or some example? for "manual" parallelization, see examples/GRID_example P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed Mar 28 23:06:41 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 28 Mar 2012 23:06:41 +0200 Subject: [Pw_forum] How to parallelize phonons In-Reply-To: <734CB6B2-1B81-494C-9EDD-739929EC18A0@democritos.it> References: <734CB6B2-1B81-494C-9EDD-739929EC18A0@democritos.it> Message-ID: <39935049-863F-4E69-8DB7-30CC1D4DC916@democritos.it> On Mar 28, 2012, at 23:00 , Paolo Giannozzi wrote: > The reference paper is unfortunately published in an exotic place: exotic but freely downloadable: http://users.ictp.it/~pub_off/lectures/lns024/10-giannozzi/10- giannozzi.pdf > P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed Mar 28 23:08:22 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 28 Mar 2012 23:08:22 +0200 Subject: [Pw_forum] How to parallelize phonons In-Reply-To: <348C4E21-9C24-4E10-A46A-D3437F65AF66@anl.gov> References: <348C4E21-9C24-4E10-A46A-D3437F65AF66@anl.gov> Message-ID: On Mar 28, 2012, at 21:47 , William Parker wrote: > The second step does generate all of the right dynamical matrix > entries, > but I have been unable to get the recover step to complete > successfully > yet, though I am currently working on this (if anyone else on the > list has > any comments on this, please speak up). why have you been unable to perform the last step? what happens? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From arebol2 at uic.edu Wed Mar 28 23:10:25 2012 From: arebol2 at uic.edu (=?iso-8859-1?Q?=22Alejandro_R=E9bola=22?=) Date: Wed, 28 Mar 2012 16:10:25 -0500 Subject: [Pw_forum] How to parallelize phonons In-Reply-To: <39935049-863F-4E69-8DB7-30CC1D4DC916@democritos.it> References: <734CB6B2-1B81-494C-9EDD-739929EC18A0@democritos.it> <39935049-863F-4E69-8DB7-30CC1D4DC916@democritos.it> Message-ID: Dear Paolo, Thanks a lot! Alejandro On Wed, March 28, 2012 4:06 pm, Paolo Giannozzi wrote: > > On Mar 28, 2012, at 23:00 , Paolo Giannozzi wrote: > >> The reference paper is unfortunately published in an exotic place: > > exotic but freely downloadable: > http://users.ictp.it/~pub_off/lectures/lns024/10-giannozzi/10- > giannozzi.pdf >> > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > From wparker at anl.gov Thu Mar 29 05:16:46 2012 From: wparker at anl.gov (William Parker) Date: Wed, 28 Mar 2012 22:16:46 -0500 Subject: [Pw_forum] How to parallelize phonons In-Reply-To: References: <348C4E21-9C24-4E10-A46A-D3437F65AF66@anl.gov> Message-ID: <8683BB35-5EEF-4F84-A2C9-3574B645A230@anl.gov> Thanks for the followup, Paolo. The recover step happens, producing the appropriate "Restart after Phonon calculation" message, but the output insists the representations calculated on other images are still "To be done." ph.x produces a new .dyn file for the first q-point but no others. So, the remaining .dyn files from the other images are incorrect because they are incomplete, even though all the data are correctly stored in the data-file.*.xml files in the _ph*/(prefix).phsave/ directories. Any ideas? Need any more information? --William On Mar 28, 2012, at 4:08 PM, Paolo Giannozzi wrote: > > On Mar 28, 2012, at 21:47 , William Parker wrote: > >> The second step does generate all of the right dynamical matrix entries, >> but I have been unable to get the recover step to complete successfully >> yet, though I am currently working on this (if anyone else on the list has >> any comments on this, please speak up). > > why have you been unable to perform the last step? what happens? > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > ********************************************************* William D. Parker phone: (630) 252-4834 Computational Postdoctoral Fellow fax: (630) 252-4798 MSD-212, Rm. C-215 Argonne National Laboratory 9700 S. Cass Ave. Argonne, IL 60439 ********************************************************* From solayinka at biu.edu.ng Thu Mar 29 07:26:56 2012 From: solayinka at biu.edu.ng (Olayinka, Samson A.) Date: Thu, 29 Mar 2012 06:26:56 +0100 Subject: [Pw_forum] How to extract high symmetry kpoints from SCF calculation Message-ID: I need to extract kpoints from my scf calculation in order to get the K_POINTS for my bands calculation. Olayinka Samson Ph.D student University of Benin,Edo State, nigeria solayinka at biu.edu.ng From tkaloni at gmail.com Thu Mar 29 11:55:13 2012 From: tkaloni at gmail.com (Thaneshwor Kaloni) Date: Thu, 29 Mar 2012 12:55:13 +0300 Subject: [Pw_forum] regarding to SOC Message-ID: Dear QE_users, I am interested to apply spin-orbit effects in 2-D system, in particular, graphene. I have seen a example22 in the version 4.3.1. I wanted to know what type of formalism has been used, like Rashba type, Dressulhouse type or zeeman type? Thank you very much in advance. Best, Kaloni PhD student *King Abdullah University of Science and Technology* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120329/62436ce8/attachment.htm From giuseppe.mattioli at ism.cnr.it Thu Mar 29 12:26:04 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Thu, 29 Mar 2012 12:26:04 +0200 