From sh.shapt at gmail.com Sun Nov 1 03:54:23 2009 From: sh.shapt at gmail.com (Shaptrishi Sharma) Date: Sat, 31 Oct 2009 19:54:23 -0700 Subject: [Pw_forum] How do we choose Emin and Emax while calculating the Density of states? Message-ID: Hi Quantum espresso users! I want to calculate Density of states however I do not know what value shall I give for Emin and Emax. To be honest I have not understood what Emin and Emax, as from the manual I can predict that it is the range of energy from where i would like to like to plot my DOS. But when I gave a value Emin=-15 and Emax=15, the calculation crashes. Suggestions welcome! Thanks S -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091031/27244eba/attachment.htm From ttduyle at gmail.com Sun Nov 1 05:37:23 2009 From: ttduyle at gmail.com (Duy Le) Date: Sun, 1 Nov 2009 00:37:23 -0400 Subject: [Pw_forum] How do we choose Emin and Emax while calculating the Density of states? In-Reply-To: References: Message-ID: <8974d3b20910312137h4d5dc7b5yed349ecf3542ee29@mail.gmail.com> I want to calculate Density of states however I do not know what value shall > I give for Emin and Emax. To be honest I have not understood what Emin and > Emax, as from the manual I can predict that it is the range of energy from > where i would like to like to plot my DOS. Yes, it is. > But when I gave a value Emin=-15 and Emax=15, the calculation crashes. > You should look in the scf (or nscf) output. There would be eigenvalues corresponding to each k-point. From those eigenvalue you can estimate Emin, Emax. -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091101/2260b0c1/attachment.htm From degironc at sissa.it Sun Nov 1 05:39:35 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sun, 01 Nov 2009 05:39:35 +0100 Subject: [Pw_forum] How do we choose Emin and Emax while calculating the Density of states? In-Reply-To: References: Message-ID: <4AED1107.2070406@sissa.it> dear S, please provide your affiliation. are you sure the problem is related to definition of emin and emax ? is the code working if you do not specify any value for them ? are you sure you are not typing in some control character? best, stefano de gironcoli - SISSA and DEMOCRITOS Shaptrishi Sharma wrote: > Hi Quantum espresso users! > > I want to calculate Density of states however I do not know what value > shall I give for Emin and Emax. To be honest I have not understood > what Emin and Emax, as from the manual I can predict that it is the > range of energy from where i would like to like to plot my DOS. But > when I gave a value Emin=-15 and Emax=15, the calculation crashes. > > Suggestions welcome! > > Thanks > > S > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at democritos.it Sun Nov 1 09:11:35 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 1 Nov 2009 09:11:35 +0100 Subject: [Pw_forum] which is the local potential In-Reply-To: References: Message-ID: <1DBC8766-3B48-435D-8BC8-0E9BE2B9EC7B@democritos.it> On Oct 31, 2009, at 10:23 , wujianchun wrote: > The question is which one, 1 total potential V_bare+V_H+V_xc, > 11 the V_bare+V_H potential or 12 the electric field potential in > plot_num, corresponds the above-mentioned "local potentials"? definitely not 12; the local potential is 1. The case "11" is useful to calculate the average potential far from a surface (e.g. for work function calculation) since the XC potential has often a nasty behavior when the charge density vanishes > PS: which is the unit of the potentials in the outfiles, eV or Ry? Ry P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From baroni at sissa.it Sun Nov 1 11:56:41 2009 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 1 Nov 2009 11:56:41 +0100 Subject: [Pw_forum] which is the local potential In-Reply-To: <1DBC8766-3B48-435D-8BC8-0E9BE2B9EC7B@democritos.it> References: <1DBC8766-3B48-435D-8BC8-0E9BE2B9EC7B@democritos.it> Message-ID: one further reason why the bare+Hartree potential should be used for estimating the value of the potential in the vacuum far from a surface (or from a molecule), even if the simple LDA is used, is that the exchange potential tends to zero as (\rho)^{1\over 3}, while the Hartree+bare potential tends to zero as \rho, hence faster. SB On Nov 1, 2009, at 9:11 AM, Paolo Giannozzi wrote: > > On Oct 31, 2009, at 10:23 , wujianchun wrote: > >> The question is which one, 1 total potential V_bare+V_H+V_xc, >> 11 the V_bare+V_H potential or 12 the electric field potential in >> plot_num, corresponds the above-mentioned "local potentials"? > > definitely not 12; the local potential is 1. The case "11" is useful > to calculate the average potential far from a surface (e.g. for > work function calculation) since the XC potential has often a > nasty behavior when the charge density vanishes > >> PS: which is the unit of the potentials in the outfiles, eV or Ry? > > Ry > > P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget 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/20091101/b8c9e3f7/attachment.htm From jcwu.suda at hotmail.com Sun Nov 1 12:11:30 2009 From: jcwu.suda at hotmail.com (wujianchun) Date: Sun, 1 Nov 2009 19:11:30 +0800 Subject: [Pw_forum] which is the local potential In-Reply-To: References: <1DBC8766-3B48-435D-8BC8-0E9BE2B9EC7B@democritos.it> Message-ID: Dear Paolo and Stefano, That's very helpful Indeed, Thanks a lot! Regards Jianchun Wu PhD candidate Department of Phyiscs, Soochow University, China From: baroni at sissa.it To: pw_forum at pwscf.org Date: Sun, 1 Nov 2009 11:56:41 +0100 Subject: Re: [Pw_forum] which is the local potential one further reason why the bare+Hartree potential should be used for estimating the value of the potential in the vacuum far from a surface (or from a molecule), even if the simple LDA is used, is that the exchange potential tends to zero as (\rho)^{1\over 3}, while the Hartree+bare potential tends to zero as \rho, hence faster. SB On Nov 1, 2009, at 9:11 AM, Paolo Giannozzi wrote: On Oct 31, 2009, at 10:23 , wujianchun wrote: The question is which one, 1 total potential V_bare+V_H+V_xc, 11 the V_bare+V_H potential or 12 the electric field potential in plot_num, corresponds the above-mentioned "local potentials"? definitely not 12; the local potential is 1. The case "11" is useful to calculate the average potential far from a surface (e.g. for work function calculation) since the XC potential has often a nasty behavior when the charge density vanishes PS: which is the unit of the potentials in the outfiles, eV or Ry? Ry P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html _________________________________________________________________ MSN????????MSN??????????? http://10.msn.com.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091101/35e76fe7/attachment.htm From tabebaw at ictp.it Sun Nov 1 15:02:45 2009 From: tabebaw at ictp.it (Abebaw_Assefa Tadesse) Date: Sun, 1 Nov 2009 15:02:45 +0100 (CET) Subject: [Pw_forum] confirm eeb733b0f43e6ef4e462730785414abfa728bef2 In-Reply-To: References: Message-ID: <39533.10.41.25.17.1257084165.squirrel@webmail.ictp.it> Dear sir/madam, I would like to subscribe to the forum and thanks for accepting my request. kind regards, Tadesse > Mailing list subscription confirmation notice for mailing list > Pw_forum > > We have received a request from proxy2-e.ictp.it for subscription of > your email address, "tabebaw at ictp.it", to the pw_forum at pwscf.org > mailing list. To confirm that you want to be added to this mailing > list, simply reply to this message, keeping the Subject: header > intact. Or visit this web page: > > http://www.democritos.it/mailman/confirm/pw_forum/eeb733b0f43e6ef4e462730785414abfa728bef2 > > > Or include the following line -- and only the following line -- in a > message to pw_forum-request at pwscf.org: > > confirm eeb733b0f43e6ef4e462730785414abfa728bef2 > > Note that simply sending a `reply' to this message should work from > most mail readers, since that usually leaves the Subject: line in the > right form (additional "Re:" text in the Subject: is okay). > > If you do not wish to be subscribed to this list, please simply > disregard this message. If you think you are being maliciously > subscribed to the list, or have any other questions, send them to > pw_forum-owner at pwscf.org. > From wangqj1 at 126.com Sun Nov 1 14:55:45 2009 From: wangqj1 at 126.com (Q.J.Wang) Date: Sun, 1 Nov 2009 21:55:45 +0800 (CST) Subject: [Pw_forum] optimize the geometry Message-ID: <11678831.252351257083745570.JavaMail.coremail@bj126app29.126.com> Dear pwscf users I want to caculate ferroelectic properties of BaTiO3 under finite electric field. Is it necessary to optimize the geometry with lefield =.ture. ? Any advice will be appreciated . -- Best regards Q.J.Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091101/7ed1e580/attachment-0001.htm From sh.shapt at gmail.com Sun Nov 1 18:23:30 2009 From: sh.shapt at gmail.com (Shaptrishi Sharma) Date: Sun, 1 Nov 2009 17:23:30 +0000 Subject: [Pw_forum] Problem crashes without any error message Message-ID: Hi there, Many of problem crashes without giving me any error message, as from the manual, I understood that a program carshes only if there is memory problem or instalation problem. Well I run the same calculation at different processors 64, 80 and 48 for 3 k points, but still it keeps on crashing without any error message. suggestions welcome SS -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091101/8b1dd362/attachment.htm From degironc at sissa.it Sun Nov 1 19:28:31 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sun, 01 Nov 2009 19:28:31 +0100 Subject: [Pw_forum] Problem crashes without any error message In-Reply-To: References: Message-ID: <4AEDD34F.9040901@sissa.it> dear SS, please provide your affiliation. have you tried a small job in serial ? stefano de Gironcoli - SISSA and DEMOCRITOS Shaptrishi Sharma wrote: > Hi there, > > Many of problem crashes without giving me any error message, as from > the manual, I understood that a program carshes only if there is > memory problem or instalation problem. Well I run the same calculation > at different processors 64, 80 and 48 for 3 k points, but still it > keeps on crashing without any error message. > suggestions welcome > > SS > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From ustc0200 at gmail.com Mon Nov 2 02:54:19 2009 From: ustc0200 at gmail.com (Zhu Xi) Date: Mon, 2 Nov 2009 09:54:19 +0800 Subject: [Pw_forum] how to make scf converged for a (3,0) CNT? Message-ID: Hi PW users, I can't make the scf converged for a (3.0) CNT, can anyone give some advice? Thanks! the input is ++++++++++++++++++++++++++++++++++++++++++ &control calculation='relax', PSEUDO_DIR='./', restart_mode='from_scratch', prefix='cnt30', forc_conv_thr=1.0D-4, outdir='./' , wf_collect=.true. , / &SYSTEM ibrav = 0, celldm(1)=0, nat = 12, ntyp = 1, ecutwfc = 30.0 , ecutrho = 300, nbnd = 30, / &electrons conv_thr = 1.D-6, mixing_beta = 0.2, / &IONS ion_dynamics = 'damp' / CELL_PARAMETERS 8.0502333261 0.0 0.0 0.0 18.897261329 0.0 0.0 0.0 18.897261329 ATOMIC_SPECIES C 12.00000 C.pz-rrkjus.UPF ATOMIC_POSITIONS (crystal) C 0.8333333333333349 0.5587165273624200 0.3982999913642820 C 0.3333333333333350 0.4412834726375799 0.6017000086357180 C 0.6666666666666640 0.4412834726375799 0.3982999913642820 C 0.3333333333333350 0.4412834726375799 0.3982999913642820 C 0.6666666666666640 0.4412834726375799 0.6017000086357180 C 0.8333333333333349 0.5587165273624200 0.6017000086357180 C 0.6666666666666640 0.6174330547248399 0.4999999999999999 C 0.3333333333333350 0.6174330547248399 0.4999999999999999 C 0.8333333333333349 0.3825669452751600 0.4999999999999999 C 0.1666666666666630 0.5587165273624200 0.6017000086357180 C 0.1666666666666630 0.5587165273624200 0.3982999913642820 C 0.1666666666666640 0.3825669452751600 0.4999999999999999 K_POINTS {automatic} 21 1 1 0 0 0 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ the out put is ============================================================ ethr = 1.21E-06, avg # of iterations = 1.0 negative rho (up, down): 0.642E-04 0.000E+00 total cpu time spent up to now is 0.62 secs total energy = -135.75618000 Ry Harris-Foulkes estimate = -135.75624906 Ry estimated scf accuracy < 0.01236748 Ry End of self-consistent calculation convergence NOT achieved, stopping Writing output data file cnt30.save PWSCF : 0m 0.62s CPU time, 57m23.48s wall time init_run : 0.00s CPU electrons : 0.62s CPU ================================================================= compiler flag is -O2 -axW by ifort10.1015 and mpich2.1.08 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091102/4c461fb1/attachment.htm From mulazzi at spring8.or.jp Mon Nov 2 04:59:43 2009 From: mulazzi at spring8.or.jp (Mulazzi Mattia) Date: Mon, 02 Nov 2009 12:59:43 +0900 Subject: [Pw_forum] LDA+U problem on Mac In-Reply-To: References: Message-ID: <4AEE592F.6040804@spring8.or.jp> Dear Gabriele, thank you for the prompt reply. Here are my comments: >I don't understand a thing: starting_ns_eigenvalue is used only on the species on which >you put +U (i.e. Hubbard_U(?)>0), so if you cannot not use LDA+U for V with your QE >installation, how could you say that using starting_ns_eigenvalue does not change the >result? I thought that the starting_ns_eigenvalue function might have worked also without the LDA+U being set to true. So I tried, but the result was the same as doing a calculation without setting the occupations. >One other important point is that occupations are symmetrized according to the symmetry >of the system. So that, perhaps, retrying after breaking some symmetry or using >nosym=.TRUE. may change something. I will try to use nosym=.true., but then, I guess, I cannot use the automatice generation of the k-points and I have to supply to the input file a list of k-points covering the whole non-irreducible Brilluoin zone. Am I right? >Which version of QE are you using? Please check if the Vanadium case has already been >inserted in tabd.f90 and set_hubbard_l.f90 files. >If not pw.x should stop with an error message like "pseudopotential not yet inserted" >before causing any segmentation fault. From version 4.1 on, LDA+U should be working >with any of the transition metal elements. If you have previous versions, you can >easily get it working modifying those two files. I am using the 4.0.5 version of QE. I tried to use the 4.1.1 (since it now suports the LDA+U for all the transition metals as well as for the rare earths), but it does not compile on my Mac, even using the same configuration parameters that I used for the compilation of the 4.0.5 version. So for now, I gave up. About the LDA+U, I did more testing on it both on my PC (using cygwin under WinXP) and on the Mac. The cygwin compilation recognises without problems the V pseudopotential included in the QE library. The same calculations done on the Mac require first a small modification of the tabd.f90 file. After doing that (and recompiling pw), no more "pseudopotential not yet inserted" message. However, using on the Mac the same input file that I use on the PC gives the bloody "segmentation fault". However, I found out that the segmentation fault error only appears when I use one Vanadium atom per unit cell and if I label it "V" in the ATOMIC_SPECIES name card. In this case just fixing lda_plus_u to true triggers the segmentation fault, even if the Hubbard_U is on another atom. If I do a calculation in a larger cell with two Vanadium atoms labelled V1 and V2 (pointing to the same pseudopotential file) then I see no segmentation fault. If I use a fictitious alloy system (say MnV or FeV in a symple cubic cell with the V atom at the 0.5 0.5 0.5 position), then I see no segmentation fault even if I label the Vanadium as "V". But if I want to calculate my system, VS2, then I have the segmentation fault. If I put a second V in the calculation and I use two labels (again V1 and V2) then no problem. I thought it was a problem of the xc functional, but it seems it doesn't, using either PZ- or PBE-generated (ultrasoft) pseudopotentials does not solve the problem. I tried to generate the norm-conserving pseudopotentials using the ld1.x program, but PW does not recognise the pseudopotentials. I think that this last problem is related to a naming problem that Dr. de Gironcoli was explaining in the pw forum archives. I don't think it can be solved without editind the code itself. Did any other user report on such or similar "segmentation fault" problems? >Please report to us if the problem persists in v4.1 and if it is reproducible. >Thanks, >GS Thank you very much, Mattia Mulazzi FPR Fellow of RIKEN at Spring8 Excitation Order Research Team 1-1-1 Sayo-cho Sayo-gun, Hyogo Japan From lanhaiping at gmail.com Mon Nov 2 08:13:37 2009 From: lanhaiping at gmail.com (lan haiping) Date: Mon, 2 Nov 2009 15:13:37 +0800 Subject: [Pw_forum] how to make scf converged for a (3,0) CNT? In-Reply-To: References: Message-ID: Hi, CNT (3,0) should be a metallic system, therefore, you need specify the smearing scheme for it. And , please supply your affiliation. regards On Mon, Nov 2, 2009 at 9:54 AM, Zhu Xi wrote: > Hi PW users, > I can't make the scf converged for a (3.0) CNT, can anyone give some > advice? Thanks! > > the input is > ++++++++++++++++++++++++++++++++++++++++++ > &control > calculation='relax', > PSEUDO_DIR='./', > restart_mode='from_scratch', > prefix='cnt30', > forc_conv_thr=1.0D-4, > outdir='./' , > wf_collect=.true. , > / > &SYSTEM > ibrav = 0, > celldm(1)=0, > nat = 12, > ntyp = 1, > ecutwfc = 30.0 , > ecutrho = 300, > nbnd = 30, > / > &electrons > conv_thr = 1.D-6, > mixing_beta = 0.2, > / > &IONS > ion_dynamics = 'damp' > / > CELL_PARAMETERS > 8.0502333261 0.0 0.0 > 0.0 18.897261329 0.0 > 0.0 0.0 18.897261329 > ATOMIC_SPECIES > C 12.00000 C.pz-rrkjus.UPF > ATOMIC_POSITIONS (crystal) > C 0.8333333333333349 0.5587165273624200 0.3982999913642820 > C 0.3333333333333350 0.4412834726375799 0.6017000086357180 > C 0.6666666666666640 0.4412834726375799 0.3982999913642820 > C 0.3333333333333350 0.4412834726375799 0.3982999913642820 > C 0.6666666666666640 0.4412834726375799 0.6017000086357180 > C 0.8333333333333349 0.5587165273624200 0.6017000086357180 > C 0.6666666666666640 0.6174330547248399 0.4999999999999999 > C 0.3333333333333350 0.6174330547248399 0.4999999999999999 > C 0.8333333333333349 0.3825669452751600 0.4999999999999999 > C 0.1666666666666630 0.5587165273624200 0.6017000086357180 > C 0.1666666666666630 0.5587165273624200 0.3982999913642820 > C 0.1666666666666640 0.3825669452751600 0.4999999999999999 > K_POINTS {automatic} > 21 1 1 0 0 0 > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > > > > the out put is > ============================================================ > ethr = 1.21E-06, avg # of iterations = 1.0 > > negative rho (up, down): 0.642E-04 0.000E+00 > > total cpu time spent up to now is 0.62 secs > > total energy = -135.75618000 Ry > Harris-Foulkes estimate = -135.75624906 Ry > estimated scf accuracy < 0.01236748 Ry > > End of self-consistent calculation > > convergence NOT achieved, stopping > > Writing output data file cnt30.save > > PWSCF : 0m 0.62s CPU time, 57m23.48s wall time > > init_run : 0.00s CPU > electrons : 0.62s CPU > ================================================================= > > > compiler flag is -O2 -axW by ifort10.1015 and mpich2.1.08 > > > _______________________________________________ > 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/20091102/8b0d5e29/attachment.htm From bipulrr at gmail.com Mon Nov 2 09:15:06 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Mon, 2 Nov 2009 13:45:06 +0530 Subject: [Pw_forum] fixing the angle. Message-ID: <3a749910911020015x5edbd69fubfd4d246076bb1e4@mail.gmail.com> Dear PwSCF users, I am want to do calculation of SiO2. What I want is to optimise the structure, using vc-relax. Beside I also want that, the angle should not change between the atoms and vc-relax give me an optimised structure. So is it possible? If so then what i have to modify in my input file? Means what additional string I have to add. I am sending my input file for vc-relax. thanks -- Bipul Rakshit Research Fellow, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091102/182f2da7/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: SiO2.vc-relax.in Type: application/octet-stream Size: 3267 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091102/182f2da7/attachment.obj From paulatto at sissa.it Mon Nov 2 09:32:51 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 2 Nov 2009 09:32:51 +0100 (CET) Subject: [Pw_forum] fixing the angle. In-Reply-To: <3a749910911020015x5edbd69fubfd4d246076bb1e4@mail.gmail.com> References: <3a749910911020015x5edbd69fubfd4d246076bb1e4@mail.gmail.com> Message-ID: <55897.78.12.172.175.1257150771.squirrel@webmail.sissa.it> In data 02 novembre 2009 alle ore 09:15:06, Bipul Rakshit ha scritto: > What I want is to optimise the structure, using vc-relax. Beside I also > want that, the angle should not change between the atoms and vc-relax give me > an optimised structure. Dear Bipul, it's not very clear to me which angle do you want to keep fixed, but it doesn't really matter. You can nail the atoms to their initial positions setting the additional flags in the atomic position lines; this will work if you are using crystal or alat coordinates (you are), it will only allow the cell volume to change. Otherwise you can set a constrain, you can find the documentation in Doc/INPUT_PW.txt. It is not difficult at all, but it does not work with bfgs, so you'll have to use damp dynamics for the atoms relaxation. 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/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From bipulrr at gmail.com Mon Nov 2 10:13:50 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Mon, 2 Nov 2009 14:43:50 +0530 Subject: [Pw_forum] fixing the angle. In-Reply-To: <55897.78.12.172.175.1257150771.squirrel@webmail.sissa.it> References: <3a749910911020015x5edbd69fubfd4d246076bb1e4@mail.gmail.com> <55897.78.12.172.175.1257150771.squirrel@webmail.sissa.it> Message-ID: <3a749910911020113x44c2c593v27ddd78bf2707841@mail.gmail.com> Dear Lorenzo Paulatto, Thanks for your kind mail. I got your points. I saw the Doc/INPUT_PW.txt file, there is a flag called CARD: CONSTRAINTS in which there is 'planar_angle' and 'torsional_angle', but it will be more helpful if you send me one input file for constraining the angle. Actually after running vc-relax with the input file which i send to you, the CELL_PARAMETER changes, that means angle also changing.... I draw the output file with xcrysden and find the angles (Si-O-Si) changes. So if possible just send me some input file for constraining the angles. On Mon, Nov 2, 2009 at 2:02 PM, Lorenzo Paulatto wrote: > In data 02 novembre 2009 alle ore 09:15:06, Bipul Rakshit > ha scritto: > > What I want is to optimise the structure, using vc-relax. Beside I also > > want that, the angle should not change between the atoms and vc-relax > give me > > an optimised structure. > > Dear Bipul, > it's not very clear to me which angle do you want to keep fixed, but it > doesn't really matter. > > You can nail the atoms to their initial positions setting the additional > flags in the atomic position lines; this will work if you are using > crystal or alat coordinates (you are), it will only allow the cell volume > to change. > > Otherwise you can set a constrain, you can find the documentation in > Doc/INPUT_PW.txt. It is not difficult at all, but it does not work with > bfgs, so you'll have to use damp dynamics for the atoms relaxation. > > 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/ > > > ---------------------------------------------------------------- > 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 > -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091102/7c5eca81/attachment.htm From gbilalbegovic at gmail.com Mon Nov 2 10:19:43 2009 From: gbilalbegovic at gmail.com (Goranka Bilalbegovic) Date: Mon, 2 Nov 2009 10:19:43 +0100 Subject: [Pw_forum] GIPAW: write tensor field Message-ID: <7332fead0911020119oa1dc041lacdfea1f84d2b644@mail.gmail.com> Hello, In the GIPAW directory there is a file "write_tensor_field.f90". However, it looks as writing of tensor fields is not implemented. I would like to know if there are some problems with this implementation, or "write_tensor_field" is just not implemented till now. Best regards, Goranka Bilalbegovic Department of Physics, Faculty of Science University of Zagreb, Croatia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091102/1d418e64/attachment.htm From paulatto at sissa.it Mon Nov 2 10:25:18 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 2 Nov 2009 10:25:18 +0100 (CET) Subject: [Pw_forum] fixing the angle. In-Reply-To: <3a749910911020113x44c2c593v27ddd78bf2707841@mail.gmail.com> References: <3a749910911020015x5edbd69fubfd4d246076bb1e4@mail.gmail.com> <55897.78.12.172.175.1257150771.squirrel@webmail.sissa.it> <3a749910911020113x44c2c593v27ddd78bf2707841@mail.gmail.com> Message-ID: <39331.78.12.172.175.1257153918.squirrel@webmail.sissa.it> On Mon, November 2, 2009 10:13, Bipul Rakshit wrote: > I saw the Doc/INPUT_PW.txt file, there is a flag called CARD: CONSTRAINTS > in which there is 'planar_angle' and 'torsional_angle', but it will be > more helpful if you send me one input file for constraining the angle. I don't have any. > Actually after running vc-relax with the input file which i send to you, > the CELL_PARAMETER changes, that means angle also changing.... Of course, if you squeeze the cell along one direction the structure will deform accordingly. If you want to rescale the whole structure maintaining all the angles constant you have to change ONLY celldm(1). There is no automatic way to do it, the cell_dofree input parameter can constrain cell deformation but not in this way. > I draw the output file with xcrysden and find the angles (Si-O-Si) > changes. Yes, I understand what's going on. But what's wrong with it changing in the first place? > So if possible just send me some input file for constraining the angles. I don't have a secret library of input files... best 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 paulatto at sissa.it Mon Nov 2 10:36:28 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 2 Nov 2009 10:36:28 +0100 (CET) Subject: [Pw_forum] GIPAW: write tensor field In-Reply-To: <7332fead0911020119oa1dc041lacdfea1f84d2b644@mail.gmail.com> References: <7332fead0911020119oa1dc041lacdfea1f84d2b644@mail.gmail.com> Message-ID: <39365.78.12.172.175.1257154588.squirrel@webmail.sissa.it> On Mon, November 2, 2009 10:19, Goranka Bilalbegovic wrote: > In the GIPAW directory there is a file "write_tensor_field.f90". However, > it looks as writing of tensor fields is not implemented. I would like to > know if there are some problems with this implementation, or > "write_tensor_field" is just not > implemented till now. Dear Goranka, the write_tensor_field subroutine is used by suscept_crystal.f90 which will write two files (one containing the current, the other containing the B field, I guess) but only if you have set the input variables filcurr and filfield. To be honest, I'm not totally sure of what will actually go in the file, but I suspect you know more than me on this subject. best 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 dimpy.sharma at tyndall.ie Mon Nov 2 11:45:51 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Mon, 2 Nov 2009 10:45:51 -0000 Subject: [Pw_forum] Problem in Calculating Projected density of states Message-ID: Hi QEs users, I have tried to calculate projected density of states first by performing scf calculation, then nscf calculation and then Projected density of states, but I am getting the folowing error. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from davcio : error # 10 error while reading from file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% my pdos input file is &inputpp prefix = 'unoptimisedsilane' outdir = '/sfiwork/dsharma/PDOSSilane/scf/scfunopt' degauss = 0, Emin = -14.6313, Emax = 0.8754, ngauss = 0, DeltaE = 0.01, filpdos = 'pdosout', /end and my script file is #!/bin/bash #PBS -N pdos #PBS -l nodes=16 ##PBS -1 waltime=90:00:00 #PBS -q big500 #PBS -V ## #PATH of the parallel abinit executable export pw_path='/usr/local/espresso-4.0.5/bin' ### PATH to the mpirun binary: export mpirun_path='/opt/mpi/bin' export calc_name='pdos' ### go in the working directory: cd $PBS_O_WORKDIR ## Count the number of cpu requested NP=`wc -l $PBS_NODEFILE` echo $NP > $calc_name.txt $mpirun_path/mpirun -machinefile $PBS_NODEFILE -np $NP $pw_path/projwfc.x -npool1 < pdos > pdosout Suggestions welcome. Thanks and regards Dimpy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091102/83d165a5/attachment-0001.htm From paulatto at sissa.it Mon Nov 2 12:27:35 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 2 Nov 2009 12:27:35 +0100 (CET) Subject: [Pw_forum] Problem in Calculating Projected density of states In-Reply-To: References: Message-ID: <34355.78.12.172.175.1257161255.squirrel@webmail.sissa.it> On Mon, November 2, 2009 11:45, Dimpy Sharma wrote: > I have tried to calculate projected density of states first by performing > scf calculation, then nscf calculation and then Projected density of > states, but I am getting the folowing error. > ... > from davcio : error # 10 Dear Dimpy, the error code (10) means that the error happened while reading the wavefunctions. If you are using a different number of processors for the ncsf calculation and the projwfc calculation then you MUST use wf_collect=.true. for the nscf calculation. 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 kazempoor2000 at yahoo.com Mon Nov 2 14:48:34 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Mon, 2 Nov 2009 05:48:34 -0800 (PST) Subject: [Pw_forum] (no subject) Message-ID: <994846.44636.qm@web112508.mail.gq1.yahoo.com> Hi All I am interested to see the importance of electron-phonon interaction in semiconductor like Tio2. I made the script like example 7 and run the script but it takes the error: from init : error # 1 nc already filled: wrong q grid or wrong nr What is the reason? Thanks This is the script I use: PW_COMMAND="/p5/batch/kazempou/q-e-scm-2009-08-12/espresso/bin/pw.x " PH_COMMAND="/p5/batch/kazempou/q-e-scm-2009-08-12/espresso/bin/ph.x " Q2R_COMMAND="/p5/batch/kazempou/q-e-scm-2009-08-12/espresso/bin/q2r.x " MATDYN_COMMAND="/p5/batch/kazempou/q-e-scm-2009-08-12/espresso/bin/matdyn.x " # # SCF at dense k-mesh, good enough for electronic DOS # cat > al.scf.fit.in << EOF &control calculation='scf' restart_mode='from_scratch', prefix='al', pseudo_dir = './', outdir='./' / &system ibrav= 6, celldm(1) =8.73,celldm(3)=0.643, nat= 6, ntyp= 2, ecutwfc =15.0,occupations='smearing', smearing='methfessel-paxton', degauss=0.05 la2F = .true., / &electrons conv_thr = 1.0d-8 mixing_beta = 0.7 / ATOMIC_SPECIES Ti 47.86700 Ti.pbe-sp-van_ak.UPF O 15.99940 O.pbe-van_bm.UPF ATOMIC_POSITIONS crystal Ti 0.000000000 0.000000000 0.000000000 Ti 0.500000000 0.500000000 0.500000000 O 0.3053 0.3053 0.000000000 O -0.3053 -0.3053 0.000000000 O 0.8053 0.1947 0.5 O 0.1947 0.8053 0.5 K_POINTS {automatic} 16 16 16 0 0 0 EOF $PW_COMMAND < al.scf.fit.in > al.scf.fit.out # # SCF at k-mesh good enough for phonons # cat > al.scf.in << EOF &control calculation='scf' restart_mode='from_scratch', prefix='al', pseudo_dir = './', outdir='./' / &system ibrav= 6, celldm(1) =8.73,celldm(3)=0.643, nat= 6, ntyp= 2, ecutwfc =15.0,occupations='smearing', smearing='methfessel-paxton', degauss=0.05 / &electrons conv_thr = 1.0d-8 mixing_beta = 0.7 / ATOMIC_SPECIES Ti 47.86700 Ti.pbe-sp-van_ak.UPF O 15.99940 O.pbe-van_bm.UPF ATOMIC_POSITIONS crystal Ti 0.000000000 0.000000000 0.000000000 Ti 0.500000000 0.500000000 0.500000000 O 0.3053 0.3053 0.000000000 O -0.3053 -0.3053 0.000000000 O 0.8053 0.1947 0.5 O 0.1947 0.8053 0.5 K_POINTS {automatic} 8 8 8 0 0 0 EOF $PW_COMMAND < al.scf.in > al.scf.out # cat > al.elph.in << EOF Electron-phonon coefficients for Al &inputph tr2_ph=1.0d-10, prefix='al', fildvscf='aldv', amass(1)=47.86, outdir='./', fildyn='tio2.dyn', elph=.true., trans=.true., ldisp=.true. nq1=4, nq2=4, nq3=4 / EOF $PH_COMMAND < al.elph.in > al.elph.out # q2r and matdyn # cat > q2r.in << EOF &input zasr='simple', fildyn='tio2.dyn', flfrc='tio2444.fc', la2F=.true. / EOF $Q2R_COMMAND < q2r.in > q2r.out # cat > matdyn.in.freq << EOF &input asr='simple', amass(1)=47.86, flfrc='tio2444.fc', flfrq='tio2444.freq', la2F=.true., dos=.false. / 36 0.0 0.0 0.0 0 0.1 0.0 0.0 0 0.2 0.0 0.0 0 0.3 0.0 0.0 0 0.4 0.0 0.0 0 0.5 0.0 0.0 0 0.5 0.0 0.1 0 0.5 0.0 0.2 0 0.5 0.0 0.3 0 0.5 0.0 0.4 0 0.5 0.0 0.5 0 0.4 0.0 0.5 0 0.3 0.0 0.5 0 0.2 0.0 0.5 0 0.1 0.0 0.5 0 0.0 0.0 0.5 0 0.0 0.0 0.4 0 0.0 0.0 0.3 0 0.0 0.0 0.2 0 0.0 0.0 0.1 0 0.0 0.0 0.0 0 0.1 0.1 0.0 0 0.2 0.2 0.0 0 0.3 0.3 0.0 0 0.4 0.4 0.0 0 0.5 0.5 0.0 0 0.5 0.5 0.1 0 0.5 0.5 0.2 0 0.5 0.5 0.3 0 0.5 0.5 0.4 0 0.5 0.5 0.5 0 0.4 0.4 0.5 0 0.3 0.3 0.5 0 0.2 0.2 0.5 0 0.1 0.1 0.5 0 0.0 0.0 0.5 0 EOF $MATDYN_COMMAND < matdyn.in.freq > matdyn.out.freq # cat > matdyn.in.dos << EOF &input asr='simple', amass(1)=47.86, flfrc='tio2444.fc', flfrq='tio2444.freq', la2F=.true., dos=.true. fldos='phonon.dos', nk1=10, nk2=10, nk3=10, ndos=50 / EOF $MATDYN_COMMAND < matdyn.in.dos > matdyn.out.dos Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091102/7c1433d9/attachment.htm From ceresoli at MIT.EDU Mon Nov 2 14:51:10 2009 From: ceresoli at MIT.EDU (Davide Ceresoli) Date: Mon, 02 Nov 2009 08:51:10 -0500 Subject: [Pw_forum] GIPAW: write tensor field In-Reply-To: <7332fead0911020119oa1dc041lacdfea1f84d2b644@mail.gmail.com> References: <7332fead0911020119oa1dc041lacdfea1f84d2b644@mail.gmail.com> Message-ID: <4AEEE3CE.7020807@mit.edu> Goranka Bilalbegovic wrote: > > Hello, > > In the GIPAW directory there is a file "write_tensor_field.f90". > However, it looks as writing of tensor fields is not implemented. I > would like to know if there are > some problems with this implementation, or "write_tensor_field" is just > not implemented till now. > > Best regards, > Goranka Bilalbegovic > Department of Physics, Faculty of Science > University of Zagreb, Croatia > Hi Goranka, the rank-2 tensor field (the induced current or the induced magnetic field) is split into 3 cartesian components, and written into 3 separate files, as vector fields When I first implemented the routine, I didn't have any fancy visualization code in mind (like OpenDX, MayaVi, VTK, ...) and I've implemented instead for Xcrysden. Xcrysden can output small 'arrows' associated to fake atoms. The problem is that the visualization becomes extremely slow. This said, the format is open, and if you have ideas and suggestions, they are welcome. Davide From arvifis at gmail.com Mon Nov 2 15:04:30 2009 From: arvifis at gmail.com (Arles V. Gil Rebaza) Date: Mon, 2 Nov 2009 12:04:30 -0200 Subject: [Pw_forum] About hyperfine interaction Message-ID: Hi, I would like calculate hyperfine properties of metals, is possible this with QE 4.1...?? I read a mail ago, but, in the manual about GIPAW no appears the job (job='hyperfine') and i'm don't know the inputs...!! Best. Arles V. Gil Rebaza Intituto de F?sica de La Plata La Plata - Argentina. ---------- Forwarded message ---------- From: Davide Ceresoli Date: 2009/9/29 Subject: Re: [Pw_forum] Hyperfine interaction in Li-Mn compounds? To: PWSCF Forum Gregor Mali wrote: > Dear PWscf/GIPAW users. > > I am studying lithium-manganese oxides and lithium-manganese silicates. > Isotropic shifts of 6Li MAS NMR signals in these compounds are > predominantly determined by the contact hyperfine interaction (Fermi > shifts), i.e. by the interaction between 6Li nuclei and unpaired > electronic spins. > > Is it possible to calculate these hyperfine shifts or the magnitude of > hyperfine interaction by the PWsfc/GIPAW module using job = 'hyperfine'. > I also wonder if the corresponding GIPAW input file requires any > additional input parameters. The option 'hyperfine' is, namely, not > documented in the INPUT_GIPAW.html file. > Dear Gregor, the extra information to enter are the nuclear g-factors for the isotopes. Here is an example for MnO (55Mn and 18O). &inputgipaw job = 'hyperfine' prefix = 'mno' tmp_dir = './scratch/' spline_ps = .true. hfi_output_unit = 'MHz' hfi_nuclear_g_factor(1) = 1.387487 ! 55Mn hfi_nuclear_g_factor(2) = -0.757520 ! 18O / I've got the numbers from webelements.com, under "NMR properties". There, the gyromangnetic ratio \gamma is listed in 10^7 rad T^{-1} s^{-1}. To obtain the g-factor, multiply \hbar and divide by the nuclear magneton (\mu_N): E.g. using the command 'units': You have: 6.6452546e7 hbar / nuclearmagneton T s You want: Definition: 1.3874872 If the nuclear spin is N/2, N>1, you need to divide the output quantities by N. For Li, you should get good results for the Fermi contact, because the unpaired electron are in the 2s orbital. But if the magnetization comes form p and d orbitals, I've found that the core electrons (those not included in the pseudopotential!) polarize opposite to the valence, giving rise to large cancellations in the Fermi contact. I've implemented the core relaxation in an experimental version of the code. I haven't put it in the CVS, because it's not perfect, and one should carefully check if the results make sense. If you are interested, send me an e-mail. > Best regards. > > Gregor Mali Best, Davide -- ###---------> Arles V. <---------### -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091102/6a926280/attachment.htm From smogunov at sissa.it Mon Nov 2 16:32:37 2009 From: smogunov at sissa.it (Alexander Smogunov) Date: Mon, 02 Nov 2009 16:32:37 +0100 Subject: [Pw_forum] Left and right going Bloch's states from PWCOND In-Reply-To: References: Message-ID: <1257175957.3672.13.camel@alex-laptop> Dear Manoj. The new parameter lorb is simply used to give in output the scattering states so that you could plot them, it does not affect the transmission calculation itself. If it is .false. the code will run normally as before... It is true that this new option does not work for ikind=2, but you can still calculate transmission and reflection amplitudes. To calculate t and r from right to left you should simply call the transmit routine in do_cond.f90 with the last argument to set to .false. By default the code does not compute the case of right --> left scattering since the total transmission is the same as in left --> right case. Only if you want to plot the scattering states (lorb=.true.) it does that. It is how the things are implemented now ... Best regards, Alexander On Fri, 2009-10-30 at 14:04 -0400, Manoj Srivastava wrote: > Just to add one more question. > what is 'lorb' switch. I get following- > lorb, & ! if .t. calculate the scattering (or Bloch) states > so, i guess for transmission calculation i will have to set it to > 't'. now- > IF (lorb.and.ikind.eq.2) call errore('do_cond','lorb not working with > ikind = 2',1) > so, it seems that calculation for r and t for right and left going > state, when left and right leads are different doesnot work. Is that > correct? A possible work around may be rotating the whole system by 180 > degree, which would be like treating left lead as right lead and > scattering region rotated. Can I do that? > > Regards, > Manoj > > On Fri, 30 Oct 2009, Manoj Srivastava wrote: > > > Dear Alexander, > > Thank you very much! I read the code, it seems that there are > > quiet a few changes in 4.1.1 compared to 4.0.4 :) .So, just to make sure, > > if I want to calculate r and t for left going Bloch's state as well as > > right going Bloch's state, I need to run the code two times, one time with > > 'left_to_right' switch true, and another time false. I dont need to change > > scattering region or interchange left and right leads. > > > > Regards, > > Manoj Srivastava > > On Thu, 29 Oct 2009, Alexander > > Smogunov wrote: > > > > > Dear Manoj > > > > > > On Wed, 2009-10-28 at 01:49 -0400, Manoj Srivastava wrote: > > > > Dear Alexander, > > > > You are correct, left and right moving states are in general not > > > > related. I was wrong about trying to create a pair. Thanks for > > > > clarification. > > > > I have a few more questions. > > > > 1. I want to find out the reflection coefficient in the code. In > > > > transmit.f90, transmission coefficient is |tmat(ig,n)|^2, where tmat is > > > > vec1(ntran-n2d-npol*nocrosr+ig,n). (line 206, of version 4.0.5). > > > > Reflection is not explicitly calculated in the code, but it should be > > > > modulus square of vec1(2*n2d+npol*norbs+ig,n) (line 234). Am I correct? > > > > > > in the 4.1 version there is output of both t and r. > > > > > > > > > > > > > > 2. In the code reflection and transmission coefficients are calculated > > > > for one direction lets say t++ and t+-, which is transmission and > > > > reflection coefficient for Bloch' state moving from - to + , or in other > > > > words, left to right. To calculate transmission and reflection for Bloch's > > > > state going from right to left, what should I do? Should i just rotate my > > > > system 180 degree, that way leads get interchanged and also scattering > > > > area has orientation 180 different from before. > > > > > > > > > > again in the 4.1 version you have possibility to calculate t and r for > > > both directions, in the do_cond.f90 the transmit routine is called with > > > an extra parameter which is true (false) if you want to calculate > > > scattering states propagating from the left (from the right). > > > > > > > 3. In the subroutine sunitary.f90, is raux measure of conservation of > > > > flux? If I sum all the transmission and reflecion coefficient for > > > > a particular Bloch's state, I should get 1, and computationally a number > > > > close to 1. How large could it be for S matrix not to be unitary, i m > > > > getting raux more than one e.g. 1.0011 but code still considers smatrix > > > > to be unitary. > > > > > > in the case when |R + T - 1| > 1.d-4 for some band, it should print out > > > the value of R+T but continues to run anyway. > > > > > > All the best, > > > Alexander > > > > > > > > > > > > > > > > > Regards, > > > > Manoj Srivastava > > > > University of Florida, Gainesville, FL > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Thu, 22 > > > > Oct 2009, Alexander Smogunov wrote: > > > > > > > > > On Thu, 2009-10-22 at 11:34 -0400, Manoj Srivastava wrote: > > > > > > Dear Alexander, > > > > > > Thanks for your answer. I just want to make sure. Imagine we have total > > > > > > number of channels in the left lead 2, so total number of Bloch's state > > > > > > are 4. 2 of them left going say a and b, and 2 right going say c and d. > > > > > > So, are you saying that for left going state a, the corresponding right > > > > > > going state is c? Are they ordered this way? > > > > > > > > > > what do you mean by corresponding? Left and right moving Bloch > > > > > states are in general not related one to another, you can even have > > > > > different number of them ... Only if you have some symmetry S which > > > > > brings kz to -kz conserving k_parallel, then the state with > > > > > \psi_{-kz} will be S \psi{kz}. This is true for example at 2D G point > > > > > when you have time reversal operation. > > > > > > > > > > Now the code simply arranges the propagating states in the order of > > > > > increasing |k_z|... > > > > > > > > > > Regards, Alexander > > > > > > > > > > > > > > > > > > > > > > Regards, > > > > > > Manoj > > > > > > > > > > > > > > > > > > On Thu, 22 Oct 2009, Alexander > > > > > > Smogunov wrote: > > > > > > > > > > > > > Dear Manoj. > > > > > > > > > > > > > > The output of complex k vectors is performed in > > > > > > > summary_band.f90 routine. If you want to see all > > > > > > > the complex k vectors, not only propagating ones, > > > > > > > you can change at the end of this routine: > > > > > > > > > > > > > > ------------------- > > > > > > > do i = 1, nchanl > > > > > > > WRITE( stdout,'(3f12.7)') DBLE(kvall(i)), AIMAG(kvall(i)), eev > > > > > > > enddo > > > > > > > ------------------- > > > > > > > > > > > > > > to > > > > > > > ------------------- > > > > > > > > > > > > > > do i = 1, 2*nstl > > > > > > > WRITE( stdout,'(3f12.7)') DBLE(kvall(i)), AIMAG(kvall(i)), eev > > > > > > > enddo > > > > > > > ------------------- > > > > > > > > > > > > > > Altogether there are 2*nstl (or 2*nstr) Bloch states in the left > > > > > > > (or right) lead. First half, [1,nstl], are propagating or decaying to > > > > > > > the right states, another half, [nstl+1,2*nstl], - propagating or > > > > > > > decaying to the left. In each group, first nchanl states are propagating > > > > > > > states. > > > > > > > > > > > > > > The propagating states are normalized by the current and are arranged in > > > > > > > the above order at the end of jbloch.f90 routine, after the following > > > > > > > lines: > > > > > > > > > > > > > > ! > > > > > > > ! Right ordering (+, >, -, <) > > > > > > > ! > > > > > > > > > > > > > > > > > > > > > > > > > > > > Notice, that in the last versions the code gives in output > > > > > > > both propagating to the right and to the left states. > > > > > > > > > > > > > > Hope this helps, > > > > > > > Alexander > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Wed, 2009-10-21 at 14:13 -0400, Manoj Srivastava wrote: > > > > > > > > Dear All, > > > > > > > > I am trying to figure out the left and right going Bloch's states in the > > > > > > > > lead from PWCOND. For a given (kx,ky)and energy we get kz. The code only > > > > > > > > prints out Bloch's state moving in one direction. eg. in one of the > > > > > > > > calculation- > > > > > > > > k//=(0.375,-0.375) > > > > > > > > Nchannels of the left tip = 1 > > > > > > > > k1(2pi/a) k2(2pi/a) E-Ef (eV) > > > > > > > > > > > > > > > > 0.3157801 0.0000000 0.0000000 > > > > > > > > > > > > > > > > Now if I want Bloch's state moving in right as well as left direction, I > > > > > > > > can go to kbloch.f90 subroutine, and print out all the eigen values of > > > > > > > > AX=exp(ikd)BX, and out of those the ones with real solution would be our > > > > > > > > Bloch's state, so I get for each channel two solutions- > > > > > > > > kval (-0.275409421993275,1.823688001395235E-010) > > > > > > > > kval (0.315780119742506,-3.611201785292708E-012) > > > > > > > > > > > > > > > > To figure out the direction, I can calculate current associated with these > > > > > > > > Bloch's sate and if the current is +ive it is right moving , and if '-'ive > > > > > > > > its left moving Bloch's state. I can print out current from jbloch.f90 > > > > > > > > subroutine which are - > > > > > > > > current eigenvalue -1.86502143831863 1.59149029314457 > > > > > > > > > > > > > > > > So, clearly the first state with kval=-0.2754094 is left moving and the > > > > > > > > other one right moving. Upto here its clear to me how to identify left and > > > > > > > > right moving states. > > > > > > > > > > > > > > > > I get confused when for a given (kx,ky,E), I have more than one Bloch' > > > > > > > > state. In another calculation where i get multiple Bloch's state- > > > > > > > > Nchannels of the left tip = 5 > > > > > > > > k1(2pi/a) k2(2pi/a) E-Ef (eV) > > > > > > > > > > > > > > > > -0.0746301 0.0000000 0.0000000 > > > > > > > > 0.1205527 0.0000000 0.0000000 > > > > > > > > 0.3112908 0.0000000 0.0000000 > > > > > > > > 0.4200218 0.0000000 0.0000000 > > > > > > > > -0.4935150 0.0000000 0.0000000 > > > > > > > > > > > > > > > > so i did the same trick i did above to first print out kz and then > > > > > > > > current, which gives me - > > > > > > > > kval (-0.420023481074359,1.979595081419732E-010) (call it a) > > > > > > > > kval (0.420023367986768,2.500979698670295E-011) (b) > > > > > > > > kval (-0.306507431678779,-1.236804629184431E-011) (c) > > > > > > > > kval (-0.125376071175573,-6.134512510438736E-011) (d) > > > > > > > > kval (-7.945001124706894E-002,6.683546930037856E-011)(e) > > > > > > > > kval (0.106554601758169,-6.427946951285107E-011) (f) > > > > > > > > kval (8.866867725358024E-002,8.342250371574646E-011) (g) > > > > > > > > kval (0.325333314672671,1.260810749228185E-011) (h) > > > > > > > > kval (-0.488725859521576,1.769197678346003E-010) (i) > > > > > > > > kval (0.479509832763231,1.765499400037283E-010) (j) > > > > > > > > > > > > > > > > current eigenvalue -9.31389492882581 -1.24296522993488 > > > > > > > > -1.21324078359658 -1.11950286753963 -1.08166842367443 > > > > > > > > 1.08187482164864 1.11973146584263 1.21295295042188 > > > > > > > > 1.24280031534940 9.313897787790 > > > > > > > > > > > > > > > > So, the first 5 are left moving and rest are right moving. But I dont know > > > > > > > > the pairs. for example for left moving state a, what is the corresponding > > > > > > > > right moving state whether its f or g ... j ? > > > > > > > > > > > > > > > > Any help would be appreciated. > > > > > > > > > > > > > > > > Regards, > > > > > > > > Manoj Srivastava > > > > > > > > University of Florida, Gainesville. > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > Pw_forum mailing list > > > > > > > > Pw_forum at pwscf.org > > > > > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > -- > > > > > > > e-mail: 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 > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > Pw_forum mailing list > > > > > > Pw_forum at pwscf.org > > > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > > > > > e-mail: 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 > > > > > > > > > > > > > _______________________________________________ > > > > Pw_forum mailing list > > > > Pw_forum at pwscf.org > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > -- > > > e-mail: 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 > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- e-mail: smogunov at sissa.it home-page: http://people.sissa.it/~smogunov From dimpy.sharma at tyndall.ie Mon Nov 2 19:47:34 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Mon, 2 Nov 2009 18:47:34 -0000 Subject: [Pw_forum] Calculating Projected density of states Message-ID: Hi QEs users, I have tried to calculate projected density of states first by performing scf calculation, then nscf calculation and then Projected density of states, but I am getting the following error. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 0 from projwfc : error # 4324 reading inputpp namelist %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% my pdos input file is &inputpp prefix = 'unoptimisedsilane', outdir = '/sfiwork/dsharma/PDOSSilane/scfn/scfunopt' degauss = 0.0, Emin = -12.6653, Emax = 12, ngauss = 0, DeltaE = 0.01, filpdos = 'pdosout', and my script file is #!/bin/bash #PBS -N pdos #PBS -l nodes=4 ##PBS -1 waltime=24:00:00 #PBS -q walton #PBS -V ## #PATH of the parallel abinit executable export pw_path='/usr/local/espresso-4.0.5/bin' ### PATH to the mpirun binary: export mpirun_path='/opt/mpi/bin' export calc_name='pdos' ### go in the working directory: cd $PBS_O_WORKDIR ## Count the number of cpu requested NP=`wc -l $PBS_NODEFILE` echo $NP > $calc_name.txt $mpirun_path/mpirun -machinefile $PBS_NODEFILE -np $NP $pw_path/projwfc.x -npool1 < pdos > pdosout My scf output file is End of self-consistent calculation k = 0.0000 0.0000 0.0000 ( 6983 PWs) bands (ev): -12.6653 -9.5380 -7.2586 -6.0976 -5.0908 -3.8305 -0.6212 0.5917 0.8368 1.6400 k = 0.2500 0.0000 0.0000 ( 6959 PWs) bands (ev): -12.1861 -9.7498 -6.9945 -6.2237 -5.5081 -5.1444 0.3355 1.0465 1.4373 1.9502 k =-0.5000 0.0000 0.0000 ( 6966 PWs) bands (ev): -10.9343 -10.8970 -6.6489 -6.3817 -5.9690 -5.5686 0.3422 0.8657 1.1277 1.7350 highest occupied, lowest unoccupied level (ev): -3.8305 -0.6212 One more thing I want to ask, I have choosen the Emin and Emax value from the scf calculation, is this correct? Suggestions welcome. Thanks and regards Dimpy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091102/d80f5dd0/attachment.htm From dimpy.sharma at tyndall.ie Mon Nov 2 19:51:32 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Mon, 2 Nov 2009 18:51:32 -0000 Subject: [Pw_forum] Calculating Projected density of states Message-ID: Hi QEs users, I have tried to calculate projected density of states first by performing scf calculation, then nscf calculation and then Projected density of states, but I am getting the following error. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 0 from projwfc : error # 4324 reading inputpp namelist %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% my pdos input file is &inputpp prefix = 'unoptimisedsilane', outdir = '/sfiwork/dsharma/PDOSSilane/scfn/scfunopt' degauss = 0.0, Emin = -12.6653, Emax = 12, ngauss = 0, DeltaE = 0.01, filpdos = 'pdosout', and my script file is #!/bin/bash #PBS -N pdos #PBS -l nodes=4 ##PBS -1 waltime=24:00:00 #PBS -q walton #PBS -V ## #PATH of the parallel abinit executable export pw_path='/usr/local/espresso-4.0.5/bin' ### PATH to the mpirun binary: export mpirun_path='/opt/mpi/bin' export calc_name='pdos' ### go in the working directory: cd $PBS_O_WORKDIR ## Count the number of cpu requested NP=`wc -l $PBS_NODEFILE` echo $NP > $calc_name.txt $mpirun_path/mpirun -machinefile $PBS_NODEFILE -np $NP $pw_path/projwfc.x -npool1 < pdos > pdosout suggestions welcome. Thanks and regards Dimpy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091102/a47c0dd3/attachment.htm From somesh.kb at gmail.com Mon Nov 2 19:55:13 2009 From: somesh.kb at gmail.com (Somesh Kumar Bhattacharya) Date: Mon, 2 Nov 2009 19:55:13 +0100 Subject: [Pw_forum] Calculating Projected density of states In-Reply-To: References: Message-ID: Hi Dimpy, Put the Emax value as real as mentioned in INPUT_PP. You have provided an integer . Regards, Somesh On Mon, Nov 2, 2009 at 7:51 PM, Dimpy Sharma wrote: > Hi QEs users, > I have tried to calculate projected density of states first by performing > scf calculation, then nscf calculation and then Projected density of states, > but I am getting the following error. > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > task # 0 > from projwfc : error # 4324 > reading inputpp namelist > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > my pdos input file is > > &inputpp > prefix = 'unoptimisedsilane', > outdir = '/sfiwork/dsharma/PDOSSilane/scfn/scfunopt' > degauss = 0.0, > Emin = -12.6653, > Emax = 12, > ngauss = 0, > DeltaE = 0.01, > filpdos = 'pdosout', > > and my script file is > > #!/bin/bash > #PBS -N pdos > #PBS -l nodes=4 > ##PBS -1 waltime=24:00:00 > #PBS -q walton > #PBS -V > ## #PATH of the parallel abinit executable > export pw_path='/usr/local/espresso-4.0.5/bin' > > ### PATH to the mpirun binary: > export mpirun_path='/opt/mpi/bin' > > export calc_name='pdos' > > ### go in the working directory: > cd $PBS_O_WORKDIR > > ## Count the number of cpu requested > NP=`wc -l $PBS_NODEFILE` > echo $NP > $calc_name.txt > > $mpirun_path/mpirun -machinefile $PBS_NODEFILE -np $NP $pw_path/projwfc.x > -npool1 < pdos > pdosout > > suggestions welcome. > > Thanks and regards > > Dimpy > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Somesh Kr. Bhattacharya Post Doctoral Fellow Room No. 263, Leonardo Building, The Abdus Salam International Centre for Theoretical Physics Strada Costiera, 11 I-34014 Trieste Italy Phone: +39-040-2240399 http://portal.ictp.it/cmsp/members/postdoctoral-fellows/somesh-kumar-bhattacharya/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091102/88457d00/attachment.htm From dimpy.sharma at tyndall.ie Mon Nov 2 19:56:30 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Mon, 2 Nov 2009 18:56:30 -0000 Subject: [Pw_forum] Problem in Calculating Projected density of states Message-ID: Hi QEs users, I have tried to calculate projected density of states first by performing scf calculation, then nscf calculation and then Projected density of states, but I am getting the following error. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 0 from projwfc : error # 4324 reading inputpp namelist %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% my pdos input file is &inputpp prefix = 'unoptimisedsilane', outdir = '/sfiwork/dsharma/PDOSSilane/scfn/scfunopt' degauss = 0.0, Emin = -12.6653, Emax = 12, ngauss = 0, DeltaE = 0.01, filpdos = 'pdosout', and my script file is #!/bin/bash #PBS -N pdos #PBS -l nodes=4 ##PBS -1 waltime=24:00:00 #PBS -q walton #PBS -V ## #PATH of the parallel abinit executable export pw_path='/usr/local/espresso-4.0.5/bin' ### PATH to the mpirun binary: export mpirun_path='/opt/mpi/bin' export calc_name='pdos' ### go in the working directory: cd $PBS_O_WORKDIR ## Count the number of cpu requested NP=`wc -l $PBS_NODEFILE` echo $NP > $calc_name.txt $mpirun_path/mpirun -machinefile $PBS_NODEFILE -np $NP $pw_path/projwfc.x -npool1 < pdos > pdosout My scf output file is End of self-consistent calculation k = 0.0000 0.0000 0.0000 ( 6983 PWs) bands (ev): -12.6653 -9.5380 -7.2586 -6.0976 -5.0908 -3.8305 -0.6212 0.5917 0.8368 1.6400 k = 0.2500 0.0000 0.0000 ( 6959 PWs) bands (ev): -12.1861 -9.7498 -6.9945 -6.2237 -5.5081 -5.1444 0.3355 1.0465 1.4373 1.9502 k =-0.5000 0.0000 0.0000 ( 6966 PWs) bands (ev): -10.9343 -10.8970 -6.6489 -6.3817 -5.9690 -5.5686 0.3422 0.8657 1.1277 1.7350 highest occupied, lowest unoccupied level (ev): -3.8305 -0.6212 One more thing I want to ask, I have choosen the Emin and Emax value from the scf calculation, is this correct? suggestion welcome Thanks and regards Dimpy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091102/8364117d/attachment.htm From dimpy.sharma at tyndall.ie Mon Nov 2 20:04:11 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Mon, 2 Nov 2009 19:04:11 -0000 Subject: [Pw_forum] Calculating Projected density of states Message-ID: Hi QEs users, I have tried to calculate projected density of states first by performing scf calculation, then nscf calculation and then Projected density of states, but I am getting the following error. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 0 from projwfc : error # 4324 reading inputpp namelist %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% my pdos input file is &inputpp prefix = 'unoptimisedsilane', outdir = '/sfiwork/dsharma/PDOSSilane/scfn/scfunopt' degauss = 0.0, Emin = -12.6653, Emax = 12, ngauss = 0, DeltaE = 0.01, filpdos = 'pdosout', and my script file is #!