From giannozz at democritos.it Fri Oct 1 09:43:30 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 01 Oct 2010 09:43:30 +0200 Subject: [Pw_forum] parallel machine In-Reply-To: References: Message-ID: <4CA59122.90608@democritos.it> mayank gupta wrote: > I am facing problem during phonon calculation in parallel machine for > silver oxide, while the same calculation with same parameters has been > successfully executed in single PC. if you are absolutely sure that the same calculations, with the same parameters, works in serial execution and doesn't in parallel execution, with the same version of QE (please specify which one), please provide the input so that your calculatio can be reproduced on a different machine. Even better, file a bug report on qe-forge: http://qe-forge.org/tracker/?atid=133&group_id=10&func=browse P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Fri Oct 1 09:49:25 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 01 Oct 2010 09:49:25 +0200 Subject: [Pw_forum] the keyword in the pw.x In-Reply-To: <201009302103032657359@gmail.com> References: <201009302103032657359@gmail.com> Message-ID: <4CA59285.6050202@democritos.it> archygu wrote: > nbnd: acturally I do not know how to use this parameter if you don't know what the number of Kohn-Sham states is, you shouldn't start a calculation > nosym nosym is for special purposes only. Beginners shouldn't do anything special, just normal things. > nraise: how can we define one "nraise" step, it is the same as one time > step if we set nraise=1 it is. Do you need to perform molecular dynamics at a given temperature? if not, you do not need to know what nraise is P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Fri Oct 1 09:57:05 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 01 Oct 2010 09:57:05 +0200 Subject: [Pw_forum] EXX on 1D supercells fail In-Reply-To: <38919.63978.qm@web53308.mail.re2.yahoo.com> References: <38919.63978.qm@web53308.mail.re2.yahoo.com> Message-ID: <4CA59451.2040405@democritos.it> Madan Mithra. L. M wrote: > calculation including EXX (PBE0) fails on 1D supercell. > However, the same job ran without dumping the core with pwscf 4.1.3. the treatment of the singularity for q->0 of the exchange potential is tricky for 1D systems. It was changed in the last version to a supposedly better version. Please provide an example or file a bug report on qe-forge: http://qe-forge.org/tracker/?atid=133&group_id=10&func=browse P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From sclauzer at sissa.it Fri Oct 1 10:05:28 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 01 Oct 2010 10:05:28 +0200 Subject: [Pw_forum] [SOLVED ?] Re: weird phonon frequencies for 3X 3X 1 KPOINTS In-Reply-To: References: <4CA494FB.9040506@sissa.it> Message-ID: <4CA59648.7070501@sissa.it> On 09/30/2010 08:47 PM, Mehmet Topsakal wrote: > Dear Gabriele, > > Thank you very much for your suggestion. After including some > smearing, -5000 frequencies disappeared. But this > still cannot explain the 3X 3X 1 situation. Why is this situation so special? BTW, I cannot find any result about this case in your repository. > For this reason, I plotted the positions of scf KPOINTS (see the > attachments) > and realized that the corner of the Brillouin zone, which is also > known as K-special-point, is NOT included for KPOINTS > other than 3X 3X 1. For graphene, K-special-point also corresponds to > the Dirac-Point where zero-band-gap occurs. From your nice drawing of the k-points, I guess that the "Dirac" K-point is included also in the 9x9x1 and 12x12x1 meshes (without shift, at least that's what your have written in the picture and in the input files), so this may explain why you get strange results for those meshes without smearing. > As a result, problem should be related with K-special-point. If you include the shift I think that the K-point will never be included (excepting the 3x3x1 grid perhaps). I suggest you to study the convergence of the frequencies separately for the shifted and unshifted grids (both with smearing) and see if they converge to the same result. Some people believe that including the K-point in the BZ sampling is of vital importance, even with dense meshes. I'm not sure of that. > > BUT. Still I cannot understand why inclusion of a point in BZ > corresponds to such a HUGE difference in phonon frequencies. > Maybe someone in this list gives a better explanation for that.... I cannot explain this, sorry. Let's wait for an answer from a graphene or phonon expert (or both). Regards GS > > All of the files are available at http://db.tt/xK2Jtu1 > > Ragards. > > > On Thu, Sep 30, 2010 at 4:47 PM, Gabriele Sclauzero > wrote: > > Dear Mehmet, > > graphene has zero gap, hence you probably need to include > smearing of the occupations in the scf calculations. > > > HTH > > GS > > > On 09/29/2010 04:54 PM, Mehmet Topsakal wrote: >> Dear all, >> >> For graphene structure, I noticed that I get completely wrong >> phonon frequencies when I use KPOINTS such as 9 9 1, 12 12 1, 15 15 1 >> >> For example: >> >> K_POINTS {automatic} >> 11 11 1 0 0 0 >> >> gives realistic frequencies as in 11.phonon.out file >> >> BUT >> >> K_POINTS {automatic} >> 12 12 1 0 0 0 >> >> gives "omega( 1) = -149.592762 [THz] = -4989.910586 [cm-1]" >> as in 12.phonon.out >> >> >> What should be the reason ???? >> >> Thanks. >> >> -- >> >> Mehmet Topsakal (Ph.D. Student) >> UNAM-Institute of Materials Science and Nanotechnology. >> Bilkent University. 06800 Bilkent, Ankara/T?rkiye >> Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365 >> UNAM-web : www.nano.org.tr >> >> >> _______________________________________________ >> 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 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > > Mehmet Topsakal (Ph.D. Student) > UNAM-Institute of Materials Science and Nanotechnology. > Bilkent University. 06800 Bilkent, Ankara/T?rkiye > Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365 > UNAM-web : www.nano.org.tr > > > _______________________________________________ > 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/20101001/45b11a0b/attachment.htm From chakraa at tcd.ie Fri Oct 1 12:21:08 2010 From: chakraa at tcd.ie (Aurab) Date: Fri, 1 Oct 2010 11:21:08 +0100 Subject: [Pw_forum] Calculating g-tensor using gipaw In-Reply-To: References: Message-ID: Dear Apsi, Thank you for the reply. I checked my pseudopotential files and yes you are right! The core radii cutoff has been read zero! Is it just a bug in the ld1.x code or there is particular reason behind. I can't think of any. Thanks a ton, Aurab On 30 September 2010 14:58, Ari P Seitsonen wrote: > > Dear Aurab, > > One possibility is that the core radii read from the GIPAW file are zero; > those are automatically written into to UPF file by the atomic/ld1 code, but > for some reason that is not completely clear to me some of them are > sometimes zero (occurs only for empty states). One way to check if this is > your case you can try > > #> awk '/ > if the UPF file is in format version 1.*, similarly for format version 2.*. > > If you don't find the origin of the problem you could post the your UPF > and complete input file. > > Greetings, > > apsi > > > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- > Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ > Physikalisch-Chemisches Institut der Universitaet Zuerich > Tel: +41 44 63 54 497 / Mobile: +41 79 71 90 935 > > > On Thu, 30 Sep 2010, Aurab wrote: > > Dear QE users and developers, >> I started to do the g-tensor calculation of ZnO using gipaw and got stuck >> with the error. >> >> from init_gipaw_1 : error # 1 >> impossible value for nrc >> >> I am using my own pseudopotentials with gipaw enabled. I looked into the >> source and found that the program init_gipaw_1.f90 (Version >> espresso-4.2.1) >> has it in line 133. Could you please instruct me how to get past this and >> what is the correct way to calculate g-tensor using gipaw. >> The gipaw input is given below, >> >> inputgipaw >> job = 'g_tensor' >> prefix = 'ZnO' >> tmp_dir = './' >> isolve = 0 >> iverbosity = 1 >> file_reconstruction(1) = 'Zn.pbe-gipaw.recon' >> file_reconstruction(2) = 'O.pbe-gipaw.recon' >> q_gipaw = 0.01 >> / >> >> Regards, >> >> Aurab D. Chakrabarty >> Trinity College Dublin >> *=*=*=*=*=*=*=*=*=*=*=*=*=*=* >> >> > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- =*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* Aurab D. Chakrabarty Postgraduate Student (Research) Room 2.22 The Lloyd Institute School of Physics Trinity College Dublin Dublin 2 Ireland Telephone: +353-1-896-8453 *=*=*=*=*=*=*=*=*=*=*=*=*=*=* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101001/3167f285/attachment.htm From mayankaditya at gmail.com Fri Oct 1 13:05:17 2010 From: mayankaditya at gmail.com (mayank gupta) Date: Fri, 1 Oct 2010 16:35:17 +0530 Subject: [Pw_forum] parallel version Message-ID: HI Sir I am using QE 4.2 version. I have used 8 processors and 4 pools in my parallel caclulation the SCF run executed succesfully but the phonon calculation break. the input file for my calculation are : &control calculation='scf' restart_mode='from_scratch', tstress = .true. tprnfor = .true. prefix='cuo', pseudo_dir = '/home/usr031/mayankg/pseudo/', outdir='/home/usr031/mayankg/tmp_cuo_zero1/' / &system ibrav= 1 , celldm(1)= 8.125 , nat= 6 , ntyp=2, ecutwfc= 65.00000000 ecutrho= 1300.00000000 !occupations='smearing', smearing='gaussian', degauss=0.02 / &electrons mixing_beta=0.3 conv_thr=1.0D-8 diagonalization='david' diago_david_ndim=10 / &ions / ATOMIC_SPECIES Cu 63.54 Cu.pw91-n-van_ak.UPF O 15.99 O.pw91-van_ak.UPF ATOMIC_POSITIONS Cu .0 .0 .0 Cu .5 .5 .0 Cu .5 .0 .5 Cu .0 .5 .5 O .25 .25 .25 O .75 .75 .75 K_POINTS automatic 8 8 8 1 1 1 &inputph tr2_ph=1.0e-14 prefix='cuo', epsil=.true. ldisp=.true., nq1=2, nq2=2, nq3=2 amass(1)=63.54, amass(2)=15.99, !recover=.true. outdir='/home/usr031/mayankg/tmp_cuo_zero1', fildyn='cuo.dyn', / and the error message Electric Fields Calculation Alpha used in Ewald sum = 2.8000 PHONON : 18m13.85s CPU time, 21m33.29s WALL time Electric Fields Calculation iter # 1 total cpu time : 3808.9 secs av.it.: 11.4 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.690E-08 iter # 1 total cpu time : 3877.4 secs av.it.: 11.4 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.690E-08 iter # 1 total cpu time : 3898.0 secs av.it.: 11.4 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.690E-08 iter # 1 total cpu time : 3980.0 secs av.it.: 11.4 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.690E-08 iter # 2 total cpu time : 5046.2 secs av.it.: 20.4 thresh= 0.831E-05 alpha_mix = 0.700 |ddv_scf|^2 = 0.210E-09 iter # 2 total cpu time : 5054.7 secs av.it.: 20.4 thresh= 0.831E-05 alpha_mix = 0.700 |ddv_scf|^2 = 0.210E-09 iter # 2 total cpu time : 5066.5 secs av.it.: 18.9 thresh= 0.831E-05 alpha_mix = 0.700 |ddv_scf|^2 = 0.210E-09 iter # 2 total cpu time : 5071.4 secs av.it.: 21.8 thresh= 0.831E-05 alpha_mix = 0.700 |ddv_scf|^2 = 0.210E-09 kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 3 ibnd 29 solve_e: root not converged NaN iter # 3 total cpu time : 6246.2 secs av.it.: 21.0 thresh= 0.145E-05 alpha_mix = 0.700 |ddv_scf|^2 = 0.296E-10 iter # 3 total cpu time : 6297.6 secs av.it.: 21.2 thresh= 0.145E-05 alpha_mix = 0.700 |ddv_scf|^2 = 0.142E-10 iter # 3 total cpu time : 6298.1 secs av.it.: 20.2 thresh= 0.145E-05 alpha_mix = 0.700 |ddv_scf|^2 = 0.296E-10 kpoint 3 ibnd 29 solve_e: root not converged NaN kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 3 ibnd 29 solve_e: root not converged NaN kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 4 ibnd 29 solve_e: root not converged NaN kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 4 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 4 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 5 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 5 ibnd 29 solve_e: root not converged NaN kpoint 3 ibnd 29 solve_e: root not converged NaN kpoint 3 ibnd 29 solve_e: root not converged NaN kpoint 3 ibnd 29 solve_e: root not converged NaN kpoint 5 ibnd 29 solve_e: root not converged NaN kpoint 3 ibnd 29 solve_e: root not converged NaN kpoint 3 ibnd 29 solve_e: root not converged NaN kpoint 3 ibnd 29 solve_e: root not converged NaN kpoint 6 ibnd 29 solve_e: root not converged NaN kpoint 3 ibnd 29 solve_e: root not converged NaN kpoint 3 ibnd 29 solve_e: root not converged NaN kpoint 3 ibnd 29 solve_e: root not converged NaN kpoint 6 ibnd 29 solve_e: root not converged NaN kpoint 4 ibnd 29 solve_e: root not converged NaN kpoint 4 ibnd 29 solve_e: root not converged NaN kpoint 4 ibnd 29 solve_e: root not converged NaN kpoint 6 ibnd 29 solve_e: root not converged NaN kpoint 4 ibnd 29 solve_e: root not converged NaN kpoint 4 ibnd 29 solve_e: root not converged NaN kpoint 4 ibnd 29 solve_e: root not converged NaN kpoint 7 ibnd 29 solve_e: root not converged NaN kpoint 4 ibnd 29 solve_e: root not converged NaN kpoint 4 ibnd 29 solve_e: root not converged NaN kpoint 4 ibnd 29 solve_e: root not converged NaN kpoint 7 ibnd 29 solve_e: root not converged NaN kpoint 5 ibnd 29 solve_e: root not converged NaN kpoint 5 ibnd 29 solve_e: root not converged NaN kpoint 5 ibnd 29 solve_e: root not converged NaN kpoint 7 ibnd 29 solve_e: root not converged NaN kpoint 5 ibnd 29 solve_e: root not converged NaN kpoint 5 ibnd 29 solve_e: root not converged NaN kpoint 5 ibnd 29 solve_e: root not converged NaN kpoint 8 ibnd 29 solve_e: root not converged NaN kpoint 5 ibnd 29 solve_e: root not converged NaN kpoint 5 ibnd 29 solve_e: root not converged NaN kpoint 5 ibnd 29 solve_e: root not converged NaN kpoint 8 ibnd 29 solve_e: root not converged NaN kpoint 6 ibnd 29 solve_e: root not converged NaN kpoint 6 ibnd 29 solve_e: root not converged NaN kpoint 6 ibnd 29 solve_e: root not converged NaN kpoint 8 ibnd 29 solve_e: root not converged NaN kpoint 6 ibnd 29 solve_e: root not converged NaN kpoint 6 ibnd 29 solve_e: root not converged NaN kpoint 6 ibnd 29 solve_e: root not converged NaN kpoint 9 ibnd 29 solve_e: root not converged NaN kpoint 6 ibnd 29 solve_e: root not converged NaN kpoint 6 ibnd 29 solve_e: root not converged NaN kpoint 6 ibnd 29 solve_e: root not converged NaN kpoint 9 ibnd 29 solve_e: root not converged NaN kpoint 7 ibnd 29 solve_e: root not converged NaN kpoint 7 ibnd 29 solve_e: root not converged NaN kpoint 7 ibnd 29 solve_e: root not converged NaN kpoint 9 ibnd 29 solve_e: root not converged NaN kpoint 7 ibnd 29 solve_e: root not converged NaN kpoint 7 ibnd 29 solve_e: root not converged NaN kpoint 7 ibnd 29 solve_e: root not converged NaN kpoint 10 ibnd 29 solve_e: root not converged NaN kpoint 7 ibnd 29 solve_e: root not converged NaN kpoint 7 ibnd 29 solve_e: root not converged NaN kpoint 7 ibnd 29 solve_e: root not converged NaN kpoint 10 ibnd 29 solve_e: root not converged NaN kpoint 8 ibnd 29 solve_e: root not converged NaN kpoint 8 ibnd 29 solve_e: root not converged NaN kpoint 8 ibnd 29 solve_e: root not converged NaN kpoint 10 ibnd 29 solve_e: root not converged NaN kpoint 8 ibnd 29 solve_e: root not converged NaN kpoint 8 ibnd 29 solve_e: root not converged NaN kpoint 8 ibnd 29 solve_e: root not converged NaN kpoint 11 ibnd 29 solve_e: root not converged NaN kpoint 8 ibnd 29 solve_e: root not converged NaN kpoint 8 ibnd 29 solve_e: root not converged NaN kpoint 8 ibnd 29 solve_e: root not converged NaN kpoint 11 ibnd 29 solve_e: root not converged NaN kpoint 9 ibnd 29 solve_e: root not converged NaN kpoint 9 ibnd 29 solve_e: root not converged NaN kpoint 9 ibnd 29 solve_e: root not converged NaN kpoint 11 ibnd 29 solve_e: root not converged NaN kpoint 9 ibnd 29 solve_e: root not converged NaN kpoint 9 ibnd 29 solve_e: root not converged NaN kpoint 9 ibnd 29 solve_e: root not converged NaN kpoint 12 ibnd 29 solve_e: root not converged NaN kpoint 9 ibnd 29 solve_e: root not converged NaN kpoint 9 ibnd 29 solve_e: root not converged NaN kpoint 9 ibnd 29 solve_e: root not converged NaN kpoint 12 ibnd 29 solve_e: root not converged NaN kpoint 10 ibnd 29 solve_e: root not converged NaN kpoint 10 ibnd 29 solve_e: root not converged NaN kpoint 10 ibnd 29 solve_e: root not converged NaN kpoint 12 ibnd 29 solve_e: root not converged NaN kpoint 10 ibnd 29 solve_e: root not converged NaN kpoint 10 ibnd 29 solve_e: root not converged NaN kpoint 10 ibnd 29 solve_e: root not converged NaN kpoint 13 ibnd 29 solve_e: root not converged NaN kpoint 10 ibnd 29 solve_e: root not converged NaN kpoint 10 ibnd 29 solve_e: root not converged NaN kpoint 10 ibnd 29 solve_e: root not converged NaN kpoint 13 ibnd 29 solve_e: root not converged NaN kpoint 11 ibnd 29 solve_e: root not converged NaN kpoint 11 ibnd 29 solve_e: root not converged NaN kpoint 11 ibnd 29 solve_e: root not converged NaN kpoint 13 ibnd 29 solve_e: root not converged NaN kpoint 11 ibnd 29 solve_e: root not converged NaN kpoint 11 ibnd 29 solve_e: root not converged NaN kpoint 11 ibnd 29 solve_e: root not converged NaN kpoint 14 ibnd 29 solve_e: root not converged NaN kpoint 11 ibnd 29 solve_e: root not converged NaN kpoint 11 ibnd 29 solve_e: root not converged NaN kpoint 11 ibnd 29 solve_e: root not converged NaN kpoint 14 ibnd 29 solve_e: root not converged NaN kpoint 12 ibnd 29 solve_e: root not converged NaN kpoint 12 ibnd 29 solve_e: root not converged NaN kpoint 12 ibnd 29 solve_e: root not converged NaN kpoint 14 ibnd 29 solve_e: root not converged NaN kpoint 12 ibnd 29 solve_e: root not converged NaN kpoint 12 ibnd 29 solve_e: root not converged NaN kpoint 12 ibnd 29 solve_e: root not converged NaN kpoint 15 ibnd 29 solve_e: root not converged NaN kpoint 12 ibnd 29 solve_e: root not converged NaN kpoint 12 ibnd 29 solve_e: root not converged NaN kpoint 12 ibnd 29 solve_e: root not converged NaN kpoint 15 ibnd 29 solve_e: root not converged NaN kpoint 13 ibnd 29 solve_e: root not converged NaN kpoint 13 ibnd 29 solve_e: root not converged NaN kpoint 13 ibnd 29 solve_e: root not converged NaN kpoint 15 ibnd 29 solve_e: root not converged NaN kpoint 13 ibnd 29 solve_e: root not converged NaN kpoint 13 ibnd 29 solve_e: root not converged NaN kpoint 13 ibnd 29 solve_e: root not converged NaN kpoint 16 ibnd 29 solve_e: root not converged NaN kpoint 13 ibnd 29 solve_e: root not converged NaN kpoint 13 ibnd 29 solve_e: root not converged NaN kpoint 13 ibnd 29 solve_e: root not converged NaN kpoint 16 ibnd 29 solve_e: root not converged NaN kpoint 14 ibnd 29 solve_e: root not converged NaN kpoint 14 ibnd 29 solve_e: root not converged NaN kpoint 14 ibnd 29 solve_e: root not converged NaN kpoint 16 ibnd 29 solve_e: root not converged NaN kpoint 14 ibnd 29 solve_e: root not converged NaN kpoint 14 ibnd 29 solve_e: root not converged NaN kpoint 14 ibnd 29 solve_e: root not converged NaN kpoint 17 ibnd 29 solve_e: root not converged NaN kpoint 14 ibnd 29 solve_e: root not converged NaN kpoint 14 ibnd 29 solve_e: root not converged NaN kpoint 14 ibnd 29 solve_e: root not converged NaN kpoint 17 ibnd 29 solve_e: root not converged NaN kpoint 15 ibnd 29 solve_e: root not converged NaN kpoint 15 ibnd 29 solve_e: root not converged NaN kpoint 15 ibnd 29 solve_e: root not converged NaN kpoint 17 ibnd 29 solve_e: root not converged NaN kpoint 15 ibnd 29 solve_e: root not converged NaN kpoint 15 ibnd 29 solve_e: root not converged NaN kpoint 15 ibnd 29 solve_e: root not converged NaN kpoint 18 ibnd 29 solve_e: root not converged NaN kpoint 15 ibnd 29 solve_e: root not converged NaN kpoint 15 ibnd 29 solve_e: root not converged NaN kpoint 15 ibnd 29 solve_e: root not converged NaN kpoint 18 ibnd 29 solve_e: root not converged NaN kpoint 16 ibnd 29 solve_e: root not converged NaN kpoint 16 ibnd 29 solve_e: root not converged NaN kpoint 16 ibnd 29 solve_e: root not converged NaN kpoint 18 ibnd 29 solve_e: root not converged NaN kpoint 16 ibnd 29 solve_e: root not converged NaN kpoint 16 ibnd 29 solve_e: root not converged NaN kpoint 16 ibnd 29 solve_e: root not converged NaN kpoint 19 ibnd 29 solve_e: root not converged NaN kpoint 16 ibnd 29 solve_e: root not converged NaN kpoint 16 ibnd 29 solve_e: root not converged NaN kpoint 16 ibnd 29 solve_e: root not converged NaN kpoint 19 ibnd 29 solve_e: root not converged NaN kpoint 17 ibnd 29 solve_e: root not converged NaN kpoint 17 ibnd 29 solve_e: root not converged NaN kpoint 17 ibnd 29 solve_e: root not converged NaN kpoint 19 ibnd 29 solve_e: root not converged NaN kpoint 17 ibnd 29 solve_e: root not converged NaN kpoint 17 ibnd 29 solve_e: root not converged NaN kpoint 17 ibnd 29 solve_e: root not converged NaN kpoint 20 ibnd 29 solve_e: root not converged NaN kpoint 17 ibnd 29 solve_e: root not converged NaN kpoint 17 ibnd 29 solve_e: root not converged NaN kpoint 17 ibnd 29 solve_e: root not converged NaN kpoint 20 ibnd 29 solve_e: root not converged NaN kpoint 18 ibnd 29 solve_e: root not converged NaN kpoint 18 ibnd 29 solve_e: root not converged NaN kpoint 18 ibnd 29 solve_e: root not converged NaN kpoint 20 ibnd 29 solve_e: root not converged NaN kpoint 18 ibnd 29 solve_e: root not converged NaN iter # 3 total cpu time : 15037.6 secs av.it.: 200.0 thresh= 0.145E-05 alpha_mix = 0.700 |ddv_scf|^2 = NaN kpoint 18 ibnd 29 solve_e: root not converged NaN kpoint 18 ibnd 29 solve_e: root not converged NaN kpoint 18 ibnd 29 solve_e: root not converged NaN kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 18 ibnd 29 solve_e: root not converged NaN kpoint 18 ibnd 29 solve_e: root not converged NaN kpoint 19 ibnd 29 solve_e: root not converged NaN kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 19 ibnd 29 solve_e: root not converged NaN kpoint 19 ibnd 29 solve_e: root not converged NaN kpoint 19 ibnd 29 solve_e: root not converged NaN kpoint 1 ibnd 29 solve_e: root not converged NaN kpoint 19 ibnd 29 solve_e: root not converged NaN kpoint 19 ibnd 29 solve_e: root not converged NaN kpoint 19 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 19 ibnd 29 solve_e: root not converged NaN kpoint 19 ibnd 29 solve_e: root not converged NaN kpoint 20 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 20 ibnd 29 solve_e: root not converged NaN kpoint 20 ibnd 29 solve_e: root not converged NaN kpoint 20 ibnd 29 solve_e: root not converged NaN kpoint 2 ibnd 29 solve_e: root not converged NaN kpoint 20 ibnd 29 solve_e: root not converged NaN kpoint 20 ibnd 29 solve_e: root not converged NaN kpoint 20 ibnd 29 solve_e: root not converged NaN kpoint 3 ibnd 29 solve_e: root not converged NaN %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from broyden : error # 1 factorization %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... kpoint 20 ibnd 29 solve_e: root not converged NaN kpoint 20 ibnd 29 solve_e: root not converged NaN %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from broyden : error # 1 factorization %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from broyden : error # 1 factorization From tunderaji at gmail.com Fri Oct 1 14:58:11 2010 From: tunderaji at gmail.com (Raji Abdulrafiu) Date: Fri, 1 Oct 2010 14:58:11 +0200 Subject: [Pw_forum] Problem running EXX_example Message-ID: Dear QE community, I tried to run the example file embedded in EXX_example in QE version 4.2, i.e. the one involving the hybrid functional. However, the job suddenly stopped with the following error message beow. I experienced the same problem while using the QE version 4.1.....Thanks ================================================== /home/araji/Codes/espresso-4.1/examples/EXX_example : starting This example shows how to use pw.x to calculate the total energy and of silicon and a few small molecules using hybrid functionals. executables directory: /home/araji/Codes/espresso-4.1/bin pseudo directory: /home/araji/Codes/espresso-4.1/pseudo temporary directory: /home/araji/tmp checking that needed directories and files exist... done running pw.x as: /home/araji/Codes/espresso-4.1/bin/pw.x cleaning /home/araji/tmp... done running PBE0 calculation for Si with nq=1,2,4 running the scf calculation for Si with nq = 1 ...Cannot match namelist object name nqx1 namelist read: misplaced = sign Cannot match namelist object name 1 Cannot match namelist object name nqx2 namelist read: misplaced = sign Cannot match namelist object name 1 Cannot match namelist object name nqx3 namelist read: misplaced = sign Cannot match namelist object name 1 STOP 2 done !!! Please, verify this is what you really want ! running the scf calculation for Si with nq = 2 ...Cannot match namelist object name nqx1 namelist read: misplaced = sign Cannot match namelist object name 2 Cannot match namelist object name nqx2 namelist read: misplaced = sign Cannot match namelist object name 2 Cannot match namelist object name nqx3 namelist read: misplaced = sign Cannot match namelist object name 2 STOP 2 done !!! Please, verify this is what you really want ! running the scf calculation for Si with nq = 4 ...Cannot match namelist object name nqx1 namelist read: misplaced = sign Cannot match namelist object name 4 Cannot match namelist object name nqx2 namelist read: misplaced = sign Cannot match namelist object name 4 Cannot match namelist object name nqx3 namelist read: misplaced = sign Cannot match namelist object name 4 STOP 2 done !!! Please, verify this is what you really want ! running now a few molecules with Gamma sampling ... pseudo directory changed to: ../Pseudo running oxygen atom..STOP 2 done running carbon atom..STOP 2 done running nitrogen atom..STOP 2 done running n2 molecule..STOP 2 done running co molecule..STOP 2 done running o2 molecule..STOP 2 done summarize N2 : 0 O2 : 0 CO : 0 ========================================================= -- Raji Abdulrafiu Tunde, Solid state and Material Physics Group, Department of Physics, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town. South Africa. Cell: +27730639756 Fax: +27216503342 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101001/35dd716a/attachment.htm From giannozz at democritos.it Fri Oct 1 15:42:19 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 1 Oct 2010 15:42:19 +0200 Subject: [Pw_forum] Problem running EXX_example In-Reply-To: References: Message-ID: <255C60C3-57FC-4BF7-BAF4-50570900F0A1@democritos.it> On Oct 1, 2010, at 14:58 , Raji Abdulrafiu wrote: > Cannot match namelist object name nqx1 you need to recompile with DFLAGS=-DEXX ... P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From elie.moujaes at hotmail.co.uk Fri Oct 1 16:12:04 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Fri, 1 Oct 2010 15:12:04 +0100 Subject: [Pw_forum] Bilayer graphene with an electric field applied In-Reply-To: References: , <4CA2F0D7.1040205@sissa.it>, , Message-ID: Dear Professor Paulatto, thanks for bringing this up. Indeed, I was plotting the band energies of the regukar k grid instead. Everything seems right now.. Regards Elie > To: pw_forum at pwscf.org > Date: Thu, 30 Sep 2010 17:46:39 +0200 > From: Lorenzo.Paulatto at impmc.upmc.fr > Subject: Re: [Pw_forum] Bilayer graphene with an electric field applied > > In data 30 settembre 2010 alle ore 15:30:01, Elie Moujaes > ha scritto: > > The thing is there are no problems in the DOS calculations; only in the > > band structure. > > Are you sure you did a proper band plot along a path in the Brillouin zone > (like example01) and not just plot of the band energies of the regular > grid of k-points? > > regards > > -- > Lorenzo Paulatto > post-doc @ IMPMC/UPMC - Universit? Paris 6 > phone: +33 (0)1 44 27 74 89 > www: http://www-int.impmc.upmc.fr/~paulatto/ > > previously (take note of the change!): > phd student @ SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > www: http://people.sissa.it/~paulatto/ > _______________________________________________ > 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/20101001/87cc26fe/attachment.htm From somnath.bhowmick at gmail.com Fri Oct 1 16:35:42 2010 From: somnath.bhowmick at gmail.com (Somnath) Date: Fri, 1 Oct 2010 20:05:42 +0530 Subject: [Pw_forum] Question regarding the charge density Message-ID: Dear members, Is it possible to get the electronic and ionic charge density together ? I think pp.x just gives the electronic charge density. Should i look into charge-density.dat file or is there any easier way to do it ? thanks in advance. -- -------------------------------------------------- Somnath Bhowmick Room No. 201, Department of Mechanical Engineering & Materials Science. Rice University, 6100 Main Street. Houston, TX 77005-1827, USA. Office: 713 348 8079 Somnath.Bhowmick at rice.edu somnath.bhowmick at gmail.com http://somnath.bhowmick.googlepages.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101001/5c87f140/attachment.htm From manoj at phys.ufl.edu Fri Oct 1 23:04:33 2010 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Fri, 1 Oct 2010 17:04:33 -0400 (EDT) Subject: [Pw_forum] how to choose bds in PWCOND? Message-ID: Dear All, I am confused about choosing bds parameter in the transmission calculation of PWCOND. My question is about example on Smogunov's website Monatomic Ni wire with a spin reversal, which can be accessed at http://people.sissa.it/~smogunov/ The manual says- right boundary of the scatt. reg. (left one is at 0 if prefixs is used and = bdl if prefixt is used) Now in this example bds is chosen to be at 1.0, but if I let the system relax and atom at z=1.0 moves away from z=1, would bds still be equal to 1.0? I am guessing so, but I am not sure. Would someone mind explaining this? -Manoj Srivastava Department of Physics, University of Florida, Gainesville, FL From bliu520 at gmail.com Sat Oct 2 04:57:57 2010 From: bliu520 at gmail.com (Baowei Liu) Date: Fri, 1 Oct 2010 22:57:57 -0400 Subject: [Pw_forum] Potentials between two charged particles Message-ID: Dear all members, I am trying to calculate the potential between two ions, -- A(+2) and A(+1) for example. When the two ions are far away from each other, there's only Coulumb potential. But when the two ions are close enough, the electron distribution will be important for the potential. Can QE be used to calculate the energy or charge density for a system of two charged particles? It will be great if QE can give the energy for different distances. Just setting the tot_charge (=+3 in this example) is kind of not what I want. Thanks in advance. Baowei Liu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101001/30657bd4/attachment.htm From baroni at sissa.it Sat Oct 2 07:47:03 2010 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 2 Oct 2010 07:47:03 +0200 Subject: [Pw_forum] relaxation and TS In-Reply-To: References: Message-ID: On Sep 30, 2010, at 3:49 PM, Masoud Nahali wrote: > > Dear Prof. Stefano Baroni and Vega Lew > > > ** shows the step in which the energy rises. I don't think that these points indicate a TS or something like that since one may see such points through any optimization procedure; am I correct ? Yes. Let me rephrase my previous statement: if you can reach B from A through an overdumped dynamics (which is equivalent to a smooth steepest-descent minimization), then there is non energy barrier. allegedly smarter minimization algorithms can occasionally incur energy bumps. SB --- 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 Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101002/946c1789/attachment-0001.htm From baroni at sissa.it Sat Oct 2 08:30:08 2010 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 2 Oct 2010 08:30:08 +0200 Subject: [Pw_forum] job vacancy Message-ID: <770133C1-5D7E-4997-8193-FBA809AAA14F@sissa.it> A 2-years postdoctoral position is open at SISSA to work on the Liouville-Lanczos approach to TDDFT [PRL 96, 113001 (2006), JCP 128, 154105 (2008)], with applications to dye-sensitized solar cells. The post is available immediately and the salary is 1800 ?/year. If you are interested, please contact me at baroni at sissa.it (do NOT hit "reply" to the present message). Best wishes - Stefano B --- 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 Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101002/bfcdfa5e/attachment.htm From baroni at sissa.it Sat Oct 2 08:38:34 2010 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 2 Oct 2010 08:38:34 +0200 Subject: [Pw_forum] Fwd: job vacancy References: <770133C1-5D7E-4997-8193-FBA809AAA14F@sissa.it> Message-ID: <94AB4DB7-6E39-4F71-B90F-6BACA9DAF347@sissa.it> Of course, the salary is 1800 ?/MONTH ... Begin forwarded message: > From: Stefano Baroni > Date: October 2, 2010 8:30:08 AM GMT+02:00 > To: PWSCF Forum > Subject: job vacancy > > A 2-years postdoctoral position is open at SISSA to work on the Liouville-Lanczos approach to TDDFT [PRL 96, 113001 (2006), JCP 128, 154105 (2008)], with applications to dye-sensitized solar cells. The post is available immediately and the salary is 1800 ?/year. If you are interested, please contact me at baroni at sissa.it (do NOT hit "reply" to the present message). Best wishes - Stefano B > > --- > 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 > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > --- 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 Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101002/9c558e78/attachment-0001.htm From daijiayu at nudt.edu.cn Sat Oct 2 10:18:17 2010 From: daijiayu at nudt.edu.cn (jiayudai) Date: Sat, 02 Oct 2010 16:18:17 +0800 Subject: [Pw_forum] negative values in XANES (jiayu dai) Message-ID: Dear matteo calandra, Thanks for your instructions. I did the comparision as you said. The DOS and the xanes before occupied cutting can be comparable (I will send the files to you seperately). However, whatever i did, the xanes after occupied cutting was strange. I attached the files i used, maybe there was something error or lost information, but i never found them. The strange thing was that even there are values larger than zero in the xanes before cutting, the xanes after cutting is most zero except in a narrow area in energy (x-aixs). I did not know where the values gone. Thanks a lot?and best wishes. Jiayu Date: Thu, 30 Sep 2010 15:50:01 +0200 From: matteo calandra Subject: Re: [Pw_forum] negative values in XANES (jiayudai) To: pw_forum at pwscf.org Message-ID: Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Dear Jiayudai, it is a bit difficult to understand what do you mean without having a picture. Maybe you can try the following for the high pressure case. You take a GIPAW pseudopotential compatible with XSPECTRA without core hole and do again the calculation without cutting occupied states but inserting your ef_r value. Then you compare your results with the corresponding projected density of states calcolated with projwfc. For corresponding I mean corresponding to the choice of your polarization (and k-vector if you are calculating the quadrupolar part). They should be the same (or very similar as probably you don't have all the same parameters in the two calculations, number of bands, broadening...) except for a prefactor along the y axis. So you can check if you are not making a mistake somewhere. All the best, M. > > Message: 3 > Date: Thu, 30 Sep 2010 19:54:51 +0800 > From: "jiayudai" > Subject: Re: [Pw_forum] negative values in XANES > To: pw_forum at pwscf.org > Message-ID: > Content-Type: text/plain; charset="gb2312" > > Dear matteo, > > Thanks for your reply to me. The "negative" means the negative > position in x-axis. And i added the "ef_r" in the input file, and > the position of the absorption is reasonable now. However, when the > pressure is high (high density), the fermi energy should be also > very high. Even i added the "ef_r", the absorption after cutting the > contribution of occupied states is only a isolated peak. In the same > case but with lower density, there is not this problem. And the > analysis of density of states for the system tells me that there > should be absorption at the position of high energy. In this case, > the absorption before occ_cut and after occ_cut is very different > (the intensity is very weak, about 10-8). So, i can not find physcal > reason to explain it. Is there also some problems in my calculation? > > By the way, i changed some parameters of &occ_cut& part, but the > results were the same. > > Thanks again, and best wishes. > > Jiayu > > > Subject: Re: [Pw_forum] negative values in XANES (jiayudai) > To: PWSCF Forum > > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Matteo, thank you for taking the time to participate in the > discussion. In the future, please hit "reply" when answering a post, > rather than starting a new thread. Have all a good day - Stefano B > > On Sep 30, 2010, at 9:13 AM, matteo calandra wrote: > >> Dear Jiayu, >> >> I assume you're using XSPECTRA to calculate Xanes K-edge. >> Maybe you can better specify what does it means "negative >> absorption". If this means that the value on the XANES intensity is negative >> then you must have some problem somewhere as the cross section >> implemented in XSPECTRA is positive definite. >> >> However, from your e-mail it is not very clear if the >> absorption is positive definite (as you say) or if the energy scale >> (the x axis in the plot) >> is negative but not the X-ray absorption intensity (y-axis in the plot). >> If y is positive and x is negative, then you simply forgot >> to specify the variable >> ef_r in the XSPECTRA input file. This variable tells you the zero >> energy of the scale. From the XSPECTRA input file: >> >> ef_r real(DP) >> DEFAULT=0.0 >> Fermi energy in Rydberg. This value combined >> with the option cut_occupied_states can be >> used to exclude the occupied states in a >> smooth way from the final plot. >> >> I hope it helps, >> >> M. >> >> >>> Dear developers and users, >>> >>> I am doing the calculation for the XANES of CHx system. There is a >>> problem that the absorption is always negative, locating at about >>> -100 eV. According to my >understanding, the absorption should be >>> positive. Besides, the fermi energy in >my systems is very high, >>> about tens of eV (high pressure). Therefore, if i used the cutoff of >>> fermi energy, the absorption should be very small. Is it >>>> reasonable? Or there is some problems in the calculations? >>> >>> Thanks in advance. >>> >>> Jiayu >> >> ---------------------------------------------------------------- >> This message was sent using IMP, the Internet Messaging Program. >> >> >> _______________________________________________ >> 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 > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20100930/c1998bf7/attachment.