Subject: [Pw_forum] How to extract high symmetry kpoints from SCF calculation In-Reply-To: References: Message-ID: <201203291226.04742.giuseppe.mattioli@ism.cnr.it> Dear Olayinka You cannot directly extract a band structure from a scf calculation. You should already know the k- point path connecting high-symmetry points (paths for cubic and hexagonal systems can be found here: http://cst-www.nrl.navy.mil/bind/kpts/index.html), and perform a non-self-consistent calculation to produce a band structure, as shown in yourQE/examples/example01. HTH Giuseppe On Thursday 29 March 2012 07:26:56 Olayinka, Samson A. wrote: > I need to extract kpoints from my scf calculation in order to get the > K_POINTS for my bands calculation. > > > Olayinka Samson > Ph.D student > University of Benin,Edo State, nigeria > solayinka at biu.edu.ng > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: From luox at ihpc.a-star.edu.sg Thu Mar 29 13:12:16 2012 From: luox at ihpc.a-star.edu.sg (Luo Xin (IHPC)) Date: Thu, 29 Mar 2012 19:12:16 +0800 Subject: [Pw_forum] error in the phonon calculation for LO-TO splitting with spin-orbit coupling Message-ID: Dear all, I am doing the phonon calculation with spin-orbit coupling, and found that the dynmat.x can not read the .xml format. Latter I test the example 24 in the espresso-4.3.2, I found it also has this problems, Is anybody encounter this problem, or is it a bug? the error report in the example 24 is : [luox at queksy_ws results]$ dynmat.x < ptphG.dyn.in > ptphG.dyn.out Fatal error in PMPI_Barrier: Invalid communicator, error stack: PMPI_Barrier(425): MPI_Barrier(comm=0x0) failed PMPI_Barrier(385): Invalid communicator And my ptphG.dyn.in contents is: [luox at queksy_ws results]$ cat ptphG.dyn.in &input fildyn='ptdyn.xml', asr='simple' / And the contents of ptdyn.xml is : [luox at queksy_ws results]$ cat ptdyn.xml 1 1 2 1 7.550000000000000E+000 0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000 cubic -5.000000000000000E-001 0.000000000000000E+000 5.000000000000000E-001 0.000000000000000E+000 5.000000000000000E-001 5.000000000000000E-001 -5.000000000000000E-001 5.000000000000000E-001 0.000000000000000E+000 -1.000000000000000E+000 -1.000000000000000E+000 1.000000000000000E+000 1.000000000000000E+000 1.000000000000000E+000 1.000000000000000E+000 -1.000000000000000E+000 1.000000000000000E+000 -1.000000000000000E+000 1.075922187500000E+002 Pt 1.778027198666795E+005 3 1.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000 4.788570990310177E-001, 0.000000000000000E+000 2.775557561562891E-017, 0.000000000000000E+000 2.775557561562891E-017, 0.000000000000000E+000 -2.775557561562891E-017, 0.000000000000000E+000 1.985408035348115E-001, 0.000000000000000E+000 -2.775557561562891E-017, 0.000000000000000E+000 2.775557561562891E-017, 0.000000000000000E+000 2.775557561562891E-017, 0.000000000000000E+000 1.985408035348115E-001, 0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000 1.000000000000000E+000 1.985408035348115E-001, 0.000000000000000E+000 -1.387778780781446E-017, 0.000000000000000E+000 1.387778780781446E-017, 0.000000000000000E+000 -1.387778780781446E-017, 0.000000000000000E+000 1.985408035348115E-001, 0.000000000000000E+000 -1.387778780781446E-017, 0.000000000000000E+000 2.775557561562891E-017, 0.000000000000000E+000 2.775557561562891E-017, 0.000000000000000E+000 4.788570990310176E-001, 0.000000000000000E+000 0.000000000000000E+000 1.000000000000000E+000 0.000000000000000E+000 1.985408035348115E-001, 0.000000000000000E+000 -2.775557561562891E-017, 0.000000000000000E+000 2.775557561562891E-017, 0.000000000000000E+000 -2.775557561562891E-017, 0.000000000000000E+000 4.788570990310177E-001, 0.000000000000000E+000 -2.775557561562891E-017, 0.000000000000000E+000 2.775557561562891E-017, 0.000000000000000E+000 2.775557561562891E-017, 0.000000000000000E+000 1.985408035348114E-001, 0.000000000000000E+000 3.476407859655458E+000 1.159604842245717E+002 0.000000000000000E+000, 0.000000000000000E+000 7.009835776274842E-001, 0.000000000000000E+000 7.131774140398537E-001, 0.000000000000000E+000 3.476407859655459E+000 1.159604842245717E+002 1.412518191627151E-016, 0.000000000000000E+000 7.131774140398538E-001, 0.000000000000000E+000 -7.009835776274841E-001, 0.000000000000000E+000 5.398943723973670E+000 1.800893778313019E+002 -1.000000000000000E+000, 0.000000000000000E+000 1.007376071188902E-016, 0.000000000000000E+000 -9.901520554307043E-017, 0.000000000000000E+000 IHPC Values :: Impact :: Honesty :: Performance :: Co-operation This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120329/9b5f52a5/attachment-0001.htm From Michael.Mehl at nrl.navy.mil Thu Mar 29 16:17:10 2012 From: Michael.Mehl at nrl.navy.mil (Michael Mehl) Date: Thu, 29 Mar 2012 10:17:10 -0400 Subject: [Pw_forum] How to extract high symmetry kpoints from SCF calculation In-Reply-To: <201203291226.04742.giuseppe.mattioli@ism.cnr.it> References: <201203291226.04742.giuseppe.mattioli@ism.cnr.it> Message-ID: <4F746EE6.5070906@nrl.navy.mil> And for other lattice systems have a look at the Bilbao Crystallographic Server's k-point and Brillouin