From yccheng.nju at gmail.com Wed Apr 1 08:34:05 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Wed, 1 Apr 2009 14:34:05 +0800 Subject: [Pw_forum] Nitrogen PP for spin-orbital interaction calculation Message-ID: Dear QE users, Recently, I try to study AlN with spin-orbital interaction. However,there is no N pseudopotential for relativistic calculation in pwscf website. Can anybody provide me such N pseudopotential or give me some advices to get it? Thank you in advance! -- Y. C. Cheng Department of Phyics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090401/f421585b/attachment.htm From dalcorso at sissa.it Wed Apr 1 09:14:43 2009 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Wed, 01 Apr 2009 09:14:43 +0200 Subject: [Pw_forum] Nitrogen PP for spin-orbital interaction calculation In-Reply-To: References: Message-ID: <1238570083.3255.12.camel@dhpc-5-20.sissa.it> On Wed, 2009-04-01 at 14:34 +0800, ??? wrote: > Dear QE users, > Recently, I try to study AlN with spin-orbital interaction. > However,there is no N pseudopotential for relativistic calculation in > pwscf website. Can anybody provide me such N pseudopotential or give > me some advices to get it? Thank you in advance! > atomic_doc/pseudo_library/LDA/REL/N.rel-pz-rrkjus.in or atomic_doc/pseudo_library/PBE/REL/N.rel-pbe-rrkjus.in Please use the one on the cvs version and let us know if it works. Note that ld1.x of espresso 4.0.X has a bug in the new format so you need to set upf_v1_format=.true. to obtain a working PP. The bug has been corrected in ld1.x of the cvs version. Hope this helps, Andrea > -- > Y. C. Cheng > Department of Phyics > Nanjing University > Nanjing 210093 > P. R. China > Tel: 86-25-83592907 > Email: yccheng.nju 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 Beirut 2/4 Fax. 0039-040-3787528 34014 Trieste (Italy) e-mail: dalcorso at sissa.it From lfhuang at theory.issp.ac.cn Wed Apr 1 11:03:46 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Wed, 01 Apr 2009 17:03:46 +0800 Subject: [Pw_forum] =?utf-8?q?about_the_quantum_tunneling_of_diffusing_ato?= =?utf-8?q?ms?= Message-ID: <20090401090346.1149.qmail@ms.hfcas.ac.cn> Dear Prof. Kohlmeyer: Thank you very much for your kind attention! And I appreciate your patient instruction very much! Best Wishes! Yours Sincerely L. F. Huang > From: Axel Kohlmeyer > Subject: Re: [Pw_forum] about the quantum tunneling of diffusing atoms > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset="UTF-8" > > On Tue, 2009-03-31 at 08:07 +0200, Stefano Baroni wrote: > > Dear LF Huang, > > > > > > no code will ever be a substitute of common sense. What you need is > > simply the potential energy (i.e. "total energy" in the usual DFT > > parlance) of a system, as a function of the coordinates of the > > diffusing atom. As simple (or as complicated) as that! > > please let me add my 2 cents to this. > > you can go back to a quantum mechanics text book and look up > for example the discussions of quantum particle vs. wall cases. > the potential doesn't change whether the particle is quantum > or classical! > > what you seem to be looking for is some kind of > "barrier crossing probability". now, wrt to that i'd have several > concerns: > > - how accurate is your "classical" barrier potential to begin with? > you are doing graphite and hydrogen and use plain DFT. the > interaction between a benzene molecule and a hydrogen molecule is > a frequently used test case for methods that add dispersion > interactions corrections to DFT. hmmm... > > - is tunneling relevant at all? at T > 0K the carbon atoms move and > your barrier will fluctuate, that will affect the crossing > probability. similarly, if your hydrogen has enough kinetic energy, > tunneling is irrelevant. > > - what is the correlation length of your system? only if it is long > quantum effects of the atom core matter. since you seem to be > doing a solid state vacuum system, you should be good on that. > > after you've made sure that all of the above is not rendering any > further studies of the quantum effects pointless, _then_ i would look > into path-integral methods (e.g. the works of mark tuckerman and dominik > marx) that allow studying probability distributions at finite > temperature, albeit mostly in imaginary time. mind you, those > calculations are hugely expensive and you may be best off to first > make some tests with a classical potential. in fact, i would not > be surprised if a suitably chosen classical potential would give > you a better representation of the potential barrier than DFT. > > cheers, > axel. ------ ====================================================================== L.F.Huang(???) lfhuang at theory.issp.ac.cn ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(office) Fax: 86-551-5591434 Web: http://theory.issp.ac.cn (website of our theory group) http://www.issp.ac.cn (website of our institute) ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090401/85a2c7d2/attachment.htm From panda.deng.pan at gmail.com Wed Apr 1 11:16:48 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Wed, 1 Apr 2009 17:16:48 +0800 Subject: [Pw_forum] disconverge about phonon calculation Message-ID: Dear All, I am doing a calculation of the LaFeAsO. And when I run the ph.x, the disconverge happens in the Representation # 3 mode # 3. I am appraciate for any comment and suggustiong.I wonder what should I do to avoid the disconvergence like this. here is my inputs ph.in LaFeAsO &inputph amass(1)= 139.9055, amass(2)= 55.845, amass(3)= 74.9216, amass(4)= 15.9994, prefix='LaFeAsO' fildyn='LaFeAsO.dyn', tr2_ph=1.0d-8, lnscf=.true., iverbosity=1, outdir='/disk2/xgwan/tmp/', ldisp=.true., nq1=4, nq2=4, nq3=4 / and scf.in &control calculation = 'scf' restart_mode='from_scratch' prefix='LaFeAsO', pseudo_dir = '/disk2/xgwan/Quantum-Espresso/espresso-4.0.3/pseudo/', outdir='/disk2/xgwan/tmp/' / &system ibrav=6, celldm(1)=7.6232, celldm(3)=2.1676, nat=8, ntyp=4, ecutwfc = 40.0, ecutrho = 300.0, occupations= 'smearing' degauss = 0.03 smearing = 'marzari-vanderbilt' / &electrons mixing_beta = 0.7 conv_thr = 1.0d-11 / ATOMIC_SPECIES La 57.0 La.pbe-nsp-van.UPF Fe 28.0 Fe.pbe-sp-van.UPF As 33.0 As.pbe-n-van.UPF O 16.0 O.pbe-rrkjus.UPF ATOMIC_POSITIONS {crystal} La 0.250000000 0.250000000 0.139792601 La 0.750000000 0.750000000 0.860207399 Fe 0.750000000 0.250000000 0.500000000 Fe 0.250000000 0.750000000 0.500000000 As 0.250000000 0.250000000 0.636557422 As 0.750000000 0.750000000 0.363442578 O 0.750000000 0.250000000 0.000000000 O 0.250000000 0.750000000 0.000000000 K_POINTS {automatic} 8 8 8 0 0 0 in addition all the atiomic positions have been relaxed. cheers Deng Pan Nanjing University From chenhanghuipwscf at gmail.com Wed Apr 1 16:48:10 2009 From: chenhanghuipwscf at gmail.com (hanghui chen) Date: Wed, 1 Apr 2009 10:48:10 -0400 Subject: [Pw_forum] maybe a bug in the QE 4.0.4 Message-ID: <22ae3ca40904010748n50db3ef4qc86e14df7e78806c@mail.gmail.com> Dear PWscf developers and in particular Professor Baroni, Thank you very much for your instructions. I did the test to check the forces and stress in the Berry phase method with the ultrasoft pseudopotential. The forces are correct but the stress is around 50% smaller. I am not sure whether it is due to the ultrasoft pseudopotential or not. I would greatly appreciate it if the developers of QE could reexamine the calculation of stress in the Berry phase method with the ultrasoft pseudopotential. Best wishes. Hanghui Chen Department of Physics, Yale University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090401/474a6e52/attachment.htm From baroni at sissa.it Wed Apr 1 16:50:46 2009 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 1 Apr 2009 16:50:46 +0200 Subject: [Pw_forum] maybe a bug in the QE 4.0.4 In-Reply-To: <22ae3ca40904010748n50db3ef4qc86e14df7e78806c@mail.gmail.com> References: <22ae3ca40904010748n50db3ef4qc86e14df7e78806c@mail.gmail.com> Message-ID: <4D921E71-5679-40F6-BA04-E5D80A114FD7@sissa.it> Is your calculated stress OK with USPP at vaishing electric field? SB On Apr 1, 2009, at 4:48 PM, hanghui chen wrote: > Dear PWscf developers and in particular Professor Baroni, > Thank you very much for your instructions. > I did the test to check the forces and stress in the Berry > phase method with the ultrasoft pseudopotential. The forces are > correct but the stress is around 50% smaller. I am not sure whether > it is due to the ultrasoft pseudopotential or not. > I would greatly appreciate it if the developers of QE could > reexamine the calculation of stress in the Berry phase method with > the ultrasoft pseudopotential. > Best wishes. > > Hanghui Chen > Department of Physics, > Yale University > _______________________________________________ > 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 [+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/20090401/cab043e6/attachment-0001.htm From umari at democritos.it Wed Apr 1 17:08:51 2009 From: umari at democritos.it (umari at democritos.it) Date: Wed, 01 Apr 2009 17:08:51 +0200 Subject: [Pw_forum] maybe a bug in the QE 4.0.4 (Paolo Umari) Message-ID: <20090401170851.xzv9td3ag0okggkk@mail.democritos.it> Dear Hanghui, > I did the test to check the forces and stress in the Berry phase > method with the ultrasoft pseudopotential. The forces are correct but the > stress is around 50% smaller. I am not sure whether it is due to the > ultrasoft pseudopotential or not. At this moment, With a finite electric field, the forces are calculated correctly also with ultrasoft pseudopotentials. However, this is not the case of stress, which is calculated correctly only for normconserving pseudopotentials. The US case requires an extra term for the stress which we still have to implement. Best regards, Paolo Umari (Democritos) ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From carlo.nervi at unito.it Wed Apr 1 21:16:25 2009 From: carlo.nervi at unito.it (Carlo Nervi) Date: Wed, 1 Apr 2009 21:16:25 +0200 (CEST) Subject: [Pw_forum] cp.x and UPF Message-ID: <1823.151.59.234.44.1238613385.squirrel@mail.unito.it> Dear all, I suppose I've correctly generated some pseudopotentials using the atomic tool ld1.x included in QE: H.pbe-rrkjus.UPF Ru.pbe-rrkjus.UPF C.pbe-rrkjus.UPF N.pbe-rrkjus.UPF The pseudoptentials apparently works fine in geometry optimizations performed with pw.x However, when I try to use cp.x for MD the following message appears: Reading pseudopotential for specie # 1 from file : /opt/QE/pseudo/H.pbe-rrkjus.UPF file type is 0: Old CPV NC PP %%%%%%%%%%%%%%%% from readpp : error # 2 file format no longer supported Perhaps I missed some readings/informations from the manual, but I would appreciate any suggestions. Thank you, Carlo -- ------------------------------------------------------ Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 Fax: +39 011 6707855 - Dipartimento di Chimica IFM via P. Giuria 7, 10125 Torino, Italy http://lem.ch.unito.it/ From kazempoor2000 at yahoo.com Wed Apr 1 21:39:08 2009 From: kazempoor2000 at yahoo.com (ali kazempoor) Date: Wed, 1 Apr 2009 12:39:08 -0700 (PDT) Subject: [Pw_forum] Ti Message-ID: <523687.87891.qm@web33106.mail.mud.yahoo.com> Dear all Has anyone Ti pseudopotential in norm-conserving format? Thanks Ali Kazempour,Isfahan Univ. of Technology,Iran -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090401/6b6b2328/attachment.htm From manoj at phys.ufl.edu Wed Apr 1 22:57:26 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Wed, 1 Apr 2009 16:57:26 -0400 (EDT) Subject: [Pw_forum] Transmission calculation using PWCOND Message-ID: Dear PWSCF users and developers, I have been trying to understand the PWCOND code for transmission calculation, basically 'transmit.f90' file. The wavefunction in the left lead, right lead and scattering region is given by - psi_k+sum_{k'}r_{kk'}psi_k' psi= sum_{n} a_n psi_n+ sum_{\alpha l m} C_{\alpha l m}psi_{\alpha l m} sum_{k'}t_{kk'}psi_k' The above expression is from Choi & Ihm's paper, on which I believe PWCOND is based on. Now undetermined coefficients in above expression are r_{kk'}, a_n, C_{\alpha,l,m}, t_kk'. I am confused on code evaluates these coefficients. My understanding is you first get the wavefunction in the leads and then solve scattering region the same way to get the wavefunction in scattering region, so at this point you have already determined a_n and C_{\alpha,l,m}. At last do boundary matching condition between leads and scattering region to get reflection and transmission coefficient. Am I right? My thinking is based on simple quantum mechanics scattering problem where we solve schrodinger's equation in each region and then do boundary matching to get reflection and transmission coefficients. Now looking at the subroutine 'transmit.f90', this does not appear to be the case. It seems as if we are solving the Schrodinger's equation in the scattering region and doing boundary matching at the same time. Using a big matrix and solving something like AX=B. Would anybody mind explaing what's going on in subroutine transmit.f90? Regards, Manoj Srivastava Physics Graduate Student University Of Florida, Gainesville, FL From chenhanghuipwscf at gmail.com Thu Apr 2 07:12:03 2009 From: chenhanghuipwscf at gmail.com (hanghui chen) Date: Thu, 2 Apr 2009 01:12:03 -0400 Subject: [Pw_forum] maybe a bug in the QE 4.0.4 (Stefano Baroni) Message-ID: <22ae3ca40904012212o4fab3f37p5f60e4fab9e87617@mail.gmail.com> Yes. At vanish electric field, even with USPP the stress is the same as the normal calculation (without using Berry Phase method). Hope this helps. Is your calculated stress OK with USPP at vaishing electric field? SB On Apr 1, 2009, at 4:48 PM, hanghui chen wrote: > Dear PWscf developers and in particular Professor Baroni, > Thank you very much for your instructions. > I did the test to check the forces and stress in the Berry > phase method with the ultrasoft pseudopotential. The forces are > correct but the stress is around 50% smaller. I am not sure whether > it is due to the ultrasoft pseudopotential or not. > I would greatly appreciate it if the developers of QE could > reexamine the calculation of stress in the Berry phase method with > the ultrasoft pseudopotential. > Best wishes. > > Hanghui Chen > Department of Physics, > Yale University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090402/5c539e17/attachment.htm From baroni at sissa.it Thu Apr 2 08:03:50 2009 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 2 Apr 2009 08:03:50 +0200 Subject: [Pw_forum] maybe a bug in the QE 4.0.4 (Stefano Baroni) In-Reply-To: <22ae3ca40904012212o4fab3f37p5f60e4fab9e87617@mail.gmail.com> References: <22ae3ca40904012212o4fab3f37p5f60e4fab9e87617@mail.gmail.com> Message-ID: <5D469DEC-F20E-442B-8D87-6AD62912BB14@sissa.it> I am confused: no electric field, no Berry phase - what I suggested you to try is whether the stress calculated from finite differences and from the Hellmann-Feynman theorem give the same result (no Berry phase in either case). I am confident they do. SB On Apr 2, 2009, at 7:12 AM, hanghui chen wrote: > Yes. At vanish electric field, even with USPP the stress is the same > as the normal calculation (without using Berry Phase method). > Hope this helps. > > Is your calculated stress OK with USPP at vaishing electric field? > SB > > On Apr 1, 2009, at 4:48 PM, hanghui chen wrote: > > > Dear PWscf developers and in particular Professor Baroni, > > Thank you very much for your instructions. > > I did the test to check the forces and stress in the Berry > > phase method with the ultrasoft pseudopotential. The forces are > > correct but the stress is around 50% smaller. I am not sure whether > > it is due to the ultrasoft pseudopotential or not. > > I would greatly appreciate it if the developers of QE could > > reexamine the calculation of stress in the Berry phase method with > > the ultrasoft pseudopotential. > > Best wishes. > > > > Hanghui Chen > > Department of Physics, > > Yale University > _______________________________________________ > 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/20090402/d783182b/attachment.htm From fedainanir at yahoo.com Thu Apr 2 08:16:35 2009 From: fedainanir at yahoo.com (fedai inanir) Date: Wed, 1 Apr 2009 23:16:35 -0700 (PDT) Subject: [Pw_forum] I Message-ID: <848909.62461.qm@web110813.mail.gq1.yahoo.com> I desire to attend yout forum Regards Fedai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090401/5a941b47/attachment.htm From carlo.nervi at unito.it Thu Apr 2 09:51:08 2009 From: carlo.nervi at unito.it (Carlo Nervi) Date: Thu, 02 Apr 2009 09:51:08 +0200 Subject: [Pw_forum] cp.x and UPF In-Reply-To: <1823.151.59.234.44.1238613385.squirrel@mail.unito.it> References: <1823.151.59.234.44.1238613385.squirrel@mail.unito.it> Message-ID: <49D46E6C.1030006@unito.it> I forgot to mention that I'm using the 4.1CVS version of QE. Does anybody could suggest me what I'm doing wrong? Thank you, Carlo Carlo Nervi ha scritto: > Dear all, > I suppose I've correctly generated some pseudopotentials > using the atomic tool ld1.x included in QE: > H.pbe-rrkjus.UPF > Ru.pbe-rrkjus.UPF > C.pbe-rrkjus.UPF > N.pbe-rrkjus.UPF > > The pseudoptentials apparently works fine in geometry > optimizations performed with pw.x > However, when I try to use cp.x for MD the following > message appears: > > Reading pseudopotential for specie # 1 from file : > /opt/QE/pseudo/H.pbe-rrkjus.UPF > file type is 0: Old CPV NC PP > > %%%%%%%%%%%%%%%% > from readpp : error # 2 > file format no longer supported > > Perhaps I missed some readings/informations from the > manual, but I would appreciate any suggestions. > Thank you, > Carlo > From giannozz at democritos.it Thu Apr 2 09:52:37 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 2 Apr 2009 09:52:37 +0200 Subject: [Pw_forum] cp.x and UPF In-Reply-To: <1823.151.59.234.44.1238613385.squirrel@mail.unito.it> References: <1823.151.59.234.44.1238613385.squirrel@mail.unito.it> Message-ID: On Apr 1, 2009, at 21:16 , Carlo Nervi wrote: > However, when I try to use cp.x for MD the following message appears: > > Reading pseudopotential for specie # 1 from file : > /opt/QE/pseudo/H.pbe-rrkjus.UPF > file type is 0: Old CPV NC PP $ grep 'file type is' */*f90 (found in CPV/read_pseudo.f90) $ vi CPV/read_pseudo.f90 ... info = check_file_type( is ) SELECT CASE (info) CASE (0) WRITE( stdout,"(3X,'file type is ',I2,': Old CPV NC PP')") info ... let us look into check_file_type: ! 0 file is unknown (guess: old CPV norm-conserving format) ... ! 20 file is UPF So we get 0 instead of the correct code 20, set here: OPEN( UNIT = pseudounit, FILE = TRIM(filename), STATUS = 'OLD' ) header_loop: do while (ios == 0) read ( pseudounit, *, iostat = ios, err = 200) dummy if (matches ("", dummy) ) then info = 20 exit header_loop So is not found in the upf file. Is it there or not? P. --- Paolo Giannozzi, Democritos and University of Udine, Italy From carlo.nervi at unito.it Thu Apr 2 10:42:59 2009 From: carlo.nervi at unito.it (Carlo Nervi) Date: Thu, 02 Apr 2009 10:42:59 +0200 Subject: [Pw_forum] cp.x and UPF In-Reply-To: References: <1823.151.59.234.44.1238613385.squirrel@mail.unito.it> Message-ID: <49D47A93.10709@unito.it> Thanks Paolo. Below there is the output of the command "head -55 /opt/QE/pseudo/H.pbe-rrkjus.UPF" The pseudopotential was generated using ld1.x as included in 4.1CVS version. There is a line with ". Also, the line "generated=..." should not be within the PP_INFO section? I tried to generate the pseudopotentials again (in the dir atomic_doc/pseudo_library_PBE/SR, but I got the same output. Is this the problem? This means also that in my previous geometry optimization the pw.x misunderstood ? I tried to seek into the source code (write_upf.f90), but I cannot figure out if something is wrong or not. For example, st line 105 there is write (ounps, '(//a11)', err = 100, iostat = ios) "" but I cannot see the corresponding output. Furthermore, I found no line code that write "" to the file, so I do not know if all the code used to write the .UPF file is in write_upf.f90 Thanks, Carlo -------- Generated using "atomic" code by A. Dal Corso (espresso distribution) Author: ADC Generation date: 18Mar2009 Pseudopotential type: USPP Element: H Functional: PBE Suggested minimum cutoff for wavefunctions: 33. Ry Suggested minimum cutoff for charge density: 409. Ry The Pseudo was generated with a Scalar-Relativistic Calculation L component and cutoff radius for Local Potential: 1 1.1000 Valence configuration: nl pn l occ Rcut Rcut US E pseu 1S 1 0 1.00 1.100 1.200 -0.477209 Generation configuration: 1S 1 0 1.00 1.100 1.200 -0.477206 1S 1 0 0.00 1.100 1.200 -0.100000 2P 2 1 0.00 1.100 1.100 0.100000 Pseudization used: rrkj Paolo Giannozzi ha scritto: > On Apr 1, 2009, at 21:16 , Carlo Nervi wrote: > >> However, when I try to use cp.x for MD the following message appears: >> >> Reading pseudopotential for specie # 1 from file : >> /opt/QE/pseudo/H.pbe-rrkjus.UPF >> file type is 0: Old CPV NC PP > > $ grep 'file type is' */*f90 > (found in CPV/read_pseudo.f90) > > $ vi CPV/read_pseudo.f90 > ... > info = check_file_type( is ) > SELECT CASE (info) > CASE (0) > WRITE( stdout,"(3X,'file type is ',I2,': Old CPV NC > PP')") info > ... > > let us look into check_file_type: > > ! 0 file is unknown (guess: old CPV norm-conserving format) > ... > ! 20 file is UPF > > So we get 0 instead of the correct code 20, set here: > > OPEN( UNIT = pseudounit, FILE = TRIM(filename), STATUS = 'OLD' ) > header_loop: do while (ios == 0) > read ( pseudounit, *, iostat = ios, err = 200) dummy > if (matches ("", dummy) ) then > info = 20 > exit header_loop > > So is not found in the upf file. Is it there or not? > > 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 > > -- ------------------------------------------------------ Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 Fax: +39 011 6707855 - Dipartimento di Chimica IFM via P. Giuria 7, 10125 Torino, Italy http://lem.ch.unito.it/ From baroni at sissa.it Thu Apr 2 10:45:32 2009 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 2 Apr 2009 10:45:32 +0200 Subject: [Pw_forum] I In-Reply-To: <848909.62461.qm@web110813.mail.gq1.yahoo.com> References: <848909.62461.qm@web110813.mail.gq1.yahoo.com> Message-ID: <2D6FA887-3518-4B29-98C9-B5968DEE0C79@sissa.it> welcome! SB On Apr 2, 2009, at 8:16 AM, fedai inanir wrote: > I desire to attend yout forum > Regards > Fedai > > _______________________________________________ > 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/20090402/1b833d1e/attachment.htm From dalcorso at sissa.it Thu Apr 2 11:56:32 2009 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Thu, 02 Apr 2009 11:56:32 +0200 Subject: [Pw_forum] Choice of irreducible representations with ph.x In-Reply-To: <49D21327.6090106@unibo.it> References: <49D21327.6090106@unibo.it> Message-ID: <1238666192.3247.6.camel@dhpc-5-20.sissa.it> I rechecked the nrapp option in the cvs version of ph.x, but I cannot find any problem. Could you please send the input of pw.x, just to see if I can reproduce your problem. Andrea On Tue, 2009-03-31 at 14:57 +0200, Cristian Degli Esposti Boschi wrote: > I would like to perform a phonon calculation > at Gamma making a choice of only a selected number > of irreducible representations. After a proper scf > calculation I use with ph.x with an input file > like the following one: > > Phononic spectrum (1) of CoM (at Gamma) > &inputph > amass(1)=1.00794, > amass(2)=12.011, > amass(3)=14.007, > amass(4)=15.999, > amass(5)=55.845, > prefix='CoM', > outdir='/scratch/userinfm/cne0fm4a/CoM/results/', > iverbosity=1, > epsil=.false., > fildyn='CoM.dm', > nrapp=1, > / > 0.0 0.0 0.0 > 1 > > > The problem is that the calculation seems to proceed ignoring > the nrapp value and the list of numbers I put in the last line > and all the irreps are considered. This happens both for nrapp=1 > (one value in the list) or nrapp>1 (nrapp values in the list). > pw.x and ph.x are run on the CINECA cluster where there appears to be QE > ver. 4.1CVS and I would liketo save cpu time by excluding the undesired > irreps. > > Using the same syntax (nrapp and the list of irreps at the end) > to modify the scripts of example02 I successfully select only one of the > two irreps for Si with QE ver. 3.2 installed on a desktop pc (reporting > the message "Not done in this run"). Might it be a version issue? > > Thanks a lot for your help and time. -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Beirut 2/4 Fax. 0039-040-3787528 34014 Trieste (Italy) e-mail: dalcorso at sissa.it From eyvaz_isaev at yahoo.com Thu Apr 2 13:10:31 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 2 Apr 2009 04:10:31 -0700 (PDT) Subject: [Pw_forum] disconverge about phonon calculation In-Reply-To: Message-ID: <39151.20450.qm@web65711.mail.ac4.yahoo.com> Hi, Try using reduced alpha_mix(1)=0.1 (in *.ph.in), default is 0.7. > tr2_ph=1.0d-8, > lnscf=.true., You use quite high threshold for phonons, default is 1.e-10. At least my experience tells me you do not need lnscf keyword if you use nq1,2,3 and ldisp=.true. options. It is quite useful if you choose a particular q-point. > ecutwfc = 40.0, > ecutrho = 300.0, ecutrho looks small, more reliable one should be around 10 times of ecutwfc, you can test it. > conv_thr = 1.0d-11 This one is quite low. You can increase it, I think 1.d-8 is a good choice. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Wed, 4/1/09, ?? wrote: > From: ?? > Subject: [Pw_forum] disconverge about phonon calculation > To: pw_forum at pwscf.org > Date: Wednesday, April 1, 2009, 1:16 PM > Dear All, > > I am doing a calculation of the LaFeAsO. And when I run > the ph.x, > the disconverge happens in the Representation # 3 mode # > 3. I am > appraciate for any comment and suggustiong.I wonder what > should I do > to avoid the disconvergence like this. > here is my inputs > ph.in > LaFeAsO > &inputph > amass(1)= 139.9055, > amass(2)= 55.845, > amass(3)= 74.9216, > amass(4)= 15.9994, > prefix='LaFeAsO' > fildyn='LaFeAsO.dyn', > tr2_ph=1.0d-8, > lnscf=.true., > iverbosity=1, > outdir='/disk2/xgwan/tmp/', > ldisp=.true., > nq1=4, nq2=4, nq3=4 > / > and scf.in > &control > calculation = 'scf' > restart_mode='from_scratch' > prefix='LaFeAsO', > pseudo_dir = > '/disk2/xgwan/Quantum-Espresso/espresso-4.0.3/pseudo/', > outdir='/disk2/xgwan/tmp/' > / > &system > ibrav=6, > celldm(1)=7.6232, > celldm(3)=2.1676, > nat=8, > ntyp=4, > ecutwfc = 40.0, > ecutrho = 300.0, > occupations= 'smearing' > degauss = 0.03 > smearing = 'marzari-vanderbilt' > / > &electrons > mixing_beta = 0.7 > conv_thr = 1.0d-11 > / > ATOMIC_SPECIES > La 57.0 La.pbe-nsp-van.UPF > Fe 28.0 Fe.pbe-sp-van.UPF > As 33.0 As.pbe-n-van.UPF > O 16.0 O.pbe-rrkjus.UPF > ATOMIC_POSITIONS {crystal} > La 0.250000000 0.250000000 0.139792601 > La 0.750000000 0.750000000 0.860207399 > Fe 0.750000000 0.250000000 0.500000000 > Fe 0.250000000 0.750000000 0.500000000 > As 0.250000000 0.250000000 0.636557422 > As 0.750000000 0.750000000 0.363442578 > O 0.750000000 0.250000000 0.000000000 > O 0.250000000 0.750000000 0.000000000 > K_POINTS {automatic} > 8 8 8 0 0 0 > > > in addition all the atiomic positions have been relaxed. > cheers > > Deng Pan > Nanjing University > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From yukihiro_okuno at fujifilm.co.jp Thu Apr 2 14:45:38 2009 From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp) Date: Thu, 2 Apr 2009 21:45:38 +0900 Subject: [Pw_forum] PLOT for Electron Localization Function Message-ID: Dear PWSCF users. I want to plot ELF (electron localization function) in 2D figure. I found some points of values of ELF are negative. I think it should be 0 < ELF(x) < 1.0. I used USPP pseudo potential. Can't we use USPP pseudo potential for ELF calculation ? Sincerely. Yukihiro Okuno. From giannozz at democritos.it Thu Apr 2 15:00:41 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 2 Apr 2009 15:00:41 +0200 Subject: [Pw_forum] PLOT for Electron Localization Function In-Reply-To: References: Message-ID: <17E07471-CC5E-4B84-A8E2-E50584F6EB5F@democritos.it> On Apr 2, 2009, at 14:45 , yukihiro_okuno at fujifilm.co.jp wrote: > Can't we use USPP pseudo potential for ELF calculation ? didn't you notice a message warning: elf + US not fully implemented in the output file? See also: http://www.democritos.it/pipermail/pw_forum/2008-July/009537.html Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From paulatto at sissa.it Thu Apr 2 17:50:11 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 02 Apr 2009 17:50:11 +0200 Subject: [Pw_forum] cp.x and UPF In-Reply-To: <49D47A93.10709@unito.it> References: <1823.151.59.234.44.1238613385.squirrel@mail.unito.it> <49D47A93.10709@unito.it> Message-ID: On Thu, 02 Apr 2009 10:42:59 +0200, Carlo Nervi wrote: > This means also that in my previous geometry optimization the pw.x > misunderstood ? Try to remove the ">" from the CP code and recompile, then it shall work. In theory it should have worked before as well, but it seems like the change was lost somewhere in time. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From cristian.degliesposti at unibo.it Thu Apr 2 18:55:17 2009 From: cristian.degliesposti at unibo.it (Cristian Degli Esposti Boschi) Date: Thu, 02 Apr 2009 18:55:17 +0200 Subject: [Pw_forum] Choice of irreducible representations with ph.x Message-ID: <49D4EDF5.9000702@unibo.it> Here follows the input file for the preliminary scf calculation done using pw.x: Thanks, Cristian --- &CONTROL calculation = "scf", prefix = "CoM", pseudo_dir = "/scratch/userinfm/cne0fm4a/pseudo/", outdir = "/scratch/userinfm/cne0fm4a/CoM/results/", verbosity = "high", / &SYSTEM ibrav = 0, celldm(1) = 1.8897261D0, nat = 48, ntyp = 5, ecutwfc = 100.D0, ecutrho = 400.D0, nbnd = 100, / &ELECTRONS electron_maxstep = 500, conv_thr = 1.D-6, mixing_beta = 0.7D0, diagonalization = "david", / CELL_PARAMETERS cubic 20.0 0.0 0.0 0.0 20.0 0.0 0.0 0.0 15.0 ATOMIC_SPECIES H 1.00794 H.pbe-van_ak.UPF C 12.011 C.pbe-van_ak.UPF N 14.007 N.pbe-van_ak.UPF O 15.999 O.pbe-van_ak.UPF Fe 55.845 Fe.pbe-sp-van_ak.UPF ATOMIC_POSITIONS {angstrom} Fe 0.000000000 0.000000000 0.000000000 0 0 0 N -2.015936221 0.000000000 0.038768204 N -0.000013925 -2.014702715 0.046905328 N 2.017269908 0.000000000 0.040458155 N -0.000013925 2.014652715 0.046905328 C -2.847040814 1.101001374 0.021528526 C -2.847040814 -1.101001374 0.021528526 C -1.099901325 -2.845127136 0.035557609 C 1.099672879 -2.845475866 0.033358015 C 2.848427407 -1.101716959 0.018059959 C 2.848427407 1.101716959 0.018059959 C 1.099672879 2.845475866 0.033358015 C -1.099901325 2.845127136 0.035557609 C -2.424089030 2.424582315 0.023330214 C -2.424089030 -2.424582315 0.023330214 C 2.424273228 -2.425359652 0.019740116 C 2.424273228 2.425359652 0.019740116 C -4.226164834 0.682755749 0.013419289 C -4.226164834 -0.682755749 0.013419289 C -0.682749799 -4.225087959 0.031048576 C 0.682057949 -4.225434105 0.029188709 C 4.226987371 -0.683186680 0.002120738 C 4.226987371 0.683186680 0.002120738 C 0.682057949 4.225434105 0.029188709 C -0.682749799 4.225087959 0.031048576 H -3.194929270 3.196716641 0.005583502 H -3.194929270 -3.196716641 0.005583502 H 3.194370362 -3.198147171 -0.001036024 H 3.194370362 3.198147171 -0.001036024 H -5.076004919 1.361487055 0.008732438 H -5.076004919 -1.361487055 0.008732438 H -1.361920855 -5.074396365 0.029488844 H 1.360598646 -5.075191580 0.024602540 H 5.077216872 -1.361288276 -0.011051138 H 5.077216872 1.361288276 -0.011051138 H 1.360598646 5.075191580 0.024602540 H -1.361920855 5.074396365 0.029488844 N -0.005537284 0.000000000 2.101372675 C 1.071489062 0.000000000 2.880387333 C -1.100816954 0.000000000 2.946533090 N 0.704089722 0.000000000 4.188705635 C -0.674259140 0.000000000 4.251114030 C -0.006438108 0.000000000 -1.731247148 O -0.017672814 0.000000000 -2.897017310 H -2.113804696 0.000000000 2.562350854 H 2.100245178 0.000000000 2.539608359 H 1.339496592 0.000000000 4.980002249 H -1.211591117 0.000000000 5.192219697 K_POINTS 1 0.0 0.0 0.0 1.0 -- ___________________________________________________ Cristian Degli Esposti Boschi CNR, CNISM, Unita' di Ricerca di Bologna, c/o Dipartimento di Fisica, Universita' di Bologna viale Berti-Pichat, 6/2, 40127, Bologna, Italia tel. ++39 051 2095114 fax ++39 051 2095113 e-mail: cristian.degliesposti -AT- unibo.it web: http://www.df.unibo.it/fismat/theory ___________________________________________________ From giannozz at democritos.it Thu Apr 2 19:16:13 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 2 Apr 2009 19:16:13 +0200 Subject: [Pw_forum] Ti In-Reply-To: <523687.87891.qm@web33106.mail.mud.yahoo.com> References: <523687.87891.qm@web33106.mail.mud.yahoo.com> Message-ID: <2802ECD0-BA1B-42F6-8800-FF0A3260DDBA@democritos.it> On Apr 1, 2009, at 21:39 , ali kazempoor wrote: > Has anyone Ti pseudopotential in norm-conserving format? with semicore electrons in core or in valence? for which XC functional? Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090402/cbe0ff03/attachment.htm From carlo.nervi at unito.it Thu Apr 2 21:37:36 2009 From: carlo.nervi at unito.it (Carlo Nervi) Date: Thu, 2 Apr 2009 21:37:36 +0200 (CEST) Subject: [Pw_forum] cp.x and UPF In-Reply-To: References: <1823.151.59.234.44.1238613385.squirrel@mail.unito.it><49D47A93.10709@unito.it> Message-ID: <1908.151.62.48.76.1238701056.squirrel@mail.unito.it> > Try to remove the ">" from the CP code and recompile, then > it shall work. In theory it should have worked before as > well, but it seems like the change was lost somewhere in > time. I recompiled the CP code removing the ">" and it works! Thank you Lorenzo, Carlo From giannozz at democritos.it Thu Apr 2 22:14:00 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 2 Apr 2009 22:14:00 +0200 Subject: [Pw_forum] Recently generated Ultrasoft PP (IMPORTANT) Message-ID: <089E8489-3335-4E93-99F0-7E265466FED6@democritos.it> Just a reminder: * USPP generated with ld1.x may have been incorrectly written to UPF format v.2 in all 4.0.x versions . The error may have been small enough to go unnoticed but may be not negligible. All USPP in UPF format tagged as version 2.0.0 should be regenerated. Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From anjmanqi at yahoo.com.cn Fri Apr 3 02:25:01 2009 From: anjmanqi at yahoo.com.cn (jiming an) Date: Fri, 3 Apr 2009 08:25:01 +0800 (CST) Subject: [Pw_forum] Infared and Raman cross section Message-ID: <657714.33340.qm@web15004.mail.cnb.yahoo.com> Dear PWSCF user, I download the example of Infared and Raman cross section from http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_advph.html, and find that in example advph.tgz the scripts of sih4.ph.in and sih4.cs.in?are missed.?If someone who know how to write?? the script of sih4.cs.in, please?tell me, thank you. Best Regards, Jiming An ___________________________________________________________ ????????????????? http://card.mail.cn.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090403/1a0f7fb7/attachment.htm From yccheng.nju at gmail.com Fri Apr 3 03:07:15 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Fri, 3 Apr 2009 09:07:15 +0800 Subject: [Pw_forum] Nitrogen PP for spin-orbital interaction calculation In-Reply-To: <1238570083.3255.12.camel@dhpc-5-20.sissa.it> References: <1238570083.3255.12.camel@dhpc-5-20.sissa.it> Message-ID: Thank you for your advice, and the N PP works fine. 2009/4/1 Dal Corso Andrea > On Wed, 2009-04-01 at 14:34 +0800, ??? wrote: > > Dear QE users, > > Recently, I try to study AlN with spin-orbital interaction. > > However,there is no N pseudopotential for relativistic calculation in > > pwscf website. Can anybody provide me such N pseudopotential or give > > me some advices to get it? Thank you in advance! > > > > atomic_doc/pseudo_library/LDA/REL/N.rel-pz-rrkjus.inor > atomic_doc/pseudo_library/PBE/REL/N.rel-pbe-rrkjus.in > > Please use the one on the cvs version and let us know if it works. Note > that ld1.x of espresso 4.0.X has a bug in the new format so you need to > set upf_v1_format=.true. to obtain a working PP. The bug has been > corrected in ld1.x of the cvs version. > > Hope this helps, > > Andrea > > > -- > > Y. C. Cheng > > Department of Phyics > > Nanjing University > > Nanjing 210093 > > P. R. China > > Tel: 86-25-83592907 > > Email: yccheng.nju 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 Beirut 2/4 Fax. 0039-040-3787528 > 34014 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 > -- Y. C. Cheng Department of Phyics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090403/bc6343d9/attachment.htm From xuzp at MIT.EDU Fri Apr 3 03:18:05 2009 From: xuzp at MIT.EDU (Zhiping Xu) Date: Thu, 2 Apr 2009 21:18:05 -0400 Subject: [Pw_forum] Possible reason for "ortho went bananas" Message-ID: <001001c9b3fa$0aeab680$6400a8c0@zpt61p> Dear all: I performed a calculation using cp.x. However I always get "ortho went bananas" errors either using calculation = 'scf' or 'cp'. Previous post on this issue says it's convergence problem. My system converges well using pw.x. I totally have no idea about this bananas error, can someone help me on this? Thanks. Best, ZP -----cp.in-------- &CONTROL calculation = 'scf', restart_mode= 'from_scratch', pseudo_dir = '/home/xuzp/bin/lib/pwscf_pot/', outdir = './', prefix = 'cp', max_seconds = 20000., dt = 50., nstep = 20, iprint = 20, isave = 20, ndr = 90, !input_restart unit ndw = 91, !output_restart unit / &SYSTEM ibrav = 14, a = 40.000, b = 2.4519514633, c = 20.000, cosbc = 0., cosac = 0., cosab = 0., nat = 20, ntyp = 4, ecutwfc = 30., ecutrho = 240., nspin = 1, nr1b = 16, nr2b = 16, nr3b = 16, / &ELECTRONS electron_maxstep = 100, conv_thr = 1.D-6, electron_dynamics = 'damp', electron_damping = 0.2, electron_velocities = 'default', emass = 400., emass_cutoff = 2.5, orthogonalization = 'ortho', ortho_eps = 1.D-8, ortho_max = 100, / &IONS ion_dynamics = 'verlet', ion_nstepe = 1, ion_temperature = 'nose', tempw = 300.D0, fnosep = 1.D0, nhpcl = 1, nhptyp = 0, ndega = 0, tolp = 100.D0, tranp = .false., remove_rigid_rot = .true., / ATOMIC_SPECIES C 12.0107 C.pbe-rrkjus.UPF H 1.00794 H.pbe-rrkjus.UPF N 14.00674 N.pbe-rrkjus.UPF O 15.9994 O.pbe-rrkjus.UPF K_POINTS automatic 1 8 1 0 0 0 ATOMIC_POSITIONS angstrom C 5.8598630590 1.2261622260 10.0000000000 C 4.4498769380 1.2259421420 10.0000000000 -------------------------------------------------------------- -- XU Zhiping, Ph. D Civil and Environmental Engineering MIT, Cambridge, MA 02139 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090402/9add80a1/attachment-0001.htm From yccheng.nju at gmail.com Fri Apr 3 05:10:29 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Fri, 3 Apr 2009 11:10:29 +0800 Subject: [Pw_forum] The symmetry of bands Message-ID: Dear pwscf users, I calculated band structure of AlN considering spin-orbital interaction. Some published reports showed that considering spin-orbital interaction the top of valence band is split into the Gamma7, Gamma9 and Gamma7 states by crystal field and spin-orbital coupling (Appl. Phys. Lett. 83, 5163). However, my calculated band structure is different from the published one. The following is the input files: scf.in &control title = 2h_aln, prefix = '2h_band', calculation = 'scf' , restart_mode = 'from_scratch' , wf_collect = .false. , outdir = './' , wfcdir = './' , pseudo_dir = './' , tstress = .true. , tprnfor = .true. , wf_collect = .true. , / &SYSTEM ibrav = 4, celldm(1) = 5.904838149212, celldm(3) = 1.603024550651, nat = 4, ntyp = 2, ecutwfc = 80, nosym = .false. , lspinorb = .true., noncolin= .true., starting_magnetization=0.00, / &ELECTRONS electron_maxstep = 100, conv_thr = 1.D-12, / ATOMIC_SPECIES N 14.00700 N.rel-pbe-rrkjus.UPF Al 26.98200 Al.rel-pbe-rrkj.UPF ATOMIC_POSITIONS (crystal) N 0.333333333 0.666666667 0.379371803 N 0.666666667 0.333333333 0.879371803 Al 0.333333333 0.666666667 -0.002269507 Al 0.666666667 0.333333333 0.497730493 K_POINTS automatic 4 4 4 1 1 1 band.in &control title = 2h_aln, prefix = '2h_band', calculation = 'bands' , restart_mode = 'from_scratch' , wf_collect = .false. , outdir = './' , wfcdir = './' , pseudo_dir = './' , / &SYSTEM ibrav = 4, celldm(1) = 5.904838149212, celldm(3) = 1.603024550651, nat = 4, ntyp = 2, ecutwfc = 80, occupations='fixed', nbnd=30, lspinorb = .true., noncolin= .true., starting_magnetization=0.00, / &ELECTRONS electron_maxstep = 100, conv_thr = 1.D-12, / ATOMIC_SPECIES N 14.00700 N.rel-pbe-rrkjus.UPF Al 26.98200 Al.rel-pbe-rrkj.UPF ATOMIC_POSITIONS (crystal) N 0.333333333 0.666666667 0.379371803 N 0.666666667 0.333333333 0.879371803 Al 0.333333333 0.666666667 -0.002269507 Al 0.666666667 0.333333333 0.497730493 K_POINTS 1 0.000000 0.000000 0.000000 1.00 bands.in for bands.x to get band symmetry information &inputpp prefix='2h_band' outdir='./' filband='spin.dat' lsigma(3)=.true. lsym=.true. / The calculated results of the band structure at Gamma point is as following: spin.dat: &plot nbnd= 30, nks= 1 / 0.000000 0.000000 0.000000 -8.070 -8.070 -5.968 -5.968 1.092 1.092 6.154 6.154 6.169 6.169 6.803 6.803 6.816 6.816 7.015 7.015 11.136 11.136 13.603 13.603 17.513 17.513 18.094 18.094 18.118 18.118 19.967 19.967 20.042 20.042 spin.dat.rap: &plot_rap nbnd_rap= 30, nks_rap= 1 / 0.000000 0.000000 0.000000 T 1 2 5 6 5 6 5 6 3 4 1 2 3 4 1 2 1 2 5 6 5 6 1 2 3 4 1 2 5 6 My questions are: 1. Why the calculated top of valence bands (15th, and 16th ) do not split as reported work (Appl. Phys. Lett.83,5163)? 2. In the spin.dat.rap file, what does the symbol "T" stand for? And what does the "1 2 5 6 5 6 5 ..." mean? Thank you in advance! -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090403/9a0fe047/attachment.htm From yccheng.nju at gmail.com Fri Apr 3 05:21:09 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Fri, 3 Apr 2009 11:21:09 +0800 Subject: [Pw_forum] Infared and Raman cross section In-Reply-To: <657714.33340.qm@web15004.mail.cnb.yahoo.com> References: <657714.33340.qm@web15004.mail.cnb.yahoo.com> Message-ID: dynmat ! Input data (namelist "input") ! ! fildyn character input file containing the dynamical matrix ! (default: fildyn='matdyn') ! q(3) real calculate LO modes (add nonanalytic terms) along ! the direction q (default: q=(0,0,0) ) ! amass(nt) real mass for atom type nt, a.u. ! (default: amass is read from file fildyn) ! asr character indicates the type of Acoustic Sum Rule imposed ! - 'no': no Acoustic Sum Rules imposed (default) ! - 'simple': previous implementation of the asr used ! (3 translational asr imposed by correction of ! the diagonal elements of the dynamical matrix) ! - 'crystal': 3 translational asr imposed by optimized ! correction of the dyn. matrix (projection). ! - 'one-dim': 3 translational asr + 1 rotational asr ! imposed by optimized correction of the dyn. mat. (the ! rotation axis is the direction of periodicity; it ! will work only if this axis considered is one of ! the cartesian axis). ! - 'zero-dim': 3 translational asr + 3 rotational asr ! imposed by optimized correction of the dyn. mat. ! Note that in certain cases, not all the rotational asr ! can be applied (e.g. if there are only 2 atoms in a ! molecule or if all the atoms are aligned, etc.). ! In these cases the supplementary asr are cancelled ! during the orthonormalization procedure (see below). ! Finally, in all cases except 'no' a simple correction ! on the effective charges is performed (same as in the ! previous implementation). ! axis integer indicates the rotation axis for a 1D system ! (1=Ox, 2=Oy, 3=Oz ; default =3) ! filout character output file containing frequencies and modes ! (default: filout='dynmat.out') ! filmol character as above, in a format suitable for 'molden' ! (default: filmol='dynmat.mold') ! filxsf character as above, in axsf format suitable for xcrysden ! (default: filmol='dynmat.axsf') In this tutorial, i think the file sih4.cs.in is replaced by sih4.ir.in !!! 2009/4/3 jiming an > Dear PWSCF user, > I download the example of Infared and Raman cross section from > http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_advph.html, and > find that in example advph.tgz the scripts of sih4.ph.in and sih4.cs.in are > missed. If someone who know how to write the script of sih4.cs.in, > please tell me, thank you. > Best Regards, > Jiming An > > > ------------------------------ > ????????????????? > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Y. C. Cheng Department of Phyics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090403/658f03f4/attachment-0001.htm From marzari at MIT.EDU Fri Apr 3 08:31:11 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Fri, 03 Apr 2009 02:31:11 -0400 Subject: [Pw_forum] Possible reason for "ortho went bananas" In-Reply-To: <001001c9b3fa$0aeab680$6400a8c0@zpt61p> References: <001001c9b3fa$0aeab680$6400a8c0@zpt61p> Message-ID: <49D5AD2F.609@mit.edu> Zhiping Xu wrote: > Dear all: > I performed a calculation using cp.x. However I always get "ortho > went bananas" errors either using calculation = 'scf' or 'cp'. Previous > post on this issue says it's convergence problem. My system converges > well using pw.x. I totally have no idea about this bananas error, can > someone help me on this? Thanks. > Best, > ZP At the very beginning, dt needs to be small - a few steps with dt=5 or so would be good - this is because the initial random wavefunctions change a lot in the first steps. Also, your script has bot ionic dynamics and damped electronic dyanmics; this is not a car-parrinello procedure. Suppose you want to do a real cp run, this is what you need to do: a few electronic steps with ions fixed, small dt (1 to 5) to let the random wavefunctions get reasonable in shape. ~100 elecronic steps with ions fixed, and either damped electronic dynamics or conjugate gradients minimization, to let the electrons converge very weel to their ground state. start the cp runs, with verlet dynamics on the ions and on the electrons. To become expert with the stuff, do not use any thermostat at first - thus you can see how your electronic and ionic energy go. dt at most 10, probably small. There are few videos on the web (linked from the page) with lectures on ab-initio md (mostly by me, not that I am the most qualified person on the topic). What is your system, also ? A carbon dimer ? A carobn chain ? why the other pseudos ??? Note tha tthe carbon dimer is a "metal", since as it vibrates it has level crossings between homo and lumo - the only way to deal with it is with a direct minimization (in cp there is something called ensemble-dft, not too tested, thought). Please read more on the cp method (e.g. the online paper by Hutter and Marx) before continuing. Once used properly, it does work extremely well. 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 smogunov at sissa.it Fri Apr 3 09:04:14 2009 From: smogunov at sissa.it (Alexander Smogunov) Date: Fri, 3 Apr 2009 09:04:14 +0200 Subject: [Pw_forum] Transmission calculation using PWCOND In-Reply-To: References: Message-ID: <200904030904.14965.smogunov@sissa.it> Dear Manoj On Wednesday 01 April 2009 22:57, Manoj Srivastava wrote: > Dear PWSCF users and developers, > I have been trying to understand the PWCOND code for transmission > calculation, basically 'transmit.f90' file. The wavefunction in the left > lead, right lead and scattering region is given by - > > psi_k+sum_{k'}r_{kk'}psi_k' > psi= sum_{n} a_n psi_n+ sum_{\alpha l m} C_{\alpha l m}psi_{\alpha l m} > sum_{k'}t_{kk'}psi_k' > > The above expression is from Choi & Ihm's paper, on which I believe PWCOND > is based on. Now undetermined coefficients in above expression are > r_{kk'}, a_n, C_{\alpha,l,m}, t_kk'. I am confused on code evaluates these > coefficients. My understanding is you first get the wavefunction in the > leads and then solve scattering region the same way to get the > wavefunction in scattering region, so at this point you have already > determined a_n and C_{\alpha,l,m}. At last do boundary matching condition > between leads and scattering region to get reflection and transmission > coefficient. Am I right? No, the scattering state (SS) is completely determined by unknown coefficients which are: {r_kk', a_n, a_alpha, t_kk'}, the first defines the SS in the left lead, the two next in the scattering region, and the last one in the right lead. What you have found before are just basis solutions phi_n and phi_alpha of the Sroedinger eq. in the scattering region over which you expand the SS with coefficients (unknown yet) a_n and a_alpha. Hope this helps, Alexander > My thinking is based on simple quantum mechanics > scattering problem where we solve schrodinger's equation in each region > and then do boundary matching to get reflection and transmission > coefficients. > > Now looking at the subroutine 'transmit.f90', this does not appear to be > the case. It seems as if we are solving the Schrodinger's equation in the > scattering region and doing boundary matching at the same time. Using a > big matrix and solving something like AX=B. Would anybody mind explaing > what's going on in subroutine transmit.f90? > > Regards, > Manoj Srivastava > Physics Graduate Student > University Of Florida, Gainesville, FL > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From dalcorso at sissa.it Fri Apr 3 09:23:59 2009 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Fri, 03 Apr 2009 09:23:59 +0200 Subject: [Pw_forum] Choice of irreducible representations with ph.x In-Reply-To: <49D4EDF5.9000702@unibo.it> References: <49D4EDF5.9000702@unibo.it> Message-ID: <1238743439.3251.15.camel@dhpc-5-20.sissa.it> You are using k=0 and q=0 so the phonon code uses the gamma_gamma tricks. The problem is that the option nrapp with gamma_gamma tricks is not supported. In the present version of ph.x there is no input variable to disable the gamma gamma tricks when k=0 and q=0. I have added one variable in the cvs version. At the moment if you really need to use the nrapp option you can disable the gamma gamma tricks adding the instruction lgamma_gamma=.FALSE. after the lines: IF (nkstot==1.OR.(nkstot==2.AND.nspin==2)) THEN lgamma_gamma=(lgamma.AND.(ABS(xk(1,1))<1.D-12) & .AND.(ABS(xk(2,1))<1.D-12) & .AND.(ABS(xk(3,1))<1.D-12) ) ENDIF in PH/phq_readin.f90 and recompile. However the option nrapp does not produce any frequency. You have to write a small code to collect the pieces of the dynamical matrix that you need and to diagonalize it. Hope this helps, Andrea On Thu, 2009-04-02 at 18:55 +0200, Cristian Degli Esposti Boschi wrote: > Here follows the input file for the preliminary scf calculation > done using pw.x: > > Thanks, Cristian > > --- > > &CONTROL > calculation = "scf", > prefix = "CoM", > pseudo_dir = "/scratch/userinfm/cne0fm4a/pseudo/", > outdir = "/scratch/userinfm/cne0fm4a/CoM/results/", > verbosity = "high", > / > &SYSTEM > ibrav = 0, > celldm(1) = 1.8897261D0, > nat = 48, > ntyp = 5, > ecutwfc = 100.D0, > ecutrho = 400.D0, > nbnd = 100, > / > &ELECTRONS > electron_maxstep = 500, > conv_thr = 1.D-6, > mixing_beta = 0.7D0, > diagonalization = "david", > / > CELL_PARAMETERS cubic > 20.0 0.0 0.0 > 0.0 20.0 0.0 > 0.0 0.0 15.0 > ATOMIC_SPECIES > H 1.00794 H.pbe-van_ak.UPF > C 12.011 C.pbe-van_ak.UPF > N 14.007 N.pbe-van_ak.UPF > O 15.999 O.pbe-van_ak.UPF > Fe 55.845 Fe.pbe-sp-van_ak.UPF > ATOMIC_POSITIONS {angstrom} > Fe 0.000000000 0.000000000 0.000000000 0 0 0 > N -2.015936221 0.000000000 0.038768204 > N -0.000013925 -2.014702715 0.046905328 > N 2.017269908 0.000000000 0.040458155 > N -0.000013925 2.014652715 0.046905328 > C -2.847040814 1.101001374 0.021528526 > C -2.847040814 -1.101001374 0.021528526 > C -1.099901325 -2.845127136 0.035557609 > C 1.099672879 -2.845475866 0.033358015 > C 2.848427407 -1.101716959 0.018059959 > C 2.848427407 1.101716959 0.018059959 > C 1.099672879 2.845475866 0.033358015 > C -1.099901325 2.845127136 0.035557609 > C -2.424089030 2.424582315 0.023330214 > C -2.424089030 -2.424582315 0.023330214 > C 2.424273228 -2.425359652 0.019740116 > C 2.424273228 2.425359652 0.019740116 > C -4.226164834 0.682755749 0.013419289 > C -4.226164834 -0.682755749 0.013419289 > C -0.682749799 -4.225087959 0.031048576 > C 0.682057949 -4.225434105 0.029188709 > C 4.226987371 -0.683186680 0.002120738 > C 4.226987371 0.683186680 0.002120738 > C 0.682057949 4.225434105 0.029188709 > C -0.682749799 4.225087959 0.031048576 > H -3.194929270 3.196716641 0.005583502 > H -3.194929270 -3.196716641 0.005583502 > H 3.194370362 -3.198147171 -0.001036024 > H 3.194370362 3.198147171 -0.001036024 > H -5.076004919 1.361487055 0.008732438 > H -5.076004919 -1.361487055 0.008732438 > H -1.361920855 -5.074396365 0.029488844 > H 1.360598646 -5.075191580 0.024602540 > H 5.077216872 -1.361288276 -0.011051138 > H 5.077216872 1.361288276 -0.011051138 > H 1.360598646 5.075191580 0.024602540 > H -1.361920855 5.074396365 0.029488844 > N -0.005537284 0.000000000 2.101372675 > C 1.071489062 0.000000000 2.880387333 > C -1.100816954 0.000000000 2.946533090 > N 0.704089722 0.000000000 4.188705635 > C -0.674259140 0.000000000 4.251114030 > C -0.006438108 0.000000000 -1.731247148 > O -0.017672814 0.000000000 -2.897017310 > H -2.113804696 0.000000000 2.562350854 > H 2.100245178 0.000000000 2.539608359 > H 1.339496592 0.000000000 4.980002249 > H -1.211591117 0.000000000 5.192219697 > K_POINTS > 1 > 0.0 0.0 0.0 1.0 > > -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Beirut 2/4 Fax. 0039-040-3787528 34014 Trieste (Italy) e-mail: dalcorso at sissa.it From sclauzer at sissa.it Fri Apr 3 09:44:32 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 03 Apr 2009 09:44:32 +0200 Subject: [Pw_forum] The symmetry of bands In-Reply-To: References: Message-ID: <49D5BE60.7060307@sissa.it> > My questions are: > 1. Why the calculated top of valence bands (15th, and 16th ) do not > split as reported work (Appl. Phys. Lett.83,5163)? > 2. In the spin.dat.rap file, what does the symbol "T" stand for? And > what does the "1 2 5 6 5 6 5 ..." mean? I can reply to the second, for the moment: T is a flag, needed by plotband.x program, which identifies k-point which have a different symmetry with respect to the preceeding. It is meant to identify the special k-point in your k-point path used for plotting the bands. Since you have only one k-point in this calculation, you should not worry about this flag. The numbers on the rows are the representations to which the corresponding eigenvalues (those listed in the filband file) belong. The representations are listed in the standard output of bands.x, so that to each number you can associate an irreducible representation. GS > The calculated results of the band structure at Gamma point is as following: > spin.dat: > &plot nbnd= 30, nks= 1 / > 0.000000 0.000000 0.000000 > -8.070 -8.070 -5.968 -5.968 1.092 1.092 6.154 6.154 > 6.169 6.169 > 6.803 6.803 6.816 6.816 7.015 7.015 11.136 11.136 > 13.603 13.603 > 17.513 17.513 18.094 18.094 18.118 18.118 19.967 19.967 > 20.042 20.042 > > spin.dat.rap: > &plot_rap nbnd_rap= 30, nks_rap= 1 / > 0.000000 0.000000 0.000000 T > 1 2 5 6 5 6 5 6 > 3 4 > 1 2 3 4 1 2 1 2 > 5 6 > 5 6 1 2 3 4 1 2 > 5 6 -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From giannozz at democritos.it Fri Apr 3 09:46:25 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 03 Apr 2009 09:46:25 +0200 Subject: [Pw_forum] Infared and Raman cross section In-Reply-To: <657714.33340.qm@web15004.mail.cnb.yahoo.com> References: <657714.33340.qm@web15004.mail.cnb.yahoo.com> Message-ID: <49D5BED1.5050101@democritos.it> jiming an wrote: > in example advph.tgz the scripts of sih4.ph.in and sih4.cs.in are missed. there is a mismatch between file names cited in the tutorial and their names in the .tgz file: sih4.ph.in => sih4.nm.in sih4.cs.in => sih4.ir.in P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From dalcorso at sissa.it Fri Apr 3 10:14:20 2009 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Fri, 03 Apr 2009 10:14:20 +0200 Subject: [Pw_forum] The symmetry of bands In-Reply-To: References: Message-ID: <1238746460.3251.23.camel@dhpc-5-20.sissa.it> On my PC, with your input I obtain: &plot nbnd= 30, nks= 1 / 0.000000 0.000000 0.000000 -8.070 -8.070 -5.968 -5.968 1.092 1.092 6.154 6.154 6.169 6.169 6.802 6.802 6.816 6.816 7.016 7.016 11.136 11.136 13.603 13.603 17.514 17.514 18.094 18.094 18.118 18.118 19.967 19.967 20.042 20.042 That compare quite well with your bands: &plot nbnd= 30, nks= 1 / 0.000000 0.000000 0.000000 -8.070 -8.070 -5.968 -5.968 1.092 1.092 6.154 6.154 6.169 6.169 6.803 6.803 6.816 6.816 7.015 7.015 11.136 11.136 13.603 13.603 17.513 17.513 18.094 18.094 18.118 18.118 19.967 19.967 20.042 20.042 The output of bands.x says that the code is using the group C_6v to classify the bands xk=( 0.00000, 0.00000, 0.00000 ) double point group C_6v (6mm) there are 9 classes and 3 irreducible representations the character table: E -E C2 2C3 -2C3 2C6 -2C6 3s_v 3s_d -C2 -3s_v -3s_d G_7 2.00 -2.00 0.00 1.00 -1.00 1.73 -1.73 0.00 0.00 G_8 2.00 -2.00 0.00 1.00 -1.00 -1.73 1.73 0.00 0.00 G_9 2.00 -2.00 0.00 -2.00 2.00 0.00 0.00 0.00 0.00 That has only three representations. An actally the .rap file contains only 1 2 or 3: &plot_rap nbnd_rap= 30, nks_rap= 1 / 0.000000 0.000000 0.000000 T 1 1 2 2 2 2 2 2 3 3 1 1 3 3 1 1 1 1 2 2 2 2 1 1 3 3 1 1 2 2 So the two bands 11-12 at 6.803 are 1 -> Gamma_7, the two bands 13-14 at 6.816 are 3-> \Gamma_9 and the two bands 15-16 7.015 are 1 -> \Gamma_7. The splitting is 13 meV and 0.199 meV in reasonable agreement with the APL that you mention. It seems that you have the correct bands but bands.x is not using C_6v to classify the bands. Which is the output of bands.x? Andrea On Fri, 2009-04-03 at 11:10 +0800, ??? wrote: > Dear pwscf users, > I calculated band structure of AlN considering spin-orbital > interaction. Some published reports showed that considering > spin-orbital interaction the top of valence band is split into the > Gamma7, Gamma9 and Gamma7 states by crystal field and spin-orbital > coupling (Appl. Phys. Lett. 83, 5163). However, my calculated band > structure is different from the published one. The following is the > input files: > scf.in > &control > title = 2h_aln, > prefix = '2h_band', > calculation = 'scf' , > restart_mode = 'from_scratch' , > wf_collect = .false. , > outdir = './' , > wfcdir = './' , > pseudo_dir = './' , > tstress = .true. , > tprnfor = .true. , > wf_collect = .true. , > / > &SYSTEM > ibrav = 4, > celldm(1) = 5.904838149212, > celldm(3) = 1.603024550651, > nat = 4, > ntyp = 2, > ecutwfc = 80, > nosym = .false. , > lspinorb = .true., > noncolin= .true., > starting_magnetization=0.00, > / > &ELECTRONS > electron_maxstep = 100, > conv_thr = 1.D-12, > / > ATOMIC_SPECIES > N 14.00700 N.rel-pbe-rrkjus.UPF > Al 26.98200 Al.rel-pbe-rrkj.UPF > ATOMIC_POSITIONS (crystal) > N 0.333333333 0.666666667 0.379371803 > N 0.666666667 0.333333333 0.879371803 > Al 0.333333333 0.666666667 -0.002269507 > Al 0.666666667 0.333333333 0.497730493 > K_POINTS automatic > 4 4 4 1 1 1 > band.in > &control > title = 2h_aln, > prefix = '2h_band', > calculation = 'bands' , > restart_mode = 'from_scratch' , > wf_collect = .false. , > outdir = './' , > wfcdir = './' , > pseudo_dir = './' , > / > &SYSTEM > ibrav = 4, > celldm(1) = 5.904838149212, > celldm(3) = 1.603024550651, > nat = 4, > ntyp = 2, > ecutwfc = 80, > occupations='fixed', > nbnd=30, > lspinorb = .true., > noncolin= .true., > starting_magnetization=0.00, > / > &ELECTRONS > electron_maxstep = 100, > conv_thr = 1.D-12, > / > ATOMIC_SPECIES > N 14.00700 N.rel-pbe-rrkjus.UPF > Al 26.98200 Al.rel-pbe-rrkj.UPF > ATOMIC_POSITIONS (crystal) > N 0.333333333 0.666666667 0.379371803 > N 0.666666667 0.333333333 0.879371803 > Al 0.333333333 0.666666667 -0.002269507 > Al 0.666666667 0.333333333 0.497730493 > K_POINTS > 1 > 0.000000 0.000000 0.000000 1.00 > > bands.in for bands.x to get band symmetry information > > &inputpp > prefix='2h_band' > outdir='./' > filband='spin.dat' > lsigma(3)=.true. > lsym=.true. > / > The calculated results of the band structure at Gamma point is as > following: > spin.dat: > &plot nbnd= 30, nks= 1 / > 0.000000 0.000000 0.000000 > -8.070 -8.070 -5.968 -5.968 1.092 1.092 6.154 6.154 > 6.169 6.169 > 6.803 6.803 6.816 6.816 7.015 7.015 11.136 11.136 > 13.603 13.603 > 17.513 17.513 18.094 18.094 18.118 18.118 19.967 19.967 > 20.042 20.042 > > spin.dat.rap: > &plot_rap nbnd_rap= 30, nks_rap= 1 / > 0.000000 0.000000 0.000000 T > 1 2 5 6 5 6 5 6 > 3 4 > 1 2 3 4 1 2 1 2 > 5 6 > 5 6 1 2 3 4 1 2 > 5 6 > > My questions are: > 1. Why the calculated top of valence bands (15th, and 16th ) do not > split as reported work (Appl. Phys. Lett.83,5163)? > 2. In the spin.dat.rap file, what does the symbol "T" stand for? And > what does the "1 2 5 6 5 6 5 ..." > mean? > > Thank you in advance! > > -- > Y. C. Cheng > Department of Physics > Nanjing University > Nanjing 210093 > P. R. China > Tel: 86-25-83592907 > Email: yccheng.nju 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 Beirut 2/4 Fax. 0039-040-3787528 34014 Trieste (Italy) e-mail: dalcorso at sissa.it From miguel.martinez at ehu.es Fri Apr 3 12:27:31 2009 From: miguel.martinez at ehu.es (Miguel =?UTF-8?B?TWFydMOtbmV6?=) Date: Fri, 3 Apr 2009 12:27:31 +0200 Subject: [Pw_forum] Recently generated Ultrasoft PP (IMPORTANT) In-Reply-To: <089E8489-3335-4E93-99F0-7E265466FED6@democritos.it> References: <089E8489-3335-4E93-99F0-7E265466FED6@democritos.it> Message-ID: <20090403122731.072b269a@lcpybm> Dear Paolo, On Thu, 2 Apr 2009 22:14:00 +0200 Paolo Giannozzi wrote: > Just a reminder: > > * USPP generated with ld1.x may have been incorrectly written to > UPF format v.2 in all 4.0.x versions . The error may have been > small enough to go unnoticed but may be not negligible. All USPP > in UPF format tagged as version 2.0.0 should be regenerated. Excuse me for making a couple of questions: * Does this mean regenerating USPPs with the CVS version of ld1.x? * Are there any plans to release a 4.0.5 version with more bugfixes or will 4.1.0 be the next version? * Also, I suppose that multiple-projector PPs have been correctly generated as long as rcut and rcutus are the same, right? Regards, Miguel -- ---------------------------------------- Miguel Mart?nez Canales Condensed Matter Physics Dpt. UPV/EHU Faculty of Science and Technology Apdo. 644 48080 Bilbao (Spain) Fax: +34 94 601 3500 Tlf: +34 94 601 5326 ---------------------------------------- "If you have an apple and I have an apple and we exchange these apples then you and I will still each have one apple. But if you have an idea and I have an idea and we exchange these ideas, then each of us will have two ideas." George Bernard Shaw From sks.jnc at gmail.com Fri Apr 3 13:43:27 2009 From: sks.jnc at gmail.com (S. K. S.) Date: Fri, 3 Apr 2009 17:13:27 +0530 Subject: [Pw_forum] Xcrysden Message-ID: Dear Users, I have a couple of questions regarding Xcrysden. 1. Usually xcrysden files use the following format: PRIMVEC 5.5246078800 0.0000000000 0.0000000000 0.0000000000 3.9064878040 0.0000000000 0.0000000000 0.0000000000 19.5324384880 PRIMCOORD 14 1 31 0.3031580950 0.0000000000 -0.3114762280 31 2.6436116560 1.9532436370 -1.8580462820 31 -0.0518106620 0.0000000000 -3.8817233780 31 2.7623039400 1.9532436370 -5.8597314410 31 0.0000000000 0.0000000000 -7.8129756070 31 2.7623039400 1.9532436370 -9.7662192440 33 1.4763662580 1.9532436370 0.3364242780 where atomic positions are not written in crystal co-ordinates. Is it possible to specify atomic positions in crystal co-ordinates in any of .xyz or .xsf xcrysden input files (except .pwi or .pwo files). 2. How to print the thermometer in Xcrysden??? Everytime I get an error saying "could not execute /usr/bin/convert". I'll be highly obliged if anyone kindly discuss the above issues. regards, SKS JNCASR Bangalore From lanhaiping at gmail.com Fri Apr 3 14:05:40 2009 From: lanhaiping at gmail.com (lan haiping) Date: Fri, 3 Apr 2009 20:05:40 +0800 Subject: [Pw_forum] Xcrysden In-Reply-To: References: Message-ID: On Fri, Apr 3, 2009 at 7:43 PM, S. K. S. wrote: > Dear Users, > > I have a couple of questions regarding Xcrysden. > 1. Usually xcrysden files use the following format: > > PRIMVEC > 5.5246078800 0.0000000000 0.0000000000 > 0.0000000000 3.9064878040 0.0000000000 > 0.0000000000 0.0000000000 19.5324384880 > PRIMCOORD > 14 1 > 31 0.3031580950 0.0000000000 -0.3114762280 > 31 2.6436116560 1.9532436370 -1.8580462820 > 31 -0.0518106620 0.0000000000 -3.8817233780 > 31 2.7623039400 1.9532436370 -5.8597314410 > 31 0.0000000000 0.0000000000 -7.8129756070 > 31 2.7623039400 1.9532436370 -9.7662192440 > 33 1.4763662580 1.9532436370 0.3364242780 > > where atomic positions are not written in crystal co-ordinates. > Is it possible to specify atomic positions in crystal co-ordinates in any > of .xyz or .xsf xcrysden input files (except .pwi or .pwo files). > Yes, you can, please have a look at the format of XSF file. > > 2. How to print the thermometer in Xcrysden??? > Everytime I get an error saying "could not execute /usr/bin/convert". > You should install GIMP, a GNU image processor. > > I'll be highly obliged if anyone kindly discuss the above issues. > regards, > SKS > JNCASR > Bangalore > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090403/bccfe097/attachment.htm From tone.kokalj at ijs.si Fri Apr 3 14:16:25 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 03 Apr 2009 14:16:25 +0200 Subject: [Pw_forum] Xcrysden In-Reply-To: References: Message-ID: <1238760985.11942.37.camel@walk.ijs.si> On Fri, 2009-04-03 at 17:13 +0530, S. K. S. wrote: > Dear Users, > > I have a couple of questions regarding Xcrysden. > 1. Usually xcrysden files use the following format: > > PRIMVEC > 5.5246078800 0.0000000000 0.0000000000 > 0.0000000000 3.9064878040 0.0000000000 > 0.0000000000 0.0000000000 19.5324384880 > PRIMCOORD > 14 1 > 31 0.3031580950 0.0000000000 -0.3114762280 > 31 2.6436116560 1.9532436370 -1.8580462820 > 31 -0.0518106620 0.0000000000 -3.8817233780 > 31 2.7623039400 1.9532436370 -5.8597314410 > 31 0.0000000000 0.0000000000 -7.8129756070 > 31 2.7623039400 1.9532436370 -9.7662192440 > 33 1.4763662580 1.9532436370 0.3364242780 > > where atomic positions are not written in crystal co-ordinates. > Is it possible to specify atomic positions in crystal co-ordinates in any > of .xyz or .xsf xcrysden input files No! XSF uses Carthesian coordinates (Angstrom units). > 2. How to print the thermometer in Xcrysden??? > Everytime I get an error saying "could not execute /usr/bin/convert". You need ImageMagick suite of programs (convert is a member of it) for "printing" in xcrysden (actually the new xcrysden version will also try to use netbpm if image-magick is missing). For ImageMagick see: http://www.imagemagick.org Note however that (probably) all linux distributions have it. So you may find the package corresponding to your distribution. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From yccheng.nju at gmail.com Fri Apr 3 14:16:53 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Fri, 3 Apr 2009 20:16:53 +0800 Subject: [Pw_forum] The symmetry of bands In-Reply-To: <1238746460.3251.23.camel@dhpc-5-20.sissa.it> References: <1238746460.3251.23.camel@dhpc-5-20.sissa.it> Message-ID: Dear dalcorso, Thank you for your detailed reply. The initial output I posted is not consistent with your output because I changed the "starting_magnetization=0.00," to 0.01. Though the energy is the same, the symmetry is different. I recalculate it with "starting_magnetization=0.00," and the output is same as your output. In addition, I want to know how to calculate the exciton energy level ? Is that possible in recent pwscf? 2009/4/3 Dal Corso Andrea > > On my PC, with your input I obtain: > > &plot nbnd= 30, nks= 1 / > 0.000000 0.000000 0.000000 > -8.070 -8.070 -5.968 -5.968 1.092 1.092 6.154 6.154 6.169 > 6.169 > 6.802 6.802 6.816 6.816 7.016 7.016 11.136 11.136 13.603 > 13.603 > 17.514 17.514 18.094 18.094 18.118 18.118 19.967 19.967 20.042 > 20.042 > > That compare quite well with your bands: > > &plot nbnd= 30, nks= 1 / > 0.000000 0.000000 0.000000 > -8.070 -8.070 -5.968 -5.968 1.092 1.092 6.154 6.154 6.169 > 6.169 > 6.803 6.803 6.816 6.816 7.015 7.015 11.136 11.136 13.603 > 13.603 > 17.513 17.513 18.094 18.094 18.118 18.118 19.967 19.967 20.042 > 20.042 > > The output of bands.x says that the code is using the group C_6v > to classify the bands > > xk=( 0.00000, 0.00000, 0.00000 ) > > double point group C_6v (6mm) > there are 9 classes and 3 irreducible representations > the character table: > > E -E C2 2C3 -2C3 2C6 -2C6 3s_v 3s_d > -C2 -3s_v -3s_d > G_7 2.00 -2.00 0.00 1.00 -1.00 1.73 -1.73 0.00 0.00 > G_8 2.00 -2.00 0.00 1.00 -1.00 -1.73 1.73 0.00 0.00 > G_9 2.00 -2.00 0.00 -2.00 2.00 0.00 0.00 0.00 0.00 > > That has only three representations. An actally the .rap file contains > only 1 2 or 3: > > &plot_rap nbnd_rap= 30, nks_rap= 1 / > 0.000000 0.000000 0.000000 T > 1 1 2 2 2 2 2 2 3 > 3 > 1 1 3 3 1 1 1 1 2 > 2 > 2 2 1 1 3 3 1 1 2 > 2 > > So the two bands 11-12 at 6.803 are 1 -> Gamma_7, the two bands 13-14 at > 6.816 are 3-> \Gamma_9 and > the two bands 15-16 7.015 are 1 -> \Gamma_7. The splitting is 13 meV and > 0.199 meV in reasonable agreement with the APL that you mention. > > It seems that you have the correct bands but bands.x is not using C_6v > to classify the bands. > Which is the output of bands.x? > > Andrea > > > > On Fri, 2009-04-03 at 11:10 +0800, ??? wrote: > > Dear pwscf users, > > I calculated band structure of AlN considering spin-orbital > > interaction. Some published reports showed that considering > > spin-orbital interaction the top of valence band is split into the > > Gamma7, Gamma9 and Gamma7 states by crystal field and spin-orbital > > coupling (Appl. Phys. Lett. 83, 5163). However, my calculated band > > structure is different from the published one. The following is the > > input files: > > scf.in > > &control > > title = 2h_aln, > > prefix = '2h_band', > > calculation = 'scf' , > > restart_mode = 'from_scratch' , > > wf_collect = .false. , > > outdir = './' , > > wfcdir = './' , > > pseudo_dir = './' , > > tstress = .true. , > > tprnfor = .true. , > > wf_collect = .true. , > > / > > &SYSTEM > > ibrav = 4, > > celldm(1) = 5.904838149212, > > celldm(3) = 1.603024550651, > > nat = 4, > > ntyp = 2, > > ecutwfc = 80, > > nosym = .false. , > > lspinorb = .true., > > noncolin= .true., > > starting_magnetization=0.00, > > / > > &ELECTRONS > > electron_maxstep = 100, > > conv_thr = 1.D-12, > > / > > ATOMIC_SPECIES > > N 14.00700 N.rel-pbe-rrkjus.UPF > > Al 26.98200 Al.rel-pbe-rrkj.UPF > > ATOMIC_POSITIONS (crystal) > > N 0.333333333 0.666666667 0.379371803 > > N 0.666666667 0.333333333 0.879371803 > > Al 0.333333333 0.666666667 -0.002269507 > > Al 0.666666667 0.333333333 0.497730493 > > K_POINTS automatic > > 4 4 4 1 1 1 > > band.in > > &control > > title = 2h_aln, > > prefix = '2h_band', > > calculation = 'bands' , > > restart_mode = 'from_scratch' , > > wf_collect = .false. , > > outdir = './' , > > wfcdir = './' , > > pseudo_dir = './' , > > / > > &SYSTEM > > ibrav = 4, > > celldm(1) = 5.904838149212, > > celldm(3) = 1.603024550651, > > nat = 4, > > ntyp = 2, > > ecutwfc = 80, > > occupations='fixed', > > nbnd=30, > > lspinorb = .true., > > noncolin= .true., > > starting_magnetization=0.00, > > / > > &ELECTRONS > > electron_maxstep = 100, > > conv_thr = 1.D-12, > > / > > ATOMIC_SPECIES > > N 14.00700 N.rel-pbe-rrkjus.UPF > > Al 26.98200 Al.rel-pbe-rrkj.UPF > > ATOMIC_POSITIONS (crystal) > > N 0.333333333 0.666666667 0.379371803 > > N 0.666666667 0.333333333 0.879371803 > > Al 0.333333333 0.666666667 -0.002269507 > > Al 0.666666667 0.333333333 0.497730493 > > K_POINTS > > 1 > > 0.000000 0.000000 0.000000 1.00 > > > > bands.in for bands.x to get band symmetry information > > > > &inputpp > > prefix='2h_band' > > outdir='./' > > filband='spin.dat' > > lsigma(3)=.true. > > lsym=.true. > > / > > The calculated results of the band structure at Gamma point is as > > following: > > spin.dat: > > &plot nbnd= 30, nks= 1 / > > 0.000000 0.000000 0.000000 > > -8.070 -8.070 -5.968 -5.968 1.092 1.092 6.154 6.154 > > 6.169 6.169 > > 6.803 6.803 6.816 6.816 7.015 7.015 11.136 11.136 > > 13.603 13.603 > > 17.513 17.513 18.094 18.094 18.118 18.118 19.967 19.967 > > 20.042 20.042 > > > > spin.dat.rap: > > &plot_rap nbnd_rap= 30, nks_rap= 1 / > > 0.000000 0.000000 0.000000 T > > 1 2 5 6 5 6 5 6 > > 3 4 > > 1 2 3 4 1 2 1 2 > > 5 6 > > 5 6 1 2 3 4 1 2 > > 5 6 > > > > My questions are: > > 1. Why the calculated top of valence bands (15th, and 16th ) do not > > split as reported work (Appl. Phys. Lett.83,5163)? > > 2. In the spin.dat.rap file, what does the symbol "T" stand for? And > > what does the "1 2 5 6 5 6 5 ..." > > mean? > > > > Thank you in advance! > > > > -- > > Y. C. Cheng > > Department of Physics > > Nanjing University > > Nanjing 210093 > > P. R. China > > Tel: 86-25-83592907 > > Email: yccheng.nju 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 Beirut 2/4 Fax. 0039-040-3787528 > 34014 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 > -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090403/a8ab9b36/attachment-0001.htm From paulatto at sissa.it Fri Apr 3 14:07:46 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 03 Apr 2009 14:07:46 +0200 Subject: [Pw_forum] Xcrysden In-Reply-To: References: Message-ID: On Fri, 03 Apr 2009 14:05:40 +0200, lan haiping wrote: >> 2. How to print the thermometer in Xcrysden??? >> Everytime I get an error saying "could not execute /usr/bin/convert". >> > You should install GIMP, a GNU image processor. convert is part of the ImageMagick (note the spelling!) package, not of gimp. It used to not be included in some distributions for licence/patents reasons; as far as I know most distributions include it nowadays. -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From yccheng.nju at gmail.com Fri Apr 3 14:22:48 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Fri, 3 Apr 2009 20:22:48 +0800 Subject: [Pw_forum] The symmetry of bands In-Reply-To: <49D5BE60.7060307@sissa.it> References: <49D5BE60.7060307@sissa.it> Message-ID: Thank you for your help concerning plotband.x and bands.x. 2009/4/3 Gabriele Sclauzero > > > > > My questions are: > > 1. Why the calculated top of valence bands (15th, and 16th ) do not > > split as reported work (Appl. Phys. Lett.83,5163)? > > 2. In the spin.dat.rap file, what does the symbol "T" stand for? And > > what does the "1 2 5 6 5 6 5 ..." > mean? > > I can reply to the second, for the moment: > T is a flag, needed by plotband.x program, which identifies k-point which > have a different > symmetry with respect to the preceeding. It is meant to identify the > special k-point in > your k-point path used for plotting the bands. Since you have only one > k-point in this > calculation, you should not worry about this flag. > > The numbers on the rows are the representations to which the corresponding > eigenvalues > (those listed in the filband file) belong. The representations are listed > in the standard > output of bands.x, so that to each number you can associate an irreducible > representation. > > GS > > > The calculated results of the band structure at Gamma point is as > following: > > spin.dat: > > &plot nbnd= 30, nks= 1 / > > 0.000000 0.000000 0.000000 > > -8.070 -8.070 -5.968 -5.968 1.092 1.092 6.154 6.154 > > 6.169 6.169 > > 6.803 6.803 6.816 6.816 7.015 7.015 11.136 11.136 > > 13.603 13.603 > > 17.513 17.513 18.094 18.094 18.118 18.118 19.967 19.967 > > 20.042 20.042 > > > > spin.dat.rap: > > &plot_rap nbnd_rap= 30, nks_rap= 1 / > > 0.000000 0.000000 0.000000 T > > 1 2 5 6 5 6 5 6 > > 3 4 > > 1 2 3 4 1 2 1 2 > > 5 6 > > 5 6 1 2 3 4 1 2 > > 5 6 > > > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Y. C. Cheng Department of Phyics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090403/23dfeede/attachment.htm From dalcorso at sissa.it Fri Apr 3 14:36:39 2009 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Fri, 03 Apr 2009 14:36:39 +0200 Subject: [Pw_forum] The symmetry of bands In-Reply-To: References: <1238746460.3251.23.camel@dhpc-5-20.sissa.it> Message-ID: <1238762199.3251.37.camel@dhpc-5-20.sissa.it> On Fri, 2009-04-03 at 20:16 +0800, ??? wrote: > Dear dalcorso, > Thank you for your detailed reply. The initial output I posted > is not consistent with your output because I changed the > "starting_magnetization=0.00," to 0.01. Though the energy is the same, > the symmetry is different. I recalculate it with > "starting_magnetization=0.00," and the output is same as your output. > > In addition, I want to know how to calculate the exciton energy > level ? Is that possible in recent pwscf? > As far as I know the answer is no. But maybe somebody else knows better than me how to do this. Andrea > 2009/4/3 Dal Corso Andrea > > On my PC, with your input I obtain: > > &plot nbnd= 30, nks= 1 / > 0.000000 0.000000 0.000000 > -8.070 -8.070 -5.968 -5.968 1.092 1.092 6.154 > 6.154 6.169 > 6.169 > > 6.802 6.802 6.816 6.816 7.016 7.016 11.136 > 11.136 13.603 > 13.603 > 17.514 17.514 18.094 18.094 18.118 18.118 19.967 > 19.967 20.042 > 20.042 > > That compare quite well with your bands: > > &plot nbnd= 30, nks= 1 / > 0.000000 0.000000 0.000000 > -8.070 -8.070 -5.968 -5.968 1.092 1.092 6.154 > 6.154 6.169 > 6.169 > 6.803 6.803 6.816 6.816 7.015 7.015 11.136 > 11.136 13.603 > 13.603 > 17.513 17.513 18.094 18.094 18.118 18.118 19.967 > 19.967 20.042 > 20.042 > > > The output of bands.x says that the code is using the group > C_6v > to classify the bands > > xk=( 0.00000, 0.00000, 0.00000 ) > > double point group C_6v (6mm) > there are 9 classes and 3 irreducible representations > the character table: > > E -E C2 2C3 -2C3 2C6 -2C6 3s_v 3s_d > -C2 -3s_v -3s_d > G_7 2.00 -2.00 0.00 1.00 -1.00 1.73 -1.73 0.00 0.00 > G_8 2.00 -2.00 0.00 1.00 -1.00 -1.73 1.73 0.00 0.00 > G_9 2.00 -2.00 0.00 -2.00 2.00 0.00 0.00 0.00 0.00 > > That has only three representations. An actally the .rap file > contains > only 1 2 or 3: > > &plot_rap nbnd_rap= 30, nks_rap= 1 / > 0.000000 0.000000 0.000000 T > > 1 1 2 2 2 2 2 > 2 3 > 3 > 1 1 3 3 1 1 1 > 1 2 > 2 > 2 2 1 1 3 3 1 > 1 2 > 2 > > So the two bands 11-12 at 6.803 are 1 -> Gamma_7, the two > bands 13-14 at > 6.816 are 3-> \Gamma_9 and > the two bands 15-16 7.015 are 1 -> \Gamma_7. The splitting is > 13 meV and > 0.199 meV in reasonable agreement with the APL that you > mention. > > It seems that you have the correct bands but bands.x is not > using C_6v > to classify the bands. > Which is the output of bands.x? > > Andrea > > > > > On Fri, 2009-04-03 at 11:10 +0800, ??? wrote: > > Dear pwscf users, > > I calculated band structure of AlN considering > spin-orbital > > interaction. Some published reports showed that considering > > spin-orbital interaction the top of valence band is split > into the > > Gamma7, Gamma9 and Gamma7 states by crystal field and > spin-orbital > > coupling (Appl. Phys. Lett. 83, 5163). However, my > calculated band > > structure is different from the published one. The > following is the > > input files: > > scf.in > > &control > > title = 2h_aln, > > prefix = '2h_band', > > calculation = 'scf' , > > restart_mode = 'from_scratch' , > > wf_collect = .false. , > > outdir = './' , > > wfcdir = './' , > > pseudo_dir = './' , > > tstress = .true. , > > tprnfor = .true. , > > wf_collect = .true. , > > / > > &SYSTEM > > ibrav = 4, > > celldm(1) = 5.904838149212, > > celldm(3) = 1.603024550651, > > nat = 4, > > ntyp = 2, > > ecutwfc = 80, > > nosym = .false. , > > lspinorb = .true., > > noncolin= .true., > > starting_magnetization=0.00, > > / > > &ELECTRONS > > electron_maxstep = 100, > > conv_thr = 1.D-12, > > / > > ATOMIC_SPECIES > > N 14.00700 N.rel-pbe-rrkjus.UPF > > Al 26.98200 Al.rel-pbe-rrkj.UPF > > ATOMIC_POSITIONS (crystal) > > N 0.333333333 0.666666667 0.379371803 > > N 0.666666667 0.333333333 0.879371803 > > Al 0.333333333 0.666666667 -0.002269507 > > Al 0.666666667 0.333333333 0.497730493 > > K_POINTS automatic > > 4 4 4 1 1 1 > > band.in > > &control > > title = 2h_aln, > > prefix = '2h_band', > > calculation = 'bands' , > > restart_mode = 'from_scratch' , > > wf_collect = .false. , > > outdir = './' , > > wfcdir = './' , > > pseudo_dir = './' , > > / > > &SYSTEM > > ibrav = 4, > > celldm(1) = 5.904838149212, > > celldm(3) = 1.603024550651, > > nat = 4, > > ntyp = 2, > > ecutwfc = 80, > > occupations='fixed', > > nbnd=30, > > lspinorb = .true., > > noncolin= .true., > > starting_magnetization=0.00, > > / > > &ELECTRONS > > electron_maxstep = 100, > > conv_thr = 1.D-12, > > / > > ATOMIC_SPECIES > > N 14.00700 N.rel-pbe-rrkjus.UPF > > Al 26.98200 Al.rel-pbe-rrkj.UPF > > ATOMIC_POSITIONS (crystal) > > N 0.333333333 0.666666667 0.379371803 > > N 0.666666667 0.333333333 0.879371803 > > Al 0.333333333 0.666666667 -0.002269507 > > Al 0.666666667 0.333333333 0.497730493 > > K_POINTS > > 1 > > 0.000000 0.000000 0.000000 1.00 > > > > bands.in for bands.x to get band symmetry information > > > > &inputpp > > prefix='2h_band' > > outdir='./' > > filband='spin.dat' > > lsigma(3)=.true. > > lsym=.true. > > / > > The calculated results of the band structure at Gamma point > is as > > following: > > spin.dat: > > &plot nbnd= 30, nks= 1 / > > 0.000000 0.000000 0.000000 > > -8.070 -8.070 -5.968 -5.968 1.092 1.092 6.154 > 6.154 > > 6.169 6.169 > > 6.803 6.803 6.816 6.816 7.015 7.015 11.136 > 11.136 > > 13.603 13.603 > > 17.513 17.513 18.094 18.094 18.118 18.118 19.967 > 19.967 > > 20.042 20.042 > > > > spin.dat.rap: > > &plot_rap nbnd_rap= 30, nks_rap= 1 / > > 0.000000 0.000000 0.000000 T > > 1 2 5 6 5 6 5 > 6 > > 3 4 > > 1 2 3 4 1 2 1 > 2 > > 5 6 > > 5 6 1 2 3 4 1 > 2 > > 5 6 > > > > My questions are: > > 1. Why the calculated top of valence bands (15th, and 16th ) > do not > > split as reported work (Appl. Phys. Lett.83,5163)? > > 2. In the spin.dat.rap file, what does the symbol "T" stand > for? And > > what does the "1 2 5 6 5 6 > 5 ..." > > mean? > > > > Thank you in advance! > > > > -- > > Y. C. Cheng > > Department of Physics > > Nanjing University > > Nanjing 210093 > > P. R. China > > Tel: 86-25-83592907 > > Email: yccheng.nju 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 Beirut 2/4 Fax. 0039-040-3787528 > 34014 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 > > > > > -- > Y. C. Cheng > Department of Physics > Nanjing University > Nanjing 210093 > P. R. China > Tel: 86-25-83592907 > Email: yccheng.nju 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 Beirut 2/4 Fax. 0039-040-3787528 34014 Trieste (Italy) e-mail: dalcorso at sissa.it From giannozz at democritos.it Fri Apr 3 14:49:46 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 03 Apr 2009 14:49:46 +0200 Subject: [Pw_forum] Recently generated Ultrasoft PP (IMPORTANT) In-Reply-To: <20090403122731.072b269a@lcpybm> References: <089E8489-3335-4E93-99F0-7E265466FED6@democritos.it> <20090403122731.072b269a@lcpybm> Message-ID: <49D605EA.7050306@democritos.it> Miguel Mart?nez wrote: > * Does this mean regenerating USPPs with the CVS version of ld1.x? yes > * Are there any plans to release a 4.0.5 version with more bugfixes or > will 4.1.0 be the next version? a 4.0.5 version is actually already out (without the fix). I didn't announce it because it was a sort of experiment. It is in the download page ion qe-forge.org . I think it will be the last of the series. > * Also, I suppose that multiple-projector PPs have been correctly > generated as long as rcut and rcutus are the same, right? right P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From sks.jnc at gmail.com Fri Apr 3 15:34:16 2009 From: sks.jnc at gmail.com (S. K. S.) Date: Fri, 3 Apr 2009 19:04:16 +0530 Subject: [Pw_forum] Xcrysden In-Reply-To: <1238760985.11942.37.camel@walk.ijs.si> References: <1238760985.11942.37.camel@walk.ijs.si> Message-ID: Dear all, Thanks a lot for your kind and helpful reply. Few things about Xcrysden are yet to be known. 1. Now I can print the thermometer after installing ImageMagick. However, it prints the thermometer separately. Please have a look on the attached file. Is it possible in XCrysden to print the thermometer together with the background "Xcrysden charge-density" plot???? 2. >No! XSF uses Carthesian coordinates (Angstrom units). Then, is there any other smart way to change Angstrom coordinates to crystal coordinates in Xcrysden??? The usual pen and paper (analytical and manual) method is not always time-saving especially for non-cubic (for instance, hexagonal) systems. 3. Another thing I would like to know, whether it is possible to increase the size of the "XYZ co-ordinate symbol" in Xcrysden??? One can easily zoom the picture of a molecule or a crystal in the Xcrysden and print the larger size picture because Xcrysden's print is an XWD window dump. But what about co-ordinate symbol??? Is it possible to make its size bigger????? regards, SKS -------------- next part -------------- A non-text attachment was scrubbed... Name: mol-urea2D.jpg Type: image/jpeg Size: 4822 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090403/fe5fcd38/attachment-0001.jpg From tone.kokalj at ijs.si Fri Apr 3 15:44:46 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 03 Apr 2009 15:44:46 +0200 Subject: [Pw_forum] Xcrysden In-Reply-To: References: <1238760985.11942.37.camel@walk.ijs.si> Message-ID: <1238766286.11942.45.camel@walk.ijs.si> On Fri, 2009-04-03 at 19:04 +0530, S. K. S. wrote: > Dear all, > > Thanks a lot for your kind and helpful reply. > Few things about Xcrysden are yet to be known. > > 1. Now I can print the thermometer after installing > ImageMagick. However, it prints the thermometer > separately. Please have a look on the attached file. > Is it possible in XCrysden to print the thermometer together > with the background "Xcrysden charge-density" plot???? This is why image manipulation or some other presentation programs are used for. Take as many "primitive" images as you like and assemble a master image there. > 2. >No! XSF uses Carthesian coordinates (Angstrom units). > > Then, is there any other smart way to change Angstrom coordinates > to crystal coordinates in Xcrysden??? The usual pen and paper > (analytical and manual) method is not always time-saving especially for > non-cubic (for instance, hexagonal) systems. There is! Instead of making XSF, make a plain pw.x input file and specify ATOMIC_POSITIONS in crystal units, then load that pw.x input file into xcrysden. Now you can pass to Carthesian if you wish so (i.e. save the loaded file as XSF). > > 3. Another thing I would like to know, whether it is possible to increase > the size of the "XYZ co-ordinate symbol" in Xcrysden??? > One can easily zoom the picture of a molecule or a crystal in the > Xcrysden and print the larger size picture because Xcrysden's print is > an XWD window dump. But what about co-ordinate symbol??? > Is it possible to make its size bigger????? Unfortunately not. (you can make it manual though: print it as it is so that you will have the directions, and then make a new one in some image processing program) Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From spaul at ncsu.edu Fri Apr 3 16:55:56 2009 From: spaul at ncsu.edu (sujata Paul) Date: Fri, 03 Apr 2009 10:55:56 -0400 Subject: [Pw_forum] PP for Planar average of all |psi|^2 In-Reply-To: 1238435159.30989.0.camel@archimedes Message-ID: <1238770557.11303.12.camel@archimedes> Hi Gabriele, This is regarding the calculation of Planar Average of |psi^2| using "PP/plan_avg.f90". So according to your suggestion I tried this input file: ========================================= &inputpp prefix='CO2', outdir './' filplot = 'CO2-psi-plan_avg.pot' / ========================================= Before that I did SCF calculations using Gamma Kpoint. "K_POINTS {automatic} 1 1 1 0 0 0" With this recipe the error I got is this: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from plan_avg : error # 2 planar average with gamma tricks not yet implemented %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% So I can't calculate |psi^2| planar average for k= (0.0000000 0.0000000 0.0000000)? Thanks and Regards -- SUJATA PAUL GRADUATE STUDENT PHYSICS DEPARTMENT NORTH CAROLINA STATE UNIVERSITY USA It was written in the error message you posted at the beginning: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from punch_plot : error # 1 no longer implemented, see PP/plan_avg.f90 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% So I guessed "plot_num=9" is not implemented in post processing. You have to use the program plan_avg.x in place of pp.x for this task. Though I never used it, from a glance to the source I guess it should be simple to use: NAMELIST / inputpp / outdir, prefix, filplot You simply need to specify these three strings... GS From kazempoor2000 at yahoo.com Fri Apr 3 17:09:32 2009 From: kazempoor2000 at yahoo.com (ali kazempoor) Date: Fri, 3 Apr 2009 08:09:32 -0700 (PDT) Subject: [Pw_forum] Ti Message-ID: <493353.16993.qm@web33108.mail.mud.yahoo.com> Dear paolo For valence in LDA thanks --- On Thu, 4/2/09, Paolo Giannozzi wrote: From: Paolo Giannozzi Subject: Re: [Pw_forum] Ti To: "PWSCF Forum" Date: Thursday, April 2, 2009, 10:16 AM On Apr 1, 2009, at 21:39 , ali kazempoor wrote: Has anyone Ti pseudopotential in norm-conserving format? with semicore electrons in core or in valence? for which XC functional? Paolo --- Paolo Giannozzi,?Democritos and?University of Udine, Italy -----Inline Attachment Follows----- _______________________________________________ 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/20090403/13801d4a/attachment.htm From sclauzer at sissa.it Fri Apr 3 17:21:56 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 03 Apr 2009 17:21:56 +0200 Subject: [Pw_forum] PP for Planar average of all |psi|^2 In-Reply-To: <1238770557.11303.12.camel@archimedes> References: <1238770557.11303.12.camel@archimedes> Message-ID: <49D62994.3080204@sissa.it> Dear Paul, sujata Paul wrote: > Hi Gabriele, > This is regarding the calculation of Planar Average of > |psi^2| using "PP/plan_avg.f90". So according to your suggestion I tried > this input file: > ========================================= > &inputpp > prefix='CO2', > outdir './' > filplot = 'CO2-psi-plan_avg.pot' > / > ========================================= > > Before that I did SCF calculations using Gamma Kpoint. > "K_POINTS {automatic} > 1 1 1 0 0 0" > > With this recipe the error I got is this: > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from plan_avg : error # 2 > planar average with gamma tricks not yet implemented > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% That's strange, as far as I know gamma triks are used only if you specify K_POINTS GAMMA The gamma_only flag should be enabled only when using this K_POINTS setting. Please verify if this is true (you can examine the data-file.xml in your .save directory or add a print statement). GS > So I can't calculate |psi^2| planar average for > k= (0.0000000 0.0000000 0.0000000)? > > Thanks and Regards > -- > SUJATA PAUL > GRADUATE STUDENT > PHYSICS DEPARTMENT > NORTH CAROLINA STATE UNIVERSITY > USA > > > > It was written in the error message you posted at the beginning: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from punch_plot : error # 1 > no longer implemented, see PP/plan_avg.f90 > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > So I guessed "plot_num=9" is not implemented in post processing. > > You have to use the program plan_avg.x in place of pp.x for this task. > Though I never used it, from a glance to the source I guess it should be simple to use: > > NAMELIST / inputpp / outdir, prefix, filplot > > You simply need to specify these three strings... > > > GS > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From babderre at physics.auth.gr Sat Apr 4 15:38:21 2009 From: babderre at physics.auth.gr (babderre at physics.auth.gr) Date: Sat, 4 Apr 2009 16:38:21 +0300 Subject: [Pw_forum] Fermi surface Message-ID: <20090404163821.11411cgjanxan45c@mail.physics.auth.gr> Dear pwscf users, 1-I calculated the fermi surface of Po without spin-orbit Zval = 6.00 with nbnd=7, It works fine . 