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 39, Issue 57 > **************************************** > > > > ---------------------------- ---------------- ------------------------------------------- Jiayu Dai Department of Physics National University of Defense Technology, Changsha, 410073, P R China ----------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101002/16c30ad0/attachment.htm From Matthieu.Verstraete at ulg.ac.be Sat Oct 2 11:27:43 2010 From: Matthieu.Verstraete at ulg.ac.be (matthieu verstraete) Date: Sat, 2 Oct 2010 11:27:43 +0200 Subject: [Pw_forum] d3 errors in file reading In-Reply-To: <4CA32AD3.3080606@democritos.it> References: <513A18AF-BE20-44D4-A458-2B57D3DA2B29@democritos.it> <4CA32AD3.3080606@democritos.it> Message-ID: Hello again - some progress: I have made d3 work for the gamma point, with the mpi executable and a single processor (and -inp thanks to Paolo's patch). Now I would like to get the corrections for other q-points, and I'm again getting davcio error messages. I have isolated the possible calls to phq_init (called from d3toten), wherein there are two calls to davcio: one for all q and one which is not used for q=Gamma (line 196 to get evq) - the likely culprit. The strange things are 1) this has been called before, during the phonon run, and everything was fine 2) the wfc file is complete: I used wf_collect = .true. so there is no reason davcio could be looking for something else. Could the call to phq_init from d3toten be looking for other files that ph.x did not need? Are there other files which need to be "collected" because I did the phonons in parallel? I have also tried d3 in parallel (32 procs like the phonons) and it fails very quickly. Log file: >>> READING PATTERNS FROM FILE sb.drho02.pat READING PATTERNS FROM FILE sb.drho01.pat <<< sb.drho01 is present. Error file: <<< "io_pattern.F90", line 45: 1525-001 The READ statement on the file ./_ph0sb.sb.drho01.pat cannot be completed because the end of the file was reached. The program will stop. >>> Again, _ph0sb.sb.drho01.pat is present. Any hints? I have the impression it's not a bug, but I have no way of knowing which file is corrupted or missing... Thanks Matthieu On Wed, Sep 29, 2010 at 2:02 PM, Paolo Giannozzi wrote: > matthieu verstraete wrote: > >> - is d3 fully parallelized? Can I run it with more? > > you can, but I think you need to run d3 on the same number > of processors as for ph.x > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Prof. Matthieu Verstraete Universite de Li?ge Institut de Physique, Bat. B5, 3/7 All?e du 6 aout, 17 B- 4000 Sart Tilman, Li?ge Belgium Associate member European Theoretical Spectroscopy Facility (ETSF http://www.etsf.eu) Phone : +32 4 366 90 17 Fax?? : +32 4 366 36 29 Mail : matthieu.verstraete at ulg.ac.be ? ? ? ? ? matthieu.jean.verstraete at gmail.com From sclauzer at sissa.it Sat Oct 2 15:51:16 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Sat, 2 Oct 2010 15:51:16 +0200 Subject: [Pw_forum] how to choose bds in PWCOND? In-Reply-To: References: Message-ID: <8812CA7C-CEC2-4FAC-A2B1-26ADA7FAF22D@sissa.it> Dear Manoj, Il giorno 01/ott/2010, alle ore 23.04, Manoj Srivastava ha scritto: > Dear All, > I am confused about choosing bds parameter in the transmission > calculation of PWCOND. My question is about example on Smogunov's website > Monatomic Ni wire with a spin reversal, which can be accessed at > http://people.sissa.it/~smogunov/ > The manual says- right boundary of the scatt. reg. (left one is at 0 if > prefixs is used and = bdl if prefixt is used) Now in this example bds is > chosen to be at 1.0, but if I let the system relax and atom at z=1.0 moves > away from z=1, would bds still be equal to 1.0? I think that's not correct. If you keep the same left lead, then there must be an atom exactly at the right boundary of the Scattering Region. If you let relax the atoms in the larger cell, then you should change bds according to the position of the rightmost atom that you want to include in the S.R. for the pwcond calculation. Be careful that the scf potential in a periodic unit cell (i.e. that corresponding to the infinite, equally spaced chain) close to the right boundary of the S.R. must be, to a good approximation, equal to that in the left lead (the same applies to the right boundary). Hence you may need to include more atoms in the larger supercell and fix the atomic positions of those that will correspond to the leftmost and rightmost regions inside the S.R. (according to your choice of bdl and bds). HTH GS > I am guessing so, but I am > not sure. Would someone mind explaining this? > > -Manoj Srivastava > Department of Physics, > University of Florida, > Gainesville, FL > > _______________________________________________ > 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/20101002/ea4831bd/attachment-0001.htm From degironc at sissa.it Sat Oct 2 15:58:39 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sat, 02 Oct 2010 15:58:39 +0200 Subject: [Pw_forum] Potentials between two charged particles In-Reply-To: References: Message-ID: <4CA73A8F.6090502@sissa.it> the code can perform calculation for charged system using the variable tot_charge. By default the code performs the calculation for a periodic system (adding a compensating background to eliminate the G=0 divergence). In the limit of large cells this eventually converge to the isolated case. There are various techniques to perform calculations for isolated systems with smaller cells. Read carefully the description of assume_isolated variable in the system namelist best, Stefano de Gironcoli - SISSA and DEMOCRITOS Baowei Liu wrote: > Dear all members, > > I am trying to calculate the potential between two ions, -- A(+2) and A(+1) > for example. When the two ions are far away from each other, there's only > Coulumb potential. But when the two ions are close enough, the electron > distribution will be important for the potential. Can QE be used to > calculate the energy or charge density for a system of two charged > particles? It will be great if QE can give the energy for different > distances. Just setting the tot_charge (=+3 in this example) is kind of not > what I want. > Thanks in advance. > > Baowei Liu > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From bliu520 at gmail.com Sun Oct 3 02:24:54 2010 From: bliu520 at gmail.com (Baowei Liu) Date: Sat, 2 Oct 2010 20:24:54 -0400 Subject: [Pw_forum] Potentials between two charged particles In-Reply-To: <4CA73A8F.6090502@sissa.it> References: <4CA73A8F.6090502@sissa.it> Message-ID: Hi Prof. Gironcoli, Thank you for your fast reply. I tried the following calculation. It gives me ! total energy = -325.65235136 Ry. But Some of rho values are negative when I do post processing. What could be the possible reason? &control calculation = 'scf' restart_mode='from_scratch', prefix='Ge', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' &system ibrav= 0, nat= 2, ntyp= 2, occupations = 'smearing',smearing='marzari-vanderbilt', degauss=0.05, nosym=.true., ecutwfc = 110 ecutrho = 880 tot_charge = +3, assume_isolated=.true. / &electrons diagonalization = 'david', mixing_mode = 'plain', mixing_beta = 0.7 conv_thr = 1.0d-7 electron_maxstep=200 / CELL_PARAMETERS cubic 40.0 0.0 0.0 0.0 40.0 0.0 0.0 0.0 40.0 ATOMIC_SPECIES Ge1 72.61 Ge.pbe-paw_kj.UPF Ge2 72.61 Ge.pbe-paw_kj.UPF ATOMIC_POSITIONS Ge1 0.50 0.50 0.50 0 0 0 Ge2 0.5 0.50 0.70 0 0 0 0 K_POINTS {automatic} 1 1 1 0 0 0 Thanks and Best Regards, Baowei Liu On Sat, Oct 2, 2010 at 9:58 AM, Stefano de Gironcoli wrote: > the code can perform calculation for charged system using the variable > tot_charge. > By default the code performs the calculation for a periodic system > (adding a compensating background to eliminate the G=0 divergence). > In the limit of large cells this eventually converge to the isolated case. > There are various techniques to perform calculations for isolated > systems with smaller cells. > Read carefully the description of assume_isolated variable in the system > namelist > best, > > Stefano de Gironcoli - SISSA and DEMOCRITOS > > Baowei Liu wrote: > > Dear all members, > > > > I am trying to calculate the potential between two ions, -- A(+2) and > A(+1) > > for example. When the two ions are far away from each other, there's only > > Coulumb potential. But when the two ions are close enough, the electron > > distribution will be important for the potential. Can QE be used to > > calculate the energy or charge density for a system of two charged > > particles? It will be great if QE can give the energy for different > > distances. Just setting the tot_charge (=+3 in this example) is kind of > not > > what I want. > > Thanks in advance. > > > > Baowei Liu > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101002/a725fa68/attachment.htm From degironc at sissa.it Mon Oct 4 08:54:33 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 04 Oct 2010 08:54:33 +0200 Subject: [Pw_forum] Potentials between two charged particles In-Reply-To: References: <4CA73A8F.6090502@sissa.it> Message-ID: <4CA97A29.9020401@sissa.it> dear Baowei Liu , when using USPP or paw, charge density can acquire small negative contributions due to an incomplete Fourier expansion of the augmentation charge density. This appears in particular when the system has large portion of vacuum (surface or molecules) since all other relevant contributions to the charge density vanish... However your cutoff values (both ecutwfc and ecutrho) are quite high so I'm a bit surprised you see negative charges. How large are these negative values ? stefano Baowei Liu wrote: > Hi Prof. Gironcoli, > > Thank you for your fast reply. I tried the following calculation. It gives > me > ! total energy = -325.65235136 Ry. > But Some of rho values are negative when I do post processing. What could be > the possible reason? > > &control > calculation = 'scf' > restart_mode='from_scratch', > prefix='Ge', > pseudo_dir = '$PSEUDO_DIR/', > outdir='$TMP_DIR/' > &system > ibrav= 0, > nat= 2, ntyp= 2, > occupations = 'smearing',smearing='marzari-vanderbilt', > degauss=0.05, > nosym=.true., > ecutwfc = 110 > ecutrho = 880 > tot_charge = +3, > assume_isolated=.true. > / > &electrons > diagonalization = 'david', > mixing_mode = 'plain', > mixing_beta = 0.7 > conv_thr = 1.0d-7 > electron_maxstep=200 > / > > CELL_PARAMETERS cubic > 40.0 0.0 0.0 > 0.0 40.0 0.0 > 0.0 0.0 40.0 > ATOMIC_SPECIES > Ge1 72.61 Ge.pbe-paw_kj.UPF > Ge2 72.61 Ge.pbe-paw_kj.UPF > ATOMIC_POSITIONS > Ge1 0.50 0.50 0.50 0 0 0 > Ge2 0.5 0.50 0.70 0 0 0 0 > > K_POINTS {automatic} > 1 1 1 0 0 0 > > Thanks and Best Regards, > Baowei Liu > > On Sat, Oct 2, 2010 at 9:58 AM, Stefano de Gironcoli wrote: > > >> the code can perform calculation for charged system using the variable >> tot_charge. >> By default the code performs the calculation for a periodic system >> (adding a compensating background to eliminate the G=0 divergence). >> In the limit of large cells this eventually converge to the isolated case. >> There are various techniques to perform calculations for isolated >> systems with smaller cells. >> Read carefully the description of assume_isolated variable in the system >> namelist >> best, >> >> Stefano de Gironcoli - SISSA and DEMOCRITOS >> >> Baowei Liu wrote: >> >>> Dear all members, >>> >>> I am trying to calculate the potential between two ions, -- A(+2) and >>> >> A(+1) >> >>> for example. When the two ions are far away from each other, there's only >>> Coulumb potential. But when the two ions are close enough, the electron >>> distribution will be important for the potential. Can QE be used to >>> calculate the energy or charge density for a system of two charged >>> particles? It will be great if QE can give the energy for different >>> distances. Just setting the tot_charge (=+3 in this example) is kind of >>> >> not >> >>> what I want. >>> Thanks in advance. >>> >>> Baowei Liu >>> >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> 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 >> >> > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From steve.ndengue at yahoo.fr Mon Oct 4 12:54:45 2010 From: steve.ndengue at yahoo.fr (=?iso-8859-1?Q?steve_ndengu=E9?=) Date: Mon, 4 Oct 2010 11:54:45 +0100 (BST) Subject: [Pw_forum] Request about the "real" total energy Message-ID: <899488.30605.qm@web29508.mail.ird.yahoo.com> Dear all, We have an enquiry about some results appearing in the output file of the pw.x run. We are trying to perform computations on isolated atoms to try to get a significance of the results given by the code. We have to recall that we are new users of QE. And as far as we know it is not too much indicated for such kind of computations but it is rather a first try to get some understanding on the "behaviour" of the code. So the problem is that when performing the computations on He for example we obtain the correct ground state energy up to the Hartree-Fock limit. But when applied to other atoms (Li, Na, Be, C, ...) the value obtained do not correspond at all to the known value. We thus have 2 questions: 1- Why is it that the level of refinement obtained is the Hartree-Fock limit; we may have expected a better accuracy? Is it linked to the use of pseudo-potentials? 2- What can we do to recover the correct (up to the Hartree-Fock limit at least) total energy for the other atoms? ? Sincerely Yours, On behalf of the Groupe? de Structure et Dynamique des Atomes et Molecules Laboratoire de Physique Fondamentale D?partement de Physique Universit? de Douala. Steve. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101004/58a8fca1/attachment.htm From degironc at sissa.it Mon Oct 4 13:11:50 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 04 Oct 2010 13:11:50 +0200 Subject: [Pw_forum] Request about the "real" total energy In-Reply-To: <899488.30605.qm@web29508.mail.ird.yahoo.com> References: <899488.30605.qm@web29508.mail.ird.yahoo.com> Message-ID: <4CA9B676.5070801@sissa.it> the pw codes in the QE distribution calculate the total energy in the pseudopotential framework. Pseudopotentials should be good at computing energy differences (at the forzen-core level) . If you wish a total energy to be compared with an all-electron (forzen-core)energy you need to calculate the formation energy of your system relative to isolated atoms and then use the difference between the isolated atom computed by the pseudopotential and with an all-electron code to correct it. Within the QE dsitribution, you can perform both all-electron and pseudopotential calculation in the atomic case with the ld1.x code . stefano steve ndengu? wrote: > Dear all, > > We have an enquiry about some results appearing in the output file of the pw.x run. > > We > are trying to perform computations on isolated atoms to try to get a > significance of the results given by the code. We have to recall that we > are new users of QE. And as far as we know it is not too much indicated > for such kind of computations but it is rather a first try to get some > understanding on the "behaviour" of the code. > > So the problem is > that when performing the computations on He for example we obtain the > correct ground state energy up to the Hartree-Fock limit. But when > applied to other atoms (Li, Na, Be, C, ...) the value obtained do not > correspond at all to the known value. > > We thus have 2 > questions: > > 1- Why is it that the level of refinement obtained is > the Hartree-Fock limit; we may have expected a better accuracy? Is it > linked to the use of pseudo-potentials? > 2- What can we do to recover the correct (up to the Hartree-Fock limit at least) total energy for the other atoms? > > Sincerely Yours, > On behalf of the > Groupe de Structure et Dynamique des Atomes et Molecules > Laboratoire de Physique Fondamentale > D?partement de Physique > Universit? de Douala. > > Steve. > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From marzari at MIT.EDU Mon Oct 4 13:13:54 2010 From: marzari at MIT.EDU (Nicola Marzari) Date: Mon, 04 Oct 2010 12:13:54 +0100 Subject: [Pw_forum] Request about the "real" total energy In-Reply-To: <899488.30605.qm@web29508.mail.ird.yahoo.com> References: <899488.30605.qm@web29508.mail.ird.yahoo.com> Message-ID: <4CA9B6F2.5080909@mit.edu> Dear Steve, Indeed, you are freezing the core electrons in a pseudopotential - if atomic energies are what you are interested in, use the ld1.x code. Of course, plane waves are not really the best choice for Hartree Fock calculations (use a quantum chemistry codes) but if you are concerned about comparisons, maybe you could look at potential energy surfaces - e.g. the dissociation of a molecule, or the frequency normal modes - there you could compare Hartree-Fock within pw.x with other known results. Still, there could be better choices to get acqainted with the code - maybe browse, from the q-e website, the lectures/videos/tutorials of the 2009 Santa Barbara school. nicola steve ndengu? wrote: > Dear all, > > We have an enquiry about some results appearing in the output file of > the pw.x run. > > We are trying to perform computations on isolated atoms to try to get > a significance of the results given by the code. We have to recall > that we are new users of QE. And as far as we know it is not too much > indicated for such kind of computations but it is rather a first try > to get some understanding on the "behaviour" of the code. > > So the problem is that when performing the computations on He for > example we obtain the correct ground state energy up to the > Hartree-Fock limit. But when applied to other atoms (Li, Na, Be, C, > ...) the value obtained do not correspond at all to the known value. > > We thus have 2 questions: > > 1- Why is it that the level of refinement obtained is the Hartree-Fock > limit; we may have expected a better accuracy? Is it linked to the use > of pseudo-potentials? > 2- What can we do to recover the correct (up to the Hartree-Fock limit > at least) total energy for the other atoms? > > Sincerely Yours, > On behalf of the > Groupe de Structure et Dynamique des Atomes et Molecules > Laboratoire de Physique Fondamentale > D?partement de Physique > Universit? de Douala. > -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From bipulrr at gmail.com Mon Oct 4 15:07:00 2010 From: bipulrr at gmail.com (Bipul Rakshit) Date: Mon, 4 Oct 2010 18:37:00 +0530 Subject: [Pw_forum] Displacements corresponding to -ve Phonon modes Message-ID: Dear PWSCF users, I am doing Phonon of KO2 compound. I find some -ve phonon modes at gamma point. (After applying ASR also) Following is the dynamical matrix formed by the phonon programme during the run. I just want to study the displacement corresponding to -ve modes. So Is it enough to plot the eigen vectors given below corresponding to each mode. Strange things what I feel in these eigen vectors are the 'K' is also moving almost with the same magnitude as 'O' and there is no imaginary part of eigen vectors though the frequencies are -ve. kindly suggest. q = ( 0.000000000 0.000000000 0.000000000 ) ************************************************************************** omega( 1) = -1.178253 [THz] = -39.302564 [cm-1] ( 0.000000 0.000000 0.000000 0.000000 0.383086 0.000000 ) ( 0.000000 0.000000 0.000000 0.000000 0.386148 0.000000 ) ( 0.000000 0.000000 0.000000 0.000000 0.424830 0.000000 ) ( 0.000000 0.000000 0.000000 0.000000 0.424830 0.000000 ) ( 0.000000 0.000000 0.000000 0.000000 0.414231 0.000000 ) ( 0.000000 0.000000 0.000000 0.000000 0.414231 0.000000 ) omega( 2) = -1.150241 [THz] = -38.368174 [cm-1] ( 0.424996 0.000000 -0.085875 0.000000 0.000000 0.000000 ) ( -0.413054 0.000000 0.083462 0.000000 0.000000 0.000000 ) ( 0.396157 0.000000 -0.080048 0.000000 0.000000 0.000000 ) ( 0.396157 0.000000 -0.080048 0.000000 0.000000 0.000000 ) ( -0.384485 0.000000 0.077689 0.000000 0.000000 0.000000 ) ( -0.384485 0.000000 0.077689 0.000000 0.000000 0.000000 ) omega( 3) = -1.150241 [THz] = -38.368174 [cm-1] ( -0.085875 0.000000 -0.424996 0.000000 0.000000 0.000000 ) ( 0.083462 0.000000 0.413054 0.000000 0.000000 0.000000 ) ( -0.080048 0.000000 -0.396157 0.000000 0.000000 0.000000 ) ( -0.080048 0.000000 -0.396157 0.000000 0.000000 0.000000 ) ( 0.077689 0.000000 0.384485 0.000000 0.000000 0.000000 ) ( 0.077689 0.000000 0.384485 0.000000 0.000000 0.000000 ) -- Bipul Rakshit Research Fellow, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101004/69fabd6d/attachment.htm From bliu520 at gmail.com Mon Oct 4 17:14:07 2010 From: bliu520 at gmail.com (Baowei Liu) Date: Mon, 4 Oct 2010 11:14:07 -0400 Subject: [Pw_forum] Potentials between two charged particles In-Reply-To: <4CA97A29.9020401@sissa.it> References: <4CA73A8F.6090502@sissa.it> <4CA97A29.9020401@sissa.it> Message-ID: Hi Prof. Gironcoli, The absolute values of these negative rhos are actually very small, around 10^-7. If I change them to be zero, I'm able to plot the charge density with plotrho.x. I was curious why negative rho appears. Thank you for your explanation. Best Regards, Baowei Liu On Mon, Oct 4, 2010 at 2:54 AM, Stefano de Gironcoli wrote: > dear Baowei Liu , > when using USPP or paw, charge density can acquire small negative > contributions due to an incomplete Fourier expansion of the > augmentation charge density. This appears in particular when the system > has large portion of vacuum (surface or molecules) since all other > relevant contributions to the charge density vanish... > However your cutoff values (both ecutwfc and ecutrho) are quite high > so I'm a bit surprised you see negative charges. > How large are these negative values ? > > stefano > > Baowei Liu wrote: > > Hi Prof. Gironcoli, > > > > Thank you for your fast reply. I tried the following calculation. It > gives > > me > > ! total energy = -325.65235136 Ry. > > But Some of rho values are negative when I do post processing. What could > be > > the possible reason? > > > > &control > > calculation = 'scf' > > restart_mode='from_scratch', > > prefix='Ge', > > pseudo_dir = '$PSEUDO_DIR/', > > outdir='$TMP_DIR/' > > &system > > ibrav= 0, > > nat= 2, ntyp= 2, > > occupations = 'smearing',smearing='marzari-vanderbilt', > > degauss=0.05, > > nosym=.true., > > ecutwfc = 110 > > ecutrho = 880 > > tot_charge = +3, > > assume_isolated=.true. > > / > > &electrons > > diagonalization = 'david', > > mixing_mode = 'plain', > > mixing_beta = 0.7 > > conv_thr = 1.0d-7 > > electron_maxstep=200 > > / > > > > CELL_PARAMETERS cubic > > 40.0 0.0 0.0 > > 0.0 40.0 0.0 > > 0.0 0.0 40.0 > > ATOMIC_SPECIES > > Ge1 72.61 Ge.pbe-paw_kj.UPF > > Ge2 72.61 Ge.pbe-paw_kj.UPF > > ATOMIC_POSITIONS > > Ge1 0.50 0.50 0.50 0 0 0 > > Ge2 0.5 0.50 0.70 0 0 0 0 > > > > K_POINTS {automatic} > > 1 1 1 0 0 0 > > > > Thanks and Best Regards, > > Baowei Liu > > > > On Sat, Oct 2, 2010 at 9:58 AM, Stefano de Gironcoli >wrote: > > > > > >> the code can perform calculation for charged system using the variable > >> tot_charge. > >> By default the code performs the calculation for a periodic system > >> (adding a compensating background to eliminate the G=0 divergence). > >> In the limit of large cells this eventually converge to the isolated > case. > >> There are various techniques to perform calculations for isolated > >> systems with smaller cells. > >> Read carefully the description of assume_isolated variable in the system > >> namelist > >> best, > >> > >> Stefano de Gironcoli - SISSA and DEMOCRITOS > >> > >> Baowei Liu wrote: > >> > >>> Dear all members, > >>> > >>> I am trying to calculate the potential between two ions, -- A(+2) and > >>> > >> A(+1) > >> > >>> for example. When the two ions are far away from each other, there's > only > >>> Coulumb potential. But when the two ions are close enough, the electron > >>> distribution will be important for the potential. Can QE be used to > >>> calculate the energy or charge density for a system of two charged > >>> particles? It will be great if QE can give the energy for different > >>> distances. Just setting the tot_charge (=+3 in this example) is kind of > >>> > >> not > >> > >>> what I want. > >>> Thanks in advance. > >>> > >>> Baowei Liu > >>> > >>> > >>> > ------------------------------------------------------------------------ > >>> > >>> _______________________________________________ > >>> 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 > >> > >> > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101004/b210cfb6/attachment-0001.htm From wumindt2 at zju.edu.cn Mon Oct 4 18:42:50 2010 From: wumindt2 at zju.edu.cn (wumindt2) Date: Tue, 05 Oct 2010 00:42:50 +0800 Subject: [Pw_forum] problem with Xspectra Message-ID: Hi, I'm a new user of Xspectra. In the Xspectra example given in the pwscf code, it calculates the XAS using the pseudopotential without core hole level. In this case, we need to extract the core wavefunction from the GIPAW pseudopotential when we run the xspectra.x. Now there are pseudopotentials with core hole, normally named as *.star1s*.UPF. So here is my question, after the SCF calculation, do we still need to extract the core wavefunction from the peusopotential of the absorbing atom? If the answer is yes, then why we choose the core wavefunction from the pseudopotential as the ground state, rather than the core wavefunction after the SCF calculation? Thanks! Min Wu 2010-10-4 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101005/9e5fe0f8/attachment.htm From baroni at sissa.it Tue Oct 5 07:45:32 2010 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 5 Oct 2010 07:45:32 +0200 Subject: [Pw_forum] Displacements corresponding to -ve Phonon modes In-Reply-To: References: Message-ID: <25EF7B55-2146-4BD3-8542-EB8F07B88F74@sissa.it> On Oct 4, 2010, at 3:07 PM, Bipul Rakshit wrote: > Dear PWSCF users, > > I am doing Phonon of KO2 compound. I find some -ve phonon modes at gamma point. (After applying ASR also) > Following is the dynamical matrix formed by the phonon programme during the run. > I just want to study the displacement corresponding to -ve modes. So Is it enough to plot the eigen vectors given below corresponding to each mode. > Strange things what I feel in these eigen vectors are the 'K' is also moving almost with the same magnitude as 'O' Not so strange for zone-center acoustic modes (their frequency is zero exactly because they correspond to a rigid translation) > and there is no imaginary part of eigen vectors though the frequencies are -ve. why should there be any? what do you mean by "-ve"? SB --- 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 Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101005/a31206af/attachment.htm From matteo.calandra at impmc.jussieu.fr Tue Oct 5 10:49:48 2010 From: matteo.calandra at impmc.jussieu.fr (matteo calandra) Date: Tue, 5 Oct 2010 10:49:48 +0200 Subject: [Pw_forum] problem with Xspectra In-Reply-To: References: Message-ID: <20101005104948.86147kozm1qczquk@www1.impmc.upmc.fr> Dear Min Wu, the pseudopotentials to be used for the absorbing atom in Xspectra are those having the label _gipaw, two examples are: Fe.pbe-sp-mt_gipaw.UPF Fe.star1s-pbe-sp-mt_gipaw.UPF The first one has no core-hole and has full gipaw informations while the second one has core-hole and full gipaw informations. Gipaw informations mean many things. What you need to know is that GIPAW informations include the presence of the all-electron wavefunction for the 1s core state. Now when you run a simulation you first need to calculate the charge density in the presence of a core-hole and thus use pseudo Fe.star1s-pbe-sp-mt_gipaw.UPF . This is done by a standard pw.x scf calculation using this pseudo. In a second step you need to calcuate the Xanes cross section and this is done by the Xspectra code. In the calculation of the matrix element appearing in the Xanes cross-section (Fermi golden rule) the initial 1s state IN THE ABSENCE of a core hole is needed. This information is contanined in the pseudo potential WITHOUT the core hole (Fe.pbe-sp-mt_gipaw.UPF). Thus you simply extract this wavefunction using the script given with the Xspectra disribution and you put the name of the file produced by the script in the input file of the Xspectra program. You cannot use the 1s core function with the core hole simply because this is wrong as the matrix element inthe cross section involves the product between the initial and final states and the initial state has no core hole. M. > Message: 1 > Date: Tue, 05 Oct 2010 00:42:50 +0800 > From: "wumindt2" > Subject: [Pw_forum] problem with Xspectra > To: pw_forum at pwscf.org > Message-ID: > Content-Type: text/plain; charset="gb2312" > > Hi, > > I'm a new user of Xspectra. > > In the Xspectra example given in the pwscf code, it calculates the > XAS using the pseudopotential > without core hole level. In this case, we need to extract the core > wavefunction from the GIPAW > pseudopotential when we run the xspectra.x. > > Now there are pseudopotentials with core hole, normally named as > *.star1s*.UPF. So here is > my question, after the SCF calculation, do we still need to extract > the core wavefunction from the > peusopotential of the absorbing atom? > > If the answer is yes, then why we choose the core wavefunction from > the pseudopotential as the ground > state, rather than the core wavefunction after the SCF calculation? > > Thanks! > > Min Wu > 2010-10-4 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From dcchrzan at berkeley.edu Tue Oct 5 20:36:17 2010 From: dcchrzan at berkeley.edu (Daryl Chrzan) Date: Tue, 5 Oct 2010 11:36:17 -0700 Subject: [Pw_forum] Si diamond-cubic to beta-Sn transformation Message-ID: <89D923D3-6703-4CF7-8109-55AFBC2623E1@berkeley.edu> Colleagues, I am working through a problem that I have assigned to my Computational Materials Science class - computation of the transition pressure for the diamond-cubic to beta-Sn structures in diamond using pw.x. The problem I have is that pw.x produces answers that are inconsistent with those produced by VASP, and those published in the literature. I have used similar ultrasoft pseudopotentials in both calculations (both based on PW91 correlation). There may be differences, between the two cases, but I have tried a number of pseudopotentials in pw.x and find essentially the same results). I have installed the QE software version 4.2.1 using both gfortran and ifort, using entirely internal libraries and with MKL (32 bit) libraries, both openMPI and single processor mode, and the tests of pw.x all conclude successfully). The software is installed on a Mac OSX 10.6 laptop. I have compiled in 32 and 64 bit mode for gfortran. If memory serves me correctly, all produce essentially the same results. Though I have generated a number of discrepancies, I think the most simple manifestation is the difference in total energy per atom for the equilibrium structures as predicted by VASP. More specifically, I find: (1) Diamond cubic structure in VASP. Relaxed structure (pressure ~ 0). K=Point mesh is 12 x 12 x 12, symmetrized. The lattice parameter comes out to be 5.456 Ang. Ultrasoft pseudopotential, PW91 exchange-correlation, cutoff chosen to be 400 eV. Total energy of relaxed cell = -10.866660 eV. (2) Diamond cubic structure run using beta-Sn POSCAR with c/a = sqrt(2). Produces the same lattice parameter and the same total energy per relaxed cell = -10.866649 eV. (3) Beta-Sn structure also relaxed using the same potential yields a lattice parameter a = 4.832 Ang, and the ratio c/a = 0.547. Using the same k-point mesh (perhaps not completely converged, but close enough for our purposes) one finds a total energy of this phase to be -10.191998 eV. (4) Using these numbers, and noting that there are two atoms per unit cell, one finds that the energy difference per atom between the structures is given by E(BetaSn Si)- E(DC Si) = (-10.191998+10.866660)/2 eV/atom = 0.34 eV/atom This value is in very good agreement with published results. We can now take these structural parameters and run pw.x from QE to compute the energy difference. I will use the beta-Sn unit cell for both calculations (the natural diamond cubic cell produces essentially the same results). I also used a MP grid 12x12x12 and an energy cutoff of 400 eV (12*400 eV for the charge density). (5) The total energy of the beta-Sn structure, per atom, predicted by QE is -130.192 eV. The total energy of the dc structure, per atom, predicted by QE is -130.982 eV. The difference in energy is, therefore, 0.79 eV/atom, more than a factor of two larger than predicted by VASP. I've attached the input files and the output files for your perusal. Sorry about the size of this message. Any insight you can lend will be more than appreciated. Thank you, Daryl C. Chrzan Professor, Materials Science and Engineering University of California Berkeley, CA 94720 and Materials Sciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720 ph./fax: 510 643 1624 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101005/d4c6dbf1/attachment-0005.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: Si.DC.in Type: application/octet-stream Size: 705 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101005/d4c6dbf1/attachment-0004.obj -------------- next part -------------- An HTML attachment was scrubbed... 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URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101005/d4c6dbf1/attachment-0008.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: Si.DC.out Type: application/octet-stream Size: 77242 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101005/d4c6dbf1/attachment-0007.obj -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101005/d4c6dbf1/attachment-0009.htm From wumindt2 at zju.edu.cn Tue Oct 5 20:53:07 2010 From: wumindt2 at zju.edu.cn (wumindt2) Date: Wed, 06 Oct 2010 02:53:07 +0800 Subject: [Pw_forum] problem with Xspectra Message-ID: Dear matteo, Thank you very much! I've got the picture now. BTW, in my previous calculation, i mistakenly extract the core wavefunction from the pseudopotential WITH a core hole. But the result seems good when compared with the experiment. Does it happen often? Cheers, Min Wu 2010-10-5 >From: matteo calandra >Reply-To: PWSCF Forum >To: pw_forum at pwscf.org >Subject: Re:[Pw_forum] problem with Xspectra >Date: Tue, 5 Oct 2010 10:49:48 +0200 > >Dear Min Wu, > > the pseudopotentials to be used for the absorbing atom >in Xspectra are those having >the label _gipaw, two examples are: > >Fe.pbe-sp-mt_gipaw.UPF >Fe.star1s-pbe-sp-mt_gipaw.UPF > >The first one has no core-hole and has full gipaw informations >while the second one has core-hole and full gipaw informations. >Gipaw informations mean many things. What you need to know is that >GIPAW informations include the presence of the >all-electron wavefunction for the 1s core state. > >Now when you run a simulation you first need to calculate the charge >density in the presence of a core-hole and thus use pseudo >Fe.star1s-pbe-sp-mt_gipaw.UPF . This is done by a standard pw.x >scf calculation using this pseudo. >In a second step you need to calcuate the Xanes cross >section and this is done by the Xspectra code. > >In the calculation of the matrix element appearing in the >Xanes cross-section (Fermi golden rule) the initial 1s state >IN THE ABSENCE of a core hole is needed. This information is contanined >in the pseudo potential WITHOUT the core hole (Fe.pbe-sp-mt_gipaw.UPF). >Thus you simply extract this wavefunction using the script given with the >Xspectra disribution and you put the name of the file produced by the script >in the input file of the Xspectra program. > >You cannot use the 1s core function with the core hole simply because this is >wrong as the matrix element inthe cross section involves the product >between the initial and final states and the initial state has no core hole. > >M. >> Message: 1 >> Date: Tue, 05 Oct 2010 00:42:50 +0800 >> From: "wumindt2" >> Subject: [Pw_forum] problem with Xspectra >> To: pw_forum at pwscf.org >> Message-ID: >> Content-Type: text/plain; charset="gb2312" >> >> Hi, >> >> I'm a new user of Xspectra. >> >> In the Xspectra example given in the pwscf code, it calculates the >> XAS using the pseudopotential >> without core hole level. In this case, we need to extract the core >> wavefunction from the GIPAW >> pseudopotential when we run the xspectra.x. >> >> Now there are pseudopotentials with core hole, normally named as >> *.star1s*.UPF. So here is >> my question, after the SCF calculation, do we still need to extract >> the core wavefunction from the >> peusopotential of the absorbing atom? >> >> If the answer is yes, then why we choose the core wavefunction from >> the pseudopotential as the ground >> state, rather than the core wavefunction after the SCF calculation? >> >> Thanks! >> >> Min Wu >> 2010-10-4 > > >---------------------------------------------------------------- >This message was sent using IMP, the Internet Messaging Program. > > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > From Michael.Mehl at nrl.navy.mil Tue Oct 5 23:55:17 2010 From: Michael.Mehl at nrl.navy.mil (Mike Mehl) Date: Tue, 05 Oct 2010 17:55:17 -0400 Subject: [Pw_forum] Si diamond-cubic to beta-Sn transformation In-Reply-To: <89D923D3-6703-4CF7-8109-55AFBC2623E1@berkeley.edu> References: <89D923D3-6703-4CF7-8109-55AFBC2623E1@berkeley.edu> Message-ID: <4CAB9EC5.3010900@nrl.navy.mil> Dayrl, Looking at your output, it seems that you are very far from the minimum energy beta-Sn structure: entering subroutine stress ... total stress (Ry/bohr**3) (kbar) P= 42.95 0.00079257 0.00000000 0.00000000 116.59 0.00 0.00 0.00000000 0.00079725 0.00000001 0.00 117.28 0.00 0.00000000 0.00000001 -0.00071388 0.00 0.00 -105.01 If you find the actual minimum energy structure for beta-Sn you'll get a much smaller difference in energy. I recently did this calculation using Si.pbe-n-van.UPF, rather than Si.pw91-n-van.UPF, and got an energy difference of 0.29 eV/atom, rather in better agreement with VASP and other published results. Ideally, all ultrasoft pseudopotentials should give the same result, but unfortunately they often don't. On 10/05/2010 02:36 PM, Daryl Chrzan wrote: > Colleagues, > > I am working through a problem that I have assigned to my Computational > Materials Science class - computation of the transition pressure for the > diamond-cubic to beta-Sn structures in diamond using pw.x. -- Michael J. Mehl Head, Center for Computational Materials Science Naval Research Laboratory Code 6390 Washington DC From dcchrzan at berkeley.edu Wed Oct 6 00:39:48 2010 From: dcchrzan at berkeley.edu (Daryl Chrzan) Date: Tue, 5 Oct 2010 15:39:48 -0700 Subject: [Pw_forum] Si diamond-cubic to beta-Sn transformation Message-ID: <868BD350-E25A-43B2-8EAC-B6EFBC708F67@berkeley.edu> Input files were stripped on the previous message. Here they are as part of the message: Diamond Cubic: &control calculation='scf' restart_mode='from_scratch', prefix='silicon', tstress= .true. tprnfor= .true. pseudo_dir='/Users/darylchrzan/ResearchProjects/PSEUDOS/', outdir='/Users/darylchrzan/Desktop/MSE215Fall2010/Assignments/One/BetaSn/tmp/' / &system ibrav=0, celldm(1)=7.29052, nat=2, ntyp=1, ecutwfc=29.3991, ecutrho=352.789, nbnd=8, smearing = 'gaussian', degauss = 0.02, / &electrons diagonalization='cg' mixing_mode='plain' mixing_beta=0.7, conv_thr=3.0d-7, / ATOMIC_SPECIES Si 28.086 Si.pw91-n-van.UPF ATOMIC_POSITIONS crystal Si -0.125 0.125 -0.250 0 0 0 Si 0.125 -0.125 0.250 0 0 0 K_POINTS automatic 12 12 12 0 0 0 CELL_PARAMETERS -0.5 0.5 0.707107 0.5 -0.5 0.707107 0.5 0.5 -0.707107 Beta-Sn: &control calculation='scf' restart_mode='from_scratch', prefix='silicon', tstress= .true. tprnfor= .true. pseudo_dir='/Users/darylchrzan/ResearchProjects/PSEUDOS/', outdir='/Users/darylchrzan/Desktop/MSE215Fall2010/Assignments/One/BetaSn/tmp/' / &system ibrav=0, celldm(1)=9.13116, nat=2, ntyp=1, ecutwfc=29.3991, ecutrho=352.789, nbnd=8, smearing = 'gaussian', degauss = 0.02, / &electrons diagonalization='cg' mixing_mode='plain' mixing_beta=0.7, conv_thr=3.0d-7, / ATOMIC_SPECIES Si 28.086 Si.pw91-n-van.UPF ATOMIC_POSITIONS crystal Si -0.125 0.125 -0.250 0 0 0 Si 0.125 -0.125 0.250 0 0 0 K_POINTS automatic 12 12 12 0 0 0 CELL_PARAMETERS -0.5 0.5 0.2735 0.5 -0.5 0.2735 0.5 0.5 -0.2735 Daryl C. Chrzan Professor, Materials Science and Engineering University of California Berkeley, CA 94720 and Materials Sciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720 ph./fax: 510 643 1624 From chan.mithra at gmail.com Wed Oct 6 10:25:34 2010 From: chan.mithra at gmail.com (Mithra Chan) Date: Wed, 6 Oct 2010 10:25:34 +0200 Subject: [Pw_forum] split q for electron-phonon coupling calculations Message-ID: Hello, everyone, I am trying splitting q points for electron-phonon coupling calculations on a computer cluster. Though jobs were finished after successful running, I was not given by file elph$qpoint . I did these calculations on example07 as follows: 1) a electronic scf calculation on a very dense k mesh with la2f=.true., 2) a scf calculation on a medium k mesh without la2f, 3) split q point using following INPUT. Electron-phonon coefficients for Al &inputph tr2_ph=1.0d-12, prefix='al', amass(1)=26.98, outdir='$OUTDIR', fildyn='al.dyn', ldisp=.true., nq1=4, nq2=4, nq3=4 start_irr=0, last_irr=0, / 4) copy file $prefix.a2Fsave, $prefix.wfc*, $prefix.dyn0, and _ph0$prefix.phsave(including both data-file.xml and data-file.xml.$qpoint) to corresponding sub-job. Then a ph.x run for electron-phonon coupling using following INPUT. phonons of al &inputph tr2_ph=1.0d-12, nq1=4, nq2=4, nq3=4 amass(1)=26.98, prefix='$prefix' start_q=$i, last_q=$i, recover=.true., outdir='$INDIR/$i', fildyn='$prefix.dyn', fildvscf='$prefix.dv', elph=.true., trans=.true., ldisp=.true., / 5) a run of ph.x by setting trans=.false. Though the job runs successfully, it does not give me the file elph$qpoint. Having browsed the source code, the PH should produce files elph$qpoint when elph=.true. Any suggestion would be appreciated. Thanks a lot. Mithra Chan -- Dr. Mithra Chan, Department of Physics, National University of Singapore, Singapore chan.mithra at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101006/e98fb0cd/attachment.htm From dalcorso at sissa.it Wed Oct 6 10:38:54 2010 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Wed, 06 Oct 2010 10:38:54 +0200 Subject: [Pw_forum] split q for electron-phonon coupling calculations In-Reply-To: References: Message-ID: <1286354334.2123.16.camel@localhost.localdomain> On Wed, 2010-10-06 at 10:25 +0200, Mithra Chan wrote: > Hello, everyone, > > I am trying splitting q points for electron-phonon coupling > calculations on a computer cluster. Though jobs were finished after > successful running, I was not given by file elph$qpoint . I did these > calculations on example07 as follows: > 1) a electronic scf calculation on a very dense k mesh with > la2f=.true., > 2) a scf calculation on a medium k mesh without la2f, > 3) split q point using following INPUT. > > Electron-phonon coefficients for Al > &inputph > tr2_ph=1.0d-12, > prefix='al', > amass(1)=26.98, > outdir='$OUTDIR', > fildyn='al.dyn', > ldisp=.true., > nq1=4, nq2=4, nq3=4 > start_irr=0, > last_irr=0, > / > > 4) copy file $prefix.a2Fsave, $prefix.wfc*, $prefix.dyn0, and _ph0 > $prefix.phsave(including both data-file.xml and data-file.xml.$qpoint) > to corresponding sub-job. Then a ph.x run for electron-phonon coupling > using following INPUT. > > phonons of al > &inputph > tr2_ph=1.0d-12, > nq1=4, nq2=4, nq3=4 > amass(1)=26.98, > prefix='$prefix' > start_q=$i, > last_q=$i, > recover=.true., > outdir='$INDIR/$i', > fildyn='$prefix.dyn', > fildvscf='$prefix.dv', > elph=.true., > trans=.true., > ldisp=.true., > / > > 5) a run of ph.x by setting trans=.false. > > Though the job runs successfully, it does not give me the file elph > $qpoint. Having browsed the source code, the PH should produce files > elph$qpoint when elph=.true. > Any suggestion would be appreciated. > The automatic split of the q points is not yet implemented for el-ph calculation. So you cannot split the q points in this way. You have to prepare many single q inputs of ph.x with ldisp=.false., giving the q point in input. Andrea > Thanks a lot. > > Mithra Chan > > -- > Dr. Mithra Chan, > Department of Physics, National University of Singapore, Singapore > chan.mithra at gmail.com > > _______________________________________________ > 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 From chan.mithra at gmail.com Wed Oct 6 11:33:43 2010 From: chan.mithra at gmail.com (Mithra Chan) Date: Wed, 6 Oct 2010 11:33:43 +0200 Subject: [Pw_forum] split q for electron-phonon coupling calculations In-Reply-To: <1286354334.2123.16.camel@localhost.localdomain> References: <1286354334.2123.16.camel@localhost.localdomain> Message-ID: Dear Andrea, Thanks for you reply. You are right. It would be fine if we can have the same feature as calculations of phonon since EPC calculations can be done for a single mode. Best regards, Mithra Chan 2010/10/6 Dal Corso Andrea > On Wed, 2010-10-06 at 10:25 +0200, Mithra Chan wrote: > > Hello, everyone, > > > > I am trying splitting q points for electron-phonon coupling > > calculations on a computer cluster. Though jobs were finished after > > successful running, I was not given by file elph$qpoint . I did these > > calculations on example07 as follows: > > 1) a electronic scf calculation on a very dense k mesh with > > la2f=.true., > > 2) a scf calculation on a medium k mesh without la2f, > > 3) split q point using following INPUT. > > > > Electron-phonon coefficients for Al > > &inputph > > tr2_ph=1.0d-12, > > prefix='al', > > amass(1)=26.98, > > outdir='$OUTDIR', > > fildyn='al.dyn', > > ldisp=.true., > > nq1=4, nq2=4, nq3=4 > > start_irr=0, > > last_irr=0, > > / > > > > 4) copy file $prefix.a2Fsave, $prefix.wfc*, $prefix.dyn0, and _ph0 > > $prefix.phsave(including both data-file.xml and data-file.xml.