zone page: http://www.cryst.ehu.es/cryst/get_kvec.html which covers all the lattice types and space groups. (What can I say? They have graduate students, I don't.) On 03/29/2012 06:26 AM, Giuseppe Mattioli wrote: > Dear Olayinka > You cannot directly extract a band structure from a scf calculation. You should already know the k- > point path connecting high-symmetry points (paths for cubic and hexagonal systems can be found > here: http://cst-www.nrl.navy.mil/bind/kpts/index.html), and perform a non-self-consistent > calculation to produce a band structure, as shown in yourQE/examples/example01. > HTH > > Giuseppe > > On Thursday 29 March 2012 07:26:56 Olayinka, Samson A. wrote: >> I need to extract kpoints from my scf calculation in order to get the >> K_POINTS for my bands calculation. -- Michael J. Mehl Head, Center for Computational Materials Science Naval Research Laboratory Code 6390 Washington DC From payam.norouzzadeh at gmail.com Thu Mar 29 17:22:37 2012 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Thu, 29 Mar 2012 10:22:37 -0500 Subject: [Pw_forum] control of relaxation procedure In-Reply-To: References: Message-ID: Thank you very much Prof.Giannozi for your comment. Best regards,Payam Norouzzadeh On Thu, Mar 29, 2012 at 3:42 AM, Paolo Giannozzi wrote: > > On Mar 28, 2012, at 21:05 , Payam Norouzzadeh wrote: > > etot_conv_thr = 1.0E-9 , >> forc_conv_thr = 1.0D-4 >> > > these are very strict thresholds, especially the first one. I do not think > you will ever need such a level of convergence > > Also note that some optimization algorithms do not honor some > convergence criteria, if I remember correclty > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > 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://www.democritos.it/pipermail/pw_forum/attachments/20120329/b68f7010/attachment.htm From laiwei at msu.edu Fri Mar 30 03:13:58 2012 From: laiwei at msu.edu (Wei Lai) Date: Thu, 29 Mar 2012 21:13:58 -0400 Subject: [Pw_forum] test case with structure relaxation In-Reply-To: References: Message-ID: Dear Paolo, Denser k-point grid still yielded a converged ratio of 1.427 which is far from the expected 1.414 but thanks for the advice. Regards, Wei On Wed, Mar 28, 2012 at 3:01 PM, Paolo Giannozzi wrote: > > On Mar 28, 2012, at 15:25 , Wei Lai wrote: > > I created a virtual tetragonal MgO cell with c/a ratio as 1.4. >> I was expecting this ratio will become close to 1.4142 (cubic) >> after relaxation. >> > > > your k-point grid is not symmetric and produces a small > symmetry breaking. A denser grid yields a more symmetric > final structure > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > 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://www.democritos.it/pipermail/pw_forum/attachments/20120329/2f4f1dce/attachment.htm From bahadira at buffalo.edu Fri Mar 30 04:07:27 2012 From: bahadira at buffalo.edu (bahadir) Date: Thu, 29 Mar 2012 22:07:27 -0400 Subject: [Pw_forum] gam.lines file problem and suggestion for a fix Message-ID: <4F75155F.6080307@buffalo.edu> i had a problem of formating of gam.lines file which gives the values in first column as '*****'. after checking the matdyn.f90 source, i realized that the values are formatted as INTEGER so cannot display float numbers so it shows stars. i just overcome this problem just changing the code block as in below and defining a new FORMAT as numbered 1031. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! if(.not.dos.and.ionode) then write(20,'(" Broadening ",F8.4)') deg(isig) write(6,'(" Broadening ",F8.4)') deg(isig) do n=1, nq write(20,1031) n ! this line is added write(20,1030) (gamma(i,n)*RY_TO_THZ,i=1,3*nat) ! this line is changed write(6,1040) n, (gamma(i,n),i=1,3*nat) end do endif 1031 FORMAT( 3x,I5) ! new format style !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! hope this helps people who get the same problem. ps: output format can be changed in the same way if neccesary bahadir -- Dr.Bahadir Altintas * Dept. of Chemistry SUNY Buffalo NY,USA * Abant Izzet Baysal University Dept. of Computer Education Bolu,Turkey From bahadira at buffalo.edu Fri Mar 30 04:16:29 2012 From: bahadira at buffalo.edu (bahadir) Date: Thu, 29 Mar 2012 22:16:29 -0400 Subject: [Pw_forum] gam.lines file problem and suggestion for a fix In-Reply-To: <4F75155F.6080307@buffalo.edu> References: <4F75155F.6080307@buffalo.edu> Message-ID: <4F75177D.9010202@buffalo.edu> Forgot to tell, this problem occurs if you have more then 9 modes. bahadir On 03/29/2012 10:07 PM, bahadir wrote: > i had a problem of formating of gam.lines file which gives the values in > first column as '*****'. after checking the matdyn.f90 source, i > realized that the values are formatted as INTEGER so cannot display > float numbers so it shows stars. i just overcome this problem just > changing the code block as in below > and defining a new FORMAT as numbered 1031. > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > if(.not.dos.and.ionode) then > write(20,'(" Broadening ",F8.4)') deg(isig) > write(6,'(" Broadening ",F8.4)') deg(isig) > do n=1, nq > write(20,1031) n ! this line is