2-considering spin-orbital interaction Zval = 16.0 ,nbnd= 24 i get error , i think this is related to nbnd =24 with three lines !! so I want to know the change of which parameters lead to this problem? thanks in advance belabbes. http://parsem.physics.auth.gr/belabbes.htm From babderre at physics.auth.gr Sat Apr 4 15:51:43 2009 From: babderre at physics.auth.gr (babderre at physics.auth.gr) Date: Sat, 4 Apr 2009 16:51:43 +0300 Subject: [Pw_forum] Fermi surface Message-ID: <20090404165143.18625qqax3133f48@mail.physics.auth.gr> Dear PWSCF users. 1-I calculated the fermi surface of Po without spin-orbit Zval = 6.00 with nbnd=7, It works fine 2-considering spin-orbital interaction Zval = 16.0 ,nbnd= 24 i get error , i think this is related to nbnd =24 with three lines !! so I want to know the change of which parameters lead to this problem? thanks in advance! belabbes. http://parsem.physics.auth.gr/belabbes.htm From eyvaz_isaev at yahoo.com Sat Apr 4 16:31:41 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sat, 4 Apr 2009 07:31:41 -0700 (PDT) Subject: [Pw_forum] Fermi surface In-Reply-To: <20090404165143.18625qqax3133f48@mail.physics.auth.gr> Message-ID: <571874.83550.qm@web65705.mail.ac4.yahoo.com> Dear Belabbes, Have you tried the recent bands_FS.f90 I posted. At least, it worked for spin-polarized cases. If you can send me your output file I will try to fix the error. I do not think it is connected to bands number, as the free format is used for this purpose. Bests, Eyvaz. --- On Sat, 4/4/09, babderre at physics.auth.gr wrote: > From: babderre at physics.auth.gr > Subject: [Pw_forum] Fermi surface > To: pw_forum at pwscf.org > Date: Saturday, April 4, 2009, 5:51 PM > Dear PWSCF users. > > 1-I calculated the fermi surface of Po without spin-orbit > Zval = 6.00 with nbnd=7, It works fine > > 2-considering spin-orbital interaction Zval = 16.0 ,nbnd= > 24 > i get error , i think this is related to nbnd =24 > with three lines !! > > so I want to know the change of which parameters lead > to this problem? > > thanks in advance! > belabbes. > http://parsem.physics.auth.gr/belabbes.htm > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From stewart at cnf.cornell.edu Sat Apr 4 20:13:34 2009 From: stewart at cnf.cornell.edu (Derek Stewart) Date: Sat, 04 Apr 2009 14:13:34 -0400 Subject: [Pw_forum] effect of symmetry warning on final band symmetry analysis In-Reply-To: <49D605EA.7050306@democritos.it> References: <089E8489-3335-4E93-99F0-7E265466FED6@democritos.it> <20090403122731.072b269a@lcpybm> <49D605EA.7050306@democritos.it> Message-ID: <20090404181334.97313.qmail@mail.spidergraphics.com> Hi everyone, I am doing some analysis of the symmetry of bands in a crystal. When I run the initial scf calculation, I get the warning associated with the fractional coordinates that has been discussed many times in the forum. warning: symmetry operation # 2 not allowed. fractional translation: -0.4999997 0.5000000 0.4999996 in crystal coordinates I know this does not cause any problems in calculating the general properties of the system. I did however want to confirm that it will not have any effect on the band symmetry analysis that is performed with bands.x when lsym=.true. (ie thinking the system has a lower symmetry than it actually does). Thanks, Derek ################################ Derek Stewart, Ph. D. Scientific Computation Associate http://www.people.cornell.edu/pages/das248/ 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 From giannozz at democritos.it Sat Apr 4 21:36:57 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 4 Apr 2009 21:36:57 +0200 Subject: [Pw_forum] effect of symmetry warning on final band symmetry analysis In-Reply-To: <20090404181334.97313.qmail@mail.spidergraphics.com> References: <089E8489-3335-4E93-99F0-7E265466FED6@democritos.it> <20090403122731.072b269a@lcpybm> <49D605EA.7050306@democritos.it> <20090404181334.97313.qmail@mail.spidergraphics.com> Message-ID: On Apr 4, 2009, at 20:13 , Derek Stewart wrote: > warning: symmetry operation # 2 not allowed. fractional > translation: > -0.4999997 0.5000000 0.4999996 in crystal coordinates > [...] > I did however want to confirm that it will not have any effect on > the band > symmetry analysis that is performed with bands.x when lsym=.true. (ie > thinking the system has a lower symmetry than it actually does). it will: the code will assume a lower symmetry than the true one (unless you are dealing with a supercell, where "fractional" is not really fractional; if the code recognizes that there is a fractional translation in a supercell, it should disable their usage, though) Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From stewart at cnf.cornell.edu Sat Apr 4 21:41:45 2009 From: stewart at cnf.cornell.edu (Derek Stewart) Date: Sat, 04 Apr 2009 15:41:45 -0400 Subject: [Pw_forum] effect of symmetry warning on final band symmetry analysis In-Reply-To: References: <089E8489-3335-4E93-99F0-7E265466FED6@democritos.it> <20090403122731.072b269a@lcpybm> <49D605EA.7050306@democritos.it> <20090404181334.97313.qmail@mail.spidergraphics.com> Message-ID: <20090404194145.98415.qmail@mail.spidergraphics.com> Hi Paolo, Thanks for your very quick reply. It looks like I will need to make sure all the symmetries are properly accounted for. Best regards, Derek Paolo Giannozzi writes: > > On Apr 4, 2009, at 20:13 , Derek Stewart wrote: > >> warning: symmetry operation # 2 not allowed. fractional >> translation: >> -0.4999997 0.5000000 0.4999996 in crystal coordinates >> [...] >> I did however want to confirm that it will not have any effect on >> the band >> symmetry analysis that is performed with bands.x when lsym=.true. (ie >> thinking the system has a lower symmetry than it actually does). > > it will: the code will assume a lower symmetry than the true one > (unless > you are dealing with a supercell, where "fractional" is not really > fractional; > if the code recognizes that there is a fractional translation in a > supercell, > it should disable their usage, though) > > 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 > ################################ Derek Stewart, Ph. D. Scientific Computation Associate http://www.people.cornell.edu/pages/das248/ 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 From manoj at phys.ufl.edu Sat Apr 4 22:19:48 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Sat, 4 Apr 2009 16:19:48 -0400 (EDT) Subject: [Pw_forum] Transmission calculation using PWCOND In-Reply-To: <200904030904.14965.smogunov@sissa.it> Message-ID: Thank you Alexander! -Manoj On Fri, 3 Apr 2009, Alexander Smogunov wrote: > Dear Manoj > > On Wednesday 01 April 2009 22:57, Manoj Srivastava wrote: > > Dear PWSCF users and developers, > > I have been trying to understand the PWCOND code for transmission > > calculation, basically 'transmit.f90' file. The wavefunction in the left > > lead, right lead and scattering region is given by - > > > > psi_k+sum_{k'}r_{kk'}psi_k' > > psi= sum_{n} a_n psi_n+ sum_{\alpha l m} C_{\alpha l m}psi_{\alpha l m} > > sum_{k'}t_{kk'}psi_k' > > > > The above expression is from Choi & Ihm's paper, on which I believe PWCOND > > is based on. Now undetermined coefficients in above expression are > > r_{kk'}, a_n, C_{\alpha,l,m}, t_kk'. I am confused on code evaluates these > > coefficients. My understanding is you first get the wavefunction in the > > leads and then solve scattering region the same way to get the > > wavefunction in scattering region, so at this point you have already > > determined a_n and C_{\alpha,l,m}. At last do boundary matching condition > > between leads and scattering region to get reflection and transmission > > coefficient. Am I right? > No, the scattering state (SS) is completely determined by unknown > coefficients which are: {r_kk', a_n, a_alpha, t_kk'}, the first defines the > SS in the left lead, the two next in the scattering region, and the last one > in the right lead. What you have found before are just basis solutions phi_n > and phi_alpha of the Sroedinger eq. in the scattering region over which you > expand the SS with coefficients (unknown yet) a_n and a_alpha. > > Hope this helps, > Alexander > > > My thinking is based on simple quantum mechanics > > scattering problem where we solve schrodinger's equation in each region > > and then do boundary matching to get reflection and transmission > > coefficients. > > > > Now looking at the subroutine 'transmit.f90', this does not appear to be > > the case. It seems as if we are solving the Schrodinger's equation in the > > scattering region and doing boundary matching at the same time. Using a > > big matrix and solving something like AX=B. Would anybody mind explaing > > what's going on in subroutine transmit.f90? > > > > Regards, > > Manoj Srivastava > > Physics Graduate Student > > University Of Florida, Gainesville, FL > > > > _______________________________________________ > > 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 baroni at sissa.it Sun Apr 5 07:53:46 2009 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 5 Apr 2009 07:53:46 +0200 Subject: [Pw_forum] effect of symmetry warning on final band symmetry analysis In-Reply-To: <20090404194145.98415.qmail@mail.spidergraphics.com> References: <089E8489-3335-4E93-99F0-7E265466FED6@democritos.it> <20090403122731.072b269a@lcpybm> <49D605EA.7050306@democritos.it> <20090404181334.97313.qmail@mail.spidergraphics.com> <20090404194145.98415.qmail@mail.spidergraphics.com> Message-ID: <346CF0CB-1A67-45AB-8A73-933819EA2368@sissa.it> On Apr 4, 2009, at 9:41 PM, Derek Stewart wrote: > Hi Paolo, > > Thanks for your very quick reply. It looks like I will need to make > sure > all the symmetries are properly accounted for. or else you learn how to assign the symmetry of each electronic state the ol' good way (i.e. using a table of characters ;-) Stefano --- 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/20090405/deeab10e/attachment-0001.htm From kazempoor2000 at yahoo.com Sun Apr 5 12:34:09 2009 From: kazempoor2000 at yahoo.com (ali kazempoor) Date: Sun, 5 Apr 2009 03:34:09 -0700 (PDT) Subject: [Pw_forum] Ti-GGA pseudo Message-ID: <465776.89652.qm@web33105.mail.mud.yahoo.com> Dear all Has anyone Ti pseudopotential with GGA xc functional in norm-conserving format(valence? electron)? thanks ?Ali Kazempour, Isfahan university of technology,Iran -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090405/93a07d7a/attachment.htm From quantumdft at gmail.com Sun Apr 5 13:06:41 2009 From: quantumdft at gmail.com (vega lew) Date: Sun, 5 Apr 2009 19:06:41 +0800 Subject: [Pw_forum] How to plot molecular hybrid orbitals for surface slab geometry? Message-ID: <412f6c680904050406k6fb170dtde2abe879ddd3e45@mail.gmail.com> Dear all, I'm studying the water splitting behavior on certain surfaces. And I have identified a special structural features of the surface for water dissociation. But I can't tell why that kind of feature did a positive effect on water dissociation. One visitor to our group thought this behavior has a strong dependence of molecular hybrid orbitals of atoms near the surface. From akohlmey at cmm.chem.upenn.edu Sun Apr 5 16:17:06 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sun, 05 Apr 2009 10:17:06 -0400 Subject: [Pw_forum] How to plot molecular hybrid orbitals for surface slab geometry? In-Reply-To: <412f6c680904050406k6fb170dtde2abe879ddd3e45@mail.gmail.com> References: <412f6c680904050406k6fb170dtde2abe879ddd3e45@mail.gmail.com> Message-ID: <1238941026.16967.22.camel@zero> On Sun, 2009-04-05 at 19:06 +0800, vega lew wrote: > Dear all, > > I'm studying the water splitting behavior on certain surfaces. And I > have identified a special structural features of the surface for water > dissociation. > But I can't tell why that kind of feature did a positive effect on > water dissociation. One visitor to our group thought this behavior has > a strong dependence of molecular hybrid orbitals of atoms near the was this person by any chance an organic chemist?? > surface. From a Structural Chemistry viewpoint, certain atomic > structure could result in different hybrid styles of molecular > orbitals. The feature I identified may have a favorable shape of > hybrid orbitals for water approaching and dissociating. you have to forget about the nice orbital pictures that you see in chemistry text books. they are a visual crutch to break a problem where everything interacts with everything into individual additive components. it still works surprisingly well, but only after the fact, i.e. you can rationalize findings that you got elsewhere in a simplified form. > > I wonder whether QE has a function for ploting the shape of hybrid > molecular orbitals near the surface. this is what the gods of quantum chemistry created the population analysis for. after you project on atomic (pseudo) wavefunctions you can determine the amount of s-,p-,d-character of your individual states. this is not without problems, though. the partitioning is somewhat arbitrary and the projection from plane waves to atomic orbitals is not complete, i.e. you are missing out on some contributions that do not fit into the atomic orbital basis you provide. cheers, axel. > > thank you for reading > > best, > > vega > > -- > ================================================================================== > Vega Lew ( weijia liu) > PH.D Candidate in Chemical Engineering > State Key Laboratory of Materials-oriented Chemical Engineering > College of Chemistry and Chemical Engineering > Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > ****************************************************************************************************************** > Email: vegalew at gmail.com > Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, > Nanjing, Jiangsu, China > ****************************************************************************************************************** > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From quantumdft at gmail.com Sun Apr 5 18:27:30 2009 From: quantumdft at gmail.com (vega lew) Date: Mon, 6 Apr 2009 00:27:30 +0800 Subject: [Pw_forum] How to plot molecular hybrid orbitals for surface slab geometry? In-Reply-To: <1238941026.16967.22.camel@zero> References: <412f6c680904050406k6fb170dtde2abe879ddd3e45@mail.gmail.com> <1238941026.16967.22.camel@zero> Message-ID: <412f6c680904050927l3b084076jf90d3e47e5b5a664@mail.gmail.com> Dear sir, >>was this person by any chance an organic chemist?? to some extent. >>this is what the gods of quantum chemistry created the population >>analysis for. after you project on atomic (pseudo) wavefunctions you >>can determine the amount of s-,p-,d-character of your individual states. >>this is not without problems, though. the partitioning is somewhat >>arbitrary and the projection from plane waves to atomic orbitals is >>not complete, i.e. you are missing out on some contributions that do >>not fit into the atomic orbital basis you provide. Do you mean the projwfc.x could help me quite a lot? If so, i would be very happy. I just identify a kind of structural feature for certain atomic arrangement. if the atom near the surface arrange that way, dissociative adsorption of water could be favourable. But I can't tell why that rules is correct? so I tried to explain something at electronic scale. Do you think I could explain this just by plotting some DoS/pDoS for certain atoms? Is there a systemic tutorial or text book for it? By the way, I'm considering intel Quadcore XEON 5500 series CPU and corresponding dual socket motherboard. the memory bandwith could be tripled as I7 series. May I have your opinion about QE performance on 5500 series servers? Do you think it is really a sensible decision to spend ~$20,000 for four XEON 5500 servers. thank you for your time vega On Sun, Apr 5, 2009 at 10:17 PM, Axel Kohlmeyer wrote: > On Sun, 2009-04-05 at 19:06 +0800, vega lew wrote: > > Dear all, > > > > I'm studying the water splitting behavior on certain surfaces. And I > > have identified a special structural features of the surface for water > > dissociation. > > But I can't tell why that kind of feature did a positive effect on > > water dissociation. One visitor to our group thought this behavior has > > a strong dependence of molecular hybrid orbitals of atoms near the > > was this person by any chance an organic chemist?? > > > surface. From a Structural Chemistry viewpoint, certain atomic > > structure could result in different hybrid styles of molecular > > orbitals. The feature I identified may have a favorable shape of > > hybrid orbitals for water approaching and dissociating. > > > > you have to forget about the nice orbital pictures that you see in > chemistry text books. they are a visual crutch to break a problem > where everything interacts with everything into individual additive > components. it still works surprisingly well, but only after the fact, > i.e. you can rationalize findings that you got elsewhere in a simplified > form. > > > > > > > I wonder whether QE has a function for ploting the shape of hybrid > > molecular orbitals near the surface. > > this is what the gods of quantum chemistry created the population > analysis for. after you project on atomic (pseudo) wavefunctions you > can determine the amount of s-,p-,d-character of your individual states. > this is not without problems, though. the partitioning is somewhat > arbitrary and the projection from plane waves to atomic orbitals is > not complete, i.e. you are missing out on some contributions that do > not fit into the atomic orbital basis you provide. > > cheers, > axel. > > > > > thank you for reading > > > > best, > > > > vega > > > > -- > > > ================================================================================== > > Vega Lew ( weijia liu) > > PH.D Candidate in Chemical Engineering > > State Key Laboratory of Materials-oriented Chemical Engineering > > College of Chemistry and Chemical Engineering > > Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > > > ****************************************************************************************************************** > > Email: vegalew at gmail.com > > Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, > > Nanjing, Jiangsu, China > > > ****************************************************************************************************************** > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090406/b4401e35/attachment.htm From Andrea.Marini at roma2.infn.it Sun Apr 5 21:44:36 2009 From: Andrea.Marini at roma2.infn.it (Andrea Marini) Date: Sun, 5 Apr 2009 21:44:36 +0200 (CEST) Subject: [Pw_forum] Yambo: news and announcements Message-ID: Dear colleagues, The Yambo GPL project is now in full swing! We are happy to inform you of a few recent developments regarding the code. * At http://www.yambo-code.org , you can now download a recent version of the code, browse the documentation on the web, and download and try out some tutorials that we use at the TDDFT school in Benasque (Spain) (Sept. 2008 and Jan. 2010). * Soon to appear in Computer Physics Communications is the related paper, "Yambo: an ab initio tool for excited state calculations" Andrea Marini, Conor Hogan, Myrta Gr?ning, Daniele Varsano Comp. Phys. Comm. (2009), in press. doi:10.1016/j.cpc.2009.02.003. But you can download the online version at: http://www.yambo-code.org/counter/click.php?id=17 * Finally, we have recently opened a discussion forum (bulletin board) at http://www.yambo-code.org/forum where anyone can join the community of users and developers in posting queries about the code or look for support in using Yambo. We invite you and your students to download and use Yambo for your reseach. In case you will do so, please keep us updated and send us your feedback ! And that's all! Thank you for your interest in Yambo! Please don't hesitate to contact us at yambo at yambo-code.org, or via the Forum itself. Best regards, The Yambo team Andrea Marini Conor Hogan Myrta Gruning Daniele Varsano -------------------------------------------------------------------------- Andrea MARINI Physics Department, University of Rome "Tor Vergata" (Italy) - phone: +39-0672594894 - fax: +39-062023507 - - andrea.marini at roma2.infn.it -- http://www.yambo-code.org/people/andrea - From quantumdft at gmail.com Mon Apr 6 07:48:50 2009 From: quantumdft at gmail.com (vega lew) Date: Mon, 6 Apr 2009 13:48:50 +0800 Subject: [Pw_forum] Yambo: news and announcements In-Reply-To: References: Message-ID: <412f6c680904052248o6c8af524g52342956f0be05cb@mail.gmail.com> Dear friend, Could Yambo cooperate with PWScf 4.0 or later? thank you vega On Mon, Apr 6, 2009 at 3:44 AM, Andrea Marini wrote: > Dear colleagues, > > The Yambo GPL project is now in full swing! We are happy to inform > you of a few recent developments regarding the code. > > * At http://www.yambo-code.org , you can now download a recent version of > the code, browse the documentation on the web, and download and try out some > tutorials that we use at the TDDFT school in Benasque (Spain) (Sept. 2008 > and Jan. 2010). > > * Soon to appear in Computer Physics Communications is the related paper, > "Yambo: an ab initio tool for excited state calculations" Andrea Marini, > Conor Hogan, Myrta Gr?ning, Daniele Varsano Comp. Phys. Comm. (2009), in > press. doi:10.1016/j.cpc.2009.02.003. But you can download the online > version at: > > http://www.yambo-code.org/counter/click.php?id=17 > > * Finally, we have recently opened a discussion forum (bulletin board) at > > http://www.yambo-code.org/forum > > where anyone can join the community of users and developers in posting > queries about the code or look for support in using Yambo. > > We invite you and your students to download and use Yambo for your reseach. > In case you will do so, please keep us updated and send us your feedback ! > > And that's all! Thank you for your interest in Yambo! Please don't hesitate > to contact us at yambo at yambo-code.org, or via the Forum itself. > > Best regards, > > The Yambo team > > Andrea Marini > Conor Hogan > Myrta Gruning > Daniele Varsano > > -------------------------------------------------------------------------- > Andrea MARINI > > Physics Department, University of Rome "Tor Vergata" (Italy) > - phone: +39-0672594894 - fax: +39-062023507 - > > - andrea.marini at roma2.infn.it -- http://www.yambo-code.org/people/andrea - > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090406/554258c3/attachment.htm From quantumdft at gmail.com Mon Apr 6 07:56:42 2009 From: quantumdft at gmail.com (vega lew) Date: Mon, 6 Apr 2009 13:56:42 +0800 Subject: [Pw_forum] PPEPPD2010 Call for Abstract now! Message-ID: <412f6c680904052256x4bf89303j28503a03c2f01232@mail.gmail.com> ############ For more information please click www.ppeppd2010.cn###################### ######## Second Announcement: http://www.ppeppd2010.cn/PDF/2nd_Broadcasting.pdf ######## Dear Sir or Madam, We warmly invite you to attend PPEPPD2010 which will be held between May 16-21, 2010, at Suzhou, China. PPEPPD stands for Properties and Phase Equilibria for Product and Process Design. This conference is basically a thermo conference and has been held every three years for the past 33 years. The conference site for PPEPPD2010 is a wonderful resort near Shanghai. This conference will provide you great opportunity to socialize with a lot of people. PPEPPD is held every three years, alternating among the North America, South America, Europe, and Asia. The Conference brings together up to 250 academic, governmental and industrial researchers from as many as 35 countries to focus on fundamentals and applications of properties and phase equilibria in a wide range of industries, such as oil, gas, chemical, pharmaceutical, materials, biotechnology and food. The proceedings are published in Fluid Phase Equilibria. Attached is a list of the session titles which may give you an idea of the major topics to be discussed in this Conference. General information about the conference is provided on the web page http://www.ppeppd2010.cn/. Furthermore, we want to show you a glance of the conference site. The city of Suzhou, one of most scenic towns in China, is a UNESCO World Heritage Site (http://whc.unesco.org/en/list/813). Since 42% area of the city is covered by water, including many ponds, streams and canals, Suzhou is praised as the ?Oriental Venice?.Taihu Lake, four-fifths of which is in the territory of Suzhou, is the third largest fresh lake in China, with East Hill (location of PPEPPD2010), West Hill and other scenic spots in its vicinity. The region offers uniquely delicious cuisine and is a center of silk manufacture. Several tours and activities are planned for accompanying persons. You could also enjoy your unforgettable experience of World Expo Shanghai 2010 after the conference. PPEPPD2010 Themes: Quantum Computation and Force Fields Surfaces, Interfaces and Confinement Effects Molecular Simulation and Multiscale Simulation Nanoscience and Nanotechnology Phase Equilibria (Theory and Experiments) Materials (Metals, inorganic solids, polymers and liquid crystals) Biological and Pharmaceutical Systems Energy, Environment and Sustainability Product and Process Engineering Enclosed is the conference information in detail. And you could get more on our website, http://www.ppeppd2010.cn/. We look forward to seeing you in beautiful Suzhou! Yours sincerely, Xiaohua LU Professor Xiaohua LU Chairman of the International Organizing Committee, PPEPPD 2010 State Key Laboratory of Material Oriented Chemical Engineering Nanjing University of Technology, Nanjing, 210009, China With all best wishes on behalf of the International Organizing Committee, Xiao-Hua, Lu (Nanjing University of Technology, China, Chair ) Hong-Lai, Liu (East China University of Science and Technology, China, Vice Chair) Susana Bottini (University Nacional del Sur, Argentina) Kwong-Yu, Chan (The University of Hong Kong, China) Chau-Chyun, Chen (ASPEN TECH. Inc., USA) Peter Cummings (Vanderbilt University, USA) Ioannis Economou (NRCPS"Demokritos", Greece) Carol Hall (North Carolina State University, USA) Seiya Hirohama (Invensys Process Systems Japan Inc., Japan) Hiroshi Inomata (Tohoku University, Japan) George Jackson (Imperial College London, UK) John O'Connell (University of Virginia, USA) Athanassios Panagiotopoulos (Princeton University, USA) Cor Peters (Delft University of Technology, Netherlands) Gabriele Sadowski (University of Dortmund, Germany) Doros Theodorou (National Technical University of Athens, Greece) Ki Pung Yoo (Sogang University, Korea) ############ For more information please click www.ppeppd2010.cn###################### ######## Second Announcement: http://www.ppeppd2010.cn/PDF/2nd_Broadcasting.pdf ######## thank you for your time vega -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090406/32345292/attachment.htm From Andrea.Marini at roma2.infn.it Mon Apr 6 09:55:38 2009 From: Andrea.Marini at roma2.infn.it (Andrea Marini) Date: Mon, 6 Apr 2009 09:55:38 +0200 (CEST) Subject: [Pw_forum] Yambo is interfaced with PWscf In-Reply-To: <412f6c680904052248o6c8af524g52342956f0be05cb@mail.gmail.com> References: <412f6c680904052248o6c8af524g52342956f0be05cb@mail.gmail.com> Message-ID: Dear collegues, to integrate my previous E-mail about the Yambo code I'd like to remind you what we have already posted in the forum some time ago ( http://www.democritos.it/pipermail/pw_forum/2008-September/009974.html ) "Yambo is a multi-purpose C/Fortran code which can compute various excited state properties (GW corrections, absorption spectra including excitonic effects, etc) using many body perturbation theory. We invite you to download the code freely at http://www.yambo-code.org. Yambo is interfaced with the PWscf code, following a standard non-self-consistent run. The interface makes use of the IOTK library of Giovanni Bussi, now part of the standard QE distribution, and the QEXML library routies of Andrea Ferretti. See the webpage for instructions for use, tutorials, and so on." Many thanks ! Andrea On Mon, 6 Apr 2009, vega lew wrote: > Dear friend, > > Could Yambo cooperate with PWScf 4.0 or later? > > thank you > > vega > > ================================================================================== > Vega Lew ( weijia liu) > PH.D Candidate in Chemical Engineering > State Key Laboratory of Materials-oriented Chemical Engineering > College of Chemistry and Chemical Engineering > Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > ************************************************************************************* -------------------------------------------------------------------------- Andrea MARINI Physics Department, University of Rome "Tor Vergata" (Italy) - phone: +39-0672594894 - fax: +39-062023507 - - andrea.marini at roma2.infn.it -- http://www.yambo-code.org/people/andrea - From gennaro.oliva at cnr.it Mon Apr 6 19:57:38 2009 From: gennaro.oliva at cnr.it (gennaro.oliva at cnr.it) Date: Mon, 6 Apr 2009 19:57:38 +0200 Subject: [Pw_forum] Parallel File System suggestion Message-ID: <20090406175738.GA23742@lavezzi.sic.rm.cnr.it> Hi there I'm trying to set up a good environment for multiple espresso users on my cluster. I have a blade center with 14 dual processor quad-core servers interconnected with infiniband + 2 gigE networks and a fibre channel storage area network. I want to allow the users to run and restart espresso jobs but they can't use their home (located on the SAN) for temporary files. I have read "Understanding parallel I/O" on the faq page where it is suggested to use a parallel file system. Which one would you suggest? I'm running centos 5.2 + openmpi 1.2.7. Thanks for your help -- Gennaro Oliva From anavat_ila at yahoo.com Tue Apr 7 09:27:05 2009 From: anavat_ila at yahoo.com (Ali Tavana) Date: Tue, 7 Apr 2009 00:27:05 -0700 (PDT) Subject: [Pw_forum] e-ph Message-ID: <594186.81163.qm@web51810.mail.re2.yahoo.com> Dear all, Does somebody know the reason of following error in e-ph calculations (when q!=0)? It is not so trivial as I have tested many solutions and I am sure every thing in input files is OK. ---------------------------------------------------------------------------------------------------------- ???? Mode symmetry, C_2h (2/m)? point group: ???? omega(? 1 -? 1) =??????? -42.4? [cm-1]?? --> A_g??????????????? ???? omega(? 2 -? 2) =???????? 54.7? [cm-1]?? -->?? ? ???? omega(? 2 -? 2) =???????? 54.7? [cm-1]?? -->?? 0B_g??????????????? ???? omega(? 2 -? 2) =???????? 54.7? [cm-1]?? -->?? ? ???? omega(? 2 -? 2) =???????? 54.7? [cm-1]?? --> A_u??????????????? ???? omega(? 3 -? 3) =???????? 57.7? [cm-1]?? -->?? ? ???? omega(? 3 -? 3) =???????? 57.7? [cm-1]?? --> B_g??????????????? ???? omega(? 3 -? 3) =???????? 57.7? [cm-1]?? -->?? ? ???? omega(? 3 -? 3) =???????? 57.7? [cm-1]?? -->?? 0A_u??????????????? ???? omega(? 4 -? 4) =???????? 87.0? [cm-1]?? --> B_u??????????????? ???? omega(? 5 -? 5) =??????? 112.0? [cm-1]?? -->?? ? ???? omega(? 5 -? 5) =??????? 112.0? [cm-1]?? --> A_g??????????????? ???? omega(? 5 -? 5) =??????? 112.0? [cm-1]?? -->?? ? ???? omega(? 5 -? 5) =??????? 112.0? [cm-1]?? -->?? 0B_u??????????????? ???? omega(? 6 -? 6) =??????? 122.1? [cm-1]?? -->?? ? ???? omega(? 6 -? 6) =??????? 122.1? [cm-1]?? -->?? 0A_g??????????????? ???? omega(? 6 -? 6) =??????? 122.1? [cm-1]?? -->?? ? ???? omega(? 6 -? 6) =??????? 122.1? [cm-1]?? --> B_u??????????????? ???? omega(? 7 -? 7) =??????? 156.0? [cm-1]?? --> B_u??????????????? ???? omega(? 8 -? 8) =??????? 172.2? [cm-1]?? --> A_u??????????????? ???? omega(? 9 -? 9) =??????? 175.2? [cm-1]?? --> A_g??????????????? ???? omega( 10 - 10) =??????? 175.8? [cm-1]?? --> B_u??????????????? ???? omega( 11 - 11) =??????? 192.2? [cm-1]?? -->?? ? ???? omega( 11 - 11) =??????? 192.2? [cm-1]?? --> B_g??????????????? ???? omega( 11 - 11) =??????? 192.2? [cm-1]?? -->?? ? ???? omega( 11 - 11) =??????? 192.2? [cm-1]?? -->?? 0A_u??????????????? ???? omega( 12 - 12) =??????? 204.8? [cm-1]?? --> A_u??????????????? ???? omega( 13 - 13) =??????? 274.3? [cm-1]?? --> B_u??????????????? ???? omega( 14 - 14) =??????? 287.1? [cm-1]?? --> B_g??????????????? ???? omega( 15 - 15) =??????? 289.4? [cm-1]?? -->?? ? ???? omega( 15 - 15) =??????? 289.4? [cm-1]?? --> A_g??????????????? ???? omega( 15 - 15) =??????? 289.4? [cm-1]?? -->?? ? ???? omega( 15 - 15) =??????? 289.4? [cm-1]?? -->?? 0B_u??????????????? ???? omega( 16 - 16) =??????? 291.9? [cm-1]?? --> B_u??????????????? ???? omega( 17 - 17) =??????? 339.3? [cm-1]?? --> B_u??????????????? ???? omega( 18 - 18) =??????? 410.7? [cm-1]?? -->?? ? ???? omega( 18 - 18) =??????? 410.7? [cm-1]?? --> A_g??????????????? ???? omega( 18 - 18) =??????? 410.7? [cm-1]?? -->?? ? ???? omega( 18 - 18) =??????? 410.7? [cm-1]?? -->?? 0B_u??????????????? ???? omega( 19 - 19) =??????? 436.0? [cm-1]?? --> B_u??????????????? ???? omega( 20 - 20) =??????? 583.9? [cm-1]?? --> A_g??????????????? ???? omega( 21 - 21) =??????? 693.7? [cm-1]?? --> A_u??????????????? ?************************************************************************** ???? electron-phonon interaction? ... ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ???? from lint : error #??????? 38 ???? cannot remap grid on k-point list ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ???? stopping ... -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090407/396db425/attachment.htm From giannozz at democritos.it Tue Apr 7 09:44:50 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 7 Apr 2009 09:44:50 +0200 Subject: [Pw_forum] e-ph In-Reply-To: <594186.81163.qm@web51810.mail.re2.yahoo.com> References: <594186.81163.qm@web51810.mail.re2.yahoo.com> Message-ID: On Apr 7, 2009, at 9:27 , Ali Tavana wrote: > Does somebody know the reason of following error in e-ph > calculations (when q!=0)? everybody knows the reason, since the same question has been asked 1001 times, and the answer is always the same. See example07/README: The dense grid must contain all k and k+q grid points used in the subsequent electron-phonon calculation and must be dense enough to produce accurate el-phon coefficients (in particular the double- delta integral at Ef is very critical). Note that you have to use unshifted grids (k1=k2=k3=0) only, that include k=0! P. --- Paolo Giannozzi, Democritos and University of Udine, Italy From rezaebraahimi at yahoo.com Tue Apr 7 12:00:18 2009 From: rezaebraahimi at yahoo.com (Reza Ebraahimi) Date: Tue, 7 Apr 2009 03:00:18 -0700 (PDT) Subject: [Pw_forum] strange results in phonon calculation Message-ID: <636062.3365.qm@web59402.mail.ac4.yahoo.com> Hi Trying to?run phonon calculation at Gamma point for my case, the code gives the following result for?some of the modes:????? ???? omega( 1) =*************** [THz] =*************** [cm-1] ???? omega( 2) =*************** [THz] =*************** [cm-1] ???? omega( 3) =*************** [THz] =*************** [cm-1] What does these mean? How should i fix this? Thanx Reza Ebraahimi - Graduate student Tehran University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090407/a25aec0c/attachment.htm From paulatto at sissa.it Tue Apr 7 12:16:33 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 07 Apr 2009 12:16:33 +0200 Subject: [Pw_forum] strange results in phonon calculation In-Reply-To: <636062.3365.qm@web59402.mail.ac4.yahoo.com> References: <636062.3365.qm@web59402.mail.ac4.yahoo.com> Message-ID: On Tue, 07 Apr 2009 12:00:18 +0200, Reza Ebraahimi wrote: > Hi > Trying to run phonon calculation at Gamma point for my case, the code > gives the following result for some of the modes: > > omega( 1) =*************** [THz] =*************** [cm-1] > omega( 2) =*************** [THz] =*************** [cm-1] > omega( 3) =*************** [THz] =*************** [cm-1] > > What does these mean? How should i fix this? Dear Reza, it means that the computed frequencies cannot fit in the output format used to print them. As the format is quite generous (15 characters for a 6 decimal places fixed-point number) it means that your frequencies are larger or equal than 10^9 THz or negative and smaller or equal than 10^8 THz (the minus counts as one character). In other words, it means that your scf calculation was already wrong in the first place, e.g. not enough converged or not properly relaxed and is giving you some non-realistic frequencies. It may also be some code bug, but it is less likely. Please provide more detail? if you want a more insightful explanation of your problem. regards [1] inputs and outputs of the scf and phonon calculations -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From eyvaz_isaev at yahoo.com Tue Apr 7 12:21:36 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 7 Apr 2009 03:21:36 -0700 (PDT) Subject: [Pw_forum] strange results in phonon calculation In-Reply-To: <636062.3365.qm@web59402.mail.ac4.yahoo.com> Message-ID: <223389.9805.qm@web65712.mail.ac4.yahoo.com> Dear Reza, No one is able to tell you exactly, why you got "banana" until you post your input files. At least, check your structure and see pressure in output file. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Tue, 4/7/09, Reza Ebraahimi wrote: > From: Reza Ebraahimi > Subject: [Pw_forum] strange results in phonon calculation > To: pw_forum at pwscf.org > Date: Tuesday, April 7, 2009, 2:00 PM > Hi > Trying to?run phonon calculation at Gamma point for my > case, the code gives the following result for?some of the > modes:????? > > ???? omega( 1) =*************** [THz] =*************** > [cm-1] > ???? omega( 2) =*************** [THz] =*************** > [cm-1] > ???? omega( 3) =*************** [THz] =*************** > [cm-1] > > What does these mean? How should i fix this? > Thanx > Reza Ebraahimi - Graduate student > Tehran University > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From mansourehp at gmail.com Tue Apr 7 14:50:49 2009 From: mansourehp at gmail.com (Mansoureh Pashangpour) Date: Tue, 7 Apr 2009 16:20:49 +0330 Subject: [Pw_forum] phonon Message-ID: Dear all I'm trying to calculate phonon frequencies( Raman and infrared) with LDA+U method. how can I perform this calculation? Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090407/7bbdf225/attachment.htm From eyvaz_isaev at yahoo.com Tue Apr 7 15:52:19 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 7 Apr 2009 06:52:19 -0700 (PDT) Subject: [Pw_forum] phonon In-Reply-To: Message-ID: <349500.82042.qm@web65714.mail.ac4.yahoo.com> > phonon frequencies( Raman and infrared) with LDA+U ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Tue, 4/7/09, Mansoureh Pashangpour wrote: > From: Mansoureh Pashangpour > Subject: [Pw_forum] phonon > To: "PWSCF Forum" > Date: Tuesday, April 7, 2009, 4:50 PM > Dear all > I'm trying to calculate phonon frequencies( Raman and > infrared) with LDA+U > method. how can I perform this calculation? > Thanks > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From eyvaz_isaev at yahoo.com Tue Apr 7 15:53:16 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 7 Apr 2009 06:53:16 -0700 (PDT) Subject: [Pw_forum] phonon In-Reply-To: Message-ID: <962372.58983.qm@web65705.mail.ac4.yahoo.com> > phonon frequencies( Raman and infrared) with LDA+U Not yet. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Tue, 4/7/09, Mansoureh Pashangpour wrote: > From: Mansoureh Pashangpour > Subject: [Pw_forum] phonon > To: "PWSCF Forum" > Date: Tuesday, April 7, 2009, 4:50 PM > Dear all > I'm trying to calculate phonon frequencies( Raman and > infrared) with LDA+U > method. how can I perform this calculation? > Thanks > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From dimpy.sharma at tyndall.ie Tue Apr 7 15:57:32 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Tue, 7 Apr 2009 14:57:32 +0100 Subject: [Pw_forum] Queries Message-ID: Hi, I am not getting my output . My input file is given below. I have kept the kinetic energy cut of for the wavefunction (ecutwfc) as 35Ry. Can you please tell me. &CONTROL calculation ='relax' restart_mode = 'from_scratch' outdir = '/sfiwork/dsharma/silane/wfc4' pseudo_dir = '/sfiwork/dsharma/QE_Pseudos/' prefix = '5' tstress = .false. tprnfor = .true. etot_conv_thr = 1.D-4 forc_conv_thr = 1.D-3 nstep = 600 / &SYSTEM ibrav = 0 celldm(1) =7.1516 nat = 6 ntyp = 2 ecutwfc = 35.0 ecutrho = 100.0 nbnd = 10 / &ELECTRONS diagonalization ='david' mixing_mode = 'plain' conv_thr = 1.0d-1 mixing_beta = 0.7 / &IONS / &CELL cell_dynamics='none' / CELL_PARAMETERS cubic 1.000000000 0.000000000 0.000000000 0.000000000 2.000000000 0.000000000 0.000000000 0.000000000 2.000000000 ATOMIC_SPECIES Si 28.08600 Si.pz-vbc.UPF H 1.00800 H.pz-vbc.UPF ATOMIC_POSITIONS angstroms Si 2.95020 -0.66592 -0.12341 Si 4.90939 0.61749 0.11358 H 5.11746 1.46255 -1.09398 H 4.69823 1.55915 1.25968 H 2.84169 -1.61779 1.02344 H 3.00948 -1.48841 -1.36525 K_POINTS automatic 4 1 1 0 0 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090407/a62334da/attachment.htm From prasenjit.jnc at gmail.com Tue Apr 7 16:14:43 2009 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Tue, 7 Apr 2009 16:14:43 +0200 Subject: [Pw_forum] Queries In-Reply-To: References: Message-ID: <627e0ffa0904070714o99634a3ma8856b939f0f4966@mail.gmail.com> What do you mean by "I'm not getting my output"?? Moreover for electronic minimization, conv_thr = 1.0d-1 is too high. You should go to much lower values, of the order of 1.0d-08 (or atleast the default value) to get any meaningful results. Prasenjit. 2009/4/7 Dimpy Sharma > Hi, > > I am not getting my output . My input file is given below. I have kept the > kinetic energy cut of for the wavefunction (ecutwfc) as 35Ry. Can you please > tell me. > &CONTROL > calculation ='relax' > restart_mode = 'from_scratch' > outdir = '/sfiwork/dsharma/silane/wfc4' > pseudo_dir = '/sfiwork/dsharma/QE_Pseudos/' > prefix = '5' > tstress = .false. > tprnfor = .true. > etot_conv_thr = 1.D-4 > forc_conv_thr = 1.D-3 > nstep = 600 > / > &SYSTEM > ibrav = 0 > celldm(1) =7.1516 > nat = 6 > ntyp = 2 > ecutwfc = 35.0 > ecutrho = 100.0 > nbnd = 10 > / > &ELECTRONS > diagonalization ='david' > mixing_mode = 'plain' > conv_thr = 1.0d-1 > mixing_beta = 0.7 > / > &IONS > / > &CELL > cell_dynamics='none' > > / > CELL_PARAMETERS cubic > 1.000000000 0.000000000 0.000000000 > 0.000000000 2.000000000 0.000000000 > 0.000000000 0.000000000 2.000000000 > ATOMIC_SPECIES > Si 28.08600 Si.pz-vbc.UPF > H 1.00800 H.pz-vbc.UPF > ATOMIC_POSITIONS angstroms > Si 2.95020 -0.66592 -0.12341 > Si 4.90939 0.61749 0.11358 > H 5.11746 1.46255 -1.09398 > H 4.69823 1.55915 1.25968 > H 2.84169 -1.61779 1.02344 > H 3.00948 -1.48841 -1.36525 > K_POINTS automatic > 4 1 1 0 0 0 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- PRASENJIT GHOSH, POST-DOC, ROOM NO: 265, MAIN BUILDING, CM SECTION, ICTP, STRADA COSTERIA 11, TRIESTE, 34104, ITALY PHONE: +39 040 2240 369 (O) +39 3807528672 (M) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090407/4723de5e/attachment.htm From prasenjit.jnc at gmail.com Tue Apr 7 16:17:56 2009 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Tue, 7 Apr 2009 16:17:56 +0200 Subject: [Pw_forum] Queries In-Reply-To: References: Message-ID: <627e0ffa0904070717v25466ac4u93555ebc72e48907@mail.gmail.com> Also ecutrho should be atleast 10-12 times ecutwfc, you should check the convergence of the quantity of interest wrt ecutrho, ecutwfc & k-points. Prasenjit. 2009/4/7 Dimpy Sharma > Hi, > > I am not getting my output . My input file is given below. I have kept the > kinetic energy cut of for the wavefunction (ecutwfc) as 35Ry. Can you please > tell me. > &CONTROL > calculation ='relax' > restart_mode = 'from_scratch' > outdir = '/sfiwork/dsharma/silane/wfc4' > pseudo_dir = '/sfiwork/dsharma/QE_Pseudos/' > prefix = '5' > tstress = .false. > tprnfor = .true. > etot_conv_thr = 1.D-4 > forc_conv_thr = 1.D-3 > nstep = 600 > / > &SYSTEM > ibrav = 0 > celldm(1) =7.1516 > nat = 6 > ntyp = 2 > ecutwfc = 35.0 > ecutrho = 100.0 > nbnd = 10 > / > &ELECTRONS > diagonalization ='david' > mixing_mode = 'plain' > conv_thr = 1.0d-1 > mixing_beta = 0.7 > / > &IONS > / > &CELL > cell_dynamics='none' > > / > CELL_PARAMETERS cubic > 1.000000000 0.000000000 0.000000000 > 0.000000000 2.000000000 0.000000000 > 0.000000000 0.000000000 2.000000000 > ATOMIC_SPECIES > Si 28.08600 Si.pz-vbc.UPF > H 1.00800 H.pz-vbc.UPF > ATOMIC_POSITIONS angstroms > Si 2.95020 -0.66592 -0.12341 > Si 4.90939 0.61749 0.11358 > H 5.11746 1.46255 -1.09398 > H 4.69823 1.55915 1.25968 > H 2.84169 -1.61779 1.02344 > H 3.00948 -1.48841 -1.36525 > K_POINTS automatic > 4 1 1 0 0 0 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- PRASENJIT GHOSH, POST-DOC, ROOM NO: 265, MAIN BUILDING, CM SECTION, ICTP, STRADA COSTERIA 11, TRIESTE, 34104, ITALY PHONE: +39 040 2240 369 (O) +39 3807528672 (M) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090407/8dcd9162/attachment-0001.htm From dimpy.sharma at tyndall.ie Tue Apr 7 16:25:33 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Tue, 7 Apr 2009 15:25:33 +0100 Subject: [Pw_forum] (no subject) Message-ID: Hi, Can anyone please explain me the significance of ecutwfc and ecutrho in quantum espresso input file. And what is the diffeence between these two values. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090407/24f1be34/attachment.htm From adams_mejl at hotmail.com Tue Apr 7 16:36:56 2009 From: adams_mejl at hotmail.com (Adam Jacobsson) Date: Tue, 7 Apr 2009 16:36:56 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: References: Message-ID: Hi, Why not look into the documentation? Date: Tue, 7 Apr 2009 15:25:33 +0100 From: dimpy.sharma at tyndall.ie To: pw_forum at pwscf.org Subject: [Pw_forum] (no subject) Hi, Can anyone please explain me the significance of ecutwfc and ecutrho in quantum espresso input file. And what is the diffeence between these two values. _________________________________________________________________ Vi vet vem du passar ihop med! Klicka h?r f?r att f? veta! http://dejting.se.msn.com/channel/index.aspx?trackingid=1002952 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090407/03e06269/attachment.htm From prasenjit.jnc at gmail.com Tue Apr 7 16:43:35 2009 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Tue, 7 Apr 2009 16:43:35 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: References: Message-ID: <627e0ffa0904070743i68af4599icdd028a33817727f@mail.gmail.com> ecutwfc determines the size of the plane wave you are using for your cal. (Note that PWscf is a plane wave based code, i.e., the wave functions are expanded in a plane wave basis). If you use ultrasoft pseudopotential, you introduce augmentation charges (because norm-conserving condition is not satisfied by these pp's). For those one uses ecutrho. In your case you are using norm-conserving pseudopotentials. Therefore for ecutrho you can use the default value (ecutrho=4*ecutwfc). However, it is better to use ultrasoft PP because you need lower value of ecutwfc, i.e., fewer no. of plane waves and therefore faster calculations. There are plenty of good books & papers available. Please go through them before you do the cal. or ask ur questions in the forum. Also look into the manual & the mailing list archive. Prasenjit. PS: Don't forget to add ur affiliation.....its a netiquette for this forum. 2009/4/7 Dimpy Sharma > > Hi, > > Can anyone please explain me the significance of ecutwfc and ecutrho in > quantum espresso input file. And what is the diffeence between these two > values. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- PRASENJIT GHOSH, POST-DOC, ROOM NO: 265, MAIN BUILDING, CM SECTION, ICTP, STRADA COSTERIA 11, TRIESTE, 34104, ITALY PHONE: +39 040 2240 369 (O) +39 3807528672 (M) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090407/4a3408ce/attachment.htm From dimpy.sharma at tyndall.ie Tue Apr 7 20:11:25 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Tue, 7 Apr 2009 19:11:25 +0100 Subject: [Pw_forum] (no subject) Message-ID: Hi everybody, can anybody please tell me why my the following program get crashed. &CONTROL calculation ='relax' restart_mode = 'from_scratch' outdir = '/sfiwork/dsharma/silane/wfc5' pseudo_dir = '/sfiwork/dsharma/QE_Pseudos/' prefix = '1' tstress = .false. tprnfor = .true. etot_conv_thr = 1.D-3 forc_conv_thr = 1.D-4 nstep = 600 / &SYSTEM ibrav = 0 celldm(1) =6.9371 nat = 6 ntyp = 2 ecutwfc = 35.0 ecutrho = 100 nbnd = 10 / &ELECTRONS diagonalization ='david' mixing_mode = 'plain' conv_thr = 1.0d-8 mixing_beta = 0.7 / &IONS / &CELL cell_dynamics='none' / CELL_PARAMETERS cubic 1.000000000 0.000000000 0.000000000 0.000000000 2.000000000 0.000000000 0.000000000 0.000000000 2.000000000 ATOMIC_SPECIES Si 28.08600 Si.pz-vbc.UPF H 1.00800 H.pz-vbc.UPF ATOMIC_POSITIONS angstroms Si 2.95020 -0.66592 -0.12341 Si 4.90939 0.61749 0.11358 H 5.11746 1.46255 -1.09398 H 4.69823 1.55915 1.25968 H 2.84169 -1.61779 1.02344 H 3.00948 -1.48841 -1.36525 K_POINTS automatic 4 1 1 0 0 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090407/6ac39bbb/attachment.htm From akohlmey at cmm.chem.upenn.edu Tue Apr 7 20:23:30 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 07 Apr 2009 14:23:30 -0400 Subject: [Pw_forum] (no subject) In-Reply-To: References: Message-ID: <1239128610.2923.143.camel@zero> On Tue, 2009-04-07 at 19:11 +0100, Dimpy Sharma wrote: > > Hi everybody, > can anybody please tell me why my the following program get crashed. most likely due to PEBCAC and lack of RTFM or STFW. cheers, axel. > > &CONTROL > calculation ='relax' > restart_mode = 'from_scratch' > outdir = '/sfiwork/dsharma/silane/wfc5' > pseudo_dir = '/sfiwork/dsharma/QE_Pseudos/' > prefix = '1' > tstress = .false. > tprnfor = .true. > etot_conv_thr = 1.D-3 > forc_conv_thr = 1.D-4 > nstep = 600 > / > &SYSTEM > ibrav = 0 > celldm(1) =6.9371 > nat = 6 > ntyp = 2 > ecutwfc = 35.0 > ecutrho = 100 > nbnd = 10 > / > &ELECTRONS > diagonalization ='david' > mixing_mode = 'plain' > conv_thr = 1.0d-8 > mixing_beta = 0.7 > / > &IONS > / > &CELL > cell_dynamics='none' > > / > CELL_PARAMETERS cubic > > 1.000000000 0.000000000 0.000000000 > 0.000000000 2.000000000 0.000000000 > 0.000000000 0.000000000 2.000000000 > ATOMIC_SPECIES > Si 28.08600 Si.pz-vbc.UPF > H 1.00800 H.pz-vbc.UPF > ATOMIC_POSITIONS angstroms > Si 2.95020 -0.66592 -0.12341 > Si 4.90939 0.61749 0.11358 > H 5.11746 1.46255 -1.09398 > H 4.69823 1.55915 1.25968 > H 2.84169 -1.61779 1.02344 > H 3.00948 -1.48841 -1.36525 > K_POINTS automatic > 4 1 1 0 0 0 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From matteo at umn.edu Tue Apr 7 20:20:54 2009 From: matteo at umn.edu (Matteo Cococcioni) Date: Tue, 07 Apr 2009 13:20:54 -0500 Subject: [Pw_forum] (no subject) In-Reply-To: References: Message-ID: <49DB9986.7050301@umn.edu> Dear Dimpy, from a very quick look at your input: for sure ecutrho needs to be 4*ecutwfc. I'm not sure the code does this automatically if it finds ecutrho in the input. what is the error message? Matteo Dimpy Sharma wrote: > > Hi everybody, > can anybody please tell me why my the following program get crashed. > > > &CONTROL > calculation ='relax' > restart_mode = 'from_scratch' > outdir = '/sfiwork/dsharma/silane/wfc5' > pseudo_dir = '/sfiwork/dsharma/QE_Pseudos/' > prefix = '1' > tstress = .false. > tprnfor = .true. > etot_conv_thr = 1.D-3 > forc_conv_thr = 1.D-4 > nstep = 600 > / > &SYSTEM > ibrav = 0 > celldm(1) =6.9371 > nat = 6 > ntyp = 2 > ecutwfc = 35.0 > ecutrho = 100 > nbnd = 10 > / > &ELECTRONS > diagonalization ='david' > mixing_mode = 'plain' > conv_thr = 1.0d-8 > mixing_beta = 0.7 > / > &IONS > / > &CELL > cell_dynamics='none' > > / > CELL_PARAMETERS cubic > > 1.000000000 0.000000000 0.000000000 > 0.000000000 2.000000000 0.000000000 > 0.000000000 0.000000000 2.000000000 > ATOMIC_SPECIES > Si 28.08600 Si.pz-vbc.UPF > H 1.00800 H.pz-vbc.UPF > ATOMIC_POSITIONS angstroms > Si 2.95020 -0.66592 -0.12341 > Si 4.90939 0.61749 0.11358 > H 5.11746 1.46255 -1.09398 > H 4.69823 1.55915 1.25968 > H 2.84169 -1.61779 1.02344 > H 3.00948 -1.48841 -1.36525 > K_POINTS automatic > 4 1 1 0 0 0 > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 Fax +1 612 626 7246 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From eyvaz_isaev at yahoo.com Tue Apr 7 22:32:44 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 7 Apr 2009 13:32:44 -0700 (PDT) Subject: [Pw_forum] (no subject) In-Reply-To: Message-ID: <683450.11644.qm@web65714.mail.ac4.yahoo.com> Dear Dimpy, Did you try carry out another calculation using your executable pw.x? Is it serial or parallel? As your input file seems to be OK except some comments given before, and it works on my notebook, it might be you have a miscompiled executable. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Tue, 4/7/09, Dimpy Sharma wrote: > From: Dimpy Sharma > Subject: [Pw_forum] (no subject) > To: pw_forum at pwscf.org > Date: Tuesday, April 7, 2009, 10:11 PM > Hi everybody, > can anybody please tell me why my the following program get > crashed. > > > &CONTROL > calculation ='relax' > restart_mode = 'from_scratch' > outdir = '/sfiwork/dsharma/silane/wfc5' > pseudo_dir = '/sfiwork/dsharma/QE_Pseudos/' > prefix = '1' > tstress = .false. > tprnfor = .true. > etot_conv_thr = 1.D-3 > forc_conv_thr = 1.D-4 > nstep = 600 > / > &SYSTEM > ibrav = 0 > celldm(1) =6.9371 > nat = 6 > ntyp = 2 > ecutwfc = 35.0 > ecutrho = 100 > nbnd = 10 > / > &ELECTRONS > diagonalization ='david' > mixing_mode = 'plain' > conv_thr = 1.0d-8 > mixing_beta = 0.7 > / > &IONS > / > &CELL > cell_dynamics='none' > > / > CELL_PARAMETERS cubic > > 1.000000000 0.000000000 0.000000000 > 0.000000000 2.000000000 0.000000000 > 0.000000000 0.000000000 2.000000000 > ATOMIC_SPECIES > Si 28.08600 Si.pz-vbc.UPF > H 1.00800 H.pz-vbc.UPF > ATOMIC_POSITIONS angstroms > Si 2.95020 -0.66592 -0.12341 > Si 4.90939 0.61749 0.11358 > H 5.11746 1.46255 -1.09398 > H 4.69823 1.55915 1.25968 > H 2.84169 -1.61779 1.02344 > H 3.00948 -1.48841 -1.36525 > K_POINTS automatic > 4 1 1 0 0 0 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From yccheng.nju at gmail.com Wed Apr 8 13:01:28 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Wed, 8 Apr 2009 19:01:28 +0800 Subject: [Pw_forum] optimize monoclinic cell Message-ID: Dear Pwscf users, I did a variable cell calculations for a base centered monoclinic crystal. The cell displayed in xcrysden is correct, and PWscf can find the symmetry. However, in the optimizing process, the cell parameter changed unexpectedly, which may be wrong. In the user's guide of PWscf, the base centered monoclinic cell is defined as follows: base centered monoclinic ============================= v1 = ( a/2, 0, -c/2), v2 = (b*cos(gamma), b*sin(gamma), 0), v3 = ( a/2, 0, c/2), where gamma is the angle between axis a and b ============================= In the first step of optimize process, the cell is changed as following: CELL_PARAMETERS (alat) 0.483414893 0.003687739 -0.271981740 -1.013180906 0.556415406 0.000000000 0.483414893 0.003687739 0.271981740 My question is : why the quantities of second row of v1, v3 vector do not retain zero! Any suggestion and comment is appriciated. Thank you in advance! The input file is attached! &CONTROL title = 'c2', prefix = 'li', calculation = 'vc-relax' , restart_mode = 'from_scratch' , outdir = './' , wfcdir = './' , pseudo_dir = './' , tstress = .true. , tprnfor = .true. , etot_conv_thr = 1.0D-5, forc_conv_thr = 1.0D-4, / &SYSTEM ibrav = 13, celldm(1) = 14.7756, celldm(2) = 1.20528, celldm(3) = 0.56348, celldm(4) = -0.873177, nat = 12, ntyp = 1, ecutwfc = 200, nosym = .false. , / &ELECTRONS electron_maxstep = 100, conv_thr = 1.D-10, / &IONS ion_dynamics='bfgs', / &CELL cell_dynamics='bfgs', press=900, / ATOMIC_SPECIES Li 6.914 Li.pz-s-mt.UPF ATOMIC_POSITIONS (crystal) Li -0.46080 0.21740 1.49640 Li -0.02770 0.02590 1.28350 Li -0.80760 0.63690 0.91840 Li 0.23010 0.43900 0.29270 Li 0.06870 0.87600 0.40410 Li -0.04760 0.70260 1.56000 Li -1.49640 -0.21740 0.46080 Li -1.28350 -0.02590 0.02770 Li -0.91840 -0.63690 0.80760 Li -0.29270 -0.43900 -0.23010 Li -0.40410 -0.87600 -0.06870 Li -1.56000 -0.70260 0.04760 K_POINTS automatic 8 8 8 1 1 1 -- Y. C. Cheng Department of Phyics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090408/c91bec55/attachment.htm From yccheng.nju at gmail.com Wed Apr 8 13:34:25 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Wed, 8 Apr 2009 19:34:25 +0800 Subject: [Pw_forum] the missing symmetry of bands Message-ID: Dear PWscf users, In my recent calculation of 4H-AlN (ABCB stacking sequence), the band symmetry seems to be missed in bands.x calculation. The output of bands.x is as following: ************************************************************************** xk=( 0.00000, 0.00000, 0.00000 ) double point group C_6v (6mm) there are 9 classes and 3 irreducible representations the character table: E -E C2 2C3 -2C3 2C6 -2C6 3s_v 3s_d -C2 -3s_v -3s_d G_7 2.00 -2.00 0.00 1.00 -1.00 1.73 -1.73 0.00 0.00 G_8 2.00 -2.00 0.00 1.00 -1.00 -1.73 1.73 0.00 0.00 G_9 2.00 -2.00 0.00 -2.00 2.00 0.00 0.00 0.00 0.00 the symmetry operations in each class: E 1 C2 -C2 2 -2 2C6 3 4 2C3 5 6 3s_v-3s_v 7 -7 9 10 -10 -9 3s_d-3s_d 8 -8 12 -11 11 -12 -E -1 -2C6 -3 -4 -2C3 -5 -6 Band symmetry, C_6v (6mm) double point group: e( 1 - 2) = -8.01764 eV 2 --> ? e( 3 - 4) = -7.17573 eV 2 --> ? e( 5 - 6) = -7.13551 eV 2 --> ? e( 7 - 8) = -5.93881 eV 2 --> ? e( 9 - 10) = 1.12077 eV 2 --> G_7 e( 9 - 10) = 1.12077 eV 2 --> 0 G_8 e( 11 - 12) = 3.70317 eV 2 --> 0 G_7 e( 11 - 12) = 3.70317 eV 2 --> G_8 e( 13 - 14) = 3.76782 eV 2 --> ? e( 15 - 16) = 6.34352 eV 2 --> ? e( 17 - 18) = 6.35869 eV 2 --> G_9 e( 19 - 20) = 6.58061 eV 2 --> ? e( 21 - 22) = 6.59473 eV 2 --> G_9 e( 23 - 24) = 6.65103 eV 2 --> ? e( 25 - 26) = 6.66500 eV 2 --> G_9 e( 27 - 28) = 6.91040 eV 2 --> ? e( 29 - 30) = 6.92400 eV 2 --> G_9 e( 31 - 32) = 7.00967 eV 2 --> G_7 e( 31 - 32) = 7.00967 eV 2 --> 0 G_8 e( 33 - 34) = 11.19288 eV 2 --> ? e( 35 - 36) = 13.31415 eV 2 --> ? e( 37 - 38) = 13.59769 eV 2 --> ? e( 39 - 40) = 14.02975 eV 2 --> ? e( 41 - 42) = 17.15974 eV 2 --> ? e( 43 - 44) = 17.32327 eV 2 --> ? e( 45 - 46) = 17.92003 eV 2 --> ? ************************************************************************** My question are : 1. what does "?" mean in " e( 1 - 2) = -8.01764 eV 2 --> ?" ? 2. what does "0" mean in " e( 9 - 10) = 1.12077 eV 2 --> 0 G_8" ? 3. In 2H-AlN(AB stacking sequence), all the symmetries of bands are shown. Why in 4H-AlN, it seems much more complicated. The input files about 4H-AlN for pw.x and bands.x are as following: scf.in &control title = 2h_aln, prefix = '4h_band', calculation = 'scf' , restart_mode = 'from_scratch' , wf_collect = .false. , outdir = './' , wfcdir = './' , pseudo_dir = './' , tstress = .true. , tprnfor = .true. , wf_collect = .true. , / &SYSTEM ibrav = 4, celldm(1) = 5.866002785691, celldm(3) = 3.238615289089, nat = 8, ntyp = 2, ecutwfc = 80, nbnd = 46, nosym = .false. , lspinorb = .true., noncolin= .true., starting_magnetization=0.00, / &ELECTRONS electron_maxstep = 100, conv_thr = 1.D-10, / ATOMIC_SPECIES N 14.00700 N.rel-pbe-rrkjus.UPF Al 26.98200 Al.rel-pbe-rrkj.UPF ATOMIC_POSITIONS (crystal) N 0.000000000 0.000000000 -0.000722968 N 0.000000000 0.000000000 0.499277032 N 0.333333333 0.666666667 0.249293699 N 0.666666667 0.333333333 0.749293699 Al 0.000000000 0.000000000 0.188800277 Al 0.000000000 0.000000000 0.688800277 Al 0.333333333 0.666666667 0.437593675 Al 0.666666667 0.333333333 0.937793675 K_POINTS automatic 8 8 8 1 1 1 band.in &control title = 2h_aln, prefix = '4h_band', calculation = 'bands' , restart_mode = 'from_scratch' , wf_collect = .false. , outdir = './' , wfcdir = './' , pseudo_dir = './' , / &SYSTEM ibrav = 4, celldm(1) = 5.866002785691, celldm(3) = 3.238615289089, nat = 8, ntyp = 2, ecutwfc = 80, nbnd=46, lspinorb = .true., noncolin= .true., starting_magnetization=0.0, / &ELECTRONS electron_maxstep = 100, conv_thr = 1.D-10, / ATOMIC_SPECIES N 14.00700 N.rel-pbe-rrkjus.UPF Al 26.98200 Al.rel-pbe-rrkj.UPF ATOMIC_POSITIONS (crystal) N 0.000000000 0.000000000 -0.000722968 N 0.000000000 0.000000000 0.499277032 N 0.333333333 0.666666667 0.249293699 N 0.666666667 0.333333333 0.749293699 Al 0.000000000 0.000000000 0.188800277 Al 0.000000000 0.000000000 0.688800277 Al 0.333333333 0.666666667 0.437593675 Al 0.666666667 0.333333333 0.937793675 K_POINTS 2 0.000000 0.000000 0.000000 1.00 0.000000 0.000000 0.083333 1.00 bands.in &inputpp prefix='4h_band' outdir='./' filband='spin.dat' lsigma(3)=.true. lsym=.true. / Thank you in advance! -- Y. C. Cheng Department of Phyics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090408/c5151b5a/attachment.htm From dalcorso at sissa.it Wed Apr 8 14:49:58 2009 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Wed, 08 Apr 2009 14:49:58 +0200 Subject: [Pw_forum] the missing symmetry of bands In-Reply-To: References: Message-ID: <1239194998.3263.26.camel@dhpc-5-20.sissa.it> On Wed, 2009-04-08 at 19:34 +0800, ??? wrote: > Dear PWscf users, > In my recent calculation of 4H-AlN (ABCB stacking sequence), > the band symmetry seems to be missed in bands.x calculation. The > output of bands.x is as following: > ************************************************************************** > xk=( 0.00000, 0.00000, 0.00000 ) > double point group C_6v (6mm) > there are 9 classes and 3 irreducible representations > the character table: > E -E C2 2C3 -2C3 2C6 -2C6 3s_v 3s_d > -C2 -3s_v -3s_d > G_7 2.00 -2.00 0.00 1.00 -1.00 1.73 -1.73 0.00 0.00 > G_8 2.00 -2.00 0.00 1.00 -1.00 -1.73 1.73 0.00 0.00 > G_9 2.00 -2.00 0.00 -2.00 2.00 0.00 0.00 0.00 0.00 > the symmetry operations in each class: > E 1 > C2 -C2 2 -2 > 2C6 3 4 > 2C3 5 6 > 3s_v-3s_v 7 -7 9 10 -10 -9 > 3s_d-3s_d 8 -8 12 -11 11 -12 > -E -1 > -2C6 -3 -4 > -2C3 -5 -6 > Band symmetry, C_6v (6mm) double point group: > e( 1 - 2) = -8.01764 eV 2 --> ? > e( 3 - 4) = -7.17573 eV 2 --> ? > e( 5 - 6) = -7.13551 eV 2 --> ? > e( 7 - 8) = -5.93881 eV 2 --> ? > e( 9 - 10) = 1.12077 eV 2 --> G_7 > e( 9 - 10) = 1.12077 eV 2 --> 0 G_8 > e( 11 - 12) = 3.70317 eV 2 --> 0 G_7 > e( 11 - 12) = 3.70317 eV 2 --> G_8 > e( 13 - 14) = 3.76782 eV 2 --> ? > e( 15 - 16) = 6.34352 eV 2 --> ? > e( 17 - 18) = 6.35869 eV 2 --> G_9 > e( 19 - 20) = 6.58061 eV 2 --> ? > e( 21 - 22) = 6.59473 eV 2 --> G_9 > e( 23 - 24) = 6.65103 eV 2 --> ? > e( 25 - 26) = 6.66500 eV 2 --> G_9 > e( 27 - 28) = 6.91040 eV 2 --> ? > e( 29 - 30) = 6.92400 eV 2 --> G_9 > e( 31 - 32) = 7.00967 eV 2 --> G_7 > e( 31 - 32) = 7.00967 eV 2 --> 0 G_8 > e( 33 - 34) = 11.19288 eV 2 --> ? > e( 35 - 36) = 13.31415 eV 2 --> ? > e( 37 - 38) = 13.59769 eV 2 --> ? > e( 39 - 40) = 14.02975 eV 2 --> ? > e( 41 - 42) = 17.15974 eV 2 --> ? > e( 43 - 44) = 17.32327 eV 2 --> ? > e( 45 - 46) = 17.92003 eV 2 --> ? > ************************************************************************** > My question are : > 1. what does "?" mean in " e( 1 - 2) = -8.01764 eV 2 It means that the symmetry finder is confused. The bands have not a symmetry that it recognizes. There are several reasons for this: 1) The 'scf' and 'bands' calculations have been run with slightly different parameters. (solution: recheck your input) 2) Your atomic positions are not sufficiently accurate: the number of digits is sufficient for pw.x to find the symmetries but the wavefunctions are sufficiently inaccurate to confuse the symmetry analyzer. (solution: correct your atomic positions) 3) If 1) and 2) do not work and you are sure about your coordinates, then probably there is a bug in the symmetry analyzer. (solution: report to the forum. I will try to solve it if I can). In your particular case: I am confused. On my PC the symmetry found with your coordinates is C_3v and the symmetry analyzer seems to work. So please recheck your run. If you still find C_6v please recheck your atomic positions. Hope this helps. Andrea > --> ?" ? > 2. what does "0" mean in " e( 9 - 10) = 1.12077 eV 2 > --> 0 G_8" ? > 3. In 2H-AlN(AB stacking sequence), all the symmetries of bands are > shown. Why in 4H-AlN, it seems much more complicated. > > The input files about 4H-AlN for pw.x and bands.x are as following: > scf.in > &control > title = 2h_aln, > prefix = '4h_band', > calculation = 'scf' , > restart_mode = 'from_scratch' , > wf_collect = .false. , > outdir = './' , > wfcdir = './' , > pseudo_dir = './' , > tstress = .true. , > tprnfor = .true. , > wf_collect = .true. , > / > &SYSTEM > ibrav = 4, > celldm(1) = 5.866002785691, > celldm(3) = 3.238615289089, > nat = 8, > ntyp = 2, > ecutwfc = 80, > nbnd = 46, > nosym = .false. , > lspinorb = .true., > noncolin= .true., > starting_magnetization=0.00, > / > &ELECTRONS > electron_maxstep = 100, > conv_thr = 1.D-10, > / > ATOMIC_SPECIES > N 14.00700 N.rel-pbe-rrkjus.UPF > Al 26.98200 Al.rel-pbe-rrkj.UPF > ATOMIC_POSITIONS (crystal) > N 0.000000000 0.000000000 -0.000722968 > N 0.000000000 0.000000000 0.499277032 > N 0.333333333 0.666666667 0.249293699 > N 0.666666667 0.333333333 0.749293699 > Al 0.000000000 0.000000000 0.188800277 > Al 0.000000000 0.000000000 0.688800277 > Al 0.333333333 0.666666667 0.437593675 > Al 0.666666667 0.333333333 0.937793675 > K_POINTS automatic > 8 8 8 1 1 1 > > band.in > &control > title = 2h_aln, > prefix = '4h_band', > calculation = 'bands' , > restart_mode = 'from_scratch' , > wf_collect = .false. , > outdir = './' , > wfcdir = './' , > pseudo_dir = './' , > / > &SYSTEM > ibrav = 4, > celldm(1) = 5.866002785691, > celldm(3) = 3.238615289089, > nat = 8, > ntyp = 2, > ecutwfc = 80, > nbnd=46, > lspinorb = .true., > noncolin= .true., > starting_magnetization=0.0, > / > &ELECTRONS > electron_maxstep = 100, > conv_thr = 1.D-10, > / > ATOMIC_SPECIES > N 14.00700 N.rel-pbe-rrkjus.UPF > Al 26.98200 Al.rel-pbe-rrkj.UPF > ATOMIC_POSITIONS (crystal) > N 0.000000000 0.000000000 -0.000722968 > N 0.000000000 0.000000000 0.499277032 > N 0.333333333 0.666666667 0.249293699 > N 0.666666667 0.333333333 0.749293699 > Al 0.000000000 0.000000000 0.188800277 > Al 0.000000000 0.000000000 0.688800277 > Al 0.333333333 0.666666667 0.437593675 > Al 0.666666667 0.333333333 0.937793675 > K_POINTS > 2 > 0.000000 0.000000 0.000000 1.00 > 0.000000 0.000000 0.083333 1.00 > > > bands.in > &inputpp > prefix='4h_band' > outdir='./' > filband='spin.dat' > lsigma(3)=.true. > lsym=.true. > / > > Thank you in advance! > > > -- > Y. C. Cheng > Department of Phyics > Nanjing University > Nanjing 210093 > P. R. China > Tel: 86-25-83592907 > Email: yccheng.nju 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 Beirut 2/4 Fax. 0039-040-3787528 34014 Trieste (Italy) e-mail: dalcorso at sissa.it From akohlmey at cmm.chem.upenn.edu Wed Apr 8 15:11:22 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 08 Apr 2009 09:11:22 -0400 Subject: [Pw_forum] optimize monoclinic cell In-Reply-To: References: Message-ID: <1239196282.2923.235.camel@zero> On Wed, 2009-04-08 at 19:01 +0800, ??? wrote: > Dear Pwscf users, > I did a variable cell calculations for a base centered > monoclinic crystal. The cell displayed in xcrysden is correct, and > PWscf can find the symmetry. However, in the optimizing process, the > cell parameter changed unexpectedly, which may be wrong. In the no. it is most likely not wrong, but rather an indication of the level of numerical accuracy with which you computed your forces and stress tensor. cheers, axel > user's guide of PWscf, the base centered monoclinic cell is defined > as follows: > base centered monoclinic > ============================= > v1 = ( a/2, 0, -c/2), > v2 = (b*cos(gamma), b*sin(gamma), 0), > v3 = ( a/2, 0, c/2), > where gamma is the angle between axis a and b > ============================= > In the first step of optimize process, the cell is changed as > following: > CELL_PARAMETERS (alat) > 0.483414893 0.003687739 -0.271981740 > -1.013180906 0.556415406 0.000000000 > 0.483414893 0.003687739 0.271981740 > My question is : why the quantities of second row of v1, v3 vector do > not retain zero! > > Any suggestion and comment is appriciated. Thank you in advance! > > The input file is attached! > &CONTROL > title = 'c2', > prefix = 'li', > calculation = 'vc-relax' , > restart_mode = 'from_scratch' , > outdir = './' , > wfcdir = './' , > pseudo_dir = './' , > tstress = .true. , > tprnfor = .true. , > etot_conv_thr = 1.0D-5, > forc_conv_thr = 1.0D-4, > / > &SYSTEM > ibrav = 13, > celldm(1) = 14.7756, > celldm(2) = 1.20528, > celldm(3) = 0.56348, > celldm(4) = -0.873177, > nat = 12, > ntyp = 1, > ecutwfc = 200, > nosym = .false. , > / > &ELECTRONS > electron_maxstep = 100, > conv_thr = 1.D-10, > / > &IONS > ion_dynamics='bfgs', > / > &CELL > cell_dynamics='bfgs', > press=900, > / > ATOMIC_SPECIES > Li 6.914 Li.pz-s-mt.UPF > ATOMIC_POSITIONS (crystal) > Li -0.46080 0.21740 1.49640 > Li -0.02770 0.02590 1.28350 > Li -0.80760 0.63690 0.91840 > Li 0.23010 0.43900 0.29270 > Li 0.06870 0.87600 0.40410 > Li -0.04760 0.70260 1.56000 > Li -1.49640 -0.21740 0.46080 > Li -1.28350 -0.02590 0.02770 > Li -0.91840 -0.63690 0.80760 > Li -0.29270 -0.43900 -0.23010 > Li -0.40410 -0.87600 -0.06870 > Li -1.56000 -0.70260 0.04760 > K_POINTS automatic > 8 8 8 1 1 1 > > -- > Y. C. Cheng > Department of Phyics > Nanjing University > Nanjing 210093 > P. R. China > Tel: 86-25-83592907 > Email: yccheng.nju at gmail.com > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From dimpy.sharma at tyndall.ie Wed Apr 8 15:20:34 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Wed, 8 Apr 2009 14:20:34 +0100 Subject: [Pw_forum] Hi Message-ID: Hi everybody, Can anybody please tell me how to recognise whether the input values for DFT calculations involve norm conserving pseudopotentials. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090408/edbdf42e/attachment.htm From paulatto at sissa.it Wed Apr 8 15:24:57 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 08 Apr 2009 15:24:57 +0200 Subject: [Pw_forum] Hi In-Reply-To: References: Message-ID: On Wed, 08 Apr 2009 15:20:34 +0200, Dimpy Sharma wrote: > > Hi everybody, > > Can anybody please tell me how to recognise whether the input values for > DFT calculations involve norm conserving pseudopotentials. Dear Dimpy, it does not depend on any input parameter, but on the pseudopotential files you are using. You can find the information you are looking for at the beginning of the psudopotential file (you can open it with a text editor). regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From akohlmey at cmm.chem.upenn.edu Wed Apr 8 15:28:12 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 08 Apr 2009 09:28:12 -0400 Subject: [Pw_forum] Hi In-Reply-To: References: Message-ID: <1239197292.2923.250.camel@zero> On Wed, 2009-04-08 at 14:20 +0100, Dimpy Sharma wrote: > > Hi everybody, > > Can anybody please tell me how to recognise whether the input values > for DFT calculations involve norm conserving pseudopotentials. RTFM. http://www.quantum-espresso.org/wiki/index.php/Unified_pseudopotential_format > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From baris.malcioglu at gmail.com Wed Apr 8 15:31:53 2009 From: baris.malcioglu at gmail.com (O. Baris Malcioglu) Date: Wed, 8 Apr 2009 15:31:53 +0200 Subject: [Pw_forum] Hi In-Reply-To: References: Message-ID: Dear Dimpy, This information can most simply be accessed looking at the pseudopotentials themselves (do not be scared, they are ascii files) Two examples $>head -40 C.pbe-rrkjus.UPF |grep pseudopotential US Ultrasoft pseudopotential $>head -40 C.blyp-mt.UPF |grep pseudopotential NC Norm - Conserving pseudopotential Cheers, Baris SISSA CM sector. On Wed, Apr 8, 2009 at 3:20 PM, Dimpy Sharma wrote: > > Hi everybody, > > Can anybody please tell me how to recognise whether the input values for DFT > calculations involve norm conserving pseudopotentials. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From daijiayu at nudt.edu.cn Wed Apr 8 16:01:43 2009 From: daijiayu at nudt.edu.cn (Jiayu Dai) Date: Wed, 08 Apr 2009 22:01:43 +0800 Subject: [Pw_forum] God bless Italy. Message-ID: <439199303.24157@nudt.edu.cn> There is an earthquake in Itlay in these days, a lot of lives gone, and a lot of people injury. I hope everything can be better soon, and God bless Italian people. Regards. ------------------------------ Jiayu Dai National University of Defense Technology, P R China From yccheng.nju at gmail.com Wed Apr 8 16:46:13 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Wed, 8 Apr 2009 22:46:13 +0800 Subject: [Pw_forum] the missing symmetry of bands In-Reply-To: <1239194998.3263.26.camel@dhpc-5-20.sissa.it> References: <1239194998.3263.26.camel@dhpc-5-20.sissa.it> Message-ID: Thank you for your advices. In my provided input file, the cell parameters and atomic positions are from a variable optimization using Non-Relativistic PP. But in the following scf run I changed to use Relativistic Pseudopotential containing additional information for spin-orbit calculations. Because the current version of PWscf can not do nonline+ GGA stress calculation, I think I can try to do an vc-relax using Relativistic Pseudopotential +LDA. 2009/4/8 Dal Corso Andrea > On Wed, 2009-04-08 at 19:34 +0800, ??? wrote: > > Dear PWscf users, > > In my recent calculation of 4H-AlN (ABCB stacking sequence), > > the band symmetry seems to be missed in bands.x calculation. The > > output of bands.x is as following: > > > ************************************************************************** > > xk=( 0.00000, 0.00000, 0.00000 ) > > double point group C_6v (6mm) > > there are 9 classes and 3 irreducible representations > > the character table: > > E -E C2 2C3 -2C3 2C6 -2C6 3s_v 3s_d > > -C2 -3s_v -3s_d > > G_7 2.00 -2.00 0.00 1.00 -1.00 1.73 -1.73 0.00 0.00 > > G_8 2.00 -2.00 0.00 1.00 -1.00 -1.73 1.73 0.00 0.00 > > G_9 2.00 -2.00 0.00 -2.00 2.00 0.00 0.00 0.00 0.00 > > the symmetry operations in each class: > > E 1 > > C2 -C2 2 -2 > > 2C6 3 4 > > 2C3 5 6 > > 3s_v-3s_v 7 -7 9 10 -10 -9 > > 3s_d-3s_d 8 -8 12 -11 11 -12 > > -E -1 > > -2C6 -3 -4 > > -2C3 -5 -6 > > Band symmetry, C_6v (6mm) double point group: > > e( 1 - 2) = -8.01764 eV 2 --> ? > > e( 3 - 4) = -7.17573 eV 2 --> ? > > e( 5 - 6) = -7.13551 eV 2 --> ? > > e( 7 - 8) = -5.93881 eV 2 --> ? > > e( 9 - 10) = 1.12077 eV 2 --> G_7 > > e( 9 - 10) = 1.12077 eV 2 --> 0 G_8 > > e( 11 - 12) = 3.70317 eV 2 --> 0 G_7 > > e( 11 - 12) = 3.70317 eV 2 --> G_8 > > e( 13 - 14) = 3.76782 eV 2 --> ? > > e( 15 - 16) = 6.34352 eV 2 --> ? > > e( 17 - 18) = 6.35869 eV 2 --> G_9 > > e( 19 - 20) = 6.58061 eV 2 --> ? > > e( 21 - 22) = 6.59473 eV 2 --> G_9 > > e( 23 - 24) = 6.65103 eV 2 --> ? > > e( 25 - 26) = 6.66500 eV 2 --> G_9 > > e( 27 - 28) = 6.91040 eV 2 --> ? > > e( 29 - 30) = 6.92400 eV 2 --> G_9 > > e( 31 - 32) = 7.00967 eV 2 --> G_7 > > e( 31 - 32) = 7.00967 eV 2 --> 0 G_8 > > e( 33 - 34) = 11.19288 eV 2 --> ? > > e( 35 - 36) = 13.31415 eV 2 --> ? > > e( 37 - 38) = 13.59769 eV 2 --> ? > > e( 39 - 40) = 14.02975 eV 2 --> ? > > e( 41 - 42) = 17.15974 eV 2 --> ? > > e( 43 - 44) = 17.32327 eV 2 --> ? > > e( 45 - 46) = 17.92003 eV 2 --> ? > > > ************************************************************************** > > My question are : > > 1. what does "?" mean in " e( 1 - 2) = -8.01764 eV 2 > > It means that the symmetry finder is confused. The bands have not a > symmetry that it recognizes. > There are several reasons for this: > > 1) The 'scf' and 'bands' calculations have been run with slightly > different parameters. (solution: recheck your input) > > 2) Your atomic positions are not sufficiently accurate: the number of > digits is sufficient for pw.x to find the symmetries but the > wavefunctions are sufficiently inaccurate to confuse the symmetry > analyzer. (solution: correct your atomic positions) > > 3) If 1) and 2) do not work and you are sure about your coordinates, > then probably there is a bug in the symmetry analyzer. (solution: report > to the forum. I will try to solve it if I can). > > In your particular case: I am confused. On my PC the symmetry found with > your coordinates is C_3v and the symmetry analyzer seems to work. So > please recheck your run. If you still find C_6v please recheck your > atomic positions. > > Hope this helps. > > Andrea > > > > > --> ?" ? > > 2. what does "0" mean in " e( 9 - 10) = 1.12077 eV 2 > > --> 0 G_8" ? > > 3. In 2H-AlN(AB stacking sequence), all the symmetries of bands are > > shown. Why in 4H-AlN, it seems much more complicated. > > > > The input files about 4H-AlN for pw.x and bands.x are as following: > > scf.in > > &control > > title = 2h_aln, > > prefix = '4h_band', > > calculation = 'scf' , > > restart_mode = 'from_scratch' , > > wf_collect = .false. , > > outdir = './' , > > wfcdir = './' , > > pseudo_dir = './' , > > tstress = .true. , > > tprnfor = .true. , > > wf_collect = .true. , > > / > > &SYSTEM > > ibrav = 4, > > celldm(1) = 5.866002785691, > > celldm(3) = 3.238615289089, > > nat = 8, > > ntyp = 2, > > ecutwfc = 80, > > nbnd = 46, > > nosym = .false. , > > lspinorb = .true., > > noncolin= .true., > > starting_magnetization=0.00, > > / > > &ELECTRONS > > electron_maxstep = 100, > > conv_thr = 1.D-10, > > / > > ATOMIC_SPECIES > > N 14.00700 N.rel-pbe-rrkjus.UPF > > Al 26.98200 Al.rel-pbe-rrkj.UPF > > ATOMIC_POSITIONS (crystal) > > N 0.000000000 0.000000000 -0.000722968 > > N 0.000000000 0.000000000 0.499277032 > > N 0.333333333 0.666666667 0.249293699 > > N 0.666666667 0.333333333 0.749293699 > > Al 0.000000000 0.000000000 0.188800277 > > Al 0.000000000 0.000000000 0.688800277 > > Al 0.333333333 0.666666667 0.437593675 > > Al 0.666666667 0.333333333 0.937793675 > > K_POINTS automatic > > 8 8 8 1 1 1 > > > > band.in > > &control > > title = 2h_aln, > > prefix = '4h_band', > > calculation = 'bands' , > > restart_mode = 'from_scratch' , > > wf_collect = .false. , > > outdir = './' , > > wfcdir = './' , > > pseudo_dir = './' , > > / > > &SYSTEM > > ibrav = 4, > > celldm(1) = 5.866002785691, > > celldm(3) = 3.238615289089, > > nat = 8, > > ntyp = 2, > > ecutwfc = 80, > > nbnd=46, > > lspinorb = .true., > > noncolin= .true., > > starting_magnetization=0.0, > > / > > &ELECTRONS > > electron_maxstep = 100, > > conv_thr = 1.D-10, > > / > > ATOMIC_SPECIES > > N 14.00700 N.rel-pbe-rrkjus.UPF > > Al 26.98200 Al.rel-pbe-rrkj.UPF > > ATOMIC_POSITIONS (crystal) > > N 0.000000000 0.000000000 -0.000722968 > > N 0.000000000 0.000000000 0.499277032 > > N 0.333333333 0.666666667 0.249293699 > > N 0.666666667 0.333333333 0.749293699 > > Al 0.000000000 0.000000000 0.188800277 > > Al 0.000000000 0.000000000 0.688800277 > > Al 0.333333333 0.666666667 0.437593675 > > Al 0.666666667 0.333333333 0.937793675 > > K_POINTS > > 2 > > 0.000000 0.000000 0.000000 1.00 > > 0.000000 0.000000 0.083333 1.00 > > > > > > bands.in > > &inputpp > > prefix='4h_band' > > outdir='./' > > filband='spin.dat' > > lsigma(3)=.true. > > lsym=.true. > > / > > > > Thank you in advance! > > > > > > -- > > Y. C. Cheng > > Department of Phyics > > Nanjing University > > Nanjing 210093 > > P. R. China > > Tel: 86-25-83592907 > > Email: yccheng.nju 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 Beirut 2/4 Fax. 0039-040-3787528 > 34014 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 > -- Y. C. Cheng Department of Phyics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090408/3c138f86/attachment-0001.htm From yccheng.nju at gmail.com Wed Apr 8 16:58:11 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Wed, 8 Apr 2009 22:58:11 +0800 Subject: [Pw_forum] optimize monoclinic cell In-Reply-To: <1239196282.2923.235.camel@zero> References: <1239196282.2923.235.camel@zero> Message-ID: Thank you for your reply. Do you mean that I can neglect this numerical error? 2009/4/8 Axel Kohlmeyer > On Wed, 2009-04-08 at 19:01 +0800, ??? wrote: > > Dear Pwscf users, > > I did a variable cell calculations for a base centered > > monoclinic crystal. The cell displayed in xcrysden is correct, and > > PWscf can find the symmetry. However, in the optimizing process, the > > cell parameter changed unexpectedly, which may be wrong. In the > > no. it is most likely not wrong, but rather an indication of the > level of numerical accuracy with which you computed your forces > and stress tensor. > > cheers, > axel > > > user's guide of PWscf, the base centered monoclinic cell is defined > > as follows: > > base centered monoclinic > > ============================= > > v1 = ( a/2, 0, -c/2), > > v2 = (b*cos(gamma), b*sin(gamma), 0), > > v3 = ( a/2, 0, c/2), > > where gamma is the angle between axis a and b > > ============================= > > In the first step of optimize process, the cell is changed as > > following: > > CELL_PARAMETERS (alat) > > 0.483414893 0.003687739 -0.271981740 > > -1.013180906 0.556415406 0.000000000 > > 0.483414893 0.003687739 0.271981740 > > My question is : why the quantities of second row of v1, v3 vector do > > not retain zero! > > > > Any suggestion and comment is appriciated. Thank you in advance! > > > > The input file is attached! > > &CONTROL > > title = 'c2', > > prefix = 'li', > > calculation = 'vc-relax' , > > restart_mode = 'from_scratch' , > > outdir = './' , > > wfcdir = './' , > > pseudo_dir = './' , > > tstress = .true. , > > tprnfor = .true. , > > etot_conv_thr = 1.0D-5, > > forc_conv_thr = 1.0D-4, > > / > > &SYSTEM > > ibrav = 13, > > celldm(1) = 14.7756, > > celldm(2) = 1.20528, > > celldm(3) = 0.56348, > > celldm(4) = -0.873177, > > nat = 12, > > ntyp = 1, > > ecutwfc = 200, > > nosym = .false. , > > / > > &ELECTRONS > > electron_maxstep = 100, > > conv_thr = 1.D-10, > > / > > &IONS > > ion_dynamics='bfgs', > > / > > &CELL > > cell_dynamics='bfgs', > > press=900, > > / > > ATOMIC_SPECIES > > Li 6.914 Li.pz-s-mt.UPF > > ATOMIC_POSITIONS (crystal) > > Li -0.46080 0.21740 1.49640 > > Li -0.02770 0.02590 1.28350 > > Li -0.80760 0.63690 0.91840 > > Li 0.23010 0.43900 0.29270 > > Li 0.06870 0.87600 0.40410 > > Li -0.04760 0.70260 1.56000 > > Li -1.49640 -0.21740 0.46080 > > Li -1.28350 -0.02590 0.02770 > > Li -0.91840 -0.63690 0.80760 > > Li -0.29270 -0.43900 -0.23010 > > Li -0.40410 -0.87600 -0.06870 > > Li -1.56000 -0.70260 0.04760 > > K_POINTS automatic > > 8 8 8 1 1 1 > > > > -- > > Y. C. Cheng > > Department of Phyics > > Nanjing University > > Nanjing 210093 > > P. R. China > > Tel: 86-25-83592907 > > Email: yccheng.nju at gmail.com > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Y. C. Cheng Department of Phyics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090408/f1d82251/attachment.htm From akohlmey at cmm.chem.upenn.edu Wed Apr 8 17:31:51 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 08 Apr 2009 11:31:51 -0400 Subject: [Pw_forum] optimize monoclinic cell In-Reply-To: References: <1239196282.2923.235.camel@zero> Message-ID: <1239204711.2923.279.camel@zero> On Wed, 2009-04-08 at 22:58 +0800, ??? wrote: > Thank you for your reply. > Do you mean that I can neglect this numerical error? i would not say "neglect". you have to be aware of it, but you also have to consider that for as long as it is within the error limits of your method, it would be without negative consequences. like for any numerical calculation there are no absolute truths and the GIGO (=garbage-in, garbage-out) principle holds. cheers, axel. > > > 2009/4/8 Axel Kohlmeyer > On Wed, 2009-04-08 at 19:01 +0800, ??? wrote: > > Dear Pwscf users, > > I did a variable cell calculations for a base > centered > > monoclinic crystal. The cell displayed in xcrysden is > correct, and > > PWscf can find the symmetry. However, in the optimizing > process, the > > cell parameter changed unexpectedly, which may be wrong. In > the > > > no. it is most likely not wrong, but rather an indication of > the > level of numerical accuracy with which you computed your > forces > and stress tensor. > > cheers, > axel > > > > user's guide of PWscf, the base centered monoclinic cell is > defined > > as follows: > > base centered monoclinic > > ============================= > > v1 = ( a/2, 0, -c/2), > > v2 = (b*cos(gamma), b*sin(gamma), 0), > > v3 = ( a/2, 0, c/2), > > where gamma is the angle between axis a and b > > ============================= > > In the first step of optimize process, the cell is changed > as > > following: > > CELL_PARAMETERS (alat) > > 0.483414893 0.003687739 -0.271981740 > > -1.013180906 0.556415406 0.000000000 > > 0.483414893 0.003687739 0.271981740 > > My question is : why the quantities of second row of v1, v3 > vector do > > not retain zero! > > > > Any suggestion and comment is appriciated. Thank you in > advance! > > > > The input file is attached! > > &CONTROL > > title = 'c2', > > prefix = 'li', > > calculation = 'vc-relax' , > > restart_mode = 'from_scratch' , > > outdir = './' , > > wfcdir = './' , > > pseudo_dir = './' , > > tstress = .true. , > > tprnfor = .true. , > > etot_conv_thr = 1.0D-5, > > forc_conv_thr = 1.0D-4, > > / > > &SYSTEM > > ibrav = 13, > > celldm(1) = 14.7756, > > celldm(2) = 1.20528, > > celldm(3) = 0.56348, > > celldm(4) = -0.873177, > > nat = 12, > > ntyp = 1, > > ecutwfc = 200, > > nosym = .false. , > > / > > &ELECTRONS > > electron_maxstep = 100, > > conv_thr = 1.D-10, > > / > > &IONS > > ion_dynamics='bfgs', > > / > > &CELL > > cell_dynamics='bfgs', > > press=900, > > / > > ATOMIC_SPECIES > > Li 6.914 Li.pz-s-mt.UPF > > ATOMIC_POSITIONS (crystal) > > Li -0.46080 0.21740 1.49640 > > Li -0.02770 0.02590 1.28350 > > Li -0.80760 0.63690 0.91840 > > Li 0.23010 0.43900 0.29270 > > Li 0.06870 0.87600 0.40410 > > Li -0.04760 0.70260 1.56000 > > Li -1.49640 -0.21740 0.46080 > > Li -1.28350 -0.02590 0.02770 > > Li -0.91840 -0.63690 0.80760 > > Li -0.29270 -0.43900 -0.23010 > > Li -0.40410 -0.87600 -0.06870 > > Li -1.56000 -0.70260 0.04760 > > K_POINTS automatic > > 8 8 8 1 1 1 > > > > -- > > Y. C. Cheng > > Department of Phyics > > Nanjing University > > Nanjing 210093 > > P. R. China > > Tel: 86-25-83592907 > > Email: yccheng.nju at gmail.com > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu > http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of > Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA > 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: > 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a > better idiot. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > Y. C. Cheng > Department of Phyics > Nanjing University > Nanjing 210093 > P. R. China > Tel: 86-25-83592907 > Email: yccheng.nju at gmail.com > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From meheut at impmc.jussieu.fr Wed Apr 8 21:16:54 2009 From: meheut at impmc.jussieu.fr (merlin meheut) Date: Wed, 08 Apr 2009 21:16:54 +0200 Subject: [Pw_forum] I/O problem with qe 4.0.4 In-Reply-To: <1237948920.3075.2.camel@zero> References: <20090325031905.20615692nloa4mft@www-ext.impmc.jussieu.fr> <1237948920.3075.2.camel@zero> Message-ID: <20090408211654.762358f34hml34ti@www-ext.impmc.jussieu.fr> Quoting Axel Kohlmeyer : > On Wed, 2009-03-25 at 03:19 +0100, merlin meheut wrote: >> Dear PWSCF users, >> >> I am trying calculating a big structure (72 atoms) with quantum >> espresso 4.0.4. With qe 3.0, I had no particular problem, but with qe >> 4.0.4 I have this error message: >> >> >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> from davcio : error # 99 >> error while writing to file >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> stopping ... > >> This is strange because it happened twice at the same point, >> approximately half-way to the end of the calculation. >> >> It may be related to different problems, such as hardware, but I will >> be happy if you have any hints to make myself a more precise idea of >> the problem. > > > i'd first check if you have enough free disk space on the > device that you are writing to and sufficient quota, in case > your installation uses quotas. > > axel. > Hi, sorry for this late reply, it was a problem of space on the nodes memory. I solved the problem by writing the big output files (wavefunctions etc..) directly on the main folder. So this was exactly the correct answer. Thank you axel! Merlin Meheut ESS department at UCLA -- Merlin M?heut professional adress: 595 Charles Young Drive East 3806 Geology Building Los Angeles, California 90095-1597 United States of America tel: 310 825 7934 cell phone: 310 893 4253 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From lfhuang at theory.issp.ac.cn Thu Apr 9 06:44:52 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Thu, 09 Apr 2009 12:44:52 +0800 Subject: [Pw_forum] =?utf-8?q?God_bless_Italy?= Message-ID: <20090409044452.2006.qmail@ms.hfcas.ac.cn> God bless Italian people! And appreciation to those brave people! Best Wishes! L.F.Huang From the Institute of Solid State Physics of China > Date: Wed, 08 Apr 2009 22:01:43 +0800 > From: "Jiayu Dai" > Subject: [Pw_forum] God bless Italy. > To: pw_forum at pwscf.org > Message-ID: > Content-Type: text/plain > > There is an earthquake in Itlay in these days, a lot of lives gone, and a lot of > people injury. I hope everything can be better soon, and God bless Italian people. > > > Regards. > > ------------------------------ > Jiayu Dai > National University of Defense Technology, P R China ------ ====================================================================== L.F.Huang(???) lfhuang at theory.issp.ac.cn ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(office) Fax: 86-551-5591434 Web: http://theory.issp.ac.cn (website of our theory group) http://www.issp.ac.cn (website of our institute) ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090409/f31d1cb6/attachment-0001.htm From jianping09 at gmail.com Thu Apr 9 07:18:08 2009 From: jianping09 at gmail.com (Jianping Dai) Date: Thu, 9 Apr 2009 13:18:08 +0800 Subject: [Pw_forum] what is the different pseudopotential? Message-ID: <486e50d80904082218k57209b0h5f7b5172e2066bab@mail.gmail.com> Dear All, I am a new user of PWSCF. I want to the difference between the two pseudopotentials: *Zn.pbe-van.UPF* ( *details*) Perdew-Burke-Ernzerhof (PBE) exch-corr Vanderbilt ultrasoft *Zn.bp-van_ak.UPF* (*details* ) Becke-Perdew gradient-corrected functional Vanderbilt ultrasoft author: ak It just generated by differnent author? Thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090409/e86b684c/attachment.htm From sclauzer at sissa.it Thu Apr 9 08:43:41 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 09 Apr 2009 08:43:41 +0200 Subject: [Pw_forum] what is the different pseudopotential? In-Reply-To: <486e50d80904082218k57209b0h5f7b5172e2066bab@mail.gmail.com> References: <486e50d80904082218k57209b0h5f7b5172e2066bab@mail.gmail.com> Message-ID: <49DD991D.3070404@sissa.it> Jianping Dai wrote: > Dear All, > > I am a new user of PWSCF. I want to the difference between the two > pseudopotentials: > > > *Zn.pbe-van.UPF* > > (*details* > ) > > Perdew-Burke-Ernzerhof (PBE) exch-corr > Vanderbilt ultrasoft > > *Zn.bp-van_ak.UPF* > > (*details* > ) > > > Becke-Perdew gradient-corrected functional > Vanderbilt ultrasoft > author: ak > > It just generated by differnent author? No, I think they use different exchange and correlation functional. In order to understand which XC functional has been used to build a PP file (before using it), you should look inside the file itself (which is plain ASCII text). In this case you would find these strings: In Zn.pbe-van.UPF: SLA PW PBE PBE PBE Exchange-Correlation functional while in Zn.bp-van_ak.UPF: SLA PZ B88 P86 BP Exchange-Correlation functional The first two codes indicate exchange and correlation functionals for the local spin density, while the third and fourth for the gradient corrected part. The fifth is the identification code for the whole functional (if existing). These codes are those reported, for instance, at the beginning of the output of a pw.x calculation. Each code is mapped to an integer defined inside Modules/functionals.f90. These codes are then used to access the corresponding formulas for the exchange and correlations parts, which you can find inside flib/functionals.f90 and flib/lsda_functionals.f90 for the spin-polarized versions. HTH GS > > > > Thanks! > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From yccheng.nju at gmail.com Thu Apr 9 09:53:51 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Thu, 9 Apr 2009 15:53:51 +0800 Subject: [Pw_forum] the missing symmetry of bands In-Reply-To: <1239194998.3263.26.camel@dhpc-5-20.sissa.it> References: <1239194998.3263.26.camel@dhpc-5-20.sissa.it> Message-ID: Actually the symmetry of 4H-AlN is C_6v, but the pw.x can not find all the 12 operations. So I followed the user's guide Page 60, I changed PW/eqvect.f90. The value of accep is changed to be 10^-3. The changed pw.x can find all 12 operations. This change is the reason why you got C_3v symmetry. After I rechanged the value of accep to be 10^-5, pw.x only can find 6 operations. Can you give some additional advices to find other operations ? 2009/4/8 Dal Corso Andrea > On Wed, 2009-04-08 at 19:34 +0800, ??? wrote: > > Dear PWscf users, > > In my recent calculation of 4H-AlN (ABCB stacking sequence), > > the band symmetry seems to be missed in bands.x calculation. The > > output of bands.x is as following: > > > ************************************************************************** > > xk=( 0.00000, 0.00000, 0.00000 ) > > double point group C_6v (6mm) > > there are 9 classes and 3 irreducible representations > > the character table: > > E -E C2 2C3 -2C3 2C6 -2C6 3s_v 3s_d > > -C2 -3s_v -3s_d > > G_7 2.00 -2.00 0.00 1.00 -1.00 1.73 -1.73 0.00 0.00 > > G_8 2.00 -2.00 0.00 1.00 -1.00 -1.73 1.73 0.00 0.00 > > G_9 2.00 -2.00 0.00 -2.00 2.00 0.00 0.00 0.00 0.00 > > the symmetry operations in each class: > > E 1 > > C2 -C2 2 -2 > > 2C6 3 4 > > 2C3 5 6 > > 3s_v-3s_v 7 -7 9 10 -10 -9 > > 3s_d-3s_d 8 -8 12 -11 11 -12 > > -E -1 > > -2C6 -3 -4 > > -2C3 -5 -6 > > Band symmetry, C_6v (6mm) double point group: > > e( 1 - 2) = -8.01764 eV 2 --> ? > > e( 3 - 4) = -7.17573 eV 2 --> ? > > e( 5 - 6) = -7.13551 eV 2 --> ? > > e( 7 - 8) = -5.93881 eV 2 --> ? > > e( 9 - 10) = 1.12077 eV 2 --> G_7 > > e( 9 - 10) = 1.12077 eV 2 --> 0 G_8 > > e( 11 - 12) = 3.70317 eV 2 --> 0 G_7 > > e( 11 - 12) = 3.70317 eV 2 --> G_8 > > e( 13 - 14) = 3.76782 eV 2 --> ? > > e( 15 - 16) = 6.34352 eV 2 --> ? > > e( 17 - 18) = 6.35869 eV 2 --> G_9 > > e( 19 - 20) = 6.58061 eV 2 --> ? > > e( 21 - 22) = 6.59473 eV 2 --> G_9 > > e( 23 - 24) = 6.65103 eV 2 --> ? > > e( 25 - 26) = 6.66500 eV 2 --> G_9 > > e( 27 - 28) = 6.91040 eV 2 --> ? > > e( 29 - 30) = 6.92400 eV 2 --> G_9 > > e( 31 - 32) = 7.00967 eV 2 --> G_7 > > e( 31 - 32) = 7.00967 eV 2 --> 0 G_8 > > e( 33 - 34) = 11.19288 eV 2 --> ? > > e( 35 - 36) = 13.31415 eV 2 --> ? > > e( 37 - 38) = 13.59769 eV 2 --> ? > > e( 39 - 40) = 14.02975 eV 2 --> ? > > e( 41 - 42) = 17.15974 eV 2 --> ? > > e( 43 - 44) = 17.32327 eV 2 --> ? > > e( 45 - 46) = 17.92003 eV 2 --> ? > > > ************************************************************************** > > My question are : > > 1. what does "?" mean in " e( 1 - 2) = -8.01764 eV 2 > > It means that the symmetry finder is confused. The bands have not a > symmetry that it recognizes. > There are several reasons for this: > > 1) The 'scf' and 'bands' calculations have been run with slightly > different parameters. (solution: recheck your input) > > 2) Your atomic positions are not sufficiently accurate: the number of > digits is sufficient for pw.x to find the symmetries but the > wavefunctions are sufficiently inaccurate to confuse the symmetry > analyzer. (solution: correct your atomic positions) > > 3) If 1) and 2) do not work and you are sure about your coordinates, > then probably there is a bug in the symmetry analyzer. (solution: report > to the forum. I will try to solve it if I can). > > In your particular case: I am confused. On my PC the symmetry found with > your coordinates is C_3v and the symmetry analyzer seems to work. So > please recheck your run. If you still find C_6v please recheck your > atomic positions. > > Hope this helps. > > Andrea > > > > > --> ?" ? > > 2. what does "0" mean in " e( 9 - 10) = 1.12077 eV 2 > > --> 0 G_8" ? > > 3. In 2H-AlN(AB stacking sequence), all the symmetries of bands are > > shown. Why in 4H-AlN, it seems much more complicated. > > > > The input files about 4H-AlN for pw.x and bands.x are as following: > > scf.in > > &control > > title = 2h_aln, > > prefix = '4h_band', > > calculation = 'scf' , > > restart_mode = 'from_scratch' , > > wf_collect = .false. , > > outdir = './' , > > wfcdir = './' , > > pseudo_dir = './' , > > tstress = .true. , > > tprnfor = .true. , > > wf_collect = .true. , > > / > > &SYSTEM > > ibrav = 4, > > celldm(1) = 5.866002785691, > > celldm(3) = 3.238615289089, > > nat = 8, > > ntyp = 2, > > ecutwfc = 80, > > nbnd = 46, > > nosym = .false. , > > lspinorb = .true., > > noncolin= .true., > > starting_magnetization=0.00, > > / > > &ELECTRONS > > electron_maxstep = 100, > > conv_thr = 1.D-10, > > / > > ATOMIC_SPECIES > > N 14.00700 N.rel-pbe-rrkjus.UPF > > Al 26.98200 Al.rel-pbe-rrkj.UPF > > ATOMIC_POSITIONS (crystal) > > N 0.000000000 0.000000000 -0.000722968 > > N 0.000000000 0.000000000 0.499277032 > > N 0.333333333 0.666666667 0.249293699 > > N 0.666666667 0.333333333 0.749293699 > > Al 0.000000000 0.000000000 0.188800277 > > Al 0.000000000 0.000000000 0.688800277 > > Al 0.333333333 0.666666667 0.437593675 > > Al 0.666666667 0.333333333 0.937793675 > > K_POINTS automatic > > 8 8 8 1 1 1 > > > > band.in > > &control > > title = 2h_aln, > > prefix = '4h_band', > > calculation = 'bands' , > > restart_mode = 'from_scratch' , > > wf_collect = .false. , > > outdir = './' , > > wfcdir = './' , > > pseudo_dir = './' , > > / > > &SYSTEM > > ibrav = 4, > > celldm(1) = 5.866002785691, > > celldm(3) = 3.238615289089, > > nat = 8, > > ntyp = 2, > > ecutwfc = 80, > > nbnd=46, > > lspinorb = .true., > > noncolin= .true., > > starting_magnetization=0.0, > > / > > &ELECTRONS > > electron_maxstep = 100, > > conv_thr = 1.D-10, > > / > > ATOMIC_SPECIES > > N 14.00700 N.rel-pbe-rrkjus.UPF > > Al 26.98200 Al.rel-pbe-rrkj.UPF > > ATOMIC_POSITIONS (crystal) > > N 0.000000000 0.000000000 -0.000722968 > > N 0.000000000 0.000000000 0.499277032 > > N 0.333333333 0.666666667 0.249293699 > > N 0.666666667 0.333333333 0.749293699 > > Al 0.000000000 0.000000000 0.188800277 > > Al 0.000000000 0.000000000 0.688800277 > > Al 0.333333333 0.666666667 0.437593675 > > Al 0.666666667 0.333333333 0.937793675 > > K_POINTS > > 2 > > 0.000000 0.000000 0.000000 1.00 > > 0.000000 0.000000 0.083333 1.00 > > > > > > bands.in > > &inputpp > > prefix='4h_band' > > outdir='./' > > filband='spin.dat' > > lsigma(3)=.true. > > lsym=.true. > > / > > > > Thank you in advance! > > > > > > -- > > Y. C. Cheng > > Department of Phyics > > Nanjing University > > Nanjing 210093 > > P. R. China > > Tel: 86-25-83592907 > > Email: yccheng.nju 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 Beirut 2/4 Fax. 0039-040-3787528 > 34014 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 > -- Y. C. Cheng Department of Phyics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090409/80863453/attachment.htm From degironc at sissa.it Thu Apr 9 10:17:49 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 09 Apr 2009 10:17:49 +0200 Subject: [Pw_forum] the missing symmetry of bands In-Reply-To: References: <1239194998.3263.26.camel@dhpc-5-20.sissa.it> Message-ID: <49DDAF2D.3010503@sissa.it> ??? wrote: > Actually the symmetry of 4H-AlN is C_6v, but the pw.x can not find all > the 12 operations. So I followed the user's guide Page 60, I changed > PW/eqvect.f90. The value of accep is changed to be 10^-3. The changed > pw.x can find all 12 operations. This change is the reason why you > got C_3v symmetry. > > After I rechanged the value of accep to be 10^-5, pw.x only can find 6 > operations. Can you give some additional advices to find other > operations ? specify atomic coordinates with a larger number of (correct) digits.. Stefano de Gironcoli - SISSA and DEMOCRITOS > 2009/4/8 Dal Corso Andrea > > > On Wed, 2009-04-08 at 19:34 +0800, ??? wrote: > > Dear PWscf users, > > In my recent calculation of 4H-AlN (ABCB stacking sequence), > > the band symmetry seems to be missed in bands.x calculation. The > > output of bands.x is as following: > > > ************************************************************************** > > xk=( 0.00000, 0.00000, 0.00000 ) > > double point group C_6v (6mm) > > there are 9 classes and 3 irreducible representations > > the character table: > > E -E C2 2C3 -2C3 2C6 -2C6 3s_v 3s_d > > -C2 -3s_v -3s_d > > G_7 2.00 -2.00 0.00 1.00 -1.00 1.73 -1.73 0.00 0.00 > > G_8 2.00 -2.00 0.00 1.00 -1.00 -1.73 1.73 0.00 0.00 > > G_9 2.00 -2.00 0.00 -2.00 2.00 0.00 0.00 0.00 0.00 > > the symmetry operations in each class: > > E 1 > > C2 -C2 2 -2 > > 2C6 3 4 > > 2C3 5 6 > > 3s_v-3s_v 7 -7 9 10 -10 -9 > > 3s_d-3s_d 8 -8 12 -11 11 -12 > > -E -1 > > -2C6 -3 -4 > > -2C3 -5 -6 > > Band symmetry, C_6v (6mm) double point group: > > e( 1 - 2) = -8.01764 eV 2 --> ? > > e( 3 - 4) = -7.17573 eV 2 --> ? > > e( 5 - 6) = -7.13551 eV 2 --> ? > > e( 7 - 8) = -5.93881 eV 2 --> ? > > e( 9 - 10) = 1.12077 eV 2 --> G_7 > > e( 9 - 10) = 1.12077 eV 2 --> 0 G_8 > > e( 11 - 12) = 3.70317 eV 2 --> 0 G_7 > > e( 11 - 12) = 3.70317 eV 2 --> G_8 > > e( 13 - 14) = 3.76782 eV 2 --> ? > > e( 15 - 16) = 6.34352 eV 2 --> ? > > e( 17 - 18) = 6.35869 eV 2 --> G_9 > > e( 19 - 20) = 6.58061 eV 2 --> ? > > e( 21 - 22) = 6.59473 eV 2 --> G_9 > > e( 23 - 24) = 6.65103 eV 2 --> ? > > e( 25 - 26) = 6.66500 eV 2 --> G_9 > > e( 27 - 28) = 6.91040 eV 2 --> ? > > e( 29 - 30) = 6.92400 eV 2 --> G_9 > > e( 31 - 32) = 7.00967 eV 2 --> G_7 > > e( 31 - 32) = 7.00967 eV 2 --> 0 G_8 > > e( 33 - 34) = 11.19288 eV 2 --> ? > > e( 35 - 36) = 13.31415 eV 2 --> ? > > e( 37 - 38) = 13.59769 eV 2 --> ? > > e( 39 - 40) = 14.02975 eV 2 --> ? > > e( 41 - 42) = 17.15974 eV 2 --> ? > > e( 43 - 44) = 17.32327 eV 2 --> ? > > e( 45 - 46) = 17.92003 eV 2 --> ? > > > ************************************************************************** > > My question are : > > 1. what does "?" mean in " e( 1 - 2) = -8.01764 eV 2 > > It means that the symmetry finder is confused. The bands have not a > symmetry that it recognizes. > There are several reasons for this: > > 1) The 'scf' and 'bands' calculations have been run with slightly > different parameters. (solution: recheck your input) > > 2) Your atomic positions are not sufficiently accurate: the number of > digits is sufficient for pw.x to find the symmetries but the > wavefunctions are sufficiently inaccurate to confuse the symmetry > analyzer. (solution: correct your atomic positions) > > 3) If 1) and 2) do not work and you are sure about your coordinates, > then probably there is a bug in the symmetry analyzer. (solution: > report > to the forum. I will try to solve it if I can). > > In your particular case: I am confused. On my PC the symmetry > found with > your coordinates is C_3v and the symmetry analyzer seems to work. So > please recheck your run. If you still find C_6v please recheck your > atomic positions. > > Hope this helps. > > Andrea > > > > > --> ?" ? > > 2. what does "0" mean in " e( 9 - 10) = 1.12077 eV 2 > > --> 0 G_8" ? > > 3. In 2H-AlN(AB stacking sequence), all the symmetries of bands are > > shown. Why in 4H-AlN, it seems much more complicated. > > > > The input files about 4H-AlN for pw.x and bands.x are as following: > > scf.in > > &control > > title = 2h_aln, > > prefix = '4h_band', > > calculation = 'scf' , > > restart_mode = 'from_scratch' , > > wf_collect = .false. , > > outdir = './' , > > wfcdir = './' , > > pseudo_dir = './' , > > tstress = .true. , > > tprnfor = .true. , > > wf_collect = .true. , > > / > > &SYSTEM > > ibrav = 4, > > celldm(1) = 5.866002785691, > > celldm(3) = 3.238615289089, > > nat = 8, > > ntyp = 2, > > ecutwfc = 80, > > nbnd = 46, > > nosym = .false. , > > lspinorb = .true., > > noncolin= .true., > > starting_magnetization=0.00, > > / > > &ELECTRONS > > electron_maxstep = 100, > > conv_thr = 1.D-10, > > / > > ATOMIC_SPECIES > > N 14.00700 N.rel-pbe-rrkjus.UPF > > Al 26.98200 Al.rel-pbe-rrkj.UPF > > ATOMIC_POSITIONS (crystal) > > N 0.000000000 0.000000000 -0.000722968 > > N 0.000000000 0.000000000 0.499277032 > > N 0.333333333 0.666666667 0.249293699 > > N 0.666666667 0.333333333 0.749293699 > > Al 0.000000000 0.000000000 0.188800277 > > Al 0.000000000 0.000000000 0.688800277 > > Al 0.333333333 0.666666667 0.437593675 > > Al 0.666666667 0.333333333 0.937793675 > > K_POINTS automatic > > 8 8 8 1 1 1 > > > > band.in > > &control > > title = 2h_aln, > > prefix = '4h_band', > > calculation = 'bands' , > > restart_mode = 'from_scratch' , > > wf_collect = .false. , > > outdir = './' , > > wfcdir = './' , > > pseudo_dir = './' , > > / > > &SYSTEM > > ibrav = 4, > > celldm(1) = 5.866002785691, > > celldm(3) = 3.238615289089, > > nat = 8, > > ntyp = 2, > > ecutwfc = 80, > > nbnd=46, > > lspinorb = .true., > > noncolin= .true., > > starting_magnetization=0.0, > > / > > &ELECTRONS > > electron_maxstep = 100, > > conv_thr = 1.D-10, > > / > > ATOMIC_SPECIES > > N 14.00700 N.rel-pbe-rrkjus.UPF > > Al 26.98200 Al.rel-pbe-rrkj.UPF > > ATOMIC_POSITIONS (crystal) > > N 0.000000000 0.000000000 -0.000722968 > > N 0.000000000 0.000000000 0.499277032 > > N 0.333333333 0.666666667 0.249293699 > > N 0.666666667 0.333333333 0.749293699 > > Al 0.000000000 0.000000000 0.188800277 > > Al 0.000000000 0.000000000 0.688800277 > > Al 0.333333333 0.666666667 0.437593675 > > Al 0.666666667 0.333333333 0.937793675 > > K_POINTS > > 2 > > 0.000000 0.000000 0.000000 1.00 > > 0.000000 0.000000 0.083333 1.00 > > > > > > bands.in > > &inputpp > > prefix='4h_band' > > outdir='./' > > filband='spin.dat' > > lsigma(3)=.true. > > lsym=.true. > > / > > > > Thank you in advance! > > > > > > -- > > Y. C. Cheng > > Department of Phyics > > Nanjing University > > Nanjing 210093 > > P. R. China > > Tel: 86-25-83592907 > > Email: yccheng.nju 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 Beirut 2/4 Fax. 0039-040-3787528 > 34014 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 > > > > > -- > Y. C. Cheng > Department of Phyics > Nanjing University > Nanjing 210093 > P. R. China > Tel: 86-25-83592907 > Email: yccheng.nju at gmail.com > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From dalcorso at sissa.it Thu Apr 9 10:23:38 2009 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Thu, 09 Apr 2009 10:23:38 +0200 Subject: [Pw_forum] the missing symmetry of bands In-Reply-To: References: <1239194998.3263.26.camel@dhpc-5-20.sissa.it> Message-ID: <1239265418.3254.20.camel@dhpc-5-20.sissa.it> On Thu, 2009-04-09 at 15:53 +0800, ??? wrote: > Actually the symmetry of 4H-AlN is C_6v, but the pw.x can not find all > the 12 operations. So I followed the user's guide Page 60, I changed > PW/eqvect.f90. The value of accep is changed to be 10^-3. The changed > pw.x can find all 12 operations. This change is the reason why you > got C_3v symmetry. > > After I rechanged the value of accep to be 10^-5, pw.x only can find 6 > operations. Can you give some additional advices to find other > operations ? If you want to classify the bands with C_6v symmetry you need coordinates that have C_6v symmetry. Probably, you have to check your coordinates by writing a small code and change the coordinates that break the symmetry. Are you sure that you started vc-relax with coordinates that had C_6v symmetry? I think that in this case you should obtain final coordinates with the same symmetry. If it is vc-relax that breaks the symmetry then, please, report the input of vc-relax because this should not happen. However I am not an expert on this part of QE, so maybe somebody else will look into this. Andrea > > > 2009/4/8 Dal Corso Andrea > > On Wed, 2009-04-08 at 19:34 +0800, ??? wrote: > > Dear PWscf users, > > In my recent calculation of 4H-AlN (ABCB stacking > sequence), > > the band symmetry seems to be missed in bands.x > calculation. The > > output of bands.x is as following: > > > ************************************************************************** > > xk=( 0.00000, 0.00000, 0.00000 ) > > double point group C_6v (6mm) > > there are 9 classes and 3 irreducible representations > > the character table: > > E -E C2 2C3 -2C3 2C6 -2C6 3s_v 3s_d > > -C2 -3s_v -3s_d > > G_7 2.00 -2.00 0.00 1.00 -1.00 1.73 -1.73 0.00 0.00 > > G_8 2.00 -2.00 0.00 1.00 -1.00 -1.73 1.73 0.00 0.00 > > G_9 2.00 -2.00 0.00 -2.00 2.00 0.00 0.00 0.00 0.00 > > the symmetry operations in each class: > > E 1 > > C2 -C2 2 -2 > > 2C6 3 4 > > 2C3 5 6 > > 3s_v-3s_v 7 -7 9 10 -10 -9 > > 3s_d-3s_d 8 -8 12 -11 11 -12 > > -E -1 > > -2C6 -3 -4 > > -2C3 -5 -6 > > Band symmetry, C_6v (6mm) double point group: > > e( 1 - 2) = -8.01764 eV 2 --> ? > > e( 3 - 4) = -7.17573 eV 2 --> ? > > e( 5 - 6) = -7.13551 eV 2 --> ? > > e( 7 - 8) = -5.93881 eV 2 --> ? > > e( 9 - 10) = 1.12077 eV 2 --> G_7 > > e( 9 - 10) = 1.12077 eV 2 --> 0 G_8 > > e( 11 - 12) = 3.70317 eV 2 --> 0 G_7 > > e( 11 - 12) = 3.70317 eV 2 --> G_8 > > e( 13 - 14) = 3.76782 eV 2 --> ? > > e( 15 - 16) = 6.34352 eV 2 --> ? > > e( 17 - 18) = 6.35869 eV 2 --> G_9 > > e( 19 - 20) = 6.58061 eV 2 --> ? > > e( 21 - 22) = 6.59473 eV 2 --> G_9 > > e( 23 - 24) = 6.65103 eV 2 --> ? > > e( 25 - 26) = 6.66500 eV 2 --> G_9 > > e( 27 - 28) = 6.91040 eV 2 --> ? > > e( 29 - 30) = 6.92400 eV 2 --> G_9 > > e( 31 - 32) = 7.00967 eV 2 --> G_7 > > e( 31 - 32) = 7.00967 eV 2 --> 0 G_8 > > e( 33 - 34) = 11.19288 eV 2 --> ? > > e( 35 - 36) = 13.31415 eV 2 --> ? > > e( 37 - 38) = 13.59769 eV 2 --> ? > > e( 39 - 40) = 14.02975 eV 2 --> ? > > e( 41 - 42) = 17.15974 eV 2 --> ? > > e( 43 - 44) = 17.32327 eV 2 --> ? > > e( 45 - 46) = 17.92003 eV 2 --> ? > > > ************************************************************************** > > My question are : > > 1. what does "?" mean in " e( 1 - 2) = -8.01764 eV > 2 > > > It means that the symmetry finder is confused. The bands have > not a > symmetry that it recognizes. > There are several reasons for this: > > 1) The 'scf' and 'bands' calculations have been run with > slightly > different parameters. (solution: recheck your input) > > 2) Your atomic positions are not sufficiently accurate: the > number of > digits is sufficient for pw.x to find the symmetries but the > wavefunctions are sufficiently inaccurate to confuse the > symmetry > analyzer. (solution: correct your atomic positions) > > 3) If 1) and 2) do not work and you are sure about your > coordinates, > then probably there is a bug in the symmetry analyzer. > (solution: report > to the forum. I will try to solve it if I can). > > In your particular case: I am confused. On my PC the symmetry > found with > your coordinates is C_3v and the symmetry analyzer seems to > work. So > please recheck your run. If you still find C_6v please recheck > your > atomic positions. > > Hope this helps. > > Andrea > > > > > > --> ?" ? > > 2. what does "0" mean in " e( 9 - 10) = 1.12077 > eV 2 > > --> 0 G_8" ? > > 3. In 2H-AlN(AB stacking sequence), all the symmetries of > bands are > > shown. Why in 4H-AlN, it seems much more complicated. > > > > The input files about 4H-AlN for pw.x and bands.x are as > following: > > scf.in > > &control > > title = 2h_aln, > > prefix = '4h_band', > > calculation = 'scf' , > > restart_mode = 'from_scratch' , > > wf_collect = .false. , > > outdir = './' , > > wfcdir = './' , > > pseudo_dir = './' , > > tstress = .true. , > > tprnfor = .true. , > > wf_collect = .true. , > > / > > &SYSTEM > > ibrav = 4, > > celldm(1) = 5.866002785691, > > celldm(3) = 3.238615289089, > > nat = 8, > > ntyp = 2, > > ecutwfc = 80, > > nbnd = 46, > > nosym = .false. , > > lspinorb = .true., > > noncolin= .true., > > starting_magnetization=0.00, > > / > > &ELECTRONS > > electron_maxstep = 100, > > conv_thr = 1.D-10, > > / > > ATOMIC_SPECIES > > N 14.00700 N.rel-pbe-rrkjus.UPF > > Al 26.98200 Al.rel-pbe-rrkj.UPF > > ATOMIC_POSITIONS (crystal) > > N 0.000000000 0.000000000 -0.000722968 > > N 0.000000000 0.000000000 0.499277032 > > N 0.333333333 0.666666667 0.249293699 > > N 0.666666667 0.333333333 0.749293699 > > Al 0.000000000 0.000000000 0.188800277 > > Al 0.000000000 0.000000000 0.688800277 > > Al 0.333333333 0.666666667 0.437593675 > > Al 0.666666667 0.333333333 0.937793675 > > K_POINTS automatic > > 8 8 8 1 1 1 > > > > band.in > > &control > > title = 2h_aln, > > prefix = '4h_band', > > calculation = 'bands' , > > restart_mode = 'from_scratch' , > > wf_collect = .false. , > > outdir = './' , > > wfcdir = './' , > > pseudo_dir = './' , > > / > > &SYSTEM > > ibrav = 4, > > celldm(1) = 5.866002785691, > > celldm(3) = 3.238615289089, > > nat = 8, > > ntyp = 2, > > ecutwfc = 80, > > nbnd=46, > > lspinorb = .true., > > noncolin= .true., > > starting_magnetization=0.0, > > / > > &ELECTRONS > > electron_maxstep = 100, > > conv_thr = 1.D-10, > > / > > ATOMIC_SPECIES > > N 14.00700 N.rel-pbe-rrkjus.UPF > > Al 26.98200 Al.rel-pbe-rrkj.UPF > > ATOMIC_POSITIONS (crystal) > > N 0.000000000 0.000000000 -0.000722968 > > N 0.000000000 0.000000000 0.499277032 > > N 0.333333333 0.666666667 0.249293699 > > N 0.666666667 0.333333333 0.749293699 > > Al 0.000000000 0.000000000 0.188800277 > > Al 0.000000000 0.000000000 0.688800277 > > Al 0.333333333 0.666666667 0.437593675 > > Al 0.666666667 0.333333333 0.937793675 > > K_POINTS > > 2 > > 0.000000 0.000000 0.000000 1.00 > > 0.000000 0.000000 0.083333 1.00 > > > > > > bands.in > > &inputpp > > prefix='4h_band' > > outdir='./' > > filband='spin.dat' > > lsigma(3)=.true. > > lsym=.true. > > / > > > > Thank you in advance! > > > > > > -- > > Y. C. Cheng > > Department of Phyics > > Nanjing University > > Nanjing 210093 > > P. R. China > > Tel: 86-25-83592907 > > Email: yccheng.nju 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 Beirut 2/4 Fax. 0039-040-3787528 > 34014 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 > > > > -- > Y. C. Cheng > Department of Phyics > Nanjing University > Nanjing 210093 > P. R. China > Tel: 86-25-83592907 > Email: yccheng.nju 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 Beirut 2/4 Fax. 0039-040-3787528 34014 Trieste (Italy) e-mail: dalcorso at sissa.it From sclauzer at sissa.it Thu Apr 9 10:24:18 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 09 Apr 2009 10:24:18 +0200 Subject: [Pw_forum] the missing symmetry of bands In-Reply-To: References: <1239194998.3263.26.camel@dhpc-5-20.sissa.it> Message-ID: <49DDB0B2.60805@sissa.it> Actually the solution was in point (2) of the reply you got by Andrea: > 2) Your atomic positions are not sufficiently accurate: the number of > digits is sufficient for pw.x to find the symmetries but the > wavefunctions are sufficiently inaccurate to confuse the symmetry > analyzer. (solution: correct your atomic positions) If you get your position from a relax calculation, most probably it means that the symmetry of the starting atomic configuration was already C_3v, since during the relaxations steps the symmetry should be conserved (unless exceptional cases). So please check the initial symmetry in your relax calculation and eventually change the starting configuration. If you don't want to repeat the calculations you can try to fix the atomic positions by hand. I think that what you are missing to recover the full symmetry is a fractional translation of (0,0,0.5) in crystal axis. For instance, the last two Al are 0.5002 apart along the z direction, instead of 0.500000. HTH GS ??? wrote: > Actually the symmetry of 4H-AlN is C_6v, but the pw.x can not find all > the 12 operations. So I followed the user's guide Page 60, I changed > PW/eqvect.f90. The value of accep is changed to be 10^-3. The changed > pw.x can find all 12 operations. This change is the reason why you got > C_3v symmetry. > > After I rechanged the value of accep to be 10^-5, pw.x only can find 6 > operations. Can you give some additional advices to find other operations ? > > 2009/4/8 Dal Corso Andrea > > > On Wed, 2009-04-08 at 19:34 +0800, ??? wrote: > > Dear PWscf users, > > In my recent calculation of 4H-AlN (ABCB stacking sequence), > > the band symmetry seems to be missed in bands.x calculation. The > > output of bands.x is as following: > > > ************************************************************************** > > xk=( 0.00000, 0.00000, 0.00000 ) > > double point group C_6v (6mm) > > there are 9 classes and 3 irreducible representations > > the character table: > > E -E C2 2C3 -2C3 2C6 -2C6 3s_v 3s_d > > -C2 -3s_v -3s_d > > G_7 2.00 -2.00 0.00 1.00 -1.00 1.73 -1.73 0.00 0.00 > > G_8 2.00 -2.00 0.00 1.00 -1.00 -1.73 1.73 0.00 0.00 > > G_9 2.00 -2.00 0.00 -2.00 2.00 0.00 0.00 0.00 0.00 > > the symmetry operations in each class: > > E 1 > > C2 -C2 2 -2 > > 2C6 3 4 > > 2C3 5 6 > > 3s_v-3s_v 7 -7 9 10 -10 -9 > > 3s_d-3s_d 8 -8 12 -11 11 -12 > > -E -1 > > -2C6 -3 -4 > > -2C3 -5 -6 > > Band symmetry, C_6v (6mm) double point group: > > e( 1 - 2) = -8.01764 eV 2 --> ? > > e( 3 - 4) = -7.17573 eV 2 --> ? > > e( 5 - 6) = -7.13551 eV 2 --> ? > > e( 7 - 8) = -5.93881 eV 2 --> ? > > e( 9 - 10) = 1.12077 eV 2 --> G_7 > > e( 9 - 10) = 1.12077 eV 2 --> 0 G_8 > > e( 11 - 12) = 3.70317 eV 2 --> 0 G_7 > > e( 11 - 12) = 3.70317 eV 2 --> G_8 > > e( 13 - 14) = 3.76782 eV 2 --> ? > > e( 15 - 16) = 6.34352 eV 2 --> ? > > e( 17 - 18) = 6.35869 eV 2 --> G_9 > > e( 19 - 20) = 6.58061 eV 2 --> ? > > e( 21 - 22) = 6.59473 eV 2 --> G_9 > > e( 23 - 24) = 6.65103 eV 2 --> ? > > e( 25 - 26) = 6.66500 eV 2 --> G_9 > > e( 27 - 28) = 6.91040 eV 2 --> ? > > e( 29 - 30) = 6.92400 eV 2 --> G_9 > > e( 31 - 32) = 7.00967 eV 2 --> G_7 > > e( 31 - 32) = 7.00967 eV 2 --> 0 G_8 > > e( 33 - 34) = 11.19288 eV 2 --> ? > > e( 35 - 36) = 13.31415 eV 2 --> ? > > e( 37 - 38) = 13.59769 eV 2 --> ? > > e( 39 - 40) = 14.02975 eV 2 --> ? > > e( 41 - 42) = 17.15974 eV 2 --> ? > > e( 43 - 44) = 17.32327 eV 2 --> ? > > e( 45 - 46) = 17.92003 eV 2 --> ? > > > ************************************************************************** > > My question are : > > 1. what does "?" mean in " e( 1 - 2) = -8.01764 eV 2 > > It means that the symmetry finder is confused. The bands have not a > symmetry that it recognizes. > There are several reasons for this: > > 1) The 'scf' and 'bands' calculations have been run with slightly > different parameters. (solution: recheck your input) > > 2) Your atomic positions are not sufficiently accurate: the number of > digits is sufficient for pw.x to find the symmetries but the > wavefunctions are sufficiently inaccurate to confuse the symmetry > analyzer. (solution: correct your atomic positions) > > 3) If 1) and 2) do not work and you are sure about your coordinates, > then probably there is a bug in the symmetry analyzer. (solution: report > to the forum. I will try to solve it if I can). > > In your particular case: I am confused. On my PC the symmetry found with > your coordinates is C_3v and the symmetry analyzer seems to work. So > please recheck your run. If you still find C_6v please recheck your > atomic positions. > > Hope this helps. > > Andrea > > > > > --> ?" ? > > 2. what does "0" mean in " e( 9 - 10) = 1.12077 eV 2 > > --> 0 G_8" ? > > 3. In 2H-AlN(AB stacking sequence), all the symmetries of bands are > > shown. Why in 4H-AlN, it seems much more complicated. > > > > The input files about 4H-AlN for pw.x and bands.x are as following: > > scf.in > > &control > > title = 2h_aln, > > prefix = '4h_band', > > calculation = 'scf' , > > restart_mode = 'from_scratch' , > > wf_collect = .false. , > > outdir = './' , > > wfcdir = './' , > > pseudo_dir = './' , > > tstress = .true. , > > tprnfor = .true. , > > wf_collect = .true. , > > / > > &SYSTEM > > ibrav = 4, > > celldm(1) = 5.866002785691, > > celldm(3) = 3.238615289089, > > nat = 8, > > ntyp = 2, > > ecutwfc = 80, > > nbnd = 46, > > nosym = .false. , > > lspinorb = .true., > > noncolin= .true., > > starting_magnetization=0.00, > > / > > &ELECTRONS > > electron_maxstep = 100, > > conv_thr = 1.D-10, > > / > > ATOMIC_SPECIES > > N 14.00700 N.rel-pbe-rrkjus.UPF > > Al 26.98200 Al.rel-pbe-rrkj.UPF > > ATOMIC_POSITIONS (crystal) > > N 0.000000000 0.000000000 -0.000722968 > > N 0.000000000 0.000000000 0.499277032 > > N 0.333333333 0.666666667 0.249293699 > > N 0.666666667 0.333333333 0.749293699 > > Al 0.000000000 0.000000000 0.188800277 > > Al 0.000000000 0.000000000 0.688800277 > > Al 0.333333333 0.666666667 0.437593675 > > Al 0.666666667 0.333333333 0.937793675 > > K_POINTS automatic > > 8 8 8 1 1 1 > > > > band.in > > &control > > title = 2h_aln, > > prefix = '4h_band', > > calculation = 'bands' , > > restart_mode = 'from_scratch' , > > wf_collect = .false. , > > outdir = './' , > > wfcdir = './' , > > pseudo_dir = './' , > > / > > &SYSTEM > > ibrav = 4, > > celldm(1) = 5.866002785691, > > celldm(3) = 3.238615289089, > > nat = 8, > > ntyp = 2, > > ecutwfc = 80, > > nbnd=46, > > lspinorb = .true., > > noncolin= .true., > > starting_magnetization=0.0, > > / > > &ELECTRONS > > electron_maxstep = 100, > > conv_thr = 1.D-10, > > / > > ATOMIC_SPECIES > > N 14.00700 N.rel-pbe-rrkjus.UPF > > Al 26.98200 Al.rel-pbe-rrkj.UPF > > ATOMIC_POSITIONS (crystal) > > N 0.000000000 0.000000000 -0.000722968 > > N 0.000000000 0.000000000 0.499277032 > > N 0.333333333 0.666666667 0.249293699 > > N 0.666666667 0.333333333 0.749293699 > > Al 0.000000000 0.000000000 0.188800277 > > Al 0.000000000 0.000000000 0.688800277 > > Al 0.333333333 0.666666667 0.437593675 > > Al 0.666666667 0.333333333 0.937793675 > > K_POINTS > > 2 > > 0.000000 0.000000 0.000000 1.00 > > 0.000000 0.000000 0.083333 1.00 > > > > > > bands.in > > &inputpp > > prefix='4h_band' > > outdir='./' > > filband='spin.dat' > > lsigma(3)=.true. > > lsym=.true. > > / > > > > Thank you in advance! > > > > > > -- > > Y. C. Cheng > > Department of Phyics > > Nanjing University > > Nanjing 210093 > > P. R. China > > Tel: 86-25-83592907 > > Email: yccheng.nju 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 Beirut 2/4 Fax. 0039-040-3787528 > 34014 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 > > > > > -- > Y. C. Cheng > Department of Phyics > Nanjing University > Nanjing 210093 > P. R. China > Tel: 86-25-83592907 > Email: yccheng.nju at gmail.com > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From yccheng.nju at gmail.com Thu Apr 9 11:22:39 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Thu, 9 Apr 2009 17:22:39 +0800 Subject: [Pw_forum] the missing symmetry of bands In-Reply-To: <49DDB0B2.60805@sissa.it> References: <1239194998.3263.26.camel@dhpc-5-20.sissa.it> <49DDB0B2.60805@sissa.it> Message-ID: Thank you for your kindly help! It is indeed the problem about sufficiency of digital number for pw.x to find the symmetries. After changing the atom position to satisfy the fractional translation of (0,0,0.5) , pw.x can find all the operation. 2009/4/9 Gabriele Sclauzero > Actually the solution was in point (2) of the reply you got by Andrea: > > > 2) Your atomic positions are not sufficiently accurate: the number > of > > digits is sufficient for pw.x to find the symmetries but the > > wavefunctions are sufficiently inaccurate to confuse the symmetry > > analyzer. (solution: correct your atomic positions) > > If you get your position from a relax calculation, most probably it means > that the > symmetry of the starting atomic configuration was already C_3v, since > during the > relaxations steps the symmetry should be conserved (unless exceptional > cases). > So please check the initial symmetry in your relax calculation and > eventually change the > starting configuration. > If you don't want to repeat the calculations you can try to fix the atomic > positions by > hand. I think that what you are missing to recover the full symmetry is a > fractional > translation of (0,0,0.5) in crystal axis. For instance, the last two Al are > 0.5002 apart > along the z direction, instead of 0.500000. > > HTH > > GS > > ??? wrote: > > Actually the symmetry of 4H-AlN is C_6v, but the pw.x can not find all > > the 12 operations. So I followed the user's guide Page 60, I changed > > PW/eqvect.f90. The value of accep is changed to be 10^-3. The changed > > pw.x can find all 12 operations. This change is the reason why you got > > C_3v symmetry. > > > > After I rechanged the value of accep to be 10^-5, pw.x only can find 6 > > operations. Can you give some additional advices to find other > operations ? > > > > 2009/4/8 Dal Corso Andrea > > > > > On Wed, 2009-04-08 at 19:34 +0800, ??? wrote: > > > Dear PWscf users, > > > In my recent calculation of 4H-AlN (ABCB stacking > sequence), > > > the band symmetry seems to be missed in bands.x calculation. The > > > output of bands.x is as following: > > > > > > ************************************************************************** > > > xk=( 0.00000, 0.00000, 0.00000 ) > > > double point group C_6v (6mm) > > > there are 9 classes and 3 irreducible representations > > > the character table: > > > E -E C2 2C3 -2C3 2C6 -2C6 3s_v 3s_d > > > -C2 -3s_v -3s_d > > > G_7 2.00 -2.00 0.00 1.00 -1.00 1.73 -1.73 0.00 0.00 > > > G_8 2.00 -2.00 0.00 1.00 -1.00 -1.73 1.73 0.00 0.00 > > > G_9 2.00 -2.00 0.00 -2.00 2.00 0.00 0.00 0.00 0.00 > > > the symmetry operations in each class: > > > E 1 > > > C2 -C2 2 -2 > > > 2C6 3 4 > > > 2C3 5 6 > > > 3s_v-3s_v 7 -7 9 10 -10 -9 > > > 3s_d-3s_d 8 -8 12 -11 11 -12 > > > -E -1 > > > -2C6 -3 -4 > > > -2C3 -5 -6 > > > Band symmetry, C_6v (6mm) double point group: > > > e( 1 - 2) = -8.01764 eV 2 --> ? > > > e( 3 - 4) = -7.17573 eV 2 --> ? > > > e( 5 - 6) = -7.13551 eV 2 --> ? > > > e( 7 - 8) = -5.93881 eV 2 --> ? > > > e( 9 - 10) = 1.12077 eV 2 --> G_7 > > > e( 9 - 10) = 1.12077 eV 2 --> 0 G_8 > > > e( 11 - 12) = 3.70317 eV 2 --> 0 G_7 > > > e( 11 - 12) = 3.70317 eV 2 --> G_8 > > > e( 13 - 14) = 3.76782 eV 2 --> ? > > > e( 15 - 16) = 6.34352 eV 2 --> ? > > > e( 17 - 18) = 6.35869 eV 2 --> G_9 > > > e( 19 - 20) = 6.58061 eV 2 --> ? > > > e( 21 - 22) = 6.59473 eV 2 --> G_9 > > > e( 23 - 24) = 6.65103 eV 2 --> ? > > > e( 25 - 26) = 6.66500 eV 2 --> G_9 > > > e( 27 - 28) = 6.91040 eV 2 --> ? > > > e( 29 - 30) = 6.92400 eV 2 --> G_9 > > > e( 31 - 32) = 7.00967 eV 2 --> G_7 > > > e( 31 - 32) = 7.00967 eV 2 --> 0 G_8 > > > e( 33 - 34) = 11.19288 eV 2 --> ? > > > e( 35 - 36) = 13.31415 eV 2 --> ? > > > e( 37 - 38) = 13.59769 eV 2 --> ? > > > e( 39 - 40) = 14.02975 eV 2 --> ? > > > e( 41 - 42) = 17.15974 eV 2 --> ? > > > e( 43 - 44) = 17.32327 eV 2 --> ? > > > e( 45 - 46) = 17.92003 eV 2 --> ? > > > > > > ************************************************************************** > > > My question are : > > > 1. what does "?" mean in " e( 1 - 2) = -8.01764 eV 2 > > > > It means that the symmetry finder is confused. The bands have not a > > symmetry that it recognizes. > > There are several reasons for this: > > > > 1) The 'scf' and 'bands' calculations have been run with slightly > > different parameters. (solution: recheck your input) > > > > 2) Your atomic positions are not sufficiently accurate: the number of > > digits is sufficient for pw.x to find the symmetries but the > > wavefunctions are sufficiently inaccurate to confuse the symmetry > > analyzer. (solution: correct your atomic positions) > > > > 3) If 1) and 2) do not work and you are sure about your coordinates, > > then probably there is a bug in the symmetry analyzer. (solution: > report > > to the forum. I will try to solve it if I can). > > > > In your particular case: I am confused. On my PC the symmetry found > with > > your coordinates is C_3v and the symmetry analyzer seems to work. So > > please recheck your run. If you still find C_6v please recheck your > > atomic positions. > > > > Hope this helps. > > > > Andrea > > > > > > > > > --> ?" ? > > > 2. what does "0" mean in " e( 9 - 10) = 1.12077 eV > 2 > > > --> 0 G_8" ? > > > 3. In 2H-AlN(AB stacking sequence), all the symmetries of bands > are > > > shown. Why in 4H-AlN, it seems much more complicated. > > > > > > The input files about 4H-AlN for pw.x and bands.x are as > following: > > > scf.in > > > &control > > > title = 2h_aln, > > > prefix = '4h_band', > > > calculation = 'scf' , > > > restart_mode = 'from_scratch' , > > > wf_collect = .false. , > > > outdir = './' , > > > wfcdir = './' , > > > pseudo_dir = './' , > > > tstress = .true. , > > > tprnfor = .true. , > > > wf_collect = .true. , > > > / > > > &SYSTEM > > > ibrav = 4, > > > celldm(1) = 5.866002785691, > > > celldm(3) = 3.238615289089, > > > nat = 8, > > > ntyp = 2, > > > ecutwfc = 80, > > > nbnd = 46, > > > nosym = .false. , > > > lspinorb = .true., > > > noncolin= .true., > > > starting_magnetization=0.00, > > > / > > > &ELECTRONS > > > electron_maxstep = 100, > > > conv_thr = 1.D-10, > > > / > > > ATOMIC_SPECIES > > > N 14.00700 N.rel-pbe-rrkjus.UPF > > > Al 26.98200 Al.rel-pbe-rrkj.UPF > > > ATOMIC_POSITIONS (crystal) > > > N 0.000000000 0.000000000 -0.000722968 > > > N 0.000000000 0.000000000 0.499277032 > > > N 0.333333333 0.666666667 0.249293699 > > > N 0.666666667 0.333333333 0.749293699 > > > Al 0.000000000 0.000000000 0.188800277 > > > Al 0.000000000 0.000000000 0.688800277 > > > Al 0.333333333 0.666666667 0.437593675 > > > Al 0.666666667 0.333333333 0.937793675 > > > K_POINTS automatic > > > 8 8 8 1 1 1 > > > > > > band.in > > > &control > > > title = 2h_aln, > > > prefix = '4h_band', > > > calculation = 'bands' , > > > restart_mode = 'from_scratch' , > > > wf_collect = .false. , > > > outdir = './' , > > > wfcdir = './' , > > > pseudo_dir = './' , > > > / > > > &SYSTEM > > > ibrav = 4, > > > celldm(1) = 5.866002785691, > > > celldm(3) = 3.238615289089, > > > nat = 8, > > > ntyp = 2, > > > ecutwfc = 80, > > > nbnd=46, > > > lspinorb = .true., > > > noncolin= .true., > > > starting_magnetization=0.0, > > > / > > > &ELECTRONS > > > electron_maxstep = 100, > > > conv_thr = 1.D-10, > > > / > > > ATOMIC_SPECIES > > > N 14.00700 N.rel-pbe-rrkjus.UPF > > > Al 26.98200 Al.rel-pbe-rrkj.UPF > > > ATOMIC_POSITIONS (crystal) > > > N 0.000000000 0.000000000 -0.000722968 > > > N 0.000000000 0.000000000 0.499277032 > > > N 0.333333333 0.666666667 0.249293699 > > > N 0.666666667 0.333333333 0.749293699 > > > Al 0.000000000 0.000000000 0.188800277 > > > Al 0.000000000 0.000000000 0.688800277 > > > Al 0.333333333 0.666666667 0.437593675 > > > Al 0.666666667 0.333333333 0.937793675 > > > K_POINTS > > > 2 > > > 0.000000 0.000000 0.000000 1.00 > > > 0.000000 0.000000 0.083333 1.00 > > > > > > > > > bands.in > > > &inputpp > > > prefix='4h_band' > > > outdir='./' > > > filband='spin.dat' > > > lsigma(3)=.true. > > > lsym=.true. > > > / > > > > > > Thank you in advance! > > > > > > > > > -- > > > Y. C. Cheng > > > Department of Phyics > > > Nanjing University > > > Nanjing 210093 > > > P. R. China > > > Tel: 86-25-83592907 > > > Email: yccheng.nju 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 Beirut 2/4 Fax. 0039-040-3787528 > > 34014 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 > > > > > > > > > > -- > > Y. C. Cheng > > Department of Phyics > > Nanjing University > > Nanjing 210093 > > P. R. China > > Tel: 86-25-83592907 > > Email: yccheng.nju at gmail.com > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090409/793fe527/attachment-0001.htm From dimpy.sharma at tyndall.ie Thu Apr 9 13:47:31 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Thu, 9 Apr 2009 12:47:31 +0100 Subject: [Pw_forum] (no subject) Message-ID: Hi Can anybody please tell me the difference meaning of ecut_conv_thr and forc_conv_thr -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090409/9a849e2a/attachment.htm From paulatto at sissa.it Thu Apr 9 13:51:16 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 09 Apr 2009 13:51:16 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: References: Message-ID: On Thu, 09 Apr 2009 13:47:31 +0200, Dimpy Sharma wrote: > > Hi > Can anybody please tell me the difference meaning of ecut_conv_thr and > forc_conv_thr The first doe not exist, the latter is the threshold for convergence of total force in a relax calculation. If instead of ecut_conv_thr you meant to write etot_conv_thr, than it would have been the threshold for convergence of total energy in a relax calculation (as a function of ions positions). It has not to be confused with conv_thr which is the convergence of scf energy in a single step of a relax calculation. Please, have a look at the documentation in the Doc/ directory. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From degironc at sissa.it Thu Apr 9 13:52:20 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 09 Apr 2009 13:52:20 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: References: Message-ID: <49DDE174.1040804@sissa.it> Relaxation stops when subsequent total energies differs by less than ecut_conv_thr (in Ry) AND each force component on any atom is less than force_conv_thr (in Ry/a.u.). BOTH conditions must be satisfied. usually the determining one is the one on forces. Stefano de Gironcoli - SISSA and DEMOCRITOS PS: Please do not forget to provide your affiliation Dimpy Sharma wrote: > Hi > > Can anybody please tell me the difference meaning of ecut_conv_thr and > forc_conv_thr > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From carlo.nervi at unito.it Thu Apr 9 21:48:49 2009 From: carlo.nervi at unito.it (Carlo Nervi) Date: Thu, 9 Apr 2009 21:48:49 +0200 (CEST) Subject: [Pw_forum] again on "charge is wrong" error Message-ID: <1319.151.62.48.5.1239306529.squirrel@mail.unito.it> Dear all, I've read some of the past messages about the "charge is wrong" error, since I faced it too. Well, I tried to increase nbnd but the result was only a longer time before crash. I read http://qe-forge.org/tracker/index.php?func=detail&aid=6&group_id=10&atid=133 that suggest a compiler problem. I used MKL 10.1.1.019 and ifort 11.0.081 compiling the version CVS4.1. Inthe input file I switched from diagonalization = 'david' to diagonalization = 'cg' and in my case magically it works. Previously was reported that the diag method does not influence the purported bug. In my case it does. Below is the input file I used. I generated PP with ld1 which includes gipaw and paw (if necssary I can post also this input file). So I cannot understand if it is a bad input file (or unlikely the PP), a compiler/library bug, or there are some other reasons. Cheers, Carlo &CONTROL title = opt_Hexametylbenzene calculation = 'scf' verbosity = 'high' restart_mode = 'from_scratch' outdir = '/home/nervi/calc/Barbiturico/Michele_periodico/Hex_opt2' wfcdir = '/home/nervi/calc/Barbiturico/Michele_periodico/Hex_opt2' pseudo_dir = '/opt/QE/pseudo/' tstress = .false. tprnfor = .true. nstep = 200 prefix = 'Hex_scf2' / &SYSTEM ibrav = 14 A = 5.2602 B = 6.1990 C = 8.0040 cosAB = -0.23883853663434945639315144328238d0 cosAC = -0.15157135729098039184458626927334d0 cosBC = -0.1769473189631088683332049444808d0 nat = 30 ntyp = 2 ! nelec = 66 ! nbnd = 43 nosym = .true. ecutwfc = 60 ecutrho = 400 / &ELECTRONS diagonalization = 'cg' conv_thr = 1.0d-12 mixing_mode = 'plain' mixing_beta = 0.7 electron_maxstep = 800 / ATOMIC_SPECIES H 1.00794 H.pbe-tm-gipaw_CN.UPF C 12.01070 C.pbe-tm-gipaw_CN.UPF ATOMIC_POSITIONS angstrom C 1.480397773 1.612313649 2.444441309 C 0.567917143 2.576536963 2.912448759 C 2.398248842 1.016955503 3.333293664 C 1.458567352 1.197000496 0.992534797 C -0.390137179 3.238330523 1.951641575 C 3.424801493 0.044743239 2.809820675 H 1.584075172 2.045815584 0.307303297 H 0.500805783 0.728127864 0.720359738 H 2.239781168 0.471645652 0.762057598 H -0.457043850 4.319305135 2.119989739 H 3.849201391 2.846663344 2.063331085 H -0.094884507 3.092803886 0.908990630 H 4.212652583 -0.148282042 3.538235815 H 1.511394708 5.096586242 2.526556736 H 3.920433573 0.445290897 1.916401289 C 0.552060959 2.923991539 4.277926921 C 1.470203101 2.328901527 5.167310621 C 2.382255680 1.363811124 4.698964273 C 3.339744478 0.703097622 5.658479146 H 3.407382859 -0.378164308 5.491314032 H -0.898773017 1.094722561 5.547308946 H 3.045747097 0.848022744 6.702191454 C 1.491410825 2.742208586 6.617237692 H 1.366101010 1.894427124 7.303910857 H 2.448208749 3.213147289 6.891196900 H 0.708636653 3.467720853 6.848772588 C -0.473956442 3.896108675 4.801178466 H -1.263190322 4.088213149 4.072554504 H 1.439086797 -1.155263370 5.082385329 H -0.969233483 3.496601812 5.694367685 K_POINTS automatic 3 3 3 0 0 0 -- ------------------------------------------------------ Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 Fax: +39 011 6707855 - Dipartimento di Chimica IFM via P. Giuria 7, 10125 Torino, Italy http://lem.ch.unito.it/ From paulatto at sissa.it Fri Apr 10 10:20:11 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 10 Apr 2009 10:20:11 +0200 Subject: [Pw_forum] again on "charge is wrong" error In-Reply-To: <1319.151.62.48.5.1239306529.squirrel@mail.unito.it> References: <1319.151.62.48.5.1239306529.squirrel@mail.unito.it> Message-ID: On Thu, 09 Apr 2009 21:48:49 +0200, Carlo Nervi wrote: > I generated PP with ld1 > which includes gipaw and paw (if necssary I can post also > this input file). Hi Carlo, I'm sorry to say, but if you've generated the paw dataset yourself, there are good chances there is a ghost state, probably at high enough energy that it does not cause problems most of the time. Please send the inputs (privately, if you so wish) so I can check them. cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From jianping09 at gmail.com Fri Apr 10 10:35:41 2009 From: jianping09 at gmail.com (Jianping Dai) Date: Fri, 10 Apr 2009 16:35:41 +0800 Subject: [Pw_forum] what is the different pseudopotential? In-Reply-To: <49DD991D.3070404@sissa.it> References: <486e50d80904082218k57209b0h5f7b5172e2066bab@mail.gmail.com> <49DD991D.3070404@sissa.it> Message-ID: <486e50d80904100135o6356b38ekccb90e67497ecfae@mail.gmail.com> Dear Sclauzero, Thanks a lot! 2009/4/9 Gabriele Sclauzero > > Jianping Dai wrote: > > Dear All, > > > > I am a new user of PWSCF. I want to the difference between the two > > pseudopotentials: > > > > > > *Zn.pbe-van.UPF* > > > > (*details* > > < > http://www.quantum-espresso.org/pseudo/upfdetails.php?upf=Zn.pbe-van.UPF>) > > > > Perdew-Burke-Ernzerhof (PBE) exch-corr > > Vanderbilt ultrasoft > > > > *Zn.bp-van_ak.UPF* > > > > (*details* > > < > http://www.quantum-espresso.org/pseudo/upfdetails.php?upf=Zn.bp-van_ak.UPF > >) > > > > > > Becke-Perdew gradient-corrected functional > > Vanderbilt ultrasoft > > author: ak > > > > It just generated by differnent author? > > No, I think they use different exchange and correlation functional. In > order to understand > which XC functional has been used to build a PP file (before using it), you > should look > inside the file itself (which is plain ASCII text). > In this case you would find these strings: > > In Zn.pbe-van.UPF: > SLA PW PBE PBE PBE Exchange-Correlation functional > > while in Zn.bp-van_ak.UPF: > SLA PZ B88 P86 BP Exchange-Correlation functional > > The first two codes indicate exchange and correlation functionals for the > local spin > density, while the third and fourth for the gradient corrected part. The > fifth is the > identification code for the whole functional (if existing). > These codes are those reported, for instance, at the beginning of the > output of a pw.x > calculation. > Each code is mapped to an integer defined inside Modules/functionals.f90. > These codes are > then used to access the corresponding formulas for the exchange and > correlations parts, > which you can find inside flib/functionals.f90 and > flib/lsda_functionals.f90 for the > spin-polarized versions. > > HTH > > GS > > > > > > > > > Thanks! > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > 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/20090410/9d8a4fa6/attachment.htm From mambom1902 at yahoo.com Fri Apr 10 11:05:19 2009 From: mambom1902 at yahoo.com (loc duong ding) Date: Fri, 10 Apr 2009 02:05:19 -0700 (PDT) Subject: [Pw_forum] Definition of Fermi level in PWscf Message-ID: <529285.42743.qm@web38802.mail.mud.yahoo.com> Dear all users, I?try to calculate the work function of CNTs.?However, I?am not?clear the definition of Fermi level in PWscf code.?How we can define?Fermi level in?case of metal and semiconductor by DFT??? I?greatly appeciate for all your helps. Best regards,----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com From sporevoyager at gmail.com Fri Apr 10 11:41:16 2009 From: sporevoyager at gmail.com (shangy) Date: Fri, 10 Apr 2009 17:41:16 +0800 Subject: [Pw_forum] Does anyone has Ge and B norm-conserving pseudopotentials with PBE type? Message-ID: <94be399f0904100241q1c5d06deoc1bc54ea7c7cab83@mail.gmail.com> Dear all: Does anyone has Ge and B norm-conserving pseudopotentials with PBE type?I'm very appreicated that if you could share it with me. Thanks in advance! Best regard! shangy Graduate unversity of Chinese academy of sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090410/995344ef/attachment.htm From panda.deng.pan at gmail.com Fri Apr 10 14:04:20 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Fri, 10 Apr 2009 20:04:20 +0800 Subject: [Pw_forum] Definition of Fermi level in PWscf In-Reply-To: <529285.42743.qm@web38802.mail.mud.yahoo.com> References: <529285.42743.qm@web38802.mail.mud.yahoo.com> Message-ID: I strongly suggest that I search the archive first where your problem had been explained. From eyvaz_isaev at yahoo.com Fri Apr 10 14:42:35 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 10 Apr 2009 05:42:35 -0700 (PDT) Subject: [Pw_forum] Definition of Fermi level in PWscf In-Reply-To: Message-ID: <274637.83208.qm@web65702.mail.ac4.yahoo.com> Please see next links: http://www.democritos.it/pipermail/pw_forum/2008-August/009764.html http://www.democritos.it/pipermail/pw_forum/2008-August/009771.html Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Fri, 4/10/09, ?? wrote: > From: ?? > Subject: Re: [Pw_forum] Definition of Fermi level in PWscf > To: "PWSCF Forum" > Date: Friday, April 10, 2009, 4:04 PM > I strongly suggest that I search the archive first where > your problem > had been explained. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From quantumdft at gmail.com Sat Apr 11 09:15:33 2009 From: quantumdft at gmail.com (vega lew) Date: Sat, 11 Apr 2009 15:15:33 +0800 Subject: [Pw_forum] what's the unit of charge density Message-ID: <412f6c680904110015u46e6be86x448f9d1c84868a11@mail.gmail.com> Dear all I just ploted the 3D charge density using pp.x code. And XCRYSDEN was used for displaying the 3D isosurface of charge density. When I set the isovalue for different number, such as 0.15 or less, I fould the overlap of electron cloud is quite meanful for different systems of distinct catalysis activities. I wonder what the unit of charge density? and whether the absolute value of it could be directly comparable for different systems ( same number of atoms, same element, only different in geometry of the model)? if I adjust the same isovalue (~0.15) for two systems, I found the the electron cloud is overlapped at reacive site for more reactive system and the electron cloud is separated for less reactive system. Could I say the chemical bond is stronger in reactive system and that bond is responsible for the activities? By the way, is there a tutorial for population analysis? I wonder where I could find the value of overap population for a pair of atoms. thank you for reading, any hints will be deeply appreciated. vega -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090411/36c228e2/attachment.htm From mansourehp at gmail.com Sat Apr 11 10:04:18 2009 From: mansourehp at gmail.com (Mansoureh Pashangpour) Date: Sat, 11 Apr 2009 12:34:18 +0430 Subject: [Pw_forum] bulk modulus unit Message-ID: Dear all I"m calculating bulk modulus for a system with PWscf. As you know Etot unit is Ry and V unit is a,u.^3. how can I find (K0 and K'0) bulk modulus in Gpa unit. Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090411/69fbe774/attachment.htm From yccheng.nju at gmail.com Sat Apr 11 10:41:58 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Sat, 11 Apr 2009 16:41:58 +0800 Subject: [Pw_forum] bulk modulus unit In-Reply-To: References: Message-ID: Maybe 14722 GPa/(Ry/au.^3). You can translate Ry and au to J and meter yourself. 2009/4/11 Mansoureh Pashangpour > Dear all > I"m calculating bulk modulus for a system with PWscf. As you know Etot unit > is Ry and V unit is a,u.^3. > how can I find (K0 and K'0) bulk modulus in Gpa unit. > Thanks > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090411/0a1cc546/attachment.htm From mansourehp at gmail.com Sat Apr 11 10:47:40 2009 From: mansourehp at gmail.com (Mansoureh Pashangpour) Date: Sat, 11 Apr 2009 13:17:40 +0430 Subject: [Pw_forum] bulk modulus unit In-Reply-To: References: Message-ID: Thank for your quick reply On Sat, Apr 11, 2009 at 1:11 PM, ??? wrote: > Maybe 14722 GPa/(Ry/au.^3). You can translate Ry and au to J and meter > yourself. > > 2009/4/11 Mansoureh Pashangpour > >> Dear all >> I"m calculating bulk modulus for a system with PWscf. As you know Etot >> unit is Ry and V unit is a,u.^3. >> how can I find (K0 and K'0) bulk modulus in Gpa unit. >> Thanks >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > Y. C. Cheng > Department of Physics > Nanjing University > Nanjing 210093 > P. R. China > Tel: 86-25-83592907 > Email: yccheng.nju at gmail.com > > _______________________________________________ > 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/20090411/a5ac4cd8/attachment.htm From paulatto at sissa.it Sat Apr 11 12:07:42 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sat, 11 Apr 2009 12:07:42 +0200 (CEST) Subject: [Pw_forum] bulk modulus unit In-Reply-To: References: Message-ID: <49648.78.12.163.141.1239444462.squirrel@webmail.sissa.it> On Sab, Aprile 11, 2009 10:04, Mansoureh Pashangpour wrote: > Dear all > I"m calculating bulk modulus for a system with PWscf. As you know Etot > unit > is Ry and V unit is a,u.^3. > how can I find (K0 and K'0) bulk modulus in Gpa unit. > Thanks in the pwtools directory there is a small utility calle eos.x to fit volume/energy curves. It prints the bulk modulus directly in GPa. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From eyvaz_isaev at yahoo.com Sat Apr 11 12:40:10 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sat, 11 Apr 2009 03:40:10 -0700 (PDT) Subject: [Pw_forum] bulk modulus unit In-Reply-To: <49648.78.12.163.141.1239444462.squirrel@webmail.sissa.it> Message-ID: <554647.14428.qm@web65704.mail.ac4.yahoo.com> Hi, 2 small comments: a) ev.x, but not eos.x in pwtools. Though, something may be has changed. b) B' (or K') is dimensionless by its definition. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Sat, 4/11/09, Lorenzo Paulatto wrote: > From: Lorenzo Paulatto > Subject: Re: [Pw_forum] bulk modulus unit > To: "PWSCF Forum" > Date: Saturday, April 11, 2009, 2:07 PM > On Sab, Aprile 11, 2009 10:04, Mansoureh Pashangpour wrote: > > Dear all > > I"m calculating bulk modulus for a system with > PWscf. As you know Etot > > unit > > is Ry and V unit is a,u.^3. > > how can I find (K0 and K'0) bulk modulus in Gpa > unit. > > Thanks > > in the pwtools directory there is a small utility calle > eos.x to fit > volume/energy curves. It prints the bulk modulus directly > in GPa. > > regards > > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by SquirrelMail http://www.squirrelmail.org/ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From kazempoor2000 at yahoo.com Sat Apr 11 13:08:46 2009 From: kazempoor2000 at yahoo.com (ali kazempoor) Date: Sat, 11 Apr 2009 04:08:46 -0700 (PDT) Subject: [Pw_forum] charged defect Message-ID: <119632.33260.qm@web33106.mail.mud.yahoo.com> From kazempoor2000 at yahoo.com Sat Apr 11 13:26:26 2009 From: kazempoor2000 at yahoo.com (ali kazempoor) Date: Sat, 11 Apr 2009 04:26:26 -0700 (PDT) Subject: [Pw_forum] charged defect Message-ID: <886978.17615.qm@web33101.mail.mud.yahoo.com> Dear all I want to study O vacancy in TiO2 bulk . So , I need to know about different charged vacancy and then simulation of the large supercell containing the vacancy. I have two questions : 1- How can I find that how many possibilities are exist for charged vacancies ( I mean that wheather I have nuetral O or O+ or O- or etc). Is these charged state related to experimental data or only determind by theory? 2- After, How can I make supercell input file that has charged vacancy. I mean that which parameter shoud be modified or added to make a supercell include charged defect? and how can I check they are correct? Thanks a lot Ali Kazempour,Isfahan University of technology,physics Dept From anvari_meh at physics.iust.ac.ir Sat Apr 11 14:59:51 2009 From: anvari_meh at physics.iust.ac.ir (Mehrnaz Anvari) Date: Sat, 11 Apr 2009 16:29:51 +0330 Subject: [Pw_forum] vc-rx Message-ID: Hello I have a question about the number of iterations which have to be done for density calculations in each step of vc-rx calculations. I mean do they have to be decreased ? For instance does it have to be converged after 2-3 iterations, after a few steps. Best Regards M.Anvari Iran University Of Science & Technology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090411/aef34e77/attachment.htm From rcjhawk at gmail.com Sat Apr 11 17:32:13 2009 From: rcjhawk at gmail.com (Michael Mehl) Date: Sat, 11 Apr 2009 11:32:13 -0400 Subject: [Pw_forum] bulk modulus unit In-Reply-To: References: Message-ID: <49E0B7FD.5080803@gmail.com> "units" [ http://en.wikipedia.org/wiki/Units_(Unix) ] is your friend $ units 2445 units, 71 prefixes, 33 nonlinear units You have: 1 rydberg/bohrradius^3 You want: gigapascal * 14710.505 / 6.7978632e-05 With the Ubuntu version, at least, using "au" instead of "bohrradius" produces interesting results. It helps to read the documentation. Mansoureh Pashangpour wrote: > Dear all > I"m calculating bulk modulus for a system with PWscf. As you know Etot > unit is Ry and V unit is a,u.^3. > how can I find (K0 and K'0) bulk modulus in Gpa unit. > Thanks > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Michael J. Mehl Naval Research Laboratory Washington DC Currently at Duke University (This is not my work email) From sanjeev0302 at rediffmail.com Sun Apr 12 20:22:53 2009 From: sanjeev0302 at rediffmail.com (Sanjeev K. Gupta) Date: 12 Apr 2009 18:22:53 -0000 Subject: [Pw_forum] electron-phonon coefficient Message-ID: <20090412182253.46206.qmail@f4mail-234-240.rediffmail.com> ? Dear PWSCF users, 1. I want to calculate the electron-phonon coefficient "lamda" and the function "square of alpha" F(w) plot, how i do? 2. I also want to calculate IR spectra and Raman spectra? Thanks in advance!! Kind Regards Sanjeev Gupta S. K. Gupta PhD Candidate, Dept. of Physics, Bhavnagar University. Bhavnagar, 364 002., Gujarat. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090412/7b9436b3/attachment.htm From azgre at azgre.com Sun Apr 12 23:06:26 2009 From: azgre at azgre.com (AZGlobal) Date: Sun, 12 Apr 2009 17:06:26 -0400 Subject: [Pw_forum] electron-phonon coefficient In-Reply-To: <20090412182253.46206.qmail@f4mail-234-240.rediffmail.com> References: <20090412182253.46206.qmail@f4mail-234-240.rediffmail.com> Message-ID: <49E257D2.2000905@azgre.com> Well, there are several ways to skin the cat. 1. The most correct way is to calculate "aph2F(w)". How you do this: you have to numerically get double integral over the calculated Fermi surface for the function *ds*ds'. You will need partial spherical FS), you can use pseudopotential matrix element, and double integral converts into single integral over dq3 for expanded zone. You can pull it out using tetrahedron, or whatever BZ integration method. Much easier, I think it is in Ziman too. 4. You may voluntary ignore the fact that "alpha2" really depends on omega. It does, but most people don't even think about writing so involved code. The matter is decided by balance of time at hand, ambition, braveness and laziness of specific individual. Anyway, if you believe that your "alpha2" is practically constant, you can use Hopfield-McMillan approach. It lets you to derive lambda and lambda(k,k'), but there is some risk (at very extreme this may cost you 20-25% error for lambda). All you will need in this case will be partial state densities at Ef. You simply circumvent all phonon dependence of "apha2", and bravely use and . 5. Finally, if you are extremely lucky, you may find experimental tunnel spectra or point-contact spectra for your compound. But it is really a rarity. Now, where to read more. First of all, look at Ziman. Going beyond that : it is not a self-promotion, it is just easier for me to do it this way. Go to http://www.azgre.com/PERSONAL/zhtpersonal.htm, and from the list of publications look at 4., 8., 9., 13., 14., 57, and 59 (this one is hard to find, it's on "pseudizm" in EPI). Look at references in these articles. Good luck, and please don't hesitate to ask more questions. W/regards Dr. A.Zhako-Titarenko > > > Dear PWSCF users, > > 1. I want to calculate the electron-phonon coefficient "lamda" and the > function "square of alpha" F(w) plot, how i do? > > 2. I also want to calculate IR spectra and Raman spectra? > > Thanks in advance!! > > Kind Regards > Sanjeev Gupta > > S. K. Gupta > PhD Candidate, > Dept. of Physics, > Bhavnagar University. > Bhavnagar, 364 002., Gujarat. > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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/20090412/091cfd7d/attachment.htm From eyvaz_isaev at yahoo.com Mon Apr 13 00:08:02 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sun, 12 Apr 2009 15:08:02 -0700 (PDT) Subject: [Pw_forum] electron-phonon coefficient In-Reply-To: <20090412035132.18541.qmail@f4mail207.rediffmail.com> Message-ID: <942267.89138.qm@web65708.mail.ac4.yahoo.com> Dear Sanjeev, Please have look at elph.tar.gz attached. I think it contains almost all information everybody needs to calculate electron-phonon interaction (run_example file is taken from /example07 directory). I have included revised elphon.f90 and lambda.f90. The first one is useful if you do not have elph-files (like elph.qx.qy.qz) using QE distribution, then replace standard (from QE distribution) elphon.f90 and recompile ph.x. The second one has one more useful output as T_c using the Allen-Dynes formula. I would suggest official lambda.f90 might be replaced by this one. As concerns Raman and IR spectra: If you are interested in IR and Raman active modes see phonon output file for Gamma point. If you need Raman and IR cross sections see dynmat.f90 (and then use dynmat.x). If you need Raman tensors then setup lraman=.true. in phonon input file. As you need Born effective charges Z* you also should specfy epsil=.true. keyword. See /Doc/INPUT_PH.txt and header part of /PH/dynmat.f90 file. Bests Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Sun, 4/12/09, Sanjeev K. Gupta wrote: From: Sanjeev K. Gupta Subject: electron-phonon coefficient To: "eyvaz_isaev" Date: Sunday, April 12, 2009, 7:51 AM Respected Sir, 1. I want to calculate the electron-phonon coefficient "lamda" and the function "square of alpha" F(w) plot, how i do? 2. I also want to calculate IR spectra and Raman spectra? Thanks in advance!! Sanjeev Gupta S. K.?Gupta PhD Candidate, Dept. of?Physics, Bhavnagar University. Bhavnagar, 364?002., Gujarat. -------------- next part -------------- A non-text attachment was scrubbed... Name: elph.tar.gz Type: application/x-gzip Size: 12807 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090412/af797dac/attachment-0001.bin From azgre at azgre.com Sun Apr 12 23:15:13 2009 From: azgre at azgre.com (AZGlobal) Date: Sun, 12 Apr 2009 17:15:13 -0400 Subject: [Pw_forum] vc-rx In-Reply-To: References: Message-ID: <49E259E1.4030100@azgre.com> Normally you iterate until calculated parameter stabilizes within prescribed error interval. Back when I was running SCF on my own, I needed 10-20 to have stabilized results for X-ray spectra for binary alloys in APW, and circa 200-250 for Fermi surface. This gives an idea of how numbers may vary. IMHO there is no other way, but to try, see, and use common sense. Best regards A.Zhalko-Titarenko > Hello > > I have a question about the number of iterations which have to be done > for density calculations in each step of vc-rx calculations. I mean do > they have to be decreased ? > For instance does it have to be converged after 2-3 iterations, after > a few steps. > Best Regards > M.Anvari > Iran University Of Science & Technology > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090412/a4e5cac6/attachment.htm From mambom1902 at yahoo.com Mon Apr 13 02:32:06 2009 From: mambom1902 at yahoo.com (loc duong ding) Date: Sun, 12 Apr 2009 17:32:06 -0700 (PDT) Subject: [Pw_forum] Definition of Fermi level in PWscf In-Reply-To: References: Message-ID: <61600.34891.qm@web38801.mail.mud.yahoo.com> > http://www.democritos.it/pipermail/pw_forum/2008-August/009764.html > > http://www.democritos.it/pipermail/pw_forum/2008-August/009771.html > >>By definition: the Fermi energy is an energy which separates the valence (occupied) electrons from the >>conductivity (unoccupied) electrons. >>In our DFT calculations there is no "real" Fermi energy (E_F), only the one for which \int_{E_min}^{E_F)N(E)dE = >>N is fulfilled (N(E) is the DOS, N is total number of valence electrons). ?Because the DOS in the bandgap is 0, we can put the Fermi level everywhere in the bandgap. Thus, following this?definition (?\int_{E_min}^{E_F)N(E)dE = N), we can have many (or infinite number of solution for Fermi level). But when using the code, there is only one value. I check DOS results.?I see the Fermi level laying near the conduction band and It can be layed near the valance band. I wonder what is the critical of choosing Fermi level in Pwscf algorithm? By?the way,?Fermi level is? equal to?the chemical potential?at?0K. So, It is a very important physical meaning and?it must be a specific value at 0K?in metal, semiconductor and insulator.?Does choosing any value of Fermi level?in the bandgap lose?its physical meaning?? I?post the input file of my calculation. It?shows?Fermi level moving around?in the bandgap. Model 1: C8O &CONTROL ????? calculation = 'nscf', ????? prefix='C8O_LDA', ????? restart_mode = 'restart', ????? pseudo_dir ='./', ????? outdir='./' ????? tstress = .true. , ????? tprnfor = .true. , ????? nstep =? 100? , ????? etot_conv_thr = 1.0E-4 , ????? forc_conv_thr = 1.0D-3 , ????? dt = 20 , / &SYSTEM ????? ibrav= 4,? celldm(1) = 9.4518, celldm(3)=2, nat = 9, ntyp = 2, nspin=2, ????? ecutwfc =20, ecutrho = 210, occupations='tetrahedra', ????? starting_magnetization(1) = 0.0, ????? starting_magnetization(2) = 0.3, ????? starting_magnetization(3) = 0.5??? / &ELECTRONS ??? startingwfc = 'atomic' ??? mixing_mode = 'plain' ??? mixing_beta = 0.6 ??? conv_thr = 1.0e-6 ??? electron_maxstep= 150 / &IONS ??? upscale = 15 / &CELL ?? cell_dynamics = 'bfgs' , ?? press = 0.00 , ?? wmass =? 0.00150000? , / ATOMIC_SPECIES ?C? 12.011? C.pz-rrkjus.UPF ?O? 15.9994 O.pz-rrkjus.UPF ATOMIC_POSITIONS {angstrom} C??????? 4.132585975?? 4.832995059?? 0.302530806 C??????? 5.456020552?? 5.597038625?? 0.302477533 O??????? 4.794489489?? 5.215547072?? 1.572012872 C??????? 1.698357183?? 4.846620591?? 0.084098745 C??????? 2.888975237?? 5.584067069?? 0.084077187 C??????? 2.927154758?? 2.718125473?? 0.084310286 C??????? 4.161227149?? 3.380362792?? 0.084418771 C??????? 0.411042607?? 2.684363968?? 0.116522861 C??????? 1.676147051?? 3.414879352?? 0.116550940 K_POINTS {automatic} 9 9 1 0 0 0 Model 2: C8O2? &CONTROL ????? calculation = 'nscf', ????? prefix='C8O2_LDA', ????? restart_mode = 'restart', ????? pseudo_dir ='./', ????? outdir='./' ????? tstress = .true. , ????? tprnfor = .true. , ????? nstep =? 100? , ????? etot_conv_thr = 1.0E-4 , ????? forc_conv_thr = 1.0D-3 , ????? dt = 20 , / &SYSTEM ????? ibrav= 4,? celldm(1) = 9.4518, celldm(3)=2, nat = 10, ntyp = 2, nspin=2, ????? ecutwfc =35, ecutrho = 210, occupations='tetrahedra', ????? starting_magnetization(1) = 0.0, ????? starting_magnetization(2) = 0.3, ????? starting_magnetization(3) = 0.5??? / &ELECTRONS ??? startingwfc = 'atomic' ??? mixing_mode = 'plain' ??? mixing_beta = 0.6 ??? conv_thr = 1.0e-6 ??? electron_maxstep= 150 / &IONS ??? upscale = 15 / &CELL ?? cell_dynamics = 'bfgs' , ?? press = 0.00 , ?? wmass =? 0.00150000? , / ATOMIC_SPECIES ?C? 12.011? C.pz-rrkjus.UPF ?O? 15.9994 O.pz-rrkjus.UPF ATOMIC_POSITIONS {angstrom} C??????? 0.896514978?? 5.847447161?? 0.369684249 C??????? 2.166323242?? 5.100308876?? 0.369426937 C??????? 3.396879855?? 5.847835514?? 0.029522644 C??????? 4.666783051?? 5.100388577?? 0.029864650 C??????? 2.169717969?? 3.638682147?? 0.193058463 C??????? 3.393684393?? 2.977581062?? 0.193531103 C??????? 4.670322202?? 3.639102512?? 0.208350961 C??????? 5.894369614?? 2.977777255?? 0.207910567 O??????? 1.532383787?? 5.473020020?? 1.633770223 O??????? 4.031020909?? 5.472856877? -1.234119799 K_POINTS {automatic} 9 9 1 0 0 0 ----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com From devsharma1983 at yahoo.co.in Mon Apr 13 06:04:46 2009 From: devsharma1983 at yahoo.co.in (dev sharma) Date: Mon, 13 Apr 2009 09:34:46 +0530 (IST) Subject: [Pw_forum] (no subject) Message-ID: <792671.63110.qm@web94505.mail.in2.yahoo.com> hi, there is one DOC-def folder in pwscf and there is one file of making the inputs file for SCF calucltaion, there u will find the meaning of all the parameters likhe ecut_conv_thr etc tc Dev Sharma --- On Thu, 9/4/09, Dimpy Sharma wrote: From: Dimpy Sharma Subject: [Pw_forum] (no subject) To: pw_forum at pwscf.org Date: Thursday, 9 April, 2009, 5:17 PM Hi Can anybody please tell me the difference meaning of ecut_conv_thr and forc_conv_thr -----Inline Attachment Follows----- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090413/31367816/attachment.htm From eyvaz_isaev at yahoo.com Mon Apr 13 11:56:12 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 13 Apr 2009 02:56:12 -0700 (PDT) Subject: [Pw_forum] (no subject) In-Reply-To: <792671.63110.qm@web94505.mail.in2.yahoo.com> Message-ID: <596798.92427.qm@web65701.mail.ac4.yahoo.com> Dear Sharma, Please have a look a /Doc/INPUT_PW.txt and example files in /examples. You will be surprized, there are lots of examples. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Mon, 4/13/09, dev sharma wrote: > From: dev sharma > Subject: Re: [Pw_forum] (no subject) > To: "PWSCF Forum" > Date: Monday, April 13, 2009, 8:04 AM > hi, there is one DOC-def folder in pwscf and there is one > file of making the inputs file for SCF calucltaion, there u > will find the meaning of all the parameters likhe > ecut_conv_thr etc > tc > Dev Sharma > --- On Thu, 9/4/09, Dimpy Sharma > wrote: > > > From: Dimpy Sharma > Subject: [Pw_forum] (no subject) > To: pw_forum at pwscf.org > Date: Thursday, 9 April, 2009, 5:17 PM > > > > > Hi > Can anybody please tell me the difference meaning of > ecut_conv_thr and forc_conv_thr > -----Inline Attachment Follows----- > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > Add more friends to your messenger and enjoy! Go to > http://messenger.yahoo.com/invite/_______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From asafis at yahoo.com.br Mon Apr 13 18:53:57 2009 From: asafis at yahoo.com.br (=?iso-8859-1?Q?=C1lvaro_Alves?=) Date: Mon, 13 Apr 2009 09:53:57 -0700 (PDT) Subject: [Pw_forum] Pseudopotential generation Message-ID: <979340.55504.qm@web52303.mail.re2.yahoo.com> Hello everyone. I need pseudopotencial of cobalt with spin-orbit. I'm trying to create it using the ld1.x of PWscf. For the all-electron calculation l used the electron configuration [Ar] 3d10 4s2. What?s the configuration should I use to generate the pseudopotencial, since the calculation that needs to have the cobalt ion Co (II)? ???????????????????????????????????????????? Sincerely, Alvaro Veja quais s?o os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090413/802fe0ac/attachment.htm From giannozz at democritos.it Mon Apr 13 22:29:16 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 13 Apr 2009 22:29:16 +0200 Subject: [Pw_forum] Definition of Fermi level in PWscf In-Reply-To: <61600.34891.qm@web38801.mail.mud.yahoo.com> References: <61600.34891.qm@web38801.mail.mud.yahoo.com> Message-ID: <200904132229.16412.giannozz@democritos.it> On Monday 13 April 2009 02:32, loc duong ding wrote: > I wonder what is the critical of choosing Fermi level in Pwscf algorithm? and I wonder what you mean. The Fermi energy calculated by PWscf for an insulator can be anywhere in the gap. Its exact location is unpredictable, irrelevant, and has no meaning anyway. The phisical Fermi energy for intrinsic semiconductors is located in the middle of the band gap (this is a textbook problem, by the way). > By?the way,?Fermi level is? equal to?the chemical potential?at?0K. So, It > is a very important physical meaning and?it must be a specific value at > 0K?in metal, semiconductor and insulator.? the Fermi energy for metals is correctly calculated (within the chosen approximation). For semiconductors and metals, see above Paolo -- Paolo Giannozzi, Democritos and Udine University From meheut at impmc.jussieu.fr Tue Apr 14 01:30:57 2009 From: meheut at impmc.jussieu.fr (merlin meheut) Date: Tue, 14 Apr 2009 01:30:57 +0200 Subject: [Pw_forum] vc-relax on "loose" strctures Message-ID: <20090414013057.98301uipbyk187xt@www-ext.impmc.jussieu.fr> Dear PWSCF users, I am trying to relax a structure consisting of a molecule surrounded by water molecules (a solvated molecule). When I realize a vc-relax calculation it gives me a good final structure. But when I am making an scf calculation on this structure, if the interatomic forces are ok, the pressure is too high (by 5 kbars). I guess it is related to the vc-relax algorithms, but the problem is that I cannot take this structure once again and relax it again, because in this case, the chosen temperature is very low (0.1K), maybe because the forces are well converged, and therefore it converges very, very slowly. Is that possible to force pwscf to start with a given temperature? Sincerely, Merlin Meheut, ESS Department at UCLA -- Merlin M?heut professional adress: 595 Charles Young Drive East 3806 Geology Building Los Angeles, California 90095-1597 United States of America tel: 310 825 7934 cell phone: 310 893 4253 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From sporevoyager at gmail.com Tue Apr 14 05:19:27 2009 From: sporevoyager at gmail.com (shangy) Date: Tue, 14 Apr 2009 11:19:27 +0800 Subject: [Pw_forum] Help on converting from fhi to UPF form! Message-ID: <94be399f0904132019v55f17edcuc02ae4c659ea0d3f@mail.gmail.com> Dear all: Some input confused me when I used the fhi2upf.x to converter some pseudopotentials (from ABINIT FHI form) to UPF form. Take Ge as example, the header information of 32-Ge.GGA.fhi are ---------------------------------- germanium, fhi98PP : Trouiller-Martins-type, GGA Perdew/Burke/Ernzerhof (1996), l= 0 local 32.000 4.000 011001 zatom,zion,pspdat 6 11 3 0 529 0 pspcod,pspxc,lmax,lloc,mmax,r2well 0.000 0.000 0.000 rchrg, fchrg, qchrg ----------------------------------- One may note that Ge has 4 valence and the LMAX=3(F) and LOC=0(S). When I run the fhi2upf.x, it asked the "Wavefunction label and occupancy". I know the circle is controlled by nwfs=LMAX+1, so it seems that there are 4 wavefunction to be inputted. However, the only 4 valences are not enough to feed them. I tried it like this --------------------- Wavefunction # 1: label, occupancy > 4s 2 Wavefunction # 2: label, occupancy > 4p 2 Wavefunction # 3: label, occupancy > 4d 0 Wavefunction # 4: label, occupancy > 4f 0 --------------------- but I don't know if it is right? I searched some related information in the maillist, it indicated another input may like this --------------------- Wavefunction # 1: label, occupancy > 3p 6 Wavefunction # 2: label, occupancy > 3d 10 Wavefunction # 3: label, occupancy > 4s 2 Wavefunction # 4: label, occupancy > 4p 2 -------------------- However, it conflict with the 4 valence in this case. Additionally, how to determine the wavefunction order? According to their energy level and from inner to outer? If it is, it seems 4s is lower than 3d and it should be ------------------ Wavefunction # 1: label, occupancy > 3p 6 Wavefunction # 2: label, occupancy > 4s 2 Wavefunction # 3: label, occupancy > 3d 10 Wavefunction # 4: label, occupancy > 4p 2 ------------------ I don't know which input is right and how to clear the above problems. Could someone lighten me? Any ideas are appreciated! Thanks in advance! Best regards! shangy Graduate unversity of Chinese academy of sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090414/4d19e7e6/attachment.htm From manoj at phys.ufl.edu Tue Apr 14 07:22:01 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Tue, 14 Apr 2009 01:22:01 -0400 (EDT) Subject: [Pw_forum] input file for transmission Message-ID: Dear PWSCF users and developers, I wish to do a transmission calculation and confused about the input file. I have a question on example 12 of the package, where transmission of monoatomic Al wire with a H atom adsorbed on the side is done. The SCF run in the device region is done with (some part of input file is given below) &system ibrav = 6, celldm(1) =12.0, celldm(3) =1.875, where the atomic postions of different atoms is Al 0.00000000 0.00000000 0.0000 Al 0.00000000 0.00000000 0.375 Al -0.02779870 0.00000000 .75537515 H 0.19269012 0.00000000 .93750000 Al -0.02779870 0.00000000 1.11962485 Al 0.00000000 0.00000000 1.5 So, looking at the z coordinate of above system, we notice that device region is periodic with period 1.875. So, physically we are solving for an infinite device region, but in the physical setting of a transmission problem leads are semi-infinite and device is finite. Shouldn't we use some kind of vacum, i.e. taking 3rd lattice vector large, which effectively would represent the finite device region? Also how much part of the leads should be taken as part of device region, Is there some kind of convergence criterion? Is it like keep increasing part of lead in the device reion till further increase does not substantial change device behavior, e.g. Bloch's state? Regards, Manoj Srivastava Ph.D. student Department of Physics University of Florida, Gainesville, FL From sclauzer at sissa.it Tue Apr 14 09:35:03 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 14 Apr 2009 09:35:03 +0200 Subject: [Pw_forum] input file for transmission In-Reply-To: References: Message-ID: <49E43CA7.8010804@sissa.it> Manoj Srivastava wrote: > Dear PWSCF users and developers, > I wish to do a transmission calculation and confused about the input > file. I have a question on example 12 of the package, where transmission > of monoatomic Al wire with a H atom adsorbed on the side is done. The SCF > run in the device region is done with (some part of input file is given > below) it is usually called the "scattering region" > > &system > ibrav = 6, > celldm(1) =12.0, > celldm(3) =1.875, > > where the atomic postions of different atoms is > Al 0.00000000 0.00000000 0.0000 > Al 0.00000000 0.00000000 0.375 > Al -0.02779870 0.00000000 .75537515 > H 0.19269012 0.00000000 .93750000 > Al -0.02779870 0.00000000 1.11962485 > Al 0.00000000 0.00000000 1.5 > > So, looking at the z coordinate of above system, we notice that device > region is periodic with period 1.875. You are right, the scattering region is a periodic system, since pwscf always uses PBCs. The lenght of the scattering region id 12.0*1.875 a.u. and contains all 5 Al and the H impurity. > So, physically we are solving for an > infinite device region, but in the physical setting of a transmission > problem leads are semi-infinite and device is finite. Shouldn't we use > some kind of vacum, i.e. taking 3rd lattice vector large, which > effectively would represent the finite device region? > Also how much part > of the leads should be taken as part of device region, I don't understand this point. The leads are conceptually different thing than the scattering region. The lead is a periodic unit of the "bulk" region (in this case an infinitely long monatomic wire) and it is used to compute the generalized Bloch states, which in turn are propagated in the scattering region. > Is there some kind > of convergence criterion? Is it like keep increasing part of lead in the > device reion till further increase does not substantial change device > behavior, e.g. Bloch's state? There is a main convergence criterion (though I don't understand if you are actually refering to this). You have to increase the scattering region, adding more Al atoms in the wire, such that the complex band structure with real wave-vectors computed using the leftmost periodic unit of the wire included in the supercell (the H impurity being in the middle of the s.c.) converges to the band structure of an impurity-free wire, obtained for instance from a pwscf calculation (or from a pwcond calculation with a 1 atom cell containing an Al atom). To do this you can use pwcond with ... prefixt='prefix of the scattering region' bdl=ratio between the lenght of the periodic unit and celldm(1) ikind=0 band_file='name of file containing the CBS' ... then compare the real bands (contained in .re) with those from pwscf (obtained using the 1 atom cell). Also convergence of the transmission with the lenght of the scattering region can be used, but it is quite more cheap to check convergence of CBS (which can also help to understand if everything is going fine), and when the CBS of your "bulk" region (leads) is correctly reproduced the transmission should be converged as well. HTH GS > > Regards, > Manoj Srivastava > Ph.D. student > 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 > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Tue Apr 14 09:44:38 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 14 Apr 2009 09:44:38 +0200 Subject: [Pw_forum] vc-rx In-Reply-To: References: Message-ID: <49E43EE6.7030100@sissa.it> Mehrnaz Anvari wrote: > Hello > > I have a question about the number of iterations which have to be done > for density calculations in each step of vc-rx calculations. I mean do > they have to be decreased ? I'm not sure I really understand what you're speaking about, but if you are asking on how many iterations are needed to converge the charge density in an scf calculation (which is one step of a vc-relax calculation), well, it depends. It depends on many parameters, but mainly on the mixing_beta and mixing_mode. You don't have to chose on "how many" iterations an scf has to converge, the converge criterion is on the "distance" (norm of the difference) of the charge density at two successive iterations, and it can be reached after a very variable number of iterations, depending on your system and on the initial guess. > For instance does it have to be converged after 2-3 iterations, after a > few steps. After the first steps of a relax calculation the number of iterations needed usually decreases, since the atomic positions do not change dramatically and the in initial guess of the charge density is not as bad as it was at the first scf calculation. Again, the precise number of steps depends on lot of conditions and parameters, you can only say that it usually decreases. HTH GS > Best Regards > M.Anvari > Iran University Of Science & Technology > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From giannozz at democritos.it Tue Apr 14 11:29:55 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 14 Apr 2009 11:29:55 +0200 Subject: [Pw_forum] Help on converting from fhi to UPF form! In-Reply-To: <94be399f0904132019v55f17edcuc02ae4c659ea0d3f@mail.gmail.com> References: <94be399f0904132019v55f17edcuc02ae4c659ea0d3f@mail.gmail.com> Message-ID: <200904141129.55913.giannozz@democritos.it> On Tuesday 14 April 2009 05:19, shangy wrote: > When I run the fhi2upf.x, it asked the "Wavefunction label and occupancy" > [...] I tried it like this > --------------------- > Wavefunction # 1: label, occupancy > 4s 2 > Wavefunction # 2: label, occupancy > 4p 2 > Wavefunction # 3: label, occupancy > 4d 0 > Wavefunction # 4: label, occupancy > 4f 0 > --------------------- > but I don't know if it is right? the FHI format doesn't contain - to the best of my very limited knowledge - any information on the electronic configuration used to generate the pseudopotential. Atomic orbitals are actually used only to produce the starting wavefunctions and charge density for self-consistency. You should specify the labels of l=0 to lmax valence orbitals (in the order:s,p,d,f,..) and a reasonable value for their occupancy. You have Ge with 4 valence electrons, so your choice seems to be correct. Paolo -- Paolo Giannozzi, Democritos and Udine University From tone.kokalj at ijs.si Tue Apr 14 12:15:11 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 14 Apr 2009 12:15:11 +0200 Subject: [Pw_forum] what's the unit of charge density In-Reply-To: <412f6c680904110015u46e6be86x448f9d1c84868a11@mail.gmail.com> References: <412f6c680904110015u46e6be86x448f9d1c84868a11@mail.gmail.com> Message-ID: <1239704111.17996.45.camel@walk.ijs.si> On Sat, 2009-04-11 at 15:15 +0800, vega lew wrote: > Dear all > > I just ploted the 3D charge density using pp.x code. And XCRYSDEN was > used for displaying the 3D isosurface of charge density. When I set > the isovalue for different number, such as 0.15 or less, I fould the > overlap of electron cloud is quite meanful for different systems of > distinct catalysis activities. I wonder what the unit of charge > density? xcrysden does not assume any units, and merely takes the values as stated in the file. The unit is therefore up to the creator of the XSF file. If the XSF file was produced by pp.x, then the unit of charge is electron/bohr^3. > and whether the absolute value of it could be directly comparable for > different systems ( same number of atoms, same element, only different > in geometry of the model)? Yes, because the unit is electron/bohr^3 (for pp.x). > By the way, is there a tutorial for population analysis? I wonder > where I could find the value of overap population for a pair of > atoms. The PWscf uses Lowdin population analysis that can be performed by projwfc.x. Note however the ingredients are lowdin oribtals, which are orthonormal, i.e.: LowdinOrb_\mu = \sum_\nu S_{\mu,\nu}^{1/2} AO_\nu, where S_{\mu,\nu}^{1/2} is the element of the square root inverse of the overlap matrix S of the atomic orbitals AO. Because lowdin orbitals are orthogonal there is no overlap between them ==> no overlap population! I am not aware of any tool in the distribution that can do overlap populations. Perhaps, instead of overlap population, you may plot the atomic projected-densities of states (using projwfc.x), and you can look how good is the PDOS "alignment" between the atoms in question ... Or you may plot the 2D contour plot of either charge density difference or integrated local density of states along the bond direction. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From manoj at phys.ufl.edu Tue Apr 14 19:59:52 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Tue, 14 Apr 2009 13:59:52 -0400 (EDT) Subject: [Pw_forum] input file for transmission In-Reply-To: <49E43CA7.8010804@sissa.it> Message-ID: Dear Gabriele, Thank you very much quick reply. I have some follow up questions on this. On Tue, 14 Apr 2009, Gabriele Sclauzero wrote: > > Manoj Srivastava wrote: > > Dear PWSCF users and developers, > > I wish to do a transmission calculation and confused about the input > > file. I have a question on example 12 of the package, where transmission > > of monoatomic Al wire with a H atom adsorbed on the side is done. The SCF > > run in the device region is done with (some part of input file is given > > below) > > it is usually called the "scattering region" > > > > > > &system > > ibrav = 6, > > celldm(1) =12.0, > > celldm(3) =1.875, > > > > where the atomic postions of different atoms is > > Al 0.00000000 0.00000000 0.0000 > > Al 0.00000000 0.00000000 0.375 > > Al -0.02779870 0.00000000 .75537515 > > H 0.19269012 0.00000000 .93750000 > > Al -0.02779870 0.00000000 1.11962485 > > Al 0.00000000 0.00000000 1.5 > > > > So, looking at the z coordinate of above system, we notice that device > > region is periodic with period 1.875. > > You are right, the scattering region is a periodic system, since pwscf always uses PBCs. > The lenght of the scattering region id 12.0*1.875 a.u. and contains all 5 Al and the H > impurity. But that is exactly the trouble I am having in this. The scattering region should not be periodic like leads, as now we have infinite scattering region! But PWSCF always has PBC, so we should have a large 3rd lattice vector to make the scattering region practically finite. I dont see any super cell here. a_3 is just 1.875*a_0, where a_0 is lattice constant. The atomic postions are all in a_0 unit, which makes me believe that it is a practically infinite system with a_3=1.875*a_0. > > > So, physically we are solving for an > > infinite device region, but in the physical setting of a transmission > > problem leads are semi-infinite and device is finite. Shouldn't we use > > some kind of vacum, i.e. taking 3rd lattice vector large, which > > effectively would represent the finite device region? > > > > Also how much part > > of the leads should be taken as part of device region, > > I don't understand this point. The leads are conceptually different thing than the > scattering region. The lead is a periodic unit of the "bulk" region (in this case an > infinitely long monatomic wire) and it is used to compute the generalized Bloch states, > which in turn are propagated in the scattering region. In the above example, in principle we can have one atom H as scattering region, and Al wire as left and righ leads, but we have taken few Al atoms with H and treated it as scattering region. Thats what I meant by how much part of leads should be taken as scattering region. > > > Is there some kind > > of convergence criterion? Is it like keep increasing part of lead in the > > device reion till further increase does not substantial change device > > behavior, e.g. Bloch's state? > > There is a main convergence criterion (though I don't understand if you are actually > refering to this). You have to increase the scattering region, adding more Al atoms in the > wire, such that the complex band structure with real wave-vectors computed using the > leftmost periodic unit of the wire included in the supercell (the H impurity being in the > middle of the s.c.) converges to the band structure of an impurity-free wire, obtained for > instance from a pwscf calculation (or from a pwcond calculation with a 1 atom cell > containing an Al atom). > > To do this you can use pwcond with > ... > prefixt='prefix of the scattering region' > bdl=ratio between the lenght of the periodic unit and celldm(1) > ikind=0 > band_file='name of file containing the CBS' > ... > > > then compare the real bands (contained in .re) with those from pwscf (obtained > using the 1 atom cell). > > Also convergence of the transmission with the lenght of the scattering region can be used, > but it is quite more cheap to check convergence of CBS (which can also help to understand > if everything is going fine), and when the CBS of your "bulk" region (leads) is correctly > reproduced the transmission should be converged as well. > > HTH > > GS > > > > > > > Regards, > > Manoj Srivastava > > Ph.D. student > > 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 > > > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From meheut at impmc.jussieu.fr Tue Apr 14 23:48:28 2009 From: meheut at impmc.jussieu.fr (merlin meheut) Date: Tue, 14 Apr 2009 23:48:28 +0200 Subject: [Pw_forum] parallel compilation on core2duo cluster Message-ID: <20090414234828.116321c6mtudxj8s@www-ext.impmc.jussieu.fr> Dear pwscf users, I am trying to run pwscf in parallel on a core2duo cluster. It seems to compile fine (I am using mpiifort), and I am able to send a parallel calculation on two cores (therefore two processes but only one processor). Unfortunately, when I want to use more cores, and therefore more than one processor, for example: > mpirun -np 4 pw.x -npool 1 < scf.inp this runs four processes but only on two cores, with the following error at the beginning of the output: > You can't run mpdboot on ['compute-0-5'] version of python must be > >= 2.4, current [''] I have been said that this error could be corrected by adding -r ssh, with: > mpirun -r ssh -np 4 pw.x -npool 1 < scf.inp but actually, this does not make any difference. Would you have any idea on the origin of this error and how to correct it? Best regards, Merlin Meheut, ESS Department at UCLA -- Merlin M?heut professional adress: 595 Charles Young Drive East 3806 Geology Building Los Angeles, California 90095-1597 United States of America tel: 310 825 7934 cell phone: 310 893 4253 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From akohlmey at cmm.chem.upenn.edu Wed Apr 15 00:09:21 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 14 Apr 2009 18:09:21 -0400 Subject: [Pw_forum] parallel compilation on core2duo cluster In-Reply-To: <20090414234828.116321c6mtudxj8s@www-ext.impmc.jussieu.fr> References: <20090414234828.116321c6mtudxj8s@www-ext.impmc.jussieu.fr> Message-ID: <1239746961.2867.971.camel@zero> On Tue, 2009-04-14 at 23:48 +0200, merlin meheut wrote: > Dear pwscf users, > > I am trying to run pwscf in parallel on a core2duo cluster. It seems > to compile fine (I am using mpiifort), and I am able to send a > parallel calculation on two cores (therefore two processes but only > one processor). Unfortunately, when I want to use more cores, and > therefore more than one processor, for example: > > > mpirun -np 4 pw.x -npool 1 < scf.inp > > this runs four processes but only on two cores, with the following > error at the beginning of the output: > > > You can't run mpdboot on ['compute-0-5'] version of python must be > > >= 2.4, current [''] > > I have been said that this error could be corrected by adding -r ssh, with: > > > mpirun -r ssh -np 4 pw.x -npool 1 < scf.inp > > but actually, this does not make any difference. of course not. either have a word with your sysadmins. it looks as if on the compute-0-5 node is a much older version of python installed than what was use to compile MPICH-2 or use a different MPI implementation that does not depend on python to launch the parallel environment. cheers, axel. > > Would you have any idea on the origin of this error and how to correct it? > > Best regards, > > Merlin Meheut, ESS Department at UCLA > > > > -- > Merlin M?heut > professional adress: > 595 Charles Young Drive East > 3806 Geology Building > Los Angeles, California 90095-1597 > United States of America > tel: 310 825 7934 > cell phone: 310 893 4253 > > ---------------------------------------------------------------- > 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 -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From sporevoyager at gmail.com Wed Apr 15 06:18:22 2009 From: sporevoyager at gmail.com (shangy) Date: Wed, 15 Apr 2009 12:18:22 +0800 Subject: [Pw_forum] Help on converting from fhi to UPF form! In-Reply-To: <200904141129.55913.giannozz@democritos.it> References: <94be399f0904132019v55f17edcuc02ae4c659ea0d3f@mail.gmail.com> <200904141129.55913.giannozz@democritos.it> Message-ID: <94be399f0904142118n6b18a8ebv7bdba7fe6c489fb7@mail.gmail.com> Dear Paolo: Thanks for your kindly reply. I got it. Thanks again. Best regards! shangy Graduate unversity of Chinese academy of sciences 2009/4/14 Paolo Giannozzi > On Tuesday 14 April 2009 05:19, shangy wrote: > > > When I run the fhi2upf.x, it asked the "Wavefunction label and occupancy" > > [...] I tried it like this > > --------------------- > > Wavefunction # 1: label, occupancy > 4s 2 > > Wavefunction # 2: label, occupancy > 4p 2 > > Wavefunction # 3: label, occupancy > 4d 0 > > Wavefunction # 4: label, occupancy > 4f 0 > > --------------------- > > but I don't know if it is right? > > the FHI format doesn't contain - to the best of my very limited > knowledge - any information on the electronic configuration > used to generate the pseudopotential. Atomic orbitals are > actually used only to produce the starting wavefunctions > and charge density for self-consistency. You should specify > the labels of l=0 to lmax valence orbitals (in the order:s,p,d,f,..) > and a reasonable value for their occupancy. You have Ge with > 4 valence electrons, so your choice seems to be correct. > > Paolo > -- > Paolo Giannozzi, Democritos and Udine University > _______________________________________________ > 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/20090415/766270ec/attachment.htm From sclauzer at sissa.it Wed Apr 15 09:03:11 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 15 Apr 2009 09:03:11 +0200 Subject: [Pw_forum] input file for transmission In-Reply-To: References: Message-ID: <49E586AF.6030105@sissa.it> Manoj Srivastava wrote: > > But that is exactly the trouble I am having in this. The scattering > region should not be periodic like leads, as now we have infinite > scattering region! But PWSCF always has PBC, so we should have a large 3rd > lattice vector to make the scattering region practically finite. But in this way you would have a cluster made of 5Al and one hydrogen, with the Al atoms at the edges disconnected from the leads. You want the charge density at the edge atoms to be as similar as possible to that of the leads (in this case an infinite monatomic chain). Even if the scattering region is computed as a periodic system with PBCs, the KS potential inside the cell is not k-dependent and you can use it to solve the scattering problem with different boundary conditions (not periodic). The k-dependent KS eigenstates obtained from pw.x calculations are not used in the pwcond calculation, only the V_KS(G) in the (super)-cell is needed (super because it needs to be larger than the periodicity of the monatomic wire). > I dont > see any super cell here. a_3 is just 1.875*a_0, where a_0 is lattice > constant. The atomic postions are all in a_0 unit, which makes me believe > that it is a practically infinite system with a_3=1.875*a_0. > >>> So, physically we are solving for an >>> infinite device region, but in the physical setting of a transmission >>> problem leads are semi-infinite and device is finite. Shouldn't we use >>> some kind of vacum, i.e. taking 3rd lattice vector large, which >>> effectively would represent the finite device region? >> >>> Also how much part >>> of the leads should be taken as part of device region, >> I don't understand this point. The leads are conceptually different thing than the >> scattering region. The lead is a periodic unit of the "bulk" region (in this case an >> infinitely long monatomic wire) and it is used to compute the generalized Bloch states, >> which in turn are propagated in the scattering region. > > In the above example, in principle we can have one atom H as scattering > region, and Al wire as left and righ leads, but we have taken few Al atoms > with H and treated it as scattering region. Thats what I > meant by how much part of leads should be taken as scattering region. OK, I got it now. I think I have already replied to this somehow, when speaking about the convergence criterion. The H impurity perturbs the charge density of the wire (with respect to the pristine wire configuration, that you take as the lead region) not only on the Al atoms hosting the hydrogen, but also on further atoms. You have to include in the scattering region as many Al atoms as needed, such that the perturbation on the charge density induced by H on the edge atoms is negligible (you can check this from the CBS, as pointed out in my previous reply). In this way the charge density will not change abruptly when crossing the border between the lead and the scattering region and the KS potential will not have discontinuities. GS -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From anvari_meh at physics.iust.ac.ir Wed Apr 15 14:03:54 2009 From: anvari_meh at physics.iust.ac.ir (Mehrnaz Anvari) Date: Wed, 15 Apr 2009 15:33:54 +0330 Subject: [Pw_forum] vc-rx Message-ID: Hell I read your answers, but I think (it maybe wrong) after density calculating in each step of vc-rx calculations, the program should use it in the next step. so because of trivial changes in cell parameters the number of iterations should decrease in each step, shouldn't? I have another question about introducing one layer to code. How could I select c parameter along z direction ,I mean how large it should be? Could I say if stress along z direction become zero after 2-3 steps in vc-rx my selection is correct? Best Regards M.Anvari Iran University Of Science & Technology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090415/62e32b94/attachment.htm From sclauzer at sissa.it Wed Apr 15 13:31:31 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 15 Apr 2009 13:31:31 +0200 Subject: [Pw_forum] vc-rx In-Reply-To: References: Message-ID: <49E5C593.7010508@sissa.it> Mehrnaz Anvari wrote: > Hell > > I read your answers, but I think (it maybe wrong) after density > calculating in each step of vc-rx calculations, the program should use > it in the next step. I don't know much about vc-rx calculation, but I can tell you for sure that in the relax calculations it does. The self-consistent charge density at the previous relaxation step(s) is(are) saved and used as initial guess for the next step. > so because of trivial changes in cell parameters trivial? > the number of iterations should decrease in each step, shouldn't? In principle it should, but if the atomic configuration changes a lot from a step to the other (as it can happen at the beginning of the relaxation) this cannot be guaranteed. > I have another question about introducing one layer to code. How could > I select c parameter along z direction ,I mean how large it should be? In principle with the option cell_dofree you could chose which of the lattice parameters you want to relax and which to keep fixed at the value specified on input. From previous posts I suspect this option is not always working as expected. You can try it and report problems, and possibly try/help to fix them if you are really interested in using it. > Could I say if stress along z direction become zero after 2-3 steps in > vc-rx my selection is correct? At the end of a variable cell calculation all stress components should be below the convergence threshold. If you want a lattice parameter to be fixed at a value other than the equilibrium one, either you try cell_dofree or implement constraints on cell parameters... Maybe I don't understand exactly what is your aim. GS > Best Regards > M.Anvari > Iran University Of Science & Technology > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From meheut at impmc.jussieu.fr Wed Apr 15 20:13:54 2009 From: meheut at impmc.jussieu.fr (merlin meheut) Date: Wed, 15 Apr 2009 20:13:54 +0200 Subject: [Pw_forum] parallel compilation on core2duo cluster In-Reply-To: <1239746961.2867.971.camel@zero> References: <20090414234828.116321c6mtudxj8s@www-ext.impmc.jussieu.fr> <1239746961.2867.971.camel@zero> Message-ID: <20090415201354.7528293pc909jaaq@www-ext.impmc.jussieu.fr> Quoting Axel Kohlmeyer : > On Tue, 2009-04-14 at 23:48 +0200, merlin meheut wrote: >> Dear pwscf users, >> >> I am trying to run pwscf in parallel on a core2duo cluster. It seems >> to compile fine (I am using mpiifort), and I am able to send a >> parallel calculation on two cores (therefore two processes but only >> one processor). Unfortunately, when I want to use more cores, and >> therefore more than one processor, for example: >> >> > mpirun -np 4 pw.x -npool 1 < scf.inp >> >> this runs four processes but only on two cores, with the following >> error at the beginning of the output: >> >> > You can't run mpdboot on ['compute-0-5'] version of python must be >> > >= 2.4, current [''] >> >> I have been said that this error could be corrected by adding -r ssh, with: >> >> > mpirun -r ssh -np 4 pw.x -npool 1 < scf.inp >> >> but actually, this does not make any difference. > > of course not. either have a word with your sysadmins. > it looks as if on the compute-0-5 node is a much > older version of python installed than what was > use to compile MPICH-2 or use a different MPI implementation > that does not depend on python to launch the parallel environment. > > cheers, > axel. > > Actually, the issue was simply that I could not ssh on the nodes without password. Sorry for this post. cheers, Merlin >> >> Would you have any idea on the origin of this error and how to correct it? >> >> Best regards, >> >> Merlin Meheut, ESS Department at UCLA >> >> >> >> -- >> Merlin M?heut >> professional adress: >> 595 Charles Young Drive East >> 3806 Geology Building >> Los Angeles, California 90095-1597 >> United States of America >> tel: 310 825 7934 >> cell phone: 310 893 4253 >> >> ---------------------------------------------------------------- >> 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 > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Merlin M?heut professional adress: 595 Charles Young Drive East 3806 Geology Building Los Angeles, California 90095-1597 United States of America tel: 310 825 7934 cell phone: 310 893 4253 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From sunyang198498 at gmail.com Thu Apr 16 03:43:33 2009 From: sunyang198498 at gmail.com (=?GB2312?B?y+/R9A==?=) Date: Wed, 15 Apr 2009 20:43:33 -0500 Subject: [Pw_forum] Convergence Problem Message-ID: <98e7a0810904151843t374d9d87x82655784fb4ff5@mail.gmail.com> Dear All, When I do the calculation of the electronic structure of slab Palladium under the external electric field, convergence problems appear. The typical problem is that the estimated scf accuracy value drop down down and bounce back. It seems that the calculation does not know where the system would go for minimizing the total energy. The electric field that I applied is saw-tooth like one. I tried many things like increasing the mixing_ndim, decreasing the mixing_betta to 0.1, adding empty bands changing the mixing mode and even increase the degauss. But, none of them would work for the scf accuracy oscillating problem. Below is the input file. Any suggestion is highly appreciated. &control calculation='scf' restart_mode='from_scratch', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' prefix='Pd' tefield = .true. dipfield = .true. nstep = 300 / &system ibrav = 6 celldm(1) = 7.3331 nspin = 2 celldm(3) = 4.5 edir = 3 emaxpos=0.72 eopreg=0.28 eamp = -0.001944 starting_magnetization=0.05 ntyp = 1 nat= 14 ecutwfc = 25.0, ecutrho = 500.0, occupations='smearing', degauss=0.2 nbnd=160 / &electrons conv_thr = 1.0e-4 mixing_mode='local-TF' mixing_beta = 0.05 mixing_ndim = 12 / ATOMIC_SPECIES Pd 100 Pd.pz-nd-rrkjus.UPF ATOMIC_POSITIONS Pd 0.500000000 0.000000000 -1.496126804 Pd 0.000000000 0.500000000 -1.496126804 Pd 0.000000000 0.000000000 -1.002542052 Pd 0.500000000 0.500000000 -1.002542051 Pd 0.500000000 0.000000000 -0.501470158 Pd 0.000000000 0.500000000 -0.501470158 Pd 0.000000000 0.000000000 0.000000000 Pd 0.500000000 0.500000000 0.000000000 Pd 0.500000000 0.000000000 0.501470158 Pd 0.000000000 0.500000000 0.501470158 Pd 0.000000000 0.000000000 1.002542052 Pd 0.500000000 0.500000000 1.002542051 Pd 0.500000000 0.000000000 1.496126804 Pd 0.000000000 0.500000000 1.496126804 K_POINTS (automatic) 8 8 1 0 0 0 -- University of Nebraska at Lincoln From azgre at azgre.com Thu Apr 16 04:06:55 2009 From: azgre at azgre.com (AZGlobal) Date: Wed, 15 Apr 2009 22:06:55 -0400 Subject: [Pw_forum] Convergence Problem In-Reply-To: <98e7a0810904151843t374d9d87x82655784fb4ff5@mail.gmail.com> References: <98e7a0810904151843t374d9d87x82655784fb4ff5@mail.gmail.com> Message-ID: <49E692BF.1020008@azgre.com> Usually oscillating SCF process is result of some flat band (lots of low-dispersion bands in Pd near Ef) flipping below/above Ef from iteration to iteration, when you iterate. The cure is smaller admixing. Takes much more processor time, but you can iterate for weeks with too big admix and no result. Hope this helps. > Dear All, > > When I do the calculation of the electronic structure of slab > Palladium under the external electric field, > convergence problems appear. The typical problem is that the estimated > scf accuracy value drop down > down and bounce back. It seems that the calculation does not know > where the system would go for > minimizing the total energy. The electric field that I applied is > saw-tooth like one. I tried many things like > increasing the mixing_ndim, decreasing the mixing_betta to 0.1, adding > empty bands changing the mixing > mode and even increase the degauss. But, none of them would work for > the scf accuracy oscillating problem. > Below is the input file. Any suggestion is highly appreciated. > > > > > &control > calculation='scf' > restart_mode='from_scratch', > pseudo_dir = '$PSEUDO_DIR/', > outdir='$TMP_DIR/' > prefix='Pd' > tefield = .true. > dipfield = .true. > nstep = 300 > > / > &system > ibrav = 6 > celldm(1) = 7.3331 > nspin = 2 > celldm(3) = 4.5 > edir = 3 > emaxpos=0.72 > eopreg=0.28 > eamp = -0.001944 > starting_magnetization=0.05 > ntyp = 1 > nat= 14 > ecutwfc = 25.0, > ecutrho = 500.0, > occupations='smearing', > degauss=0.2 > nbnd=160 > / > > &electrons > conv_thr = 1.0e-4 > mixing_mode='local-TF' > mixing_beta = 0.05 > mixing_ndim = 12 > > / > ATOMIC_SPECIES > Pd 100 Pd.pz-nd-rrkjus.UPF > ATOMIC_POSITIONS > Pd 0.500000000 0.000000000 -1.496126804 > Pd 0.000000000 0.500000000 -1.496126804 > Pd 0.000000000 0.000000000 -1.002542052 > Pd 0.500000000 0.500000000 -1.002542051 > Pd 0.500000000 0.000000000 -0.501470158 > Pd 0.000000000 0.500000000 -0.501470158 > Pd 0.000000000 0.000000000 0.000000000 > Pd 0.500000000 0.500000000 0.000000000 > Pd 0.500000000 0.000000000 0.501470158 > Pd 0.000000000 0.500000000 0.501470158 > Pd 0.000000000 0.000000000 1.002542052 > Pd 0.500000000 0.500000000 1.002542051 > Pd 0.500000000 0.000000000 1.496126804 > Pd 0.000000000 0.500000000 1.496126804 > > > > > K_POINTS (automatic) > 8 8 1 0 0 0 > > > > From sunyang198498 at gmail.com Thu Apr 16 05:21:00 2009 From: sunyang198498 at gmail.com (=?GB2312?B?y+/R9A==?=) Date: Wed, 15 Apr 2009 22:21:00 -0500 Subject: [Pw_forum] Convergence Problem In-Reply-To: <49E692BF.1020008@azgre.com> References: <98e7a0810904151843t374d9d87x82655784fb4ff5@mail.gmail.com> <49E692BF.1020008@azgre.com> Message-ID: <98e7a0810904152021w7924dac7x34103bb03adfaad4@mail.gmail.com> Hi, Dr.A.Zhako Titarenko and other users, You mean the mixing betta. My value for mixing betta is 0.05, is it still too high? Thank you in advance. Yang 2009/4/15 AZGlobal : > Usually oscillating ?SCF process is result of some flat band ?(lots of > low-dispersion bands in Pd near Ef) flipping below/above Ef from > iteration to iteration, when you iterate. The cure is smaller admixing. > Takes much more processor time, but you can iterate for weeks with too > big admix and no result. Hope this helps. >> Dear All, >> >> When I do the calculation of the electronic structure of slab >> Palladium under the external electric field, >> convergence problems appear. The typical problem is that the estimated >> scf accuracy value drop down >> down and bounce back. It seems that the calculation does not know >> where the system would go for >> minimizing the total energy. The electric field that I applied is >> saw-tooth like one. I tried many things like >> increasing the mixing_ndim, decreasing the mixing_betta to 0.1, adding >> empty bands changing the mixing >> mode and even increase the degauss. But, none of them would work for >> the scf accuracy oscillating problem. >> Below is the input file. Any suggestion is highly appreciated. >> >> >> >> >> &control >> ? ? calculation='scf' >> ? ? restart_mode='from_scratch', >> ? ? pseudo_dir = '$PSEUDO_DIR/', >> ? ? outdir='$TMP_DIR/' >> ? ? prefix='Pd' >> ? ? tefield = .true. >> ? ? dipfield = .true. >> ? ? nstep = 300 >> >> ?/ >> ?&system >> ? ? ibrav = 6 >> ? ? celldm(1) = 7.3331 >> ? ? nspin = 2 >> ? ? celldm(3) = 4.5 >> ? ? edir = 3 >> ? ? emaxpos=0.72 >> ? ? eopreg=0.28 >> ? ? eamp = -0.001944 >> ? ? starting_magnetization=0.05 >> ? ? ntyp = 1 >> ? ? nat= 14 >> ? ? ecutwfc = 25.0, >> ? ? ecutrho = 500.0, >> ? ? occupations='smearing', >> ? ? degauss=0.2 >> ? ? nbnd=160 >> ?/ >> >> ?&electrons >> ? ? conv_thr = 1.0e-4 >> ? ? mixing_mode='local-TF' >> ? ? mixing_beta = 0.05 >> ? ? mixing_ndim = 12 >> >> ?/ >> ATOMIC_SPECIES >> ?Pd ?100 ?Pd.pz-nd-rrkjus.UPF >> ATOMIC_POSITIONS >> Pd ? ? ? 0.500000000 ? 0.000000000 ?-1.496126804 >> Pd ? ? ? 0.000000000 ? 0.500000000 ?-1.496126804 >> Pd ? ? ? 0.000000000 ? 0.000000000 ?-1.002542052 >> Pd ? ? ? 0.500000000 ? 0.500000000 ?-1.002542051 >> Pd ? ? ? 0.500000000 ? 0.000000000 ?-0.501470158 >> Pd ? ? ? 0.000000000 ? 0.500000000 ?-0.501470158 >> Pd ? ? ? 0.000000000 ? 0.000000000 ? 0.000000000 >> Pd ? ? ? 0.500000000 ? 0.500000000 ? 0.000000000 >> Pd ? ? ? 0.500000000 ? 0.000000000 ? 0.501470158 >> Pd ? ? ? 0.000000000 ? 0.500000000 ? 0.501470158 >> Pd ? ? ? 0.000000000 ? 0.000000000 ? 1.002542052 >> Pd ? ? ? 0.500000000 ? 0.500000000 ? 1.002542051 >> Pd ? ? ? 0.500000000 ? 0.000000000 ? 1.496126804 >> Pd ? ? ? 0.000000000 ? 0.500000000 ? 1.496126804 >> >> >> >> >> K_POINTS (automatic) >> ?8 8 1 0 0 0 >> >> >> >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- University of Nebraska at Lincoln From panda.deng.pan at gmail.com Thu Apr 16 05:31:53 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Thu, 16 Apr 2009 11:31:53 +0800 Subject: [Pw_forum] Convergence Problem In-Reply-To: <98e7a0810904152021w7924dac7x34103bb03adfaad4@mail.gmail.com> References: <98e7a0810904151843t374d9d87x82655784fb4ff5@mail.gmail.com> <49E692BF.1020008@azgre.com> <98e7a0810904152021w7924dac7x34103bb03adfaad4@mail.gmail.com> Message-ID: maybe the ecutwfc value is small. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090416/db25a9e5/attachment.htm From sunyang198498 at gmail.com Thu Apr 16 05:42:42 2009 From: sunyang198498 at gmail.com (=?GB2312?B?y+/R9A==?=) Date: Wed, 15 Apr 2009 22:42:42 -0500 Subject: [Pw_forum] Convergence Problem In-Reply-To: References: <98e7a0810904151843t374d9d87x82655784fb4ff5@mail.gmail.com> <49E692BF.1020008@azgre.com> <98e7a0810904152021w7924dac7x34103bb03adfaad4@mail.gmail.com> Message-ID: <98e7a0810904152042y7cb45757v5ee316165c8a8315@mail.gmail.com> Thanks for your advice, Deng. Yang 2009/4/15 ?? : > maybe the ecutwfc value is small. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- University of Nebraska at Lincoln From prasenjit.jnc at gmail.com Thu Apr 16 07:57:38 2009 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Thu, 16 Apr 2009 07:57:38 +0200 Subject: [Pw_forum] Convergence Problem In-Reply-To: <98e7a0810904152042y7cb45757v5ee316165c8a8315@mail.gmail.com> References: <98e7a0810904151843t374d9d87x82655784fb4ff5@mail.gmail.com> <49E692BF.1020008@azgre.com> <98e7a0810904152021w7924dac7x34103bb03adfaad4@mail.gmail.com> <98e7a0810904152042y7cb45757v5ee316165c8a8315@mail.gmail.com> Message-ID: <627e0ffa0904152257r2552670cg902685e718d73022@mail.gmail.com> Hi Yang, Here are a few general suggestions: (1) Check the convergence wrt to vacuum (distance between periodic images). In ur case it seems too small to me, as a result of which the periodic images are interacting. I think this is specially important for ur case because ur having an external electric field. (2) check convergence wrt ecutrho & ecutwfc. Ususally ecutrho is 10-12 times ecutwfc. (probably ur wave fn is not converged) (3) a value of mixing beta=0.05 is too low. Such a low value often implies that you don't move the electrons at all......hence its not very effective........according to my experience, at least for cal. without electric field, a value of 0.2-0.3 works well. (4) Also you are doing a slab cal. and usually either a few layers at the bottom or a few in the middle are kept fixed (although this should not affect ur electronic minimization). With regards, Prasenjit. (5) ur value of conv_thr seem too high.....at least u should use the default value. But I would suggest u to use something of the order of 10^-8. 2009/4/16 ?? > Thanks for your advice, Deng. > > Yang > > 2009/4/15 ?? : > > maybe the ecutwfc value is small. > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > University of Nebraska at Lincoln > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- PRASENJIT GHOSH, POST-DOC, ROOM NO: 265, MAIN BUILDING, CM SECTION, ICTP, STRADA COSTERIA 11, TRIESTE, 34104, ITALY PHONE: +39 040 2240 369 (O) +39 3807528672 (M) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090416/e3043d76/attachment.htm From sclauzer at sissa.it Thu Apr 16 08:43:06 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 16 Apr 2009 08:43:06 +0200 Subject: [Pw_forum] Convergence Problem In-Reply-To: <98e7a0810904151843t374d9d87x82655784fb4ff5@mail.gmail.com> References: <98e7a0810904151843t374d9d87x82655784fb4ff5@mail.gmail.com> Message-ID: <49E6D37A.1090506@sissa.it> On top of what alreay said by the other users, I would suggest few more things: > Below is the input file. Any suggestion is highly appreciated. > > > > > &control > calculation='scf' > restart_mode='from_scratch', > pseudo_dir = '$PSEUDO_DIR/', > outdir='$TMP_DIR/' > prefix='Pd' > tefield = .true. > dipfield = .true. > nstep = 300 > > / > &system > ibrav = 6 > celldm(1) = 7.3331 > nspin = 2 > celldm(3) = 4.5 > edir = 3 > emaxpos=0.72 > eopreg=0.28 > eamp = -0.001944 I don't know much about efield calculations, but I suppose that you are sure that you placed the discontinuity of the potential in the vacuum, as should be done. > starting_magnetization=0.05 To be rigorous, starting_magnetization is a vector. In order to avoid strange surprises, you should specify starting_magnetization(1)=0.05 ... > ntyp = 1 > nat= 14 > ecutwfc = 25.0, > ecutrho = 500.0, > occupations='smearing', > degauss=0.2 This value of degauss (which is in Ryd, NOT eV) seems exceedingly high to me. I would use something like at least 1 order of magnitude smaller (but you should test convergence by yourself, together with the k-point mesh). You may also want to try different kind of smearing methods. Methfessel-Paxton usually works well with metals (smearing="mp") > nbnd=160 Usually there is no need to specify the number of bands when using smearing. The number of bands which will be computed is automatically increased by the program to a safe choice. > / > > &electrons > conv_thr = 1.0e-4 See Ghosh's reply... > mixing_mode='local-TF' have you tried a different mixing mode? I don't know if this is well suited for slab calculations. HTH GS > mixing_beta = 0.05 > mixing_ndim = 12 > > / > ATOMIC_SPECIES > Pd 100 Pd.pz-nd-rrkjus.UPF > ATOMIC_POSITIONS > Pd 0.500000000 0.000000000 -1.496126804 > Pd 0.000000000 0.500000000 -1.496126804 > Pd 0.000000000 0.000000000 -1.002542052 > Pd 0.500000000 0.500000000 -1.002542051 > Pd 0.500000000 0.000000000 -0.501470158 > Pd 0.000000000 0.500000000 -0.501470158 > Pd 0.000000000 0.000000000 0.000000000 > Pd 0.500000000 0.500000000 0.000000000 > Pd 0.500000000 0.000000000 0.501470158 > Pd 0.000000000 0.500000000 0.501470158 > Pd 0.000000000 0.000000000 1.002542052 > Pd 0.500000000 0.500000000 1.002542051 > Pd 0.500000000 0.000000000 1.496126804 > Pd 0.000000000 0.500000000 1.496126804 > > > > > K_POINTS (automatic) > 8 8 1 0 0 0 > > > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From pemryan at yahoo.cn Thu Apr 16 11:06:38 2009 From: pemryan at yahoo.cn (Yan) Date: Thu, 16 Apr 2009 17:06:38 +0800 Subject: [Pw_forum] plotband.x could not get filename Message-ID: <200904161706.42206.pemryan@yahoo.cn> Dear PWSCF users, I met such a problem when drawing phonon dispersion: bash-3.2$ /home/pem/espresso4/espresso.4.0/bin/plotband.x myFileName : too many arguments -1 At line 42 of file plotband.f90 (unit = 1, file = '') ------------------------------------------------------------------------------ for anything I typed after plotband.x , it gives the same error info. I find plotband.f90 and modified line 42 as bellow: call get_file ( filename ) - open(unit=1,file='filename',form='formatted') + open(unit=1,file='myFileName',form='formatted') ------------------------------------------------------------------------------- after recompilation, now /plotband.x works with this file. I think there is something wrong with the subroutine 'get_file'(from flib/inpfile.f90), but I don't know exactly where. My QE version is 4.0. I've tried the inpfile.f90 from 4.1cvs, and it gives the same error. Bests, Yan -- Ren, Yan | Tel: +8610-8264-8102 Institute of Physics, Chinese Academy of Sciences, Beijing, China --- Every describable physical law will turn out to be an error some day. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090416/ad142cde/attachment.htm From paulatto at sissa.it Thu Apr 16 11:16:27 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 16 Apr 2009 11:16:27 +0200 Subject: [Pw_forum] Convergence Problem In-Reply-To: <98e7a0810904151843t374d9d87x82655784fb4ff5@mail.gmail.com> References: <98e7a0810904151843t374d9d87x82655784fb4ff5@mail.gmail.com> Message-ID: On Thu, 16 Apr 2009 03:43:33 +0200, ????? wrote: > edir = 3 > emaxpos=0.72 > eopreg=0.28 Dear ??, This three lines mean that the field is inverted between 72% and 100% of the third basis vector, in your case along the z direction. In other words, the upper 28% percent of your cell is occupied the inverted field. The intensity of the inverted field is approximately 3 times larger than the direct field. > ATOMIC_POSITIONS > Pd 0.500000000 0.000000000 -1.496126804 > Pd 0.000000000 0.500000000 -1.496126804 > Pd 0.000000000 0.000000000 -1.002542052 > Pd 0.500000000 0.500000000 -1.002542051 > Pd 0.500000000 0.000000000 -0.501470158 > Pd 0.000000000 0.500000000 -0.501470158 All these atoms are in the inverted field region, maybe you have not understood correctly emaxpos and eopreg work. Please check you input to be sure you are actually doing what you want to do! You can also increase the number of bands, reduce the beta mixing parameter and increasing the mixing_ndim parameter, but they cannot help if the input file has some error. cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From giannozz at democritos.it Thu Apr 16 11:16:33 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 16 Apr 2009 11:16:33 +0200 Subject: [Pw_forum] plotband.x could not get filename In-Reply-To: <200904161706.42206.pemryan@yahoo.cn> References: <200904161706.42206.pemryan@yahoo.cn> Message-ID: <49E6F771.2000804@democritos.it> Yan wrote: > call get_file ( filename ) > - open(unit=1,file='filename',form='formatted') there is no such line. The correct line is open(unit=1,file=filename,form='formatted') > + open(unit=1,file='myFileName',form='formatted') this will open a file called myFileName. > after recompilation, now /plotband.x works with this file. > I think there is something wrong with the subroutine 'get_file' > (from flib/inpfile.f90), but I don't know exactly where. there is nothing wrong with subroutine get_file. It's your system call "iargc" that doesn't work (it returns -1 instead of the number of arguments) Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From paulatto at sissa.it Thu Apr 16 11:18:39 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 16 Apr 2009 11:18:39 +0200 Subject: [Pw_forum] Convergence Problem In-Reply-To: <49E6D37A.1090506@sissa.it> References: <98e7a0810904151843t374d9d87x82655784fb4ff5@mail.gmail.com> <49E6D37A.1090506@sissa.it> Message-ID: On Thu, 16 Apr 2009 08:43:06 +0200, Gabriele Sclauzero wrote: > have you tried a different mixing mode? I don't know if this is well > suited for slab > calculations. It is. cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From pemryan at yahoo.cn Thu Apr 16 11:43:19 2009 From: pemryan at yahoo.cn (Yan) Date: Thu, 16 Apr 2009 17:43:19 +0800 Subject: [Pw_forum] plotband.x could not get filename In-Reply-To: <49E6F771.2000804@democritos.it> References: <200904161706.42206.pemryan@yahoo.cn> <49E6F771.2000804@democritos.it> Message-ID: <200904161743.36147.pemryan@yahoo.cn> Dear Paolo, Thank you for your reply. I tests iargc with test.f90, it works and returns correct number of arguments. !--------test.f90--------- PROGRAM test IMPLICIT NONE INTEGER :: iargc, nargs nargs = iargc() write(*,*) nargs RETURN END PROGRAM !--------end------------- bash-3.2$ gfortran test.f90 -o test bash-3.2$ ./test 0 bash-3.2$ ./test 1 1 2 Could you give me some more hint about how to locate and fix this problem? Thank you. Yan On 2009/04/16 Thursday 17:16:33 Paolo Giannozzi wrote: > there is nothing wrong with subroutine get_file. It's your system > call "iargc" that doesn't work (it returns -1 instead of the > number of arguments) -- Ren, Yan | Tel: +8610-8264-8102 Institute of Physics, Chinese Academy of Sciences, Beijing, China --- Light is scream from another world. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090416/663128e3/attachment.htm From ylli at theory.issp.ac.cn Thu Apr 16 14:05:15 2009 From: ylli at theory.issp.ac.cn (=?utf-8?B?TGkgWUw=?=) Date: Thu, 16 Apr 2009 20:05:15 +0800 Subject: [Pw_forum] =?utf-8?q?propagation_direction_in_the_input_file_for_?= =?utf-8?q?dynmat=2Ex?= Message-ID: <20090416120515.6211.qmail@ms.hfcas.ac.cn> Dear all users, Now I've a question on the polar materials. In order to get LO-TO splitting, you know, we need to use dynmat.x. In the input file for dynmat.x, we need input q(1), q(2), and q(3), that is, the propagation direction. I don't know how to choose this direction. My system has hexagonal symmetry and its primitive cell is rhombohedral. Any suggestions are welcome. Thanks in advance. Bests, Yanling Li, Institute of Solid states physics, CAS, P. R. China. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090416/81540a1e/attachment.htm From clie at aphy.iphy.ac.cn Thu Apr 16 16:10:30 2009 From: clie at aphy.iphy.ac.cn (clie) Date: Thu, 16 Apr 2009 14:10:30 GMT Subject: [Pw_forum] How to compute the average Coulomb repulse U and exchange parameter J In-Reply-To: References: Message-ID: <20090416141031.2150.eqmail@aphy.iphy.ac.cn> Dear friends, Have you ever computed the average Coulomb repulse U and exchange parameter J by pwscf. Could someone give some more detailed explanation about how to process the output to get the U and J. I have read this pape(PHYSICAL REVIEW B 71, 035105, 2005), but I am still confusing about how to get U. Thank you in advance. All the best, Zhi Li ----------------------------------------------- Ex5 group Extreme Condition Physics, Institute of Physics, Chinese Academy of Sciences, P. O. Box 603, Beijing, 100190, People?s Republic of China pw_forum-request at pwscf.org ?: > 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: Convergence Problem (??) > 2. Re: Convergence Problem (??) > 3. Re: Convergence Problem (Prasenjit Ghosh) > 4. Re: Convergence Problem (Gabriele Sclauzero) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 16 Apr 2009 11:31:53 +0800 > From: ?? > Subject: Re: [Pw_forum] Convergence Problem > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > maybe the ecutwfc value is small. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090416/ db25a9e5/attachment.html > > ------------------------------ > > Message: 2 > Date: Wed, 15 Apr 2009 22:42:42 -0500 > From: ?? > Subject: Re: [Pw_forum] Convergence Problem > To: PWSCF Forum > Message-ID: > <98e7a0810904152042y7cb45757v5ee316165c8a8315 at mail.gmail.com> > Content-Type: text/plain; charset=GB2312 > > Thanks for your advice, Deng. > > Yang > > 2009/4/15 ?? : >> maybe the ecutwfc value is small. >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > > -- > University of Nebraska at Lincoln > > > ------------------------------ > > Message: 3 > Date: Thu, 16 Apr 2009 07:57:38 +0200 > From: Prasenjit Ghosh > Subject: Re: [Pw_forum] Convergence Problem > To: PWSCF Forum > Message-ID: > <627e0ffa0904152257r2552670cg902685e718d73022 at mail.gmail.com> > Content-Type: text/plain; charset="gb2312" > > Hi Yang, > > Here are a few general suggestions: > > (1) Check the convergence wrt to vacuum (distance between periodic images). > In ur case it seems too small to me, as a result of which the periodic > images are interacting. I think this is specially important for ur case > because ur having an external electric field. > > (2) check convergence wrt ecutrho & ecutwfc. Ususally ecutrho is 10-12 times > ecutwfc. (probably ur wave fn is not converged) > > (3) a value of mixing beta=0.05 is too low. Such a low value often implies > that you don't move the electrons at all......hence its not very > effective........according to my experience, at least for cal. without > electric field, a value of 0.2-0.3 works well. > > (4) Also you are doing a slab cal. and usually either a few layers at the > bottom or a few in the middle are kept fixed (although this should not > affect ur electronic minimization). > > With regards, > Prasenjit. > > > > (5) ur value of conv_thr seem too high.....at least u should use the default > value. But I would suggest u to use something of the order of 10^-8. > > 2009/4/16 ?? > >> Thanks for your advice, Deng. >> >> Yang >> >> 2009/4/15 ?? : >> > maybe the ecutwfc value is small. >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> > >> >> >> >> -- >> University of Nebraska at Lincoln >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > PRASENJIT GHOSH, > POST-DOC, > ROOM NO: 265, MAIN BUILDING, > CM SECTION, ICTP, > STRADA COSTERIA 11, > TRIESTE, 34104, > ITALY > PHONE: +39 040 2240 369 (O) > +39 3807528672 (M) > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090416/ e3043d76/attachment-0001.htm > > ------------------------------ > > Message: 4 > Date: Thu, 16 Apr 2009 08:43:06 +0200 > From: Gabriele Sclauzero > Subject: Re: [Pw_forum] Convergence Problem > To: PWSCF Forum > Message-ID: <49E6D37A.1090506 at sissa.it> > Content-Type: text/plain; charset=us-ascii; format=flowed > > On top of what alreay said by the other users, I would suggest few more things: >> Below is the input file. Any suggestion is highly appreciated. >> >> >> >> >> &control >> calculation='scf' >> restart_mode='from_scratch', >> pseudo_dir = '$PSEUDO_DIR/', >> outdir='$TMP_DIR/' >> prefix='Pd' >> tefield = .true. >> dipfield = .true. >> nstep = 300 >> >> / >> &system >> ibrav = 6 >> celldm(1) = 7.3331 >> nspin = 2 >> celldm(3) = 4.5 >> edir = 3 >> emaxpos=0.72 >> eopreg=0.28 >> eamp = -0.001944 > > I don't know much about efield calculations, but I suppose that you are sure that you > placed the discontinuity of the potential in the vacuum, as should be done. > >> starting_magnetization=0.05 > > To be rigorous, starting_magnetization is a vector. In order to avoid strange surprises, > you should specify > starting_magnetization(1)=0.05 > ... > >> ntyp = 1 >> nat= 14 >> ecutwfc = 25.0, >> ecutrho = 500.0, >> occupations='smearing', >> degauss=0.2 > > This value of degauss (which is in Ryd, NOT eV) seems exceedingly high to me. I would use > something like at least 1 order of magnitude smaller (but you should test convergence by > yourself, together with the k-point mesh). > > You may also want to try different kind of smearing methods. Methfessel- Paxton usually > works well with metals (smearing="mp") > >> nbnd=160 > > Usually there is no need to specify the number of bands when using smearing. The number of > bands which will be computed is automatically increased by the program to a safe choice. > >> / >> >> &electrons >> conv_thr = 1.0e-4 > > See Ghosh's reply... > >> mixing_mode='local-TF' > > have you tried a different mixing mode? I don't know if this is well suited for slab > calculations. > > > HTH > > GS > >> mixing_beta = 0.05 >> mixing_ndim = 12 >> >> / >> ATOMIC_SPECIES >> Pd 100 Pd.pz-nd-rrkjus.UPF >> ATOMIC_POSITIONS >> Pd 0.500000000 0.000000000 -1.496126804 >> Pd 0.000000000 0.500000000 -1.496126804 >> Pd 0.000000000 0.000000000 -1.002542052 >> Pd 0.500000000 0.500000000 -1.002542051 >> Pd 0.500000000 0.000000000 -0.501470158 >> Pd 0.000000000 0.500000000 -0.501470158 >> Pd 0.000000000 0.000000000 0.000000000 >> Pd 0.500000000 0.500000000 0.000000000 >> Pd 0.500000000 0.000000000 0.501470158 >> Pd 0.000000000 0.500000000 0.501470158 >> Pd 0.000000000 0.000000000 1.002542052 >> Pd 0.500000000 0.500000000 1.002542051 >> Pd 0.500000000 0.000000000 1.496126804 >> Pd 0.000000000 0.500000000 1.496126804 >> >> >> >> >> K_POINTS (automatic) >> 8 8 1 0 0 0 >> >> >> > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 22, Issue 34 > **************************************** From giannozz at democritos.it Thu Apr 16 16:17:10 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 16 Apr 2009 16:17:10 +0200 Subject: [Pw_forum] plotband.x could not get filename In-Reply-To: <200904161743.36147.pemryan@yahoo.cn> References: <200904161706.42206.pemryan@yahoo.cn> <49E6F771.2000804@democritos.it> <200904161743.36147.pemryan@yahoo.cn> Message-ID: <49E73DE6.5050904@democritos.it> Yan wrote: > Thank you for your reply. I tests iargc with test.f90, it works and > returns correct number of arguments. so it has to work in plotband.x as well (if you are linking the same object, of course) P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From eyvaz_isaev at yahoo.com Thu Apr 16 16:21:33 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 16 Apr 2009 07:21:33 -0700 (PDT) Subject: [Pw_forum] propagation direction in the input file for dynmat.x In-Reply-To: <20090416120515.6211.qmail@ms.hfcas.ac.cn> Message-ID: <720623.33627.qm@web65708.mail.ac4.yahoo.com> Dear Li, This one can be done using matdyn.x, too. >My system has hexagonal symmetry and its primitive cell is rhombohedral. If the difference in between number of atoms not too much, I would prefer hexagonal, as it has higher symmetry and this will make things easier. From eariel99 at gmail.com Fri Apr 17 00:33:05 2009 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Thu, 16 Apr 2009 18:33:05 -0400 Subject: [Pw_forum] ensemble DFT vs "PWSCF" DFT in metals Message-ID: Hi, I am curious about the difference between the ensemble DFT method implemented in CP and the smeared DFT used in PWSCF with Methfessel-Paxton smearing. ?What is better for what system? -- Eduardo Menendez Departamento de Fisica Facultad de Ciencias Universidad de Chile Phone: (56)(2)9787439 URL: http://fisica.ciencias.uchile.cl/~emenendez -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090416/c393a22d/attachment.htm From degironc at sissa.it Fri Apr 17 10:24:13 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 17 Apr 2009 10:24:13 +0200 Subject: [Pw_forum] ensemble DFT vs "PWSCF" DFT in metals In-Reply-To: References: Message-ID: <49E83CAD.9070900@sissa.it> The functional is the same but the approach used to reach the solution is different. PWscf uses a self-consistent cycle technique while ensemble DFT recast it in a global-minimization problem. Ensemble DFT is guaranteed (if I remember correctly) to be a scheme where the total energy decreases at each iteration while for the self-consistent solution sometime the energy does not monotonically decrease with the number of iteration before converging. I think that the relative efficiency of the two methods may be different for different systems and only experience can tell you wich one is more efficient for your system. Tricky systems are typically very anisotropic metallic slabs subjects to charge sloshing (dealt with mixing_mode='local-TF' in PWscf) and/or magnetic systems where many alternative solutions are close in energy (larger smearing usually helps in stabilizing the system but may wash out the physical effect... very many kpoints and a small smearing may be needed) . In these cases the always decreasing nature of ensembe-DFT may be useful. At variance with CP, PWscf exploits symmetry so for "crystals" PWscf may be preferable. I don't know how the many-k-points case, often needed for metals, is dealt with in the ensemble DFT method... in principle all partially occupied electronic states (nbnd*nks) should be treated together. But I don't know how this is done in CP. Methfessel and Paxton broadening may leads to non positive-definite occupation numbers. This is usually not a big problem for PWscf , when decent k-point sampling is used, but I think it is incompatible with the ensemble DFT scheme. Luckily other efficient smearing techniques such as the Marzari-Vanderbilt scheme are available that are positive-definite. Stefano de Gironcoli - SISSA and DEMOCRITOS Eduardo Ariel Menendez Proupin wrote: > Hi, > I am curious about the difference between the ensemble DFT method > implemented in CP and the smeared DFT used in PWSCF with > Methfessel-Paxton smearing. ?What is better for what system? > > -- > Eduardo Menendez > Departamento de Fisica > Facultad de Ciencias > Universidad de Chile > Phone: (56)(2)9787439 > URL: http://fisica.ciencias.uchile.cl/~emenendez > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From ylli at theory.issp.ac.cn Fri Apr 17 10:37:37 2009 From: ylli at theory.issp.ac.cn (=?utf-8?B?TGkgWUw=?=) Date: Fri, 17 Apr 2009 16:37:37 +0800 Subject: [Pw_forum] =?utf-8?q?propagation_direction_in_the_input_file?= Message-ID: <20090417083737.29118.qmail@ms.hfcas.ac.cn> Dear Eyvaz, Many thanks your suggestions or comments. >This one can be done using matdyn.x, too. Can you give me example file to finish LO-TO spliting using matdyn.x? I noticed that for insulator, by default, ph.x firstly calculate electric field and effective charges. Why? > If the difference in between number of atoms not too much, I would prefer hexagonal. There are much difference in between nubmers of atoms. There are 30 atoms in unit cell. But in its primitive cell, the number of atoms is only 10. By the way, now I can obtain dielectriic constants (high frequency dielectric constants) and effective charges, but I don't know how to get static dielectrin constant and polar charges? can you give me some suggestions? Thanks a lot. Best regards, Yanling Li, Institute of solid states physics, CAS, China. ------------------------------------------------------------------------- >>Dear Li, >>This one can be done using matdyn.x, too. >>My system has hexagonal symmetry and its primitive cell is rhombohedral. >>If the difference in between number of atoms not too much, I would prefer hexagonal, as it has higher symmetry >>and this will make things easier. >>From matdyn.f90: > > ! Then, if (.not.dos) : > ! nq number of q-points > ! (q(i,n), i=1,3) nq q-points in 2pi/a units > ! If q = 0, the direction qhat (q=>0) for the non-analytic part > ! is extracted from the sequence of q-points as follows: > ! qhat = q(n) - q(n-1) or qhat = q(n) - q(n+1) > ! depending on which one is available and nonzero. > ! For low-symmetry crystals, specify twice q = 0 in the list > ! if you want to have q = 0 results for two different directions > ! > Anyway, you should specify 2 directions like > x(1) y(1) z(1) > ........ > x(N-1) y(N) z(N) >0 0 0 !!!!! Gamma point x(N)=0 y(N)=0 z(N)=0 >x(N+1) y(N+1) z(N+1) > ......... > x(M) y(M) z(M) > For a hexagonal lattice you could try A (00z) --> G(000) --> K(-1/3,2/3,0), as example. > Hope this helps. > Bests, Eyvaz. >--- On Thu, 4/16/09, Li YL wrote: > Dear all users, > > Now I've a question on the polar materials. In order to > get LO-TO splitting, you know, we need to use dynmat.x. In > the input file for dynmat.x, we need input q(1), q(2), and > q(3), that is, the propagation direction. I don't know > how to choose this direction. My system has hexagonal > symmetry and its primitive cell is rhombohedral. > Any suggestions are welcome. Thanks in advance. > > Bests, > > Yanling Li, > > Institute of Solid states physics, CAS, P. R. China. Re: [Pw_forum] propagation direction in the input file -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090417/3452484e/attachment.htm From zah7903 at gmail.com Fri Apr 17 15:20:33 2009 From: zah7903 at gmail.com (Aihua Zhang) Date: Fri, 17 Apr 2009 21:20:33 +0800 Subject: [Pw_forum] general external potential Message-ID: Dear PWscf users, I am thinking about adding a general periodic local potential to my system. I noted that for the specific sawlike potential (tefield), the total energy correction (etotefield) and the force correction (forcefield) are needed in pwscf code. I wonder how to generalize these two terms for a general local potential? Could anyone give me a clue? Thank you! Best regards Zhang -- ------------------------------------------------------------------ Research Fellow, Dept. of Physics, National Univ. of Singapore 10 Kent Ridge Crescent, Singapore, 119260 Tel: +65 6516 7844 ------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090417/1b013146/attachment.htm From quantumdft at gmail.com Fri Apr 17 17:02:13 2009 From: quantumdft at gmail.com (vega lew) Date: Fri, 17 Apr 2009 23:02:13 +0800 Subject: [Pw_forum] what's the unit of charge density In-Reply-To: <1239704111.17996.45.camel@walk.ijs.si> References: <412f6c680904110015u46e6be86x448f9d1c84868a11@mail.gmail.com> <1239704111.17996.45.camel@walk.ijs.si> Message-ID: <412f6c680904170802s3e362b81mf568860ee1609c94@mail.gmail.com> Dear friend, thank you for your help. your answer is quite useful for us. >I am not aware of any tool in the distribution that can do overlap >populations. as far as I know, this function could be accomplished during Mulliken bond population analysis in CASTEP. I used to think this kind of analysis could help us to understand our promble. >Perhaps, instead of overlap population, you may plot the atomic >projected-densities of states (using projwfc.x), and you can look how >good is the PDOS "alignment" between the atoms in question ... >Or you may plot the 2D contour plot of either charge density difference >or integrated local density of states along the bond direction. could you give me some more information about plotting the charge density difference map. which command in QE should be used for that plotting? And I also found 2D contour is a little hard for our problem, because our model is a slab geometry, and the atoms on the surface goes ups and downs. Thus, we can't put all the atoms we are focus on in one 2D map. could you please tell me more about how to integrated lDoS along the bond direction? Do you mean I could plot the pDoS for certain atoms, and then integrate it to the HOMO? thank you again for your kind help best wishes, vega On Tue, Apr 14, 2009 at 6:15 PM, Tone Kokalj wrote: > On Sat, 2009-04-11 at 15:15 +0800, vega lew wrote: > > Dear all > > > > I just ploted the 3D charge density using pp.x code. And XCRYSDEN was > > used for displaying the 3D isosurface of charge density. When I set > > the isovalue for different number, such as 0.15 or less, I fould the > > overlap of electron cloud is quite meanful for different systems of > > distinct catalysis activities. I wonder what the unit of charge > > density? > > xcrysden does not assume any units, and merely takes the values as > stated in the file. The unit is therefore up to the creator of the XSF > file. > > If the XSF file was produced by pp.x, then the unit of charge is > electron/bohr^3. > > > > and whether the absolute value of it could be directly comparable for > > different systems ( same number of atoms, same element, only different > > in geometry of the model)? > > Yes, because the unit is electron/bohr^3 (for pp.x). > > > By the way, is there a tutorial for population analysis? I wonder > > where I could find the value of overap population for a pair of > > atoms. > > The PWscf uses Lowdin population analysis that can be performed by > projwfc.x. Note however the ingredients are lowdin oribtals, which are > orthonormal, i.e.: > > LowdinOrb_\mu = \sum_\nu S_{\mu,\nu}^{1/2} AO_\nu, > > where S_{\mu,\nu}^{1/2} is the element of the square root inverse of the > overlap matrix S of the atomic orbitals AO. Because lowdin orbitals are > orthogonal there is no overlap between them ==> no overlap population! > > I am not aware of any tool in the distribution that can do overlap > populations. > > Perhaps, instead of overlap population, you may plot the atomic > projected-densities of states (using projwfc.x), and you can look how > good is the PDOS "alignment" between the atoms in question ... > Or you may plot the 2D contour plot of either charge density difference > or integrated local density of states along the bond direction. > > Regards, Tone > > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint attachments. > See: http://www.gnu.org/philosophy/no-word-attachments.html > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090417/55b487cb/attachment-0001.htm From paulatto at sissa.it Fri Apr 17 17:11:08 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 17 Apr 2009 17:11:08 +0200 Subject: [Pw_forum] what's the unit of charge density In-Reply-To: <412f6c680904170802s3e362b81mf568860ee1609c94@mail.gmail.com> References: <412f6c680904110015u46e6be86x448f9d1c84868a11@mail.gmail.com> <1239704111.17996.45.camel@walk.ijs.si> <412f6c680904170802s3e362b81mf568860ee1609c94@mail.gmail.com> Message-ID: On Fri, 17 Apr 2009 17:02:13 +0200, vega lew wrote: > could you give me some more information about plotting the charge density > difference map. The second stage of post-processing - the one described in th &PLOT namelist - can process more than one filplot file at a time. All the input files are multiplied by a user-specified weight and summed together. e.g. something like this: &inputp / &plot nfile=2 filepp(1) = 'before.fil' filepp(2) = 'after.fil' weight(1) = +1 weight(2) = -1 ... / regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From tone.kokalj at ijs.si Fri Apr 17 18:20:38 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 17 Apr 2009 18:20:38 +0200 Subject: [Pw_forum] what's the unit of charge density In-Reply-To: <412f6c680904170802s3e362b81mf568860ee1609c94@mail.gmail.com> References: <412f6c680904110015u46e6be86x448f9d1c84868a11@mail.gmail.com> <1239704111.17996.45.camel@walk.ijs.si> <412f6c680904170802s3e362b81mf568860ee1609c94@mail.gmail.com> Message-ID: <1239985238.5088.34.camel@walk.ijs.si> On Fri, 2009-04-17 at 23:02 +0800, vega lew wrote: > Dear friend, > > thank you for your help. your answer is quite useful for us. > > >I am not aware of any tool in the distribution that can do overlap > >populations. > > as far as I know, this function could be accomplished during Mulliken > bond population analysis in CASTEP. > I used to think this kind of analysis could help us to understand our > promble. Right! What I meant was that there is currently no tool in quantum-espresso that can do Mulliken population. > could you please tell me more about how to integrated lDoS along the > bond direction? You do a 2D contour plot, where the bond-direction lies on the plotting plane. The cumbersome (but not difficult) part it to determine the appropriate plane (origin + 2 spanning vectors). The recipe is as given by Lorenzo in the previous email (i.e. via specifying the &PLOT namelist of pp.x). Even if not all atoms of interests lie on the plotting plane this can be still useful, moreover you may choose several plotting planes. > Do you mean > I could plot the pDoS for certain atoms, and then integrate it to the > HOMO? Yes precisely: the PDOS is a prerequisite for ILDOS. By PDOS you will determine within which energy window to integrate. You may do several energy windows. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From quantumdft at gmail.com Fri Apr 17 18:35:35 2009 From: quantumdft at gmail.com (vega lew) Date: Sat, 18 Apr 2009 00:35:35 +0800 Subject: [Pw_forum] what's the unit of charge density In-Reply-To: <1239985238.5088.34.camel@walk.ijs.si> References: <412f6c680904110015u46e6be86x448f9d1c84868a11@mail.gmail.com> <1239704111.17996.45.camel@walk.ijs.si> <412f6c680904170802s3e362b81mf568860ee1609c94@mail.gmail.com> <1239985238.5088.34.camel@walk.ijs.si> Message-ID: <412f6c680904170935h1497bb4btec74499cc5d84727@mail.gmail.com> Dear friends, many thanks to Anton Kokalj and Lorenzo Paulatto. I'm really grateful for your kind help and constructive discussion. best wishes, vega On Sat, Apr 18, 2009 at 12:20 AM, Tone Kokalj wrote: > On Fri, 2009-04-17 at 23:02 +0800, vega lew wrote: > > Dear friend, > > > > thank you for your help. your answer is quite useful for us. > > > > >I am not aware of any tool in the distribution that can do overlap > > >populations. > > > > as far as I know, this function could be accomplished during Mulliken > > bond population analysis in CASTEP. > > I used to think this kind of analysis could help us to understand our > > promble. > > Right! > > What I meant was that there is currently no tool in quantum-espresso > that can do Mulliken population. > > > could you please tell me more about how to integrated lDoS along the > > bond direction? > > You do a 2D contour plot, where the bond-direction lies on the plotting > plane. The cumbersome (but not difficult) part it to determine the > appropriate plane (origin + 2 spanning vectors). The recipe is as given > by Lorenzo in the previous email (i.e. via specifying the &PLOT namelist > of pp.x). > > Even if not all atoms of interests lie on the plotting plane this can be > still useful, moreover you may choose several plotting planes. > > > Do you mean > > I could plot the pDoS for certain atoms, and then integrate it to the > > HOMO? > > Yes precisely: the PDOS is a prerequisite for ILDOS. By PDOS you will > determine within which energy window to integrate. You may do several > energy windows. > > Regards, Tone > > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint attachments. > See: http://www.gnu.org/philosophy/no-word-attachments.html > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090418/e3e58671/attachment.htm From anvari_meh at physics.iust.ac.ir Sat Apr 18 11:22:35 2009 From: anvari_meh at physics.iust.ac.ir (Mehrnaz Anvari) Date: Sat, 18 Apr 2009 12:52:35 +0330 Subject: [Pw_forum] one layer calculations Message-ID: Hello Thanks because of your attention.first I have to say, I couldn't understand cell_dofree, I have celldm(1) & celldm(3) in my input, so how could I insert cell_dofree. Second problem is when I choose celldm(3)=10 after vc-rx the calculated stress along z become approximately zero & when I put celldm(3)=3 it reached stress=-2 (& it means that my cell is large). I know for introducing one layer to system I have to create vacuum in z so how could I choose the best value between them? Best Regards Mehrnaz Anvari Iran University Of Science & Technology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090418/7752bc7f/attachment.htm From raamesh123 at rediffmail.com Sat Apr 18 21:14:11 2009 From: raamesh123 at rediffmail.com (ramesh kumar) Date: 18 Apr 2009 19:14:11 -0000 Subject: [Pw_forum] compliation problem Message-ID: <20090418191411.22150.qmail@f5mail-237-238.rediffmail.com> Dear forum thanks for all the people who helped me many a times.... i am trying to install espresso 4.0.4 package in cluster.... As prof. Paolo suggests i went for simple configuration but i got some error messages...i browsed the full forum ...i am not able to find the answer please help me.... ./configure said success make all test -d bin || mkdir bin if test -d iotk ; then \ ( cd iotk ; if test "make" = "" ; then make TLDEPS= lib+util ; \ else make TLDEPS= lib+util ; fi ) ; fi make[1]: Entering directory `/sfs1/phd/ph06d017/ramesh/espresso-4.0.4/iotk' cd src ; make lib+util make[2]: Entering directory `/sfs1/phd/ph06d017/ramesh/espresso-4.0.4/iotk/src' mpif90 -O2 -assume byterecl -nomodule -fpp -D__INTEL -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I./ -I../Modules -I../iotk/src -I../PW -I../PH -c iotk_base.f90 mpif90 -O2 -assume byterecl -nomodule -fpp -D__INTEL -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I./ -I../Modules -I../iotk/src -I../PW -I../PH -c iotk_attr_interf.f90 mpif90 -O2 -assume byterecl -nomodule -fpp -D__INTEL -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I./ -I../Modules -I../iotk/src -I../PW -I../PH -c iotk_error_interf.f90 mpif90 -O2 -assume byterecl -nomodule -fpp -D__INTEL -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I./ -I../Modules -I../iotk/src -I../PW -I../PH -c iotk_misc_interf.f90 fortcom: Error: iotk_misc_interf.spp, line 55: Error in opening the compiled module file. Check INCLUDE paths. [IOTK_BASE] use iotk_base ------^ fortcom: Error: iotk_misc_interf.spp, line 59: This derived type name has not been declared. [IOTK_DUMMYTYPE] type(iotk_dummytype), optional :: dummy -------^ fortcom: Error: iotk_misc_interf.spp, line 54: This name does not have a type, and must have an explicit type. [DUMMY] subroutine iotk_copy_tag_x(source,dest,dummy,maxsize,ierr) ---------------------------------------^ fortcom: Error: iotk_misc_interf.spp, line 90: Error in opening the compiled module file. Check INCLUDE paths. [IOTK_BASE] use iotk_base ------^ fortcom: Error: iotk_misc_interf.spp, line 92: This derived type name has not been declared. [IOTK_DUMMYTYPE] type(iotk_dummytype),optional :: dummy -------^ fortcom: Error: iotk_misc_interf.spp, line 88: This name does not have a type, and must have an explicit type. [DUMMY] subroutine iotk_set_x(dummy,unitmin,unitmax,getline_buffer,error_warn_overflow, & ----------------------^ fortcom: Error: iotk_misc_interf.spp, line 109: Error in opening the compiled module file. Check INCLUDE paths. [IOTK_BASE] use iotk_base ------^ fortcom: Error: iotk_misc_interf.spp, line 111: This derived type name has not been declared. [IOTK_DUMMYTYPE] type(iotk_dummytype),optional :: dummy -------^ fortcom: Error: iotk_misc_interf.spp, line 107: This name does not have a type, and must have an explicit type. [DUMMY] subroutine iotk_get_x(dummy,unitmin,unitmax,getline_buffer,error_warn_overflow, & ----------------------^ fortcom: Error: iotk_misc_interf.spp, line 165: Error in opening the compiled module file. Check INCLUDE paths. [IOTK_BASE] use iotk_base ------^ fortcom: Error: iotk_misc_interf.spp, line 168: A specification expression object must be a dummy argument, a COMMON block object, or an object accessible through host or use association [IOTK_ATTLENX] character(iotk_attlenx), intent(in) :: attr ------------^ fortcom: Error: iotk_misc_interf.spp, line 189: Error in opening the compiled module file. Check INCLUDE paths. [IOTK_BASE] use iotk_base ------^ fortcom: Error: iotk_misc_interf.spp, line 191: A specification expression object must be a dummy argument, a COMMON block object, or an object accessible through host or use association [IOTK_TAGLENX] character(iotk_taglenx), intent(in) :: tag ------------^ fortcom: Error: iotk_misc_interf.spp, line 192: A specification expression object must be a dummy argument, a COMMON block object, or an object accessible through host or use association [IOTK_NAMLENX] character(iotk_namlenx), intent(out) :: name ------------^ compilation aborted for iotk_misc_interf.f90 (code 1) make[2]: *** [iotk_misc_interf.o] Error 1 make[2]: Leaving directory `/sfs1/phd/ph06d017/ramesh/espresso-4.0.4/iotk/src' make[1]: *** [lib+util] Error 2 make[1]: Leaving directory `/sfs1/phd/ph06d017/ramesh/espresso-4.0.4/iotk' make: *** [libiotk] Error 2 With regards K. Ramesh Kumar Research Scholar Department of Physics IIT-Madras Chennai-600 036 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090418/d775d0b1/attachment.htm From kyin.cn at gmail.com Sun Apr 19 10:10:18 2009 From: kyin.cn at gmail.com (Kun Yin) Date: Sun, 19 Apr 2009 16:10:18 +0800 Subject: [Pw_forum] effective charges and USPP implementation Message-ID: Dear Users and Developers: PWscf website (http://www.pwscf.org/pseudo.htm) states that "calculations of effective charges, electron-phonon coefficients, third-order derivatives are not implemented with USPPs". Does this situation still exist? My primary concern is the effective chareges calculation. Please tell me if this feature has been implemented with USPPs now, and if yes, from which version on? Thank you in advance! -- Kun Yin Ph.D. Candidate School of Earth Sciences and Engineering Nanjing University 502 Geological Laboratory Building 22 Hankou Road Nanjing 210093 P.R. China email: kyin.cn at gmail.com From degironc at sissa.it Sun Apr 19 11:42:33 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sun, 19 Apr 2009 11:42:33 +0200 Subject: [Pw_forum] effective charges and USPP implementation In-Reply-To: References: Message-ID: <49EAF209.9030202@sissa.it> Dear Kun Yin, the webpage http://www.pwscf.org/pseudo.htm is outdated and is not linked anymore from the pwscf website . effective charges and electron-phonon coefficients are implemented with USPP. third order derivatives are not. stefano de Gironcoli - SISSA and DEMOCRITOS Kun Yin wrote: > Dear Users and Developers: > > PWscf website (http://www.pwscf.org/pseudo.htm) states that "calculations of > effective charges, electron-phonon coefficients, third-order derivatives are > not implemented with USPPs". Does this situation still exist? My primary > concern is the effective chareges calculation. Please tell me if this > feature has been implemented with USPPs now, and if yes, from which version > on? Thank you in advance! > > -- > Kun Yin > Ph.D. Candidate > School of Earth Sciences and Engineering > Nanjing University > 502 Geological Laboratory Building > 22 Hankou Road > Nanjing 210093 > P.R. China > > email: kyin.cn at gmail.com > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From kyin.cn at gmail.com Sun Apr 19 13:17:25 2009 From: kyin.cn at gmail.com (Kun Yin) Date: Sun, 19 Apr 2009 19:17:25 +0800 Subject: [Pw_forum] effective charges and USPP implementation References: <49EAF209.9030202@sissa.it> Message-ID: <83318FCEC81A4C3FA81DAF282B13C1FB@workhorse> Dear Stefano de Gironcoli, Thank you for your reply! -- Kun Yin Ph.D. Candidate School of Earth Sciences and Engineering Nanjing University 502 Geological Laboratory Building 22 Hankou Road Nanjing 210093 P.R. China email: kyin.cn at gmail.com ----- Original Message ----- From: "Stefano de Gironcoli" To: "PWSCF Forum" Sent: Sunday, April 19, 2009 5:42 PM Subject: Re: [Pw_forum] effective charges and USPP implementation > Dear Kun Yin, > the webpage http://www.pwscf.org/pseudo.htm is outdated and is not > linked anymore from the pwscf website . > effective charges and electron-phonon coefficients are implemented > with USPP. > third order derivatives are not. > > stefano de Gironcoli - SISSA and DEMOCRITOS > > Kun Yin wrote: >> Dear Users and Developers: >> >> PWscf website (http://www.pwscf.org/pseudo.htm) states that "calculations >> of >> effective charges, electron-phonon coefficients, third-order derivatives >> are >> not implemented with USPPs". Does this situation still exist? My primary >> concern is the effective chareges calculation. Please tell me if this >> feature has been implemented with USPPs now, and if yes, from which >> version >> on? Thank you in advance! >> >> -- >> Kun Yin >> Ph.D. Candidate >> School of Earth Sciences and Engineering >> Nanjing University >> 502 Geological Laboratory Building >> 22 Hankou Road >> Nanjing 210093 >> P.R. China >> >> email: kyin.cn at gmail.com >> >> _______________________________________________ >> 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 giannozz at democritos.it Sun Apr 19 20:08:53 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 19 Apr 2009 20:08:53 +0200 Subject: [Pw_forum] compliation problem In-Reply-To: <20090418191411.22150.qmail@f5mail-237-238.rediffmail.com> References: <20090418191411.22150.qmail@f5mail-237-238.rediffmail.com> Message-ID: <5F045367-F9F2-4CE6-A0F5-7A79D5DA2DC8@democritos.it> On Apr 18, 2009, at 21:14 , ramesh kumar wrote: > ...i am not able to find the answer please help me.... please "help yourself". Compilation problems, especially weird problems like yours, are often due to something strange in a specific machine. Sometimes expert eyes can immediately detect what is wrong, sometimes the origin of the problem is not obvious. In the latter case only the owner of the machine can find out what is wrong by carefully looking at the error message and by trial and error. > ./configure > said success and nothing else? look for suspicious warnings and messages > mpif90 -O2 -assume byterecl -nomodule -fpp -D__INTEL -D__FFTW - > D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I./ -I../ > Modules -I../iotk/src -I../PW -I../PH -c iotk_base.f90 iotk_base.f90 is compiled... > > mpif90 -O2 -assume byterecl -nomodule -fpp -D__INTEL -D__FFTW - > D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I./ -I../ > Modules -I../iotk/src -I../PW -I../PH -c iotk_misc_interf.f90 > fortcom: Error: iotk_misc_interf.spp, line 55: Error in opening the > compiled module file. Check INCLUDE paths. [IOTK_BASE] ...module iotk_base is not found. Are there iotk/src/iotk_base.o and iotk_base.mod files (or .d, or .whatever your compiler uses)? If not, there is something wrong with your compiler or your mpif90 and you should try to understand why it doesn't produce an object file. If yes, you should try to understand why it doesn't locate a module, since options -I are correct Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From eyvaz_isaev at yahoo.com Mon Apr 20 01:12:43 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sun, 19 Apr 2009 16:12:43 -0700 (PDT) Subject: [Pw_forum] propagation direction in the input file In-Reply-To: <20090417083737.29118.qmail@ms.hfcas.ac.cn> Message-ID: <509470.27371.qm@web65713.mail.ac4.yahoo.com> Dear Li, --- On Fri, 4/17/09, Li YL wrote: > Many thanks your suggestions or comments. Welcome! > Can you give me example file to finish LO-TO spliting > using matdyn.x? See attached file. But keep in mind IFC (and the dynamical matrix at Gamma point) have to be calculated as an insulator (semiconductor). I.e. there is no need to specify occupations (and related keywords) in scf.in. At the same time add epsil=.true. to ph.in. This will give you IFC and dyn0 files with macroscopic dielectric constants and Born effective charges. Attached file is for a hexagonal lattice. You can not use it directly as you have to use your actual c/a ratio. > I noticed that for insulator, by default, > ph.x firstly calculate electric field and effective charges. > Why? > ph.x does not calculate electric field, it calculates macroscopic dielectric constants and Born effectife charges. Because of that LO-TO splitting depends on these parameters. Please read a textbook why this LO-TO splitting occurs. > There are 30 atoms in unit cell. But in its primitive cell, > the number of atoms is only 10. > Well, I see. Sure the primitive cell is more suitable. > By the way, now I can obtain dielectriic constants (high > frequency dielectric constants) and effective charges, but I > don't know how to get static dielectrin constant and > polar charges? can you give me some suggestions? Again, not "polar" charges, Born effective charges. Static dielectric constants and the charges can be calculated easily. See above. Bests, Eyvaz. > > Best regards, > > Yanling Li, > > Institute of solid states physics, CAS, China. > > > ------------------------------------------------------------------------- > > >>Dear Li, > > >>This one can be done using matdyn.x, too. > > >>My system has hexagonal symmetry and its primitive > cell is rhombohedral. > > >>If the difference in between number of atoms not > too much, I would prefer hexagonal, as it has higher > symmetry >>and this will make things easier. > > >>From matdyn.f90: > > > > ! Then, if (.not.dos) : > > ! nq number of q-points > > ! (q(i,n), i=1,3) nq q-points in 2pi/a units > > ! If q = 0, the direction qhat (q=>0) for the > non-analytic part > > ! is extracted from the sequence of q-points as > follows: > > ! qhat = q(n) - q(n-1) or qhat = q(n) - > q(n+1) > > ! depending on which one is available and nonzero. > > ! For low-symmetry crystals, specify twice q = 0 in > the list > > ! if you want to have q = 0 results for two > different directions > > ! > > Anyway, you should specify 2 directions like > > > x(1) y(1) z(1) > > ........ > > x(N-1) y(N) z(N) > >0 0 0 !!!!! Gamma point x(N)=0 y(N)=0 z(N)=0 > >x(N+1) y(N+1) z(N+1) > > ......... > > x(M) y(M) z(M) > > > For a hexagonal lattice you could try A (00z) --> > G(000) --> K(-1/3,2/3,0), as example. > > > Hope this helps. > > > Bests, Eyvaz. > > > >--- On Thu, 4/16/09, Li YL > wrote: > > > Dear all users, > > > > Now I've a question on the polar materials. In > order to > > get LO-TO splitting, you know, we need to use > dynmat.x. In > > the input file for dynmat.x, we need input q(1), q(2), > and > > q(3), that is, the propagation direction. I don't > know > > how to choose this direction. My system has hexagonal > > symmetry and its primitive cell is rhombohedral. > > Any suggestions are welcome. Thanks in advance. > > > > Bests, > > > > Yanling Li, > > > > Institute of Solid states physics, CAS, P. R. China. > > > Re: [Pw_forum] propagation direction in the input file > > > _______________________________________________ > 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: matdyn.in1.gz Type: application/x-gzip Size: 1204 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090419/04e1fecb/attachment.bin From mansourehp at gmail.com Mon Apr 20 08:26:49 2009 From: mansourehp at gmail.com (Mansoureh Pashangpour) Date: Mon, 20 Apr 2009 10:56:49 +0430 Subject: [Pw_forum] phonon wih GGA and LSDA Message-ID: Dear all I'm using phonon calculation for a system. I would like to know do calculated phonon modes change within GGA and LSDA calculation? and which of them is closer to experimental results? I would like to know the answer before testing of both calculation. regards -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090420/ca89b798/attachment.htm From sclauzer at sissa.it Mon Apr 20 09:57:51 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 20 Apr 2009 09:57:51 +0200 Subject: [Pw_forum] one layer calculations In-Reply-To: References: Message-ID: <49EC2AFF.80303@sissa.it> Hello Mehrnaz Anvari wrote: > Hello > > Thanks because of your attention.first I have to say, I couldn't > understand cell_dofree, I have celldm(1) & celldm(3) in my input, so how > could I insert cell_dofree. Well, it depends what you want to do... with so little of informations it's hard to guess. > Second problem is when I choose > celldm(3)=10 after vc-rx the calculated stress along z become > approximately zero & when I put celldm(3)=3 it reached stress=-2 (& it > means that my cell is large). Here the point is not clear at all? Where is the problem? The calculates stress depends on the cell parameters, but also on what you put inside of you cell. So you should specify what kind of system you are studying and a sample for an input file. > I know for introducing one layer to system > I have to create vacuum in z so how could I choose the best value > between them? If you want to create vacuum layers between surfaces in a slab geometry, I think you should not look at stress, but rather at the convergence of total energy as a function of the vacuum thickness. HTH GS > Best Regards > Mehrnaz Anvari > Iran University Of Science & Technology > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Mon Apr 20 10:14:28 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 20 Apr 2009 10:14:28 +0200 Subject: [Pw_forum] phonon wih GGA and LSDA In-Reply-To: References: Message-ID: <49EC2EE4.4020701@sissa.it> Mansoureh Pashangpour wrote: > Dear all > I'm using phonon calculation for a system. I would like to know do > calculated phonon modes change within GGA and LSDA calculation? Definitely they do. They can even change within LDA or GGA if you try different XC functionals. > and which of them is closer to experimental results? I don't know if anyone would give a definite answer to this... LDA and GGA are both _approximations_ to the XC functional, but gradient corrected functionals are believed to reproduce more accurately structural properties (though sometimes for some kind of systems LDA can do better, maybe because of cancellation of errors). While waiting for a more helpful answer, I suggest you to give a look at the following review and references therein: Baroni et al., RMP 73, pp 515 (2001) HTH GS > I would like to know the answer before testing of both calculation. > regards > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Mon Apr 20 10:21:20 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 20 Apr 2009 10:21:20 +0200 Subject: [Pw_forum] How to compute the average Coulomb repulse U and exchange parameter J In-Reply-To: <20090416141031.2150.eqmail@aphy.iphy.ac.cn> References: <20090416141031.2150.eqmail@aphy.iphy.ac.cn> Message-ID: <49EC3080.3020004@sissa.it> To have an idea, you can start having a look at the tutorial: http://vlab.msi.umn.edu/events/lecture.shtml Use the supercell extrapolation utility with care and counter-check results, since it has been reported on this forum that it may not be working as expected for some lattice types which have not yet been tested. HTH GS clie wrote: > Dear friends, > Have you ever computed the average Coulomb repulse U and exchange parameter J > by pwscf. Could someone give some more detailed explanation about how to > process the output to get the U and J. I have read this pape(PHYSICAL REVIEW B > 71, 035105, 2005), but I am still confusing about how to get U. Thank you in > advance. > All the best, > Zhi Li > > ----------------------------------------------- > Ex5 group Extreme Condition Physics, Institute of Physics, Chinese > Academy of Sciences, P. O. Box 603, Beijing, 100190, People?s Republic of > China > > > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From kazempoor2000 at yahoo.com Mon Apr 20 13:23:10 2009 From: kazempoor2000 at yahoo.com (ali kazempoor) Date: Mon, 20 Apr 2009 04:23:10 -0700 (PDT) Subject: [Pw_forum] reconstruction Message-ID: <40151.64085.qm@web33101.mail.mud.yahoo.com> Dear all I want to study the fingerprint of reconstruction in nanowire facets. How can I find that wheater I have surface reconstruction or not? Should I make a bigger supercell in Z direction( Z is the lenght of nanowire)? thanks Ali Kazempour.Isfahan University of Technology,Iran From clie at aphy.iphy.ac.cn Mon Apr 20 13:50:38 2009 From: clie at aphy.iphy.ac.cn (clie) Date: Mon, 20 Apr 2009 11:50:38 GMT Subject: [Pw_forum] The NWORDWPP and NWORDWF In-Reply-To: References: Message-ID: <20090420115038.31431.eqmail@aphy.iphy.ac.cn> Dear friends, When I try to compile the wannier_init.f90, the following error happened, fortcom Error, wannier_init.f90,line 64: the name does't have atype, and must have an explicit type. [NWORDWPP] ..... fortcom Error, wannier_init.f90,line 65: the name does't have atype, and must have an explicit type. [NWORDWF] How to resolve the question? Thank you in advence. All the best, Zhi Li ----------------------------------------------- Ex5 group Extreme Condition Physics, Institute of Physics, Chinese Academy of Sciences, P. O. Box 603, Beijing, 100190, People?s Republic of China pw_forum-request at pwscf.org ?: > 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. one layer calculations (Mehrnaz Anvari) > 2. compliation problem (ramesh kumar) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 18 Apr 2009 12:52:35 +0330 > From: "Mehrnaz Anvari" > Subject: [Pw_forum] one layer calculations > To: pw_forum at pwscf.org > Message-ID: > Content-Type: text/plain; charset="us-ascii" > > Hello > Thanks because of your attention.first I have to say, I couldn't understand > cell_dofree, I have celldm(1) & celldm(3) in my input, so how could I insert > cell_dofree. Second problem is when I choose celldm(3)=10 after vc-rx the > calculated stress along z become approximately zero & when I put celldm(3)=3 > it reached stress=-2 (& it means that my cell is large). I know for > introducing one layer to system I have to create vacuum in z so how could I > choose the best value between them? > Best Regards > Mehrnaz Anvari > Iran University Of Science & Technology > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090418/ 7752bc7f/attachment.html > > ------------------------------ > > Message: 2 > Date: 18 Apr 2009 19:14:11 -0000 > From: "ramesh kumar" > Subject: [Pw_forum] compliation problem > To: > Message-ID: <20090418191411.22150.qmail at f5mail-237-238.rediffmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear forum > > thanks for all the people who helped me many a times.... > > i am trying to install espresso 4.0.4 package in cluster.... > > As prof. Paolo suggests i went for simple configuration but i got some error messages...i browsed the full forum ...i am not able to find the answer please help me.... > > ./configure > said success > > make all > > test -d bin || mkdir bin > if test -d iotk ; then \ > ( cd iotk ; if test "make" = "" ; then make TLDEPS= lib+util ; \ > else make TLDEPS= lib+util ; fi ) ; fi > make[1]: Entering directory `/sfs1/phd/ph06d017/ramesh/espresso-4.0.4/iotk' > cd src ; make lib+util > make[2]: Entering directory `/sfs1/phd/ph06d017/ramesh/espresso-4.0.4/iotk/ src' > mpif90 -O2 -assume byterecl -nomodule -fpp -D__INTEL -D__FFTW - D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I./ -I../Modules -I../ iotk/src -I../PW -I../PH -c iotk_base.f90 > mpif90 -O2 -assume byterecl -nomodule -fpp -D__INTEL -D__FFTW - D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I./ -I../Modules -I../ iotk/src -I../PW -I../PH -c iotk_attr_interf.f90 > mpif90 -O2 -assume byterecl -nomodule -fpp -D__INTEL -D__FFTW - D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I./ -I../Modules -I../ iotk/src -I../PW -I../PH -c iotk_error_interf.f90 > mpif90 -O2 -assume byterecl -nomodule -fpp -D__INTEL -D__FFTW - D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I./ -I../Modules -I../ iotk/src -I../PW -I../PH -c iotk_misc_interf.f90 > fortcom: Error: iotk_misc_interf.spp, line 55: Error in opening the compiled module file. Check INCLUDE paths. [IOTK_BASE] > use iotk_base > ------^ > fortcom: Error: iotk_misc_interf.spp, line 59: This derived type name has not been declared. [IOTK_DUMMYTYPE] > type(iotk_dummytype), optional :: dummy > -------^ > fortcom: Error: iotk_misc_interf.spp, line 54: This name does not have a type, and must have an explicit type. [DUMMY] > subroutine iotk_copy_tag_x(source,dest,dummy,maxsize,ierr) > ---------------------------------------^ > fortcom: Error: iotk_misc_interf.spp, line 90: Error in opening the compiled module file. Check INCLUDE paths. [IOTK_BASE] > use iotk_base > ------^ > fortcom: Error: iotk_misc_interf.spp, line 92: This derived type name has not been declared. [IOTK_DUMMYTYPE] > type(iotk_dummytype),optional :: dummy > -------^ > fortcom: Error: iotk_misc_interf.spp, line 88: This name does not have a type, and must have an explicit type. [DUMMY] > subroutine iotk_set_x(dummy,unitmin,unitmax,getline_buffer, error_warn_overflow, & > ----------------------^ > fortcom: Error: iotk_misc_interf.spp, line 109: Error in opening the compiled module file. Check INCLUDE paths. [IOTK_BASE] > use iotk_base > ------^ > fortcom: Error: iotk_misc_interf.spp, line 111: This derived type name has not been declared. [IOTK_DUMMYTYPE] > type(iotk_dummytype),optional :: dummy > -------^ > fortcom: Error: iotk_misc_interf.spp, line 107: This name does not have a type, and must have an explicit type. [DUMMY] > subroutine iotk_get_x(dummy,unitmin,unitmax,getline_buffer, error_warn_overflow, & > ----------------------^ > fortcom: Error: iotk_misc_interf.spp, line 165: Error in opening the compiled module file. Check INCLUDE paths. [IOTK_BASE] > use iotk_base > ------^ > fortcom: Error: iotk_misc_interf.spp, line 168: A specification expression object must be a dummy argument, a COMMON block object, or an object accessible through host or use association [IOTK_ATTLENX] > character(iotk_attlenx), intent(in) :: attr > ------------^ > fortcom: Error: iotk_misc_interf.spp, line 189: Error in opening the compiled module file. Check INCLUDE paths. [IOTK_BASE] > use iotk_base > ------^ > fortcom: Error: iotk_misc_interf.spp, line 191: A specification expression object must be a dummy argument, a COMMON block object, or an object accessible through host or use association [IOTK_TAGLENX] > character(iotk_taglenx), intent(in) :: tag > ------------^ > fortcom: Error: iotk_misc_interf.spp, line 192: A specification expression object must be a dummy argument, a COMMON block object, or an object accessible through host or use association [IOTK_NAMLENX] > character(iotk_namlenx), intent(out) :: name > ------------^ > compilation aborted for iotk_misc_interf.f90 (code 1) > make[2]: *** [iotk_misc_interf.o] Error 1 > make[2]: Leaving directory `/sfs1/phd/ph06d017/ramesh/espresso-4.0.4/iotk/src' > make[1]: *** [lib+util] Error 2 > make[1]: Leaving directory `/sfs1/phd/ph06d017/ramesh/espresso-4.0.4/iotk' > make: *** [libiotk] Error 2 > > > > With regards > > K. Ramesh Kumar > Research Scholar > Department of Physics > IIT-Madras > Chennai-600 036 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090418/ d775d0b1/attachment-0001.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 22, Issue 39 > **************************************** From degironc at sissa.it Mon Apr 20 15:05:56 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 20 Apr 2009 15:05:56 +0200 Subject: [Pw_forum] The NWORDWPP and NWORDWF In-Reply-To: <20090420115038.31431.eqmail@aphy.iphy.ac.cn> References: <20090420115038.31431.eqmail@aphy.iphy.ac.cn> Message-ID: <49EC7334.1040403@sissa.it> dear Zhi Li, nwordwpp and and nwordwf are defined in Modules/io_files.f90 which is "used" by wannier_init.f90. there is some problem in the way modules are included in your installation. have you tried to start the installation from scratch ? [ make veryclean ; ./configure ; make all ] stefano de Gironcoli - SISSA and DEMOCRITOS clie wrote: > Dear friends, > When I try to compile the wannier_init.f90, the following error happened, > fortcom Error, wannier_init.f90,line 64: the name does't have atype, and must > have an explicit type. [NWORDWPP] > ..... > fortcom Error, wannier_init.f90,line 65: the name does't have atype, and must > have an explicit type. [NWORDWF] > How to resolve the question? > Thank you in advence. > All the best, > Zhi Li > > > ----------------------------------------------- > Ex5 group Extreme Condition Physics, Institute of Physics, Chinese > Academy of Sciences, P. O. Box 603, Beijing, 100190, People?s Republic of > China > > > > pw_forum-request at pwscf.org ?: > > >> 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. one layer calculations (Mehrnaz Anvari) >> 2. compliation problem (ramesh kumar) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Sat, 18 Apr 2009 12:52:35 +0330 >> From: "Mehrnaz Anvari" >> Subject: [Pw_forum] one layer calculations >> To: pw_forum at pwscf.org >> Message-ID: >> Content-Type: text/plain; charset="us-ascii" >> >> Hello >> Thanks because of your attention.first I have to say, I couldn't understand >> cell_dofree, I have celldm(1) & celldm(3) in my input, so how could I insert >> cell_dofree. Second problem is when I choose celldm(3)=10 after vc-rx the >> calculated stress along z become approximately zero & when I put celldm(3)=3 >> it reached stress=-2 (& it means that my cell is large). I know for >> introducing one layer to system I have to create vacuum in z so how could I >> choose the best value between them? >> Best Regards >> Mehrnaz Anvari >> Iran University Of Science & Technology >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090418/ >> > 7752bc7f/attachment.html > >> ------------------------------ >> >> Message: 2 >> Date: 18 Apr 2009 19:14:11 -0000 >> From: "ramesh kumar" >> Subject: [Pw_forum] compliation problem >> To: >> Message-ID: <20090418191411.22150.qmail at f5mail-237-238.rediffmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> >> Dear forum >> >> thanks for all the people who helped me many a times.... >> >> i am trying to install espresso 4.0.4 package in cluster.... >> >> As prof. Paolo suggests i went for simple configuration but i got some error >> > messages...i browsed the full forum ...i am not able to find the answer please > help me.... > >> ./configure >> said success >> >> make all >> >> test -d bin || mkdir bin >> if test -d iotk ; then \ >> ( cd iotk ; if test "make" = "" ; then make TLDEPS= lib+util ; \ >> else make TLDEPS= lib+util ; fi ) ; fi >> make[1]: Entering directory `/sfs1/phd/ph06d017/ramesh/espresso-4.0.4/iotk' >> cd src ; make lib+util >> make[2]: Entering directory `/sfs1/phd/ph06d017/ramesh/espresso-4.0.4/iotk/ >> > src' > >> mpif90 -O2 -assume byterecl -nomodule -fpp -D__INTEL -D__FFTW - >> > D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I./ -I../Modules -I../ > iotk/src -I../PW -I../PH -c iotk_base.f90 > >> mpif90 -O2 -assume byterecl -nomodule -fpp -D__INTEL -D__FFTW - >> > D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I./ -I../Modules -I../ > iotk/src -I../PW -I../PH -c iotk_attr_interf.f90 > >> mpif90 -O2 -assume byterecl -nomodule -fpp -D__INTEL -D__FFTW - >> > D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I./ -I../Modules -I../ > iotk/src -I../PW -I../PH -c iotk_error_interf.f90 > >> mpif90 -O2 -assume byterecl -nomodule -fpp -D__INTEL -D__FFTW - >> > D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I./ -I../Modules -I../ > iotk/src -I../PW -I../PH -c iotk_misc_interf.f90 > >> fortcom: Error: iotk_misc_interf.spp, line 55: Error in opening the compiled >> > module file. Check INCLUDE paths. [IOTK_BASE] > >> use iotk_base >> ------^ >> fortcom: Error: iotk_misc_interf.spp, line 59: This derived type name has not >> > been declared. [IOTK_DUMMYTYPE] > >> type(iotk_dummytype), optional :: dummy >> -------^ >> fortcom: Error: iotk_misc_interf.spp, line 54: This name does not have a type, >> > and must have an explicit type. [DUMMY] > >> subroutine iotk_copy_tag_x(source,dest,dummy,maxsize,ierr) >> ---------------------------------------^ >> fortcom: Error: iotk_misc_interf.spp, line 90: Error in opening the compiled >> > module file. Check INCLUDE paths. [IOTK_BASE] > >> use iotk_base >> ------^ >> fortcom: Error: iotk_misc_interf.spp, line 92: This derived type name has not >> > been declared. [IOTK_DUMMYTYPE] > >> type(iotk_dummytype),optional :: dummy >> -------^ >> fortcom: Error: iotk_misc_interf.spp, line 88: This name does not have a type, >> > and must have an explicit type. [DUMMY] > >> subroutine iotk_set_x(dummy,unitmin,unitmax,getline_buffer, >> > error_warn_overflow, & > >> ----------------------^ >> fortcom: Error: iotk_misc_interf.spp, line 109: Error in opening the compiled >> > module file. Check INCLUDE paths. [IOTK_BASE] > >> use iotk_base >> ------^ >> fortcom: Error: iotk_misc_interf.spp, line 111: This derived type name has >> > not been declared. [IOTK_DUMMYTYPE] > >> type(iotk_dummytype),optional :: dummy >> -------^ >> fortcom: Error: iotk_misc_interf.spp, line 107: This name does not have a >> > type, and must have an explicit type. [DUMMY] > >> subroutine iotk_get_x(dummy,unitmin,unitmax,getline_buffer, >> > error_warn_overflow, & > >> ----------------------^ >> fortcom: Error: iotk_misc_interf.spp, line 165: Error in opening the compiled >> > module file. Check INCLUDE paths. [IOTK_BASE] > >> use iotk_base >> ------^ >> fortcom: Error: iotk_misc_interf.spp, line 168: A specification expression >> > object must be a dummy argument, a COMMON block object, or an object accessible > through host or use association [IOTK_ATTLENX] > >> character(iotk_attlenx), intent(in) :: attr >> ------------^ >> fortcom: Error: iotk_misc_interf.spp, line 189: Error in opening the compiled >> > module file. Check INCLUDE paths. [IOTK_BASE] > >> use iotk_base >> ------^ >> fortcom: Error: iotk_misc_interf.spp, line 191: A specification expression >> > object must be a dummy argument, a COMMON block object, or an object accessible > through host or use association [IOTK_TAGLENX] > >> character(iotk_taglenx), intent(in) :: tag >> ------------^ >> fortcom: Error: iotk_misc_interf.spp, line 192: A specification expression >> > object must be a dummy argument, a COMMON block object, or an object accessible > through host or use association [IOTK_NAMLENX] > >> character(iotk_namlenx), intent(out) :: name >> ------------^ >> compilation aborted for iotk_misc_interf.f90 (code 1) >> make[2]: *** [iotk_misc_interf.o] Error 1 >> make[2]: Leaving directory `/sfs1/phd/ph06d017/ramesh/espresso-4.0.4/iotk/src' >> make[1]: *** [lib+util] Error 2 >> make[1]: Leaving directory `/sfs1/phd/ph06d017/ramesh/espresso-4.0.4/iotk' >> make: *** [libiotk] Error 2 >> >> >> >> With regards >> >> K. Ramesh Kumar >> Research Scholar >> Department of Physics >> IIT-Madras >> Chennai-600 036 >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090418/ >> > d775d0b1/attachment-0001.htm > >> ------------------------------ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> End of Pw_forum Digest, Vol 22, Issue 39 >> **************************************** >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From paulatto at sissa.it Mon Apr 20 15:10:23 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 20 Apr 2009 15:10:23 +0200 (CEST) Subject: [Pw_forum] The NWORDWPP and NWORDWF In-Reply-To: <20090420115038.31431.eqmail@aphy.iphy.ac.cn> References: <20090420115038.31431.eqmail@aphy.iphy.ac.cn> Message-ID: <60052.78.12.164.141.1240233023.squirrel@webmail.sissa.it> On Mon, 20 Apr 2009 13:50:38 +0200, clie wrote: have an explicit type. [NWORDWPP] have an explicit type. [NWORDWF] Those variables are included in the iofiles module, which is correctly included in wannier_init.f90. If the compiler cannot find them, it is a likely a problem with the compiler, maybe you have compiled part of quantum-espresso and then continued with another compiled without cleaning (make clean). Similar errors may also happen if you are using multi process make (make -j#), in this case they can be resolved by simpling running make again. If there is some system administrator in your institution, you should try and ask him directly, these kind of compilation problems are very general and may hint some misconfiguration in your machines. hope it helps, cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From akohlmey at cmm.chem.upenn.edu Mon Apr 20 15:57:45 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 20 Apr 2009 09:57:45 -0400 Subject: [Pw_forum] parallel make, was: Re: The NWORDWPP and NWORDWF In-Reply-To: <60052.78.12.164.141.1240233023.squirrel@webmail.sissa.it> References: <20090420115038.31431.eqmail@aphy.iphy.ac.cn> <60052.78.12.164.141.1240233023.squirrel@webmail.sissa.it> Message-ID: <1240235865.8441.350.camel@zero> On Mon, 2009-04-20 at 15:10 +0200, Lorenzo Paulatto wrote: > Similar errors may also happen if you are using multi process make (make > -j#), in this case they can be resolved by simpling running make again. lorenzo, if you want to use parallel make with Q-E properly, you must not do "make -j# all" but rather "make MFLAGS=-j# all", which should work fine, provided the dependencies are correct. i'm doing it all the time on dual quadcore machines and the compile just "flies". the toplevel makefile is by no means parallel make safe and it is next to impossible to do so without changing the behavior completely. i tried quite a long time ago, and could not make it work. but i got the subdir-makes to work properly and it has survived since (the complicated looking way of how the makefile recurses into the subdir with MFLAGS and TLDEPS and how calling make in the subdir jumps back to the toplevel to check all dependcies are the result of that). cheers, axel. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From giannozz at democritos.it Tue Apr 21 12:19:32 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 21 Apr 2009 12:19:32 +0200 Subject: [Pw_forum] charged defect In-Reply-To: <886978.17615.qm@web33101.mail.mud.yahoo.com> References: <886978.17615.qm@web33101.mail.mud.yahoo.com> Message-ID: <1CA1C5FB-8142-46E1-BFF5-79B0BA11DCD6@democritos.it> On Apr 11, 2009, at 13:26 , ali kazempoor wrote: > I want to study O vacancy in TiO2 bulk it's tricky, very tricky. May I suggest the following recent paper by Alex Zunger: Phys. Rev. B78, 235104 (2008)? it is a general paper on the problem of formation energies in charged defects. Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From giuseppe.mattioli at mlib.ism.cnr.it Tue Apr 21 15:11:55 2009 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Tue, 21 Apr 2009 15:11:55 +0200 Subject: [Pw_forum] charged defect In-Reply-To: <1CA1C5FB-8142-46E1-BFF5-79B0BA11DCD6@democritos.it> References: <886978.17615.qm@web33101.mail.mud.yahoo.com> <1CA1C5FB-8142-46E1-BFF5-79B0BA11DCD6@democritos.it> Message-ID: <200904211511.56168.giuseppe.mattioli@mlib.ism.cnr.it> Dear Ali > > I want to study O vacancy in TiO2 bulk There's a lot of people studying such an issue...! First, I suggest reading at least these papers: Phys. Rev. B vol. 73, pag. 125205 (2006). J. Chem. Phys. vol. 129, pag. 154113 (2008). Phys. Rev. B vol. 76, pag. 045217 (2007). Phys. Rev. B vol. 78, pag. 241201 (2008). Then, you will be aware that you need very large supercells and some kind of beyond-LDA (LDA+U or hybrid xc functionals) approximation in order to achieve a good description of point defects in TiO2. So, have a nice time... Dear Paolo > it's tricky, very tricky. May I suggest the following recent paper > by Alex Zunger: Phys. Rev. B78, 235104 (2008)? it is a general > paper on the problem of formation energies in charged defects. It's more than tricky... I'm starting in to think that TiO2 is not really a "regular" semiconductor. The paper by Zunger is of course an in-depth one, but native point defects in TiO2 seems to behave in a different way than, e.g., oxygen vacancies in ZnO (one of the topics of the Zunger's paper). This is not the suitable place for long debates, but I hope that such a scrap of an information can be useful to somebody. Cheers to everybody Giuseppe On Tuesday 21 April 2009 12:19:32 Paolo Giannozzi wrote: > On Apr 11, 2009, at 13:26 , ali kazempoor wrote: > > I want to study O vacancy in TiO2 bulk > > it's tricky, very tricky. May I suggest the following recent paper > by Alex Zunger: Phys. Rev. B78, 235104 (2008)? it is a general > paper on the problem of formation energies in charged defects. > > 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 -- ******************************************************** - 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: -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090421/7db70f5d/attachment.htm From zah7903 at gmail.com Tue Apr 21 15:55:29 2009 From: zah7903 at gmail.com (Aihua Zhang) Date: Tue, 21 Apr 2009 21:55:29 +0800 Subject: [Pw_forum] force in sawlike potential Message-ID: Dear all, I comment out the line to impose total force = 0 in forces.f90, and perform a calculation of one atom in sawlike potential. The input file is attached below. I had expected the force exerted on nucleus by the field would cancel the force on ion due to change in electron charge density, so the total force should vanish since the system is neutral. I also varied the cutoff energy, but failed to see a convergence behavior as shown below. Could anyone give me a clue? Thank you! Ecut(Ry) Total force(Ry/au) 30 0.002729 40 0.003052 50 0.003848 60 0.000086 70 0.000962 80 0.000137 90 0.003208 100 0.001271 The input file: ------------------------------------------------------------------------- &control calculation = 'scf' restart_mode='from_scratch', prefix='c', tstress = .true. tprnfor = .true. pseudo_dir = '.', outdir='/scratch/local' tefield=.true. / &system ibrav= 0, nat= 1, ntyp= 1, ecutwfc=100 edir=3 emaxpos=0.95 eopreg=0.1 eamp=0.001 / &electrons diagonalization='cg' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / CELL_PARAMETERS 10 0 0 0 10 0 0 0 20 ATOMIC_SPECIES C 1 C.pbe-rrkjus.UPF ATOMIC_POSITIONS {bohr} C 0.00 0.00 9.0 K_POINTS gamma ---------------------------------------------------------------------------- Best regards zah -- ------------------------------------------------------------------ Research Fellow, Dept. of Physics, National Univ. of Singapore 10 Kent Ridge Crescent, Singapore, 119260 Tel: +65 6516 7844 ------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090421/0a9c1daf/attachment.htm From paulatto at sissa.it Tue Apr 21 16:21:31 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 21 Apr 2009 16:21:31 +0200 Subject: [Pw_forum] force in sawlike potential In-Reply-To: References: Message-ID: In data 21 aprile 2009 alle ore 15:55:29, Aihua Zhang ha scritto: > I had expected the force exerted on nucleus by the field would > cancel the force on ion due to change in electron charge density, so the > total force should vanish since the system is neutral. I also varied the > cutoff energy, but failed to see a convergence behavior as shown below. > Could anyone give me a clue? Thank you! dear Aihua Zhang, that part of the code has been "fixed" more than once recently, hence the answer depends on the exact version of QE you are using. regards -- Creato con il rivoluzionario client e-mail di Opera: http://www.opera.com/mail/ From zah7903 at gmail.com Tue Apr 21 16:58:14 2009 From: zah7903 at gmail.com (Aihua Zhang) Date: Tue, 21 Apr 2009 22:58:14 +0800 Subject: [Pw_forum] force in sawlike potential In-Reply-To: References: Message-ID: Thank you! My QE version is 4.0.4. I will go for the newest version to have a look. On Tue, Apr 21, 2009 at 10:21 PM, Lorenzo Paulatto wrote: > In data 21 aprile 2009 alle ore 15:55:29, Aihua Zhang > ha scritto: > > I had expected the force exerted on nucleus by the field would > > cancel the force on ion due to change in electron charge density, so the > > total force should vanish since the system is neutral. I also varied the > > cutoff energy, but failed to see a convergence behavior as shown below. > > Could anyone give me a clue? Thank you! > > dear Aihua Zhang, > that part of the code has been "fixed" more than once recently, hence the > answer depends on the exact version of QE you are using. > > regards > > > -- > Creato con il rivoluzionario client e-mail di Opera: > http://www.opera.com/mail/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ------------------------------------------------------------------ Research Fellow, Dept. of Physics, National Univ. of Singapore 10 Kent Ridge Crescent, Singapore, 119260 Tel: +65 6516 7844 ------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090421/d8e2ba53/attachment-0001.htm From zah7903 at gmail.com Tue Apr 21 18:09:59 2009 From: zah7903 at gmail.com (Aihua Zhang) Date: Wed, 22 Apr 2009 00:09:59 +0800 Subject: [Pw_forum] force in sawlike potential In-Reply-To: References: Message-ID: Dear Paulatto, I compared the source codes under PW directory between 4.0.4 and 4.0.5. I only found a minor relevant change in compute_dip.f90. I don't think this change will affect the force. Best regards zah On Tue, Apr 21, 2009 at 10:21 PM, Lorenzo Paulatto wrote: > In data 21 aprile 2009 alle ore 15:55:29, Aihua Zhang > ha scritto: > > I had expected the force exerted on nucleus by the field would > > cancel the force on ion due to change in electron charge density, so the > > total force should vanish since the system is neutral. I also varied the > > cutoff energy, but failed to see a convergence behavior as shown below. > > Could anyone give me a clue? Thank you! > > dear Aihua Zhang, > that part of the code has been "fixed" more than once recently, hence the > answer depends on the exact version of QE you are using. > > regards > > > -- > Creato con il rivoluzionario client e-mail di Opera: > http://www.opera.com/mail/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ------------------------------------------------------------------ Research Fellow, Dept. of Physics, National Univ. of Singapore 10 Kent Ridge Crescent, Singapore, 119260 Tel: +65 6516 7844 ------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090422/e5a727a1/attachment.htm From paulatto at sissa.it Tue Apr 21 18:22:30 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 21 Apr 2009 18:22:30 +0200 Subject: [Pw_forum] force in sawlike potential In-Reply-To: References: Message-ID: In data 21 aprile 2009 alle ore 18:09:59, Aihua Zhang ha scritto: > Dear Paulatto, > > I compared the source codes under PW directory between 4.0.4 and 4.0.5. I > only found a minor relevant change in compute_dip.f90. I don't think this > change will affect the force. In fact, I was about to write there isn't any difference between 4.0.4 and 4.0.5, even though the sawtooth potential method is going through a redesign it won't be released very soon. What may be problematic is that your potential is that, in your case, emaxpos+eopreg is greater than 1. It should cause no harm, in theory, but I suspect the code may have some problem dealing with this case. What does it happen if you shift all your system half a basis vector down along the z direction? e.g. if you put the C atom in (0,0,0) and emaxpos=0.45, eopreg=0.10 regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From kazempoor2000 at yahoo.com Tue Apr 21 18:26:38 2009 From: kazempoor2000 at yahoo.com (ali kazempoor) Date: Tue, 21 Apr 2009 09:26:38 -0700 (PDT) Subject: [Pw_forum] Fw: reconstruction Message-ID: <213964.99430.qm@web33108.mail.mud.yahoo.com> --- On Mon, 4/20/09, ali kazempoor wrote: From: ali kazempoor Subject: reconstruction To: pw_forum at pwscf.org Date: Monday, April 20, 2009, 4:23 AM Dear all I want to study the fingerprint of reconstruction in nanowire facets. How can? I find that wheater I have surface reconstruction or not? Should I make a bigger supercell in Z direction( Z is the lenght of nanowire)? thanks Ali Kazempour.Isfahan University of Technology,Iran ? ? ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090421/48059560/attachment.htm From prasenjit.jnc at gmail.com Tue Apr 21 19:38:42 2009 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Tue, 21 Apr 2009 19:38:42 +0200 Subject: [Pw_forum] reconstruction In-Reply-To: <40151.64085.qm@web33101.mail.mud.yahoo.com> References: <40151.64085.qm@web33101.mail.mud.yahoo.com> Message-ID: <627e0ffa0904211038o3483973cq12d033a7e31f1f6d@mail.gmail.com> Dear Ali, Usually when you speak of simulating a nanowire, because of the periodic boundary conditions, you simulate an infinite one. If the nanowire is aligned along Z axis, which seems to be your case, then you have periodicity along the Z-direction. Therefore you need to have enough vacuum along the x & y direction so that the periodic images should not interact. Prasenjit. 2009/4/20 ali kazempoor > > Dear all > I want to study the fingerprint of reconstruction in nanowire facets. How > can I find that wheater I have surface reconstruction or not? Should I make > a bigger supercell in Z direction( Z is the lenght of nanowire)? > thanks > Ali Kazempour.Isfahan University of Technology,Iran > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- PRASENJIT GHOSH, POST-DOC, ROOM NO: 265, MAIN BUILDING, CM SECTION, ICTP, STRADA COSTERIA 11, TRIESTE, 34104, ITALY PHONE: +39 040 2240 369 (O) +39 3807528672 (M) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090421/8bb0ec8a/attachment.htm From panda.deng.pan at gmail.com Tue Apr 21 20:23:06 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Wed, 22 Apr 2009 02:23:06 +0800 Subject: [Pw_forum] question for phonon calculation Message-ID: Dear All Users, I was going to calculating phonon frequency of MgB2 at Gamma point.But I got the minus value at the lowest three branch. q = ( 0.000000000 0.000000000 0.000000000 ) ************************************************************************** omega( 1) = -1.333147 [THz] = -44.469304 [cm-1] omega( 2) = -1.333147 [THz] = -44.469304 [cm-1] omega( 3) = -1.003834 [THz] = -33.484515 [cm-1] omega( 4) = 9.706117 [THz] = 323.763351 [cm-1] omega( 5) = 9.706117 [THz] = 323.763351 [cm-1] omega( 6) = 11.666010 [THz] = 389.138778 [cm-1] omega( 7) = 15.807885 [THz] = 527.297796 [cm-1] omega( 8) = 15.807885 [THz] = 527.297796 [cm-1] omega( 9) = 20.623897 [THz] = 687.943739 [cm-1] ************************************************************************** I had already relax the lattice.And below is my inputs for scf and phonon calculation.Any suggest and comments on how to avoid the minus values was appreciated. scf.in &control calculation = 'scf' restart_mode='from_scratch' prefix='MgB2', pseudo_dir = '//Quantum-Espresso/espresso-4.0.3/pseudo/', outdir='/tmp/' / &system ibrav=4, celldm(1)=5.8398, celldm(3)=1.1420, nat=3, ntyp=2, ecutwfc = 45.0, ecutrho = 450.0, occupations= 'smearing', degauss= 0.03, smearing= 'cold', / &electrons mixing_beta = 0.7 conv_thr = 1.0d-12 / ATOMIC_SPECIES Mg 24.3 Mg.pw91-np-van.UPF B 10.8 B.pw91-n-van.UPF ATOMIC_POSITIONS Mg 0 0 0 B 0 0.57735 0.571 B 0.5 0.28868 0.571 K_POINTS {automatic} 32 32 32 0 0 0 ph.in MgB2 &inputph amass(1)= 24.3, amass(2)= 10.8, prefix='MgB2' tr2_ph=1.0d-25, alpha_mix(1)=0.5, iverbosity=1, outdir='//tmp/', / 0 0 0 I also wonder how to apply 'asr' to my calculation.I could not find any option for ph.x. Have a nice day! Deng Pan Nanjing University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090422/71018448/attachment.htm From kazempoor2000 at yahoo.com Tue Apr 21 20:55:03 2009 From: kazempoor2000 at yahoo.com (ali kazempoor) Date: Tue, 21 Apr 2009 11:55:03 -0700 (PDT) Subject: [Pw_forum] reconstruction Message-ID: <946400.24485.qm@web33102.mail.mud.yahoo.com> Dear Prasenjit Thank you for your reply, but I mean what I do to see the surface reconstruction at lateral nanowire surface. For simulation of a nanowire in z direction we add vaccum around nanowire in x and y and for z we use periodic boundary condition . So if we only suppose one unit repetation in z , we can not observe the surface reconstruction . Therefor for observing reconstruction , I think we have to make for example twice unit repetation in z or more. thanks --- On Tue, 4/21/09, Prasenjit Ghosh wrote: From: Prasenjit Ghosh Subject: Re: [Pw_forum] reconstruction To: "PWSCF Forum" Date: Tuesday, April 21, 2009, 10:38 AM Dear Ali, Usually when you speak of simulating a nanowire, because of the periodic boundary conditions, you simulate an infinite one. If the nanowire is aligned along Z axis, which seems to be your case,? then you have periodicity along the Z-direction. Therefore you need to? have enough vacuum along the x & y direction so that the periodic images should not interact. Prasenjit. 2009/4/20 ali kazempoor Dear all I want to study the fingerprint of reconstruction in nanowire facets. How can ?I find that wheater I have surface reconstruction or not? Should I make a bigger supercell in Z direction( Z is the lenght of nanowire)? thanks Ali Kazempour.Isfahan University of Technology,Iran _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- PRASENJIT GHOSH, POST-DOC, ROOM NO: 265, MAIN BUILDING, CM SECTION, ICTP, STRADA COSTERIA 11, TRIESTE, 34104, ITALY PHONE: +39 040 2240 369 (O) ? ? ? ? ? ? ?+39 3807528672 (M) -----Inline Attachment Follows----- _______________________________________________ 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/20090421/cfbed207/attachment-0001.htm From giannozz at democritos.it Tue Apr 21 21:04:44 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 21 Apr 2009 21:04:44 +0200 Subject: [Pw_forum] question for phonon calculation In-Reply-To: References: Message-ID: <1A6F8884-FD2D-4D31-84A5-63C148AFA4C3@democritos.it> On Apr 21, 2009, at 20:23 , ?? wrote: > I was going to calculating phonon frequency of MgB2 at Gamma point. > But I got the minus value at the lowest three branch. See items 1.7.2 and 1.7.3 of http://www.quantum-espresso.org/wiki/index.php/ Frequently_Asked_Questions plus a large number of postings (search for "negative phonon frequencies") > I also wonder how to apply 'asr' to my calculation code dynmat.x Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From prasenjit.jnc at gmail.com Tue Apr 21 21:11:50 2009 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Tue, 21 Apr 2009 21:11:50 +0200 Subject: [Pw_forum] reconstruction In-Reply-To: <946400.24485.qm@web33102.mail.mud.yahoo.com> References: <946400.24485.qm@web33102.mail.mud.yahoo.com> Message-ID: <627e0ffa0904211211q4487a9f7o39b14821a725ca44@mail.gmail.com> Dear Ali, It depends on the type of reconstruction the surface of the nanowire undergoes. May be if you tell a bit more about the type of reconstruction, I can tell you more. Prasenjit. 2009/4/21 ali kazempoor > Dear Prasenjit > Thank you for your reply, but I mean what I do to see the surface > reconstruction at lateral nanowire surface. For simulation of a nanowire in > z direction we add vaccum around nanowire in x and y and for z we use > periodic boundary condition . So if we only suppose one unit repetation in z > , we can not observe the surface reconstruction . Therefor for observing > reconstruction , I think we have to make for example twice unit repetation > in z or more. > thanks > > --- On *Tue, 4/21/09, Prasenjit Ghosh * wrote: > > > From: Prasenjit Ghosh > Subject: Re: [Pw_forum] reconstruction > To: "PWSCF Forum" > Date: Tuesday, April 21, 2009, 10:38 AM > > > Dear Ali, > > Usually when you speak of simulating a nanowire, because of the periodic > boundary conditions, you simulate an infinite one. If the nanowire is > aligned along Z axis, which seems to be your case, then you have > periodicity along the Z-direction. Therefore you need to have enough vacuum > along the x & y direction so that the periodic images should not interact. > > Prasenjit. > > 2009/4/20 ali kazempoor > > > >> >> Dear all >> I want to study the fingerprint of reconstruction in nanowire facets. How >> can I find that wheater I have surface reconstruction or not? Should I make >> a bigger supercell in Z direction( Z is the lenght of nanowire)? >> thanks >> Ali Kazempour.Isfahan University of Technology,Iran >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > PRASENJIT GHOSH, > POST-DOC, > ROOM NO: 265, MAIN BUILDING, > CM SECTION, ICTP, > STRADA COSTERIA 11, > TRIESTE, 34104, > ITALY > PHONE: +39 040 2240 369 (O) > +39 3807528672 (M) > > -----Inline Attachment Follows----- > > _______________________________________________ > 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 > > -- PRASENJIT GHOSH, POST-DOC, ROOM NO: 265, MAIN BUILDING, CM SECTION, ICTP, STRADA COSTERIA 11, TRIESTE, 34104, ITALY PHONE: +39 040 2240 369 (O) +39 3807528672 (M) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090421/59bd23ee/attachment.htm From marcel at physik.tu-berlin.de Tue Apr 21 21:24:23 2009 From: marcel at physik.tu-berlin.de (Marcel Mohr) Date: Tue, 21 Apr 2009 21:24:23 +0200 (CEST) Subject: [Pw_forum] reconstruction In-Reply-To: <627e0ffa0904211211q4487a9f7o39b14821a725ca44@mail.gmail.com> References: <946400.24485.qm@web33102.mail.mud.yahoo.com> <627e0ffa0904211211q4487a9f7o39b14821a725ca44@mail.gmail.com> Message-ID: Dear Ali You can start with (lateral) surface reconstruction of your bulk system. Afterwards I would try different supercells with different starting points, like number of atoms or "surface molecules". Don't forget to saturate dangling bonds (even there you can check different types). I think in Si NWs even a SiH3 group is outermost for some NWs After relaxing your structures you can check the most favorable ones by comparing energies (have a look at surface calculations for details). Good luck Marcel Mohr -- Institut f?r Festk?rperphysik TU Berlin On Tue, 21 Apr 2009, Prasenjit Ghosh wrote: > Dear Ali, > > It depends on the type of reconstruction the surface of the nanowire undergoes.? May be if you tell a bit more about the type of reconstruction, I > can tell you more. > > Prasenjit. > > 2009/4/21 ali kazempoor > Dear Prasenjit > Thank you for your reply, but I mean what I do to see the surface reconstruction at lateral nanowire surface. For simulation of a nanowire > in z direction we add vaccum around nanowire in x and y and for z we use periodic boundary condition . So if we only suppose one unit > repetation in z , we can not observe the surface reconstruction . Therefor for observing reconstruction , I think we have to make for > example twice unit repetation in z or more. > thanks > > --- On Tue, 4/21/09, Prasenjit Ghosh wrote: > > From: Prasenjit Ghosh > Subject: Re: [Pw_forum] reconstruction > To: "PWSCF Forum" > Date: Tuesday, April 21, 2009, 10:38 AM > > > Dear Ali, > > Usually when you speak of simulating a nanowire, because of the periodic boundary conditions, you simulate an infinite one. If the > nanowire is aligned along Z axis, which seems to be your case,? then you have periodicity along the Z-direction. Therefore you need > to? have enough vacuum along the x & y direction so that the periodic images should not interact. > > Prasenjit. > > 2009/4/20 ali kazempoor > > Dear all > I want to study the fingerprint of reconstruction in nanowire facets. How can ?I find that wheater I have surface > reconstruction or not? Should I make a bigger supercell in Z direction( Z is the lenght of nanowire)? > thanks > Ali Kazempour.Isfahan University of Technology,Iran > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > PRASENJIT GHOSH, > POST-DOC, > ROOM NO: 265, MAIN BUILDING, > CM SECTION, ICTP, > STRADA COSTERIA 11, > TRIESTE, 34104, > ITALY > PHONE: +39 040 2240 369 (O) > ? ? ? ? ? ? ?+39 3807528672 (M) > > -----Inline Attachment Follows----- > > _______________________________________________ > 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 > > > > > -- > PRASENJIT GHOSH, > POST-DOC, > ROOM NO: 265, MAIN BUILDING, > CM SECTION, ICTP, > STRADA COSTERIA 11, > TRIESTE, 34104, > ITALY > PHONE: +39 040 2240 369 (O) > ? ? ? ? ? ? ?+39 3807528672 (M) > > From eyvaz_isaev at yahoo.com Tue Apr 21 21:38:57 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 21 Apr 2009 12:38:57 -0700 (PDT) Subject: [Pw_forum] question for phonon calculation In-Reply-To: Message-ID: <309636.18892.qm@web65709.mail.ac4.yahoo.com> Hi, > But I got the minus value at the lowest three branch. > how to avoid the minus values Here you are incorrect, you got imaginary frequences. 5 years ago I did such kind calculations for MgB2 using my own PBE US pseudopotentials and met no problem. As far as know phonons are sensitive to parameters used to generate. Most likely, you can ignore these frequences, as applying ASR will correct them. As concerns how to apply ASR, just use matdyn.x in QE/PH or QE/bin (with keyword asr='crystal') file to generate phonon dispersion relations with correct acoustic modes at Gamma point. See example file /examples/example06. > tr2_ph=1.0d-25 Looks extremly low. As 1.d-10 is default, the use of d-12 or d-14 should be sufficient. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Tue, 4/21/09, ?? wrote: > From: ?? > Subject: [Pw_forum] question for phonon calculation > To: "pw forum" > Date: Tuesday, April 21, 2009, 10:23 PM > Dear All Users, > > I was going to calculating phonon frequency of MgB2 at > Gamma point.But I got > the minus value at the lowest three branch. > > q = ( 0.000000000 0.000000000 0.000000000 ) > > > ************************************************************************** > omega( 1) = -1.333147 [THz] = -44.469304 > [cm-1] > omega( 2) = -1.333147 [THz] = -44.469304 > [cm-1] > omega( 3) = -1.003834 [THz] = -33.484515 > [cm-1] > omega( 4) = 9.706117 [THz] = 323.763351 > [cm-1] > omega( 5) = 9.706117 [THz] = 323.763351 > [cm-1] > omega( 6) = 11.666010 [THz] = 389.138778 > [cm-1] > omega( 7) = 15.807885 [THz] = 527.297796 > [cm-1] > omega( 8) = 15.807885 [THz] = 527.297796 > [cm-1] > omega( 9) = 20.623897 [THz] = 687.943739 > [cm-1] > > ************************************************************************** > > I had already relax the lattice.And below is my inputs for > scf and phonon > calculation.Any suggest and comments on how to avoid the > minus values was > appreciated. > > scf.in > &control > calculation = 'scf' > restart_mode='from_scratch' > prefix='MgB2', > pseudo_dir = > '//Quantum-Espresso/espresso-4.0.3/pseudo/', > outdir='/tmp/' > / > &system > ibrav=4, > celldm(1)=5.8398, > celldm(3)=1.1420, > nat=3, > ntyp=2, > ecutwfc = 45.0, > ecutrho = 450.0, > occupations= 'smearing', > degauss= 0.03, > smearing= 'cold', > / > &electrons > mixing_beta = 0.7 > conv_thr = 1.0d-12 > / > ATOMIC_SPECIES > Mg 24.3 Mg.pw91-np-van.UPF > B 10.8 B.pw91-n-van.UPF > ATOMIC_POSITIONS > Mg 0 0 0 > B 0 0.57735 0.571 > B 0.5 0.28868 0.571 > K_POINTS {automatic} > 32 32 32 0 0 0 > > ph.in > > MgB2 > &inputph > amass(1)= 24.3, > amass(2)= 10.8, > prefix='MgB2' > tr2_ph=1.0d-25, > alpha_mix(1)=0.5, > iverbosity=1, > outdir='//tmp/', > / > 0 0 0 > > I also wonder how to apply 'asr' to my > calculation.I could not find any > option for ph.x. > > Have a nice day! > > Deng Pan > Nanjing University > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From eyvaz_isaev at yahoo.com Wed Apr 22 00:29:02 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 21 Apr 2009 15:29:02 -0700 (PDT) Subject: [Pw_forum] question for phonon calculation In-Reply-To: <309636.18892.qm@web65709.mail.ac4.yahoo.com> Message-ID: <372647.21149.qm@web65705.mail.ac4.yahoo.com> > parameters used to generate. Sorry, it should be "to generate a pseudopotential". Bests, Eyvaz. --- On Tue, 4/21/09, Eyvaz Isaev wrote: > From: Eyvaz Isaev > Subject: Re: [Pw_forum] question for phonon calculation > To: "PWSCF Forum" > Date: Tuesday, April 21, 2009, 11:38 PM > Hi, > > > But I got the minus value at the lowest three branch. > > > how to avoid the minus values > > Here you are incorrect, you got imaginary frequences. > > 5 years ago I did such kind calculations for MgB2 using my > own PBE US pseudopotentials and met no problem. As far as > know phonons are sensitive to parameters used to generate. > Most likely, you can ignore these frequences, as applying > ASR will correct them. As concerns how to apply ASR, just > use matdyn.x in QE/PH or QE/bin (with keyword > asr='crystal') file to generate phonon dispersion > relations with correct acoustic modes at Gamma point. See > example file /examples/example06. > > > tr2_ph=1.0d-25 > Looks extremly low. As 1.d-10 is default, the use of d-12 > or d-14 should be sufficient. > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of > Steel & Alloys, Russia, > Department of Physics, Chemistry, and Biology (IFM), > Linkoping University, Sweden > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, > eyvaz_isaev at yahoo.com > > > --- On Tue, 4/21/09, ?? > wrote: > > > From: ?? > > Subject: [Pw_forum] question for phonon calculation > > To: "pw forum" > > Date: Tuesday, April 21, 2009, 10:23 PM > > Dear All Users, > > > > I was going to calculating phonon frequency of MgB2 at > > Gamma point.But I got > > the minus value at the lowest three branch. > > > > q = ( 0.000000000 0.000000000 0.000000000 > ) > > > > > > > ************************************************************************** > > omega( 1) = -1.333147 [THz] = -44.469304 > > [cm-1] > > omega( 2) = -1.333147 [THz] = -44.469304 > > [cm-1] > > omega( 3) = -1.003834 [THz] = -33.484515 > > [cm-1] > > omega( 4) = 9.706117 [THz] = 323.763351 > > [cm-1] > > omega( 5) = 9.706117 [THz] = 323.763351 > > [cm-1] > > omega( 6) = 11.666010 [THz] = 389.138778 > > [cm-1] > > omega( 7) = 15.807885 [THz] = 527.297796 > > [cm-1] > > omega( 8) = 15.807885 [THz] = 527.297796 > > [cm-1] > > omega( 9) = 20.623897 [THz] = 687.943739 > > [cm-1] > > > > > ************************************************************************** > > > > I had already relax the lattice.And below is my inputs > for > > scf and phonon > > calculation.Any suggest and comments on how to avoid > the > > minus values was > > appreciated. > > > > scf.in > > &control > > calculation = 'scf' > > restart_mode='from_scratch' > > prefix='MgB2', > > pseudo_dir = > > '//Quantum-Espresso/espresso-4.0.3/pseudo/', > > outdir='/tmp/' > > / > > &system > > ibrav=4, > > celldm(1)=5.8398, > > celldm(3)=1.1420, > > nat=3, > > ntyp=2, > > ecutwfc = 45.0, > > ecutrho = 450.0, > > occupations= 'smearing', > > degauss= 0.03, > > smearing= 'cold', > > / > > &electrons > > mixing_beta = 0.7 > > conv_thr = 1.0d-12 > > / > > ATOMIC_SPECIES > > Mg 24.3 Mg.pw91-np-van.UPF > > B 10.8 B.pw91-n-van.UPF > > ATOMIC_POSITIONS > > Mg 0 0 0 > > B 0 0.57735 0.571 > > B 0.5 0.28868 0.571 > > K_POINTS {automatic} > > 32 32 32 0 0 0 > > > > ph.in > > > > MgB2 > > &inputph > > amass(1)= 24.3, > > amass(2)= 10.8, > > prefix='MgB2' > > tr2_ph=1.0d-25, > > alpha_mix(1)=0.5, > > iverbosity=1, > > outdir='//tmp/', > > / > > 0 0 0 > > > > I also wonder how to apply 'asr' to my > > calculation.I could not find any > > option for ph.x. > > > > Have a nice day! > > > > Deng Pan > > Nanjing University > > _______________________________________________ > > 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 daijiayu at nudt.edu.cn Wed Apr 22 04:02:28 2009 From: daijiayu at nudt.edu.cn (Jiayu Dai) Date: Wed, 22 Apr 2009 10:02:28 +0800 Subject: [Pw_forum] Fermi energy in doped material. Message-ID: <440365748.04744@nudt.edu.cn> Dear all, As we know, the fermi energy of semiconductor can be placed anywhere in the band gap. For intinsic semiconductor, the calculation using pw.x is in agreement with it. But for doped semiconductor, for example, heavily doped semiconductor, the fermi energy should shift into the conduction band or valence band(depend on the type of doping), but the gap is always there. So, the question is: How could we know the heavily doped semiconductor is a metal or semiconductor? Or, the fermi energy calculated is not appropriate in this case? Thanks a lot. ------------------------------ Jiayu Dai National University of Defense Technology, P R China From manoj at phys.ufl.edu Wed Apr 22 05:44:30 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Tue, 21 Apr 2009 23:44:30 -0400 (EDT) Subject: [Pw_forum] PWCOND Message-ID: Dear PWSCF users, I have a question regarding real band structure calculated from PWCOND. Complex band code requires kx,ky and E as input and gives kz as output. I have noticed that the answer for kz depends whether you have unit cell vectors as (a1,a2,a3) or (a1,a2,-a3). I did a calculation for Cu(001) with 2 atoms tetragonal unit cell, with the following input file - & control calculation='scf' pseudo_dir = '/home/manoj/espresso-4.0.1/pseudo', outdir='./', prefix='cu', / &system ibrav = 0, celldm(1)=4.7588286373854648 nat= 2, ntyp= 1, ecutwfc =150.0, occupations='smearing', smearing='gaussian', degauss=0.02, ecutrho=400 / &electrons conv_thr = 1.0e-8 mixing_beta=0.7 / ATOMIC_SPECIES Cu 63.55 Cu.pz-d-rrkjus.UPF ATOMIC_POSITIONS Cu 0.0 0.0 0.0 Cu 0.5 0.5 0.707106781 K_POINTS (automatic) 8 8 8 1 1 1 CELL_PARAMETERS 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.414213562 &inputcond outdir='./' prefixl='cu' band_file ='bands.cu' ikind=0 energy0=2.d0 denergy=-0.5 ewind=104.d0 epsproj=1.d-6 / 1 0.0 0.0 1.0 24 This gives me reasonable answer and it matches up with existing results. Now when I changed a3 to -a3, so that the unit cell now has become (a1,a2,-a3), the answer does not match up with the previous one. Just to give you one concrete example- at Fermi energy for kx,ky (0,0) for unit cell (a1,a2,a3) we get kz=-0.1571 while for (a1,a2,-a3) we get kz=0.07323. I understand that for two different set of unit cell vectors we should not in general expect k_z to match, but this is a very special example, as it is just mirror symmetry about xy plane. so shouldn't kz in one set have value -kz in other? Thanks for your attention. Regards, Manoj Srivastava Department of Physics University of Florida Gainesville, FL From kyin.cn at gmail.com Wed Apr 22 08:33:08 2009 From: kyin.cn at gmail.com (Kun Yin) Date: Wed, 22 Apr 2009 14:33:08 +0800 Subject: [Pw_forum] improper symmetry analysis Message-ID: <89E86BC3D8E24EC99E71E72CB70118B2@workhorse> Dear Users and Developers: I met a weird phenomenon when calculating with a fcc crystal (sg. Fd-3m). I used the same crystal structure. The only difference among the input files is the value of parameter celldm(1). The crystal symmetries recognized by pw.x are not consistent. There are also some warnings like "symmetry operation # not allowed" in the head of the output files. Below is part of my shell script including input file: primitive_volumes="1056.5261 1009.8683 972.0540 940.4584 913.4519 889.9579 869.2306 850.7331 834.0674" i=0; for v in $primitive_volumes; do a=`echo 'scale=6; e(l('$v'*0.5)/3.0)' | bc -l` i=`expr $i + 1` cat > temp.in << EOF &control calculation = 'relax' restart_mode='from_scratch', prefix='temp', tprnfor = .true. pseudo_dir = '$PSEUDO_DIR' outdir = '$TMP_DIR' / &system ibrav = 0, celldm(1)=$a, nat = 14, ntyp = 3, ecutwfc = 45.0, ecutrho = 450.0 / &electrons conv_thr = 1.0d-8 / &ions ion_dynamics='bfgs' / ATOMIC_SPECIES Mg 24.305 Mg.pw91-np-van.UPF Al 26.9815 Al.pw91-n-van.UPF O 15.9994 O.pw91-van_ak.UPF K_POINTS automatic 6 6 6 0 0 0 CELL_PARAMETERS cubic 1.0 1.0 0.0 1.0 -1.0 0.0 1.0 0.0 1.0 ATOMIC_POSITIONS crystal Mg 0.12500000 0.87500000 0.25000000 Mg 0.87500000 0.12500000 0.75000000 Al 0.50000000 0.50000000 0.00000000 Al 0.50000000 0.00000000 0.50000000 Al 0.00000000 0.50000000 0.00000000 Al 0.50000000 0.50000000 0.50000000 O 0.26230000 0.73770000 0.52460000 O 0.73770000 0.26230000 0.47540000 O 0.73770000 0.71310000 0.02460000 O 0.26230000 0.28690000 0.97540000 O 0.71310000 0.73770000 0.52460000 O 0.28690000 0.26230000 0.47540000 O 0.73770000 0.26230000 0.02460000 O 0.26230000 0.73770000 0.97540000 EOF Check symmetry operations in output files (grep 'Sym.Ops' *.out): temp-1.out: 48 Sym.Ops. (with inversion) temp-2.out: 48 Sym.Ops. (with inversion) temp-3.out: 48 Sym.Ops. (with inversion) temp-4.out: 12 Sym.Ops. (with inversion) temp-5.out: 12 Sym.Ops. (with inversion) temp-6.out: 12 Sym.Ops. (with inversion) temp-7.out: 12 Sym.Ops. (with inversion) temp-8.out: 48 Sym.Ops. (with inversion) temp-9.out: 48 Sym.Ops. (with inversion) I think the correct symmetry operations number should be 48 for this crystal. I don't know how to fix this "improper symmetry analysis" problem. Can you help me? -- Kun Yin Ph.D. Candidate School of Earth Sciences and Engineering Nanjing University 502 Geological Laboratory Building 22 Hankou Road Nanjing 210093 P.R. China email: kyin.cn at gmail.com From giannozz at democritos.it Wed Apr 22 08:46:35 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 22 Apr 2009 08:46:35 +0200 Subject: [Pw_forum] improper symmetry analysis In-Reply-To: <89E86BC3D8E24EC99E71E72CB70118B2@workhorse> References: <89E86BC3D8E24EC99E71E72CB70118B2@workhorse> Message-ID: <0D7D213B-AF56-4619-B957-707CDD7B27E5@democritos.it> On Apr 22, 2009, at 8:33 , Kun Yin wrote: > I don't know how to fix this "improper symmetry analysis" problem. > Can you help me? item 1.22 of the Troubleshooting section of the user guide --- Paolo Giannozzi, Democritos and University of Udine, Italy From smogunov at sissa.it Wed Apr 22 09:18:55 2009 From: smogunov at sissa.it (Alexander Smogunov) Date: Wed, 22 Apr 2009 09:18:55 +0200 Subject: [Pw_forum] PWCOND In-Reply-To: References: Message-ID: <1240384735.5942.3.camel@alex-laptop> Dear Manoj. The pwcond code was written assuming that the unit cell starts at z=0 and goes in positive z direction, the direction of transport. Quite probable that when you invert the cell it does not work properly... Alexander ? ???, 21/04/2009 ? 23:44 -0400, Manoj Srivastava ?????: > Dear PWSCF users, > I have a question regarding real band structure calculated from > PWCOND. Complex band code requires kx,ky and E as input and gives kz > as output. I have noticed that the answer for kz depends whether you have > unit cell vectors as (a1,a2,a3) or (a1,a2,-a3). I did a calculation for > Cu(001) with 2 atoms tetragonal unit cell, with the following input file - > > & control > calculation='scf' > pseudo_dir = '/home/manoj/espresso-4.0.1/pseudo', > outdir='./', > prefix='cu', > / > &system > ibrav = 0, > celldm(1)=4.7588286373854648 > nat= 2, > ntyp= 1, > ecutwfc =150.0, > occupations='smearing', > smearing='gaussian', > degauss=0.02, > ecutrho=400 > / > &electrons > conv_thr = 1.0e-8 > mixing_beta=0.7 > / > ATOMIC_SPECIES > Cu 63.55 Cu.pz-d-rrkjus.UPF > ATOMIC_POSITIONS > Cu 0.0 0.0 0.0 > Cu 0.5 0.5 0.707106781 > K_POINTS (automatic) > 8 8 8 1 1 1 > CELL_PARAMETERS > 1.0 0.0 0.0 > 0.0 1.0 0.0 > 0.0 0.0 1.414213562 > > &inputcond > outdir='./' > prefixl='cu' > band_file ='bands.cu' > ikind=0 > energy0=2.d0 > denergy=-0.5 > ewind=104.d0 > epsproj=1.d-6 > / > 1 > 0.0 0.0 1.0 > 24 > > This gives me reasonable answer and it matches up with existing results. > Now when I changed a3 to -a3, so that the unit cell now has become > (a1,a2,-a3), the answer does not match up with the previous one. > Just to give you one concrete example- > at Fermi energy for kx,ky (0,0) for unit cell (a1,a2,a3) we get kz=-0.1571 > while for (a1,a2,-a3) we get kz=0.07323. > I understand that for two different set of unit cell vectors we should not > in general expect k_z to match, but this is a very special example, as it > is just mirror symmetry about xy plane. so shouldn't kz in one set have > value -kz in other? > Thanks for your attention. > > Regards, > 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 -- Alexander Smogunov Email: smogunov at sissa.it Home page: http://people.sissa.it/~smogunov From kyin.cn at gmail.com Wed Apr 22 09:33:32 2009 From: kyin.cn at gmail.com (Kun Yin) Date: Wed, 22 Apr 2009 15:33:32 +0800 Subject: [Pw_forum] improper symmetry analysis References: <89E86BC3D8E24EC99E71E72CB70118B2@workhorse> <0D7D213B-AF56-4619-B957-707CDD7B27E5@democritos.it> Message-ID: <1F4283CD06DB45B887393FA4369CAE91@workhorse> Thank you, Paolo. I have read 17.22 and 17.24 sections of user guide. I think the problem of my calculations arises from "they contain a fractional translation that is incompatible with the FFT grid" since they change in unit cell volume. As a consquence, they do have different number of k points. [kyin at geohpclab results]$ grep 'number of k points=' *.out temp-1.out: number of k points= 16 temp-2.out: number of k points= 16 temp-3.out: number of k points= 16 temp-4.out: number of k points= 32 temp-5.out: number of k points= 32 temp-6.out: number of k points= 32 temp-7.out: number of k points= 32 temp-8.out: number of k points= 16 temp-9.out: number of k points= 16 I think this missing of symmetries will not affect calculation of groud state energy. But if I use this scf calculation results to do phonon calculations, can I get correct phonon band assignment? -- Kun Yin Ph.D. Candidate School of Earth Sciences and Engineering Nanjing University 502 Geological Laboratory Building 22 Hankou Road Nanjing 210093 P.R. China email: kyin.cn at gmail.com ----- Original Message ----- From: "Paolo Giannozzi" To: "PWSCF Forum" Sent: Wednesday, April 22, 2009 2:46 PM Subject: Re: [Pw_forum] improper symmetry analysis > > On Apr 22, 2009, at 8:33 , Kun Yin wrote: > >> I don't know how to fix this "improper symmetry analysis" problem. >> Can you help me? > > item 1.22 of the Troubleshooting section of the user guide > > --- > 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 From giannozz at democritos.it Wed Apr 22 09:39:29 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 22 Apr 2009 09:39:29 +0200 Subject: [Pw_forum] improper symmetry analysis In-Reply-To: <1F4283CD06DB45B887393FA4369CAE91@workhorse> References: <89E86BC3D8E24EC99E71E72CB70118B2@workhorse> <0D7D213B-AF56-4619-B957-707CDD7B27E5@democritos.it> <1F4283CD06DB45B887393FA4369CAE91@workhorse> Message-ID: <49EEC9B1.6060407@democritos.it> Kun Yin wrote: > "they contain a fractional translation that is incompatible with the FFT grid" you can force the FFT grid to values that are compatible with fractional translations, if you really need to > I think this missing of symmetries will not affect calculation of groud > state energy. it doesn't > But if I use this scf calculation results to do phonon > calculations, can I get correct phonon band assignment? you get a phonon band assignment that is be correct for the symmetry the code has found Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From paulatto at sissa.it Wed Apr 22 09:41:50 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 22 Apr 2009 09:41:50 +0200 Subject: [Pw_forum] improper symmetry analysis In-Reply-To: <1F4283CD06DB45B887393FA4369CAE91@workhorse> References: <89E86BC3D8E24EC99E71E72CB70118B2@workhorse> <0D7D213B-AF56-4619-B957-707CDD7B27E5@democritos.it> <1F4283CD06DB45B887393FA4369CAE91@workhorse> Message-ID: 22 aprile 2009 alle ore 09:33:32, Kun Yin ha scritto: > I think this missing of symmetries will not affect calculation of groud > state energy. But if I use this scf calculation results to do phonon > calculations, can I get correct phonon band assignment? Dear Kun Yin, just manually specify the dimension of the FFT grid along the direction where the symmetry operation is lost, it is printed in output in this form: G cutoff = 84.7099 ( 32329 G-vectors) FFT grid: ( 20, 20,216) or, if you have, ecutrho > 4*ecutwfc in the following form: G cutoff = 677.6793 ( 365691 G-vectors) FFT grid: ( 54, 54,300) G cutoff = 338.8396 ( 129571 G-vectors) smooth grid: ( 40, 40,216) just make sure that the dimensions of the grids are multiple of the numbers of replicas in the fractional traslation. Where they are not, you can specify them manually using the system-namelist keywords nr1, nr2 and nr3 for the FFT grid; and nr1s, nr2s and nr3s for the smooth grid. You should not decrease them from their default value, but only increase them! regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From giannozz at democritos.it Wed Apr 22 09:45:05 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 22 Apr 2009 09:45:05 +0200 Subject: [Pw_forum] improper symmetry analysis In-Reply-To: References: <89E86BC3D8E24EC99E71E72CB70118B2@workhorse> <0D7D213B-AF56-4619-B957-707CDD7B27E5@democritos.it> <1F4283CD06DB45B887393FA4369CAE91@workhorse> Message-ID: <49EECB01.8000005@democritos.it> Lorenzo Paulatto wrote: > You should not decrease them from their default value, but only increase them! actually the default should be slightly overestimated, so one can try to decrease it a little bit P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From madhura at jncasr.ac.in Wed Apr 22 10:30:45 2009 From: madhura at jncasr.ac.in (Madhura Marathe) Date: Wed, 22 Apr 2009 14:00:45 +0530 (IST) Subject: [Pw_forum] conv_thr for forces for relaxing ions Message-ID: <55694.134.105.55.77.1240389045.squirrel@134.105.55.77> Dear all, During one of the ionic relaxation calculations, I got the error message, "SCF correction compared to forces is too large, reduce conv_thr". I am using conv_thr = 1.0d-8 which is generally sufficient, so I increased the parameter upscale (from 10.0 to 100.0) in &IONS to reduce the the threshold during relaxation. This lead to the convergence till the last ionic iteration which was converged to sufficient accuracy, when again the same error message occurred. The forces then are Total force = 0.000136 Total SCF correction = 0.000016 SCF correction compared to forces is too large, reduce conv_thr There has been a recent discussion on the topic. From that, I gathered that the subsequent relaxations after this error message are not reliable. So my question is whether the forces are reliable in this last iteration? Or do I need to further reduce the conv_thr and re-run the whole calculation? Thanks for the help, Madhura. -- Madhura Marathe, PhD student, TSU, JNCASR, Bangalore. India. Phone No: +91-80-22082835 From kyin.cn at gmail.com Wed Apr 22 10:17:02 2009 From: kyin.cn at gmail.com (Kun Yin) Date: Wed, 22 Apr 2009 16:17:02 +0800 Subject: [Pw_forum] improper symmetry analysis References: <89E86BC3D8E24EC99E71E72CB70118B2@workhorse> <0D7D213B-AF56-4619-B957-707CDD7B27E5@democritos.it> <1F4283CD06DB45B887393FA4369CAE91@workhorse> <49EECB01.8000005@democritos.it> Message-ID: Thank you for your answers, Paolo and Lorenzo. First time to know using nr1,nr2,nr3 and nr1s,nr2s,nr3s keywords.^_^ Lorenzo wrote: > "just make sure that the dimensions of the grids are multiple of the > numbers of replicas in the fractional traslation." I don't quite understand this sentence. Just try to increase and decrease default nr and nrs values as suggested. There are total 9 calculations, 1-3 and 8-0 find symmetry right, 4-7 find symmetry wrong. [kyin at geohpclab results]$ grep 'FFT grid:' *.out temp-1.out: G cutoff = 744.8786 ( 170271 G-vectors) FFT grid: ( 80, 80, 80) temp-2.out: G cutoff = 722.7847 ( 162825 G-vectors) FFT grid: ( 80, 80, 80) temp-3.out: G cutoff = 704.6276 ( 156325 G-vectors) FFT grid: ( 80, 80, 80) temp-4.out: G cutoff = 689.2743 ( 151669 G-vectors) FFT grid: ( 75, 75, 75) temp-5.out: G cutoff = 676.0151 ( 147349 G-vectors) FFT grid: ( 75, 75, 75) temp-6.out: G cutoff = 664.3728 ( 143471 G-vectors) FFT grid: ( 75, 75, 75) temp-7.out: G cutoff = 654.0170 ( 140255 G-vectors) FFT grid: ( 75, 75, 75) temp-8.out: G cutoff = 644.7053 ( 136787 G-vectors) FFT grid: ( 72, 72, 72) temp-9.out: G cutoff = 636.2575 ( 134435 G-vectors) FFT grid: ( 72, 72, 72) [kyin at geohpclab results]$ grep 'smooth grid:' *.out temp-1.out: G cutoff = 297.9514 ( 43143 G-vectors) smooth grid: ( 50, 50, 50) temp-2.out: G cutoff = 289.1139 ( 41151 G-vectors) smooth grid: ( 50, 50, 50) temp-3.out: G cutoff = 281.8510 ( 39597 G-vectors) smooth grid: ( 48, 48, 48) temp-4.out: G cutoff = 275.7097 ( 38421 G-vectors) smooth grid: ( 48, 48, 48) temp-5.out: G cutoff = 270.4060 ( 37309 G-vectors) smooth grid: ( 48, 48, 48) temp-6.out: G cutoff = 265.7491 ( 36085 G-vectors) smooth grid: ( 48, 48, 48) temp-7.out: G cutoff = 261.6068 ( 35557 G-vectors) smooth grid: ( 45, 45, 45) temp-8.out: G cutoff = 257.8821 ( 34621 G-vectors) smooth grid: ( 45, 45, 45) temp-9.out: G cutoff = 254.5030 ( 34015 G-vectors) smooth grid: ( 45, 45, 45) For No. 5 calculation, defulat value is 75 and 48. I set nr1=nr2=nr3=80, nr1s=nr2s=nr3s=50. It finds symmetry right! when I decrease to nr1=nr2=nr3=72, nr1s=nr2s=nr3s=45. It reports error and crash. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 1 from fft_dlay_set : error # 8 inconsistent number of sticks %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%--Kun YinPh.D. CandidateSchool of Earth Sciences and EngineeringNanjing University502 Geological Laboratory Building22 Hankou RoadNanjing 210093P.R. Chinaemail: kyin.cn at gmail.com----- Original Message -----From: "Paolo Giannozzi" To: "PWSCF Forum" Sent: Wednesday, April 22, 2009 3:45 PMSubject: Re: [Pw_forum] improper symmetry analysis> Lorenzo Paulatto wrote:>>> You should not decrease them from their default value, but only increasethem!>> actually the default should be slightly overestimated, so one can try to> decrease it a little bit>> 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 From degironc at sissa.it Wed Apr 22 10:23:27 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 22 Apr 2009 10:23:27 +0200 Subject: [Pw_forum] conv_thr for forces for relaxing ions In-Reply-To: <55694.134.105.55.77.1240389045.squirrel@134.105.55.77> References: <55694.134.105.55.77.1240389045.squirrel@134.105.55.77> Message-ID: <49EED3FF.7010202@sissa.it> In PWscf the forces are calculated from the Hellman-Feynman theorem (strictly true only at the stationary point) plus a correction that (approximately) accounts for the residual lack of self-consistency. As such when the correction is large compared to the Hellman-Feynman term one should be careful. In your case I would say that the forces are now probably very small and therefore the structure is reliable. I would say that the actual (small) value for the force are probably correct within a few percent since the correction term is (according to the value quote) of the order of 10 % of the total (and hopefully is not completely wrong). Hope this helps, stefano de Gironcoli -SISSA and DEMOCRITOS Madhura Marathe wrote: > Dear all, > > During one of the ionic relaxation calculations, I got the error message, > "SCF correction compared to forces is too large, reduce conv_thr". I am > using conv_thr = 1.0d-8 which is generally sufficient, so I increased the > parameter upscale (from 10.0 to 100.0) in &IONS to reduce the the > threshold during relaxation. This lead to the convergence till the last > ionic iteration which was converged to sufficient accuracy, when again the > same error message occurred. The forces then are > Total force = 0.000136 Total SCF correction = 0.000016 > SCF correction compared to forces is too large, reduce conv_thr > > There has been a recent discussion on the topic. From that, I gathered > that the subsequent relaxations after this error message are not > reliable. > So my question is whether the forces are reliable in this last iteration? > Or do I need to further reduce the conv_thr and re-run the whole > calculation? > > Thanks for the help, > Madhura. > > From madhura at jncasr.ac.in Wed Apr 22 11:15:12 2009 From: madhura at jncasr.ac.in (Madhura Marathe) Date: Wed, 22 Apr 2009 14:45:12 +0530 (IST) Subject: [Pw_forum] conv_thr for forces for relaxing ions In-Reply-To: <49EED3FF.7010202@sissa.it> References: <55694.134.105.55.77.1240389045.squirrel@134.105.55.77> <49EED3FF.7010202@sissa.it> Message-ID: <54501.134.105.55.77.1240391712.squirrel@134.105.55.77> Dear Stefano, Thanks for the quick reply. This was really necessary to confirm since the calculations are expensive. And I am more interested in the ground state structure, may not use the actual value of the force for further analysis. Madhura. > In PWscf the forces are calculated from the Hellman-Feynman theorem > (strictly true only at the stationary point) plus a correction that > (approximately) accounts for the residual lack of self-consistency. As > such when the correction is large compared to the Hellman-Feynman term > one should be careful. > In your case I would say that the forces are now probably very small > and therefore the structure is reliable. > I would say that the actual (small) value for the force are probably > correct within a few percent since the correction term is (according to > the value quote) of the order of 10 % of the total (and hopefully is not > completely wrong). > Hope this helps, > stefano de Gironcoli -SISSA and DEMOCRITOS > > Madhura Marathe wrote: >> Dear all, >> >> During one of the ionic relaxation calculations, I got the error >> message, >> "SCF correction compared to forces is too large, reduce conv_thr". I am >> using conv_thr = 1.0d-8 which is generally sufficient, so I increased >> the >> parameter upscale (from 10.0 to 100.0) in &IONS to reduce the the >> threshold during relaxation. This lead to the convergence till the last >> ionic iteration which was converged to sufficient accuracy, when again >> the >> same error message occurred. The forces then are >> Total force = 0.000136 Total SCF correction = 0.000016 >> SCF correction compared to forces is too large, reduce conv_thr >> >> There has been a recent discussion on the topic. From that, I gathered >> that the subsequent relaxations after this error message are not >> reliable. >> So my question is whether the forces are reliable in this last >> iteration? >> Or do I need to further reduce the conv_thr and re-run the whole >> calculation? >> >> Thanks for the help, >> Madhura. >> >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Madhura Marathe, PhD student, TSU, JNCASR, Bangalore. India. Phone No: +91-80-22082835 From paulatto at sissa.it Wed Apr 22 11:41:33 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 22 Apr 2009 11:41:33 +0200 Subject: [Pw_forum] improper symmetry analysis In-Reply-To: References: <89E86BC3D8E24EC99E71E72CB70118B2@workhorse> <0D7D213B-AF56-4619-B957-707CDD7B27E5@democritos.it> <1F4283CD06DB45B887393FA4369CAE91@workhorse> <49EECB01.8000005@democritos.it> Message-ID: In data 22 aprile 2009 alle ore 10:17:02, Kun Yin ha scritto: > I don't quite understand this sentence. Just try to increase and decrease > default nr and nrs values as suggested. There are total 9 calculations, > 1-3 and 8-0 find symmetry right, 4-7 find symmetry wrong. There is no symmetry "right" and "wrong", in calculations 4-7 pw.x does not use certain symmetry operations because they are not compatible with the FFT grid, this will make the calculation a more expensive (as the reduced number of k-points is higher), but not wrong. Let's do some number theory: > temp-1.out: G cutoff = 744.8786 ( 170271 G-vectors) FFT grid: > ( 80, 80, 80) > temp-2.out: G cutoff = 722.7847 ( 162825 G-vectors) FFT grid: > ( 80, 80, 80) > temp-3.out: G cutoff = 704.6276 ( 156325 G-vectors) FFT grid: > ( 80, 80, 80) > temp-4.out: G cutoff = 689.2743 ( 151669 G-vectors) FFT grid: > ( 75, 75, 75) > temp-5.out: G cutoff = 676.0151 ( 147349 G-vectors) FFT grid: > ( 75, 75, 75) > temp-6.out: G cutoff = 664.3728 ( 143471 G-vectors) FFT grid: > ( 75, 75, 75) > temp-7.out: G cutoff = 654.0170 ( 140255 G-vectors) FFT grid: > ( 75, 75, 75) > temp-8.out: G cutoff = 644.7053 ( 136787 G-vectors) FFT grid: > ( 72, 72, 72) > temp-9.out: G cutoff = 636.2575 ( 134435 G-vectors) FFT grid: > ( 72, 72, 72) 80 = 2^4 * 5 75 = 3 * 5^2 72 = 2^3 * 3^2 In other words, when the size of you FFT grid is not a multiple of 2 a certain symmetry operation canot be represented properly. You should be able to guess which operation it is from your atomic positions configuration. If I remember correctly symmetry is applied only on the FFT grid, the dimensions of the smooth grid should not matter. > For No. 5 calculation, defulat value is 75 and 48. I set nr1=nr2=nr3=80, > nr1s=nr2s=nr3s=50. It finds symmetry right! As consequence of what said above. Setting nrX=80 and leaving nrXs to their default values should also work. > when I decrease to nr1=nr2=nr3=72, nr1s=nr2s=nr3s=45. It reports error > and crash. Likely they are too small with respect to what your cutoffs requires! regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From giannozz at democritos.it Wed Apr 22 12:12:22 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 22 Apr 2009 12:12:22 +0200 Subject: [Pw_forum] Fermi energy in doped material. In-Reply-To: <440365748.04744@nudt.edu.cn> References: <440365748.04744@nudt.edu.cn> Message-ID: <49EEED86.5050707@democritos.it> Jiayu Dai wrote: > How could we know the heavily doped semiconductor is a metal or semiconductor? > Or, the fermi energy calculated is not appropriate in this case? it depends on how "heavily" the semiconductor is doped. For doping in the order of a few %, you can use a supercell and everything will work. Realistic (i.e. order of magnitudes smaller) doping levels in semiconductors cannot be simulated in this way. You have to resort to phenomenological models in which the doping produces free charges and the Fermi energy determines how many of them. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From manoj at phys.ufl.edu Wed Apr 22 12:31:28 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Wed, 22 Apr 2009 06:31:28 -0400 (EDT) Subject: [Pw_forum] PWCOND In-Reply-To: <1240384735.5942.3.camel@alex-laptop> Message-ID: Dear Alexander, Thank you for your quick response. One follow up question on this. So, how do you describe your left and right leads, if they are different? If the leads are different then I need to do two calculations for the lead, one for each leads. They are semi-infinite, so periodicity in one is in +z direction and while in the other it is in -z direction. Regards, Manoj On Wed, 22 Apr 2009, Alexander Smogunov wrote: > Dear Manoj. The pwcond code was written assuming that the unit cell starts at z=0 and goes in positive z direction, the direction of transport. Quite probable that when you invert the cell it does not work properly... Alexander ?? ??????, 21/04/2009 ?? 23:44 -0400, Manoj Srivastava ??????????: > Dear PWSCF users, > I have a question regarding real band structure calculated from > PWCOND. Complex band code requires kx,ky and E as input and gives kz > as output. I have noticed that the answer for kz depends whether you have > unit cell vectors as (a1,a2,a3) or (a1,a2,-a3). I did a calculation for > Cu(001) with 2 atoms tetragonal unit cell, with the following input file - > > & control > calculation='scf' > pseudo_dir = '/home/manoj/espresso-4.0.1/pseudo', > outdir='./', > prefix='cu', > / > &system > ibrav = 0, > celldm(1)=4.7588286373854648 > nat= 2, > ntyp= 1, > ecutwfc =150.0, > occupations='smearing', > smearing='gaussian', > degauss=0.02, > ecutrho=400 > / > &electrons > conv_thr = 1.0e-8 > mixing_beta=0.7 > / > ATOMIC_SPECIES > Cu 63.55 Cu.pz-d-rrkjus.UPF > ATOMIC_POSITIONS > Cu 0.0 0.0 0.0 > Cu 0.5 0.5 0.707106781 > K_POINTS (automatic) > 8 8 8 1 1 1 > CELL_PARAMETERS > 1.0 0.0 0.0 > 0.0 1.0 0.0 > 0.0 0.0 1.414213562 > > &inputcond > outdir='./' > prefixl='cu' > band_file ='bands.cu' > ikind=0 > energy0=2.d0 > denergy=-0.5 > ewind=104.d0 > epsproj=1.d-6 > / > 1 > 0.0 0.0 1.0 > 24 > > This gives me reasonable answer and it matches up with existing results. > Now when I changed a3 to -a3, so that the unit cell now has become > (a1,a2,-a3), the answer does not match up with the previous one. > Just to give you one concrete example- > at Fermi energy for kx,ky (0,0) for unit cell (a1,a2,a3) we get kz=-0.1571 > while for (a1,a2,-a3) we get kz=0.07323. > I understand that for two different set of unit cell vectors we should not > in general expect k_z to match, but this is a very special example, as it > is just mirror symmetry about xy plane. so shouldn't kz in one set have > value -kz in other? > Thanks for your attention. > > Regards, > 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 -- Alexander Smogunov Email: smogunov at sissa.it Home page: http://people.sissa.it/~smogunov _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at democritos.it Wed Apr 22 12:34:13 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 22 Apr 2009 12:34:13 +0200 Subject: [Pw_forum] improper symmetry analysis In-Reply-To: References: <89E86BC3D8E24EC99E71E72CB70118B2@workhorse> <0D7D213B-AF56-4619-B957-707CDD7B27E5@democritos.it> <1F4283CD06DB45B887393FA4369CAE91@workhorse> <49EECB01.8000005@democritos.it> Message-ID: <49EEF2A5.3020606@democritos.it> Lorenzo Paulatto wrote: > If I remember correctly symmetry is applied only on the FFT grid, the > dimensions of the smooth grid should not matter. you remeber correctly, but actuyally there is no ]strong reason for such choice: the part of the charge density that has to be symmetrized is calculated in the smooth grid > Likely they are too small with respect to what your cutoffs requires! one can try to reduce a little bit the fft dimensions, but success is not guaranteed! anyway the code should loudly complain P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From smogunov at sissa.it Wed Apr 22 13:00:01 2009 From: smogunov at sissa.it (Alexander Smogunov) Date: Wed, 22 Apr 2009 13:00:01 +0200 Subject: [Pw_forum] PWCOND In-Reply-To: References: Message-ID: <1240398001.5942.19.camel@alex-laptop> The leads are semi-infinite in the scattering problem set-up when they are connected by a scattering region. To find the scattering states you need the generalised Bloch states in the parts of leads (their unit cells) adjacent to the scattering region. These you calculate from INFINITE leads taking the unit cell ... You can have a look at my home page (still very draft), where there are some notes and examples in pwcond section. Alexander. ? ???, 22/04/2009 ? 06:31 -0400, Manoj Srivastava ?????: > Dear Alexander, > Thank you for your quick response. One follow up question on this. So, > how do you describe your left and right leads, if they are different? If > the leads are different then I need to do two calculations for the lead, > one for each leads. They are semi-infinite, so periodicity in one is in +z > direction and while in the other it is in -z direction. > > Regards, > Manoj > > > On > Wed, 22 Apr 2009, Alexander Smogunov wrote: > > > Dear Manoj. > The pwcond code was written assuming that the unit cell > starts at z=0 and goes in positive z direction, the direction > of transport. Quite probable that when you invert the > cell it does not work properly... > Alexander > > > ? ???, 21/04/2009 ? 23:44 -0400, Manoj Srivastava ?????: > > Dear PWSCF users, > > I have a question regarding real band structure calculated from > > PWCOND. Complex band code requires kx,ky and E as input and gives kz > > as output. I have noticed that the answer for kz depends whether you have > > unit cell vectors as (a1,a2,a3) or (a1,a2,-a3). I did a calculation for > > Cu(001) with 2 atoms tetragonal unit cell, with the following input file - > > > > & control > > calculation='scf' > > pseudo_dir = '/home/manoj/espresso-4.0.1/pseudo', > > outdir='./', > > prefix='cu', > > / > > &system > > ibrav = 0, > > celldm(1)=4.7588286373854648 > > nat= 2, > > ntyp= 1, > > ecutwfc =150.0, > > occupations='smearing', > > smearing='gaussian', > > degauss=0.02, > > ecutrho=400 > > / > > &electrons > > conv_thr = 1.0e-8 > > mixing_beta=0.7 > > / > > ATOMIC_SPECIES > > Cu 63.55 Cu.pz-d-rrkjus.UPF > > ATOMIC_POSITIONS > > Cu 0.0 0.0 0.0 > > Cu 0.5 0.5 0.707106781 > > K_POINTS (automatic) > > 8 8 8 1 1 1 > > CELL_PARAMETERS > > 1.0 0.0 0.0 > > 0.0 1.0 0.0 > > 0.0 0.0 1.414213562 > > > > &inputcond > > outdir='./' > > prefixl='cu' > > band_file ='bands.cu' > > ikind=0 > > energy0=2.d0 > > denergy=-0.5 > > ewind=104.d0 > > epsproj=1.d-6 > > / > > 1 > > 0.0 0.0 1.0 > > 24 > > > > This gives me reasonable answer and it matches up with existing results. > > Now when I changed a3 to -a3, so that the unit cell now has become > > (a1,a2,-a3), the answer does not match up with the previous one. > > Just to give you one concrete example- > > at Fermi energy for kx,ky (0,0) for unit cell (a1,a2,a3) we get kz=-0.1571 > > while for (a1,a2,-a3) we get kz=0.07323. > > I understand that for two different set of unit cell vectors we should not > > in general expect k_z to match, but this is a very special example, as it > > is just mirror symmetry about xy plane. so shouldn't kz in one set have > > value -kz in other? > > Thanks for your attention. > > > > Regards, > > 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 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Alexander Smogunov Email: smogunov at sissa.it Home page: http://people.sissa.it/~smogunov From mambom1902 at yahoo.com Wed Apr 22 14:06:44 2009 From: mambom1902 at yahoo.com (loc duong ding) Date: Wed, 22 Apr 2009 05:06:44 -0700 (PDT) Subject: [Pw_forum] Work function of Carbon nanotube Message-ID: <361674.89706.qm@web38801.mail.mud.yahoo.com> Dear all, I try to calculate the work function of CNT. I follow all steps in the?work function example and no error in the calculation steps. I compare my result with?some papers and I see my results is smaller?and the?dependence of work function?in diameter is inverted. My results is 4.2, 3.8, 3.6 eV for (4,4), (5,5) and (6,6) tube. It looks strange. ? This?is my?input file: input_pw &CONTROL ????? calculation = 'scf', ????? prefix='CNT0404', ????? restart_mode = 'restart', ????? pseudo_dir ='./', ????? outdir='./' ????? tstress = .true. , ????? tprnfor = .true. , ????? nstep =? 100? , ????? etot_conv_thr = 1.0E-4 , ????? forc_conv_thr = 1.0D-3 , ????? dt = 20 , / &SYSTEM ????? ibrav= 0,? celldm(1) = 47.259, nat = 16, ntyp = 1, nspin=1, ????? ecutwfc =35, ecutrho = 210, occupations='smearing', degauss=0.0001, ????? starting_magnetization(1) = 0.0, ????? starting_magnetization(2) = 0.3, ????? starting_magnetization(3) = 0.5??? / &ELECTRONS ??? startingwfc = 'atomic' ??? mixing_mode = 'plain' ??? mixing_beta = 0.6 ??? conv_thr = 1.0e-6 ??? electron_maxstep= 150 / &IONS ??? upscale = 15 / &CELL ?? cell_dynamics = 'bfgs' , ?? press = 0.00 , ?? wmass =? 0.00150000? , / ATOMIC_SPECIES ?C? 12.011? C.pbe-rrkjus.UPF ATOMIC_POSITIONS {angstrom} C??? 6.553412225?? 2.494247153?? 0.724930481 C??? 6.384209537?? 3.189335516?? 1.955034374 C??? 4.921037485?? 4.725404700?? 0.724938769 C??? 5.532498571?? 4.353613294?? 1.955042803 C??? 1.264191320?? 3.317569203?? 0.724981489 C??? 3.495616015?? 4.948134701?? 0.724939100 C??? 2.800526187?? 4.779818582?? 1.955052266 C??? 1.043153150?? 1.891599899?? 0.724952105 C??? 1.212815843?? 1.196984732?? 1.955055225 C??? 1.636733754?? 3.927573140?? 1.955082857 C??? 2.673787862? -0.341212987?? 0.724950680 C??? 2.063329729?? 0.030888435?? 1.955053025 C??? 6.331514885?? 1.068488114?? 0.724935334 C??? 4.099852762? -0.563295810?? 0.724948544 C??? 4.794456495? -0.394248320?? 1.955057038 C??? 5.959864180?? 0.457099648?? 1.955045909 K_POINTS {automatic} 1 1 9 0 0 0 CELL_PARAMETERS ?1.0?? 0.0?? 0.0 ?0.0?? 1.0?? 0.0 ?0.0?? 0.0?? 0.09838 input_pp &inputPP ?prefix='CNT0404' ? outdir='./' ? plot_num= 1 ? filplot='CNT0404' / &plot ? iflag=3, ? output_format=3 ? fileout='CNT0404.total.potential.xsf' / input_average 1?????? CNT0404 1? 500? 1? 2 Could you please give me some sugestions to adjust the calculations? What?factors should I change?? I great appreciate for your help. Best regards,----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com From carlo.nervi at unito.it Wed Apr 22 14:32:09 2009 From: carlo.nervi at unito.it (Carlo Nervi) Date: Wed, 22 Apr 2009 14:32:09 +0200 Subject: [Pw_forum] GIPAW: impossible value for nrc Message-ID: <49EF0E49.8050203@unito.it> Dear all, I'm trying to use GIPAW module for NMR calculations. With the very helpful suggestions of Lorenzo Paulatto I generated the PAW Pseudopotentials of C and H, including gipaw. With these PP I performed geometry optimization whithin the cell (calculation='relax') and subsequently run the "calculation='scf'". When I try to run gipaw.x module, I always get from init_gipaw_1 : error # 1 impossible value for nrc The values for rc, rs, nrc, nrs, nt, msh(nt) are: 0.000000000000000E+000 0.000000000000000E+000 0 0 1 745 so both nrc and nrs are zero, whereas they are required to be >=1. I tried also to copy the original PP files into the directory .save created by pw.x, but with no success. The gipaw input I used is: &inputgipaw job = 'nmr' tmp_dir = '/home/nervi/calc/Barbiturico/Michele_periodico/GIPAW_Hex/' file_reconstruction ( 1 ) = 'H.pbe-paw-gipaw.recon' file_reconstruction ( 2 ) = 'C.pbe-paw-gipaw.recon' isolve = 0 iverbosity = 1 q_gipaw = 0.01 spline_ps = .true. use_nmr_macroscopic_shape = .true. prefix = 'Hex1' / Is there anything that I missed? Could somebody give yto me further hints on what I have to do? Thank you in advance, Carlo -- ------------------------------------------------------ Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 Fax: +39 011 6707855 - Dipartimento di Chimica IFM via P. Giuria 7, 10125 Torino, Italy http://lem.ch.unito.it/ From paulatto at sissa.it Wed Apr 22 14:37:37 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 22 Apr 2009 14:37:37 +0200 Subject: [Pw_forum] GIPAW: impossible value for nrc In-Reply-To: <49EF0E49.8050203@unito.it> References: <49EF0E49.8050203@unito.it> Message-ID: In data 22 aprile 2009 alle ore 14:32:09, Carlo Nervi ha scritto: > Dear all, > I'm trying to use GIPAW module for NMR calculations. > With the very helpful suggestions of Lorenzo Paulatto I generated the > PAW Pseudopotentials of C and H, including gipaw. With these PP I > performed geometry optimization whithin the cell (calculation='relax') > and subsequently run the "calculation='scf'". Sorry Carlo, I thought you had been following the bug report I'd opened on qe-forge, so I didn't bothered to alert you when I was able to "fix" it. The problem is quite complicated, but the resolution is simple: you have to explicitly specify the &test namelist when generating a pseudopotential with GIPAW data, otherwise if you have a "local" channel it won't be stored correctly in the GIPAW section of the UPF file. Then, you have to rerun the scf calculations! Or, at least, overwrite manually the UPF files in the $OUTDIR/$PREFIX.save directory, because GIPAW takes the UPF files from there, and only from there. Whatever you've put in your pseudo directory is totally ignored by GIPAW (and most of the post-processing tools). cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From kyin.cn at gmail.com Wed Apr 22 16:18:01 2009 From: kyin.cn at gmail.com (YIN Kun) Date: Wed, 22 Apr 2009 22:18:01 +0800 Subject: [Pw_forum] improper symmetry analysis References: <89E86BC3D8E24EC99E71E72CB70118B2@workhorse> <0D7D213B-AF56-4619-B957-707CDD7B27E5@democritos.it> <1F4283CD06DB45B887393FA4369CAE91@workhorse> <49EECB01.8000005@democritos.it> <49EEF2A5.3020606@democritos.it> Message-ID: <001101c9c355$287284c0$7200a8c0@eeepc701> Thanks a lot for explaining, Lorenzo. Perhaps using "right" and "wrong" is not suitable to describe problem. They just meant the symmetry which I intend to get or not. Follow your instructions, I get the "right" symmetry which I intend to. I think I know "how" to solve this problem now. And I have to spend more time to learn about FFT grid so as to totally understand "why" doing this way. L & P, Thank you again! ----- Original Message ----- From: "Paolo Giannozzi" To: "PWSCF Forum" Sent: Wednesday, April 22, 2009 6:34 PM Subject: Re: [Pw_forum] improper symmetry analysis > Lorenzo Paulatto wrote: > >> If I remember correctly symmetry is applied only on the FFT grid, the >> dimensions of the smooth grid should not matter. > > you remeber correctly, but actuyally there is no ]strong reason for > such choice: the part of the charge density that has to be symmetrized > is calculated in the smooth grid > >> Likely they are too small with respect to what your cutoffs requires! > > one can try to reduce a little bit the fft dimensions, but success is > not guaranteed! anyway the code should loudly complain > > 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 From asafis at yahoo.com.br Wed Apr 22 16:21:55 2009 From: asafis at yahoo.com.br (=?iso-8859-1?Q?=C1lvaro_Alves?=) Date: Wed, 22 Apr 2009 07:21:55 -0700 (PDT) Subject: [Pw_forum] fully relativistic pseudopotential for Co Message-ID: <179555.13347.qm@web52310.mail.re2.yahoo.com> Hi all. I build a fully relativistic pseudopotencial for cobalt. When testing it I found the following results for lattice parameters: a = 2.44 A, c = 4.03 A and c / a = 1.65. The experimental values are 2.51 A, 4.07 A and 1.62.? I want to improve these results. Do you have any suggestions? My input is below. ?&input ??? title='Co', ??? prefix='Co-rel' ??? zed=27., ??? rel=2, ??? rlderiv=2.50, ??? eminld=-4.0, ??? emaxld=4.0 ??? deld=0.02, ??? nld=3, ??? config='[Ar] 3d7.0 4s2.0 4p0.0', ??? iswitch=3, ??? dft='PBE' ?/ ?&inputp ?? lloc=0, ?? pseudotype=3, ?? file_pseudopw='Co.rel-pbe.rrkjus.UPF', ?? nlcc=.true., ?? rcore=1.2, ?? author='ASA', ?/ 7 4P? 2? 1? 0.00 -0.10? 2.40? 2.40? 0.5 4P? 2? 1? 0.00 -0.10? 2.40? 2.40? 1.5 3D? 3? 2? 4.00? 0.00? 1.50? 2.10? 1.5 3D? 3? 