$qpoint) > > to corresponding sub-job. Then a ph.x run for electron-phonon coupling > > using following INPUT. > > > > phonons of al > > &inputph > > tr2_ph=1.0d-12, > > nq1=4, nq2=4, nq3=4 > > amass(1)=26.98, > > prefix='$prefix' > > start_q=$i, > > last_q=$i, > > recover=.true., > > outdir='$INDIR/$i', > > fildyn='$prefix.dyn', > > fildvscf='$prefix.dv', > > elph=.true., > > trans=.true., > > ldisp=.true., > > / > > > > 5) a run of ph.x by setting trans=.false. > > > > Though the job runs successfully, it does not give me the file elph > > $qpoint. Having browsed the source code, the PH should produce files > > elph$qpoint when elph=.true. > > Any suggestion would be appreciated. > > > > The automatic split of the q points is not yet implemented for el-ph > calculation. So you cannot split the q points in this way. You have to > prepare many single q inputs of ph.x with ldisp=.false., giving the q > point in input. > > Andrea > > > Thanks a lot. > > > > Mithra Chan > > > > -- > > Dr. Mithra Chan, > > Department of Physics, National University of Singapore, Singapore > > chan.mithra at gmail.com > > > > _______________________________________________ > > 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 > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Mithra Chan, Department of Physics, National University of Singapore, Singapore chan.mithra at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101006/282fe99e/attachment.htm From matteo.calandra at impmc.jussieu.fr Wed Oct 6 11:57:40 2010 From: matteo.calandra at impmc.jussieu.fr (matteo calandra) Date: Wed, 6 Oct 2010 11:57:40 +0200 Subject: [Pw_forum] problem with Xspectra In-Reply-To: References: Message-ID: <20101006115740.13113mq7e05kq5uc@www1.impmc.upmc.fr> Dear Min Wu, usually the mistake you did (using the 1s wavefunction with the core-hole instead of that without the core-hole) leads to small differences in the case of K-edge, as the two wavefunction are probably very similar. This is not true for L1 edges (that you can calculate with the current program) or generally speaking, less deep edges (L,M and so on). However, even in the case of K-edges it can be important. So I suggest you repeat the last step of your calculation (the XSPECTRA one) using the core wfc without a core-hole as this is the correct thing to do. All the best, M. > > Message: 1 > Date: Wed, 06 Oct 2010 02:53:07 +0800 > From: "wumindt2" > Subject: Re: [Pw_forum] problem with Xspectra > To: pw_forum at pwscf.org > Message-ID: > Content-Type: text/plain; charset="gb2312" > > Dear matteo, > > Thank you very much! > I've got the picture now. > > BTW, in my previous calculation, i mistakenly extract the core wavefunction > from the pseudopotential WITH a core hole. But the result seems good > when compared > with the experiment. Does it happen often? > > Cheers, > > Min Wu > 2010-10-5 > > > >> From: matteo calandra >> Reply-To: PWSCF Forum >> To: pw_forum at pwscf.org >> Subject: Re:[Pw_forum] problem with Xspectra >> Date: Tue, 5 Oct 2010 10:49:48 +0200 >> >> Dear Min Wu, >> >> the pseudopotentials to be used for the absorbing atom >> in Xspectra are those having >> the label _gipaw, two examples are: >> >> Fe.pbe-sp-mt_gipaw.UPF >> Fe.star1s-pbe-sp-mt_gipaw.UPF >> >> The first one has no core-hole and has full gipaw informations >> while the second one has core-hole and full gipaw informations. >> Gipaw informations mean many things. What you need to know is that >> GIPAW informations include the presence of the >> all-electron wavefunction for the 1s core state. >> >> Now when you run a simulation you first need to calculate the charge >> density in the presence of a core-hole and thus use pseudo >> Fe.star1s-pbe-sp-mt_gipaw.UPF . This is done by a standard pw.x >> scf calculation using this pseudo. >> In a second step you need to calcuate the Xanes cross >> section and this is done by the Xspectra code. >> >> In the calculation of the matrix element appearing in the >> Xanes cross-section (Fermi golden rule) the initial 1s state >> IN THE ABSENCE of a core hole is needed. This information is contanined >> in the pseudo potential WITHOUT the core hole (Fe.pbe-sp-mt_gipaw.UPF). >> Thus you simply extract this wavefunction using the script given with the >> Xspectra disribution and you put the name of the file produced by the script >> in the input file of the Xspectra program. >> >> You cannot use the 1s core function with the core hole simply >> because this is >> wrong as the matrix element inthe cross section involves the product >> between the initial and final states and the initial state has no core hole. >> >> M. >>> Message: 1 >>> Date: Tue, 05 Oct 2010 00:42:50 +0800 >>> From: "wumindt2" > >>> Subject: [Pw_forum] problem with Xspectra >>> To: pw_forum at pwscf.org >>> Message-ID: > >>> Content-Type: text/plain; charset="gb2312" >>> >>> Hi, >>> >>> I'm a new user of Xspectra. >>> >>> In the Xspectra example given in the pwscf code, it calculates the >>> XAS using the pseudopotential >>> without core hole level. In this case, we need to extract the core >>> wavefunction from the GIPAW >>> pseudopotential when we run the xspectra.x. >>> >>> Now there are pseudopotentials with core hole, normally named as >>> *.star1s*.UPF. So here is >>> my question, after the SCF calculation, do we still need to extract >>> the core wavefunction from the >>> peusopotential of the absorbing atom? >>> >>> If the answer is yes, then why we choose the core wavefunction from >>> the pseudopotential as the ground >>> state, rather than the core wavefunction after the SCF calculation? >>> >>> Thanks! >>> >>> Min Wu >>> 2010-10-4 >> >> >> ---------------------------------------------------------------- >> This message was sent using IMP, the Internet Messaging Program. >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From parwana.habibi at cea.fr Wed Oct 6 15:18:31 2010 From: parwana.habibi at cea.fr (HABIBI Parwana) Date: Wed, 6 Oct 2010 15:18:31 +0200 Subject: [Pw_forum] USPP creation using ld1.x Message-ID: Dear all, I have already emailed you about uspp generation,and the initial input I had was describing the electron occupation like it should. However, I get this error message : %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from ld1_setup : error # 1 mismatched all-electron/pseudo occupations %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% This suggests me that the occupations I wrote in the input are incorrect. Like I said, they are supposed to be correct the way I described them. Could you tell me how I can create a pseudo with the occupations I want? Shall I change lines in ld1_setup.f90? I attached once again the input. Thank you, Parwana, Ph.D student, CEA-Saclay, DSM/IRAMIS/SPCSI PS : the rel_dist tag is not supposed to be the problem...I get the same error with and without the tag. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101006/e7b6c1d9/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: Cr_us_pbe_6rel.in.2 Type: application/octet-stream Size: 885 bytes Desc: Cr_us_pbe_6rel.in.2 Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101006/e7b6c1d9/attachment-0001.obj From Lorenzo.Paulatto at impmc.upmc.fr Wed Oct 6 15:29:05 2010 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Wed, 06 Oct 2010 15:29:05 +0200 Subject: [Pw_forum] USPP creation using ld1.x In-Reply-To: References: Message-ID: Dear Parwana, less then one month ago you asked a very similar question and I gave you relatively detailed answer. If something in my previous answer was not very clear you should have asked for clarification... Anyway, if you cannot understand which are the occupation in the all-electron configuration, just set "iswitch=1" in your input file. If you then run it with ld1.x it will only do the all-electron calculation, included printing the occupations of the orbitals (and a lot of other funny numbers). best regards -- Lorenzo Paulatto post-doc @ IMPMC/UPMC - Universit? Paris 6 phone: +33 (0)1 44 27 74 89 www: http://www-int.impmc.upmc.fr/~paulatto/ previously (take note of the change!): phd student @ SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 www: http://people.sissa.it/~paulatto/ From izaakw89 at yahoo.com Wed Oct 6 22:41:22 2010 From: izaakw89 at yahoo.com (Izaak Williamson) Date: Wed, 6 Oct 2010 13:41:22 -0700 (PDT) Subject: [Pw_forum] Differing bond lengths from relax calculation Message-ID: <510207.23107.qm@web44807.mail.sp1.yahoo.com> Dear members, I am running a relax calculation on trimers of the type M-N-M where M describes a magnetic atom. I am running them as spin-polarized calculations with Hubbard-U. The shape of the unit cell is cubic. I want to find out the equilibrium bond length (M-N). Since the cluster is symmetric, I would expect that both M-N-M bond lengths would be same. But, it turns out that two bond lengths are different. Why is this happening? Any help would be much appreciated. Thanks for any help, Izaak Williamson Research Assistant Physics Department Boise State University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101006/d62bae24/attachment.htm From mohnish.iitk at gmail.com Thu Oct 7 05:23:02 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Thu, 7 Oct 2010 08:53:02 +0530 Subject: [Pw_forum] Si diamond-cubic to beta-Sn transformation In-Reply-To: <868BD350-E25A-43B2-8EAC-B6EFBC708F67@berkeley.edu> References: <868BD350-E25A-43B2-8EAC-B6EFBC708F67@berkeley.edu> Message-ID: Dear Prof Daryl ! Can you please attach your VASP file also so that I can have a closer look at your VASP file. In fact I did the calculation with your input file and after optimizing the structure I was getting the energy difference of 0.69 ev/atom. I just wanted to see the structures. On Wed, Oct 6, 2010 at 4:09 AM, Daryl Chrzan wrote: > Input files were stripped on the previous message. Here they are as part > of the message: > > Diamond Cubic: > > &control > calculation='scf' > restart_mode='from_scratch', > prefix='silicon', > tstress= .true. > tprnfor= .true. > pseudo_dir='/Users/darylchrzan/ResearchProjects/PSEUDOS/', > > outdir='/Users/darylchrzan/Desktop/MSE215Fall2010/Assignments/One/BetaSn/tmp/' > / > &system > ibrav=0, > celldm(1)=7.29052, > nat=2, > ntyp=1, > ecutwfc=29.3991, > ecutrho=352.789, > nbnd=8, > smearing = 'gaussian', > degauss = 0.02, > / > &electrons > diagonalization='cg' > mixing_mode='plain' > mixing_beta=0.7, > conv_thr=3.0d-7, > / > ATOMIC_SPECIES > Si 28.086 Si.pw91-n-van.UPF > ATOMIC_POSITIONS crystal > Si -0.125 0.125 -0.250 0 0 0 > Si 0.125 -0.125 0.250 0 0 0 > K_POINTS automatic > 12 12 12 0 0 0 > CELL_PARAMETERS > -0.5 0.5 0.707107 > 0.5 -0.5 0.707107 > 0.5 0.5 -0.707107 > > > Beta-Sn: > > &control > calculation='scf' > restart_mode='from_scratch', > prefix='silicon', > tstress= .true. > tprnfor= .true. > pseudo_dir='/Users/darylchrzan/ResearchProjects/PSEUDOS/', > > outdir='/Users/darylchrzan/Desktop/MSE215Fall2010/Assignments/One/BetaSn/tmp/' > / > &system > ibrav=0, > celldm(1)=9.13116, > nat=2, > ntyp=1, > ecutwfc=29.3991, > ecutrho=352.789, > nbnd=8, > smearing = 'gaussian', > degauss = 0.02, > / > &electrons > diagonalization='cg' > mixing_mode='plain' > mixing_beta=0.7, > conv_thr=3.0d-7, > / > ATOMIC_SPECIES > Si 28.086 Si.pw91-n-van.UPF > ATOMIC_POSITIONS crystal > Si -0.125 0.125 -0.250 0 0 0 > Si 0.125 -0.125 0.250 0 0 0 > K_POINTS automatic > 12 12 12 0 0 0 > CELL_PARAMETERS > -0.5 0.5 0.2735 > 0.5 -0.5 0.2735 > 0.5 0.5 -0.2735 > > > > Daryl C. Chrzan > Professor, Materials Science and Engineering > University of California > Berkeley, CA 94720 > > and > > Materials Sciences Division > Lawrence Berkeley National Laboratory > Berkeley, CA 94720 > > ph./fax: 510 643 1624 > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101007/b758d7c3/attachment.htm From mirnezhad.mm at gmail.com Thu Oct 7 09:20:28 2010 From: mirnezhad.mm at gmail.com (Mahdi Mirnezhad) Date: Thu, 7 Oct 2010 14:20:28 +0700 Subject: [Pw_forum] Question about Young's modulus Message-ID: Dear all, I calculated Young's modulusfor graphene and i got correct answer but when I want to calculate Young's modulus for CNT(3,3) for a axial strain with the same condition (same PS) i got a wrong answer? Any suggestion appreciated, tanks mahdi mirnezhade From giuseppe.mattioli at mlib.ism.cnr.it Thu Oct 7 10:29:47 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Thu, 7 Oct 2010 10:29:47 +0200 Subject: [Pw_forum] Differing bond lengths from relax calculation In-Reply-To: <510207.23107.qm@web44807.mail.sp1.yahoo.com> References: <510207.23107.qm@web44807.mail.sp1.yahoo.com> Message-ID: <201010071029.47212.giuseppe.mattioli@mlib.ism.cnr.it> Dear Izaak Difficult to say, without looking at your input file. Do you obtain similar results without the U correction? Yours Giuseppe On Wednesday 06 October 2010 22:41:22 Izaak Williamson wrote: > Dear members, > > I am running a relax calculation on trimers of the type M-N-M where M > describes a magnetic atom. I am running them as spin-polarized calculations > with Hubbard-U. The shape of the unit cell is cubic. I want to find out the > equilibrium bond length (M-N). Since the cluster is symmetric, I would > expect that both M-N-M bond lengths would be same. But, it turns out that > two bond lengths are different. Why is this happening? Any help would be > much appreciated. > > Thanks for any help, > > Izaak Williamson > Research Assistant > Physics Department > Boise State University -- ******************************************************** - 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 00016 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From giannozz at democritos.it Thu Oct 7 11:12:19 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 07 Oct 2010 11:12:19 +0200 Subject: [Pw_forum] Question regarding the charge density In-Reply-To: References: Message-ID: <4CAD8EF3.5090407@democritos.it> Somnath wrote: > Is it possible to get the electronic and ionic charge density together ? the "ionic charge density" is a sum of delta functions centered at atomic positions: not really easy to visualize. You can replace delta functions with gaussians and get something more manageable (this is by the way how the CP code calculates the total energy). It is however not currently implemented in pp.x Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From mayankaditya at gmail.com Fri Oct 8 09:32:04 2010 From: mayankaditya at gmail.com (mayank gupta) Date: Fri, 8 Oct 2010 13:02:04 +0530 Subject: [Pw_forum] Negative rho is large Message-ID: Dear All QE users I am doing caclulation for ZrO2 monoclinic phase. In scf calculation I took ecutwfc=75 Ry and ecut_rho=750. I am getting message negative rho up down 0.261e0.00 0.00 in output. i have used ultrasoft pseudo potential. how to improve my result. Here I paste my input scf file. &control calculation='scf' restart_mode='from_scratch', tstress = .true. tprnfor = .true. prefix='zro', pseudo_dir = '/home/mayank/pseudo/', outdir='/home/mayank/tmp2/' / &system ibrav= 12 ,celldm(1)=10.0928877,celldm(2)=0.967796293,celldm(3)=0.979591837, celldm(4)=-0.16074,celldm(5)=0.0,celldm(6)=0.0, nat= 12 , ntyp=2, ecutwfc= 75.00000000 ecutrho=750 / &electrons conv_thr=1.0D-8 mixing_beta=0.3 diagonalization='david' / &ions / ATOMIC_SPECIES Zr 91.22 Zr.pw91-nsp-van.UPF O 15.99 O.pw91-van_ak.UPF ATOMIC_POSITIONS {crystal} Zr 0.209735100 0.276043346 0.042234007 Zr 0.290264900 0.723956654 0.542234007 Zr 0.790264900 0.723956654 0.957765993 Zr 0.709735100 0.276043346 0.457765993 O 0.344714661 0.068493659 0.332481802 O 0.155285339 0.931506341 0.832481802 O 0.655285339 0.931506341 0.667518198 O 0.844714661 0.068493659 0.167518198 O 0.478408144 0.449572291 0.757453977 O 0.021591856 0.550427709 0.257453977 O 0.521591856 0.550427709 0.242546023 O 0.978408144 0.449572291 0.742546023 K_POINTS automatic 4 4 4 1 1 1 Thanks -- Mayank kumar gupta Contact No- 9869834437 ? ? ? ? ? ? ? ? ? 8097400037 ? ? ? ? ? ? ? ? ?8080458227 From sd.wang000 at gmail.com Fri Oct 8 10:36:50 2010 From: sd.wang000 at gmail.com (shudong wang) Date: Fri, 8 Oct 2010 16:36:50 +0800 Subject: [Pw_forum] plot the wave functions Message-ID: Dear developers and users: How can I get the wave functions of top valence band and bottom conduction band? I want to plot the functions at some special points like gamma. Thanks! S.D.Wang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101008/15af4a5b/attachment.htm From giannozz at democritos.it Fri Oct 8 11:14:49 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 08 Oct 2010 11:14:49 +0200 Subject: [Pw_forum] Si diamond-cubic to beta-Sn transformation In-Reply-To: <868BD350-E25A-43B2-8EAC-B6EFBC708F67@berkeley.edu> References: <868BD350-E25A-43B2-8EAC-B6EFBC708F67@berkeley.edu> Message-ID: <4CAEE109.6090409@democritos.it> Daryl Chrzan wrote: > smearing = 'gaussian', > degauss = 0.02, you need occupations='smearing' as well, or else the code will silently default to fixed occupations. There should be a check and a warning, but there isn't any. Using QE in teaching is a great way to find all kinds of problems. I noticed it because this statement looked weird to me: highest occupied, lowest unoccupied level (ev): 11.4054 5.2182 and no, the numbers were not printed in revers order. It doesn't make any difference for diamond Si, but it does for beta-Sn Si. I got betatin.out:! total energy = -19.20675112 Ry diamond.out:! total energy = -19.25371607 Ry i.e. 0.32eV/atoms > Beta-Sn: > nat=2 I was convinced that beta-Sn has 4 atoms per unit cell, not 2. I am interested because I also have used QE for teaching, and the diamond to beta-tin transition is a good exercise Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From janfelix.binder at epfl.ch Fri Oct 8 14:01:46 2010 From: janfelix.binder at epfl.ch (Jan Felix Binder) Date: Fri, 08 Oct 2010 14:01:46 +0200 Subject: [Pw_forum] plot the wave functions In-Reply-To: References: Message-ID: <4CAF082A.5070108@epfl.ch> use the post processing program pp.x. for the input you can use something like this: &INPUTPP prefix='Ge64-k8', outdir='/home/jfbinder/Ge/xps/cube8/temp/' filplot = 'wave.dat', plot_num = 7, kpoint = 1, kband=294, lsign=.true. / &PLOT nfile = 1, fileout = 'wave.cube', iflag = 3, output_format = 6, / shudong wang wrote: > Dear developers and users: > How can I get the wave functions of top valence band and bottom > conduction band? I want to plot the functions at some special points > like gamma. > > Thanks! > > S.D.Wang > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From dcchrzan at berkeley.edu Fri Oct 8 21:55:45 2010 From: dcchrzan at berkeley.edu (Daryl Chrzan) Date: Fri, 8 Oct 2010 12:55:45 -0700 Subject: [Pw_forum] Si diamond-cubic to beta-Sn transformation Message-ID: <61B5C6A6-D00F-4A62-A7E7-F7686B1B5600@berkeley.edu> Michael, Thank you for the response. I agree that I am far from the minimum. However, when I do get to the minimum, I end up with a c/a ratio that is far off, and an energy difference of 0.6 eV, about twice what you find. (I have, I believe, accounted for the proper number of atoms, etc.) I have done the calculation with the PAW potential and the PZ-vbc potential and obtained the same results. Obviously I am doing something wrong but I simply cannot see it. I'll try the Si.pbe-n-van.UPF and see if I can reproduce your 0.29 eV energy difference. Did you c/a work out to be around 0.547? Daryl Daryl C. Chrzan Professor, Materials Science and Engineering University of California Berkeley, CA 94720 and Materials Sciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720 ph./fax: 510 643 1624 From dcchrzan at berkeley.edu Fri Oct 8 22:05:47 2010 From: dcchrzan at berkeley.edu (Daryl Chrzan) Date: Fri, 8 Oct 2010 13:05:47 -0700 Subject: [Pw_forum] Si diamond-cubic to beta-Sn transformation Message-ID: <4F1642DC-8ECC-4B6C-80BC-CA78BEF01CC4@berkeley.edu> Paolo, The smearing flag solved the problems. Thank you much for the tip (on behalf of myself and my class). I agree this is an excellent teaching exercise. Mark Asta suggested it to me, and it seems perfect. I still believe that there are 2 atoms per unit cell in the beta-Sn structure, so I am a bit confused by your final statement. I suppose this depends on the choice of lattice vectors... Daryl Daryl C. Chrzan Professor, Materials Science and Engineering University of California Berkeley, CA 94720 and Materials Sciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720 ph./fax: 510 643 1624 From giannozz at democritos.it Fri Oct 8 22:28:42 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 8 Oct 2010 22:28:42 +0200 Subject: [Pw_forum] Si diamond-cubic to beta-Sn transformation In-Reply-To: <4F1642DC-8ECC-4B6C-80BC-CA78BEF01CC4@berkeley.edu> References: <4F1642DC-8ECC-4B6C-80BC-CA78BEF01CC4@berkeley.edu> Message-ID: On Oct 8, 2010, at 22:05 , Daryl Chrzan wrote: > I still believe that there are 2 atoms per unit cell in the beta-Sn > structure, so I am a bit confused by your final statement > don't take it too seriously: I interpreted the "4a" positions mentioned in http://cst-www.nrl.navy.mil/lattice/struk/a5.html as meaning that there are 4 atoms in the unit cell, but I am too lazy to go and check the International Tables of Cristallography! P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From Michael.Mehl at nrl.navy.mil Sat Oct 9 00:33:19 2010 From: Michael.Mehl at nrl.navy.mil (Mike Mehl) Date: Fri, 08 Oct 2010 18:33:19 -0400 Subject: [Pw_forum] Si diamond-cubic to beta-Sn transformation In-Reply-To: <61B5C6A6-D00F-4A62-A7E7-F7686B1B5600@berkeley.edu> References: <61B5C6A6-D00F-4A62-A7E7-F7686B1B5600@berkeley.edu> Message-ID: <4CAF9C2F.8040402@nrl.navy.mil> Not quite: celldm(1) =11.15433936, celldm(3) =0.54170527 On 10/08/2010 03:55 PM, Daryl Chrzan wrote: > Michael, > > Thank you for the response. I agree that I am far from the minimum. However, when I do get to the minimum, I end up with a c/a ratio that is far off, and an energy difference of 0.6 eV, about twice what you find. (I have, I believe, accounted for the proper number of atoms, etc.) > > I have done the calculation with the PAW potential and the PZ-vbc potential and obtained the same results. Obviously I am doing something wrong but I simply cannot see it. I'll try the Si.pbe-n-van.UPF and see if I can reproduce your 0.29 eV energy difference. Did you c/a work out to be around 0.547? > > Daryl -- Michael J. Mehl Head, Center for Computational Materials Science Naval Research Laboratory Code 6390 Washington DC From bobjohn.lzu at gmail.com Sat Oct 9 03:24:02 2010 From: bobjohn.lzu at gmail.com (john Bob) Date: Sat, 9 Oct 2010 09:24:02 +0800 Subject: [Pw_forum] Some questions about IFC from PWSCF Message-ID: Dear Pwscf users: I have some questions about IFC from pwscf. I have read some threads about interatomic force constants in PWSCF maillist. I get confused when trying to analysis the IFC of NiTi alloy, and also the example06 AsAl. 1. F(R) and R=(i-1)*a + (j-1)*b +(k-1)*c. It means F(1 2 1) should equal to F(1 1 2) and F(2 1 1) for cubic lattice. But in B2 NiTi alloy ( CsCl strucuture) F(1 1 2) = F(1 2 1) /= F(2 1 1). and in example06 F(2 1 1) = F(1 1 2) /= F(1 2 1). It seems some extra-things added to some direction. Why? 2. How to interpret the "1 1 1 1" section, F_{xx}^{1,1}(0). Does it means the force along x axis on Atom1 when Atom1 has a small displacement along the x direction? 3. The section after the "diagonalizing the dynamical matrix". I find the vectors in xx.dyn file xx.vec file (after matdyn.x) are different, rotated. Are these vectors eigen-displacements or just eigen-vector after diagonalizing? Best regards Dr. Zhou Bo Northwest University, Xi'an China NiTi.fc ... 6 6 6 1 1 1 1 1 1 1 4.30811843056E-02 2 1 1 1.49655475926E-02 3 1 1 7.47266388889E-04 4 1 1 -2.16783699074E-03 5 1 1 7.47266388889E-04 6 1 1 1.49655475926E-02 1 2 1 2.68996333333E-03 2 2 1 6.60210833333E-04 3 2 1 3.81960555556E-04 4 2 1 -2.61037222222E-04 5 2 1 3.81960555556E-04 6 2 1 6.60210833333E-04 1 3 1 -6.84333333333E-06 2 3 1 -6.65476851852E-05 3 3 1 -2.73466666667E-05 4 3 1 -1.06576851852E-04 5 3 1 -2.73466666667E-05 6 3 1 -6.65476851852E-05 1 4 1 4.48548611111E-05 2 4 1 -1.11791388889E-04 3 4 1 -1.06166666667E-05 4 4 1 -2.20306944444E-05 5 4 1 -1.06166666667E-05 6 4 1 -1.11791388889E-04 1 5 1 -6.84333333333E-06 2 5 1 -6.65476851852E-05 3 5 1 -2.73466666667E-05 4 5 1 -1.06576851852E-04 5 5 1 -2.73466666667E-05 6 5 1 -6.65476851852E-05 1 6 1 2.68996333333E-03 2 6 1 6.60210833333E-04 3 6 1 3.81960555556E-04 4 6 1 -2.61037222222E-04 5 6 1 3.81960555556E-04 6 6 1 6.60210833333E-04 1 1 2 2.68996333333E-03 2 1 2 6.60210833333E-04 3 1 2 3.81960555556E-04 4 1 2 -2.61037222222E-04 5 1 2 3.81960555556E-04 6 1 2 6.60210833333E-04 1 2 2 1.07580273148E-03 2 2 2 -8.68419537037E-04 3 2 2 -1.26556851852E-04 4 2 2 4.42628240741E-05 5 2 2 -1.26556851852E-04 6 2 2 -8.68419537037E-04 1 3 2 1.78201250000E-04 2 3 2 1.02706111111E-04 3 3 2 -6.21652777778E-05 4 3 2 1.27609722222E-05 5 3 2 -6.21652777778E-05 6 3 2 1.02706111111E-04 1 4 2 2.77759259259E-06 2 4 2 -6.13445370370E-05 3 4 2 7.55775925926E-05 4 4 2 -1.15009259259E-05 5 4 2 7.55775925926E-05 6 4 2 -6.13445370370E-05 1 5 2 1.78201250000E-04 2 5 2 1.02706111111E-04 3 5 2 -6.21652777778E-05 4 5 2 1.27609722222E-05 5 5 2 -6.21652777778E-05 6 5 2 1.02706111111E-04 1 6 2 1.07580273148E-03 2 6 2 -8.68419537037E-04 3 6 2 -1.26556851852E-04 4 6 2 4.42628240741E-05 5 6 2 -1.26556851852E-04 6 6 2 -8.68419537037E-04 1 1 3 -6.84333333333E-06 2 1 3 -6.65476851852E-05 3 1 3 -2.73466666667E-05 4 1 3 -1.06576851852E-04 5 1 3 -2.73466666667E-05 6 1 3 -6.65476851852E-05 1 2 3 1.78201250000E-04 2 2 3 1.02706111111E-04 3 2 3 -6.21652777778E-05 4 2 3 1.27609722222E-05 5 2 3 -6.21652777778E-05 6 2 3 1.02706111111E-04 1 3 3 -4.81876388889E-05 2 3 3 -4.36212962963E-06 3 3 3 -5.60238888889E-05 4 3 3 4.51591203704E-05 5 3 3 -5.60238888889E-05 6 3 3 -4.36212962963E-06 1 4 3 -2.30238888889E-05 2 4 3 -1.50694444444E-06 3 4 3 2.35983333333E-05 4 4 3 2.81166666667E-06 5 4 3 2.35983333333E-05 6 4 3 -1.50694444444E-06 1 5 3 -4.81876388889E-05 2 5 3 -4.36212962963E-06 3 5 3 -5.60238888889E-05 4 5 3 4.51591203704E-05 5 5 3 -5.60238888889E-05 6 5 3 -4.36212962963E-06 1 6 3 1.78201250000E-04 2 6 3 1.02706111111E-04 3 6 3 -6.21652777778E-05 4 6 3 1.27609722222E-05 5 6 3 -6.21652777778E-05 6 6 3 1.02706111111E-04 1 1 4 4.48548611111E-05 2 1 4 -1.11791388889E-04 3 1 4 -1.06166666667E-05 4 1 4 -2.20306944444E-05 5 1 4 -1.06166666667E-05 6 1 4 -1.11791388889E-04 1 2 4 2.77759259259E-06 2 2 4 -6.13445370370E-05 3 2 4 7.55775925926E-05 4 2 4 -1.15009259259E-05 5 2 4 7.55775925926E-05 6 2 4 -6.13445370370E-05 1 3 4 -2.30238888889E-05 2 3 4 -1.50694444444E-06 3 3 4 2.35983333333E-05 4 3 4 2.81166666667E-06 5 3 4 2.35983333333E-05 6 3 4 -1.50694444444E-06 1 4 4 -9.10425462963E-05 2 4 4 2.44929629630E-05 3 4 4 -1.40046296296E-06 4 4 4 1.51428240741E-05 5 4 4 -1.40046296296E-06 6 4 4 2.44929629630E-05 1 5 4 -2.30238888889E-05 2 5 4 -1.50694444444E-06 3 5 4 2.35983333333E-05 4 5 4 2.81166666667E-06 5 5 4 2.35983333333E-05 6 5 4 -1.50694444444E-06 1 6 4 2.77759259259E-06 2 6 4 -6.13445370370E-05 3 6 4 7.55775925926E-05 4 6 4 -1.15009259259E-05 5 6 4 7.55775925926E-05 6 6 4 -6.13445370370E-05 1 1 5 -6.84333333333E-06 2 1 5 -6.65476851852E-05 3 1 5 -2.73466666667E-05 4 1 5 -1.06576851852E-04 5 1 5 -2.73466666667E-05 6 1 5 -6.65476851852E-05 1 2 5 1.78201250000E-04 2 2 5 1.02706111111E-04 3 2 5 -6.21652777778E-05 4 2 5 1.27609722222E-05 5 2 5 -6.21652777778E-05 6 2 5 1.02706111111E-04 1 3 5 -4.81876388889E-05 2 3 5 -4.36212962963E-06 3 3 5 -5.60238888889E-05 4 3 5 4.51591203704E-05 5 3 5 -5.60238888889E-05 6 3 5 -4.36212962963E-06 1 4 5 -2.30238888889E-05 2 4 5 -1.50694444444E-06 3 4 5 2.35983333333E-05 4 4 5 2.81166666667E-06 5 4 5 2.35983333333E-05 6 4 5 -1.50694444444E-06 1 5 5 -4.81876388889E-05 2 5 5 -4.36212962963E-06 3 5 5 -5.60238888889E-05 4 5 5 4.51591203704E-05 5 5 5 -5.60238888889E-05 6 5 5 -4.36212962963E-06 1 6 5 1.78201250000E-04 2 6 5 1.02706111111E-04 3 6 5 -6.21652777778E-05 4 6 5 1.27609722222E-05 5 6 5 -6.21652777778E-05 6 6 5 1.02706111111E-04 1 1 6 2.68996333333E-03 2 1 6 6.60210833333E-04 3 1 6 3.81960555556E-04 4 1 6 -2.61037222222E-04 5 1 6 3.81960555556E-04 6 1 6 6.60210833333E-04 1 2 6 1.07580273148E-03 2 2 6 -8.68419537037E-04 3 2 6 -1.26556851852E-04 4 2 6 4.42628240741E-05 5 2 6 -1.26556851852E-04 6 2 6 -8.68419537037E-04 1 3 6 1.78201250000E-04 2 3 6 1.02706111111E-04 3 3 6 -6.21652777778E-05 4 3 6 1.27609722222E-05 5 3 6 -6.21652777778E-05 6 3 6 1.02706111111E-04 1 4 6 2.77759259259E-06 2 4 6 -6.13445370370E-05 3 4 6 7.55775925926E-05 4 4 6 -1.15009259259E-05 5 4 6 7.55775925926E-05 6 4 6 -6.13445370370E-05 1 5 6 1.78201250000E-04 2 5 6 1.02706111111E-04 3 5 6 -6.21652777778E-05 4 5 6 1.27609722222E-05 5 5 6 -6.21652777778E-05 6 5 6 1.02706111111E-04 1 6 6 1.07580273148E-03 2 6 6 -8.68419537037E-04 3 6 6 -1.26556851852E-04 4 6 6 4.42628240741E-05 5 6 6 -1.26556851852E-04 6 6 6 -8.68419537037E-04 1 1 1 2 1 1 1 -8.74218916667E-03 2 1 1 -8.74218976551E-03 3 1 1 -2.35019119479E-03 4 1 1 -7.60084259259E-05 5 1 1 -7.60088052061E-05 ... -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101009/1144fc38/attachment-0001.htm From wumindt2 at zju.edu.cn Sat Oct 9 05:11:16 2010 From: wumindt2 at zju.edu.cn (wumindt2) Date: Sat, 09 Oct 2010 11:11:16 +0800 Subject: [Pw_forum] Xspectra calculation Message-ID: Dear Xspectra users, I met a problem when calculating the X-ray absorption spectra with the Xspectra code. Concern about the polarization, ?// is the polarization along the c axis, while ?? is the polariztion in the plane. It's easy to define the ?// , since normally (0,0,1) is the direction of c axis. But for ?? polarization, what does "in plane" mean? Are any directions in the a,b plane will cause the same result? For instance, will (1,0,0) ,(0,1,0) or (1,1,0) polarization direction have the same spectra? Thank you very much for any help. Cheers, Min Wu 2010-10-8 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101009/5fd9f157/attachment.htm From degironc at sissa.it Sat Oct 9 10:23:36 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sat, 09 Oct 2010 10:23:36 +0200 Subject: [Pw_forum] Some questions about IFC from PWSCF In-Reply-To: References: Message-ID: <4CB02688.7000609@sissa.it> Dear John Bob, answer to 1. & 2: IFC have four indices and depend on a lattice vector : F_(alpha,beta)^(na,nb)(R) this is the force in direction alpha (cartesian) on atom na in the unit cell at the origin when atom nb in the unit cell identified by R is displaced in direction beta. The header of each block (the four integers 1 1 1 1 for instance) etc. are just alpha,beta,na,nb and the subsequent lines contain i j k F_(alpha,beta)^(na,nb)(R) where R=(i-1)*a + (j-1)*b +(k-1)*c. There are 6x6x6 lines in your case because your q-points grid had these dimensions and a grid of q in the BZ translate in a set of R in real space. In order to compare individual IFC you must take into consideration the fact that they are tensorial quantities (matrices) and not scalar For instance if the system is cubic you expect F_{xx}{11} (0) = F_{yy}{11}(0) = F_{zz}{11} (0) = something while F_{xy}{11}(0) = F_{yx}{11}(0) =F_{yz}{11}(0) =F_{zy}{11}(0) =F_{xz}{11}(0) = F_{zx}{11}(0) = 0 where the R=0 is the first element (i,j,k=1,1,1) after the header of each block (alpha,beta,na,nb) you should have F_{xx}{11}(2 1 1) = F_{yy}{11}(1 2 1) = F_{zz}{11} (1 1 2) and also F_{xx}{11}(2 1 1) = F_{xx}{11}(6 1 1) = F_{yy}{11}(1 6 1) = F_{zz}{11} (1 1 6) for your 6x6x6 grid. and many other relations that links rotations of the linking vector R and rotations of the alpha,beta indices answer to 3: The written vectors are normalized displacements i.e. are eigenvectors rescaled with the sqrt of the atomic mass and remormalized. In case of doubts the routine that does that is PH/dyndia.f90 and the corresponding section (look for "Diagonalizing the " in dyndia.f90) should be quite transparent stefano === John Bob wrote: > Dear Pwscf users: > I have some questions about IFC from pwscf. I have read some threads > about interatomic force constants in PWSCF maillist. I get confused when > trying to analysis the IFC of NiTi alloy, and also the example06 AsAl. > > 1. F(R) and R=(i-1)*a + (j-1)*b +(k-1)*c. It means F(1 2 1) should equal > to F(1 1 2) and F(2 1 1) for cubic lattice. But in B2 NiTi alloy ( CsCl > strucuture) F(1 1 2) = F(1 2 1) /= F(2 1 1). and in example06 F(2 1 1) = F(1 > 1 2) /= F(1 2 1). It seems some extra-things added to some direction. Why? > > 2. How to interpret the "1 1 1 1" section, F_{xx}^{1,1}(0). Does it means > the force along x axis on Atom1 when Atom1 has a small displacement along > the x direction? > > 3. The section after the "diagonalizing the dynamical matrix". I find the > vectors in xx.dyn file xx.vec file (after matdyn.x) are different, rotated. > Are these vectors eigen-displacements or just eigen-vector after > diagonalizing? > > Best regards > > Dr. Zhou Bo > Northwest University, Xi'an China > > NiTi.fc > > ... > 6 6 6 > 1 1 1 1 > 1 1 1 4.30811843056E-02 > 2 1 1 1.49655475926E-02 > 3 1 1 7.47266388889E-04 > 4 1 1 -2.16783699074E-03 > 5 1 1 7.47266388889E-04 > 6 1 1 1.49655475926E-02 > 1 2 1 2.68996333333E-03 > 2 2 1 6.60210833333E-04 > 3 2 1 3.81960555556E-04 > 4 2 1 -2.61037222222E-04 > 5 2 1 3.81960555556E-04 > 6 2 1 6.60210833333E-04 > 1 3 1 -6.84333333333E-06 > 2 3 1 -6.65476851852E-05 > 3 3 1 -2.73466666667E-05 > 4 3 1 -1.06576851852E-04 > 5 3 1 -2.73466666667E-05 > 6 3 1 -6.65476851852E-05 > 1 4 1 4.48548611111E-05 > 2 4 1 -1.11791388889E-04 > 3 4 1 -1.06166666667E-05 > 4 4 1 -2.20306944444E-05 > 5 4 1 -1.06166666667E-05 > 6 4 1 -1.11791388889E-04 > 1 5 1 -6.84333333333E-06 > 2 5 1 -6.65476851852E-05 > 3 5 1 -2.73466666667E-05 > 4 5 1 -1.06576851852E-04 > 5 5 1 -2.73466666667E-05 > 6 5 1 -6.65476851852E-05 > 1 6 1 2.68996333333E-03 > 2 6 1 6.60210833333E-04 > 3 6 1 3.81960555556E-04 > 4 6 1 -2.61037222222E-04 > 5 6 1 3.81960555556E-04 > 6 6 1 6.60210833333E-04 > 1 1 2 2.68996333333E-03 > 2 1 2 6.60210833333E-04 > 3 1 2 3.81960555556E-04 > 4 1 2 -2.61037222222E-04 > 5 1 2 3.81960555556E-04 > 6 1 2 6.60210833333E-04 > 1 2 2 1.07580273148E-03 > 2 2 2 -8.68419537037E-04 > 3 2 2 -1.26556851852E-04 > 4 2 2 4.42628240741E-05 > 5 2 2 -1.26556851852E-04 > 6 2 2 -8.68419537037E-04 > 1 3 2 1.78201250000E-04 > 2 3 2 1.02706111111E-04 > 3 3 2 -6.21652777778E-05 > 4 3 2 1.27609722222E-05 > 5 3 2 -6.21652777778E-05 > 6 3 2 1.02706111111E-04 > 1 4 2 2.77759259259E-06 > 2 4 2 -6.13445370370E-05 > 3 4 2 7.55775925926E-05 > 4 4 2 -1.15009259259E-05 > 5 4 2 7.55775925926E-05 > 6 4 2 -6.13445370370E-05 > 1 5 2 1.78201250000E-04 > 2 5 2 1.02706111111E-04 > 3 5 2 -6.21652777778E-05 > 4 5 2 1.27609722222E-05 > 5 5 2 -6.21652777778E-05 > 6 5 2 1.02706111111E-04 > 1 6 2 1.07580273148E-03 > 2 6 2 -8.68419537037E-04 > 3 6 2 -1.26556851852E-04 > 4 6 2 4.42628240741E-05 > 5 6 2 -1.26556851852E-04 > 6 6 2 -8.68419537037E-04 > 1 1 3 -6.84333333333E-06 > 2 1 3 -6.65476851852E-05 > 3 1 3 -2.73466666667E-05 > 4 1 3 -1.06576851852E-04 > 5 1 3 -2.73466666667E-05 > 6 1 3 -6.65476851852E-05 > 1 2 3 1.78201250000E-04 > 2 2 3 1.02706111111E-04 > 3 2 3 -6.21652777778E-05 > 4 2 3 1.27609722222E-05 > 5 2 3 -6.21652777778E-05 > 6 2 3 1.02706111111E-04 > 1 3 3 -4.81876388889E-05 > 2 3 3 -4.36212962963E-06 > 3 3 3 -5.60238888889E-05 > 4 3 3 4.51591203704E-05 > 5 3 3 -5.60238888889E-05 > 6 3 3 -4.36212962963E-06 > 1 4 3 -2.30238888889E-05 > 2 4 3 -1.50694444444E-06 > 3 4 3 2.35983333333E-05 > 4 4 3 2.81166666667E-06 > 5 4 3 2.35983333333E-05 > 6 4 3 -1.50694444444E-06 > 1 5 3 -4.81876388889E-05 > 2 5 3 -4.36212962963E-06 > 3 5 3 -5.60238888889E-05 > 4 5 3 4.51591203704E-05 > 5 5 3 -5.60238888889E-05 > 6 5 3 -4.36212962963E-06 > 1 6 3 1.78201250000E-04 > 2 6 3 1.02706111111E-04 > 3 6 3 -6.21652777778E-05 > 4 6 3 1.27609722222E-05 > 5 6 3 -6.21652777778E-05 > 6 6 3 1.02706111111E-04 > 1 1 4 4.48548611111E-05 > 2 1 4 -1.11791388889E-04 > 3 1 4 -1.06166666667E-05 > 4 1 4 -2.20306944444E-05 > 5 1 4 -1.06166666667E-05 > 6 1 4 -1.11791388889E-04 > 1 2 4 2.77759259259E-06 > 2 2 4 -6.13445370370E-05 > 3 2 4 7.55775925926E-05 > 4 2 4 -1.15009259259E-05 > 5 2 4 7.55775925926E-05 > 6 2 4 -6.13445370370E-05 > 1 3 4 -2.30238888889E-05 > 2 3 4 -1.50694444444E-06 > 3 3 4 2.35983333333E-05 > 4 3 4 2.81166666667E-06 > 5 3 4 2.35983333333E-05 > 6 3 4 -1.50694444444E-06 > 1 4 4 -9.10425462963E-05 > 2 4 4 2.44929629630E-05 > 3 4 4 -1.40046296296E-06 > 4 4 4 1.51428240741E-05 > 5 4 4 -1.40046296296E-06 > 6 4 4 2.44929629630E-05 > 1 5 4 -2.30238888889E-05 > 2 5 4 -1.50694444444E-06 > 3 5 4 2.35983333333E-05 > 4 5 4 2.81166666667E-06 > 5 5 4 2.35983333333E-05 > 6 5 4 -1.50694444444E-06 > 1 6 4 2.77759259259E-06 > 2 6 4 -6.13445370370E-05 > 3 6 4 7.55775925926E-05 > 4 6 4 -1.15009259259E-05 > 5 6 4 7.55775925926E-05 > 6 6 4 -6.13445370370E-05 > 1 1 5 -6.84333333333E-06 > 2 1 5 -6.65476851852E-05 > 3 1 5 -2.73466666667E-05 > 4 1 5 -1.06576851852E-04 > 5 1 5 -2.73466666667E-05 > 6 1 5 -6.65476851852E-05 > 1 2 5 1.78201250000E-04 > 2 2 5 1.02706111111E-04 > 3 2 5 -6.21652777778E-05 > 4 2 5 1.27609722222E-05 > 5 2 5 -6.21652777778E-05 > 6 2 5 1.02706111111E-04 > 1 3 5 -4.81876388889E-05 > 2 3 5 -4.36212962963E-06 > 3 3 5 -5.60238888889E-05 > 4 3 5 4.51591203704E-05 > 5 3 5 -5.60238888889E-05 > 6 3 5 -4.36212962963E-06 > 1 4 5 -2.30238888889E-05 > 2 4 5 -1.50694444444E-06 > 3 4 5 2.35983333333E-05 > 4 4 5 2.81166666667E-06 > 5 4 5 2.35983333333E-05 > 6 4 5 -1.50694444444E-06 > 1 5 5 -4.81876388889E-05 > 2 5 5 -4.36212962963E-06 > 3 5 5 -5.60238888889E-05 > 4 5 5 4.51591203704E-05 > 5 5 5 -5.60238888889E-05 > 6 5 5 -4.36212962963E-06 > 1 6 5 1.78201250000E-04 > 2 6 5 1.02706111111E-04 > 3 6 5 -6.21652777778E-05 > 4 6 5 1.27609722222E-05 > 5 6 5 -6.21652777778E-05 > 6 6 5 1.02706111111E-04 > 1 1 6 2.68996333333E-03 > 2 1 6 6.60210833333E-04 > 3 1 6 3.81960555556E-04 > 4 1 6 -2.61037222222E-04 > 5 1 6 3.81960555556E-04 > 6 1 6 6.60210833333E-04 > 1 2 6 1.07580273148E-03 > 2 2 6 -8.68419537037E-04 > 3 2 6 -1.26556851852E-04 > 4 2 6 4.42628240741E-05 > 5 2 6 -1.26556851852E-04 > 6 2 6 -8.68419537037E-04 > 1 3 6 1.78201250000E-04 > 2 3 6 1.02706111111E-04 > 3 3 6 -6.21652777778E-05 > 4 3 6 1.27609722222E-05 > 5 3 6 -6.21652777778E-05 > 6 3 6 1.02706111111E-04 > 1 4 6 2.77759259259E-06 > 2 4 6 -6.13445370370E-05 > 3 4 6 7.55775925926E-05 > 4 4 6 -1.15009259259E-05 > 5 4 6 7.55775925926E-05 > 6 4 6 -6.13445370370E-05 > 1 5 6 1.78201250000E-04 > 2 5 6 1.02706111111E-04 > 3 5 6 -6.21652777778E-05 > 4 5 6 1.27609722222E-05 > 5 5 6 -6.21652777778E-05 > 6 5 6 1.02706111111E-04 > 1 6 6 1.07580273148E-03 > 2 6 6 -8.68419537037E-04 > 3 6 6 -1.26556851852E-04 > 4 6 6 4.42628240741E-05 > 5 6 6 -1.26556851852E-04 > 6 6 6 -8.68419537037E-04 > 1 1 1 2 > 1 1 1 -8.74218916667E-03 > 2 1 1 -8.74218976551E-03 > 3 1 1 -2.35019119479E-03 > 4 1 1 -7.60084259259E-05 > 5 1 1 -7.60088052061E-05 > ... > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From matteo.calandra at impmc.jussieu.fr Sat Oct 9 11:30:54 2010 From: matteo.calandra at impmc.jussieu.fr (matteo calandra) Date: Sat, 9 Oct 2010 11:30:54 +0200 Subject: [Pw_forum] Xspectra calculation In-Reply-To: References: Message-ID: <20101009113054.30054xq5t9dknlu6@www1.impmc.upmc.fr> Dear Wumindt2, the fact that different polarization directions can be equivalent or not in a solid depends only on the symmetry of your lattice (thus on the crystal structure) only. So the general response to your question is given by the theory of crystal symmetries. M. > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 09 Oct 2010 11:11:16 +0800 > From: "wumindt2" > Subject: [Pw_forum] Xspectra calculation > To: pw_forum at pwscf.org > Message-ID: > Content-Type: text/plain; charset="gb2312" > > Dear Xspectra users, > > I met a problem when calculating the X-ray absorption spectra with > the Xspectra code. > Concern about the polarization, ?// is the polarization along the c > axis, while ?? is the polariztion > in the plane. It's easy to define the ?