[Pw_forum] dynmat.x - segmentation fault error
I would like to kindly thank Prof Gianozzi for giving me the solution for the problem. Indeed, providing suggested changes was the point. Now dynmat.x works fine even for few-hundred atomic unit cells, with the only limitation of using ASR=simple. Thank you! Kacper Druzbicki, Faculty of Chemistry, Department of Chemical Physics, Jagiellonian University, Ingardena Street 3, 30-060 Cracow, Poland phone: +48 12 6632265 - Original Message - From: Paolo Giannozzi Date: Thursday, December 1, 2011 10:06 am Subject: Re: [Pw_forum] dynmat.x - segmentation fault error To: PWSCF Forum > Try to replace routine set_asr in dynmat.f90 with the attached > version - no warranty > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum
[Pw_forum] dynmat.x - segmentation fault error
Dear QE users, I get the following error while trying to diagonalize the dynamic matrix for the 186 atomic system. " Reading Dynamical Matrix from file matdyn ...Force constants read ...epsilon and Z* read Segmentation fault " Below you can find the dynmat file and the input for dynmat.x. http://www.sendspace.com/file/pd9w9u Any ideas? I would appreciate if one could check the file on his machine. Thank you in advance, Casper Kacper Dru?bicki, Faculty of Chemistry, Department of Chemical Physics, Jagiellonian University, Ingardena Street 3, 30-060 Krak?w, Poland phone: +48 12 6632265
[Pw_forum] ODP: Re: Ph.x problem. No results. Wrong irreducible representations number.
Thank you, Sir! It's seems that now it's finally running. The program has already turned into Electric Fields Calculation section, and it looks that it's ok now. It progressively iterating. I still wonder why it lost the thread of symmetry, giving the inproper normal modes number. It's monoclinic system (which I notice that QE define in a specific way) and I built the geometry by importing the coordinates and the cell parameters from CASTEP. When opened via Xcrysden or J-Ice, the geometry seems to be allright. All the cell parameters are correct. Loss of normal mode symmetry for such a low symmetric system is not a problem to me. However, It's courious. With kind regards, Casper Kacper Dru?bicki, Faculty of Chemistry, Department of Chemical Physics, Jagiellonian University, Ingardena Street 3, 30-060 Krak?w, Poland phone: +48 12 6632265 - Wiadomo?? oryginalna - Od: Paolo Giannozzi Data: Niedziela, Wrzesie? 11, 2011 6:46 pm Temat: Re: [Pw_forum] Ph.x problem. No results. Wrong irreducible representations number. Do: PWSCF Forum > On Sep 10, 2011, at 18:55 , Kacper Dru?bicki wrote: > > > london = .true. > > this is not currently implemented in the phonon code (and could > cause the latter to crash / hang) > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum
[Pw_forum] ODP: Sulfur, Nitrogen, Chlorine PBE Norm-Conserving PP
The problem have been solved by Emine Kucukbenli, who linked me to pslibrary project in qe-forge. Just to summarize and educate newbies like me: http://qe-forge.org/projects/pslibrary/ I also got the needed pseudos from the abinit page: http://www.abinit.org/downloads/psp-links/pseudopotentials Thank you very much! Casper Definitely it's a great library. Did not know about it. I found all the data I needed. I looked for NC pseudos due to some ph.x restrictions. Besides, I wanted to get PBE NC, and the sulfur pseudo with D orbitals included. I also found