2? 0.00 -0.30? 1.50? 2.10? 1.5 3D? 3? 2? 3.00? 0.00? 1.50? 2.10? 2.5 3D? 3? 2? 0.00 -0.30? 1.50? 2.10? 2.5 4S? 1? 0? 2.00? 0.00? 2.20? 2.20? 0.5 ??????????????????????????????????????????????????????? Regards, Alvaro Veja quais s?o os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090422/cedec17f/attachment.htm From raamesh123 at rediffmail.com Wed Apr 22 18:03:34 2009 From: raamesh123 at rediffmail.com (ramesh kumar) Date: 22 Apr 2009 16:03:34 -0000 Subject: [Pw_forum] compilation problem-solved Message-ID: <20090422160334.65067.qmail@f5mail-236-233.rediffmail.com> Dear All Thank you very much Prof. Paolo. the problem is solved by using the iotk_base.o and iotk_base.mod as they were missing in the //../iotk/src folder.. With regards K. Ramesh Kumar Research Scholar Department of Physics IIT-Madras Chennai-600 036 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090422/d8131863/attachment.htm From akohlmey at cmm.chem.upenn.edu Wed Apr 22 18:15:11 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 22 Apr 2009 12:15:11 -0400 Subject: [Pw_forum] fully relativistic pseudopotential for Co In-Reply-To: <179555.13347.qm@web52310.mail.re2.yahoo.com> References: <179555.13347.qm@web52310.mail.re2.yahoo.com> Message-ID: <1240416911.5982.42.camel@zero> On Wed, 2009-04-22 at 07:21 -0700, ?lvaro Alves wrote: > > Hi all. I build a fully relativistic pseudopotencial for cobalt. When > testing it I found the following results for lattice parameters: a = > 2.44 A, c = 4.03 A and c / a = 1.65. The experimental values are 2.51 > A, 4.07 A and 1.62. I want to improve these results. Do you have any > suggestions? My input is below. > alvaro, you can try sacrificing five chickens or a goat, bow five times to mecca or pray 5 ave marias. other than that, i'd say that you have a less than 3% overbinding for the lattice parameter and 1% deviation in c and and since both errors are towards the same direction you have an error of 2% in c/a. to the best of my knowledge, this is pretty much of what people report as typical error margins for a gradient corrected functional, only that i remember seeing underbinding more commonly than overbinding (the latter would be more common in LDA). at this point, the black magic of pseudopotential generation begins. you can twiddle with cutoffs and electron configuration and see if this shifts the results closer to what you want, while not harming transferability (how transferable is this potential anyways? did you test it?). cheers, axel. -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090422/4ee95d57/attachment.htm From m.abbasnejad at gmail.com Wed Apr 22 18:38:22 2009 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Wed, 22 Apr 2009 09:38:22 -0700 Subject: [Pw_forum] relax with casino pseudopotential Message-ID: <7699a1950904220938x74085bfboddb76a4bf86aa273@mail.gmail.com> Dear all, Why does the stresses in the run with the converted CASINO pseudopotential, using 1 1 1 k points, have the undiagonal elements? Thanks in advance. Yours, Mohaddeseh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090422/b00b7a06/attachment.htm From ceresoli at MIT.EDU Wed Apr 22 19:57:15 2009 From: ceresoli at MIT.EDU (Davide Ceresoli) Date: Wed, 22 Apr 2009 13:57:15 -0400 Subject: [Pw_forum] GIPAW: impossible value for nrc In-Reply-To: References: <49EF0E49.8050203@unito.it> Message-ID: <49EF5A7B.90009@mit.edu> Lorenzo Paulatto wrote: > In data 22 aprile 2009 alle ore 14:32:09, Carlo Nervi > ha scritto: > >> Dear all, >> I'm trying to use GIPAW module for NMR calculations. >> With the very helpful suggestions of Lorenzo Paulatto I generated the >> PAW Pseudopotentials of C and H, including gipaw. With these PP I A small clairification to the Espresso community: right now, the GIPAW code works only with norm-conserving pseudopotentials. No ultrasoft/PAW yet. Davide -- +----------------------------------------------------------+ Davide Ceresoli DMSE 13-4084 Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge, MA 02139-4307 Phone: (617) 253-6026 Mobile: +39-347-1001570 Skype: dceresoli +----------------------------------------------------------+ From baroni at sissa.it Wed Apr 22 20:19:15 2009 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 22 Apr 2009 20:19:15 +0200 Subject: [Pw_forum] relax with casino pseudopotential In-Reply-To: <7699a1950904220938x74085bfboddb76a4bf86aa273@mail.gmail.com> References: <7699a1950904220938x74085bfboddb76a4bf86aa273@mail.gmail.com> Message-ID: which system? with which input data? SB On Apr 22, 2009, at 6:38 PM, mohaddeseh abbasnejad wrote: > > Dear all, > > Why does the stresses in the run with the converted CASINO > pseudopotential, using 1 1 1 > k points, have the undiagonal elements? > > Thanks in advance. > > Yours, > Mohaddeseh > > > > > > _______________________________________________ > 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/20090422/ec17df3d/attachment-0001.htm From nemeth at anl.gov Thu Apr 23 02:25:59 2009 From: nemeth at anl.gov (Karoly Nemeth) Date: Wed, 22 Apr 2009 19:25:59 -0500 (CDT) Subject: [Pw_forum] inhomogenious k-points distribution In-Reply-To: References: Message-ID: Hi, I was wondering whether it would be possible to define sub-regions in the Brillouin-zone where PWSCF would calculate bands at an increased resolution as compared to the rest of the Brillouin zone. This might be useful in spectroscopy, when one wants to study direct transitions happening at a specific k-points region. Thanks: Karoly *********************************************************************** Karoly Nemeth, Ph.D. Argonne National Laboratory 9700 S. Cass Ave. Argonne, IL 60439. Advanced Photon Source X-Ray Science Division Building 401, Room B4198 Tel. 630-252-5813 Fax: 630-252-3222 *********************************************************************** From sd.wang000 at 163.com Thu Apr 23 03:57:16 2009 From: sd.wang000 at 163.com (sd.wang000) Date: Thu, 23 Apr 2009 09:57:16 +0800 Subject: [Pw_forum] (no subject) Message-ID: <200904230957153205146@163.com> Dear all users: I have calculated phonons at Gamma point,and I found erro following? from phq_readin : error # 17 reading inputph namelist stopping ... The input file is? phonons of NaCoO at Gamma &inputph tr2_ph=1.0d-14, prefix='pwscf', epsil=.true., amass(Na)=22.989, amass(Co)=58.999, amass(O)=15.999, outdir='/root/tmp/', fildyn='nco.dynG', / 0.0 0.0 0.0 Why does it happen? Thanks in advance! 2009-04-23 sd.wang000 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090423/72cb8d0a/attachment.htm From yirigui321 at 126.com Thu Apr 23 04:42:56 2009 From: yirigui321 at 126.com (yirigui321) Date: Thu, 23 Apr 2009 10:42:56 +0800 (CST) Subject: [Pw_forum] =?gbk?b?wLTX1HlpcmlndWkzMjFAMTI2LmNvbbXE08q8/g==?= Message-ID: <12223393.126751240454576743.JavaMail.coremail@bj126app103.126.com> from read_namelists;error# reading namelist electrons -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090423/e04be9d8/attachment.htm From degironc at sissa.it Thu Apr 23 06:47:54 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 23 Apr 2009 06:47:54 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: <200904230957153205146@163.com> References: <200904230957153205146@163.com> Message-ID: <49EFF2FA.2030704@sissa.it> name and affiliation ? Stefano de Gironcoli - SISSA and DEMOCRITOS sd.wang000 wrote: > Dear all users: > I have calculated phonons at Gamma point,and I found erro following? > > from phq_readin : error # 17 > reading inputph namelist > > stopping ... > > The input file is? > phonons of NaCoO at Gamma > &inputph > tr2_ph=1.0d-14, > prefix='pwscf', > epsil=.true., > amass(Na)=22.989, > amass(Co)=58.999, > amass(O)=15.999, > outdir='/root/tmp/', > fildyn='nco.dynG', > / > 0.0 0.0 0.0 > Why does it happen? > Thanks in advance! > 2009-04-23 > ------------------------------------------------------------------------ > sd.wang000 > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From m.abbasnejad at gmail.com Thu Apr 23 07:33:55 2009 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Thu, 23 Apr 2009 10:03:55 +0430 Subject: [Pw_forum] relax with casino pseudopotential In-Reply-To: References: <7699a1950904220938x74085bfboddb76a4bf86aa273@mail.gmail.com> Message-ID: <7699a1950904222233k3855ccf5hc6b99b453ef82465@mail.gmail.com> I run the calculation for the Si. The input data were as follows: ibrav= 2, celldm(1) =10.57, nat= 2, ntyp= 1, ecutwfc =18.0, nosym=.true., K_POINTS {automatic} 1 1 1 1 1 1 Yours, Mohaddeseh On Wed, Apr 22, 2009 at 10:49 PM, Stefano Baroni wrote: > which system? with which input data? SB > > On Apr 22, 2009, at 6:38 PM, mohaddeseh abbasnejad wrote: > > > Dear all, > > Why does the stresses in the run with the converted CASINO > pseudopotential, using 1 1 1 > k points, have the undiagonal elements? > > Thanks in advance. > > Yours, > Mohaddeseh > > > > > > _______________________________________________ > 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 > > > > > > > > > _______________________________________________ > 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/20090423/8a37b49a/attachment.htm From baroni at sissa.it Thu Apr 23 07:34:43 2009 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 23 Apr 2009 07:34:43 +0200 Subject: [Pw_forum] inhomogenious k-points distribution In-Reply-To: References: Message-ID: Hi! I think that would be useful, and not difficult to implement. At the very least, I think that it would be enough to pass "manually" custom-defined sets of k points (with the associated weights) to bands.x Just a word of warning for the younger members of this forum. NO transition (direct or indirect) ever occurs at a specific point of the BZ. What Karoly meant is that in order to resolve the contribution of "critical points" to the absorption intensity (which give rise to Van Hove singularities in the spectrum), it would be useful to increase the k-point resulution in specific regions of the BZ. Stefano On Apr 23, 2009, at 2:25 AM, Karoly Nemeth wrote: > > Hi, > > I was wondering whether it would be possible to define sub-regions > in the > Brillouin-zone where PWSCF would calculate bands at an increased > resolution as compared to the rest of the Brillouin zone. This might > be > useful in spectroscopy, when one wants to study direct transitions > happening at a specific k-points region. > Thanks: > > Karoly > > *********************************************************************** > Karoly Nemeth, Ph.D. > Argonne National Laboratory > 9700 S. Cass Ave. Argonne, IL 60439. > Advanced Photon Source > X-Ray Science Division > Building 401, Room B4198 > Tel. 630-252-5813 > Fax: 630-252-3222 > *********************************************************************** > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From baroni at sissa.it Thu Apr 23 07:42:31 2009 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 23 Apr 2009 07:42:31 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: <200904230957153205146@163.com> References: <200904230957153205146@163.com> Message-ID: On Apr 23, 2009, at 3:57 AM, sd.wang000 wrote: > Dear all users: > I have calculated phonons at Gamma point,and I found erro following? > > from phq_readin : error # 17 > reading inputph namelist > > stopping ... > > The input file is? > phonons of NaCoO at Gamma > &inputph > tr2_ph=1.0d-14, > prefix='pwscf', > epsil=.true., > amass(Na)=22.989, > amass(Co)=58.999, > amass(O)=15.999, a minimum proficiency in FORTRAN would help anybody willing to do numerical simulations ... as the syntax clearly indicates, "amass" is an array. in fortran you can only address elements in an aray by their (numerical) position: amass(1), amass(2), amass(3), ... As Stefano de Gironcoli (as well as zillions of others) was suggesting, providing your name and affiliation is considered a sign of respect in this mailng list. please, stick at this custom, if you can. Stefano Baroni --- 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/20090423/c5e9075e/attachment-0001.htm From baroni at sissa.it Thu Apr 23 07:45:54 2009 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 23 Apr 2009 07:45:54 +0200 Subject: [Pw_forum] relax with casino pseudopotential In-Reply-To: <7699a1950904222233k3855ccf5hc6b99b453ef82465@mail.gmail.com> References: <7699a1950904220938x74085bfboddb76a4bf86aa273@mail.gmail.com> <7699a1950904222233k3855ccf5hc6b99b453ef82465@mail.gmail.com> Message-ID: <0B7120EC-FB63-4CC3-95F1-177AD2CECE61@sissa.it> On Apr 23, 2009, at 7:33 AM, mohaddeseh abbasnejad wrote: > > I run the calculation for the Si. > The input data were as follows: > > ibrav= 2, celldm(1) =10.57, nat= 2, ntyp= 1, > ecutwfc =18.0, nosym=.true., how can you expect nondiagonal elements of any tensor to anish if you do NOT impose symmetry? You can avoid to impose symmetry (why?) if you use a complete mesh of k points (i.e. one spanning the entire BZ, and not only its irreducible wedge). > K_POINTS {automatic} > 1 1 1 1 1 1 > > Yours, > Mohaddeseh providing your affiliation is alwasy considered a sign of politeness in this mailing list. 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/20090423/605266cd/attachment.htm From m.abbasnejad at gmail.com Thu Apr 23 07:50:58 2009 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Thu, 23 Apr 2009 10:20:58 +0430 Subject: [Pw_forum] relax with casino pseudopotential In-Reply-To: <7699a1950904222233k3855ccf5hc6b99b453ef82465@mail.gmail.com> References: <7699a1950904220938x74085bfboddb76a4bf86aa273@mail.gmail.com> <7699a1950904222233k3855ccf5hc6b99b453ef82465@mail.gmail.com> Message-ID: <7699a1950904222250q456ebf59sa5e8d58a3b449784@mail.gmail.com> I have attached the full input. Is it neccessary to send you the pseudopotential file too. Yours, Mohaddeseh On Thu, Apr 23, 2009 at 10:03 AM, mohaddeseh abbasnejad < m.abbasnejad at gmail.com> wrote: > > I run the calculation for the Si. > The input data were as follows: > > ibrav= 2, celldm(1) =10.57, nat= 2, ntyp= 1, > > ecutwfc =18.0, nosym=.true., > K_POINTS {automatic} > > 1 1 1 1 1 1 > > Yours, > Mohaddeseh > > > > On Wed, Apr 22, 2009 at 10:49 PM, Stefano Baroni wrote: > >> which system? with which input data? SB >> >> On Apr 22, 2009, at 6:38 PM, mohaddeseh abbasnejad wrote: >> >> >> Dear all, >> >> Why does the stresses in the run with the converted CASINO >> pseudopotential, using 1 1 1 >> k points, have the undiagonal elements? >> >> Thanks in advance. >> >> Yours, >> Mohaddeseh >> >> >> >> >> >> _______________________________________________ >> 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 >> >> >> >> >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > > -- --------------------------------------------------------- Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran, North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 Cellphone: +989177317514 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir --------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090423/e72ef05c/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: relax.in Type: application/octet-stream Size: 744 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090423/e72ef05c/attachment.obj From marzari at MIT.EDU Thu Apr 23 07:51:02 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Thu, 23 Apr 2009 01:51:02 -0400 Subject: [Pw_forum] inhomogenious k-points distribution In-Reply-To: References: Message-ID: <49F001C6.2080803@mit.edu> Dear Karoly, another option would be using Wannier functions to interpolate the bands - they capture van Hove singularities very well (Lee PRL 2007, Yates PRB 2007). Learning how to do this is a project in itself, though, so it would be worth only if you have a long term plan on studying transitions. nicola Stefano Baroni wrote: > Hi! I think that would be useful, and not difficult to implement. > At the very least, I think that it would be enough to pass "manually" > custom-defined sets of k points (with the associated weights) to bands.x > > Just a word of warning for the younger members of this forum. > NO transition (direct or indirect) ever occurs at a specific point of > the BZ. What Karoly meant is that in order to resolve the contribution > of "critical points" to the absorption intensity (which give rise to > Van Hove singularities in the spectrum), it would be useful to > increase the k-point resulution in specific regions of the BZ. > > Stefano > > On Apr 23, 2009, at 2:25 AM, Karoly Nemeth wrote: > >> Hi, >> >> I was wondering whether it would be possible to define sub-regions >> in the >> Brillouin-zone where PWSCF would calculate bands at an increased >> resolution as compared to the rest of the Brillouin zone. This might >> be >> useful in spectroscopy, when one wants to study direct transitions >> happening at a specific k-points region. >> Thanks: >> >> Karoly >> >> *********************************************************************** >> Karoly Nemeth, Ph.D. >> Argonne National Laboratory >> 9700 S. Cass Ave. Argonne, IL 60439. >> Advanced Photon Source >> X-Ray Science Division >> Building 401, Room B4198 >> Tel. 630-252-5813 >> Fax: 630-252-3222 >> *********************************************************************** -- --------------------------------------------------------------------- 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 m.abbasnejad at gmail.com Thu Apr 23 07:59:42 2009 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Thu, 23 Apr 2009 10:29:42 +0430 Subject: [Pw_forum] relax with casino pseudopotential In-Reply-To: <7699a1950904222250q456ebf59sa5e8d58a3b449784@mail.gmail.com> References: <7699a1950904220938x74085bfboddb76a4bf86aa273@mail.gmail.com> <7699a1950904222233k3855ccf5hc6b99b453ef82465@mail.gmail.com> <7699a1950904222250q456ebf59sa5e8d58a3b449784@mail.gmail.com> Message-ID: <7699a1950904222259n6c9e7ad5jb8935badbef6b765@mail.gmail.com> Thank you for your attention. How can I run the calculation with using a complete mesh of k points? Sincerely yours, Mohaddeseh On Thu, Apr 23, 2009 at 10:20 AM, mohaddeseh abbasnejad < m.abbasnejad at gmail.com> wrote: > I have attached the full input. > Is it neccessary to send you the pseudopotential file too. > > Yours, > Mohaddeseh > On Thu, Apr 23, 2009 at 10:03 AM, mohaddeseh abbasnejad < > m.abbasnejad at gmail.com> wrote: > >> >> I run the calculation for the Si. >> The input data were as follows: >> >> ibrav= 2, celldm(1) =10.57, nat= 2, ntyp= 1, >> >> ecutwfc =18.0, nosym=.true., >> K_POINTS {automatic} >> >> 1 1 1 1 1 1 >> >> Yours, >> Mohaddeseh >> >> >> >> On Wed, Apr 22, 2009 at 10:49 PM, Stefano Baroni wrote: >> >>> which system? with which input data? SB >>> >>> On Apr 22, 2009, at 6:38 PM, mohaddeseh abbasnejad wrote: >>> >>> >>> Dear all, >>> >>> Why does the stresses in the run with the converted CASINO >>> pseudopotential, using 1 1 1 >>> k points, have the undiagonal elements? >>> >>> Thanks in advance. >>> >>> Yours, >>> Mohaddeseh >>> >>> >>> >>> >>> >>> _______________________________________________ >>> 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 >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> >> -- >> >> > > > -- > --------------------------------------------------------- > > Mohaddeseh Abbasnejad, > Room No. 323, Department of Physics, > University of Tehran, North Karegar Ave., > Tehran, P.O. Box: 14395-547- IRAN > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 > Cellphone: +989177317514 > E-Mail: m.abbasnejad at gmail.com > Website: http://physics.ut.ac.ir > > --------------------------------------------------------- > > -- --------------------------------------------------------- Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran, North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 Cellphone: +989177317514 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir --------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090423/66a2f313/attachment.htm From baroni at sissa.it Thu Apr 23 08:12:59 2009 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 23 Apr 2009 08:12:59 +0200 Subject: [Pw_forum] relax with casino pseudopotential In-Reply-To: <7699a1950904222259n6c9e7ad5jb8935badbef6b765@mail.gmail.com> References: <7699a1950904220938x74085bfboddb76a4bf86aa273@mail.gmail.com> <7699a1950904222233k3855ccf5hc6b99b453ef82465@mail.gmail.com> <7699a1950904222250q456ebf59sa5e8d58a3b449784@mail.gmail.com> <7699a1950904222259n6c9e7ad5jb8935badbef6b765@mail.gmail.com> Message-ID: On Apr 23, 2009, at 7:59 AM, mohaddeseh abbasnejad wrote: > > Thank you for your attention. > How can I run the calculation with using a complete mesh of k points? provide the code with a complete mesh of points, and us with you affiliation SB > > Sincerely yours, > Mohaddeseh > > On Thu, Apr 23, 2009 at 10:20 AM, mohaddeseh abbasnejad > wrote: > I have attached the full input. > Is it neccessary to send you the pseudopotential file too. > > Yours, > Mohaddeseh > On Thu, Apr 23, 2009 at 10:03 AM, mohaddeseh abbasnejad > wrote: > > I run the calculation for the Si. > The input data were as follows: > > ibrav= 2, celldm(1) =10.57, nat= 2, ntyp= 1, > ecutwfc =18.0, nosym=.true., > K_POINTS {automatic} > 1 1 1 1 1 1 > > Yours, > Mohaddeseh > > > > On Wed, Apr 22, 2009 at 10:49 PM, Stefano Baroni > wrote: > which system? with which input data? > SB > > On Apr 22, 2009, at 6:38 PM, mohaddeseh abbasnejad wrote: > >> >> Dear all, >> >> Why does the stresses in the run with the converted CASINO >> pseudopotential, using 1 1 1 >> k points, have the undiagonal elements? >> >> Thanks in advance. >> >> Yours, >> Mohaddeseh >> >> >> >> >> >> _______________________________________________ >> 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 > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > > > > > -- > --------------------------------------------------------- > > Mohaddeseh Abbasnejad, > Room No. 323, Department of Physics, > University of Tehran, North Karegar Ave., > Tehran, P.O. Box: 14395-547- IRAN > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 > Cellphone: +989177317514 > E-Mail: m.abbasnejad at gmail.com > Website: http://physics.ut.ac.ir > > --------------------------------------------------------- > > > > > -- > --------------------------------------------------------- > > Mohaddeseh Abbasnejad, > Room No. 323, Department of Physics, > University of Tehran, North Karegar Ave., > Tehran, P.O. Box: 14395-547- IRAN > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 > Cellphone: +989177317514 > E-Mail: m.abbasnejad at gmail.com > Website: http://physics.ut.ac.ir > > --------------------------------------------------------- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- 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/20090423/d54ab27d/attachment-0001.htm From m.abbasnejad at gmail.com Thu Apr 23 08:28:42 2009 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Thu, 23 Apr 2009 10:58:42 +0430 Subject: [Pw_forum] relax with casino pseudopotential In-Reply-To: References: <7699a1950904220938x74085bfboddb76a4bf86aa273@mail.gmail.com> <7699a1950904222233k3855ccf5hc6b99b453ef82465@mail.gmail.com> <7699a1950904222250q456ebf59sa5e8d58a3b449784@mail.gmail.com> <7699a1950904222259n6c9e7ad5jb8935badbef6b765@mail.gmail.com> Message-ID: <7699a1950904222328p181796d5k932e9890649e0b6d@mail.gmail.com> Dear Professor Baroni, I am Mohaddeseh Abbasnejad, the PhD student of Tehran university. I work on Quantum Monte Carlo. Yours, Mohaddeseh Abbasnejad --------------------------------------------------------- Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran, North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 Cellphone: +989177317514 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir --------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090423/3f24b092/attachment.htm From giannozz at democritos.it Thu Apr 23 09:17:34 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 23 Apr 2009 09:17:34 +0200 Subject: [Pw_forum] relax with casino pseudopotential In-Reply-To: <7699a1950904222250q456ebf59sa5e8d58a3b449784@mail.gmail.com> References: <7699a1950904220938x74085bfboddb76a4bf86aa273@mail.gmail.com> <7699a1950904222233k3855ccf5hc6b99b453ef82465@mail.gmail.com> <7699a1950904222250q456ebf59sa5e8d58a3b449784@mail.gmail.com> Message-ID: <49F0160E.2070405@democritos.it> mohaddeseh abbasnejad wrote: > calculation = 'relax' it's silicon, they is no need to relax anything > tprnfor = .true. forces are zero by symmetry > diagonalization='cg' it's slower than the default (not that it matters in this case) If you want to calculate all k-points and not only those in the irreducible Brillouin Zone, use option nosym=.true. and provide the entire grid (pwtools/kpoints.x will give the complete list) Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From carlo.nervi at unito.it Thu Apr 23 10:57:17 2009 From: carlo.nervi at unito.it (Carlo Nervi) Date: Thu, 23 Apr 2009 10:57:17 +0200 Subject: [Pw_forum] GIPAW: impossible value for nrc In-Reply-To: <49EF5A7B.90009@mit.edu> References: <49EF0E49.8050203@unito.it> <49EF5A7B.90009@mit.edu> Message-ID: <49F02D6D.1060500@unito.it> Dear all, I'm getting crazy with GIPAW... :-) Finally I did a step back and did the nmr-example provided by Seitsonen on his web pages, using the Si_pbe-20070930.UPF PP. All works! I got exactly the same results. Well, than I decided to use the Si.pbe-rrkj.in included in the pseudo_library/PBE/SR dir. Here it is, just to make sure all is okay: &input title='Si', zed=14.0, rel=1, config="[Ne] 3s2.0 3p2.0 3d-2.0" iswitch=3, dft='PBE', / &inputp lloc=2, pseudotype=1, file_pseudopw='Si.pbe-rrkj.UPF', author='ADC', / 3 3S 1 0 2.00 0.00 2.20 2.20 3P 2 1 2.00 0.00 2.40 2.40 3D 3 2 -2.00 0.20 2.40 2.40 If I use this generated PP the scf.out looks okay. Than I modified it in order to create the PP for gipaw: &input title='Si', zed=14.0, rel=1, config="[Ne] 3s2.0 3p2.0 3d-2.0" iswitch=3, dft='PBE', / &inputp lloc=2, pseudotype=1, file_pseudopw='Si.pbe-rrkj.UPF', file_recon='Si.pbe-rrkj.recon', lgipaw_reconstruction = .true. tm = .true. author='ADC', / 3 3S 1 0 2.00 0.00 2.20 2.20 3P 2 1 2.00 0.00 2.40 2.40 3D 3 2 -2.00 0.20 2.40 2.40 &test / 3 3S 1 0 2.00 0.00 2.20 2.20 3P 2 1 2.00 0.00 2.40 2.40 3D 3 2 -2.00 0.20 2.40 2.40 If I use this generated PP the scf.out contain WARNING: Pseudopotential # 1 file : H.pbe-tm-gipaw.UPF WARNING: WFC # 1(1S) IS NOT CORRECTLY NORMALIZED: norm= 1.421108 WARNING: WFC HAS BEEN NOW RENORMALIZED WARNING: Pseudopotential # 1 file : H.pbe-tm-gipaw.UPF WARNING: WFC # 2(2P) IS NOT CORRECTLY NORMALIZED: norm= 26.282579 WARNING: WFC HAS BEEN NOW RENORMALIZED Is this output from pw.x normal? Furthermore, the gipaw crash every time. One error message is: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from cdiaghg : error # 87 diagonalization (ZHEGV*) failed %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% The parallel version of gipaw.x crash in a different way, mumbling something about glibc and malloc() (out of memory I suppose...) I'm using the 4.1CVS version, snapshot of January 2009. Any help would be greately appreciated! Thank you, Carlo -- ------------------------------------------------------ Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 Fax: +39 011 6707855 - Dipartimento di Chimica IFM via P. Giuria 7, 10125 Torino, Italy http://lem.ch.unito.it/ From alain.allouche at univ-provence.fr Thu Apr 23 10:57:18 2009 From: alain.allouche at univ-provence.fr (Alain Allouche) Date: Thu, 23 Apr 2009 10:57:18 +0200 Subject: [Pw_forum] Fwd: configure error with intel 11 compiler References: Message-ID: <5D77F946-3429-44C8-B364-B237B023ACFD@univ-provence.fr> > Dear Espressonists > I have an error configuring QE4.0.5, ./configure produces the message: > > configure:3127: error: C preprocessor "/lib/cpp" fails sanity check > > I saw in the archive that ifort is usual of this error but I do not > know how to cure it > Thank you for your help > > ALLOUCHE Alain Physique des Interactions Ioniques et Moleculaires CNRS / Universite de Provence Campus Saint Jerome Service 242 Avenue de l'Escadrille Normandie-Niemen 13397 Marseille Cedex 20 - France Tel : +33 (0) 4 91 28 85 76 Cellphone: +33 (0) 6 81 84 80 66 Fax : +33 (0) 4.91.28.91.94 email: Alain.Allouche at univ-provence.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090423/eef464b3/attachment.htm From giannozz at democritos.it Thu Apr 23 12:21:45 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 23 Apr 2009 12:21:45 +0200 Subject: [Pw_forum] Fwd: configure error with intel 11 compiler In-Reply-To: <5D77F946-3429-44C8-B364-B237B023ACFD@univ-provence.fr> References: <5D77F946-3429-44C8-B364-B237B023ACFD@univ-provence.fr> Message-ID: <49F04139.6020006@democritos.it> Alain Allouche wrote: >> configure:3127: error: C preprocessor "/lib/cpp" fails sanity check >> >> I saw in the archive that ifort is usual of this error Alain, this is NOT usual. There is something wrong in the configuration of your machine. If you have CPP set to /lib/cpp, try to unset it. For reasons I ignore, "configure" doesn't seem to like compilers with the path specified Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From mazouz_moulay at yahoo.fr Thu Apr 23 14:44:33 2009 From: mazouz_moulay at yahoo.fr (mazouz moulay) Date: Thu, 23 Apr 2009 12:44:33 +0000 (GMT) Subject: [Pw_forum] Phonon calculation Message-ID: <472892.89087.qm@web25507.mail.ukl.yahoo.com> Dear all, I perfomed a calculation on ?TlAs, the electronic band shows a semi-metallic behavior, and I want to calculate the phonons dispersion, in this case, we ?use the metallic option in the scf input? or we consider this compound as semiconductor in order to have the dynamical properties (Born effective ?charge and the dielectric tensor)? Thanks you in advance. ? ?Moulay Mazouz D?partement de Physique Universit? des Sciences et de la Technologie d'Oran. USTO. Oran.?Alg?rie -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090423/32dd09e3/attachment.htm From akohlmey at cmm.chem.upenn.edu Thu Apr 23 15:38:10 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 23 Apr 2009 09:38:10 -0400 Subject: [Pw_forum] Fwd: configure error with intel 11 compiler In-Reply-To: <5D77F946-3429-44C8-B364-B237B023ACFD@univ-provence.fr> References: <5D77F946-3429-44C8-B364-B237B023ACFD@univ-provence.fr> Message-ID: <1240493890.5982.356.camel@zero> On Thu, 2009-04-23 at 10:57 +0200, Alain Allouche wrote: > > Dear Espressonists > > > I have an error configuring QE4.0.5, ./configure produces the > > message: > > > > > > configure:3127: error: C preprocessor "/lib/cpp" fails sanity check > > > > > > I saw in the archive that ifort is usual of this error but I do not alain, please show me where this is usual. and furthermore it is an error message from the configure script and _not_ ifort. "as usual", you don't provide any information about your installation, so nobody can help you right now. if you want the doctor to help you, you have to not only tell him, _that_ it hurts, but _where_ and _how_, too... cheers, axel. > > know how to cure it > > Thank you for your help > > > > > > > > > > ALLOUCHE Alain > Physique des Interactions Ioniques et Moleculaires > CNRS / Universite de Provence > Campus Saint Jerome Service 242 > Avenue de l'Escadrille Normandie-Niemen > 13397 Marseille Cedex 20 - France > Tel : +33 (0) 4 91 28 85 76 > Cellphone: +33 (0) 6 81 84 80 66 > Fax : +33 (0) 4.91.28.91.94 > email: Alain.Allouche at univ-provence.fr > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From carlo.nervi at unito.it Thu Apr 23 15:46:23 2009 From: carlo.nervi at unito.it (Carlo Nervi) Date: Thu, 23 Apr 2009 15:46:23 +0200 Subject: [Pw_forum] GIPAW: impossible value for nrc In-Reply-To: <49EF5A7B.90009@mit.edu> References: <49EF0E49.8050203@unito.it> <49EF5A7B.90009@mit.edu> Message-ID: <49F0712F.5090403@unito.it> Sorry, in the previous email I copy&paste another very similar error from another job. The error message regarding the nmr-example is the following: If I use this generated PP the scf.out contain Program GIPAW v.4.1CVS starts ... Today is 23Apr2009 at 15:16:35 Parallel version (MPI) Number of processors in use: 1 WARNING: Pseudopotential # 1 file : Si.pbe-rrkj-gipaw.UPF WARNING: WFC # 1(3S) IS NOT CORRECTLY NORMALIZED: norm= 1.439008 WARNING: WFC HAS BEEN NOW RENORMALIZED WARNING: Pseudopotential # 1 file : Si.pbe-rrkj-gipaw.UPF WARNING: WFC # 2(3P) IS NOT CORRECTLY NORMALIZED: norm= 1.940790 WARNING: WFC HAS BEEN NOW RENORMALIZED ... chi_bare vGv (VV) in 10^{-6} cm^3/mol: -47.9269 0.0000 0.0000 0.0000 -47.9269 0.0000 0.0000 0.0000 -47.9269 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from grid_gather : error # 63936 f_out too small %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... First: I cannot understand why I got the warnings after scf calculations after simply adding the gipaw_recontruction=.true. Sorry for bothering a lot... Carlo -- ------------------------------------------------------ Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 Fax: +39 011 6707855 - Dipartimento di Chimica IFM via P. Giuria 7, 10125 Torino, Italy http://lem.ch.unito.it/ From yccheng.nju at gmail.com Thu Apr 23 16:20:04 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Thu, 23 Apr 2009 22:20:04 +0800 Subject: [Pw_forum] Phonon calculation In-Reply-To: <472892.89087.qm@web25507.mail.ukl.yahoo.com> References: <472892.89087.qm@web25507.mail.ukl.yahoo.com> Message-ID: I think you can consider this compound as semiconductor. As far as I know, a semi-metal can be considered as an indirect semiconductor with a minus bandgap. 2009/4/23 mazouz moulay > Dear all, > > I perfomed a calculation on TlAs, the electronic band shows a > semi-metallic behavior, and I want to calculate the phonons dispersion, in > this case, we use the metallic option in the scf input or we consider > this compound as semiconductor in order to have the dynamical properties > (Born effective charge and the dielectric tensor)? > > Thanks you in advance. > > > > Moulay Mazouz > D?partement de Physique > Universit? des Sciences et de la Technologie d'Oran. > USTO. Oran. Alg?rie > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090423/58b04c92/attachment.htm From eyvaz_isaev at yahoo.com Thu Apr 23 17:42:51 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 23 Apr 2009 08:42:51 -0700 (PDT) Subject: [Pw_forum] Phonon calculation In-Reply-To: <472892.89087.qm@web25507.mail.ukl.yahoo.com> Message-ID: <831884.4184.qm@web65715.mail.ac4.yahoo.com> Dear Mazouz, > the electronic band shows a semi-metallic behavior If you have non-vanishing density of states at the Fermi level (so that bands are separated, but overlapping of valence and conduction bands takes place), your system should be considered as metallic. If you will consider your system as a semiconductor, you lose some amount of electrons. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Thu, 4/23/09, mazouz moulay wrote: > From: mazouz moulay > Subject: [Pw_forum] Phonon calculation > To: pw_forum at pwscf.org > Date: Thursday, April 23, 2009, 4:44 PM > Dear all, > I perfomed a calculation on ?TlAs, the electronic band > shows a semi-metallic behavior, and I want to calculate the > phonons dispersion, in this case, we ?use the metallic > option in the scf input? or we consider this compound as > semiconductor in order to have the dynamical properties > (Born effective ?charge and the dielectric tensor)? > Thanks you in advance. > ? > ?Moulay Mazouz > D?partement de Physique > Universit? des Sciences et de la Technologie d'Oran. > USTO. Oran.?Alg?rie > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From eyvaz_isaev at yahoo.com Thu Apr 23 17:50:06 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 23 Apr 2009 08:50:06 -0700 (PDT) Subject: [Pw_forum] Phonon calculation In-Reply-To: Message-ID: <121108.30264.qm@web65711.mail.ac4.yahoo.com> --- On Thu, 4/23/09, ??? wrote: > From: ??? > Subject: Re: [Pw_forum] Phonon calculation > I think you can consider this compound as semiconductor. > > As far as I know, a semi-metal can be considered as an > indirect semiconductor with a minus bandgap. Well, and then how the DOS (with a negative band gap) will look like? Please also provide your affiliation when you post to this forum. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > 2009/4/23 mazouz moulay > > > Dear all, > > > > I perfomed a calculation on TlAs, the electronic band > shows a > > semi-metallic behavior, and I want to calculate the > phonons dispersion, in > > this case, we use the metallic option in the scf > input or we consider > > this compound as semiconductor in order to have the > dynamical properties > > (Born effective charge and the dielectric tensor)? > > > > Thanks you in advance. > > > > > > > > Moulay Mazouz > > D?partement de Physique > > Universit? des Sciences et de la Technologie > d'Oran. > > USTO. Oran. Alg?rie > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > -- > Y. C. Cheng > Department of Physics > Nanjing University > Nanjing 210093 > P. R. China > Tel: 86-25-83592907 > Email: yccheng.nju at gmail.com > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From lex at phys.ufl.edu Thu Apr 23 18:35:12 2009 From: lex at phys.ufl.edu (Lex Kemper) Date: Thu, 23 Apr 2009 12:35:12 -0400 Subject: [Pw_forum] Fractional magnetization Message-ID: <49F098C0.1090906@phys.ufl.edu> Hello everyone, I have a question regarding constrained magnetization calculations. I notice in the manual that both multiplicity and tot_magnetization are integers. However, systems are not always found in an integer spin state. Furthermore, being able to specify a non-integer spin state is useful for making systems converge to a particular desired solution. At the moment, the only way I can specify a non-integer spin state is by using the nelec/nelup/neldw combination. The manual says this is obsolete though, and to use the other variables instead. Should (at least one) of these be changed to a real instead of an integer? Thanks, Lex Kemper Department of Physics & QTP University of Florida From nemeth at anl.gov Thu Apr 23 21:55:11 2009 From: nemeth at anl.gov (Karoly Nemeth) Date: Thu, 23 Apr 2009 14:55:11 -0500 (CDT) Subject: [Pw_forum] inhomogenious k-points distribution In-Reply-To: References: Message-ID: Dear Stefano and Nicola, Thanks a lot for the valuable comments! 1. I still feel like a younger member of the forum though... 2. I use MATLAB to manipulate the bands extracted by pw2casino from PWSCF outputs. Of course it is quite simple to increase resolution of the bands by nice interpolations available in MATLAB. However interpolation of the wavefunction coefficients (crystal orbital coefficients) would be dangerous, e.g. because loss of normalization could happen, or there may be sign issues. My guess is though that it is perhaps not as dangerous as it might look like. As of longer term work on these transitions I can't tell much yet. Perhaps. Since the bands are normally smooth enough for interpolation (using a moderate but not too small number of k-points) my best guess is that one should try to do some sort of interpolation, perhaps not on individual wavefunction coeffs, but on whole coeff vectors (wavefunctions). At least, numerically that seems to be the cheapest thing to do and perhaps not of too bad quality. Cheers: Karoly *********************************************************************** Karoly Nemeth, Ph.D. Argonne National Laboratory 9700 S. Cass Ave. Argonne, IL 60439. Advanced Photon Source X-Ray Science Division Building 401, Room B4198 Tel. 630-252-5813 Fax: 630-252-3222 *********************************************************************** From: Stefano Baroni Subject: Re: [Pw_forum] inhomogenious k-points distribution To: PWSCF Forum Message-ID: Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Hi! I think that would be useful, and not difficult to implement. At the very least, I think that it would be enough to pass "manually" custom-defined sets of k points (with the associated weights) to bands.x Just a word of warning for the younger members of this forum. NO transition (direct or indirect) ever occurs at a specific point of the BZ. What Karoly meant is that in order to resolve the contribution of "critical points" to the absorption intensity (which give rise to Van Hove singularities in the spectrum), it would be useful to increase the k-point resulution in specific regions of the BZ. Stefano > > Hi, > > I was wondering whether it would be possible to define > sub-regions > in the > Brillouin-zone where PWSCF would calculate bands at an > increased > resolution as compared to the rest of the Brillouin zone. This > might > be > useful in spectroscopy, when one wants to study direct > transitions > happening at a specific k-points region. > Thanks: > > Karoly Message: 3 Date: Thu, 23 Apr 2009 01:51:02 -0400 From: Nicola Marzari Subject: Re: [Pw_forum] inhomogenious k-points distribution To: PWSCF Forum Message-ID: <49F001C6.2080803 at mit.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Dear Karoly, another option would be using Wannier functions to interpolate the bands - they capture van Hove singularities very well (Lee PRL 2007, Yates PRB 2007). Learning how to do this is a project in itself, though, so it would be worth only if you have a long term plan on studying transitions. nicola From yccheng.nju at gmail.com Fri Apr 24 03:25:37 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Fri, 24 Apr 2009 09:25:37 +0800 Subject: [Pw_forum] Phonon calculation In-Reply-To: <121108.30264.qm@web65711.mail.ac4.yahoo.com> References: <121108.30264.qm@web65711.mail.ac4.yahoo.com> Message-ID: A well know disadvantage of DFT is underestimate the bandgap of semiconductor. To get the exact bandgap, a much more expensive calculation should be done, for example GW calculation. I don't know whether TIAs is semimetal in experiments. If the TIAs is the exactly semimetal in experiments, Prof. Eyvaz's opinion is right. If the TIAs is not the semimetal in experiments, to find the exactly bandgap is needed. > > Well, and then how the DOS (with a negative band gap) will look like? > > Please also provide your affiliation when you post to this forum. > > Bests, > Eyvaz. > Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090424/bf67c72f/attachment.htm From pc229 at kent.ac.uk Fri Apr 24 15:55:12 2009 From: pc229 at kent.ac.uk (Pieremanuele Canepa) Date: Fri, 24 Apr 2009 15:55:12 +0200 Subject: [Pw_forum] how can I create a supercell in PWSCF? Message-ID: <8b443ba10904240655w3ea42fachd4d16385c0fd7191@mail.gmail.com> Dear all, does exist a script or a small program in Quantum espresso that allow me to create a suitable supercell (for instance 2x2x1) starting from a primitive cell of PWSCF? Best regards, Piero -- Pieremanuele Canepa Room 230 School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom ----------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090424/b394bcac/attachment.htm From baroni at sissa.it Fri Apr 24 16:31:27 2009 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 24 Apr 2009 16:31:27 +0200 Subject: [Pw_forum] how can I create a supercell in PWSCF? In-Reply-To: <8b443ba10904240655w3ea42fachd4d16385c0fd7191@mail.gmail.com> References: <8b443ba10904240655w3ea42fachd4d16385c0fd7191@mail.gmail.com> Message-ID: xcrysden? SB On Apr 24, 2009, at 3:55 PM, Pieremanuele Canepa wrote: > Dear all, > does exist a script or a small program in Quantum espresso that > allow me to create a suitable supercell (for instance 2x2x1) > starting from a primitive cell of PWSCF? > Best regards, Piero > > -- > Pieremanuele Canepa > Room 230 > School of Physical Sciences, Ingram Building, > University of Kent, Canterbury, Kent, > CT2 7NH > United Kingdom > ----------------------------------------------------------- > > _______________________________________________ > 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/20090424/3941c15b/attachment.htm From pc229 at kent.ac.uk Fri Apr 24 16:41:54 2009 From: pc229 at kent.ac.uk (pc229 at kent.ac.uk) Date: Fri, 24 Apr 2009 16:41:54 +0200 Subject: [Pw_forum] how can I create a supercell in PWSCF? In-Reply-To: References: <8b443ba10904240655w3ea42fachd4d16385c0fd7191@mail.gmail.com> Message-ID: It doesn't. Xcrysden?let me only visualize the output structure without manipulate it. I can? create the supercell?using the command unit repetition but? I can export the final structure. Should I do it by hand? Best Regards, Piero Nobody knows any shortcut to avoid to write it by hand? ----- Original Message ----- From: Stefano?Baroni? Date: Friday, April 24, 2009 4:31 pm Subject: Re: [Pw_forum] how can I create a supercell?in PWSCF? To: PWSCF?Forum > xcrysden? > SB > > On Apr?24, 2009, at 3:55 PM, Pieremanuele?Canepa?wrote: > > > Dear all, > > does exist a script or a? small program? in Quantum > espresso?that? > > allow me to? create a suitable supercell?(for instance > 2x2x1)? > > starting from a primitive cell of PWSCF? > > Best regards, Piero > > > > -- > > Pieremanuele?Canepa > > Room 230 > > School of Physical Sciences, Ingram Building, > > University of Kent, Canterbury, Kent, > > CT2 7NH > > United Kingdom > > ----------------------------------------------------------- > > > > _______________________________________________ > > 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 > attachmentsWhy? See:? http://www.gnu.org/philosophy/no-word- > attachments.html > > > > > > > --- Pieremanuele Canepa Room 230 School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090424/07b151cf/attachment.htm From pc229 at kent.ac.uk Fri Apr 24 16:45:44 2009 From: pc229 at kent.ac.uk (pc229 at kent.ac.uk) Date: Fri, 24 Apr 2009 16:45:44 +0200 Subject: [Pw_forum] how can I create a supercell in PWSCF? In-Reply-To: References: <8b443ba10904240655w3ea42fachd4d16385c0fd7191@mail.gmail.com> Message-ID: ?It doesn't. Xcrysden?let me only visualize the output structure ?without manipulate it. I can? create the supercell?using the ?command unit repetition but? I cannot export the final structure. ?Should I do it by hand? ?Best Regards, Piero ? ?Nobody knows any shortcut to avoid to write it by hand? > ----- Original Message ----- > From: Stefano?Baroni? > Date: Friday, April 24, 2009 4:31 pm > Subject: Re: [Pw_forum] how can I create a supercell?in PWSCF? > To: PWSCF?Forum > > > xcrysden? > > SB > > > > On Apr?24, 2009, at 3:55 PM, Pieremanuele?Canepa?wrote: > > > > > Dear all, > > > does exist a script or a? small program? in Quantum > > espresso?that? > > > allow me to? create a suitable supercell?(for instance > > 2x2x1)? > > > starting from a primitive cell of PWSCF? > > > Best regards, Piero > > > > > > -- > > > Pieremanuele?Canepa > > > Room 230 > > > School of Physical Sciences, Ingram Building, > > > University of Kent, Canterbury, Kent, > > > CT2 7NH > > > United Kingdom > > > ----------------------------------------------------------- > > > > > > _______________________________________________ > > > 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 > > attachmentsWhy? See:? http://www.gnu.org/philosophy/no-word- > > attachments.html > > > > > > > > > > > > > > > > --- > Pieremanuele Canepa > Room 230 > School of Physical Sciences, Ingram Building, > University of Kent, Canterbury, Kent, > CT2 7NH > United Kingdom > > > > > > > > > > > > > > --- Pieremanuele Canepa Room 230 School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090424/96a294d3/attachment-0001.htm From akohlmey at cmm.chem.upenn.edu Fri Apr 24 16:48:00 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 24 Apr 2009 10:48:00 -0400 Subject: [Pw_forum] how can I create a supercell in PWSCF? In-Reply-To: References: <8b443ba10904240655w3ea42fachd4d16385c0fd7191@mail.gmail.com> Message-ID: <1240584480.18574.70.camel@zero> On Fri, 2009-04-24 at 16:41 +0200, pc229 at kent.ac.uk wrote: > It doesn't. Xcrysden let me only visualize the output structure > without manipulate it. I can create the supercell using the command > unit repetition but I can export the final structure. Should I do it > by hand? what is so difficult about it?? you can just write a little script using awk/perl/python/tcl/... to do one translation/scaling operation and then cut and paste the final (or initial) alat based coordinates from a previous run into this and piece the different translations together and make one input from it. this needs to be adjusted most of the time anyways. cheers, axel. > Best Regards, Piero > > Nobody knows any shortcut to avoid to write it by hand? > > ----- Original Message ----- > From: Stefano Baroni > Date: Friday, April 24, 2009 4:31 pm > Subject: Re: [Pw_forum] how can I create a supercell in PWSCF? > To: PWSCF Forum > > > xcrysden? > > SB > > > > On Apr 24, 2009, at 3:55 PM, Pieremanuele Canepa wrote: > > > > > Dear all, > > > does exist a script or a small program in Quantum > > espresso that > > > allow me to create a suitable supercell (for instance > > 2x2x1) > > > starting from a primitive cell of PWSCF? > > > Best regards, Piero > > > > > > -- > > > Pieremanuele Canepa > > > Room 230 > > > School of Physical Sciences, Ingram Building, > > > University of Kent, Canterbury, Kent, > > > CT2 7NH > > > United Kingdom > > > ----------------------------------------------------------- > > > > > > _______________________________________________ > > > 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 > > attachmentsWhy? See: http://www.gnu.org/philosophy/no-word- > > attachments.html > > > > > > > > > > > > > > > > --- > Pieremanuele Canepa > Room 230 > School of Physical Sciences, Ingram Building, > University of Kent, Canterbury, Kent, > CT2 7NH > United Kingdom > > > > > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From tone.kokalj at ijs.si Fri Apr 24 16:51:31 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 24 Apr 2009 16:51:31 +0200 Subject: [Pw_forum] how can I create a supercell in PWSCF? In-Reply-To: References: <8b443ba10904240655w3ea42fachd4d16385c0fd7191@mail.gmail.com> Message-ID: <1240584691.5164.36.camel@walk.ijs.si> On Fri, 2009-04-24 at 16:41 +0200, pc229 at kent.ac.uk wrote: > It doesn't. Xcrysden let me only visualize the output structure > without manipulate it. This is true. > I can create the supercell using the command unit repetition but I > can export the final structure. Should I do it by hand? This is very clever (never thought about that)! To make it right, make sure you switch to the co-called "translational asymmetruc unit" display (click second left image at the bottom toolbox). Then you save an XSF file. This file will contain a lot of info. Search for ATOMS section. These are atoms you need! Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From pc229 at kent.ac.uk Fri Apr 24 16:53:03 2009 From: pc229 at kent.ac.uk (pc229 at kent.ac.uk) Date: Fri, 24 Apr 2009 16:53:03 +0200 Subject: [Pw_forum] how can I create a supercell in PWSCF? In-Reply-To: <1240584480.18574.70.camel@zero> References: <8b443ba10904240655w3ea42fachd4d16385c0fd7191@mail.gmail.com> <1240584480.18574.70.camel@zero> Message-ID: I know Thanks. I thought there was by far a simpler way already prepared! ----- Original Message ----- From: Axel Kohlmeyer Date: Friday, April 24, 2009 4:49 pm Subject: Re: [Pw_forum] how can I create a supercell in PWSCF? To: PWSCF Forum > On Fri, 2009-04-24 at 16:41 +0200, pc229 at kent.ac.uk wrote: > > It doesn't. Xcrysden let me only visualize the output structure > > without manipulate it. I can? create the supercell using > the command > > unit repetition but? I can export the final structure. > Should I do it > > by hand? > > what is so difficult about it?? > > you can just write a little script using awk/perl/python/tcl/... > to do one translation/scaling operation and then cut and paste > the final (or initial) alat based coordinates from a previous > run into this and piece the different translations together and > make one input from it. this needs to be adjusted most of the > time anyways. > > cheers, > ?? axel. > > > Best Regards, Piero > > > > Nobody knows any shortcut to avoid to write it by hand? > > > > ----- Original Message ----- > > From: Stefano Baroni > > Date: Friday, April 24, 2009 4:31 pm > > Subject: Re: [Pw_forum] how can I create a supercell in PWSCF? > > To: PWSCF Forum > > > > > xcrysden? > > > SB > > > > > > On Apr 24, 2009, at 3:55 PM, Pieremanuele Canepa wrote: > > > > > > > Dear all, > > > > does exist a script or a? small program? in > Quantum > > > espresso that? > > > > allow me to? create a suitable supercell (for > instance > > > 2x2x1)? > > > > starting from a primitive cell of PWSCF? > > > > Best regards, Piero > > > > > > > > -- > > > > Pieremanuele Canepa > > > > Room 230 > > > > School of Physical Sciences, Ingram Building, > > > > University of Kent, Canterbury, Kent, > > > > CT2 7NH > > > > United Kingdom > > > > ----------------------------------------------------------- > > > > > > > > _______________________________________________ > > > > 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 > > > attachmentsWhy? See:? http://www.gnu.org/philosophy/no- > word- > > > attachments.html > > > > > > > > > > > > > > > > > > > > > > > > > --- > > Pieremanuele Canepa > > Room 230 > > School of Physical Sciences, Ingram Building, > > University of Kent, Canterbury, Kent, > > CT2 7NH > > United Kingdom > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > ======================================================================= > Axel Kohlmeyer?? > akohlmey at cmm.chem.upenn.edu?? http://www.cmm.upenn.edu > ?? Center for Molecular Modeling?? -- > ?? University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA > 19104-6323 > tel: 1-215-898-1582,? fax: 1-215-573-6233,? office- > tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better > idiot. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > --- Pieremanuele Canepa Room 230 School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090424/dd8eed0f/attachment.htm From pc229 at kent.ac.uk Fri Apr 24 16:54:14 2009 From: pc229 at kent.ac.uk (pc229 at kent.ac.uk) Date: Fri, 24 Apr 2009 16:54:14 +0200 Subject: [Pw_forum] how can I create a supercell in PWSCF? In-Reply-To: <1240584691.5164.36.camel@walk.ijs.si> References: <8b443ba10904240655w3ea42fachd4d16385c0fd7191@mail.gmail.com> <1240584691.5164.36.camel@walk.ijs.si> Message-ID: Thank you tone ----- Original Message ----- From: Tone Kokalj Date: Friday, April 24, 2009 4:51 pm Subject: Re: [Pw_forum] how can I create a supercell in PWSCF? To: PWSCF Forum > On Fri, 2009-04-24 at 16:41 +0200, pc229 at kent.ac.uk wrote: > > It doesn't. Xcrysden let me only visualize the output structure > > without manipulate it. > > This is true. > > > I can? create the supercell using the command unit > repetition but? I > > can export the final structure. Should I do it by hand? > > This is very clever (never thought about that)! > > To make it right, make sure you switch to the co-called "translational > asymmetruc unit" display (click second left image at the bottom > toolbox). Then you save an XSF file. This file will contain a > lot of > info. Search for ATOMS section. These are atoms you need! > > Regards, Tone > > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint attachments. > See:? http://www.gnu.org/philosophy/no-word-attachments.html > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > --- Pieremanuele Canepa Room 230 School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090424/5ad91764/attachment-0001.htm From paulatto at sissa.it Fri Apr 24 17:07:20 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 24 Apr 2009 17:07:20 +0200 Subject: [Pw_forum] how can I create a supercell in PWSCF? In-Reply-To: <1240584691.5164.36.camel@walk.ijs.si> References: <8b443ba10904240655w3ea42fachd4d16385c0fd7191@mail.gmail.com> <1240584691.5164.36.camel@walk.ijs.si> Message-ID: In data 24 aprile 2009 alle ore 16:51:31, Tone Kokalj ha scritto: > To make it right, make sure you switch to the co-called "translational > asymmetruc unit" display (click second left image at the bottom > toolbox). Then you save an XSF file. This file will contain a lot of > info. Search for ATOMS section. These are atoms you need! this is nice, I have used it a couple of time myself, it has a couple of minor drawback though that you have to be aware of: 1. the new atomic positions will be in angstrom units 2. you have to redefine the unit cell by hand (the one defined in the PRIMVEC section of the XSF file is in Angstrom, not rescaled to fit the supercell) In the CVS version of QE there is a tentative and experimental support for aritmetic expression, with this in mind you can define a supercell easily if you are using alat units in this way: 1. use ibrav=0 and specify the cell axis by hand, leaving celldm(0) (aka alat) unchanged, e.g. if you are doing a 2x2x1 FCC you will have: CELL (alat) -1 0 1 0 1 1 -0.5 0.5 0 2. you can then copy/past the atomic position four times (in units of alat) and change them by adding one each time, i.e. let's suppose you have silicon: Si 0 0 0 Si 1/4 1/4 1/4 Si 1 0 0 Si 1/4+1 0 0 ... Si 1/4+1 1/4+1 0 A major drwaback is that you have to do it by hand/script and that the resulting input file is not readable by xrysden. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From akohlmey at cmm.chem.upenn.edu Fri Apr 24 17:13:32 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 24 Apr 2009 11:13:32 -0400 Subject: [Pw_forum] how can I create a supercell in PWSCF? In-Reply-To: References: <8b443ba10904240655w3ea42fachd4d16385c0fd7191@mail.gmail.com> <1240584480.18574.70.camel@zero> Message-ID: <1240586012.18574.75.camel@zero> On Fri, 2009-04-24 at 16:53 +0200, pc229 at kent.ac.uk wrote: > I know Thanks. I thought there was by far a simpler way already > prepared! as with almost any open source project, people primarily focus on what they personally think to be the most important. i consider the method i outlined quite simple and it allows for very large flexibility. if you think differently, then this is _your_ chance. write it and contribute it. this is the best way to pay back the developers of Q-E for all their efforts. cheers, axel. > > ----- Original Message ----- > From: Axel Kohlmeyer > Date: Friday, April 24, 2009 4:49 pm > Subject: Re: [Pw_forum] how can I create a supercell in PWSCF? > To: PWSCF Forum > > > On Fri, 2009-04-24 at 16:41 +0200, pc229 at kent.ac.uk wrote: > > > It doesn't. Xcrysden let me only visualize the output structure > > > without manipulate it. I can create the supercell using > > the command > > > unit repetition but I can export the final structure. > > Should I do it > > > by hand? > > > > what is so difficult about it?? > > > > you can just write a little script using awk/perl/python/tcl/... > > to do one translation/scaling operation and then cut and paste > > the final (or initial) alat based coordinates from a previous > > run into this and piece the different translations together and > > make one input from it. this needs to be adjusted most of the > > time anyways. > > > > cheers, > > axel. > > > > > Best Regards, Piero > > > > > > Nobody knows any shortcut to avoid to write it by hand? > > > > > > ----- Original Message ----- > > > From: Stefano Baroni > > > Date: Friday, April 24, 2009 4:31 pm > > > Subject: Re: [Pw_forum] how can I create a supercell in PWSCF? > > > To: PWSCF Forum > > > > > > > xcrysden? > > > > SB > > > > > > > > On Apr 24, 2009, at 3:55 PM, Pieremanuele Canepa wrote: > > > > > > > > > Dear all, > > > > > does exist a script or a small program in > > Quantum > > > > espresso that > > > > > allow me to create a suitable supercell (for > > instance > > > > 2x2x1) > > > > > starting from a primitive cell of PWSCF? > > > > > Best regards, Piero > > > > > > > > > > -- > > > > > Pieremanuele Canepa > > > > > Room 230 > > > > > School of Physical Sciences, Ingram Building, > > > > > University of Kent, Canterbury, Kent, > > > > > CT2 7NH > > > > > United Kingdom > > > > > ----------------------------------------------------------- > > > > > > > > > > _______________________________________________ > > > > > 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 > > > > attachmentsWhy? See: http://www.gnu.org/philosophy/no- > > word- > > > > attachments.html > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > --- > > > Pieremanuele Canepa > > > Room 230 > > > School of Physical Sciences, Ingram Building, > > > University of Kent, Canterbury, Kent, > > > CT2 7NH > > > United Kingdom > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > > > ======================================================================= > > Axel Kohlmeyer > > akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > > Center for Molecular Modeling -- > > University of Pennsylvania > > Department of Chemistry, 231 S.34th Street, Philadelphia, PA > > 19104-6323 > > tel: 1-215-898-1582, fax: 1-215-573-6233, office- > > tel: 1-215-898-5425 > > > ======================================================================= > > If you make something idiot-proof, the universe creates a better > > idiot. > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > --- > Pieremanuele Canepa > Room 230 > School of Physical Sciences, Ingram Building, > University of Kent, Canterbury, Kent, > CT2 7NH > United Kingdom > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From tone.kokalj at ijs.si Fri Apr 24 17:22:13 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 24 Apr 2009 17:22:13 +0200 Subject: [Pw_forum] how can I create a supercell in PWSCF? In-Reply-To: References: <8b443ba10904240655w3ea42fachd4d16385c0fd7191@mail.gmail.com> <1240584691.5164.36.camel@walk.ijs.si> Message-ID: <1240586533.5164.55.camel@walk.ijs.si> On Fri, 2009-04-24 at 17:07 +0200, Lorenzo Paulatto wrote: > this is nice, I have used it a couple of time myself, it has a couple of > minor drawback though that you have to be aware of: > 1. the new atomic positions will be in angstrom units not a big problem, because one may use "ATOMIC_POSITIONS angstrom" ... > 2. you can then copy/past the atomic position four times (in units of > alat) and change them by adding one each time, i.e. let's suppose you have > silicon: > Si 0 0 0 > Si 1/4 1/4 1/4 > Si 1 0 0 > Si 1/4+1 0 0 > ... > Si 1/4+1 1/4+1 0 > > A major drwaback is that you have to do it by hand/script and that the > resulting input file is not readable by xrysden. Thanks for pointing this out. I have to think about the solution. This new input syntax will have to become readable by xcrysden. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From pc229 at kent.ac.uk Fri Apr 24 17:27:42 2009 From: pc229 at kent.ac.uk (Pieremanuele Canepa) Date: Fri, 24 Apr 2009 17:27:42 +0200 Subject: [Pw_forum] how can I create a supercell in PWSCF? In-Reply-To: <1240586012.18574.75.camel@zero> References: <8b443ba10904240655w3ea42fachd4d16385c0fd7191@mail.gmail.com> <1240584480.18574.70.camel@zero> <1240586012.18574.75.camel@zero> Message-ID: <8b443ba10904240827g1c716769x5d46e37a38fd207d@mail.gmail.com> You are right man ! Cheers, Piero On Fri, Apr 24, 2009 at 5:13 PM, Axel Kohlmeyer wrote: > On Fri, 2009-04-24 at 16:53 +0200, pc229 at kent.ac.uk wrote: > > I know Thanks. I thought there was by far a simpler way already > > prepared! > > as with almost any open source project, people primarily > focus on what they personally think to be the most important. > > i consider the method i outlined quite simple and it > allows for very large flexibility. if you think differently, > then this is _your_ chance. write it and contribute it. > this is the best way to pay back the developers of Q-E > for all their efforts. > > cheers, > axel. > > > > > ----- Original Message ----- > > From: Axel Kohlmeyer > > Date: Friday, April 24, 2009 4:49 pm > > Subject: Re: [Pw_forum] how can I create a supercell in PWSCF? > > To: PWSCF Forum > > > > > On Fri, 2009-04-24 at 16:41 +0200, pc229 at kent.ac.uk wrote: > > > > It doesn't. Xcrysden let me only visualize the output structure > > > > without manipulate it. I can create the supercell using > > > the command > > > > unit repetition but I can export the final structure. > > > Should I do it > > > > by hand? > > > > > > what is so difficult about it?? > > > > > > you can just write a little script using awk/perl/python/tcl/... > > > to do one translation/scaling operation and then cut and paste > > > the final (or initial) alat based coordinates from a previous > > > run into this and piece the different translations together and > > > make one input from it. this needs to be adjusted most of the > > > time anyways. > > > > > > cheers, > > > axel. > > > > > > > Best Regards, Piero > > > > > > > > Nobody knows any shortcut to avoid to write it by hand? > > > > > > > > ----- Original Message ----- > > > > From: Stefano Baroni > > > > Date: Friday, April 24, 2009 4:31 pm > > > > Subject: Re: [Pw_forum] how can I create a supercell in PWSCF? > > > > To: PWSCF Forum > > > > > > > > > xcrysden? > > > > > SB > > > > > > > > > > On Apr 24, 2009, at 3:55 PM, Pieremanuele Canepa wrote: > > > > > > > > > > > Dear all, > > > > > > does exist a script or a small program in > > > Quantum > > > > > espresso that > > > > > > allow me to create a suitable supercell (for > > > instance > > > > > 2x2x1) > > > > > > starting from a primitive cell of PWSCF? > > > > > > Best regards, Piero > > > > > > > > > > > > -- > > > > > > Pieremanuele Canepa > > > > > > Room 230 > > > > > > School of Physical Sciences, Ingram Building, > > > > > > University of Kent, Canterbury, Kent, > > > > > > CT2 7NH > > > > > > United Kingdom > > > > > > ----------------------------------------------------------- > > > > > > > > > > > > _______________________________________________ > > > > > > 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 > > > > > attachmentsWhy? See: http://www.gnu.org/philosophy/no- > > > word- > > > > > attachments.html > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > --- > > > > Pieremanuele Canepa > > > > Room 230 > > > > School of Physical Sciences, Ingram Building, > > > > University of Kent, Canterbury, Kent, > > > > CT2 7NH > > > > United Kingdom > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > Pw_forum mailing list > > > > Pw_forum at pwscf.org > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > > > > > ======================================================================= > > > Axel Kohlmeyer > > > akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > > > Center for Molecular Modeling -- > > > University of Pennsylvania > > > Department of Chemistry, 231 S.34th Street, Philadelphia, PA > > > 19104-6323 > > > tel: 1-215-898-1582, fax: 1-215-573-6233, office- > > > tel: 1-215-898-5425 > > > > > ======================================================================= > > > If you make something idiot-proof, the universe creates a better > > > idiot. > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > --- > > Pieremanuele Canepa > > Room 230 > > School of Physical Sciences, Ingram Building, > > University of Kent, Canterbury, Kent, > > CT2 7NH > > United Kingdom > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Pieremanuele Canepa Room 230 School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom ----------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090424/3feab555/attachment-0001.htm From pc229 at kent.ac.uk Fri Apr 24 17:32:07 2009 From: pc229 at kent.ac.uk (Pieremanuele Canepa) Date: Fri, 24 Apr 2009 17:32:07 +0200 Subject: [Pw_forum] how can I create a supercell in PWSCF? In-Reply-To: <8b443ba10904240827g1c716769x5d46e37a38fd207d@mail.gmail.com> References: <8b443ba10904240655w3ea42fachd4d16385c0fd7191@mail.gmail.com> <1240584480.18574.70.camel@zero> <1240586012.18574.75.camel@zero> <8b443ba10904240827g1c716769x5d46e37a38fd207d@mail.gmail.com> Message-ID: <8b443ba10904240832u7fd2b9f7s13da43d7faad324b@mail.gmail.com> Anyway thanks to everybody for helping me! On Fri, Apr 24, 2009 at 5:27 PM, Pieremanuele Canepa wrote: > You are right man ! > Cheers, Piero > > > On Fri, Apr 24, 2009 at 5:13 PM, Axel Kohlmeyer < > akohlmey at cmm.chem.upenn.edu> wrote: > >> On Fri, 2009-04-24 at 16:53 +0200, pc229 at kent.ac.uk wrote: >> > I know Thanks. I thought there was by far a simpler way already >> > prepared! >> >> as with almost any open source project, people primarily >> focus on what they personally think to be the most important. >> >> i consider the method i outlined quite simple and it >> allows for very large flexibility. if you think differently, >> then this is _your_ chance. write it and contribute it. >> this is the best way to pay back the developers of Q-E >> for all their efforts. >> >> cheers, >> axel. >> >> > >> > ----- Original Message ----- >> > From: Axel Kohlmeyer >> > Date: Friday, April 24, 2009 4:49 pm >> > Subject: Re: [Pw_forum] how can I create a supercell in PWSCF? >> > To: PWSCF Forum >> > >> > > On Fri, 2009-04-24 at 16:41 +0200, pc229 at kent.ac.uk wrote: >> > > > It doesn't. Xcrysden let me only visualize the output structure >> > > > without manipulate it. I can create the supercell using >> > > the command >> > > > unit repetition but I can export the final structure. >> > > Should I do it >> > > > by hand? >> > > >> > > what is so difficult about it?? >> > > >> > > you can just write a little script using awk/perl/python/tcl/... >> > > to do one translation/scaling operation and then cut and paste >> > > the final (or initial) alat based coordinates from a previous >> > > run into this and piece the different translations together and >> > > make one input from it. this needs to be adjusted most of the >> > > time anyways. >> > > >> > > cheers, >> > > axel. >> > > >> > > > Best Regards, Piero >> > > > >> > > > Nobody knows any shortcut to avoid to write it by hand? >> > > > >> > > > ----- Original Message ----- >> > > > From: Stefano Baroni >> > > > Date: Friday, April 24, 2009 4:31 pm >> > > > Subject: Re: [Pw_forum] how can I create a supercell in PWSCF? >> > > > To: PWSCF Forum >> > > > >> > > > > xcrysden? >> > > > > SB >> > > > > >> > > > > On Apr 24, 2009, at 3:55 PM, Pieremanuele Canepa wrote: >> > > > > >> > > > > > Dear all, >> > > > > > does exist a script or a small program in >> > > Quantum >> > > > > espresso that >> > > > > > allow me to create a suitable supercell (for >> > > instance >> > > > > 2x2x1) >> > > > > > starting from a primitive cell of PWSCF? >> > > > > > Best regards, Piero >> > > > > > >> > > > > > -- >> > > > > > Pieremanuele Canepa >> > > > > > Room 230 >> > > > > > School of Physical Sciences, Ingram Building, >> > > > > > University of Kent, Canterbury, Kent, >> > > > > > CT2 7NH >> > > > > > United Kingdom >> > > > > > ----------------------------------------------------------- >> > > > > > >> > > > > > _______________________________________________ >> > > > > > 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 >> > > > > attachmentsWhy? See: http://www.gnu.org/philosophy/no- >> > > word- >> > > > > attachments.html >> > > > > >> > > > > >> > > > > >> > > > > >> > > > > >> > > > > >> > > > > >> > > > >> > > > --- >> > > > Pieremanuele Canepa >> > > > Room 230 >> > > > School of Physical Sciences, Ingram Building, >> > > > University of Kent, Canterbury, Kent, >> > > > CT2 7NH >> > > > United Kingdom >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > _______________________________________________ >> > > > Pw_forum mailing list >> > > > Pw_forum at pwscf.org >> > > > http://www.democritos.it/mailman/listinfo/pw_forum >> > > >> > > -- >> > > >> > ======================================================================= >> > > Axel Kohlmeyer >> > > akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu >> > > Center for Molecular Modeling -- >> > > University of Pennsylvania >> > > Department of Chemistry, 231 S.34th Street, Philadelphia, PA >> > > 19104-6323 >> > > tel: 1-215-898-1582, fax: 1-215-573-6233, office- >> > > tel: 1-215-898-5425 >> > > >> > ======================================================================= >> > > If you make something idiot-proof, the universe creates a better >> > > idiot. >> > > _______________________________________________ >> > > Pw_forum mailing list >> > > Pw_forum at pwscf.org >> > > http://www.democritos.it/mailman/listinfo/pw_forum >> > > >> > >> > --- >> > Pieremanuele Canepa >> > Room 230 >> > School of Physical Sciences, Ingram Building, >> > University of Kent, Canterbury, Kent, >> > CT2 7NH >> > United Kingdom >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> >> -- >> ======================================================================= >> Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu >> Center for Molecular Modeling -- University of Pennsylvania >> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 >> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 >> ======================================================================= >> If you make something idiot-proof, the universe creates a better idiot. >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > Pieremanuele Canepa > Room 230 > School of Physical Sciences, Ingram Building, > University of Kent, Canterbury, Kent, > CT2 7NH > United Kingdom > ----------------------------------------------------------- > > -- Pieremanuele Canepa Room 230 School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom ----------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090424/25d699f4/attachment.htm From eyvaz_isaev at yahoo.com Fri Apr 24 17:55:12 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 24 Apr 2009 08:55:12 -0700 (PDT) Subject: [Pw_forum] how can I create a supercell in PWSCF? In-Reply-To: <8b443ba10904240827g1c716769x5d46e37a38fd207d@mail.gmail.com> Message-ID: <172659.32197.qm@web65706.mail.ac4.yahoo.com> Dear all, Let me add (again!!!) my 5 cent words to this issue: If you need to create a supercell (and too lazy to create a small program to translate atoms), use Dario's PHON code. http://chianti.geol.ucl.ac.uk/~dario/ As Dario and QE have the same origin, Triest, they are compatible. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Fri, 4/24/09, Pieremanuele Canepa wrote: > From: Pieremanuele Canepa > Subject: Re: [Pw_forum] how can I create a supercell in PWSCF? > To: "PWSCF Forum" > Date: Friday, April 24, 2009, 7:27 PM > You are right man ! > Cheers, Piero > > On Fri, Apr 24, 2009 at 5:13 PM, Axel Kohlmeyer > > wrote: > > > On Fri, 2009-04-24 at 16:53 +0200, pc229 at kent.ac.uk > wrote: > > > I know Thanks. I thought there was by far a > simpler way already > > > prepared! > > > > as with almost any open source project, people > primarily > > focus on what they personally think to be the most > important. > > > > i consider the method i outlined quite simple and it > > allows for very large flexibility. if you think > differently, > > then this is _your_ chance. write it and contribute > it. > > this is the best way to pay back the developers of Q-E > > for all their efforts. > > > > cheers, > > axel. > > > > > > > > ----- Original Message ----- > > > From: Axel Kohlmeyer > > > > Date: Friday, April 24, 2009 4:49 pm > > > Subject: Re: [Pw_forum] how can I create a > supercell in PWSCF? > > > To: PWSCF Forum > > > > > > > On Fri, 2009-04-24 at 16:41 +0200, > pc229 at kent.ac.uk wrote: > > > > > It doesn't. Xcrysden let me only > visualize the output structure > > > > > without manipulate it. I can create > the supercell using > > > > the command > > > > > unit repetition but I can export the > final structure. > > > > Should I do it > > > > > by hand? > > > > > > > > what is so difficult about it?? > > > > > > > > you can just write a little script using > awk/perl/python/tcl/... > > > > to do one translation/scaling operation and > then cut and paste > > > > the final (or initial) alat based > coordinates from a previous > > > > run into this and piece the different > translations together and > > > > make one input from it. this needs to be > adjusted most of the > > > > time anyways. > > > > > > > > cheers, > > > > axel. > > > > > > > > > Best Regards, Piero > > > > > > > > > > Nobody knows any shortcut to avoid to > write it by hand? > > > > > > > > > > ----- Original Message ----- > > > > > From: Stefano Baroni > > > > > > Date: Friday, April 24, 2009 4:31 pm > > > > > Subject: Re: [Pw_forum] how can I > create a supercell in PWSCF? > > > > > To: PWSCF Forum > > > > > > > > > > > > xcrysden? > > > > > > SB > > > > > > > > > > > > On Apr 24, 2009, at 3:55 PM, > Pieremanuele Canepa wrote: > > > > > > > > > > > > > Dear all, > > > > > > > does exist a script or a > small program in > > > > Quantum > > > > > > espresso that > > > > > > > allow me to create a > suitable supercell (for > > > > instance > > > > > > 2x2x1) > > > > > > > starting from a primitive > cell of PWSCF? > > > > > > > Best regards, Piero > > > > > > > > > > > > > > -- > > > > > > > Pieremanuele Canepa > > > > > > > Room 230 > > > > > > > School of Physical Sciences, > Ingram Building, > > > > > > > University of Kent, > Canterbury, Kent, > > > > > > > CT2 7NH > > > > > > > United Kingdom > > > > > > > > ----------------------------------------------------------- > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > 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 > > > > > > attachmentsWhy? See: > http://www.gnu.org/philosophy/no- > > > > word- > > > > > > attachments.html > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > --- > > > > > Pieremanuele Canepa > > > > > Room 230 > > > > > School of Physical Sciences, Ingram > Building, > > > > > University of Kent, Canterbury, Kent, > > > > > CT2 7NH > > > > > United Kingdom > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > Pw_forum mailing list > > > > > Pw_forum at pwscf.org > > > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > > > > > > > > ======================================================================= > > > > Axel Kohlmeyer > > > > akohlmey at cmm.chem.upenn.edu > http://www.cmm.upenn.edu > > > > Center for Molecular Modeling -- > > > > University of Pennsylvania > > > > Department of Chemistry, 231 S.34th Street, > Philadelphia, PA > > > > 19104-6323 > > > > tel: 1-215-898-1582, fax: 1-215-573-6233, > office- > > > > tel: 1-215-898-5425 > > > > > > > > ======================================================================= > > > > If you make something idiot-proof, the > universe creates a better > > > > idiot. > > > > > _______________________________________________ > > > > Pw_forum mailing list > > > > Pw_forum at pwscf.org > > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > --- > > > Pieremanuele Canepa > > > Room 230 > > > School of Physical Sciences, Ingram Building, > > > University of Kent, Canterbury, Kent, > > > CT2 7NH > > > United Kingdom > > > > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > > > ======================================================================= > > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu > http://www.cmm.upenn.edu > > Center for Molecular Modeling -- University of > Pennsylvania > > Department of Chemistry, 231 S.34th Street, > Philadelphia, PA 19104-6323 > > tel: 1-215-898-1582, fax: 1-215-573-6233, > office-tel: 1-215-898-5425 > > > ======================================================================= > > If you make something idiot-proof, the universe > creates a better idiot. > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > Pieremanuele Canepa > Room 230 > School of Physical Sciences, Ingram Building, > University of Kent, Canterbury, Kent, > CT2 7NH > United Kingdom > ----------------------------------------------------------- > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From kyin.cn at gmail.com Sat Apr 25 05:38:04 2009 From: kyin.cn at gmail.com (Kun Yin) Date: Sat, 25 Apr 2009 11:38:04 +0800 Subject: [Pw_forum] how can I create a supercell in PWSCF? References: <172659.32197.qm@web65706.mail.ac4.yahoo.com> Message-ID: Dear all: Share my solutions. (1) Make supercell, primitive cell and conventional unit-cell positions -- "spacegroup" program in EXCITING package (http://exciting.sourceforge.net, seems changing name). I edited very little code of "spacegroup" program, recompiled to make it output file format of PWSCF alike and POSCAR (for VASP and fropho). Usage: after program compiled, make a file containing lattice parameters, wyckoff positions, supercell size,etc called spacegroup.in and then execute command: spacegroup spacegroup.in (2) Check symmetry -- I use "fropho" (http://fropho.sourceforge.net), something like PHON, but I think newer and better. Usage: after program compiled, just execute command: echo 'find_symmetry' | fropho or echo 'find_symmetry = xxx' | fropho (xxx is the precision, e.g., 1.0d-6) Hope helpful. -- Kun Yin Ph.D. Candidate School of Earth Sciences and Engineering Nanjing University 502 Geological Laboratory Building 22 Hankou Road Nanjing 210093 P.R. China email: kyin.cn at gmail.com ----- Original Message ----- From: "Eyvaz Isaev" To: "PWSCF Forum" Sent: Friday, April 24, 2009 11:55 PM Subject: Re: [Pw_forum] how can I create a supercell in PWSCF? Dear all, Let me add (again!!!) my 5 cent words to this issue: If you need to create a supercell (and too lazy to create a small program to translate atoms), use Dario's PHON code. http://chianti.geol.ucl.ac.uk/~dario/ As Dario and QE have the same origin, Triest, they are compatible. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Fri, 4/24/09, Pieremanuele Canepa wrote: > From: Pieremanuele Canepa > Subject: Re: [Pw_forum] how can I create a supercell in PWSCF? > To: "PWSCF Forum" > Date: Friday, April 24, 2009, 7:27 PM > You are right man ! > Cheers, Piero > > On Fri, Apr 24, 2009 at 5:13 PM, Axel Kohlmeyer > > wrote: > > > On Fri, 2009-04-24 at 16:53 +0200, pc229 at kent.ac.uk > wrote: > > > I know Thanks. I thought there was by far a > simpler way already > > > prepared! > > > > as with almost any open source project, people > primarily > > focus on what they personally think to be the most > important. > > > > i consider the method i outlined quite simple and it > > allows for very large flexibility. if you think > differently, > > then this is _your_ chance. write it and contribute > it. > > this is the best way to pay back the developers of Q-E > > for all their efforts. > > > > cheers, > > axel. > > > > > > > > ----- Original Message ----- > > > From: Axel Kohlmeyer > > > > Date: Friday, April 24, 2009 4:49 pm > > > Subject: Re: [Pw_forum] how can I create a > supercell in PWSCF? > > > To: PWSCF Forum > > > > > > > On Fri, 2009-04-24 at 16:41 +0200, > pc229 at kent.ac.uk wrote: > > > > > It doesn't. Xcrysden let me only > visualize the output structure > > > > > without manipulate it. I can create > the supercell using > > > > the command > > > > > unit repetition but I can export the > final structure. > > > > Should I do it > > > > > by hand? > > > > > > > > what is so difficult about it?? > > > > > > > > you can just write a little script using > awk/perl/python/tcl/... > > > > to do one translation/scaling operation and > then cut and paste > > > > the final (or initial) alat based > coordinates from a previous > > > > run into this and piece the different > translations together and > > > > make one input from it. this needs to be > adjusted most of the > > > > time anyways. > > > > > > > > cheers, > > > > axel. > > > > > > > > > Best Regards, Piero > > > > > > > > > > Nobody knows any shortcut to avoid to > write it by hand? > > > > > > > > > > ----- Original Message ----- > > > > > From: Stefano Baroni > > > > > > Date: Friday, April 24, 2009 4:31 pm > > > > > Subject: Re: [Pw_forum] how can I > create a supercell in PWSCF? > > > > > To: PWSCF Forum > > > > > > > > > > > > xcrysden? > > > > > > SB > > > > > > > > > > > > On Apr 24, 2009, at 3:55 PM, > Pieremanuele Canepa wrote: > > > > > > > > > > > > > Dear all, > > > > > > > does exist a script or a > small program in > > > > Quantum > > > > > > espresso that > > > > > > > allow me to create a > suitable supercell (for > > > > instance > > > > > > 2x2x1) > > > > > > > starting from a primitive > cell of PWSCF? > > > > > > > Best regards, Piero > > > > > > > > > > > > > > -- > > > > > > > Pieremanuele Canepa > > > > > > > Room 230 > > > > > > > School of Physical Sciences, > Ingram Building, > > > > > > > University of Kent, > Canterbury, Kent, > > > > > > > CT2 7NH > > > > > > > United Kingdom > > > > > > > > ----------------------------------------------------------- > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > 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 > > > > > > attachmentsWhy? See: > http://www.gnu.org/philosophy/no- > > > > word- > > > > > > attachments.html > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > --- > > > > > Pieremanuele Canepa > > > > > Room 230 > > > > > School of Physical Sciences, Ingram > Building, > > > > > University of Kent, Canterbury, Kent, > > > > > CT2 7NH > > > > > United Kingdom > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > Pw_forum mailing list > > > > > Pw_forum at pwscf.org > > > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > > > > > > > > ======================================================================= > > > > Axel Kohlmeyer > > > > akohlmey at cmm.chem.upenn.edu > http://www.cmm.upenn.edu > > > > Center for Molecular Modeling -- > > > > University of Pennsylvania > > > > Department of Chemistry, 231 S.34th Street, > Philadelphia, PA > > > > 19104-6323 > > > > tel: 1-215-898-1582, fax: 1-215-573-6233, > office- > > > > tel: 1-215-898-5425 > > > > > > > > ======================================================================= > > > > If you make something idiot-proof, the > universe creates a better > > > > idiot. > > > > > _______________________________________________ > > > > Pw_forum mailing list > > > > Pw_forum at pwscf.org > > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > --- > > > Pieremanuele Canepa > > > Room 230 > > > School of Physical Sciences, Ingram Building, > > > University of Kent, Canterbury, Kent, > > > CT2 7NH > > > United Kingdom > > > > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > > > ======================================================================= > > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu > http://www.cmm.upenn.edu > > Center for Molecular Modeling -- University of > Pennsylvania > > Department of Chemistry, 231 S.34th Street, > Philadelphia, PA 19104-6323 > > tel: 1-215-898-1582, fax: 1-215-573-6233, > office-tel: 1-215-898-5425 > > > ======================================================================= > > If you make something idiot-proof, the universe > creates a better idiot. > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > Pieremanuele Canepa > Room 230 > School of Physical Sciences, Ingram Building, > University of Kent, Canterbury, Kent, > CT2 7NH > United Kingdom > ----------------------------------------------------------- > _______________________________________________ > 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 wangweiphysics at yahoo.com.cn Sat Apr 25 17:39:28 2009 From: wangweiphysics at yahoo.com.cn (=?utf-8?B?546uIOeOiw==?=) Date: Sat, 25 Apr 2009 23:39:28 +0800 (CST) Subject: [Pw_forum] from phq_readin : error # 1 , no elec. field with metals Message-ID: <60951.11396.qm@web15208.mail.cnb.yahoo.com> Dear all, ?? I want to calculate phonon frequencies at Gamma for superconductor KOs2O6, according to the example02, first I run scf calculation using pw.x command without any error, but when I perform the phonon calculation, the error appears as forrows: ?? from phq_readin: error #?????? 1 ?? no elec. field with metals Who can tell me why? Thank you very much! ? The input files as follows: kos2o6.scf.in ??&CONTROL ???????????????? calculation = 'scf' , ??????????????? restart_mode = 'from_scratch' , ????????????????????? outdir = '/home/ww/data/kos2o6/' , ????????????????????? wfcdir = '/home/ww/data/kos2o6/' , ????????????????? pseudo_dir = '/home/ww/PWscf/pseudo/' , ????????????????????? prefix = 'kos2o6' , ?/ ?&SYSTEM ?????????????????????? ibrav = 2, ?????????????????? celldm(1) = 19.0945, ???????????????????????? nat = 18, ??????????????????????? ntyp = 3, ???????????????????? ecutwfc = 60 , ???????????????????? ecutrho = 600 , ???????????????? occupations = 'smearing' , ???????????????????? degauss = 0.03 ??????????????????? smearing = 'gauss' , ?/ ?&ELECTRONS ??????????????????? conv_thr = 1.0D-8 , ???????????????? mixing_beta = 0.7 , ?/ ATOMIC_SPECIES ??? K?? 39.10000? K.pbe-sp.UPF ?? Os? 190.20000? Os.pbe-n-van.UPF ??? O?? 16.00000? O.pbe-van_ak.UPF ATOMIC_POSITIONS crystal ?? .... K_POINTS {automatic} ? 