// , since normally (0,0,1) > is the direction of c axis. > But for ?? polarization, what does "in plane" mean? Are any > directions in the a,b plane > will cause the same result? For instance, will (1,0,0) ,(0,1,0) or > (1,1,0) polarization direction > have the same spectra? > > Thank you very much for any help. > > Cheers, > > Min Wu > 2010-10-8 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20101009/5fd9f157/attachment.html > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 40, Issue 16 > **************************************** > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From wumindt2 at zju.edu.cn Sat Oct 9 16:48:53 2010 From: wumindt2 at zju.edu.cn (wumindt2) Date: Sat, 09 Oct 2010 22:48:53 +0800 Subject: [Pw_forum] Xspectra calculation Message-ID: Dear matteo, Thanks. For dichroism compound, do we just need the in-plane and the c-axis polarization vectors? While for trichroism compound, do we need to calculate three different polarization vectors? Am i right? Best regards, Min Wu 2010-10-9 >From: matteo calandra >Reply-To: PWSCF Forum >To: pw_forum at pwscf.org >Subject: Re: [Pw_forum] Xspectra calculation >Date: Sat, 9 Oct 2010 11:30:54 +0200 > >Dear Wumindt2, > > the fact that different polarization directions can be equivalent or not >in a solid depends only on the symmetry of your lattice (thus on the crystal >structure) only. >So the general response to your question is given by the theory of crystal >symmetries. > >M. > > >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Sat, 09 Oct 2010 11:11:16 +0800 >> From: "wumindt2" >> Subject: [Pw_forum] Xspectra calculation >> To: pw_forum at pwscf.org >> Message-ID: >> Content-Type: text/plain; charset="gb2312" >> >> Dear Xspectra users, >> >> I met a problem when calculating the X-ray absorption spectra with >> the Xspectra code. >> Concern about the polarization, ?// is the polarization along the c >> axis, while ?? is the polariztion >> in the plane. It's easy to define the ?// , since normally (0,0,1) >> is the direction of c axis. >> But for ?? polarization, what does "in plane" mean? Are any >> directions in the a,b plane >> will cause the same result? For instance, will (1,0,0) ,(0,1,0) or >> (1,1,0) polarization direction >> have the same spectra? >> >> Thank you very much for any help. >> >> Cheers, >> >> Min Wu >> 2010-10-8 >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://www.democritos.it/pipermail/pw_forum/attachments/20101009/5fd9f157/attachment.html >> >> ------------------------------ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> End of Pw_forum Digest, Vol 40, Issue 16 >> **************************************** >> > > > >---------------------------------------------------------------- >This message was sent using IMP, the Internet Messaging Program. > > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > From mohnish.iitk at gmail.com Mon Oct 11 06:46:32 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Mon, 11 Oct 2010 10:16:32 +0530 Subject: [Pw_forum] Way to do calculation using charge density of coarse grid for fine grid... Message-ID: Dear QE users, I am doing calculations for large supercells. The way I am trying to do is first I do calculation for gamma point(which will be quit less time consuming), then what I want to do is use the charge density obtained form gamma point to do the calculation for 2x2x1 and then 2x2x1 to do 3x3x1 k-point grid. I there anyway to do this because when I am using the charge density of coarser grid to the calculation for finer grid I am getting the error "davcio error". I am also using the wave-function of the coarser grid for fine grid calculation. Thanks in advance -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101011/cf143f4f/attachment.htm From giannozz at democritos.it Mon Oct 11 09:32:24 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 11 Oct 2010 09:32:24 +0200 Subject: [Pw_forum] Way to do calculation using charge density of coarse grid for fine grid... In-Reply-To: References: Message-ID: <239AF225-4FD5-4501-A0FA-AFBD7755AF4A@democritos.it> On Oct 11, 2010, at 6:46 , mohnish pandey wrote: > I there anyway to do this because when I am using the > charge density of coarser grid to the calculation for finer grid > I am getting the error "davcio error". I am also using the > wave-function of the coarser grid for fine grid calculation. if I remember correctly, you should be able to read the charge density produced by a Gamma-only calculation into a k-point calculation, but only if you have the same FFT grids: use "startingpot='file'". You cannot re-use wavefunctions, though. Paolo --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From matteo.calandra at impmc.jussieu.fr Mon Oct 11 10:08:16 2010 From: matteo.calandra at impmc.jussieu.fr (Matteo Calandra) Date: Mon, 11 Oct 2010 10:08:16 +0200 Subject: [Pw_forum] Xspectra calculation (wumindt2) In-Reply-To: References: Message-ID: <4CB2C5F0.7010100@impmc.jussieu.fr> Dear I assume you are talking of the dipolar part only. For the quadrupolar it is substantially more complicate. The number of independent calculations that you have to perform to obtain the isotropic cross section (powder) depends on the point group of the space group of your crystal. It is 1 for a cubic or tetraedric crystal, 2 for a uniaxial crystal and it is 3, 4, 6 for a biaxial (ot trichroic) crystal. I suggest you read C. Brouder J. Phys.: Condens. Matter 2 (1990) 701-738 for more details. M. > > Message: 3 > Date: Sat, 09 Oct 2010 22:48:53 +0800 > From: "wumindt2" > Subject: Re: [Pw_forum] Xspectra calculation > To: pw_forum at pwscf.org > Message-ID: > Content-Type: text/plain; charset="gb2312" > > Dear matteo, > > Thanks. > > For dichroism compound, do we just need the in-plane and the c-axis > polarization vectors? > While for trichroism compound, do we need to calculate three different > polarization vectors? > Am i right? > > Best regards, > From bobjohn.lzu at gmail.com Mon Oct 11 11:22:18 2010 From: bobjohn.lzu at gmail.com (john Bob) Date: Mon, 11 Oct 2010 17:22:18 +0800 Subject: [Pw_forum] Some questions about IFC from PWSCF In-Reply-To: <4CB02688.7000609@sissa.it> References: <4CB02688.7000609@sissa.it> Message-ID: Dear Stefano: Thank you very much for the answers. I lernt much from those. In some textbook the force constant matrix are ( L L' ) F ( ) alpha,beta ( K K' ) L is the index of cells, K index of different atoms. (1) Can I rewrite the F_(alpha,beta)^(na,nb)(R) as ( 0 L' ) F ( ) while L' is L(a,b,c) L(R) ? alpha,beta ( na nb ) (2) F_{alpha,beta} matrix is 3X3 matrix. And It acts like other two rank tensor ( dielectric tensor, electric conductivity tensor) under symmetry operations ? The independent parameters can be decided by group theory ? one for cubic system. (3) I pick up the " x x 1 1 2 1 1 x.xxxx " lines ================ 1 1 1 1 1 1 1 4.30811843056E-02 2 1 1 1.49655475926E-02 1 2 1 1 1 1 1 0.00000000000E+00 2 1 1 0.00000000000E+00 1 3 1 1 1 1 1 0.00000000000E+00 2 1 1 0.00000000000E+00 2 1 1 1 1 1 1 0.00000000000E+00 2 1 1 0.00000000000E+00 2 2 1 1 1 1 1 4.30811843056E-02 2 1 1 2.68996333333E-03 2 3 1 1 1 1 1 0.00000000000E+00 2 1 1 0.00000000000E+00 3 1 1 1 1 1 1 0.00000000000E+00 2 1 1 0.00000000000E+00 3 2 1 1 1 1 1 0.00000000000E+00 2 1 1 0.00000000000E+00 3 3 1 1 1 1 1 4.30811843056E-02 2 1 1 2.68996333333E-03 ========================== why Fxx /= Fyy = Fzz ? I am sorry for my poor english. Also sorry for so many annoying question, self-teaching is a hard and careful work. Dr Zhou Bo Norhwest University Xi'an China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101011/65cb4c6c/attachment.htm From wongkc81 at gmail.com Mon Oct 11 14:51:21 2010 From: wongkc81 at gmail.com (Wong Kelvin) Date: Mon, 11 Oct 2010 20:51:21 +0800 Subject: [Pw_forum] simulation of poisson effect in thin film Message-ID: Dear all, I am simulating the material behaviour of metal under biaxial strain. (although so-called thin film, the cell does not include any vacuum. it's still bulk). so i strain the crystal in a and b direction by certain percent. Accordingly the stress in x and y , also z direction go up significantly. I try to reduce the stress in Z direction by changing the C length of the crystal while keeping strain (length of) in A and B. I understanding that i took poisson effect into account by doing so. Is my understanding correct? Pls comments. Wong -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101011/29a15a29/attachment.htm From degironc at sissa.it Mon Oct 11 15:21:31 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 11 Oct 2010 15:21:31 +0200 Subject: [Pw_forum] Some questions about IFC from PWSCF In-Reply-To: References: <4CB02688.7000609@sissa.it> Message-ID: <4CB30F5B.2000307@sissa.it> dear Zhou Bo the IFC between atoms in cell L and L' only depends on L-L' hence the answer to 1) is yes. 2) for any given L , na,nb F_alpha,beta is a 3x3 matrix but when you apply symmetry you must not oly rotate alpha and beta but also L,na and nb... so ... yes: symmetry determines the structure of the matrix but .. no: it's not the global symmetry of the crystal but the one of the pair of atoms. 3) think of a simple cubic system with a nearest neighbor spring: if you displace the atom in the origin in the x direction this gives a certain (big) force in the x direction to the first n.n. atom in the x direction ... and a different (smaller) force to n.n. atoms in y and z directions. If you move the atom in the y direction the big force will be on the y direction on atom n.n. along y while on atoms along x and z the force will be smaller... stefano john Bob wrote: > Dear Stefano: > > Thank you very much for the answers. I lernt much from those. In some > textbook the force constant matrix are > ( L L' ) > F ( ) > alpha,beta ( K K' ) L is the index of cells, K index of > different atoms. > > (1) Can I rewrite the F_(alpha,beta)^(na,nb)(R) as > ( 0 L' ) > F ( ) while L' is L(a,b,c) > L(R) ? > alpha,beta ( na nb ) > > (2) F_{alpha,beta} matrix is 3X3 matrix. And It acts like other two rank > tensor ( dielectric tensor, electric conductivity tensor) under symmetry > operations ? The independent parameters can be decided by group theory ? > one for cubic system. > > (3) I pick up the > " x x 1 1 > 2 1 1 x.xxxx " > lines > ================ > 1 1 1 1 > 1 1 1 4.30811843056E-02 > 2 1 1 1.49655475926E-02 > 1 2 1 1 > 1 1 1 0.00000000000E+00 > 2 1 1 0.00000000000E+00 > 1 3 1 1 > 1 1 1 0.00000000000E+00 > 2 1 1 0.00000000000E+00 > 2 1 1 1 > 1 1 1 0.00000000000E+00 > 2 1 1 0.00000000000E+00 > 2 2 1 1 > 1 1 1 4.30811843056E-02 > 2 1 1 2.68996333333E-03 > 2 3 1 1 > 1 1 1 0.00000000000E+00 > 2 1 1 0.00000000000E+00 > 3 1 1 1 > 1 1 1 0.00000000000E+00 > 2 1 1 0.00000000000E+00 > 3 2 1 1 > 1 1 1 0.00000000000E+00 > 2 1 1 0.00000000000E+00 > 3 3 1 1 > 1 1 1 4.30811843056E-02 > 2 1 1 2.68996333333E-03 > ========================== > why Fxx /= Fyy = Fzz ? > > I am sorry for my poor english. Also sorry for so many annoying question, > self-teaching is a hard and careful work. > > > Dr Zhou Bo > > Norhwest University Xi'an China > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From bobjohn.lzu at gmail.com Mon Oct 11 16:05:10 2010 From: bobjohn.lzu at gmail.com (john Bob) Date: Mon, 11 Oct 2010 22:05:10 +0800 Subject: [Pw_forum] Some questions about IFC from PWSCF In-Reply-To: <4CB30F5B.2000307@sissa.it> References: <4CB02688.7000609@sissa.it> <4CB30F5B.2000307@sissa.it> Message-ID: Dear Stefano: I got it. Thank you so much Dr. Zhou Bo Northwest University Xi'an China From wumindt2 at zju.edu.cn Tue Oct 12 08:59:33 2010 From: wumindt2 at zju.edu.cn (wumindt2) Date: Tue, 12 Oct 2010 14:59:33 +0800 Subject: [Pw_forum] Xspectra calculation (wumindt2) Message-ID: Dear Matteo, Thanks for the information, i read the C. Brouder the paper a little bit. I'am still not sure how to choose the polarization vector. For instance, we have a crystal with spacegroup of P42/MNM, point group of 4/mmm. According to the Table in C. Brouder's paper, this is a dichroism compound. Thus, how can we choose the polarization vector when calculating the XAS of this compound? Can you please show me how? Thanks so much! Cheers, Min Wu 2010-10-12 >From: Matteo Calandra >Reply-To: PWSCF Forum >To: pw_forum at pwscf.org >Subject: Re: [Pw_forum] Xspectra calculation (wumindt2) >Date: Mon, 11 Oct 2010 10:08:16 +0200 > >Dear > > I assume you are talking of the dipolar part only. >For the quadrupolar it is substantially more complicate. >The number of independent calculations that you have >to perform to obtain the isotropic cross section (powder) >depends on the point group of the space group >of your crystal. >It is 1 for a cubic or tetraedric crystal, >2 for a uniaxial crystal and it is 3, 4, 6 for a biaxial >(ot trichroic) crystal. >I suggest you read >C. Brouder J. Phys.: Condens. Matter 2 (1990) 701-738 >for more details. > >M. > > >> >> Message: 3 >> Date: Sat, 09 Oct 2010 22:48:53 +0800 >> From: "wumindt2" >> Subject: Re: [Pw_forum] Xspectra calculation >> To: pw_forum at pwscf.org >> Message-ID: >> Content-Type: text/plain; charset="gb2312" >> >> Dear matteo, >> >> Thanks. >> >> For dichroism compound, do we just need the in-plane and the c-axis >> polarization vectors? >> While for trichroism compound, do we need to calculate three different >> polarization vectors? >> Am i right? >> >> Best regards, >> >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > From matteo.calandra at impmc.jussieu.fr Tue Oct 12 10:14:42 2010 From: matteo.calandra at impmc.jussieu.fr (matteo calandra) Date: Tue, 12 Oct 2010 10:14:42 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 40, Issue 19 In-Reply-To: References: Message-ID: <20101012101442.84091vx35nxcb3zm@www1.impmc.upmc.fr> Dear Min Wu, I think you should sit down a bit and try to solve this issue by yourself. This is not a problem concerning the code as you would have the same problem with any other code, but it concerns basic physics and group theory. In the future we plan to write a program to find the isotropic cross section with the sallest number of calculations possible from the knowledge of the symmetries of the lattice. However this is not yet done (I am not aware of any program doing this). So, as I always do in these case, you should si down,try to understand Ch. Bouder's paper and find the polarization vectors necessary to obtain the isotropic cross section. M. > > Message: 6 > Date: Tue, 12 Oct 2010 14:59:33 +0800 > From: "wumindt2" > Subject: Re: [Pw_forum] Xspectra calculation (wumindt2) > To: pw_forum at pwscf.org > Message-ID: > Content-Type: text/plain; charset="gb2312" > > Dear Matteo, > > Thanks for the information, i read the C. Brouder the paper a little bit. > I'am still not sure how to choose the polarization vector. > For instance, we have a crystal with spacegroup of P42/MNM, point > group of 4/mmm. > According to the Table in C. Brouder's paper, this is a dichroism compound. > Thus, how can we choose the polarization vector when calculating the XAS > of this compound? > Can you please show me how? > > Thanks so much! > > Cheers, > > Min Wu > 2010-10-12 > > >> From: Matteo Calandra >> Reply-To: PWSCF Forum >> To: pw_forum at pwscf.org >> Subject: Re: [Pw_forum] Xspectra calculation (wumindt2) >> Date: Mon, 11 Oct 2010 10:08:16 +0200 >> >> Dear >> >> I assume you are talking of the dipolar part only. >> For the quadrupolar it is substantially more complicate. >> The number of independent calculations that you have >> to perform to obtain the isotropic cross section (powder) >> depends on the point group of the space group >> of your crystal. >> It is 1 for a cubic or tetraedric crystal, >> 2 for a uniaxial crystal and it is 3, 4, 6 for a biaxial >> (ot trichroic) crystal. >> I suggest you read >> C. Brouder J. Phys.: Condens. Matter 2 (1990) 701-738 >> for more details. >> >> M. >> >> >>> >>> Message: 3 >>> Date: Sat, 09 Oct 2010 22:48:53 +0800 >>> From: "wumindt2" > >>> Subject: Re: [Pw_forum] Xspectra calculation >>> To: pw_forum at pwscf.org >>> Message-ID: > >>> Content-Type: text/plain; charset="gb2312" >>> >>> Dear matteo, >>> >>> Thanks. >>> >>> For dichroism compound, do we just need the in-plane and the c-axis >>> polarization vectors? >>> While for trichroism compound, do we need to calculate three different >>> polarization vectors? >>> Am i right? >>> >>> Best regards, >>> >> _______________________________________________ >> 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 > > > End of Pw_forum Digest, Vol 40, Issue 19 > **************************************** > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From physik.shyam at gmail.com Tue Oct 12 12:36:25 2010 From: physik.shyam at gmail.com (Shyam Khambholja) Date: Tue, 12 Oct 2010 17:36:25 +0700 Subject: [Pw_forum] cohesive energy Message-ID: Hello all, scf calculation can give us total energy. but how to calculate cohesive energy of elements like aluminium from total energy ? thanks in advance -- Mr. Shyam G Khambholja Research student, Depratment of Physics, Sardar Patel University, Gujarat -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101012/8cf3d73e/attachment.htm From mirnezhad.mm at gmail.com Tue Oct 12 14:55:00 2010 From: mirnezhad.mm at gmail.com (Mahdi Mirnezhad) Date: Tue, 12 Oct 2010 16:25:00 +0330 Subject: [Pw_forum] Question about Young's modulus In-Reply-To: References: Message-ID: Dear Developers, I think there is a problem in the calculation of stress in Quantum Esperesso. This problem concern with the volume of unit cell. For bulk structures there is no problem for determination of Volume but in the super cell method code calculate stress according to unit cell volume so when i calculate Young's Modulus for graphene with two method (strees/strain or (E=(1/V)*second derivative of energy) ) i get different answer. What is your suggestion? Thanks for your reply. Mahdi Mirnezhad Msc student of Mechanics Guilan University. On 10/7/10, Mahdi Mirnezhad wrote: > Dear all, > I calculated Young's modulusfor graphene and i got correct answer but > when I want to calculate Young's modulus for CNT(3,3) for a axial > strain with the same condition (same PS) i got a wrong answer? > Any suggestion appreciated, > tanks > > mahdi mirnezhade > From degironc at sissa.it Tue Oct 12 15:01:29 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 12 Oct 2010 15:01:29 +0200 Subject: [Pw_forum] Question about Young's modulus In-Reply-To: References: Message-ID: <4CB45C29.6070908@sissa.it> for a 2-D system I guess that the definition of stress will involve the area and not the volume ... stefano Mahdi Mirnezhad wrote: > Dear Developers, > I think there is a problem in the calculation of stress in Quantum > Esperesso. This problem concern with the volume of unit cell. For bulk > structures there is no problem for determination of Volume but in the > super cell method code calculate stress according to unit cell volume > so when i calculate Young's Modulus for graphene with two method > (strees/strain or (E=(1/V)*second derivative of energy) ) i get > different answer. > What is your suggestion? > Thanks for your reply. > > Mahdi Mirnezhad > Msc student of Mechanics > Guilan University. > > > > On 10/7/10, Mahdi Mirnezhad wrote: > >> Dear all, >> I calculated Young's modulusfor graphene and i got correct answer but >> when I want to calculate Young's modulus for CNT(3,3) for a axial >> strain with the same condition (same PS) i got a wrong answer? >> Any suggestion appreciated, >> tanks >> >> mahdi mirnezhade >> >> > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From degironc at sissa.it Tue Oct 12 15:07:28 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 12 Oct 2010 15:07:28 +0200 Subject: [Pw_forum] cohesive energy In-Reply-To: References: Message-ID: <4CB45D90.9030502@sissa.it> the cohesive energy is the energy per atom of the bulk minus the energy of an isolated atom. stefano Shyam Khambholja wrote: > Hello all, > scf calculation can give us total energy. but how to calculate > cohesive energy of elements like aluminium from total energy ? thanks in > advance > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From kissi at uni-mainz.de Tue Oct 12 20:02:00 2010 From: kissi at uni-mainz.de (Kiss, Ioan) Date: Tue, 12 Oct 2010 18:02:00 +0000 Subject: [Pw_forum] pw.x crash on LSF/mvapich Message-ID: Dear PWSCF users and developers, I have a problem running pw.x in our computer center. The MPI environment is mvapich_1.1, the queuing system is LSF, and I have compiled PWSCF with the Intel compiler suite together with MKL libraries. The threading via MKL is turned off by exporting OMP_NUM_THREADS=1. The machines are 8 core Xeons with QDR Infiniband and 48GB of ECC memory/node. I would like to perform some geometry optimizations on Cd doped CuInSe2 with PWSCF version 4.1.2. The FFT grid for the respective slab is 150:150:144, and it does run on 24 CPUs (i.e. 3 nodes with 8 cores). However, by taking the same binary and input file, if I would like to use 48, 72 or 144 CPU cores, than the job will crash right after the WFC initialization: Self-consistent Calculation iteration # 1 ecut= 25.00 Ry beta=0.70 Davidson diagonalization with overlap Signal 15 received. . . . Signal 15 received. Job /usr/local/lsf/7.0/linux2.6-glibc2.3-x86_64/bin/mvapich_wrapper VIADEV_USE_SHMEM_ALLREDUCE=0 VIADEV_USE_SHMEM_REDUCE=0 VIADEV_USE_SHMEM_BARRIER=0 DISABLE_RDMA_ALLTOALL=1 DISABLE_RDMA_ALLGATHER=1 DISABLE_RDMA_BARRIER=1 MV2_CPU_MAPPING=0:1:2:3:4:5:6:7 ./pwTest.x -in INP-PWSCF TID HOST_NAME COMMAND_LINE STATUS TERMINATION_TIME ===== ========== ================ ======================= =================== 00000 moment1 /usr/local/lsf/l Exit (1) 10/12/2010 19:20:36 . . . 00001 moment1 /usr/local/lsf/l Exit (174) 10/12/2010 19:20:36 As you can see, I have already tried to deactivate the shared memory optimizations implemented in mvapich in the Nemesis routines, but that did not help either. Strangely, on the same machine I can run CPMD without any issues, so I am really wondering what I am doing wrong or what should I change to fix this problem. I have tried several different MKL versions and so forth, but to be honest it seems to me that I just cannot fix it. Also, using the same input file and 48-72 CPUs the job will nicely finish in Juelich supercomputer center and also in the department's tiny local cluster running OpenMPI. Do you have some ideas why the machine under LSF/mvapich is not fully cooperating with PWSCF above 24 CPU cores, or what should be done to remedy this issue? Thanks in advance for any helpful comment, Janos. ========================================== 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 maxim_espresso at mail.ru Wed Oct 13 15:03:06 2010 From: maxim_espresso at mail.ru (Maxim) Date: Wed, 13 Oct 2010 20:03:06 +0700 Subject: [Pw_forum] LDA+U calculation, difference in U values of one sort of atom. Message-ID: <1286974986.4373.7.camel@nto-2.mn.isp.nsc.ru> Dear pwscf users, I have obtained Hubbard U values for Ta atoms in Ta2O5 system. The values are 1.9 eV and 2.8 eV for two not equivalent atoms. I am confused about such relevant difference in the the values. As I understand Hubbard U characterizes the sort of atom and its coordination should not influence on the value. Could you help me to figure out what is wrong? Thank you in advance, Maxim From physik.shyam at gmail.com Wed Oct 13 12:54:41 2010 From: physik.shyam at gmail.com (Shyam Khambholja) Date: Wed, 13 Oct 2010 17:54:41 +0700 Subject: [Pw_forum] Pw_forum Digest, Vol 40, Issue 20 In-Reply-To: References: Message-ID: Thank you Prof. Stefano, how to calculate energy of an isolated atom ? shyam On Wed, Oct 13, 2010 at 2:32 PM, wrote: > 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. Re: Pw_forum Digest, Vol 40, Issue 19 (matteo calandra) > 2. cohesive energy (Shyam Khambholja) > 3. Re: Question about Young's modulus (Mahdi Mirnezhad) > 4. Re: Question about Young's modulus (Stefano de Gironcoli) > 5. Re: cohesive energy (Stefano de Gironcoli) > 6. pw.x crash on LSF/mvapich (Kiss, Ioan) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 12 Oct 2010 10:14:42 +0200 > From: matteo calandra > Subject: Re: [Pw_forum] Pw_forum Digest, Vol 40, Issue 19 > To: pw_forum at pwscf.org > Message-ID: <20101012101442.84091vx35nxcb3zm at www1.impmc.upmc.fr> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Dear Min Wu, > > I think you should sit down a bit and try to solve this issue > by yourself. This is not a problem concerning the code as you would have > the same problem with any other code, but it concerns basic > physics and group theory. > In the future we plan to write a program to find the isotropic cross > section > with the sallest number of calculations possible from the knowledge of > the symmetries of the lattice. > However this is not yet done (I am not aware of any program doing this). > > So, as I always do in these case, you should si down,try to understand > Ch. Bouder's paper and find the polarization vectors necessary to > obtain the isotropic cross section. > > M. > > > > > Message: 6 > > Date: Tue, 12 Oct 2010 14:59:33 +0800 > > From: "wumindt2" > > Subject: Re: [Pw_forum] Xspectra calculation (wumindt2) > > To: pw_forum at pwscf.org > > Message-ID: > > Content-Type: text/plain; charset="gb2312" > > > > Dear Matteo, > > > > Thanks for the information, i read the C. Brouder the paper a little bit. > > I'am still not sure how to choose the polarization vector. > > For instance, we have a crystal with spacegroup of P42/MNM, point > > group of 4/mmm. > > According to the Table in C. Brouder's paper, this is a dichroism > compound. > > Thus, how can we choose the polarization vector when calculating the XAS > > of this compound? > > Can you please show me how? > > > > Thanks so much! > > > > Cheers, > > > > Min Wu > > 2010-10-12 > > > > > >> From: Matteo Calandra > >> Reply-To: PWSCF Forum > >> To: pw_forum at pwscf.org > >> Subject: Re: [Pw_forum] Xspectra calculation (wumindt2) > >> Date: Mon, 11 Oct 2010 10:08:16 +0200 > >> > >> Dear > >> > >> I assume you are talking of the dipolar part only. > >> For the quadrupolar it is substantially more complicate. > >> The number of independent calculations that you have > >> to perform to obtain the isotropic cross section (powder) > >> depends on the point group of the space group > >> of your crystal. > >> It is 1 for a cubic or tetraedric crystal, > >> 2 for a uniaxial crystal and it is 3, 4, 6 for a biaxial > >> (ot trichroic) crystal. > >> I suggest you read > >> C. Brouder J. Phys.: Condens. Matter 2 (1990) 701-738 > >> for more details. > >> > >> M. > >> > >> > >>> > >>> Message: 3 > >>> Date: Sat, 09 Oct 2010 22:48:53 +0800 > >>> From: "wumindt2" > > > >>> Subject: Re: [Pw_forum] Xspectra calculation > >>> To: pw_forum at pwscf.org > >>> Message-ID: > > > >>> Content-Type: text/plain; charset="gb2312" > >>> > >>> Dear matteo, > >>> > >>> Thanks. > >>> > >>> For dichroism compound, do we just need the in-plane and the c-axis > >>> polarization vectors? > >>> While for trichroism compound, do we need to calculate three different > >>> polarization vectors? > >>> Am i right? > >>> > >>> Best regards, > >>> > >> _______________________________________________ > >> 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 > > > > > > End of Pw_forum Digest, Vol 40, Issue 19 > > **************************************** > > > > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > > > ------------------------------ > > Message: 2 > Date: Tue, 12 Oct 2010 17:36:25 +0700 > From: Shyam Khambholja > Subject: [Pw_forum] cohesive energy > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hello all, > scf calculation can give us total energy. but how to calculate > cohesive energy of elements like aluminium from total energy ? thanks in > advance > > -- > Mr. Shyam G Khambholja > Research student, > Depratment of Physics, > Sardar Patel University, Gujarat > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20101012/8cf3d73e/attachment.html > > ------------------------------ > > Message: 3 > Date: Tue, 12 Oct 2010 16:25:00 +0330 > From: Mahdi Mirnezhad > Subject: Re: [Pw_forum] Question about Young's modulus > To: pw_forum > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Developers, > I think there is a problem in the calculation of stress in Quantum > Esperesso. This problem concern with the volume of unit cell. For bulk > structures there is no problem for determination of Volume but in the > super cell method code calculate stress according to unit cell volume > so when i calculate Young's Modulus for graphene with two method > (strees/strain or (E=(1/V)*second derivative of energy) ) i get > different answer. > What is your suggestion? > Thanks for your reply. > > Mahdi Mirnezhad > Msc student of Mechanics > Guilan University. > > > > On 10/7/10, Mahdi Mirnezhad wrote: > > Dear all, > > I calculated Young's modulusfor graphene and i got correct answer but > > when I want to calculate Young's modulus for CNT(3,3) for a axial > > strain with the same condition (same PS) i got a wrong answer? > > Any suggestion appreciated, > > tanks > > > > mahdi mirnezhade > > > > > ------------------------------ > > Message: 4 > Date: Tue, 12 Oct 2010 15:01:29 +0200 > From: Stefano de Gironcoli > Subject: Re: [Pw_forum] Question about Young's modulus > To: PWSCF Forum > Message-ID: <4CB45C29.6070908 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > for a 2-D system I guess that the definition of stress will involve the > area and not the volume ... > stefano > > > Mahdi Mirnezhad wrote: > > Dear Developers, > > I think there is a problem in the calculation of stress in Quantum > > Esperesso. This problem concern with the volume of unit cell. For bulk > > structures there is no problem for determination of Volume but in the > > super cell method code calculate stress according to unit cell volume > > so when i calculate Young's Modulus for graphene with two method > > (strees/strain or (E=(1/V)*second derivative of energy) ) i get > > different answer. > > What is your suggestion? > > Thanks for your reply. > > > > Mahdi Mirnezhad > > Msc student of Mechanics > > Guilan University. > > > > > > > > On 10/7/10, Mahdi Mirnezhad wrote: > > > >> Dear all, > >> I calculated Young's modulusfor graphene and i got correct answer but > >> when I want to calculate Young's modulus for CNT(3,3) for a axial > >> strain with the same condition (same PS) i got a wrong answer? > >> Any suggestion appreciated, > >> tanks > >> > >> mahdi mirnezhade > >> > >> > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ------------------------------ > > Message: 5 > Date: Tue, 12 Oct 2010 15:07:28 +0200 > From: Stefano de Gironcoli > Subject: Re: [Pw_forum] cohesive energy > To: PWSCF Forum > Message-ID: <4CB45D90.9030502 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > the cohesive energy is the energy per atom of the bulk minus the energy > of an isolated atom. > stefano > > Shyam Khambholja wrote: > > Hello all, > > scf calculation can give us total energy. but how to > calculate > > cohesive energy of elements like aluminium from total energy ? thanks in > > advance > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ------------------------------ > > Message: 6 > Date: Tue, 12 Oct 2010 18:02:00 +0000 > From: "Kiss, Ioan" > Subject: [Pw_forum] pw.x crash on LSF/mvapich > To: "pw_forum at pwscf.org" > Message-ID: > < > C2A03FEA95390F46839DC92BB46F57741D19C449 at e14mdb-01.zdv.Uni-Mainz.DE> > Content-Type: text/plain; charset="iso-8859-1" > > Dear PWSCF users and developers, > > I have a problem running pw.x in our computer center. > The MPI environment is mvapich_1.1, the queuing system is LSF, and I have > compiled PWSCF with the Intel compiler suite together with MKL libraries. > The threading via MKL is turned off by exporting OMP_NUM_THREADS=1. > The machines are 8 core Xeons with QDR Infiniband and 48GB of ECC > memory/node. > > I would like to perform some geometry optimizations on Cd doped > CuInSe2 with PWSCF version 4.1.2. > The FFT grid for the respective slab is 150:150:144, and it does run > on 24 CPUs (i.e. 3 nodes with 8 cores). > However, by taking the same binary and input file, if I would like to use > 48, 72 > or 144 CPU cores, than the job will crash right after the WFC > initialization: > > Self-consistent Calculation > > iteration # 1 ecut= 25.00 Ry beta=0.70 > Davidson diagonalization with overlap > Signal 15 received. > . > . > . > Signal 15 received. > Job /usr/local/lsf/7.0/linux2.6-glibc2.3-x86_64/bin/mvapich_wrapper > VIADEV_USE_SHMEM_ALLREDUCE=0 > VIADEV_USE_SHMEM_REDUCE=0 VIADEV_USE_SHMEM_BARRIER=0 > DISABLE_RDMA_ALLTOALL=1 > DISABLE_RDMA_ALLGATHER=1 DISABLE_RDMA_BARRIER=1 > MV2_CPU_MAPPING=0:1:2:3:4:5:6:7 ./pwTest.x -in INP-PWSCF > > TID HOST_NAME COMMAND_LINE STATUS > TERMINATION_TIME > ===== ========== ================ ======================= > =================== > 00000 moment1 /usr/local/lsf/l Exit (1) 10/12/2010 > 19:20:36 > . > . > . > 00001 moment1 /usr/local/lsf/l Exit (174) 10/12/2010 > 19:20:36 > > As you can see, I have already tried to deactivate the shared memory > optimizations > implemented in mvapich in the Nemesis routines, but that did not help > either. > Strangely, on the same machine I can run CPMD without any issues, so I am > really wondering > what I am doing wrong or what should I change to fix this problem. I have > tried several different > MKL versions and so forth, but to be honest it seems to me that I just > cannot fix it. > Also, using the same input file and 48-72 CPUs the job will nicely finish > in Juelich supercomputer > center and also in the department's tiny local cluster running OpenMPI. > > Do you have some ideas why the machine under LSF/mvapich is not fully > cooperating with > PWSCF above 24 CPU cores, or what should be done to remedy this issue? > > > Thanks in advance for any helpful comment, > > Janos. > > > ========================================== > 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 > > > End of Pw_forum Digest, Vol 40, Issue 20 > **************************************** > -- Mr. Shyam G Khambholja Reseach student, Depratment of Physics, Sardar Patel University, Gujarat Cell No. : +91 999 888 3867 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101013/8e5430ed/attachment-0001.htm From degironc at sissa.it Wed Oct 13 13:49:50 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 13 Oct 2010 13:49:50 +0200 Subject: [Pw_forum] cohesive energy In-Reply-To: References: Message-ID: <4CB59CDE.5060908@sissa.it> Dear Shyam Khambholja, PLEASE DO NOT REPLY TO A DIGEST MESSAGE: try to keep an informative subject line. > Thank you Prof. Stefano, > how to calculate energy of an isolated > atom ? > > shyam place an atom in a large box and calculate its energy with the same cutoff (wfc and rho) values. pay attention that atoms are often magnetic even if the solid is not and that in order to attain the lowest possible energy rotational symmetry may need to be broken... hence use nspin=2, nosym=.true., starting_wfc=random, tot_magnetization=a few values you think appropriate and chose the lowest energy. stefano Shyam Khambholja wrote: > Hello all, > scf calculation can give us total energy. but how to calculate > cohesive energy of elements like aluminium from total energy ? thanks in > advance > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From marzari at MIT.EDU Wed Oct 13 15:16:58 2010 From: marzari at MIT.EDU (Nicola Marzari) Date: Wed, 13 Oct 2010 14:16:58 +0100 Subject: [Pw_forum] LDA+U calculation, difference in U values of one sort of atom. In-Reply-To: <1286974986.4373.7.camel@nto-2.mn.isp.nsc.ru> References: <1286974986.4373.7.camel@nto-2.mn.isp.nsc.ru> Message-ID: <4CB5B14A.9050309@mit.edu> On 10/13/10 2:03 PM, Maxim wrote: > Dear pwscf users, > > I have obtained Hubbard U values for Ta atoms in Ta2O5 system. The > values are 1.9 eV and 2.8 eV for two not equivalent atoms. I am confused > about such relevant difference in the the values. As I understand > Hubbard U characterizes the sort of atom and its coordination should not > influence on the value. > Could you help me to figure out what is wrong? > > Thank you in advance, > Maxim Dear Maxim, I'd rather take the opposite view - each atom has its own "U", that depends in principle on everything - even as you stretch a bond the U will change, but it is always well-defined, and fully ab-initio (following the Cococcioni/de Gironcoli PRB 2005). Some delicate points to consider are the fact that you cannot really compare energies for different values of U, in the functional, and so you need, at the end, to choose an average U that is as much as possible in the right ballpark. Note that in most cases that works very well, but if you go through significant changes in coordination/bond breaking, you might go through electronic states where the value of U calculated by linear response is very different from your ballpark. We have written a few things on this with Heather Kulik (PRL and JCP). nicola --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From sd.wang000 at gmail.com Wed Oct 13 16:01:38 2010 From: sd.wang000 at gmail.com (shudong wang) Date: Wed, 13 Oct 2010 22:01:38 +0800 Subject: [Pw_forum] About fhi2UPF.x Message-ID: Dear developers and users: I want to use fhi2upf.x to convert 27-Co.LDA.fhi to upf format, but I have some questions: 1.What the wavefunction1-4 should I write? For my Co atom, which is right below? Wavefunction # 1: label, occupancy > 4S 2 Wavefunction # 2: label, occupancy > 4P 0 Wavefunction # 3: label, occupancy > 3D 7 Wavefunction # 4: label, occupancy > 4F 0 or Wavefunction # 1: label, occupancy > 3S 2 Wavefunction # 2: label, occupancy > 3P 6 Wavefunction # 3: label, occupancy > 4S 2 Wavefunction # 4: label, occupancy > 3D 7 How can I dicide the label for different atom? What is the "rule" for this? Another quetion: If my converted pp is not precise, how can I solve this? Which parameters should I change to enhance the precision?? Thanks! SDWang Southeast University in Nanjing,China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101013/5fd7b415/attachment.htm From giannozz at democritos.it Wed Oct 13 16:52:59 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 13 Oct 2010 16:52:59 +0200 Subject: [Pw_forum] About fhi2UPF.x In-Reply-To: References: Message-ID: <4CB5C7CB.9070409@democritos.it> shudong wang wrote: > I want to use fhi2upf.x to convert 27-Co.LDA.fhi to upf format, but I > have some questions: > 1.What the wavefunction1-4 should I write? you should ask this to whoever generated that pseudopotential. The FHI format does not contain all the info needed to be used with other codes. You should in any case know how many valence electrons there are. Occupancies are used only for starting the calculation and are not critical. The correct angular momentum is important. I think it is s,p,d,f, in this order, but no warranty. > If my converted pp is not precise, how can I solve this? Which > parameters should I change to enhance the precision?? this is a big question that doesn't have a quick answer. Please have a look at the atomic_doc/pseudo-gen.pdf file P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From sclauzer at sissa.it Wed Oct 13 17:09:37 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 13 Oct 2010 17:09:37 +0200 Subject: [Pw_forum] About fhi2UPF.x In-Reply-To: <4CB5C7CB.9070409@democritos.it> References: <4CB5C7CB.9070409@democritos.it> Message-ID: <12D71F37-39DB-443F-85FF-0F5F22D58DDD@sissa.it> Il giorno 13/ott/2010, alle ore 16.52, Paolo Giannozzi ha scritto: > shudong wang wrote: > >> I want to use fhi2upf.x to convert 27-Co.LDA.fhi to upf format, but I >> have some questions: >> 1.What the wavefunction1-4 should I write? > > you should ask this to whoever generated that pseudopotential. > The FHI format does not contain all the info needed to be used > with other codes. > > You should in any case know how many valence electrons there > are. Occupancies are used only for starting the calculation > and are not critical. The correct angular momentum is important. > I think it is s,p,d,f, in this order, but no warranty. I think Paolo is right: for every element, in the corresponding PP there is one projector per angular momentum l, for l=0,1,2,3, and they should be stored in that ordered. To check that everything is OK, one could first convert from FHI to UPF (as you already did), then extract the wavefunctions using read_upf_to file.x . The wavefunctions on output can be compared to those obtained from an all-electron calculation for the same element, to see if they match for r > r_core. HTH GS > > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > 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/20101013/b0718000/attachment.htm From giannozz at democritos.it Wed Oct 13 17:35:44 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 13 Oct 2010 17:35:44 +0200 Subject: [Pw_forum] pw.x crash on LSF/mvapich In-Reply-To: References: Message-ID: <4CB5D1D0.1060307@democritos.it> Kiss, Ioan wrote: > Thanks in advance for any helpful comment, unfortunately I have only a useless comment, and it is the one in the FAQ: 11.5.0.5 Why is my parallel job crashing with mysterious errors? Mysterious, unpredictable, erratic errors in parallel execution are almost always coming from bugs in the compiler or/and in the MPI libraries and sometimes even to flacky hardware. Sorry, not our fault. A slightly expanded version: http://www.quantum-espresso.org/user_guide/node50.html#SECTION0001110120000000000000 P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From m_pazoki at physics.sharif.edu Thu Oct 14 13:27:56 2010 From: m_pazoki at physics.sharif.edu (meysam pazoki) Date: Thu, 14 Oct 2010 14:57:56 +0330 Subject: [Pw_forum] a questoin about pressure and bulk modulus of system Message-ID: Dear PWSCF users I have a queston about bulk modulus and pressure of a system. We know from