added > write(20,1030) (gamma(i,n)*RY_TO_THZ,i=1,3*nat) ! this line > is changed > write(6,1040) n, (gamma(i,n),i=1,3*nat) > end do > endif > > 1031 FORMAT( 3x,I5) ! new format style > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > > hope this helps people who get the same problem. > > ps: output format can be changed in the same way if neccesary > > bahadir > -- Dr.Bahadir Altintas * Dept. of Chemistry SUNY Buffalo NY,USA * Abant Izzet Baysal University Dept. of Computer Education Bolu,Turkey From luox at ihpc.a-star.edu.sg Fri Mar 30 11:31:54 2012 From: luox at ihpc.a-star.edu.sg (Luo Xin (IHPC)) Date: Fri, 30 Mar 2012 17:31:54 +0800 Subject: [Pw_forum] error in the phonon calculation for LO-TO splitting with spin-orbit coupling In-Reply-To: <1333037510.3781.44.camel@ulisse.cm.sissa.it> References: <1333022921.3781.3.camel@ulisse.cm.sissa.it> <1333037510.3781.44.camel@ulisse.cm.sissa.it> Message-ID: Dear all, I compiled the 4.3.1 and 4.3.2 version in serial, and found that dynmat.x can read the .xml format without any problems (so it also solve my problem), I think it is a mpi problems. Regards! Luo Xin -----Original Message----- From: Andrea Dal Corso [mailto:dalcorso at sissa.it] Sent: Friday, March 30, 2012 12:12 AM To: Luo Xin (IHPC) Subject: RE: [Pw_forum] error in the phonon calculation for LO-TO splitting with spin-orbit coupling I do not know. The svn version is working in my PC with ptdyn.xml. The 4.3.1 version of dynmat.x runs but with a single processor, not in parallel. If in your case it is not working with a single processor, please send me your dynamical matrix xml file. Andrea On Thu, 2012-03-29 at 20:36 +0800, Luo Xin (IHPC) wrote: > In fact, I think it can read the .xml file, but some error occur after that. > For example, after we run the dynmat.x. > It gives the error report, and if we look at the output file phphG.dyn.out > [luox at queksy_ws results]$ cat ptphG.dyn.out > Reading Dynamical Matrix from file ptdyn.xml > > We can see that it is reading the matrix in *.xml file, but didn't finished. > I encounter this problem in espresso-4.3.1, and I have compiled it on different machines, it always report this error. > > Regards! > Luo Xin > > > -----Original Message----- > From: Andrea Dal Corso [mailto:dalcorso at sissa.it] > Sent: Thursday, March 29, 2012 8:09 PM > To: Luo Xin (IHPC) > Subject: Re: [Pw_forum] error in the phonon calculation for LO-TO splitting with spin-orbit coupling > > You need to add the .xml extension to the fildyn filename to read a xml > file. > > HTH, > > Andrea > > On Thu, 2012-03-29 at 19:12 +0800, Luo Xin (IHPC) wrote: > > Dear all, > > > > > > > > I am doing the phonon calculation with spin-orbit coupling, and found > > that the dynmat.x can not read the .xml format. Latter I test the > > example 24 in the espresso-4.3.2, I found it also has this problems, > > Is anybody encounter this problem, or is it a bug? > > > > > > > > > > > > the error report in the example 24 is : > > > > > > > > > > > > [luox at queksy_ws results]$ dynmat.x < ptphG.dyn.in > ptphG.dyn.out > > > > > > > > Fatal error in PMPI_Barrier: Invalid communicator, error stack: > > > > > > > > PMPI_Barrier(425): MPI_Barrier(comm=0x0) failed > > > > > > > > PMPI_Barrier(385): Invalid communicator > > > > > > > > > > > > And my ptphG.dyn.in contents is: > > > > > > > > [luox at queksy_ws results]$ cat ptphG.dyn.in > > > > > > > > &input > > > > > > > > fildyn='ptdyn.xml', > > > > > > > > asr='simple' > > > > > > > > / > > > > > > > > > > > > And the contents of ptdyn.xml is : > > > > > > > > [luox at queksy_ws results]$ cat ptdyn.xml > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 1 > > > > > > > > > > > > > > > > > > > > > > > > 1 > > > > > > > > > > > > > > > > > > > > > > > > 2 > > > > > > > > > > > > > > > > > > > > > > > > 1 > > > > > > > > > > > > > > > > > > > > > > > > 7.550000000000000E+000 > > > > > > > > 0.000000000000000E+000 > > > > > > > > 0.000000000000000E+000 > > > > > > > > 0.000000000000000E+000 > > > > > > > > 0.000000000000000E+000 > > > > > > > > 0.000000000000000E+000 > > > > > > > > > > > > > > > > > > > > > > > > cubic > > > > > > > > > > > > > > > > > > > > > > > > -5.000000000000000E-001 0.000000000000000E+000 > > 5.000000000000000E-001 > > > > > > > > 0.000000000000000E+000 5.000000000000000E-001 > > 5.000000000000000E-001 > > > > > > > > -5.000000000000000E-001 5.000000000000000E-001 0.000000000000000E > > +000 > > > > > > > > > > > > > > > > > > > > > > > > -1.000000000000000E+000 -1.000000000000000E+000 1.000000000000000E > > +000 > > > > > > > > 1.000000000000000E+000 1.000000000000000E+000 1.000000000000000E > > +000 > > > > > > > > -1.000000000000000E+000 1.000000000000000E+000 -1.000000000000000E > > +000 > > > > > > > > > > > > > > > > > > > > > > > > 1.075922187500000E+002 > > > > > > > > > > > > > > > > > > > > > > > > Pt > > > > > > > > > > > > > > > > > > > > > > > > 1.778027198666795E+005 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 3 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 1.