/bin/bash #PBS -N pdos #PBS -l nodes=4 ##PBS -1 waltime=24:00:00 #PBS -q walton #PBS -V ## #PATH of the parallel abinit executable export pw_path='/usr/local/espresso-4.0.5/bin' ### PATH to the mpirun binary: export mpirun_path='/opt/mpi/bin' export calc_name='pdos' ### go in the working directory: cd $PBS_O_WORKDIR ## Count the number of cpu requested NP=`wc -l $PBS_NODEFILE` echo $NP > $calc_name.txt $mpirun_path/mpirun -machinefile $PBS_NODEFILE -np $NP $pw_path/projwfc.x -npool1 < pdos > pdosout My scf output file is End of self-consistent calculation k = 0.0000 0.0000 0.0000 ( 6983 PWs) bands (ev): -12.6653 -9.5380 -7.2586 -6.0976 -5.0908 -3.8305 -0.6212 0.5917 0.8368 1.6400 k = 0.2500 0.0000 0.0000 ( 6959 PWs) bands (ev): -12.1861 -9.7498 -6.9945 -6.2237 -5.5081 -5.1444 0.3355 1.0465 1.4373 1.9502 k =-0.5000 0.0000 0.0000 ( 6966 PWs) bands (ev): -10.9343 -10.8970 -6.6489 -6.3817 -5.9690 -5.5686 0.3422 0.8657 1.1277 1.7350 highest occupied, lowest unoccupied level (ev): -3.8305 -0.6212 One more thing I want to ask, I have choosen the Emin and Emax value from the scf calculation, is this correct? suggestion welcome Thanks and regards Dimpy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091102/ae9667d9/attachment-0001.htm From paulatto at sissa.it Mon Nov 2 20:06:18 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 2 Nov 2009 20:06:18 +0100 (CET) Subject: [Pw_forum] Calculating Projected density of states In-Reply-To: References: Message-ID: <33369.78.12.172.175.1257188778.squirrel@webmail.sissa.it> On Mon, November 2, 2009 20:04, Dimpy Sharma wrote: > reading inputpp namelist Dear Dimpy, you have to terminate with a "/". P.S. Keep Cool! We already got your email some time ago. -- 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 dimpy.sharma at tyndall.ie Mon Nov 2 20:10:14 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Mon, 2 Nov 2009 19:10:14 -0000 Subject: [Pw_forum] sorry for my repeated message as the mail keeps on bouncing continously. Message-ID: Hi QEss users, I apologis for my previous repeated eamils of mine as in my mail inbox it was showing me that the mail is bounched. I am sorry for this. Thanks Dimpy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091102/415f3f11/attachment.htm From tb283 at cornell.edu Tue Nov 3 00:21:15 2009 From: tb283 at cornell.edu (Turan Birol) Date: Mon, 2 Nov 2009 18:21:15 -0500 Subject: [Pw_forum] Calculation of specific irreps only Message-ID: <135f09040911021521j5ad074b1x632b694c0eb7f95@mail.gmail.com> Dear members of the pwscf community, I am calculating the phonon frequencies of Sr4 Ti3 O10 at gamma point. What I am interested in particular is a soft mode, which, unfortunately, is the hardest one to converge. So, I was wondering if it is possible to get the frequencies of only a group of phonons, without doing the whole calculation. The topic have been apparently briefly discussed in the forum in July 2006, but I believe the suggestion given there (use of modenum) is not suitable for my purpose. Instead I specified the relevant representations in the following way: &inputph tr2_ph=1.0d-16, prefix='Sr2TiO4', lnscf=.true., nrapp=2, / 0.0 0.0 0.0 5 6 in the input of ph.x. However, the code stops, after doing the calculation and achieving convergence for only the relevant modes as wished, saying: Stopping because representation 1 is not done and timing analysis follows. But the frequencies of these modes are not given. As I understand it, using the nrapp keyword as I have done it should be possible to calculate the frequencies of phonons belonging to specific representations, without having to calculate all the phonons at the given wave vector. Is this correct? If not, is it due to the way things are implemented, or is it not possible in DFPT, in which case I have to resort to frozen phonons? (I do not see a reason for the latter, as different irreps correspond to different types of distortions which -in principle- are decoupled; however, there are people in the list who know more about DFPT than me, for sure. :-) ) Thank you very much for your time. Regards, Turan Birol Phd student, Cornell University Department of Physics, USA From brad.malone at gmail.com Tue Nov 3 02:20:03 2009 From: brad.malone at gmail.com (Brad Malone) Date: Mon, 2 Nov 2009 17:20:03 -0800 Subject: [Pw_forum] fhi2upf.f90 and 'reasonable assumption' of nwfs=lmax_+1 Message-ID: Hi, I'm trying to convert a Ga pseudopotential from FHI to UPF format. The pseudopotential was generated from the following FHI input file: -------------------- 31.00 6 2 8 1.00 : z nc nv iexc rnlc 1 0 2.00 : n l f 2 0 2.00 2 1 6.00 3 0 2.00 3 1 6.00 3 2 10.00 4 0 2.00 4 1 1.00 2 t : lmax s_pp_def 2 0.00 5.00 t : lt rct et s_pp_type -------------------- I'm keeping the 3d states in the core, but treating it with a NLCC. Anyway, when I try to convert this file it asks me to specify the wavefunctions and occupancies. So I typed in Wavefunction # 1: label, occupancy > 4S,2 Wavefunction # 2: label, occupancy > 4P,1 However, the code asks for one more wavefunction, under the 'reasonable assumption' that nwfs = lmax_+1 (see below from fhi2upf.f90) > ! reasonable assumption > rel = 1 > rcloc = 0.0d0 > nwfs = lmax_+1 <---- > I imagine I'm missing something here, but why is this a reasonable assumption? Is not reasonable for me to pseudize only the valence 4s and 4p states in Gallium? Being unafraid of being called unreasonable, I changed this line to be "nwfs=lmax_" and entered in only my 4s and 4p wavefunctions (treating l=0 as the local component) and my pseudopotential was then generated "successfully". I then tried out this pseudopotential along with an As one that I also generated with FHI (and similarly hacked fhi2upf.f90 to convert it) on a GaAs system and received the following error: > from read_pseudo_nl : error # 1 > Reading pseudo file (BETA) > from read_pseudo_nl : error # 1 > Reading pseudo file (BETA) > So it looks like something isn't working out here, and I wonder if it's this 'reasonable assumption' that I don't understand. Thanks in advance for any feedback or advice on this. Best, Brad Malone UC Berkeley -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091102/d6c591e8/attachment.htm From bipulrr at gmail.com Tue Nov 3 05:43:11 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Tue, 3 Nov 2009 10:13:11 +0530 Subject: [Pw_forum] Particular Phonon mode Message-ID: <3a749910911022043u17b013efnb5e02272e5e994f3@mail.gmail.com> Dear PWscf users, I am doing gamma Phonon calculation on LaMnO3. Since the unit cell contain 20 atoms, so at gamma i am getting 60 frequencies (3 acoustic modes ~ 0) If I am just interested in just the first three frequencies ( the acoustic modes), what changes i have to made in the input file. phonons of LaMnO3-pero &inputph tr2_ph=1.0d-10, alpha_mix(1)= 0.7, prefix='lamno3', ! epsil=.true., ! ldisp=.true., ! nq1=2, nq2=2, nq3=2 ! iq1=6, iq2=6, iq3=6 ! lnscf= .true. amass(1)= 138.9055, amass(2)=54.938049, amass(3)=15.9994, outdir = './OUT', fildyn='LaMnO3.dynG', / 0.0 0.0 0.0 -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091103/4174389b/attachment.htm From kajalmh18 at gmail.com Tue Nov 3 07:55:23 2009 From: kajalmh18 at gmail.com (kajal jindal) Date: Tue, 3 Nov 2009 12:25:23 +0530 Subject: [Pw_forum] magnetization value Message-ID: Hi, I am studying spin polarized DFT with GGA for exchange and correlation..I am aware that i can get to know the total magnetic moment for my structure..but i want to know how can i get the magnetic moment on each atom and the contribution from the corresponding orbitals? sincerely, Miss Kajal (UTA)(University of Delhi) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091103/2c96e977/attachment.htm From jibiaoli at gmail.com Tue Nov 3 08:08:20 2009 From: jibiaoli at gmail.com (Clark Lee) Date: Tue, 3 Nov 2009 08:08:20 +0100 Subject: [Pw_forum] Problem in Calculating Projected density of states In-Reply-To: References: Message-ID: Do you mean Fermi level?, if so then Ef from your nscf calculation could be better. On Mon, Nov 2, 2009 at 7:56 PM, Dimpy Sharma wrote: > > One more thing I want to ask, I have choosen the Emin and Emax value from > the scf calculation, is this correct? > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091103/66065675/attachment.htm From madhura at jncasr.ac.in Tue Nov 3 08:07:22 2009 From: madhura at jncasr.ac.in (Madhura Marathe) Date: Tue, 3 Nov 2009 12:37:22 +0530 (IST) Subject: [Pw_forum] magnetization value In-Reply-To: References: Message-ID: <56446.172.16.1.1.1257232042.squirrel@172.16.1.1> Dear Kajal, What you need is projected density of states (projwfc.x) calculations. Have a look at Doc/INPUT_PROJWFC.* in the documentation of espresso package. Regards, Madhura. > Hi, > > I am studying spin polarized DFT with GGA for exchange and correlation..I > am > aware that i can get to know the total magnetic moment for my > structure..but > i want to know how can i get the magnetic moment on each atom and the > contribution from the corresponding orbitals? > > sincerely, > Miss Kajal > (UTA)(University of Delhi) > _______________________________________________ > 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 sclauzer at sissa.it Tue Nov 3 09:21:49 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 3 Nov 2009 09:21:49 +0100 Subject: [Pw_forum] magnetization value In-Reply-To: References: Message-ID: <20091103092149.vgf8jm8dhcwocok0@webmail.sissa.it> Dear Kajal Quoting kajal jindal : > Hi, > > I am studying spin polarized DFT with GGA for exchange and correlation..I am > aware that i can get to know the total magnetic moment for my structure..but > i want to know how can i get the magnetic moment on each atom and the I suppose that you are already awaew that in a planewaves code there is no clear definition of the "borders" between atoms in a solid. Anyway you can try to define, for instance, atomic charges by projecting onto atomic orbitals or integrating the charge density within spheres centered on nuclei, or whatever. The projwfc.x postprocessing utility uses atomic orbitals to estimate atomic occupations in the solid, but as far as I know cannot compute atomic magnetization. Anyway you can try to extend the code (sources in PP/) to meet your needs. Another solution would be to perform a non-collinear calculation (but it can be much more expensive...): in fact, in the noncollinear case the code determines in some way to which atom belongs each point in the real space grid. This method is used to compute atomic charges and atomic magnetic moments. Maybe you can use those subroutines to compute the same thing in the collinear case (again, this will require some coding from your side...). > contribution from the corresponding orbitals? This is maybe trickier to obtain: as I said above, you should try to extend the projwfc.x code. HTH GS > > sincerely, > Miss Kajal > (UTA)(University of Delhi) > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From sclauzer at sissa.it Tue Nov 3 09:40:12 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 3 Nov 2009 09:40:12 +0100 Subject: [Pw_forum] LDA+U problem on Mac In-Reply-To: <4AEE592F.6040804@spring8.or.jp> References: <4AEE592F.6040804@spring8.or.jp> Message-ID: <20091103094012.y0a5n4brgg4kkwc0@webmail.sissa.it> Dear Mattia, Quoting Mulazzi Mattia : > Dear Gabriele, > > thank you for the prompt reply. Here are my comments: > >> I don't understand a thing: starting_ns_eigenvalue is used only on >> the species on which >> you put +U (i.e. Hubbard_U(?)>0), so if you cannot not use LDA+U >> for V with your QE >> installation, how could you say that using starting_ns_eigenvalue >> does not change the >> result? > > I thought that the starting_ns_eigenvalue function might have worked > also without the LDA+U being set to true. This is not the case. > So I tried, but the result was the same as doing a calculation > without setting the occupations. If lda_plus_u=.FALSE., then this is the case. Even if you enable LDA+U, it is not granted that changing starting_ns_eigenvalue will do anything. This feature is needed to gently push the calculation to the LDA+U ground state when it is very distant to the plain LDA one. However, it is not granted that the LDA+U ground state will correspond to the atomic orbitals occupations that you have in mind. > >> One other important point is that occupations are symmetrized >> according to the symmetry >of the system. So that, perhaps, >> retrying after breaking some symmetry or using >nosym=.TRUE. may >> change something. > > I will try to use nosym=.true., but then, I guess, I cannot use the > automatice generation of the k-points and I have to supply to the > input file a list of k-points covering the whole non-irreducible > Brilluoin zone. Am I right? I think that you can still use the automatic generation of k-points. Simply they will not be reduced by symmetry and the calculation will be longer. Anyway, you may not actually need to use nosym, if the supercell with two V types has already low enough symmetry to break the degeneracy of states that you want to occupy with different weights. > >> Which version of QE are you using? Please check if the Vanadium >> case has already been >inserted in tabd.f90 and set_hubbard_l.f90 >> files. >> If not pw.x should stop with an error message like "pseudopotential >> not yet inserted" >> before causing any segmentation fault. From version 4.1 on, LDA+U >> should be working >with any of the transition metal elements. If >> you have previous versions, you can >easily get it working >> modifying those two files. > > I am using the 4.0.5 version of QE. I tried to use the 4.1.1 (since > it now suports the LDA+U for all the transition metals as well as > for the rare earths), but it does not compile on my Mac, even using > the same configuration parameters that I used for the compilation > of the 4.0.5 version. So for now, I gave up. Why does it not compile? The two versions are not much different. Try to address this issue (in a separate thread), maybe other Mac users have this problem. I will try ASAP to compile on Mac. You need also to specify which compiler, which libraries, error messages,... > About the LDA+U, I did more testing on it both on my PC (using > cygwin under WinXP) and on the Mac. The cygwin compilation > recognises without problems the V pseudopotential included in the QE > library. The same calculations done on the Mac require first a > small modification of the tabd.f90 file. Not only! As I said also set_hubbard_l.f90 needs to be modified accordingly. For the moment, you can take those two files from 4.1.1 and put in 4.0.5 version (and recompile). They should work. After doing that (and recompiling > pw), no more "pseudopotential not yet inserted" message. However, > using on the Mac the same input file that I use on the PC gives the > bloody "segmentation fault". However, I found out that the > segmentation fault error only appears when I use one Vanadium atom > per unit cell and if I label it "V" in the ATOMIC_SPECIES name card. > In this case just fixing lda_plus_u to true triggers the > segmentation fault, even if the Hubbard_U is on another atom. > If I do a calculation in a larger cell with two Vanadium atoms > labelled V1 and V2 (pointing to the same pseudopotential file) then > I see no segmentation fault. OK, I think that there was a problem with atomic labels made by one single character; it should be fixed in 4.1.x. Retry using V1 in place of V even if you have only one Vanadium type, it should work. > If I use a fictitious alloy system (say MnV or FeV in a symple cubic > cell with the V atom at the 0.5 0.5 0.5 position), then I see no > segmentation fault even if I label the Vanadium as "V". But if I > want to calculate my system, VS2, then I have the segmentation > fault. If I put a second V in the calculation and I use two labels > (again V1 and V2) then no problem. This is strange. Anyway keep in mind that the problem shows up only if you put the +U on the single-character named species. > I thought it was a problem of the xc functional, but it seems it > doesn't, using either PZ- or PBE-generated (ultrasoft) > pseudopotentials does not solve the problem. I tried to generate the > norm-conserving pseudopotentials using the ld1.x program, but PW > does not recognise the pseudopotentials. I think that this last > problem is related to a naming problem that Dr. de Gironcoli was > explaining in the pw forum archives. I don't think it can be solved > without editind the code itself. Yes it is not a problem of the PP. If you still have problems, after replacing those two files of above, or using V1 in place of V, please report it. HTH GS > > Did any other user report on such or similar "segmentation fault" problems? PS: After all, I'm still a bit surprised that this problem I mentioned shows up as a segmentaion fault. Maybe it is something else... > >> Please report to us if the problem persists in v4.1 and if it is >> reproducible. > >> Thanks, > >> GS > > Thank you very much, > > Mattia Mulazzi > > FPR Fellow of RIKEN at Spring8 > Excitation Order Research Team > 1-1-1 Sayo-cho Sayo-gun, Hyogo > Japan > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From bipulrr at gmail.com Tue Nov 3 11:38:19 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Tue, 3 Nov 2009 16:08:19 +0530 Subject: [Pw_forum] fixing the angle. In-Reply-To: <39331.78.12.172.175.1257153918.squirrel@webmail.sissa.it> References: <3a749910911020015x5edbd69fubfd4d246076bb1e4@mail.gmail.com> <55897.78.12.172.175.1257150771.squirrel@webmail.sissa.it> <3a749910911020113x44c2c593v27ddd78bf2707841@mail.gmail.com> <39331.78.12.172.175.1257153918.squirrel@webmail.sissa.it> Message-ID: <3a749910911030238w40b72343tcf95e3af31176b7a@mail.gmail.com> Dear Lorenzo Paulatto and pwscf users using vc-relax, i am doing simple LaSb (NaCl structure) with some lattice parameter and lattice vectors (CELL_PARAMETERS) 0.0 0.5 0.5 0.5 0.0 0.5 0.5 0.5 0.0 but after the relaxation it converts to 0.0 0.4999999 0.499999 0.4999999 0.00 0.4999999 0.4999999 0.4999999 0.0 Although the change is very small, and when i draw the structure the angle deviate from 60 to 59.999 degree So if I just want to fix the angle exactly in 60 degree only or want to the exact CELL_PARAMETERS as input, then how can i use the constraints flags? Or is there some other option? Actually there is no such documentation for using constraints. please guide me in this reference. On Mon, Nov 2, 2009 at 2:55 PM, Lorenzo Paulatto wrote: > > On Mon, November 2, 2009 10:13, Bipul Rakshit wrote: > > I saw the Doc/INPUT_PW.txt file, there is a flag called CARD: > CONSTRAINTS > > in which there is 'planar_angle' and 'torsional_angle', but it will be > > more helpful if you send me one input file for constraining the angle. > > I don't have any. > > > Actually after running vc-relax with the input file which i send to you, > > the CELL_PARAMETER changes, that means angle also changing.... > > Of course, if you squeeze the cell along one direction the structure will > deform accordingly. If you want to rescale the whole structure maintaining > all the angles constant you have to change ONLY celldm(1). There is no > automatic way to do it, the cell_dofree input parameter can constrain cell > deformation but not in this way. > > > I draw the output file with xcrysden and find the angles (Si-O-Si) > > changes. > > Yes, I understand what's going on. But what's wrong with it changing in > the first place? > > > So if possible just send me some input file for constraining the angles. > > I don't have a secret library of input files... > > best 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 > -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091103/164472fc/attachment.htm From paulatto at sissa.it Tue Nov 3 11:50:58 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 3 Nov 2009 11:50:58 +0100 (CET) Subject: [Pw_forum] fixing the angle. In-Reply-To: <3a749910911030238w40b72343tcf95e3af31176b7a@mail.gmail.com> References: <3a749910911020015x5edbd69fubfd4d246076bb1e4@mail.gmail.com> <55897.78.12.172.175.1257150771.squirrel@webmail.sissa.it> <3a749910911020113x44c2c593v27ddd78bf2707841@mail.gmail.com> <39331.78.12.172.175.1257153918.squirrel@webmail.sissa.it> <3a749910911030238w40b72343tcf95e3af31176b7a@mail.gmail.com> Message-ID: <48998.78.12.172.175.1257245458.squirrel@webmail.sissa.it> On Tue, November 3, 2009 11:38, Bipul Rakshit wrote: > but after the relaxation > it converts to > 0.0 0.4999999 0.499999 > 0.4999999 0.00 0.4999999 > 0.4999999 0.4999999 0.0 > ... the angle > deviate from 60 to 59.999 degree It does not, at least not in the output configuration you have printed above. If you notice, what's happened is that the cell basis vectors have rescaled of the same amount, they have just shrink all together. If, from the data above, you have measured a change in the cell angles you have to buy a new pocket calculator. > So if I just want to fix the angle exactly in 60 degree only or want to > the exact CELL_PARAMETERS as input, then how can i use the constraints > flags? No, constrains are used for inter-atomic angles, not for the cell. > Or is there some other option? Yes, there is one. It does not work with bfgs, but you are using damp-w so it should not be a problem. It is called cell_dofree, you will find the documentation in the input format manual. > Actually there is no such documentation for using constraints. > please guide me in this reference. It is in the input format manual: Doc/INPUT_PW.txt or Doc/INPUT_PW.html, it is toward the end of the file, you will have to scroll down a bit. best 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 siyouber at yahoo.fr Tue Nov 3 14:25:07 2009 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Tue, 3 Nov 2009 13:25:07 +0000 (GMT) Subject: [Pw_forum] Pair correlation function Message-ID: <23090.34363.qm@web26505.mail.ukl.yahoo.com> Dear all, I posted a message on how to get pair correlation functions from QE outputs.? I got some solutions but until now the problem is not solved. I search the web and got some fortran code, but none of them is able to do it(may be because I am not quite an expert). Please could somebody help me with a code to extract the pair correlation functions? Another problem is how to visualize the trajectory of a dynamic from CP.x with Xcrysden? Thanks very much for your help ******************************** Bertrand SITAMTZE YOUMBI Laboratory of Material Sciences Department of Physics University of Yaound? I-Cameroon PO Box 812 Yaound? ************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091103/727b4469/attachment.htm From zucco at dipteris.unige.it Tue Nov 3 16:05:10 2009 From: zucco at dipteris.unige.it (Marino Vetuschi Zuccolini) Date: Tue, 3 Nov 2009 16:05:10 +0100 Subject: [Pw_forum] LDA+U problem on Mac In-Reply-To: <20091103094012.y0a5n4brgg4kkwc0@webmail.sissa.it> References: <4AEE592F.6040804@spring8.or.jp> <20091103094012.y0a5n4brgg4kkwc0@webmail.sissa.it> Message-ID: <71B892F2-E273-4021-8AAD-0F2FED747983@dipteris.unige.it> Hello to all, I think that part of the problem in QE compilation on Mac (Snow Leopard 10.6 using gfortran-4.0 in serial) can be related to what enlightened by Giannozzi in his email of the Oct 25 suggesting this *** in include/c_defs.h, there should be two lines (produced by "configure") that look like #define F77_FUNC(name,NAME) name ## _ #define F77_FUNC_(name,NAME) name ## _ *** Writing this two lines of c_defs.h solved the problem for me. m. On 3 Nov 2009, at 9:40, Gabriele Sclauzero wrote: > Dear Mattia, > > Quoting Mulazzi Mattia : > >> Dear Gabriele, >> >> thank you for the prompt reply. Here are my comments: >> >>> I don't understand a thing: starting_ns_eigenvalue is used only on >>> the species on which >>> you put +U (i.e. Hubbard_U(?)>0), so if you cannot not use LDA+U >>> for V with your QE >>> installation, how could you say that using starting_ns_eigenvalue >>> does not change the >>> result? >> >> I thought that the starting_ns_eigenvalue function might have worked >> also without the LDA+U being set to true. > > This is not the case. > >> So I tried, but the result was the same as doing a calculation >> without setting the occupations. > > If lda_plus_u=.FALSE., then this is the case. Even if you enable > LDA+U, it is not granted that changing starting_ns_eigenvalue will do > anything. This feature is needed to gently push the calculation to > the LDA+U ground state when it is very distant to the plain LDA one. > However, it is not granted that the LDA+U ground state will correspond > to the atomic orbitals occupations that you have in mind. > >> >>> One other important point is that occupations are symmetrized >>> according to the symmetry >of the system. So that, perhaps, >>> retrying after breaking some symmetry or using >nosym=.TRUE. may >>> change something. >> >> I will try to use nosym=.true., but then, I guess, I cannot use the >> automatice generation of the k-points and I have to supply to the >> input file a list of k-points covering the whole non-irreducible >> Brilluoin zone. Am I right? > > I think that you can still use the automatic generation of k-points. > Simply they will not be reduced by symmetry and the calculation will > be longer. Anyway, you may not actually need to use nosym, if the > supercell with two V types has already low enough symmetry to break > the degeneracy of states that you want to occupy with different > weights. > >> >>> Which version of QE are you using? Please check if the Vanadium >>> case has already been >inserted in tabd.f90 and set_hubbard_l.f90 >>> files. >>> If not pw.x should stop with an error message like "pseudopotential >>> not yet inserted" >>> before causing any segmentation fault. From version 4.1 on, LDA+U >>> should be working >with any of the transition metal elements. If >>> you have previous versions, you can >easily get it working >>> modifying those two files. >> >> I am using the 4.0.5 version of QE. I tried to use the 4.1.1 (since >> it now suports the LDA+U for all the transition metals as well as >> for the rare earths), but it does not compile on my Mac, even using >> the same configuration parameters that I used for the compilation >> of the 4.0.5 version. So for now, I gave up. > > Why does it not compile? The two versions are not much different. Try > to address this issue (in a separate thread), maybe other Mac users > have this problem. I will try ASAP to compile on Mac. You need also to > specify which compiler, which libraries, error messages,... > >> About the LDA+U, I did more testing on it both on my PC (using >> cygwin under WinXP) and on the Mac. The cygwin compilation >> recognises without problems the V pseudopotential included in the QE >> library. The same calculations done on the Mac require first a >> small modification of the tabd.f90 file. > > Not only! As I said also set_hubbard_l.f90 needs to be modified > accordingly. For the moment, you can take those two files from 4.1.1 > and put in 4.0.5 version (and recompile). They should work. > > > After doing that (and recompiling >> pw), no more "pseudopotential not yet inserted" message. However, >> using on the Mac the same input file that I use on the PC gives the >> bloody "segmentation fault". However, I found out that the >> segmentation fault error only appears when I use one Vanadium atom >> per unit cell and if I label it "V" in the ATOMIC_SPECIES name card. >> In this case just fixing lda_plus_u to true triggers the >> segmentation fault, even if the Hubbard_U is on another atom. >> If I do a calculation in a larger cell with two Vanadium atoms >> labelled V1 and V2 (pointing to the same pseudopotential file) then >> I see no segmentation fault. > > > OK, I think that there was a problem with atomic labels made by one > single character; it should be fixed in 4.1.x. Retry using V1 in place > of V even if you have only one Vanadium type, it should work. > >> If I use a fictitious alloy system (say MnV or FeV in a symple cubic >> cell with the V atom at the 0.5 0.5 0.5 position), then I see no >> segmentation fault even if I label the Vanadium as "V". But if I >> want to calculate my system, VS2, then I have the segmentation >> fault. If I put a second V in the calculation and I use two labels >> (again V1 and V2) then no problem. > > This is strange. Anyway keep in mind that the problem shows up only if > you put the +U on the single-character named species. > >> I thought it was a problem of the xc functional, but it seems it >> doesn't, using either PZ- or PBE-generated (ultrasoft) >> pseudopotentials does not solve the problem. I tried to generate the >> norm-conserving pseudopotentials using the ld1.x program, but PW >> does not recognise the pseudopotentials. I think that this last >> problem is related to a naming problem that Dr. de Gironcoli was >> explaining in the pw forum archives. I don't think it can be solved >> without editind the code itself. > > Yes it is not a problem of the PP. If you still have problems, after > replacing those two files of above, or using V1 in place of V, please > report it. > > > HTH > > GS > > >> >> Did any other user report on such or similar "segmentation fault" >> problems? > > > PS: After all, I'm still a bit surprised that this problem I mentioned > shows up as a segmentaion fault. Maybe it is something else... > >> >>> Please report to us if the problem persists in v4.1 and if it is >>> reproducible. >> >>> Thanks, >> >>> GS >> >> Thank you very much, >> >> Mattia Mulazzi >> >> FPR Fellow of RIKEN at Spring8 >> Excitation Order Research Team >> 1-1-1 Sayo-cho Sayo-gun, Hyogo >> Japan >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by Horde http://www.horde.org/ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ******************************************************* Marino Vetuschi Zuccolini zucco at dipteris.unige.it Researcher / Geochemist Laboratory of Geochemistry DIPartimento per lo studio della TErra e delle sue RISorse - Universit? di Genova Tel. ++39 010 3538136 Fax. ++39 010 352169 Corso Europa 26, 16132 - Genova - Italy From dimpy.sharma at tyndall.ie Tue Nov 3 20:04:17 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Tue, 3 Nov 2009 19:04:17 -0000 Subject: [Pw_forum] scf stops after finishing 100 iteration Message-ID: Hi Quantum espresso users, I tired to perform scf calculation but it shows me the following error 'convergence NOT achieved after 100 iterations: stopping' However the nscf calculation and projected density of states run successfully, why is this so? My input file is as follows &CONTROL calculation ='scf' restart_mode = 'from_scratch' outdir = '/sfiwork/dsharma/PDOSSilane/PDOSsi/si_wfc' pseudo_dir = '/sfiwork/dsharma/QE_Pseudos/' prefix = 'si' tstress = .true. tprnfor = .true. etot_conv_thr = 1.D-4 forc_conv_thr = 1.D-3 nstep = 600 wf_collect =.true. / &SYSTEM ibrav = 0 celldm(1) =7.4088 nat = 6 ntyp = 1 ecutwfc = 40 ecutrho = 160.0 nbnd = 12 / &ELECTRONS diagonalization ='david' mixing_mode = 'plain' conv_thr = 1.0d-6 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 ATOMIC_POSITIONS angstroms Si 2.95020 -0.66592 -0.12341 Si 4.90939 0.61749 0.11358 Si 0.99475 0.65272 -0.16138 Si -0.98472 -0.62740 -0.15123 Si -2.94624 0.68229 -0.12124 Si -4.89549 -0.61534 0.11905 K_POINTS automatic 4 1 1 0 0 0 Can anybody give me any suggestions? Thanks Dimpy Dimpy Sharma, PhD Electronics Theory Group UCC,Cork Ireland -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091103/cab30b1f/attachment.htm From degironc at sissa.it Tue Nov 3 22:05:42 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 03 Nov 2009 22:05:42 +0100 Subject: [Pw_forum] scf stops after finishing 100 iteration In-Reply-To: References: Message-ID: <4AF09B26.4020300@sissa.it> have you verified that your crystal structure is reasonable using a visualizer like xcrysden or similar ? it appears to me that a couple of atoms are very very close to each other. stefano Dimpy Sharma wrote: > > Hi Quantum espresso users, > > I tired to perform scf calculation but it shows me the following error > 'convergence NOT achieved after 100 iterations: stopping' > > However the nscf calculation and projected density of states run > successfully, why is this so? > > My input file is as follows > > &CONTROL > calculation ='scf' > restart_mode = 'from_scratch' > outdir = '/sfiwork/dsharma/PDOSSilane/PDOSsi/si_wfc' > pseudo_dir = '/sfiwork/dsharma/QE_Pseudos/' > prefix = 'si' > tstress = .true. > tprnfor = .true. > etot_conv_thr = 1.D-4 > forc_conv_thr = 1.D-3 > nstep = 600 > wf_collect =.true. > / > &SYSTEM > ibrav = 0 > celldm(1) =7.4088 > nat = 6 > ntyp = 1 > ecutwfc = 40 > ecutrho = 160.0 > nbnd = 12 > / > &ELECTRONS > diagonalization ='david' > mixing_mode = 'plain' > conv_thr = 1.0d-6 > 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 > ATOMIC_POSITIONS angstroms > Si 2.95020 -0.66592 -0.12341 > Si 4.90939 0.61749 0.11358 > Si 0.99475 0.65272 -0.16138 > Si -0.98472 -0.62740 -0.15123 > Si -2.94624 0.68229 -0.12124 > Si -4.89549 -0.61534 0.11905 > K_POINTS automatic > 4 1 1 0 0 0 > > Can anybody give me any suggestions? > > Thanks > > Dimpy > > Dimpy Sharma, > PhD > Electronics Theory Group > UCC,Cork > Ireland > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From mulazzi at spring8.or.jp Wed Nov 4 04:04:55 2009 From: mulazzi at spring8.or.jp (Mulazzi Mattia) Date: Wed, 4 Nov 2009 12:04:55 +0900 Subject: [Pw_forum] LDA+U problem on Mac In-Reply-To: References: Message-ID: <94EA28A8-3EA3-4BD4-9243-15875A4EB064@spring8.or.jp> Dear Gabriele, >>> One other important point is that occupations are symmetrized >>> according to the symmetry >of the system. So that, perhaps, >>> retrying after breaking some symmetry or using >nosym=.TRUE. may >>> change something. >> >> I will try to use nosym=.true., but then, I guess, I cannot use the >> automatic generation of the k-points and I have to supply to the >> input file a list of k-points covering the whole non-irreducible >> Brillouin zone. Am I right? > > I think that you can still use the automatic generation of k-points. > Simply they will not be reduced by symmetry and the calculation will > be longer. Anyway, you may not actually need to use nosym, if the > supercell with two V types has already low enough symmetry to break > the degeneracy of states that you want to occupy with different > weights. I am trying a calculation with nosym=.true. and the automatic k-point generation. I will then use project_wf.x to actually get the atomic- and orbitally-projected density of the states as a function of energy. That would be a good way to check the orbital order in my system. >>> Which version of QE are you using? Please check if the Vanadium >>> case has already been >inserted in tabd.f90 and set_hubbard_l.f90 >>> files. >>> If not pw.x should stop with an error message like "pseudopotential >>> not yet inserted" >>> before causing any segmentation fault. From version 4.1 on, LDA+U >>> should be working >with any of the transition metal elements. If >>> you have previous versions, you can >easily get it working >>> modifying those two files. >> >> I am using the 4.0.5 version of QE. I tried to use the 4.1.1 (since >> it now suports the LDA+U for all the transition metals as well as >> for the rare earths), but it does not compile on my Mac, even using >> the same configuration parameters that I used for the compilation >> of the 4.0.5 version. So for now, I gave up. > > Why does it not compile? The two versions are not much different. Try > to address this issue (in a separate thread), maybe other Mac users > have this problem. I will try ASAP to compile on Mac. You need also to > specify which compiler, which libraries, error messages,... Briefly, there are errors on something called 'iotk', not much more info. I am soon posting new info about it. >> About the LDA+U, I did more testing on it both on my PC (using >> cygwin under WinXP) and on the Mac. The cygwin compilation >> recognises without problems the V pseudopotential included in the QE >> library. The same calculations done on the Mac require first a >> small modification of the tabd.f90 file. > > Not only! As I said also set_hubbard_l.f90 needs to be modified > accordingly. For the moment, you can take those two files from 4.1.1 > and put in 4.0.5 version (and recompile). They should work. I did not need to modify the set_hubbard_l.f90 file to have the LDA+U running, but just the tab_d.f90. > After doing that (and recompiling >> pw), no more "pseudopotential not yet inserted" message. However, >> using on the Mac the same input file that I use on the PC gives the >> bloody "segmentation fault". However, I found out that the >> segmentation fault error only appears when I use one Vanadium atom >> per unit cell and if I label it "V" in the ATOMIC_SPECIES name card. >> In this case just fixing lda_plus_u to true triggers the >> segmentation fault, even if the Hubbard_U is on another atom. >> If I do a calculation in a larger cell with two Vanadium atoms >> labelled V1 and V2 (pointing to the same pseudopotential file) then >> I see no segmentation fault. > > > OK, I think that there was a problem with atomic labels made by one > single character; it should be fixed in 4.1.x. Retry using V1 in place > of V even if you have only one Vanadium type, it should work. > >> If I use a fictitious alloy system (say MnV or FeV in a symple cubic >> cell with the V atom at the 0.5 0.5 0.5 position), then I see no >> segmentation fault even if I label the Vanadium as "V". But if I >> want to calculate my system, VS2, then I have the segmentation >> fault. If I put a second V in the calculation and I use two labels >> (again V1 and V2) then no problem. > > This is strange. Anyway keep in mind that the problem shows up only if > you put the +U on the single-character named species. I checked and there is also a segmentation fault when I use the MnS2 system, and for it also when I do a calculation with one Mn atom per cell there is a segmentation fault. On the other hand a calculation with two Mn atoms, Mn1 and Mn2, does not give a segmentation fault. So the problem is not in the atomic pseudopotential naming. >> I thought it was a problem of the xc functional, but it seems it >> doesn't, using either PZ- or PBE-generated (ultrasoft) >> pseudopotentials does not solve the problem. I tried to generate the >> norm-conserving pseudopotentials using the ld1.x program, but PW >> does not recognise the pseudopotentials. I think that this last >> problem is related to a naming problem that Dr. de Gironcoli was >> explaining in the pw forum archives. I don't think it can be solved >> without editind the code itself. > > Yes it is not a problem of the PP. If you still have problems, after > replacing those two files of above, or using V1 in place of V, please > report it. I did a test after changing from V.pbe-n-van.UPF to V1.pbe-n-van.UPF, but I still have the segmentation fault. > HTH > > GS > PS: After all, I'm still a bit surprised that this problem I mentioned > shows up as a segmentaion fault. Maybe it is something else... At first I thought about a compiler bug (as suggested in the QE troubleshooting pages), but it is quite unlikely it is the case. Why should the compiler be buggy only with a one atom per cell system. Mattia FPR Fellow of RIKEN at Spring8 Excitation Order Research Team 1-1-1 Sayo-cho Sayo-gun, Hyogo Japan From wanghui.jilin at gmail.com Wed Nov 4 04:20:58 2009 From: wanghui.jilin at gmail.com (Hui Wang) Date: Wed, 4 Nov 2009 11:20:58 +0800 Subject: [Pw_forum] [Help] I need a NC pseudopotential (PBE) of Ca with 10 valence electrons Message-ID: <66c76c8e0911031920p71d6adb4k58c9d77254e94723@mail.gmail.com> Dear all, I need a NC pseudopotential (PBE) of Ca with 10 valence electrons, nl pn l occ 3S 3 0 2.00 3P 3 1 6.00 4S 4 0 2.00 3D 3 2 0.00 Could some one help me ? *************************************** Hui Wang PhD State Key Lab of Superhard Materials, Jilin University 2699 Qianjin Str. 130012, Changchun P. R. China Email: *wanghui.jilin at gmail.com* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091104/05112226/attachment.htm From mulazzi at spring8.or.jp Wed Nov 4 05:03:26 2009 From: mulazzi at spring8.or.jp (Mulazzi Mattia) Date: Wed, 4 Nov 2009 13:03:26 +0900 Subject: [Pw_forum] Qe 4.1 compilation problem on Mac solved In-Reply-To: References: Message-ID: Dear Marco, I am using a OS 10.5.6 Mac, no Snow Leopard and the compiler is g95. Today I tried again a compilation of QE 4.1 and it seems it works using different parameters for the configure script(basically compiling as serial). Thanks for the help, Mattia > Message: 6 > Date: Tue, 3 Nov 2009 16:05:10 +0100 > From: Marino Vetuschi Zuccolini > Subject: Re: [Pw_forum] LDA+U problem on Mac > To: PWSCF Forum > Message-ID: <71B892F2-E273-4021-8AAD-0F2FED747983 at dipteris.unige.it> > Content-Type: text/plain; charset=iso-8859-1; format=flowed; delsp=yes > > Hello to all, > > I think that part of the problem in QE compilation on Mac (Snow > Leopard 10.6 using gfortran-4.0 in serial) can be related to what > enlightened by Giannozzi in his email of the Oct 25 suggesting this > > *** > in include/c_defs.h, there should be two lines (produced by > "configure") > that look like > #define F77_FUNC(name,NAME) name ## _ > #define F77_FUNC_(name,NAME) name ## _ > *** > > Writing this two lines of c_defs.h solved the problem for me. > > m. From brad.malone at gmail.com Wed Nov 4 06:26:06 2009 From: brad.malone at gmail.com (Brad Malone) Date: Tue, 3 Nov 2009 21:26:06 -0800 Subject: [Pw_forum] fhi2upf.f90 and 'reasonable assumption' of nwfs=lmax_+1 In-Reply-To: References: Message-ID: The solution seems to be to simply specify the higher states with zero occupancy, in this case 4D,0 The pseudopotentials converted in this way seem to work fine. Best, Brad On Mon, Nov 2, 2009 at 5:20 PM, Brad Malone wrote: > Hi, I'm trying to convert a Ga pseudopotential from FHI to UPF format. The > pseudopotential was generated from the following FHI input file: > -------------------- > 31.00 6 2 8 1.00 : z nc nv iexc rnlc > 1 0 2.00 : n l f > 2 0 2.00 > 2 1 6.00 > 3 0 2.00 > 3 1 6.00 > 3 2 10.00 > 4 0 2.00 > 4 1 1.00 > 2 t : lmax s_pp_def > 2 0.00 5.00 t : lt rct et s_pp_type > -------------------- > > I'm keeping the 3d states in the core, but treating it with a NLCC. Anyway, > when I try to convert this file it asks me to specify the wavefunctions and > occupancies. So I typed in > > Wavefunction # 1: label, occupancy > 4S,2 > Wavefunction # 2: label, occupancy > 4P,1 > > However, the code asks for one more wavefunction, under the 'reasonable > assumption' that nwfs = lmax_+1 (see below from fhi2upf.f90) > >> ! reasonable assumption >> rel = 1 >> rcloc = 0.0d0 >> nwfs = lmax_+1 <---- >> > > I imagine I'm missing something here, but why is this a reasonable > assumption? Is not reasonable for me to pseudize only the valence 4s and 4p > states in Gallium? Being unafraid of being called unreasonable, I changed > this line to be "nwfs=lmax_" and entered in only my 4s and 4p wavefunctions > (treating l=0 as the local component) and my pseudopotential was then > generated "successfully". I then tried out this pseudopotential along with > an As one that I also generated with FHI (and similarly hacked fhi2upf.f90 > to convert it) on a GaAs system and received the following error: > >> from read_pseudo_nl : error # 1 >> Reading pseudo file (BETA) >> from read_pseudo_nl : error # 1 >> Reading pseudo file (BETA) >> > > So it looks like something isn't working out here, and I wonder if it's > this 'reasonable assumption' that I don't understand. Thanks in advance for > any feedback or advice on this. > > Best, > Brad Malone > UC Berkeley > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091103/462d9a63/attachment-0001.htm From kajalmh18 at gmail.com Wed Nov 4 06:50:59 2009 From: kajalmh18 at gmail.com (kajal jindal) Date: Wed, 4 Nov 2009 11:20:59 +0530 Subject: [Pw_forum] magnetic interaction Message-ID: Hi, I am trying to study the magnetic interaction between two atoms...and I want to determine the stability of the ferromagnetic versus antiferromagnetic state..So for this, I need to calculate the total energies corresponding to both ferromagnetic and antiferromagnetic spin alignments...So.can anyone guide me how to calculate the energy by specifying the spin alignments..? sincerely, Miss Kajal (UTA)(University of Delhi) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091104/35e81e0c/attachment.htm From udayagiri3 at gmail.com Wed Nov 4 07:17:51 2009 From: udayagiri3 at gmail.com (udayagiri sai babu) Date: Wed, 4 Nov 2009 11:47:51 +0530 Subject: [Pw_forum] scf stops after finishing 100 iteration In-Reply-To: <4AF09B26.4020300@sissa.it> References: <4AF09B26.4020300@sissa.it> Message-ID: Dear Dimpy Sharma you modify your electrons card as below. i.e add the option electron_maxstep=1000 by default it is 100. If convergence is not achieved in 100 steps then it stops. So put the variable electron_maxstep to a high value say 1000 so that the scf calculation runs till it is converged. &ELECTRONS diagonalization ='david' mixing_mode = 'plain' conv_thr = 1.0d-6 mixing_beta = 0.7 electron_maxstep=1000 On Wed, Nov 4, 2009 at 2:35 AM, Stefano de Gironcoli wrote: > have you verified that your crystal structure is reasonable using a > visualizer like xcrysden or similar ? > it appears to me that a couple of atoms are very very close to each other. > stefano > > Dimpy Sharma wrote: > > > > Hi Quantum espresso users, > > > > I tired to perform scf calculation but it shows me the following error > > 'convergence NOT achieved after 100 iterations: stopping' > > > > However the nscf calculation and projected density of states run > > successfully, why is this so? > > > > My input file is as follows > > > > &CONTROL > > calculation ='scf' > > restart_mode = 'from_scratch' > > outdir = '/sfiwork/dsharma/PDOSSilane/PDOSsi/si_wfc' > > pseudo_dir = '/sfiwork/dsharma/QE_Pseudos/' > > prefix = 'si' > > tstress = .true. > > tprnfor = .true. > > etot_conv_thr = 1.D-4 > > forc_conv_thr = 1.D-3 > > nstep = 600 > > wf_collect =.true. > > / > > &SYSTEM > > ibrav = 0 > > celldm(1) =7.4088 > > nat = 6 > > ntyp = 1 > > ecutwfc = 40 > > ecutrho = 160.0 > > nbnd = 12 > > / > > &ELECTRONS > > diagonalization ='david' > > mixing_mode = 'plain' > > conv_thr = 1.0d-6 > > 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 > > ATOMIC_POSITIONS angstroms > > Si 2.95020 -0.66592 -0.12341 > > Si 4.90939 0.61749 0.11358 > > Si 0.99475 0.65272 -0.16138 > > Si -0.98472 -0.62740 -0.15123 > > Si -2.94624 0.68229 -0.12124 > > Si -4.89549 -0.61534 0.11905 > > K_POINTS automatic > > 4 1 1 0 0 0 > > > > Can anybody give me any suggestions? > > > > Thanks > > > > Dimpy > > > > Dimpy Sharma, > > PhD > > Electronics Theory Group > > UCC,Cork > > Ireland > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 > -- U.Saibabu PhD student, Deformation mechanisms modeling group, Materials engineering department, IISc Bangalore, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091104/e4754d2b/attachment.htm From mighfar at jncasr.ac.in Wed Nov 4 09:09:06 2009 From: mighfar at jncasr.ac.in (Mighfar Imam) Date: Wed, 4 Nov 2009 13:39:06 +0530 (IST) Subject: [Pw_forum] magnetic interaction In-Reply-To: References: Message-ID: <43995.172.16.1.1.1257322146.squirrel@172.16.1.1> You can specify equal but opposite (-ve) values of starting_magnetization(i) for the two atoms to cosider antiferromagnetic interaction. Mighfar Imam PhD Student, Theoretical Sciences Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur, Bangalore-64, India. Ph.(Lab.) +91 -(80) 22082835 Cell: +919480336087 kajal jindal > Hi, > > I am trying to study the magnetic interaction between two atoms...and I > want > to determine the stability of the ferromagnetic versus antiferromagnetic > state..So for this, I need to calculate the total energies corresponding > to > both ferromagnetic and antiferromagnetic spin alignments...So.can anyone > guide me how to calculate the energy by specifying the spin alignments..? > > sincerely, > Miss Kajal > (UTA)(University of Delhi) > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From sclauzer at sissa.it Wed Nov 4 09:46:50 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 4 Nov 2009 09:46:50 +0100 Subject: [Pw_forum] Fwd: LDA+U problem on Mac Message-ID: <20091104094650.79p9kec09ww4o4ss@webmail.sissa.it> > Da: Gabriele Sclauzero > Data: 04 novembre 2009 9:43:12 GMT+01:00 > A: PWSCF Forum > Oggetto: Re: [Pw_forum] LDA+U problem on Mac > > > Il giorno 04/nov/09, alle ore 04:04, Mulazzi Mattia ha scritto: > >> >>>> About the LDA+U, I did more testing on it both on my PC (using >>>> cygwin under WinXP) and on the Mac. The cygwin compilation >>>> recognises without problems the V pseudopotential included in the QE >>>> library. The same calculations done on the Mac require first a >>>> small modification of the tabd.f90 file. >>> >>> Not only! As I said also set_hubbard_l.f90 needs to be modified >>> accordingly. For the moment, you can take those two files from 4.1.1 >>> and put in 4.0.5 version (and recompile). They should work. >> >> I did not need to modify the set_hubbard_l.f90 file to have the LDA+U >> running, but just the tab_d.f90. > > This sounds strange to me! If I remember well, there should be a > check in both subroutines, and the program should stop complaining > if either of the two subroutines has not been modified properly. Be > careful that you might not be obtaining correct results. You should > check that Hubbard_l=2 (it shuold be written at the beginning of > output) and starting local occupation on V is 3 (nsum=3 before the > first iteration). > >>> This is strange. Anyway keep in mind that the problem shows up only if >>> you put the +U on the single-character named species. >> >> I checked and there is also a segmentation fault when I use the MnS2 >> system, and for it also when I do a calculation with one Mn atom per >> cell there is a segmentation fault. On the other hand a calculation >> with two Mn atoms, Mn1 and Mn2, does not give a segmentation fault. So >> the problem is not in the atomic pseudopotential naming. > > >>> >>> Yes it is not a problem of the PP. If you still have problems, after >>> replacing those two files of above, or using V1 in place of V, please >>> report it. >> >> I did a test after changing from V.pbe-n-van.UPF to V1.pbe-n-van.UPF, >> but I still have the segmentation fault. > > Can you please send me some input files which give the crash > (together with details of compilation and QE version used) > > >> >>> HTH >>> >>> GS >>> PS: After all, I'm still a bit surprised that this problem I mentioned >>> shows up as a segmentaion fault. Maybe it is something else... >> At first I thought about a compiler bug (as suggested in the QE >> troubleshooting pages), but it is quite unlikely it is the case. Why >> should the compiler be buggy only with a one atom per cell system. > > I've always been told that g95 is not much reliable to do serious > calculations, since it may contain many bugs. Can you recompile with > gfortran, it is free software as well. You could also try with > ifort, but you need a license for Mac. > > Gabriele -- SISSA & Democritos > >> >> Mattia >> >> FPR Fellow of RIKEN at Spring8 >> Excitation Order Research Team >> 1-1-1 Sayo-cho Sayo-gun, Hyogo >> Japan >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > ? Gabriele Sclauzero ? > email: gurlomail at gmail.com > office: sclauzer at sissa.it > +39 040 3787511 > skype: gurlonotturno > ? Gabriele Sclauzero ? email: gurlomail at gmail.com office: sclauzer at sissa.it +39 040 3787511 skype: gurlonotturno ----- Fine del messaggio inoltrato ----- ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ -------------- next part -------------- Inizio messaggio inoltrato: > Da: Gabriele Sclauzero > Data: 04 novembre 2009 9:43:12 GMT+01:00 > A: PWSCF Forum > Oggetto: Re: [Pw_forum] LDA+U problem on Mac > > > Il giorno 04/nov/09, alle ore 04:04, Mulazzi Mattia ha scritto: > >> >>>> About the LDA+U, I did more testing on it both on my PC (using >>>> cygwin under WinXP) and on the Mac. The cygwin compilation >>>> recognises without problems the V pseudopotential included in the >>>> QE >>>> library. The same calculations done on the Mac require first a >>>> small modification of the tabd.f90 file. >>> >>> Not only! As I said also set_hubbard_l.f90 needs to be modified >>> accordingly. For the moment, you can take those two files from 4.1.1 >>> and put in 4.0.5 version (and recompile). They should work. >> >> I did not need to modify the set_hubbard_l.f90 file to have the LDA+U >> running, but just the tab_d.f90. > > This sounds strange to me! If I remember well, there should be a > check in both subroutines, and the program should stop complaining > if either of the two subroutines has not been modified properly. Be > careful that you might not be obtaining correct results. You should > check that Hubbard_l=2 (it shuold be written at the beginning of > output) and starting local occupation on V is 3 (nsum=3 before the > first iteration). > >>> This is strange. Anyway keep in mind that the problem shows up >>> only if >>> you put the +U on the single-character named species. >> >> I checked and there is also a segmentation fault when I use the MnS2 >> system, and for it also when I do a calculation with one Mn atom per >> cell there is a segmentation fault. On the other hand a calculation >> with two Mn atoms, Mn1 and Mn2, does not give a segmentation fault. >> So >> the problem is not in the atomic pseudopotential naming. > > >>> >>> Yes it is not a problem of the PP. If you still have problems, after >>> replacing those two files of above, or using V1 in place of V, >>> please >>> report it. >> >> I did a test after changing from V.pbe-n-van.UPF to V1.pbe-n-van.UPF, >> but I still have the segmentation fault. > > Can you please send me some input files which give the crash > (together with details of compilation and QE version used) > > >> >>> HTH >>> >>> GS >>> PS: After all, I'm still a bit surprised that this problem I >>> mentioned >>> shows up as a segmentaion fault. Maybe it is something else... >> At first I thought about a compiler bug (as suggested in the QE >> troubleshooting pages), but it is quite unlikely it is the case. Why >> should the compiler be buggy only with a one atom per cell system. > > I've always been told that g95 is not much reliable to do serious > calculations, since it may contain many bugs. Can you recompile with > gfortran, it is free software as well. You could also try with > ifort, but you need a license for Mac. > > Gabriele -- SISSA & Democritos > >> >> Mattia >> >> FPR Fellow of RIKEN at Spring8 >> Excitation Order Research Team >> 1-1-1 Sayo-cho Sayo-gun, Hyogo >> Japan >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > ? Gabriele Sclauzero ? > email: gurlomail at gmail.com > office: sclauzer at sissa.it > +39 040 3787511 > skype: gurlonotturno > ? Gabriele Sclauzero ? email: gurlomail at gmail.com office: sclauzer at sissa.it +39 040 3787511 skype: gurlonotturno -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091104/d564f3cd/attachment.htm From sh.shapt at gmail.com Wed Nov 4 12:59:03 2009 From: sh.shapt at gmail.com (Shaptrishi Sharma) Date: Wed, 4 Nov 2009 11:59:03 +0000 Subject: [Pw_forum] Is it possible to calculate projected density of states for only one H in a chain of different atoms Message-ID: Hi there, I would like to know, is it possible to calculate the projected density of states for only one atom like Hydrogen or Nitrogen in a chain of of different atoms, as I have tired using the coordinate of a single hydrogen I mean I gave as 0.00 0.00 0.00 coordinates of Hydrogen, in this case the calculation does not run . Thanks SS -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091104/9f696dc5/attachment.htm From paulatto at sissa.it Wed Nov 4 13:06:31 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 04 Nov 2009 13:06:31 +0100 Subject: [Pw_forum] Is it possible to calculate projected density of states for only one H in a chain of different atoms In-Reply-To: References: Message-ID: In data 04 novembre 2009 alle ore 12:59:03, Shaptrishi Sharma ha scritto: > I would like to know, is it possible to calculate the projected density > of states for only one atom like Hydrogen or Nitrogen in a chain of of > different atoms, Dear Shaptrishi, it is possible, of course, but it is not implemented. However, unless you have seriously limited computing power you can just compute the pdos for all atoms; then just don't use the ones you don't need. > as I have tired using the coordinate of a single hydrogen I mean I gave > as > > 0.00 0.00 0.00 > coordinates of Hydrogen, > in this case the calculation does not run . Well, the program can only do what it's programmed to do. 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 nkxirainbow at gmail.com Wed Nov 4 13:07:40 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Wed, 4 Nov 2009 20:07:40 +0800 Subject: [Pw_forum] Is it possible to calculate projected density of states for only one H in a chain of different atoms In-Reply-To: References: Message-ID: <21fbc4790911040407p23ffa12as3ae9991c6f57415e@mail.gmail.com> After pdos calculated, ESPRESSO will give pdos for each atom in unit cell. On Wed, Nov 4, 2009 at 7:59 PM, Shaptrishi Sharma wrote: > Hi there, > > I would like to know, is it possible to calculate the projected density of > states for only one atom like Hydrogen or Nitrogen in a chain of of > different atoms, as I have tired using the coordinate of a single hydrogen I > mean I gave as > > 0.00 0.00 0.00 > coordinates of Hydrogen, > > in this case the calculation does not run . > Thanks > > ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091104/694c347f/attachment.htm From kajalmh18 at gmail.com Thu Nov 5 06:47:26 2009 From: kajalmh18 at gmail.com (kajal jindal) Date: Thu, 5 Nov 2009 11:17:26 +0530 Subject: [Pw_forum] magnetic interaction In-Reply-To: <43995.172.16.1.1.1257322146.squirrel@172.16.1.1> References: <43995.172.16.1.1.1257322146.squirrel@172.16.1.1> Message-ID: Hi, Thanks for ur previous reply, but i think this will work if the two atoms considered are of different types. Actually i m working on ZnO and I am substituting two O atoms with two N atoms and hence ,want to consider the magnetic interaction between them..So how to proceed in that case coz I have to consider ferromagnetic and antiferromagnetic spin alignments for the two N atoms only.. Thanks, sincerely, Miss Kajal (UTA)(University of Delhi) On Wed, Nov 4, 2009 at 1:39 PM, Mighfar Imam wrote: > You can specify equal but opposite (-ve) values of > starting_magnetization(i) for the two atoms to cosider antiferromagnetic > interaction. > > > Mighfar Imam > PhD Student, > Theoretical Sciences Unit, > Jawaharlal Nehru Center for > Advanced Scientific Research, > Jakkur, Bangalore-64, India. > Ph.(Lab.) +91 -(80) 22082835 > Cell: +919480336087 > > > kajal jindal > > Hi, > > > > I am trying to study the magnetic interaction between two atoms...and I > > want > > to determine the stability of the ferromagnetic versus antiferromagnetic > > state..So for this, I need to calculate the total energies corresponding > > to > > both ferromagnetic and antiferromagnetic spin alignments...So.can anyone > > guide me how to calculate the energy by specifying the spin alignments..? > > > > sincerely, > > Miss Kajal > > (UTA)(University of Delhi) > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091105/7caf7323/attachment-0001.htm From ttduyle at gmail.com Thu Nov 5 07:02:57 2009 From: ttduyle at gmail.com (Duy Le) Date: Thu, 5 Nov 2009 01:02:57 -0500 Subject: [Pw_forum] magnetic interaction In-Reply-To: References: <43995.172.16.1.1.1257322146.squirrel@172.16.1.1> Message-ID: <8974d3b20911042202m2faf98a4pb6667970b86e4ff5@mail.gmail.com> The code does not understand your 2 oxygen atoms are of the same type unless you tell it to understand so (O Mass PP). You just need to define 2 different type (for oxygen): O1 Mass PP O2 Mass PP .... -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Thu, Nov 5, 2009 at 12:47 AM, kajal jindal wrote: > Hi, > > Thanks for ur previous reply, but i think this will work if the two atoms > considered are of different types. Actually i m working on ZnO and I am > substituting two O atoms with two N atoms and hence ,want to consider the > magnetic interaction between them..So how to proceed in that case coz I have > to consider ferromagnetic and antiferromagnetic spin alignments for the two > N atoms only.. > > Thanks, > > > sincerely, > Miss Kajal > (UTA)(University of Delhi) > > > On Wed, Nov 4, 2009 at 1:39 PM, Mighfar Imam wrote: > >> You can specify equal but opposite (-ve) values of >> starting_magnetization(i) for the two atoms to cosider antiferromagnetic >> interaction. >> >> >> Mighfar Imam >> PhD Student, >> Theoretical Sciences Unit, >> Jawaharlal Nehru Center for >> Advanced Scientific Research, >> Jakkur, Bangalore-64, India. >> Ph.(Lab.) +91 -(80) 22082835 >> Cell: +919480336087 >> >> >> kajal jindal >> > Hi, >> > >> > I am trying to study the magnetic interaction between two atoms...and I >> > want >> > to determine the stability of the ferromagnetic versus >> antiferromagnetic >> > state..So for this, I need to calculate the total energies >> corresponding >> > to >> > both ferromagnetic and antiferromagnetic spin alignments...So.can anyone >> > guide me how to calculate the energy by specifying the spin >> alignments..? >> > >> > sincerely, >> > Miss Kajal >> > (UTA)(University of Delhi) >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091105/fff277a1/attachment.htm From baroni at sissa.it Thu Nov 5 07:43:58 2009 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 5 Nov 2009 07:43:58 +0100 Subject: [Pw_forum] magnetic interaction In-Reply-To: References: <43995.172.16.1.1.1257322146.squirrel@172.16.1.1> Message-ID: give them a different type label. the code will treat them as different, even though they have the same pp SB On Nov 5, 2009, at 6:47 AM, kajal jindal wrote: > Hi, > > Thanks for ur previous reply, but i think this will work if the two > atoms considered are of different types. Actually i m working on ZnO > and I am substituting two O atoms with two N atoms and hence ,want > to consider the magnetic interaction between them..So how to proceed > in that case coz I have to consider ferromagnetic and > antiferromagnetic spin alignments for the two N atoms only.. > > Thanks, > > sincerely, > Miss Kajal > (UTA)(University of Delhi) > > > On Wed, Nov 4, 2009 at 1:39 PM, Mighfar Imam > wrote: > You can specify equal but opposite (-ve) values of > starting_magnetization(i) for the two atoms to cosider > antiferromagnetic > interaction. > > > Mighfar Imam > PhD Student, > Theoretical Sciences Unit, > Jawaharlal Nehru Center for > Advanced Scientific Research, > Jakkur, Bangalore-64, India. > Ph.(Lab.) +91 -(80) 22082835 > Cell: +919480336087 > > > kajal jindal > > Hi, > > > > I am trying to study the magnetic interaction between two > atoms...and I > > want > > to determine the stability of the ferromagnetic versus > antiferromagnetic > > state..So for this, I need to calculate the total energies > corresponding > > to > > both ferromagnetic and antiferromagnetic spin alignments...So.can > anyone > > guide me how to calculate the energy by specifying the spin > alignments..? > > > > sincerely, > > Miss Kajal > > (UTA)(University of Delhi) > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- 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/20091105/e4b76fa2/attachment.htm From giannozz at democritos.it Thu Nov 5 11:22:20 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 05 Nov 2009 11:22:20 +0100 Subject: [Pw_forum] Fwd: LDA+U problem on Mac In-Reply-To: <20091104094650.79p9kec09ww4o4ss@webmail.sissa.it> References: <20091104094650.79p9kec09ww4o4ss@webmail.sissa.it> Message-ID: <4AF2A75C.2070304@democritos.it> Gabriele Sclauzero wrote: >>> At first I thought about a compiler bug (as suggested in the QE >>> troubleshooting pages), but it is quite unlikely it is the case. Why >>> should the compiler be buggy only with a one atom per cell system. Because. If bugs were predictable, they would be predicted. >> I've always been told that g95 is not much reliable to do serious >> calculations, since it may contain many bugs. Can you recompile with >> gfortran, it is free software as well. in my experience, g95 for Intel is one of the most reliable compilers around. Not sure about g95 for mac, but it looks quite reliable as well. Gfortran is much less reliable: it may or may not work. In any case: no claim of bugginess in QE will be taken seriously until reproduced on a different machine or software configuration. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From eariel99 at gmail.com Thu Nov 5 13:19:10 2009 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Thu, 5 Nov 2009 09:19:10 -0300 Subject: [Pw_forum] wave functions extrapolated written in outdir Message-ID: Hi, I think I found a strange behaviour of pw.x . I am runnning a calculation with this options outdir = './temp', wfcdir = '/tmp', disk_io = 'none', pot_extrapolation = 'second_order', wfc_extrapolation = 'second_order', It seems that the wfc extrapolation is conflicting with disk_io= none. OK, Fine, but the code writes the wave functions (*.oldwfc and *.old2wfc*) in outdir, instead of wfcdir. Should them be written in wfcdir ? I noted it when the code halted when writeng 64 wfc files for a system of 136 atoms (i. e., tons of bytes), in the NFS exported directory specified by outdir. Writing output data file cdse.save second order wave-functions extrapolation %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from davcio : error # 11 error while reading from file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% etc, etc. stopping ... Thank you. -- 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/20091105/c82ac979/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Thu Nov 5 14:30:03 2009 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Thu, 5 Nov 2009 15:30:03 +0200 Subject: [Pw_forum] magnetic interaction In-Reply-To: References: <43995.172.16.1.1.1257322146.squirrel@172.16.1.1> Message-ID: <200911051430.04563.giuseppe.mattioli@mlib.ism.cnr.it> You can also force the total magnetization of your system, for example by using the 'tot_magnetization' key: tot_magnetization=0.0 a diamagnetic or antiferromagnetic state, depending upon the 'starting_magnetization(n)' switch on your N atoms. tot_magnetization=2.0 a ferromagnetic (triplet) state. For the sake of curiosity, are you sure that a ferromagnetic or antiferromagnetic coupling can be obtained by N doping of ZnO? I have heard of Co or Mn doped ZnO. I have heard about the role of O vacancies... Let us know! Yours Giuseppe On Thursday 05 November 2009 06:47:26 kajal jindal wrote: > Hi, > > Thanks for ur previous reply, but i think this will work if the two atoms > considered are of different types. Actually i m working on ZnO and I am > substituting two O atoms with two N atoms and hence ,want to consider the > magnetic interaction between them..So how to proceed in that case coz I > have to consider ferromagnetic and antiferromagnetic spin alignments for > the two N atoms only.. > > Thanks, > > sincerely, > Miss Kajal > (UTA)(University of Delhi) > > On Wed, Nov 4, 2009 at 1:39 PM, Mighfar Imam wrote: > > You can specify equal but opposite (-ve) values of > > starting_magnetization(i) for the two atoms to cosider antiferromagnetic > > interaction. > > > > > > Mighfar Imam > > PhD Student, > > Theoretical Sciences Unit, > > Jawaharlal Nehru Center for > > Advanced Scientific Research, > > Jakkur, Bangalore-64, India. > > Ph.(Lab.) +91 -(80) 22082835 > > Cell: +919480336087 > > > > > > kajal jindal > > > > > Hi, > > > > > > I am trying to study the magnetic interaction between two atoms...and I > > > want > > > to determine the stability of the ferromagnetic versus > > > antiferromagnetic state..So for this, I need to calculate the total > > > energies corresponding to > > > both ferromagnetic and antiferromagnetic spin alignments...So.can > > > anyone guide me how to calculate the energy by specifying the spin > > > alignments..? > > > > > > sincerely, > > > Miss Kajal > > > (UTA)(University of Delhi) > > > _______________________________________________ > > > 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 -- ******************************************************** - 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/20091105/7361386a/attachment.htm From sclauzer at sissa.it Thu Nov 5 15:34:51 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 05 Nov 2009 15:34:51 +0100 Subject: [Pw_forum] scf stops after finishing 100 iteration In-Reply-To: References: <4AF09B26.4020300@sissa.it> Message-ID: <4AF2E28B.1080704@sissa.it> udayagiri sai babu wrote: > Dear Dimpy Sharma > you modify your electrons card as below. i.e add the option > electron_maxstep=1000 by default it is 100. If convergence is not > achieved in 100 steps then it stops. So put the variable > electron_maxstep to a high value say 1000 so that the scf calculation > runs till it is converged. Or until it reaches 1000 steps. If two atoms are too close because of wrong input coordinates, as Stefano was suggesting, you will probably never reach convergence and lose 10 times the cputime you've already lost before... when a calculation does not converge in 100 steps, it is always better to ask ourselves why it did not. Instead of increasing electron_maxstep one could for instance check the structure, check cutoffs, smearing... and play a bit with mixing_beta and mixinng_mode. Cheers GS > > &ELECTRONS > diagonalization ='david' > mixing_mode = 'plain' > conv_thr = 1.0d-6 > mixing_beta = 0.7 > electron_maxstep=1000 > > On Wed, Nov 4, 2009 at 2:35 AM, Stefano de Gironcoli > wrote: > > have you verified that your crystal structure is reasonable using a > visualizer like xcrysden or similar ? > it appears to me that a couple of atoms are very very close to each > other. > stefano > > Dimpy Sharma wrote: > > > > Hi Quantum espresso users, > > > > I tired to perform scf calculation but it shows me the following > error > > 'convergence NOT achieved after 100 iterations: stopping' > > > > However the nscf calculation and projected density of states run > > successfully, why is this so? > > > > My input file is as follows > > > > &CONTROL > > calculation ='scf' > > restart_mode = 'from_scratch' > > outdir = '/sfiwork/dsharma/PDOSSilane/PDOSsi/si_wfc' > > pseudo_dir = '/sfiwork/dsharma/QE_Pseudos/' > > prefix = 'si' > > tstress = .true. > > tprnfor = .true. > > etot_conv_thr = 1.D-4 > > forc_conv_thr = 1.D-3 > > nstep = 600 > > wf_collect =.true. > > / > > &SYSTEM > > ibrav = 0 > > celldm(1) =7.4088 > > nat = 6 > > ntyp = 1 > > ecutwfc = 40 > > ecutrho = 160.0 > > nbnd = 12 > > / > > &ELECTRONS > > diagonalization ='david' > > mixing_mode = 'plain' > > conv_thr = 1.0d-6 > > 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 > > ATOMIC_POSITIONS angstroms > > Si 2.95020 -0.66592 -0.12341 > > Si 4.90939 0.61749 0.11358 > > Si 0.99475 0.65272 -0.16138 > > Si -0.98472 -0.62740 -0.15123 > > Si -2.94624 0.68229 -0.12124 > > Si -4.89549 -0.61534 0.11905 > > K_POINTS automatic > > 4 1 1 0 0 0 > > > > Can anybody give me any suggestions? > > > > Thanks > > > > Dimpy > > > > Dimpy Sharma, > > PhD > > Electronics Theory Group > > UCC,Cork > > Ireland > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 > > > > > -- > U.Saibabu > PhD student, > Deformation mechanisms modeling group, > Materials engineering department, > IISc Bangalore, > India. > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 Nov 5 15:52:39 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 05 Nov 2009 15:52:39 +0100 Subject: [Pw_forum] Fwd: LDA+U problem on Mac In-Reply-To: <4AF2A75C.2070304@democritos.it> References: <20091104094650.79p9kec09ww4o4ss@webmail.sissa.it> <4AF2A75C.2070304@democritos.it> Message-ID: <4AF2E6B7.4000802@sissa.it> Paolo Giannozzi wrote: > Gabriele Sclauzero wrote: > >>> I've always been told that g95 is not much reliable to do serious >>> calculations, since it may contain many bugs. Can you recompile with >>> gfortran, it is free software as well. > > in my experience, g95 for Intel is one of the most reliable compilers > around. Not sure about g95 for mac, but it looks quite reliable as > well. Gfortran is much less reliable: it may or may not work. About this point, I'm always remembering the wrong way round... GS > > In any case: no claim of bugginess in QE will be taken seriously until > reproduced on a different machine or software configuration. > > Paolo -- 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 Nov 5 17:24:58 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 05 Nov 2009 17:24:58 +0100 Subject: [Pw_forum] Particular Phonon mode In-Reply-To: <3a749910911022043u17b013efnb5e02272e5e994f3@mail.gmail.com> References: <3a749910911022043u17b013efnb5e02272e5e994f3@mail.gmail.com> Message-ID: <4AF2FC5A.7050005@sissa.it> Bipul Rakshit wrote: > Dear PWscf users, > I am doing gamma Phonon calculation on LaMnO3. Since the unit cell > contain 20 atoms, so at gamma i am getting 60 frequencies (3 acoustic > modes ~ 0) > > If I am just interested in just the first three frequencies ( the > acoustic modes), what changes i have to made in the input file. You could try to specity nrapp=1 in the namelist and add a line containing the index of the representation you are interested in. I suppose that acoustic modes should be done first and should fall in one single representation, so that you can add 1 at the end of the input file. I'm not sure if this is the correct way, so look carefully to what you will obtain on output. HTH GS > > phonons of LaMnO3-pero > &inputph > tr2_ph=1.0d-10, > alpha_mix(1)= 0.7, > prefix='lamno3', > ! epsil=.true., > ! ldisp=.true., > ! nq1=2, nq2=2, nq3=2 > ! iq1=6, iq2=6, iq3=6 > ! lnscf= .true. > amass(1)= 138.9055, > amass(2)=54.938049, > amass(3)=15.9994, > outdir = './OUT', > fildyn='LaMnO3.dynG', > / > 0.0 0.0 0.0 > > -- > Dr. Bipul Rakshit > Research Associate, > S N Bose Centre for Basic Sciences, > Salt Lake, > Kolkata 700 098 > India > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 quantumdft at gmail.com Fri Nov 6 04:35:39 2009 From: quantumdft at gmail.com (vega lew) Date: Fri, 6 Nov 2009 11:35:39 +0800 Subject: [Pw_forum] where is the end of an unconverged NEB calculation Message-ID: <412f6c680911051935g630b2649tab527978ec7a50cb@mail.gmail.com> Dear all, During my NEB calculations, I found there are two possible situation. First, the calculation could be converged after about 100 iterations. Second, the calculation never converged in more than 300 iterations. And for the second case, the energy barrier went down and down to a certain value, and then the reported energy barrier went up gradually. For example in my resent job, the energy barrier goes to 1.49 eV from the intial 2.99 eV in about 120 iterations. Then the energy barrier rise to 1.73 eV bit by bit in following 40 iterations. And the calculation is still running while this value is still going up. How could I deal with this situation? Could I take the lowest value as the energy barrier of the reaction? How could I know whether there will be another smaller value in the longer calculation? thank you for reading. Ang hints will be deeply appreciated. best, vega -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091106/8d483e02/attachment.htm From lfhuang at theory.issp.ac.cn Fri Nov 6 09:50:04 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Fri, 06 Nov 2009 16:50:04 +0800 Subject: [Pw_forum] =?utf-8?q?where_is_the_end_of_an_unconverged_NEB_calcu?= =?utf-8?q?lation?= Message-ID: <20091106085004.14387.qmail@ms.hfcas.ac.cn> Dear vega lew: Have you gone into the ./tmp directory to see the energy convergence of every image? The calculational statuses of all the images can be found there, and I guess your convergence problem may be due to the same reasons as ordinary electronic structrue calculations, which may be modified by change some parameters e.g. k-points numbers, smearing, nband. Or there may be some defects in the pseudopotential and you should better change for another one. May these be helpful. Best Wishes! Yours Sincerely L.F.Huang > Date: Fri, 6 Nov 2009 11:35:39 +0800 > From: vega lew > Subject: [Pw_forum] where is the end of an unconverged NEB calculation > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > > During my NEB calculations, I found there are two possible situation. First, > the calculation could be converged after about 100 iterations. Second, the > calculation never converged in more than 300 iterations. And for the second > case, the energy barrier went down and down to a certain value, and then the > reported energy barrier went up gradually. For example in my resent job, the > energy barrier goes to 1.49 eV from the intial 2.99 eV in about 120 > iterations. Then the energy barrier rise to 1.73 eV bit by bit in following > 40 iterations. And the calculation is still running while this value is > still going up. How could I deal with this situation? Could I take the > lowest value as the energy barrier of the reaction? How could I know whether > there will be another smaller value in the longer calculation? > > thank you for reading. Ang hints will be deeply appreciated. > > best, > > vega > > -- > ================================================================================== > Vega Lew ( weijia liu) > Graduate student > 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 > ****************************************************************************************************************** ------ ====================================================================== L.F.Huang(???) ph.D candidate, DFT and phonon physics ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(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/20091106/5700ddb1/attachment.htm From quantumdft at gmail.com Fri Nov 6 10:35:00 2009 From: quantumdft at gmail.com (vega lew) Date: Fri, 6 Nov 2009 17:35:00 +0800 Subject: [Pw_forum] where is the end of an unconverged NEB calculation In-Reply-To: <20091106085004.14387.qmail@ms.hfcas.ac.cn> References: <20091106085004.14387.qmail@ms.hfcas.ac.cn> Message-ID: <412f6c680911060135wc4db9d3r4aaaea3814b8465a@mail.gmail.com> Dear frined in CAS, My convergence of every single NEB iteration is very well. My convergence problem is about the calculated "activation energy" (I call it as energy barrier in last mail.), not for the energy convergence of every image. here is a few lines from my output file, Program PWSCF v.4.0.3 starts ... Today is 8Oct2009 at 23:53:20 Parallel version (MPI) Number of processors in use: 5 path-images division: nimage = 5 For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW Current dimensions of program pwscf are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 gamma-point specific algorithms are used initial path length = 7.8290 bohr initial inter-image distance = 1.3048 bohr calculation = neb restart_mode = from_scratch opt_scheme = quick-min num_of_images = 7 nstep = 9999 CI_scheme = no-CI first_last_opt = F coarse-grained phase-space = F use_freezing = F ds = 1.0000 a.u. k_max = 0.1000 a.u. k_min = 0.1000 a.u. suggested k_max = 0.6169 a.u. suggested k_min = 0.6169 a.u. path_thr = 0.0500 eV / A ------------------------------ iteration 1 ------------------------------ cpu = 0 tcpu = 0.2 self-consistency for image 1 cpu = 3 tcpu = 0.2 self-consistency for image 5 cpu = 4 tcpu = 0.2 self-consistency for image 6 cpu = 2 tcpu = 0.2 self-consistency for image 4 cpu = 1 tcpu = 0.2 self-consistency for image 7 cpu = 0 tcpu = 23616.8 self-consistency for image 2 cpu = 1 tcpu = 25603.1 self-consistency for image 3 activation energy (->) = 3.272591 eV activation energy (<-) = 2.990961 eV image energy (eV) error (eV/A) frozen 1 -119085.6620746 0.024462 T 2 -119084.9563724 2.640583 F 3 -119083.3975295 2.385012 F 4 -119082.3894835 2.896402 F 5 -119083.2192599 2.998904 F 6 -119084.7252314 2.403066 F 7 -119085.3804446 0.025165 T path length = 7.829 bohr inter-image distance = 1.305 bohr ------------------------------ iteration 2 ------------------------------ cpu = 2 tcpu = 29648.3 self-consistency for image 4 cpu = 0 tcpu = 42567.1 self-consistency for image 2 cpu = 1 tcpu = 44477.8 self-consistency for image 3 cpu = 3 tcpu = 30626.8 self-consistency for image 5 cpu = 4 tcpu = 32197.2 self-consistency for image 6 activation energy (->) = 3.093816 eV activation energy (<-) = 2.812186 eV image energy (eV) error (eV/A) frozen 1 -119085.6620746 0.024462 T 2 -119085.0987352 2.105271 F 3 -119083.6078363 2.170459 F 4 -119082.5682586 2.050101 F 5 -119083.5224117 1.596776 F 6 -119084.8769055 1.343862 F 7 -119085.3804446 0.025165 T path length = 7.843 bohr inter-image distance = 1.307 bohr ...... ...... ------------------------------ iteration 120 ------------------------------ cpu = 2 tcpu = ******** self-consistency for image 4 cpu = 0 tcpu = ******** self-consistency for image 2 cpu = 3 tcpu = ******** self-consistency for image 5 cpu = 4 tcpu = ******** self-consistency for image 6 cpu = 1 tcpu = ******** self-consistency for image 3 activation energy (->) = 1.786596 eV activation energy (<-) = 1.504966 eV image energy (eV) error (eV/A) frozen 1 -119085.6620746 0.024462 T 2 -119085.4786718 0.223126 F 3 -119083.9049529 0.170985 F 4 -119083.8754787 0.076161 F 5 -119085.1083173 0.075946 F 6 -119085.3050720 0.015511 F 7 -119085.3804446 0.025165 T path length = 9.729 bohr inter-image distance = 1.621 bohr ------------------------------ iteration 121 ------------------------------ cpu = 2 tcpu = ******** self-consistency for image 4 cpu = 3 tcpu = ******** self-consistency for image 5 cpu = 0 tcpu = ******** self-consistency for image 2 cpu = 4 tcpu = ******** self-consistency for image 6 cpu = 1 tcpu = ******** self-consistency for image 3 activation energy (->) = 1.775789 eV activation energy (<-) = 1.494159 eV image energy (eV) error (eV/A) frozen 1 -119085.6620746 0.024462 T 2 -119085.4781477 0.130868 F 3 -119083.8862860 0.275250 F 4 -119083.8905252 0.089256 F 5 -119085.1088347 0.047586 F 6 -119085.3051231 0.015512 F 7 -119085.3804446 0.025165 T path length = 9.725 bohr inter-image distance = 1.621 bohr ------------------------------ iteration 122 ------------------------------ cpu = 2 tcpu = ******** self-consistency for image 4 cpu = 3 tcpu = ******** self-consistency for image 5 cpu = 0 tcpu = ******** self-consistency for image 2 cpu = 1 tcpu = ******** self-consistency for image 3 cpu = 4 tcpu = ******** self-consistency for image 6 activation energy (->) = 1.791716 eV activation energy (<-) = 1.510086 eV image energy (eV) error (eV/A) frozen 1 -119085.6620746 0.024462 T 2 -119085.4766388 0.150020 F 3 -119083.8703582 0.360096 F 4 -119083.9053588 0.136487 F 5 -119085.1096015 0.054464 F 6 -119085.3051878 0.017319 F 7 -119085.3804446 0.025165 T ...... ...... ...... ------------------------------ iteration 160 ------------------------------ cpu = 2 tcpu = ******** self-consistency for image 4 cpu = 0 tcpu = ******** self-consistency for image 2 cpu = 3 tcpu = ******** self-consistency for image 5 cpu = 1 tcpu = ******** self-consistency for image 3 cpu = 4 tcpu = ******** self-consistency for image 6 activation energy (->) = 2.015566 eV activation energy (<-) = 1.733936 eV image energy (eV) error (eV/A) frozen 1 -119085.6620746 0.024462 T 2 -119085.4084826 0.122618 F 3 -119083.6465085 0.151901 F 4 -119084.1207907 0.114239 F 5 -119085.1378794 0.024820 F 6 -119085.3093981 0.014540 F 7 -119085.3804446 0.025165 T path length = 9.760 bohr inter-image distance = 1.627 bohr ------------------------------ iteration 161 ------------------------------ cpu = 2 tcpu = ******** self-consistency for image 4 cpu = 3 tcpu = ******** self-consistency for image 5 cpu = 0 tcpu = ******** self-consistency for image 2 cpu = 4 tcpu = ******** self-consistency for image 6 cpu = 1 tcpu = ******** self-consistency for image 3 activation energy (->) = 2.019415 eV activation energy (<-) = 1.737785 eV image energy (eV) error (eV/A) frozen 1 -119085.6620746 0.024462 T 2 -119085.4066890 0.190727 F 3 -119083.6426594 0.205492 F 4 -119084.1216091 0.058992 F 5 -119085.1383781 0.022947 F 6 -119085.3094981 0.024415 F 7 -119085.3804446 0.025165 T path length = 9.765 bohr inter-image distance = 1.627 bohr ...... ...... ...... as I said last mail, the activation energy goes to 1.49 eV from the intial 2.99 eV in about 120 iterations. Then the energy barrier rise to 1.73 eV bit by bit in following 40 iterations. And the calculation is still running while this value is still going up. How could I deal with this? thank you for reading and reply best, vega On Fri, Nov 6, 2009 at 4:50 PM, lfhuang wrote: > Dear vega lew: > Have you gone into the ./tmp directory to see the energy convergence of > every image? The calculational statuses of all the images can be found > there, and I guess your convergence problem may be due to the same reasons > as ordinary electronic structrue calculations, which may be modified by > change some parameters e.g. k-points numbers, smearing, nband. Or there may > be some defects in the pseudopotential and you should better change for > another one. May these be helpful. > > Best Wishes! > Yours Sincerely > L.F.Huang > > > Date: Fri, 6 Nov 2009 11:35:39 +0800 > > From: vega lew > > Subject: [Pw_forum] where is the end of an unconverged NEB calculation > > To: PWSCF Forum > > Message-ID: > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear all, > > > > During my NEB calculations, I found there are two possible situation. > First, > > the calculation could be converged after about 100 iterations. Second, > the > > calculation never converged in more than 300 iterations. And for the > second > > case, the energy barrier went down and down to a certain value, and then > the > > reported energy barrier went up gradually. For example in my resent job, > the > > energy barrier goes to 1.49 eV from the intial 2.99 eV in about 120 > > iterations. Then the energy barrier rise to 1.73 eV bit by bit in > following > > 40 iterations. And the calculation is still running while this value is > > still going up. How could I deal with this situation? Could I take the > > lowest value as the energy barrier of the reaction? How could I know > whether > > there will be another smaller value in the longer calculation? > > > > thank you for reading. Ang hints will be deeply appreciated. > > > > best, > > > > vega > > > > -- > > > ================================================================================== > > > Vega Lew ( weijia liu) > > Graduate student > > 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 > > > ****************************************************************************************************************** > > > ------ > ====================================================================== > L.F.Huang(???) ph.D candidate, DFT and phonon physics > ====================================================================== > Add: Research Laboratory for Computational Materials Sciences, > Instutue of Solid State Physics,the Chinese Academy of Sciences, > P.O.Box 1129, Hefei 230031, P.R.China > Tel: 86-551-5591464-328(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) > ====================================================================== > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091106/4210da57/attachment-0001.htm From lfhuang at theory.issp.ac.cn Fri Nov 6 12:32:06 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Fri, 06 Nov 2009 19:32:06 +0800 Subject: [Pw_forum] =?utf-8?q?where_is_the_end_of_an_unconverged_NEB_calcu?= =?utf-8?q?lation?= Message-ID: <20091106113206.13037.qmail@ms.hfcas.ac.cn> Dear vega lew: I see you use normal NEB method, why don't use the Climbing-Image NEB? CI-NEB will let you find the saddle-point state. And I see the path length is about 5.0 anstrong, which is a little long path that 7 images in no-CI maybe not many enough if the potential energy surface is not smooth enough. Also, increasing the spring constants k_min and k_max and decreasing the atomic masses in the input file may help some. The meanings of these parameters can be found in the original papers on Dimer and NEB methods, which can be found in the bibliography in the Q_E homepage. In addition, It seems I have not made you understand me in the previous email, and I meant the convergence of the electronic-structure calculations for every image can be checked only when you open the PW.out files in the directory ./tmp/**_i (i=1,2...7). The potential barrier is just the energy difference between the saddle-point state (not well difined in the no-CI method) and the initial state, so when there is something wrong with the convergence of E_ac, there must be something wrong with the energy convergence of the "saddle-point state" and the initital state, which can be modified by changing some parameters e.g. k-points numbers, smearing, nband. Or there may be some defects in the pseudopotential and you should better change for another one. Probably the no-CI method also can result in this kind of convergence problem due to that the structure with highest energy can not stablized during your calculations. One important note: the NEB is cpu time consuming, and can eaily cost over 100 iterations to converge if your parameters are not optimized, so you'd better take some tests on smaller systems to find the optimum parameters before more complicated calculations. May these be helpful for you! Best Wishes! Yours Sincerely L.F.Huang > My convergence of every single NEB iteration is very well. My convergence > problem is about the calculated "activation energy" (I call it as energy > barrier in last mail.), not for the energy convergence of every image. > > here is a few lines from my output file, > > Program PWSCF v.4.0.3 starts ... > Today is 8Oct2009 at 23:53:20 > > Parallel version (MPI) > > Number of processors in use: 5 > path-images division: nimage = 5 > > For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW > > Current dimensions of program pwscf are: > Max number of different atomic species (ntypx) = 10 > Max number of k-points (npk) = 40000 > Max angular momentum in pseudopotentials (lmaxx) = 3 > > gamma-point specific algorithms are used > > > initial path length = 7.8290 bohr > initial inter-image distance = 1.3048 bohr > > calculation = neb > restart_mode = from_scratch > opt_scheme = quick-min > num_of_images = 7 > nstep = 9999 > CI_scheme = no-CI > first_last_opt = F > coarse-grained phase-space = F > use_freezing = F > ds = 1.0000 a.u. > k_max = 0.1000 a.u. > k_min = 0.1000 a.u. > suggested k_max = 0.6169 a.u. > suggested k_min = 0.6169 a.u. > path_thr = 0.0500 eV / A > > ------------------------------ iteration 1 > ------------------------------ > > cpu = 0 tcpu = 0.2 self-consistency for image 1 > cpu = 3 tcpu = 0.2 self-consistency for image 5 > cpu = 4 tcpu = 0.2 self-consistency for image 6 > cpu = 2 tcpu = 0.2 self-consistency for image 4 > cpu = 1 tcpu = 0.2 self-consistency for image 7 > cpu = 0 tcpu = 23616.8 self-consistency for image 2 > cpu = 1 tcpu = 25603.1 self-consistency for image 3 > > activation energy (->) = 3.272591 eV > activation energy ( > image energy (eV) error (eV/A) frozen > > 1 -119085.6620746 0.024462 T > 2 -119084.9563724 2.640583 F > 3 -119083.3975295 2.385012 F > 4 -119082.3894835 2.896402 F > 5 -119083.2192599 2.998904 F > 6 -119084.7252314 2.403066 F > 7 -119085.3804446 0.025165 T > > path length = 7.829 bohr > inter-image distance = 1.305 bohr > > ------------------------------ iteration 2 > ------------------------------ > > cpu = 2 tcpu = 29648.3 self-consistency for image 4 > cpu = 0 tcpu = 42567.1 self-consistency for image 2 > cpu = 1 tcpu = 44477.8 self-consistency for image 3 > cpu = 3 tcpu = 30626.8 self-consistency for image 5 > cpu = 4 tcpu = 32197.2 self-consistency for image 6 > > activation energy (->) = 3.093816 eV > activation energy ( > image energy (eV) error (eV/A) frozen > > 1 -119085.6620746 0.024462 T > 2 -119085.0987352 2.105271 F > 3 -119083.6078363 2.170459 F > 4 -119082.5682586 2.050101 F > 5 -119083.5224117 1.596776 F > 6 -119084.8769055 1.343862 F > 7 -119085.3804446 0.025165 T > > path length = 7.843 bohr > inter-image distance = 1.307 bohr > ...... > ...... > ------------------------------ iteration 120 > ------------------------------ > > cpu = 2 tcpu = ******** self-consistency for image 4 > cpu = 0 tcpu = ******** self-consistency for image 2 > cpu = 3 tcpu = ******** self-consistency for image 5 > cpu = 4 tcpu = ******** self-consistency for image 6 > cpu = 1 tcpu = ******** self-consistency for image 3 > > activation energy (->) = 1.786596 eV > activation energy ( > image energy (eV) error (eV/A) frozen > > 1 -119085.6620746 0.024462 T > 2 -119085.4786718 0.223126 F > 3 -119083.9049529 0.170985 F > 4 -119083.8754787 0.076161 F > 5 -119085.1083173 0.075946 F > 6 -119085.3050720 0.015511 F > 7 -119085.3804446 0.025165 T > > path length = 9.729 bohr > inter-image distance = 1.621 bohr > > ------------------------------ iteration 121 > ------------------------------ > > cpu = 2 tcpu = ******** self-consistency for image 4 > cpu = 3 tcpu = ******** self-consistency for image 5 > cpu = 0 tcpu = ******** self-consistency for image 2 > cpu = 4 tcpu = ******** self-consistency for image 6 > cpu = 1 tcpu = ******** self-consistency for image 3 > > activation energy (->) = 1.775789 eV > activation energy ( > image energy (eV) error (eV/A) frozen > > 1 -119085.6620746 0.024462 T > 2 -119085.4781477 0.130868 F > 3 -119083.8862860 0.275250 F > 4 -119083.8905252 0.089256 F > 5 -119085.1088347 0.047586 F > 6 -119085.3051231 0.015512 F > 7 -119085.3804446 0.025165 T > > path length = 9.725 bohr > inter-image distance = 1.621 bohr > > ------------------------------ iteration 122 > ------------------------------ > > cpu = 2 tcpu = ******** self-consistency for image 4 > cpu = 3 tcpu = ******** self-consistency for image 5 > cpu = 0 tcpu = ******** self-consistency for image 2 > cpu = 1 tcpu = ******** self-consistency for image 3 > cpu = 4 tcpu = ******** self-consistency for image 6 > > activation energy (->) = 1.791716 eV > activation energy ( > image energy (eV) error (eV/A) frozen > > 1 -119085.6620746 0.024462 T > 2 -119085.4766388 0.150020 F > 3 -119083.8703582 0.360096 F > 4 -119083.9053588 0.136487 F > 5 -119085.1096015 0.054464 F > 6 -119085.3051878 0.017319 F > 7 -119085.3804446 0.025165 T > ...... > ...... > ...... > ------------------------------ iteration 160 > ------------------------------ > > cpu = 2 tcpu = ******** self-consistency for image 4 > cpu = 0 tcpu = ******** self-consistency for image 2 > cpu = 3 tcpu = ******** self-consistency for image 5 > cpu = 1 tcpu = ******** self-consistency for image 3 > cpu = 4 tcpu = ******** self-consistency for image 6 > > activation energy (->) = 2.015566 eV > activation energy ( > image energy (eV) error (eV/A) frozen > > 1 -119085.6620746 0.024462 T > 2 -119085.4084826 0.122618 F > 3 -119083.6465085 0.151901 F > 4 -119084.1207907 0.114239 F > 5 -119085.1378794 0.024820 F > 6 -119085.3093981 0.014540 F > 7 -119085.3804446 0.025165 T > > path length = 9.760 bohr > inter-image distance = 1.627 bohr > > ------------------------------ iteration 161 > ------------------------------ > > cpu = 2 tcpu = ******** self-consistency for image 4 > cpu = 3 tcpu = ******** self-consistency for image 5 > cpu = 0 tcpu = ******** self-consistency for image 2 > cpu = 4 tcpu = ******** self-consistency for image 6 > cpu = 1 tcpu = ******** self-consistency for image 3 > > activation energy (->) = 2.019415 eV > activation energy ( > image energy (eV) error (eV/A) frozen > > 1 -119085.6620746 0.024462 T > 2 -119085.4066890 0.190727 F > 3 -119083.6426594 0.205492 F > 4 -119084.1216091 0.058992 F > 5 -119085.1383781 0.022947 F > 6 -119085.3094981 0.024415 F > 7 -119085.3804446 0.025165 T > > path length = 9.765 bohr > inter-image distance = 1.627 bohr > ...... > ...... > ...... > > as I said last mail, the activation energy goes to 1.49 eV from the intial > 2.99 eV in about 120 iterations. Then the energy barrier rise to 1.73 eV bit > by bit in following 40 iterations. And the calculation is still running > while this value is still going up. > > How could I deal with this? > > thank you for reading and reply > > best, > > vega > On Fri, Nov 6, 2009 at 4:50 PM, lfhuang wrote: > > > Dear vega lew: > > Have you gone into the ./tmp directory to see the energy convergence of > > every image? The calculational statuses of all the images can be found > > there, and I guess your convergence problem may be due to the same reasons > > as ordinary electronic structrue calculations, which may be modified by > > change some parameters e.g. k-points numbers, smearing, nband. Or there may > > be some defects in the pseudopotential and you should better change for > > another one. May these be helpful. > > > > Best Wishes! > > Yours Sincerely > > L.F.Huang > > > > > Date: Fri, 6 Nov 2009 11:35:39 +0800 > > > From: vega lew > > > Subject: [Pw_forum] where is the end of an unconverged NEB calculation > > > To: PWSCF Forum > > > Message-ID: > > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Dear all, > > > > > > During my NEB calculations, I found there are two possible situation. > > First, > > > the calculation could be converged after about 100 iterations. Second, > > the > > > calculation never converged in more than 300 iterations. And for the > > second > > > case, the energy barrier went down and down to a certain value, and then > > the > > > reported energy barrier went up gradually. For example in my resent job, > > the > > > energy barrier goes to 1.49 eV from the intial 2.99 eV in about 120 > > > iterations. Then the energy barrier rise to 1.73 eV bit by bit in > > following > > > 40 iterations. And the calculation is still running while this value is > > > still going up. How could I deal with this situation? Could I take the > > > lowest value as the energy barrier of the reaction? How could I know > > whether > > > there will be another smaller value in the longer calculation? > > > > > > thank you for reading. Ang hints will be deeply appreciated. > > > > > > best, > > > > > > vega > > > > > > -- > > > > > ================================================================================== > > > > > Vega Lew ( weijia liu) > > > Graduate student > > > 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 > > > > > ****************************************************************************************************************** > > > > > > ------ > > ====================================================================== > > L.F.Huang(???) ph.D candidate, DFT and phonon physics > > ====================================================================== > > Add: Research Laboratory for Computational Materials Sciences, > > Instutue of Solid State Physics,the Chinese Academy of Sciences, > > P.O.Box 1129, Hefei 230031, P.R.China > > Tel: 86-551-5591464-328(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) > > ====================================================================== > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > -- > ================================================================================== > Vega Lew ( weijia liu) > Graduate student > 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/20091106/4210da57/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 29, Issue 15 > **************************************** > ------ ====================================================================== L.F.Huang(???) ph.D candidate, DFT and phonon physics ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(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/20091106/2320d006/attachment-0001.htm From paulatto at sissa.it Fri Nov 6 14:00:03 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 06 Nov 2009 14:00:03 +0100 Subject: [Pw_forum] where is the end of an unconverged NEB calculation In-Reply-To: <412f6c680911051935g630b2649tab527978ec7a50cb@mail.gmail.com> References: <412f6c680911051935g630b2649tab527978ec7a50cb@mail.gmail.com> Message-ID: In data 06 novembre 2009 alle ore 04:35:39, vega lew ha scritto: > During my NEB calculations, I found there are two possible situation. > First, the calculation could be converged after about 100 iterations. > Second, the calculation never converged in more than 300 iterations. Dear Vega, NEB calculation are a bit tricky in general and require extreme care to be setup correctly. NEB also takes easily hunders of iteration to converge, of course depending on the number of atoms and of images. Here is some free advice I can give, although only practice make prefection. 1. don't use climbing image at the beginning, CI makes convergence slower; especially if the special image changes during the convergence process (it may happen if CI_scheme='auto') this does ususally mess up everything. Converge your calculation than restart from the last configuration with the climbing image (note that this will *increase* the barrier!) 2. carefully choose the initial path, remember that QE assumens continuity between the first and last image at the initial condition. In other words, periodic images are NOT used, you may have to manually translate an atom by one or more unit cell base vectors in order to have a meaningful initial path. 3. you can try to start the NEB process with most of the atoms fixed in position, in order to have the more "problematic" one to converge, before freeing all of them. 4. especially for larger systems, you can start the NEB with lower accuracy (less k-points, lower cutoff) and then increase it when it has converged to refine your calculation. 5. use the Broyden algorithm instead of the default one, it is a bit more fragile, but it removes the oscillation problem. If this happens, and you cannot afford more images, focus to a smaller problem, decompose it to pieces. 6. you can grossly estimate the number of iterations required as number_of_images * number_of_atoms * 3 (the atoms that don't move should not be counted). It may take half that many iterations, or twice as many, but more or less that's the order of magnitude, unless you start from a very accurate or very bad initial guess. good luck -- 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 padmaja_patnaik at yahoo.co.uk Fri Nov 6 20:26:16 2009 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Fri, 6 Nov 2009 19:26:16 +0000 (GMT) Subject: [Pw_forum] Density of states Message-ID: <704795.21212.qm@web26102.mail.ukl.yahoo.com> Dear all I am working on semiconductors with impurities and calculating with quantum espresso code. The density of states plot for unrelaxed condition shows the band gap and when relaxed the plot shows no band gap (please refer to the attached file). Is this enough to tell that its half-metallic after relaxation? Or do i have to look at some other values also? If yes what should i look at. Thanx in advance. Regards Padmaja Patnaik Research Scholar Dept of Physics IIT Bombay Mumbai, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091106/9e9911ef/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: DOS.pdf Type: application/pdf Size: 9535 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091106/9e9911ef/attachment.pdf From padmaja_patnaik at yahoo.co.uk Fri Nov 6 21:27:55 2009 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Fri, 6 Nov 2009 20:27:55 +0000 (GMT) Subject: [Pw_forum] Density of states Message-ID: <293634.59178.qm@web26102.mail.ukl.yahoo.com> Dear all I am working on semiconductors with impurities and calculating with quantum espresso code. The density of states plot for unrelaxed condition shows the band gap and when relaxed the plot shows no band gap (Would like to attach pfd of the plot but mail delivery fails with attachment pdf file). Is this enough to tell that its half-metallic after relaxation? Or do i have to look at some other values also? If yes what should i look at. Thanx in advance. Regards Padmaja Patnaik Research Scholar Dept of Physics IIT Bombay Mumbai, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091106/7f61a662/attachment.htm From giannozz at democritos.it Fri Nov 6 21:45:14 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 6 Nov 2009 21:45:14 +0100 Subject: [Pw_forum] fhi2upf.f90 and 'reasonable assumption' of nwfs=lmax_+1 In-Reply-To: References: Message-ID: <752BB22D-0405-481B-8EF4-A5B96F1FFDD8@democritos.it> On Nov 3, 2009, at 2:20 , Brad Malone wrote: > However, the code asks for one more wavefunction, under the > 'reasonable assumption' that nwfs = lmax_+1 (see below from > fhi2upf.f90) [...] > I imagine I'm missing something here, but why is this a reasonable > assumption? > Is not reasonable for me to pseudize only the valence 4s and 4p > states in Gallium? typically for an atom like Ga you need s, p, d pseudopotentials, and it is convenient to use the d potential as local reference term; so lmax=1, nwfs=2. If you use p or s or something else as local reference, the above does not hold. P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From padmaja_patnaik at yahoo.co.uk Fri Nov 6 21:46:41 2009 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Fri, 6 Nov 2009 20:46:41 +0000 (GMT) Subject: [Pw_forum] Density of states Message-ID: <524358.58556.qm@web26108.mail.ukl.yahoo.com> Dear all I am working on semiconductors with impurities and calculating with quantum espresso code. The density of states plot for unrelaxed condition shows the band gap and when relaxed the plot shows no band gap (please refer to the attached file). Is this enough to tell that its half-metallic after relaxation? Or do i have to look at some other values also? If yes what should i look at. Thanx in advance. Regards Padmaja Patnaik Research Scholar Dept of Physics IIT Bombay Mumbai, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091106/20a39743/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: DOS.pdf Type: application/pdf Size: 9535 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091106/20a39743/attachment-0001.pdf From giannozz at democritos.it Fri Nov 6 22:33:36 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 6 Nov 2009 22:33:36 +0100 Subject: [Pw_forum] wave functions extrapolated written in outdir In-Reply-To: References: Message-ID: <4FC43EEB-9808-4F09-981F-DFC8725285F3@democritos.it> On Nov 5, 2009, at 13:19 , Eduardo Ariel Menendez Proupin wrote: > It seems that the wfc extrapolation is conflicting with disk_io= none. quite likely: disk_io='none' is useful only for "one-shot" calculations, when you are interested only in quantities that are printed on output. Maybe this should be clearly stated in the documentation. > the code writes the wave functions (*.oldwfc and *.old2wfc*) in > outdir, > instead of wfcdir. Should them be written in wfcdir ? I think so. The problem is that little-used and little-known options are also little-tested... P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From zubaexy at gmail.com Sat Nov 7 01:46:41 2009 From: zubaexy at gmail.com (Zubaer Hossain) Date: Fri, 6 Nov 2009 18:46:41 -0600 Subject: [Pw_forum] k-mesh in pwcond Message-ID: <51ec861d0911061646v37aa44ffh43f1af3594dfe99d@mail.gmail.com> Dear QE users, Is there any rule for choosing k-meshes for the lead and the scattering region along the transport direction? Thanks in advance, Zubaer UIUC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091106/da803f68/attachment.htm From eyvaz_isaev at yahoo.com Sat Nov 7 03:42:34 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 6 Nov 2009 18:42:34 -0800 (PST) Subject: [Pw_forum] Density of states In-Reply-To: <524358.58556.qm@web26108.mail.ukl.yahoo.com> Message-ID: <242187.92974.qm@web65709.mail.ac4.yahoo.com> Dear Padmaya, --- On Fri, 11/6/09, Padmaja Patnaik wrote: > > I am working on semiconductors with impurities and > calculating with quantum espresso code. The density of > states plot for unrelaxed condition shows the band gap and when relaxed > the plot shows no band gap (please refer to the attached file). Is this > enough to tell that its half-metallic after relaxation? No, because it is absolutely not related with the half-metallic systems (at least what you have shown). Please have a look at the web page: http://en.wikipedia.org/wiki/Half-metal to understand what is "Half-metallic system". And then look at your DOS pictures to figure out what do you have, metallic or half-metallic system. >Or do i have to look at some > other values also? If yes what should i look at. Looking at your DOS pictures it is quite strange to see that after relaxation the DOS is completely different from the original one. Yes, usually some extra bands (in the band gap) appear due to relaxation (lowering the symmetry), nevertheless it almost conserves the shape of the original (unrelaxed) DOS. So, it seems in your calculations something went in the wrong way. Bests, Eyvaz. P.S. Please avoid repeating a message to the forum, this will not give you more chance to get a reply. ------------------------------------------------------------------- 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 From nkxirainbow at gmail.com Sat Nov 7 04:07:29 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Sat, 7 Nov 2009 03:07:29 +0000 Subject: [Pw_forum] k-mesh in pwcond In-Reply-To: <51ec861d0911061646v37aa44ffh43f1af3594dfe99d@mail.gmail.com> References: <51ec861d0911061646v37aa44ffh43f1af3594dfe99d@mail.gmail.com> Message-ID: <21fbc4790911061907k60e31182w5f11428e57e8419a@mail.gmail.com> Dear ? I do not think pwcond can set k-mesh along the transport direction. Instead, you can set k-mesh perpendicular to the transport direction. The transport device can be period perpendicular to the transport direction. However, it is not period along the transport direction On Sat, Nov 7, 2009 at 12:46 AM, Zubaer Hossain wrote: > Dear QE users, > > Is there any rule for choosing k-meshes for the lead and the scattering > region along the transport direction? > > Thanks in advance, > Zubaer > UIUC > > > -- ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091107/8f63f420/attachment.htm From quantumdft at gmail.com Sat Nov 7 07:45:18 2009 From: quantumdft at gmail.com (vega lew) Date: Sat, 7 Nov 2009 14:45:18 +0800 Subject: [Pw_forum] where is the end of an unconverged NEB calculation In-Reply-To: References: <412f6c680911051935g630b2649tab527978ec7a50cb@mail.gmail.com> Message-ID: <412f6c680911062245xcd266b7ue94ba626d4d715a3@mail.gmail.com> Dear friends from CAS and Italy, Thank you for your advice, I will try to adjust the parameters that you just mentioned above. At last, I found QE has been upgraded to 4.1.1, but the QE I used is 4.0.3. I wonder whether the new vision of QE could do better than the older one. Thank you again for your time. best, vega On Fri, Nov 6, 2009 at 9:00 PM, Lorenzo Paulatto wrote: > In data 06 novembre 2009 alle ore 04:35:39, vega lew > ha scritto: > > During my NEB calculations, I found there are two possible situation. > > First, the calculation could be converged after about 100 iterations. > > Second, the calculation never converged in more than 300 iterations. > > Dear Vega, > NEB calculation are a bit tricky in general and require extreme care to be > setup correctly. NEB also takes easily hunders of iteration to converge, > of course depending on the number of atoms and of images. Here is some > free advice I can give, although only practice make prefection. > > 1. don't use climbing image at the beginning, CI makes convergence slower; > especially if the special image changes during the convergence process (it > may happen if CI_scheme='auto') this does ususally mess up everything. > Converge your calculation than restart from the last configuration with > the climbing image (note that this will *increase* the barrier!) > > 2. carefully choose the initial path, remember that QE assumens continuity > between the first and last image at the initial condition. In other words, > periodic images are NOT used, you may have to manually translate an atom > by one or more unit cell base vectors in order to have a meaningful > initial path. > > 3. you can try to start the NEB process with most of the atoms fixed in > position, in order to have the more "problematic" one to converge, before > freeing all of them. > > 4. especially for larger systems, you can start the NEB with lower > accuracy (less k-points, lower cutoff) and then increase it when it has > converged to refine your calculation. > > > 5. use the Broyden algorithm instead of the default one, it is a bit more > fragile, but it removes the oscillation problem. If this happens, and you > cannot afford more images, focus to a smaller problem, decompose it to > pieces. > > 6. you can grossly estimate the number of iterations required as > number_of_images * number_of_atoms * 3 (the atoms that don't move should > not be counted). It may take half that many iterations, or twice as many, > but more or less that's the order of magnitude, unless you start from a > very accurate or very bad initial guess. > > good luck > > -- > 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 > -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091107/3f2f3fd9/attachment.htm From vamsi.iisc at gmail.com Sat Nov 7 07:48:34 2009 From: vamsi.iisc at gmail.com (vamsi kv) Date: Sat, 7 Nov 2009 12:18:34 +0530 Subject: [Pw_forum] choosing oxygen and Hydrogen pseudopotentials Message-ID: <84ff69170911062248h1a3cc788y56513660ca8e6bab@mail.gmail.com> Dear all, I have done some work on metals using PWscf code. No i want to see how gases adsorb on metals. Inorder to do that i want to know how to choose pseudopotentials for gases say Oxygen and Hydrogen and how to tune the parameters of pseudopotentials to perform the calculations. K V Vamsi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091107/52858a9a/attachment.htm From baroni at sissa.it Sat Nov 7 08:46:11 2009 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 7 Nov 2009 08:46:11 +0100 Subject: [Pw_forum] Density of states In-Reply-To: <524358.58556.qm@web26108.mail.ukl.yahoo.com> References: <524358.58556.qm@web26108.mail.ukl.yahoo.com> Message-ID: OK, OK, we got it. No need to repost. "without" relaxation, you mean *with* impurities, but with all the atoms at the position they would have *without* impurities, right? Or rather the system without any impurities? One thing you should pay attention to is the density of impurities. In computer simulations, this may be order of magnitudes larger than in the experiment, because of the need of using small supercells. (if this is the case, the closure of the gap could be the spurious consequence of the formation of a broad impurity band, instead of isolated, localazed states. SB On Nov 6, 2009, at 9:46 PM, Padmaja Patnaik wrote: > Dear all > > I am working on semiconductors with impurities and calculating with > quantum espresso code. The density of states plot for unrelaxed > condition shows the band gap and when relaxed the plot shows no band > gap (please refer to the attached file). Is this enough to tell that > its half-metallic after relaxation? Or do i have to look at some > other values also? If yes what should i look at. > > Thanx in advance. > Regards > > Padmaja Patnaik > Research Scholar > Dept of Physics > IIT Bombay > Mumbai, India > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget 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/20091107/38517c30/attachment-0001.htm From giannozz at democritos.it Sat Nov 7 12:59:33 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 7 Nov 2009 12:59:33 +0100 Subject: [Pw_forum] where is the end of an unconverged NEB calculation In-Reply-To: <412f6c680911062245xcd266b7ue94ba626d4d715a3@mail.gmail.com> References: <412f6c680911051935g630b2649tab527978ec7a50cb@mail.gmail.com> <412f6c680911062245xcd266b7ue94ba626d4d715a3@mail.gmail.com> Message-ID: <0FC999C6-E7B9-4FA1-80AF-245360AB1097@democritos.it> On Nov 7, 2009, at 7:45 , vega lew wrote: > At last, I found QE has been upgraded to 4.1.1, but the QE I used > is 4.0.3. > I wonder whether the new vision of QE could do better than the > older one. it does a few things better for sure, but I don't remember major improvements to NEB P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From jhouska at kfy.zcu.cz Sat Nov 7 14:15:35 2009 From: jhouska at kfy.zcu.cz (Jiri Houska) Date: Sat, 07 Nov 2009 14:15:35 +0100 Subject: [Pw_forum] total projections < 1 Message-ID: <20091107141535.nltl4d9j5wgs00sg@webmail.zcu.cz> Hello, am wondering about the following problem: using calculated file "Projections", I made a sum for each electronic state over all atoms (211 occupied + 43 unoccupied states, amorphous insulator). (1) For low energy states, the sum is sufficiently close to 1.00 (>0.99). (2) However, several states below Fermi level the sum starts to decrease almost monotonously with increasing energy, being around 0.80 only for the highest unoccupied state calculated. Please does it indicate a problem, or is it what I have to expect for some reason? Thanks a lot! Jiri Houska Department of Physics University of West Bohemia From paulatto at sissa.it Sat Nov 7 16:00:38 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sat, 7 Nov 2009 16:00:38 +0100 (CET) Subject: [Pw_forum] total projections < 1 In-Reply-To: <20091107141535.nltl4d9j5wgs00sg@webmail.zcu.cz> References: <20091107141535.nltl4d9j5wgs00sg@webmail.zcu.cz> Message-ID: <51445.78.12.172.175.1257606038.squirrel@webmail.sissa.it> Dear Jiri, first of all, welcome to the QE forum. > am wondering about the following problem: using calculated file > "Projections", I made a sum for each electronic state over all atoms > (211 occupied + 43 unoccupied states, amorphous insulator). I guess you are using projwfc.x to compute the projected densi ty of states, if I'm wrong please correct me. > (1) For low energy states, the sum is sufficiently close to 1.00 (>0.99). > > (2) However, several states below Fermi level the sum starts to > decrease almost monotonously with increasing energy, being around 0.80 > only for the highest unoccupied state calculated. Please does it > indicate a problem, or is it what I have to expect for some reason? The lack of charge is a well known issue of projected density of states, if you look at the output of the program you will notice that it reports the "spilling factor", which is exactly what you have computed. There are several possible explanations for the fenomenom you are observing, I'll try to list them. First of all, the projections only collect charge from the neighbourhood of atoms, if some electron wish to go far away from the atom, it will not be caught in the projection! High-energy empty states are more likely to be highly delocalized, and they are computed to a lower accuracy during self-consistency, which may be enough to explain what you see. Second, computing integrals from the density of states may not be the most sensible way to do it. The projected dos depends on the choice of smearing and on the energy step; they are often chosen for aesthetic purpose (i.e. to get a nice plot) more than to compute accurate integrals. best 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 ttduyle at gmail.com Sat Nov 7 16:44:26 2009 From: ttduyle at gmail.com (Duy Le) Date: Sat, 7 Nov 2009 10:44:26 -0500 Subject: [Pw_forum] choosing oxygen and Hydrogen pseudopotentials In-Reply-To: <84ff69170911062248h1a3cc788y56513660ca8e6bab@mail.gmail.com> References: <84ff69170911062248h1a3cc788y56513660ca8e6bab@mail.gmail.com> Message-ID: <8974d3b20911070744h26a4a91ch1f7f9155cf65ea45@mail.gmail.com> Go to this page, and choose the pps you want to use and download them. http://www.quantum-espresso.org/pseudo.php :) -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Sat, Nov 7, 2009 at 1:48 AM, vamsi kv wrote: > Dear all, > > I have done some work on metals using PWscf code. > No i want to see how gases adsorb on metals. Inorder to do that i want to > know how to choose pseudopotentials for gases say Oxygen and Hydrogen and > how to tune the parameters of pseudopotentials to perform the calculations. > > > K V Vamsi > > > > _______________________________________________ > 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/20091107/ed418da2/attachment.htm From marzari at MIT.EDU Sat Nov 7 18:12:24 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Sat, 07 Nov 2009 12:12:24 -0500 Subject: [Pw_forum] choosing oxygen and Hydrogen pseudopotentials In-Reply-To: <8974d3b20911070744h26a4a91ch1f7f9155cf65ea45@mail.gmail.com> References: <84ff69170911062248h1a3cc788y56513660ca8e6bab@mail.gmail.com> <8974d3b20911070744h26a4a91ch1f7f9155cf65ea45@mail.gmail.com> Message-ID: <4AF5AA78.6080409@mit.edu> Indeed - although it's difficult to get accurate results for this particular problem with most xc functionals. A safe bet would be to start from PBE or revPBE or PBEsol; for the pseudo the US RKKJ tend to have been tested quite extensively. nicola Duy Le wrote: > Go to this page, and choose the pps you want to use and download them. > http://www.quantum-espresso.org/pseudo.php > :) > > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > > "Men don't need hand to do things" > > > On Sat, Nov 7, 2009 at 1:48 AM, vamsi kv > wrote: > > Dear all, > > I have done some work on metals using PWscf code. > No i want to see how gases adsorb on metals. Inorder to do that i > want to know how to choose pseudopotentials for gases say Oxygen > and Hydrogen and how to tune the parameters of pseudopotentials to > perform the calculations. > > > K V Vamsi > > > -- --------------------------------------------------------------------- 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 snd2mra at yahoo.com Sat Nov 7 19:27:51 2009 From: snd2mra at yahoo.com (snd2mra at yahoo.com) Date: Sat, 7 Nov 2009 10:27:51 -0800 (PST) Subject: [Pw_forum] Can not restart EXX-PBE0 Relaxation calculation. Message-ID: <743155.32088.qm@web53306.mail.re2.yahoo.com> Dear All, I am not able to restart the EXX-PBE0 relaxation calculation (pwscf Ver 4.1.1 compiled in IBM Power5 - MPI version). Setting "max_seconds = 223200.0D0" made the job to terminate in a clean manner, saving the required results to restart the job. However, on restarting the job, it read atomic positions and unit cell parameters as well as the initial density from the previous run. However, on checking "dexx", i found that the job is just redoing the calculation all from beginning. The job was restarted five times and I am giving the result of "dexx" in each case. As one can see, they all look almost the same: Run1 ---- dexx = 0.00132657 Ry dexx = 0.00070419 Ry dexx = 0.00047010 Ry dexx = 0.00022185 Ry dexx = 0.00010279 Ry dexx = 0.00006006 Ry dexx = 0.00004655 Ry Run2 ---- dexx = 0.00132658 Ry dexx = 0.00070419 Ry dexx = 0.00047008 Ry dexx = 0.00022184 Ry dexx = 0.00010279 Ry dexx = 0.00006006 Ry dexx = 0.00004655 Ry dexx = 0.00004333 Ry dexx = 0.00004407 Ry dexx = 0.00004622 Ry Run3 ---- dexx = 0.00132657 Ry dexx = 0.00070413 Ry dexx = 0.00047011 Ry dexx = 0.00022185 Ry dexx = 0.00010279 Ry Run4 ---- dexx = 0.00132657 Ry dexx = 0.00070412 Ry dexx = 0.00047012 Ry dexx = 0.00022186 Ry dexx = 0.00010279 Ry dexx = 0.00006005 Ry dexx = 0.00004654 Ry dexx = 0.00004332 Ry dexx = 0.00004405 Ry dexx = 0.00004620 Ry dexx = 0.00004763 Ry dexx = 0.00004607 Ry Run5 ---- dexx = 0.00132660 Ry dexx = 0.00070419 Ry dexx = 0.00047007 Ry dexx = 0.00022183 Ry dexx = 0.00010278 Ry dexx = 0.00006006 Ry dexx = 0.00004655 Ry dexx = 0.00004334 Ry dexx = 0.00004407 Ry dexx = 0.00004622 Ry dexx = 0.00004764 Ry dexx = 0.00004607 Ry ------ In put file ---- &CONTROL calculation='relax' restart_mode='restart', prefix='ACManEXX', pseudo_dir = '/home/phd/04/mit/cnode/pwscfjobs/EXX/psps_NC', outdir='/home/hpcscratch/mit/cnodepwout/EXX' wfcdir='/home/hpcscratch/mit/cnodepwout/EXX/temp' etot_conv_thr = 1.0000D-7, forc_conv_thr = 1.0000D-5, wf_collect = .true. , tprnfor = .true. , nstep = 500, max_seconds = 223200.0D0, / &SYSTEM ibrav = 0, nat = 6, ntyp = 2, ecutwfc = 66.148D0 , ecutrho = 264.595D0, tot_charge = 0.000000, occupations = 'fixed' , nspin = 1 , nbnd = 26, input_dft = 'pbe0', / &ELECTRONS electron_maxstep = 180 , mixing_mode = 'local-TF', mixing_beta = 0.2D0, conv_thr = 1.0000D-9 , / &IONS ion_dynamics = 'bfgs', bfgs_ndim = 4, upscale = 10.D0, / CELL_PARAMETERS 22.676713595 0.0 0.0 0.0 22.676713595 0.0 0.0 0.0 4.91234355 ATOMIC_SPECIES C 12.0107 c_pbe.upf H 1.00800 h_pbe.upf ATOMIC_POSITIONS angstrom X 5.93894434 4.62657861 1.87816198 X 5.86347344 5.24631253 0.60776799 X 5.99291940 6.69889806 0.53341804 X 6.18414736 7.42038361 1.69948775 X 5.84262660 3.54534419 1.93381763 X 6.28046619 8.50161892 1.64383194 K_POINTS automatic 1 1 51 0 0 0 --------- end ---- Could comeone please help to make restart work properly ? Thank you - Madan ---------------------------------------- Madan Mithra . L. M, Senior Research Fellow Dept.of Physics Indian Institute of Science Bangalore - 560 012 INDIA ......................................... Phone : 91-80-22932313 (Lab) FAX : (080) 360 2602 ----------------------------------------- From sxu2 at ncsu.edu Sat Nov 7 21:22:16 2009 From: sxu2 at ncsu.edu (shu xu) Date: Sat, 7 Nov 2009 15:22:16 -0500 Subject: [Pw_forum] "cannot open xml_recover file for writing" In-Reply-To: <36d476df0911071220q7d4f1cc1s3c82772f1da411c8@mail.gmail.com> References: <36d476df0910191228l32a9f74dube8f94be4be5602d@mail.gmail.com> <36d476df0910191230x2840c5eeq701cbab56a2100b1@mail.gmail.com> <4ADD75B9.6070102@democritos.it> <4ADEC506.2030807@democritos.it> <36d476df0911071220q7d4f1cc1s3c82772f1da411c8@mail.gmail.com> Message-ID: <36d476df0911071222u51cedd31s99d6952f34ae1505@mail.gmail.com> > Hi all > > I tried espresso-4.0.5 and the restart worked fine. But both 4.1 and 4.1.1 > complained "cannot open xml...". > > I compared 4.0.5 version with 4.1. The difference is that 4.0.5 only has > SC.save directory which contains the > > data-file.xml file. (the prefix is SC). However, 4.1 would create a > _phSC.phsave directory which contains 3 files > > data-file.xml , data-file.xml.1 data-file.xml.1.0 besides the > data-file.xml in SC.save. > > So I guess the phonon restarting problem is probably because the program > cannot locate the multiple xml files in > > _phSC.phsave directory or two data-file.xml files with the same name exist > on SC.save and _phSC.phsave directiory. > > Anyone has an idea to fix this bug? > > > Shu Xu > Dept. of Physics > NCSU > USA > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091107/5ce92aab/attachment.htm From anvari_meh at physics.iust.ac.ir Sun Nov 8 09:31:53 2009 From: anvari_meh at physics.iust.ac.ir (Mehrnaz Anvari) Date: Sun, 08 Nov 2009 12:01:53 +0330 Subject: [Pw_forum] question Message-ID: Hello Recently when I send a messege to forum I get faild message and no one answers my questions. However, my questions exite in archieve. Now what is the reason of this matter? What can I do? Best Mehrnaz Anvari -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091108/54563740/attachment.htm From manoj at phys.ufl.edu Sun Nov 8 09:49:15 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Sun, 8 Nov 2009 03:49:15 -0500 (EST) Subject: [Pw_forum] Left and right going Bloch's states from PWCOND In-Reply-To: <1257175957.3672.13.camel@alex-laptop> Message-ID: Dear Alexander, Thanks for answering my question. I have two more questions. I understand that for muliple channels in the leads, Bloch's states are arranged in order of increasing |kz|. For example- Nchannels of the left tip = 4 k1(2pi/a) k2(2pi/a) E-Ef (eV) -0.2937447 0.0000000 0.0000000 0.3140648 0.0000000 0.0000000 -0.3882921 0.0000000 0.0000000 0.4084626 0.0000000 0.0000000 Nchannels of the right tip = 4 k1(2pi/a) k2(2pi/a) E-Ef (eV) 0.2117188 0.0000000 0.0000000 0.3140394 0.0000000 0.0000000 -0.3915554 0.0000000 0.0000000 -0.4937163 0.0000000 0.0000000 Now when I calculate transmission, code prints out - 1 --> 1 0.0198530 1 --> 2 0.0638572 1 --> 3 0.0193576 1 --> 4 0.5152587 0.61833 and three more sets like this (I am not writing it down). In above 1,2,3,4 correspond to Bloch's states in left and right lead. My question is, are transmission coefficients arranged in the same order as kz 's are. e.g. does transmission coefficient in 1 -->1 stand for transmission coefficient of state kz= -0.2937447 in left lead to state with kz=0.2117188 in the right lead? similarly, 1-->2 mean kz=-0.2937447 to kz=0.3140394 , and so on ? Also, what is eigenchannel decomposition, if I want to get transmission coefficient, code prints out as T_ij for propagating states: 1 --> 1 0.0198530 1 --> 2 0.0638572 1 --> 3 0.0193576 1 --> 4 0.5152587 0.61833 2 --> 1 0.1840566 2 --> 2 0.3834998 2 --> 3 0.0693121 2 --> 4 0.1578845 0.79475 3 --> 1 0.1853693 3 --> 2 0.0321809 3 --> 3 0.1536389 3 --> 4 0.0309744 0.40216 4 --> 1 0.1601806 4 --> 2 0.0132465 4 --> 3 0.2321587 4 --> 4 0.1197219 0.52531 then what information does eigenchannel decomposition contain? Eigenchannel decomposition: @ 1 0.00000 0.10086 0.31024 0.09173 0.36027 0.23776 @ 2 0.00000 0.47744 0.03523 0.03500 0.49217 0.43760 @ 3 0.00000 0.84821 0.42617 0.44674 0.06122 0.06587 @ 4 0.00000 0.91404 0.22836 0.42652 0.08634 0.25877 I dont know what to think of these numbers. Thanks for your help. Regards, Manoj On Mon, 2 Nov 2009, Alexander Smogunov wrote: > Dear Manoj. > The new parameter lorb is simply used to give in output the scattering > states so that you could plot them, it does not affect the transmission > calculation itself. If it is .false. the code will run normally as > before... It is true that this new option does not work for ikind=2, > but you can still calculate transmission and reflection amplitudes. > To calculate t and r from right to left you should simply > call the transmit routine in do_cond.f90 with the last argument > to set to .false. By default the code does not compute the > case of right --> left scattering since the total transmission > is the same as in left --> right case. Only if you want to plot the > scattering states (lorb=.true.) it does that. > It is how the things are implemented now ... > Best regards, > Alexander > > > > > On Fri, 2009-10-30 at 14:04 -0400, Manoj Srivastava wrote: > > Just to add one more question. > > what is 'lorb' switch. I get following- > > lorb, & ! if .t. calculate the scattering (or Bloch) states > > so, i guess for transmission calculation i will have to set it to > > 't'. now- > > IF (lorb.and.ikind.eq.2) call errore('do_cond','lorb not working with > > ikind = 2',1) > > so, it seems that calculation for r and t for right and left going > > state, when left and right leads are different doesnot work. Is that > > correct? A possible work around may be rotating the whole system by 180 > > degree, which would be like treating left lead as right lead and > > scattering region rotated. Can I do that? > > > > Regards, > > Manoj > > > > On Fri, 30 Oct 2009, Manoj Srivastava wrote: > > > > > Dear Alexander, > > > Thank you very much! I read the code, it seems that there are > > > quiet a few changes in 4.1.1 compared to 4.0.4 :) .So, just to make sure, > > > if I want to calculate r and t for left going Bloch's state as well as > > > right going Bloch's state, I need to run the code two times, one time with > > > 'left_to_right' switch true, and another time false. I dont need to change > > > scattering region or interchange left and right leads. > > > > > > Regards, > > > Manoj Srivastava > > > On Thu, 29 Oct 2009, Alexander > > > Smogunov wrote: > > > > > > > Dear Manoj > > > > > > > > On Wed, 2009-10-28 at 01:49 -0400, Manoj Srivastava wrote: > > > > > Dear Alexander, > > > > > You are correct, left and right moving states are in general not > > > > > related. I was wrong about trying to create a pair. Thanks for > > > > > clarification. > > > > > I have a few more questions. > > > > > 1. I want to find out the reflection coefficient in the code. In > > > > > transmit.f90, transmission coefficient is |tmat(ig,n)|^2, where tmat is > > > > > vec1(ntran-n2d-npol*nocrosr+ig,n). (line 206, of version 4.0.5). > > > > > Reflection is not explicitly calculated in the code, but it should be > > > > > modulus square of vec1(2*n2d+npol*norbs+ig,n) (line 234). Am I correct? > > > > > > > > in the 4.1 version there is output of both t and r. > > > > > > > > > > > > > > > > > > 2. In the code reflection and transmission coefficients are calculated > > > > > for one direction lets say t++ and t+-, which is transmission and > > > > > reflection coefficient for Bloch' state moving from - to + , or in other > > > > > words, left to right. To calculate transmission and reflection for Bloch's > > > > > state going from right to left, what should I do? Should i just rotate my > > > > > system 180 degree, that way leads get interchanged and also scattering > > > > > area has orientation 180 different from before. > > > > > > > > > > > > > again in the 4.1 version you have possibility to calculate t and r for > > > > both directions, in the do_cond.f90 the transmit routine is called with > > > > an extra parameter which is true (false) if you want to calculate > > > > scattering states propagating from the left (from the right). > > > > > > > > > 3. In the subroutine sunitary.f90, is raux measure of conservation of > > > > > flux? If I sum all the transmission and reflecion coefficient for > > > > > a particular Bloch's state, I should get 1, and computationally a number > > > > > close to 1. How large could it be for S matrix not to be unitary, i m > > > > > getting raux more than one e.g. 1.0011 but code still considers smatrix > > > > > to be unitary. > > > > > > > > in the case when |R + T - 1| > 1.d-4 for some band, it should print out > > > > the value of R+T but continues to run anyway. > > > > > > > > All the best, > > > > Alexander > > > > > > > > > > > > > > > > > > > > > > Regards, > > > > > Manoj Srivastava > > > > > University of Florida, Gainesville, FL > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Thu, 22 > > > > > Oct 2009, Alexander Smogunov wrote: > > > > > > > > > > > On Thu, 2009-10-22 at 11:34 -0400, Manoj Srivastava wrote: > > > > > > > Dear Alexander, > > > > > > > Thanks for your answer. I just want to make sure. Imagine we have total > > > > > > > number of channels in the left lead 2, so total number of Bloch's state > > > > > > > are 4. 