thermodynamics that the energy of our electronic system is E=TS-PV+? N.In the zero temrature(T=0) we have E=-PV+?N and p=-?E/?v.In the limit of born openhimer approximation with freezed ions, we can calculate the pressure of our system(electrons+ions) by partial derrivative of energy with respect to volume of system.But in literature I see that calculate pressure from this term: p=-dE/dV and neglect the ?E/?? term.Is it correct? In the zero temrature chemical potential is equal to fermi energy and We should expect that the fermi energy have no changes by variation in volume of system.Is it correct for finite temratures,too? Best Regards Meysam Pazoki SUT -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101014/47d8a52e/attachment.htm From m_pazoki at physics.sharif.edu Thu Oct 14 13:38:56 2010 From: m_pazoki at physics.sharif.edu (meysam pazoki) Date: Thu, 14 Oct 2010 15:08:56 +0330 Subject: [Pw_forum] enthalpy of adsorbtion of o2 molecule on a ZnO supercell Message-ID: Dear PWSCF users I want to calculte the enthalpy of adsorbtion of o2 molecule on the surface of a ZnO.Can i use variable cell relaxation for the supercell and use the enthalpy that printed in output file? I can also run a series of scf jobs with different cell volumes,and then calculate the pressure of system from E-V diagram and then calculate enthalpy by H=E+PV from my data.Is it also true? Thanks Best Regards Meysam Pazoki SUT -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101014/05c43a74/attachment.htm From mohnish.iitk at gmail.com Thu Oct 14 19:30:13 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Thu, 14 Oct 2010 23:00:13 +0530 Subject: [Pw_forum] enthalpy of adsorbtion of o2 molecule on a ZnO supercell In-Reply-To: References: Message-ID: Dear Meysam, First you relax the supecell using "relax" calculation, it will make all the atoms to attain an equilibrium position. Then adsorb the atom (make it close enough so that your surface is interacting with the adorbate) and make the "relaax" calculation again. The energy that you get from latter step subtract the "former energy of the supercell+energy of the isolated adsorbate"..This difference should give the adsorption energy. In fact I have not done any adsorption calculations but intuitively what I have said seems correct to me. On Thu, Oct 14, 2010 at 5:08 PM, meysam pazoki wrote: > Dear PWSCF users > > I want to calculte the enthalpy of adsorbtion of o2 molecule on the surface > of a ZnO.Can i use variable cell relaxation for the supercell and use the > enthalpy that printed in output file? > I can also run a series of scf jobs with different cell volumes,and then > calculate the pressure of system from E-V diagram and then calculate > enthalpy by H=E+PV from my data.Is it also true? > > Thanks > Best Regards > Meysam Pazoki > SUT > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101014/880f149b/attachment.htm From trambui at u.boisestate.edu Thu Oct 14 21:14:57 2010 From: trambui at u.boisestate.edu (Tram Bui) Date: Thu, 14 Oct 2010 13:14:57 -0600 Subject: [Pw_forum] Pw_forum Digest, Vol 40, Issue 20 In-Reply-To: References: Message-ID: Hi, My name is Tram Bui and i'm new to the forum so i'm not quite sure how the Q&A work, but today I want to try the forum with my very first question is that: If i want to calculate the total energy based on lattice parameters of SiC, how do you determine (or find) the ecutoff (kinetic energy cutoff of wave function) value for a material structure such as SiC? Thank you, Tram On Wed, Oct 13, 2010 at 4:54 AM, Shyam Khambholja wrote: > Thank you Prof. Stefano, > how to calculate energy of an isolated > atom ? > > shyam > > > On Wed, Oct 13, 2010 at 2:32 PM, wrote: > >> 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. Re: Pw_forum Digest, Vol 40, Issue 19 (matteo calandra) >> 2. cohesive energy (Shyam Khambholja) >> 3. Re: Question about Young's modulus (Mahdi Mirnezhad) >> 4. Re: Question about Young's modulus (Stefano de Gironcoli) >> 5. Re: cohesive energy (Stefano de Gironcoli) >> 6. pw.x crash on LSF/mvapich (Kiss, Ioan) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 12 Oct 2010 10:14:42 +0200 >> From: matteo calandra >> Subject: Re: [Pw_forum] Pw_forum Digest, Vol 40, Issue 19 >> To: pw_forum at pwscf.org >> Message-ID: <20101012101442.84091vx35nxcb3zm at www1.impmc.upmc.fr> >> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; >> format="flowed" >> >> Dear Min Wu, >> >> I think you should sit down a bit and try to solve this issue >> by yourself. This is not a problem concerning the code as you would have >> the same problem with any other code, but it concerns basic >> physics and group theory. >> In the future we plan to write a program to find the isotropic cross >> section >> with the sallest number of calculations possible from the knowledge of >> the symmetries of the lattice. >> However this is not yet done (I am not aware of any program doing this). >> >> So, as I always do in these case, you should si down,try to understand >> Ch. Bouder's paper and find the polarization vectors necessary to >> obtain the isotropic cross section. >> >> M. >> >> > >> > Message: 6 >> > Date: Tue, 12 Oct 2010 14:59:33 +0800 >> > From: "wumindt2" >> > Subject: Re: [Pw_forum] Xspectra calculation (wumindt2) >> > To: pw_forum at pwscf.org >> > Message-ID: >> > Content-Type: text/plain; charset="gb2312" >> > >> > Dear Matteo, >> > >> > Thanks for the information, i read the C. Brouder the paper a little >> bit. >> > I'am still not sure how to choose the polarization vector. >> > For instance, we have a crystal with spacegroup of P42/MNM, point >> > group of 4/mmm. >> > According to the Table in C. Brouder's paper, this is a dichroism >> compound. >> > Thus, how can we choose the polarization vector when calculating the XAS >> > of this compound? >> > Can you please show me how? >> > >> > Thanks so much! >> > >> > Cheers, >> > >> > Min Wu >> > 2010-10-12 >> > >> > >> >> From: Matteo Calandra >> >> Reply-To: PWSCF Forum >> >> To: pw_forum at pwscf.org >> >> Subject: Re: [Pw_forum] Xspectra calculation (wumindt2) >> >> Date: Mon, 11 Oct 2010 10:08:16 +0200 >> >> >> >> Dear >> >> >> >> I assume you are talking of the dipolar part only. >> >> For the quadrupolar it is substantially more complicate. >> >> The number of independent calculations that you have >> >> to perform to obtain the isotropic cross section (powder) >> >> depends on the point group of the space group >> >> of your crystal. >> >> It is 1 for a cubic or tetraedric crystal, >> >> 2 for a uniaxial crystal and it is 3, 4, 6 for a biaxial >> >> (ot trichroic) crystal. >> >> I suggest you read >> >> C. Brouder J. Phys.: Condens. Matter 2 (1990) 701-738 >> >> for more details. >> >> >> >> M. >> >> >> >> >> >>> >> >>> Message: 3 >> >>> Date: Sat, 09 Oct 2010 22:48:53 +0800 >> >>> From: "wumindt2" >> > >> >>> Subject: Re: [Pw_forum] Xspectra calculation >> >>> To: pw_forum at pwscf.org >> >>> Message-ID: >> > >> >>> Content-Type: text/plain; charset="gb2312" >> >>> >> >>> Dear matteo, >> >>> >> >>> Thanks. >> >>> >> >>> For dichroism compound, do we just need the in-plane and the c-axis >> >>> polarization vectors? >> >>> While for trichroism compound, do we need to calculate three different >> >>> polarization vectors? >> >>> Am i right? >> >>> >> >>> Best regards, >> >>> >> >> _______________________________________________ >> >> 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 >> > >> > >> > End of Pw_forum Digest, Vol 40, Issue 19 >> > **************************************** >> > >> >> >> >> ---------------------------------------------------------------- >> This message was sent using IMP, the Internet Messaging Program. >> >> >> >> >> ------------------------------ >> >> Message: 2 >> Date: Tue, 12 Oct 2010 17:36:25 +0700 >> From: Shyam Khambholja >> Subject: [Pw_forum] cohesive energy >> To: pw_forum at pwscf.org >> Message-ID: >> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hello all, >> scf calculation can give us total energy. but how to calculate >> cohesive energy of elements like aluminium from total energy ? thanks in >> advance >> >> -- >> Mr. Shyam G Khambholja >> Research student, >> Depratment of Physics, >> Sardar Patel University, Gujarat >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://www.democritos.it/pipermail/pw_forum/attachments/20101012/8cf3d73e/attachment.html >> >> ------------------------------ >> >> Message: 3 >> Date: Tue, 12 Oct 2010 16:25:00 +0330 >> From: Mahdi Mirnezhad >> Subject: Re: [Pw_forum] Question about Young's modulus >> To: pw_forum >> Message-ID: >> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> Dear Developers, >> I think there is a problem in the calculation of stress in Quantum >> Esperesso. This problem concern with the volume of unit cell. For bulk >> structures there is no problem for determination of Volume but in the >> super cell method code calculate stress according to unit cell volume >> so when i calculate Young's Modulus for graphene with two method >> (strees/strain or (E=(1/V)*second derivative of energy) ) i get >> different answer. >> What is your suggestion? >> Thanks for your reply. >> >> Mahdi Mirnezhad >> Msc student of Mechanics >> Guilan University. >> >> >> >> On 10/7/10, Mahdi Mirnezhad wrote: >> > Dear all, >> > I calculated Young's modulusfor graphene and i got correct answer but >> > when I want to calculate Young's modulus for CNT(3,3) for a axial >> > strain with the same condition (same PS) i got a wrong answer? >> > Any suggestion appreciated, >> > tanks >> > >> > mahdi mirnezhade >> > >> >> >> ------------------------------ >> >> Message: 4 >> Date: Tue, 12 Oct 2010 15:01:29 +0200 >> From: Stefano de Gironcoli >> Subject: Re: [Pw_forum] Question about Young's modulus >> To: PWSCF Forum >> Message-ID: <4CB45C29.6070908 at sissa.it> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> for a 2-D system I guess that the definition of stress will involve the >> area and not the volume ... >> stefano >> >> >> Mahdi Mirnezhad wrote: >> > Dear Developers, >> > I think there is a problem in the calculation of stress in Quantum >> > Esperesso. This problem concern with the volume of unit cell. For bulk >> > structures there is no problem for determination of Volume but in the >> > super cell method code calculate stress according to unit cell volume >> > so when i calculate Young's Modulus for graphene with two method >> > (strees/strain or (E=(1/V)*second derivative of energy) ) i get >> > different answer. >> > What is your suggestion? >> > Thanks for your reply. >> > >> > Mahdi Mirnezhad >> > Msc student of Mechanics >> > Guilan University. >> > >> > >> > >> > On 10/7/10, Mahdi Mirnezhad wrote: >> > >> >> Dear all, >> >> I calculated Young's modulusfor graphene and i got correct answer but >> >> when I want to calculate Young's modulus for CNT(3,3) for a axial >> >> strain with the same condition (same PS) i got a wrong answer? >> >> Any suggestion appreciated, >> >> tanks >> >> >> >> mahdi mirnezhade >> >> >> >> >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> >> >> ------------------------------ >> >> Message: 5 >> Date: Tue, 12 Oct 2010 15:07:28 +0200 >> From: Stefano de Gironcoli >> Subject: Re: [Pw_forum] cohesive energy >> To: PWSCF Forum >> Message-ID: <4CB45D90.9030502 at sissa.it> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> the cohesive energy is the energy per atom of the bulk minus the energy >> of an isolated atom. >> stefano >> >> Shyam Khambholja wrote: >> > Hello all, >> > scf calculation can give us total energy. but how to >> calculate >> > cohesive energy of elements like aluminium from total energy ? thanks >> in >> > advance >> > >> > >> > ------------------------------------------------------------------------ >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> >> >> ------------------------------ >> >> Message: 6 >> Date: Tue, 12 Oct 2010 18:02:00 +0000 >> From: "Kiss, Ioan" >> Subject: [Pw_forum] pw.x crash on LSF/mvapich >> To: "pw_forum at pwscf.org" >> Message-ID: >> < >> C2A03FEA95390F46839DC92BB46F57741D19C449 at e14mdb-01.zdv.Uni-Mainz.DE> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Dear PWSCF users and developers, >> >> I have a problem running pw.x in our computer center. >> The MPI environment is mvapich_1.1, the queuing system is LSF, and I have >> compiled PWSCF with the Intel compiler suite together with MKL libraries. >> The threading via MKL is turned off by exporting OMP_NUM_THREADS=1. >> The machines are 8 core Xeons with QDR Infiniband and 48GB of ECC >> memory/node. >> >> I would like to perform some geometry optimizations on Cd doped >> CuInSe2 with PWSCF version 4.1.2. >> The FFT grid for the respective slab is 150:150:144, and it does run >> on 24 CPUs (i.e. 3 nodes with 8 cores). >> However, by taking the same binary and input file, if I would like to use >> 48, 72 >> or 144 CPU cores, than the job will crash right after the WFC >> initialization: >> >> Self-consistent Calculation >> >> iteration # 1 ecut= 25.00 Ry beta=0.70 >> Davidson diagonalization with overlap >> Signal 15 received. >> . >> . >> . >> Signal 15 received. >> Job /usr/local/lsf/7.0/linux2.6-glibc2.3-x86_64/bin/mvapich_wrapper >> VIADEV_USE_SHMEM_ALLREDUCE=0 >> VIADEV_USE_SHMEM_REDUCE=0 VIADEV_USE_SHMEM_BARRIER=0 >> DISABLE_RDMA_ALLTOALL=1 >> DISABLE_RDMA_ALLGATHER=1 DISABLE_RDMA_BARRIER=1 >> MV2_CPU_MAPPING=0:1:2:3:4:5:6:7 ./pwTest.x -in INP-PWSCF >> >> TID HOST_NAME COMMAND_LINE STATUS >> TERMINATION_TIME >> ===== ========== ================ ======================= >> =================== >> 00000 moment1 /usr/local/lsf/l Exit (1) 10/12/2010 >> 19:20:36 >> . >> . >> . >> 00001 moment1 /usr/local/lsf/l Exit (174) 10/12/2010 >> 19:20:36 >> >> As you can see, I have already tried to deactivate the shared memory >> optimizations >> implemented in mvapich in the Nemesis routines, but that did not help >> either. >> Strangely, on the same machine I can run CPMD without any issues, so I am >> really wondering >> what I am doing wrong or what should I change to fix this problem. I have >> tried several different >> MKL versions and so forth, but to be honest it seems to me that I just >> cannot fix it. >> Also, using the same input file and 48-72 CPUs the job will nicely finish >> in Juelich supercomputer >> center and also in the department's tiny local cluster running OpenMPI. >> >> Do you have some ideas why the machine under LSF/mvapich is not fully >> cooperating with >> PWSCF above 24 CPU cores, or what should be done to remedy this issue? >> >> >> Thanks in advance for any helpful comment, >> >> Janos. >> >> >> ========================================== >> 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 >> >> >> End of Pw_forum Digest, Vol 40, Issue 20 >> **************************************** >> > > > > -- > Mr. Shyam G Khambholja > Reseach student, > Depratment of Physics, > Sardar Patel University, Gujarat > Cell No. : +91 999 888 3867 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Tram Bui B.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/20101014/bbb3b74b/attachment-0001.htm From ttduyle at gmail.com Thu Oct 14 21:33:34 2010 From: ttduyle at gmail.com (Duy Le) Date: Thu, 14 Oct 2010 15:33:34 -0400 Subject: [Pw_forum] Pw_forum Digest, Vol 40, Issue 20 In-Reply-To: References: Message-ID: On Thu, Oct 14, 2010 at 3:14 PM, Tram Bui wrote: > Hi, Welcome! > ? My name is Tram Bui and i'm new to the forum so i'm not quite sure how the > Q&A work, You can email any question to the mailing list. Make sure to use a clear subject and sign in the end of your email. If you reply from a PW-forum digest, please remove all irrelevant content so that other member can follow easily. >but today I want to try the forum with my very first question is > that: If i want to calculate the total energy based on lattice parameters of > SiC, how do you determine (or find) the ecutoff (kinetic energy cutoff of > wave function) value for a material structure such as SiC? You need to test this value. The total energy of a system will converge as increasing energy cutoff. > > Thank you, > Tram > > -- > Tram Bui > > B.S. Materials Science & Engineering > trambui at u.boisestate.edu -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" From giannozz at democritos.it Thu Oct 14 21:48:02 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 14 Oct 2010 21:48:02 +0200 Subject: [Pw_forum] Choice of cutoff (was: Pw_forum Digest, Vol 40, Issue 20) In-Reply-To: References: Message-ID: <2664414B-5483-493F-AFE8-0231BDB375D7@democritos.it> On Oct 14, 2010, at 21:14 , Tram Bui wrote: > My name is Tram Bui and i'm new to the forum so i'm not quite > sure how the Q&A work definitely so: you have already violated a number of basic rules, such as - choose a meaningful subject - do not use "reply" to start a new thread: it will confuse the ordering of messages into threads - do not use "reply" with a Digest!!! - do not quote a bunch of irrelevant stuff in your reply > how do you determine (or find) the ecutoff (kinetic energy cutoff > of wave function) > value for a material structure such as SiC? the answer is left as an exercise to the reader. Really: you have to decide a convergence criterion on some physical property, then verify which cutoff gives you a converged answer. As a rule, it depends a lot upon pseudopotentials For more: http://www.quantum-espresso.org/learn.php P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From prasenjit.jnc at gmail.com Fri Oct 15 06:04:41 2010 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Fri, 15 Oct 2010 09:34:41 +0530 Subject: [Pw_forum] enthalpy of adsorbtion of o2 molecule on a ZnO supercell In-Reply-To: References: Message-ID: Dear Meysam, When you do a supercell calculation you do not need to relax the lattice parameters because the cell vectors perpendicular to the surface is ficticious in the sense that you simply use a value large enough so that the periodic images perpendicular to the surface do not interact with each other. The inplane lattice vectors are determined by your theoretically obtained bulk lattice parameter for ZnO. So you should follow the procedure suggested by Mohnish. Just another addition, all the calculations, the ZnO surface, O2+ZnO surface and the O2 molecule in vacuum (the gas phase) should be done using the same supercell. Also be careful when you do calculations for O2 molecule in gas phase, you should do a spin polarized calculation becase the ground state of O2 is spin triplet. Hope this helps. Prasenjit. On 14 October 2010 23:00, mohnish pandey wrote: > Dear Meysam, > ?? ? ? ? ? ? ? ? ? ? ? ?First you relax the supecell using "relax" > calculation, it will make all the atoms to attain an equilibrium position. > Then ?adsorb the atom (make it close enough so that your surface is > interacting with the adorbate) and make the "relaax" calculation again. The > energy that you get from latter step subtract the "former energy of the > supercell+energy of the isolated adsorbate"..This difference should give the > adsorption energy. In fact I have not done any adsorption calculations but > intuitively what I have said seems correct to me. > > On Thu, Oct 14, 2010 at 5:08 PM, meysam pazoki > wrote: >> >> Dear PWSCF users >> >> I want to calculte the enthalpy of adsorbtion of o2 molecule on the >> surface of a ZnO.Can i use variable cell relaxation for the supercell and >> use the enthalpy that printed in output file? >> I can also run a series of scf jobs with different cell volumes,and then >> calculate the pressure of system from E-V diagram and then calculate >> enthalpy by H=E+PV from my data.Is it also true? >> >> Thanks >> Best Regards >> Meysam Pazoki >> SUT >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > Regards, > MOHNISH, > ----------------------------------------------------------------- > Mohnish Pandey > Y6927262,5th Year dual degree student, > Department of Chemical Engineering, > IIT KANPUR, UP, INDIA > ----------------------------------------------------------------- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- PRASENJIT GHOSH, Assistant Professor, IISER Pune, First floor, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan Pune, Maharashtra 411021, India Phone: +91 (20) 2590 8203 Fax: +91 (20) 2589 9790 From 1009ukumar at gmail.com Fri Oct 15 07:42:39 2010 From: 1009ukumar at gmail.com (sonu kumar) Date: Fri, 15 Oct 2010 11:12:39 +0530 Subject: [Pw_forum] problem in generation of PP with semicore states? Message-ID: Dear All QE users and developers, I have problems with generation of PP for Cu(+0.5) with TM pseudization scheme , when i include semicore states. Without semicore state, i don't have any problem. But when i include 3s and 3p states in valence, error comes like- negative rho, problem in finding qi coeffs. Rho problem is solved with PSQ aug functions, but finding of qi coeffs is still there. Please see below for input file---------------------------- &input title='Cu' zed=29, eminld=-10.0, emaxld=3.0, rlderiv=2.5, nld=3, iswitch=3, config="[Ar] 3d9.0 4s1.3 4p0.2" dft='LDA' rel=1, / &inputp pseudotype=3, nlcc=.true., new_core_ps = .true. rcore=0.6000 lloc=-1, rcloc=2.0000, file_pseudopw='Cu_1.UPF' zval=19, lpaw=.false. lnc2paw=.false. which_augfun ='PSQ', rmatch_augfun= 2.0000, author='sk', tm =.true. !rho0=0.01, !nX n l occ nrg rmin rcut / 8 3S 1 0 2.00 0.00 0.650 3.0000 1 3P 2 1 6.00 0.00 0.650 3.0000 1 3D 3 2 9.00 0.00 0.650 2.0000 1 !1.9000 1 3D 3 2 0.00 0.10 0.650 2.0000 1 !1.9000 1 4S 1 0 1.30 0.00 2.000 3.2000 1 4S 1 0 0.00 1.95 2.000 3.2000 1 4P 2 1 0.20 0.00 2.600 3.6000 1 4P 2 1 0.00 0.05 2.600 3.6000 1 ! doubt: ! !is it ok if I take one 3s and one 4s so that two proj/angular !momentum. similarly for for 3p and 4p ? -------------------------input file end------------------------------------------- i shall be very thankful to you for your help. With Kind regards, Sonu Kumar Phd Student, Physics Department Indian Institute of Technology Delhi-110016, India web:-http://www.iitd.ac.in/ From baroni at sissa.it Fri Oct 15 08:10:53 2010 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 15 Oct 2010 08:10:53 +0200 Subject: [Pw_forum] a questoin about pressure and bulk modulus of system In-Reply-To: References: Message-ID: <35BBAB56-61BB-4F76-9771-2E404883DDEC@sissa.it> Dear Meysam, your post seems the result of an intricate intertwining of thermodynamics, quantum mechanics, and condensed matter misunderstandings ... Let me try to sort them out. 1) In the Born-Oppenheimer approximation, which you are correctly referring too, you can just forget about electronic degrees of freedom, when dealing with the thermodynamics of the system. The chemical potential that may (or may not, see below) appear in your thermodynamics equation has nothing to do with the Fermi energy, in this case: it is the energy required to add or subtract one "particle" (atom, molecule) to/from your system. In fact, you should have one different chemical potential per atomic/molecular species. 2) When quoting any thermodynamic relation, you should always keep in mind which are the "natural" variables you are adopting. In standard treatments, the "natural" variables of the energy as an extensive quantity are the volume, the entropy, and the number of of particles: E=E(S,V,N) [see e.g. D. Chandler, Introduction to Modern Statistical Mechanics, Oxford University Press, New York (1987), Chapt. 1]. This being the case, the pressure is defined as p=-?E/?V - no other derivatives are involved in this definition. 2') The thermodynamic relation you are quoting looks very obscure to me. Where have you taken it from? Which "natural" variables would the energy depend on? 3) All the above is a complication of real life. In real-life DFT calculations (which, I presume, are what you are interested in) the number of atoms is fixed, and the temperature (and, hence, the entropy) is zero (unless you do molecular dynamics / Monte Carlo, which I understand is not the case). Hence the energy is a function of the volume alone (as well as of any other applied field, but this would open another thread), and the pressure is just the negative of the derivative of the energy with respect to the only extensive quantity it can depend on, i.e. the volume ... as simple as that! 4) The Fermi energy of any metal does depend on volume (think of the simple jellium model of simple metals), both at zero and at finite temperature, but, as said, this has nothing to do with the calculation of the pressure (but for the fact that when calculating the total energy of a metal as a function of volume, you should recalculate the Fermi energy for every volume you are considering). Hope this clarifies/helps a bit Stefano B. On Oct 14, 2010, at 1:27 PM, meysam pazoki wrote: > Dear PWSCF users > > I have a queston about bulk modulus and pressure of a system. > We know from thermodynamics that the energy of our electronic > system is E=TS-PV+? N.In the zero temrature(T=0) we have E=-PV+?N and p=-?E/?v.In the limit of born openhimer approximation with freezed ions, we can calculate the pressure of our system(electrons+ions) by partial derrivative of energy with respect to volume of system.But in literature I see that calculate pressure from this term: p=-dE/dV and neglect the ?E/?? term.Is it correct? > In the zero temrature chemical potential is equal to fermi energy and We should expect that the fermi energy have no changes by variation in volume of system.Is it correct for finite temratures,too? > > Best Regards > Meysam Pazoki > SUT > _______________________________________________ > 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 Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101015/f2dcd4a6/attachment-0001.htm From georgemanyali at gmail.com Fri Oct 15 10:12:04 2010 From: georgemanyali at gmail.com (george manyali) Date: Fri, 15 Oct 2010 11:12:04 +0300 Subject: [Pw_forum] perdew zunger pseudo potential for Sc,Cr and V. Message-ID: Hi everyone, Does any one know where I can get perdew zunger pseudo potential for Sc,Cr and V.They are not included in the Quantum espresso pseudo potential package. Thanks G S .MANYALI POSTGRADUATE STUDENT KENYA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101015/4b39f5ee/attachment.htm From m_pazoki at physics.sharif.edu Fri Oct 15 10:48:36 2010 From: m_pazoki at physics.sharif.edu (meysam pazoki) Date: Fri, 15 Oct 2010 12:18:36 +0330 Subject: [Pw_forum] enthalpy of adsorbtion of o2 molecule on a ZnO supercell Message-ID: Dear mohnish and Prasenjit Thanks for your good answers ,I have another question :"Is enthalpy of adsorbtion equals to energy of adsorbtion?" I want to calculate enthalpy of adsorbtion and your answers are about energy of adsorbtion. Regards Meysam Pazoki SUT -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101015/f31de22a/attachment.htm From m_pazoki at physics.sharif.edu Fri Oct 15 11:27:20 2010 From: m_pazoki at physics.sharif.edu (meysam pazoki) Date: Fri, 15 Oct 2010 12:57:20 +0330 Subject: [Pw_forum] a questoin about pressure and bulk modulus of system In-Reply-To: References: Message-ID: Dear Stefano Thanks for your good answer.I am an experimentalist and I learn good new things from your answer. My mistake was that I didnt know in calculation of pressure,we neglect electronic degrres of freedom(I will be thankfull to you,if you introduce a reference about this subject). I have another question :Is these terms are right? E=-PV+uN+TS => dE=-PdV-VdP+udN+Ndu+Tds+SdT and we know from first law of thermodynamics that dE=-PdV+udN+Tds and we conclude that -VdP+Ndu+SdT=0 and in zero temrature and fixed number of atoms we have dE=-PdV and P=-dE/dV Thanks Meysam pazoki SUT -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101015/acd26890/attachment.htm From prasenjit.jnc at gmail.com Fri Oct 15 13:18:59 2010 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Fri, 15 Oct 2010 16:48:59 +0530 Subject: [Pw_forum] enthalpy of adsorbtion of o2 molecule on a ZnO supercell In-Reply-To: References: Message-ID: Dear Meysam, In principle they are different quantities. Generally enthalpy (H) is related to the internal energy (E) as H=E+PV (P=pressure V=volume)....so change in enthalpy upon adsorption of a molecule (enthalpy of adsorption) is given by dH=dE+PdV+VdP where dE is the adsorption energy for your case (and is -ve if the molecule binds). Now if you consider your system to be the surface with molecule adsorbed on it, then for a given coverage, the volume & pressure is constant.....so in that case dH=-dE, i.e. the enthalpy of adsorption is -(adsorption energy) Prasenjit On 15 October 2010 14:18, meysam pazoki wrote: > Dear mohnish and Prasenjit > > Thanks? for your good answers ,I have another question :"Is enthalpy of > adsorbtion equals to energy of adsorbtion?" > I want to calculate enthalpy of adsorbtion and your answers are about energy > of adsorbtion. > > Regards > Meysam Pazoki > SUT > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- PRASENJIT GHOSH, Assistant Professor, IISER Pune, First floor, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan Pune, Maharashtra 411021, India Phone: +91 (20) 2590 8203 Fax: +91 (20) 2589 9790 From baroni at sissa.it Fri Oct 15 16:18:21 2010 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 15 Oct 2010 16:18:21 +0200 Subject: [Pw_forum] a questoin about pressure and bulk modulus of system In-Reply-To: References: Message-ID: <8B6DB539-A808-4F1D-AFD2-1CFE459EFE94@sissa.it> On Oct 15, 2010, at 11:27 AM, meysam pazoki wrote: > > Dear Stefano > > Thanks for your good answer.I am an experimentalist and I learn good new things from your answer. > My mistake was that I didnt know in calculation of pressure,we neglect electronic degrres of freedom(I will be thankfull to you,if you introduce a reference about this subject). I am sorry to keep correcting you. I don't think I ever said that you can disregard the electronic degrees of freedom when calculating the pressure. I said you can neglect them *in the BO approximation*, when dealing with thermodynamics. I could have been more precise by saying that when doing thermodynamics in the BO approximation, you can safely assume that the "electronic temperature" is zero, i.e. that electrons can be considered in their ground state. In the BO approximations, electrons are kind of slaves who keep atoms together, but do participate in the (thermo) dynamics. The fact that they are slave does imply that you can do without them ... > I have another question :Is these terms are right? > E=-PV+uN+TS => dE=-PdV-VdP+udN+Ndu+Tds+SdT NO - this is nonsense. Nor the energy, nor its differential are what you write. As said in my previous post, the energy is an extensive function of the three extensive quantities S,V,N: E=E(S,V,N) ? -PV+uN+TS. In calculating its differential, you should vary only the variables it depends upon (i.e., S,V,N). > and we know from first law of thermodynamics that dE=-PdV+udN+Tds This is correct, in fact it is different from the expression you gave before. Form this relation you can conclude that P=-?E/?V; T=?E/?S, ?=?E/?N. The first relation is what you need > and we conclude that -VdP+Ndu+SdT=0 NO - see above > and in zero temrature and fixed number of atoms > we have dE=-PdV and P=-dE/dV right, for the wrong reason (i.e. your conclusion is correct, the argument you use to derive it is not) > Thanks You are welcome. You asked a well posed question, and it is a pleasure to answer well posed questions. I think you should study some basic thermodynamics / statistical mechanics. Chandler's book is a very good starting point. Regards - SB --- 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 Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101015/b53e3557/attachment.htm From cristian.degliesposti at unibo.it Fri Oct 15 16:28:15 2010 From: cristian.degliesposti at unibo.it (Cristian Degli Esposti Boschi) Date: Fri, 15 Oct 2010 16:28:15 +0200 Subject: [Pw_forum] Bond-order-corrected (or BOLS) pseudopotentials Message-ID: <8CEC16238EFDFF43865B9ECB4D43E03147D925ABD5@EXVS01.personale.dir.unibo.it> We would like to understand better the so-called bond order length strength (BOLS) correlation approach [Chang Q. Sun an co-workers, basic ref. is Prog. Solid. State Chem. 35, pag. 1 (2007)] to structures with under-coordinated atoms (surfaces, ribbons, rods, etc.) Sometimes it is stated that the BOLS approach is incorportated with DFT calculations, and in particular quoting from [J. Phys. Chem. C, 112, 18927 (2008)] "...Unfortunately, the presence and polarization of the nonbonding states are hardly described from the self-consistent optimization in DFT or tight-binding approximations at the present because of the limitation of interatomic potentials. Potentials suitable for the broken-bond-induced local strain and quantum trapping that are sometimes several folds deeper than the potential at the usual atomic site in the bulk and potentials suitable for the weak interaction between the nonbonding and the polarized antibonding states are highly desirable for computations." It seems to me that they would call for pseudopotentials corrected by the fact of going to represent atoms with low coordination or nonbonding states/electrons. Typically, in such a situation, the neighboring bonds tend to shrink and the bonding energies (in magnitude) tend to increase. Should one then consider a "BOLS-corrected" pseudpotential? Are you aware of problems of this kind, or is the question correctly posed at all? Thanks again for your time. Cristian From baroni at sissa.it Fri Oct 15 16:45:15 2010 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 15 Oct 2010 16:45:15 +0200 Subject: [Pw_forum] a questoin about pressure and bulk modulus of system In-Reply-To: <8B6DB539-A808-4F1D-AFD2-1CFE459EFE94@sissa.it> References: <8B6DB539-A808-4F1D-AFD2-1CFE459EFE94@sissa.it> Message-ID: <2FE8A085-4E66-4EF8-89AD-268670891C03@sissa.it> On Oct 15, 2010, at 4:18 PM, Stefano Baroni wrote: > dered in their ground state. In the BO approximations, electrons are kind of slaves who keep atoms together, but do participate in the (thermo) what I meant here, of course is that " ... electrons ... do NOT participate ... " sorry for the misunderstanding I may have created SB --- 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 Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101015/1d078663/attachment-0001.htm From cristian.degliesposti at unibo.it Fri Oct 15 16:50:11 2010 From: cristian.degliesposti at unibo.it (Cristian Degli Esposti Boschi) Date: Fri, 15 Oct 2010 16:50:11 +0200 Subject: [Pw_forum] Bond-order-corrected (or BOLS) pseudopotentials Message-ID: <8CEC16238EFDFF43865B9ECB4D43E03147D925ABD7@EXVS01.personale.dir.unibo.it> Sorry for forgetting it in my previous post; my affiliation (now) is: Cristian Degli Esposti Boschi CNR-IMM, Sezione di Bologna, via Gobetti, 101, 40129, Bologna, Italia From baroni at sissa.it Fri Oct 15 17:19:52 2010 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 15 Oct 2010 17:19:52 +0200 Subject: [Pw_forum] a questoin about pressure and bulk modulus of system In-Reply-To: <8B6DB539-A808-4F1D-AFD2-1CFE459EFE94@sissa.it> References: <8B6DB539-A808-4F1D-AFD2-1CFE459EFE94@sissa.it> Message-ID: <6C64873D-9D17-47D7-89AC-B0DA559C502B@sissa.it> Folks: a distinguished colleague of mine just made me notice that if I were a student I would probably fail the first-year thermodynamics exam. Some of my statements are right, but my claims of Meyasam being wrong are partially wrong (and he was therefore partially right!). Let me point out my own mistakes: >> I have another question :Is these terms are right? >> E=-PV+uN+TS Contrary to my claims, this equation is correct, as it is a consequence of Euler's theorem on homogeneous functions [E(?S,?V,?N)=?E(S,V,N) implies E= S ?E/?S + V ?E/?V +N ?E/?N] - Notice that you need Euler's theorem *AND* the definition of T,P,? as energy derivatives to establish the equation. >> => dE=-PdV-VdP+udN+Ndu+Tds+SdT > > NO - this is nonsense. Nor the energy, nor its differential are what you write. As said in my previous post, the energy is an extensive function of the three extensive quantities S,V,N: E=E(S,V,N) ? -PV+uN+TS. In calculating its differential, you should vary only the variables it depends upon (i.e., S,V,N). MY comment is wrong. As said, E=-PV+uN+TS is a consequence of Euler's theorem, and it is legitimate to take the formal differential the way Meyasam did. > >> and we know from first law of thermodynamics that dE=-PdV+udN+Tds > > This is correct, in fact it is different from the expression you gave before. Form this relation you can conclude that P=-?E/?V; T=?E/?S, ?=?E/?N. The first relation is what you need > >> and we conclude that -VdP+Ndu+SdT=0 > > NO - see above RIGHT for a more subtle reason than I was able to guess at first sight the above equation even has a distinguished name: its is know as the Gibbs-Duhem equation > >> and in zero temrature and fixed number of atoms >> we have dE=-PdV and P=-dE/dV > > right, for the wrong reason (i.e. your conclusion is correct, the argument you use to derive it is not) my last negative statement is less wrong than others, in the sense that you do not need the Gibbs-Duhem equation to establish that P=-?E/?V. This relation is instead a definition of the pressure, as the derivative of the energy with respect to one of its natural variables, and it is indeed needed to establish the Gibbs-Duhem equation. Sorry for the mess I may have created. I can only conclude that I could have directed the recommendation to study more thermodynamics to myself in the first place ... In any event, I now know more than I did before, and so I hope will some of you. Thank you for making me (re-) learn something that I had long forgotten ... Stefano B --- 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 Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101015/56c640aa/attachment.htm From kajalmh18 at gmail.com Sat Oct 16 07:54:54 2010 From: kajalmh18 at gmail.com (kajal jindal) Date: Sat, 16 Oct 2010 11:24:54 +0530 Subject: [Pw_forum] calculation of transition level Message-ID: Hi, I want to calculate the transition level with Nitrogen doping in ZnO. For that, I have to calculate the total energy of the defect by substituting O by N in the neutral and single negative (1- ) charge states. I don't have much idea on how to proceed with the calculation of energy in different charge states. I think that in my scf calculation file, within the atomic species I have to use the atomic mass of Nitrogen itself and pseudopotential of oxygen in place of single negative N state. I am really confused as is this the right way for charged species or are there different pseudopotential for ions.Can anybody please guide me in doing so??? sincerely, Miss Kajal (UTA)(University of Delhi) Junior Research Fellow -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101016/43f236f2/attachment.htm From snd2mra at yahoo.com Sat Oct 16 08:56:36 2010 From: snd2mra at yahoo.com (Madan Mithra. L. M) Date: Fri, 15 Oct 2010 23:56:36 -0700 (PDT) Subject: [Pw_forum] EXX on 1D supercells fail - solved In-Reply-To: Message-ID: <876644.64602.qm@web53305.mail.re2.yahoo.com> Dear Prof. Giannozzi, I have found that removing 'ecutrho' from the input file makes the job to run. Thank you - Madan > Date: Thu, 30 Sep 2010 12:40:14 -0700 (PDT) > From: "Madan Mithra. L. M" > Subject: [Pw_forum] EXX on 1D supercells fail > To: pw_forum at pwscf.org > Message-ID: <38919.63978.qm at web53308.mail.re2.yahoo.com> > Content-Type: text/plain; charset=us-ascii > > Dear All, > > I compiled the latest version of pwscf (4.2.1) on IBM > Power5 machine (xlf compiler) as well as on Dell Cluster > (Intel ifort 11.1.056). In both cases, calculation including > EXX (PBE0) fails on 1D supercell. However, the same job ran > without dumping the core with pwscf 4.1.3. Any suggestion ? > I would like to use the latest version as it supports > restarting the EXX calculation. > > Thank you > > - Madan ---------------------------------------- Madan Mithra .L.M Senior Research Fellow Dept.of Physics Indian Institute of Science Bangalore - 560 012 INDIA ......................................... e-mail : mit at physics.iisc.ernet.in : snd2mra at yahoo.com Phone : 91-80-22932313 (Lab) FAX : (080) 360 2602 ----------------------------------------- From m_pazoki at physics.sharif.edu Sat Oct 16 09:36:28 2010 From: m_pazoki at physics.sharif.edu (meysam pazoki) Date: Sat, 16 Oct 2010 11:06:28 +0330 Subject: [Pw_forum] enthalpy of adsorbtion of o2 molecule on a ZnO Message-ID: Dear Prasenjit Thanks indeed for your comment Regards meysam Sharif university of technology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101016/4254ebaa/attachment.htm From farzad_c81 at yahoo.com Sat Oct 16 14:30:38 2010 From: farzad_c81 at yahoo.com (Farzad Molani) Date: Sat, 16 Oct 2010 05:30:38 -0700 (PDT) Subject: [Pw_forum] k_point for sheet in bands calculation Message-ID: <268890.83351.qm@web55701.mail.re3.yahoo.com> Hello, I'm goimg to study electronic stucture of nano sheet and I have a question about the K-point. I think for sheet we need sampling from gamma to K. Is it true? So in bands calculation for k-point I should choice { crystal }. Am I right? I couldn't undrestand about points of { crystal } in k-point from gamma to K. what are these points depends on? 