the needed data at abinit webpage, but the one for Sulfur does not include D states, which are IMO important in structural studies of sulfur including organic compounds. I also found BLYP norm conserving pps at QE page. However, I performed some benchmark for the compound I study, within isolated molecule approach. As a result I found that PBE works as good as B3LYP in the prediction of vibrational spectra in this case, and also works well with CASTEP and DMOL3, while BLYP delivered the worst results, along with OLYP and LDA. Thank you! With the best wishes, Casper Kacper Dru?bicki, Faculty of Chemistry, Department of Chemical Physics, Jagiellonian University, Ingardena Street 3, 30-060 Krak?w, Poland phone: +48 12 6632265 - Wiadomo?? oryginalna - Od: "Kacper Dru?bicki" Data: Niedziela, Wrzesie? 11, 2011 6:16 pm Temat: [Pw_forum] Sulfur, Nitrogen, Chlorine PBE Norm-Conserving PP Do: pw_forum at pwscf.org > Dear QE users, > > I hope that you wouldn't mind if I ask does anybody know any source of > PBE Norm-Conserving PP for Sulfur, Nitrogen and Chlorine? I cannot > found them anywhere. I would appreciate if someone could share them > with me... > > With kind regards, > Casper > > Kacper Dru?bicki, > Faculty of Chemistry, > Department of Chemical Physics, > Jagiellonian University, > Ingardena Street 3, 30-060 Krak?w, Poland > phone: +48 12 6632265 > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum
[Pw_forum] Sulfur, Nitrogen, Chlorine PBE Norm-Conserving PP
Dear QE users, I hope that you wouldn't mind if I ask does anybody know any source of PBE Norm-Conserving PP for Sulfur, Nitrogen and Chlorine? I cannot found them anywhere. I would appreciate if someone could share them with me... With kind regards, Casper Kacper Dru?bicki, Faculty of Chemistry, Department of Chemical Physics, Jagiellonian University, Ingardena Street 3, 30-060 Krak?w, Poland phone: +48 12 6632265
[Pw_forum] ODP: Re: Ph.x problem. No results. Wrong irreducible representations number.
Dear Prof. Gianozzi, Thank you for your suggestion. Well, actually I am interested only (or at least) in the IR spectrum. I would like to use USPP so I would like to avoid the gamma trick. I know it's a quite big system, however, I found no problems with the system size when using CASTEP in this purpose. Thus, I thought that QE might also handle it. I have more serious computation resources for QE that for CASTEP. QE solve SCF step for this system in ~20 seconds. I solve the wrong irreducible representations number by turning off the symmetry. However it didn't solve the whole problem. The ph.x still idles. With best wishes, Casper Kacper Dru?bicki, Faculty of Chemistry, Department of Chemical Physics, Jagiellonian University, Ingardena Street 3, 30-060 Krak?w, Poland phone: +48 12 6632265 - Wiadomo?? oryginalna - Od: Paolo Giannozzi Data: Niedziela, Wrzesie? 11, 2011 5:46 pm Temat: Re: [Pw_forum] Ph.x problem. No results. Wrong irreducible representations number. Do: PWSCF Forum > On Sep 10, 2011, at 18:55 , Kacper Dru?bicki wrote: > > > However, when I turned into bigger system, with the 186 atomic unit > > > cell > > a phonon calculation for such a big cell will take a serious amount > of time. > You should try to estimate it from smaller calculations. > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum
[Pw_forum] Ph.x problem. No results. Wrong irreducible representations number.