10? 10? 10? 0? 0? 0 kos2o6.phG.in: ???? phonons of kos2o6 at Gamma ?&inputph ? tr2_ph=1.0d-14, ? prefix='kos2o6', ? epsil=.true., ? amass(1)=39.10, ? amass(2)=190.2, ? amass(3)=16.00, ? outdir='/home/ww/data/kos2o6/', ? fildyn='kos2o6.dynG', ?/ 0.0 0.0 0.0 ___________________________________________________________ ????????????????? http://card.mail.cn.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090425/0cb9cf45/attachment.htm From lanhaiping at gmail.com Sat Apr 25 18:56:47 2009 From: lanhaiping at gmail.com (lan haiping) Date: Sun, 26 Apr 2009 00:56:47 +0800 Subject: [Pw_forum] from phq_readin : error # 1 , no elec. field with metals In-Reply-To: <60951.11396.qm@web15208.mail.cnb.yahoo.com> References: <60951.11396.qm@web15208.mail.cnb.yahoo.com> Message-ID: Hi, According to INPUT_PH, epsil LOGICAL *Default:* .false. If .true. in a q=0 calculation for a non metal the macroscopic dielectric constant of the system is computed. Do not set epsil to .true. if you have a metallic system or q/=0: the code will complain and stop. Therefore, your system should be a metal, and phonon code complained and stopped. Please supply your affiliation! Regards, On Sat, Apr 25, 2009 at 11:39 PM, ? ? wrote: > Dear all, > I want to calculate phonon frequencies at Gamma for superconductor > KOs2O6, according to the example02, first I run scf calculation using pw.x > command without any error, but when I perform the phonon calculation, the > error appears as forrows: > from phq_readin: error # 1 > no elec. field with metals > Who can tell me why? Thank you very much! > > The input files as follows: > kos2o6.scf.in > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > outdir = '/home/ww/data/kos2o6/' , > wfcdir = '/home/ww/data/kos2o6/' , > pseudo_dir = '/home/ww/PWscf/pseudo/' , > prefix = 'kos2o6' , > / > &SYSTEM > ibrav = 2, > celldm(1) = 19.0945, > nat = 18, > ntyp = 3, > ecutwfc = 60 , > ecutrho = 600 , > occupations = 'smearing' , > degauss = 0.03 > smearing = 'gauss' , > / > &ELECTRONS > conv_thr = 1.0D-8 , > mixing_beta = 0.7 , > / > ATOMIC_SPECIES > K 39.10000 K.pbe-sp.UPF > Os 190.20000 Os.pbe-n-van.UPF > O 16.00000 O.pbe-van_ak.UPF > ATOMIC_POSITIONS crystal > .... > K_POINTS {automatic} > 10 10 10 0 0 0 > kos2o6.phG.in: > phonons of kos2o6 at Gamma > &inputph > tr2_ph=1.0d-14, > prefix='kos2o6', > epsil=.true., > amass(1)=39.10, > amass(2)=190.2, > amass(3)=16.00, > outdir='/home/ww/data/kos2o6/', > fildyn='kos2o6.dynG', > / > 0.0 0.0 0.0 > > ------------------------------ > ????????????????? > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090426/edc33cb1/attachment.htm From eyvaz_isaev at yahoo.com Sat Apr 25 18:59:58 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sat, 25 Apr 2009 09:59:58 -0700 (PDT) Subject: [Pw_forum] from phq_readin : error # 1 , no elec. field with metals In-Reply-To: <60951.11396.qm@web15208.mail.cnb.yahoo.com> Message-ID: <950057.79544.qm@web65704.mail.ac4.yahoo.com> Dear unknown user, First of all, all questions put in this forum should be signed properly, i.e. you should provide your name and affiliation. As concerns your question it is quite simple, and very basic. Can you please tell us what is macroscopic dielectric constant for metals? If you know the answer, you can fix the problem quite easily. By the way, the message from phq_readin.f90 almost contains the answer what you should do. Read carefully INPUT_PH.txt (in /Doc) to learn more about parameters you included in pn.in file. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Sat, 4/25/09, ? ? wrote: > From: ? ? > Subject: [Pw_forum] from phq_readin : error # 1 , no elec. field with metals > To: pw_forum at pwscf.org > Date: Saturday, April 25, 2009, 7:39 PM > Dear all, > ?? I want to calculate phonon frequencies at Gamma for > superconductor KOs2O6, according to the example02, first I > run scf calculation using pw.x command without any error, > but when I perform the phonon calculation, the error appears > as forrows: > ?? from phq_readin: error #?????? 1 > ?? no elec. field with metals > Who can tell me why? Thank you very much! > ? > The input files as follows: > kos2o6.scf.in > ??&CONTROL > ???????????????? calculation = > 'scf' , > ??????????????? restart_mode = > 'from_scratch' , > ????????????????????? outdir = > '/home/ww/data/kos2o6/' , > ????????????????????? wfcdir = > '/home/ww/data/kos2o6/' , > ????????????????? pseudo_dir = > '/home/ww/PWscf/pseudo/' , > ????????????????????? prefix = > 'kos2o6' , > ?/ > ?&SYSTEM > ?????????????????????? ibrav = 2, > ?????????????????? celldm(1) = 19.0945, > ???????????????????????? nat = 18, > ??????????????????????? ntyp = 3, > ???????????????????? ecutwfc = 60 , > ???????????????????? ecutrho = 600 , > ???????????????? occupations = > 'smearing' , > ???????????????????? degauss = 0.03 > ??????????????????? smearing = > 'gauss' , > ?/ > ?&ELECTRONS > ??????????????????? conv_thr = 1.0D-8 , > ???????????????? mixing_beta = 0.7 , > ?/ > ATOMIC_SPECIES > ??? K?? 39.10000? K.pbe-sp.UPF > ?? Os? 190.20000? Os.pbe-n-van.UPF > ??? O?? 16.00000? O.pbe-van_ak.UPF > ATOMIC_POSITIONS crystal > ?? .... > K_POINTS {automatic} > ? 10? 10? 10? 0? 0? 0 > > kos2o6.phG.in: > ???? phonons of kos2o6 at Gamma > ?&inputph > ? tr2_ph=1.0d-14, > ? prefix='kos2o6', > ? epsil=.true., > ? amass(1)=39.10, > ? amass(2)=190.2, > ? amass(3)=16.00, > ? outdir='/home/ww/data/kos2o6/', > ? fildyn='kos2o6.dynG', > ?/ > 0.0 0.0 0.0 > > > > > ___________________________________________________________ > ????????????????? > http://card.mail.cn.yahoo.com/_______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From eariel99 at gmail.com Sat Apr 25 23:48:27 2009 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Sat, 25 Apr 2009 17:48:27 -0400 Subject: [Pw_forum] -nimage -npool -ntg -ndiag Message-ID: Hi, I found in the new, or maybe not so new, users guide, that 1000 atoms or so can be calculated, and new ways to paralelize. The example in the manual is mpirun -np 4096 ./pw.x -nimage 8 -npool 2 -ntg 8 -ndiag 144 -input myinput.in I have played a bit, but not with a massive computer, and I have found that the default options are always better than my unexpert choices. So, I would like to see some hints, in addition to what is reproduced below (from the users guide), about the good choices of -ntg and -ndiag. Maybe some examples is enough to understand it. From giannozz at democritos.it Sun Apr 26 18:36:34 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 26 Apr 2009 18:36:34 +0200 Subject: [Pw_forum] -nimage -npool -ntg -ndiag In-Reply-To: References: Message-ID: Hi Eduardo > mpirun -np 4096 ./pw.x -nimage 8 -npool 2 -ntg 8 -ndiag 144 -input > myinput.in presently, -nimage is relevant only for NEB calculations; -npools, only in presence of k-points. In the following I am assuming nimage=npool=1. > I would like to see some hints, in addition to what is reproduced > below (from the users guide), about the good choices of -ntg and - > ndiag > -ntg is useful if the number of processors you want to use is ~ or > than nr3s (fft dimension along axis 3). In that case it may be interesting to perform FFTs in parallel on ntg grous of electronic states, parallelizing each FFT on np/ntg procs. -ndiag should be such that ndiag^2 <= np . The default is the largest possible ndiag; the ideal choice is the one that gives the best performances and depends upon many factors (dimension of the matrices to be manipulated, communication hardware, phase of the moon...). The larger ndiag, the smaller the memory usage (all matrices that are manipulated are distributed across ndiag^2 processors) and the smaller the amount of floating point operations per processor, but eventually the overall performances will flatten and then degrade due to communication overhead. Don't even think trying this on slow communication hardware. Some time ago I was asked to write the proceedings for some Italian conference on high-performance computing. As a rule I don't write anything that doesn't contain something new or at least something useful. The result of my and Carlo Cavazzoni's effort to reduce the waste of bits is the following small paper: http://www.fisica.uniud.it/~giannozz/Papers/rimini08.pdf containing some information on parallelization levels in quantum- espresso. Whether it is useful or not, the reader will judge. Paolo From jasius_1 at yahoo.com Mon Apr 27 02:26:11 2009 From: jasius_1 at yahoo.com (Jonas Baltrusaitis) Date: Sun, 26 Apr 2009 17:26:11 -0700 (PDT) Subject: [Pw_forum] can't read wavefunction and coords Message-ID: <922459.3274.qm@web54403.mail.yahoo.com> Hi all, I am following an example 9 in trying to setup a single input to: 1. optimize structure at gamma point 2. calculate scf 3. phonon calculation 4. IR cross section calculation What's absolutely not clear from example 9 is how (why) the wavefunction and coords gets read from scf calculation part to latter parts. It just does. Whereas it does not into scf run if I add optimization run before scf and start scf with restart directive. It simply disregards my restart command. I was pretty convinced that restart will read previous wavefunction but now I just don't know I attached my input, would appreciate any suggestions Jonas Baltrusaitis University of Iowa #!/bin/sh # run from directory where this script is cd `echo $0 | sed 's/\(.*\)\/.*/\1/'` # extract pathname EXAMPLE_DIR=/home/jbaltrus/$PBS_JOBNAME # check whether echo has the -e option if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi $ECHO $ECHO "$EXAMPLE_DIR : starting" $ECHO $ECHO "This example shows how to use pw.x and phcg.x to calculate the normal" $ECHO "modes of a molecule (SiH4) at Gamma." $ECHO $ECHO # set the needed environment variables PREFIX=`pwd` BIN_DIR=/share/apps/espresso-4.0.4/bin PSEUDO_DIR=/share/apps/espresso-4.0.4/pseudo TMP_DIR=/share/apps/scratch/ mkdir $EXAMPLE_DIR/results PARA_PREFIX="mpiexec -n 8 -machinefile $PBS_NODEFILE" PARA_POSTFIX="-rmpool 0 -nodes 2 -procs 4" # required executables and pseudopotentials BIN_LIST="pw.x phcg.x ph.x" PSEUDO_LIST="Si.vbc.UPF H.vbc.UPF C.pz-rrkjus.UPF H.vbc.UPF" $ECHO $ECHO " executables directory: $BIN_DIR" $ECHO " pseudo directory: $PSEUDO_DIR" $ECHO " temporary directory: $TMP_DIR" $ECHO " checking that needed directories and files exist...\c" # check for directories for DIR in "$BIN_DIR" "$PSEUDO_DIR" ; do if test ! -d $DIR ; then $ECHO $ECHO "ERROR: $DIR not existent or not a directory" $ECHO "Aborting" exit 1 fi done for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do if test ! -d $DIR ; then mkdir $DIR fi done cd $EXAMPLE_DIR/results # check for executables for FILE in $BIN_LIST ; do if test ! -x $BIN_DIR/$FILE ; then $ECHO $ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable" $ECHO "Aborting" exit 1 fi done # check for pseudopotentials for FILE in $PSEUDO_LIST ; do if test ! -r $PSEUDO_DIR/$FILE ; then $ECHO $ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable" $ECHO "Aborting" exit 1 fi done $ECHO " done" # how to run executables PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX" PH_COMMAND="$PARA_PREFIX $BIN_DIR/ph.x $PARA_POSTFIX" PHCG_COMMAND="$PARA_PREFIX $BIN_DIR/phcg.x $PARA_POSTFIX" DYNMAT_COMMAND=" $BIN_DIR/dynmat.x" $ECHO $ECHO " running pw.x as: $PW_COMMAND" $ECHO " running ph.x as: $PH_COMMAND" $ECHO " running phcg.x as: $PHCG_COMMAND" $ECHO " running dynmat.x as: $DYNMAT_COMMAND" $ECHO # clean TMP_DIR $ECHO " cleaning $TMP_DIR...\c" rm -rf $TMP_DIR/* $ECHO " done" # geometry optimization calculation cat > sih4.opt.in << EOF &control calculation='relax' pseudo_dir = '$PSEUDO_DIR/', restart_mode = ?from_scratch?, outdir='$TMP_DIR/' title='Test Silane SiH4 gamma only' prefix='sih4' tprnfor=.true., tstress=.true. / &system ibrav=2, celldm(1) =12.0, nat=5, ntyp= 2, ecutwfc =16.0 / &electrons mixing_mode='plain' mixing_beta = 0.7, conv_thr = 1.0d-8 / &IONS / ATOMIC_SPECIES Si 28.086 Si.vbc.UPF H 1.008 H.vbc.UPF ATOMIC_POSITIONS (angstrom) Si -0.117489394 -0.768144287 0.335809279 H -0.211023980 -0.607144136 1.652050052 H -1.814442124 -1.682247277 -0.460054024 H -0.023954807 0.421221649 -0.250551950 H 0.963879018 -1.487802354 0.053153717 K_POINTS (gamma) EOF $ECHO " running the geometry opt calculation for SiH4...\c" $PW_COMMAND < sih4.opt.in > sih4.opt.out check_failure $? $ECHO " done" # self-consistent calculation cat > sih4.scf.in << EOF &control calculation='scf' pseudo_dir = '$PSEUDO_DIR/', restart_mode = ?restart?, outdir='$TMP_DIR/' title='Test Silane SiH4 gamma only' prefix='sih4' tprnfor=.true., tstress=.true. / &system ibrav=2, celldm(1) =12.0, nat=5, ntyp= 2, ecutwfc =16.0 / &electrons mixing_mode='plain' mixing_beta = 0.7, conv_thr = 1.0d-8 / ATOMIC_SPECIES Si 28.086 Si.vbc.UPF H 1.008 H.vbc.UPF ATOMIC_POSITIONS (angstrom) Si -0.117489394 -0.768144287 0.335809279 H -0.211023980 -0.607144136 1.652050052 H -1.814442124 -1.682247277 -0.460054024 H -0.023954807 0.421221649 -0.250551950 H 0.963879018 -1.487802354 0.053153717 K_POINTS (gamma) EOF $ECHO " running the scf calculation for SiH4...\c" $PW_COMMAND < sih4.scf.in > sih4.scf.out check_failure $? $ECHO " done" # normal mode calculation for SiH4 cat > sih4.nm.in << EOF normal modes for sih4 &inputph tr2_ph=1.0d-14, prefix='sih4', amass(1)=28.086, amass(2)=1.008, outdir='$TMP_DIR/', epsil=.true., trans=.true., asr=.true. raman=.false. fildyn='sih4.dyn' / 0.0 0.0 0.0 EOF $ECHO " running normal mode calculation for SiH4...\c" $PHCG_COMMAND < sih4.nm.in > sih4.nm.out check_failure $? $ECHO " done" # IR cross sections for SiH4 cat > sih4.dyn.in << EOF &input fildyn='sih4.dyn', asr='zero-dim' / EOF $ECHO " running IR cross section calculation for SiH4...\c" $DYNMAT_COMMAND < sih4.dyn.in > sih4.dyn.out check_failure $? $ECHO " done" $ECHO $ECHO "$EXAMPLE_DIR: done" From rfaccio at fq.edu.uy Mon Apr 27 07:20:44 2009 From: rfaccio at fq.edu.uy (Ricardo Faccio) Date: Mon, 27 Apr 2009 02:20:44 -0300 Subject: [Pw_forum] LDA+U and occupations matrix problems / call for NC PP Cu & Co References: <922459.3274.qm@web54403.mail.yahoo.com> Message-ID: <000b01c9c6f7$eb611640$0402a8c0@ricardof> Dear Pwscf users I'm a newbie using pwscf, and I?m trying to reproduce some full-potential all-electrons results from a previous work using WIEN2k. My system is a cuprate/colbatite YBaCuCoO5. I succeed running the lda+u calculations, but I found the previous discussed problem regarding the lack of normalization in some PP (non norm-conserving). I worked with the UPF's files from the QE web page: Cu.pbe-d-rrkjus.UPF and Co.pbe-nd-rrkjus.UPF. The problem of occupations higher than 1 was resolved with the flag: U_projection_type = 'norm-atomic'. But I am interested in checking the stresses and forces, in order to verify my previous equilibrium solution and these are not implemented for such correction ('norm-atomic'). For these reason I would like to ask you for a PBE-Norm-conserving PP for Cu and Co, if anyone has it available. I think this is the fattest solution in order to avoid the U dependency upon normalization (through U_projection_type) and for checking my previous results. But, if I have no answers, I will try to generate these files from myself (but it is a little bit more complicated that ATOMS implemented in SIESTA). Thanks in advance and sorry for the inconvenience. Ricardo Faccio ------------------------------------------------------------------------- Dr. Ricardo Faccio Prof. Adjunto de F?sica Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA Facultad de Qu?mica, Universidad de la Rep?blica Av. Gral. Flores 2124, C.C. 1157 C.P. 11800, Montevideo, Uruguay. E-mail: rfaccio at fq.edu.uy Phone: 598 2 924 98 59 598 2 929 06 48 Fax: 598 2 9241906 Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm From degironc at sissa.it Mon Apr 27 08:49:42 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 27 Apr 2009 08:49:42 +0200 Subject: [Pw_forum] LDA+U and occupations matrix problems / call for NC PP Cu & Co In-Reply-To: <000b01c9c6f7$eb611640$0402a8c0@ricardof> References: <922459.3274.qm@web54403.mail.yahoo.com> <000b01c9c6f7$eb611640$0402a8c0@ricardof> Message-ID: <49F55586.9000407@sissa.it> Dear Ricardo Faccio, The problem of normalization of atomic wavefunctions in LDA+U should have been solved about one year ago in the cvs version and incorporated in recent distributions. I include below the CVS log message of that correction that should clarify the change. It should be possible to repeat your calculations without the norm-atomic flag on and atomic wavefunctions should be renormalized on the atomic grid, that is in a configuration independent way, hence forces and stress should be ok). Please report any problem that you may experience, best, stefano > > date: 2008/07/14 21:50:33; author: degironc; state: Exp; lines: +84 -0 > Normalization of atomic wavefuncitons is checked (only for those with > non-negative occupation) after pseudopotential reading and if it found to > be different from 1 by more than 1.d-6 the wavefunction is renormalized. > > Should make no difference in all usual cases since atomic wfcs are only > used in order to generate the initial set of trial wfcs and normalization > is not important there... > > It is VERY important for LDA+U calculations using atomic wfc in the > progector > (the default case) since proper normalization is assumed and lack of > it leads > to disasters. > > Hopefully this will solve many of the difficulties people have encounterd > when using LDA+U with older RRKJ pseudopotentials, where normalization > was not imposed properly (and nobody realizes except when doing LDA+U) or > pseudopotentials of unknown origin. Ricardo Faccio wrote: > Dear Pwscf users > > I'm a newbie using pwscf, and I?m trying to reproduce some full-potential > all-electrons results from a previous work using WIEN2k. My system is a > cuprate/colbatite YBaCuCoO5. I succeed running the lda+u calculations, but I > found the previous discussed problem regarding the lack of normalization in > some PP (non norm-conserving). I worked with the UPF's files from the QE web > page: Cu.pbe-d-rrkjus.UPF and Co.pbe-nd-rrkjus.UPF. The problem of > occupations higher than 1 was resolved with the flag: U_projection_type = > 'norm-atomic'. But I am interested in checking the stresses and forces, in > order to verify my previous equilibrium solution and these are not > implemented for such correction ('norm-atomic'). > > For these reason I would like to ask you for a PBE-Norm-conserving PP for Cu > and Co, if anyone has it available. I think this is the fattest solution in > order to avoid the U dependency upon normalization (through > U_projection_type) and for checking my previous results. But, if I have no > answers, I will try to generate these files from myself (but it is a little > bit more complicated that ATOMS implemented in SIESTA). > > Thanks in advance and sorry for the inconvenience. > > Ricardo Faccio > > ------------------------------------------------------------------------- > Dr. Ricardo Faccio > Prof. Adjunto de F?sica > Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA > Facultad de Qu?mica, Universidad de la Rep?blica > Av. Gral. Flores 2124, C.C. 1157 > C.P. 11800, Montevideo, Uruguay. > E-mail: rfaccio at fq.edu.uy > Phone: 598 2 924 98 59 > 598 2 929 06 48 > Fax: 598 2 9241906 > Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From sclauzer at sissa.it Mon Apr 27 10:50:47 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 27 Apr 2009 10:50:47 +0200 Subject: [Pw_forum] can't read wavefunction and coords In-Reply-To: <922459.3274.qm@web54403.mail.yahoo.com> References: <922459.3274.qm@web54403.mail.yahoo.com> Message-ID: <49F571E7.40104@sissa.it> Dear Jonas Jonas Baltrusaitis wrote: > Hi all, > > I am following an example 9 in trying to setup a single input to: 1. optimize structure > at gamma point 2. calculate scf 3. phonon calculation 4. IR cross section calculation > > What's absolutely not clear from example 9 is how (why) the wavefunction and coords > gets read from scf calculation part to latter parts. It just does. Informations (system configuration, scf potential, wavefunctions...) are exchaged between successive steps of a calculations with the programs included in QE through the files contained in the directory you specify in outdir variable, and will have prefix as prefix (eg. yourprefix.save contains system configuration, PPs, charge density..., yourprefix.wfc contains the wavefunction coefficients...) > Whereas it does not > into scf run if I add optimization run before scf and start scf with restart > directive. It simply disregards my restart command. I was pretty convinced that restart > will read previous wavefunction but now I just don't know In principle, if you specify the same prefix and outdir, it should. Have you some evidence that it does not? Anyway, I think you don't need to do an scf after the relax run. You can use the data produced by this run as if it was an scf run (in fact it is a sequence of scf steps). HTH GS -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Mon Apr 27 11:09:41 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 27 Apr 2009 11:09:41 +0200 Subject: [Pw_forum] Fractional magnetization In-Reply-To: <49F098C0.1090906@phys.ufl.edu> References: <49F098C0.1090906@phys.ufl.edu> Message-ID: <49F57655.70604@sissa.it> Dear Lex Lex Kemper wrote: > Hello everyone, > > I have a question regarding constrained magnetization calculations. I > notice in the manual that both multiplicity and tot_magnetization are > integers. Because these are meant for calculations with fixed (integer) occupations, therefore you can have only integer total magnetization. > However, systems are not always found in an integer spin > state. Furthermore, being able to specify a non-integer spin state is > useful for making systems converge to a particular desired solution. > > At the moment, the only way I can specify a non-integer spin state is > by using the nelec/nelup/neldw combination. That's not true, you can fix the total magnetization (and also some "local" magnetic moments or even angles in noncolinear calculations) if you use broadening in the occupations (smearing) and specify you constraints through constrained_magnetization keyword and related variables. Please have a look at the corresponding sections of the INPUT_PW manual. HTH GS > The manual says this is > obsolete though, and to use the other variables instead. Should (at > least one) of these be changed to a real instead of an integer? > > Thanks, > > Lex Kemper > Department of Physics & QTP > University of Florida > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From anavat_ila at yahoo.com Mon Apr 27 11:39:27 2009 From: anavat_ila at yahoo.com (Ali Tavana) Date: Mon, 27 Apr 2009 02:39:27 -0700 (PDT) Subject: [Pw_forum] e-ph double delta integration Message-ID: <636132.6143.qm@web51808.mail.re2.yahoo.com> Dear all, First thanks to Paollo for his guides. I think its better to be mentioned explicitly somewhere in the documentations that k and q points are not divided (kx, Ky, Kz) and are (ka, Kb, kc), As many codes use kx,ky,kz scheme. Second: I want to know if the df(Ep)/dEp quantity in the evaluation of e-ph interaction is replaced with delta function or not. And the third question: How can estimate the accuracy of calculated lambdas based on its values for different Gaussian broadenings (what is this Gaussian broadening it self as it is mentioned that it is not the broadening of the distribution of electrons on the Fermi level. Thank you in anticipation, Ali From yccheng.nju at gmail.com Mon Apr 27 14:42:05 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Mon, 27 Apr 2009 20:42:05 +0800 Subject: [Pw_forum] Can PWscf calculate "Transition dipole moment"? Message-ID: Dear PWscf users, For a semiconductor, the transition dipole moment is useful for determining if transitions are allowed between valence bands and conduction bands. I have searched forum, and got no information concerning about transition dipole moment. Can PWscf calculate "Transition dipole moment"? -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090427/4986075d/attachment.htm From lanhaiping at gmail.com Mon Apr 27 14:46:09 2009 From: lanhaiping at gmail.com (lan haiping) Date: Mon, 27 Apr 2009 20:46:09 +0800 Subject: [Pw_forum] Can PWscf calculate "Transition dipole moment"? In-Reply-To: References: Message-ID: I think you can have a look at $QE/Doc/eps_man.pdf. As far as i know, QE can handle dielectric properties of semiconductors such as absorption spectrum in KS-RPA framework. Regards, Hai-Ping On Mon, Apr 27, 2009 at 8:42 PM, ??? wrote: > Dear PWscf users, > For a semiconductor, the transition dipole moment is useful for > determining if transitions are allowed between valence bands and conduction > bands. I have searched forum, and got no information concerning about > transition dipole moment. Can PWscf calculate "Transition dipole moment"? > -- > Y. C. Cheng > Department of Physics > Nanjing University > Nanjing 210093 > P. R. China > Tel: 86-25-83592907 > Email: yccheng.nju at gmail.com > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090427/6dc8fb48/attachment.htm From yccheng.nju at gmail.com Mon Apr 27 14:47:48 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Mon, 27 Apr 2009 20:47:48 +0800 Subject: [Pw_forum] Can PWscf calculate "Transition dipole moment"? In-Reply-To: References: Message-ID: Thank you for your quick reply! 2009/4/27 lan haiping > I think you can have a look at $QE/Doc/eps_man.pdf. > As far as i know, QE can handle dielectric properties of semiconductors > such as absorption spectrum in KS-RPA framework. > > Regards, > Hai-Ping > > On Mon, Apr 27, 2009 at 8:42 PM, ??? wrote: > >> Dear PWscf users, >> For a semiconductor, the transition dipole moment is useful for >> determining if transitions are allowed between valence bands and conduction >> bands. I have searched forum, and got no information concerning about >> transition dipole moment. Can PWscf calculate "Transition dipole moment"? >> -- >> Y. C. Cheng >> Department of Physics >> Nanjing University >> Nanjing 210093 >> P. R. China >> Tel: 86-25-83592907 >> Email: yccheng.nju at gmail.com >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > Hai-Ping Lan > Department of Electronics , > Peking University , Bejing, 100871 > lanhaiping at gmail.com, hplan at pku.edu.cn > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090427/aa15051f/attachment.htm From glevita at units.it Mon Apr 27 15:12:22 2009 From: glevita at units.it (glevita at units.it) Date: Mon, 27 Apr 2009 15:12:22 +0200 Subject: [Pw_forum] Pseudopotentials for potassium chloride In-Reply-To: <412f6c680904170802s3e362b81mf568860ee1609c94@mail.gmail.com> References: <412f6c680904110015u46e6be86x448f9d1c84868a11@mail.gmail.com> <1239704111.17996.45.camel@walk.ijs.si> <412f6c680904170802s3e362b81mf568860ee1609c94@mail.gmail.com> Message-ID: <20090427151222.227970k4kasgk3k0@wmail1.units.it> Dear PWSCF users, I'd like to run a test-system with a KCl monolayer on a copper surface. In the PWSCF pseudopotential library it seems options are somewhat narrow, namely PZ or BLYP, and no ultrasoft pseudos which can match both elements. I'd just like to know if someone else has ever used any ultrasoft approach for potassium chloride, with pseudos which are maybe not reported in the library. If not, would you deem 80 ryd a relatively safe cutoff for either the BLYP and the PZ norm-conserving pseudos? Anyway I'll run some tests on both, to check which combination better suits my needs.... Thanks a lot, Giacomo Levita (MPI Stuttgart- abt. Kern) ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From jasius_1 at yahoo.com Mon Apr 27 16:19:51 2009 From: jasius_1 at yahoo.com (Jonas Baltrusaitis) Date: Mon, 27 Apr 2009 07:19:51 -0700 (PDT) Subject: [Pw_forum] can't read wavefunction and coords In-Reply-To: <49F571E7.40104@sissa.it> Message-ID: <173714.47975.qm@web54406.mail.yahoo.com> Gabriele, thanks for your response. I reran input without the SCF step. I don't thin it's reading coords right. The source of confusion is that I am inputting and outputing coords in angstroms in optimization but it gets transferred into alat in normal mode calcs. Still, this is what I backcalculate with xcrysden: Optimized coords: ATOMIC POSITIONS Si -0.053476533 -0.187541319 +0.057950773 ... Normal mode calculation coords: ATOMIC_POSITIONS Si -0.037813604 -0.132611686 0.040977368 H -0.042235675 -0.102590555 0.268983495 H -0.221511706 -0.243919610 -0.030796850 H -0.032400640 0.077902395 -0.042412224 H 0.144511653 -0.248234756 -0.027243038 below is my latest input incidently, is there a way to tell pwscf to use only angstroms in output? It is convenient for me to use angstroms when setting up the initial input so I'd like to stay with angstroms JOnas #!/bin/sh # run from directory where this script is cd `echo $0 | sed 's/\(.*\)\/.*/\1/'` # extract pathname EXAMPLE_DIR=/home/jbaltrus/$PBS_JOBNAME # check whether echo has the -e option if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi $ECHO $ECHO "$EXAMPLE_DIR : starting" $ECHO $ECHO "This example shows how to use pw.x and phcg.x to calculate the normal" $ECHO "modes of a molecule (SiH4) at Gamma." $ECHO $ECHO # set the needed environment variables PREFIX=`pwd` BIN_DIR=/share/apps/espresso-4.0.4/bin PSEUDO_DIR=/share/apps/espresso-4.0.4/pseudo TMP_DIR=/share/apps/scratch/ mkdir $EXAMPLE_DIR/results PARA_PREFIX="mpiexec -n 8 -machinefile $PBS_NODEFILE" PARA_POSTFIX="-rmpool 0 -nodes 2 -procs 4" # required executables and pseudopotentials BIN_LIST="pw.x phcg.x ph.x" PSEUDO_LIST="Si.vbc.UPF H.vbc.UPF C.pz-rrkjus.UPF H.vbc.UPF" $ECHO $ECHO " executables directory: $BIN_DIR" $ECHO " pseudo directory: $PSEUDO_DIR" $ECHO " temporary directory: $TMP_DIR" $ECHO " checking that needed directories and files exist...\c" # check for directories for DIR in "$BIN_DIR" "$PSEUDO_DIR" ; do if test ! -d $DIR ; then $ECHO $ECHO "ERROR: $DIR not existent or not a directory" $ECHO "Aborting" exit 1 fi done for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do if test ! -d $DIR ; then mkdir $DIR fi done cd $EXAMPLE_DIR/results # check for executables for FILE in $BIN_LIST ; do if test ! -x $BIN_DIR/$FILE ; then $ECHO $ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable" $ECHO "Aborting" exit 1 fi done # check for pseudopotentials for FILE in $PSEUDO_LIST ; do if test ! -r $PSEUDO_DIR/$FILE ; then $ECHO $ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable" $ECHO "Aborting" exit 1 fi done $ECHO " done" # how to run executables PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX" PH_COMMAND="$PARA_PREFIX $BIN_DIR/ph.x $PARA_POSTFIX" PHCG_COMMAND="$PARA_PREFIX $BIN_DIR/phcg.x $PARA_POSTFIX" DYNMAT_COMMAND=" $BIN_DIR/dynmat.x" $ECHO $ECHO " running pw.x as: $PW_COMMAND" $ECHO " running ph.x as: $PH_COMMAND" $ECHO " running phcg.x as: $PHCG_COMMAND" $ECHO " running dynmat.x as: $DYNMAT_COMMAND" $ECHO # clean TMP_DIR $ECHO " cleaning $TMP_DIR...\c" rm -rf $TMP_DIR/* $ECHO " done" # geometry optimization calculation cat > sih4.opt.in << EOF &control calculation='relax' pseudo_dir = '$PSEUDO_DIR/', restart_mode = ?from_scratch?, outdir='$TMP_DIR/' title='Test Silane SiH4 gamma only' prefix='sih4' tprnfor=.true., tstress=.true. / &system ibrav=2, celldm(1) =12.0, nat=5, ntyp= 2, ecutwfc =16.0 / &electrons mixing_mode='plain' mixing_beta = 0.7, conv_thr = 1.0d-8 / &IONS / ATOMIC_SPECIES Si 28.086 Si.vbc.UPF H 1.008 H.vbc.UPF ATOMIC_POSITIONS (angstrom) Si -0.117489394 -0.768144287 0.335809279 H -0.211023980 -0.607144136 1.652050052 H -1.814442124 -1.682247277 -0.460054024 H -0.023954807 0.421221649 -0.250551950 H 0.963879018 -1.487802354 0.053153717 K_POINTS (gamma) EOF $ECHO " running the geometry opt calculation for SiH4...\c" $PW_COMMAND < sih4.opt.in > sih4.opt.out check_failure $? $ECHO " done" # normal mode calculation for SiH4 cat > sih4.nm.in << EOF normal modes for sih4 &inputph tr2_ph=1.0d-14, prefix='sih4', amass(1)=28.086, amass(2)=1.008, outdir='$TMP_DIR/', epsil=.true., trans=.true., asr=.true. raman=.false. fildyn='sih4.dyn' / 0.0 0.0 0.0 EOF $ECHO " running normal mode calculation for SiH4...\c" $PHCG_COMMAND < sih4.nm.in > sih4.nm.out check_failure $? $ECHO " done" # IR cross sections for SiH4 cat > sih4.dyn.in << EOF &input fildyn='sih4.dyn', asr='zero-dim' / EOF $ECHO " running IR cross section calculation for SiH4...\c" $DYNMAT_COMMAND < sih4.dyn.in > sih4.dyn.out check_failure $? $ECHO " done" $ECHO $ECHO "$EXAMPLE_DIR: done" --- On Mon, 4/27/09, Gabriele Sclauzero wrote: > From: Gabriele Sclauzero > Subject: Re: [Pw_forum] can't read wavefunction and coords > To: "PWSCF Forum" > Date: Monday, April 27, 2009, 1:50 AM > Dear Jonas > > Jonas Baltrusaitis wrote: > > Hi all, > > > > I am following an example 9 in trying to setup a > single input to: 1. optimize structure > > at gamma point 2. calculate scf 3. phonon calculation > 4. IR cross section calculation > > > > What's absolutely not clear from example 9 is how > (why) the wavefunction and coords > > gets read from scf calculation part to latter parts. > It just does. > > Informations (system configuration, scf potential, > wavefunctions...) are exchaged between > successive steps of a calculations with the programs > included in QE through the files > contained in the directory you specify in outdir variable, > and will have prefix as prefix > (eg. yourprefix.save contains system configuration, PPs, > charge density..., yourprefix.wfc > contains the wavefunction coefficients...) > > > Whereas it does not > > into scf run if I add optimization run before scf and > start scf with restart > > directive. It simply disregards my restart command. I > was pretty convinced that restart > > will read previous wavefunction but now I just > don't know > > In principle, if you specify the same prefix and outdir, it > should. Have you some evidence > that it does not? > > Anyway, I think you don't need to do an scf after the > relax run. You can use the data > produced by this run as if it was an scf run (in fact it is > a sequence of scf steps). > > HTH > > GS > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at democritos.it Mon Apr 27 16:23:05 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 27 Apr 2009 16:23:05 +0200 Subject: [Pw_forum] can't read wavefunction and coords In-Reply-To: <173714.47975.qm@web54406.mail.yahoo.com> References: <173714.47975.qm@web54406.mail.yahoo.com> Message-ID: <49F5BFC9.8020500@democritos.it> Jonas Baltrusaitis wrote: > I don't thin it's reading coords right which version of the code are you talking about? P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From rfaccio at fq.edu.uy Mon Apr 27 16:26:48 2009 From: rfaccio at fq.edu.uy (Ricardo Faccio) Date: Mon, 27 Apr 2009 11:26:48 -0300 Subject: [Pw_forum] LDA+U and occupations matrix problems / call for NC P Cu & Co References: <922459.3274.qm@web54403.mail.yahoo.com><000b01c9c6f7$eb611640$0402a8c0@ricardof> <49F55586.9000407@sissa.it> Message-ID: <024b01c9c744$33d35040$0402a8c0@ricardof> Dear Stefano Thanks for your quick response. I found the CVS log in the mailing list, but I decided to write you since the problem persist. Now I'm attaching my input file, which I used to perform U=1.0d-8 eV, U= 3.5 eV and U= 7 eV. Making a revision of the problem, I found the only difference regards in the GGA xc-potential. Maybe it is the problem; I found some early posts indicating that GGA+U is not yet implemented. If it is the case sorry, but in the meanwhile I'll comment I little bit on the problem. 1) U=1.0d-8 eV, everything is ok, since there is no U and pwscf runs in the normal GGA procedure, this is the initial occupations matrix for one Co atom atom 5 spin 1 occupations 0.400 0.000 0.000 0.000 0.000 0.000 0.400 0.000 0.000 0.000 0.000 0.000 0.400 0.000 0.000 0.000 0.000 0.000 0.400 0.000 0.000 0.000 0.000 0.000 0.400 atom 5 spin 2 occupations 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 This is normal for the d7 pseudo for Co, and in the last step we found: occupations atom 5 spin 1 occupations 0.532 0.000 0.000 0.000 0.000 0.000 0.434 0.000 0.000 0.000 0.000 0.000 0.434 0.000 0.000 0.000 0.000 0.000 0.993 0.000 0.000 0.000 0.000 0.000 0.435 atom 5 spin 2 occupations 0.976 0.000 0.000 0.000 0.000 0.000 0.992 0.000 0.000 0.000 0.000 0.000 0.992 0.000 0.000 0.000 0.000 0.000 0.995 0.000 0.000 0.000 0.000 0.000 0.935 2) In the case of U=3.5 eV (for both Cu & Co) In the first scf cycle the occupations matrix looks like the one in the U=0 case, but in the second scf step I found: atom 5 Tr[ns(na)]= 14.9317605 atom 5 spin 1 eigenvalues: 0.2107738 0.2794264 0.2794264 0.5053719 0.5799705 eigenvectors 1 0.0000000 0.0000000 0.0000000 -1.0000000 0.0000000 2 0.0000000 -0.8886367 0.4586119 0.0000000 0.0000000 3 0.0000000 -0.4586119 -0.8886367 0.0000000 0.0000000 4 0.0000000 0.0000000 0.0000000 0.0000000 -1.0000000 5 -1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 occupations 0.580 0.000 0.000 0.000 0.000 0.000 0.279 0.000 0.000 0.000 0.000 0.000 0.279 0.000 0.000 0.000 0.000 0.000 0.211 0.000 0.000 0.000 0.000 0.000 0.505 atom 5 spin 2 eigenvalues: 2.5970604 2.6187425 2.6187425 2.6211004 2.6211456 eigenvectors 1 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 2 0.0000000 -0.8592401 0.5115724 0.0000000 0.0000000 3 0.0000000 0.5115724 0.8592401 0.0000000 0.0000000 4 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 5 0.0000000 0.0000000 0.0000000 -1.0000000 0.0000000 occupations 2.597 0.000 0.000 0.000 0.000 0.000 2.619 0.000 0.000 0.000 0.000 0.000 2.619 0.000 0.000 0.000 0.000 0.000 2.621 0.000 0.000 0.000 0.000 0.000 2.621 The occupations jumps from 1 to 2.6 always in the second scf, and stands in this value until the end of the scf procedure. As I mentioned before, I didn't use the U_projection_type flag for these three cases. I resolved the problem adding the explicitly the flag: U_projection_type = 'norm-atomic', since 'atomic' leads to the same erratic occupations matrix. The problem is only related with Co electrons, since Cu always presents occupations terms in the range of 0 to 1. But as I mentioned before, maybe the problem is that ?GGA+U? is not yet implemented. Thanks once again Ricardo ------------------------------------------------------------------------- Dr. Ricardo Faccio Prof. Adjunto de F?sica Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA Facultad de Qu?mica, Universidad de la Rep?blica Av. Gral. Flores 2124, C.C. 1157 C.P. 11800, Montevideo, Uruguay. E-mail: rfaccio at fq.edu.uy Phone: 598 2 924 98 59 598 2 929 06 48 Fax: 598 2 9241906 Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm --------------------------------------------------------------------------------- ----- Original Message ----- From: "Stefano de Gironcoli" To: "PWSCF Forum" Sent: Monday, April 27, 2009 3:49 AM Subject: Re: [Pw_forum] LDA+U and occupations matrix problems / call for NC PP Cu & Co > Dear Ricardo Faccio,The problem of normalization of atomic wavefunctions > in LDA+U should have been solved about one year ago in the cvs version and > incorporated in recent distributions. I include below the CVS log message > of that correction that should clarify the change.It should be possible to > repeat your calculations without the norm-atomic flag on and atomic > wavefunctions should be renormalized on the atomic grid, that is in a > configuration independent way, hence forces and stress should be > ok).Please report any problem that you may experience,best, stefano>> > date: 2008/07/14 21:50:33; author: degironc; state: Exp; lines: +84 -0> > Normalization of atomic wavefuncitons is checked (only for those with> > non-negative occupation) after pseudopotential reading and if it found to> > be different from 1 by more than 1.d-6 the wavefunction is renormalized.>> > Should make no difference in all usual cases since atomic wfcs are only> > used in order to generate the initial set of trial wfcs and normalization> > is not important there...>> It is VERY important for LDA+U calculations > using atomic wfc in the > progector> (the default case) since proper > normalization is assumed and lack of > it leads> to disasters.>> Hopefully > this will solve many of the difficulties people have encounterd> when > using LDA+U with older RRKJ pseudopotentials, where normalization> was not > imposed properly (and nobody realizes except when doing LDA+U) or> > pseudopotentials of unknown origin. > > > > > Ricardo Faccio wrote:> Dear Pwscf users>> I'm a newbie using pwscf, and I?m > trying to reproduce some full-potential > all-electrons results from a > previous work using WIEN2k. My system is a > cuprate/colbatite YBaCuCoO5. > I succeed running the lda+u calculations, but I > found the previous > discussed problem regarding the lack of normalization in > some PP (non > norm-conserving). I worked with the UPF's files from the QE web > page: > Cu.pbe-d-rrkjus.UPF and Co.pbe-nd-rrkjus.UPF. The problem of > > occupations higher than 1 was resolved with the flag: U_projection_type = > > 'norm-atomic'. But I am interested in checking the stresses and forces, > in > order to verify my previous equilibrium solution and these are not > > implemented for such correction ('norm-atomic').>> For these reason I > would like to ask you for a PBE-Norm-conserving PP for Cu > and Co, if > anyone has it available. I think this is the fattest solution in > order > to avoid the U dependency upon normalization (through > U_projection_type) > and for checking my previous results. But, if I have no > answers, I will > try to generate these files from myself (but it is a little > bit more > complicated that ATOMS implemented in SIESTA).>> Thanks in advance and > sorry for the inconvenience.>> Ricardo > Faccio>> -------------------------------------------------------------------------> > Dr. Ricardo Faccio> Prof. Adjunto de F?sica> Mail: Cryssmat-Lab., > C?tedra de F?sica, DETEMA> Facultad de Qu?mica, Universidad de la > Rep?blica> Av. Gral. Flores 2124, C.C. 1157> C.P. 11800, > Montevideo, Uruguay.> E-mail: rfaccio at fq.edu.uy> Phone: 598 2 924 98 > 59> 598 2 929 06 48> Fax: 598 2 9241906> Web: > http://cryssmat.fq.edu.uy/ricardo/ricardo.htm>> > _______________________________________________> Pw_forum mailing list> > Pw_forum at pwscf.org> http://www.democritos.it/mailman/listinfo/pw_forum> > _______________________________________________Pw_forum mailing > listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- A non-text attachment was scrubbed... Name: y.pw.in Type: application/octet-stream Size: 3384 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090427/d09985b3/attachment.obj From akohlmey at cmm.chem.upenn.edu Mon Apr 27 16:28:55 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 27 Apr 2009 10:28:55 -0400 Subject: [Pw_forum] can't read wavefunction and coords In-Reply-To: <173714.47975.qm@web54406.mail.yahoo.com> References: <173714.47975.qm@web54406.mail.yahoo.com> Message-ID: <1240842535.18574.497.camel@zero> On Mon, 2009-04-27 at 07:19 -0700, Jonas Baltrusaitis wrote: > Gabriele, > > thanks for your response. I reran input without the SCF step. I don't thin it's reading coords right. The source of confusion is that I am inputting and outputing coords in angstroms in optimization but it gets transferred into alat in normal mode calcs. jonas, please _read_ the documentation and don't assume that one DFT program follows the logic of another. restart_mode='restart' is meant to restart an interrupted calculation of the _same_ input, _not_ to continue from a previous calculation. you have to use some shell script magic to transfer final coordinates from one calculation to another, but this is why pw.x outputs coordinates in a format that is consistent with the input. to read back the potential and/or wavefunction from a previous run you have to use startingpot='file' and startingwfc='file'. check out the docs on them, too, and the restrictions. > Still, this is what I backcalculate with xcrysden: > > Optimized coords: > ATOMIC POSITIONS > Si -0.053476533 -0.187541319 +0.057950773 > ... > > Normal mode calculation coords: > ATOMIC_POSITIONS > Si -0.037813604 -0.132611686 0.040977368 > H -0.042235675 -0.102590555 0.268983495 > H -0.221511706 -0.243919610 -0.030796850 > H -0.032400640 0.077902395 -0.042412224 > H 0.144511653 -0.248234756 -0.027243038 > > below is my latest input > incidently, is there a way to tell pwscf to use only angstroms in > output? It is convenient for me to use angstroms when setting up the > initial input so I'd like to stay with angstroms no. not unless you implement it, that is. ...and for the majority of problems that QE codes are used on, fractional coordinates are the much more convenient choice. cheers, axel. > JOnas > > #!/bin/sh > > # run from directory where this script is > cd `echo $0 | sed 's/\(.*\)\/.*/\1/'` # extract pathname > EXAMPLE_DIR=/home/jbaltrus/$PBS_JOBNAME > > # check whether echo has the -e option > if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi > > $ECHO > $ECHO "$EXAMPLE_DIR : starting" > $ECHO > $ECHO "This example shows how to use pw.x and phcg.x to calculate the normal" > $ECHO "modes of a molecule (SiH4) at Gamma." > $ECHO > $ECHO > > # set the needed environment variables > PREFIX=`pwd` > BIN_DIR=/share/apps/espresso-4.0.4/bin > PSEUDO_DIR=/share/apps/espresso-4.0.4/pseudo > TMP_DIR=/share/apps/scratch/ > > mkdir $EXAMPLE_DIR/results > > PARA_PREFIX="mpiexec -n 8 -machinefile $PBS_NODEFILE" > PARA_POSTFIX="-rmpool 0 -nodes 2 -procs 4" > > > # required executables and pseudopotentials > BIN_LIST="pw.x phcg.x ph.x" > PSEUDO_LIST="Si.vbc.UPF H.vbc.UPF C.pz-rrkjus.UPF H.vbc.UPF" > > $ECHO > $ECHO " executables directory: $BIN_DIR" > $ECHO " pseudo directory: $PSEUDO_DIR" > $ECHO " temporary directory: $TMP_DIR" > $ECHO " checking that needed directories and files exist...\c" > > # check for directories > for DIR in "$BIN_DIR" "$PSEUDO_DIR" ; do > if test ! -d $DIR ; then > $ECHO > $ECHO "ERROR: $DIR not existent or not a directory" > $ECHO "Aborting" > exit 1 > fi > done > for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do > if test ! -d $DIR ; then > mkdir $DIR > fi > done > cd $EXAMPLE_DIR/results > > # check for executables > for FILE in $BIN_LIST ; do > if test ! -x $BIN_DIR/$FILE ; then > $ECHO > $ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable" > $ECHO "Aborting" > exit 1 > fi > done > > # check for pseudopotentials > for FILE in $PSEUDO_LIST ; do > if test ! -r $PSEUDO_DIR/$FILE ; then > $ECHO > $ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable" > $ECHO "Aborting" > exit 1 > fi > done > $ECHO " done" > > # how to run executables > PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX" > PH_COMMAND="$PARA_PREFIX $BIN_DIR/ph.x $PARA_POSTFIX" > PHCG_COMMAND="$PARA_PREFIX $BIN_DIR/phcg.x $PARA_POSTFIX" > DYNMAT_COMMAND=" $BIN_DIR/dynmat.x" > $ECHO > $ECHO " running pw.x as: $PW_COMMAND" > $ECHO " running ph.x as: $PH_COMMAND" > $ECHO " running phcg.x as: $PHCG_COMMAND" > $ECHO " running dynmat.x as: $DYNMAT_COMMAND" > $ECHO > > # clean TMP_DIR > $ECHO " cleaning $TMP_DIR...\c" > rm -rf $TMP_DIR/* > $ECHO " done" > > # geometry optimization calculation > cat > sih4.opt.in << EOF > &control > calculation='relax' > pseudo_dir = '$PSEUDO_DIR/', > restart_mode = ?from_scratch?, > outdir='$TMP_DIR/' > title='Test Silane SiH4 gamma only' > prefix='sih4' > tprnfor=.true., tstress=.true. > / > &system > ibrav=2, celldm(1) =12.0, nat=5, ntyp= 2, > ecutwfc =16.0 > / > &electrons > mixing_mode='plain' > mixing_beta = 0.7, > conv_thr = 1.0d-8 > / > &IONS > / > ATOMIC_SPECIES > Si 28.086 Si.vbc.UPF > H 1.008 H.vbc.UPF > ATOMIC_POSITIONS (angstrom) > Si -0.117489394 -0.768144287 0.335809279 > H -0.211023980 -0.607144136 1.652050052 > H -1.814442124 -1.682247277 -0.460054024 > H -0.023954807 0.421221649 -0.250551950 > H 0.963879018 -1.487802354 0.053153717 > K_POINTS (gamma) > EOF > $ECHO " running the geometry opt calculation for SiH4...\c" > $PW_COMMAND < sih4.opt.in > sih4.opt.out > check_failure $? > $ECHO " done" > > > # normal mode calculation for SiH4 > cat > sih4.nm.in << EOF > normal modes for sih4 > &inputph > tr2_ph=1.0d-14, > prefix='sih4', > amass(1)=28.086, > amass(2)=1.008, > outdir='$TMP_DIR/', > epsil=.true., > trans=.true., asr=.true. > raman=.false. > fildyn='sih4.dyn' > / > 0.0 0.0 0.0 > EOF > $ECHO " running normal mode calculation for SiH4...\c" > $PHCG_COMMAND < sih4.nm.in > sih4.nm.out > check_failure $? > $ECHO " done" > > # IR cross sections for SiH4 > cat > sih4.dyn.in << EOF > &input fildyn='sih4.dyn', asr='zero-dim' / > EOF > > $ECHO " running IR cross section calculation for SiH4...\c" > $DYNMAT_COMMAND < sih4.dyn.in > sih4.dyn.out > check_failure $? > $ECHO " done" > > > $ECHO > $ECHO "$EXAMPLE_DIR: done" > > > --- On Mon, 4/27/09, Gabriele Sclauzero wrote: > > > From: Gabriele Sclauzero > > Subject: Re: [Pw_forum] can't read wavefunction and coords > > To: "PWSCF Forum" > > Date: Monday, April 27, 2009, 1:50 AM > > Dear Jonas > > > > Jonas Baltrusaitis wrote: > > > Hi all, > > > > > > I am following an example 9 in trying to setup a > > single input to: 1. optimize structure > > > at gamma point 2. calculate scf 3. phonon calculation > > 4. IR cross section calculation > > > > > > What's absolutely not clear from example 9 is how > > (why) the wavefunction and coords > > > gets read from scf calculation part to latter parts. > > It just does. > > > > Informations (system configuration, scf potential, > > wavefunctions...) are exchaged between > > successive steps of a calculations with the programs > > included in QE through the files > > contained in the directory you specify in outdir variable, > > and will have prefix as prefix > > (eg. yourprefix.save contains system configuration, PPs, > > charge density..., yourprefix.wfc > > contains the wavefunction coefficients...) > > > > > Whereas it does not > > > into scf run if I add optimization run before scf and > > start scf with restart > > > directive. It simply disregards my restart command. I > > was pretty convinced that restart > > > will read previous wavefunction but now I just > > don't know > > > > In principle, if you specify the same prefix and outdir, it > > should. Have you some evidence > > that it does not? > > > > Anyway, I think you don't need to do an scf after the > > relax run. You can use the data > > produced by this run as if it was an scf run (in fact it is > > a sequence of scf steps). > > > > HTH > > > > GS > > > > -- > > > > > > o ------------------------------------------------ o > > | Gabriele Sclauzero, PhD Student | > > | c/o: SISSA & CNR-INFM Democritos, | > > | via Beirut 2-4, 34014 Trieste (Italy) | > > | email: sclauzer at sissa.it | > > | phone: +39 040 3787 511 | > > | skype: gurlonotturno | > > o ------------------------------------------------ o > > _______________________________________________ > > 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 -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From sclauzer at sissa.it Mon Apr 27 16:37:20 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 27 Apr 2009 16:37:20 +0200 Subject: [Pw_forum] can't read wavefunction and coords In-Reply-To: <173714.47975.qm@web54406.mail.yahoo.com> References: <173714.47975.qm@web54406.mail.yahoo.com> Message-ID: <49F5C320.3040801@sissa.it> Jonas Baltrusaitis wrote: > Gabriele, > > thanks for your response. I reran input without the SCF step. I don't thin it's reading > coords right. The source of confusion is that I am inputting and outputing coords in > angstroms in optimization but it gets transferred into alat in normal mode calcs. I think reading and writing coordinates is treated properly in pwscf (i.e. it is internally consistent). You can specify input coordinates in different formats, alat (Cartesian axes, celldm(1) units), crystal,... At the beginning of the output the read coordinates are written in alat units (correctly transformed, if you used an input with a different format), and in crystal units if you use verbosity='high'. In relax calculations the coordinated are written after each scf step in the format you used for the input. So, if you use (angstrom) as input format, you'll get ATOMIC_POSITION in angstrom units on output, so that you can copy and paste those positions if you need them to build another input. For me it always worked: if I give input coordinates as ATOMIC_POSITIONS (angstrom) ... I will get ATOMIC_POSITIONS (angstrom) ... after each ions move in a relax calculation. If you restart, the program should not care about the atomic positions you give on input, but read those store in the restart files. HTH GS > > Still, this is what I backcalculate with xcrysden: > > Optimized coords: ATOMIC POSITIONS Si -0.053476533 -0.187541319 +0.057950773 ... > > Normal mode calculation coords: ATOMIC_POSITIONS Si -0.037813604 -0.132611686 > 0.040977368 H -0.042235675 -0.102590555 0.268983495 H -0.221511706 > -0.243919610 -0.030796850 H -0.032400640 0.077902395 -0.042412224 H > 0.144511653 -0.248234756 -0.027243038 > > below is my latest input incidently, is there a way to tell pwscf to use only angstroms > in output? > It is convenient for me to use angstroms when setting up the initial input > so I'd like to stay with angstroms > > JOnas -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From jasius_1 at yahoo.com Mon Apr 27 18:13:51 2009 From: jasius_1 at yahoo.com (Jonas Baltrusaitis) Date: Mon, 27 Apr 2009 09:13:51 -0700 (PDT) Subject: [Pw_forum] can't read wavefunction and coords In-Reply-To: <49F5BFC9.8020500@democritos.it> Message-ID: <33152.80152.qm@web54410.mail.yahoo.com> 4.0.4 --- On Mon, 4/27/09, Paolo Giannozzi wrote: > From: Paolo Giannozzi > Subject: Re: [Pw_forum] can't read wavefunction and coords > To: jasius_1 at yahoo.com, "PWSCF Forum" > Date: Monday, April 27, 2009, 7:23 AM > Jonas Baltrusaitis wrote: > > > I don't thin it's reading coords right > > which version of the code are you talking about? > > P. > -- Paolo Giannozzi, Democritos and University of Udine, > Italy From giannozz at democritos.it Mon Apr 27 18:32:35 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 27 Apr 2009 18:32:35 +0200 Subject: [Pw_forum] can't read wavefunction and coords In-Reply-To: <33152.80152.qm@web54410.mail.yahoo.com> References: <33152.80152.qm@web54410.mail.yahoo.com> Message-ID: <49F5DE23.8020703@democritos.it> Jonas Baltrusaitis wrote: > 4.0.4 then it is not related to a recent change for non-scf calculations (coordinates are read from data file and no longer from input). Nothing interesting for me :-) Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From meheut at impmc.jussieu.fr Mon Apr 27 18:58:54 2009 From: meheut at impmc.jussieu.fr (merlin meheut) Date: Mon, 27 Apr 2009 18:58:54 +0200 Subject: [Pw_forum] relaxation of ice Ic with qe404 Message-ID: <20090427185854.13426kpdby0ec28e@www-ext.impmc.jussieu.fr> Dear PWSCF users, I have had a symetry problem during the relaxation of ice Ic, which happened on two platforms where I have compiled the 4.0.4 version, whereas the 3.0 version seemed to work fine. My input is : ------------------------------------------------------------------------- glace Ic modele Parravicini 1973 &control calculation = 'vc-relax', restart_mode = 'from_scratch' , prefix = 'ICEIc', disk_io = 'default' , pseudo_dir = './', outdir = '/tmp/', tprnfor = .true., tstress = .true., nstep = 300, /&endi &system ibrav =2, celldm(1)=12.0, nat = 6, ntyp = 2, ecutwfc =80,nr1=60,nr2=60,nr3=60 /&end &electrons electron_maxstep = 30, conv_thr = 1.d-9 , mixing_mode = 'plain', startingwfc = 'atomic', mixing_beta = 0.5, diagonalization = 'david_overlap', /&end &ions /&end &cell cell_dynamics='damp-w', /&end ATOMIC_SPECIES O 15.9949 O.pbe H 1.0078 H.pbe2 ATOMIC_POSITIONS crystal O 0.0000000000000000 0.0000000000000000 0.0000000000000000 O -0.2500000000000000 0.7500000000000000 -0.2500000000000000 H -0.0875 0.2625 -0.0875 H -0.0875 -0.0875 -0.0875 H -0.1625 0.8375 -0.5125 H -0.5125 0.8375 -0.1625 K_POINTS {automatic} 2 2 2 1 1 1 ----------------------------------------------------------- and the output: ----------------------------------------------------------- (...) ATOMIC_POSITIONS (crystal) O 0.000786430 -0.000786430 0.000786430 O -0.249213570 0.749213570 -0.249213570 H -0.094054219 0.277467614 -0.094054219 H -0.094054219 -0.089359175 -0.094054219 H -0.160640825 0.844054219 -0.527467614 H -0.527467614 0.844054219 -0.160640825 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from checkallsym : error # 1 some of the original symmetry operations not satisfied %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... ----------------------------------------------------------------------- Since I happened to make it work with the 3.0 version, I do not really need to solve the problem, but in case you would like more information about this problem, I will do my best. Merlin Meheut, ESS Department at UCLA -- Merlin M?heut professional adress: 595 Charles Young Drive East 3806 Geology Building Los Angeles, California 90095-1597 United States of America tel: 310 825 7934 cell phone: 310 893 4253 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From jasius_1 at yahoo.com Tue Apr 28 03:51:08 2009 From: jasius_1 at yahoo.com (Jonas Baltrusaitis) Date: Mon, 27 Apr 2009 18:51:08 -0700 (PDT) Subject: [Pw_forum] can't read wavefunction and coords In-Reply-To: <49F5C320.3040801@sissa.it> Message-ID: <557930.57670.qm@web54409.mail.yahoo.com> Gabriele et al, I rerun input with alat and, yes , it reads nicely. I assume it will read and convert ansgtroms from geom opt to alat in the next step no prob. Last thing I want to add to my input (after or before normal modes calcs) is DOS calcs. And this is where I got stuck as it wouldn't read last optimized coordinates (in fact it would miss ATOMIC SPECIES field if I didn't add it in ncsf part in hope that guess will get read). If I added ATOMIC SPECIES in ncsf it would use those instead of converting them from the optimization run. So my questions is how to combined DOS calcs so it uses optimized coordinates, so in one input I can 1) optimize, 2) normal modes and crossections and 3) DOS and PDOS calcs from optimized geometries I attached the input that succeded in nm calcls but failed in DOS calcs: didn;t read coords and produced empty output files thanks Jonas #!/bin/sh # run from directory where this script is cd `echo $0 | sed 's/\(.*\)\/.*/\1/'` # extract pathname EXAMPLE_DIR=/home/jbaltrus/$PBS_JOBNAME # check whether echo has the -e option if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi $ECHO $ECHO "$EXAMPLE_DIR : starting" $ECHO $ECHO "This example shows how to use pw.x and phcg.x to calculate the normal" $ECHO "modes of a molecule (SiH4) at Gamma." $ECHO $ECHO # set the needed environment variables PREFIX=`pwd` BIN_DIR=/share/apps/espresso-4.0.4/bin PSEUDO_DIR=/share/apps/espresso-4.0.4/pseudo TMP_DIR=/share/apps/scratch mkdir $EXAMPLE_DIR/results PARA_PREFIX="mpiexec -n 8 -machinefile $PBS_NODEFILE" PARA_POSTFIX="-rmpool 0 -nodes 2 -procs 4" # required executables and pseudopotentials BIN_LIST="pw.x phcg.x ph.x" PSEUDO_LIST="Si.vbc.UPF H.vbc.UPF C.pz-rrkjus.UPF H.vbc.UPF" $ECHO $ECHO " executables directory: $BIN_DIR" $ECHO " pseudo directory: $PSEUDO_DIR" $ECHO " temporary directory: $TMP_DIR" $ECHO " checking that needed directories and files exist...\c" # check for directories for DIR in "$BIN_DIR" "$PSEUDO_DIR" ; do if test ! -d $DIR ; then $ECHO $ECHO "ERROR: $DIR not existent or not a directory" $ECHO "Aborting" exit 1 fi done for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do if test ! -d $DIR ; then mkdir $DIR fi done cd $EXAMPLE_DIR/results # check for executables for FILE in $BIN_LIST ; do if test ! -x $BIN_DIR/$FILE ; then $ECHO $ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable" $ECHO "Aborting" exit 1 fi done # check for pseudopotentials for FILE in $PSEUDO_LIST ; do if test ! -r $PSEUDO_DIR/$FILE ; then $ECHO $ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable" $ECHO "Aborting" exit 1 fi done $ECHO " done" # how to run executables PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX" PH_COMMAND="$PARA_PREFIX $BIN_DIR/ph.x $PARA_POSTFIX" PHCG_COMMAND="$PARA_PREFIX $BIN_DIR/phcg.x $PARA_POSTFIX" DYNMAT_COMMAND=" $BIN_DIR/dynmat.x" $ECHO $ECHO " running pw.x as: $PW_COMMAND" $ECHO " running ph.x as: $PH_COMMAND" $ECHO " running phcg.x as: $PHCG_COMMAND" $ECHO " running dynmat.x as: $DYNMAT_COMMAND" $ECHO # clean TMP_DIR $ECHO " cleaning $TMP_DIR...\c" rm -rf $TMP_DIR/* $ECHO " done" # geometry optimization calculation cat > sih4.opt.in << EOF &control calculation='relax' pseudo_dir = '$PSEUDO_DIR/', restart_mode = ?from_scratch?, outdir='$TMP_DIR/' title='Test Silane SiH4 gamma only' prefix='sih4' tprnfor=.true. / &system ibrav=2, celldm(1) =12.0, nat=5, ntyp= 2, ecutwfc =16.0 / &electrons mixing_mode='plain' mixing_beta = 0.7, conv_thr = 1.0d-8 / &IONS / ATOMIC_SPECIES Si 28.086 Si.vbc.UPF H 1.008 H.vbc.UPF ATOMIC_POSITIONS (alat) Si 0.000000000 0.000000000 0.000000000 H 0.128530744 0.128530744 0.128530744 H -0.128530744 -0.128530744 0.128530744 H -0.128530744 0.128530744 -0.128530744 H 0.128530744 -0.128530744 -0.148530744 K_POINTS (gamma) EOF $ECHO " running the geometry opt calculation for SiH4...\c" $PW_COMMAND < sih4.opt.in > sih4.opt.out $ECHO " done" # normal mode calculation for SiH4 cat > sih4.nm.in << EOF normal modes for sih4 &inputph tr2_ph=1.0d-14, prefix='sih4', amass(1)=28.086, amass(2)=1.008, outdir='$TMP_DIR/', epsil=.true., trans=.true., asr=.true. raman=.false. fildyn='sih4.dyn' / 0.0 0.0 0.0 EOF $ECHO " running normal mode calculation for SiH4...\c" $PHCG_COMMAND < sih4.nm.in > sih4.nm.out $ECHO " done" # IR cross sections for SiH4 cat > sih4.dyn.in << EOF &input fildyn='sih4.dyn', asr='zero-dim' / EOF $ECHO " running IR cross section calculation for SiH4...\c" $DYNMAT_COMMAND < sih4.dyn.in > sih4.dyn.out $ECHO " done" # DOS calculation for sih4 cat > sih4.dos.in << EOF &control calculation='nscf' prefix='sih4', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' / &system ibrav=2, celldm(1) =12.0, nat=5, ntyp= 2, ecutwfc =16.0 / &electrons mixing_mode='plain' mixing_beta = 0.7, conv_thr = 1.0d-8 / ATOMIC_SPECIES Si 28.086 Si.vbc.UPF H 1.008 H.vbc.UPF ATOMIC_POSITIONS (alat) Si 0.000000000 0.000000000 0.000000000 H 0.128530744 0.128530744 0.128530744 H -0.128530744 -0.128530744 0.128530744 H -0.128530744 0.128530744 -0.128530744 H 0.128530744 -0.128530744 -0.148530744 K_POINTS {automatic} 12 12 12 0 0 0 EOF cat > sih4.dos2.in << EOF &inputpp outdir='$TMP_DIR/' prefix='sih4' fildos='sih4.dos', Emin=5.0, Emax=25.0, DeltaE=0.1 / EOF $ECHO " running DOS calculation for sih4...\c" $PW_COMMAND < sih4.dos.in > sih4.dos.out check_failure $? $DOS_COMMAND < sih4.dos2.in > sih4.dos2.out $ECHO " done" cat > sih4.pdos.in << EOF &inputpp outdir='$TMP_DIR/' prefix='sih4' Emin=5.0, Emax=25.0, DeltaE=0.1 ngauss=1, degauss=0.02 / EOF $ECHO " running PDOS calculation for Ni...\c" $PROJWFC_COMMAND < sih4.pdos.in > sih4.pdos.out $ECHO " done" $ECHO $ECHO "$EXAMPLE_DIR: done" --- On Mon, 4/27/09, Gabriele Sclauzero wrote: > From: Gabriele Sclauzero > Subject: Re: [Pw_forum] can't read wavefunction and coords > To: "PWSCF Forum" > Date: Monday, April 27, 2009, 7:37 AM > Jonas Baltrusaitis wrote: > > Gabriele, > > > > thanks for your response. I reran input without the > SCF step. I don't thin it's reading > > coords right. The source of confusion is that I am > inputting and outputing coords in > > angstroms in optimization but it gets transferred into > alat in normal mode calcs. > > I think reading and writing coordinates is treated properly > in pwscf (i.e. it is > internally consistent). You can specify input coordinates > in different formats, alat > (Cartesian axes, celldm(1) units), crystal,... > At the beginning of the output the read coordinates are > written in alat units (correctly > transformed, if you used an input with a different format), > and in crystal units if you > use verbosity='high'. > In relax calculations the coordinated are written after > each scf step in the format you > used for the input. So, if you use (angstrom) as input > format, you'll get ATOMIC_POSITION > in angstrom units on output, so that you can copy and paste > those positions if you need > them to build another input. > For me it always worked: if I give input coordinates as > ATOMIC_POSITIONS (angstrom) > ... > > I will get > ATOMIC_POSITIONS (angstrom) > ... > > after each ions move in a relax calculation. > If you restart, the program should not care about the > atomic positions you give on input, > but read those store in the restart files. > > HTH > > GS > > > > > > Still, this is what I backcalculate with xcrysden: > > > > Optimized coords: ATOMIC POSITIONS Si -0.053476533 > -0.187541319 +0.057950773 ... > > > > Normal mode calculation coords: ATOMIC_POSITIONS Si > -0.037813604 -0.132611686 > > 0.040977368 H -0.042235675 -0.102590555 > 0.268983495 H -0.221511706 > > -0.243919610 -0.030796850 H -0.032400640 > 0.077902395 -0.042412224 H > > 0.144511653 -0.248234756 -0.027243038 > > > > below is my latest input incidently, is there a way to > tell pwscf to use only angstroms > > in output? > > It is convenient for me to use angstroms when setting > up the initial input > > so I'd like to stay with angstroms > > > > JOnas > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From sclauzer at sissa.it Tue Apr 28 09:05:00 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 28 Apr 2009 09:05:00 +0200 Subject: [Pw_forum] can't read wavefunction and coords In-Reply-To: <557930.57670.qm@web54409.mail.yahoo.com> References: <557930.57670.qm@web54409.mail.yahoo.com> Message-ID: <49F6AA9C.6060109@sissa.it> Jonas Baltrusaitis wrote: > Gabriele et al, > > I rerun input with alat and, yes , it reads nicely. I assume it will read and convert > ansgtroms from geom opt to alat in the next step no prob. > > Last thing I want to add to my input (after or before normal modes calcs) is DOS calcs. > And this is where I got stuck as it wouldn't read last optimized coordinates (in fact > it would miss ATOMIC SPECIES field if I didn't add it in ncsf part in hope that guess > will get read). If I added ATOMIC SPECIES in ncsf it would use those instead of > converting them from the optimization run. Sorry I cannot follow your logic, it seems to me that you are confusing things a bit... You must always have ATOMIC_SPECIES card if you want to include any atom in your calcs. > > So my questions is how to combined DOS calcs so it uses optimized coordinates, so in > one input I can 1) optimize, 2) normal modes and crossections and 3) DOS and PDOS calcs > from optimized geometries I don't see any problem, apart from the fact that in version 4.0.4 ATOMIC_POSITIONS are read from input instead of being read from the .save directory (but now in the CVS the coords should be read from the scf restart files, as it seems more logical to me, since the charge density is read from there as well). Anyway what I suggest to do (since you want to do everything in a single script) is: first the relaxation, then grep the final atomic positions with something like this nat=5 grep -A$((nat+5)) CELL_PARAMETERS | tail -$((nat+1)) > atpos.tmp then use the positions in this temp file to add them at the end of any successive input file which needs them (_after_ removing the old ones from the middle of the file, obviously) cat > sih4.dos.in << EOF &control calculation='nscf' prefix='sih4', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' / &system ibrav=2, celldm(1) =12.0, nat=5, ntyp= 2, ecutwfc =16.0 / &electrons mixing_mode='plain' mixing_beta = 0.7, conv_thr = 1.0d-8 / ATOMIC_SPECIES Si 28.086 Si.vbc.UPF H 1.008 H.vbc.UPF K_POINTS {automatic} 12 12 12 0 0 0 EOF cat atpos.tmp >> sih4.dos.in for instance. In this way you don't have to care about the format of the positions. You can do the same to build an scf run before the nscf one, if you wish. Then you can calculate dos, pdos, ..., whatever needs scf charge density and/or wfcs from the relaxed configuration. > > I attached the input that succeded in nm calcls but failed in DOS calcs: didn;t read > coords and produced empty output files This seems another "problem", not related with atomic positions... Did it give you an error? Are you sure that the fildos file is not present? ...? GS > > thanks > > Jonas > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From kazempoor2000 at yahoo.com Tue Apr 28 09:54:43 2009 From: kazempoor2000 at yahoo.com (ali kazempoor) Date: Tue, 28 Apr 2009 00:54:43 -0700 (PDT) Subject: [Pw_forum] vc -relax converge Message-ID: <184001.10586.qm@web33104.mail.mud.yahoo.com> Dear all I use vc -relax to obtain the optimized lattice constant(tetragonal cell) and also the atomic position around O vacancy in TiO2 (2*2*3 supercell),but after 2 weeks , the pressure slowly goes from -100 kbar to -56 kbar( two far from 0.00. The input file is at following: &control calculation = 'vc-relax' restart_mode='restart', prefix='rutile-71atom' tstress = .true. tprnfor = .true. pseudo_dir = './', outdir='/ptmp/javad/scratch/' nstep=1000, dt=70, / &system ibrav= 6 , celldm(1) =17.36,celldm(3)=0.9663585, nat= 71, ntyp= 2, ecutwfc =35.0,ecutrho=400 / &electrons diagonalization='' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-6 / &IONS / &CELL cell_dynamics = 'damp-w', press=00.0 / ATOMIC_SPECIES Ti 43.0 Ti.pz-sp-van.UPF O 16.0 O.pz-van_ak.UPF ATOMIC_POSITIONS crystal Ti 0.00000000 0.00000000 0.00000000 Ti 0.50000000 0.00000000 0.00000000 Ti 0.00000000 0.50000000 0.00000000 Ti 0.50000000 0.50000000 0.00000000 Ti 0.00000000 0.00000000 0.33333333 Ti 0.50000000 0.00000000 0.33333333 Ti 0.00000000 0.50000000 0.33333333 Ti 0.50000000 0.50000000 0.33333333 Ti 0.00000000 0.00000000 0.66666667 Ti 0.50000000 0.00000000 0.66666667 Ti 0.00000000 0.50000000 0.66666667 Ti 0.50000000 0.50000000 0.66666667 Ti 0.25000000 0.25000000 0.16666667 Ti 0.75000000 0.25000000 0.16666667 Ti 0.25000000 0.75000000 0.16666667 Ti 0.75000000 0.75000000 0.16666667 Ti 0.25000000 0.25000000 0.50000000 Ti 0.75000000 0.25000000 0.50000000 Ti 0.25000000 0.75000000 0.50000000 Ti 0.75000000 0.75000000 0.50000000 Ti 0.25000000 0.25000000 0.83333333 Ti 0.75000000 0.25000000 0.83333333 Ti 0.25000000 0.75000000 0.83333333 Ti 0.75000000 0.75000000 0.83333333 O 0.65265000 0.15265000 0.00000000 O 0.15265000 0.65265000 0.00000000 O 0.65265000 0.65265000 0.00000000 O 0.15265000 0.15265000 0.33333333 O 0.65265000 0.15265000 0.33333333 O 0.15265000 0.65265000 0.33333333 O 0.65265000 0.65265000 0.33333333 O 0.15265000 0.15265000 0.66666667 O 0.65265000 0.15265000 0.66666667 O 0.15265000 0.65265000 0.66666667 O 0.65265000 0.65265000 0.66666667 O 0.34735000 0.34735000 0.00000000 O 0.84735000 0.34735000 0.00000000 O 0.34735000 0.84735000 0.00000000 O 0.84735000 0.84735000 0.00000000 O 0.34735000 0.34735000 0.33333333 O 0.84735000 0.34735000 0.33333333 O 0.34735000 0.84735000 0.33333333 O 0.84735000 0.84735000 0.33333333 O 0.34735000 0.34735000 0.66666667 O 0.84735000 0.34735000 0.66666667 O 0.34735000 0.84735000 0.66666667 O 0.84735000 0.84735000 0.66666667 O 0.40265000 0.09735000 0.16666667 O 0.90265000 0.09735000 0.16666667 O 0.40265000 0.59735000 0.16666667 O 0.90265000 0.59735000 0.16666667 O 0.40265000 0.09735000 0.50000000 O 0.90265000 0.09735000 0.50000000 O 0.40265000 0.59735000 0.50000000 O 0.90265000 0.59735000 0.50000000 O 0.40265000 0.09735000 0.83333333 O 0.90265000 0.09735000 0.83333333 O 0.40265000 0.59735000 0.83333333 O 0.90265000 0.59735000 0.83333333 O 0.09735000 0.40265000 0.16666667 O 0.59735000 0.40265000 0.16666667 O 0.09735000 0.90265000 0.16666667 O 0.59735000 0.90265000 0.16666667 O 0.09735000 0.40265000 0.50000000 O 0.59735000 0.40265000 0.50000000 O 0.09735000 0.90265000 0.50000000 O 0.59735000 0.90265000 0.50000000 O 0.09735000 0.40265000 0.83333333 O 0.59735000 0.40265000 0.83333333 O 0.09735000 0.90265000 0.83333333 O 0.59735000 0.90265000 0.83333333 K_POINTS automatic 4 4 4 0 0 0 Have you any comment to accelerate the convergence? Thanks A lt Ali KAzempour,Isfahan University of Technology,Physics Dept From degironc at sissa.it Tue Apr 28 10:48:11 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 28 Apr 2009 10:48:11 +0200 Subject: [Pw_forum] vc -relax converge In-Reply-To: <184001.10586.qm@web33104.mail.mud.yahoo.com> References: <184001.10586.qm@web33104.mail.mud.yahoo.com> Message-ID: <49F6C2CB.5030106@sissa.it> I think that usually it is convenient to relax the internal coordinates before staring moving the cell. did you tried that? have you tried to use the bfgs algorithm in vc-relax ? Stefano de Gironcoli - SISSA and DEMOCRITOS ali kazempoor wrote: > Dear all > I use vc -relax to obtain the optimized lattice constant(tetragonal cell) and also the atomic position around O vacancy in TiO2 (2*2*3 supercell),but after 2 weeks , the pressure slowly goes from -100 kbar to -56 kbar( two far from 0.00. The input file is at following: > &control > calculation = 'vc-relax' > restart_mode='restart', > prefix='rutile-71atom' > tstress = .true. > tprnfor = .true. > pseudo_dir = './', > outdir='/ptmp/javad/scratch/' > nstep=1000, > dt=70, > / > &system > ibrav= 6 , celldm(1) =17.36,celldm(3)=0.9663585, nat= 71, ntyp= 2, > ecutwfc =35.0,ecutrho=400 > / > &electrons > diagonalization='' > mixing_mode = 'plain' > mixing_beta = 0.7 > conv_thr = 1.0d-6 > / > &IONS > / > &CELL > cell_dynamics = 'damp-w', > press=00.0 > / > ATOMIC_SPECIES > Ti 43.0 Ti.pz-sp-van.UPF > O 16.0 O.pz-van_ak.UPF > ATOMIC_POSITIONS crystal > Ti 0.00000000 0.00000000 0.00000000 > Ti 0.50000000 0.00000000 0.00000000 > Ti 0.00000000 0.50000000 0.00000000 > Ti 0.50000000 0.50000000 0.00000000 > Ti 0.00000000 0.00000000 0.33333333 > Ti 0.50000000 0.00000000 0.33333333 > Ti 0.00000000 0.50000000 0.33333333 > Ti 0.50000000 0.50000000 0.33333333 > Ti 0.00000000 0.00000000 0.66666667 > Ti 0.50000000 0.00000000 0.66666667 > Ti 0.00000000 0.50000000 0.66666667 > Ti 0.50000000 0.50000000 0.66666667 > Ti 0.25000000 0.25000000 0.16666667 > Ti 0.75000000 0.25000000 0.16666667 > Ti 0.25000000 0.75000000 0.16666667 > Ti 0.75000000 0.75000000 0.16666667 > Ti 0.25000000 0.25000000 0.50000000 > Ti 0.75000000 0.25000000 0.50000000 > Ti 0.25000000 0.75000000 0.50000000 > Ti 0.75000000 0.75000000 0.50000000 > Ti 0.25000000 0.25000000 0.83333333 > Ti 0.75000000 0.25000000 0.83333333 > Ti 0.25000000 0.75000000 0.83333333 > Ti 0.75000000 0.75000000 0.83333333 > O 0.65265000 0.15265000 0.00000000 > O 0.15265000 0.65265000 0.00000000 > O 0.65265000 0.65265000 0.00000000 > O 0.15265000 0.15265000 0.33333333 > O 0.65265000 0.15265000 0.33333333 > O 0.15265000 0.65265000 0.33333333 > O 0.65265000 0.65265000 0.33333333 > O 0.15265000 0.15265000 0.66666667 > O 0.65265000 0.15265000 0.66666667 > O 0.15265000 0.65265000 0.66666667 > O 0.65265000 0.65265000 0.66666667 > O 0.34735000 0.34735000 0.00000000 > O 0.84735000 0.34735000 0.00000000 > O 0.34735000 0.84735000 0.00000000 > O 0.84735000 0.84735000 0.00000000 > O 0.34735000 0.34735000 0.33333333 > O 0.84735000 0.34735000 0.33333333 > O 0.34735000 0.84735000 0.33333333 > O 0.84735000 0.84735000 0.33333333 > O 0.34735000 0.34735000 0.66666667 > O 0.84735000 0.34735000 0.66666667 > O 0.34735000 0.84735000 0.66666667 > O 0.84735000 0.84735000 0.66666667 > O 0.40265000 0.09735000 0.16666667 > O 0.90265000 0.09735000 0.16666667 > O 0.40265000 0.59735000 0.16666667 > O 0.90265000 0.59735000 0.16666667 > O 0.40265000 0.09735000 0.50000000 > O 0.90265000 0.09735000 0.50000000 > O 0.40265000 0.59735000 0.50000000 > O 0.90265000 0.59735000 0.50000000 > O 0.40265000 0.09735000 0.83333333 > O 0.90265000 0.09735000 0.83333333 > O 0.40265000 0.59735000 0.83333333 > O 0.90265000 0.59735000 0.83333333 > O 0.09735000 0.40265000 0.16666667 > O 0.59735000 0.40265000 0.16666667 > O 0.09735000 0.90265000 0.16666667 > O 0.59735000 0.90265000 0.16666667 > O 0.09735000 0.40265000 0.50000000 > O 0.59735000 0.40265000 0.50000000 > O 0.09735000 0.90265000 0.50000000 > O 0.59735000 0.90265000 0.50000000 > O 0.09735000 0.40265000 0.83333333 > O 0.59735000 0.40265000 0.83333333 > O 0.09735000 0.90265000 0.83333333 > O 0.59735000 0.90265000 0.83333333 > K_POINTS automatic > 4 4 4 0 0 0 > Have you any comment to accelerate the convergence? > Thanks A lt > Ali KAzempour,Isfahan University of Technology,Physics Dept > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at democritos.it Tue Apr 28 12:08:08 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 28 Apr 2009 12:08:08 +0200 Subject: [Pw_forum] relaxation of ice Ic with qe404 In-Reply-To: <20090427185854.13426kpdby0ec28e@www-ext.impmc.jussieu.fr> References: <20090427185854.13426kpdby0ec28e@www-ext.impmc.jussieu.fr> Message-ID: <49F6D588.9060106@democritos.it> merlin meheut wrote: > I have had a symetry problem during the relaxation of ice Ic, > which happened on two platforms where I have compiled the > 4.0.4 version, whereas the 3.0 version seemed to work fine. the problem you mention appeared in v.3.1 (and is still there), apparently after a change of the damped-dynamics algorithm. In lines 824-826 of PW/vcsubs.f90, note the following: ! if(.true. ) = original version modified by Cesar Da Silva ! if(.false.) = modified algorithm by SdG if (.true.) then The last line was "if(.false.) then" in v.3.0 and it was change to the current one in v.3.1, because CDS said that his version was more tested. If you revert to the previous version, the problem you mention disappears. I cannot say whether this means that there is something fishy in the current algorithm. In any case: cell_dynamics='bfgs' is faster, at least in this case. By the way, diagonalization='david_overlap' is obsolete and will issue an error message in the new version. Use diagonalization='david' Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giuseppe.mattioli at mlib.ism.cnr.it Tue Apr 28 12:52:41 2009 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Tue, 28 Apr 2009 12:52:41 +0200 Subject: [Pw_forum] vc -relax converge In-Reply-To: <184001.10586.qm@web33104.mail.mud.yahoo.com> References: <184001.10586.qm@web33104.mail.mud.yahoo.com> Message-ID: <200904281252.42446.giuseppe.mattioli@mlib.ism.cnr.it> Dear Ali You have surely your good reasons to work with a 72-atom cell, but have you think about optimizing your lattice parameters by using a 6-atom cell and then building a supercell with an O vacancy? This is the best speed-up I can suggest. By the way, in a vc-relax calculation you should calculate forces and stress very accurately. You should decrease conv_thr (=1.0d-9) and insert within the &control box etot_conv_thr=1.0E-5, forc_conv_thr=1.0D-4, Moreover, in my experience a 4*4*4 k-point mesh is a very robust one for a 72- atom TiO2 supercell. A 2*2*2 mesh should give reliable and well converged results. Finally, give a chance to the vc-bfgs... And don't forget that you should use some beyond-LDA calculation in order to achieve a good description of reduced TiO2. Yours Giuseppe On Tuesday 28 April 2009 09:54:43 ali kazempoor wrote: > Dear all > I use vc -relax to obtain the optimized lattice constant(tetragonal cell) > and also the atomic position around O vacancy in TiO2 (2*2*3 > supercell),but after 2 weeks , the pressure slowly goes from -100 kbar to > -56 kbar( two far from 0.00. The input file is at following: &control > calculation = 'vc-relax' > restart_mode='restart', > prefix='rutile-71atom' > tstress = .true. > tprnfor = .true. > pseudo_dir = './', > outdir='/ptmp/javad/scratch/' > nstep=1000, > dt=70, > / > &system > ibrav= 6 , celldm(1) =17.36,celldm(3)=0.9663585, nat= 71, ntyp= 2, > ecutwfc =35.0,ecutrho=400 > / > &electrons > diagonalization='' > mixing_mode = 'plain' > mixing_beta = 0.7 > conv_thr = 1.0d-6 > / > &IONS > / > &CELL > cell_dynamics = 'damp-w', > press=00.0 > / > ATOMIC_SPECIES > Ti 43.0 Ti.pz-sp-van.UPF > O 16.0 O.pz-van_ak.UPF > ATOMIC_POSITIONS crystal > Ti 0.00000000 0.00000000 0.00000000 > Ti 0.50000000 0.00000000 0.00000000 > Ti 0.00000000 0.50000000 0.00000000 > Ti 0.50000000 0.50000000 0.00000000 > Ti 0.00000000 0.00000000 0.33333333 > Ti 0.50000000 0.00000000 0.33333333 > Ti 0.00000000 0.50000000 0.33333333 > Ti 0.50000000 0.50000000 0.33333333 > Ti 0.00000000 0.00000000 0.66666667 > Ti 0.50000000 0.00000000 0.66666667 > Ti 0.00000000 0.50000000 0.66666667 > Ti 0.50000000 0.50000000 0.66666667 > Ti 0.25000000 0.25000000 0.16666667 > Ti 0.75000000 0.25000000 0.16666667 > Ti 0.25000000 0.75000000 0.16666667 > Ti 0.75000000 0.75000000 0.16666667 > Ti 0.25000000 0.25000000 0.50000000 > Ti 0.75000000 0.25000000 0.50000000 > Ti 0.25000000 0.75000000 0.50000000 > Ti 0.75000000 0.75000000 0.50000000 > Ti 0.25000000 0.25000000 0.83333333 > Ti 0.75000000 0.25000000 0.83333333 > Ti 0.25000000 0.75000000 0.83333333 > Ti 0.75000000 0.75000000 0.83333333 > O 0.65265000 0.15265000 0.00000000 > O 0.15265000 0.65265000 0.00000000 > O 0.65265000 0.65265000 0.00000000 > O 0.15265000 0.15265000 0.33333333 > O 0.65265000 0.15265000 0.33333333 > O 0.15265000 0.65265000 0.33333333 > O 0.65265000 0.65265000 0.33333333 > O 0.15265000 0.15265000 0.66666667 > O 0.65265000 0.15265000 0.66666667 > O 0.15265000 0.65265000 0.66666667 > O 0.65265000 0.65265000 0.66666667 > O 0.34735000 0.34735000 0.00000000 > O 0.84735000 0.34735000 0.00000000 > O 0.34735000 0.84735000 0.00000000 > O 0.84735000 0.84735000 0.00000000 > O 0.34735000 0.34735000 0.33333333 > O 0.84735000 0.34735000 0.33333333 > O 0.34735000 0.84735000 0.33333333 > O 0.84735000 0.84735000 0.33333333 > O 0.34735000 0.34735000 0.66666667 > O 0.84735000 0.34735000 0.66666667 > O 0.34735000 0.84735000 0.66666667 > O 0.84735000 0.84735000 0.66666667 > O 0.40265000 0.09735000 0.16666667 > O 0.90265000 0.09735000 0.16666667 > O 0.40265000 0.59735000 0.16666667 > O 0.90265000 0.59735000 0.16666667 > O 0.40265000 0.09735000 0.50000000 > O 0.90265000 0.09735000 0.50000000 > O 0.40265000 0.59735000 0.50000000 > O 0.90265000 0.59735000 0.50000000 > O 0.40265000 0.09735000 0.83333333 > O 0.90265000 0.09735000 0.83333333 > O 0.40265000 0.59735000 0.83333333 > O 0.90265000 0.59735000 0.83333333 > O 0.09735000 0.40265000 0.16666667 > O 0.59735000 0.40265000 0.16666667 > O 0.09735000 0.90265000 0.16666667 > O 0.59735000 0.90265000 0.16666667 > O 0.09735000 0.40265000 0.50000000 > O 0.59735000 0.40265000 0.50000000 > O 0.09735000 0.90265000 0.50000000 > O 0.59735000 0.90265000 0.50000000 > O 0.09735000 0.40265000 0.83333333 > O 0.59735000 0.40265000 0.83333333 > O 0.09735000 0.90265000 0.83333333 > O 0.59735000 0.90265000 0.83333333 > K_POINTS automatic > 4 4 4 0 0 0 > Have you any comment to accelerate the convergence? > Thanks A lt > Ali KAzempour,Isfahan University of Technology,Physics Dept > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00016 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090428/0c8c4bfc/attachment-0001.htm From yk.majid at gmail.com Tue Apr 28 13:52:49 2009 From: yk.majid at gmail.com (majid yazdani) Date: Tue, 28 Apr 2009 16:22:49 +0430 Subject: [Pw_forum] 3D charge density with Xcrysden Message-ID: *Dear all users,* *I want to know how could I visualize a 3D charge density plot with xcrsden.?* ** *Besr regards,* *Majid* *Department of Physics, University of Kashan, Iran.* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090428/b7e52023/attachment.htm From lanhaiping at gmail.com Tue Apr 28 14:07:15 2009 From: lanhaiping at gmail.com (lan haiping) Date: Tue, 28 Apr 2009 20:07:15 +0800 Subject: [Pw_forum] 3D charge density with Xcrysden In-Reply-To: References: Message-ID: Just have a look at this url, http://www.xcrysden.org/doc/density.html On Tue, Apr 28, 2009 at 7:52 PM, majid yazdani wrote: > *Dear all users,* > *I want to know how could I visualize a 3D charge density plot with > xcrsden.?* > ** > *Besr regards,* > *Majid* > *Department of Physics, University of Kashan, Iran.* > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090428/f4b62c34/attachment.htm From paulatto at sissa.it Tue Apr 28 14:08:29 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 28 Apr 2009 14:08:29 +0200 Subject: [Pw_forum] 3D charge density with Xcrysden In-Reply-To: References: Message-ID: In data 28 aprile 2009 alle ore 13:52:49, majid yazdani ha scritto: > *Dear all users,* > *I want to know how could I visualize a 3D charge density plot with > xcrsden.?* You have to generate an appropriate charge density file with pp.x, like its is done in example 05 and 16, but using the xcrysden output format (please see Doc/INPUT_PP.html for details). Than follow the link pointed by Ian for additional details on how to convince xcrysden to show the data to you. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From Giovanni.Cantele at na.infn.it Tue Apr 28 14:18:35 2009 From: Giovanni.Cantele at na.infn.it (Giovanni Cantele) Date: Tue, 28 Apr 2009 14:18:35 +0200 Subject: [Pw_forum] 3D charge density with Xcrysden In-Reply-To: References: Message-ID: <49F6F41B.903@na.infn.it> majid yazdani wrote: > *Dear all users,* > *I want to know how could I visualize a 3D charge density plot with > xcrsden.?* > ** > *Besr regards,* > *Majid* > *Department of Physics, University of Kashan, Iran.* > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > First step should, of course, to generate a file with Xcrysden format (http://www.xcrysden.org/doc/XSF.html#scalar-field) containing information on your crystal (lattice, atomic positions), the spatial grid on which the charge density is calculated and the values of the charge density on the points of that grid. This is done using the post-processing tools of Quantum-Espresso, documented in Doc/INPUT_PP.txt Basically, you should: i) make an scf run, using pw.x ; ii) post-process your results, using pp.x the input file of the latter should contain both the &INPUTPP and the &PLOT (see the above mentioned doc for further reference) Then, you'll end up with a *.xsf file, which can be directly read by XCrysDen. Here there is a description on how to load the file and the charge density data inside: http://www.xcrysden.org/doc/density.html Here there is a description on how to change some parameters controlling the display of the isosurfaces: http://www.xcrysden.org/doc/isocontrol.html Once all this is done, you may also play with 2D cuts of you charge density (projection onto a plane), which are directly handled by XCrysDen. Giovanni -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: giovanni.cantele at cnr.it giovanni.cantele at na.infn.it Web: http://people.na.infn.it/~cantele Research Group: http://www.nanomat.unina.it From zhaohscas at yahoo.com.cn Tue Apr 28 14:49:29 2009 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Tue, 28 Apr 2009 20:49:29 +0800 Subject: [Pw_forum] 3D charge density with Xcrysden In-Reply-To: <49F6F41B.903@na.infn.it> References: <49F6F41B.903@na.infn.it> Message-ID: <233932368.20090428204929@yahoo.com.cn> On Tuesday, April 28, 2009 at 20:18, Giovanni.Cantele at na.infn.it wrote: [snip] > Once all this is done, you may also play with 2D cuts of you charge > density (projection onto a plane), > which are directly handled by XCrysDen. What do you mean? Do you mean the XCrysDen itself can extract a 2D charge density plot for a specific plane based on the 3D one. If so, what's the concrete steps? Best regards, -- Hongsheng Zhao Xinjiang Technical Institute of Physics and Chemistry Chinese Academy of Sciences GnuPG DSA: 0xD108493 2009-4-28 From Giovanni.Cantele at na.infn.it Tue Apr 28 15:52:52 2009 From: Giovanni.Cantele at na.infn.it (Giovanni Cantele) Date: Tue, 28 Apr 2009 15:52:52 +0200 Subject: [Pw_forum] 3D charge density with Xcrysden In-Reply-To: <233932368.20090428204929@yahoo.com.cn> References: <49F6F41B.903@na.infn.it> <233932368.20090428204929@yahoo.com.cn> Message-ID: <49F70A34.1020407@na.infn.it> Hongsheng Zhao wrote: > On Tuesday, April 28, 2009 at 20:18, Giovanni.Cantele at na.infn.it wrote: > [snip] > >> Once all this is done, you may also play with 2D cuts of you charge >> density (projection onto a plane), >> which are directly handled by XCrysDen. >> > > What do you mean? Do you mean the XCrysDen itself can extract a > 2D charge density plot for a specific plane based on the 3D one. If > so, what's the concrete steps? > > Best regards, > (sorry, just replying again, maybe the previous answer was not successfull because of a "SPAM" flag in the subject of the e-mail I was replying to) Yes! even if (at least this is what I've always used!) only xy, yz,xz planes, at the moment it should not possible to specify an arbitrary plane. once you have opened your xsf file with Xcrysden and the "isosurface controls" window (see previous post links), in the same window you find 4 tabs, one is "isosurface" the other three are "Plane1", "Plane2", "Plane3" or similar, each of them allows to select a plane (xy, yz, xz) and its position, as well as how to display on it isolines, colours, etc. Details in http://www.xcrysden.org/doc/plane1control.html Giovanni -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: giovanni.cantele at cnr.it giovanni.cantele at na.infn.it Web: http://people.na.infn.it/~cantele Research Group: http://www.nanomat.unina.it From jasius_1 at yahoo.com Wed Apr 29 02:23:27 2009 From: jasius_1 at yahoo.com (Jonas Baltrusaitis) Date: Tue, 28 Apr 2009 17:23:27 -0700 (PDT) Subject: [Pw_forum] can't read wavefunction and coords In-Reply-To: <49F6AA9C.6060109@sissa.it> Message-ID: <124688.32679.qm@web54406.mail.yahoo.com> Gabriele, I am almost there. I appreciate you helping me I added coordinates, read nicely. However when calculating DOS in produces empty dos2 and pdos output files with no error and doesn't generate fildos at all. I suspect it has problems reading guess I am confused as I am following Example 8, thus should be pretty straightforward but it's not. My latest input is below Jonas #!