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/20101016/28ed0471/attachment.htm From 1009ukumar at gmail.com Sat Oct 16 15:17:37 2010 From: 1009ukumar at gmail.com (sonu kumar) Date: Sat, 16 Oct 2010 18:47:37 +0530 Subject: [Pw_forum] Again: unable( impossible ) to generation PP with semicore states and NLCC ? Message-ID: Dear All QE users and developers, I am very sorry for this mail again. I am unable generation of PP for Cu with TM (also with rrkj scheme) pseudization scheme , when i include semicore states 3s and 3p and NLCC, after making many-many tries ( variations in rc's, logder, V_loc, matching rad for aug func etc....) The most comman problem is "negative rho " problem. I also want to use PAW , but unfortunately even unable to generate USPP. This is leading me to think (not 100% sure through very limited experience) that atomic code is unable to generate pp with both NLCC and semicore states and also loosing my faith in atomic code. So i need help from PP expert or any one willing to help. Please see below for input file---------------------------- &input title='Cu' zed=29, eminld=-10.0, emaxld=3.0, rlderiv=2.5, nld=3, iswitch=3, config="[Ne] 3s2 3p6 3d10.0 4s0.3 4p0.2" dft='LDA' rel=1, / &inputp pseudotype=3, nlcc=.true., new_core_ps = .true. rcore=0.6000 lloc=-1, rcloc=2.0000, file_pseudopw='Cu_1.UPF' zval=19, lpaw=.false. lnc2paw=.false. which_augfun ='PSQ', rmatch_augfun= 2.0000, author='sk', tm =.true. !rho0=0.01, !nX n l occ nrg rmin rcut / 8 3S 1 0 2.00 0.00 0.650 3.0000 1 3P 2 1 6.00 0.00 0.650 3.0000 1 3D 3 2 10.0 0.00 0.650 2.0000 1 3D 3 2 0.00 0.10 0.650 2.0000 1 4S 1 0 0.30 0.00 2.000 3.2000 1 4S 1 0 0.00 1.95 2.000 3.2000 1 4P 2 1 0.20 0.00 2.600 3.6000 1 4P 2 1 0.00 0.05 2.600 3.6000 1 -------------------input file end------------------------------------------- With Kind Regards, Sonu IITD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101016/103b15ec/attachment.htm From ttduyle at gmail.com Sat Oct 16 15:28:46 2010 From: ttduyle at gmail.com (Duy Le) Date: Sat, 16 Oct 2010 09:28:46 -0400 Subject: [Pw_forum] Again: unable( impossible ) to generation PP with semicore states and NLCC ? In-Reply-To: References: Message-ID: Why do you need a +0.5 pp? Can you make pp with semicore for regular Cu? -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Sat, Oct 16, 2010 at 9:17 AM, sonu kumar <1009ukumar at gmail.com> wrote: > Dear All QE users and developers, > > I am very sorry for this mail again. > I am unable ?generation of PP for Cu with TM (also with rrkj scheme) > pseudization scheme , when i ?include semicore states 3s and 3p and NLCC, > after making > many-many tries ( variations in ?rc's, logder, V_loc, matching rad for aug > func etc....) > The most comman problem is "negative rho " problem. > I also want to use PAW , but unfortunately even unable to generate USPP. > This is leading ?me to think (not 100% sure through ?very limited > experience) that atomic code is unable to generate pp with both NLCC > and?semicore states and also loosing ?my faith in atomic?code. So i need > help from PP expert or any one willing to help. > > Please see below ?for input file---------------------------- > ?&input > ?? ? title='Cu' > ?? ? zed=29, > ?? ? eminld=-10.0, > ?? ? emaxld=3.0, > ?? ? rlderiv=2.5, > ?? ? nld=3, > ?? ? iswitch=3, > ?? ? config="[Ne] 3s2 3p6 3d10.0 4s0.3 4p0.2" > ?? ? dft='LDA' > ?? ? rel=1, > ??/ > ??&inputp > ?? ?pseudotype=3, > ?? ?nlcc=.true., > ?? ? ?new_core_ps = .true. > ?? ? ?rcore=0.6000 > ?? ?lloc=-1, > ?? ? ?rcloc=2.0000, > ?? ?file_pseudopw='Cu_1.UPF' > ?? ?zval=19, > ?? ?lpaw=.false. > ?? ? ?lnc2paw=.false. > ?? ? ?which_augfun ='PSQ', > ?? ? ?rmatch_augfun= 2.0000, > ?? ?author='sk', > ?? ?tm =.true. > ?? ?!rho0=0.01, > > !nX n l ? occ ? nrg ? rmin ? rcut > ??/ > ?8 > ?3S ?1 0 ?2.00 ? ?0.00 ? ?0.650 ? ?3.0000 ?1 > ?3P ?2 1 ?6.00 ? ?0.00 ? ?0.650 ? ?3.0000 ?1 > ?3D ?3 2 ?10.0 ? ?0.00 ? ?0.650 ? ?2.0000 ? 1 > ?3D ?3 2 ?0.00 ? ?0.10 ? ?0.650 ? ?2.0000 ? 1 > ?4S ?1 0 ?0.30 ? ?0.00 ? ?2.000 ? ?3.2000 ?1 > ?4S ?1 0 ?0.00 ? ?1.95 ? ?2.000 ? ?3.2000 ?1 > ?4P ?2 1 ?0.20 ? ?0.00 ? ?2.600 ? ?3.6000 ?1 > ?4P ?2 1 ?0.00 ? ?0.05 ? ?2.600 ? ?3.6000 ?1 > > ?-------------------input > file?end------------------------------------------- > > > > With Kind Regards, > Sonu > > IITD > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From giannozz at democritos.it Sat Oct 16 16:16:53 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 16 Oct 2010 16:16:53 +0200 Subject: [Pw_forum] EXX on 1D supercells fail - solved In-Reply-To: <876644.64602.qm@web53305.mail.re2.yahoo.com> References: <876644.64602.qm@web53305.mail.re2.yahoo.com> Message-ID: On Oct 16, 2010, at 8:56 , Madan Mithra. L. M wrote: > I have found that removing 'ecutrho' from the input file makes the > job to run. thank you for the info. I don't think however that removing ecutrho as ONLY change can make your job run. In your job, ecutrho=4*ecutwfc. This is correct and is the default, so if you remove it, nothing should change. I have noticed is that your job uses many bands (approx. two times more than actually needed) a large cutoff and a large number of k-points. Since in exact-exchange calculations all wavefunctions are stored into memory, you may easily exceed thr available memory limits Paolo --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From ttduyle at gmail.com Sat Oct 16 16:19:17 2010 From: ttduyle at gmail.com (Duy Le) Date: Sat, 16 Oct 2010 10:19:17 -0400 Subject: [Pw_forum] k_point for sheet in bands calculation In-Reply-To: <268890.83351.qm@web55701.mail.re3.yahoo.com> References: <268890.83351.qm@web55701.mail.re3.yahoo.com> Message-ID: On Sat, Oct 16, 2010 at 8:30 AM, Farzad Molani wrote: > Hello, > I'm goimg to study electronic stucture of nano sheet and I have a question > about the > K-point. I think for sheet we need sampling from gamma to K. > Is it true? > Any direction you want. Depends on the structure of your nano sheet. So in bands calculation for k-point I should choice { crystal }. Am I > right? > I couldn't undrestand about points of { crystal } in k-point from gamma to > K. > what are these points depends on? > Go to pwsfc website. In the Tutorial section you will see a link about Summer school at Santa Barbara (2009). Download the exercise of week 1, day 1. Details and example of a band structure calculation can be found in this exercise. -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" > 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:/ > > > _______________________________________________ > 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/20101016/202533d5/attachment.htm From jiejiangnc at gmail.com Sat Oct 16 23:28:23 2010 From: jiejiangnc at gmail.com (Jie Jiang) Date: Sat, 16 Oct 2010 17:28:23 -0400 Subject: [Pw_forum] Zn PAW pseudopotential Message-ID: * Dear pwscf users ** Has anyone generated a Zn paw pseudopotential? would you **share the UPF file and/or the ld1 input file. * Jie -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101016/570d7d57/attachment.htm From m_pazoki at physics.sharif.edu Sun Oct 17 09:14:09 2010 From: m_pazoki at physics.sharif.edu (meysam pazoki) Date: Sun, 17 Oct 2010 10:44:09 +0330 Subject: [Pw_forum] a question about pressure of system Message-ID: Dear Prof Stefano Baroni Thanks a lot for your good comments.They were very useful indeed. Regards meysam Pazoki SUT -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101017/a95f18a2/attachment.htm From chakraa at tcd.ie Sun Oct 17 12:46:30 2010 From: chakraa at tcd.ie (Aurab) Date: Sun, 17 Oct 2010 11:46:30 +0100 Subject: [Pw_forum] Too large susceptibility in NMR/ g-tensor calculations using GIPAW Message-ID: Dear QE users and developers, I am facing a strange problem calculating g tensor of Al doped ZnO systems. Some elements of the susceptibility tensor (chi_bare) is printed as ****** . I assume this is probably due to occurrence of a very large number for that element. Could you please tell me why the susceptibility is blowing up and also what is chi_bare pGv and chi_bare vGv. The block of the output file is given below. End of magnetic susceptibility calculation f-sum rule: -285.026632 1.736420 0.008960 1.735646 -277.370374 0.014146 0.008277 0.011673 -280.653668 f-sum rule (symmetrized): -281.198503 0.000000 0.000000 0.000000 -281.198503 0.000000 0.000000 0.000000 -280.653668 chi_bare pGv (HH) in paratec units: 90907.501059 ************ 9207.951760 ************ ************ 23.037180 13509.227748 -26.194227 ************ ************ 0.000000 0.000000 0.000000 ************ 0.000000 0.000000 0.000000 ************ chi_bare vGv (VV) in paratec units: 60335.176596 ************ 6700.192197 ************ 71027.408187 73.369691 6701.964050 73.241903 ************ 65681.292392 0.000000 0.000000 0.000000 65681.292392 0.000000 0.000000 0.000000 ************ ********************************************** Many regards, Aurab -- =*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* Aurab D. Chakrabarty Room 2.22 The Lloyd Institute School of Physics Trinity College Dublin Dublin 2 Ireland Telephone: +353-1-896-8453 *=*=*=*=*=*=*=*=*=*=*=*=*=*=* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101017/146b8d10/attachment.htm From davide.ceresoli at materials.ox.ac.uk Sun Oct 17 14:52:20 2010 From: davide.ceresoli at materials.ox.ac.uk (Davide Ceresoli) Date: Sun, 17 Oct 2010 13:52:20 +0100 Subject: [Pw_forum] Too large susceptibility in NMR/ g-tensor calculations using GIPAW In-Reply-To: References: Message-ID: <4CBAF184.5010407@materials.ox.ac.uk> On 10/17/2010 11:46 AM, Aurab wrote: > Dear QE users and developers, > I am facing a strange problem calculating g tensor of Al doped ZnO > systems. Some elements of the susceptibility tensor (chi_bare) is > printed as ****** . I assume this is probably due to occurrence of a > very large number for that element. Could you please tell me why the > susceptibility is blowing up and also what is chi_bare pGv and chi_bare > vGv. The block of the output file is given below. > > > > End of magnetic susceptibility calculation > > f-sum rule: > -285.026632 1.736420 0.008960 > 1.735646 -277.370374 0.014146 > 0.008277 0.011673 -280.653668 > > f-sum rule (symmetrized): > -281.198503 0.000000 0.000000 > 0.000000 -281.198503 0.000000 > 0.000000 0.000000 -280.653668 Dear Aurab, it would be useful if you could post your input files. In the meanwhile I can only guess: is your cell hexagonal? GIPAW is incompatible with symmetries that do not map cartesian axis on themselves. Try nosym = .true. How many electrons do you have? the f-sum rule is a good indicator of the convergence of GIPAW calculations. In my experience, the % error on chemical shift is similar to the % error on the f-sum rule, but the error on susceptibilities is much larger. Is your system spin-polarized? To converge the f-sum rule, you must increase the number of k-points. HTH. Cheers, Davide From 1009ukumar at gmail.com Sun Oct 17 15:41:25 2010 From: 1009ukumar at gmail.com (sonu kumar) Date: Sun, 17 Oct 2010 19:11:25 +0530 Subject: [Pw_forum] Again: unable( impossible ) to generation PP with semicore states and NLCC ? Message-ID: Thank you Duy Le for your reply. >Why do you need a +0.5 pp? Can you make pp with semicore for regular Cu? PP for an ionic state can be used like neutral pp for the same atom and "ideally" should be same. I hope i would be able to generate required PP. Thank you very much Duy Le and QE forum. with regards, sonu IITD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101017/45525709/attachment.htm From anna.ferrari at unito.it Sun Oct 17 15:37:23 2010 From: anna.ferrari at unito.it (anna.ferrari at unito.it) Date: Sun, 17 Oct 2010 13:37:23 +0000 Subject: [Pw_forum] R: Too large susceptibility in NMR/ g-tensor calculationsusing GIPAW Message-ID: <628655786-1287322647-cardhu_decombobulator_blackberry.rim.net-603705160-@bda049.bisx.produk.on.blackberry> Le mail ti raggiungono ovunque con BlackBerry? from Vodafone! From giannozz at democritos.it Sun Oct 17 22:51:30 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 17 Oct 2010 22:51:30 +0200 Subject: [Pw_forum] Again: unable( impossible ) to generation PP with semicore states and NLCC ? In-Reply-To: References: Message-ID: <28E8E59F-3694-432F-841E-AD853C520856@democritos.it> On Oct 16, 2010, at 15:17 , sonu kumar wrote: > I am unable generation of PP for Cu with TM (also with rrkj > scheme) pseudization > scheme [...] The most comman problem is "negative rho " problem how can you get a "negative rho" problem with norm-conserving PPs? > This is leading me to think (not 100% sure through very limited > experience) that > atomic code is unable to generate pp with both NLCC and semicore > states typically you need NLCC when you do not want to include semicore states. Can you generate simpler PPs? if no, you shouldn't attempt to generate PPs in more complex cases. Have you read the documentation on how to generate PPs? the case of semicore state is mentioned. It is not trivial. > and also loosing my faith in atomic code. the atomic code works, but it cannot do everything, and sometimes it is hard to generate PPs. P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From wumindt2 at zju.edu.cn Sun Oct 17 23:03:50 2010 From: wumindt2 at zju.edu.cn (wumindt2) Date: Mon, 18 Oct 2010 05:03:50 +0800 Subject: [Pw_forum] Xspectra calculation (wumindt2) Message-ID: Dear Matteo, I met some problem when calculating the XASs with the Xspectra. I tested the example of quartz, and got the consistent result with the published work. Then i moved on to test another example of solid CO2, which has an isotropic symmetry according to C. Brouder's paper. But the X-ray absorption spectrum i got was totally wrong. The first sharp peak which is well-known existing in CO2 was not found. We also tested a single CO2 molecule which is still a clear-cut example. The C atom and the two O atoms are all in the Z axis. So the polarization vectors of (0,0,1) and (1,0,0) are enough for this case. However, we still cannot get the right XAS. To make it easier for you to understand my problem, I attached the input files of this calculation. The GIPAW pseudopotentials i used were downloaded from the website of QE. Thanks a lot for the help. Best regards, Min Wu 2010-10-17 >From: Matteo Calandra >Reply-To: PWSCF Forum >To: pw_forum at pwscf.org >Subject: Re: [Pw_forum] Xspectra calculation (wumindt2) >Date: Mon, 11 Oct 2010 10:08:16 +0200 > >Dear > > I assume you are talking of the dipolar part only. >For the quadrupolar it is substantially more complicate. >The number of independent calculations that you have >to perform to obtain the isotropic cross section (powder) >depends on the point group of the space group >of your crystal. >It is 1 for a cubic or tetraedric crystal, >2 for a uniaxial crystal and it is 3, 4, 6 for a biaxial >(ot trichroic) crystal. >I suggest you read >C. Brouder J. Phys.: Condens. Matter 2 (1990) 701-738 >for more details. > >M. > > >> >> Message: 3 >> Date: Sat, 09 Oct 2010 22:48:53 +0800 >> From: "wumindt2" >> Subject: Re: [Pw_forum] Xspectra calculation >> To: pw_forum at pwscf.org >> Message-ID: >> Content-Type: text/plain; charset="gb2312" >> >> Dear matteo, >> >> Thanks. >> >> For dichroism compound, do we just need the in-plane and the c-axis >> polarization vectors? >> While for trichroism compound, do we need to calculate three different >> polarization vectors? >> Am i right? >> >> Best regards, >> >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: scf.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20101018/1834f743/attachment.txt -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: CO2-moleculer.xspectra_b.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20101018/1834f743/attachment.asc -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: CO2-moleculer.xspectra_c.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20101018/1834f743/attachment-0001.txt From physik.shyam at gmail.com Mon Oct 18 06:36:26 2010 From: physik.shyam at gmail.com (Shyam Khambholja) Date: Sun, 17 Oct 2010 21:36:26 -0700 Subject: [Pw_forum] optical properties Message-ID: Can we calculate optical properties using pwscf ? -- Mr. Shyam G Khambholja Reseach student, Depratment of Physics, Sardar Patel University, Gujarat Cell No. : +91 999 888 3867 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101017/48ecb573/attachment.htm From mambom1902 at yahoo.com Mon Oct 18 08:20:51 2010 From: mambom1902 at yahoo.com (loc duong ding) Date: Sun, 17 Oct 2010 23:20:51 -0700 (PDT) Subject: [Pw_forum] How to draw the wave function Message-ID: <263223.60838.qm@web38802.mail.mud.yahoo.com> Dear all, I want to draw the wave function shape ( some KS orbitals near the Fermi level). I check the input of Post processing but there is no option to draw wave function. Can we extract the shape of the wave function by PWscf? If possible, could you gives some instructions how to do that? I appreciate all your helps. Sincerely, ----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com, ddloc at skku.edu From sclauzer at sissa.it Mon Oct 18 09:04:35 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 18 Oct 2010 09:04:35 +0200 Subject: [Pw_forum] k_point for sheet in bands calculation In-Reply-To: <268890.83351.qm@web55701.mail.re3.yahoo.com> References: <268890.83351.qm@web55701.mail.re3.yahoo.com> Message-ID: <08C1230C-90C5-41AE-B853-C69592EBCEFF@sissa.it> Hello, Il giorno 16/ott/2010, alle ore 14.30, Farzad Molani ha scritto: > Hello, > I'm goimg to study electronic stucture of nano sheet and I have a question about the > K-point. I think for sheet we need sampling from gamma to K. > Is it true? If your system is two-dimensional you will need to sample a 2D Brillouin zone, as well as to choose the cell size in the third direction big enough to avoid a spurious interaction between periodic replicas of the sheet. > So in bands calculation for k-point I should choice { crystal }. Am I right? You can get the correct k-points whatever option you specify to K_POINTS (tpiba, automatic,...), as long as you know what are the k-points that you need and what this options mean. Please read the documentation and the tutorials, as suggested by Duy Le. GS > I couldn't undrestand about points of { crystal } in k-point from gamma to K. > what are these points depends on? > > 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:/ > > > _______________________________________________ > 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/20101018/127e8351/attachment-0001.htm From sclauzer at sissa.it Mon Oct 18 09:14:14 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 18 Oct 2010 09:14:14 +0200 Subject: [Pw_forum] How to draw the wave function In-Reply-To: <263223.60838.qm@web38802.mail.mud.yahoo.com> References: <263223.60838.qm@web38802.mail.mud.yahoo.com> Message-ID: <27AF261F-C2F9-459B-BBE3-3CC4415BB97D@sissa.it> Il giorno 18/ott/2010, alle ore 08.20, loc duong ding ha scritto: > Dear all, > > I want to draw the wave function shape ( some KS orbitals near the Fermi level). > I check the input of Post processing but there is no option to draw wave > function. Have you read the documentation in Doc/INPUT_PP.txt ? ... +-------------------------------------------------------------------- Variable: plot_num Type: INTEGER Description: selects what to save in filplot: 0 = charge 1 = total potential V_bare + V_H + V_xc 2 = local ionic potential V_bare 3 = local density of states at e_fermi 4 = local density of electronic entropy 5 = STM images 6 = spin polarization (rho(up)-rho(down)) 7 = contribution of a selected wavefunction to the (pseudo-)charge density. Noncollinear case: contribution of the given state to the charge or to the magnetization along the direction indicated by spin_component (0 = charge, 1 = x, 2 = y, 3 = z ) GS > > > > Can we extract the shape of the wave function by PWscf? If possible, could you > gives some instructions how to do that? > > > I appreciate all your helps. > > Sincerely, > ----------------------------------------------- > Loc Duong Dinh > Ms-Ph.D Student > Sungkyunkwan Advanced Institute of Nanotechnology, > Sungkyunkwan University, > Suwon, 440-746, Korea > Email: mambom1902 at yahoo.com, ddloc at skku.edu > > > > > _______________________________________________ > 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/20101018/6b2e7d49/attachment.htm From matteo.calandra at impmc.jussieu.fr Mon Oct 18 09:35:10 2010 From: matteo.calandra at impmc.jussieu.fr (Matteo Calandra) Date: Mon, 18 Oct 2010 09:35:10 +0200 Subject: [Pw_forum] xspectra calculation (wumindt2) In-Reply-To: References: Message-ID: <4CBBF8AE.9070705@impmc.jussieu.fr> dear Min Wu, the attachment do not go through the pw_forum, so I cannot do much about it. What I can tell you is that we calculate Co and LiCoO2 and we get a good agreement with experiments. Maybe you can try to compare with the following paper: Juhin et al. Phys. Rev. B 81, 115115 (2010) http://link.aps.org/doi/10.1103/PhysRevB.81.115115 Anyway, from four message what seems to be wrong (assuming the scf run to be correct) are the unit of the polarization vector (assuming you're dealing with the dipolar part only and assuming the peak you're referring to is dipolar). Did you set xcoordcrys to the proper value (see below)? For zhqt concerns CoO2, note that the pre-edge of CoO2 at the Co K-edge has a quadrupolar part, so if you stick to the dipolar calculation you want be able to reproduce the pre-edge peak. Note also that in the case of LiCoO2, which is probably not so different from yours, DFT fails in the pre-edge and you have to use DFT+U. In particular, remember that if you don't set the variable xcoordcrys=.false. your xepsilon and xkvec are in reduced coordinates. From Doc/INPUT_XSPECTRA xkvec(1:3) real(DP) DEFAULT=(1.0,0 .0,0.0) coordinates of the x-ray momentum k xepsilon(1:3) real(DP) DEFAULT=(1.0,0 .0,0.0) coordinates of the incident x-ray polarization vector xcoordcrys logical DEFAULT=.true. .true. to use crystal coordinates for k and epsilon Maybe you could try to reproduce our calculation on LiCoO2 so that you are sure of not having any errors with the input file. The paper is very detailed so you can compare every step in the calculation. All the best, M. >Message: 6 >Date: Mon, 18 Oct 2010 05:03:50 +0800 >From: "wumindt2" >Subject: Re: [Pw_forum] Xspectra calculation (wumindt2) >To: pw_forum at pwscf.org >Message-ID: >Content-Type: text/plain; charset="gb2312" >Dear Matteo, >I met some problem when calculating the XASs with the Xspectra. >I tested the example of quartz, and got the consistent result with the >published work. >Then i moved on to test another example of solid CO2, which has an >isotropic >symmetry according to C. Brouder's paper. But the X-ray absorption >spectrum >i got was totally wrong. The first sharp peak which is well-known >existing >in CO2 was not found. >We also tested a single CO2 molecule which is still a clear-cut >example. >The C atom and the two O atoms are all in the Z axis. So the >polarization vectors >of (0,0,1) and (1,0,0) are enough for this case. However, we still >cannot get the >right XAS. To make it easier for you to understand my problem, I >attached the input files of this calculation. >The GIPAW pseudopotentials i used were downloaded from the website of >QE. >Thanks a lot for the help. >Best regards, >Min Wu From 1009ukumar at gmail.com Mon Oct 18 09:40:04 2010 From: 1009ukumar at gmail.com (sonu kumar) Date: Mon, 18 Oct 2010 13:10:04 +0530 Subject: [Pw_forum] Again: unable( impossible ) to generation PP with semicore states and NLCC ? Message-ID: Thank you Prof. Paolo Giannozzi for your reply. >how can you get a "negative rho" problem with norm-conserving PPs? negative rho problem is (must be) with USPP while pseudizing the q functions. i am sorry for the incomplete info. >typically you need NLCC when you do not want to include semicore states. sometimes we may need both semicore and NLCC like in magnetic properties and lattice dynamics of complex oxides(in which an atoms have different environments depending upon its site symmetry). Anyone having experience in this regard can support my argument. >Can you generate simpler PPs? Yes,Sir. >Have you read the documentation on how to >generate PPs? very well sir. >the case of semicore state is mentioned. It is not >trivial. I am optimistic and will be able to generate required PP. >the atomic code works, but it cannot do everything, and sometimes it is hard to generate PPs. thank you for keeping my faith in atomic code. with kind regards, Sonu IITD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101018/289307dd/attachment.htm From chan.mithra at gmail.com Mon Oct 18 10:41:58 2010 From: chan.mithra at gmail.com (Mithra Chan) Date: Mon, 18 Oct 2010 10:41:58 +0200 Subject: [Pw_forum] network problem for parallel calculations Message-ID: Dear all, I am suffering the problem of network caused by transferring data for parallel runnings on PC clusters. It seems the pw.x occupies a lot of network from nodes to the server. If I run several pw.x jobs, the network of cluster got stuck. I noted that this is due to the pw.x write data (such as wave functions) to my HOME directory, the server, but not the temporary directory. My job file like #$ -N SCF #$ -q quad0 #$ -pe orte 16 #$ -j n INDIR=`pwd` echo $TMP > $INDIR/tmpdir cd $TMP cp $INDIR/JOB.scf.in . mpirun -np 16 $PATH_TO_PW/pw.x -npool 4 < JOB.scf.in > scf.out cd $INDIR cp $TMP/* . Then I copied the pw.x to the temporary directory, and run it locally. However, the pw.x still write files to my home directory. In this step my job file is : #$ -N SCF #$ -q quad0 #$ -pe orte 16 #$ -j n INDIR=`pwd` echo $TMP > $INDIR/tmpdir cd $TMP cp $INDIR/JOB.scf.in . cp $INDIR/pw.x . mpirun -np 16 pw.x -npool 4 < JOB.scf.in > scf.out cd $INDIR cp $TMP/* . How can I make the pw.x just writes data to the $TMP and after its running copies the resulting files to my home directory, i.e. the server? Any suggestion would be appreciated. Thanks a lot. Mithra Chan -- Dr. Mithra Chan, Department of Physics, National University of Singapore, Singapore chan.mithra at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101018/35c478b3/attachment.htm From Lorenzo.Paulatto at impmc.upmc.fr Mon Oct 18 10:48:27 2010 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Mon, 18 Oct 2010 10:48:27 +0200 Subject: [Pw_forum] network problem for parallel calculations In-Reply-To: References: Message-ID: Dear Mithra, by default, QE should use the current directory as temporary space. However, you can control this behavior busing the keyword outdir="/whatever/directory" in the &control namelist (check the manual Doc/INPUT_PW.txt !!!). > INDIR=`pwd` > echo $TMP > $INDIR/tmpdir > cd $TMP This should work, but if $TMP is empty, than it will just use the home directory! > cp $TMP/* . are you sure copying everything to the home directory is not stalling the network? best regards -- Lorenzo Paulatto post-doc @ IMPMC/UPMC - Universit? Paris 6 phone: +33 (0)1 44 27 74 89 www: http://www-int.impmc.upmc.fr/~paulatto/ previously (take note of the change!): phd student @ SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 www: http://people.sissa.it/~paulatto/ From chan.mithra at gmail.com Mon Oct 18 11:06:48 2010 From: chan.mithra at gmail.com (Mithra Chan) Date: Mon, 18 Oct 2010 11:06:48 +0200 Subject: [Pw_forum] network problem for parallel calculations In-Reply-To: References: Message-ID: Dear Lorenzo, Thanks for you suggestion. I think that would not work. Because the job is distributed randomly, I do not know which node it will lated at. I tried by setting outdir='./' and coy the INPUT file to $TMP then run it locally. In this case it write files locally, but I got an error which says "from davcio : error # 10 error while writing to file". Best regards, Mithra Chan 2010/10/18 Lorenzo Paulatto > Dear Mithra, > by default, QE should use the current directory as temporary space. > However, you can control this behavior busing the keyword > outdir="/whatever/directory" in the &control namelist (check the manual > Doc/INPUT_PW.txt !!!). > > > INDIR=`pwd` > > echo $TMP > $INDIR/tmpdir > > cd $TMP > > This should work, but if $TMP is empty, than it will just use the home > directory! > > > cp $TMP/* . > > are you sure copying everything to the home directory is not stalling the > network? > > best regards > > > > -- > Lorenzo Paulatto > post-doc @ IMPMC/UPMC - Universit? Paris 6 > phone: +33 (0)1 44 27 74 89 > www: http://www-int.impmc.upmc.fr/~paulatto/ > > previously (take note of the change!): > phd student @ SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > www: http://people.sissa.it/~paulatto/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Mithra Chan, Department of Physics, National University of Singapore, Singapore chan.mithra at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101018/435bafec/attachment.htm From chan.mithra at gmail.com Mon Oct 18 11:18:03 2010 From: chan.mithra at gmail.com (Mithra Chan) Date: Mon, 18 Oct 2010 11:18:03 +0200 Subject: [Pw_forum] network problem for parallel calculations In-Reply-To: References: Message-ID: Dear Lorenzo, It seems we can use 'disk_io' to do that. I am trying, we will see. Regards, Mithra Chan 2010/10/18 Mithra Chan > Dear Lorenzo, > > Thanks for you suggestion. I think that would not work. Because the job is > distributed randomly, I do not know which node it will lated at. I tried by > setting outdir='./' and coy the INPUT file to $TMP then run it locally. In > this case it write files locally, but I got an error which says "from davcio > : error # 10 error while writing to file". > > Best regards, > > Mithra Chan > > > 2010/10/18 Lorenzo Paulatto > > Dear Mithra, >> by default, QE should use the current directory as temporary space. >> However, you can control this behavior busing the keyword >> outdir="/whatever/directory" in the &control namelist (check the manual >> Doc/INPUT_PW.txt !!!). >> >> > INDIR=`pwd` >> > echo $TMP > $INDIR/tmpdir >> > cd $TMP >> >> This should work, but if $TMP is empty, than it will just use the home >> directory! >> >> > cp $TMP/* . >> >> are you sure copying everything to the home directory is not stalling the >> network? >> >> best regards >> >> >> >> -- >> Lorenzo Paulatto >> post-doc @ IMPMC/UPMC - Universit? Paris 6 >> phone: +33 (0)1 44 27 74 89 >> www: http://www-int.impmc.upmc.fr/~paulatto/ >> >> previously (take note of the change!): >> phd student @ SISSA & DEMOCRITOS (Trieste) >> phone: +39 040 3787 511 >> www: http://people.sissa.it/~paulatto/ >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > Dr. Mithra Chan, > Department of Physics, National University of Singapore, Singapore > chan.mithra at gmail.com > > -- Dr. Mithra Chan, Department of Physics, National University of Singapore, Singapore chan.mithra at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101018/2f055cb6/attachment.htm From giannozz at democritos.it Mon Oct 18 11:25:28 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 18 Oct 2010 11:25:28 +0200 Subject: [Pw_forum] network problem for parallel calculations In-Reply-To: References: Message-ID: <4CBC1288.2040609@democritos.it> Mithra Chan wrote: > It seems we can use 'disk_io' to do that. I am trying, we will see. please see the section "Understanding parallel I/O" in the user guide P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From hqzhou at nju.edu.cn Mon Oct 18 12:41:05 2010 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Mon, 18 Oct 2010 18:41:05 +0800 Subject: [Pw_forum] Bug in PlotPhon Message-ID: Eyvaz, There is a tiny bug or typo in ../PlotPhon/Scripts/Lines. When $cell == 8, b2a=`head -1 $FC_name.fc | cut -c 22-33 ` should be b2a=`head -1 $FC_name.fc | cut -c 23-33 ` I'm using PlotPhon in qe 4.2.1. zhou huiqun @earth sciences, nanjing university, china -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101018/32fd5be5/attachment.htm From mambom1902 at yahoo.com Mon Oct 18 13:51:54 2010 From: mambom1902 at yahoo.com (loc duong ding) Date: Mon, 18 Oct 2010 04:51:54 -0700 (PDT) Subject: [Pw_forum] Pw_forum Digest, Vol 40, Issue 29 In-Reply-To: References: Message-ID: <222409.43362.qm@web38808.mail.mud.yahoo.com> Could you please explain me a little more about that? Is it plot number 7 for the wave function? What is the meaning of psi ? If I want to draw the wave function of two state nearest Fermi level, how should I do? If possible, can you give me some hint to set up the input file for that? I hope to receive more help from you? > > > Dear all, > > > > I want to draw the wave function shape ( some KS orbitals near the Fermi >level). > > > I check the input of Post processing but there is no option to draw wave > > function. > > Have you read the documentation in Doc/INPUT_PP.txt ? > > ... > > +-------------------------------------------------------------------- > Variable: plot_num > > Type: INTEGER > Description: selects what to save in filplot: > > 0 = charge > > 1 = total potential V_bare + V_H + V_xc > > 2 = local ionic potential V_bare > > 3 = local density of states at e_fermi > > 4 = local density of electronic entropy > > 5 = STM images > > 6 = spin polarization (rho(up)-rho(down)) > > 7 = contribution of a selected wavefunction to the > (pseudo-)charge density. Noncollinear case: > contribution of the given state to the charge or > to the magnetization along the direction indicated > by spin_component (0 = charge, 1 = x, 2 = y, 3 = z >) > > > > GS > > > > > > > > > Can we extract the shape of the wave function by PWscf? If possible, could >you > > > gives some instructions how to do that? > > > > > > I appreciate all your helps. > > > > Sincerely, ----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com, ddloc at skku.edu From degironc at sissa.it Mon Oct 18 13:52:17 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 18 Oct 2010 13:52:17 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 40, Issue 29 In-Reply-To: <222409.43362.qm@web38808.mail.mud.yahoo.com> References: <222409.43362.qm@web38808.mail.mud.yahoo.com> Message-ID: <4CBC34F1.8000104@sissa.it> DO NOT REPLY TO A DIGEST MESSSAGE. stefano loc duong ding wrote: > Could you please explain me a little more about that? Is it plot number 7 for > the wave function? What is the meaning of psi ? If I want to draw the wave > function of two state nearest Fermi level, how should I do? > > > If possible, can you give me some hint to set up the input file for that? > > I hope to receive more help from you? > > >>> Dear all, >>> >>> I want to draw the wave function shape ( some KS orbitals near the Fermi >>> >> level). >> >> >>> I check the input of Post processing but there is no option to draw wave >>> function. >>> >> Have you read the documentation in Doc/INPUT_PP.txt ? >> >> ... >> >> +-------------------------------------------------------------------- >> Variable: plot_num >> >> Type: INTEGER >> Description: selects what to save in filplot: >> >> 0 = charge >> >> 1 = total potential V_bare + V_H + V_xc >> >> 2 = local ionic potential V_bare >> >> 3 = local density of states at e_fermi >> >> 4 = local density of electronic entropy >> >> 5 = STM images >> >> 6 = spin polarization (rho(up)-rho(down)) >> >> 7 = contribution of a selected wavefunction to the >> (pseudo-)charge density. Noncollinear case: >> contribution of the given state to the charge or >> to the magnetization along the direction >> > indicated > >> by spin_component (0 = charge, 1 = x, 2 = y, 3 = z >> ) >> >> >> >> GS >> >> >>> >>> Can we extract the shape of the wave function by PWscf? If possible, could >>> >> you >> >> >>> gives some instructions how to do that? >>> >>> >>> I appreciate all your helps. >>> >>> Sincerely, >>> > > > ----------------------------------------------- > Loc Duong Dinh > Ms-Ph.D Student > Sungkyunkwan Advanced Institute of Nanotechnology, > Sungkyunkwan University, > Suwon, 440-746, Korea > Email: mambom1902 at yahoo.com, ddloc at skku.edu > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From eyvaz_isaev at yahoo.com Mon Oct 18 19:38:24 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 18 Oct 2010 10:38:24 -0700 (PDT) Subject: [Pw_forum] Bug in PlotPhon In-Reply-To: References: Message-ID: <203631.46845.qm@web65716.mail.ac4.yahoo.com> Hi, Thanks! Mostly typos. I will check it again and then correct. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: Huiqun Zhou To: pw_forum at pwscf.org Sent: Mon, October 18, 2010 12:41:05 PM Subject: [Pw_forum] Bug in PlotPhon Eyvaz, There is a tiny bug or typo in ../PlotPhon/Scripts/Lines. When $cell == 8, b2a=`head -1 $FC_name.fc | cut -c 22-33 ` should be b2a=`head -1 $FC_name.fc | cut -c 23-33 ` I'm using PlotPhon in qe 4.2.1. zhou huiqun @earth sciences, nanjing university, china -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101018/5e48b7be/attachment.htm From wumindt2 at zju.edu.cn Tue Oct 19 01:21:35 2010 From: wumindt2 at zju.edu.cn (wumindt2) Date: Tue, 19 Oct 2010 07:21:35 +0800 Subject: [Pw_forum] xspectra calculation (wumindt2) Message-ID: Dear Matteo, It seems i have found the problem. It's not the problem of the xcoordcrys. I set it as .true. and the polarization vectors are (0,0,1) and (0,1,0). The xray k vector is the default value (1,0,0). BTW, can we use the same vector for polarization and xay k moment? e.g. Both of them are (1,0,0). Is it OK? The problem i found is that i set the "cut_occ_states" = .true. Then it cut all the occupied state that i expected to see. When i reset it to .false., i saw the expected peak. I have another problem, what does the "ef_r" do in the calculation? For instance, i got fermi level of -5 eV with scf calculation. The i set ef_r= -5/13.6 Ry. Then, in the calculated xspectra data, where is the Fermi level? It is ajusted to 0 eV, or still is the -5 eV? Sorry to bother you again. Thanks so much. Cheers, Min Wu 2010-10-18 >From: Matteo Calandra >Reply-To: PWSCF Forum >To: pw_forum at pwscf.org >Subject: Re:[Pw_forum] xspectra calculation (wumindt2) >Date: Mon, 18 Oct 2010 09:35:10 +0200 > >dear Min Wu, > > the attachment do not go through the pw_forum, so I cannot >do much about it. What I can tell you is that we calculate >Co and LiCoO2 and we get a good agreement with experiments. >Maybe you can try to compare with the following paper: > >Juhin et al. Phys. Rev. B 81, 115115 (2010) >http://link.aps.org/doi/10.1103/PhysRevB.81.115115 > >Anyway, from four message what seems to be wrong (assuming the scf >run to be correct) are the unit of the polarization vector >(assuming you're dealing with the dipolar part only and assuming >the peak you're referring to is dipolar). Did you set xcoordcrys to >the proper value (see below)? > >For zhqt concerns CoO2, note that the pre-edge >of CoO2 at the Co K-edge has a quadrupolar part, so if you stick >to the dipolar calculation you want be able to reproduce the pre-edge >peak. Note also that in the case of LiCoO2, which is probably >not so different from yours, DFT fails in the >pre-edge and you have to use DFT+U. > >In particular, remember that if you don't set the variable >xcoordcrys=.false. your xepsilon and xkvec are in reduced coordinates. > From Doc/INPUT_XSPECTRA > >xkvec(1:3) real(DP) >DEFAULT=(1.0,0 >.0,0.0) > coordinates of the x-ray momentum k > > >xepsilon(1:3) real(DP) >DEFAULT=(1.0,0 >.0,0.0) > coordinates of the incident x-ray > polarization vector > >xcoordcrys logical >DEFAULT=.true. > .true. to use crystal coordinates for > k and epsilon > > >Maybe you could try to reproduce our calculation on LiCoO2 so that >you are sure of not having any errors with the input file. >The paper is very detailed so you can compare every step in the calculation. > >All the best, M. > > >Message: 6 > >Date: Mon, 18 Oct 2010 05:03:50 +0800 > >From: "wumindt2" > >Subject: Re: [Pw_forum] Xspectra calculation (wumindt2) > >To: pw_forum at pwscf.org > >Message-ID: > >Content-Type: text/plain; charset="gb2312" > > >Dear Matteo, > > >I met some problem when calculating the XASs with the Xspectra. > >I tested the example of quartz, and got the consistent result with the > >published work. > >Then i moved on to test another example of solid CO2, which has an > >isotropic > >symmetry according to C. Brouder's paper. But the X-ray absorption > >spectrum > >i got was totally wrong. The first sharp peak which is well-known > >existing > >in CO2 was not found. > >We also tested a single CO2 molecule which is still a clear-cut >example. > >The C atom and the two O atoms are all in the Z axis. So the > >polarization vectors > >of (0,0,1) and (1,0,0) are enough for this case. However, we still > >cannot get the > >right XAS. To make it easier for you to understand my problem, I > >attached the input files of this calculation. > >The GIPAW pseudopotentials i used were downloaded from the website of >QE. > > >Thanks a lot for the help. > > >Best regards, > > >Min Wu >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > From archygu at gmail.com Tue Oct 19 11:14:04 2010 From: archygu at gmail.com (archygu) Date: Tue, 19 Oct 2010 17:14:04 +0800 Subject: [Pw_forum] calculation error Message-ID: <201010191714025622492@gmail.com> Dear All, I build my own cluster with several PCs, and normally QE run well on it. However, several days befor I get the problem, when I run the ./pp.x, I always get the following problem: At line 81 of file error_handler.f90 Fortran runtime error: Read-only file system At line 81 of file error_handler.f90 Fortran runtime error: Read-only file system At line 81 of file error_handler.f90 Fortran runtime error: Read-only file system At line 81 of file error_handler.f90 Fortran runtime error: Read-only file system At line 81 of file error_handler.f90 Fortran runtime error: Read-only file system mean while, the ./pw.x still run very well. I have check with the error_handler.f90, but can not find the reason. is there any one can share your experince to solve this problem with me? Thanks a lot, Best Regards, Archy GU Nanyang Technological University, SG 2010-10-19 archygu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101019/617c185b/attachment.htm From matteo.calandra at impmc.jussieu.fr Tue Oct 19 16:28:30 2010 From: matteo.calandra at impmc.jussieu.fr (Matteo Calandra) Date: Tue, 19 Oct 2010 16:28:30 +0200 Subject: [Pw_forum] xspectra calculation In-Reply-To: References: Message-ID: <4CBDAB0E.8020108@impmc.jussieu.fr> Dear Min Wu, > >It seems i have found the problem. It's not the problem of the >xcoordcrys. I set it as .true. and the polarization vectors are (0,0,1) >and >(0,1,0). The xray k vector is the default value (1,0,0). >BTW, can we use the same vector for polarization and xay k moment? >e.g. Both of them are (1,0,0). Is it OK? Of course epsilon and k MUST be ortogonal otherwise what you are doing is meaningless. If you calculate the dipolar part only then the k-vector is not used and can take any value. > >The problem i found is that i set the "cut_occ_states" = .true. >Then it cut all the occupied state that i expected to see. >When i reset it to .false., i saw the expected peak. > Maybe your ef_r is not in the correct units... Of course you put the Fermi level in the presence of a core-hole, don't you ? >I have another problem, what does the "ef_r" do in the calculation? >For instance, i got fermi level of -5 eV with scf calculation. >The i set ef_r= -5/13.6 Ry. Then, in the calculated xspectra data, >where is >the Fermi level? It is ajusted to 0 eV, or still is the -5 eV? > zero, the energies are simply shifted. M. -- * * * * Matteo Calandra, Charge de Recherche (CR1) Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris Universit? Pierre et Marie Curie, tour 16, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra From wumindt2 at zju.edu.cn Wed Oct 20 01:07:16 2010 From: wumindt2 at zju.edu.cn (wumindt2) Date: Wed, 20 Oct 2010 07:07:16 +0800 Subject: [Pw_forum] xspectra calculation Message-ID: Dear Matteo, So when we just do the dipolar part, we don't need to care about the k vector, right? Besides, in order to compare with an experimental spectrum, is it necessary to cut the occupied state below Fermi energy level within our Xspectra calculation ? In that case, we should set "cut_occ_states" = .true. and "ef_r" equal to the fermi energy we got in the scf calculation. Is it? Best regards, Min Wu 2010-10 >From: Matteo Calandra >Reply-To: PWSCF Forum >To: pw_forum at pwscf.org >Subject: Re: [Pw_forum] xspectra calculation >Date: Tue, 19 Oct 2010 16:28:30 +0200 > >Dear Min Wu, > > > > >It seems i have found the problem. It's not the problem of the > >xcoordcrys. I set it as .true. and the polarization vectors are >(0,0,1) >and > >(0,1,0). The xray k vector is the default value (1,0,0). > >BTW, can we use the same vector for polarization and xay k moment? > >e.g. Both of them are (1,0,0). Is it OK? > >Of course epsilon and k MUST be ortogonal otherwise what you are doing >is meaningless. If you calculate the dipolar part only then >the k-vector is not used and can take any value. > > > > >The problem i found is that i set the "cut_occ_states" = .true. > >Then it cut all the occupied state that i expected to see. > >When i reset it to .false., i saw the expected peak. > > > >Maybe your ef_r is not in the correct units... Of course you put the >Fermi level in the presence of a core-hole, don't you ? > > >I have another problem, what does the "ef_r" do in the calculation? > >For instance, i got fermi level of -5 eV with scf calculation. > >The i set ef_r= -5/13.6 Ry. Then, in the calculated xspectra data, > >where is > >the Fermi level? It is ajusted to 0 eV, or still is the -5 eV? > > > >zero, the energies are simply shifted. > >M. > >-- >* * * * >Matteo Calandra, Charge de Recherche (CR1) >Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris >Universit? Pierre et Marie Curie, tour 16, case 115 >4 Place Jussieu, 75252 Paris Cedex 05 France >Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 >http://www.impmc.jussieu.fr/~calandra >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > From mambom1902 at yahoo.com Wed Oct 20 04:49:36 2010 From: mambom1902 at yahoo.com (loc duong ding) Date: Tue, 19 Oct 2010 19:49:36 -0700 (PDT) Subject: [Pw_forum] How to draw the wave function Message-ID: <309269.93205.qm@web38806.mail.mud.yahoo.com> > DO NOT REPLY TO A DIGEST MESSSAGE. > stefano > I am sorry for my stupid mistake. By the way, I hope to receive replies from all of you. I appreciate to all your help. Sincerely, > loc duong ding wrote: > > Could you please explain me a little more about that? Is it plot number 7 >for > > > the wave function? What is the meaning of psi ? If I want to draw the wave > > function of two state nearest Fermi level, how should I do? > > > > > > If possible, can you give me some hint to set up the input file for that? > > > > I hope to receive more help from you? > > > > > >>> Dear all, > >>> > >>> I want to draw the wave function shape ( some KS orbitals near the Fermi > >>> > >> level). > >> > >> > >>> I check the input of Post processing but there is no option to draw wave > >>> function. > >>> > >> Have you read the documentation in Doc/INPUT_PP.txt ? > >> > >> ... > >> > >> +-------------------------------------------------------------------- > >> Variable: plot_num > >> > >> Type: INTEGER > >> Description: selects what to save in filplot: > >> > >> 0 = charge > >> > >> 1 = total potential V_bare + V_H + V_xc > >> > >> 2 = local ionic potential V_bare > >> > >> 3 = local density of states at e_fermi > >> > >> 4 = local density of electronic entropy > >> > >> 5 = STM images > >> > >> 6 = spin polarization (rho(up)-rho(down)) > >> > >> 7 = contribution of a selected wavefunction to >the > >> (pseudo-)charge density. Noncollinear case: > >> contribution of the given state to the charge >or > >> to the magnetization along the direction > >> > > indicated > > > >> by spin_component (0 = charge, 1 = x, 2 = y, >3 = z > > >> ) > >> > >> > >> > >> GS > >> > >> > >>> > >>> Can we extract the shape of the wave function by PWscf? If possible, >could > > >>> > >> you > >> > >> > >>> gives some instructions how to do that? > >>> > >>> > >>> I appreciate all your helps. > >>> > >>> Sincerely, > >>> ----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com, ddloc at skku.edu From wumindt2 at zju.edu.cn Wed Oct 20 09:23:43 2010 From: wumindt2 at zju.edu.cn (wumindt2) Date: Wed, 20 Oct 2010 15:23:43 +0800 Subject: [Pw_forum] Nscf calculation problem Message-ID: Dear All, I met a problem with Nscf calculation. The K mesh i used is 12*12*12, and then there are 868 independent K points. But it takes about 450 seconds to calculate only one K point. If in this case, it will takes me 4.5 days to do such a nscf calculation. The tested energy cutoff i used is 60 Ry. Is there any way to accelerate the nscf calculation? If i'm right, the nscf calculation just take the charge density calculated from scf calculation, and there should be few way can accelerate the nscf calculation. Is it? Thanks for any help. Min Wu 2010-10-20 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101020/e775353b/attachment.htm From daijiayu at nudt.edu.cn Wed Oct 20 12:11:34 2010 From: daijiayu at nudt.edu.cn (jiayudai) Date: Wed, 20 Oct 2010 18:11:34 +0800 Subject: [Pw_forum] xspectra calculation Message-ID: Dear Matteo and Min Wu, Several daysa ago, i said a problem in my calculations with high pressure. With the help of Matteo, the problem has been solved, and that is because of my fault, where i misread the units of ef_r (in Ry here). Thank Matteo. And i think even for dipolar part, the direction of k vector should be important in some cases, such as the SiO2 in the example. And if we want to compare the results with some experiments, we should cut the contribution of occupied states, that is, cut_occ_states = .true. should be used. But we should shift the position by hand in order to compare the results, cause i think it is very difficult to get the accurate position in DFT, or even in atomic physics, it is a difficult problem to determine the position of spectra. The "ef_r" should be the fermi energy in scf calculation with core-hole, i think. Am i right? Jiayu ------------------------------ Message: 3 Date: Wed, 20 Oct 2010 07:07:16 +0800 From: "wumindt2" Subject: Re: [Pw_forum] xspectra calculation To: pw_forum at pwscf.org Message-ID: Content-Type: text/plain; charset="gb2312" Dear Matteo, So when we just do the dipolar part, we don't need to care about the k vector, right? Besides, in order to compare with an experimental spectrum, is it necessary to cut the occupied state below Fermi energy level within our Xspectra calculation ? In that case, we should set "cut_occ_states" = .true. and "ef_r" equal to the fermi energy we got in the scf calculation. Is it? Best regards, Min Wu 2010-10 ---------------- ------------------------------------------- Jiayu Dai Department of Physics National University of Defense Technology, Changsha, 410073, P R China ----------------------------------------- From giannozz at democritos.it Wed Oct 20 12:49:30 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 20 Oct 2010 12:49:30 +0200 Subject: [Pw_forum] calculation error In-Reply-To: <201010191714025622492@gmail.com> References: <201010191714025622492@gmail.com> Message-ID: <4CBEC93A.60506@democritos.it> archygu wrote: > At line 81 of file error_handler.f90 > Fortran runtime error: Read-only file system go to line 81 of file error_handler.f90 and print crash_file. Most likely it is a nonexistent directory, or not what you expect. Try to figure out why. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Wed Oct 20 12:51:12 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 20 Oct 2010 12:51:12 +0200 Subject: [Pw_forum] Nscf calculation problem In-Reply-To: References: Message-ID: <4CBEC9A0.90304@democritos.it> wumindt2 wrote: > Is there any way to accelerate the nscf calculation? reduce the number of states (nbnd) to the minimum P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Wed Oct 20 12:54:21 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 20 Oct 2010 12:54:21 +0200 Subject: [Pw_forum] How to draw the wave function In-Reply-To: <309269.93205.qm@web38806.mail.mud.yahoo.com> References: <309269.93205.qm@web38806.mail.mud.yahoo.com> Message-ID: <4CBECA5D.3040105@democritos.it> loc duong ding wrote: > By the way, I hope to receive replies from all of you really? there are 1200 subscribers to pw_forum There are examples, there is input documentation. Generically asking for more help is a sure way to irritate people. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From matteo.calandra at impmc.jussieu.fr Wed Oct 20 17:13:39 2010 From: matteo.calandra at impmc.jussieu.fr (Matteo Calandra) Date: Wed, 20 Oct 2010 17:13:39 +0200 Subject: [Pw_forum] xspectra calculation In-Reply-To: References: Message-ID: <4CBF0723.9030508@impmc.jussieu.fr> >Dear Matteo, >So when we just do the dipolar part, we don't need to care about the >k vector, right? yes, it is not used. >Besides, in order to compare with an experimental spectrum, is it necessary to cut >the occupied state below Fermi energy level within our Xspectra calculation ? >In that case, we should set "cut_occ_states" = .true. and >"ef_r" equal to the fermi energy we got in the scf calculation. Is it? Yes. However if you have a small gap insulator, introduction of a core-hole can lead to a metallic system (close the gap). In this case it is not clear where to cut. Actually in this case the static core-hole approximation is probably incorrect. For metals it is even worst. M. Best regards, Min Wu 2010-10 -- * * * * Matteo Calandra, Charge de Recherche (CR1) Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris Universit? Pierre et Marie Curie, tour 16, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra From wumindt2 at zju.edu.cn Wed Oct 20 19:15:17 2010 From: wumindt2 at zju.edu.cn (wumindt2) Date: Thu, 21 Oct 2010 01:15:17 +0800 Subject: [Pw_forum] pseudopotential Message-ID: Dear All, Since there are limited pseudopotentials available on the website of QE. Can we mix Norm-conserving pseudo and Ultrasoft pseudo in one calculation? Thanks. Min Wu 2010-10-20 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101021/57df3cc6/attachment.htm From giannozz at democritos.it Wed Oct 20 21:17:23 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 20 Oct 2010 21:17:23 +0200 Subject: [Pw_forum] pseudopotential In-Reply-To: References: Message-ID: <5F2E9CDD-6D50-4469-82F6-1AEA0BE2F4E6@democritos.it> On Oct 20, 2010, at 19:15 , wumindt2 wrote: > Since there are limited pseudopotentials available on the website > of QE. > Can we mix Norm-conserving pseudo and Ultrasoft pseudo in one > calculation? you didn't try to search "mix pseudopotentials" in the web site, did you? > Of course you can P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From matteo.calandra at impmc.jussieu.fr Thu Oct 21 11:37:45 2010 From: matteo.calandra at impmc.jussieu.fr (Matteo Calandra) Date: Thu, 21 Oct 2010 11:37:45 +0200 Subject: [Pw_forum] xspectra calculation In-Reply-To: References: Message-ID: <4CC009E9.3000106@impmc.jussieu.fr> Dear Jiayu >And i think even for dipolar part, the direction of k vector should be >important in some cases, such as the SiO2 in the example. No, this is incorrect. The dipolar part cross section does not depend on k. >And if we >want to compare the results with some experiments, we should cut the >contribution of occupied states, that is, cut_occ_states = .true. >should be used. But we should shift the position by hand in order to >compare the results, cause i think it is very difficult to get the >accurate position in DFT, or even in atomic physics, it is a difficult >problem to determine the position of spectra. The "ef_r" should be the >fermi energy in scf calculation with core-hole, i think. On this second point you are right in the method but not on the reason why one should cut at somewhat lower values with respect to e_f. The problems that you can face are the following: 1) You have a system with a gap even in the presence of a core-hole . In this case if you cut exactly at the bottom of the conduction band (empty states) then the cut_occ_states procecure can miss this peak. So it is safer to cut at somewhat lower energy than the bottom of the conduction band. 2) You have a system without gap in the presence of a core-hole (either because it was a metal even without core-hole or because it was a small gap semiconductor that becomes a metal when the core-hole is inserted). In this case identification of where to cut is ill defined. In this case you should keep in mind that probably core hole effects are not correctly described. Of course, if DFT underestimates the gap you can easily end up in a metallic solution. All the best, M. Jiayu -- * * * * Matteo Calandra, Charge de Recherche (CR1) Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris Universit? Pierre et Marie Curie, tour 16, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra From daijiayu at nudt.edu.cn Thu Oct 21 15:06:12 2010 From: daijiayu at nudt.edu.cn (jiayudai) Date: Thu, 21 Oct 2010 21:06:12 +0800 Subject: [Pw_forum] xspectra calculation Message-ID: Dear Matteo, Do you think what's the difference between the method in XSpectra code and the method in Abinit (see the ref: http://prl.aps.org/abstract/PRL/v101/i15/e155001, http://prb.aps.org/abstract/PRB/v80/i6/e064110). I think the treatment is very similar, but they consider the Fermi-Dirac distribution for electrons. It seems that they also cut the occupied states when they calculate the xanes. So, do you think if we consider the Fermi distribution of electrons, this model can be used for metals? Regards. Jiayu ------------------------------ Message: 5 Date: Wed, 20 Oct 2010 17:13:39 +0200 From: Matteo Calandra Subject: Re: [Pw_forum] xspectra calculation To: pw_forum at pwscf.org Message-ID: <4CBF0723.9030508 at impmc.jussieu.fr> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >Dear Matteo, >So when we just do the dipolar part, we don't need to care about the >k vector, right? yes, it is not used. >Besides, in order to compare with an experimental spectrum, is it necessary to cut >the occupied state below Fermi energy level within our Xspectra calculation ? >In that case, we should set "cut_occ_states" = .true. and >"ef_r" equal to the fermi energy we got in the scf calculation. Is it? Yes. However if you have a small gap insulator, introduction of a core-hole can lead to a metallic system (close the gap). In this case it is not clear where to cut. Actually in this case the static core-hole approximation is probably incorrect. For metals it is even worst. M. Best regards, From clie at aphy.iphy.ac.cn Fri Oct 22 10:29:15 2010 From: clie at aphy.iphy.ac.cn (clie at aphy.iphy.ac.cn) Date: Fri, 22 Oct 2010 16:29:15 +0800 (CST) Subject: [Pw_forum] gipaw.x In-Reply-To: References: Message-ID: <45ab0.8a1a.12bd30e5d55.Coremail.clie@aphy.iphy.ac.cn> Dear All, I encounter with a problem when using gipaw.x, *** glibc detected *** /work/3256069.jms/home/clie/QE/QE4.2/bin/gipaw.x: double free or corruption (out): 0x000000000c116a10 *** Any ideal? All the best, Zhi Li > -----????----- > ???: pw_forum-request at pwscf.org > ????: 2010?10?21? ??? > ???: pw_forum at pwscf.org > ??: > ??: Pw_forum Digest, Vol 40, Issue 33 > > 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. Re: xspectra calculation (jiayudai) > 2. Re: calculation error (Paolo Giannozzi) > 3. Re: Nscf calculation problem (Paolo Giannozzi) > 4. Re: How to draw the wave function (Paolo Giannozzi) > 5. Re: xspectra calculation (Matteo Calandra) > 6. pseudopotential (wumindt2) > 7. Re: pseudopotential (Paolo Giannozzi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 20 Oct 2010 18:11:34 +0800 > From: "jiayudai" > Subject: Re: [Pw_forum] xspectra calculation > To: pw_forum at pwscf.org > Message-ID: > Content-Type: text/plain; charset="gb2312" > > Dear Matteo and Min Wu, > > Several daysa ago, i said a problem in my calculations with high pressure. With the help of Matteo, the problem has been solved, and that is because of my fault, where i misread the units of ef_r (in Ry here). Thank Matteo. > > And i think even for dipolar part, the direction of k vector should be important in some cases, such as the SiO2 in the example. And if we want to compare the results with some experiments, we should cut the contribution of occupied states, that is, cut_occ_states = .true. should be used. But we should shift the position by hand in order to compare the results, cause i think it is very difficult to get the accurate position in DFT, or even in atomic physics, it is a difficult problem to determine the position of spectra. The "ef_r" should be the fermi energy in scf calculation with core-hole, i think. > > Am i right? > > Jiayu > > > ------------------------------ > > Message: 3 > Date: Wed, 20 Oct 2010 07:07:16 +0800 > From: "wumindt2" > Subject: Re: [Pw_forum] xspectra calculation > To: pw_forum at pwscf.org > Message-ID: > Content-Type: text/plain; charset="gb2312" > > Dear Matteo, > > So when we just do the dipolar part, we don't need to care about the > k vector, right? > > Besides, in order to compare with an experimental spectrum, is it necessary to cut > the occupied state below Fermi energy level within our Xspectra calculation ? > In that case, we should set "cut_occ_states" = .true. and > "ef_r" equal to the fermi energy we got in the scf calculation. Is it? > > Best regards, > > Min Wu > 2010-10 > > ---------------- > ------------------------------------------- > Jiayu Dai > Department of Physics > National University of Defense Technology, > Changsha, 410073, P R China > ----------------------------------------- > > ------------------------------ > > Message: 2 > Date: Wed, 20 Oct 2010 12:49:30 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] calculation error > To: PWSCF Forum > Message-ID: <4CBEC93A.60506 at democritos.it> > Content-Type: text/plain; charset=GB2312 > > archygu wrote: > > > At line 81 of file error_handler.f90 > > Fortran runtime error: Read-only file system > > go to line 81 of file error_handler.f90 and print crash_file. > Most likely it is a nonexistent directory, or not what you > expect. Try to figure out why. > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > ------------------------------ > > Message: 3 > Date: Wed, 20 Oct 2010 12:51:12 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] Nscf calculation problem > To: wumindt2 , PWSCF Forum > Message-ID: <4CBEC9A0.90304 at democritos.it> > Content-Type: text/plain; charset=GB2312 > > wumindt2 wrote: > > > Is there any way to accelerate the nscf calculation? > > reduce the number of states (nbnd) to the minimum > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > ------------------------------ > > Message: 4 > Date: Wed, 20 Oct 2010 12:54:21 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] How to draw the wave function > To: PWSCF Forum > Message-ID: <4CBECA5D.3040105 at democritos.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > loc duong ding wrote: > > > By the way, I hope to receive replies from all of you > > really? there are 1200 subscribers to pw_forum > > There are examples, there is input documentation. Generically > asking for more help is a sure way to irritate people. > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > ------------------------------ > > Message: 5 > Date: Wed, 20 Oct 2010 17:13:39 +0200 > From: Matteo Calandra > Subject: Re: [Pw_forum] xspectra calculation > To: pw_forum at pwscf.org > Message-ID: <4CBF0723.9030508 at impmc.jussieu.fr> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > >Dear Matteo, > > >So when we just do the dipolar part, we don't need to care about the > >k vector, right? > > yes, it is not used. > > >Besides, in order to compare with an experimental spectrum, is it necessary to cut > >the occupied state below Fermi energy level within our Xspectra calculation ? > >In that case, we should set "cut_occ_states" = .true. and > >"ef_r" equal to the fermi energy we got in the scf calculation. Is it? > > Yes. However if you have a small gap insulator, introduction of a > core-hole can lead to a metallic system (close the gap). In this case it is > not clear where to cut. Actually in this case the static core-hole > approximation is probably incorrect. > For metals it is even worst. > > M. > > Best regards, > > Min Wu > 2010-10 > > > -- > * * * * > Matteo Calandra, Charge de Recherche (CR1) > Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris > Universit? Pierre et Marie Curie, tour 16, case 115 > 4 Place Jussieu, 75252 Paris Cedex 05 France > Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 > http://www.impmc.jussieu.fr/~calandra > > > ------------------------------ > > Message: 6 > Date: Thu, 21 Oct 2010 01:15:17 +0800 > From: "wumindt2" > Subject: [Pw_forum] pseudopotential > To: pw_forum at pwscf.org > Message-ID: > Content-Type: text/plain; charset="gb2312" > > Dear All, > > Since there are limited pseudopotentials available on the website of QE. > Can we mix Norm-conserving pseudo and Ultrasoft pseudo in one calculation? > > Thanks. > > Min Wu > 2010-10-20 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101021/57df3cc6/attachment.html > > ------------------------------ > > Message: 7 > Date: Wed, 20 Oct 2010 21:17:23 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] pseudopotential > To: wumindt2 , PWSCF Forum > Message-ID: <5F2E9CDD-6D50-4469-82F6-1AEA0BE2F4E6 at democritos.it> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > > On Oct 20, 2010, at 19:15 , wumindt2 wrote: > > > Since there are limited pseudopotentials available on the website > > of QE. > > Can we mix Norm-conserving pseudo and Ultrasoft pseudo in one > > calculation? > > you didn't try to search "mix pseudopotentials" in the web site, did > you? > > > > Of course you can > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics, 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 > > > End of Pw_forum Digest, Vol 40, Issue 33 > **************************************** From giannozz at democritos.it Fri Oct 22 11:26:51 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 22 Oct 2010 11:26:51 +0200 Subject: [Pw_forum] Guidelines for posting Message-ID: <4CC158DB.5070703@democritos.it> Everybody is invited to have a look at the Guidelines for Posting to this mailing list: http://www.quantum-espresso.org/wiki/index.php/Pw_users and to the Guidelines for reporting problems: http://www.quantum-espresso.org/wiki/index.php/Bugs P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From davide.ceresoli at materials.ox.ac.uk Fri Oct 22 11:37:49 2010 From: davide.ceresoli at materials.ox.ac.uk (Davide Ceresoli) Date: Fri, 22 Oct 2010 10:37:49 +0100 Subject: [Pw_forum] gipaw.x In-Reply-To: <45ab0.8a1a.12bd30e5d55.Coremail.clie@aphy.iphy.ac.cn> References: <45ab0.8a1a.12bd30e5d55.Coremail.clie@aphy.iphy.ac.cn> Message-ID: <4CC15B6D.4010809@materials.ox.ac.uk> On 10/22/2010 09:29 AM, clie at aphy.iphy.ac.cn wrote: > Dear All, > I encounter with a problem when using gipaw.x, > *** glibc detected *** /work/3256069.jms/home/clie/QE/QE4.2/bin/gipaw.x: double free or corruption (out): 0x000000000c116a10 *** > Any ideal? > All the best, > Zhi Li I've thoroughly tested GIPAW against memory corruption on Linux machines, with the Intel compiler (-check all), and never found problems. Could you give us some details on your machine-compiler-MPI, and your input files? Davide From lihongfuture at gmail.com Fri Oct 22 13:31:14 2010 From: lihongfuture at gmail.com (Lihong shi) Date: Fri, 22 Oct 2010 19:31:14 +0800 Subject: [Pw_forum] electron-phonon interaction in semiconductor Message-ID: Dear all: I am a new user to qespresso. I wonder whether this software can calculate the electron-phonon interaction coefficient in semiconductors. Because in the manual, it is referred that it can calculate this coefficient in metals and can not in insulators. Does anybody know this? Thanks in advance! Lihong -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101022/b34530d2/attachment.htm From cyrille.barreteau at cea.fr Fri Oct 22 14:05:25 2010 From: cyrille.barreteau at cea.fr (Cyrille Barreteau) Date: Fri, 22 Oct 2010 14:05:25 +0200 Subject: [Pw_forum] question about pseudo and lowdin analysis Message-ID: <4CC17E05.8080508@cea.fr> Dear all, I have a question concerning pseudopotential and lowdin charge analysis (projwfc). I have done calculation on Ni/Au(111) system (1 layer of Nickel on 15 layers of Au) with a Nickel pseudopotential for which the p wavefunction are not included and a Gold pseudo for which they are included. Doing the local charge analysis with projwfc I got the following result (where Atom 1 is the surface Ni atom and Atom 2 is the Au sublayer atom). Therefore it seems that there is a charge transfer between the Nickel atom and the Gold atom. Atom # 1: total charge = 9.5860, s = 0.6508, p = 0.0000, d = 8.9352, spin up = 5.1427, s = 0.3140, p = 0.0000, d = 4.8288, spin down = 4.4433, s = 0.3369, p = 0.0000, d = 4.1064, polarization = 0.6995, s = -0.0229, p = 0.0000, d = 0.7224, Atom # 2: total charge = 11.3424, s = 0.4993, p = 1.2324, d = 9.6107, spin up = 5.6558, s = 0.2460, p = 0.6055, d = 4.8043, spin down = 5.6866, s = 0.2533, p = 0.6268, d = 4.8065, polarization = -0.0308, s = -0.0073, p = -0.0213, d = -0.0022, Spilling Parameter: 0.0011 Since I suspected a kind of artefact due to the slight inconsistency between Au and Ni pseudo I have redone the calculation with a pseudo of Nickel including p wavefunctions and I got the following result. The charge transfer seems to have disappeared. However the total magnetic moment is almost identical. Atom # 1: total charge = 9.9425, s = 0.4115, p = 0.7846, d = 8.7464, spin up = 5.3347, s = 0.2000, p = 0.3710, d = 4.7637, spin down = 4.6079, s = 0.2115, p = 0.4136, d = 3.9827, polarization = 0.7268, s = -0.0115, p = -0.0426, d = 0.7810, Atom # 2: total charge = 11.0206, s = 0.4441, p = 1.0158, d = 9.5607, spin up = 5.4973, s = 0.2188, p = 0.4993, d = 4.7792, spin down = 5.5233, s = 0.2253, p = 0.5164, d = 4.7815, polarization = -0.0260, s = -0.0065, p = -0.0171, d = -0.0023, Spilling Parameter: 0.0010 I do not really understand the exact meaning of this lowdin charge analysis. It seems that the electrons of p chararacter of Nickel which cannot be projected on p wavefunction in the first pseudo are "evaporating" into s and p orbitals of Nickel or Gold atoms. I am also puzzled by the fact that the spilling parameter is equally good in both calculation while I would expect a larger value for the first case. How can that be possible? I also have a question concerning the generation of pseudopotential. How the inclusion or not of p wavefunction affects the quality of the pseudo? It seems that both pseudo are equally good but it is just an artefact of the projection procedure which can lead to different local charge analysis. thank you very much in advance for enligthening up this point. best wishes cyrille -- ================================================================== Cyrille Barreteau | phone : +33 (0)1 69 08 29 51 CEA Saclay | fax : +33 (0)1 69 08 84 46 IRAMIS, SPCSI | email cyrille.barreteau at cea.fr Batiment 462 | 91191 Gif sur Yvette Cedex FRANCE ~~~~~~~~~~~~~~~~~~~~~~~~ http://iramis.cea.fr/Pisp/cyrille.barreteau/ ================================================================== From mambom1902 at yahoo.com Fri Oct 22 17:56:11 2010 From: mambom1902 at yahoo.com (loc duong ding) Date: Fri, 22 Oct 2010 08:56:11 -0700 (PDT) Subject: [Pw_forum] How to draw the wave function In-Reply-To: References: Message-ID: <31684.33804.qm@web38807.mail.mud.yahoo.com> >> By the way, I hope to receive replies from all of you >really? there are 1200 subscribers to pw_forum >There are examples, there is input documentation. Generically >asking for more help is a sure way to irritate people. I try to read the input document for pp processing. There are some points I can not understand. The input for k_point is integer. Does it mean the order of k-point we use in the input file to calculate band structure? Example for calculation band, I put these K-points: K_points {crystal} 5 0 0 0 1 0 0 0.1 1 0 0 0.3 1 0 0 0.4 1 0 0 0.5 1 If I chose k-point =2, it is at the (0, 0, 0.1) point? Another point is the band we want to draw. If I want to draw the band just below the fermi level, how I can know the order of the band? I appreciate all your help. Sincerely, ----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com, ddloc at skku.edu From ttduyle at gmail.com Fri Oct 22 18:47:56 2010 From: ttduyle at gmail.com (Duy Le) Date: Fri, 22 Oct 2010 12:47:56 -0400 Subject: [Pw_forum] Nscf calculation problem In-Reply-To: <4CBEC9A0.90304@democritos.it> References: <4CBEC9A0.90304@democritos.it> Message-ID: More cores may help :) -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Wed, Oct 20, 2010 at 6:51 AM, Paolo Giannozzi wrote: > wumindt2 wrote: > > > Is there any way to accelerate the nscf calculation? > > reduce the number of states (nbnd) to the minimum > > P. > -- > Paolo Giannozzi, 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/20101022/910d7a1f/attachment.htm From giannozz at democritos.it Fri Oct 22 19:08:16 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 22 Oct 2010 19:08:16 +0200 Subject: [Pw_forum] question about pseudo and lowdin analysis In-Reply-To: <4CC17E05.8080508@cea.fr> References: <4CC17E05.8080508@cea.fr> Message-ID: <4CC1C500.90806@democritos.it> Cyrille Barreteau wrote: > How the inclusion or not of p wavefunction affects the quality of the > pseudo? if the pseudopotential is the same and you just add a p atomic orbital to the PP file, nothing will change in the calculation (apart from a small difference in slef-consistency because the starting point is slightly different). The Lowdin charges will change, as they always do since they depend upon the set of atomic orbitals used for the projection. A difference of 1/3 of an electron is rather surprising, but I don't see any reason to think that there is anything wrong in the algorithm. Likely, yet another indication that "atomic" charges should be taken with a (rather large) grain of salt Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Fri Oct 22 19:48:57 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 22 Oct 2010 19:48:57 +0200 Subject: [Pw_forum] How to draw the wave function In-Reply-To: <31684.33804.qm@web38807.mail.mud.yahoo.com> References: <31684.33804.qm@web38807.mail.mud.yahoo.com> Message-ID: On Oct 22, 2010, at 17:56 , loc duong ding wrote: > The input for k_point is integer. Does it mean the order of k-point > we use in the input file to calculate band structure? yes > Another point is the band we want to draw. If I want to draw the band > just below the fermi level, how I can know the order of the band? look into the output, look at the Fermi energy (or the top of the valence band), count the bands at the k-point you want to plot. P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From david.grifith at gmail.com Sat Oct 23 13:59:24 2010 From: david.grifith at gmail.com (david grifith) Date: Sat, 23 Oct 2010 15:29:24 +0330 Subject: [Pw_forum] positive fermi energy Message-ID: Dear All I get positive fermi energy (+7.8 eV) for bulk graphite by Quantum Espresso. Positive energy is meaningless for me here. Would you please say me that in whcih way QE selects the zero energy? As I know the vacuum should be considered as zero energy. I appreciate you in advance to solve the problem. -- Sincerely Yours David G. JCU -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101023/e3a63a6f/attachment.htm From cyrille.barreteau at cea.fr Sat Oct 23 14:07:47 2010 From: cyrille.barreteau at cea.fr (BARRETEAU Cyrille) Date: Sat, 23 Oct 2010 14:07:47 +0200 Subject: [Pw_forum] =?iso-8859-1?q?RE=A0=3A__positive_fermi_energy?= References: Message-ID: <18E4AC9C2FAC504E994A6759DE5ABE8DE313F4@DIODON.extra.cea.fr> David, You should know that within DFT calculations the zero of energy of a periodic system is NOT the vacuum. If you want to get the energy of vacuum you can simulate for example a surface with the "supercell" method ie including empty space between slabs. You will get the vacuum energy (and therefore also the work function) by plotting the potential far away from you slabs in the "empty" region. cyrille ================================================================== Cyrille Barreteau phone : +33 (0)1 69 08 29 51 CEA Saclay fax : +33 (0)1 69 08 84 46 IRAMIS, SPCSI, Batiment 462 email cyrille.barreteau at cea.fr 91191 Gif sur Yvette Cedex FRANCE ~~~~~~~~~~~~~~~~~~~~~~~~ Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/ ================================================================== ________________________________ De: pw_forum-bounces at pwscf.org de la part de david grifith Date: sam. 23/10/2010 13:59 ?: PwSCF Forum Objet : [Pw_forum] positive fermi energy Dear All I get positive fermi energy (+7.8 eV) for bulk graphite by Quantum Espresso. Positive energy is meaningless for me here. Would you please say me that in whcih way QE selects the zero energy? As I know the vacuum should be considered as zero energy. I appreciate you in advance to solve the problem. -- Sincerely Yours David G. JCU -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 5742 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101023/b353be7d/attachment.bin From baroni at sissa.it Sat Oct 23 15:50:35 2010 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 23 Oct 2010 15:50:35 +0200 Subject: [Pw_forum] electron-phonon interaction in semiconductor In-Reply-To: References: Message-ID: <909C9225-D927-4FB2-B97A-BEA262FD5518@sissa.it> yes - enjoy QE - SB On Oct 22, 2010, at 1:31 PM, Lihong shi wrote: > Dear all: > > I am a new user to qespresso. I wonder whether this software can calculate the electron-phonon interaction coefficient in semiconductors. Because in the manual, it is referred that it can calculate this coefficient in metals and can not in insulators. Does anybody know this? > > Thanks in advance! > > Lihong > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From sd.wang000 at gmail.com Sat Oct 23 17:35:45 2010 From: sd.wang000 at gmail.com (shudong wang) Date: Sat, 23 Oct 2010 23:35:45 +0800 Subject: [Pw_forum] Supercell in GWW calculations Message-ID: Dear developers: I confused about the size of supercell in GWW calculations. What the supercell should I use,2x2x2 or 3x3x3 ....? Does it must be used in the GWW? Thanks in advance! S. D. Wang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101023/f06ebf71/attachment.htm From wumindt2 at zju.edu.cn Sat Oct 23 18:03:34 2010 From: wumindt2 at zju.edu.cn (wumindt2) Date: Sun, 24 Oct 2010 00:03:34 +0800 Subject: [Pw_forum] xspectra calculation Message-ID: Dear Matteo, When i cut the occupied state with "cut_occ_states=.true.", there is a small peak appeared at the energy of ef_r i set. In the element of "cut_occ", only cut_desmooth = 0.01 was set. The others are using default value. So what's the reason of this small peak? How to cut the occupied states smoothly? Thanks. With Regards, Min Wu 2010-10-23 From cyrille.barreteau at cea.fr Sat Oct 23 20:43:49 2010 From: cyrille.barreteau at cea.fr (BARRETEAU Cyrille) Date: Sat, 23 Oct 2010 20:43:49 +0200 Subject: [Pw_forum] =?iso-8859-1?q?RE=A0=3A__question_about_pseudo_and_low?= =?iso-8859-1?q?din_analysis?= References: <4CC17E05.8080508@cea.fr> <4CC1C500.90806@democritos.it> Message-ID: <18E4AC9C2FAC504E994A6759DE5ABE8DE313F6@DIODON.extra.cea.fr> Thank you Paolo for your answer. I am quite sure there is nothing wrong in the lowdin charge analysis algorithm. I was just a bit surprised of the result. By the way I have also tested with a similar system Co/Au(111) and got the same tendancy. cyrille ================================================================== Cyrille Barreteau phone : +33 (0)1 69 08 29 51 CEA Saclay fax : +33 (0)1 69 08 84 46 IRAMIS, SPCSI, Batiment 462 email cyrille.barreteau at cea.fr 91191 Gif sur Yvette Cedex FRANCE ~~~~~~~~~~~~~~~~~~~~~~~~ Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/ ================================================================== ________________________________ De: pw_forum-bounces at pwscf.org de la part de Paolo Giannozzi Date: ven. 22/10/2010 19:08 ?: PWSCF Forum Objet : Re: [Pw_forum] question about pseudo and lowdin analysis Cyrille Barreteau wrote: > How the inclusion or not of p wavefunction affects the quality of the > pseudo? if the pseudopotential is the same and you just add a p atomic orbital to the PP file, nothing will change in the calculation (apart from a small difference in slef-consistency because the starting point is slightly different). The Lowdin charges will change, as they always do since they depend upon the set of atomic orbitals used for the projection. A difference of 1/3 of an electron is rather surprising, but I don't see any reason to think that there is anything wrong in the algorithm. Likely, yet another indication that "atomic" charges should be taken with a (rather large) grain of salt Paolo -- Paolo Giannozzi, 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 -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 6190 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101023/ffaef928/attachment-0001.bin From david.grifith at gmail.com Sat Oct 23 21:57:31 2010 From: david.grifith at gmail.com (david grifith) Date: Sat, 23 Oct 2010 23:27:31 +0330 Subject: [Pw_forum] positive Fermi energy Message-ID: Dear Cyrille and Users Thanks for your answer. However, I don't want to calculate the energy of vacuum; Really I want to draw the DOS and PDOS of the BULK graphite correctly. I don't know that I should use the +7.8 eV as the Fermi energy in the DOS diagram either set it to zero and rescale the other energies or something else ? You should know that within DFT calculations the zero of energy of a > periodic system is NOT the vacuum. > where is the zero of energy here ? and in which way the QE chooses it ? Also, can one compare this Fermi energy with the Fermi energy of another material, or is such comparison reliable ? > If you want to get the energy of vacuum you can simulate for example a > surface with the "supercell" method ie including empty space between slabs. > You will get the vacuum energy (and therefore also the work function) by > plotting the potential far away from you slabs in the "empty" region. > > cyrille > > Dear All > > I get positive Fermi energy (+7.8 eV) for bulk graphite by Quantum > Espresso. > Positive energy is meaningless for me here. Would you please say me that in > whcih way QE selects the zero energy? > As I know the vacuum should be considered as zero energy. I appreciate you > in advance to solve the problem. > > -- > Sincerely Yours > David G. > JCU > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101023/0c20f8c8/attachment.htm From metokal at gmail.com Sat Oct 23 22:35:43 2010 From: metokal at gmail.com (Mehmet Topsakal) Date: Sat, 23 Oct 2010 22:35:43 +0200 Subject: [Pw_forum] Supercell in GWW calculations In-Reply-To: References: Message-ID: Supercell ??? As far as I know, GWW is ONLY for gamma-point calculations. So if you are studying finite molecules, only relevant parameter is the vacuum distance. For periodic systems, you can try YAMBO (http://www.yambo-code.org) to obtain quasi-particle energies and band structure.... Regards, On Sat, Oct 23, 2010 at 5:35 PM, shudong wang wrote: > Dear developers: > I confused about the size of supercell in GWW calculations. What the > supercell should I use,2x2x2 or 3x3x3 ....? Does it must be used in the GWW? > > > Thanks in advance! > > S. D. Wang > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Mehmet Topsakal (Ph.D. Student) UNAM-Institute of Materials Science and Nanotechnology. Bilkent University. 