2 of them left going say a and b, and 2 right going say c and d. > > > > > > > So, are you saying that for left going state a, the corresponding right > > > > > > > going state is c? Are they ordered this way? > > > > > > > > > > > > what do you mean by corresponding? Left and right moving Bloch > > > > > > states are in general not related one to another, you can even have > > > > > > different number of them ... Only if you have some symmetry S which > > > > > > brings kz to -kz conserving k_parallel, then the state with > > > > > > \psi_{-kz} will be S \psi{kz}. This is true for example at 2D G point > > > > > > when you have time reversal operation. > > > > > > > > > > > > Now the code simply arranges the propagating states in the order of > > > > > > increasing |k_z|... > > > > > > > > > > > > Regards, Alexander > > > > > > > > > > > > > > > > > > > > > > > > > > Regards, > > > > > > > Manoj > > > > > > > > > > > > > > > > > > > > > On Thu, 22 Oct 2009, Alexander > > > > > > > Smogunov wrote: > > > > > > > > > > > > > > > Dear Manoj. > > > > > > > > > > > > > > > > The output of complex k vectors is performed in > > > > > > > > summary_band.f90 routine. If you want to see all > > > > > > > > the complex k vectors, not only propagating ones, > > > > > > > > you can change at the end of this routine: > > > > > > > > > > > > > > > > ------------------- > > > > > > > > do i = 1, nchanl > > > > > > > > WRITE( stdout,'(3f12.7)') DBLE(kvall(i)), AIMAG(kvall(i)), eev > > > > > > > > enddo > > > > > > > > ------------------- > > > > > > > > > > > > > > > > to > > > > > > > > ------------------- > > > > > > > > > > > > > > > > do i = 1, 2*nstl > > > > > > > > WRITE( stdout,'(3f12.7)') DBLE(kvall(i)), AIMAG(kvall(i)), eev > > > > > > > > enddo > > > > > > > > ------------------- > > > > > > > > > > > > > > > > Altogether there are 2*nstl (or 2*nstr) Bloch states in the left > > > > > > > > (or right) lead. First half, [1,nstl], are propagating or decaying to > > > > > > > > the right states, another half, [nstl+1,2*nstl], - propagating or > > > > > > > > decaying to the left. In each group, first nchanl states are propagating > > > > > > > > states. > > > > > > > > > > > > > > > > The propagating states are normalized by the current and are arranged in > > > > > > > > the above order at the end of jbloch.f90 routine, after the following > > > > > > > > lines: > > > > > > > > > > > > > > > > ! > > > > > > > > ! Right ordering (+, >, -, <) > > > > > > > > ! > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Notice, that in the last versions the code gives in output > > > > > > > > both propagating to the right and to the left states. > > > > > > > > > > > > > > > > Hope this helps, > > > > > > > > Alexander > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Wed, 2009-10-21 at 14:13 -0400, Manoj Srivastava wrote: > > > > > > > > > Dear All, > > > > > > > > > I am trying to figure out the left and right going Bloch's states in the > > > > > > > > > lead from PWCOND. For a given (kx,ky)and energy we get kz. The code only > > > > > > > > > prints out Bloch's state moving in one direction. eg. in one of the > > > > > > > > > calculation- > > > > > > > > > k//=(0.375,-0.375) > > > > > > > > > Nchannels of the left tip = 1 > > > > > > > > > k1(2pi/a) k2(2pi/a) E-Ef (eV) > > > > > > > > > > > > > > > > > > 0.3157801 0.0000000 0.0000000 > > > > > > > > > > > > > > > > > > Now if I want Bloch's state moving in right as well as left direction, I > > > > > > > > > can go to kbloch.f90 subroutine, and print out all the eigen values of > > > > > > > > > AX=exp(ikd)BX, and out of those the ones with real solution would be our > > > > > > > > > Bloch's state, so I get for each channel two solutions- > > > > > > > > > kval (-0.275409421993275,1.823688001395235E-010) > > > > > > > > > kval (0.315780119742506,-3.611201785292708E-012) > > > > > > > > > > > > > > > > > > To figure out the direction, I can calculate current associated with these > > > > > > > > > Bloch's sate and if the current is +ive it is right moving , and if '-'ive > > > > > > > > > its left moving Bloch's state. I can print out current from jbloch.f90 > > > > > > > > > subroutine which are - > > > > > > > > > current eigenvalue -1.86502143831863 1.59149029314457 > > > > > > > > > > > > > > > > > > So, clearly the first state with kval=-0.2754094 is left moving and the > > > > > > > > > other one right moving. Upto here its clear to me how to identify left and > > > > > > > > > right moving states. > > > > > > > > > > > > > > > > > > I get confused when for a given (kx,ky,E), I have more than one Bloch' > > > > > > > > > state. In another calculation where i get multiple Bloch's state- > > > > > > > > > Nchannels of the left tip = 5 > > > > > > > > > k1(2pi/a) k2(2pi/a) E-Ef (eV) > > > > > > > > > > > > > > > > > > -0.0746301 0.0000000 0.0000000 > > > > > > > > > 0.1205527 0.0000000 0.0000000 > > > > > > > > > 0.3112908 0.0000000 0.0000000 > > > > > > > > > 0.4200218 0.0000000 0.0000000 > > > > > > > > > -0.4935150 0.0000000 0.0000000 > > > > > > > > > > > > > > > > > > so i did the same trick i did above to first print out kz and then > > > > > > > > > current, which gives me - > > > > > > > > > kval (-0.420023481074359,1.979595081419732E-010) (call it a) > > > > > > > > > kval (0.420023367986768,2.500979698670295E-011) (b) > > > > > > > > > kval (-0.306507431678779,-1.236804629184431E-011) (c) > > > > > > > > > kval (-0.125376071175573,-6.134512510438736E-011) (d) > > > > > > > > > kval (-7.945001124706894E-002,6.683546930037856E-011)(e) > > > > > > > > > kval (0.106554601758169,-6.427946951285107E-011) (f) > > > > > > > > > kval (8.866867725358024E-002,8.342250371574646E-011) (g) > > > > > > > > > kval (0.325333314672671,1.260810749228185E-011) (h) > > > > > > > > > kval (-0.488725859521576,1.769197678346003E-010) (i) > > > > > > > > > kval (0.479509832763231,1.765499400037283E-010) (j) > > > > > > > > > > > > > > > > > > current eigenvalue -9.31389492882581 -1.24296522993488 > > > > > > > > > -1.21324078359658 -1.11950286753963 -1.08166842367443 > > > > > > > > > 1.08187482164864 1.11973146584263 1.21295295042188 > > > > > > > > > 1.24280031534940 9.313897787790 > > > > > > > > > > > > > > > > > > So, the first 5 are left moving and rest are right moving. But I dont know > > > > > > > > > the pairs. for example for left moving state a, what is the corresponding > > > > > > > > > right moving state whether its f or g ... j ? > > > > > > > > > > > > > > > > > > Any help would be appreciated. > > > > > > > > > > > > > > > > > > Regards, > > > > > > > > > Manoj Srivastava > > > > > > > > > University of Florida, Gainesville. > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > > Pw_forum mailing list > > > > > > > > > Pw_forum at pwscf.org > > > > > > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > > > > > > > > e-mail: 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 > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > Pw_forum mailing list > > > > > > > Pw_forum at pwscf.org > > > > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > > > > > > e-mail: 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 > > > > > > > > > > > > > > > > _______________________________________________ > > > > > Pw_forum mailing list > > > > > Pw_forum at pwscf.org > > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > > > > e-mail: 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 > > > > > > > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > -- > e-mail: 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 Sun Nov 8 10:45:23 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 8 Nov 2009 10:45:23 +0100 Subject: [Pw_forum] question In-Reply-To: References: Message-ID: <56B5221E-FEC2-44BA-B5D4-664242B83E01@democritos.it> On Nov 8, 2009, at 9:31 , Mehrnaz Anvari wrote: > Recently when I send a messege to forum I get faild message > and no one answers my questions. However, my questions exite > in archieve. Now what is the reason of this matter? What can I do? try to reformulate your question in an understandable format --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sun Nov 8 16:03:02 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 8 Nov 2009 16:03:02 +0100 Subject: [Pw_forum] "cannot open xml_recover file for writing" In-Reply-To: <36d476df0911071222u51cedd31s99d6952f34ae1505@mail.gmail.com> References: <36d476df0910191228l32a9f74dube8f94be4be5602d@mail.gmail.com> <36d476df0910191230x2840c5eeq701cbab56a2100b1@mail.gmail.com> <4ADD75B9.6070102@democritos.it> <4ADEC506.2030807@democritos.it> <36d476df0911071220q7d4f1cc1s3c82772f1da411c8@mail.gmail.com> <36d476df0911071222u51cedd31s99d6952f34ae1505@mail.gmail.com> Message-ID: On Nov 7, 2009, at 21:22 , shu xu wrote: > So I guess the phonon restarting problem is probably because the > program cannot locate the multiple xml files in _phSC.phsave > directory or two data-file.xml files with the same name exist on > SC.save and _phSC.phsave directiory. > > Anyone has an idea to fix this bug? if you are really convinced that there is a bug, please file a bug report (see http://qe-forge.org/tracker/?atid=133&group_id=10) with a description of the exact conditions leading to incorrect behavior and a (preferrably small) test job. I couldn't see anything obviously wrong in phonon restart. P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From quantumdft at gmail.com Sun Nov 8 16:32:58 2009 From: quantumdft at gmail.com (vega lew) Date: Sun, 8 Nov 2009 23:32:58 +0800 Subject: [Pw_forum] Something about the bandwith of memory Message-ID: <412f6c680911080732p2e03ddfdk4d8a5b9e2273ed84@mail.gmail.com> Dear all, Intel E5500 seriers CPU has a triple channel to enhance the bandwidth of the memory. And sometime earlier, Axel told me that the bandwidth of memory is one of the most important thing for the performance of QE. So we try to make a contract with the seller of intel server based on XEON Nahelem processors. But we find the bandwidth of memory is not only depends on the CPU, chipset and memory module et al., but is also depends on something else. For example, the server made by HP, and DELL of the same CPU an DDR3 memory would show different bandwidth performance evaluating by ScienceMark v2.0. But ScienceMark v2.0 only could be run in Windows. So I wonder is there a small tool to test the bandwith of memory in Linux? think you for reading vega -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091108/29f49e3e/attachment-0001.htm From giannozz at democritos.it Sun Nov 8 17:16:57 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 8 Nov 2009 17:16:57 +0100 Subject: [Pw_forum] "cannot open xml_recover file for writing" In-Reply-To: References: <36d476df0910191228l32a9f74dube8f94be4be5602d@mail.gmail.com> <36d476df0910191230x2840c5eeq701cbab56a2100b1@mail.gmail.com> <4ADD75B9.6070102@democritos.it> <4ADEC506.2030807@democritos.it> <36d476df0911071220q7d4f1cc1s3c82772f1da411c8@mail.gmail.com> <36d476df0911071222u51cedd31s99d6952f34ae1505@mail.gmail.com> Message-ID: <8B3C8262-8005-45E2-A18C-C8687878D311@democritos.it> On Nov 8, 2009, at 16:03 , Paolo Giannozzi wrote: > I couldn't see anything obviously wrong in phonon restart. actually, there is something wrong, but it is not obvious what why ... P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From snd2mra at yahoo.com Sun Nov 8 20:30:09 2009 From: snd2mra at yahoo.com (Madan Mithra. L. M) Date: Sun, 8 Nov 2009 11:30:09 -0800 (PST) Subject: [Pw_forum] Can not restart EXX-PBE0 Relaxation calculation. Message-ID: <158137.42920.qm@web53301.mail.re2.yahoo.com> From: snd2mra at yahoo.com Subject: Can not restart EXX-PBE0 Relaxation calculation. To: pw_forum at pwscf.org Date: Saturday, November 7, 2009, 11:57 PM Dear All, I am not able to restart the EXX-PBE0 relaxation calculation (pwscf Ver 4.1.1 compiled in IBM Power5 - MPI version). Setting "max_seconds = 223200.0D0" made the job to terminate in a clean manner, saving the required results to restart the job. However, on restarting the job, it read atomic positions and unit cell parameters as well as the initial density from the previous run. However, on checking "dexx", i found that the job is just redoing the calculation all from beginning. The job was restarted five times and I am giving the result of "dexx" in each case. As one can see, they all look almost the same: > Run1 > ---- > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00132657 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00070419 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00047010 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00022185 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00010279 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00006006 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00004655 Ry > > Run2 > ---- > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00132658 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00070419 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00047008 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00022184 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00010279 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00006006 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00004655 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00004333 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00004407 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00004622 Ry > > Run3 > ---- > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00132657 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00070413 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00047011 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00022185 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00010279 Ry > > Run4 > ---- > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00132657 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00070412 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00047012 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00022186 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00010279 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00006005 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00004654 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00004332 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00004405 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00004620 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00004763 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00004607 Ry > > Run5 > ---- > > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00132660 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00070419 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00047007 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00022183 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00010278 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00006006 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00004655 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00004334 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00004407 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00004622 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00004764 Ry > ? ???dexx? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.00004607 Ry > > ------ In put file ---- > > &CONTROL > ? ? calculation='relax' > ? ? restart_mode='restart', > ? ? prefix='ACManEXX', > ? ? pseudo_dir = > '/home/phd/04/mit/cnode/pwscfjobs/EXX/psps_NC', > ? ? outdir='/home/hpcscratch/mit/cnodepwout/EXX' > ? ? > wfcdir='/home/hpcscratch/mit/cnodepwout/EXX/temp' > ? ? etot_conv_thr = 1.0000D-7, > ? ? forc_conv_thr = 1.0000D-5, > ? ? wf_collect = .true. , > ? ? tprnfor = .true. , > ? ? nstep = 500, > ? ? max_seconds = 223200.0D0, > / > &SYSTEM > ? ? ? ? ? ? ? ? > ? ? ???ibrav = 0, > ? ? ? ? ? ? ? ? > ? ? ? ???nat = 6, > ? ? ? ? ? ? ? ? > ? ? ? ? ntyp = 2, > ? ? ? ? ? ? ? ? > ? ???ecutwfc = 66.148D0 , > ? ? ? ? ? ? ? ? > ? ???ecutrho = 264.595D0, > ? ? ? ? ? ? ? ? > ? tot_charge = 0.000000, > ? ? ? ? ? ? ? > ???occupations = 'fixed' , > ? ? ? ? ? ? ? ? > ? ? ???nspin = 1 , > ? ? ? ? ? ? ? ? > ? ? ? ? nbnd = 26, > ? ? ? ? ? ? ? ? > ???input_dft = 'pbe0', > / > &ELECTRONS > ? ? ? ? ? ? electron_maxstep > = 180 , > ? ? ? ? ? ? ? > ???mixing_mode = 'local-TF', > ? ? ? ? ? ? ? > ???mixing_beta = 0.2D0, > ? ? ? ? ? ? ? ? > ? ? conv_thr = 1.0000D-9 , > / > &IONS > ? ? ? ? ? ? ? ? > ion_dynamics = 'bfgs', > ? ? ? ? ? ? ? ? > ???bfgs_ndim = 4, > ? ? ? ? ? ? ? ? > ? ???upscale = 10.D0, > / > > CELL_PARAMETERS > 22.676713595 0.0 0.0 > 0.0 22.676713595 0.0 > 0.0 0.0 4.91234355 > > ATOMIC_SPECIES > ? ? C? ? 12.0107? c_pbe.upf > ? ? H? ? 1.00800? h_pbe.upf > > ATOMIC_POSITIONS angstrom > X???5.93894434? ? > 4.62657861? ? 1.87816198 > X???5.86347344? ? > 5.24631253? ? 0.60776799 > X???5.99291940? ? > 6.69889806? ? 0.53341804 > X???6.18414736? ? > 7.42038361? ? 1.69948775 > X???5.84262660? ? > 3.54534419? ? 1.93381763 > X???6.28046619? ? > 8.50161892? ? 1.64383194 > > K_POINTS automatic > ? 1 1 51???0 0 0 > > --------- end ---- Could comeone please help to make restart work properly ? Thank you - Madan > ? ? ? ? ? ? ? ? > ? ? ? > ???---------------------------------------- > ? ? ? ? ? ? ? ? > ? ? ? ???Madan Mithra . L. M, > ? ? ? ? ? ? ? ? > ? ? ? ???Senior Research > Fellow > ? ? ? ? ? ? ? ? > ? ? ? ???Dept.of Physics > ? ? ? ? ? ? ? ? > ? ? ? ???Indian Institute of > Science > ? ? ? ? ? ? ? ? > ? ? ? ???Bangalore - 560 012 > ? ? ? ? ? ? ? ? > ? ? ? ???INDIA > ? ? ? ? ? ? ? ? > ? ? ? > ???......................................... > ? ? ? ? ? ? ? ? > ? ? ? ???Phone? : > 91-80-22932313? ? (Lab) > ? ? ? ? ? ? ? ? > ? ? ? ???FAX? ? : > (080) 360 2602 > ? ? ? ? ? ? ? ? > ? ? ? > ???----------------------------------------- > > > > ? ? ? > From giannozz at democritos.it Sun Nov 8 21:05:58 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 8 Nov 2009 21:05:58 +0100 Subject: [Pw_forum] Can not restart EXX-PBE0 Relaxation calculation. In-Reply-To: <158137.42920.qm@web53301.mail.re2.yahoo.com> References: <158137.42920.qm@web53301.mail.re2.yahoo.com> Message-ID: <160FFD05-C936-4B4D-85F7-C83245C3283C@democritos.it> On Nov 8, 2009, at 20:30 , Madan Mithra. L. M wrote: > The job was restarted five times ...and are you going to send the same message five times as well? As I said no less than two days ago, lesser-used options are also less tested than others. Exact exchange is something reatively new and restarting from interrupted calculations is not guaranteed to work. It will be fixed sooner or later. P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From sclauzer at sissa.it Mon Nov 9 11:20:24 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 09 Nov 2009 11:20:24 +0100 Subject: [Pw_forum] k-mesh in pwcond In-Reply-To: <21fbc4790911061907k60e31182w5f11428e57e8419a@mail.gmail.com> References: <51ec861d0911061646v37aa44ffh43f1af3594dfe99d@mail.gmail.com> <21fbc4790911061907k60e31182w5f11428e57e8419a@mail.gmail.com> Message-ID: <4AF7ECE8.4050304@sissa.it> xirainbow wrote: > Dear ? > I do not think pwcond can set k-mesh along the transport direction. > Instead, you can set k-mesh perpendicular to the transport direction. > > The transport device can be period perpendicular to the transport direction. > However, it is not period along the transport direction This is right, in the pwcond calculation the Born-von Karman PBCs are removed along the transport direction, and you need to take care only of the 2D BZ sampling in the perpendicular directions. Anyway, in the preceding pwscf calculation, periodicity is still there in all 3 directions, hence you need a proper k-point sampling also along the transport direction, especially for the leads, which usually are a bulk periodic unit (hence they may not be a supercell). HTH GS > > On Sat, Nov 7, 2009 at 12:46 AM, Zubaer Hossain > wrote: > > Dear QE users, > > Is there any rule for choosing k-meshes for the lead and the > scattering region along the transport direction? > > Thanks in advance, > Zubaer > UIUC > > > > > -- > ____________________________________ > Hui Wang > School of physics, Nankai University, Tianjin, China > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 Nov 9 11:32:06 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 09 Nov 2009 11:32:06 +0100 Subject: [Pw_forum] total projections < 1 In-Reply-To: <20091107141535.nltl4d9j5wgs00sg@webmail.zcu.cz> References: <20091107141535.nltl4d9j5wgs00sg@webmail.zcu.cz> Message-ID: <4AF7EFA6.4040007@sissa.it> Jiri Houska wrote: > Hello, > am wondering about the following problem: using calculated file > "Projections", I made a sum for each electronic state over all atoms > (211 occupied + 43 unoccupied states, amorphous insulator). From where are you collecting the occupations? From the standard output of projwfc.x or from filpdos? You should be aware that in the former case, when writing the "local charge decomposition" of each KS eigenstate, the program gives on standard output only contributions from atomic orbitals with an overlap (on that state) which is larger than 0.001. HTH GS > > (1) For low energy states, the sum is sufficiently close to 1.00 (>0.99). > > (2) However, several states below Fermi level the sum starts to > decrease almost monotonously with increasing energy, being around 0.80 > only for the highest unoccupied state calculated. Please does it > indicate a problem, or is it what I have to expect for some reason? > > Thanks a lot! > > Jiri Houska > Department of Physics > University of West Bohemia > > > _______________________________________________ > 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 sh.shapt at gmail.com Mon Nov 9 14:05:26 2009 From: sh.shapt at gmail.com (Shaptrishi Sharma) Date: Mon, 9 Nov 2009 13:05:26 +0000 Subject: [Pw_forum] About K Points while running scf and nscf calculation Message-ID: Hi There, I would like to know one thing,when I run a scf calculation I ahve to assign k points as automatic, while runningn a nscf calculation I must give it Crystal, and if it is written automatic it wont run. why is it so? One more question : what is the difference between running a scf calculation with K points as 6 1 1 0 0 0 and the same nscf calculations with 50 kpoints? Regards S Shapt Sharma Msc (Physics), Pune -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091109/d118bab8/attachment.htm From paulatto at sissa.it Mon Nov 9 14:13:10 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 09 Nov 2009 14:13:10 +0100 Subject: [Pw_forum] About K Points while running scf and nscf calculation In-Reply-To: References: Message-ID: In data 09 novembre 2009 alle ore 14:05:26, Shaptrishi Sharma ha scritto: > I would like to know one thing,when I run a scf calculation I ahve to > assign > k points as automatic, while runningn a nscf calculation I must give it > Crystal, and if it is written automatic it wont run. why is it so? Dear Shaptrishi, It is not. I'm sure you can use automatic k-point generation in ncsf calculations too. If you are having some issue in a specific case, please report that case. > One more question : what is the difference between running a scf > calculation with K points as > 6 1 1 0 0 0 > and the same nscf calculations with 50 kpoints? You are the only one that can tell, we cannot tell the difference of something we don't know. For sure they have different k-points and one is not self-consistent while the other is not. 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 kazempoor2000 at yahoo.com Mon Nov 9 14:32:52 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Mon, 9 Nov 2009 05:32:52 -0800 (PST) Subject: [Pw_forum] constraints Message-ID: <599421.51225.qm@web112510.mail.gq1.yahoo.com> Dear All I want to fix the distance between two atom during relaxation , the distance is 1.98 , but the code crash and the error is target = 3.67419827 dmax = 2.79062000 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from init_constraint : error # 1 the target for constraint 1 is larger than the largest possible value %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% why does it happen and what can I do? this is my input file: &CONTROL title = 'routile lattice BFGS' , calculation = 'relax' , restart_mode = 'from_scratch' , outdir = '/ptmp/kazempou/scratch' , pseudo_dir = './' , prefix = 'routil lattice default' , etot_conv_thr = 0.000000735 , forc_conv_thr = 0.0011668141375 , / &SYSTEM ibrav = 6, celldm(1) = 8.68, celldm(3) = 0.643, nat = 6, ntyp = 2, ecutwfc = 15 , ecutrho = 400 , / &ELECTRONS conv_thr = 1.0D-4 , / &IONS / ATOMIC_SPECIES Ti 47.86700 ti.optgga2.fhi.UPF O 15.99940 o.optgga1.fhi.UPF ATOMIC_POSITIONS crystal Ti 0.000000000 0.000000000 0.000000000 Ti 0.500000000 0.500000000 0.500000000 O 0.305300000 0.305300000 0.000000000 O -0.305300000 -0.305300000 0.000000000 O 0.805300000 0.194700000 0.500000000 O 0.194700000 0.805300000 0.500000000 K_POINTS automatic 8 8 10 0 0 0 CONSTRAINTS 1 1.98 'distance' 2 4 thanks a lot Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091109/2361e13c/attachment.htm From paulatto at sissa.it Mon Nov 9 14:39:17 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 09 Nov 2009 14:39:17 +0100 Subject: [Pw_forum] constraints In-Reply-To: <599421.51225.qm@web112510.mail.gq1.yahoo.com> References: <599421.51225.qm@web112510.mail.gq1.yahoo.com> Message-ID: In data 09 novembre 2009 alle ore 14:32:52, ali kazempour ha scritto: > Dear All > I want to fix the distance between two atom during relaxation , the > distance is 1.98 , but the code crash and the error is > target = 3.67419827 > dmax = 2.79062000 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from init_constraint : error # 1 > the target for constraint 1 is larger than the largest possible > value > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > why does it happen and what can I do? Dear Ali, the constraint is in unit of celldm(1), in your specific case you have asked the two atoms to be about 16 Angstrom apart, which is impossible in periodic boundary conditions with such a unit cell. 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 kazempoor2000 at yahoo.com Mon Nov 9 14:49:31 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Mon, 9 Nov 2009 05:49:31 -0800 (PST) Subject: [Pw_forum] constraints In-Reply-To: References: <599421.51225.qm@web112510.mail.gq1.yahoo.com> Message-ID: <90134.9293.qm@web112517.mail.gq1.yahoo.com> Dear Lorenzo Thank you for reply. IF I change the value of 1.98 to 0.4 then it should work or not? Do I choose bigger cell?Which parameter should be modified? thanks Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German ________________________________ From: Lorenzo Paulatto To: PWSCF Forum Sent: Mon, November 9, 2009 2:39:17 PM Subject: Re: [Pw_forum] constraints In data 09 novembre 2009 alle ore 14:32:52, ali kazempour ha scritto: > Dear All > I want to fix the distance between two atom during relaxation , the > distance is 1.98 , but the code crash and the error is > target = 3.67419827 > dmax = 2.79062000 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from init_constraint : error # 1 > the target for constraint 1 is larger than the largest possible > value > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > why does it happen and what can I do? Dear Ali, the constraint is in unit of celldm(1), in your specific case you have asked the two atoms to be about 16 Angstrom apart, which is impossible in periodic boundary conditions with such a unit cell. 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091109/6c9d125f/attachment-0001.htm From paulatto at sissa.it Mon Nov 9 14:54:05 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 09 Nov 2009 14:54:05 +0100 Subject: [Pw_forum] constraints In-Reply-To: <90134.9293.qm@web112517.mail.gq1.yahoo.com> References: <599421.51225.qm@web112510.mail.gq1.yahoo.com> <90134.9293.qm@web112517.mail.gq1.yahoo.com> Message-ID: In data 09 novembre 2009 alle ore 14:49:31, ali kazempour ha scritto: > Thank you for reply. IF I change the value of 1.98 to 0.4 then it > should work or not? Do I choose bigger cell?Which parameter should be > modified? Whoops! I've noticed I misinterpreted you previous email... your input is actually correct (although, strange) and should not give such a problem, I will investigate further into it, but it will take a while. For now, notice that the value 1.98 you have specified it the constraint tolerance, and it is far too high... the constraint target goes on the same line of the constraint, like this: CONSTRAINTS 1 1.d-4 'distance' 2 4 0.4 The algorithm that re-wraps atomic coordinates inside the unit cell should work in your case, not give that error... as a quick solution you can try to translate atom #2 inside the unit cell by hand. 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 cristian.degliesposti at unibo.it Mon Nov 9 17:16:24 2009 From: cristian.degliesposti at unibo.it (Cristian Degli Esposti Boschi) Date: Mon, 09 Nov 2009 17:16:24 +0100 Subject: [Pw_forum] e: "cannot open xml_recover file for writing" Message-ID: <4AF84058.6010803@unibo.it> Well, by comparing the output of my (several) aborted runs on SP6 (CINECA) with what reported in Shu Xu's messages (of 8/11/2009 and 20/10/2009) it seems that I have exactly the same problem when trying to restart a phonon run (ph.x) with QuantumESPRESSO 4.1, that is an error message cannot open xml_recover file for writing I also suspect that it is due to a different directory structure in version 4.1, so I encourage to report a bug as suggested by Paolo Giannozzi. Otherwise I will do it as soon as I have completed one more check... Thanks for your time, Cristian -- ___________________________________________________ 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 anvari_meh at physics.iust.ac.ir Mon Nov 9 19:49:46 2009 From: anvari_meh at physics.iust.ac.ir (Mehrnaz Anvari) Date: Mon, 09 Nov 2009 22:19:46 +0330 Subject: [Pw_forum] elph question Message-ID: Hi First, thanks a lot because of your answer, it assured me that you can recieve my mails. Secondly, I performed elph calculations for graphene and I got a wrong answer for lambda(about 0.0173), so I want to know that is it possible to do elph calculations for graphene ? or because it has zero DOS at fermi surface this calculations are forbbiden for this material. Best Mehrnaz Iran university of science & technology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091109/5feb208c/attachment.htm From modaresi.mohsen at gmail.com Mon Nov 9 20:04:21 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Mon, 9 Nov 2009 22:04:21 +0300 Subject: [Pw_forum] HI Message-ID: Hi I faced with a problem. I made a file with "pwgui" but when i run "pw.x" i faced with this message from iosys : error # 1 invalid dual? What it means? And i send that file. With especial thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091109/f87ff789/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: pw.in Type: application/octet-stream Size: 2535 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091109/f87ff789/attachment.obj From anvari_meh at physics.iust.ac.ir Mon Nov 9 19:56:47 2009 From: anvari_meh at physics.iust.ac.ir (Mehrnaz Anvari) Date: Mon, 09 Nov 2009 22:26:47 +0330 Subject: [Pw_forum] phonon dispersion Message-ID: Hi I've tried to plot phonon dispersion of graphene in gamma ,M,K,gamma direction. Although I used asr=crystal in my calculations, the acoustic phonons at first gamma point are not exactly zero. what is the reason of this happening? does it relate to choosing c/a in difinition of graphene? Mehrnaz -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091109/6ba074d7/attachment.htm From ttduyle at gmail.com Mon Nov 9 20:19:17 2009 From: ttduyle at gmail.com (Duy Le) Date: Mon, 9 Nov 2009 14:19:17 -0500 Subject: [Pw_forum] HI In-Reply-To: References: Message-ID: <8974d3b20911091119u2072f9c5k18b69d62bf323ff0@mail.gmail.com> pwgui is good, but you should know what you are doing. There are too many UNPHYSICAL parameters in the given input. There are plenty tutorials you may need to look at them before doing serious calculations http://www.fisica.uniud.it/~giannozz/QE-Tutorial/ -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Mon, Nov 9, 2009 at 2:04 PM, mohsen modaresi wrote: > Hi > I faced with a problem. > I made a file with "pwgui" but when i run "pw.x" i faced with this message > from iosys : error # 1 > invalid dual? > What it means? > And i send that file. > With especial thanks. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091109/903ba15a/attachment.htm From giannozz at democritos.it Mon Nov 9 20:34:02 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 9 Nov 2009 20:34:02 +0100 Subject: [Pw_forum] phonon dispersion In-Reply-To: References: Message-ID: On Nov 9, 2009, at 19:56 , Mehrnaz Anvari wrote: > Although I used asr=crystal in my calculations, the acoustic > phonons at first gamma point are not exactly zero. > what is the reason of this happening? does it relate to > choosing c/a in difinition of graphene? short answers: 1) I don't know 2) no. Even after ASR is imposed, a very small nonzero frequency (fractions of cm^{-1)) is still obtained as the rsult of the diagonalization. It might be numrical noise in the diagonalization, though P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Mon Nov 9 20:36:37 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 9 Nov 2009 20:36:37 +0100 Subject: [Pw_forum] elph question In-Reply-To: References: Message-ID: <0C74430D-A74F-4243-ACE1-AAFA541023C0@democritos.it> On Nov 9, 2009, at 19:49 , Mehrnaz Anvari wrote: > I performed elph calculations for graphene and I got a > wrong answer for lambda(about 0.0173), so I want to > know that is it possible to do elph calculations for graphene ? > there are several papers by the Paris group (Mauri, Lazzeri et al) about the calculation of electron-phonon coefficients in graphene. It is a tricky problem that cannot be solved simply by "brute force" P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From zubaexy at gmail.com Mon Nov 9 22:29:30 2009 From: zubaexy at gmail.com (Zubaer Hossain) Date: Mon, 9 Nov 2009 15:29:30 -0600 Subject: [Pw_forum] k-mesh in pwcond In-Reply-To: <4AF7ECE8.4050304@sissa.it> References: <51ec861d0911061646v37aa44ffh43f1af3594dfe99d@mail.gmail.com> <21fbc4790911061907k60e31182w5f11428e57e8419a@mail.gmail.com> <4AF7ECE8.4050304@sissa.it> Message-ID: <51ec861d0911091329t5fdc3798v42260e6dbc533872@mail.gmail.com> Thanks for your replies. I know there's no k-mesh input in the input file for pwcond. Actually, I was getting different transmission coefficient values with respect to a change in the k-mesh values for the lead and scat calculations. I realized that the complex band structures were actually not converged w.r.t the k-mesh. Seems like pwcond requires quite a dense k-mesh for convergence, especially for metallic systems. However, now I am getting good results. Zubaer On Mon, Nov 9, 2009 at 4:20 AM, Gabriele Sclauzero wrote: > > > xirainbow wrote: > > Dear ? > > I do not think pwcond can set k-mesh along the transport direction. > > Instead, you can set k-mesh perpendicular to the transport direction. > > > > The transport device can be period perpendicular to the transport > direction. > > However, it is not period along the transport direction > > This is right, in the pwcond calculation the Born-von Karman PBCs are > removed along the > transport direction, and you need to take care only of the 2D BZ sampling > in the > perpendicular directions. > Anyway, in the preceding pwscf calculation, periodicity is still there in > all 3 > directions, hence you need a proper k-point sampling also along the > transport direction, > especially for the leads, which usually are a bulk periodic unit (hence > they may not be a > supercell). > > HTH > > GS > > > > > On Sat, Nov 7, 2009 at 12:46 AM, Zubaer Hossain > > wrote: > > > > Dear QE users, > > > > Is there any rule for choosing k-meshes for the lead and the > > scattering region along the transport direction? > > > > Thanks in advance, > > Zubaer > > UIUC > > > > > > > > > > -- > > ____________________________________ > > Hui Wang > > School of physics, Nankai University, Tianjin, China > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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/20091109/af86c9ce/attachment-0001.htm From jcwu.suda at hotmail.com Tue Nov 10 08:26:10 2009 From: jcwu.suda at hotmail.com (wujianchun) Date: Tue, 10 Nov 2009 15:26:10 +0800 Subject: [Pw_forum] May I get the occupation of the bands Message-ID: Dear , How can I get the information of the occupation of the bands in Pwscf? In VASP, the "outcar" can give the "band No. ", " band energies" and " occupation" simultaneously. filband in Pwscf only gives the K pionts and energies. May I get the corresponding occupation of each bands? Thanks a lot! Regards Jianchun Department of physics Soochow University, China _________________________________________________________________ ?????????????????msn????? http://ditu.live.com/?form=TL&swm=1 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091110/35b1c532/attachment.htm From mohnish.iitk at gmail.com Tue Nov 10 08:59:14 2009 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Tue, 10 Nov 2009 13:29:14 +0530 Subject: [Pw_forum] convergence issue for energy calculation of thin film Message-ID: Dear users, I am trying to calculation energy of zinc oxide thin films of different number of atomic layer, but the energy is not converging, I have varied the value of beta in the range of (0.1- 0.7) , energy cutoff in the range of (15 - 50), but the energy is not converging. I am copying my input file for vc-relax calculation of energy of 4 atomic layer thin film. Can anybody suggest me something for convergence. Thanks in advance... &control calculation = 'vc-relax', restart_mode='from_scratch', nstep=200, outdir='/home/rajpala/Desktop/wurtzite4', pseudo_dir='/home/rajpala/Desktop/wurtzite4' prefix='zno', tstress = .true., tprnfor = .true., / &system nosym =.TRUE.,ibrav= 4, a = 3.2858, c = 26,nat= 8, ntyp= 2, ecutwfc = 25 / &electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.5 electron_maxstep=200 conv_thr = 1.0d-6 / &IONS ion_dynamics='bfgs' / &CELL cell_dynamics='damp-w' / ATOMIC_SPECIES Zn 65.390 Zn.pbe-van.UPF O 15.099 O.pbe-rrkjus.UPF ATOMIC_POSITIONS (crystal) Zn 0.33333333 0.66666666 0.09995 Zn 0.33333333 0.66666666 0.2999 Zn 0.00 0.00 0.1999 Zn 0.00 0.00 0.40 O 0.0 0.0 0.06899 O 0.0 0.0 0.26885 O 0.33333333 0.66666666 0.1689 O 0.33333333 0.66666666 0.3689 K_POINTS (automatic) 4 4 1 0 0 0 -- Mohnish Pandey Y6262,4th Year Undergraduate, Department of Chemical Engineering, IIT KANPUR -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091110/9b2ae5b9/attachment.htm From sclauzer at sissa.it Tue Nov 10 09:52:01 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 10 Nov 2009 09:52:01 +0100 Subject: [Pw_forum] k-mesh in pwcond In-Reply-To: <51ec861d0911091329t5fdc3798v42260e6dbc533872@mail.gmail.com> References: <51ec861d0911061646v37aa44ffh43f1af3594dfe99d@mail.gmail.com> <21fbc4790911061907k60e31182w5f11428e57e8419a@mail.gmail.com> <4AF7ECE8.4050304@sissa.it> <51ec861d0911091329t5fdc3798v42260e6dbc533872@mail.gmail.com> Message-ID: <4AF929B1.9070909@sissa.it> Zubaer Hossain wrote: > Thanks for your replies. > > I know there's no k-mesh input in the input file for pwcond. That's not true: after the namelist you must specify a list of 2D k-points, either manually (with correct weights) or automatically generated (somehow in the same way as for K_POINTS AUTOMATIC in pw.x, but here in 2D instead of 3D). Actually, I > was getting different transmission coefficient values with respect to a > change in the k-mesh values for the lead and scat calculations. If you said that "there's no k-mesh input in the input file for pwcond", how could you see those changes in the transmission? Do you mean that you are changing k-points in the pw.x calculation, instead? > > I realized that the complex band structures were actually not converged > w.r.t the k-mesh. This statement does not make much sense to me: k-dependent transmissions need to be converged wrt k-mesh, while CBS (which can be computed, for any k_perp point, as a function of energy to obtain a k_z VS e_{k_z} plot) has to be converged wrt to ewind and epsproj parameters (in order to match with sufficient precision the corresponding bands plot from pw.x) > Seems like pwcond requires quite a dense k-mesh for > convergence, especially for metallic systems. However, now I am getting > good results. Which kind of system are you computing? If it is a tipless geometry with 1D periodicity (like a monatomic wire with an impurity), you don't need to sample k_perp, since the transmission should be k_perp-independent (if you have chosen the cell correctly). If you are studying a geometry with k-dependent transmission (like tunnel junctions or wire between bulk leads), then the convergence of transmission may depend a lot on the scattering energy. Of course you will have metallic leads... what other kind of leads would be of interest to you? I think that the convergence of transmission is related to the CBS of the leads, and in particular to the location of band edges in energy. HTH GS > > Zubaer > > > > On Mon, Nov 9, 2009 at 4:20 AM, Gabriele Sclauzero > wrote: > > > > xirainbow wrote: > > Dear ? > > I do not think pwcond can set k-mesh along the transport direction. > > Instead, you can set k-mesh perpendicular to the transport > direction. > > > > The transport device can be period perpendicular to the transport > direction. > > However, it is not period along the transport direction > > This is right, in the pwcond calculation the Born-von Karman PBCs > are removed along the > transport direction, and you need to take care only of the 2D BZ > sampling in the > perpendicular directions. > Anyway, in the preceding pwscf calculation, periodicity is still > there in all 3 > directions, hence you need a proper k-point sampling also along the > transport direction, > especially for the leads, which usually are a bulk periodic unit > (hence they may not be a > supercell). > > HTH > > GS > > > > > On Sat, Nov 7, 2009 at 12:46 AM, Zubaer Hossain > > > >> wrote: > > > > Dear QE users, > > > > Is there any rule for choosing k-meshes for the lead and the > > scattering region along the transport direction? > > > > Thanks in advance, > > Zubaer > > UIUC > > > > > > > > > > -- > > ____________________________________ > > Hui Wang > > School of physics, Nankai University, Tianjin, China > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 sclauzer at sissa.it Tue Nov 10 10:03:10 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 10 Nov 2009 10:03:10 +0100 Subject: [Pw_forum] HI In-Reply-To: References: Message-ID: <4AF92C4E.5060702@sissa.it> Dear Mohsen, first of all, in this forum we encourage people to sign their mails and put their affiliation. We will be grateful to you! Inspecting your input file, I saw plenty of pw input keywords that I didn't even know that actually existed... seriously: one good thing of using namelists for input is that you need to specify only the parameters that you need to change. For the others the default is usually good, or at least it is better not to change them unless you know exactly what you are doing. On the other hand some parameters need to be changed (to check for numerical accuracy, for instance). Two of these are the plane waves cutoff of the wavefunctions and the charge density. In your file I found: ecutwfc = 5 , ecutrho = 5 , Which are very low values and moreover not compatible. ecutrho must be at least 4*ecutwfc (this is the default and it is fine for normconserving PPs, while for ultrasoft you may need much higher ratio ecutrho/ecutwfc, which is also called "dual") HTH GS mohsen modaresi wrote: > Hi > I faced with a problem. > I made a file with "pwgui" but when i run "pw.x" i faced with this message > from iosys : error # 1 > invalid dual? > What it means? > And i send that file. > With especial 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 paulatto at sissa.it Tue Nov 10 10:04:49 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 10 Nov 2009 10:04:49 +0100 Subject: [Pw_forum] May I get the occupation of the bands In-Reply-To: References: Message-ID: In data 10 novembre 2009 alle ore 08:26:10, wujianchun ha scritto: > How can I get the information of the occupation of the bands in Pwscf? Dear Jianchun, they are printed at convergence, if you set verbosity='high'. best regards P.S. -- 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 Tue Nov 10 10:06:58 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 10 Nov 2009 10:06:58 +0100 Subject: [Pw_forum] May I get the occupation of the bands In-Reply-To: References: Message-ID: <4AF92D32.2090801@sissa.it> Dear Jianchun, wujianchun wrote: > Dear , > > How can I get the information of the occupation of the bands in Pwscf? use verbosity='high' in the &control namelist Cheers GS > > In VASP, the "outcar" can give the "band No. ", " band energies" and > " occupation" simultaneously. > filband in Pwscf only gives the K pionts and energies. > > May I get the corresponding occupation of each bands? > > Thanks a lot! > > Regards > Jianchun > Department of physics > Soochow University, China > > > ------------------------------------------------------------------------ > ??????????MSN??? ????? > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 paulatto at sissa.it Tue Nov 10 10:11:33 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 10 Nov 2009 10:11:33 +0100 Subject: [Pw_forum] HI In-Reply-To: <4AF92C4E.5060702@sissa.it> References: <4AF92C4E.5060702@sissa.it> Message-ID: In data 10 novembre 2009 alle ore 10:03:10, Gabriele Sclauzero ha scritto: > Inspecting your input file, I saw plenty of pw input keywords that I > didn't even know that actually existed... To add a bit on this: I've seen you have used pwgui to generate the file. It is ok, but does not save you from reading the documentation. Quantum-ESPRESSO does only work for systems that make sense, so the input have to be consistent both syntactically and physically. Is a good thing that you are trying to use it, and with some patience you will learn. Instead of starting with random input (the Montecarlo algorithm is not effective for humans) you should start by checking the examples and the tutorial that you can find here: . There is also a serie of video-lectures here: . 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 Tue Nov 10 11:09:01 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 10 Nov 2009 11:09:01 +0100 Subject: [Pw_forum] convergence issue for energy calculation of thin film In-Reply-To: References: Message-ID: <4AF93BBD.709@democritos.it> mohnish pandey wrote: > I am trying to calculation energy of zinc oxide thin films > of different number of atomic layer, but the energy is not > converging, I have varied the value of beta in the range of > (0.1- 0.7) , energy cutoff in the range of (15 - 50), > but the energy is not converging. try mixing_mode='local-TF' (good for surfaces) and/or adding a few conduction bands and a small broadening (prevents trouble if the system becomes metallic during self-consistency) P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From jhouska at kfy.zcu.cz Tue Nov 10 11:21:07 2009 From: jhouska at kfy.zcu.cz (Jiri Houska) Date: Tue, 10 Nov 2009 11:21:07 +0100 Subject: [Pw_forum] total projections < 1 In-Reply-To: <4AF7EFA6.4040007@sissa.it> References: <20091107141535.nltl4d9j5wgs00sg@webmail.zcu.cz> <4AF7EFA6.4040007@sissa.it> Message-ID: <20091110112107.ad8oazv9kgsogo0g@webmail.zcu.cz> Hello, thanks Gabriele and Lorenzo for the answers. I used the file Projections (that is, generated by projwfc.x but different from standard output of projwfc.x). I see there also weights well below 0.001 (see the short example below). The Lorenzo's answer (parts of high-energy electrons can be far from all atoms) seems most likely to me now (so hopefully it was not my mistake :) ). Regards, Jiri 400 1 254 F F 1 1Si 1 0 1 1 1 0.0007622327 1 2 0.0002113878 1 3 0.0000141535 1 4 0.0000003404 1 5 0.0003379727 1 6 0.0012689268 1 7 0.0000030462 1 8 0.0003089662 1 9 0.0021086488 1 10 0.0004881924 1 11 0.0240786863 1 12 0.0003211811 1 13 0.0001706586 1 14 0.0004463602 1 15 0.0000001926 1 16 0.0000075481 1 17 0.0005386425 1 18 0.0023389087 Quoting Gabriele Sclauzero : > From where are you collecting the occupations? From the standard > output of projwfc.x or > from filpdos? You should be aware that in the former case, when > writing the "local charge > decomposition" of each KS eigenstate, the program gives on standard > output only > contributions from atomic orbitals with an overlap (on that state) > which is larger than 0.001. > > HTH > > GS > > >> >> (1) For low energy states, the sum is sufficiently close to 1.00 (>0.99). >> >> (2) However, several states below Fermi level the sum starts to >> decrease almost monotonously with increasing energy, being around 0.80 >> only for the highest unoccupied state calculated. Please does it >> indicate a problem, or is it what I have to expect for some reason? >> >> Thanks a lot! >> >> Jiri Houska >> Department of Physics >> University of West Bohemia >> >> >> _______________________________________________ >> 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 giannozz at democritos.it Tue Nov 10 11:22:17 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 10 Nov 2009 11:22:17 +0100 Subject: [Pw_forum] [Help] I need a NC pseudopotential (PBE) of Ca with 10 valence electrons In-Reply-To: <66c76c8e0911031920p71d6adb4k58c9d77254e94723@mail.gmail.com> References: <66c76c8e0911031920p71d6adb4k58c9d77254e94723@mail.gmail.com> Message-ID: <4AF93ED9.5020200@democritos.it> Hui Wang wrote: > I need a NC pseudopotential (PBE) of Ca with 10 valence electrons, once upon a time (3 years ago) I generated one (more exactly, two). Whoever asked for it (I don't remember any longer who) never reported whether it was working or not. Here are the input. Use at your risk. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: ca.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20091110/7d24955d/attachment.asc -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: casp1.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20091110/7d24955d/attachment.txt -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: casp1-test.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20091110/7d24955d/attachment-0001.asc -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: casp2.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20091110/7d24955d/attachment-0001.txt -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: casp2-test.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20091110/7d24955d/attachment-0002.asc From giannozz at democritos.it Tue Nov 10 13:42:02 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 10 Nov 2009 13:42:02 +0100 Subject: [Pw_forum] e: "cannot open xml_recover file for writing" In-Reply-To: <4AF84058.6010803@unibo.it> References: <4AF84058.6010803@unibo.it> Message-ID: <4AF95F9A.50505@democritos.it> Cristian Degli Esposti Boschi wrote: > I also suspect that it is due to a different directory > structure in version 4.1, so I encourage to report > a bug as suggested by Paolo Giannozzi. Otherwise I will > do it as soon as I have completed one more check... thank you. I had again a look it at, and ADC as well (he knows better than anybody else phonon restarting). It seems to work (unless the file is corrupted, which occasionally happens, especially if stopping execution with control-C as I was doing), also in parallel execution. I had the "xml error" a few days ago and didn't understand why; now I cannot reproduce it any longer. The directory structure has changed (after my insistance on not overwriting data from self-consistency) but the restart mechanism was changed accordingly. Maybe it happens in some specific cases, but it is hard to say until one finds which specific cases P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From ppzang at gmail.com Tue Nov 10 13:58:26 2009 From: ppzang at gmail.com (Chenpeng Zang) Date: Tue, 10 Nov 2009 20:58:26 +0800 Subject: [Pw_forum] Problem in running the software Message-ID: I have unpacked the xc-1.5.21-linux_x86_64-semishared.tar.gzand run the xcConfigure, just like what the Installation Instructions says. However when I run the software using ./xcrysden, an error occurred, which is "./xcrysden: line 215: /home/Zangcp/software/XCrySDen-1.5.21-bin-semishared/bin/xcrys: cannot execute binary file". The OS is Fedora 11. Who can tell me what happened. Thanks a lot. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091110/10ff1903/attachment.htm From mohnish.iitk at gmail.com Tue Nov 10 13:59:16 2009 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Tue, 10 Nov 2009 18:29:16 +0530 Subject: [Pw_forum] convergence issue for energy calculation of thin film In-Reply-To: References: Message-ID: Thank you so much Paolo for help... On Tue, Nov 10, 2009 at 1:29 PM, mohnish pandey wrote: > Dear users, > I am trying to calculation energy of zinc oxide thin films > of different number of atomic layer, but the energy is not converging, I > have varied the value of beta in the range of (0.1- 0.7) , energy cutoff in > the range of (15 - 50), but the energy is not converging. I am copying my > input file for vc-relax calculation of energy of 4 atomic layer thin film. > Can anybody suggest me something for convergence. > Thanks in advance... > > &control > calculation = 'vc-relax', > restart_mode='from_scratch', > nstep=200, > outdir='/home/rajpala/Desktop/wurtzite4', > pseudo_dir='/home/rajpala/Desktop/wurtzite4' > prefix='zno', > tstress = .true., > tprnfor = .true., > / > &system > nosym =.TRUE.,ibrav= 4, a = 3.2858, c = 26,nat= 8, ntyp= 2, > ecutwfc = 25 > / > &electrons > diagonalization='david' > mixing_mode = 'plain' > mixing_beta = 0.5 > electron_maxstep=200 > conv_thr = 1.0d-6 > / > &IONS > ion_dynamics='bfgs' > / > &CELL > cell_dynamics='damp-w' > / > ATOMIC_SPECIES > Zn 65.390 Zn.pbe-van.UPF > O 15.099 O.pbe-rrkjus.UPF > ATOMIC_POSITIONS (crystal) > Zn 0.33333333 0.66666666 0.09995 > Zn 0.33333333 0.66666666 0.2999 > Zn 0.00 0.00 0.1999 > Zn 0.00 0.00 0.40 > O 0.0 0.0 0.06899 > O 0.0 0.0 0.26885 > O 0.33333333 0.66666666 0.1689 > O 0.33333333 0.66666666 0.3689 > K_POINTS (automatic) > 4 4 1 0 0 0 > > > -- > Mohnish Pandey > Y6262,4th Year Undergraduate, > Department of Chemical Engineering, > IIT KANPUR > -- Mohnish Pandey Y6262,4th Year Undergraduate, Department of Chemical Engineering, IIT KANPUR -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091110/706febd7/attachment.htm From paulatto at sissa.it Tue Nov 10 14:02:41 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 10 Nov 2009 14:02:41 +0100 Subject: [Pw_forum] Problem in running the software In-Reply-To: References: Message-ID: In data 10 novembre 2009 alle ore 13:58:26, Chenpeng Zang ha scritto: > /home/Zangcp/software/XCrySDen-1.5.21-bin-semishared/bin/xcrys: cannot > execute binary file". Dear Chenpeng Zang, if the file is actually there and has execution permissions (check with "ls -l filename") than it is your system administrator that has mounted the home directory with the noexec option (you'll have to complain with him). Please note that there is an XCrysDen mailing list, which may be a more appropriate place for this kind of questions: http://www.democritos.it/mailman/listinfo/xcrysden 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 ppzang at gmail.com Tue Nov 10 14:06:49 2009 From: ppzang at gmail.com (Chenpeng Zang) Date: Tue, 10 Nov 2009 21:06:49 +0800 Subject: [Pw_forum] Problem in running the software In-Reply-To: References: Message-ID: Lorenzo Paulatto: Thank you response so fast, which actually surprised me. Thank you for your help. God bless you! Chenpeng Zang 2009/11/10 Lorenzo Paulatto > In data 10 novembre 2009 alle ore 13:58:26, Chenpeng Zang > ha scritto: > > /home/Zangcp/software/XCrySDen-1.5.21-bin-semishared/bin/xcrys: cannot > > execute binary file". > > Dear Chenpeng Zang, > if the file is actually there and has execution permissions (check with > "ls -l filename") than it is your system administrator that has mounted > the home directory with the noexec option (you'll have to complain with > him). > > Please note that there is an XCrysDen mailing list, which may be a more > appropriate place for this kind of questions: > http://www.democritos.it/mailman/listinfo/xcrysden > > 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/ > _______________________________________________ > 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/20091110/b2b95720/attachment.htm From paulatto at sissa.it Tue Nov 10 14:26:41 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 10 Nov 2009 14:26:41 +0100 Subject: [Pw_forum] constraints In-Reply-To: References: <599421.51225.qm@web112510.mail.gq1.yahoo.com> <90134.9293.qm@web112517.mail.gq1.yahoo.com> Message-ID: In data 09 novembre 2009 alle ore 14:54:05, Lorenzo Paulatto ha scritto: > The algorithm that re-wraps atomic coordinates inside the unit cell > should work in your case, not give that error... as a quick solution you > can try > to translate atom #2 inside the unit cell by hand. So, apparently there is an error in how the algorithm estimates the maximum possible distance between two atoms. Currently it uses half the shorter basis vector, while it should be half the longest cell diagonal (the demonstration is left as exercise ;-). You can get the new file from here: http://qe-forge.org/scm/viewvc.php/*checkout*/espresso/Modules/constraints_module.f90?revision=1.53&root=q-e please replace the old file (Modules/constraints_module.f90) and recompile the code. Don't forget to report if you find any problem. 