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000 > > > > > > > > > > > > > > > > > > > > > > > > 4.788570990310177E-001, 0.000000000000000E+000 > > > > > > > > 2.775557561562891E-017, 0.000000000000000E+000 > > > > > > > > 2.775557561562891E-017, 0.000000000000000E+000 > > > > > > > > -2.775557561562891E-017, 0.000000000000000E+000 > > > > > > > > 1.985408035348115E-001, 0.000000000000000E+000 > > > > > > > > -2.775557561562891E-017, 0.000000000000000E+000 > > > > > > > > 2.775557561562891E-017, 0.000000000000000E+000 > > > > > > > > 2.775557561562891E-017, 0.000000000000000E+000 > > > > > > > > 1.985408035348115E-001, 0.000000000000000E+000 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 0.000000000000000E+000 0.000000000000000E+000 1.000000000000000E+000 > > > > > > > > > > > > > > > > > > > > > > > > 1.985408035348115E-001, 0.000000000000000E+000 > > > > > > > > -1.387778780781446E-017, 0.000000000000000E+000 > > > > > > > > 1.387778780781446E-017, 0.000000000000000E+000 > > > > > > > > -1.387778780781446E-017, 0.000000000000000E+000 > > > > > > > > 1.985408035348115E-001, 0.000000000000000E+000 > > > > > > > > -1.387778780781446E-017, 0.000000000000000E+000 > > > > > > > > 2.775557561562891E-017, 0.000000000000000E+000 > > > > > > > > 2.775557561562891E-017, 0.000000000000000E+000 > > > > > > > > 4.788570990310176E-001, 0.000000000000000E+000 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 0.000000000000000E+000 1.000000000000000E+000 0.000000000000000E+000 > > > > > > > > > > > > > > > > > > > > > > > > 1.985408035348115E-001, 0.000000000000000E+000 > > > > > > > > -2.775557561562891E-017, 0.000000000000000E+000 > > > > > > > > 2.775557561562891E-017, 0.000000000000000E+000 > > > > > > > > -2.775557561562891E-017, 0.000000000000000E+000 > > > > > > > > 4.788570990310177E-001, 0.000000000000000E+000 > > > > > > > > -2.775557561562891E-017, 0.000000000000000E+000 > > > > > > > > 2.775557561562891E-017, 0.000000000000000E+000 > > > > > > > > 2.775557561562891E-017, 0.000000000000000E+000 > > > > > > > > 1.985408035348114E-001, 0.000000000000000E+000 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 3.476407859655458E+000 1.159604842245717E+002 > > > > > > > > > > > > > > > > > > > > > > > > 0.000000000000000E+000, 0.000000000000000E+000 > > > > > > > > 7.009835776274842E-001, 0.000000000000000E+000 > > > > > > > > 7.131774140398537E-001, 0.000000000000000E+000 > > > > > > > > > > > > > > > > > > > > > > > > 3.476407859655459E+000 1.159604842245717E+002 > > > > > > > > > > > > > > > > > > > > > > > > 1.412518191627151E-016, 0.000000000000000E+000 > > > > > > > > 7.131774140398538E-001, 0.000000000000000E+000 > > > > > > > > -7.009835776274841E-001, 0.000000000000000E+000 > > > > > > > > > > > > > > > > > > > > > > > > 5.398943723973670E+000 1.800893778313019E+002 > > > > > > > > > > > > > > > > > > > > > > > > -1.000000000000000E+000, 0.000000000000000E+000 > > > > > > > > 1.007376071188902E-016, 0.000000000000000E+000 > > > > > > > > -9.901520554307043E-017, 0.000000000000000E+000 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > IHPC Values :: Impact :: Honesty :: Performance :: Co-operation > > This email is confidential and may be privileged. If you are not the > > intended recipient, please delete it and notify us immediately. Please > > do not copy or use it for any purpose, or disclose its contents to any > > other person. Thank you. > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > -- > Andrea Dal Corso Tel. 0039-040-3787428 > SISSA, Via Bonomea 265 Fax. 0039-040-3787249 > I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it > > > > IHPC Values :: Impact :: Honesty :: Performance :: Co-operation > This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Bonomea 265 Fax. 0039-040-3787249 I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it IHPC Values :: Impact :: Honesty :: Performance :: Co-operation This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. From giannozz at democritos.it Fri Mar 30 12:10:05 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 30 Mar 2012 12:10:05 +0200 Subject: [Pw_forum] test case with structure relaxation In-Reply-To: References: Message-ID: <1333102205.19070.66.camel@fe12lx.fisica.uniud.it> On Thu, 2012-03-29 at 21:13 -0400, Wei Lai wrote: > Denser k-point grid still yielded a converged ratio of 1.427 which is far from the expected 1.414 but thanks for the advice. grid: 3 3 2 1 1 1 c/a: 1.3949 grid: 4 4 3 1 1 1 c/a: 1.4099 grid: 6 6 4 1 1 1 c/a: 1.4126 grid: 8 8 6 1 1 1 c/a: 1.4132 http://www.fisica.uniud.it/~giannozz/public/mgo.tar.gz P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From ramzialaya at hotmail.fr Fri Mar 30 13:20:29 2012 From: ramzialaya at hotmail.fr (ramzi alaya) Date: Fri, 30 Mar 2012 12:20:29 +0100 Subject: [Pw_forum] regarding to SOC In-Reply-To: References: Message-ID: Dear Thaneshwor Kaloni; Use a relativistic pseudopotential. Date: Thu, 29 Mar 2012 12:55:13 +0300 From: tkaloni at gmail.com To: pw_forum at pwscf.org Subject: [Pw_forum] regarding to SOC Dear QE_users, I am interested to apply spin-orbit effects in 2-D system, in particular, graphene. I have seen a