06800 Bilkent, Ankara/T?rkiye Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365 UNAM-web : www.nano.org.tr -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101023/d16d4921/attachment.htm From cyrille.barreteau at cea.fr Sun Oct 24 07:42:22 2010 From: cyrille.barreteau at cea.fr (BARRETEAU Cyrille) Date: Sun, 24 Oct 2010 07:42:22 +0200 Subject: [Pw_forum] =?iso-8859-1?q?RE=A0=3A__positive_Fermi_energy?= References: Message-ID: <18E4AC9C2FAC504E994A6759DE5ABE8DE313F8@DIODON.extra.cea.fr> David, Ef=7.8eV is probably the right value and therefore you can plot the DOS and define Ef as the new zero of energy if you wish... cyrille ================================================================== Cyrille Barreteau phone : +33 (0)1 69 08 29 51 CEA Saclay fax : +33 (0)1 69 08 84 46 IRAMIS, SPCSI, Batiment 462 email cyrille.barreteau at cea.fr 91191 Gif sur Yvette Cedex FRANCE ~~~~~~~~~~~~~~~~~~~~~~~~ Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/ ================================================================== ________________________________ De: pw_forum-bounces at pwscf.org de la part de david grifith Date: sam. 23/10/2010 21:57 ?: pw_forum at pwscf.org Objet : Re: [Pw_forum] positive Fermi energy Dear Cyrille and Users Thanks for your answer. However, I don't want to calculate the energy of vacuum; Really I want to draw the DOS and PDOS of the BULK graphite correctly. I don't know that I should use the +7.8 eV as the Fermi energy in the DOS diagram either set it to zero and rescale the other energies or something else ? You should know that within DFT calculations the zero of energy of a periodic system is NOT the vacuum. where is the zero of energy here ? and in which way the QE chooses it ? Also, can one compare this Fermi energy with the Fermi energy of another material, or is such comparison reliable ? If you want to get the energy of vacuum you can simulate for example a surface with the "supercell" method ie including empty space between slabs. You will get the vacuum energy (and therefore also the work function) by plotting the potential far away from you slabs in the "empty" region. cyrille Dear All I get positive Fermi energy (+7.8 eV) for bulk graphite by Quantum Espresso. Positive energy is meaningless for me here. Would you please say me that in whcih way QE selects the zero energy? As I know the vacuum should be considered as zero energy. I appreciate you in advance to solve the problem. -- Sincerely Yours David G. JCU -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 6410 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101024/56395ccd/attachment.bin From giannozz at democritos.it Sun Oct 24 09:40:07 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 24 Oct 2010 09:40:07 +0200 Subject: [Pw_forum] positive Fermi energy In-Reply-To: References: Message-ID: <804E5C32-E5E9-491D-99BD-EBE4AD0F1F65@democritos.it> On Oct 23, 2010, at 21:57 , david grifith wrote: > Also, can one compare this Fermi energy with the Fermi > energy of another material no; you have to resort to some trick to align the Fermi energies (e.g. align the average electrostatic potential far from the surface, if any, or align deep levels, if any) Paolo --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From david.grifith at gmail.com Sun Oct 24 12:07:07 2010 From: david.grifith at gmail.com (david grifith) Date: Sun, 24 Oct 2010 13:37:07 +0330 Subject: [Pw_forum] positive Fermi energy Message-ID: Dear Professor Giannozzi and Cyrille Thanks for your attentions and helps; Now I get your mean about DOS and comparision of Fermi energies completely but yet I have not understood where is selected as zero energy in the Bulk graphite by QE ? or generally where is selected as zero energy in QE calculations? > cyrille : > > Ef=7.8eV is probably the right value and therefore you can plot the DOS > and define Ef as the new zero of energy if you wish... > > Also, can one compare this Fermi energy with the Fermi energy of another > material, or is such comparison reliable ? > > Paolo Giannozzi : > > no; you have to resort to some trick to align the Fermi > energies (e.g. align the average electrostatic potential > far from the surface, if any, or align deep levels, if any) > > > > > > > > > > > > > -- Sincerely Yours David G. JCU -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101024/7d59b81b/attachment.htm From gexiaoch at sissa.it Sun Oct 24 14:26:05 2010 From: gexiaoch at sissa.it (Xiaochuan Ge) Date: Sun, 24 Oct 2010 14:26:05 +0200 (CEST) Subject: [Pw_forum] Energy in output Message-ID: <52739.147.122.49.58.1287923165.squirrel@webmail.sissa.it> Hello everyone! My name is Ge Xiaochuan, I have some puzzles in the energy items in the output of PW. the Fermi energy is -6.4869 ev ! total energy = -0.94493686 Ry Harris-Foulkes estimate = -0.94493686 Ry estimated scf accuracy < 5.8E-16 Ry The total energy is the sum of the following terms: one-electron contribution = -0.88071975 Ry hartree contribution = 0.52197977 Ry xc contribution = -0.50124138 Ry ewald contribution = -0.05674602 Ry smearing contrib. (-TS) = -0.02820948 Ry I have two questions: 1.The Atom which I calculated is H. But why the hartree and xc contributions exist when there is only one electron in the cell. If the 'self-interaction' is included, when there is only one electon, the sum of hartree and xc part should be zero. 2.what is the relation of the orbit energy and the one-electron contribution. Thanks in advanced for your kind replying. Ge Xiaochuan ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From giannozz at democritos.it Sun Oct 24 14:38:11 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 24 Oct 2010 14:38:11 +0200 Subject: [Pw_forum] Energy in output In-Reply-To: <52739.147.122.49.58.1287923165.squirrel@webmail.sissa.it> References: <52739.147.122.49.58.1287923165.squirrel@webmail.sissa.it> Message-ID: On Oct 24, 2010, at 14:26 , Xiaochuan Ge wrote: > 1.The Atom which I calculated is H. But why the hartree and xc > contributions exist when there is only one electron in the cell. > If the 'self-interaction' is included, when there is only one electon, > the sum of hartree and xc part should be zero. find an approximate functional that has such a property and you will solve 90% of the problems of DFT. If furthermore it is also easy to use, you will become famous. P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sun Oct 24 15:04:00 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 24 Oct 2010 15:04:00 +0200 Subject: [Pw_forum] positive Fermi energy In-Reply-To: References: Message-ID: <038F187E-5585-4079-931A-02B07ACD8403@democritos.it> On Oct 24, 2010, at 12:07 , david grifith wrote: > yet I have not understood where is selected as zero energy > in the Bulk graphite by QE ? or generally where is selected > as zero energy in QE calculations? nothing is selected as "zero energy". One-electron energies, including the Fermi energy, are calculated with respect to some arbitrary reference energy (see the paper cited in the first of the following links). If you want to set your zero of the energy at the Fermi energy, you can do it in your preferred plotting program. If instead you want to know how this arbitrary reference level is calculatd in the code, see the notes in the last link. http://www.democritos.it/pipermail/pw_forum/2004-August/001240.html http://www.democritos.it/pipermail/pw_forum/2007-April/006351.html http://www.democritos.it/pipermail/pw_forum/2009-June/013231.html http://www.democritos.it/pipermail/pw_forum/2009-June/013232.html P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From stenuit at sissa.it Sun Oct 24 15:31:37 2010 From: stenuit at sissa.it (Geoffrey Stenuit) Date: Sun, 24 Oct 2010 15:31:37 +0200 Subject: [Pw_forum] Supercell in GWW calculations In-Reply-To: References: Message-ID: <20101024153137.l6w55efpc00gs00g@webmail.sissa.it> Dear S.D. Wang, It depends on what you are computing: molecule or periodic system. For a molecule, as you know, the answer is a 1x1x1 sc with enough vacuum around it. For a periodic system, it depends on the size of the cell in the real space. Anyway for both cases, the GWW code computes only the GWW eigenvalues at the gamma point. Nevertheless, a 2X2X2 or 3x3x3 or beyond sc should be used for improving the accuracy of the exchange part of the eigenvalues. For more informations, please have a look on your webpage (tutorial part) http://gww.qe-forge.org/index.php?page=tutorial Hope it helps, Joe Quoting shudong wang : > Dear developers: > I confused about the size of supercell in GWW calculations. What the > supercell should I use,2x2x2 or 3x3x3 ....? Does it must be used in the GWW? > > > Thanks in advance! > > S. D. Wang > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From marzari at MIT.EDU Sun Oct 24 18:16:16 2010 From: marzari at MIT.EDU (Nicola Marzari) Date: Sun, 24 Oct 2010 17:16:16 +0100 Subject: [Pw_forum] =?utf-8?q?RE=C2=A0=3A__positive_Fermi_energy?= In-Reply-To: <18E4AC9C2FAC504E994A6759DE5ABE8DE313F8@DIODON.extra.cea.fr> References: <18E4AC9C2FAC504E994A6759DE5ABE8DE313F8@DIODON.extra.cea.fr> Message-ID: <4CC45BD0.90007@mit.edu> On this thread - let me also stress that lacking an absolute scale of energies is an intrinsic feature of calculations done in periodic-boundary conditions, and not a feature or a defect of q-e. It's universal to any solid-state code (abinit, vasp, castep...). it's also very instructive to understand why it happens, and an extensive discussion of the issues related to finding the position of the vacuum level and the electrostatic averaging technique (Baldereschi et al Phys. Rev. Lett. 61, 734 (1988)) can be found in Caspar Fall's thesis http://library.epfl.ch/en/theses/?nr=1955 or in Singh-Miller et al Phys. Rev. B 80, 235407 (2009), while the issues related to electrostatics in periodic-boundary conditions are discussed in Dabo et al Phys. Rev. B 77 115139 (2008). nicola ? -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From s.m.rezaeisani at gmail.com Mon Oct 25 09:35:07 2010 From: s.m.rezaeisani at gmail.com (Seyed Mojtaba Rezaei Sani) Date: Mon, 25 Oct 2010 11:05:07 +0330 Subject: [Pw_forum] vc-relax output Message-ID: Dear all what does T indicate in vc-relax output? It isn't the temperature that calculation has been done in, is it? -- ========================================== Seyed Mojtaba Rezaei Sani Computational Condensed Matter Research Lab Physics Department, Isfahan University of Technology 84156-83111 Isfahan, Iran Tel lab: +98 311 391 3731 Fax Office: +98 311 391 3746 http://physics.iut.ac.ir/cms/ s.rezaeisani at ph.iut.ac.ir =========================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101025/25cf390a/attachment.htm From kazempoor2000 at yahoo.com Mon Oct 25 10:48:55 2010 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Mon, 25 Oct 2010 01:48:55 -0700 (PDT) Subject: [Pw_forum] vc-relax-temperature Message-ID: <685696.74397.qm@web114406.mail.gq1.yahoo.com> Dear all what does T indicate in vc-relax output?? It isn't the temperature that calculation has been done in, is it? Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101025/13d12869/attachment.htm From david.grifith at gmail.com Mon Oct 25 15:06:03 2010 From: david.grifith at gmail.com (David Grifith) Date: Mon, 25 Oct 2010 16:36:03 +0330 Subject: [Pw_forum] positive Fermi energy Message-ID: Dear Professor Giannozi and Marzari Many thanks for your helpful comments. david grifith wrote: > > > yet I have not understood where is selected as zero energy > > in the Bulk graphite by QE ? or generally where is selected > > as zero energy in QE calculations? > > nothing is selected as "zero energy". One-electron energies, > including the Fermi energy, are calculated with respect to some > arbitrary reference energy (see the paper cited in the first of > the following links). If you want to set your zero of the energy > at the Fermi energy, you can do it in your preferred plotting > program. If instead you want to know how this arbitrary reference > level is calculatd in the code, see the notes in the last link. > > http://www.democritos.it/pipermail/pw_forum/2004-August/001240.html > http://www.democritos.it/pipermail/pw_forum/2007-April/006351.html > http://www.democritos.it/pipermail/pw_forum/2009-June/013231.html > http://www.democritos.it/pipermail/pw_forum/2009-June/013232.html > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > On this thread - let me also stress that lacking an absolute > scale of energies is an intrinsic feature of calculations > done in periodic-boundary conditions, and not a feature or a > defect of q-e. It's universal to any solid-state code (abinit, > vasp, castep...). it's also very instructive to understand > why it happens, and an extensive discussion of the issues related > to finding the position of the vacuum level and the electrostatic > averaging technique (Baldereschi et al Phys. Rev. Lett. 61, > 734 (1988)) can be found in Caspar Fall's thesis > http://library.epfl.ch/en/theses/?nr=1955 or in > Singh-Miller et al Phys. Rev. B 80, 235407 (2009), while the > issues related to electrostatics in periodic-boundary conditions > are discussed in Dabo et al Phys. Rev. B 77 115139 (2008). > > nicola > ? > > -- > --------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials Science and Engineering > 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA > tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu > > > -- > Sincerely Yours > David G. > JCU > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101025/9f253e55/attachment.htm From mambom1902 at yahoo.com Tue Oct 26 03:26:30 2010 From: mambom1902 at yahoo.com (loc duong ding) Date: Mon, 25 Oct 2010 18:26:30 -0700 (PDT) Subject: [Pw_forum] How to draw the wave function In-Reply-To: References: Message-ID: <924168.39882.qm@web38804.mail.mud.yahoo.com> > > The input for k_point is integer. Does it mean the order of k-point > > we use in the input file to calculate band structure? > > yes > > > Another point is the band we want to draw. If I want to draw the band > > just below the fermi level, how I can know the order of the band? > > look into the output, look at the Fermi energy (or the top of > the valence band), count the bands at the k-point you want > to plot. Where is the first kband (kband=1)? Is it the minimum value of energy (the first value in the out-put (-20)) or at the valence band? Actually, I want to consider whether certain states are localized or delocalized. From the calculation, how we can know one state is localized or delocalized? > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > ----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com, ddloc at skku.edu From daijiayu at nudt.edu.cn Tue Oct 26 06:04:01 2010 From: daijiayu at nudt.edu.cn (jiayudai) Date: Tue, 26 Oct 2010 12:04:01 +0800 Subject: [Pw_forum] The problem of calculating electron localization function (ELF) in QE-4.2.1 Message-ID: Dear developers, Recently, when i was calculating the ELF using the new version of code, i found that there were some problems. The elf using 4.2.1 code was not right, the values were from 0.0 to 1.0, but the exact values should be from 0.5 to 1.0. Besides, when i changed to use the 4.0.5 code, the values were right.. I diff the two source codes, there are some difference in them. So, could you please fix the problem in the new code? Thanks. Jiayu ---------------- ------------------------------------------- Jiayu Dai Department of Physics National University of Defense Technology, Changsha, 410073, P R China ----------------------------------------- From sclauzer at sissa.it Tue Oct 26 09:53:29 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 26 Oct 2010 09:53:29 +0200 Subject: [Pw_forum] How to draw the wave function In-Reply-To: <924168.39882.qm@web38804.mail.mud.yahoo.com> References: <924168.39882.qm@web38804.mail.mud.yahoo.com> Message-ID: <4CC688F9.2030408@sissa.it> On 10/26/2010 03:26 AM, loc duong ding wrote: > > >>> The input for k_point is integer. Does it mean the order of k-point >>> we use in the input file to calculate band structure? >>> >> yes >> >> >>> Another point is the band we want to draw. If I want to draw the band >>> just below the fermi level, how I can know the order of the band? >>> >> look into the output, look at the Fermi energy (or the top of >> the valence band), count the bands at the k-point you want >> to plot. >> > Where is the first kband (kband=1)? Is it the minimum value of energy (the first > value in the out-put (-20)) or at the valence band? > The first possibility you've mentioned, of course. At the end of the scf or nscf calculation, for each k-point the bands are written on output in order of increasing eigenvalue (energy). kband=1 correspond to the lowest eigenvalue, then comes kband=2, etc. up to kband=nbnd. > > Actually, I want to consider whether certain states are localized or > delocalized. From the calculation, how we can know one state is localized or > delocalized? Look at the electronic band dispersions. HTH GS > > > >> P. >> --- >> Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine >> via delle Scienze 208, 33100 Udine, Italy >> Phone +39-0432-558216, fax +39-0432-558222 >> >> > ----------------------------------------------- > Loc Duong Dinh > Ms-Ph.D Student > Sungkyunkwan Advanced Institute of Nanotechnology, > Sungkyunkwan University, > Suwon, 440-746, Korea > Email: mambom1902 at yahoo.com, ddloc at skku.edu > > > > _______________________________________________ > 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 From barfi.koa at gmail.com Tue Oct 26 14:04:33 2010 From: barfi.koa at gmail.com (B. Koa) Date: Tue, 26 Oct 2010 15:34:33 +0330 Subject: [Pw_forum] batch file Message-ID: Dear QE users Is there a way for running a batch of QE's input files by a command line? (It means when a job is completed, the next file should begin running.) -- B. Koa NIT -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101026/793afe3c/attachment.htm From Lorenzo.Paulatto at impmc.upmc.fr Tue Oct 26 14:27:24 2010 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Tue, 26 Oct 2010 14:27:24 +0200 Subject: [Pw_forum] batch file In-Reply-To: References: Message-ID: On Tue, 26 Oct 2010 14:04:33 +0200, B. Koa wrote: > Dear QE users > > Is there a way for running a batch of QE's input files by a command line? > (It means when a job is completed, the next file should begin running.) > Dear Koa, I assume you what to do a simple serial run, in a Linux or similar environment; if my guess is not correct, you should provide more details on your system. In general what you are asking for is noting fancy at all, in general a batch file (known as "script" in unix) is just a sequence of operations to be executed one after the other. In particular, if you create a text file called "pw_batch.sh" and write in it something like this: #!/bin/bash # beginning of the file "pw_batch.sh" /wherever/it/is/pw.x -in file1.in > file1.out /wherever/it/is/pw.x -in file2.in > file2.out /wherever/it/is/pw.x -in file3.in > file3.out # end of file And the execute it with the command "sh pw_batch.sh" it will execute pw.x with the input1, then with input2 and finally with input3. In general, this is a very basic unix questions, you should address similar questions to the technical support of your institution: they can surely provide you all the help you need. best regards -- Lorenzo Paulatto post-doc @ IMPMC/UPMC - Universit? Paris 6 phone: +33 (0)1 44 27 74 89 www: http://www-int.impmc.upmc.fr/~paulatto/ previously (take note of the change!): phd student @ SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 www: http://people.sissa.it/~paulatto/ From archygu at gmail.com Wed Oct 27 03:52:55 2010 From: archygu at gmail.com (chenjie gu) Date: Wed, 27 Oct 2010 09:52:55 +0800 Subject: [Pw_forum] problem in electron localization function Message-ID: Dearv All, when I do the electron localization function calculation by use ./pp.x, there always has the error as follows, At line 81 of file error_handler.f90 Fortran runtime error: Read-only file system At line 81 of file error_handler.f90 Fortran runtime error: Read-only file system At line 81 of file error_handler.f90 Fortran runtime error: Read-only file system At line 81 of file error_handler.f90 Fortran runtime error: Read-only file system At line 81 of file error_handler.f90 Fortran runtime error: Read-only file system is there any one has the same problem, and can give me some suggestion? Thanks in advance. -- Yours Regards, chenjie GU EEE,Nanyang Technoligical University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101027/4d2812f9/attachment.htm From archygu at gmail.com Wed Oct 27 03:54:52 2010 From: archygu at gmail.com (chenjie gu) Date: Wed, 27 Oct 2010 09:54:52 +0800 Subject: [Pw_forum] The problem of calculating electron localization function (ELF) in QE-4.2.1 In-Reply-To: References: Message-ID: Dear Jiayu, even so, I can not do the calculation because of the error as follows, At line 81 of file error_handler.f90 Fortran runtime error: Read-only file system At line 81 of file error_handler.f90 Fortran runtime error: Read-only file system At line 81 of file error_handler.f90 Fortran runtime error: Read-only file system At line 81 of file error_handler.f90 Fortran runtime error: Read-only file system At line 81 of file error_handler.f90 Fortran runtime error: Read-only file system 2010/10/26 jiayudai > Dear developers, > > Recently, when i was calculating the ELF using the new version of code, i > found that there were some problems. The elf using 4.2.1 code was not right, > the values were from 0.0 to 1.0, but the exact values should be from 0.5 to > 1.0. Besides, when i changed to use the 4.0.5 code, the values were right.. > I diff the two source codes, there are some difference in them. So, could > you please fix the problem in the new code? > > Thanks. > > Jiayu > ---------------- > ------------------------------------------- > Jiayu Dai > Department of Physics > National University of Defense Technology, > Changsha, 410073, P R China > ----------------------------------------- > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Yours Regards, chenjie GU EEE,Nanyang Technoligical University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101027/12ca49b0/attachment.htm From chan.mithra at gmail.com Wed Oct 27 12:39:10 2010 From: chan.mithra at gmail.com (Mithra Chan) Date: Wed, 27 Oct 2010 12:39:10 +0200 Subject: [Pw_forum] anything wrong with my wannier calculation? Message-ID: Dear all, I am doing a test on the WANNIER90. The system is very simple, GaAs, which is the same as EXAMPLE01. I did the wannier calculations after SCF, NSCF and pw2wan. For the wannier orbitals, I want to interplate 8 for which the initial projection is based on Ga:l=0;l=1 and As:l=0;l=1. However, the final result of $NAME_hr.dat shows that the wannier orbitals are nonorthogonal on the same site because the overlap matrix has non-zero elements among wannier orbitals either on the Ga or on the As. Is there anything wrong with my Calculation? Any suggestion will be appreciated. Thanks a lot. Best regards, Mithra Chan -- Dr. Mithra Chan, Department of Physics, National University of Singapore, Singapore chan.mithra at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101027/44f8c846/attachment.htm From giannozz at democritos.it Wed Oct 27 12:44:12 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 27 Oct 2010 12:44:12 +0200 Subject: [Pw_forum] vc-relax-temperature In-Reply-To: <685696.74397.qm@web114406.mail.gq1.yahoo.com> References: <685696.74397.qm@web114406.mail.gq1.yahoo.com> Message-ID: <4CC8027C.3020409@democritos.it> ali kazempour wrote: > what does T indicate in vc-relax output? in damped dynamics? average kinetic energy of the atoms = 3K_b T/2. If you are not at equilibrium, the kinetic energy will increase, then decrease during the simulation due to the damping P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From marzari at MIT.EDU Wed Oct 27 12:44:43 2010 From: marzari at MIT.EDU (Nicola Marzari) Date: Wed, 27 Oct 2010 11:44:43 +0100 Subject: [Pw_forum] anything wrong with my wannier calculation? In-Reply-To: References: Message-ID: <4CC8029B.1050701@mit.edu> Dear Mithra, 1) start by plotting the wannier functions, and see if they look like sp3 orbitals. 2) Have you done a proper disentanglement ? What you want is to extract 4 bands from the conduction manifold (plus the 4 valence). 3) maybe post followups (with more detail) on the wannier 90 mailing list, rather than pw_forum: http://www.wannier.org/forum.html nicola On 10/27/10 11:39 AM, Mithra Chan wrote: > Dear all, > > I am doing a test on the WANNIER90. The system is very simple, GaAs, > which is the same as EXAMPLE01. I did the wannier calculations after > SCF, NSCF and pw2wan. For the wannier orbitals, I want to interplate 8 > for which the initial projection is based on Ga:l=0;l=1 and > As:l=0;l=1. However, the final result of $NAME_hr.dat shows that the > wannier orbitals are nonorthogonal on the same site because the > overlap matrix has non-zero elements among wannier orbitals either on > the Ga or on the As. Is there anything wrong with my Calculation? Any > suggestion will be appreciated. > > Thanks a lot. > > Best regards, > > Mithra Chan > > -- > Dr. Mithra Chan, > Department of Physics, National University of Singapore, Singapore > chan.mithra at gmail.com -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101027/cc1b3588/attachment.htm From max.n.popov at gmail.com Wed Oct 27 16:27:10 2010 From: max.n.popov at gmail.com (=?KOI8-R?B?7cHL08nNIPDP0M/X?=) Date: Wed, 27 Oct 2010 16:27:10 +0200 Subject: [Pw_forum] 'Tetrahedra' and 'scf' Message-ID: Hi everyone, according to changelog-4.2, the tetrahedron method was forbidden to be used for scf at *2010-03-25.* What is the reason? Probably, the best person to answer the question is Prof. Gianozzi. -- Best regards, Max Popov Ph.D. student Materials center Leoben (MCL), Leoben, Austria. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101027/41396cd3/attachment.htm From giannozz at democritos.it Wed Oct 27 16:35:59 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 27 Oct 2010 16:35:59 +0200 Subject: [Pw_forum] 'Tetrahedra' and 'scf' In-Reply-To: References: Message-ID: <4CC838CF.8020006@democritos.it> ?????? ????? wrote: > according to changelog-4.2, the tetrahedron method was forbidden to be > used for scf at *2010-03-25.* > What is the reason? forces are not variational, i.e. are not the derivative of the energy. This shouldn't be a big problem if you do not calculate forces, though. > Probably, the best person to answer the question is Prof. Gianozzi. I don't know any Prof. "Gianozzi". Who is he? P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From marzari at MIT.EDU Wed Oct 27 16:40:19 2010 From: marzari at MIT.EDU (Nicola Marzari) Date: Wed, 27 Oct 2010 15:40:19 +0100 Subject: [Pw_forum] 'Tetrahedra' and 'scf' In-Reply-To: <4CC838CF.8020006@democritos.it> References: <4CC838CF.8020006@democritos.it> Message-ID: <4CC839D3.3010605@mit.edu> On 10/27/10 3:35 PM, Paolo Giannozzi wrote: >> Probably, the best person to answer the question is Prof. Gianozzi. > I don't know any Prof. "Gianozzi". Who is he? The good-humored, but unhelpful, brother. nicola :-) -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From max.n.popov at gmail.com Wed Oct 27 16:44:37 2010 From: max.n.popov at gmail.com (=?KOI8-R?B?7cHL08nNIPDP0M/X?=) Date: Wed, 27 Oct 2010 16:44:37 +0200 Subject: [Pw_forum] 'Tetrahedra' and 'scf' In-Reply-To: <4CC838CF.8020006@democritos.it> References: <4CC838CF.8020006@democritos.it> Message-ID: Dear Prof. Giannozzi, first of all, I'm sorry for the typo. Thank you for the quick reply too! It is true that Hellmann-Feynman theorem does not work for the tetrahedron method, but for scf it should not be a problem. Should it? 2010/10/27 Paolo Giannozzi > ?????? ????? wrote: > > > according to changelog-4.2, the tetrahedron method was forbidden to be > > used for scf at *2010-03-25.* > > What is the reason? > > forces are not variational, i.e. are not the derivative of the energy. > This shouldn't be a big problem if you do not calculate forces, though. > > > Probably, the best person to answer the question is Prof. Gianozzi. > > I don't know any Prof. "Gianozzi". Who is he? > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Best regards, Max Popov Ph.D. student Materials center Leoben (MCL), Leoben, Austria. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101027/8adb4ded/attachment.htm From hasanx at gmail.com Wed Oct 27 22:16:15 2010 From: hasanx at gmail.com (=?ISO-8859-9?Q?HASAN_SAH=DDN?=) Date: Wed, 27 Oct 2010 23:16:15 +0300 Subject: [Pw_forum] a2F calculation Message-ID: Hi, I have ben trying to calculate spectral function a2F with respect to phonon frequency cm-1. At the end of my calculation I get the files: dyna2F, a2Fdos, a2Fq2r I see that they contain some column data. Which one of these files does contain the information of a2F-frequency ? Hasan Sahin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101027/590f0ea6/attachment.htm From eyvaz_isaev at yahoo.com Wed Oct 27 22:48:17 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 27 Oct 2010 13:48:17 -0700 (PDT) Subject: [Pw_forum] a2F calculation In-Reply-To: References: Message-ID: <350550.66510.qm@web65716.mail.ac4.yahoo.com> Hi, Definitely, a2Fdos! The first column is \omega, the second one is total a2Fdos, others are mode-projected a2Fdos. Please, provide your affiliation when post a question to the forum. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: HASAN SAH?N To: pw_forum at pwscf.org Sent: Wed, October 27, 2010 10:16:15 PM Subject: [Pw_forum] a2F calculation Hi, I have ben trying to calculate spectral function a2F with respect to phonon frequency cm-1. At the end of my calculation I get the files: dyna2F, a2Fdos, a2Fq2r I see that they contain some column data. Which one of these files does contain the information of a2F-frequency ? Hasan Sahin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101027/2d6c1b47/attachment-0001.htm From eariel99 at gmail.com Wed Oct 27 23:02:53 2010 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Wed, 27 Oct 2010 18:02:53 -0300 Subject: [Pw_forum] 'Tetrahedra' and 'scf' Message-ID: Hi, I think it would be helpful and appreciated to keep scf with tetrahedron method, at least to make accurate SCF calculations. It would also be fine if the program just don't calculate the forces when the tetrahedron methos is chosen, and give a warning for the beginners "forces are not variational. Use other smearing method" > according to changelog-4.2, the tetrahedron method was forbidden to be used > for scf at *2010-03-25.* > What is the reason? > >forces are not variational, i.e. are not the derivative of the energy. >This shouldn't be a big problem if you do not calculate forces, though. Best regards -- Eduardo Menendez Departamento de Fisica Facultad de Ciencias Universidad de Chile Phone: (56)(2)9787439 URL: http://fisica.ciencias.uchile.cl/~emenendez They did it! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101027/8e32b84a/attachment.htm From elie.moujaes at hotmail.co.uk Thu Oct 28 19:22:59 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Thu, 28 Oct 2010 18:22:59 +0100 Subject: [Pw_forum] Brillouin Zone for my supercell Message-ID: Dear All, I am working with a supercell of 60 Carbon atoms. I am trying to do scf and band structure calculations. Is there anything in QE that is used to draw the Brillouin zone for my supercell as I need to find the coordinates of the points that are intercepts with the walls of the Brillouin zone or maybe find coordinates of high symmetry points in the BZ? How can I get such information? Regards Elie Moujaes University of Nottingham BG7 2RD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101028/e163be36/attachment.htm From ttduyle at gmail.com Thu Oct 28 19:28:59 2010 From: ttduyle at gmail.com (Duy Le) Date: Thu, 28 Oct 2010 13:28:59 -0400 Subject: [Pw_forum] Brillouin Zone for my supercell In-Reply-To: References: Message-ID: I doubt that QE has. Try Xcrysden. -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Thu, Oct 28, 2010 at 1:22 PM, Elie Moujaes wrote: > Dear All, > > I am working with a supercell of 60 Carbon atoms. I am trying to do scf and > band structure calculations. Is there anything in QE that is used to draw > the Brillouin zone for my supercell as I need to find the coordinates of the > points that are intercepts with the walls of the Brillouin zone or maybe > find coordinates of high symmetry points in the BZ? How can I get such > information? > > Regards > > Elie Moujaes > University of Nottingham > BG7 2RD > > _______________________________________________ > 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/20101028/9070a385/attachment.htm From giannozz at democritos.it Thu Oct 28 19:39:00 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 28 Oct 2010 19:39:00 +0200 Subject: [Pw_forum] 'Tetrahedra' and 'scf' In-Reply-To: References: Message-ID: <95CEF9EE-996A-4342-A0FB-5692D3ACEEF6@democritos.it> On Oct 27, 2010, at 23:02 , Eduardo Ariel Menendez Proupin wrote: > I think it would be helpful and appreciated to keep scf with > tetrahedron method it is still working: it is sufficient to comment out a check in PW/ input.f90 . Anyway, I'll set a les restrictive condition > It would also be fine if the program just don't calculate the > forces when the tetrahedron > method is chosen, and give a warning for the beginners "forces are > not variational. > Use other smearing method" beginners don't read warnings, and when they do, they don't understand it ... P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Thu Oct 28 19:40:31 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 28 Oct 2010 19:40:31 +0200 Subject: [Pw_forum] The problem of calculating electron localization function (ELF) in QE-4.2.1 In-Reply-To: References: Message-ID: On Oct 26, 2010, at 6:04 , jiayudai wrote: > So, could you please fix the problem in the new code? a simple test showing the problem would be helpful (it would be even more helpful to fix than to ask to fix) P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From pasianot at cnea.gov.ar Thu Oct 28 18:45:21 2010 From: pasianot at cnea.gov.ar (R.C.Pasianot) Date: Thu, 28 Oct 2010 14:45:21 -0200 (ARST) Subject: [Pw_forum] Brillouin Zone for my supercell In-Reply-To: References: Message-ID: Hi, Whatever the size of your supercell, its Bravais lattice must be one among the well known 14 (which is it ?), each one possessing a known BZ. The only thing is that with 60 atoms you're going to have many bands. Regards, Roberto On Thu, 28 Oct 2010, Elie Moujaes wrote: > > Dear All, > > I am working with a supercell of 60 Carbon atoms. I am trying to do scf and band structure calculations. Is there anything in QE that is used to draw the Brillouin zone for my supercell as I need to find the coordinates of the points that are intercepts with the walls of the Brillouin zone or maybe find coordinates of high symmetry points in the BZ? How can I get such information? > > Regards > > Elie Moujaes > University of Nottingham > BG7 2RD From eyvaz_isaev at yahoo.com Thu Oct 28 20:03:40 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 28 Oct 2010 11:03:40 -0700 (PDT) Subject: [Pw_forum] Brillouin Zone for my supercell In-Reply-To: References: Message-ID: <576508.92030.qm@web65710.mail.ac4.yahoo.com> Hi, Let me add that BZ is defined by crystal lattice type (irrespective of supercell or simple lattice). So, if you know (should know) Brave lattice type (ibrav), then have look at Bradley and Cracknell textbook "The Mathematical Theory of Symmetry in Solids: Representation Theory for Point Groups and Space Groups" or visit Bilbao Crystallographic Server. Yes, XCrysDen is helpful if you have a complex structure (non-cubic and non-hexagonal) where the shape of IBZ depends on the axis ratio. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: Duy Le To: PWSCF Forum Sent: Thu, October 28, 2010 7:28:59 PM Subject: Re: [Pw_forum] Brillouin Zone for my supercell I doubt that QE has. Try Xcrysden. -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Thu, Oct 28, 2010 at 1:22 PM, Elie Moujaes wrote: Dear All, > >I am working with a supercell of 60 Carbon atoms. I am trying to do scf and band >structure calculations. Is there anything in QE that is used to draw the >Brillouin zone for my supercell as I need to find the coordinates of the points >that are intercepts with the walls of the Brillouin zone or maybe find >coordinates of high symmetry points in the BZ? How can I get such information? > >Regards > >Elie Moujaes >University of Nottingham >BG7 2RD > >_______________________________________________ >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/20101028/50e61165/attachment.htm From ismotochi at gmail.com Thu Oct 28 20:05:50 2010 From: ismotochi at gmail.com (isaac motochi) Date: Thu, 28 Oct 2010 21:05:50 +0300 Subject: [Pw_forum] Brillouin Zone for my supercell In-Reply-To: References: Message-ID: Hi Elie, You can find the information you want on high symmetry points by working in Xcrysden. Motochi Isaac Moi University- Kenya From elie.moujaes at hotmail.co.uk Thu Oct 28 20:21:25 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Thu, 28 Oct 2010 19:21:25 +0100 Subject: [Pw_forum] Brillouin Zone for my supercell In-Reply-To: References: , Message-ID: Thank you all for the information. I will be having a look at XCrysDen and looking at other books as well... Regards Elie > Date: Thu, 28 Oct 2010 21:05:50 +0300 > From: ismotochi at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] Brillouin Zone for my supercell > > Hi Elie, You can find the information you want on high symmetry points > by working in Xcrysden. > > Motochi Isaac > Moi University- Kenya > _______________________________________________ > 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/20101028/dfa22635/attachment.htm From koidoly at gmail.com Sat Oct 30 06:04:49 2010 From: koidoly at gmail.com (Sangkook Choi) Date: Fri, 29 Oct 2010 21:04:49 -0700 Subject: [Pw_forum] norm conserving pseudopotential with multiple projectors and semicores Message-ID: Dear all, 1) is it possible to generate norm conserving pseudopotentials with multiple projectors, and semicores by LD1? For example, Pb with 5s, 5p, 5d, 6s, 6p? 2) if possible, what is nns number in "inputp" for each orbital? is below choice correct? 5s:1 5p:2 5d:3 6s:4 6p:5 Thanks:) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101029/5d995c0e/attachment.htm From amar.shugani at gmail.com Sat Oct 30 11:12:21 2010 From: amar.shugani at gmail.com (amar shugani) Date: Sat, 30 Oct 2010 14:42:21 +0530 Subject: [Pw_forum] (no subject) Message-ID: I am trying to run nscf but the error is occuring # From IOTK LIBRARY VERSION 1.2.0 #UNRECOVERABLE ERROR (ierr=1) #ERROR IN :iotk_scan_end (iotk_scan.spp:233) #cvs revision :1.23 #foundl #ERROR IN :iotk_close_read(iotk_files.spp:645) #cvs revision:1.20 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101030/77b4c7ed/attachment.htm From barfi.koa at gmail.com Sun Oct 31 21:42:43 2010 From: barfi.koa at gmail.com (B. Koa) Date: Mon, 1 Nov 2010 00:12:43 +0330 Subject: [Pw_forum] GDIS Message-ID: Dear QE Users I can not visualize input and output files of QE by GDIS which has been introduced in the TOOLS. Is there any trick ? or is it only useful to visualize some specific properties ? Many Thanks -- B. Koa NIT -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101101/c7e8711d/attachment.htm From degironc at sissa.it Sun Oct 31 21:50:06 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sun, 31 Oct 2010 21:50:06 +0100 Subject: [Pw_forum] GDIS In-Reply-To: References: Message-ID: <4CCDD67E.7010107@sissa.it> Dear B. Koa what is GDIS and what is TOOLS ? Stefano de Gironcoli - SISSA and DEMOCRITOS B. Koa wrote: > Dear QE Users > > I can not visualize input and output files of QE by GDIS which has been > introduced in the TOOLS. Is there any trick ? or is it only useful to > visualize some specific properties ? Many Thanks > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From ttduyle at gmail.com Sun Oct 31 22:13:24 2010 From: ttduyle at gmail.com (Duy Le) Date: Sun, 31 Oct 2010 17:13:24 -0400 Subject: [Pw_forum] GDIS In-Reply-To: <4CCDD67E.7010107@sissa.it> References: <4CCDD67E.7010107@sissa.it> Message-ID: GDIS is a visualization software. Koa, you need to learn which formats GDIS supports. -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Sun, Oct 31, 2010 at 4:50 PM, Stefano de Gironcoli wrote: > Dear B. Koa > what is GDIS and what is TOOLS ? > Stefano de Gironcoli - SISSA and DEMOCRITOS > > B. Koa wrote: > > Dear QE Users > > > > I can not visualize input and output files of QE by GDIS which has been > > introduced in the TOOLS. Is there any trick ? or is it only useful to > > visualize some specific properties ? Many Thanks > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101031/c68edc82/attachment.htm