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 kazempoor2000 at yahoo.com Tue Nov 10 14:39:19 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Tue, 10 Nov 2009 05:39:19 -0800 (PST) Subject: [Pw_forum] oxygen molecule Message-ID: <162880.97919.qm@web112510.mail.gq1.yahoo.com> Hi 2 All I want the chemical potential of oxygen molecule , but the binding energy that I get is too far from experiment and theoretical results. Could anyone help me How can I improve my calculation. &CONTROL calculation = "relax", restart_mode='from_scratch' prefix = "o2", pseudo_dir = "./", outdir = "/p5/batch/kazempou/", verbosity='high' / &SYSTEM ibrav = 1, celldm(1)=20 nat = 2, nosym=.true. ntyp = 1, ecutwfc = 45.D0, ecutrho = 400.D0, occupations='smearing', smearing='mp', degauss= 0.001,nspin=2,starting_magnetization(1)= 1.0, / &ELECTRONS conv_thr = 1.D-5, mixing_beta = 0.7D0, / &IONS / ATOMIC_SPECIES O 1.00 o.optgga1.fhi.UPF ATOMIC_POSITIONS crystal O 0.5 0.5 0.5 0 0 0 O 0.5 0.5 0.0 K_POINTS {Gamma} thanks a lot Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091110/c9c1d5f0/attachment-0001.htm From smogunov at sissa.it Tue Nov 10 14:46:02 2009 From: smogunov at sissa.it (Alexander Smogunov) Date: Tue, 10 Nov 2009 14:46:02 +0100 Subject: [Pw_forum] Left and right going Bloch's states from PWCOND In-Reply-To: References: Message-ID: <1257860762.11470.15.camel@alex-laptop> Dear Manoj On Sun, 2009-11-08 at 03:49 -0500, Manoj Srivastava wrote: > Dear Alexander, > Thanks for answering my question. I have two more questions. I understand > that for muliple channels in the leads, Bloch's states are arranged in > order of increasing |kz|. For example- > Nchannels of the left tip = 4 > k1(2pi/a) k2(2pi/a) E-Ef (eV) > > -0.2937447 0.0000000 0.0000000 > 0.3140648 0.0000000 0.0000000 > -0.3882921 0.0000000 0.0000000 > 0.4084626 0.0000000 0.0000000 > Nchannels of the right tip = 4 > k1(2pi/a) k2(2pi/a) E-Ef (eV) > > 0.2117188 0.0000000 0.0000000 > 0.3140394 0.0000000 0.0000000 > -0.3915554 0.0000000 0.0000000 > -0.4937163 0.0000000 0.0000000 > > Now when I calculate transmission, code prints out - > 1 --> 1 0.0198530 > 1 --> 2 0.0638572 > 1 --> 3 0.0193576 > 1 --> 4 0.5152587 > 0.61833 > and three more sets like this (I am not writing it down). In above > 1,2,3,4 correspond to Bloch's states in left and right lead. My question > is, are transmission coefficients arranged in the same order as kz 's are. > e.g. does transmission coefficient in 1 -->1 stand for transmission > coefficient of state kz= -0.2937447 in left lead to state with > kz=0.2117188 in the right lead? similarly, 1-->2 mean kz=-0.2937447 to > kz=0.3140394 , and so on ? > That's right. > Also, what is eigenchannel decomposition, if I want to get transmission > coefficient, code prints out as > T_ij for propagating states: > 1 --> 1 0.0198530 > 1 --> 2 0.0638572 > 1 --> 3 0.0193576 > 1 --> 4 0.5152587 > 0.61833 > 2 --> 1 0.1840566 > 2 --> 2 0.3834998 > 2 --> 3 0.0693121 > 2 --> 4 0.1578845 > 0.79475 > 3 --> 1 0.1853693 > 3 --> 2 0.0321809 > 3 --> 3 0.1536389 > 3 --> 4 0.0309744 > 0.40216 > 4 --> 1 0.1601806 > 4 --> 2 0.0132465 > 4 --> 3 0.2321587 > 4 --> 4 0.1197219 > 0.52531 > then what information does eigenchannel decomposition contain? > Eigenchannel decomposition: > @ 1 0.00000 0.10086 > 0.31024 > 0.09173 > 0.36027 > 0.23776 > @ 2 0.00000 0.47744 > 0.03523 > 0.03500 > 0.49217 > 0.43760 > @ 3 0.00000 0.84821 > 0.42617 > 0.44674 > 0.06122 > 0.06587 > @ 4 0.00000 0.91404 > 0.22836 > 0.42652 > 0.08634 > 0.25877 > I dont know what to think of these numbers. Thanks for your help. > As you may know, the eigenchannels (and their transmissions) are defined as eigenvectors, say A_{ij} (and eigenvalues t_{j}) of the Hermitian matrix T^{+} T, where T is the transmission matrix from the left to the right. Here there are 4 eigenchannels (the same number as Nchannel in the left lead), and for each of them the code prints its number j, energy (here it is the E_F), and its transmission t_j. The following 4 numbers in the column are the squared components of the eigenchannel over the left lead bands, i.e. |A_{ij}|^2. All the best, Alexander > Regards, > Manoj > > > On Mon, 2 Nov 2009, Alexander Smogunov wrote: > > > Dear Manoj. > > The new parameter lorb is simply used to give in output the scattering > > states so that you could plot them, it does not affect the transmission > > calculation itself. If it is .false. the code will run normally as > > before... It is true that this new option does not work for ikind=2, > > but you can still calculate transmission and reflection amplitudes. > > To calculate t and r from right to left you should simply > > call the transmit routine in do_cond.f90 with the last argument > > to set to .false. By default the code does not compute the > > case of right --> left scattering since the total transmission > > is the same as in left --> right case. Only if you want to plot the > > scattering states (lorb=.true.) it does that. > > It is how the things are implemented now ... > > Best regards, > > Alexander > > > > > > > > > > On Fri, 2009-10-30 at 14:04 -0400, Manoj Srivastava wrote: > > > Just to add one more question. > > > what is 'lorb' switch. I get following- > > > lorb, & ! if .t. calculate the scattering (or Bloch) states > > > so, i guess for transmission calculation i will have to set it to > > > 't'. now- > > > IF (lorb.and.ikind.eq.2) call errore('do_cond','lorb not working with > > > ikind = 2',1) > > > so, it seems that calculation for r and t for right and left going > > > state, when left and right leads are different doesnot work. Is that > > > correct? A possible work around may be rotating the whole system by 180 > > > degree, which would be like treating left lead as right lead and > > > scattering region rotated. Can I do that? > > > > > > Regards, > > > Manoj > > > > > > On Fri, 30 Oct 2009, Manoj Srivastava wrote: > > > > > > > Dear Alexander, > > > > Thank you very much! I read the code, it seems that there are > > > > quiet a few changes in 4.1.1 compared to 4.0.4 :) .So, just to make sure, > > > > if I want to calculate r and t for left going Bloch's state as well as > > > > right going Bloch's state, I need to run the code two times, one time with > > > > 'left_to_right' switch true, and another time false. I dont need to change > > > > scattering region or interchange left and right leads. > > > > > > > > Regards, > > > > Manoj Srivastava > > > > On Thu, 29 Oct 2009, Alexander > > > > Smogunov wrote: > > > > > > > > > Dear Manoj > > > > > > > > > > On Wed, 2009-10-28 at 01:49 -0400, Manoj Srivastava wrote: > > > > > > Dear Alexander, > > > > > > You are correct, left and right moving states are in general not > > > > > > related. I was wrong about trying to create a pair. Thanks for > > > > > > clarification. > > > > > > I have a few more questions. > > > > > > 1. I want to find out the reflection coefficient in the code. In > > > > > > transmit.f90, transmission coefficient is |tmat(ig,n)|^2, where tmat is > > > > > > vec1(ntran-n2d-npol*nocrosr+ig,n). (line 206, of version 4.0.5). > > > > > > Reflection is not explicitly calculated in the code, but it should be > > > > > > modulus square of vec1(2*n2d+npol*norbs+ig,n) (line 234). Am I correct? > > > > > > > > > > in the 4.1 version there is output of both t and r. > > > > > > > > > > > > > > > > > > > > > > 2. In the code reflection and transmission coefficients are calculated > > > > > > for one direction lets say t++ and t+-, which is transmission and > > > > > > reflection coefficient for Bloch' state moving from - to + , or in other > > > > > > words, left to right. To calculate transmission and reflection for Bloch's > > > > > > state going from right to left, what should I do? Should i just rotate my > > > > > > system 180 degree, that way leads get interchanged and also scattering > > > > > > area has orientation 180 different from before. > > > > > > > > > > > > > > > > again in the 4.1 version you have possibility to calculate t and r for > > > > > both directions, in the do_cond.f90 the transmit routine is called with > > > > > an extra parameter which is true (false) if you want to calculate > > > > > scattering states propagating from the left (from the right). > > > > > > > > > > > 3. In the subroutine sunitary.f90, is raux measure of conservation of > > > > > > flux? If I sum all the transmission and reflecion coefficient for > > > > > > a particular Bloch's state, I should get 1, and computationally a number > > > > > > close to 1. How large could it be for S matrix not to be unitary, i m > > > > > > getting raux more than one e.g. 1.0011 but code still considers smatrix > > > > > > to be unitary. > > > > > > > > > > in the case when |R + T - 1| > 1.d-4 for some band, it should print out > > > > > the value of R+T but continues to run anyway. > > > > > > > > > > All the best, > > > > > Alexander > > > > > > > > > > > > > > > > > > > > > > > > > > > Regards, > > > > > > Manoj Srivastava > > > > > > University of Florida, Gainesville, FL > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Thu, 22 > > > > > > Oct 2009, Alexander Smogunov wrote: > > > > > > > > > > > > > On Thu, 2009-10-22 at 11:34 -0400, Manoj Srivastava wrote: > > > > > > > > Dear Alexander, > > > > > > > > Thanks for your answer. I just want to make sure. Imagine we have total > > > > > > > > number of channels in the left lead 2, so total number of Bloch's state > > > > > > > > are 4. 2 of them left going say a and b, and 2 right going say c and d. > > > > > > > > So, are you saying that for left going state a, the corresponding right > > > > > > > > going state is c? Are they ordered this way? > > > > > > > > > > > > > > what do you mean by corresponding? Left and right moving Bloch > > > > > > > states are in general not related one to another, you can even have > > > > > > > different number of them ... Only if you have some symmetry S which > > > > > > > brings kz to -kz conserving k_parallel, then the state with > > > > > > > \psi_{-kz} will be S \psi{kz}. This is true for example at 2D G point > > > > > > > when you have time reversal operation. > > > > > > > > > > > > > > Now the code simply arranges the propagating states in the order of > > > > > > > increasing |k_z|... > > > > > > > > > > > > > > Regards, Alexander > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Regards, > > > > > > > > Manoj > > > > > > > > > > > > > > > > > > > > > > > > On Thu, 22 Oct 2009, Alexander > > > > > > > > Smogunov wrote: > > > > > > > > > > > > > > > > > Dear Manoj. > > > > > > > > > > > > > > > > > > The output of complex k vectors is performed in > > > > > > > > > summary_band.f90 routine. If you want to see all > > > > > > > > > the complex k vectors, not only propagating ones, > > > > > > > > > you can change at the end of this routine: > > > > > > > > > > > > > > > > > > ------------------- > > > > > > > > > do i = 1, nchanl > > > > > > > > > WRITE( stdout,'(3f12.7)') DBLE(kvall(i)), AIMAG(kvall(i)), eev > > > > > > > > > enddo > > > > > > > > > ------------------- > > > > > > > > > > > > > > > > > > to > > > > > > > > > ------------------- > > > > > > > > > > > > > > > > > > do i = 1, 2*nstl > > > > > > > > > WRITE( stdout,'(3f12.7)') DBLE(kvall(i)), AIMAG(kvall(i)), eev > > > > > > > > > enddo > > > > > > > > > ------------------- > > > > > > > > > > > > > > > > > > Altogether there are 2*nstl (or 2*nstr) Bloch states in the left > > > > > > > > > (or right) lead. First half, [1,nstl], are propagating or decaying to > > > > > > > > > the right states, another half, [nstl+1,2*nstl], - propagating or > > > > > > > > > decaying to the left. In each group, first nchanl states are propagating > > > > > > > > > states. > > > > > > > > > > > > > > > > > > The propagating states are normalized by the current and are arranged in > > > > > > > > > the above order at the end of jbloch.f90 routine, after the following > > > > > > > > > lines: > > > > > > > > > > > > > > > > > > ! > > > > > > > > > ! Right ordering (+, >, -, <) > > > > > > > > > ! > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Notice, that in the last versions the code gives in output > > > > > > > > > both propagating to the right and to the left states. > > > > > > > > > > > > > > > > > > Hope this helps, > > > > > > > > > Alexander > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Wed, 2009-10-21 at 14:13 -0400, Manoj Srivastava wrote: > > > > > > > > > > Dear All, > > > > > > > > > > I am trying to figure out the left and right going Bloch's states in the > > > > > > > > > > lead from PWCOND. For a given (kx,ky)and energy we get kz. The code only > > > > > > > > > > prints out Bloch's state moving in one direction. eg. in one of the > > > > > > > > > > calculation- > > > > > > > > > > k//=(0.375,-0.375) > > > > > > > > > > Nchannels of the left tip = 1 > > > > > > > > > > k1(2pi/a) k2(2pi/a) E-Ef (eV) > > > > > > > > > > > > > > > > > > > > 0.3157801 0.0000000 0.0000000 > > > > > > > > > > > > > > > > > > > > Now if I want Bloch's state moving in right as well as left direction, I > > > > > > > > > > can go to kbloch.f90 subroutine, and print out all the eigen values of > > > > > > > > > > AX=exp(ikd)BX, and out of those the ones with real solution would be our > > > > > > > > > > Bloch's state, so I get for each channel two solutions- > > > > > > > > > > kval (-0.275409421993275,1.823688001395235E-010) > > > > > > > > > > kval (0.315780119742506,-3.611201785292708E-012) > > > > > > > > > > > > > > > > > > > > To figure out the direction, I can calculate current associated with these > > > > > > > > > > Bloch's sate and if the current is +ive it is right moving , and if '-'ive > > > > > > > > > > its left moving Bloch's state. I can print out current from jbloch.f90 > > > > > > > > > > subroutine which are - > > > > > > > > > > current eigenvalue -1.86502143831863 1.59149029314457 > > > > > > > > > > > > > > > > > > > > So, clearly the first state with kval=-0.2754094 is left moving and the > > > > > > > > > > other one right moving. Upto here its clear to me how to identify left and > > > > > > > > > > right moving states. > > > > > > > > > > > > > > > > > > > > I get confused when for a given (kx,ky,E), I have more than one Bloch' > > > > > > > > > > state. In another calculation where i get multiple Bloch's state- > > > > > > > > > > Nchannels of the left tip = 5 > > > > > > > > > > k1(2pi/a) k2(2pi/a) E-Ef (eV) > > > > > > > > > > > > > > > > > > > > -0.0746301 0.0000000 0.0000000 > > > > > > > > > > 0.1205527 0.0000000 0.0000000 > > > > > > > > > > 0.3112908 0.0000000 0.0000000 > > > > > > > > > > 0.4200218 0.0000000 0.0000000 > > > > > > > > > > -0.4935150 0.0000000 0.0000000 > > > > > > > > > > > > > > > > > > > > so i did the same trick i did above to first print out kz and then > > > > > > > > > > current, which gives me - > > > > > > > > > > kval (-0.420023481074359,1.979595081419732E-010) (call it a) > > > > > > > > > > kval (0.420023367986768,2.500979698670295E-011) (b) > > > > > > > > > > kval (-0.306507431678779,-1.236804629184431E-011) (c) > > > > > > > > > > kval (-0.125376071175573,-6.134512510438736E-011) (d) > > > > > > > > > > kval (-7.945001124706894E-002,6.683546930037856E-011)(e) > > > > > > > > > > kval (0.106554601758169,-6.427946951285107E-011) (f) > > > > > > > > > > kval (8.866867725358024E-002,8.342250371574646E-011) (g) > > > > > > > > > > kval (0.325333314672671,1.260810749228185E-011) (h) > > > > > > > > > > kval (-0.488725859521576,1.769197678346003E-010) (i) > > > > > > > > > > kval (0.479509832763231,1.765499400037283E-010) (j) > > > > > > > > > > > > > > > > > > > > current eigenvalue -9.31389492882581 -1.24296522993488 > > > > > > > > > > -1.21324078359658 -1.11950286753963 -1.08166842367443 > > > > > > > > > > 1.08187482164864 1.11973146584263 1.21295295042188 > > > > > > > > > > 1.24280031534940 9.313897787790 > > > > > > > > > > > > > > > > > > > > So, the first 5 are left moving and rest are right moving. But I dont know > > > > > > > > > > the pairs. for example for left moving state a, what is the corresponding > > > > > > > > > > right moving state whether its f or g ... j ? > > > > > > > > > > > > > > > > > > > > Any help would be appreciated. > > > > > > > > > > > > > > > > > > > > Regards, > > > > > > > > > > Manoj Srivastava > > > > > > > > > > University of Florida, Gainesville. > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > > > Pw_forum mailing list > > > > > > > > > > Pw_forum at pwscf.org > > > > > > > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > -- > > > > > > > > > e-mail: 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 > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > Pw_forum mailing list > > > > > > > > Pw_forum at pwscf.org > > > > > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > -- > > > > > > > e-mail: 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 > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > Pw_forum mailing list > > > > > > Pw_forum at pwscf.org > > > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > > > > > e-mail: 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 > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > e-mail: 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 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- e-mail: smogunov at sissa.it home-page: http://people.sissa.it/~smogunov From emiss_pemiss at hotmail.com Tue Nov 10 14:40:49 2009 From: emiss_pemiss at hotmail.com (Mehmet Baturay) Date: Tue, 10 Nov 2009 13:40:49 +0000 Subject: [Pw_forum] from read_namelists : error # 208 Message-ID: Hi All.. i am newbie. i am trying to learn PWscf.. i am Working on Cu2MnAl. But when i clicked the run i am getting one error. if u help me i will be happy. The Error : Program PWSCF v.4.1.1 starts ... Today is 10Nov2009 at 15: 8:14 For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW Current dimensions of program pwscf are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 Waiting for input... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_namelists : error # 208 reading namelist control %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... My input Data: &CONTROL title = Cu2MnAl , calculation = 'scf' , restart_mode = 'from_scratch' , outdir = '/home/mehmet/Masa?st?/temp/' , pseudo_dir = '/home/mehmet/Masa?st?/pseudo2/' , prefix = 'cma' , tstress = .true. , tprnfor = .true. , lberry = .false. , gdir = 3 , / &SYSTEM ibrav = 2, celldm(1) = 11.172, nat = 14, ntyp = 3, ecutwfc = 30 , ecutrho = 350 , / &ELECTRONS conv_thr = 1.0D-5 , mixing_mode = 'plain' , mixing_beta = 0.7 , / ATOMIC_SPECIES Cu 63.54600 Cu.pbe-d-rrkjus.UPF Mn 54.93805 Mn.pbe-sp-van.UPF Al 26.98154 Al.pbe-rrkj.UPF ATOMIC_POSITIONS crystal Cu 0.250000000 0.250000000 0.250000000 Cu 0.750000000 0.750000000 0.750000000 Mn 0.000000000 0.000000000 0.000000000 Al 0.500000000 0.500000000 0.500000000 _________________________________________________________________ Keep your friends updated?even when you?re not signed in. http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/social-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-xm:SI_SB_5:092010 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091110/18d6e983/attachment.htm From paulatto at sissa.it Tue Nov 10 14:52:49 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 10 Nov 2009 14:52:49 +0100 Subject: [Pw_forum] from read_namelists : error # 208 In-Reply-To: References: Message-ID: Dear Mehmet, welcome on board. There is only one tiny error in your input: > title = Cu2MnAl , you have missed the quotes around the title: > title = 'Cu2MnAl' , I would not used non-ascii characters as "?" in the file names, but it may still work: > outdir = '/home/mehmet/Masa?st?/temp/' , > pseudo_dir = '/home/mehmet/Masa?st?/pseudo2/' , This should be all, good work. -- 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 Tue Nov 10 15:03:16 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 10 Nov 2009 15:03:16 +0100 Subject: [Pw_forum] oxygen molecule In-Reply-To: <162880.97919.qm@web112510.mail.gq1.yahoo.com> References: <162880.97919.qm@web112510.mail.gq1.yahoo.com> Message-ID: <4AF972A4.3070306@democritos.it> ali kazempour wrote: > I want the chemical potential of oxygen molecule , but the binding > energy that I get is too far from experiment and theoretical results from theoretical results with the same theory? once upon a time I got a binding energy for O_2 of 7.2eV with LDA, 5.7eV with PBE. Experiments: 5.12eV. > ecutwfc = 45.D0, > ecutrho = 400.D0, > O 1.00 o.optgga1.fhi.UPF this is not ultrasoft: ecutwfc is maybe too little, ecutrho shouldn't be specified P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From jcwu.suda at hotmail.com Tue Nov 10 15:16:14 2009 From: jcwu.suda at hotmail.com (wujianchun) Date: Tue, 10 Nov 2009 22:16:14 +0800 Subject: [Pw_forum] May I get the occupation of the bands In-Reply-To: <4AF92D32.2090801@sissa.it> References: Message-ID: Dear Gabriele Sclauzero and Lorenzo Paulatto, Thank you for your kind help! Regards Jianchun Department of physics Soochow University, China > Date: Tue, 10 Nov 2009 10:06:58 +0100 > From: sclauzer at sissa.it > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] May I get the occupation of the bands > > Dear Jianchun, > > wujianchun wrote: > > Dear , > > > > How can I get the information of the occupation of the bands in Pwscf? > > use verbosity='high' in the &control namelist > > > Cheers > > > GS > > > > > In VASP, the "outcar" can give the "band No. ", " band energies" and > > " occupation" simultaneously. > > filband in Pwscf only gives the K pionts and energies. > > > > May I get the corresponding occupation of each bands? > > > > Thanks a lot! > > > > Regards > > Jianchun > > Department of physics > > Soochow University, China > > > > > > ------------------------------------------------------------------------ > > ??????????MSN??? ????? > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 _________________________________________________________________ ?????????????????msn????? http://ditu.live.com/?form=TL&swm=1 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091110/f1de73ff/attachment.htm From cristian.degliesposti at unibo.it Tue Nov 10 16:49:34 2009 From: cristian.degliesposti at unibo.it (Cristian Degli Esposti Boschi) Date: Tue, 10 Nov 2009 16:49:34 +0100 Subject: [Pw_forum] e: "cannot open xml_recover file for writing" Message-ID: <4AF98B8E.3080204@unibo.it> >It seems >to work (unless the file is corrupted, which occasionally >happens, especially if stopping execution with control-C >as I was doing), also in parallel execution. More specifically all the "restart" errors I had with ph.x occurred when I try to restart a calculation stopped by the parallel scheduler on the SP6 machine (CINECA) due to the fact that the job reached the maximum allowed time on that queue. So, parallely, I notified the fact also to the administrators. Cheers, Cristian -- ___________________________________________________ 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 modaresi.mohsen at gmail.com Tue Nov 10 19:14:52 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Tue, 10 Nov 2009 21:14:52 +0300 Subject: [Pw_forum] HI In-Reply-To: <8974d3b20911091119u2072f9c5k18b69d62bf323ff0@mail.gmail.com> References: <8974d3b20911091119u2072f9c5k18b69d62bf323ff0@mail.gmail.com> Message-ID: Thank you This site very useful for me.( http://www.fisica.uniud.it/~giannozz/QE-Tutorial/ ) Mohsen Modaresi Msc student Department of physics Ferdowsi University On Mon, Nov 9, 2009 at 10:19 PM, Duy Le wrote: > pwgui is good, but you should know what you are doing. There are too many > UNPHYSICAL parameters in the given input. > There are plenty tutorials you may need to look at them before doing > serious calculations > http://www.fisica.uniud.it/~giannozz/QE-Tutorial/ > > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > > "Men don't need hand to do things" > > > On Mon, Nov 9, 2009 at 2:04 PM, mohsen modaresi > wrote: > >> Hi >> I faced with a problem. >> I made a file with "pwgui" but when i run "pw.x" i faced with this message >> from iosys : error # 1 >> invalid dual? >> What it means? >> And i send that file. >> With especial thanks. >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091110/50c7ef99/attachment.htm From modaresi.mohsen at gmail.com Tue Nov 10 20:09:14 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Tue, 10 Nov 2009 22:09:14 +0300 Subject: [Pw_forum] Special k points Message-ID: Hi I read help file and i faced with this sentences : Special k-points (xk_x/y/z) in the irreducible Brillouin Zone of the lattice (with all symmetries) and weights (wk) *See the literature for lists* of special points and the corresponding weights. which literature? I searched but i didnt find any things. thanks for your answer. Mohsen Modaresi Dep. physics Ferdowsi University Iran -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091110/d7c4587c/attachment.htm From modaresi.mohsen at gmail.com Tue Nov 10 20:16:29 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Tue, 10 Nov 2009 22:16:29 +0300 Subject: [Pw_forum] from read_namelists : error # 208 In-Reply-To: References: Message-ID: Hello Dear Mehmet I am newbie like you. I suggest to you this page( http://www.fisica.uniud.it/~giannozz/QE-Tutorial/) , It is very useful for me. I think this can help you. With best wishes Mohsen Modaresi Dep. Physics Ferdowsi University Iran 2009/11/10 Mehmet Baturay > Hi All.. i am newbie. i am trying to learn PWscf.. > i am Working on Cu2MnAl. > But when i clicke d the run i am getting one error. if u help me i will be > happy. > The Error : > > Program PWSCF v.4.1.1 starts ... > Today is 10Nov2009 at 15: 8:14 > > For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW > > Current dimensions of program pwscf are: > Max number of different atomic species (ntypx) = 10 > Max number of k-points (npk) = 40000 > Max angular momentum in pseudopotentials (lmaxx) = 3 > Waiting for input... > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_namelists : error # 208 > reading namelist control > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > My input Data: > > &CONTROL > title = Cu2MnAl , > calculation = 'scf' , > restart_mode = 'from_scratch' , > outdir = '/home/mehmet/Masa?st?/temp/' , > pseudo_dir = '/home/mehmet/Masa?st?/pseudo2/' , > prefix = 'cma' , > tstress = .true. , > tprnfor = .true. , > lberry = .false. , > gdir = 3 , > / > &SYSTEM > ibrav = 2, > celldm(1) = 11.172, > nat = 14, > ntyp = 3, > ecutwfc = 30 , > ecutrho = 350 , > / > &ELECTRONS > conv_thr = 1.0D-5 , > mixing_mode = 'plain' , > mixing_beta = 0.7 , > / > ATOMIC_SPECIES > Cu 63.54600 Cu.pbe-d-rrkjus.UPF > Mn 54.93805 Mn.pbe-sp-van.UPF > Al 26.98154 Al.pbe-rrkj.UPF > ATOMIC_POSITIONS crystal > Cu 0.250000000 0.250000000 0.250000000 > Cu 0.750000000 0.750000000 0.750000000 > Mn 0.000000000 0.000000000 0.000000000 > Al 0.500000000 0.500000000 0.500000000 > ------------------------------ > Keep your friends updated? even when you?re not signed in. > > _______________________________________________ > 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/20091110/91978190/attachment.htm From brad.malone at gmail.com Wed Nov 11 02:17:23 2009 From: brad.malone at gmail.com (Brad Malone) Date: Tue, 10 Nov 2009 17:17:23 -0800 Subject: [Pw_forum] Descriptions of FHI and UPF formats? Message-ID: Hi, I'm currently having some issues with pseudopotentials that I've converted from FHI format to UPF format using the utility fhi2upf.x. My problems might possibly be stemming from the conversion from FHI to UPF format (either due to the code itself or quite possibly incorrect usage). In the header of fhi2upf.f90 it says "May or may not work: carefully check what you get". However, without knowing the format of the two pseudo files it's not really possible for me to check this conversion directly. Is anyone aware of any good resources online that clearly describe the formats of these two files? Is http://quantum-espresso.org/wiki/index.php/Unified_pseudopotential_format up to date? If so, any explanation for FHI then? It would be nice to not simply get an understanding of the format by looking at fhi2upf.f90, since I then might not be able to tell what assumptions result in it occasionally not working. Thanks, Brad Malone UC Berkeley -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091110/b2ba9b4e/attachment-0001.htm From naromero at gmail.com Wed Nov 11 02:20:24 2009 From: naromero at gmail.com (Nichols A. Romero) Date: Tue, 10 Nov 2009 19:20:24 -0600 Subject: [Pw_forum] phonon calculations - parallelization over modes Message-ID: <6ac064b60911101720w520bb9a4x415fec24181a01a1@mail.gmail.com> Hi, Are QE phonon calculations parallel over modes (which should be embarrassingly parallel) + q-points? Also, on a completely different note, is there any way to search the mail archive? http://www.democritos.it/pipermail/pw_forum/ -- Nichols A. Romero, Ph.D. Argonne Leadership Computing Facility Argonne, IL 60490 (630) 252-3441 (O) (630) 470-0462 (C) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091110/ba809311/attachment.htm From jameslipd at gmail.com Wed Nov 11 04:30:51 2009 From: jameslipd at gmail.com (Jiaye Li) Date: Wed, 11 Nov 2009 11:30:51 +0800 Subject: [Pw_forum] Installation error on Xcrysden-1.5.21-src-all Message-ID: Dear all I tried to install the Xcrysden-1.5.21-src-all source code on my fc11 PC. I have already installed ifort10 and icc10. libXmu-devel-1.0.4-2.fc11.i586.rpm is also installed correctly. When I type 'make all' in the root directory of Xcrysden source, tcl and tk went on smoothly, but C code compiling reported the error. Please see the follows: #------------------------------# # # # Compiling XCRYSDEN C-code # # # #------------------------------# cd C; make "TOPDIR=/home/jy/Download/XCrySDen-1.5.21-src-all" compile make[1]: Entering directory `/home/jy/Download/XCrySDen-1.5.21-src-all/C' make TOPDIR=/home/jy/Download/XCrySDen-1.5.21-src-all make[2]: Entering directory `/home/jy/Download/XCrySDen-1.5.21-src-all/C' gcc -static -ansi -funroll-loops -DUSE_FONTS detnsplit.o xcAppInit.o xcballstick.o xcviewport.o xcLabels.o vectors.o xcDisplayFunc2.o xcAtomAdd.o loadValues.o hpsort.o auxilproc.o xcdebug.o 3D.o xcDisplayFunc.o readstrf.o mxmymz.o remakestr.o xcSelect.o readisodata.o lighting.o xcGLparam.o colorplane.o isorender.o polygonise.o polygonise_auxil.o xcIsoSurf.o voronoi.o xcBz.o xcSuperCell.o xcPrimitives.o setOpenGLState.o memory.o isoMalloc.o isoInterpolate.o readPlvertex.o splineInt.o paraSize.o isoline.o xcIsoSpaceSel.o cells.o xcWigner.o xcTogl.o datagrid.o sInfo.o xcIsoDataGrid.o xcColorScheme.o xcReadXSF.o xcF3toI4.o xcFractCoor.o signal.o MarchCubes.o isosurf.o xcMolSurf.o cryNewContext.o fs.o cryDispFunc.o cryDispFuncMultiFS.o crySetProj.o crySurfArgs.o crySurf.o cryTransform.o cryClip.o cryTogl.o forces.o xcForces.o gl2psPrintTogl.o ppmPrintTogl.o lcasi.o lcasif.o xcFont.o fog.o writeXSF.o hbonds.o xcHBonds.o linear.o realTimeMovie.o getline.o togl.o gl2ps.o sgiRasterFont.o sgiAux.o \ -o xcrys /home/jy/Download/XCrySDen-1.5.21-src-all/external/lib/libtk8.5.a /home/jy/Download/XCrySDen-1.5.21-src-all/external/lib/libtcl8.5.a /home/jy/Download/XCrySDen-1.5.21-src-all/external/lib/libGLU.a /home/jy/Download/XCrySDen-1.5.21-src-all/external/lib/libGL.a -L/usr/lib/X11/xdm/ -lXmu -lX11 -lXext -lpthread -lm -ldl /usr/bin/ld: cannot find -lXmu collect2: ld returned 1 exit status make[2]: *** [xcrys] Error 1 make[2]: Leaving directory `/home/jy/Download/XCrySDen-1.5.21-src-all/C' make[1]: *** [compile] Error 2 make[1]: Leaving directory `/home/jy/Download/XCrySDen-1.5.21-src-all/C' make: *** [src-C] Error 2 Considering that the the X11 lib may not be found so I made some changes to the Make.sys, where I replaced the line "X_LIB = -L/usr/lib/X11/xdm -lXmu -lX11 -lXext -lpthread" with "X_LIB = /usr/lib/X11/xdm/libXdmGreet.so -lXmu -lX11 -lXext -lpthread". Because I installed X11 already. Then type "make all", again. But error occurs again: #------------------------------# # # # Compiling XCRYSDEN C-code # # # #------------------------------# cd C; make "TOPDIR=/home/jy/Download/XCrySDen-1.5.21-src-all" compile make[1]: Entering directory `/home/jy/Download/XCrySDen-1.5.21-src-all/C' make TOPDIR=/home/jy/Download/XCrySDen-1.5.21-src-all make[2]: Entering directory `/home/jy/Download/XCrySDen-1.5.21-src-all/C' gcc -static -ansi -funroll-loops -DUSE_FONTS detnsplit.o xcAppInit.o xcballstick.o xcviewport.o xcLabels.o vectors.o xcDisplayFunc2.o xcAtomAdd.o loadValues.o hpsort.o auxilproc.o xcdebug.o 3D.o xcDisplayFunc.o readstrf.o mxmymz.o remakestr.o xcSelect.o readisodata.o lighting.o xcGLparam.o colorplane.o isorender.o polygonise.o polygonise_auxil.o xcIsoSurf.o voronoi.o xcBz.o xcSuperCell.o xcPrimitives.o setOpenGLState.o memory.o isoMalloc.o isoInterpolate.o readPlvertex.o splineInt.o paraSize.o isoline.o xcIsoSpaceSel.o cells.o xcWigner.o xcTogl.o datagrid.o sInfo.o xcIsoDataGrid.o xcColorScheme.o xcReadXSF.o xcF3toI4.o xcFractCoor.o signal.o MarchCubes.o isosurf.o xcMolSurf.o cryNewContext.o fs.o cryDispFunc.o cryDispFuncMultiFS.o crySetProj.o crySurfArgs.o crySurf.o cryTransform.o cryClip.o cryTogl.o forces.o xcForces.o gl2psPrintTogl.o ppmPrintTogl.o lcasi.o lcasif.o xcFont.o fog.o writeXSF.o hbonds.o xcHBonds.o linear.o realTimeMovie.o getline.o togl.o gl2ps.o sgiRasterFont.o sgiAux.o \ -o xcrys /home/jy/Download/XCrySDen-1.5.21-src-all/external/lib/libtk8.5.a /home/jy/Download/XCrySDen-1.5.21-src-all/external/lib/libtcl8.5.a /home/jy/Download/XCrySDen-1.5.21-src-all/external/lib/libGLU.a /home/jy/Download/XCrySDen-1.5.21-src-all/external/lib/libGL.a /usr/lib/X11/xdm/libXdmGreet.so -lXmu -lX11 -lXext -lpthread -lm -ldl /usr/bin/ld: attempted static link of dynamic object `/usr/lib/X11/xdm/libXdmGreet.so' collect2: ld returned 1 exit status make[2]: *** [xcrys] Error 1 make[2]: Leaving directory `/home/jy/Download/XCrySDen-1.5.21-src-all/C' make[1]: *** [compile] Error 2 make[1]: Leaving directory `/home/jy/Download/XCrySDen-1.5.21-src-all/C' make: *** [src-C] Error 2 At this time, it seems hard for me to find out the specific error for the compiling. What's wrong with the X11 lib or some other libs? Thank you in advance. BTW, the Make.sys file is attached. -- Sincerely yours Jiaye Li -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091111/bafd4a55/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: Makefile Type: application/octet-stream Size: 3415 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091111/bafd4a55/attachment.obj From nkxirainbow at gmail.com Wed Nov 11 08:55:10 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Wed, 11 Nov 2009 07:55:10 +0000 Subject: [Pw_forum] Special k points In-Reply-To: References: Message-ID: <21fbc4790911102355t5877d48aqab2efa1efbc0f7c@mail.gmail.com> PRB 13 5188 I hope it can help you?? On Tue, Nov 10, 2009 at 7:09 PM, mohsen modaresi wrote: > Hi > I read help file and i faced with this sentences : > > Special k-points (xk_x/y/z) in the irreducible Brillouin Zone > > of the lattice (with all symmetries) and weights (wk) > *See the literature for lists* of special points and > > the corresponding weights. > > which literature? > > I searched but i didnt find any things. > thanks for your answer. > > Mohsen Modaresi > Dep. physics Ferdowsi University Iran > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091111/cedeff23/attachment.htm From giannozz at democritos.it Wed Nov 11 09:05:46 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 11 Nov 2009 09:05:46 +0100 Subject: [Pw_forum] phonon calculations - parallelization over modes In-Reply-To: <6ac064b60911101720w520bb9a4x415fec24181a01a1@mail.gmail.com> References: <6ac064b60911101720w520bb9a4x415fec24181a01a1@mail.gmail.com> Message-ID: <4AFA705A.8080809@democritos.it> Nichols A. Romero wrote: > Are QE phonon calculations parallel over modes (which should be > embarrassingly parallel) + q-points? short answer: not yet with MPI, but it is possible to execute phonons on a GRID infrastructure (i.e. many loosely-coupled machines): http://qe-forge.org/projects/ph-on-grid/ > Also, on a completely different note, is there any way to search the > mail archive? 1) the link you find in http://www.quantum-espresso.org/tools.php 2) using google: type for example PW_forum phonon parallelization site:www.democritos.it P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From jameslipd at gmail.com Wed Nov 11 09:17:29 2009 From: jameslipd at gmail.com (Jiaye Li) Date: Wed, 11 Nov 2009 16:17:29 +0800 Subject: [Pw_forum] How to set ecutwfc and ecutrho Message-ID: Dear users I am curious about the calculation speed related to "ecutwfc" and "ecutrho". As indicated in the tutorial, ecutwfc represents the energy cutoff (Ry) and ecutrho refers to kinetic energy cutoff for charge density and potential. I cannot fully understand the meaning of that brief description. From my experience (vasp), the larger the energy cutoff, the slower the calculation would be, but more accurate. I just would like to know how to set the experience values of the two flags for the case of metal bulk (and surface) and metal oxide bulk (and surface)? Thank you. -- Sincerely yours Jiaye Li -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091111/fbadb2f5/attachment.htm From jameslipd at gmail.com Wed Nov 11 09:19:18 2009 From: jameslipd at gmail.com (Jiaye Li) Date: Wed, 11 Nov 2009 16:19:18 +0800 Subject: [Pw_forum] Installation error on Xcrysden-1.5.21-src-all Message-ID: Problems have just been solved. :-) I just export the libs of C compiler and X11, and recompile it successfully. On Wed, Nov 11, 2009 at 3:55 PM, wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. phonon calculations - parallelization over modes > (Nichols A. Romero) > 2. Installation error on Xcrysden-1.5.21-src-all (Jiaye Li) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 10 Nov 2009 19:20:24 -0600 > From: "Nichols A. Romero" > Subject: [Pw_forum] phonon calculations - parallelization over modes > To: PWSCF Forum > Message-ID: > <6ac064b60911101720w520bb9a4x415fec24181a01a1 at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > Are QE phonon calculations parallel over modes (which should be > embarrassingly parallel) + q-points? > > Also, on a completely different note, is there any way to search the mail > archive? > http://www.democritos.it/pipermail/pw_forum/ > > -- > Nichols A. Romero, Ph.D. > Argonne Leadership Computing Facility > Argonne, IL 60490 > (630) 252-3441 (O) > (630) 470-0462 (C) > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20091110/ba809311/attachment.html > > ------------------------------ > > Message: 2 > Date: Wed, 11 Nov 2009 11:30:51 +0800 > From: Jiaye Li > Subject: [Pw_forum] Installation error on Xcrysden-1.5.21-src-all > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Dear all > > I tried to install the Xcrysden-1.5.21-src-all source code on my fc11 PC. I > have already installed ifort10 and icc10. > libXmu-devel-1.0.4-2.fc11.i586.rpm > is also installed correctly. When I type 'make all' in the root directory > of > Xcrysden source, tcl and tk went on smoothly, but C code compiling reported > the error. Please see the follows: > > > #------------------------------# > # # > # Compiling XCRYSDEN C-code # > # # > #------------------------------# > > cd C; make "TOPDIR=/home/jy/Download/XCrySDen-1.5.21-src-all" compile > make[1]: Entering directory `/home/jy/Download/XCrySDen-1.5.21-src-all/C' > make TOPDIR=/home/jy/Download/XCrySDen-1.5.21-src-all > make[2]: Entering directory `/home/jy/Download/XCrySDen-1.5.21-src-all/C' > gcc -static -ansi -funroll-loops -DUSE_FONTS detnsplit.o xcAppInit.o > xcballstick.o xcviewport.o xcLabels.o vectors.o xcDisplayFunc2.o > xcAtomAdd.o > loadValues.o hpsort.o auxilproc.o xcdebug.o 3D.o xcDisplayFunc.o readstrf.o > mxmymz.o remakestr.o xcSelect.o readisodata.o lighting.o xcGLparam.o > colorplane.o isorender.o polygonise.o polygonise_auxil.o xcIsoSurf.o > voronoi.o xcBz.o xcSuperCell.o xcPrimitives.o setOpenGLState.o memory.o > isoMalloc.o isoInterpolate.o readPlvertex.o splineInt.o paraSize.o > isoline.o > xcIsoSpaceSel.o cells.o xcWigner.o xcTogl.o datagrid.o sInfo.o > xcIsoDataGrid.o xcColorScheme.o xcReadXSF.o xcF3toI4.o xcFractCoor.o > signal.o MarchCubes.o isosurf.o xcMolSurf.o cryNewContext.o fs.o > cryDispFunc.o cryDispFuncMultiFS.o crySetProj.o crySurfArgs.o crySurf.o > cryTransform.o cryClip.o cryTogl.o forces.o xcForces.o gl2psPrintTogl.o > ppmPrintTogl.o lcasi.o lcasif.o xcFont.o fog.o writeXSF.o hbonds.o > xcHBonds.o linear.o realTimeMovie.o getline.o togl.o gl2ps.o > sgiRasterFont.o > sgiAux.o \ > -o xcrys > /home/jy/Download/XCrySDen-1.5.21-src-all/external/lib/libtk8.5.a > /home/jy/Download/XCrySDen-1.5.21-src-all/external/lib/libtcl8.5.a > /home/jy/Download/XCrySDen-1.5.21-src-all/external/lib/libGLU.a > /home/jy/Download/XCrySDen-1.5.21-src-all/external/lib/libGL.a > -L/usr/lib/X11/xdm/ -lXmu -lX11 -lXext -lpthread -lm -ldl > /usr/bin/ld: cannot find -lXmu > collect2: ld returned 1 exit status > make[2]: *** [xcrys] Error 1 > make[2]: Leaving directory `/home/jy/Download/XCrySDen-1.5.21-src-all/C' > make[1]: *** [compile] Error 2 > make[1]: Leaving directory `/home/jy/Download/XCrySDen-1.5.21-src-all/C' > make: *** [src-C] Error 2 > > > Considering that the the X11 lib may not be found so I made some changes to > the Make.sys, where I replaced the line "X_LIB = -L/usr/lib/X11/xdm > -lXmu -lX11 -lXext -lpthread" with "X_LIB = > /usr/lib/X11/xdm/libXdmGreet.so -lXmu -lX11 -lXext -lpthread". Because I > installed X11 already. > > Then type "make all", again. But error occurs again: > > #------------------------------# > # # > # Compiling XCRYSDEN C-code # > # # > #------------------------------# > > cd C; make "TOPDIR=/home/jy/Download/XCrySDen-1.5.21-src-all" compile > make[1]: Entering directory `/home/jy/Download/XCrySDen-1.5.21-src-all/C' > make TOPDIR=/home/jy/Download/XCrySDen-1.5.21-src-all > make[2]: Entering directory `/home/jy/Download/XCrySDen-1.5.21-src-all/C' > gcc -static -ansi -funroll-loops -DUSE_FONTS detnsplit.o xcAppInit.o > xcballstick.o xcviewport.o xcLabels.o vectors.o xcDisplayFunc2.o > xcAtomAdd.o > loadValues.o hpsort.o auxilproc.o xcdebug.o 3D.o xcDisplayFunc.o readstrf.o > mxmymz.o remakestr.o xcSelect.o readisodata.o lighting.o xcGLparam.o > colorplane.o isorender.o polygonise.o polygonise_auxil.o xcIsoSurf.o > voronoi.o xcBz.o xcSuperCell.o xcPrimitives.o setOpenGLState.o memory.o > isoMalloc.o isoInterpolate.o readPlvertex.o splineInt.o paraSize.o > isoline.o > xcIsoSpaceSel.o cells.o xcWigner.o xcTogl.o datagrid.o sInfo.o > xcIsoDataGrid.o xcColorScheme.o xcReadXSF.o xcF3toI4.o xcFractCoor.o > signal.o MarchCubes.o isosurf.o xcMolSurf.o cryNewContext.o fs.o > cryDispFunc.o cryDispFuncMultiFS.o crySetProj.o crySurfArgs.o crySurf.o > cryTransform.o cryClip.o cryTogl.o forces.o xcForces.o gl2psPrintTogl.o > ppmPrintTogl.o lcasi.o lcasif.o xcFont.o fog.o writeXSF.o hbonds.o > xcHBonds.o linear.o realTimeMovie.o getline.o togl.o gl2ps.o > sgiRasterFont.o > sgiAux.o \ > -o xcrys > /home/jy/Download/XCrySDen-1.5.21-src-all/external/lib/libtk8.5.a > /home/jy/Download/XCrySDen-1.5.21-src-all/external/lib/libtcl8.5.a > /home/jy/Download/XCrySDen-1.5.21-src-all/external/lib/libGLU.a > /home/jy/Download/XCrySDen-1.5.21-src-all/external/lib/libGL.a > /usr/lib/X11/xdm/libXdmGreet.so -lXmu -lX11 -lXext -lpthread -lm -ldl > /usr/bin/ld: attempted static link of dynamic object > `/usr/lib/X11/xdm/libXdmGreet.so' > collect2: ld returned 1 exit status > make[2]: *** [xcrys] Error 1 > make[2]: Leaving directory `/home/jy/Download/XCrySDen-1.5.21-src-all/C' > make[1]: *** [compile] Error 2 > make[1]: Leaving directory `/home/jy/Download/XCrySDen-1.5.21-src-all/C' > make: *** [src-C] Error 2 > > > At this time, it seems hard for me to find out the specific error for the > compiling. What's wrong with the X11 lib or some other libs? Thank you in > advance. > > BTW, the Make.sys file is attached. > > -- > Sincerely yours > > Jiaye Li > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20091111/bafd4a55/attachment-0001.htm > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: Makefile > Type: application/octet-stream > Size: 3415 bytes > Desc: not available > Url : > http://www.democritos.it/pipermail/pw_forum/attachments/20091111/bafd4a55/attachment-0001.obj > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 29, Issue 29 > **************************************** > -- Sincerely yours Jiaye Li -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091111/087a2946/attachment-0001.htm From nkxirainbow at gmail.com Wed Nov 11 09:38:26 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Wed, 11 Nov 2009 08:38:26 +0000 Subject: [Pw_forum] How to set ecutwfc and ecutrho In-Reply-To: References: Message-ID: <21fbc4790911110038g1d398803o932dde721606d3e7@mail.gmail.com> Dear Li? I am curious about the calculation speed related to "ecutwfc" and "ecutrho". > As indicated in the tutorial, ecutwfc represents the energy cutoff (Ry) and > ecutrho refers to kinetic energy cutoff for charge density and potential. I > cannot fully understand the meaning of that brief description. If you use Norm-concerving PP, you can just omit the parameter "ecutrho". If you use Ultra-soft PP, you must set "ecutrho" as (8~12)X"ecutwfc". You will fully understand the "ecutrho" after reading some paper about Ultra-soft PP?? (For example?PRB, 41 7892) > From my experience (vasp), the larger the energy cutoff, the slower the > calculation would be, but more accurate. Yes? it is true for PWscf, too. I just would like to know how to set the experience values of the two flags > for the case of metal bulk (and surface) and metal oxide bulk (and surface)? > Thank you. > I think, the value is different with different kind of metal. You can take a convergence test to get proper "ecutrho" and "ecutwfc" ?? ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091111/db895df0/attachment.htm From sclauzer at sissa.it Wed Nov 11 09:58:49 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 11 Nov 2009 09:58:49 +0100 Subject: [Pw_forum] How to set ecutwfc and ecutrho In-Reply-To: References: Message-ID: <4AFA7CC9.6090108@sissa.it> Dear Jiaye, Jiaye Li wrote: > Dear users > > I am curious about the calculation speed related to "ecutwfc" and > "ecutrho". As indicated in the tutorial, ecutwfc represents the energy > cutoff (Ry) and ecutrho refers to kinetic energy cutoff for charge > density and potential. I cannot fully understand the meaning of that More precisely, ecutwfc and ecutrho are the kinetic energy cutoff of the plane wave basis used to describe the wavefunctions and the charge density, respectively. > brief description. From my experience (vasp), the larger the energy > cutoff, the slower the calculation would be, but more accurate. I just That's right and I think should be a general consideration valid for any code using plane waves. I would say "longer", rather than "slower" (which I feel more appropriate with regard to the optimization of a code or the performance of a computer). > would like to know how to set the experience values of the two flags for > the case of metal bulk (and surface) and metal oxide bulk (and surface)? The choice of the cutoffs depends only on the pseudopotentials you are using and on which quantities you are interested in (for instance, magnetic properties are harder to converge wrt total energy). Once you've chosen your PPs you can test convergence of the energy wrt to cutoffs in the cheapest system (usually in the bulk). The threshold of convergence is somehow your choice: personally I don't go below 1mRy since this is the expected order of magnitude of the errors due to PPs. For normconserving PPs you don't need to specify ecutrho, since the default (4*ecutwfc) is good (you can try to figure out why, writing down the charge density in terms of the PW expansion of the wavefunctions). For ultrasoft PPs you will need higher ecutrho due to the augmentation terms in the charge. Try to read some literature about pseudopotential and ask to some experienced people working next door and, of course, experience yourself by trying. HTH GS > Thank you. > > -- > Sincerely yours > > Jiaye Li > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 vitruss at gmail.com Wed Nov 11 10:42:13 2009 From: vitruss at gmail.com (Vit) Date: Wed, 11 Nov 2009 15:42:13 +0600 Subject: [Pw_forum] graphene scf calculation Message-ID: Dear all! I'm trying to plot graphene band structure as a part of computations of carbon based composites. But scf calculation for graphene can't achieve convergence. I've tried different mixing_beta, mixing_mode, degaus ant ecutwfc. The example input file is attached. Could you please tell me which parameters I should tune to achieve convergence? Thanks in advance, Koroteev Victor PhD student, Nikolaev Institute of Inorganic Chemistry SB RAS Novosibirsk, Russian Federation. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091111/f8afcec1/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: graphite.scf.in Type: application/octet-stream Size: 605 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091111/f8afcec1/attachment.obj From paulatto at sissa.it Wed Nov 11 10:46:03 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 11 Nov 2009 10:46:03 +0100 Subject: [Pw_forum] Descriptions of FHI and UPF formats? In-Reply-To: References: Message-ID: In data 11 novembre 2009 alle ore 02:17:23, Brad Malone ha scritto: > Is > http://quantum-espresso.org/wiki/index.php/Unified_pseudopotential_format > up to date? Yes, it is. There is a new UPF format which is quite different (the description is currently sitting in my hard disk), but fhi2upf converts to the one described on the web page. > If so, any explanation for FHI then? It would be nice to not > simply get an understanding of the format by looking at fhi2upf.f90, > since I then might not be able to tell what assumptions result in it > occasionally > not working. I see you point, but I don't know of any such description. You may be luckier on the abinit web site, although a quick google search didn't find anything for me. 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 Nov 11 10:50:14 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 11 Nov 2009 10:50:14 +0100 Subject: [Pw_forum] Descriptions of FHI and UPF formats? In-Reply-To: References: Message-ID: <4AFA88D6.9060205@democritos.it> Brad Malone wrote: > If so, any explanation for FHI then? FHI = Fritz Haber Institute...some time ago I looked for documentation of their format and found nothing P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From eyvaz_isaev at yahoo.com Wed Nov 11 12:04:08 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 11 Nov 2009 03:04:08 -0800 (PST) Subject: [Pw_forum] graphene scf calculation In-Reply-To: Message-ID: <304105.15826.qm@web65702.mail.ac4.yahoo.com> Dear Victor, > But scf calculation for graphene can't > achieve convergence. I've tried different mixing_beta, > mixing_mode, degaus ant ecutwfc. The example input file is > attached. Could you please tell me which parameters I should > tune to achieve convergence? There are several issues (according to your input file) that can affect on convergence in your case. But the main reason, most likely, is k-mesh grid, using 16x16x1 grid the convergence was OK. Please pay attention, 16x16x1, because you simulate 2D case. For Ultrasoft PsP you should use ecutrho about (8-12) times larger than ecutwfc. You have 2 carbon atoms with 4 valence electrons, so, you do not need 8 bands (only 4 is enough), if graphene is semiconducting. In this case you can omit degauss (not sure it is used, if you did not specify "occupations" keyword). Otherwise use keywords specific for metallic case (occupations='smearing', smearing='XYZ', degauss=LKJ). I used mixing_beta=0.1 and mixing_mode-'local-TF', too. 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, 11/11/09, Vit wrote: From nkxirainbow at gmail.com Wed Nov 11 12:04:17 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Wed, 11 Nov 2009 11:04:17 +0000 Subject: [Pw_forum] graphene scf calculation In-Reply-To: References: Message-ID: <21fbc4790911110304g39d379fam4e3f69b79065d9ed@mail.gmail.com> Dear Victor: I look at your input file and notice :"K_POINTS {automatic} 24 24 24 0 0 0" I think there is no need to set kz=24, because you deal with a two dimension graphene. Of couse, setting kz=24 is not wrong. The following is my graphene.rx.in (not scf.in) for graphene. I calculated it about half a year ago, and it went well?? I also put my graphene's results at http://blog.sina.com.cn/s/blog_5f15ead20100c9fu.html I hope it can help you?? &CONTROL calculation = 'vc-relax' , restart_mode = 'from_scratch' , outdir = '/home/raman/graphene/g-monolayer/' , pseudo_dir = '/home/raman/espresso-4.0.4/pseudo/' , etot_conv_thr = 1.0e-7 , forc_conv_thr = 1.0e-7 , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 4, celldm(1) = 4.608737, celldm(3) = 4.536666, nat = 2, ntyp = 1, ecutwfc = 60.D0 , nosym = .false. , nbnd = 8, nelec = 8, tot_charge = 0.000000, occupations = 'fixed' , / &ELECTRONS conv_thr = 1.D-8 , mixing_mode = 'local-TF' , mixing_beta = 0.7D0 , / &IONS ion_dynamics = 'bfgs' , pot_extrapolation = 'second_order' , wfc_extrapolation = 'second_order' , / &CELL cell_dynamics = 'bfgs' , press_conv_thr = 0.2 , cell_dofree = 'xyz' , / ATOMIC_SPECIES C 12.00000 C.pz-rrkjus.UPF ATOMIC_POSITIONS crystal C 0.000000000 0.000000000 0.000000000 1 1 1 C 0.333333333 -0.333333333 0.000000000 1 1 1 K_POINTS automatic 23 23 1 0 0 0 ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091111/b99d5b23/attachment-0001.htm From jameslipd at gmail.com Wed Nov 11 13:05:01 2009 From: jameslipd at gmail.com (Jiaye Li) Date: Wed, 11 Nov 2009 20:05:01 +0800 Subject: [Pw_forum] How to set ecutwfc and ecutrho Message-ID: Dear Hui Wang and Gabriele Sclauzero Thank you for your replies. I just start to learn how to use pwscf and there are many knowledge and skills that I should learn. Anyway, I will read more references and make more tests. On Wed, Nov 11, 2009 at 7:04 PM, wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: How to set ecutwfc and ecutrho (xirainbow) > 2. Re: How to set ecutwfc and ecutrho (Gabriele Sclauzero) > 3. graphene scf calculation (Vit) > 4. Re: Descriptions of FHI and UPF formats? (Lorenzo Paulatto) > 5. Re: Descriptions of FHI and UPF formats? (Paolo Giannozzi) > 6. Re: graphene scf calculation (Eyvaz Isaev) > 7. Re: graphene scf calculation (xirainbow) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 11 Nov 2009 08:38:26 +0000 > From: xirainbow > Subject: Re: [Pw_forum] How to set ecutwfc and ecutrho > To: PWSCF Forum > Message-ID: > <21fbc4790911110038g1d398803o932dde721606d3e7 at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Li? > > > I am curious about the calculation speed related to "ecutwfc" and > "ecutrho". > > As indicated in the tutorial, ecutwfc represents the energy cutoff (Ry) > and > > ecutrho refers to kinetic energy cutoff for charge density and potential. > I > > cannot fully understand the meaning of that brief description. > > If you use Norm-concerving PP, you can just omit the parameter "ecutrho". > If you use Ultra-soft PP, you must set "ecutrho" as (8~12)X"ecutwfc". > You will fully understand the "ecutrho" after reading some paper about > Ultra-soft PP?? (For example?PRB, 41 7892) > > > > > From my experience (vasp), the larger the energy cutoff, the slower the > > calculation would be, but more accurate. > > Yes? it is true for PWscf, too. > > I just would like to know how to set the experience values of the two flags > > for the case of metal bulk (and surface) and metal oxide bulk (and > surface)? > > Thank you. > > > I think, the value is different with different kind of metal. > You can take a convergence test to get proper "ecutrho" and "ecutwfc" ?? > > ____________________________________ > Hui Wang > School of physics, Nankai University, Tianjin, China > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20091111/db895df0/attachment-0001.htm > > ------------------------------ > > Message: 2 > Date: Wed, 11 Nov 2009 09:58:49 +0100 > From: Gabriele Sclauzero > Subject: Re: [Pw_forum] How to set ecutwfc and ecutrho > To: PWSCF Forum > Message-ID: <4AFA7CC9.6090108 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Jiaye, > > Jiaye Li wrote: > > Dear users > > > > I am curious about the calculation speed related to "ecutwfc" and > > "ecutrho". As indicated in the tutorial, ecutwfc represents the energy > > cutoff (Ry) and ecutrho refers to kinetic energy cutoff for charge > > density and potential. I cannot fully understand the meaning of that > > More precisely, ecutwfc and ecutrho are the kinetic energy cutoff of the > plane wave basis > used to describe the wavefunctions and the charge density, respectively. > > > brief description. From my experience (vasp), the larger the energy > > cutoff, the slower the calculation would be, but more accurate. I just > > That's right and I think should be a general consideration valid for any > code using plane > waves. I would say "longer", rather than "slower" (which I feel more > appropriate with > regard to the optimization of a code or the performance of a computer). > > > > would like to know how to set the experience values of the two flags for > > the case of metal bulk (and surface) and metal oxide bulk (and surface)? > > The choice of the cutoffs depends only on the pseudopotentials you are > using and on which > quantities you are interested in (for instance, magnetic properties are > harder to converge > wrt total energy). Once you've chosen your PPs you can test convergence of > the energy wrt > to cutoffs in the cheapest system (usually in the bulk). The threshold of > convergence is > somehow your choice: personally I don't go below 1mRy since this is the > expected order of > magnitude of the errors due to PPs. > For normconserving PPs you don't need to specify ecutrho, since the default > (4*ecutwfc) is > good (you can try to figure out why, writing down the charge density in > terms of the PW > expansion of the wavefunctions). > For ultrasoft PPs you will need higher ecutrho due to the augmentation > terms in the charge. > > Try to read some literature about pseudopotential and ask to some > experienced people > working next door and, of course, experience yourself by trying. > > HTH > > GS > > > > Thank you. > > > > -- > > Sincerely yours > > > > Jiaye Li > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 > > > ------------------------------ > > Message: 3 > Date: Wed, 11 Nov 2009 15:42:13 +0600 > From: Vit > Subject: [Pw_forum] graphene scf calculation > To: "PWSCF Forum" > Message-ID: > Content-Type: text/plain; charset="utf-8" > > Dear all! > I'm trying to plot graphene band structure as a part of computations of > carbon based composites. But scf calculation for graphene can't achieve > convergence. I've tried different mixing_beta, mixing_mode, degaus ant > ecutwfc. The example input file is attached. Could you please tell me > which parameters I should tune to achieve convergence? > > Thanks in advance, > Koroteev Victor > PhD student, > Nikolaev Institute of Inorganic Chemistry SB RAS > Novosibirsk, Russian Federation. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20091111/f8afcec1/attachment-0001.htm > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: graphite.scf.in > Type: application/octet-stream > Size: 605 bytes > Desc: not available > Url : > http://www.democritos.it/pipermail/pw_forum/attachments/20091111/f8afcec1/attachment-0001.obj > > ------------------------------ > > Message: 4 > Date: Wed, 11 Nov 2009 10:46:03 +0100 > From: "Lorenzo Paulatto" > Subject: Re: [Pw_forum] Descriptions of FHI and UPF formats? > To: "PWSCF Forum" > Message-ID: > Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > > In data 11 novembre 2009 alle ore 02:17:23, Brad Malone > ha scritto: > > Is > > > http://quantum-espresso.org/wiki/index.php/Unified_pseudopotential_format > > up to date? > > Yes, it is. There is a new UPF format which is quite different (the > description is currently sitting in my hard disk), but fhi2upf converts to > the one described on the web page. > > > If so, any explanation for FHI then? It would be nice to not > > simply get an understanding of the format by looking at fhi2upf.f90, > > since I then might not be able to tell what assumptions result in it > > occasionally > > not working. > > I see you point, but I don't know of any such description. You may be > luckier on the abinit web site, although a quick google search didn't find > anything for me. > > 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/ > > > ------------------------------ > > Message: 5 > Date: Wed, 11 Nov 2009 10:50:14 +0100 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] Descriptions of FHI and UPF formats? > To: PWSCF Forum > Message-ID: <4AFA88D6.9060205 at democritos.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Brad Malone wrote: > > > If so, any explanation for FHI then? > > FHI = Fritz Haber Institute...some time ago I looked for > documentation of their format and found nothing > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > ------------------------------ > > Message: 6 > Date: Wed, 11 Nov 2009 03:04:08 -0800 (PST) > From: Eyvaz Isaev > Subject: Re: [Pw_forum] graphene scf calculation > To: PWSCF Forum > Message-ID: <304105.15826.qm at web65702.mail.ac4.yahoo.com> > Content-Type: text/plain; charset=us-ascii > > Dear Victor, > > > > But scf calculation for graphene can't > > achieve convergence. I've tried different mixing_beta, > > mixing_mode, degaus ant ecutwfc. The example input file is > > attached. Could you please tell me which parameters I should > > tune to achieve convergence? > > There are several issues (according to your input file) that can affect on > convergence in your case. But the main reason, most likely, is k-mesh grid, > using 16x16x1 grid the convergence was OK. > > Please pay attention, 16x16x1, because you simulate 2D case. > > For Ultrasoft PsP you should use ecutrho about (8-12) times larger than > ecutwfc. > > You have 2 carbon atoms with 4 valence electrons, so, you do not need 8 > bands (only 4 is enough), if graphene is semiconducting. In this case you > can omit degauss (not sure it is used, if you did not specify "occupations" > keyword). Otherwise use keywords specific for metallic case > (occupations='smearing', smearing='XYZ', degauss=LKJ). > > I used mixing_beta=0.1 and mixing_mode-'local-TF', too. > > 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, 11/11/09, Vit wrote: > > > > > > > > > > > ------------------------------ > > Message: 7 > Date: Wed, 11 Nov 2009 11:04:17 +0000 > From: xirainbow > Subject: Re: [Pw_forum] graphene scf calculation > To: PWSCF Forum > Message-ID: > <21fbc4790911110304g39d379fam4e3f69b79065d9ed at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Victor: > I look at your input file and notice :"K_POINTS {automatic} 24 24 24 0 0 0" > I think there is no need to set kz=24, because you deal with a two > dimension > graphene. > Of couse, setting kz=24 is not wrong. > > The following is my graphene.rx.in (not scf.in) for graphene. > I calculated it about half a year ago, and it went well?? > I also put my graphene's results at > http://blog.sina.com.cn/s/blog_5f15ead20100c9fu.html > I hope it can help you?? > > &CONTROL > calculation = 'vc-relax' , > restart_mode = 'from_scratch' , > outdir = '/home/raman/graphene/g-monolayer/' , > pseudo_dir = '/home/raman/espresso-4.0.4/pseudo/' , > etot_conv_thr = 1.0e-7 , > forc_conv_thr = 1.0e-7 , > tstress = .true. , > tprnfor = .true. , > / > &SYSTEM > ibrav = 4, > celldm(1) = 4.608737, > celldm(3) = 4.536666, > nat = 2, > ntyp = 1, > ecutwfc = 60.D0 , > nosym = .false. , > nbnd = 8, > nelec = 8, > tot_charge = 0.000000, > occupations = 'fixed' , > / > &ELECTRONS > conv_thr = 1.D-8 , > mixing_mode = 'local-TF' , > mixing_beta = 0.7D0 , > / > &IONS > ion_dynamics = 'bfgs' , > pot_extrapolation = 'second_order' , > wfc_extrapolation = 'second_order' , > / > &CELL > cell_dynamics = 'bfgs' , > press_conv_thr = 0.2 , > cell_dofree = 'xyz' , > / > ATOMIC_SPECIES > C 12.00000 C.pz-rrkjus.UPF > ATOMIC_POSITIONS crystal > C 0.000000000 0.000000000 0.000000000 1 1 1 > C 0.333333333 -0.333333333 0.000000000 1 1 1 > K_POINTS automatic > 23 23 1 0 0 0 > > > ____________________________________ > Hui Wang > School of physics, Nankai University, Tianjin, China > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20091111/b99d5b23/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 29, Issue 31 > **************************************** > -- Sincerely yours Jiaye Li -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091111/2a8878f2/attachment-0001.htm From tb283 at cornell.edu Wed Nov 11 15:04:36 2009 From: tb283 at cornell.edu (Turan Birol) Date: Wed, 11 Nov 2009 09:04:36 -0500 Subject: [Pw_forum] Special k points In-Reply-To: <21fbc4790911102355t5877d48aqab2efa1efbc0f7c@mail.gmail.com> References: <21fbc4790911102355t5877d48aqab2efa1efbc0f7c@mail.gmail.com> Message-ID: <135f09040911110604j2400447dp66d7d64d826a0667@mail.gmail.com> Also, for every type of simple problem, I would suggest Martin's book: http://www.amazon.com/Electronic-Structure-Theory-Practical-Methods/dp/0521534402/ref=sr_1_1?ie=UTF8&s=books&qid=1257948167&sr=8-1 From stewart at cnf.cornell.edu Wed Nov 11 15:55:09 2009 From: stewart at cnf.cornell.edu (Derek Stewart) Date: Wed, 11 Nov 2009 09:55:09 -0500 Subject: [Pw_forum] graphene scf calculation Message-ID: Hi Koroteev, Just to follow up on some of the other suggestions, I would encourage you to use a very fine k-point grid in the graphene plane. For spare k-point meshes in the graphene plane, the calculated density of states will actually have a small band gap (which shouldn't occur in graphene). This probably won't affect your scf convergence, but it will be important for calculated physical properties. Best regards, Derek ################################ Derek Stewart, Ph. D. Scientific Computation Associate ** New Webpage ** http://sites.google.com/site/dft4nano/ 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 ----- Original Message ----- From: Vit [mailto:vitruss at gmail.com] To: pw_forum at pwscf.org Sent: Wed, 11 Nov 2009 15:42:13 +0600 Subject: [Pw_forum] graphene scf calculation Dear all! I'm trying to plot graphene band structure as a part of computations of carbon based composites. But scf calculation for graphene can't achieve convergence. I've tried different mixing_beta, mixing_mode, degaus ant ecutwfc. The example input file is attached. Could you please tell me which parameters I should tune to achieve convergence? Thanks in advance, Koroteev Victor PhD student, Nikolaev Institute of Inorganic Chemistry SB RAS Novosibirsk, Russian Federation. From baroni at sissa.it Wed Nov 11 18:05:20 2009 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 11 Nov 2009 18:05:20 +0100 Subject: [Pw_forum] Special k points In-Reply-To: <135f09040911110604j2400447dp66d7d64d826a0667@mail.gmail.com> References: <21fbc4790911102355t5877d48aqab2efa1efbc0f7c@mail.gmail.com> <135f09040911110604j2400447dp66d7d64d826a0667@mail.gmail.com> Message-ID: Bravo Turan! This suggestion is particularly welcome. It seems that the habit of reading (studying!) books is gradually fading in the past. Note that extended excerpts from Richard Martin's book (including the section on special points) are available on google books. http://books.google.com/books?id=dmRTFLpSGNsC&printsec=frontcover&dq=electronic+structure#v =onepage&q=&f=false SB On Nov 11, 2009, at 3:04 PM, Turan Birol wrote: > Also, for every type of simple problem, I would suggest Martin's > book: > > http://www.amazon.com/Electronic-Structure-Theory-Practical-Methods/dp/0521534402/ref=sr_1_1?ie=UTF8&s=books&qid=1257948167&sr=8-1 > _______________________________________________ > 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/20091111/23dc1240/attachment.htm From anvari_meh at physics.iust.ac.ir Thu Nov 12 07:18:43 2009 From: anvari_meh at physics.iust.ac.ir (Mehrnaz Anvari) Date: Thu, 12 Nov 2009 09:48:43 +0330 Subject: [Pw_forum] phonon dispersion Message-ID: Hi You said that if this problem(non zero acoustic frequency at gamma point ) appears even after choosing asr option, it relates to numerical noise. Now which order of this noise is acceptable? Thanks Mehrnaz -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091112/571c63d2/attachment.htm From nkxirainbow at gmail.com Thu Nov 12 08:04:19 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Thu, 12 Nov 2009 07:04:19 +0000 Subject: [Pw_forum] phonon dispersion In-Reply-To: References: Message-ID: <21fbc4790911112304j55b431a1i84899b2592991b35@mail.gmail.com> Dear Mehrnaz : 2009/11/12 Mehrnaz Anvari > Hi > You said that if this problem(non zero acoustic frequency at gamma > point ) appears even after choosing asr option, it relates to numerical > noise. > Now which order of this noise is acceptable? > I think it is up to you. In the periodic calculation, the two rotational mode never really vanish due to weak interaction with the periodic images of the molecule. Even using Gaussian03? which does not use period boundary condition, the rotational frequency never equals to zero. There is an example of Hydrogen molecule. You can find it in PW_forum: http://www.democritos.it/pipermail/pw_forum/2005-June/002615.html -- ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091112/8b5dcf34/attachment.htm From giannozz at democritos.it Thu Nov 12 11:03:48 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 12 Nov 2009 11:03:48 +0100 Subject: [Pw_forum] phonon dispersion In-Reply-To: <21fbc4790911112304j55b431a1i84899b2592991b35@mail.gmail.com> References: <21fbc4790911112304j55b431a1i84899b2592991b35@mail.gmail.com> Message-ID: <8AA0B2D4-32CF-4B22-A109-AC15A8B5C638@democritos.it> On Nov 12, 2009, at 8:04 , xirainbow wrote: > In the periodic calculation, the two rotational mode never really > vanish due to weak interaction with the periodic images of the > molecule. I think the original question was on a different subject. Even after imposing acoustic sum rule, the frequency of translation modes are not exactly zero. They shouldn't exceed a fraction of a cm^{-1}, though. Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From dimpy.sharma at tyndall.ie Thu Nov 12 14:26:42 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Thu, 12 Nov 2009 13:26:42 -0000 Subject: [Pw_forum] Problem in running nscf calculation at higher number of k points Message-ID: Hi Quantum espresso users, I need to calculate projected density of states and band structure for my system and thats why I have been running a nsf calculation with higher number of k points, but the problem is that my calculation crashes without giving me any error message. The nscf calculation runs successfully upto for 4 k points but if I increase it to 5 or higher number it crashes. I run my calculation in a very high memory of 80 nodes. Can anybody please give me any suggestion? Thanks a million! Dimpy D Sharma Theory Modelling and design UCC Ireland -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091112/09d698d7/attachment.htm From anvari_meh at physics.iust.ac.ir Thu Nov 12 16:56:22 2009 From: anvari_meh at physics.iust.ac.ir (Mehrnaz Anvari) Date: Thu, 12 Nov 2009 19:26:22 +0330 Subject: [Pw_forum] elph guestion Message-ID: Dear Paolo I've already read about brute force in your paper(PRB,39,1989) which is used to calculate perturbations in a system(such as ionic displacement). Am I rigth? Also I've studied two of Lazzeri papers about evaluated lambda in graphene.Do you mean that he doesn't use elph code directly to calculate lambda in graphene? In addition I want to know that does the elph code use new fermi energy & Dos at fermi energy after perturbation to calculate lambda? Mehrnaz Iran University of science & technology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091112/9ca31dde/attachment.htm From eyvaz_isaev at yahoo.com Thu Nov 12 19:01:53 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 12 Nov 2009 10:01:53 -0800 (PST) Subject: [Pw_forum] Problem in running nscf calculation at higher number of k points In-Reply-To: Message-ID: <832234.51518.qm@web65714.mail.ac4.yahoo.com> Dear Dimpy, --- On Thu, 11/12/09, Dimpy Sharma wrote: > I need to calculate projected density of states and band > structure for my system and thats why I have been running a > nsf calculation with higher number of k points, but the > problem is that my calculation crashes without giving me any > error message. The nscf calculation runs successfully upto > for? 4 k points but if I increase it to 5 or higher > number it crashes. I run my calculation in a very high > memory of 80 nodes. Can anybody please give me any > suggestion? The info provided is quite scarce to tell more exactly why this happens. Have you checked disk space? May be you have no free disk space. 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 From dhjung at insilicotech.co.kr Fri Nov 13 00:19:05 2009 From: dhjung at insilicotech.co.kr (Dong Hyun Jung) Date: Fri, 13 Nov 2009 08:19:05 +0900 Subject: [Pw_forum] EXX calculation error Message-ID: <81FCE705EAAE4DC29DE9830C6D9CB409@DHJUNG> Hi Quantum espresso users, I have tried to calculate CuPc crystal using EXX. Testing EXX with examples was successful. So, I believe that the compilation has no problem. However, when I apply EXX to CuPc system, there happens a segmentation fault error. Looking into the code, I found that the problem is related to the function exxenergy2. In more detail, the program stops at this loop, vc = 0.D0 do ig=1,ngm vc = vc + fac(ig) * x1 * & abs( rhoc(nls(ig)) + CONJG(rhoc(nlsm(ig))) )**2 vc = vc + fac(ig) * x2 * & abs( rhoc(nls(ig)) - CONJG(rhoc(nlsm(ig))) )**2 end do ngm is 22873 and when ig=5547, it does not go any more. Please help me to get over this problem. The following is the input. In this input, cutoff energy 35 Ryb is just a test. Thank you in advance. &control calculation='scf' pseudo_dir = '/opt/espresso-4.1/pseudo/' , wfcdir = '/scratch/dhjung-CuPc-alpha-35-1527', disk_io = 'default' , restart_mode='from_scratch', verbosity = 'high' , / &system ibrav=14 celldm(1)=7.158 celldm(2)=3.4174 celldm(3)=3.1765 celldm(4)=-0.010057 celldm(5)=-0.08916 celldm(6)=-0.0152757 input_dft='pbe0' nat=57 ecutwfc=35. ecutrho=360. ntyp=4 occupations='smearing' degauss=0.0037 smearing='gauss' nspin=2 starting_magnetization(1) = 0 starting_magnetization(2) = 0 starting_magnetization(3) = 0 starting_magnetization(4) = 1 london=.true. london_rcut = 150 london_s6 = 0.75 / &electrons electron_maxstep = 200, conv_thr = 2.0D-8 , startingpot = 'file' , startingwfc = 'file' mixing_mode = 'local-TF', mixing_beta = 0.5 , diagonalization = 'david' , diago_david_ndim = 10, / ATOMIC_SPECIES C 12.0109996796 06-C.GGA.fhi.UPF H 1.0080000162 01-H.GGA.fhi.UPF N 14.0067 N_MT_PBE.psp.UPF Cu 63.546 29-Cu.GGA.fhi.UPF K_POINTS gamma #K_POINTS {automatic} #5 2 2 1 1 1 ATOMIC_POSITIONS {crystal} H 0.077236869 0.557967715 0.205802347 H 0.622277732 -0.351874750 0.255041514 H 0.915455135 -0.336197783 0.450150538 H -0.183589645 0.450533766 0.043780800 H 0.410056523 0.476275521 0.367695525 H 0.975977982 -0.166011421 0.546947230 H 0.750172668 -0.006016814 0.450382392 H 0.503401122 0.284727572 0.370768689 H -0.077236869 -0.557967715 -0.205802347 H -0.622277732 0.351874750 -0.255041514 H -0.915455135 0.336197783 -0.450150538 H 0.183589645 -0.450533766 -0.043780800 H -0.410056523 -0.476275521 -0.367695525 H -0.975977982 0.166011421 -0.546947230 H -0.750172668 0.006016814 -0.450382392 H -0.503401122 -0.284727572 -0.370768689 C 0.404451638 -0.015164950 0.223690256 C 0.026344575 0.309332907 0.116186809 C -0.031388984 0.415466464 0.114340625 C 0.110975543 0.474357100 0.205921665 C 0.300538589 0.427730304 0.297758200 C 0.355176667 0.321232990 0.300258344 C 0.216875201 0.262706147 0.207857356 C 0.229789269 0.152910153 0.180865003 C 0.567554581 -0.090671317 0.300044092 C 0.727712507 -0.081213108 0.408679372 C -0.073446432 0.227107735 0.035445577 C 0.851513756 -0.170855207 0.461570503 C 0.815181944 -0.267584478 0.406478164 C 0.653244082 -0.277156748 0.297801234 C 0.529601926 -0.187358064 0.245141443 C 0.342719615 -0.168879141 0.136243221 C -0.404451638 0.015164950 -0.223690256 C -0.026344575 -0.309332907 -0.116186809 C 0.031388984 -0.415466464 -0.114340625 C -0.110975543 -0.474357100 -0.205921665 C -0.300538589 -0.427730304 -0.297758200 C -0.355176667 -0.321232990 -0.300258344 C -0.216875201 -0.262706147 -0.207857356 C -0.229789269 -0.152910153 -0.180865003 C -0.567554581 0.090671317 -0.300044092 C -0.727712507 0.081213108 -0.408679372 C 0.073446432 -0.227107735 -0.035445577 C -0.851513756 0.170855207 -0.461570503 C -0.815181944 0.267584478 -0.406478164 C -0.653244082 0.277156748 -0.297801234 C -0.529601926 0.187358064 -0.245141443 C -0.342719615 0.168879141 -0.136243221 N 0.390000831 0.084712273 0.249222416 N 0.053782089 0.134509668 0.076913452 N 0.273070103 -0.064716699 0.126123111 N -0.255196800 0.243833544 -0.062198110 N -0.390000831 -0.084712273 -0.249222416 N -0.053782089 -0.134509668 -0.076913452 N -0.273070103 0.064716699 -0.126123111 N 0.255196800 -0.243833544 0.062198110 Cu 0.000000000 0.000000000 0.000000000 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dong Hyun Jung, Ph. D Chief Scientist Insilicotech Co. Ltd. A-1101, Kolontripolis, 210, Geumgok-Dong, Seongnam, Gyeonggi-Do, 463-943, Korea Tel. +82-31-728-0443 Fax. +82-31-728-0444 dhjung at insilicotech.co.kr ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From giannozz at democritos.it Fri Nov 13 08:12:16 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 13 Nov 2009 08:12:16 +0100 Subject: [Pw_forum] EXX calculation error In-Reply-To: <81FCE705EAAE4DC29DE9830C6D9CB409@DHJUNG> References: <81FCE705EAAE4DC29DE9830C6D9CB409@DHJUNG> Message-ID: On Nov 13, 2009, at 24:19 , Dong Hyun Jung wrote: > ecutwfc=35. > ecutrho=360. > C 12.0109996796 06-C.GGA.fhi.UPF > H 1.0080000162 01-H.GGA.fhi.UPF > N 14.0067 N_MT_PBE.psp.UPF > Cu 63.546 29-Cu.GGA.fhi.UPF these are norm-conserving PPs. You shouldn't set ecutrho: it will be automatically set to 4*ecutwfc. Not sure this is related with your problem, though P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From sclauzer at sissa.it Fri Nov 13 08:37:40 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 13 Nov 2009 08:37:40 +0100 Subject: [Pw_forum] Problem in running nscf calculation at higher number of k points In-Reply-To: References: Message-ID: <4AFD0CC4.9080309@sissa.it> Dimpy Sharma wrote: > > Hi Quantum espresso users, > > I need to calculate projected density of states and band structure for > my system and thats why I have been running a nsf calculation with > higher number of k points, but the problem is that my calculation > crashes without giving me any error message. The nscf calculation runs > successfully upto for 4 k points but if I increase it to 5 or higher > number it crashes. Exceeded walltime? I run my calculation in a very high memory of 80 > nodes. Can anybody please give me any suggestion? If you are using 80 processors, either you have a very big system and you don't need a high number of k-points (however I wouldn't define 4-5 a high number), or you are using a lot of pools to distribute k-points. Before posting again, you should check if you meet the same problem on a smaller system or even in a serial run. Also check the logs (stderr and stdout) from the nodes where the job was running (which are usually redirected to the user at the end of a parallel job): if the program crashed there should be some (possibly obscure) error message. If you really want help please specify all the details of the calculation, where you run the job, which system, etc. etc. GS > > Thanks a million! > > Dimpy > > D Sharma > Theory Modelling and design > UCC > Ireland > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 ppzang at gmail.com Fri Nov 13 09:24:35 2009 From: ppzang at gmail.com (Chenpeng Zang) Date: Fri, 13 Nov 2009 16:24:35 +0800 Subject: [Pw_forum] Problem in running the software In-Reply-To: References: Message-ID: Dear Lorenzo Paulatto: I have checked the execution permissions of the file xcrys. It turns out to be "-rwxr-xr-x. 1 Zangcp Zangcp 887581 08-01 02:21 xcrys", which means this file is executable, right? Actually, I am the owner of the pc and system administrator, of course. For I am the beginner of linux environment, I don't know how to change the exec option of directory. Would you like to guide me? Best wishes. Chenpeng Zang 2009/11/10 Chenpeng Zang > Lorenzo Paulatto: > Thank you response so fast, which actually surprised me. > Thank you for your help. > God bless you! > > Chenpeng Zang > > 2009/11/10 Lorenzo Paulatto > > In data 10 novembre 2009 alle ore 13:58:26, Chenpeng Zang >> ha scritto: >> > /home/Zangcp/software/XCrySDen-1.5.21-bin-semishared/bin/xcrys: cannot >> > execute binary file". >> >> Dear Chenpeng Zang, >> if the file is actually there and has execution permissions (check with >> "ls -l filename") than it is your system administrator that has mounted >> the home directory with the noexec option (you'll have to complain with >> him). >> >> Please note that there is an XCrysDen mailing list, which may be a more >> appropriate place for this kind of questions: >> http://www.democritos.it/mailman/listinfo/xcrysden >> >> 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/ >> _______________________________________________ >> 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/20091113/1436fc89/attachment.htm From giannozz at democritos.it Fri Nov 13 09:54:12 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 13 Nov 2009 09:54:12 +0100 Subject: [Pw_forum] Problem in running the software In-Reply-To: References: Message-ID: <4AFD1EB4.1000904@democritos.it> Chenpeng Zang wrote: > Dear Lorenzo Paulatto: > I have checked the execution permissions of the file xcrys. It > turns out to be "-rwxr-xr-x. 1 Zangcp Zangcp 887581 08-01 02:21 xcrys", > which means this file is executable, right? Actually, I am the owner of > the pc and system administrator, of course. For I am the beginner of > linux environment, I don't know how to change the exec option of > directory. Would you like to guide me? maybe Lorenzo will, but I think he shouldn't. This is the mailing list for the quantum espresso distribution, not for all kinds of computer problems. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From paulatto at sissa.it Fri Nov 13 10:31:30 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 13 Nov 2009 10:31:30 +0100 Subject: [Pw_forum] Problem in running the software In-Reply-To: References: Message-ID: In data 13 novembre 2009 alle ore 09:24:35, Chenpeng Zang ha scritto: > I don't know how to change the exec option of directory. Would you like > to guide me? Now I've noticed that you downloaded the 64bit version of the software, are you sure you hardware is 64bit? *remember to post to the xcrysden mailing list for problems on xcrysden* 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 ppzang at gmail.com Fri Nov 13 11:48:01 2009 From: ppzang at gmail.com (Chenpeng Zang) Date: Fri, 13 Nov 2009 18:48:01 +0800 Subject: [Pw_forum] Problem in running the software In-Reply-To: References: Message-ID: I am not sure but the other version does not work either and reports the same error. I am sorry for posting the irrelevant question. I might just need some help. If it is wasting your time, it is okey to ignore my mail. Anyway thank for your patient. 2009/11/13 Lorenzo Paulatto > In data 13 novembre 2009 alle ore 09:24:35, Chenpeng Zang > ha scritto: > > I don't know how to change the exec option of directory. Would you like > > to guide me? > > Now I've noticed that you downloaded the 64bit version of the software, > are you sure you hardware is 64bit? > > *remember to post to the xcrysden mailing list for problems on xcrysden* > > 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/ > _______________________________________________ > 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/20091113/7d37b9d6/attachment.htm From paulatto at sissa.it Fri Nov 13 11:58:00 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 13 Nov 2009 11:58:00 +0100 Subject: [Pw_forum] Problem in running the software In-Reply-To: References: Message-ID: In data 13 novembre 2009 alle ore 11:48:01, Chenpeng Zang ha scritto: > I am not sure Well, you'll have to find out sooner or later. You can type uname -m to get the information: x86_64 : it's 64bit i686 : it's 32bit > but the other version does not work either and reports the > same error. First of all have a look at ~/.bashrc (it a hidden file) with a text editor and clean up any possible line related to xcrysden (leftovers from older versions, or bad installation). Then restart your system (or at least redo the login) download the correct version of xcrysden, unpack it somewhere, change to the directory and run ./xcrysden. If you're still having any problem, please post the *entire* output to the xcrysden mailing list. 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 ppzang at gmail.com Fri Nov 13 12:26:51 2009 From: ppzang at gmail.com (Chenpeng Zang) Date: Fri, 13 Nov 2009 19:26:51 +0800 Subject: [Pw_forum] Problem in running the software In-Reply-To: References: Message-ID: Finally, it works. Thank you very very much ^_^ 2009/11/13 Lorenzo Paulatto > In data 13 novembre 2009 alle ore 11:48:01, Chenpeng Zang > ha scritto: > > I am not sure > > Well, you'll have to find out sooner or later. You can type uname -m to > get the information: > x86_64 : it's 64bit > i686 : it's 32bit > > > but the other version does not work either and reports the > > same error. > > First of all have a look at ~/.bashrc (it a hidden file) with a text > editor and clean up any possible line related to xcrysden (leftovers from > older versions, or bad installation). Then restart your system (or at > least redo the login) download the correct version of xcrysden, unpack it > somewhere, change to the directory and run ./xcrysden. > > If you're still having any problem, please post the *entire* output to the > xcrysden mailing list. > > > 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/ > _______________________________________________ > 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/20091113/d7e084fe/attachment.htm From modaresi.mohsen at gmail.com Fri Nov 13 14:44:09 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Fri, 13 Nov 2009 16:44:09 +0300 Subject: [Pw_forum] some problem with ld1.x Message-ID: Dear espresso users I will be grateful if you help me with this I tried to use (ld1.x), i worked with example that i get from ( http://www.fisica.uniud.it/~giannozz/QE-Tutorial/) and i have not any problem but when i try to write a new input file for (ld1.x) i faced with problems. some of them are: 1) this is structure that used for si ( config="[Ne] 3s2 3p2 3d-1" ), Si is special case or 3d bands are special or d bands are special? we know that Si structure is ("[Ne] 3s2 3p2") why they add 3d-1 term to this structure?what it means? 2) this example is about Si, if we have a structure like GaAS what is our (config)? we must work with Ga configuration or As configuration? what is (zval)? I have this problems becuse i have only one example, Can any body get me inpute file for ld1.x? Thanks Mohsen Modaresi deppartement of physics, Msc student of Solid State Physics, Ferdowsi University, Iran -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091113/bc0a7a7a/attachment.htm From paulatto at sissa.it Fri Nov 13 14:52:44 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 13 Nov 2009 14:52:44 +0100 Subject: [Pw_forum] some problem with ld1.x In-Reply-To: References: Message-ID: Dear Mohsen, welcome in the QE community. > 1) this is structure that used for si ( config="[Ne] 3s2 3p2 3d-1" ), Si > is special case or 3d bands are special or d bands are special? we know > that Si structure is ("[Ne] 3s2 3p2") why they add 3d-1 term to this > structure?what it means? Well, the fact that Si only has electrons up to 3p in it ground state, for an isolated atom, does not imply that the same is true when you put it in a compound. The pseudopotential has to keep in account this fact. The capacity of a pps to reproduce the characteristic of an atom in a wide range of configuration is called transferability. In your specific I guess (I cannot say for sure, as you are not providing the necessary information) that the 3d orbital is used to generate the local potential. > 2) this example is about Si, if we have a structure like GaAS what is our > (config)? we must work with Ga configuration or As configuration? what is > (zval)? I don't understand what you are asking here. > I have this problems becuse i have only one example, Can any body get me > inpute file for ld1.x? > Thanks There is a whole bunch of them in the Quantum-ESPRESSO distribution; have a look a the directory atomic_doc and its subdirectories; I would also advise you to read Paolo Giannozzi's guide on pps generation pseudo_guid.tex, which you can find in the aforementioned directory. 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 modaresi.mohsen at gmail.com Fri Nov 13 15:14:42 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Fri, 13 Nov 2009 17:14:42 +0300 Subject: [Pw_forum] some problem with ld1.x In-Reply-To: References: Message-ID: Dear Lorenzo Paulatto Thanks fot your answer. yes you are right i have not enough information about pseudopotential. about my second question: all of examples work with Si,Al,Fe,Ni,... i asked that can we work with GaAs or MgO or FeO which have two elements? and if we can what is our (config) and (zval)?((we have two elements that have different configuration which configuration must be used?)) and thanks for "atomic_doc" best wishes mohsen modaresi On Fri, Nov 13, 2009 at 4:52 PM, Lorenzo Paulatto wrote: > Dear Mohsen, > welcome in the QE community. > > > 1) this is structure that used for si ( config="[Ne] 3s2 3p2 3d-1" ), Si > > is special case or 3d bands are special or d bands are special? we know > > that Si structure is ("[Ne] 3s2 3p2") why they add 3d-1 term to this > > structure?what it means? > > Well, the fact that Si only has electrons up to 3p in it ground state, for > an isolated atom, does not imply that the same is true when you put it in > a compound. The pseudopotential has to keep in account this fact. The > capacity of a pps to reproduce the characteristic of an atom in a wide > range of configuration is called transferability. In your specific I guess > (I cannot say for sure, as you are not providing the necessary > information) that the 3d orbital is used to generate the local potential. > > > > 2) this example is about Si, if we have a structure like GaAS what is our > > (config)? we must work with Ga configuration or As configuration? what is > > (zval)? > > I don't understand what you are asking here. > > > I have this problems becuse i have only one example, Can any body get me > > inpute file for ld1.x? > > Thanks > > There is a whole bunch of them in the Quantum-ESPRESSO distribution; have > a look a the directory atomic_doc and its subdirectories; I would also > advise you to read Paolo Giannozzi's guide on pps generation > pseudo_guid.tex, which you can find in the aforementioned directory. > > > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091113/e0768023/attachment.htm From paulatto at sissa.it Fri Nov 13 15:25:55 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 13 Nov 2009 15:25:55 +0100 Subject: [Pw_forum] some problem with ld1.x In-Reply-To: References: Message-ID: In data 13 novembre 2009 alle ore 15:14:42, mohsen modaresi ha scritto: > i asked that can we work with GaAs or MgO or FeO which have two elements? > and if we can what is our (config) and (zval)?((we have two elements that > have different configuration which configuration must be used?)) > and thanks for "atomic_doc" Dear Mohsen, ld1.x is "only" a pseudopotential generation program, it only computes isolated atoms. The pseudopotentials are then used by pw.x (ground state code) or cp.x (Car-Parrinello code) to simulate complex material. Normally you don't generate the pps yourself, but you take them from publicly available databases, such as the one provided by QE: . Generating the pseudopotential yourself requires a certain knowledge of the mechanism and a lot of patience. I see that you are a bit confused about all this DFT business, I think you could really benefit from watching the videos from the first few days of tutorial, available here: . 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 modaresi.mohsen at gmail.com Fri Nov 13 15:39:01 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Fri, 13 Nov 2009 17:39:01 +0300 Subject: [Pw_forum] some problem with ld1.x In-Reply-To: References: Message-ID: Dear Lorenzo Thanks for your help actually i am confused, but i think that your links can help me. Thanks for your frindly advise. mohsen modaresi On Fri, Nov 13, 2009 at 5:25 PM, Lorenzo Paulatto wrote: > In data 13 novembre 2009 alle ore 15:14:42, mohsen modaresi > ha scritto: > > i asked that can we work with GaAs or MgO or FeO which have two elements? > > and if we can what is our (config) and (zval)?((we have two elements that > > have different configuration which configuration must be used?)) > > and thanks for "atomic_doc" > > Dear Mohsen, > ld1.x is "only" a pseudopotential generation program, it only computes > isolated atoms. The pseudopotentials are then used by pw.x (ground state > code) or cp.x (Car-Parrinello code) to simulate complex material. Normally > you don't generate the pps yourself, but you take them from publicly > available databases, such as the one provided by QE: > . Generating the > pseudopotential yourself requires a certain knowledge of the mechanism and > a lot of patience. > > I see that you are a bit confused about all this DFT business, I think you > could really benefit from watching the videos from the first few days of > tutorial, available here: > . > > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091113/6b9c0abe/attachment.htm From m.c.dixon at leeds.ac.uk Fri Nov 13 16:45:34 2009 From: m.c.dixon at leeds.ac.uk (Mark Dixon) Date: Fri, 13 Nov 2009 15:45:34 +0000 (GMT) Subject: [Pw_forum] Compile of Espresso 4.1.1 fails with PGI Message-ID: I'm trying to compile Espresso 4.1.1 with the PGI compiler on SLES10 SP2 on an x86_64 platform, which fails with an assembler error. I'm getting the same error message with versions 7.1, 7.2, 8.0 and 9.0. I'm starting to wonder if it's my binutils package. In case there are any words of wisdom out there, the lines leading-up to the error show: ( cd Multigrid ; if test "make" = "" ; then make TLDEPS= all ; \ else make TLDEPS= all ; fi ) make[1]: Entering directory `/nobackup/issmcd/es/espresso-4.1.1/Multigrid' pgf77 -fast -r8 -c pded.f pgf77 -fast -r8 -c buildAd.f pgf77 -fast -r8 -c buildBd.f pgf77 -fast -r8 -c buildGd.f pgf77 -fast -r8 -c buildPd.f pgf77 -fast -r8 -c cgd.f pgf77 -fast -r8 -c cgmgd.f pgf77 -fast -r8 -c cgmgdrvd.f cpp -P -traditional -D__PGI -D__ACML -D__MPI -D__PARA -I../include maind.f90 -o maind.F90 mpif90 -fast -r8 -D__PGI -D__ACML -D__MPI -D__PARA -I../include -I./ -I../Modules -I../iotk/src -I../PW -I../PH -I../EE -I../GIPAW -c maind.F90 -o maind.o pgf77 -fast -r8 -c mainsubd.f pgf77 -fast -r8 -c matvecd.f /tmp/pgf77v0Se-_QCr57f.s: Assembler messages: /tmp/pgf77v0Se-_QCr57f.s:43755: Error: suffix or operands invalid for `movhpd' make[1]: *** [matvecd.o] Error 2 make[1]: Leaving directory `/nobackup/issmcd/es/espresso-4.1.1/Multigrid' make: *** [libs] Error 2 Any ideas? Thanks, Mark -- ----------------------------------------------------------------- Mark Dixon Email : m.c.dixon at leeds.ac.uk HPC/Grid Systems Support Tel (int): 35429 Information Systems Services Tel (ext): +44(0)113 343 5429 University of Leeds, LS2 9JT, UK ----------------------------------------------------------------- From giannozz at democritos.it Fri Nov 13 17:08:38 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 13 Nov 2009 17:08:38 +0100 Subject: [Pw_forum] Compile of Espresso 4.1.1 fails with PGI In-Reply-To: References: Message-ID: <4AFD8486.4090400@democritos.it> Mark Dixon wrote: > In case there are any words of wisdom out there I'll provide some words (wisdom not included in price) > pgf77 -fast -r8 -c matvecd.f > /tmp/pgf77v0Se-_QCr57f.s: Assembler messages: > /tmp/pgf77v0Se-_QCr57f.s:43755: Error: suffix or operands invalid for `movhpd' try to compile this file without "-fast", e.g: cd Multigrid/ ; pgf77 -r8 -c matvecd.f ; cd - ; make ... P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From vranjan at ncsu.edu Fri Nov 13 22:54:00 2009 From: vranjan at ncsu.edu (Vivek Ranjan) Date: Fri, 13 Nov 2009 16:54:00 -0500 (EST) Subject: [Pw_forum] Constrained Dynamics (vc-relax) In-Reply-To: <74264.83803.qm@web73008.mail.tp2.yahoo.com> References: <74264.83803.qm@web73008.mail.tp2.yahoo.com> Message-ID: <47968.152.14.74.117.1258149240.squirrel@webmail.ncsu.edu> Hello, I tried to run vc-relax calculation with constraints and the program stopped. I found out the following lines in "move_ions.f90". IF ( lmovecell .AND. lconstrain ) & CALL errore( 'move_ions', & & 'variable cell and constraints not implemented', 1 ) Wondering if constraint as implemented within PWSCF should not be applied when for vc-relax ? Any suggestions/discussion on this topic and possible ways to extend the implementation to relaxed cell case ? Thank you, Vivek Physics, NC State University From anvari_meh at physics.iust.ac.ir Sat Nov 14 03:56:03 2009 From: anvari_meh at physics.iust.ac.ir (Mehrnaz Anvari) Date: Sat, 14 Nov 2009 06:26:03 +0330 Subject: [Pw_forum] phonon & temperature Message-ID: Hi I want to know what is the relation between phonon calculations and temperature? I know that density & external potentials depend on ion displacements, but I couldn't understand how does code connect these displacements to temperature? also I want to know that whether ionic displacements cause any ripples or roughness in the structure of sample or not? Mehrnaz Iran University of science & technology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091114/bcc85f2e/attachment.htm From anvari_meh at physics.iust.ac.ir Sat Nov 14 04:00:47 2009 From: anvari_meh at physics.iust.ac.ir (Mehrnaz Anvari) Date: Sat, 14 Nov 2009 06:30:47 +0330 Subject: [Pw_forum] elph question Message-ID: Dear Paolo Sorry because of repeated question. the answer will clear somethig for me. I've already read about brute force in your paper(PRB,39,1989) which is used to calculate perturbations in a system(such as ionic displacement). Am I rigth? Also I've studied two of Lazzeri papers about evaluated lambda in graphene.Do you mean that he doesn't use elph code directly to calculate lambda in graphene? In addition I want to know that does the elph code use new fermi energy & Dos at fermi energy after perturbation to calculate lambda? Mehrnaz Iran University of science & technology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091114/b4d6a6c4/attachment-0001.htm From nkxirainbow at gmail.com Sat Nov 14 05:04:04 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Sat, 14 Nov 2009 12:04:04 +0800 Subject: [Pw_forum] phonon & temperature In-Reply-To: References: Message-ID: <21fbc4790911132004n70d65a20w193cac8285041a86@mail.gmail.com> Dear Mehrnaz: > Hi > I want to know what is the relation between phonon calculations and > temperature? > I think phonon frequency is independent of temperature. That means all the phonon frequency is calculated under 0 K. -- ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091114/bf18c791/attachment.htm From paulatto at sissa.it Sat Nov 14 12:26:15 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sat, 14 Nov 2009 12:26:15 +0100 (CET) Subject: [Pw_forum] Constrained Dynamics (vc-relax) In-Reply-To: <47968.152.14.74.117.1258149240.squirrel@webmail.ncsu.edu> References: <74264.83803.qm@web73008.mail.tp2.yahoo.com> <47968.152.14.74.117.1258149240.squirrel@webmail.ncsu.edu> Message-ID: <32916.78.12.162.16.1258197975.squirrel@webmail.sissa.it> On Fri, November 13, 2009 22:54, Vivek Ranjan wrote: > Wondering if constraint as implemented within PWSCF should not be applied > when for vc-relax ? Dear Vivek, that line is there for a reason! You can try to remove it and, with a bit of luck, it may even work, but it has never been tried nor tested. > Any suggestions/discussion on this topic and possible ways to extend the > implementation to relaxed cell case ? That part of the code would greatly benefit from a drastic cleanup and re-implementation; all the necessary subroutines are there but they are connected in a clumsy way. Also note that bfgs+constraint is not implemented at the moment. I think reading through the code of the specific minimization algorithm you are interested in should not be difficult and all the constraint subroutines have clear and simple purposes. If you are going to implement this functionality you're very welcome to ask for help. best 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 modaresi.mohsen at gmail.com Sat Nov 14 16:15:55 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Sat, 14 Nov 2009 18:45:55 +0330 Subject: [Pw_forum] phonon & temperature In-Reply-To: <21fbc4790911132004n70d65a20w193cac8285041a86@mail.gmail.com> References: <21fbc4790911132004n70d65a20w193cac8285041a86@mail.gmail.com> Message-ID: Dear Phonon frequency is depend on temperature, but measurements perform in fixed temperature like 0K. i think Mohsen Modaresi On Sat, Nov 14, 2009 at 7:34 AM, xirainbow wrote: > Dear Mehrnaz: > > >> Hi >> I want to know what is the relation between phonon calculations and >> temperature? >> > I think phonon frequency is independent of temperature. > That means all the phonon frequency is calculated under 0 K. > > > -- > ____________________________________ > Hui Wang > School of physics, Nankai University, Tianjin, China > > _______________________________________________ > 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/20091114/74374a04/attachment.htm From giannozz at democritos.it Sat Nov 14 19:15:52 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 14 Nov 2009 19:15:52 +0100 Subject: [Pw_forum] elph question In-Reply-To: References: Message-ID: On Nov 14, 2009, at 4:00 , Mehrnaz Anvari wrote: > Also I've studied two of Lazzeri papers about evaluated lambda in > graphene.Do you mean that he doesn't use elph code directly to > calculate > lambda in graphene? why do you keep asking me about what other people did? I vaguely remember that they treated the term at the Dirac point separately, for obvious reasons. In order to say more, I should read the papers. This is YOUR problem, not mine. > In addition I want to know that does the elph code use new fermi > energy & > Dos at fermi energy after perturbation to calculate lambda? the Fermi energy doesn't change with perturbation, except for those at q=0. In the latter case, It is likely that the Fermi energy is not updated. Somebody else noticed this a few days ago and promised to make a few tests. Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sat Nov 14 19:18:55 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 14 Nov 2009 19:18:55 +0100 Subject: [Pw_forum] phonon & temperature In-Reply-To: References: Message-ID: <3EA36BAC-29F8-4C74-8D51-AECEDF35EDD2@democritos.it> On Nov 14, 2009, at 3:56 , Mehrnaz Anvari wrote: > I want to know what is the relation between phonon calculations > and temperature? I know that density & external potentials depend > on ion displacements, but I couldn't understand how does code > connect these displacements to temperature? the code doesn't connect anything to temperature. Phonon calculations are performed at T=0. The Quasi-Harmonic Approximation allows to calculate thermal properties at finite temperature. > also I want to know that whether ionic displacements cause any ripples > or roughness in the structure of sample or not? what are you talking about? --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From modaresi.mohsen at gmail.com Sat Nov 14 19:20:06 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Sat, 14 Nov 2009 21:20:06 +0300 Subject: [Pw_forum] about output files Message-ID: dear users Where i can find more information a bout out put files? Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091114/db9d6e51/attachment.htm From modaresi.mohsen at gmail.com Sat Nov 14 19:33:41 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Sat, 14 Nov 2009 21:33:41 +0300 Subject: [Pw_forum] elph question In-Reply-To: References: Message-ID: Dear Paolo Giannozzi I think that you have a bad day. Today you have not enough patient about questions. you are right, it is not your problem but every day you have an answer for questions so every body think that you know every thing.[?] On Sat, Nov 14, 2009 at 9:15 PM, Paolo Giannozzi wrote: > > On Nov 14, 2009, at 4:00 , Mehrnaz Anvari wrote: > > Also I've studied two of Lazzeri papers about evaluated lambda in > > graphene.Do you mean that he doesn't use elph code directly to > > calculate > > lambda in graphene? > > why do you keep asking me about what other people did? I vaguely > remember > that they treated the term at the Dirac point separately, for obvious > reasons. > In order to say more, I should read the papers. This is YOUR problem, > not > mine. > > > In addition I want to know that does the elph code use new fermi > > energy & > > Dos at fermi energy after perturbation to calculate lambda? > > > the Fermi energy doesn't change with perturbation, except for those > at q=0. > In the latter case, It is likely that the Fermi energy is not > updated. Somebody > else noticed this a few days ago and promised to make a few tests. > > Paolo > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091114/4275e9af/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/gif Size: 111 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091114/4275e9af/attachment.gif From eyvaz_isaev at yahoo.com Sat Nov 14 23:04:03 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sat, 14 Nov 2009 14:04:03 -0800 (PST) Subject: [Pw_forum] elph question Message-ID: <375855.44832.qm@web65714.mail.ac4.yahoo.com> Dear Mohsen, --- On Sat, 11/14/09, mohsen modaresi wrote: >Dear Paolo Giannozzi >I think that you have a bad day. >Today you have not enough patient about questions. you are right, it is >not your problem but every day you have an answer for questions so every >body think that you know every thing. You should be more polite in this forum, otherwise you are at a risk not getting an answer to your questions. And keep in mind: NOBODY in this forum is oblidged to answer to your question, they all are volunteers to share their experience/knowledge. If you are not satisfied with the answers, please think about another place to ask. Also it is worth thinking about did you do everithing correctly. Read more about things you are going to deal with. Regards, 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 From modaresi.mohsen at gmail.com Sat Nov 14 23:10:20 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Sun, 15 Nov 2009 01:40:20 +0330 Subject: [Pw_forum] elph question In-Reply-To: <375855.44832.qm@web65714.mail.ac4.yahoo.com> References: <375855.44832.qm@web65714.mail.ac4.yahoo.com> Message-ID: Dear Eyvaz Isaev and Paolo Giannozzi I am sory for that. you are right. Mohsen Modaresi Ferdowsi University On Sun, Nov 15, 2009 at 1:34 AM, Eyvaz Isaev wrote: > Dear Mohsen, > > --- On Sat, 11/14/09, mohsen modaresi wrote: > > >Dear Paolo Giannozzi > >I think that you have a bad day. > >Today you have not enough patient about questions. you are right, it is > >not your problem but every day you have an answer for questions so every > >body think that you know every thing. > > You should be more polite in this forum, otherwise you are at a risk not > getting an answer to your questions. > > And keep in mind: NOBODY in this forum is oblidged to answer to your > question, they all are volunteers to share their experience/knowledge. If > you are not satisfied with the answers, please think about another place to > ask. Also it is worth thinking about did you do everithing correctly. Read > more about things you are going to deal with. > > Regards, > 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 > > > > > > > _______________________________________________ > 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/20091115/55171e06/attachment.htm From brad.malone at gmail.com Sun Nov 15 03:19:28 2009 From: brad.malone at gmail.com (Brad Malone) Date: Sat, 14 Nov 2009 18:19:28 -0800 Subject: [Pw_forum] Generating a pseudo with semicore states Message-ID: Hi, I'm trying to generate a pseudopotential for Gallium with the entire third shell taken as valence (i.e., I want 3s2 3p6 3d10 4s2 4s1 all in valence). I didn't see anything in the /atomic_doc/pseudo_library/ that had an example where there were multiple occupied states of the same angular momentum. My first attempt at doing so was with the following input file: &input atom = 'Ga' iswitch = 3 rel = 1 dft = 'PZ' / 8 1S 1 0 2.00 1 2S 2 0 2.00 1 2P 2 1 6.00 1 3S 3 0 2.00 1 3P 3 1 6.00 1 3D 3 2 10.00 1 4S 4 0 2.00 1 4P 4 1 1.00 1 &inputp pseudotype = 2 file_pseudopw = 'Ga.UPF' lloc = 0 nlcc = .false. tm = .true. / 3 3P 2 1 6.00 0.00 0.50 0.50 0.00 3D 3 2 10.00 0.00 0.50 0.50 0.00 3S 1 0 2.00 0.00 0.50 0.50 0.00 After generating the pseudopotential with this file, it became clear that I had the wrong valence (no 4s or 4p electrons presumably). So I tried to edit the file and add these in to the &inputp field. For the 4S and 4P I used a cutoff of 2 au, but the pseudopotential generation failed and said that I had the wrong number of nodes. Am I doing something wrong? I appreciate any help or suggestions. Thanks! Best, Brad UC Berkeley -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091114/2b8aae25/attachment-0001.htm From brad.malone at gmail.com Sun Nov 15 03:35:59 2009 From: brad.malone at gmail.com (Brad Malone) Date: Sat, 14 Nov 2009 18:35:59 -0800 Subject: [Pw_forum] Generating a pseudo with semicore states In-Reply-To: References: Message-ID: To be clear, on my second attempt the bottom of my file looks like : / 5 3P 2 1 6.00 0.00 0.50 0.50 0.00 3D 3 2 10.00 0.00 0.50 0.50 0.00 4S 2 0 2.00 0.00 2.0 2.0 0.00 4P 3 1 1.00 0.00 2.0 2.0 0.00 3S 1 0 2.00 0.00 0.50 0.50 0.00 Thanks, Brad On Sat, Nov 14, 2009 at 6:19 PM, Brad Malone wrote: > Hi, I'm trying to generate a pseudopotential for Gallium with the entire > third shell taken as valence (i.e., I want 3s2 3p6 3d10 4s2 4s1 all in > valence). I didn't see anything in the /atomic_doc/pseudo_library/ that had > an example where there were multiple occupied states of the same angular > momentum. My first attempt at doing so was with the following input file: > > &input > atom = 'Ga' > iswitch = 3 > rel = 1 > dft = 'PZ' > / > 8 > 1S 1 0 2.00 1 > 2S 2 0 2.00 1 > 2P 2 1 6.00 1 > 3S 3 0 2.00 1 > 3P 3 1 6.00 1 > 3D 3 2 10.00 1 > 4S 4 0 2.00 1 > 4P 4 1 1.00 1 > &inputp > pseudotype = 2 > file_pseudopw = 'Ga.UPF' > lloc = 0 > nlcc = .false. > tm = .true. > / > 3 > 3P 2 1 6.00 0.00 0.50 0.50 0.00 > 3D 3 2 10.00 0.00 0.50 0.50 0.00 > 3S 1 0 2.00 0.00 0.50 0.50 0.00 > > After generating the pseudopotential with this file, it became clear that I > had the wrong valence (no 4s or 4p electrons presumably). So I tried to edit > the file and add these in to the &inputp field. For the 4S and 4P I used a > cutoff of 2 au, but the pseudopotential generation failed and said that I > had the wrong number of nodes. Am I doing something wrong? I appreciate any > help or suggestions. Thanks! > > Best, > Brad > UC Berkeley > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091114/e7261335/attachment.htm From anvari_meh at physics.iust.ac.ir Sun Nov 15 05:40:13 2009 From: anvari_meh at physics.iust.ac.ir (Mehrnaz Anvari) Date: Sun, 15 Nov 2009 08:10:13 +0330 Subject: [Pw_forum] phonon & temperature Message-ID: Dear Paolo First of all thanks a lot because of your answer. But, I have to make my question clear.As you said for phonon calculations, external potential depends on ionic displacements, and these diplacements are enough small to provide harmonic conditions (I agree with this part). So, phonons can be calculated and it means tempreture isn't used directly. In. addition the source of these displacements in crystals is temperature, and it sometimes causes that crystal doesn't have smooth surface for example in room temperature. now, I want to know that can I say that the calculations consist of this surface flactuations? Best Mehrnaz -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091115/259c0155/attachment.htm From anvari_meh at physics.iust.ac.ir Sun Nov 15 06:33:21 2009 From: anvari_meh at physics.iust.ac.ir (Mehrnaz Anvari) Date: Sun, 15 Nov 2009 09:03:21 +0330 Subject: [Pw_forum] elph question Message-ID: Dear Paolo Sorry, my question had a problem, so I have to correct it. In my first question I asked you that it is possible to calculate elph coupling for 2D material such as graphene, then you answered that it is a tricky problem because it isn't solved simply with brute force. I was confused because I had read in your paper that for phonon calculations brute foce finite difference methode is used. In other hand, we need phonon calculations for next step(elph calculatins), so I thought that I have to change something in code and I couldn't use it directly,at least for graphene. Mehrnaz Iran University of science & technology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091115/edd3b3c1/attachment.htm From giannozz at democritos.it Sun Nov 15 21:52:46 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 15 Nov 2009 21:52:46 +0100 Subject: [Pw_forum] Generating a pseudo with semicore states In-Reply-To: References: Message-ID: On Nov 15, 2009, at 3:19 , Brad Malone wrote: > Hi, I'm trying to generate a pseudopotential for Gallium with the > entire third shell taken as valence (i.e., I want 3s2 3p6 3d10 4s2 > 4s1 all in valence) [...]. After generating the pseudopotential > with this file, it became clear that I had the wrong valence (no 4s > or 4p electrons presumably). you need to specify a test configuration (containing all valence states) in the &test section P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sun Nov 15 21:55:34 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 15 Nov 2009 21:55:34 +0100 Subject: [Pw_forum] phonon & temperature In-Reply-To: References: Message-ID: <4792CBA0-0490-497A-AD56-6B9B612B9358@democritos.it> On Nov 15, 2009, at 5:40 , Mehrnaz Anvari wrote: > In addition the source of these displacements in crystals is > temperature, > and it sometimes causes that crystal doesn't have smooth surface for > example in room temperature. now, I want to know that can I say that > the calculations consist of this surface flactuations? you cannot say anything about surfaces in a bulk crystal with periodic boundary conditions: there is no surface P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From brad.malone at gmail.com Mon Nov 16 00:44:12 2009 From: brad.malone at gmail.com (Brad Malone) Date: Sun, 15 Nov 2009 15:44:12 -0800 Subject: [Pw_forum] Generating a pseudo with semicore states In-Reply-To: References: Message-ID: Thanks for the quick response Paolo. I missed it in the documentation, thinking incorrectly that the &test section wouldn't have anything to do with the construction of the pseudopotential. Best, Brad UC Berkeley > you need to specify a test configuration (containing all valence > states) in the &test section > > P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > On Sat, Nov 14, 2009 at 6:35 PM, Brad Malone wrote: > To be clear, on my second attempt the bottom of my file looks like : > > / > 5 > 3P 2 1 6.00 0.00 0.50 0.50 0.00 > 3D 3 2 10.00 0.00 0.50 0.50 0.00 > 4S 2 0 2.00 0.00 2.0 2.0 0.00 > 4P 3 1 1.00 0.00 2.0 2.0 0.00 > > 3S 1 0 2.00 0.00 0.50 0.50 0.00 > > > Thanks, > Brad > > On Sat, Nov 14, 2009 at 6:19 PM, Brad Malone wrote: > >> Hi, I'm trying to generate a pseudopotential for Gallium with the entire >> third shell taken as valence (i.e., I want 3s2 3p6 3d10 4s2 4s1 all in >> valence). I didn't see anything in the /atomic_doc/pseudo_library/ that had >> an example where there were multiple occupied states of the same angular >> momentum. My first attempt at doing so was with the following input file: >> >> &input >> atom = 'Ga' >> iswitch = 3 >> rel = 1 >> dft = 'PZ' >> / >> 8 >> 1S 1 0 2.00 1 >> 2S 2 0 2.00 1 >> 2P 2 1 6.00 1 >> 3S 3 0 2.00 1 >> 3P 3 1 6.00 1 >> 3D 3 2 10.00 1 >> 4S 4 0 2.00 1 >> 4P 4 1 1.00 1 >> &inputp >> pseudotype = 2 >> file_pseudopw = 'Ga.UPF' >> lloc = 0 >> nlcc = .false. >> tm = .true. >> / >> 3 >> 3P 2 1 6.00 0.00 0.50 0.50 0.00 >> 3D 3 2 10.00 0.00 0.50 0.50 0.00 >> 3S 1 0 2.00 0.00 0.50 0.50 0.00 >> >> After generating the pseudopotential with this file, it became clear that >> I had the wrong valence (no 4s or 4p electrons presumably). So I tried to >> edit the file and add these in to the &inputp field. For the 4S and 4P I >> used a cutoff of 2 au, but the pseudopotential generation failed and said >> that I had the wrong number of nodes. Am I doing something wrong? I >> appreciate any help or suggestions. Thanks! >> >> Best, >> Brad >> UC Berkeley >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091115/fb36d3fa/attachment.htm From elenariasredondo at yahoo.es Mon Nov 16 03:40:38 2009 From: elenariasredondo at yahoo.es (Elena Redondo) Date: Mon, 16 Nov 2009 02:40:38 +0000 (GMT) Subject: [Pw_forum] Li pseudopotential Message-ID: <485422.3003.qm@web23301.mail.ird.yahoo.com> Dear Quantum-Espresso users, Does anyone have the PBE norm-conserving pseudopotential for Li at high pressure indicated by Ya et al. in PRB 79, 092103 (2009)? It includes 1s,2s and 2p in the valence with small core radius of 0.8,1.0 and 1.0. Any information would be appreciated. Thank you very much. Elena Elena Junquera Facultad de Ciencias Universidad Complutense de Madrid -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091116/a9ededc9/attachment.htm From ttduyle at gmail.com Mon Nov 16 07:11:56 2009 From: ttduyle at gmail.com (Duy Le) Date: Mon, 16 Nov 2009 01:11:56 -0500 Subject: [Pw_forum] about output files In-Reply-To: References: Message-ID: <8974d3b20911152211x59379229p19f83fa99aebb664@mail.gmail.com> output is rich enough. I don't think there is any document showing us how to read output. -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Sat, Nov 14, 2009 at 1:20 PM, mohsen modaresi wrote: > dear users > Where i can find more information a bout out put files? > Thanks > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091116/d3539966/attachment.htm From mpayami at aeoi.org.ir Mon Nov 16 08:05:31 2009 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Mon, 16 Nov 2009 10:35:31 +0330 Subject: [Pw_forum] maybe intresting for you References: <8974d3b20911152211x59379229p19f83fa99aebb664@mail.gmail.com> Message-ID: <4B3AEEBCD68F46C3B0B8FC8E1742E117@bb174365e76fae> Dear PW users, I found the link as an intresting one: http://www.aps.org/publications/apsnews/200908/zerogravity.cfm Best regards, Mahmoud Payami Physics Group AEOI Tehran-Iran -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091116/04c10eae/attachment.htm From paulatto at sissa.it Mon Nov 16 10:05:35 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 16 Nov 2009 10:05:35 +0100 Subject: [Pw_forum] Generating a pseudo with semicore states In-Reply-To: References: Message-ID: > Thanks for the quick response Paolo. I missed it in the documentation, > thinking incorrectly that the &test section wouldn't have anything to do > with the construction of the pseudopotential. It is a bit complicated. The configuration in the test section is (can be?) used for descreening the potential. I think it was useful for some kind of trick, used to generate semi-core pseudopotentials before the multi-projector form was invented. I would advise you to remove it from the input file completely, because if it is present and it has a different configuration than the generation one, it is likely to mess up the pseudopotential. 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 paulatto at sissa.it Mon Nov 16 10:09:48 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 16 Nov 2009 10:09:48 +0100 Subject: [Pw_forum] Li pseudopotential In-Reply-To: <485422.3003.qm@web23301.mail.ird.yahoo.com> References: <485422.3003.qm@web23301.mail.ird.yahoo.com> Message-ID: Replying to message "[Pw_forum] Li pseudopotential" from Elena Redondo (16/11/09): > PBE norm-conserving pseudopotential for Li > ... > It includes 1s,2s and 2p in the valence with small core radius of > 0.8,1.0 and 1.0. > Any information would be appreciated. Dear Elena, what you have should be all you need to regenerate it. Just take file atomic_doc/pseudo_library/PBE/SR/H.pbe-rrkjus.in in QE, adapt it to Lithium and change the radii to suit your needs. If you have any problem, ghost states or similar please ask again. 