Dear QE users, I started to work with organic molecular crystals, trying to simulate phonon spectra at gamma, using ultrasoft pps. I deal with monoclinic systems, with the point group P21/c. I tested the procedure with Glycine example, and everything works good and I got all the needed results. However, when I turned into bigger system, with the 186 atomic unit cell, I stuck with no progress... Being more strictly, I got the inproper phonon number 3N-7 instead of 3N and nothing more. The program gives: Atomic displacements: There are 551 irreducible representations The output ends with the listing: 'Representation 551 1 modes -B To be done' and the program does not give any more results for the next hours. I wait for the line: 'Alpha used in Ewald sum = ...' but I got nothing more than the previously mentioned line. The program seems to still work or sleep. I was given no error commands. Is there any limitation of ph.x? I have no idea. I use QE ver 4.3. Could anyone check if this error occurs also at one's machine? My pw.x input only for gamma looks like: &CONTROL title = freq , calculation = 'scf' , outdir = '...' , wfcdir = '...' , pseudo_dir = '...' , prefix = 'freq' restart_mode = 'from_scratch' , wf_collect = .true. , disk_io = 'high' , etot_conv_thr = 1.0d-6 , forc_conv_thr = 1.0d-4 , tstress = .true. , tprnfor = .true. , nstep = 1000 , / &SYSTEM ibrav = 0 , celldm(1) = 16.657934589 , nat = 186, ntyp = 4, ecutwfc = 35.0, ecutrho = 420.0, nosym = .false. , occupations = 'fixed' , london = .true. , / &ELECTRONS electron_maxstep = 100 , conv_thr = 1.D-8 , / &IONS ion_dynamics = 'bfgs' , upscale = 100 , / ATOMIC_SPECIES H 1.008162 H.pbe-van_bm.UPF C 12.0109996796 C.pbe-van_bm.UPF O 15.9989995956 O.pbe-van_bm.UPF S 32.0600013733 S.pbe-van_bm.UPF ATOMIC_POSITIONS crystal H0.661768681 0.098938508 0.027981564 H0.681762733 0.422126036 0.031147779 H0.71062 0.241252285 0.075540824 H0.911720569 0.232557783 0.003204964 H0.943244272 0.047148948 0.046896512 H0.972545308 0.440972636 0.088760388 H0.950707533 0.612471994 0.043453200 H1.185165475 0.402837986 0.019740732 H1.203284961 0.228642875 0.064947666 H1.221684226 0.614171074 0.105831184 H1.209382169 0.794360264 0.061215766 H1.453593378 0.605397048 0.041178042 H1.463518767 0.417260867 0.085244173 H1.475307338 0.982108249 0.084496779 H1.714729329 0.769004805 0.064951907 H1.715288127 0.587554612 0.109713614 H1.743518237 0.911226534 0.113518402 H1.509304424 1.247931787 0.231211728 H1.386058504 1.174258073 0.295461176 H1.191306726 0.502931257 0.245636813 H1.316250165 0.575294755 0.182169779 H0.893771048 1.295612503 0.360400800 H0.761039631 1.259598293 0.422215413 H1.008108016 0.590340566 0.452448120 H1.135128158 0.624540850 0.391020982 H0.648719144 1.227335666 0.469467460 H0.763991964 0.536420331 0.563538388 H0.896497028 0.561587838 0.501851000 H0.376539444 1.064666579 0.578561984 H0.545745742 1.212353752 0.599222472 H0.538123549 0.976303068 0.663073142 H0.369942960 0.822943867 0.644368047 H0.229716969 1.218967098 0.639126983 H0.400019790 1.387811998 0.648770996 H0.265047891 1.390814172 0.709924789 H0.433376628 1.216281792 0.718987372 H0.285565507 0.824365684 0.709221575 H0.115807400 0.995779167 0.699976088 H0.152134669 1.184020951 0.769102402 H0.38589 1.014627013 0.779622204 H0.182893915 0.619844993 0.770979600 H0.015685456 0.776052371 0.753332990 H0.002737958 0.974709477 0.821894297 H0.163534225 0.797629807 0.840392847 H0.023344300 0.408511721 0.821105841 H -0.130002493 0.581670416 0.798432853 H -0.194915353 0.436797122 0.865661373 H -0.176560036 0.759211830 0.867488521 H1.028352538 0.070629138 0.110395323 H0.519225839 1.200934848 0.530432834 H -0.661768681 0.598938508
[Pw_forum] Raman Spectra of Molecular Crystals
Dear QE Users, My name is Casper and I am a newbie in Quantum Espresso with some experience in modeling with other periodic codes (mainly CASTEP and DMOL3). Please forgive me bothering you with my question. I don't want to spam QE maillist, but I would like to kindly ask someone for some help in modeling of vibrational spectra of molecular crystals. Could anyone send me any exemplary input which allows to compute IR and Raman spectra of any simple system? I am rather disoriented while reading some manuals etc. and I am not sure how to start. I would really appreciate your help. With best wishes, Casper Kacper Dru?bicki, Faculty of Chemistry, Department of Chemical Physics, Jagiellonian University, Ingardena Street 3, 30-060 Krak?w, Poland phone: +48 12 6632265