example22 in the version 4.3.1. I wanted to know what type of formalism has been used, like Rashba type, Dressulhouse type or zeeman type? Thank you very much in advance. Best, Kaloni PhD student King Abdullah University of Science and Technology _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120330/0b0a8788/attachment.htm From laiwei at msu.edu Fri Mar 30 15:09:18 2012 From: laiwei at msu.edu (Wei Lai) Date: Fri, 30 Mar 2012 09:09:18 -0400 Subject: [Pw_forum] test case with structure relaxation In-Reply-To: <1333102205.19070.66.camel@fe12lx.fisica.uniud.it> References: <1333102205.19070.66.camel@fe12lx.fisica.uniud.it> Message-ID: Dear Paolo, Thanks for your effort. It looks like the shifted origin made a difference. Regards, Wei On 3/30/12, Paolo Giannozzi wrote: > On Thu, 2012-03-29 at 21:13 -0400, Wei Lai wrote: > >> Denser k-point grid still yielded a converged ratio of 1.427 which is far >> from the expected 1.414 but thanks for the advice. > > grid: 3 3 2 1 1 1 c/a: 1.3949 > grid: 4 4 3 1 1 1 c/a: 1.4099 > grid: 6 6 4 1 1 1 c/a: 1.4126 > grid: 8 8 6 1 1 1 c/a: 1.4132 > > http://www.fisica.uniud.it/~giannozz/public/mgo.tar.gz > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > From laiwei at msu.edu Fri Mar 30 15:09:49 2012 From: laiwei at msu.edu (Wei Lai) Date: Fri, 30 Mar 2012 09:09:49 -0400 Subject: [Pw_forum] test case with structure relaxation In-Reply-To: <1333102205.19070.66.camel@fe12lx.fisica.uniud.it> References: <1333102205.19070.66.camel@fe12lx.fisica.uniud.it> Message-ID: Dear Paolo, Thanks for your effort. It looks like the shifted origin made a difference. Regards, Wei On 3/30/12, Paolo Giannozzi wrote: > On Thu, 2012-03-29 at 21:13 -0400, Wei Lai wrote: > >> Denser k-point grid still yielded a converged ratio of 1.427 which is far >> from the expected 1.414 but thanks for the advice. > > grid: 3 3 2 1 1 1 c/a: 1.3949 > grid: 4 4 3 1 1 1 c/a: 1.4099 > grid: 6 6 4 1 1 1 c/a: 1.4126 > grid: 8 8 6 1 1 1 c/a: 1.4132 > > http://www.fisica.uniud.it/~giannozz/public/mgo.tar.gz > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > From nedya.farisia at ui.ac.id Fri Mar 30 18:36:16 2012 From: nedya.farisia at ui.ac.id (nedya.farisia at ui.ac.id) Date: Fri, 30 Mar 2012 23:36:16 +0700 Subject: [Pw_forum] dual spin polarization Message-ID: Dear quantum espresso experts, I have tried to plot spin density using pp.x. But whatever the spin I choose (spin polarization = 0,1,2) the result always the same (like total spin polarization). What can I do to divide the isosurface for spin up and spin down but in one XSF? Thank you for any information. Nedya, Undergraduate Student From giannozz at democritos.it Fri Mar 30 22:49:52 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 30 Mar 2012 22:49:52 +0200 Subject: [Pw_forum] gam.lines file problem and suggestion for a fix In-Reply-To: <4F75155F.6080307@buffalo.edu> References: <4F75155F.6080307@buffalo.edu> Message-ID: On Mar 30, 2012, at 4:07 , bahadir wrote: > i just overcome this problem just changing the code block as in below > and defining a new FORMAT as numbered 1031. > [...] > hope this helps people who get the same problem. thank you. It should be fixed in the next version P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From ptao10b at imr.ac.cn Sat Mar 31 04:03:55 2012 From: ptao10b at imr.ac.cn (=?GBK?B?zNXF9A==?=) Date: Sat, 31 Mar 2012 10:03:55 +0800 (CST) Subject: [Pw_forum] problem in generating pseudopotential Message-ID: Dear all, I'm trying to generate an LDA pseudopotential for Mo, but the generating and testing results are not the same. Here are the input and output files: ######################################################## pseudo generation: &input title='Mo', prefix='mo', iswitch=3, rlderiv=3.0, eminld=-1.0, emaxld=0.7, deld=0.01d0, nld=3, zed=42.0, config="[Kr] 4d5 5s1 5p0" dft='LDA', / &inputp lloc=1, pseudotype=1, file_pseudopw='Mo.tp_rrkj.UPF', nlcc=.true., file_core='corecharge' / 3 4D 3 2 5.00 0.00 2.50 2.50 5S 1 0 1.00 0.00 4.00 4.00 5P 2 1 0.00 -0.10 6.00 6.00 ######################################################## pseudo test: &input title='Mo', prefix='mo' iswitch=2, zed=42.0, config="[Kr] 4d5 5s1 5p0" dft='LDA', / &test file_pseudo='Mo.tp_rrkj.UPF', nconf=1, configts(1)='4d5 5s1 5p0' / ########################################################## the wfc output file of pseudo generation(mops.wfc): # r 5S 4D 5S 4D 2.013411 0.439711 0.639837 0.428222 0.627268 2.038737 0.447239 0.631527 0.438662 0.620807 2.064381 0.454716 0.623245 0.448804 0.614230 2.090348 0.462131 0.615006 0.458639 0.607545 2.116641 0.469472 0.606823 0.468161 0.600756 2.143265 0.476726 0.598704 0.477361 0.593870 2.170224 0.483879 0.590655 0.486233 0.586894 2.197522 0.490919 0.582680 0.494770 0.579832 2.225163 0.497831 0.574779 0.502967 0.572691 2.253153 0.504602 0.566947 0.510819 0.565477 2.281494 0.511218 0.559180 0.518320 0.558195 2.310191 0.517664 0.551469 0.525466 0.550850 ############################################################# the wfc output file of pseudo test(mops1.wfc) # r 5P 5S 4D 3D 4P 4S 3P 2.013411 -0.184466 0.428222 -0.627268 0.005179 