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 giannozz at democritos.it Mon Nov 16 10:15:38 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 16 Nov 2009 10:15:38 +0100 Subject: [Pw_forum] Generating a pseudo with semicore states In-Reply-To: References: Message-ID: <4B01183A.7010104@democritos.it> Lorenzo Paulatto wrote: > It is a bit complicated. The configuration in the test section is (can > be?) used for descreening the potential. I think it was useful for some > kind of trick, used to generate semi-core pseudopotentials before the > multi-projector form was invented. > > I would advise you to remove it from the input file completely, because if > it is present and it has a different configuration than the generation > one, it is likely to mess up the pseudopotential. unless something has been changed recently, I don't think the code will automatically recognize the correct number of valence electrons, even with multiple projectors, if you have electrons both in shell N and in shell N+1. This is why the test configuration is used for descreening. It would if you could specify both sehll N and shel N+1 as reference states for pseudization, but usually you cannot P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From cristian.degliesposti at unibo.it Mon Nov 16 11:09:55 2009 From: cristian.degliesposti at unibo.it (Cristian Degli Esposti Boschi) Date: Mon, 16 Nov 2009 11:09:55 +0100 Subject: [Pw_forum] cannot open xml_recover file for writing Message-ID: <4B0124F3.4080609@unibo.it> I confirm that with the same input files for the same case I succesfully completed the scf and the phonon calculation at Gamma point for a structure of 58 atoms, on a parallel system (SP6 at CINECA) with one restart in the middle due to the maximum time limit allowed by the scheduler. The restart procedure works with QuantumESPRESSO 4.05 but NOT with version 4.1, because every time one tries to restart the phonon calculation (at least on that architecture) the execution stops with the error cannot open xml_recover file for writing as commented before in this forum. I will post a bug notification on the QE forge site and inform also the administrators of SP6. Thanks, Cristian -- ___________________________________________________ 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 kazempoor2000 at yahoo.com Mon Nov 16 12:36:57 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Mon, 16 Nov 2009 03:36:57 -0800 (PST) Subject: [Pw_forum] gipaw Message-ID: <453714.61822.qm@web112518.mail.gq1.yahoo.com> Does anybody has the psupotential for Ti in GIPAW format? thanks Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091116/22d5bea5/attachment.htm From elenariasredondo at yahoo.es Mon Nov 16 18:49:58 2009 From: elenariasredondo at yahoo.es (Elena Redondo) Date: Mon, 16 Nov 2009 09:49:58 -0800 (PST) Subject: [Pw_forum] Li pseudopotential In-Reply-To: Message-ID: <619414.53699.qm@web23305.mail.ird.yahoo.com> Dear Lorenzo, ? Thanks for your e-mail. I was trying to build the PP as you suggested. According to the paper, it is a norm-conserving pseudopotential, so, I used the multiple projector scheme (pseudotype=2). I write below the input: ? &input ?? title='Li', ?? zed=3., ?? rel=0, ?? iswitch=3, ?? config='[He] 2s1 2p0' ?? dft='PBE', ?/ ?&inputp ?? pseudotype=2, ?? lloc=1, ?? file_pseudopw='Li2.TM', ?? zval=3.0, ?? tm=.true., ?/ 3 1S? 1? 0? 2.00? 0.00? 0.80 0.80 2S? 2? 0? 1.00? 0.00? 1.00 1.00 2P? 2? 1? 0.00? 0.05? 1.00 1.00 ? But, when generating it, a error message appears: ? ? Generating local pot.: lloc=1, matching radius rcloc =?? 1.0000 ????? Wfc?? 1S? rcut= 0.800? Estimated cut-off energy=????? 199.31 Ry ????? This function has??? 0 nodes for 0 < r escribi?: De: Lorenzo Paulatto Asunto: Re: [Pw_forum] Li pseudopotential Para: "PWSCF Forum" Fecha: lunes, 16 de noviembre, 2009 10:09 Replying to message "[Pw_forum] Li pseudopotential" from Elena Redondo? (16/11/09): > PBE norm-conserving pseudopotential for Li > ... > It includes 1s,2s and 2p in the valence with small core radius of? > 0.8,1.0 and 1.0. > Any information would be appreciated. Dear Elena, what you have should be all you need to regenerate it. Just? take file atomic_doc/pseudo_library/PBE/SR/H.pbe-rrkjus.in in QE, adapt it? to Lithium and change the radii to suit your needs. If you have any problem, ghost states or similar please ask again. 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091116/88cab898/attachment.htm From giannozz at democritos.it Mon Nov 16 19:04:03 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 16 Nov 2009 19:04:03 +0100 Subject: [Pw_forum] Li pseudopotential In-Reply-To: <619414.53699.qm@web23305.mail.ird.yahoo.com> References: <619414.53699.qm@web23305.mail.ird.yahoo.com> Message-ID: <4B019413.5020800@democritos.it> Elena Redondo wrote: > I think that it is because the 2s orbital has a node before rc=1.00. for sure it has a node. It has to be there. > But, Yao et al say they used a cutoff radii of 1.0 for the 2s orbital. > They also say that they generated it using the QE package. they say they generated it "in a format suitable for QE", and this is not the same as "generated using QE" P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From paulatto at sissa.it Mon Nov 16 19:20:01 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 16 Nov 2009 19:20:01 +0100 (CET) Subject: [Pw_forum] Li pseudopotential In-Reply-To: <619414.53699.qm@web23305.mail.ird.yahoo.com> References: <619414.53699.qm@web23305.mail.ird.yahoo.com> Message-ID: <49786.78.12.162.16.1258395601.squirrel@webmail.sissa.it> Replying to message "Re: [Pw_forum] Li pseudopotential" from Elena Redondo (16/11/09): > I think that it is because the 2s orbital has a node before rc=1.00. > But, Yao et al say they used a cutoff radii of 1.0 for the 2s orbital. Dear Elena, you are using the Toullier-Martin recipe to pseudize the atomic wavefunctions (tm=.true.). This method always generates node-less wavefunctions hence it cannot be used to generate norm-conserving pseudopotentials that include two orbitals with the same angular momentum (1s and 2s, in your case). In theory it should be possible to generate this kind of pseudo using some other pseudization scheme, but ld1 does not do it, or at least it thinks it does not ;-). An exception would be possible if rcut was "inside" the node of the 2s wavefunction, but this is not your case, as the node is at ~0.84 bohr. Indeed, if you put the rcut of 2s orbital to 0.80 you get a good (but very hard) pseudopotential (you also have to remove of the tm=.true. switch, otherwise it will have a ghost state). Considering what Paolo Giannozzi said, I think you could try some other pseudopotential generatio software (such as Opium) for this specific purpose. 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 baroni at sissa.it Mon Nov 16 19:40:05 2009 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 16 Nov 2009 19:40:05 +0100 Subject: [Pw_forum] Li pseudopotential In-Reply-To: <49786.78.12.162.16.1258395601.squirrel@webmail.sissa.it> References: <619414.53699.qm@web23305.mail.ird.yahoo.com> <49786.78.12.162.16.1258395601.squirrel@webmail.sissa.it> Message-ID: just out of curiosity: have you tried to ask the authors to share *their* PP? SB On Nov 16, 2009, at 7:20 PM, Lorenzo Paulatto wrote: > Replying to message "Re: [Pw_forum] Li pseudopotential" from Elena > Redondo > (16/11/09): >> I think that it is because the 2s orbital has a node before rc=1.00. >> But, Yao et al say they used a cutoff radii of 1.0 for the 2s >> orbital. > > Dear Elena, > you are using the Toullier-Martin recipe to pseudize the atomic > wavefunctions (tm=.true.). This method always generates node-less > wavefunctions hence it cannot be used to generate norm-conserving > pseudopotentials that include two orbitals with the same angular > momentum > (1s and 2s, in your case). In theory it should be possible to generate > this kind of pseudo using some other pseudization scheme, but ld1 > does not > do it, or at least it thinks it does not ;-). > > An exception would be possible if rcut was "inside" the node of the 2s > wavefunction, but this is not your case, as the node is at ~0.84 bohr. > Indeed, if you put the rcut of 2s orbital to 0.80 you get a good > (but very > hard) pseudopotential (you also have to remove of the tm=.true. > switch, > otherwise it will have a ghost state). > > Considering what Paolo Giannozzi said, I think you could try some > other > pseudopotential generatio software (such as Opium) for this specific > purpose. > > 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/ > > _______________________________________________ > 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/20091116/ec1c419c/attachment-0001.htm From mohnish.iitk at gmail.com Tue Nov 17 05:46:46 2009 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Tue, 17 Nov 2009 10:16:46 +0530 Subject: [Pw_forum] charge density plots_'charge-density.dat ' Message-ID: Dear users, I am calculating energies of zinc oxide thin films. I want to visualise the charge density of the structure. But after calculation I am getting a file name called "charge-density.dat" but it is not opening with XCRYSDEN. Can anybody please suggest me something how to fix the problem and get the charge density plots. Lot of thanks in advance, MOHNISH -- Mohnish Pandey Y6262,4th Year Undergraduate, Department of Chemical Engineering, IIT KANPUR -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091117/96c67f2e/attachment.htm From decboy9 at gmail.com Tue Nov 17 08:34:34 2009 From: decboy9 at gmail.com (dev sharma) Date: Tue, 17 Nov 2009 13:04:34 +0530 Subject: [Pw_forum] charge density plots_'charge-density.dat ' In-Reply-To: References: Message-ID: Dear Mohnish, Have u got the XSF file ???? If yes then open that with the xcrysden. Tc Dev, University of Delhi, India On Tue, Nov 17, 2009 at 10:16 AM, mohnish pandey wrote: > Dear users, > I am calculating energies of zinc oxide thin films. I > want to visualise the charge density of the structure. But after calculation > I am getting a file name called "charge-density.dat" but it is not opening > with XCRYSDEN. Can anybody please suggest me something how to fix the > problem and get the charge density plots. > Lot of thanks in advance, > > MOHNISH > > -- > Mohnish Pandey > Y6262,4th Year Undergraduate, > Department of Chemical Engineering, > IIT KANPUR > > _______________________________________________ > 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/20091117/a9ae68b6/attachment.htm From sclauzer at sissa.it Tue Nov 17 08:49:37 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 17 Nov 2009 08:49:37 +0100 Subject: [Pw_forum] charge density plots_'charge-density.dat ' In-Reply-To: References: Message-ID: <4B025591.7090903@sissa.it> Dear Mohnish, mohnish pandey wrote: > Dear users, > I am calculating energies of zinc oxide thin films. I > want to visualise the charge density of the structure. But after > calculation I am getting a file name called "charge-density.dat" but it That file is unformatted, hence is not human-, nor xcrysden-, nor gnuplot- readable. It is used to save the charge density at intermediate steps and at the end of the self consistent loop. > is not opening with XCRYSDEN. Can anybody please suggest me something You can extract the charge density from it and produce a file readable by some plotting utility by using the postprocesing utilities of QE contained in the PP/ subfolder (pp.x, average.x, ...). Before starting you should have a look at example n. 5 The first step is to run pp.x (please see Doc/INPUT_PP.txt). If you want xcrysden format there is a specific flag to specify on input. Then you should be able to load the file with xcrysden --xsf yourfile You can also get the charge density in other formats, suitable for other visualization programs or for further postprocessing steps. HTH GS > how to fix the problem and get the charge density plots. > Lot of thanks in advance, > > MOHNISH > > -- > Mohnish Pandey > Y6262,4th Year Undergraduate, > Department of Chemical Engineering, > IIT KANPUR > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 mohnish.iitk at gmail.com Tue Nov 17 11:00:47 2009 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Tue, 17 Nov 2009 15:30:47 +0530 Subject: [Pw_forum] charge density plots_'charge-density.dat ' In-Reply-To: <4B025591.7090903@sissa.it> References: <4B025591.7090903@sissa.it> Message-ID: Thank you so much dear Gabriele :) On Tue, Nov 17, 2009 at 1:19 PM, Gabriele Sclauzero wrote: > Dear Mohnish, > > mohnish pandey wrote: > > Dear users, > > I am calculating energies of zinc oxide thin films. I > > want to visualise the charge density of the structure. But after > > calculation I am getting a file name called "charge-density.dat" but it > > That file is unformatted, hence is not human-, nor xcrysden-, nor gnuplot- > readable. It is > used to save the charge density at intermediate steps and at the end of > the self > consistent loop. > > > is not opening with XCRYSDEN. Can anybody please suggest me something > > You can extract the charge density from it and produce a file readable by > some plotting > utility by using the postprocesing utilities of QE contained in the PP/ > subfolder (pp.x, > average.x, ...). > Before starting you should have a look at example n. 5 > The first step is to run pp.x (please see Doc/INPUT_PP.txt). If you want > xcrysden format > there is a specific flag to specify on input. Then you should be able to > load the file with > xcrysden --xsf yourfile > You can also get the charge density in other formats, suitable for other > visualization > programs or for further postprocessing steps. > > HTH > > GS > > > > how to fix the problem and get the charge density plots. > > Lot of thanks in advance, > > > > MOHNISH > > > > -- > > Mohnish Pandey > > Y6262,4th Year Undergraduate, > > Department of Chemical Engineering, > > IIT KANPUR > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 > -- Mohnish Pandey Y6262,4th Year Undergraduate, Department of Chemical Engineering, IIT KANPUR -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091117/1c290c98/attachment.htm From miguel.martinez at ehu.es Tue Nov 17 11:32:56 2009 From: miguel.martinez at ehu.es (Miguel =?UTF-8?B?TWFydMOtbmV6?=) Date: Tue, 17 Nov 2009 11:32:56 +0100 Subject: [Pw_forum] Li pseudopotential In-Reply-To: <49786.78.12.162.16.1258395601.squirrel@webmail.sissa.it> References: <619414.53699.qm@web23305.mail.ird.yahoo.com> <49786.78.12.162.16.1258395601.squirrel@webmail.sissa.it> Message-ID: <20091117113256.3f29888a@lcpybm> Dear Lorenzo, Does that mean that you cannot generate pseudopotentials with semicore s states for any alkali metal using Troulliers-Martins pseudization? Maybe this doesn't apply to US or PAW pseudopotentials, since I've "succesfully" created a Cs pseudo with 9 electrons using TM and both the Li-1s and the Na-2s2p inputs in the PAW library use tm. As a side note, I'm getting various errors when building the PAW library pseudopotentials with espresso 4.1.1: -Cl, Ge, P, S and Si produce a "negative rho" error -Li-1s produces a "q_i coefficients" error I've seen this in a gfortran build and in an ifort build (both x86_64 machines, though). I don't know whether this is a miscompilation or something else. Is this maybe related to the pseudopotential bug present in the 4.0.x series of espresso? A diff between reference and available output shows noticeable differences only in the bmat matrix before the crashes. Regards, Miguel On Mon, 16 Nov 2009 19:20:01 +0100 (CET) "Lorenzo Paulatto" wrote: > you are using the Toullier-Martin recipe to pseudize the atomic > wavefunctions (tm=.true.). This method always generates node-less > wavefunctions hence it cannot be used to generate norm-conserving > pseudopotentials that include two orbitals with the same angular > momentum (1s and 2s, in your case). In theory it should be possible > to generate this kind of pseudo using some other pseudization scheme, > but ld1 does not do it, or at least it thinks it does not ;-). -- ---------------------------------------- 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 paulatto at sissa.it Tue Nov 17 11:40:47 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 17 Nov 2009 11:40:47 +0100 Subject: [Pw_forum] Li pseudopotential In-Reply-To: <20091117113256.3f29888a@lcpybm> References: <619414.53699.qm@web23305.mail.ird.yahoo.com> <49786.78.12.162.16.1258395601.squirrel@webmail.sissa.it> <20091117113256.3f29888a@lcpybm> Message-ID: Replying to message "Re: [Pw_forum] Li pseudopotential" from Miguel Mart?nez (17/11/09): > Maybe this doesn't apply to US or PAW pseudopotentials, since I've > "succesfully" created a Cs pseudo with 9 electrons using TM and both > the Li-1s and the Na-2s2p inputs in the PAW library use tm. Indeed, in the ultrasoft and PAW formalism pseudo-wavefunctions do not have to be orthogonal. > As a side note, I'm getting various errors when building the PAW > library pseudopotentials with espresso 4.1.1: > -Cl, Ge, P, S and Si produce a "negative rho" error > -Li-1s produces a "q_i coefficients" error Yes, it is a recent change in the code which I haven't had time to check yet, you can get rid of it by increasing r_match_augfun, or even removing it from the input. > A diff between reference and > available output shows noticeable differences only in the bmat matrix > before the crashes. I think the bmat matrix depends on the normalization of wavefunctions, which has changed too, so this should be unrelated and harmless. Apparently when the check fails the PAW dataset would have contained a substantial amount of negative charge, which can cause some problem during the plane-wave calculation. It is better to work around it by changing the parameters a bit than just removing the check. 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 Nov 17 11:51:28 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Tue, 17 Nov 2009 02:51:28 -0800 (PST) Subject: [Pw_forum] makov-payne or ee Message-ID: <78425.22607.qm@web112505.mail.gq1.yahoo.com> Hi All I want to do charged calculation in a supercell that is not cubic. I saw esspresso can do makov-payne by " asuume_isolated=.true' in periodic boundary condition and also do ee in open boundary condition. Since my supercell is not cubic how can I use makov-payne for non-cubic supercell.? Can I use ee to correct the energy in the case of charge calculation? thanks a lot Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091117/085766e1/attachment.htm From miguel.martinez at ehu.es Tue Nov 17 12:06:52 2009 From: miguel.martinez at ehu.es (Miguel =?UTF-8?B?TWFydMOtbmV6?=) Date: Tue, 17 Nov 2009 12:06:52 +0100 Subject: [Pw_forum] Li pseudopotential In-Reply-To: References: <619414.53699.qm@web23305.mail.ird.yahoo.com> <49786.78.12.162.16.1258395601.squirrel@webmail.sissa.it> <20091117113256.3f29888a@lcpybm> Message-ID: <20091117120652.32666b8a@lcpybm> Thanks for your answer, Lorenzo. -- ---------------------------------------- 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 paulatto at sissa.it Tue Nov 17 12:08:42 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 17 Nov 2009 12:08:42 +0100 Subject: [Pw_forum] makov-payne or ee In-Reply-To: <78425.22607.qm@web112505.mail.gq1.yahoo.com> References: <78425.22607.qm@web112505.mail.gq1.yahoo.com> Message-ID: Replying to message "[Pw_forum] makov-payne or ee" from ali kazempour (17/11/09): > I want to do charged calculation in a supercell that is not cubic. I saw > esspresso can do makov-payne by " asuume_isolated=.true' in periodic > boundary condition and also do ee in open boundary condition. Since my > supercell is not cubic how can I use makov-payne for non-cubic > supercell.? No, Makov-Payne correction is only implemented for cubic lattices (ibrav=1,2,3). MP correction is based on the analytic summation of dipole and quadrupole terms it is in principle extendible to any kind of lattice. You "only" have to compute the analytical integrals and plug the expressions in the code, if you are willing to contribute the analytical part, I'm willing to give support for the implementation. 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 paulatto at sissa.it Tue Nov 17 12:10:12 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 17 Nov 2009 12:10:12 +0100 Subject: [Pw_forum] makov-payne or ee In-Reply-To: <78425.22607.qm@web112505.mail.gq1.yahoo.com> References: <78425.22607.qm@web112505.mail.gq1.yahoo.com> Message-ID: Replying to message "[Pw_forum] makov-payne or ee" from ali kazempour (17/11/09): > Can I use ee to correct the energy in the case of charge calculation? > thanks a lot Yes, this should be possible. -- 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 Tue Nov 17 12:10:13 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 17 Nov 2009 12:10:13 +0100 Subject: [Pw_forum] makov-payne or ee In-Reply-To: <78425.22607.qm@web112505.mail.gq1.yahoo.com> References: <78425.22607.qm@web112505.mail.gq1.yahoo.com> Message-ID: <4B028495.9000705@sissa.it> there are two ways you can calculate an isolated system using version 4.1.1 (three if you use cvs verison) Using 4.1.1: - Makov-Payne: just define assume_isolated = .true. the code calculate an estimate of the energy correction for the presence of images. This does not introduce a correction for the potential (except a constant shift if i recall correctly). The correction is calculated from the Madelung constant of the Bravais lattice used so there is no constraint on that. -dcc: density counter charge correction (using ee) define do_ee as .true. and then the needed variables in the auxiliary ee namelist (please refer to the INPUT_PW.html etc for a description) . The multigrid solver only works for orthorhombic cells. If you are using CVS version. one additional option has been added and the input restructured (simplified?) assume_isolated is now a CHARACTER variable whose choices are: 'none' (default): regular periodic calculation w/o any correction. 'makov-payne', 'm-p', 'mp' : the Makov-Payne correction to the total energy is computed. An estimate of the vacuum level is also calculated so that eigenvalues can be properly aligned. Theory: G.Makov, and M.C.Payne, "Periodic boundary conditions in ab initio calculations" , Phys.Rev.B 51, 4014 (1995) 'dcc' : density counter charge correction. The electrostatic problem is solved in open boundary conditions. At variance with the Makov-Payne approach that only estimates an energy correction here the scf potential is corrected as well. The OBC problem is solved useing a multi-grid algorithm that requires additional input provided in the separate namelist EE (see later). Theory described in: I.Dabo, B.Kozinsky, N.E.Singh-Miller and N.Marzari, "Electrostatic periodic boundary conditions and real-space corrections", Phys.Rev.B 77, 115139 (2008) 'martyna-tuckerman', 'm-t', 'mt' : Martyna-Tuckerman correction. As for the dcc correction the scf potential is also corrected. Implementation adapted from: G.J. Martyna, and M.E. Tuckerman, "A reciprocal space based method for treating long range interactions in ab-initio and force-field-based calculation in clusters", J.Chem.Phys. 110, 2810 (1999) -- Please have a look at the theory papers before using a given option so that you know what you are doing., The correction is VERY important for charged system. It is less critical, still usefull, for neutral molecules, especially when significant dipoles are present. Check convergence w.r.t to cell size and compare yourself the different approaches. best regards, stefano ali kazempour wrote: > Hi All > I want to do charged calculation in a supercell that is not cubic. I > saw esspresso can do makov-payne by " asuume_isolated=.true' in > periodic boundary condition and also do ee in open boundary condition. > Since my supercell is not cubic how can I use makov-payne for > non-cubic supercell.? > Can I use ee to correct the energy in the case of charge calculation? > thanks a lot > > Ali Kazempour > > Fritz-Haber-Institut fax : ++49-30-8413 4701 > der Max-Planck-Gesellschaft > Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de > D-14 195 Berlin-Dahlem / German > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From degironc at sissa.it Tue Nov 17 12:17:21 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 17 Nov 2009 12:17:21 +0100 Subject: [Pw_forum] makov-payne or ee In-Reply-To: References: <78425.22607.qm@web112505.mail.gq1.yahoo.com> Message-ID: <4B028641.80204@sissa.it> Sorry for my previous message. Lorenzo is right. Makov Payne correction is only implemented for ibrav = 1,2,3 stefano Lorenzo Paulatto wrote: > Replying to message "[Pw_forum] makov-payne or ee" from ali kazempour > (17/11/09): > >> I want to do charged calculation in a supercell that is not cubic. I saw >> esspresso can do makov-payne by " asuume_isolated=.true' in periodic >> boundary condition and also do ee in open boundary condition. Since my >> supercell is not cubic how can I use makov-payne for non-cubic >> supercell.? >> > > No, Makov-Payne correction is only implemented for cubic lattices > (ibrav=1,2,3). > > MP correction is based on the analytic summation of dipole and quadrupole > terms it is in principle extendible to any kind of lattice. You "only" > have to compute the analytical integrals and plug the expressions in the > code, if you are willing to contribute the analytical part, I'm willing to > give support for the implementation. > > regards > > > From jarodriguezm at bt.unal.edu.co Tue Nov 17 15:17:58 2009 From: jarodriguezm at bt.unal.edu.co (Jairo Arbey Rodriguez Martinez) Date: Tue, 17 Nov 2009 09:17:58 -0500 Subject: [Pw_forum] Constraints HOWTO Message-ID: <74d8a4ef0911170617m1130f748m856f82b511d69c6b@mail.gmail.com> Dear Dr. Carlo Sbraccia and users I am making a constraint that forces an atom to move on a plane defined by A*x + B*y +C*z = D, where (x,y,z) is the position of the atom. I have followed the detailed instructions of the manual "constraints_HOWTO.pdf", but what I made does not work. The atom moves freely. I attach the two modules read_cards.f90 and constrains_module.f90 with the new constraint, and I hope to get help. The code compiles, links and executes well, but the constraint does not work. The lines in the input are: -------------------------------------------------------------- CONSTRAINTS 1 0.5D-6 mov_on_plane 1 -6.178444739 2.007498388 0.000000000 0.000000000 -------------------------------------------------------------- Some lines of the output are: Waiting for input... Reading 1 constraints; tolerance: 0.000000 1) atom 1 is restricted to move on the plane/line -6.17844474 * X + 2.00749839 * Y + 0.00000000 * Z = 0.00000000 ... ... constr target set (n= 1) = T constr_target on atom 1 = 0.00000000 ... ... --------------------------------------------------------------- After that, nothing is mentioned in the output about the constraint. The scf cycles and the relaxation of the ions seem normal. Thanks in advance for your help -- Jairo Arbey Rodr?guez M. -------------- next part -------------- A non-text attachment was scrubbed... Name: read_cards.f90 Type: text/x-fortran Size: 87831 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091117/45b29006/attachment-0002.bin -------------- next part -------------- A non-text attachment was scrubbed... Name: constraints_module.f90 Type: text/x-fortran Size: 53741 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091117/45b29006/attachment-0003.bin From giannozz at democritos.it Tue Nov 17 16:39:43 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 17 Nov 2009 16:39:43 +0100 Subject: [Pw_forum] Constraints HOWTO In-Reply-To: <74d8a4ef0911170617m1130f748m856f82b511d69c6b@mail.gmail.com> References: <74d8a4ef0911170617m1130f748m856f82b511d69c6b@mail.gmail.com> Message-ID: <4B02C3BF.3050509@democritos.it> Jairo Arbey Rodriguez Martinez wrote: > After that, nothing is mentioned in the output about the constraint. constraints are implemented only in some types of MD and damped MD: is that what you did? P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From mtt_turion at hotmail.com Tue Nov 17 17:08:02 2009 From: mtt_turion at hotmail.com (mtt physics) Date: Tue, 17 Nov 2009 23:08:02 +0700 Subject: [Pw_forum] Pw_forum Digest, Vol 29, Issue 44 In-Reply-To: References: Message-ID: How about I want convert ABINIT to QE (Abdulmutta Thatribud) > From: pw_forum-request at pwscf.org > Subject: Pw_forum Digest, Vol 29, Issue 44 > To: pw_forum at pwscf.org > Date: Tue, 17 Nov 2009 15:18:01 +0100 > > 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: makov-payne or ee (Stefano de Gironcoli) > 2. Constraints HOWTO (Jairo Arbey Rodriguez Martinez) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 17 Nov 2009 12:17:21 +0100 > From: Stefano de Gironcoli > Subject: Re: [Pw_forum] makov-payne or ee > To: PWSCF Forum > Message-ID: <4B028641.80204 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Sorry for my previous message. > Lorenzo is right. Makov Payne correction is only implemented for ibrav = > 1,2,3 > stefano > > Lorenzo Paulatto wrote: > > Replying to message "[Pw_forum] makov-payne or ee" from ali kazempour > > (17/11/09): > > > >> I want to do charged calculation in a supercell that is not cubic. I saw > >> esspresso can do makov-payne by " asuume_isolated=.true' in periodic > >> boundary condition and also do ee in open boundary condition. Since my > >> supercell is not cubic how can I use makov-payne for non-cubic > >> supercell.? > >> > > > > No, Makov-Payne correction is only implemented for cubic lattices > > (ibrav=1,2,3). > > > > MP correction is based on the analytic summation of dipole and quadrupole > > terms it is in principle extendible to any kind of lattice. You "only" > > have to compute the analytical integrals and plug the expressions in the > > code, if you are willing to contribute the analytical part, I'm willing to > > give support for the implementation. > > > > regards > > > > > > > > > > ------------------------------ > > Message: 2 > Date: Tue, 17 Nov 2009 09:17:58 -0500 > From: Jairo Arbey Rodriguez Martinez > Subject: [Pw_forum] Constraints HOWTO > To: PWSCF Forum > Message-ID: > <74d8a4ef0911170617m1130f748m856f82b511d69c6b at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Dr. Carlo Sbraccia and users > > I am making a constraint that forces an atom to move on a plane > defined by A*x + B*y +C*z = D, where (x,y,z) is the position of the > atom. I have followed the detailed instructions of the manual > "constraints_HOWTO.pdf", but what I made does not work. The atom moves > freely. I attach the two modules read_cards.f90 and > constrains_module.f90 with the new constraint, and I hope to get help. > The code compiles, links and executes well, but the constraint does > not work. > > The lines in the input are: > -------------------------------------------------------------- > CONSTRAINTS > 1 0.5D-6 > mov_on_plane 1 -6.178444739 2.007498388 0.000000000 0.000000000 > -------------------------------------------------------------- > Some lines of the output are: > Waiting for input... > Reading 1 constraints; tolerance: 0.000000 > 1) atom 1 is restricted to move on the plane/line > -6.17844474 * X + 2.00749839 * Y + 0.00000000 * Z = > 0.00000000 > ... > ... constr target set (n= 1) = T > constr_target on atom 1 = 0.00000000 > ... > ... > --------------------------------------------------------------- > After that, nothing is mentioned in the output about the constraint. > The scf cycles and the relaxation of the ions seem normal. Thanks in > advance for your help > -- > Jairo Arbey Rodr?guez M. > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: read_cards.f90 > Type: text/x-fortran > Size: 87831 bytes > Desc: not available > Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091117/45b29006/attachment.bin > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: constraints_module.f90 > Type: text/x-fortran > Size: 53741 bytes > Desc: not available > Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091117/45b29006/attachment-0001.bin > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 29, Issue 44 > **************************************** _________________________________________________________________ Windows 7 ????: ????????????????????????? ????????????????? http://windows.microsoft.com/shop -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091117/c9d947bb/attachment.htm From paulatto at sissa.it Tue Nov 17 17:14:51 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 17 Nov 2009 17:14:51 +0100 Subject: [Pw_forum] Pw_forum Digest, Vol 29, Issue 44 In-Reply-To: References: Message-ID: Replying to message "Re: [Pw_forum] Pw_forum Digest, Vol 29, Issue 44" from mtt physics (17/11/09): > How about I want convert ABINIT to QE (Abdulmutta Thatribud) Well, it depends on *what* you want to convert. Anyway, have a look here: 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 ouuing at gmail.com Tue Nov 17 17:29:53 2009 From: ouuing at gmail.com (H.Y Liu) Date: Wed, 18 Nov 2009 00:29:53 +0800 Subject: [Pw_forum] nothing is written to the output file In-Reply-To: References: <20091028075354.14113.qmail@ms.hfcas.ac.cn> Message-ID: you needn't consider it. perhaps your task is expensive on performing some run. in fact, the import files about calculating are that tmp files which you should the tmp direct. so you really look if the size of tmp file is increasing. you should know the performing is ok. best regards. On Fri, Oct 30, 2009 at 7:20 PM, Hong LI wrote: > Dear users, > > We?are using espresso to relax the atomic structures of an alloy, there is a > problem that after several days of running?the size of *.out is still zero, > nothing is written to the output file. If we kill the job then the > output?file is not empty. Some?small jobs run fine, I mean the information > is?updated?from time to time?during the calculation.?It seems?this is just > an occasional case. Does anyone here encounter similar problem before, any > suggestions to solve this problem ? Many thanks. > > Best wishes. > Hong > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=**=-=**=-=**=-=*=-=*=-=*=-=*=-=*=- Hanyu Liu(???), MS. State key Laboratory of Superhard Materials, Jilin University, China Email: liuhanyu08 at mails.jlu.edu.cn ouuing at gmail.com From jarodriguezm at bt.unal.edu.co Tue Nov 17 17:53:30 2009 From: jarodriguezm at bt.unal.edu.co (Jairo Arbey Rodriguez Martinez) Date: Tue, 17 Nov 2009 11:53:30 -0500 Subject: [Pw_forum] Constraints HOWTO In-Reply-To: <4B02C3BF.3050509@democritos.it> References: <74d8a4ef0911170617m1130f748m856f82b511d69c6b@mail.gmail.com> <4B02C3BF.3050509@democritos.it> Message-ID: <74d8a4ef0911170853q5de85b58jb1ac707a136ad96@mail.gmail.com> I have used both: car-parrinello md (damped, with program cp.x ) and in pw.x, ion_dynamics = bfgs (default) 2009/11/17 Paolo Giannozzi : > Jairo Arbey Rodriguez Martinez wrote: > >> After that, nothing is mentioned in the output about the constraint. > > constraints are implemented only in some types of MD and damped MD: > is that what you did? > > 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 > -- Jairo Arbey Rodr?guez M. From yaldachem at gmail.com Tue Nov 17 20:39:29 2009 From: yaldachem at gmail.com (yaldaa kh) Date: Tue, 17 Nov 2009 11:39:29 -0800 Subject: [Pw_forum] lowdin charge Message-ID: <47431d9f0911171139se70cfb3h38dfeb3550facdc6@mail.gmail.com> dear all I performed pdos calculation(scf ,nscf pdos) for Cu slab ,but in lowdin charge, the Cu-p had some charge while p orbitals in Cu atom are unoccupied. if this result is wrong? thanks a lot yaldaa Kh. chem. student Azad university Iran -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091117/6875fad6/attachment.htm From jameslipd at gmail.com Wed Nov 18 03:24:13 2009 From: jameslipd at gmail.com (Jiaye Li) Date: Wed, 18 Nov 2009 10:24:13 +0800 Subject: [Pw_forum] Cannot run parallel jobs with openmpi Message-ID: Dear users I installed q-espresso 4.1.1, mpich2-1.2 and openmpi-1.3.3 on a single cpu PC. I tested some jobs with mpich2, which works successfully. But I met with some problems with openmpi runs. For example, when I type "mpirun -np 4 pw.x output", only one-qaurter of the cpu(25%) is taken up. In fact, when I used mpich2, 100% cpu was taken up. The openmpi should be installed correctly, because there is no error reported upon compilation and the test of vasp run with openmpi takes up 100% cpu (four processes). I am wondering if openmpi is compatible with pwscf? -- Sincerely yours Jiaye Li -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091118/ccb3e7a8/attachment.htm From ynwuyang at gmail.com Wed Nov 18 05:48:53 2009 From: ynwuyang at gmail.com (yuning wu) Date: Tue, 17 Nov 2009 23:48:53 -0500 Subject: [Pw_forum] Virtual crystal approximation for vacancy Message-ID: <4B037CB5.6040304@gmail.com> Dear all, I am considering to use virtual crystal approximation to study a system with vacancy doped, and I do not know what I am supposed to generate a VCA psuedopotential for a mixture of an atom and a vacancy. I guess it is zero for the vacancy but I am not sure. Any ideas please? Thanks very much. Best, Yuning ##################### Yuning Wu Department of Physics & Quantum Theory Project University of Florida Gainesville, FL 32611 From quantumdft at gmail.com Wed Nov 18 06:17:53 2009 From: quantumdft at gmail.com (vega lew) Date: Wed, 18 Nov 2009 13:17:53 +0800 Subject: [Pw_forum] how to set nr1b, nr2b, nr3b for cp.x when using ultrasoft pseudopotential Message-ID: <412f6c680911172117o2f9ca4f3j6725bda6658423fd@mail.gmail.com> Dear all, I used to submit an manuscript to a specialized journal about chemistry and physics. The referees suggested me to perform some molecular dynamics. I now agree with the referees that the molecular dynamics is essential to confirm the configurations from pw.x. But I have little experience in First principle molecular dynamic, but I have a good impression of classical MD. So I think I could accomplish it with some learning from more experienced people. Following the excellent manual provided by the website, I try to use cp.x code to perform molecular dynamics on my systems. Now it is running... But I have a question about the option "nr1b, nr2b, nr3b" in &SYSTEM namelist. Could you please tell me something more about it? How to determine the proper value for different systems. Do you think it could greatly increase the computational time consumption if the value is not properly set? I want to calculate a system of 147 atoms with 48 [TiO2] units and a water molecule. And following the autopilot example, I set these three value to 20 repectively. do you think it is reasonable for this system? If not, could you please tell me something about how to set it properly. thank you for reading. any suggestion is deeply appreciated. Thank you in advance. best wishes, vega -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091118/d3404b2d/attachment.htm From mtt_turion at hotmail.com Wed Nov 18 06:49:08 2009 From: mtt_turion at hotmail.com (mtt physics) Date: Wed, 18 Nov 2009 12:49:08 +0700 Subject: [Pw_forum] piezoelectric tensor in Pb(ZrxTi1-x)O3 In-Reply-To: References: Message-ID: Dear Lorenzo Paulatto and all I want to calculated piezoelectric constant from when atom displaced in the perfect tetragonal it shown polarization calculate with Berry phase method. The piezoelectric calculated from First-principles. Are there the code for calculate piezoelectric in QE regard Abdulmutta Thatribud > From: pw_forum-request at pwscf.org > Subject: Pw_forum Digest, Vol 29, Issue 45 > To: pw_forum at pwscf.org > Date: Wed, 18 Nov 2009 05:48:58 +0100 > > 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: Constraints HOWTO (Paolo Giannozzi) > 2. Re: Pw_forum Digest, Vol 29, Issue 44 (mtt physics) > 3. Re: Pw_forum Digest, Vol 29, Issue 44 (Lorenzo Paulatto) > 4. Re: nothing is written to the output file (H.Y Liu) > 5. Re: Constraints HOWTO (Jairo Arbey Rodriguez Martinez) > 6. lowdin charge (yaldaa kh) > 7. Cannot run parallel jobs with openmpi (Jiaye Li) > 8. Virtual crystal approximation for vacancy (yuning wu) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 17 Nov 2009 16:39:43 +0100 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] Constraints HOWTO > To: PWSCF Forum > Message-ID: <4B02C3BF.3050509 at democritos.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Jairo Arbey Rodriguez Martinez wrote: > > > After that, nothing is mentioned in the output about the constraint. > > constraints are implemented only in some types of MD and damped MD: > is that what you did? > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > ------------------------------ > > Message: 2 > Date: Tue, 17 Nov 2009 23:08:02 +0700 > From: mtt physics > Subject: Re: [Pw_forum] Pw_forum Digest, Vol 29, Issue 44 > To: > Message-ID: > Content-Type: text/plain; charset="windows-874" > > > How about I want convert ABINIT to QE (Abdulmutta Thatribud) > > > From: pw_forum-request at pwscf.org > > Subject: Pw_forum Digest, Vol 29, Issue 44 > > To: pw_forum at pwscf.org > > Date: Tue, 17 Nov 2009 15:18:01 +0100 > > > > 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: makov-payne or ee (Stefano de Gironcoli) > > 2. Constraints HOWTO (Jairo Arbey Rodriguez Martinez) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 17 Nov 2009 12:17:21 +0100 > > From: Stefano de Gironcoli > > Subject: Re: [Pw_forum] makov-payne or ee > > To: PWSCF Forum > > Message-ID: <4B028641.80204 at sissa.it> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Sorry for my previous message. > > Lorenzo is right. Makov Payne correction is only implemented for ibrav = > > 1,2,3 > > stefano > > > > Lorenzo Paulatto wrote: > > > Replying to message "[Pw_forum] makov-payne or ee" from ali kazempour > > > (17/11/09): > > > > > >> I want to do charged calculation in a supercell that is not cubic. I saw > > >> esspresso can do makov-payne by " asuume_isolated=.true' in periodic > > >> boundary condition and also do ee in open boundary condition. Since my > > >> supercell is not cubic how can I use makov-payne for non-cubic > > >> supercell.? > > >> > > > > > > No, Makov-Payne correction is only implemented for cubic lattices > > > (ibrav=1,2,3). > > > > > > MP correction is based on the analytic summation of dipole and quadrupole > > > terms it is in principle extendible to any kind of lattice. You "only" > > > have to compute the analytical integrals and plug the expressions in the > > > code, if you are willing to contribute the analytical part, I'm willing to > > > give support for the implementation. > > > > > > regards > > > > > > > > > > > > > > > > > ------------------------------ > > > > Message: 2 > > Date: Tue, 17 Nov 2009 09:17:58 -0500 > > From: Jairo Arbey Rodriguez Martinez > > Subject: [Pw_forum] Constraints HOWTO > > To: PWSCF Forum > > Message-ID: > > <74d8a4ef0911170617m1130f748m856f82b511d69c6b at mail.gmail.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear Dr. Carlo Sbraccia and users > > > > I am making a constraint that forces an atom to move on a plane > > defined by A*x + B*y +C*z = D, where (x,y,z) is the position of the > > atom. I have followed the detailed instructions of the manual > > "constraints_HOWTO.pdf", but what I made does not work. The atom moves > > freely. I attach the two modules read_cards.f90 and > > constrains_module.f90 with the new constraint, and I hope to get help. > > The code compiles, links and executes well, but the constraint does > > not work. > > > > The lines in the input are: > > -------------------------------------------------------------- > > CONSTRAINTS > > 1 0.5D-6 > > mov_on_plane 1 -6.178444739 2.007498388 0.000000000 0.000000000 > > -------------------------------------------------------------- > > Some lines of the output are: > > Waiting for input... > > Reading 1 constraints; tolerance: 0.000000 > > 1) atom 1 is restricted to move on the plane/line > > -6.17844474 * X + 2.00749839 * Y + 0.00000000 * Z = > > 0.00000000 > > ... > > ... constr target set (n= 1) = T > > constr_target on atom 1 = 0.00000000 > > ... > > ... > > --------------------------------------------------------------- > > After that, nothing is mentioned in the output about the constraint. > > The scf cycles and the relaxation of the ions seem normal. Thanks in > > advance for your help > > -- > > Jairo Arbey Rodr?guez M. > > -------------- next part -------------- > > A non-text attachment was scrubbed... > > Name: read_cards.f90 > > Type: text/x-fortran > > Size: 87831 bytes > > Desc: not available > > Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091117/45b29006/attachment.bin > > -------------- next part -------------- > > A non-text attachment was scrubbed... > > Name: constraints_module.f90 > > Type: text/x-fortran > > Size: 53741 bytes > > Desc: not available > > Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091117/45b29006/attachment-0001.bin > > > > ------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > End of Pw_forum Digest, Vol 29, Issue 44 > > **************************************** > > _________________________________________________________________ > Windows 7 ????: ????????????????????????? ????????????????? > http://windows.microsoft.com/shop > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091117/c9d947bb/attachment-0001.htm > > ------------------------------ > > Message: 3 > Date: Tue, 17 Nov 2009 17:14:51 +0100 > From: "Lorenzo Paulatto" > Subject: Re: [Pw_forum] Pw_forum Digest, Vol 29, Issue 44 > To: "PWSCF Forum" > Message-ID: > Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > > Replying to message "Re: [Pw_forum] Pw_forum Digest, Vol 29, Issue 44" > from mtt physics (17/11/09): > > How about I want convert ABINIT to QE (Abdulmutta Thatribud) > > Well, it depends on *what* you want to convert. Anyway, have a look here: > > > 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/ > > > ------------------------------ > > Message: 4 > Date: Wed, 18 Nov 2009 00:29:53 +0800 > From: "H.Y Liu" > Subject: Re: [Pw_forum] nothing is written to the output file > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset=UTF-8 > > you needn't consider it. perhaps your task is expensive on performing > some run. in fact, the import files about calculating are that tmp > files which you should the tmp direct. > so you really look if the size of tmp file is increasing. you should > know the performing is ok. > > best regards. > > On Fri, Oct 30, 2009 at 7:20 PM, Hong LI wrote: > > Dear users, > > > > We?are using espresso to relax the atomic structures of an alloy, there is a > > problem that after several days of running?the size of *.out is still zero, > > nothing is written to the output file. If we kill the job then the > > output?file is not empty. Some?small jobs run fine, I mean the information > > is?updated?from time to time?during the calculation.?It seems?this is just > > an occasional case. Does anyone here encounter similar problem before, any > > suggestions to solve this problem ? Many thanks. > > > > Best wishes. > > Hong > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=**=-=**=-=**=-=*=-=*=-=*=-=*=-=*=- > Hanyu Liu(???), > MS. > State key Laboratory of Superhard Materials, Jilin University, China > Email: liuhanyu08 at mails.jlu.edu.cn ouuing at gmail.com > > > ------------------------------ > > Message: 5 > Date: Tue, 17 Nov 2009 11:53:30 -0500 > From: Jairo Arbey Rodriguez Martinez > Subject: Re: [Pw_forum] Constraints HOWTO > To: PWSCF Forum > Message-ID: > <74d8a4ef0911170853q5de85b58jb1ac707a136ad96 at mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > I have used both: car-parrinello md (damped, with program cp.x ) and > in pw.x, ion_dynamics = bfgs (default) > > > 2009/11/17 Paolo Giannozzi : > > Jairo Arbey Rodriguez Martinez wrote: > > > >> After that, nothing is mentioned in the output about the constraint. > > > > constraints are implemented only in some types of MD and damped MD: > > is that what you did? > > > > 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 > > > > > > -- > Jairo Arbey Rodr?guez M. > > > ------------------------------ > > Message: 6 > Date: Tue, 17 Nov 2009 11:39:29 -0800 > From: yaldaa kh > Subject: [Pw_forum] lowdin charge > To: pw_forum > Message-ID: > <47431d9f0911171139se70cfb3h38dfeb3550facdc6 at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > dear all > I performed pdos calculation(scf ,nscf pdos) for Cu slab ,but in lowdin > charge, the Cu-p had some charge while p orbitals in Cu atom are unoccupied. > if this result is wrong? > thanks a lot > yaldaa Kh. > chem. student > Azad university Iran > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091117/6875fad6/attachment-0001.htm > > ------------------------------ > > Message: 7 > Date: Wed, 18 Nov 2009 10:24:13 +0800 > From: Jiaye Li > Subject: [Pw_forum] Cannot run parallel jobs with openmpi > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Dear users > > I installed q-espresso 4.1.1, mpich2-1.2 and openmpi-1.3.3 on a single cpu > PC. I tested some jobs with mpich2, which works successfully. But I met with > some problems with openmpi runs. For example, when I type "mpirun -np 4 pw.x > output", only one-qaurter of the cpu(25%) is taken up. In fact, when > I used mpich2, 100% cpu was taken up. The openmpi should be installed > correctly, because there is no error reported upon compilation and the test > of vasp run with openmpi takes up 100% cpu (four processes). > > I am wondering if openmpi is compatible with pwscf? > > -- > Sincerely yours > > Jiaye Li > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091118/ccb3e7a8/attachment-0001.htm > > ------------------------------ > > Message: 8 > Date: Tue, 17 Nov 2009 23:48:53 -0500 > From: yuning wu > Subject: [Pw_forum] Virtual crystal approximation for vacancy > To: pw_forum at pwscf.org > Message-ID: <4B037CB5.6040304 at gmail.com> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear all, > > I am considering to use virtual crystal approximation to study a system > with vacancy doped, and I do not know what I am supposed to generate a > VCA psuedopotential for a mixture of an atom and a vacancy. I guess it > is zero for the vacancy but I am not sure. Any ideas please? Thanks very > much. > > Best, > > Yuning > > ##################### > > Yuning Wu > Department of Physics & Quantum Theory Project > University of Florida > Gainesville, FL 32611 > > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 29, Issue 45 > **************************************** _________________________________________________________________ Windows 7 ????: ????????????????????????? ????????????????? http://windows.microsoft.com/shop -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091118/80a006ea/attachment-0001.htm From giannozz at democritos.it Wed Nov 18 08:00:21 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 18 Nov 2009 08:00:21 +0100 Subject: [Pw_forum] how to set nr1b, nr2b, nr3b for cp.x when using ultrasoft pseudopotential In-Reply-To: <412f6c680911172117o2f9ca4f3j6725bda6658423fd@mail.gmail.com> References: <412f6c680911172117o2f9ca4f3j6725bda6658423fd@mail.gmail.com> Message-ID: On Nov 18, 2009, at 6:17 , vega lew wrote: > I have a question about the option "nr1b, nr2b, nr3b" in &SYSTEM > namelist. > Could you please tell me something more about it? http://www.quantum-espresso.org/user_guide/node30.html > P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed Nov 18 08:01:25 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 18 Nov 2009 08:01:25 +0100 Subject: [Pw_forum] Virtual crystal approximation for vacancy In-Reply-To: <4B037CB5.6040304@gmail.com> References: <4B037CB5.6040304@gmail.com> Message-ID: On Nov 18, 2009, at 5:48 , yuning wu wrote: > I am considering to use virtual crystal approximation to study a > system > with vacancy doped not a good idea IMHO - P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed Nov 18 08:03:17 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 18 Nov 2009 08:03:17 +0100 Subject: [Pw_forum] Cannot run parallel jobs with openmpi In-Reply-To: References: Message-ID: On Nov 18, 2009, at 3:24 , Jiaye Li wrote: > I am wondering if openmpi is compatible with pwscf? PWscf is compatible with all MPI implementations (as long as they work) P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From sclauzer at sissa.it Wed Nov 18 08:54:25 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 18 Nov 2009 08:54:25 +0100 Subject: [Pw_forum] lowdin charge In-Reply-To: <47431d9f0911171139se70cfb3h38dfeb3550facdc6@mail.gmail.com> References: <47431d9f0911171139se70cfb3h38dfeb3550facdc6@mail.gmail.com> Message-ID: <4B03A831.6090508@sissa.it> yaldaa kh wrote: > dear all > I performed pdos calculation(scf ,nscf pdos) for Cu slab ,but in lowdin > charge, the Cu-p had some charge while p orbitals in Cu atom > are unoccupied. if this result is wrong? Not necessarily. It depends on how much is "some charge". You are right when you say that in the Cu atom p orbitals are unoccupied (strictly), but in a solid the situation is different. Also empty orbitals may be involved in the binding, for instance when some charge transfer takes place (remember that in Cu the 3d shell is full and there is place for only 1e- in the 4s). Because of this, pseudopotentials usually include among the projectors (or in the local channel) electronic states which can be empty in the atom, but not too much higher in energy wrt the occupied ones (e.g., in Cu, which is [Ar] 3d10 4s1, also 4p are included since they are only 3-4 eV higher than 4s). So, if you have the 4p channel in your PP, you will get also the 4p projection file from projwfc.x, but these states should be restricted to a high energy region. Have you checked how much 4p charge (if any) is found BELOW the Fermi energy? GS > thanks a lot > yaldaa Kh. > chem. student > Azad university Iran > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 science35 at gmail.com Wed Nov 18 09:01:17 2009 From: science35 at gmail.com (patriot pershing) Date: Wed, 18 Nov 2009 09:01:17 +0100 Subject: [Pw_forum] confirm 63d7beb150c220f0275a453fc134e323bbbcd213 In-Reply-To: References: Message-ID: <9fdec6370911180001w668d0a1id8b9bf9e87ce121c@mail.gmail.com> dear please i'm a new user of quantum espresso soft and i would run this soft under windows environemment using cygwin but i haven't arrived to do this, for this reason i would ask if any one can help me by giving me the detailed procedure ot install and run quantum espresso under cygwin thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091118/ba3e587c/attachment.htm From giannozz at democritos.it Wed Nov 18 11:35:08 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 18 Nov 2009 11:35:08 +0100 Subject: [Pw_forum] Constraints HOWTO In-Reply-To: <74d8a4ef0911170853q5de85b58jb1ac707a136ad96@mail.gmail.com> References: <74d8a4ef0911170617m1130f748m856f82b511d69c6b@mail.gmail.com> <4B02C3BF.3050509@democritos.it> <74d8a4ef0911170853q5de85b58jb1ac707a136ad96@mail.gmail.com> Message-ID: <4B03CDDC.5010107@democritos.it> Jairo Arbey Rodriguez Martinez wrote: > I have used both: car-parrinello md (damped, with program cp.x) this should work, I think > and in pw.x, ion_dynamics = bfgs (default) this is not implemented, I think. I know nothing about constraints, but you should as a first step find cases in which the existing constraint work, before adding new ones P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Wed Nov 18 11:36:47 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 18 Nov 2009 11:36:47 +0100 Subject: [Pw_forum] confirm 63d7beb150c220f0275a453fc134e323bbbcd213 In-Reply-To: <9fdec6370911180001w668d0a1id8b9bf9e87ce121c@mail.gmail.com> References: <9fdec6370911180001w668d0a1id8b9bf9e87ce121c@mail.gmail.com> Message-ID: <4B03CE3F.40503@democritos.it> patriot pershing wrote: > i'm a new user of quantum espresso soft this was already clear from the ill-chosen subject P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From jameslipd at gmail.com Wed Nov 18 12:00:01 2009 From: jameslipd at gmail.com (Jiaye Li) Date: Wed, 18 Nov 2009 19:00:01 +0800 Subject: [Pw_forum] Cannot run parallel jobs with openmpi Message-ID: The problem has been fixed. PWscf should be installed after the compilation of mpi binary. Thanks. On Wed, Nov 18, 2009 at 4:15 PM, wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: how to set nr1b, nr2b, nr3b for cp.x when using ultrasoft > pseudopotential (Paolo Giannozzi) > 2. Re: Virtual crystal approximation for vacancy (Paolo Giannozzi) > 3. Re: Cannot run parallel jobs with openmpi (Paolo Giannozzi) > 4. Re: lowdin charge (Gabriele Sclauzero) > 5. Re: confirm 63d7beb150c220f0275a453fc134e323bbbcd213 > (patriot pershing) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 18 Nov 2009 08:00:21 +0100 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] how to set nr1b, nr2b, nr3b for cp.x when > using ultrasoft pseudopotential > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > > On Nov 18, 2009, at 6:17 , vega lew wrote: > > > I have a question about the option "nr1b, nr2b, nr3b" in &SYSTEM > > namelist. > > Could you please tell me something more about it? > > http://www.quantum-espresso.org/user_guide/node30.html > > > > > P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > ------------------------------ > > Message: 2 > Date: Wed, 18 Nov 2009 08:01:25 +0100 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] Virtual crystal approximation for vacancy > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > > On Nov 18, 2009, at 5:48 , yuning wu wrote: > > > I am considering to use virtual crystal approximation to study a > > system > > with vacancy doped > > not a good idea IMHO - P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > ------------------------------ > > Message: 3 > Date: Wed, 18 Nov 2009 08:03:17 +0100 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] Cannot run parallel jobs with openmpi > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset=US-ASCII; format=flowed > > > On Nov 18, 2009, at 3:24 , Jiaye Li wrote: > > > I am wondering if openmpi is compatible with pwscf? > > PWscf is compatible with all MPI implementations (as > long as they work) > > P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > ------------------------------ > > Message: 4 > Date: Wed, 18 Nov 2009 08:54:25 +0100 > From: Gabriele Sclauzero > Subject: Re: [Pw_forum] lowdin charge > To: PWSCF Forum > Message-ID: <4B03A831.6090508 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > yaldaa kh wrote: > > dear all > > I performed pdos calculation(scf ,nscf pdos) for Cu slab ,but in lowdin > > charge, the Cu-p had some charge while p orbitals in Cu atom > > are unoccupied. if this result is wrong? > > Not necessarily. It depends on how much is "some charge". You are right > when you say that > in the Cu atom p orbitals are unoccupied (strictly), but in a solid the > situation is > different. Also empty orbitals may be involved in the binding, for instance > when some > charge transfer takes place (remember that in Cu the 3d shell is full and > there is place > for only 1e- in the 4s). > Because of this, pseudopotentials usually include among the projectors (or > in the local > channel) electronic states which can be empty in the atom, but not too much > higher in > energy wrt the occupied ones (e.g., in Cu, which is [Ar] 3d10 4s1, also 4p > are included > since they are only 3-4 eV higher than 4s). > So, if you have the 4p channel in your PP, you will get also the 4p > projection file from > projwfc.x, but these states should be restricted to a high energy region. > Have you checked > how much 4p charge (if any) is found BELOW the Fermi energy? > > > GS > > > thanks a lot > > yaldaa Kh. > > chem. student > > Azad university Iran > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 > > > ------------------------------ > > Message: 5 > Date: Wed, 18 Nov 2009 09:01:17 +0100 > From: patriot pershing > Subject: Re: [Pw_forum] confirm > 63d7beb150c220f0275a453fc134e323bbbcd213 > To: pw_forum at pwscf.org > Message-ID: > <9fdec6370911180001w668d0a1id8b9bf9e87ce121c at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > dear please > i'm a new user of quantum espresso soft and i would run this soft under > windows environemment using cygwin but i haven't arrived to do this, for > this reason i would ask if any one can help me by giving me the detailed > procedure ot install and run quantum espresso under cygwin > thanks > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20091118/ba3e587c/attachment.html > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 29, Issue 47 > **************************************** > -- Sincerely yours Jiaye Li -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091118/bee11be7/attachment.htm From sclauzer at sissa.it Wed Nov 18 12:04:51 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 18 Nov 2009 12:04:51 +0100 Subject: [Pw_forum] Cannot run parallel jobs with openmpi In-Reply-To: References: Message-ID: <4B03D4D3.2070506@sissa.it> Jiaye Li wrote: > The problem has been fixed. PWscf should be installed after the > compilation of mpi binary. Thanks. Isn't it the same with VASP? GS > > > > -- > Sincerely yours > > Jiaye Li > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 paulatto at sissa.it Wed Nov 18 12:27:19 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 18 Nov 2009 12:27:19 +0100 Subject: [Pw_forum] Cannot run parallel jobs with openmpi In-Reply-To: <4B03D4D3.2070506@sissa.it> References: <4B03D4D3.2070506@sissa.it> Message-ID: Replying to message "Re: [Pw_forum] Cannot run parallel jobs with openmpi" from Gabriele Sclauzero (18/11/09): >> The problem has been fixed. PWscf should be installed after the >> compilation of mpi binary. Thanks. > > Isn't it the same with VASP? It would be quite astonishing if you could run mpi software *without* the mpi libraries. The next step would be to try without a computer ;-). 