/bin/sh # run from directory where this script is cd `echo $0 | sed 's/\(.*\)\/.*/\1/'` # extract pathname EXAMPLE_DIR=/home/jbaltrus/$PBS_JOBNAME # check whether echo has the -e option if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi $ECHO $ECHO "$EXAMPLE_DIR : starting" $ECHO $ECHO "This example shows how to use pw.x and phcg.x to calculate the normal" $ECHO "modes of a molecule (SiH4) at Gamma." $ECHO $ECHO # set the needed environment variables PREFIX=`pwd` BIN_DIR=/share/apps/espresso-4.0.4/bin PSEUDO_DIR=/share/apps/espresso-4.0.4/pseudo TMP_DIR=/share/apps/scratch mkdir $EXAMPLE_DIR/results PARA_PREFIX="mpiexec -n 8 -machinefile $PBS_NODEFILE" PARA_POSTFIX="-rmpool 0 -nodes 2 -procs 4" # required executables and pseudopotentials BIN_LIST="pw.x phcg.x ph.x" PSEUDO_LIST="Si.vbc.UPF H.vbc.UPF C.pz-rrkjus.UPF H.vbc.UPF" $ECHO $ECHO " executables directory: $BIN_DIR" $ECHO " pseudo directory: $PSEUDO_DIR" $ECHO " temporary directory: $TMP_DIR" $ECHO " checking that needed directories and files exist...\c" # check for directories for DIR in "$BIN_DIR" "$PSEUDO_DIR" ; do if test ! -d $DIR ; then $ECHO $ECHO "ERROR: $DIR not existent or not a directory" $ECHO "Aborting" exit 1 fi done for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do if test ! -d $DIR ; then mkdir $DIR fi done cd $EXAMPLE_DIR/results # check for executables for FILE in $BIN_LIST ; do if test ! -x $BIN_DIR/$FILE ; then $ECHO $ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable" $ECHO "Aborting" exit 1 fi done # check for pseudopotentials for FILE in $PSEUDO_LIST ; do if test ! -r $PSEUDO_DIR/$FILE ; then $ECHO $ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable" $ECHO "Aborting" exit 1 fi done $ECHO " done" # how to run executables PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX" PH_COMMAND="$PARA_PREFIX $BIN_DIR/ph.x $PARA_POSTFIX" PHCG_COMMAND="$PARA_PREFIX $BIN_DIR/phcg.x $PARA_POSTFIX" DYNMAT_COMMAND=" $BIN_DIR/dynmat.x" $ECHO $ECHO " running pw.x as: $PW_COMMAND" $ECHO " running ph.x as: $PH_COMMAND" $ECHO " running phcg.x as: $PHCG_COMMAND" $ECHO " running dynmat.x as: $DYNMAT_COMMAND" $ECHO # clean TMP_DIR $ECHO " cleaning $TMP_DIR...\c" rm -rf $TMP_DIR/* $ECHO " done" # geometry optimization calculation cat > sih4.opt.in << EOF &control calculation='relax' pseudo_dir = '$PSEUDO_DIR/', restart_mode = ?from_scratch?, outdir='$TMP_DIR/' title='Test Silane SiH4 gamma only' prefix='sih4' tprnfor=.true. / &system ibrav=2, celldm(1) =12.0, nat=5, ntyp= 2, ecutwfc =16.0 / &electrons mixing_mode='plain' mixing_beta = 0.7, conv_thr = 1.0d-8 / &IONS / ATOMIC_SPECIES Si 28.086 Si.vbc.UPF H 1.008 H.vbc.UPF ATOMIC_POSITIONS (alat) Si 0.000000000 0.000000000 0.000000000 H 0.128530744 0.128530744 0.128530744 H -0.128530744 -0.128530744 0.128530744 H -0.128530744 0.128530744 -0.128530744 H 0.128530744 -0.128530744 -0.148530744 K_POINTS (gamma) EOF $ECHO " running the geometry opt calculation for SiH4...\c" $PW_COMMAND < sih4.opt.in > sih4.opt.out $ECHO " done" nat=5 grep -A$((nat+5)) CELL_PARAMETERS sih4.opt.out | tail -$((nat+1)) > atpos.tmp # normal mode calculation for SiH4 cat > sih4.nm.in << EOF normal modes for sih4 &inputph tr2_ph=1.0d-14, prefix='sih4', amass(1)=28.086, amass(2)=1.008, outdir='$TMP_DIR/', epsil=.true., trans=.true., asr=.true. raman=.false. fildyn='sih4.dyn' / 0.0 0.0 0.0 EOF $ECHO " running normal mode calculation for SiH4...\c" $PHCG_COMMAND < sih4.nm.in > sih4.nm.out $ECHO " done" # IR cross sections for SiH4 cat > sih4.dyn.in << EOF &input fildyn='sih4.dyn', asr='zero-dim' / EOF $ECHO " running IR cross section calculation for SiH4...\c" $DYNMAT_COMMAND < sih4.dyn.in > sih4.dyn.out $ECHO " done" # DOS (SCF) calculation for sih4 cat > sih4.scf.in << EOF &control calculation='scf' prefix='sih4', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' / &system ibrav=2, celldm(1) =12.0, nat=5, ntyp= 2, ecutwfc =16.0 / &electrons mixing_mode='plain' mixing_beta = 0.7, conv_thr = 1.0d-8 / ATOMIC_SPECIES Si 28.086 Si.vbc.UPF H 1.008 H.vbc.UPF K_POINTS {automatic} 12 12 12 0 0 0 EOF cat atpos.tmp >> sih4.scf.in $PW_COMMAND < sih4.scf.in > sih4.scf.out # DOS calculation for sih4 cat > sih4.dos.in << EOF &control calculation='nscf' prefix='sih4', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' / &system ibrav=2, celldm(1) =12.0, nat=5, ntyp= 2, ecutwfc =16.0 / &electrons mixing_mode='plain' mixing_beta = 0.7, conv_thr = 1.0d-8 / ATOMIC_SPECIES Si 28.086 Si.vbc.UPF H 1.008 H.vbc.UPF K_POINTS {automatic} 12 12 12 0 0 0 EOF cat atpos.tmp >> sih4.dos.in cat > sih4.dos2.in << EOF &inputpp outdir='$TMP_DIR/' prefix='sih4' fildos='sih4.dos', Emin=5.0, Emax=25.0, DeltaE=0.1 / EOF $ECHO " running DOS calculation for sih4...\c" $PW_COMMAND < sih4.dos.in > sih4.dos.out $DOS_COMMAND < sih4.dos2.in > sih4.dos2.out $ECHO " done" cat > sih4.pdos.in << EOF &inputpp outdir='$TMP_DIR/' prefix='sih4' Emin=5.0, Emax=25.0, DeltaE=0.1 ngauss=1, degauss=0.02 / EOF $ECHO " running PDOS calculation for Ni...\c" $PROJWFC_COMMAND < sih4.pdos.in > sih4.pdos.out $ECHO " done" $ECHO $ECHO "$EXAMPLE_DIR: done" --- On Tue, 4/28/09, Gabriele Sclauzero wrote: > From: Gabriele Sclauzero > Subject: Re: [Pw_forum] can't read wavefunction and coords > To: "PWSCF Forum" > Date: Tuesday, April 28, 2009, 12:05 AM > Jonas Baltrusaitis wrote: > > Gabriele et al, > > > > I rerun input with alat and, yes , it reads nicely. I > assume it will read and convert > > ansgtroms from geom opt to alat in the next step no > prob. > > > > Last thing I want to add to my input (after or before > normal modes calcs) is DOS calcs. > > And this is where I got stuck as it wouldn't read > last optimized coordinates (in fact > > it would miss ATOMIC SPECIES field if I didn't add > it in ncsf part in hope that guess > > will get read). If I added ATOMIC SPECIES in ncsf it > would use those instead of > > converting them from the optimization run. > > Sorry I cannot follow your logic, it seems to me that you > are confusing things a bit... > > You must always have ATOMIC_SPECIES card if you want to > include any atom in your calcs. > > > > > So my questions is how to combined DOS calcs so it > uses optimized coordinates, so in > > one input I can 1) optimize, 2) normal modes and > crossections and 3) DOS and PDOS calcs > > from optimized geometries > > I don't see any problem, apart from the fact that in > version 4.0.4 ATOMIC_POSITIONS are > read from input instead of being read from the .save > directory (but now in the CVS the > coords should be read from the scf restart files, as it > seems more logical to me, since > the charge density is read from there as well). > Anyway what I suggest to do (since you want to do > everything in a single script) is: first > the relaxation, then grep the final atomic positions with > something like this > > nat=5 > grep -A$((nat+5)) CELL_PARAMETERS | tail -$((nat+1)) > > atpos.tmp > > then use the positions in this temp file to add them at the > end of any successive input > file which needs them (_after_ removing the old ones from > the middle of the file, obviously) > > cat > sih4.dos.in << EOF > &control > calculation='nscf' > prefix='sih4', > pseudo_dir = '$PSEUDO_DIR/', > outdir='$TMP_DIR/' > / > &system > ibrav=2, celldm(1) =12.0, nat=5, ntyp= 2, > ecutwfc =16.0 > / > &electrons > mixing_mode='plain' > mixing_beta = 0.7, > conv_thr = 1.0d-8 > / > ATOMIC_SPECIES > Si 28.086 Si.vbc.UPF > H 1.008 H.vbc.UPF > K_POINTS {automatic} > 12 12 12 0 0 0 > EOF > > cat atpos.tmp >> sih4.dos.in > > for instance. In this way you don't have to care about > the format of the positions. You > can do the same to build an scf run before the nscf one, if > you wish. Then you can > calculate dos, pdos, ..., whatever needs scf charge density > and/or wfcs from the relaxed > configuration. > > > > > I attached the input that succeded in nm calcls but > failed in DOS calcs: didn;t read > > coords and produced empty output files > > This seems another "problem", not related with > atomic positions... > > Did it give you an error? Are you sure that the fildos file > is not present? ...? > > > GS > > > > > thanks > > > > Jonas > > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From alianoaa at gmail.com Wed Apr 29 02:28:34 2009 From: alianoaa at gmail.com (antonio aliano) Date: Tue, 28 Apr 2009 17:28:34 -0700 Subject: [Pw_forum] Carbon Pseudo-potential Message-ID: <9a321f950904281728v4526c9c3l293588abde75c1cd@mail.gmail.com> Dear Pwscf users, I'm looking for a PBE Norm-conserving Pseudopotential for Carbon; On the quantum espresso web page i found a lot of pseudopotentials for carbon but I didn't find any PBE-norm-conserving. It sound strange to me, but i could not find it. So i wonder if anyone knows if there is aparticular reason for that or if anyone know other repository or database where it is possible to find a PBE Carbon pseudopotential (.UPF). Sorry for the trivial question, Have a good day, A.A. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090428/857e384f/attachment.htm From akohlmey at cmm.chem.upenn.edu Wed Apr 29 03:21:22 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 28 Apr 2009 21:21:22 -0400 Subject: [Pw_forum] Carbon Pseudo-potential In-Reply-To: <9a321f950904281728v4526c9c3l293588abde75c1cd@mail.gmail.com> References: <9a321f950904281728v4526c9c3l293588abde75c1cd@mail.gmail.com> Message-ID: <1240968082.18574.839.camel@zero> On Tue, 2009-04-28 at 17:28 -0700, antonio aliano wrote: > Dear Pwscf users, > > I'm looking for a PBE Norm-conserving Pseudopotential for Carbon; On > the quantum espresso web page i found a lot of pseudopotentials for > carbon but I didn't find any PBE-norm-conserving. just do one yourself. carbon is rather uncritical, and use a cutoff of either 1.0 a.u. for a "hard" or 1.4 a.u. for a "soft" NC potential. or something in between. if you are willing to do some checks, i can send you an archive of similarly created files with a precursor of the atomic code that is in Q-E. they are converted to UPF, though, but i cannot guarantee they work and i don't have time to test them properly. just let me know. cheers, axel. > It sound strange to me, but i could not find it. So i wonder if anyone > knows if there is aparticular reason for that or if anyone know other > repository or database where it is possible to find a PBE Carbon > pseudopotential (.UPF). > > Sorry for the trivial question, > > Have a good day, > > A.A. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From yccheng.nju at gmail.com Wed Apr 29 03:31:44 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Wed, 29 Apr 2009 09:31:44 +0800 Subject: [Pw_forum] The stability of monolayer compound Message-ID: Dear all, Recently, the mono layered structure "graphene" is studied extensively. In graphite the link between layers is by "Van Der Waals Force" which is weaker than the ionic or covalent bond. So using scraping method, people can get graphene. However, for other compounds( AlN, BC2N, GaN, ZnO,......), in which the connection between layers are ionic bonds, the graphite-like structure have not been got in experiments. My questions are as follows: 1, Is it possible to get the mono layered compounds( AlN, BC2N, GaN, ZnO,......)? 2, From the theoretical interests, how to study the stability of mono layered compounds by first-principles calculation? Any suggestion or comment is appreciated ! Thank you in advance. -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090429/73213de7/attachment.htm From wangweiphysics at yahoo.com.cn Wed Apr 29 08:19:33 2009 From: wangweiphysics at yahoo.com.cn (=?utf-8?B?546uIOeOiw==?=) Date: Wed, 29 Apr 2009 14:19:33 +0800 (CST) Subject: [Pw_forum] from phq_readin: error # 1, no elec. field with metals Message-ID: <105371.18478.qm@web15201.mail.cnb.yahoo.com> Thank you for all response. I have fixed the proplem. epsil=.false.is the right option for metal sysytem. And I am very sorry I forget giving my affiliation last time: Wang wei, Southeast University, Nanjing, P. R. China 2009.4.29 --- 09?4?26????, pw_forum-request at pwscf.org ??? ???: pw_forum-request at pwscf.org ??: Pw_forum Digest, Vol 22, Issue 61 ???: pw_forum at pwscf.org ??: 2009?4?26?,??,??5:54 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. from phq_readin : error # 1 , no elec. field with metals (? ?) ???2. Re: from phq_readin : error # 1 ,??? no elec. field with ??? metals ? ? ? (lan haiping) ???3. Re: from phq_readin : error # 1 ,??? no elec. field with metals ? ? ? (Eyvaz Isaev) ???4. -nimage -npool -ntg -ndiag (Eduardo Ariel Menendez Proupin) ---------------------------------------------------------------------- Message: 1 Date: Sat, 25 Apr 2009 23:39:28 +0800 (CST) From: ? ? Subject: [Pw_forum] from phq_readin : error # 1 , no elec. field with ??? metals To: pw_forum at pwscf.org Message-ID: <60951.11396.qm at web15208.mail.cnb.yahoo.com> Content-Type: text/plain; charset="utf-8" Dear all, ?? I want to calculate phonon frequencies at Gamma for superconductor KOs2O6, according to the example02, first I run scf calculation using pw.x command without any error, but when I perform the phonon calculation, the error appears as forrows: ?? from phq_readin: error #?????? 1 ?? no elec. field with metals Who can tell me why? Thank you very much! ? The input files as follows: kos2o6.scf.in ??&CONTROL ???????????????? calculation = 'scf' , ??????????????? restart_mode = 'from_scratch' , ????????????????????? outdir = '/home/ww/data/kos2o6/' , ????????????????????? wfcdir = '/home/ww/data/kos2o6/' , ????????????????? pseudo_dir = '/home/ww/PWscf/pseudo/' , ????????????????????? prefix = 'kos2o6' , ?/ ?&SYSTEM ?????????????????????? ibrav = 2, ?????????????????? celldm(1) = 19.0945, ???????????????????????? nat = 18, ??????????????????????? ntyp = 3, ???????????????????? ecutwfc = 60 , ???????????????????? ecutrho = 600 , ???????????????? occupations = 'smearing' , ???????????????????? degauss = 0.03 ??????????????????? smearing = 'gauss' , ?/ ?&ELECTRONS ??????????????????? conv_thr = 1.0D-8 , ???????????????? mixing_beta = 0.7 , ?/ ATOMIC_SPECIES ??? K?? 39.10000? K.pbe-sp.UPF ?? Os? 190.20000? Os.pbe-n-van.UPF ??? O?? 16.00000? O.pbe-van_ak.UPF ATOMIC_POSITIONS crystal ?? .... K_POINTS {automatic} ? 10? 10? 10? 0? 0? 0 kos2o6.phG.in: ???? phonons of kos2o6 at Gamma ?&inputph ? tr2_ph=1.0d-14, ? prefix='kos2o6', ? epsil=.true., ? amass(1)=39.10, ? amass(2)=190.2, ? amass(3)=16.00, ? outdir='/home/ww/data/kos2o6/', ? fildyn='kos2o6.dynG', ?/ 0.0 0.0 0.0 ? ? ? ___________________________________________________________ ? ????????????????? http://card.mail.cn.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090425/0cb9cf45/attachment-0001.htm ------------------------------ Message: 2 Date: Sun, 26 Apr 2009 00:56:47 +0800 From: lan haiping Subject: Re: [Pw_forum] from phq_readin : error # 1 ,??? no elec. field ??? with ??? metals To: PWSCF Forum Message-ID: ??? Content-Type: text/plain; charset="gb2312" Hi, According to INPUT_PH, epsil LOGICAL? *Default:* .false. If .true. in a q=0 calculation for a non metal the macroscopic dielectric constant of the system is computed. Do not set epsil to .true. if you have a metallic system or q/=0: the code will complain and stop. Therefore, your system should be a metal, and phonon code complained and stopped. Please supply your affiliation! Regards, On Sat, Apr 25, 2009 at 11:39 PM, ? ? wrote: > Dear all, >? ? I want to calculate phonon frequencies at Gamma for superconductor > KOs2O6, according to the example02, first I run scf calculation using pw.x > command without any error, but when I perform the phonon calculation, the > error appears as forrows: >? ? from phq_readin: error #? ? ???1 >? ? no elec. field with metals > Who can tell me why? Thank you very much! > > The input files as follows: > kos2o6.scf.in >???&CONTROL >? ? ? ? ? ? ? ? ? calculation = 'scf' , >? ? ? ? ? ? ? ???restart_mode = 'from_scratch' , >? ? ? ? ? ? ? ? ? ? ???outdir = '/home/ww/data/kos2o6/' , >? ? ? ? ? ? ? ? ? ? ???wfcdir = '/home/ww/data/kos2o6/' , >? ? ? ? ? ? ? ? ???pseudo_dir = '/home/ww/PWscf/pseudo/' , >? ? ? ? ? ? ? ? ? ? ???prefix = 'kos2o6' , >? / >? &SYSTEM >? ? ? ? ? ? ? ? ? ? ? ? ibrav = 2, >? ? ? ? ? ? ? ? ? ? celldm(1) = 19.0945, >? ? ? ? ? ? ? ? ? ? ? ? ? nat = 18, >? ? ? ? ? ? ? ? ? ? ? ???ntyp = 3, >? ? ? ? ? ? ? ? ? ? ? ecutwfc = 60 , >? ? ? ? ? ? ? ? ? ? ? ecutrho = 600 , >? ? ? ? ? ? ? ? ? occupations = 'smearing' , >? ? ? ? ? ? ? ? ? ? ? degauss = 0.03 >? ? ? ? ? ? ? ? ? ???smearing = 'gauss' , >? / >? &ELECTRONS >? ? ? ? ? ? ? ? ? ???conv_thr = 1.0D-8 , >? ? ? ? ? ? ? ? ? mixing_beta = 0.7 , >? / > ATOMIC_SPECIES >? ???K???39.10000? K.pbe-sp.UPF >? ? Os? 190.20000? Os.pbe-n-van.UPF >? ???O???16.00000? O.pbe-van_ak.UPF > ATOMIC_POSITIONS crystal >? ? .... > K_POINTS {automatic} >???10? 10? 10? 0? 0? 0 > kos2o6.phG.in: >? ? ? phonons of kos2o6 at Gamma >? &inputph >???tr2_ph=1.0d-14, >???prefix='kos2o6', >???epsil=.true., >???amass(1)=39.10, >???amass(2)=190.2, >???amass(3)=16.00, >???outdir='/home/ww/data/kos2o6/', >???fildyn='kos2o6.dynG', >? / > 0.0 0.0 0.0 > > ------------------------------ > ????????????????? > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090426/edc33cb1/attachment-0001.htm ------------------------------ Message: 3 Date: Sat, 25 Apr 2009 09:59:58 -0700 (PDT) From: Eyvaz Isaev Subject: Re: [Pw_forum] from phq_readin : error # 1 ,??? no elec. field ??? with metals To: PWSCF Forum Message-ID: <950057.79544.qm at web65704.mail.ac4.yahoo.com> Content-Type: text/plain; charset=utf-8 Dear unknown user, First of all, all questions put in this forum should be signed properly, i.e. you should provide your name and affiliation. As concerns your question it is quite simple, and very basic. Can you please tell us what is macroscopic dielectric constant for metals? If you know the answer, you can fix the problem quite easily. By the way, the message from phq_readin.f90 almost contains the answer what you should do. Read carefully INPUT_PH.txt (in /Doc) to learn more about parameters you included in pn.in file. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Sat, 4/25/09, ? ? wrote: > From: ? ? > Subject: [Pw_forum] from phq_readin : error # 1 , no elec. field with metals > To: pw_forum at pwscf.org > Date: Saturday, April 25, 2009, 7:39 PM > Dear all, > ?? I want to calculate phonon frequencies at Gamma for > superconductor KOs2O6, according to the example02, first I > run scf calculation using pw.x command without any error, > but when I perform the phonon calculation, the error appears > as forrows: > ?? from phq_readin: error #?????? 1 > ?? no elec. field with metals > Who can tell me why? Thank you very much! > ? > The input files as follows: > kos2o6.scf.in > ??&CONTROL > ???????????????? calculation = > 'scf' , > ??????????????? restart_mode = > 'from_scratch' , > ????????????????????? outdir = > '/home/ww/data/kos2o6/' , > ????????????????????? wfcdir = > '/home/ww/data/kos2o6/' , > ????????????????? pseudo_dir = > '/home/ww/PWscf/pseudo/' , > ????????????????????? prefix = > 'kos2o6' , > ?/ > ?&SYSTEM > ?????????????????????? ibrav = 2, > ?????????????????? celldm(1) = 19.0945, > ???????????????????????? nat = 18, > ??????????????????????? ntyp = 3, > ???????????????????? ecutwfc = 60 , > ???????????????????? ecutrho = 600 , > ???????????????? occupations = > 'smearing' , > ???????????????????? degauss = 0.03 > ??????????????????? smearing = > 'gauss' , > ?/ > ?&ELECTRONS > ??????????????????? conv_thr = 1.0D-8 , > ???????????????? mixing_beta = 0.7 , > ?/ > ATOMIC_SPECIES > ??? K?? 39.10000? K.pbe-sp.UPF > ?? Os? 190.20000? Os.pbe-n-van.UPF > ??? O?? 16.00000? O.pbe-van_ak.UPF > ATOMIC_POSITIONS crystal > ?? .... > K_POINTS {automatic} > ? 10? 10? 10? 0? 0? 0 > > kos2o6.phG.in: > ???? phonons of kos2o6 at Gamma > ?&inputph > ? tr2_ph=1.0d-14, > ? prefix='kos2o6', > ? epsil=.true., > ? amass(1)=39.10, > ? amass(2)=190.2, > ? amass(3)=16.00, > ? outdir='/home/ww/data/kos2o6/', > ? fildyn='kos2o6.dynG', > ?/ > 0.0 0.0 0.0 > > > >? ? ? > ___________________________________________________________ >???????????????????? > http://card.mail.cn.yahoo.com/_______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? ? ? ------------------------------ Message: 4 Date: Sat, 25 Apr 2009 17:48:27 -0400 From: Eduardo Ariel Menendez Proupin Subject: [Pw_forum] -nimage -npool -ntg -ndiag To: pw_forum at pwscf.org Message-ID: ??? Content-Type: text/plain; charset="iso-8859-1" Hi, I found in the new, or maybe not so new, users guide, that 1000 atoms or so can be calculated, and new ways to paralelize. The example in the manual is mpirun -np 4096 ./pw.x -nimage 8 -npool 2 -ntg 8 -ndiag 144 -input myinput.in I have played a bit, but not with a massive computer, and I have found that the default options are always better than my unexpert? choices. So, I would like to see some hints, in addition to what? is reproduced below (from the users guide), about the good choices of -ntg and -ndiag. Maybe some examples is enough to understand it. >From the users guide: This execute the PWscf code on 4096 processors, to simulate a system with 8 images, each of which is distributed across 512 processors. K-points are distributed across 2 pools of 256 processors each, 3D FFT is performed using 8 task groups (64 processors each, so the 3D real-space grid is cut into 64 slices), and the diagonalization of the subspace Hamiltonian is distributed to a square grid of 144 processors (12x12). Default values are: -nimage 1 -npool 1 -ntg 1 ; ndiag is chosen by the code as the fastest n^2 (n integer) that fits into the size of each pool. *Massively parallel calculations*: For very large jobs (i.e. O(1000) atoms or so) or for very long jobs to be run on massively parallel machines (e.g. IBM BlueGene) it is crucial to use in an effective way both the "task group" and the "ortho group" parallelization. Without a judicious choice of parameters, large jobs will find a stumbling block in either memory or CPU requirements. In particular, the "ortho group" parallelization is used in the diagonalization of matrices in the subspace of Kohn-Sham states (whose dimension is as a strict minumum equal to the number of occupied states). These are stored as block-distributed matrixes (distributed across processors) and diagonalized using custom-taylored diagonalization algorithms that work on block-distributed matrixes. Thanks -- Eduardo Menendez Departamento de Fisica Facultad de Ciencias Universidad de Chile Phone: (56)(2)9787439 URL: http://fisica.ciencias.uchile.cl/~emenendez -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090425/f69ac51d/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 22, Issue 61 **************************************** ___________________________________________________________ ????????????????? http://card.mail.cn.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090429/fa47e86c/attachment-0001.htm From sclauzer at sissa.it Wed Apr 29 08:38:47 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 29 Apr 2009 08:38:47 +0200 Subject: [Pw_forum] can't read wavefunction and coords In-Reply-To: <124688.32679.qm@web54406.mail.yahoo.com> References: <124688.32679.qm@web54406.mail.yahoo.com> Message-ID: <49F7F5F7.7070105@sissa.it> Dear Jonas, I feel like I'm solving bash programming issues, than QE ones... Anyway, Jonas Baltrusaitis wrote: > Gabriele, > > I am almost there. I appreciate you helping me I added coordinates, read nicely. > However when calculating DOS in produces empty dos2 and pdos output files with no error > and doesn't generate fildos at all. I suspect it has problems reading guess You cannot blame dos.x if you don't let it even try to do something... ;-) Here you defined how to execute pw.x, ph.x, ... but dos.x and projwfc.x are missing! # how to run executables PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX" PH_COMMAND="$PARA_PREFIX $BIN_DIR/ph.x $PARA_POSTFIX" PHCG_COMMAND="$PARA_PREFIX $BIN_DIR/phcg.x $PARA_POSTFIX" DYNMAT_COMMAND=" $BIN_DIR/dynmat.x" $ECHO $ECHO " running pw.x as: $PW_COMMAND" $ECHO " running ph.x as: $PH_COMMAND" $ECHO " running phcg.x as: $PHCG_COMMAND" $ECHO " running dynmat.x as: $DYNMAT_COMMAND" $ECHO Then in your script the lines $DOS_COMMAND < sih4.dos2.in > sih4.dos2.out $PROJWFC_COMMAND < sih4.pdos.in > sih4.pdos.out and actually the output from these two lines is exactly an empty file... so everything is fine with bash and QE (unless someone will prove the contrary). cheers, GS -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Wed Apr 29 09:02:44 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 29 Apr 2009 09:02:44 +0200 Subject: [Pw_forum] LDA+U and occupations matrix problems / call for NC P Cu & Co In-Reply-To: <024b01c9c744$33d35040$0402a8c0@ricardof> References: <922459.3274.qm@web54403.mail.yahoo.com><000b01c9c6f7$eb611640$0402a8c0@ricardof> <49F55586.9000407@sissa.it> <024b01c9c744$33d35040$0402a8c0@ricardof> Message-ID: <49F7FB94.3060006@sissa.it> Ricardo Faccio wrote: > Dear Stefano > > Thanks for your quick response. I found the CVS log in the mailing list, > but I decided to write you since the problem persist. Are you meaning that using the latest CVS you found the same problem? Does it change anything from the output of the previous version. If there is a PP with wavefunctions which need to be renormalized you should find a warning at the beginning of the output. Do > Now I'm attaching > my input file, which I used to perform U=1.0d-8 eV, U= 3.5 eV and U= 7 > eV. Making a revision of the problem, I found the only difference > regards in the GGA xc-potential. Maybe it is the problem; I found some > early posts indicating that GGA+U is not yet implemented. Which posts? Please give reference. I think GGA+U can be used and it has been used extensively by the developer himself, so I think it should be safe. There is no conceptual and practical difference in using GGA+U rather than LDA+U. > If it is the > case sorry, but in the meanwhile I'll comment I little bit on the problem. > > 1) U=1.0d-8 eV, everything is ok, since there is no U and pwscf runs in > the normal GGA procedure, this is the initial occupations matrix for one > Co atom > > atom 5 spin 1 > occupations > 0.400 0.000 0.000 0.000 0.000 > 0.000 0.400 0.000 0.000 0.000 > 0.000 0.000 0.400 0.000 0.000 > 0.000 0.000 0.000 0.400 0.000 > 0.000 0.000 0.000 0.000 0.400 > atom 5 spin 2 > occupations > 1.000 0.000 0.000 0.000 0.000 > 0.000 1.000 0.000 0.000 0.000 > 0.000 0.000 1.000 0.000 0.000 > 0.000 0.000 0.000 1.000 0.000 > 0.000 0.000 0.000 0.000 1.000 > > This is normal for the d7 pseudo for Co, and in the last step we found: > > occupations > atom 5 spin 1 > occupations > > 0.532 0.000 0.000 0.000 0.000 > 0.000 0.434 0.000 0.000 0.000 > 0.000 0.000 0.434 0.000 0.000 > 0.000 0.000 0.000 0.993 0.000 > 0.000 0.000 0.000 0.000 0.435 > atom 5 spin 2 > occupations > 0.976 0.000 0.000 0.000 0.000 > 0.000 0.992 0.000 0.000 0.000 > 0.000 0.000 0.992 0.000 0.000 > 0.000 0.000 0.000 0.995 0.000 > 0.000 0.000 0.000 0.000 0.935 > > 2) In the case of U=3.5 eV (for both Cu & Co) > > In the first scf cycle the occupations matrix looks like the one in the > U=0 case, Of course, because at the first iteration occupations are fixed using Hund's rule, not calculated from projections onto atomic wavefunctions. > but in the second scf step I found: > > atom 5 Tr[ns(na)]= 14.9317605 > atom 5 spin 1 > eigenvalues: 0.2107738 0.2794264 0.2794264 0.5053719 0.5799705 > eigenvectors > 1 0.0000000 0.0000000 0.0000000 -1.0000000 0.0000000 > 2 0.0000000 -0.8886367 0.4586119 0.0000000 0.0000000 > 3 0.0000000 -0.4586119 -0.8886367 0.0000000 0.0000000 > 4 0.0000000 0.0000000 0.0000000 0.0000000 -1.0000000 > 5 -1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 > occupations > 0.580 0.000 0.000 0.000 0.000 > 0.000 0.279 0.000 0.000 0.000 > 0.000 0.000 0.279 0.000 0.000 > 0.000 0.000 0.000 0.211 0.000 > 0.000 0.000 0.000 0.000 0.505 > atom 5 spin 2 > eigenvalues: 2.5970604 2.6187425 2.6187425 2.6211004 2.6211456 > eigenvectors > 1 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 > 2 0.0000000 -0.8592401 0.5115724 0.0000000 0.0000000 > 3 0.0000000 0.5115724 0.8592401 0.0000000 0.0000000 > 4 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 > 5 0.0000000 0.0000000 0.0000000 -1.0000000 0.0000000 > occupations > 2.597 0.000 0.000 0.000 0.000 > 0.000 2.619 0.000 0.000 0.000 > 0.000 0.000 2.619 0.000 0.000 > 0.000 0.000 0.000 2.621 0.000 > 0.000 0.000 0.000 0.000 2.621 > The occupations jumps from 1 to 2.6 always in the second scf, and > stands in this value until the end of the scf procedure. These values are quite strange. If you are sure that the pseudo-atomic wavefunction from the PP file has been renormalized at the beginning, you could try to generate a new PP of Co (using ld1.x from the cvs version, which should produce already normalized wfcs) with the same cut-off radii and see if the problem persists. You can also try to fix occupations on Co for the first scf iterations using mixing_fixed_ns or try different initial occupations with starting_ns_eigenvalue. Another critical point could be convergence of local occupations ns with respect to ecutwfc and number of k-points, but the exceedingly high values you get seem to point at a different problem. HTH GS > As I mentioned > before, I didn't use the U_projection_type flag for these three cases. I > resolved the problem adding the explicitly the flag: U_projection_type = > 'norm-atomic', since 'atomic' leads to the same erratic occupations > matrix. The problem is only related with Co electrons, since Cu always > presents occupations terms in the range of 0 to 1. > > But as I mentioned before, maybe the problem is that ?GGA+U? is not yet > implemented. > > > > Thanks once again > > Ricardo > > > > > ------------------------------------------------------------------------- > Dr. Ricardo Faccio > Prof. Adjunto de F?sica > Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA > Facultad de Qu?mica, Universidad de la Rep?blica > Av. Gral. Flores 2124, C.C. 1157 > C.P. 11800, Montevideo, Uruguay. > E-mail: rfaccio at fq.edu.uy > Phone: 598 2 924 98 59 > 598 2 929 06 48 > Fax: 598 2 9241906 > Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm > --------------------------------------------------------------------------------- -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From m.abbasnejad at gmail.com Wed Apr 29 09:06:14 2009 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Wed, 29 Apr 2009 00:06:14 -0700 Subject: [Pw_forum] pw2casino.x Message-ID: <7699a1950904290006o236db6e8pbd6746e607837c2f@mail.gmail.com> Dear all, After running the exapmle01 for Si, the total energy is -14.52 Ry. and when we run the post processing pw2casino.x, the total energy becomes -7.26 Ry. Why are these results different from each other? Yours, Mohaddeseh -- --------------------------------------------------------- Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran, North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 Cellphone: +989177317514 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir --------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090429/633e8b90/attachment.htm From giannozz at democritos.it Wed Apr 29 09:12:01 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 29 Apr 2009 09:12:01 +0200 Subject: [Pw_forum] pw2casino.x In-Reply-To: <7699a1950904290006o236db6e8pbd6746e607837c2f@mail.gmail.com> References: <7699a1950904290006o236db6e8pbd6746e607837c2f@mail.gmail.com> Message-ID: <49F7FDC1.9000000@democritos.it> mohaddeseh abbasnejad wrote: > After running the exapmle01 for Si, the total energy is -14.52 Ry. and > when we run the post processing pw2casino.x, the total energy becomes > -7.26 Ry. -7.26 Ha, not Ry -- Paolo Giannozzi, Democritos and University of Udine, Italy From m.abbasnejad at gmail.com Wed Apr 29 09:15:52 2009 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Wed, 29 Apr 2009 00:15:52 -0700 Subject: [Pw_forum] pw2casino.x In-Reply-To: <49F7FDC1.9000000@democritos.it> References: <7699a1950904290006o236db6e8pbd6746e607837c2f@mail.gmail.com> <49F7FDC1.9000000@democritos.it> Message-ID: <7699a1950904290015l1ba346d4tebeff425560eec71@mail.gmail.com> Thank you. On Wed, Apr 29, 2009 at 12:12 AM, Paolo Giannozzi wrote: > mohaddeseh abbasnejad wrote: > > > After running the exapmle01 for Si, the total energy is -14.52 Ry. and > > when we run the post processing pw2casino.x, the total energy becomes > > -7.26 Ry. > > -7.26 Ha, not Ry > > -- > 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 > -- --------------------------------------------------------- Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran, North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 Cellphone: +989177317514 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir --------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090429/4fab0f06/attachment.htm From paulatto at sissa.it Wed Apr 29 12:00:27 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 29 Apr 2009 12:00:27 +0200 Subject: [Pw_forum] The stability of monolayer compound In-Reply-To: References: Message-ID: In data 29 aprile 2009 alle ore 03:31:44, ??? ha scritto: > 1, Is it possible to get the mono layered compounds( AlN, BC2N, GaN, > ZnO,......)? Dear ???, this mailing list is not intended for scientific discussion, but for technical assistance regarding Quantum-espresso; often some scientific notions are involved in the discussions, but only accidentally. Furthermore, there is little chance you will get a good answer to such a specific question frm this mailing list, although it may happen that some of ther readers have specific knowledge on your topic. Personally, I have no idea if it's possible. > 2, From the theoretical interests, how to study the stability of mono > layered compounds by first-principles calculation? This is a more pertinent question! You can do a calculation for the material in the bulk configuration first, in order to obtain the equilibrium cell parameters and atomic positions. Then you can carve out a single layer in the same way you do for graphene, extending the cell along the direction perpendicular to the plane (usually z) until the periodic images don't interact anymore (the total energy converges). At this point there are several stability tests you can do: 1. how high is the energy of an isolated plane compared to a plane in the bulk, i.e how much does the inter-layer bonds contribute to total energy? 2. does the plane structure reform spontaneously if you perturb breaking symmetry? 3. phonons can be somehow linked to structural stability, I don't know the details, but you can find lot of literature on this argument 4. ... whatever you can think of, use graphene as a reference of something that's stable good luck! best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From wangweiphysics at yahoo.com.cn Wed Apr 29 12:11:04 2009 From: wangweiphysics at yahoo.com.cn (wangwei) Date: Wed, 29 Apr 2009 18:11:04 +0800 (CST) Subject: [Pw_forum] Virtual crystal approximation? Message-ID: <61853.20015.qm@web15203.mail.cnb.yahoo.com> Dear all, Whether or not the PWSCF package can calculate by??virtual crystal approximation for doped material? Thanks a lot. ? wangwei, Southeast University, P. R. China ___________________________________________________________ ????????????????? http://card.mail.cn.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090429/23f20f5a/attachment.htm From paulatto at sissa.it Wed Apr 29 12:38:11 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 29 Apr 2009 12:38:11 +0200 Subject: [Pw_forum] Virtual crystal approximation? In-Reply-To: <61853.20015.qm@web15203.mail.cnb.yahoo.com> References: <61853.20015.qm@web15203.mail.cnb.yahoo.com> Message-ID: In data 29 aprile 2009 alle ore 12:11:04, wangwei ha scritto: > Whether or not the PWSCF package can calculate by??virtual crystal > approximation for doped material? Dear Wangwei, there is the virtual.x utility in the upftools directory of QE distribution that can be used to generate virtual pseudopotential, it's not very tested nor very mantained, as it is not used very often, but as far as I know it works. Please have a look at the mailing list archives here where the usage of virtual.x has been discussed extensively. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From lanhaiping at gmail.com Wed Apr 29 14:04:17 2009 From: lanhaiping at gmail.com (lan haiping) Date: Wed, 29 Apr 2009 20:04:17 +0800 Subject: [Pw_forum] Carbon Pseudo-potential In-Reply-To: <9a321f950904281728v4526c9c3l293588abde75c1cd@mail.gmail.com> References: <9a321f950904281728v4526c9c3l293588abde75c1cd@mail.gmail.com> Message-ID: Hi, i think you may find a proper NC PP at Opium project. Please have a look at http://www.sas.upenn.edu/rappegroup/htdocs/Research/psp_gga.html#C regards On Wed, Apr 29, 2009 at 8:28 AM, antonio aliano wrote: > Dear Pwscf users, > > I'm looking for a PBE Norm-conserving Pseudopotential for Carbon; On the > quantum espresso web page i found a lot of pseudopotentials for carbon but I > didn't find any PBE-norm-conserving. > It sound strange to me, but i could not find it. So i wonder if anyone > knows if there is aparticular reason for that or if anyone know other > repository or database where it is possible to find a PBE Carbon > pseudopotential (.UPF). > > Sorry for the trivial question, > > Have a good day, > > A.A. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090429/c55f6b03/attachment-0001.htm From shruba at gmail.com Wed Apr 29 23:43:50 2009 From: shruba at gmail.com (shruba at gmail.com) Date: Wed, 29 Apr 2009 17:43:50 -0400 Subject: [Pw_forum] problem with installing Quantum ESPRESSO CVS version Message-ID: <822f4ec80904291443h155ecd7jf16c9fd0bb92e3b3@mail.gmail.com> Dear Pwscf forum users, I was trying to install Quantum ESPRESSO (CVS) version in our university cluster the configuration of that machine is *Dual Xeon Quad Core Processors (584 Cores at 3.0 GHz) 4 Virtualization Nodes with 4 Dual-Core AMD Opteron Model 8220 each(32 Cores at 2.8 GHz 32 GB Memory per Node Dual GPU at 650 MHz Nvidia 9800 GX2 Graphics Card per node Operating System: RHEL 5.0* with the ./configure command it can sucessfully detect the parallel envirnoment but with make all command I am getting following error */apps/intel/fce/10.1.008/lib/libimf.so: warning: warning: feupdateenv is not implemented and will always fail /opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_lapack.so: undefined reference to `mkl_serv_load_fun' /opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_lapack.so: undefined reference to `mkl_serv_load_dll' make[1]: *** [pw.x] Error 1 make[1]: Leaving directory `/gpfs/fs0/work/gshruba/espressocvs/PW' make: *** [pw] Error 2 * when I contacted to the cluster management they suggested me to check weather CVS version is compatible with version 10.0.1.014 of the intel mkl? If any of you can suggest me a how to solve this problem, that will be a great help. Please let me know if I missed any relevant information. Thanks in advance. Regards Shruba Gangopadhyay -- Shruba Gangopadhyay PhD candidate Department of Chemistry University of Central Florida Orlando, FL-32826 'friendship doubles joys and reduces sorrows by half' (Francis Bacon). -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090429/f02d7a2c/attachment.htm From zqwu00 at gmail.com Thu Apr 30 00:15:18 2009 From: zqwu00 at gmail.com (zq wu) Date: Wed, 29 Apr 2009 15:15:18 -0700 Subject: [Pw_forum] phonon calculation for large system Message-ID: <3ebf88c60904291515g33a39565w68f289e6f75a021b@mail.gmail.com> Dear pwscf users, I need to do phonon calculation for large system (several hundreds atoms per cell). Since i can use lots of processors, I plan to submit many jobs, each of which will calculate 1 phonon mode. But i do not know whether it is available to get final dynamic matrix from these separate runs and how to do it. Can any one help me? Currently, phonon modes are calculated one by one in sequence in phonon calculation. Can we do some parallelization here? Can we divide the processors into several groups and let each group take care of one or more modes in a way similar to K-points parallelization? I think that the parallel efficeincy for modes parallelization should also be close to K-points parallelization since the phonon modes calculation is independent of each other. The modes parallelization should be very useful for system with large numbers of atoms. Does anyone have the idea how hard it is to do the modes parallelization? Thanks Zhongqing CACS University of Southern California -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090429/c9f3a923/attachment.htm From jasius_1 at yahoo.com Thu Apr 30 04:23:33 2009 From: jasius_1 at yahoo.com (Jonas Baltrusaitis) Date: Wed, 29 Apr 2009 19:23:33 -0700 (PDT) Subject: [Pw_forum] can't read wavefunction and coords In-Reply-To: <49F7F5F7.7070105@sissa.it> Message-ID: <965919.62156.qm@web54405.mail.yahoo.com> OK, this time I have a tricky one. Fixed bash issues (my mistake). Now my fil.dos and all PDOS files have only one line: # E (eV) dos(E) Int dos(E) Seems like it all starts with .dos2. file which is not complete, either. No crash error is produced thanks Jonas Program POST-PROC v.4.0.4 starts ... Today is 29Apr2009 at 21:15:46 Parallel version (MPI) Number of processors in use: 8 R & G space division: proc/pool = 8 Planes per process (thick) : nr3 = 24 npp = 3 ncplane = 576 Proc/ planes cols G planes cols G columns G Pool (dense grid) (smooth grid) (wavefct grid) 1 3 39 464 3 39 464 14 95 2 3 39 464 3 39 464 14 95 3 3 39 465 3 39 465 14 95 4 3 39 465 3 39 465 13 92 5 3 39 465 3 39 465 13 92 6 3 39 465 3 39 465 13 92 7 3 39 465 3 39 465 14 94 8 3 40 466 3 40 466 14 94 tot 24 313 3719 24 313 3719 109 749 Gaussian broadening (read from input): ngauss,degauss= 1 0.020000 INput: #!/bin/sh # run from directory where this script is cd `echo $0 | sed 's/\(.*\)\/.*/\1/'` # extract pathname EXAMPLE_DIR=/home/jbaltrus/$PBS_JOBNAME # check whether echo has the -e option if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi $ECHO $ECHO "$EXAMPLE_DIR : starting" $ECHO $ECHO "This example shows how to use pw.x and phcg.x to calculate the normal" $ECHO "modes of a molecule (SiH4) at Gamma." $ECHO $ECHO # set the needed environment variables PREFIX=`pwd` BIN_DIR=/share/apps/espresso-4.0.4/bin PSEUDO_DIR=/share/apps/espresso-4.0.4/pseudo TMP_DIR=/share/apps/scratch/$PBS_JOBNAME mkdir $EXAMPLE_DIR/results PARA_PREFIX="mpiexec -n 8 -machinefile $PBS_NODEFILE" PARA_POSTFIX="-rmpool 0 -nodes 2 -procs 4" # required executables and pseudopotentials BIN_LIST="pw.x phcg.x ph.x dos.x " PSEUDO_LIST="Si.vbc.UPF H.vbc.UPF C.pz-rrkjus.UPF H.vbc.UPF" $ECHO $ECHO " executables directory: $BIN_DIR" $ECHO " pseudo directory: $PSEUDO_DIR" $ECHO " temporary directory: $TMP_DIR" $ECHO " checking that needed directories and files exist...\c" # check for directories for DIR in "$BIN_DIR" "$PSEUDO_DIR" ; do if test ! -d $DIR ; then $ECHO $ECHO "ERROR: $DIR not existent or not a directory" $ECHO "Aborting" exit 1 fi done for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do if test ! -d $DIR ; then mkdir $DIR fi done cd $EXAMPLE_DIR/results # check for executables for FILE in $BIN_LIST ; do if test ! -x $BIN_DIR/$FILE ; then $ECHO $ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable" $ECHO "Aborting" exit 1 fi done # check for pseudopotentials for FILE in $PSEUDO_LIST ; do if test ! -r $PSEUDO_DIR/$FILE ; then $ECHO $ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable" $ECHO "Aborting" exit 1 fi done $ECHO " done" # how to run executables PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX" PH_COMMAND="$PARA_PREFIX $BIN_DIR/ph.x $PARA_POSTFIX" PHCG_COMMAND="$PARA_PREFIX $BIN_DIR/phcg.x $PARA_POSTFIX" DYNMAT_COMMAND=" $BIN_DIR/dynmat.x" DOS_COMMAND="$PARA_PREFIX $BIN_DIR/dos.x $PARA_POSTFIX" PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x $PARA_POSTFIX" $ECHO $ECHO " running pw.x as: $PW_COMMAND" $ECHO " running ph.x as: $PH_COMMAND" $ECHO " running phcg.x as: $PHCG_COMMAND" $ECHO " running dynmat.x as: $DYNMAT_COMMAND" $ECHO # geometry optimization calculation cat > sih4.opt.in << EOF &control calculation='relax' pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' title='Test Silane SiH4 gamma only' prefix='sih4' tprnfor=.true. / &system ibrav=2, celldm(1) =12.0, nat=5, ntyp= 2, ecutwfc =16.0 / &electrons mixing_mode='plain' mixing_beta = 0.7, conv_thr = 1.0d-8 / &IONS / ATOMIC_SPECIES Si 28.086 Si.vbc.UPF H 1.008 H.vbc.UPF ATOMIC_POSITIONS (alat) Si 0.000000000 0.000000000 0.000000000 H 0.128530744 0.128530744 0.128530744 H -0.128530744 -0.128530744 0.128530744 H -0.128530744 0.128530744 -0.128530744 H 0.128530744 -0.128530744 -0.148530744 K_POINTS (gamma) EOF $ECHO " running the geometry opt calculation for SiH4...\c" $PW_COMMAND < sih4.opt.in > sih4.opt.out $ECHO " done" nat=5 grep -A$((nat+5)) CELL_PARAMETERS sih4.opt.out | tail -$((nat+1)) > atpos.tmp # normal mode calculation for SiH4 cat > sih4.nm.in << EOF normal modes for sih4 &inputph tr2_ph=1.0d-14, prefix='sih4', amass(1)=28.086, amass(2)=1.008, outdir='$TMP_DIR/', epsil=.true., trans=.true., asr=.true. raman=.false. fildyn='sih4.dyn' / 0.0 0.0 0.0 EOF $ECHO " running normal mode calculation for SiH4...\c" $PHCG_COMMAND < sih4.nm.in > sih4.nm.out $ECHO " done" # IR cross sections for SiH4 cat > sih4.dyn.in << EOF &input fildyn='sih4.dyn', asr='zero-dim' / EOF $ECHO " running IR cross section calculation for SiH4...\c" $DYNMAT_COMMAND < sih4.dyn.in > sih4.dyn.out $ECHO " done" # DOS (SCF) calculation for sih4 cat > sih4.scf.in << EOF &control calculation='scf' prefix='sih4', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' / &system ibrav=2, celldm(1) =12.0, nat=5, ntyp= 2, ecutwfc =16.0 / &electrons mixing_mode='plain' mixing_beta = 0.7, conv_thr = 1.0d-8 / ATOMIC_SPECIES Si 28.086 Si.vbc.UPF H 1.008 H.vbc.UPF K_POINTS {automatic} 12 12 12 0 0 0 EOF cat atpos.tmp >> sih4.scf.in $PW_COMMAND < sih4.scf.in > sih4.scf.out # DOS calculation for sih4 cat > sih4.dos.in << EOF &control calculation='nscf' prefix='sih4', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' / &system ibrav=2, celldm(1) =12.0, nat=5, ntyp= 2, ecutwfc =16.0 / &electrons mixing_mode='plain' mixing_beta = 0.7, conv_thr = 1.0d-8 / ATOMIC_SPECIES Si 28.086 Si.vbc.UPF H 1.008 H.vbc.UPF K_POINTS {automatic} 12 12 12 0 0 0 EOF cat atpos.tmp >> sih4.dos.in cat > sih4.dos2.in << EOF &inputpp outdir='$TMP_DIR/' prefix='sih4' fildos='sih4.dos', Emin=5.0, Emax=25.0, DeltaE=0.1, ngauss=1, degauss=0.02 / EOF $ECHO " running DOS calculation for sih4...\c" $PW_COMMAND < sih4.dos.in > sih4.dos.out $DOS_COMMAND < sih4.dos2.in > sih4.dos2.out $ECHO " done" cat > sih4.pdos.in << EOF &inputpp outdir='$TMP_DIR/' prefix='sih4' Emin=5.0, Emax=25.0, DeltaE=0.1, ngauss=1, degauss=0.02 / EOF $ECHO " running PDOS calculation for Ni...\c" $PROJWFC_COMMAND < sih4.pdos.in > sih4.pdos.out $ECHO " done" $ECHO $ECHO "$EXAMPLE_DIR: done" From asubedi at gmail.com Thu Apr 30 04:58:27 2009 From: asubedi at gmail.com (asubedi) Date: Wed, 29 Apr 2009 22:58:27 -0400 Subject: [Pw_forum] electron-phonon coupling within rigid band approximation Message-ID: <532cb13c0904291958t4c44452fl119edecc4f121e1@mail.gmail.com> Dear all, I am trying to calculate electron-phonon coupling of an insulator, which is not possible with QE. However, can I do it by fixing the Fermi energy so that it crosses the valence bands? Thanks, Alaska From giannozz at democritos.it Thu Apr 30 09:16:33 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 30 Apr 2009 09:16:33 +0200 Subject: [Pw_forum] problem with installing Quantum ESPRESSO CVS version In-Reply-To: <822f4ec80904291443h155ecd7jf16c9fd0bb92e3b3@mail.gmail.com> References: <822f4ec80904291443h155ecd7jf16c9fd0bb92e3b3@mail.gmail.com> Message-ID: On Apr 29, 2009, at 23:43 , shruba at gmail.com wrote: > /apps/intel/fce/10.1.008/lib/libimf.so: warning: warning: > feupdateenv is not implemented > and will always fail not a problem > /opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_lapack.so: undefined > reference to `mkl_serv_load_fun' in your make.sys, you should have LDFLAGS = -i-static -openmp BLAS_LIBS = -L /opt/intel/mkl/10.0.1.014/lib/em64t -lmkl_em64t LAPACK_LIBS= and no -lmkl_lapack -lguide -lpthreads > when I contacted to the cluster management they suggested me to check > weather CVS version is compatible with version 10.0.1.014 of the > intel mkl? of course it is and it works on all machines I have tried. If you find why it doesn't in your case, please report. Most likely, the version of the intel compiler found by configure is either old ( References: <532cb13c0904291958t4c44452fl119edecc4f121e1@mail.gmail.com> Message-ID: <3CCBD25C-35E9-468D-8AD0-0085605460F6@democritos.it> On Apr 30, 2009, at 4:58 , asubedi wrote: > I am trying to calculate electron-phonon coupling of an insulator, > which is not possible with QE. However, can I do it by fixing the > Fermi energy so that it crosses the valence bands? I guess you can, but is this what you want? Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090430/a4593525/attachment.htm From sclauzer at sissa.it Thu Apr 30 09:37:20 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 30 Apr 2009 09:37:20 +0200 Subject: [Pw_forum] can't read wavefunction and coords In-Reply-To: <965919.62156.qm@web54405.mail.yahoo.com> References: <965919.62156.qm@web54405.mail.yahoo.com> Message-ID: <49F95530.6000609@sissa.it> Jonas Baltrusaitis wrote: > OK, this time I have a tricky one. Fixed bash issues (my mistake). Now my fil.dos and > all PDOS files have only one line: > > # E (eV) dos(E) Int dos(E) > > Seems like it all starts with .dos2. file which is not complete, either. No crash error is produced Are you sure of your choice of Emin, Emax? What is the highest KS eigenvalue you obtained from pw.x? You should have a look a the output produced at the intermediate steps. It is not wise to do everything blindly and simply hope that at the end you will get the correct result... GS > # DOS calculation for sih4 > cat > sih4.dos.in << EOF > &control > calculation='nscf' > prefix='sih4', > pseudo_dir = '$PSEUDO_DIR/', > outdir='$TMP_DIR/' > / > &system > ibrav=2, celldm(1) =12.0, nat=5, ntyp= 2, > ecutwfc =16.0 > / > &electrons > mixing_mode='plain' > mixing_beta = 0.7, > conv_thr = 1.0d-8 > / > ATOMIC_SPECIES > Si 28.086 Si.vbc.UPF > H 1.008 H.vbc.UPF > K_POINTS {automatic} > 12 12 12 0 0 0 > EOF > > cat atpos.tmp >> sih4.dos.in > > cat > sih4.dos2.in << EOF > &inputpp > outdir='$TMP_DIR/' > prefix='sih4' > fildos='sih4.dos', > Emin=5.0, Emax=25.0, DeltaE=0.1, > ngauss=1, degauss=0.02 > / > EOF > > $ECHO " running DOS calculation for sih4...\c" > $PW_COMMAND < sih4.dos.in > sih4.dos.out > $DOS_COMMAND < sih4.dos2.in > sih4.dos2.out > $ECHO " done" > > cat > sih4.pdos.in << EOF > &inputpp > outdir='$TMP_DIR/' > prefix='sih4' > Emin=5.0, Emax=25.0, DeltaE=0.1, > ngauss=1, degauss=0.02 > / > EOF > $ECHO " running PDOS calculation for Ni...\c" > $PROJWFC_COMMAND < sih4.pdos.in > sih4.pdos.out > $ECHO " done" > > $ECHO > $ECHO "$EXAMPLE_DIR: done" > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Thu Apr 30 09:46:41 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 30 Apr 2009 09:46:41 +0200 Subject: [Pw_forum] phonon calculation for large system In-Reply-To: <3ebf88c60904291515g33a39565w68f289e6f75a021b@mail.gmail.com> References: <3ebf88c60904291515g33a39565w68f289e6f75a021b@mail.gmail.com> Message-ID: <49F95761.5010404@sissa.it> zq wu wrote: > Dear pwscf users, > > I need to do phonon calculation for large system (several hundreds atoms > per cell). Since i can use lots of processors, I plan to submit many > jobs, each of which will calculate 1 phonon mode. But i do not know > whether it is available to get final dynamic matrix from these separate > runs and how to do it. Can any one help me? > > Currently, phonon modes are calculated one by one in sequence in phonon > calculation. Can we do some parallelization here? Can we divide the > processors into several groups and let each group take care of one or > more modes in a way similar to K-points parallelization? I think that > the parallel efficeincy for modes parallelization should also be close > to K-points parallelization since the phonon modes calculation is > independent of each other. The modes parallelization should be very > useful for system with large numbers of atoms. Does anyone have the > idea how hard it is to do the modes parallelization? If I correctly understood, i think that this kind of parallelization has already been exploited in the latest versions of CVS, in order to use ph.x on the GRID. I don't know if all the related problems have been fixed at this stage (have they, Paolo?), but you can try to download the CVS and use the keywords start_q, last_q, start_irr, last_irr (see INPUT_PH) to split your job in many independent jobs. Sorry, I don't know the details, but at least now you're aware that there is this possibility available (though not extensively tested, I think, so use _with_ _care_ and help debugging, please). HTH GS > > Thanks > > Zhongqing > > CACS University of Southern California > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From giannozz at democritos.it Thu Apr 30 09:56:11 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 30 Apr 2009 09:56:11 +0200 Subject: [Pw_forum] phonon calculation for large system In-Reply-To: <49F95761.5010404@sissa.it> References: <3ebf88c60904291515g33a39565w68f289e6f75a021b@mail.gmail.com> <49F95761.5010404@sissa.it> Message-ID: <97BACDB3-4033-4612-B470-E9CB8E943E51@democritos.it> On Apr 30, 2009, at 9:46 , Gabriele Sclauzero wrote: > i think that this kind of parallelization has already been exploited > in the latest versions of CVS, in order to use ph.x on the GRID. > I don't know if all the related problems have been fixed at this stage they have, but I am not sure you can run hundreds of atoms on the grid: the single-q, single-mode calculation has to fit into the memory of each node. P. --- Paolo Giannozzi, Democritos and University of Udine, Italy From sclauzer at sissa.it Thu Apr 30 10:13:46 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 30 Apr 2009 10:13:46 +0200 Subject: [Pw_forum] phonon calculation for large system In-Reply-To: <97BACDB3-4033-4612-B470-E9CB8E943E51@democritos.it> References: <3ebf88c60904291515g33a39565w68f289e6f75a021b@mail.gmail.com> <49F95761.5010404@sissa.it> <97BACDB3-4033-4612-B470-E9CB8E943E51@democritos.it> Message-ID: <49F95DBA.8000803@sissa.it> Paolo Giannozzi wrote: > On Apr 30, 2009, at 9:46 , Gabriele Sclauzero wrote: > >> i think that this kind of parallelization has already been exploited >> in the latest versions of CVS, in order to use ph.x on the GRID. >> I don't know if all the related problems have been fixed at this stage > > they have, but I am not sure you can run hundreds of atoms on the grid: > the single-q, single-mode calculation has to fit into the memory of > each node. Of course, you are right. Anyway, I think you can use this parallelization level even on a cluster, so that you do not have to do modes and irreps sequentially, but you can split them in concurrently running (multiprocessor) jobs so that you-ll have an actual speed-up. Or are you forced to use a single processor in order to exploit this start_q, last_q,... keywords? GS > > 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 > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From hqzhou at nju.edu.cn Thu Apr 30 12:38:22 2009 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Thu, 30 Apr 2009 18:38:22 +0800 Subject: [Pw_forum] phonon calculation for large system References: <3ebf88c60904291515g33a39565w68f289e6f75a021b@mail.gmail.com> <49F95761.5010404@sissa.it> Message-ID: <07517234C3DA4DE4BBEF7E368E5E416C@solarflare> Gabriele, I just downloaded the CVS version two days ago, but found no INPUT_PH in Doc. Should you please post one, or let me know how to generate it? Huiqun Zhou @Earth Sciences, Nanjing University, China ----- Original Message ----- From: "Gabriele Sclauzero" To: "PWSCF Forum" Sent: Thursday, April 30, 2009 3:46 PM Subject: Re: [Pw_forum] phonon calculation for large system > > > zq wu wrote: >> Dear pwscf users, >> >> I need to do phonon calculation for large system (several hundreds atoms >> per cell). Since i can use lots of processors, I plan to submit many >> jobs, each of which will calculate 1 phonon mode. But i do not know >> whether it is available to get final dynamic matrix from these separate >> runs and how to do it. Can any one help me? >> >> Currently, phonon modes are calculated one by one in sequence in phonon >> calculation. Can we do some parallelization here? Can we divide the >> processors into several groups and let each group take care of one or >> more modes in a way similar to K-points parallelization? I think that >> the parallel efficeincy for modes parallelization should also be close >> to K-points parallelization since the phonon modes calculation is >> independent of each other. The modes parallelization should be very >> useful for system with large numbers of atoms. Does anyone have the >> idea how hard it is to do the modes parallelization? > > If I correctly understood, i think that this kind of parallelization has > already been > exploited in the latest versions of CVS, in order to use ph.x on the GRID. > I don't know if > all the related problems have been fixed at this stage (have they, > Paolo?), but you can > try to download the CVS and use the keywords start_q, last_q, start_irr, > last_irr (see > INPUT_PH) to split your job in many independent jobs. Sorry, I don't know > the details, but > at least now you're aware that there is this possibility available (though > not extensively > tested, I think, so use _with_ _care_ and help debugging, please). > > HTH > > GS > > >> >> Thanks >> >> Zhongqing >> >> CACS University of Southern California >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From sclauzer at sissa.it Thu Apr 30 12:47:09 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 30 Apr 2009 12:47:09 +0200 Subject: [Pw_forum] phonon calculation for large system In-Reply-To: <07517234C3DA4DE4BBEF7E368E5E416C@solarflare> References: <3ebf88c60904291515g33a39565w68f289e6f75a021b@mail.gmail.com> <49F95761.5010404@sissa.it> <07517234C3DA4DE4BBEF7E368E5E416C@solarflare> Message-ID: <49F981AD.9020501@sissa.it> Huiqun Zhou wrote: > Gabriele, > > I just downloaded the CVS version two days ago, but found no INPUT_PH > in Doc. Should you please post one, or let me know how to generate it? try: cvs update -d doc-def you should find then a directory doc-def inside your cvs tree, and inside there will be template files for automatic generation of the documentation. From inside doc-def, type make but this probably won't work unless you have all needed tcl libraries installed. Anyway you can read directly the INPUT_PH.def file, searching for start_q, start_irr, etc. etc. GS > > Huiqun Zhou > @Earth Sciences, Nanjing University, China > > > ----- Original Message ----- > From: "Gabriele Sclauzero" > To: "PWSCF Forum" > Sent: Thursday, April 30, 2009 3:46 PM > Subject: Re: [Pw_forum] phonon calculation for large system > > >> >> zq wu wrote: >>> Dear pwscf users, >>> >>> I need to do phonon calculation for large system (several hundreds atoms >>> per cell). Since i can use lots of processors, I plan to submit many >>> jobs, each of which will calculate 1 phonon mode. But i do not know >>> whether it is available to get final dynamic matrix from these separate >>> runs and how to do it. Can any one help me? >>> >>> Currently, phonon modes are calculated one by one in sequence in phonon >>> calculation. Can we do some parallelization here? Can we divide the >>> processors into several groups and let each group take care of one or >>> more modes in a way similar to K-points parallelization? I think that >>> the parallel efficeincy for modes parallelization should also be close >>> to K-points parallelization since the phonon modes calculation is >>> independent of each other. The modes parallelization should be very >>> useful for system with large numbers of atoms. Does anyone have the >>> idea how hard it is to do the modes parallelization? >> If I correctly understood, i think that this kind of parallelization has >> already been >> exploited in the latest versions of CVS, in order to use ph.x on the GRID. >> I don't know if >> all the related problems have been fixed at this stage (have they, >> Paolo?), but you can >> try to download the CVS and use the keywords start_q, last_q, start_irr, >> last_irr (see >> INPUT_PH) to split your job in many independent jobs. Sorry, I don't know >> the details, but >> at least now you're aware that there is this possibility available (though >> not extensively >> tested, I think, so use _with_ _care_ and help debugging, please). >> >> HTH >> >> GS >> >> >>> Thanks >>> >>> Zhongqing >>> >>> CACS University of Southern California >>> >>> >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >> -- >> >> >> o ------------------------------------------------ o >> | Gabriele Sclauzero, PhD Student | >> | c/o: SISSA & CNR-INFM Democritos, | >> | via Beirut 2-4, 34014 Trieste (Italy) | >> | email: sclauzer at sissa.it | >> | phone: +39 040 3787 511 | >> | skype: gurlonotturno | >> o ------------------------------------------------ o >> _______________________________________________ >> 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 > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From manoj at phys.ufl.edu Thu Apr 30 13:23:25 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Thu, 30 Apr 2009 07:23:25 -0400 (EDT) Subject: [Pw_forum] transmission calculation Message-ID: Dear PWSCF users and developers, I have tried to do a transmission calcuation and not getting right results. I have tried to figure out the reason behind this and realized that in my set up for some reason the Bloch waves in left lead get changed resulting wrong transmission. By this I meant that, if I just try to calculate complex band of the left lead, I have a kz for each kx,ky and E but when I am doing transmission calculation, the Bloch's wave in the same lead has different kz for the same kx,ky and E, which does not make sense as why should the Bloch's wave in lead get affected by the presence of scattering region? For the right lead kz remains the same in both cases though, which I believe how it should be. I did this for several cases, I interchanged right and left leads, increased number of atoms in the scattering region, chose scattering region in different way, and everytime kz of left lead changes. Following is my input file for the scattering region - scf part - &control calculation='scf' pseudo_dir = '/home/manoj/espresso-4.0.1/pseudo', outdir='./', prefix='cus', / &system ibrav =0, celldm(1)=4.82, nat= 10, ntyp= 1, ecutwfc =50.0, occupations='smearing', smearing='gaussian', degauss=0.02, ecutrho=500 / &electrons conv_thr = 1.0e-8 mixing_beta=0.7 / ATOMIC_SPECIES Cu 63.55 Cu.pz-d-rrkjus.UPF ATOMIC_POSITIONS Cu 0.0 0.0 0.0 Cu -0.5 0.288675134 0.816496581 Cu -1.0 0.577350269 1.632993162 Cu -1.5 0.866025404 2.449489743 Cu 0.0 0.0 3.265986324 Cu 0.5 -0.288675134 4.082482905 Cu 1.0 -0.577350269 4.898979486 Cu 1.5 -0.866025404 5.715476066 Cu 1.0 -0.577350269 6.531972647 Cu 0.5 -0.288675134 7.348469228 K_POINTS (automatic) 6 6 4 1 1 1 CELL_PARAMETERS {hexagonal} 1.0 0.0 0.0 -0.5 0.866025403 0.0 0.0 0.0 8.16496581 conductance part - &inputcond outdir='./' prefixl='cul' prefixr='cur' prefixs='cus' tran_file ='trans.twin' ikind=2 ecut2d=50 energy0=0.0 denergy=0.0 ewind=5.d0 epsproj=1.d-6 nz1=25 / 2 0.000000 0.000000 1 0.5000000 -0.5000000 1 1 0.0 Thank you for your attention. Regards, Manoj Srivastava Graduate Student Department of Physics University of Florida, Gainesville, FL From paulatto at sissa.it Thu Apr 30 13:34:42 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 30 Apr 2009 13:34:42 +0200 Subject: [Pw_forum] transmission calculation In-Reply-To: References: Message-ID: In data 30 aprile 2009 alle ore 13:23:25, Manoj Srivastava ha scritto: > I did this for several cases, I interchanged right and left leads, > increased number of atoms in the scattering region, chose scattering > region in different way, and everytime kz of left lead changes. Following > is my input file for the scattering region - I'm no expert in transimission calculation, but I have had a look at your scf input file for the lead region, using XCrysDen, and I've noticed tha tlayers 4 and 5 are aligned in a strange way, reducing the system symmetry. Are you sure you have done it on purpose? Have you tried checking your input files with XCD? best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From sclauzer at sissa.it Thu Apr 30 13:38:56 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 30 Apr 2009 13:38:56 +0200 Subject: [Pw_forum] transmission calculation In-Reply-To: References: Message-ID: <49F98DD0.3080709@sissa.it> Manoj Srivastava wrote: > Dear PWSCF users and developers, > I have tried to do a transmission calcuation and not getting right > results. I have tried to figure out the reason behind this and realized > that in my set up for some reason the Bloch waves in left lead get changed > resulting wrong transmission. By this I meant that, if I just try to > calculate complex band of the left lead, I have a kz for each kx,ky and E > but when I am doing transmission calculation, the Bloch's wave in the same > lead has different kz for the same kx,ky and E, which does not make sense > as why should the Bloch's wave in lead get affected by the presence of > scattering region? For the right lead kz remains the same in both cases > though, which I believe how it should be. Does it happen also when you do not use G_perp basis reduction? Can you try again the CBS and the transmission calculation without specifying ecut2d, nz1 and putting ewind=1.d3? Better, first check the size of the reduced basis using grep n2d and see if they are very different (or if the second is too low with respect to the size of the whole basis set). Also try to understand which of the two results (kz vectors) is correct, by comparing the real part of kz with the band structure from pw.x GS > I did this for several cases, I interchanged right and left leads, > increased number of atoms in the scattering region, chose scattering > region in different way, and everytime kz of left lead changes. Following > is my input file for the scattering region - > > scf part - > > &control > calculation='scf' > pseudo_dir = '/home/manoj/espresso-4.0.1/pseudo', > outdir='./', > prefix='cus', > / > &system > ibrav =0, > celldm(1)=4.82, > nat= 10, > ntyp= 1, > ecutwfc =50.0, > occupations='smearing', > smearing='gaussian', > degauss=0.02, > ecutrho=500 > / > &electrons > conv_thr = 1.0e-8 > mixing_beta=0.7 > / > ATOMIC_SPECIES > Cu 63.55 Cu.pz-d-rrkjus.UPF > ATOMIC_POSITIONS > Cu 0.0 0.0 0.0 > Cu -0.5 0.288675134 0.816496581 > Cu -1.0 0.577350269 1.632993162 > Cu -1.5 0.866025404 2.449489743 > Cu 0.0 0.0 3.265986324 > Cu 0.5 -0.288675134 4.082482905 > Cu 1.0 -0.577350269 4.898979486 > Cu 1.5 -0.866025404 5.715476066 > Cu 1.0 -0.577350269 6.531972647 > Cu 0.5 -0.288675134 7.348469228 > K_POINTS (automatic) > 6 6 4 1 1 1 > CELL_PARAMETERS {hexagonal} > 1.0 0.0 0.0 > -0.5 0.866025403 0.0 > 0.0 0.0 8.16496581 > > > > conductance part - > > &inputcond > outdir='./' > prefixl='cul' > prefixr='cur' > prefixs='cus' > tran_file ='trans.twin' > ikind=2 > ecut2d=50 > energy0=0.0 > denergy=0.0 > ewind=5.d0 > epsproj=1.d-6 > nz1=25 > / > 2 > 0.000000 0.000000 1 > 0.5000000 -0.5000000 1 > > 1 > 0.0 > > Thank you for your attention. > > Regards, > Manoj Srivastava > Graduate Student > 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 > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From lidonglin556 at 163.com Thu Apr 30 14:13:46 2009 From: lidonglin556 at 163.com (null) Date: Thu, 30 Apr 2009 20:13:46 +0800 (CST) Subject: [Pw_forum] Pw_forum Digest, Vol 22, Issue 72 In-Reply-To: References: Message-ID: <33465711.1329331241093626811.JavaMail.coremail@app165.163.com> Re: phonon calculation for large system (Huiqun Zhou) Maybe i can give it to you, but i do not know your email. ?2009-04-30?pw_forum-request at pwscf.org ??? 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: problem with installing Quantum ESPRESSO CVS version (Paolo Giannozzi) 2. Re: electron-phonon coupling within rigid band approximation (Paolo Giannozzi) 3. Re: can't read wavefunction and coords (Gabriele Sclauzero) 4. Re: phonon calculation for large system (Gabriele Sclauzero) 5. Re: phonon calculation for large system (Paolo Giannozzi) 6. Re: phonon calculation for large system (Gabriele Sclauzero) 7. Re: phonon calculation for large system (Huiqun Zhou) ---------------------------------------------------------------------- Message: 1 Date: Thu, 30 Apr 2009 09:16:33 +0200 From: Paolo Giannozzi Subject: Re: [Pw_forum] electron-phonon coupling within rigid band approximation To: PWSCF Forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090430/016b9c13/attachment-0001.htm From smogunov at sissa.it Thu Apr 30 15:08:35 2009 From: smogunov at sissa.it (Alexander Smogunov) Date: Thu, 30 Apr 2009 15:08:35 +0200 Subject: [Pw_forum] transmission calculation In-Reply-To: References: Message-ID: <1241096915.5731.36.camel@alex-laptop> Dear Manoj Please provide also scf files for the leads. Note that in the case ikind=2 (different leads) the scattering file should be a double unit cell i.e. should contain the scattering barrier + some portion of the right lead + the scattering barrier in order to have regular periodicity in the z direction. You should also provide bds parameter which says where the scattering barrier ends (while it should start from 0). Regards, Alexander On Thu, 2009-04-30 at 07:23 -0400, Manoj Srivastava wrote: > Dear PWSCF users and developers, > I have tried to do a transmission calcuation and not getting right > results. I have tried to figure out the reason behind this and realized > that in my set up for some reason the Bloch waves in left lead get changed > resulting wrong transmission. By this I meant that, if I just try to > calculate complex band of the left lead, I have a kz for each kx,ky and E > but when I am doing transmission calculation, the Bloch's wave in the same > lead has different kz for the same kx,ky and E, which does not make sense > as why should the Bloch's wave in lead get affected by the presence of > scattering region? For the right lead kz remains the same in both cases > though, which I believe how it should be. > I did this for several cases, I interchanged right and left leads, > increased number of atoms in the scattering region, chose scattering > region in different way, and everytime kz of left lead changes. Following > is my input file for the scattering region - > > scf part - > > &control > calculation='scf' > pseudo_dir = '/home/manoj/espresso-4.0.1/pseudo', > outdir='./', > prefix='cus', > / > &system > ibrav =0, > celldm(1)=4.82, > nat= 10, > ntyp= 1, > ecutwfc =50.0, > occupations='smearing', > smearing='gaussian', > degauss=0.02, > ecutrho=500 > / > &electrons > conv_thr = 1.0e-8 > mixing_beta=0.7 > / > ATOMIC_SPECIES > Cu 63.55 Cu.pz-d-rrkjus.UPF > ATOMIC_POSITIONS > Cu 0.0 0.0 0.0 > Cu -0.5 0.288675134 0.816496581 > Cu -1.0 0.577350269 1.632993162 > Cu -1.5 0.866025404 2.449489743 > Cu 0.0 0.0 3.265986324 > Cu 0.5 -0.288675134 4.082482905 > Cu 1.0 -0.577350269 4.898979486 > Cu 1.5 -0.866025404 5.715476066 > Cu 1.0 -0.577350269 6.531972647 > Cu 0.5 -0.288675134 7.348469228 > K_POINTS (automatic) > 6 6 4 1 1 1 > CELL_PARAMETERS {hexagonal} > 1.0 0.0 0.0 > -0.5 0.866025403 0.0 > 0.0 0.0 8.16496581 > > > > conductance part - > > &inputcond > outdir='./' > prefixl='cul' > prefixr='cur' > prefixs='cus' > tran_file ='trans.twin' > ikind=2 > ecut2d=50 > energy0=0.0 > denergy=0.0 > ewind=5.d0 > epsproj=1.d-6 > nz1=25 > / > 2 > 0.000000 0.000000 1 > 0.5000000 -0.5000000 1 > > 1 > 0.0 > > Thank you for your attention. > > Regards, > Manoj Srivastava > Graduate Student > 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 -- Alexander Smogunov Email: smogunov at sissa.it Home page: http://people.sissa.it/~smogunov From ihsanas at yahoo.com Thu Apr 30 16:18:38 2009 From: ihsanas at yahoo.com (Ihsan Erikat) Date: Thu, 30 Apr 2009 07:18:38 -0700 (PDT) Subject: [Pw_forum] How to choose number of pools Message-ID: <202185.92074.qm@web52303.mail.re2.yahoo.com> Hello all I am? running pwscf on 10 CPU and? the k points in my file is 3x6x1. ? When I use? the command mpirun -np xx? pw.x -npool x , how can I choose? the effective number of processors and pools . I read the manual and the forum archive, but I don`t know how to choose these numbers. I`ll appreciate any help. best regards Ihsan Erikat Physics department-Jordan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090430/d23ac12e/attachment.htm From paulatto at sissa.it Thu Apr 30 16:22:01 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 30 Apr 2009 16:22:01 +0200 Subject: [Pw_forum] How to choose number of pools In-Reply-To: <202185.92074.qm@web52303.mail.re2.yahoo.com> References: <202185.92074.qm@web52303.mail.re2.yahoo.com> Message-ID: In data 30 aprile 2009 alle ore 16:18:38, Ihsan Erikat ha scritto: > Hello all > I am? running pwscf on 10 CPU how are they connected to each other? > and? the k points in my file is 3x6x1. how many kpoints do you have after symmetry operations have been applied? > When I use? the command mpirun -np xx? pw.x -npool x , how can I choose? > the effective number of processors and pools. All processors inside the same pool must be able to comunicate with each other with an extremely large bandwidth and low latency. You can have a benefit by taking the number of pools as a divisor of the number of kpoints, especially if the number of kpoints is small. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From giannozz at democritos.it Thu Apr 30 16:28:53 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 30 Apr 2009 16:28:53 +0200 Subject: [Pw_forum] phonon calculation for large system In-Reply-To: <49F95DBA.8000803@sissa.it> References: <3ebf88c60904291515g33a39565w68f289e6f75a021b@mail.gmail.com> <49F95761.5010404@sissa.it> <97BACDB3-4033-4612-B470-E9CB8E943E51@democritos.it> <49F95DBA.8000803@sissa.it> Message-ID: On Apr 30, 2009, at 10:13 , Gabriele Sclauzero wrote: > I think you can use this parallelization level even on a cluster, > so that you do not have to do modes and irreps sequentially, > but you can split them in concurrently running (multiprocessor) > jobs so that you-ll have an actual speed-up. sure, but it is currently not implemented in a MPI framework: it has to be done "by hand". It isn't difficult to implement it, using the "image group", though. > Or are you forced to use a single processor in order to exploit > this start_q, last_q,... keywords? no, I don't think so, or if so, it can be easily fixed Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From akohlmey at cmm.chem.upenn.edu Thu Apr 30 16:33:07 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 30 Apr 2009 10:33:07 -0400 Subject: [Pw_forum] How to choose number of pools In-Reply-To: <202185.92074.qm@web52303.mail.re2.yahoo.com> References: <202185.92074.qm@web52303.mail.re2.yahoo.com> Message-ID: <1241101987.18574.1047.camel@zero> On Thu, 2009-04-30 at 07:18 -0700, Ihsan Erikat wrote: please check out previous lengthy discussions on the subject in the mailing list archives _again_. this topic has been discussed repeatedly and people have done benchmarks to demonstrate and understand how the various parallelization options help under specific environments. particularly the number of cpus per node, cores per cpu, main memory per cpu/core, cache memory per cpu/core in combination with the interconnect (tcp/ip, infiniband/myrinet/...) can lead to different results. in some cases it may even better to not use all cpu cores in order maximize cache usage, in others it may be important to use the more communication demanding parallelization scheme to reduce the per process memory use. ... and this is only the beginning. compiler vendor and flags as well as BLAS/LAPACK and communication libraries can have and impact, not to mention the setup and configuration of machines. (e.g. modern linux distributions come with SELinux enabled which effectively trashes the cache by randomizing the stack frame location and lots of useless auto-configuration demons running that interrupt the kernel needlessly and thus create a lot of OS jitter which affects latency sensitive applications. running a "lean mean computing machine" requires some effort on many levels...). in short: do tests and figure it out yourself. what works best depends very much on your input set size, network, hard- and software. cheers, axel. > Hello all > I am running pwscf on 10 CPU and the k points in my file is 3x6x1. > > When I use the command mpirun -np xx pw.x -npool x , how can I > choose the effective number of processors and pools . I read the > manual and the forum archive, but I don`t know how to choose these > numbers. I`ll appreciate any help. > > > > best regards > Ihsan Erikat > Physics department-Jordan University > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From ihsanas at yahoo.com Thu Apr 30 16:57:46 2009 From: ihsanas at yahoo.com (Ihsan Erikat) Date: Thu, 30 Apr 2009 07:57:46 -0700 (PDT) Subject: [Pw_forum] How to choose number of pools Message-ID: <355210.41044.qm@web52308.mail.re2.yahoo.com> Thank you, the CPU are mpd connection and the home is NFS share. When I run the job in one CPU the output file gives k-point =8, best regards Ihsan Erikat Physics department , Jordan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090430/03682ba3/attachment.htm From paulatto at sissa.it Thu Apr 30 17:09:45 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 30 Apr 2009 17:09:45 +0200 Subject: [Pw_forum] How to choose number of pools In-Reply-To: <355210.41044.qm@web52308.mail.re2.yahoo.com> References: <355210.41044.qm@web52308.mail.re2.yahoo.com> Message-ID: In data 30 aprile 2009 alle ore 16:57:46, Ihsan Erikat ha scritto: > Thank you, the CPU are mpd connection I don't know what it is, if it's not faster that a 10/100/1000 ethernet card your best bet is to use 8 processors and 8 pools, leaving 2 processors idle. Also, make sure that your outdir is set to some directory local to the nodes, e.g. /tmp, otherwise the overhead introduced when saving the restart data may kill the performance. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From akohlmey at cmm.chem.upenn.edu Thu Apr 30 17:23:09 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 30 Apr 2009 11:23:09 -0400 Subject: [Pw_forum] How to choose number of pools In-Reply-To: References: <355210.41044.qm@web52308.mail.re2.yahoo.com> Message-ID: <1241104989.18574.1104.camel@zero> On Thu, 2009-04-30 at 17:09 +0200, Lorenzo Paulatto wrote: > In data 30 aprile 2009 alle ore 16:57:46, Ihsan Erikat > ha scritto: > > > Thank you, the CPU are mpd connection lorenzo, mpd are the processes that MPICH-2 generates upon initializing the parallel environment. that doesn't really help much, but it is likely that the cluster is running with GigE at best. > I don't know what it is, if it's not faster that a 10/100/1000 ethernet > card your best bet is to use 8 processors and 8 pools, leaving 2 > processors idle. Also, make sure that your outdir is set to some directory better yet. run with -np 8 and put a second job on the other two. ;-) cheers, axel. > local to the nodes, e.g. /tmp, otherwise the overhead introduced when > saving the restart data may kill the performance. > > best regards > > > > > -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From asubedi at gmail.com Thu Apr 30 17:27:15 2009 From: asubedi at gmail.com (asubedi) Date: Thu, 30 Apr 2009 11:27:15 -0400 Subject: [Pw_forum] electron-phonon coupling within rigid band approximation In-Reply-To: <3CCBD25C-35E9-468D-8AD0-0085605460F6@democritos.it> References: <532cb13c0904291958t4c44452fl119edecc4f121e1@mail.gmail.com> <3CCBD25C-35E9-468D-8AD0-0085605460F6@democritos.it> Message-ID: <532cb13c0904300827o40ee2339q61517a22a4b41467@mail.gmail.com> > I guess you can, but is this what you want? Yes, this would be equivalent calculating electron-phonon coupling of a doped material, and this is what I actually need. (In the hope that rigid-band approximation is ok for this system at small doping levels). I assume I need to do the following steps. First, I do the scf calculation for the insulator with very small gaussian smearing. Then modify the elphon.f90 file to add/substract a number to effit(isig) after the call to efermig. Please let me know if there is a better way. Thanks, Alaska From manoj at phys.ufl.edu Thu Apr 30 18:25:40 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Thu, 30 Apr 2009 12:25:40 -0400 (EDT) Subject: [Pw_forum] transmission calculation In-Reply-To: Message-ID: Dear Lorenzo, Thank you for answering. Layers 4 and 5 are supposed be like that, it is done on purpose. The file I provided was not for the lead but for the scattering region. I have visualized my structure, it looks ok. Regards, Manoj On Thu, 30 Apr 2009, Lorenzo Paulatto wrote: > In data 30 aprile 2009 alle ore 13:23:25, Manoj Srivastava > ha scritto: > > I did this for several cases, I interchanged right and left leads, > > increased number of atoms in the scattering region, chose scattering > > region in different way, and everytime kz of left lead changes. Following > > is my input file for the scattering region - > > I'm no expert in transimission calculation, but I have had a look at your > scf input file for the lead region, using XCrysDen, and I've noticed tha > tlayers 4 and 5 are aligned in a strange way, reducing the system > symmetry. Are you sure you have done it on purpose? Have you tried > checking your input files with XCD? > > best regards > > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From manoj at phys.ufl.edu Thu Apr 30 18:29:26 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Thu, 30 Apr 2009 12:29:26 -0400 (EDT) Subject: [Pw_forum] transmission calculation In-Reply-To: <49F98DD0.3080709@sissa.it> Message-ID: Dear Gabriele, Thanks for answering. On Thu, 30 Apr 2009, Gabriele Sclauzero wrote: > Manoj Srivastava wrote: > > Dear PWSCF users and developers, > > I have tried to do a transmission calcuation and not getting right > > results. I have tried to figure out the reason behind this and realized > > that in my set up for some reason the Bloch waves in left lead get changed > > resulting wrong transmission. By this I meant that, if I just try to > > calculate complex band of the left lead, I have a kz for each kx,ky and E > > but when I am doing transmission calculation, the Bloch's wave in the same > > lead has different kz for the same kx,ky and E, which does not make sense > > as why should the Bloch's wave in lead get affected by the presence of > > scattering region? For the right lead kz remains the same in both cases > > though, which I believe how it should be. > > Does it happen also when you do not use G_perp basis reduction? Can you try again the CBS > and the transmission calculation without specifying ecut2d, nz1 and putting ewind=1.d3? Yes, I have tried this. No difference, the kz value for left lead gets changed, when i switch from ikind=0 to ikind=2. > > Better, first check the size of the reduced basis using > > grep n2d > > and see if they are very different (or if the second is too low with respect to the size > of the whole basis set). > Also try to understand which of the two results (kz vectors) is correct, by comparing the > real part of kz with the band structure from pw.x The one with ikind=0 is correct. > > > GS > > > > I did this for several cases, I interchanged right and left leads, > > increased number of atoms in the scattering region, chose scattering > > region in different way, and everytime kz of left lead changes. Following > > is my input file for the scattering region - > > > > scf part - > > > > &control > > calculation='scf' > > pseudo_dir = '/home/manoj/espresso-4.0.1/pseudo', > > outdir='./', > > prefix='cus', > > / > > &system > > ibrav =0, > > celldm(1)=4.82, > > nat= 10, > > ntyp= 1, > > ecutwfc =50.0, > > occupations='smearing', > > smearing='gaussian', > > degauss=0.02, > > ecutrho=500 > > / > > &electrons > > conv_thr = 1.0e-8 > > mixing_beta=0.7 > > / > > ATOMIC_SPECIES > > Cu 63.55 Cu.pz-d-rrkjus.UPF > > ATOMIC_POSITIONS > > Cu 0.0 0.0 0.0 > > Cu -0.5 0.288675134 0.816496581 > > Cu -1.0 0.577350269 1.632993162 > > Cu -1.5 0.866025404 2.449489743 > > Cu 0.0 0.0 3.265986324 > > Cu 0.5 -0.288675134 4.082482905 > > Cu 1.0 -0.577350269 4.898979486 > > Cu 1.5 -0.866025404 5.715476066 > > Cu 1.0 -0.577350269 6.531972647 > > Cu 0.5 -0.288675134 7.348469228 > > K_POINTS (automatic) > > 6 6 4 1 1 1 > > CELL_PARAMETERS {hexagonal} > > 1.0 0.0 0.0 > > -0.5 0.866025403 0.0 > > 0.0 0.0 8.16496581 > > > > > > > > conductance part - > > > > &inputcond > > outdir='./' > > prefixl='cul' > > prefixr='cur' > > prefixs='cus' > > tran_file ='trans.twin' > > ikind=2 > > ecut2d=50 > > energy0=0.0 > > denergy=0.0 > > ewind=5.d0 > > epsproj=1.d-6 > > nz1=25 > > / > > 2 > > 0.000000 0.000000 1 > > 0.5000000 -0.5000000 1 > > > > 1 > > 0.0 > > > > Thank you for your attention. > > > > Regards, > > Manoj Srivastava > > Graduate Student > > 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 > > > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From zqwu00 at gmail.com Thu Apr 30 20:14:50 2009 From: zqwu00 at gmail.com (zq wu) Date: Thu, 30 Apr 2009 11:14:50 -0700 Subject: [Pw_forum] phonon calculation for large system In-Reply-To: References: <3ebf88c60904291515g33a39565w68f289e6f75a021b@mail.gmail.com> <49F95761.5010404@sissa.it> <97BACDB3-4033-4612-B470-E9CB8E943E51@democritos.it> <49F95DBA.8000803@sissa.it> Message-ID: <3ebf88c60904301114q2f857669mdf79bd810bf208f7@mail.gmail.com> On Thu, Apr 30, 2009 at 7:28 AM, Paolo Giannozzi wrote: > > On Apr 30, 2009, at 10:13 , Gabriele Sclauzero wrote: > > > I think you can use this parallelization level even on a cluster, > > so that you do not have to do modes and irreps sequentially, > > but you can split them in concurrently running (multiprocessor) > > jobs so that you-ll have an actual speed-up. > > sure, but it is currently not implemented in a MPI framework: > it has to be done "by hand". It isn't difficult to implement it, > using the "image group", though. > > > Or are you forced to use a single processor in order to exploit > > this start_q, last_q,... keywords? > > no, I don't think so, or if so, it can be easily fixed > > Paolo > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > Can single-q, single-mode calculation run in several nodes. If so, memory may be not a problem even for system with several hundreds atoms. Thank you very much. All these information are very helpful. I will try the latest versions of CVS. Zhongqing > > _______________________________________________ > 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/20090430/5ed0adcd/attachment.htm