0.421340 -0.297669 -0.001341 2.038737 -0.193140 0.438662 -0.620807 0.004681 0.407008 -0.284270 -0.001176 2.064381 -0.201764 0.448804 -0.614230 0.004225 0.392895 -0.271244 -0.001031 2.090348 -0.210334 0.458639 -0.607545 0.003808 0.379010 -0.258594 -0.000901 2.116641 -0.218843 0.468161 -0.600756 0.003428 0.365364 -0.246323 -0.000787 2.143265 -0.227287 0.477361 -0.593870 0.003081 0.351965 -0.234432 -0.000685 2.170224 -0.235658 0.486233 -0.586894 0.002766 0.338821 -0.222922 -0.000596 2.197522 -0.243952 0.494770 -0.579832 0.002479 0.325938 -0.211791 -0.000517 2.225163 -0.252163 0.502967 -0.572691 0.002219 0.313325 -0.201039 -0.000448 2.253153 -0.260286 0.510819 -0.565477 0.001984 0.300986 -0.190663 -0.000388 2.281494 -0.268316 0.518320 -0.558195 0.001771 0.288926 -0.180661 -0.000335 2.310191 -0.276248 0.525466 -0.550850 0.001578 0.277151 -0.171030 -0.000288 ############################################################# As you can see, the wfc in the two output files are not the same at all, and this leads to the case that the pseudowfc in the test and and the all-electron wfc are not overlapped when r>rcut. Could any nice guy tell me where the mistake is? I'm so confused now. Thank you very much! Warmest regards, Plato Tao -- ------------------------------------------------------------------- PH.D. candidate Peng Tao Magnetism and Magnetic Materials Division National Laboratory for Material Science Institute of Metal Research, Chinese Academy of Sciences Phone +86-024-83978751 ------------------------------------------------------------------- From ptao10b at imr.ac.cn Sat Mar 31 04:59:01 2012 From: ptao10b at imr.ac.cn (=?GBK?B?zNXF9A==?=) Date: Sat, 31 Mar 2012 10:59:01 +0800 (CST) Subject: [Pw_forum] problem in generating pseudopotential In-Reply-To: References: Message-ID: Sorry, I've pasted the wrong output file. and I think I should give the result when r>rcut: ######################################################### I did the test again: # r 5P 5S 4D 5P 5S 4D 7.115890 0.301985 0.126980 0.048473 0.295021 0.133672 0.041913 7.205397 0.295900 0.121607 0.046243 0.288790 0.127850 0.039868 7.296030 0.289791 0.116371 0.044088 0.282546 0.122185 0.037898 7.387803 0.283664 0.111274 0.042007 0.276295 0.116679 0.036002 7.480730 0.277525 0.106318 0.039998 0.270042 0.111333 0.034177 7.574826 0.271380 0.101502 0.038061 0.263794 0.106147 0.032422 7.670106 0.265234 0.096827 0.036194 0.257555 0.101120 0.030736 7.766584 0.259093 0.092293 0.034396 0.251333 0.096253 0.029117 You could find that the pseudowfc in the test and and the all-electron wfc are not overlapped. ########################################################## And this is the pseudo-generation wfc: # r 5S 4D 5S 4D 7.115890 0.133672 0.041913 0.133672 0.041913 7.205397 0.127850 0.039868 0.127850 0.039868 7.296030 0.122185 0.037898 0.122185 0.037898 7.387803 0.116679 0.036002 0.116679 0.036002 7.480730 0.111333 0.034177 0.111333 0.034177 7.574826 0.106147 0.032422 0.106147 0.032422 7.670106 0.101120 0.030736 0.101120 0.030736 7.766584 0.096253 0.029117 0.096253 0.029117 And you can see the consistence of pseudo and the real wfc in pseudo generation ########################################################## > -----????----- > ???: "??" > ????: 2012?3?31? ??? > ???: pw_forum > ??: > ??: problem in generating pseudopotential > > Dear all, > > I'm trying to generate an LDA pseudopotential for Mo, but the generating and testing results are not the same. Here are the input and output files: > ######################################################## > pseudo generation: > &input > title='Mo', > prefix='mo', > iswitch=3, > rlderiv=3.0, > eminld=-1.0, > emaxld=0.7, > deld=0.01d0, > nld=3, > zed=42.0, > config="[Kr] 4d5 5s1 5p0" > dft='LDA', > / > &inputp > lloc=1, > pseudotype=1, > file_pseudopw='Mo.tp_rrkj.UPF', > nlcc=.true., > file_core='corecharge' > / > 3 > 4D 3 2 5.00 0.00 2.50 2.50 > 5S 1 0 1.00 0.00 4.00 4.00 > 5P 2 1 0.00 -0.10 6.00 6.00 > ######################################################## > pseudo test: > &input > title='Mo', > prefix='mo' > iswitch=2, > zed=42.0, > config="[Kr] 4d5 5s1 5p0" > dft='LDA', > / > &test > file_pseudo='Mo.tp_rrkj.UPF', > nconf=1, > configts(1)='4d5 5s1 5p0' > / > ########################################################## > the wfc output file of pseudo generation(mops.wfc): > # r 5S 4D 5S 4D > 2.013411 0.439711 0.639837 0.428222 0.627268 > 2.038737 0.447239 0.631527 0.438662 0.620807 > 2.064381 0.454716 0.623245 0.448804 0.614230 > 2.090348 0.462131 0.615006 0.458639 0.607545 > 2.116641 0.469472 0.606823 0.468161 0.600756 > 2.143265 0.476726 0.598704 0.477361 0.593870 > 2.170224 0.483879 0.590655 0.486233 0.586894 > 2.197522 0.490919 0.582680 0.494770 0.579832 > 2.225163 0.497831 0.574779 0.502967 0.572691 > 2.253153 0.504602 0.566947 0.510819 0.565477 > 2.281494 0.511218 0.559180 0.518320 0.558195 > 2.310191 0.517664 0.551469 0.525466 0.550850 > ############################################################# > the wfc output file of pseudo test(mops1.wfc) > # r 5P 5S 4D 3D 4P 4S 3P > 2.013411 -0.184466 0.428222 -0.627268 0.005179 0.421340 -0.297669 -0.001341 > 2.038737 -0.193140 0.438662 -0.620807 0.004681 0.407008 -0.284270 -0.001176 > 2.064381 -0.201764 0.448804 -0.614230 0.004225 0.392895 -0.271244 -0.001031 > 2.090348 -0.210334 0.458639 -0.607545 0.003808 0.379010 -0.258594 -0.000901 > 2.116641 -0.218843 0.468161 -0.600756 0.003428 0.365364 -0.246323 -0.000787 > 2.143265 -0.227287 0.477361 -0.593870 0.003081 0.351965 -0.234432 -0.000685 > 2.170224 -0.235658 0.486233 -0.586894 0.002766 0.338821 -0.222922 -0.000596 > 2.197522 -0.243952 0.494770 -0.579832 0.002479 0.325938 -0.211791 -0.000517 > 2.225163 -0.252163 0.502967 -0.572691 0.002219 0.313325 -0.201039 -0.000448 > 2.253153 -0.260286 0.510819 -0.565477 0.001984 0.300986 -0.190663 -0.000388 > 2.281494 -0.268316 0.518320 -0.558195 0.001771 0.288926 -0.180661 -0.000335 > 2.310191 -0.276248 0.525466 -0.550850 0.001578 0.277151 -0.171030 -0.000288 > ############################################################# > > As you can see, the wfc in the two output files are not the same at all, and this leads to the case that the pseudowfc in the test and and the all-electron wfc are not overlapped when r>rcut. > > > Could any nice guy tell me where the mistake is? I'm so confused now. Thank you very much! > > Warmest regards, > > Plato Tao > > > -- > ------------------------------------------------------------------- > PH.D. candidate Peng Tao > Magnetism and Magnetic Materials Division > National Laboratory for Material Science > Institute of Metal Research, Chinese Academy of Sciences > Phone +86-024-83978751 > ------------------------------------------------------------------- > > > -- ------------------------------------------------------------------- PH.D. candidate Peng Tao Magnetism and Magnetic Materials Division National Laboratory for Material Science Institute of Metal Research, Chinese Academy of Sciences Phone +86-024-83978751 ------------------------------------------------------------------- From romeda_8 at yahoo.com Sat Mar 31 16:39:12 2012 From: romeda_8 at yahoo.com (Romeda Azeen) Date: Sat, 31 Mar 2012 07:39:12 -0700 (PDT) Subject: [Pw_forum] How to optimize a hexagonal closest-packed (hcp) structure? Message-ID: <1333204752.54817.YahooMailNeo@web120404.mail.ne1.yahoo.com> Dear QE developers, I have a question about optimization of a hcp structure (e.g. Ti and Zr). Any hcp structure have two lattice constants (a and c), so for scf calculation, it is nessesry to optimize both lattice constants. Method 1: Fixed celldm(3) at ideal c/a ratio (1.633) and then changed celldm(1)=a and eventually computation of total energy. Method 2: Fixed celldm(1) at experimental lattice constant and then changed celldm(3)=c/a and computing of total energy. Method 3: Fixed unit cell volume at experimental volume and then changed c/a ratio and calculation of a (Volume=fixed) and run scf calculation with different a and c/a. what is best method for optimization of a and c? Method 1, 2 , 3 or others method? I am very thankful any to help me. -- Romeda Azeen, Bhavnagar University Bhavnagar 364002 Gujarat India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120331/fedc72fb/attachment.htm From baroni at sissa.it Sat Mar 31 16:59:02 2012 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 31 Mar 2012 16:59:02 +0200 Subject: [Pw_forum] How to optimize a hexagonal closest-packed (hcp) structure? In-Reply-To: <1333204752.54817.YahooMailNeo@web120404.mail.ne1.yahoo.com> References: <1333204752.54817.YahooMailNeo@web120404.mail.ne1.yahoo.com> Message-ID: The best method is the one that you find so by direct experience, because this would teach you something that you will never learn by asking around questions that you could answer by yourself. (it would also help you clarify what you mean by "best" bethod). If you had tried by yourself, most probably you would have found that the best method is (3), because it is the one for which the number of plane waves depends the least on the parameter you vary. Questions for you: 1) is this really so? 2) why would it be best to keep the number of plane waves "as constant as possible"? Best wishes, Stefano B On Mar 31, 2012, at 4:39 PM, Romeda Azeen wrote: > Dear QE developers, > I have a question about optimization of a hcp structure (e.g. Ti and Zr). > Any hcp structure have two lattice constants (a and c), so for scf calculation, it is nessesry to optimize both lattice constants. > > > Method 1: Fixed celldm(3) at ideal c/a ratio (1.633) and then changed celldm(1)=a and eventually computation of total energy. > > Method 2: Fixed celldm(1) at experimental lattice constant and then changed celldm(3)=c/a and computing of total energy. > > Method 3: Fixed unit cell volume at experimental volume and then changed c/a ratio and calculation of a (Volume=fixed) and run scf > > calculation with different a and c/a. > > > what is best method for optimization of a and c? Method 1, 2 , 3 or others method? > > > I am very thankful any to help me. > > -- > Romeda Azeen, > Bhavnagar University Bhavnagar 364002 Gujarat India > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120331/52459a9e/attachment.htm