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 kazempoor2000 at yahoo.com Wed Nov 18 12:40:40 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Wed, 18 Nov 2009 03:40:40 -0800 (PST) Subject: [Pw_forum] ee potential Message-ID: <79307.36495.qm@web112512.mail.gq1.yahoo.com> Dear All I used EE correction for charged supercell and after that three output was generated that I don't know what are they?Could anyone tell me what are they? vloc1.dat vloc2.dat vcorrz.dat thanks a lot Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091118/c3cb6aa3/attachment-0001.htm From quantumdft at gmail.com Wed Nov 18 12:53:27 2009 From: quantumdft at gmail.com (vega lew) Date: Wed, 18 Nov 2009 19:53:27 +0800 Subject: [Pw_forum] how to set nr1b, nr2b, nr3b for cp.x when using ultrasoft pseudopotential In-Reply-To: References: <412f6c680911172117o2f9ca4f3j6725bda6658423fd@mail.gmail.com> Message-ID: <412f6c680911180353i1ae5b973g74444a0f55388109@mail.gmail.com> Dear sir, thank you for your information. could anyone tell me something about how to visualize the geometry of the output file? Is there a small tool to read the output file directly instead of converting the XYZ coordinations into another format and feeding it to VMD or VEGAZZ? thank you in advance. best wishes. vega On Wed, Nov 18, 2009 at 3:00 PM, Paolo Giannozzi wrote: > > On Nov 18, 2009, at 6:17 , vega lew wrote: > > > I have a question about the option "nr1b, nr2b, nr3b" in &SYSTEM > > namelist. > > Could you please tell me something more about it? > > http://www.quantum-espresso.org/user_guide/node30.html > > > > > P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091118/460ac795/attachment.htm From quantumdft at gmail.com Wed Nov 18 13:23:15 2009 From: quantumdft at gmail.com (vega lew) Date: Wed, 18 Nov 2009 20:23:15 +0800 Subject: [Pw_forum] how to set nr1b, nr2b, nr3b for cp.x when using ultrasoft pseudopotential In-Reply-To: <412f6c680911180353i1ae5b973g74444a0f55388109@mail.gmail.com> References: <412f6c680911172117o2f9ca4f3j6725bda6658423fd@mail.gmail.com> <412f6c680911180353i1ae5b973g74444a0f55388109@mail.gmail.com> Message-ID: <412f6c680911180423l1ae7dc5etcd1883a23c34e897@mail.gmail.com> Dear all, Sorry for last arbitrary question. I found there was a code called cppp.x. But now I encounter another serious problem with the information from pp.x of "ortho went bananas", when I try to add nose thermostat to the system at 150th step. the process as follows, First, I get the optimized geometry from the pw.x. Then I use that geometry as the initial input to pp.x. During the first 19 of cp calculation, I did a few electronic steps with ions fixed and dt=1 From nazari at iasbs.ac.ir Wed Nov 18 17:23:04 2009 From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir) Date: Wed, 18 Nov 2009 16:23:04 -0000 (UTC) Subject: [Pw_forum] Problems concerning fhi2upf In-Reply-To: <412f6c680911180353i1ae5b973g74444a0f55388109@mail.gmail.com> References: <412f6c680911172117o2f9ca4f3j6725bda6658423fd@mail.gmail.com> <412f6c680911180353i1ae5b973g74444a0f55388109@mail.gmail.com> Message-ID: <33754.213.176.122.17.1258561384.squirrel@mail.iasbs.ac.ir> Dear All, Similar to the case which discused in the FORUM ["Problems concerning fhi2upf and cpmd2upf"] I have probelm for conveting 22-Ti.GGA.fhi to UPF format. That is my pleasure if someone give me the Nomconserving pseudopotentials for Ti atom or any suggestion for converting the file. regards fariba nazari IASBS From baroni at sissa.it Wed Nov 18 17:08:29 2009 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 18 Nov 2009 17:08:29 +0100 Subject: [Pw_forum] confirm 63d7beb150c220f0275a453fc134e323bbbcd213 In-Reply-To: <9fdec6370911180001w668d0a1id8b9bf9e87ce121c@mail.gmail.com> References: <9fdec6370911180001w668d0a1id8b9bf9e87ce121c@mail.gmail.com> Message-ID: why don't you install linux on a partition of your pc? oh, yes! your taking the time of signing your posts on this forum is usually regarded as a sign of politeness and consideration. thanks - SB On Nov 18, 2009, at 9:01 AM, patriot pershing wrote: > > dear please > i'm a new user of quantum espresso soft and i would run this soft > under windows environemment using cygwin but i haven't arrived to do > this, for this reason i would ask if any one can help me by giving > me the detailed procedure ot install and run quantum espresso under > cygwin > thanks > _______________________________________________ > 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/20091118/eba064fc/attachment-0001.htm From aschauer at princeton.edu Wed Nov 18 17:37:22 2009 From: aschauer at princeton.edu (Uli Aschauer) Date: Wed, 18 Nov 2009 11:37:22 -0500 Subject: [Pw_forum] how to set nr1b, nr2b, nr3b for cp.x when using ultrasoft pseudopotential In-Reply-To: References: Message-ID: <4B0422C2.80005@princeton.edu> Dear Vega, it seems that you're mixing pw.x input in your cp.x input. There is no such such thing as mixing_beta and nosym in cp.x (check the manual). Also your system is way too large to converge the wavefunction in 80 steps, which is needed to get reasonable forces on the ions. There are other I suggest you start from a cp.x example to understand how to perform a sequence of cp.x runs. Also please not the changing the dt in AUTOPILOT does not work as the dt2bye variable is calculated outside the main loop in cpr.f90 and is thus never updated upon AUTOPILOT events. You will have to move the calculation of dt2bye inside to make it work. Best regards, -uli _________________________________________________________ Uli Aschauer Princeton University Chemistry Department Frick Laboratory, Room 213 Princeton, NJ 08544 Tel: +1-609-258-0116 Email: aschauer at princeton.edu _________________________________________________________ > > Dear all, > > Sorry for last arbitrary question. I found there was a code called cppp.x. > > But now I encounter another serious problem with the information from > pp.x of "ortho went bananas", when I try to add nose thermostat to the > system at 150th step. > > the process as follows, > First, I get the optimized geometry from the pw.x. Then I use that > geometry as the initial input to pp.x. > During the first 19 of cp calculation, I did a few electronic steps > with ions fixed and dt=1 > From 20th step to 79th step, I enlarge the dt to 3; > From 80th step to 149th step, I allow the ions to move and set dt to > 5, with no thermostat. > When I tried to add nose thermostat, the "econt" of the system became > to NaN and the vnhp became to Inf. > And then the program crashed with the information that "ortho went > bananas" > > here is a part of my input files, > &CONTROL > > title = 'CPMD' > , > calculation = 'cp' > , > restart_mode = 'from_scratch' > , > outdir = '/tmp/' , > wfcdir = '/tmp/' > , > pseudo_dir = '/home/vega/espresso-4.0/pseudo/' , > prefix = 'cp_dissociation1' , > nstep = 99999 , > dt = > 1, > / > > &SYSTEM > > ibrav = > 8, > celldm(1) =24.8624, > celldm(2) = 0.8520, > celldm(3) = 1.6964, > nat = > 147, > ntyp = 3, > nr1b = 20, > nr2b = 20, > nr3b = > 20, > nosym = .true. > , > ecutwfc = 30, > ecutrho = 300, > / > > > &ELECTRONS > mixing_mode ='local-TF', > mixing_beta = 0.4, > electron_dynamics = 'damp', > / > > &IONS > > ion_dynamics = 'none', > ion_temperature = > 'not_controlled', > / > AUTOPILOT > on_step = 20 : dt=3 > on_step = 20 : electron_dynamics = 'damp' > on_step = 80 : dt=5 > on_step = 80 : ion_dynamics = 'damp' > on_step = 150 : ion_temperature = 'nose' > ENDRULES > > ATOMIC_SPECIES > > ...... > ...... > ...... > > could you please do me a favor to tell me what is going wrong. > > best wishes, > > vega From szs_naghavi at yahoo.com Wed Nov 18 19:33:15 2009 From: szs_naghavi at yahoo.com (zahra sadat naghavi) Date: Wed, 18 Nov 2009 10:33:15 -0800 (PST) Subject: [Pw_forum] (no subject) Message-ID: <231320.77296.qm@web63004.mail.re1.yahoo.com> Dear Pwscf users, Could you please tell me is it possible to solve a system with pwscf that is not periodic? For example, I would like to calculate phonon frequencies of a molecule with a larg amount of atoms such as 500,defining this molecule in a periodic lattice is easy but its phonon caculation is impossilble here. Does anybody have any solution? Any helps are appricated. Bests -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091118/89e87f58/attachment.htm From sh.shapt at gmail.com Wed Nov 18 21:19:36 2009 From: sh.shapt at gmail.com (Shaptrishi Sharma) Date: Wed, 18 Nov 2009 20:19:36 +0000 Subject: [Pw_forum] library erro Message-ID: Hi QEs users, what does the following error means when we try to plot band structure 'lib-4220 : UNRECOVERABLE library error An internal library run-time error has occurred. Encountered during a sequential formatted WRITE to unit 6 Fortran unit 6 is connected to a sequential formatted text file (standard output). Current format: ("high-symmetry point: ",3f7.4) ^ Abort (core dumped)' suggestions welcome Thanks SS Pune India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091118/2334a7c3/attachment.htm From jdburton1 at gmail.com Wed Nov 18 20:22:14 2009 From: jdburton1 at gmail.com (J. D. Burton) Date: Wed, 18 Nov 2009 13:22:14 -0600 Subject: [Pw_forum] dedicated wfcdir for PWCOND Message-ID: <004c01ca6884$6f8b1c80$4ea15580$@com> Hi everyone, When running PWCOND, is there a way to keep .wfc* files in a dedicated directory other than outdir? I know this can be done in pw.x and it really helps minimize network communication during parallel jobs by keeping the wfc files on the worker nodes. If it's not there, then I suppose I can try to put it into PWCOND myself. unless there is some fundamental difficulty that I haven't thought of yet. Cheers, J. D. ************************************ J. D. Burton, Ph.D. jdburton1 at gmail.com University of Nebraska Lincoln Physics and Astronomy Office Ph. (402) 472 2499 Mobile Ph. (402) 419 9918 213C Ferguson Hall ************************************ "The job of a scientist is to generate wrong ideas as fast as possible." -- Murray Gell-Mann -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091118/19f569f5/attachment.htm From giannozz at democritos.it Wed Nov 18 22:39:29 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 18 Nov 2009 22:39:29 +0100 Subject: [Pw_forum] dedicated wfcdir for PWCOND In-Reply-To: <004c01ca6884$6f8b1c80$4ea15580$@com> References: <004c01ca6884$6f8b1c80$4ea15580$@com> Message-ID: <115F7FFF-A469-4153-8D3C-32A0770AAA83@democritos.it> On Nov 18, 2009, at 20:22 , J. D. Burton wrote: > When running PWCOND, is there a way to keep .wfc* files in a > dedicated directory other than outdir? I know this can be done in > pw.x and it really helps minimize network communication during > parallel jobs by keeping the wfc files on the worker nodes. > variable wfc_dir is present in PWCOND, but it is never set. Try to read it (it should be added to the namelist in do_cond.f90) and see what happens P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed Nov 18 22:41:54 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 18 Nov 2009 22:41:54 +0100 Subject: [Pw_forum] library erro In-Reply-To: References: Message-ID: <1D6B3853-4FF7-4483-BA46-8E2BEE2FB2D6@democritos.it> On Nov 18, 2009, at 21:19 , Shaptrishi Sharma wrote: > what does the following error means when we try to plot band structure > > 'lib-4220 : UNRECOVERABLE library error > An internal library run-time error has occurred. > > Encountered during a sequential formatted WRITE to unit 6 > Fortran unit 6 is connected to a sequential formatted text file > (standard output). > Current format: ("high-symmetry point: ",3f7.4) it means: error while writing to output. Look in the code for ("high-symmetry point: ",3f7.4) and try to figure out what is happening and why P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From naromero at gmail.com Wed Nov 18 22:59:08 2009 From: naromero at gmail.com (Nichols A. Romero) Date: Wed, 18 Nov 2009 13:59:08 -0800 Subject: [Pw_forum] QE postdoc opportunity @ ANL Message-ID: <6ac064b60911181359q325d3d28kec510ba24bb770c4@mail.gmail.com> Dear Colleagues, I bring to your attention computational postdoctoral fellowships at Argonne National Laboratory for those interested in working on the computational aspects of electronic structure methods. Please share this with any Ph.D. student or postdoc who would be be a good fit: http://www.cels.anl.gov/about/opportunities/ We are looking for candidates interested in the development of Quantum Espresso for massively parallel electronic structure calculations on our Blue Gene / P. In particular, their is great interest in implementing coarse-grained parallelization for phonon calculations over MPI in order to rapidly accelerate the design of complex oxide materials. This project will also require advancing the hybrid MPI-OpenMP parallelism in Quantum Espresso to maximize its peak performance on the Blue Gene / P architecture. The postdoc will work closely with staff in the Leadership Computing Facility and the Material Science Division. An ideal candidate will have experience in MPI programming and development of Quantum Espresso. For further information, please contact: Nichols A. Romero naromero at alcf.anl.gov Argonne National Laboratory offers competitive salaries. -- Nichols A. Romero, Ph.D. Argonne Leadership Computing Facility Argonne, IL 60490 (630) 252-3441 (O) (630) 470-0462 (C) From jameslipd at gmail.com Thu Nov 19 04:24:20 2009 From: jameslipd at gmail.com (Jiaye Li) Date: Thu, 19 Nov 2009 11:24:20 +0800 Subject: [Pw_forum] Cannot run parallel jobs with openmpi Message-ID: Dear Gabriele Yes, it is the same with vasp. On Wed, Nov 18, 2009 at 7:40 PM, wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: Constraints HOWTO (Paolo Giannozzi) > 2. Re: confirm 63d7beb150c220f0275a453fc134e323bbbcd213 > (Paolo Giannozzi) > 3. Cannot run parallel jobs with openmpi (Jiaye Li) > 4. Re: Cannot run parallel jobs with openmpi (Gabriele Sclauzero) > 5. Re: Cannot run parallel jobs with openmpi (Lorenzo Paulatto) > 6. ee potential (ali kazempour) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 18 Nov 2009 11:35:08 +0100 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] Constraints HOWTO > To: PWSCF Forum > Message-ID: <4B03CDDC.5010107 at democritos.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Jairo Arbey Rodriguez Martinez wrote: > > > I have used both: car-parrinello md (damped, with program cp.x) > > this should work, I think > > > and in pw.x, ion_dynamics = bfgs (default) > > this is not implemented, I think. I know nothing about constraints, > but you should as a first step find cases in which the existing > constraint work, before adding new ones > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > ------------------------------ > > Message: 2 > Date: Wed, 18 Nov 2009 11:36:47 +0100 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] confirm > 63d7beb150c220f0275a453fc134e323bbbcd213 > To: PWSCF Forum > Message-ID: <4B03CE3F.40503 at democritos.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > patriot pershing wrote: > > > i'm a new user of quantum espresso soft > > this was already clear from the ill-chosen subject > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > ------------------------------ > > Message: 3 > Date: Wed, 18 Nov 2009 19:00:01 +0800 > From: Jiaye Li > Subject: [Pw_forum] Cannot run parallel jobs with openmpi > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > The problem has been fixed. PWscf should be installed after the compilation > of mpi binary. Thanks. > > On Wed, Nov 18, 2009 at 4:15 PM, wrote: > > > Send Pw_forum mailing list submissions to > > pw_forum at pwscf.org > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://www.democritos.it/mailman/listinfo/pw_forum > > or, via email, send a message with subject or body 'help' to > > pw_forum-request at pwscf.org > > > > You can reach the person managing the list at > > pw_forum-owner at pwscf.org > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Pw_forum digest..." > > > > > > Today's Topics: > > > > 1. Re: how to set nr1b, nr2b, nr3b for cp.x when using ultrasoft > > pseudopotential (Paolo Giannozzi) > > 2. Re: Virtual crystal approximation for vacancy (Paolo Giannozzi) > > 3. Re: Cannot run parallel jobs with openmpi (Paolo Giannozzi) > > 4. Re: lowdin charge (Gabriele Sclauzero) > > 5. Re: confirm 63d7beb150c220f0275a453fc134e323bbbcd213 > > (patriot pershing) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Wed, 18 Nov 2009 08:00:21 +0100 > > From: Paolo Giannozzi > > Subject: Re: [Pw_forum] how to set nr1b, nr2b, nr3b for cp.x when > > using ultrasoft pseudopotential > > To: PWSCF Forum > > Message-ID: > > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > > > > > On Nov 18, 2009, at 6:17 , vega lew wrote: > > > > > I have a question about the option "nr1b, nr2b, nr3b" in &SYSTEM > > > namelist. > > > Could you please tell me something more about it? > > > > http://www.quantum-espresso.org/user_guide/node30.html > > > > > > > > > P. > > --- > > Paolo Giannozzi, Dept of Physics, University of Udine > > via delle Scienze 208, 33100 Udine, Italy > > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > > > > > > ------------------------------ > > > > Message: 2 > > Date: Wed, 18 Nov 2009 08:01:25 +0100 > > From: Paolo Giannozzi > > Subject: Re: [Pw_forum] Virtual crystal approximation for vacancy > > To: PWSCF Forum > > Message-ID: > > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > > > > > On Nov 18, 2009, at 5:48 , yuning wu wrote: > > > > > I am considering to use virtual crystal approximation to study a > > > system > > > with vacancy doped > > > > not a good idea IMHO - P. > > --- > > Paolo Giannozzi, Dept of Physics, University of Udine > > via delle Scienze 208, 33100 Udine, Italy > > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > > > > > > ------------------------------ > > > > Message: 3 > > Date: Wed, 18 Nov 2009 08:03:17 +0100 > > From: Paolo Giannozzi > > Subject: Re: [Pw_forum] Cannot run parallel jobs with openmpi > > To: PWSCF Forum > > Message-ID: > > Content-Type: text/plain; charset=US-ASCII; format=flowed > > > > > > On Nov 18, 2009, at 3:24 , Jiaye Li wrote: > > > > > I am wondering if openmpi is compatible with pwscf? > > > > PWscf is compatible with all MPI implementations (as > > long as they work) > > > > P. > > --- > > Paolo Giannozzi, Dept of Physics, University of Udine > > via delle Scienze 208, 33100 Udine, Italy > > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > > > > > > ------------------------------ > > > > Message: 4 > > Date: Wed, 18 Nov 2009 08:54:25 +0100 > > From: Gabriele Sclauzero > > Subject: Re: [Pw_forum] lowdin charge > > To: PWSCF Forum > > Message-ID: <4B03A831.6090508 at sissa.it> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > > > > > yaldaa kh wrote: > > > dear all > > > I performed pdos calculation(scf ,nscf pdos) for Cu slab ,but in lowdin > > > charge, the Cu-p had some charge while p orbitals in Cu atom > > > are unoccupied. if this result is wrong? > > > > Not necessarily. It depends on how much is "some charge". You are right > > when you say that > > in the Cu atom p orbitals are unoccupied (strictly), but in a solid the > > situation is > > different. Also empty orbitals may be involved in the binding, for > instance > > when some > > charge transfer takes place (remember that in Cu the 3d shell is full and > > there is place > > for only 1e- in the 4s). > > Because of this, pseudopotentials usually include among the projectors > (or > > in the local > > channel) electronic states which can be empty in the atom, but not too > much > > higher in > > energy wrt the occupied ones (e.g., in Cu, which is [Ar] 3d10 4s1, also > 4p > > are included > > since they are only 3-4 eV higher than 4s). > > So, if you have the 4p channel in your PP, you will get also the 4p > > projection file from > > projwfc.x, but these states should be restricted to a high energy region. > > Have you checked > > how much 4p charge (if any) is found BELOW the Fermi energy? > > > > > > GS > > > > > thanks a lot > > > yaldaa Kh. > > > chem. student > > > Azad university Iran > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > 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 > > > > > > ------------------------------ > > > > Message: 5 > > Date: Wed, 18 Nov 2009 09:01:17 +0100 > > From: patriot pershing > > Subject: Re: [Pw_forum] confirm > > 63d7beb150c220f0275a453fc134e323bbbcd213 > > To: pw_forum at pwscf.org > > Message-ID: > > <9fdec6370911180001w668d0a1id8b9bf9e87ce121c at mail.gmail.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > dear please > > i'm a new user of quantum espresso soft and i would run this soft under > > windows environemment using cygwin but i haven't arrived to do this, for > > this reason i would ask if any one can help me by giving me the detailed > > procedure ot install and run quantum espresso under cygwin > > thanks > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > http://www.democritos.it/pipermail/pw_forum/attachments/20091118/ba3e587c/attachment.html > > > > ------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > End of Pw_forum Digest, Vol 29, Issue 47 > > **************************************** > > > > > > -- > Sincerely yours > > Jiaye Li > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20091118/bee11be7/attachment-0001.htm > > ------------------------------ > > Message: 4 > Date: Wed, 18 Nov 2009 12:04:51 +0100 > From: Gabriele Sclauzero > Subject: Re: [Pw_forum] Cannot run parallel jobs with openmpi > To: PWSCF Forum > Message-ID: <4B03D4D3.2070506 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Jiaye Li wrote: > > The problem has been fixed. PWscf should be installed after the > > compilation of mpi binary. Thanks. > > Isn't it the same with VASP? > > GS > > > > > > > > > -- > > Sincerely yours > > > > Jiaye Li > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 > > > ------------------------------ > > Message: 5 > Date: Wed, 18 Nov 2009 12:27:19 +0100 > From: "Lorenzo Paulatto" > Subject: Re: [Pw_forum] Cannot run parallel jobs with openmpi > To: "PWSCF Forum" > Message-ID: > Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > > Replying to message "Re: [Pw_forum] Cannot run parallel jobs with openmpi" > from Gabriele Sclauzero (18/11/09): > >> The problem has been fixed. PWscf should be installed after the > >> compilation of mpi binary. Thanks. > > > > Isn't it the same with VASP? > > It would be quite astonishing if you could run mpi software *without* the > mpi libraries. The next step would be to try without a computer ;-). > > 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/ > > > ------------------------------ > > Message: 6 > Date: Wed, 18 Nov 2009 03:40:40 -0800 (PST) > From: ali kazempour > Subject: [Pw_forum] ee potential > To: pw > Message-ID: <79307.36495.qm at web112512.mail.gq1.yahoo.com> > Content-Type: text/plain; charset="us-ascii" > > Dear All > I used EE correction for charged supercell and after that three output was > generated that I don't know what are they?Could anyone tell me what are > they? > vloc1.dat > vloc2.dat > vcorrz.dat > > > thanks a lot > > Ali Kazempour > > > > > > Fritz-Haber-Institut fax : ++49-30-8413 4701 > der Max-Planck-Gesellschaft > Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de > D-14 195 Berlin-Dahlem / German > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20091118/c3cb6aa3/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 29, Issue 48 > **************************************** > -- Sincerely yours Jiaye Li -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091119/44c6bd23/attachment-0001.htm From gbilalbegovic at gmail.com Thu Nov 19 07:17:45 2009 From: gbilalbegovic at gmail.com (Goranka Bilalbegovic) Date: Thu, 19 Nov 2009 07:17:45 +0100 Subject: [Pw_forum] GIPAW, write tensor field, xsf Message-ID: <7332fead0911182217l608f3651v86e565873cc8df6d@mail.gmail.com> Hello, I am trying to plot tensor fields in GIPAW calculations. Files (such as FigFillcurr.xsf_UP_X.xsf) are formed. However, two installations of XCrySDen (Linux and Cygwin) are not able to open xsf files written by write_tensor_field. On both configurations other density xsf files are opened and shown correctly. I have tested two systems: my example of a cluster and the GIPAW CH4 molecule example. The error is: --- ERROR: while executing exec .../bin/gengeom 0 1 11 1 1 1 1 XC_gengeom.1684 /home/.../xcrys_tmp/xc_1684/FigFillcurr.xsf_UP_X.xsf.raw --- I compared the xsf part in write_tensor_field.f90 and PP/xsf.f90. Several differences exist. The head of FigFillcurr.xsf_UP_X.xsf for the CH4 GIPAW example is: --- CRYSTAL PRIMVEC 5.499998026 0.000000000 0.000000000 0.000000000 5.499998026 0.000000000 0.000000000 0.000000000 5.499998026 PRIMCOORD 91130 1 C 0.000000000 0.000000000 0.000000000 H 0.634076639 0.634076639 0.634076639 H 0.634076639 -0.634076639 -0.634076639 H -0.634076639 -0.634076639 0.634076639 H -0.634076639 0.634076639 -0.634076639 X 0.122222178 0.122222178 0.122222178 0.8078E-27 -0.5707E-06 0.1843E-05 X 0.122222178 0.122222178 0.244444357 -0.4750E-04 0.0000E+00 0.5707E-06 --- The lines with X and numbers repeat to the end of the file. Perhaps, writing of 3D datagrids in write_tensor_field.f90 should be as in xsf.f90 ? Thanks. Goranka Bilalbegovic Department of Physics, Faculty of Science University of Zagreb, Croatia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091119/33c1b662/attachment.htm From dhjung at insilicotech.co.kr Thu Nov 19 07:56:09 2009 From: dhjung at insilicotech.co.kr (Dong Hyun Jung) Date: Thu, 19 Nov 2009 15:56:09 +0900 Subject: [Pw_forum] EXX calculation error In-Reply-To: References: <81FCE705EAAE4DC29DE9830C6D9CB409@DHJUNG> Message-ID: <312E3CFE249C41DDAEBA0EC158B16C86@DHJUNG> Thank you so much. Too large ecutrho was the problem. Now I can calculate. Thank you again. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dong Hyun Jung, Ph. D Chief Scientist Insilicotech Co. Ltd. A-1101, Kolontripolis, 210, Geumgok-Dong, Seongnam, Gyeonggi-Do, 463-943, Korea Tel. +82-31-728-0443 Fax. +82-31-728-0444 dhjung at insilicotech.co.kr ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi Sent: Friday, November 13, 2009 4:12 PM To: PWSCF Forum Subject: Re: [Pw_forum] EXX calculation error On Nov 13, 2009, at 24:19 , Dong Hyun Jung wrote: > ecutwfc=35. > ecutrho=360. > C 12.0109996796 06-C.GGA.fhi.UPF > H 1.0080000162 01-H.GGA.fhi.UPF > N 14.0067 N_MT_PBE.psp.UPF > Cu 63.546 29-Cu.GGA.fhi.UPF these are norm-conserving PPs. You shouldn't set ecutrho: it will be automatically set to 4*ecutwfc. Not sure this is related with your problem, though P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From paulatto at sissa.it Thu Nov 19 08:20:05 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 19 Nov 2009 08:20:05 +0100 (CET) Subject: [Pw_forum] (no subject) In-Reply-To: <231320.77296.qm@web63004.mail.re1.yahoo.com> References: <231320.77296.qm@web63004.mail.re1.yahoo.com> Message-ID: <58164.78.12.162.16.1258615205.squirrel@webmail.sissa.it> On Wed, November 18, 2009 19:33, zahra sadat naghavi wrote: > Could you please tell me is it possible to solve a system with pwscf that > is not periodic? Dear Zahra, pw.x always uses periodic boundary conditions, it is possible to simulate an isolated non-periodic system by putting it in the middle of a big cell, so that periodic images don't interact. There are also a number of algorithms to threat this case more effectively that can be activated with input parameters. > For example, I would like to calculate phonon frequencies of a molecule > with a larg amount of atoms such as 500,defining this molecule > in a periodic lattice is easy but its phonon caculation is impossilble > here. 500 atoms are a lot for plane-wave based codes, strictly speaking what matters is the number of electrons, but unless they are all Hydrogens it does not make a big difference. You definitely can, but it will take much longer than you expect; I would not even bother trying with less than 256 processors *available all time*. You can have a look at this page where the scaling with system size is explained in detail. > Does anybody have any solution? To be honest, I would go for a localized basis set code. best tregards -- 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 sclauzer at sissa.it Thu Nov 19 08:47:11 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 19 Nov 2009 08:47:11 +0100 Subject: [Pw_forum] dedicated wfcdir for PWCOND In-Reply-To: <004c01ca6884$6f8b1c80$4ea15580$@com> References: <004c01ca6884$6f8b1c80$4ea15580$@com> Message-ID: <4B04F7FF.1070804@sissa.it> Dear JD, J. D. Burton wrote: > Hi everyone, > > > > When running PWCOND, is there a way to keep .wfc* files in a dedicated > directory other than outdir? I know this can be done in pw.x and it > really helps minimize network communication during parallel jobs by > keeping the wfc files on the worker nodes. If it?s not there, then I Actually pwcond.x in the present implementation does not use the wavefunctions produced by pw.x, but only the charge density and the informations in the data-file.xml. The only thing needed to run a standard pwcond calculation is the prefix.save directory. If the wavefunction files prefix.wfc are not present, the code will create them in outdir, but those files will NOT be used during the calculations (in fact, if you look at their size it should be zero). If there are already the wavefunction files from the previous pw.x calculation, they will be left untouched. This means also that you can do the pwcond calculation with any number of processors, irrespectively of how many you used for the pwscf one. > suppose I can try to put it into PWCOND myself? unless there is some > fundamental difficulty that I haven?t thought of yet. If you are volunteering to extend to pwcond the usage of wfc_dir feature, you're welcome! Anyway I don't feel there is the need for that at the moment, since, as I told you, there is no network communication issue related to wavefunction files in pwcond. HTH GS > > > > Cheers, > > J. D. > > > > ************************************ > > J. D. Burton, Ph.D. > > jdburton1 at gmail.com > > University of Nebraska Lincoln > > Physics and Astronomy > > Office Ph. (402) 472 2499 > > Mobile Ph. (402) 419 9918 > > 213C Ferguson Hall > > ************************************ > > "The job of a scientist is to generate wrong ideas as fast as possible." > -- Murray Gell-Mann > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 daijiayu at nudt.edu.cn Thu Nov 19 10:28:16 2009 From: daijiayu at nudt.edu.cn (Jiayu Dai) Date: Thu, 19 Nov 2009 17:28:16 +0800 Subject: [Pw_forum] pressure at finite temperature. Message-ID: <458622896.09855@nudt.edu.cn> Dear users, I met a problem when i calculated the pressure of the system at finite temperature. The preesure is much lower than that of experiments. I searched in the mailist of pwforum, and some body said the kinetic contribution of the pressure should be added, but nobody answered. Is it true? Or in pwscf, the pressure is only the pressure of electronic contribution using stress.f90? I noticed there is a new parameter in dynamics.f90: press_new. It adds the contribution of ions and virial, but it only used in NPT. Thanks a lot. Jiayu ------------------------------ ------------------------------------------- Jiayu Dai Department of Physics National University of Defense Technology, Changsha, 410073, P R China ----------------------------------------- From ceresoli at MIT.EDU Thu Nov 19 15:09:11 2009 From: ceresoli at MIT.EDU (Davide Ceresoli) Date: Thu, 19 Nov 2009 09:09:11 -0500 Subject: [Pw_forum] GIPAW, write tensor field, xsf In-Reply-To: <7332fead0911182217l608f3651v86e565873cc8df6d@mail.gmail.com> References: <7332fead0911182217l608f3651v86e565873cc8df6d@mail.gmail.com> Message-ID: <4B055187.2090004@mit.edu> Goranka Bilalbegovic wrote: > > Hello, > > I am trying to plot tensor fields in GIPAW calculations. Files (such as > FigFillcurr.xsf_UP_X.xsf) are formed. However, two installations of > XCrySDen (Linux and Cygwin) are not able to open xsf files written by > write_tensor_field. On both configurations other density xsf files are > opened and shown correctly. > > I have tested two systems: my example of a cluster and the GIPAW CH4 > molecule example. > > The error is: > --- > ERROR: while executing exec > .../bin/gengeom 0 1 11 1 1 1 1 > XC_gengeom.1684 > /home/.../xcrys_tmp/xc_1684/FigFillcurr.xsf_UP_X.xsf.raw > --- > > I compared the xsf part in write_tensor_field.f90 and PP/xsf.f90. > Several differences exist. The head of FigFillcurr.xsf_UP_X.xsf for the > CH4 GIPAW example is: > --- > CRYSTAL > PRIMVEC > 5.499998026 0.000000000 0.000000000 > 0.000000000 5.499998026 0.000000000 > 0.000000000 0.000000000 5.499998026 > PRIMCOORD > 91130 1 > C 0.000000000 0.000000000 0.000000000 > H 0.634076639 0.634076639 0.634076639 > H 0.634076639 -0.634076639 -0.634076639 > H -0.634076639 -0.634076639 0.634076639 > H -0.634076639 0.634076639 -0.634076639 > X 0.122222178 0.122222178 0.122222178 0.8078E-27 -0.5707E-06 0.1843E-05 > X 0.122222178 0.122222178 0.244444357 -0.4750E-04 0.0000E+00 0.5707E-06 This is strange, according to xcrysden documentation: http://www.xcrysden.org/doc/vectorField.html this is the right format. Maybe, something has changed in the newest Xcrysden versions. I'll test on my system and I'll let you know. Davide From jlz101 at unlserve.unl.edu Thu Nov 19 17:23:57 2009 From: jlz101 at unlserve.unl.edu (J. D. Burton) Date: Thu, 19 Nov 2009 10:23:57 -0600 Subject: [Pw_forum] dedicated wfcdir for PWCOND In-Reply-To: <4B04F7FF.1070804@sissa.it> References: <004c01ca6884$6f8b1c80$4ea15580$@com> <4B04F7FF.1070804@sissa.it> Message-ID: <000301ca6934$b1b3ffe0$151bffa0$@unl.edu> Dear Gabriele, Thanks for the info. I obviously knew the energy-dependent wavefunctions calculated in PWCOND are different from the Bloch eigenvectors generated by the periodic pw.x. I just never noticed that those wfc files made by PWCOND were empty! So I guess everything is held in the RAM on worker nodes, which means I just need to be careful about number of processors (available memory) vs system size. Thanks again, J. D. ************************************ J. D. Burton, Ph.D. jlz101 at unlserve.unl.edu University of Nebraska Lincoln Physics and Astronomy Office Ph. (402) 472 2499 Mobile Ph. (402) 419 9918 213C Ferguson Hall ************************************ "The job of a scientist is to generate wrong ideas as fast as possible." -- Murray Gell-Mann -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Gabriele Sclauzero Sent: Thursday, November 19, 2009 1:47 AM To: PWSCF Forum Subject: Re: [Pw_forum] dedicated wfcdir for PWCOND Dear JD, J. D. Burton wrote: > Hi everyone, > > > > When running PWCOND, is there a way to keep .wfc* files in a dedicated > directory other than outdir? I know this can be done in pw.x and it > really helps minimize network communication during parallel jobs by > keeping the wfc files on the worker nodes. If it's not there, then I Actually pwcond.x in the present implementation does not use the wavefunctions produced by pw.x, but only the charge density and the informations in the data-file.xml. The only thing needed to run a standard pwcond calculation is the prefix.save directory. If the wavefunction files prefix.wfc are not present, the code will create them in outdir, but those files will NOT be used during the calculations (in fact, if you look at their size it should be zero). If there are already the wavefunction files from the previous pw.x calculation, they will be left untouched. This means also that you can do the pwcond calculation with any number of processors, irrespectively of how many you used for the pwscf one. > suppose I can try to put it into PWCOND myself. unless there is some > fundamental difficulty that I haven't thought of yet. If you are volunteering to extend to pwcond the usage of wfc_dir feature, you're welcome! Anyway I don't feel there is the need for that at the moment, since, as I told you, there is no network communication issue related to wavefunction files in pwcond. HTH GS > > > > Cheers, > > J. D. > > > > ************************************ > > J. D. Burton, Ph.D. > > jdburton1 at gmail.com > > University of Nebraska Lincoln > > Physics and Astronomy > > Office Ph. (402) 472 2499 > > Mobile Ph. (402) 419 9918 > > 213C Ferguson Hall > > ************************************ > > "The job of a scientist is to generate wrong ideas as fast as possible." > -- Murray Gell-Mann > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 Nov 19 17:36:25 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 19 Nov 2009 17:36:25 +0100 Subject: [Pw_forum] dedicated wfcdir for PWCOND In-Reply-To: <000301ca6934$b1b3ffe0$151bffa0$@unl.edu> References: <004c01ca6884$6f8b1c80$4ea15580$@com> <4B04F7FF.1070804@sissa.it> <000301ca6934$b1b3ffe0$151bffa0$@unl.edu> Message-ID: <4B057409.90800@sissa.it> J. D. Burton wrote: > Dear Gabriele, > > Thanks for the info. I obviously knew the energy-dependent wavefunctions > calculated in PWCOND are different from the Bloch eigenvectors generated by > the periodic pw.x. Not necessarily. I think that the propagating Bloch waves (i.e. those at real k vector) computed in the leads should coincide with those from pw.x, while the evanescent states are not present in pw.x due to PBCs along z, obviously. > I just never noticed that those wfc files made by PWCOND > were empty! So I guess everything is held in the RAM on worker nodes, which > means I just need to be careful about number of processors (available > memory) vs system size. You are right. If the system is very big, the memory requirement may be huge and so you should be careful. You can try to reduce the G_perp basis set in the perpendicular directions by playing with ewind and epsproj parameters. HTH GS > > Thanks again, > J. D. > > ************************************ > J. D. Burton, Ph.D. > jlz101 at unlserve.unl.edu > University of Nebraska Lincoln > Physics and Astronomy > Office Ph. (402) 472 2499 > Mobile Ph. (402) 419 9918 > 213C Ferguson Hall > ************************************ > "The job of a scientist is to generate wrong ideas as fast as possible." > -- Murray Gell-Mann > > -----Original Message----- > From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On > Behalf Of Gabriele Sclauzero > Sent: Thursday, November 19, 2009 1:47 AM > To: PWSCF Forum > Subject: Re: [Pw_forum] dedicated wfcdir for PWCOND > > Dear JD, > > J. D. Burton wrote: >> Hi everyone, >> >> >> >> When running PWCOND, is there a way to keep .wfc* files in a dedicated >> directory other than outdir? I know this can be done in pw.x and it >> really helps minimize network communication during parallel jobs by >> keeping the wfc files on the worker nodes. If it's not there, then I > > Actually pwcond.x in the present implementation does not use the > wavefunctions produced by > pw.x, but only the charge density and the informations in the data-file.xml. > The only thing needed to run a standard pwcond calculation is the > prefix.save directory. > If the wavefunction files prefix.wfc are not present, the code will create > them in outdir, > but those files will NOT be used during the calculations (in fact, if you > look at their > size it should be zero). > If there are already the wavefunction files from the previous pw.x > calculation, they will > be left untouched. > This means also that you can do the pwcond calculation with any number of > processors, > irrespectively of how many you used for the pwscf one. > >> suppose I can try to put it into PWCOND myself. unless there is some >> fundamental difficulty that I haven't thought of yet. > > If you are volunteering to extend to pwcond the usage of wfc_dir feature, > you're welcome! > Anyway I don't feel there is the need for that at the moment, since, as I > told you, there > is no network communication issue related to wavefunction files in pwcond. > > > HTH > > GS > >> >> >> Cheers, >> >> J. D. >> >> >> >> ************************************ >> >> J. D. Burton, Ph.D. >> >> jdburton1 at gmail.com >> >> University of Nebraska Lincoln >> >> Physics and Astronomy >> >> Office Ph. (402) 472 2499 >> >> Mobile Ph. (402) 419 9918 >> >> 213C Ferguson Hall >> >> ************************************ >> >> "The job of a scientist is to generate wrong ideas as fast as possible." >> -- Murray Gell-Mann >> >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 jlz101 at unlserve.unl.edu Thu Nov 19 18:12:59 2009 From: jlz101 at unlserve.unl.edu (J. D. Burton) Date: Thu, 19 Nov 2009 11:12:59 -0600 Subject: [Pw_forum] dedicated wfcdir for PWCOND In-Reply-To: <4B057409.90800@sissa.it> References: <004c01ca6884$6f8b1c80$4ea15580$@com> <4B04F7FF.1070804@sissa.it> <000301ca6934$b1b3ffe0$151bffa0$@unl.edu> <4B057409.90800@sissa.it> Message-ID: <000c01ca693b$8bbcbeb0$a3363c10$@unl.edu> Dear Gabriele, >> Thanks for the info. I obviously knew the energy-dependent wavefunctions >> calculated in PWCOND are different from the Bloch eigenvectors generated by >> the periodic pw.x. >Not necessarily. I think that the propagating Bloch waves (i.e. those at real k vector) >computed in the leads should coincide with those from pw.x, while the evanescent states >are not present in pw.x due to PBCs along z, obviously. Let me rephrase: The wavefunctions generated by pw.x are, in general, fundamentally useless for the PWCOND calculation because they are only generated on a comparatively sparse k-mesh for self-consistency, whereas PWCOND uses the propagating modes (i.e. complex kz values, etc) of the leads at a given input energy (which in general is not on the list of eigenvalues found in pw.x) on a much more dense mesh of k_perp points. This is not to say that if you were to use pw.x to generate a wfc at just the right (real) k_z at just the right k_perp corresponding to just the right energy that it would be different from that found by PWCOND... it's just that would be a pointless procedure. Cheers, J. D. ************************************ J. D. Burton, Ph.D. jlz101 at unlserve.unl.edu University of Nebraska Lincoln Physics and Astronomy Office Ph. (402) 472 2499 Mobile Ph. (402) 419 9918 213C Ferguson Hall ************************************ "The job of a scientist is to generate wrong ideas as fast as possible." -- Murray Gell-Mann -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Gabriele Sclauzero Sent: Thursday, November 19, 2009 10:36 AM To: PWSCF Forum Subject: Re: [Pw_forum] dedicated wfcdir for PWCOND J. D. Burton wrote: > Dear Gabriele, > > Thanks for the info. I obviously knew the energy-dependent wavefunctions > calculated in PWCOND are different from the Bloch eigenvectors generated by > the periodic pw.x. Not necessarily. I think that the propagating Bloch waves (i.e. those at real k vector) computed in the leads should coincide with those from pw.x, while the evanescent states are not present in pw.x due to PBCs along z, obviously. > I just never noticed that those wfc files made by PWCOND > were empty! So I guess everything is held in the RAM on worker nodes, which > means I just need to be careful about number of processors (available > memory) vs system size. You are right. If the system is very big, the memory requirement may be huge and so you should be careful. You can try to reduce the G_perp basis set in the perpendicular directions by playing with ewind and epsproj parameters. HTH GS > > Thanks again, > J. D. > > ************************************ > J. D. Burton, Ph.D. > jlz101 at unlserve.unl.edu > University of Nebraska Lincoln > Physics and Astronomy > Office Ph. (402) 472 2499 > Mobile Ph. (402) 419 9918 > 213C Ferguson Hall > ************************************ > "The job of a scientist is to generate wrong ideas as fast as possible." > -- Murray Gell-Mann > > -----Original Message----- > From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On > Behalf Of Gabriele Sclauzero > Sent: Thursday, November 19, 2009 1:47 AM > To: PWSCF Forum > Subject: Re: [Pw_forum] dedicated wfcdir for PWCOND > > Dear JD, > > J. D. Burton wrote: >> Hi everyone, >> >> >> >> When running PWCOND, is there a way to keep .wfc* files in a dedicated >> directory other than outdir? I know this can be done in pw.x and it >> really helps minimize network communication during parallel jobs by >> keeping the wfc files on the worker nodes. If it's not there, then I > > Actually pwcond.x in the present implementation does not use the > wavefunctions produced by > pw.x, but only the charge density and the informations in the data-file.xml. > The only thing needed to run a standard pwcond calculation is the > prefix.save directory. > If the wavefunction files prefix.wfc are not present, the code will create > them in outdir, > but those files will NOT be used during the calculations (in fact, if you > look at their > size it should be zero). > If there are already the wavefunction files from the previous pw.x > calculation, they will > be left untouched. > This means also that you can do the pwcond calculation with any number of > processors, > irrespectively of how many you used for the pwscf one. > >> suppose I can try to put it into PWCOND myself. unless there is some >> fundamental difficulty that I haven't thought of yet. > > If you are volunteering to extend to pwcond the usage of wfc_dir feature, > you're welcome! > Anyway I don't feel there is the need for that at the moment, since, as I > told you, there > is no network communication issue related to wavefunction files in pwcond. > > > HTH > > GS > >> >> >> Cheers, >> >> J. D. >> >> >> >> ************************************ >> >> J. D. Burton, Ph.D. >> >> jdburton1 at gmail.com >> >> University of Nebraska Lincoln >> >> Physics and Astronomy >> >> Office Ph. (402) 472 2499 >> >> Mobile Ph. (402) 419 9918 >> >> 213C Ferguson Hall >> >> ************************************ >> >> "The job of a scientist is to generate wrong ideas as fast as possible." >> -- Murray Gell-Mann >> >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 Nov 19 18:20:19 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 19 Nov 2009 18:20:19 +0100 Subject: [Pw_forum] dedicated wfcdir for PWCOND In-Reply-To: <000c01ca693b$8bbcbeb0$a3363c10$@unl.edu> References: <004c01ca6884$6f8b1c80$4ea15580$@com> <4B04F7FF.1070804@sissa.it> <000301ca6934$b1b3ffe0$151bffa0$@unl.edu> <4B057409.90800@sissa.it> <000c01ca693b$8bbcbeb0$a3363c10$@unl.edu> Message-ID: <4B057E53.1070504@sissa.it> J. D. Burton wrote: > Dear Gabriele, > >>> Thanks for the info. I obviously knew the energy-dependent wavefunctions >>> calculated in PWCOND are different from the Bloch eigenvectors generated > by >>> the periodic pw.x. > >> Not necessarily. I think that the propagating Bloch waves (i.e. those at > real k vector) >> computed in the leads should coincide with those from pw.x, while the > evanescent states >> are not present in pw.x due to PBCs along z, obviously. > > Let me rephrase: The wavefunctions generated by pw.x are, in general, > fundamentally useless for the PWCOND calculation because they are only > generated on a comparatively sparse k-mesh for self-consistency, whereas > PWCOND uses the propagating modes (i.e. complex kz values, etc) of the leads > at a given input energy (which in general is not on the list of eigenvalues > found in pw.x) on a much more dense mesh of k_perp points. That's right. The convergence of total energy can be different from that of the transmission. Anyway, from my experience, it is not always said that the k_perp grid needed to converge the transmission has to be more dense than that needed for the total energy. Actually it depends on the features of the band structure next to the target scattering energy (see PRB 72, 033401 (2005) or appendix of PRB 74, 165416 (2006) for instance). HTH GS > > This is not to say that if you were to use pw.x to generate a wfc at just > the right (real) k_z at just the right k_perp corresponding to just the > right energy that it would be different from that found by PWCOND... it's > just that would be a pointless procedure. > > Cheers, > J. D. > > ************************************ > J. D. Burton, Ph.D. > jlz101 at unlserve.unl.edu > University of Nebraska Lincoln > Physics and Astronomy > Office Ph. (402) 472 2499 > Mobile Ph. (402) 419 9918 > 213C Ferguson Hall > ************************************ > "The job of a scientist is to generate wrong ideas as fast as possible." > -- Murray Gell-Mann > > > -----Original Message----- > From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On > Behalf Of Gabriele Sclauzero > Sent: Thursday, November 19, 2009 10:36 AM > To: PWSCF Forum > Subject: Re: [Pw_forum] dedicated wfcdir for PWCOND > > > > J. D. Burton wrote: >> Dear Gabriele, >> >> Thanks for the info. I obviously knew the energy-dependent wavefunctions >> calculated in PWCOND are different from the Bloch eigenvectors generated > by >> the periodic pw.x. > > Not necessarily. I think that the propagating Bloch waves (i.e. those at > real k vector) > computed in the leads should coincide with those from pw.x, while the > evanescent states > are not present in pw.x due to PBCs along z, obviously. > >> I just never noticed that those wfc files made by PWCOND >> were empty! So I guess everything is held in the RAM on worker nodes, > which >> means I just need to be careful about number of processors (available >> memory) vs system size. > > You are right. If the system is very big, the memory requirement may be huge > and so you > should be careful. You can try to reduce the G_perp basis set in the > perpendicular > directions by playing with ewind and epsproj parameters. > > HTH > > GS > >> Thanks again, >> J. D. >> >> ************************************ >> J. D. Burton, Ph.D. >> jlz101 at unlserve.unl.edu >> University of Nebraska Lincoln >> Physics and Astronomy >> Office Ph. (402) 472 2499 >> Mobile Ph. (402) 419 9918 >> 213C Ferguson Hall >> ************************************ >> "The job of a scientist is to generate wrong ideas as fast as possible." >> -- Murray Gell-Mann >> >> -----Original Message----- >> From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On >> Behalf Of Gabriele Sclauzero >> Sent: Thursday, November 19, 2009 1:47 AM >> To: PWSCF Forum >> Subject: Re: [Pw_forum] dedicated wfcdir for PWCOND >> >> Dear JD, >> >> J. D. Burton wrote: >>> Hi everyone, >>> >>> >>> >>> When running PWCOND, is there a way to keep .wfc* files in a dedicated >>> directory other than outdir? I know this can be done in pw.x and it >>> really helps minimize network communication during parallel jobs by >>> keeping the wfc files on the worker nodes. If it's not there, then I >> Actually pwcond.x in the present implementation does not use the >> wavefunctions produced by >> pw.x, but only the charge density and the informations in the > data-file.xml. >> The only thing needed to run a standard pwcond calculation is the >> prefix.save directory. >> If the wavefunction files prefix.wfc are not present, the code will create >> them in outdir, >> but those files will NOT be used during the calculations (in fact, if you >> look at their >> size it should be zero). >> If there are already the wavefunction files from the previous pw.x >> calculation, they will >> be left untouched. >> This means also that you can do the pwcond calculation with any number of >> processors, >> irrespectively of how many you used for the pwscf one. >> >>> suppose I can try to put it into PWCOND myself. unless there is some >>> fundamental difficulty that I haven't thought of yet. >> If you are volunteering to extend to pwcond the usage of wfc_dir feature, >> you're welcome! >> Anyway I don't feel there is the need for that at the moment, since, as I >> told you, there >> is no network communication issue related to wavefunction files in pwcond. >> >> >> HTH >> >> GS >> >>> >>> >>> Cheers, >>> >>> J. D. >>> >>> >>> >>> ************************************ >>> >>> J. D. Burton, Ph.D. >>> >>> jdburton1 at gmail.com >>> >>> University of Nebraska Lincoln >>> >>> Physics and Astronomy >>> >>> Office Ph. (402) 472 2499 >>> >>> Mobile Ph. (402) 419 9918 >>> >>> 213C Ferguson Hall >>> >>> ************************************ >>> >>> "The job of a scientist is to generate wrong ideas as fast as possible." >>> -- Murray Gell-Mann >>> >>> >>> >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> 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 nedward at MIT.EDU Thu Nov 19 21:52:27 2009 From: nedward at MIT.EDU (Nicholas E. Singh-Miller) Date: Thu, 19 Nov 2009 15:52:27 -0500 (EST) Subject: [Pw_forum] ee potential In-Reply-To: <79307.36495.qm@web112512.mail.gq1.yahoo.com> References: <79307.36495.qm@web112512.mail.gq1.yahoo.com> Message-ID: Hi Ali, > vloc1.dat > vloc2.dat It looks like these are the realspace ionic potentials used to calculate the correction. Thus, 1 and 2 would be the two atom types in your system. They are printed radially where the first column is r, the second is the psedo-potential, and the thrid is a gaussian approximation of the pseudo potential. As far as I can tell, these were just printed for testing and verifying. You probably will not have much use for them. > vcorrz.dat > My version (older) does not print this, but again it was probably for testing and is likely the corrective potential averaged to the z axis. hope that helps, Nick ***************************************** Nicholas E. Singh-Miller Prof. Marzari Group (quasiamore.mit.edu) Materials Science and Engineering Massachusetts Institute of Technology 13-4066 (617)324-0372 ***************************************** From ceresoli at MIT.EDU Thu Nov 19 21:59:30 2009 From: ceresoli at MIT.EDU (Davide Ceresoli) Date: Thu, 19 Nov 2009 15:59:30 -0500 Subject: [Pw_forum] GIPAW, write tensor field, xsf In-Reply-To: <7332fead0911182217l608f3651v86e565873cc8df6d@mail.gmail.com> References: <7332fead0911182217l608f3651v86e565873cc8df6d@mail.gmail.com> Message-ID: <4B05B1B2.80901@mit.edu> Goranka Bilalbegovic wrote: > > Hello, > > I have tested two systems: my example of a cluster and the GIPAW CH4 > molecule example. > > The error is: > --- > ERROR: while executing exec > .../bin/gengeom 0 1 11 1 1 1 1 > XC_gengeom.1684 > /home/.../xcrys_tmp/xc_1684/FigFillcurr.xsf_UP_X.xsf.raw The problem could be that xcrysden cannot handle such an amount of "atoms". In fact, on my machine, gengeom crashed with a "segmentation violation" error. Davide From gbilalbegovic at gmail.com Fri Nov 20 00:07:29 2009 From: gbilalbegovic at gmail.com (Goranka Bilalbegovic) Date: Fri, 20 Nov 2009 00:07:29 +0100 Subject: [Pw_forum] GIPAW, write tensor field, xsf In-Reply-To: <4B05B1B2.80901@mit.edu> References: <7332fead0911182217l608f3651v86e565873cc8df6d@mail.gmail.com> <4B05B1B2.80901@mit.edu> Message-ID: <7332fead0911191507g48a17f5fhdc0cea4bd739a22e@mail.gmail.com> On Thu, Nov 19, 2009 at 9:59 PM, Davide Ceresoli wrote: > > The problem could be that xcrysden cannot handle such an > amount of "atoms". In fact, on my machine, gengeom crashed > with a "segmentation violation" error. > > I have looked at Tone's examples and found one vector_field.xsf. It is for N_2H_4CO and some arrows, but *.xsf is: ------ ATOMS 6 0.0000000000 0.0000000000 0.0000000000 8 0.0000000000 0.0000000000 1.2614009982 7 0.0000000000 1.1482466623 -0.6997899990 7 0.0000000000 -1.1482466623 -0.6997899990 1 0.0000000000 2.0265496485 -0.2028169999 1 0.0000000000 -2.0265496485 -0.2028169999 1 0.0000000000 1.1340804828 -1.7049749982 1 0.0000000000 -1.1340804828 -1.7049749982 X 2.000 0.000 2.000 0.010 0.000 0.000 X 1.902 0.618 2.000 0.010 0.003 0.000 ... ------ I edited FigFillcurr.xsf_UP_X.xsf for the GIPAW CH4 example, deleted first 7 lines and put "ATOMS" as the first line. Now my XCrySDen opens this file, but it looks funny and definitely it takes a lot of memory. I am not able to rotate it on my home PC Cygwin. Tone's example is "is merely an "artistic" example". I wanted to get something similar to figures in Chapter 4 of Jonathan Yates's thesis. My cluster has 18 atoms. Will try tomorrow to decrease size of arrows, or something similar. Best regards, Goranka Bilalbegovic Department of Physics, -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091120/4595bae4/attachment.htm From quantumdft at gmail.com Fri Nov 20 04:26:10 2009 From: quantumdft at gmail.com (vega lew) Date: Fri, 20 Nov 2009 11:26:10 +0800 Subject: [Pw_forum] how to set nr1b, nr2b, nr3b for cp.x when using ultrasoft pseudopotential In-Reply-To: <4B0422C2.80005@princeton.edu> References: <4B0422C2.80005@princeton.edu> Message-ID: <412f6c680911191926g4bd8e5a5xf41fb5c794e3c671@mail.gmail.com> Dear Uli and all the friends in the forum, thank you very much for your reply. could you please tell me how to move the calculation dt2bye inside the main loop? I just lean from the autopilot example in the package of QE 4.0.3 version. In that example, the dt2bye is at the very beginning of the input file. Should I follow that way? Following you last suggestion, I engage more steps to make the system to coverge, and keep more attention on the total energy of the system. But this time when I add thermostat to the system, the temparature never goes up? could you please tell me why the thermostat never take effect? my input files is listed as follows, &CONTROL title = 'CPMD' , calculation = 'cp' , restart_mode = 'from_scratch' , outdir = '/disk5/nanjing/vega/cpmd/' , wfcdir = '/tmp/' , pseudo_dir = '/home/software/nanjing/vega/espresso-4.0.1/pseudo/' , prefix = 'cp_molecular' , nstep = 99999 , dt = 3, iprint = 50, / &SYSTEM ibrav = 8, celldm(1) =24.8624, celldm(2) = 0.8520, celldm(3) = 1.6964, nat = 147, ntyp = 3, nr1b = 20, nr2b = 20, nr3b = 20, nbnd = 630, # my system has 1160 electrons and I add a few more empty bands to the system. ecutwfc = 30, ecutrho = 300, / &ELECTRONS mixing_mode ='local-TF', electron_dynamics = 'damp', / &IONS ion_dynamics = 'none', ion_temperature = 'not_controlled', / AUTOPILOT on_step = 80 : ion_dynamics = 'damp' on_step = 160 : ion_temperature = 'nose' on_step = 160 : tempw =50 on_step = 240 : tempw =100 on_step = 540 : tempw =150 on_step = 1000 : tempw =200 on_step = 10000 : tempw =250 ENDRULES ATOMIC_SPECIES to output is as follows, ............. ............. in while: event_index 4 ======================================== EMPLOY RULES: CURRENT_NFI= 540 event_index= 4 event_step== 540 ======================================== RULE EVENT: tempw 150.000000000000 in while after: event_index 5 ............ ............ ATOMIC_VELOCITIES O 0.470823E-05 0.561221E-06 0.356130E-05 O -0.222964E-05 0.686844E-06 0.565589E-05 O 0.245059E-07 0.368266E-05 -0.646064E-06 O 0.340472E-06 -0.104069E-05 -0.267787E-05 O -0.141504E-05 0.140458E-05 0.176310E-05 O -0.138272E-05 -0.690043E-06 -0.113648E-05 O 0.173462E-05 0.778397E-07 -0.304404E-05 O -0.390145E-05 0.144215E-06 -0.145382E-05 O 0.000000E+00 0.000000E+00 0.000000E+00 O 0.000000E+00 0.000000E+00 0.000000E+00 O 0.000000E+00 0.000000E+00 0.000000E+00 O 0.000000E+00 0.000000E+00 0.000000E+00 O 0.000000E+00 0.000000E+00 0.000000E+00 O 0.000000E+00 0.000000E+00 0.000000E+00 O 0.000000E+00 0.000000E+00 0.000000E+00 O 0.000000E+00 0.000000E+00 0.000000E+00 .......... .......... .......... nfi ekinc temph tempp etot enthal econs econt vnhh xnhh0 vnhp xnhp0 550 0.00000 0.0 0.0 -4369.56798 -4369.56798 -4369.56796 -4369.56796 0.0000 0.0000 0.0000 0.0000 and we found the velocities of atoms is zore. that is because some of atoms is fixed in the system. the velocities of atoms with is free to move is about in range of 1E10-4~1E10-6. Do you think it is rether small? By the way, the initial geometry is from the optimized structure of pw.x. This initial geometry is a local mimima of the system, and coveged very well in the relax calculation of pw.x. So this may be the trapped geometry. Do you think this is the main cause of the system temparature never goes up? thank you very much for reading. any hints will be deeply appreciated best wishes, vega On Thu, Nov 19, 2009 at 12:37 AM, Uli Aschauer wrote: > Dear Vega, > > it seems that you're mixing pw.x input in your cp.x input. There is no > such such thing as mixing_beta and nosym in cp.x (check the manual). > Also your system is way too large to converge the wavefunction in 80 > steps, which is needed to get reasonable forces on the ions. There are > other I suggest you start from a cp.x example to understand how to > perform a sequence of cp.x runs. > > Also please not the changing the dt in AUTOPILOT does not work as the > dt2bye variable is calculated outside the main loop in cpr.f90 and is > thus never updated upon AUTOPILOT events. You will have to move the > calculation of dt2bye inside to make it work. > > Best regards, > -uli > > _________________________________________________________ > Uli Aschauer > Princeton University > Chemistry Department > Frick Laboratory, Room 213 > Princeton, NJ 08544 > Tel: +1-609-258-0116 > Email: aschauer at princeton.edu > _________________________________________________________ > > > > > Dear all, > > > > Sorry for last arbitrary question. I found there was a code called > cppp.x. > > > > But now I encounter another serious problem with the information from > > pp.x of "ortho went bananas", when I try to add nose thermostat to the > > system at 150th step. > > > > the process as follows, > > First, I get the optimized geometry from the pw.x. Then I use that > > geometry as the initial input to pp.x. > > During the first 19 of cp calculation, I did a few electronic steps > > with ions fixed and dt=1 > > From 20th step to 79th step, I enlarge the dt to 3; > > From 80th step to 149th step, I allow the ions to move and set dt to > > 5, with no thermostat. > > When I tried to add nose thermostat, the "econt" of the system became > > to NaN and the vnhp became to Inf. > > And then the program crashed with the information that "ortho went > > bananas" > > > > here is a part of my input files, > > &CONTROL > > > > title = 'CPMD' > > , > > calculation = 'cp' > > , > > restart_mode = 'from_scratch' > > , > > outdir = '/tmp/' , > > wfcdir = '/tmp/' > > , > > pseudo_dir = '/home/vega/espresso-4.0/pseudo/' , > > prefix = 'cp_dissociation1' , > > nstep = 99999 , > > dt = > > 1, > > / > > > > &SYSTEM > > > > ibrav = > > 8, > > celldm(1) =24.8624, > > celldm(2) = 0.8520, > > celldm(3) = 1.6964, > > nat = > > 147, > > ntyp = 3, > > nr1b = 20, > > nr2b = 20, > > nr3b = > > 20, > > nosym = .true. > > , > > ecutwfc = 30, > > ecutrho = 300, > > / > > > > > > &ELECTRONS > > mixing_mode ='local-TF', > > mixing_beta = 0.4, > > electron_dynamics = 'damp', > > / > > > > &IONS > > > > ion_dynamics = 'none', > > ion_temperature = > > 'not_controlled', > > / > > AUTOPILOT > > on_step = 20 : dt=3 > > on_step = 20 : electron_dynamics = 'damp' > > on_step = 80 : dt=5 > > on_step = 80 : ion_dynamics = 'damp' > > on_step = 150 : ion_temperature = 'nose' > > ENDRULES > > > > ATOMIC_SPECIES > > > > ...... > > ...... > > ...... > > > > could you please do me a favor to tell me what is going wrong. > > > > best wishes, > > > > vega > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091120/cc665c86/attachment-0001.htm From jwan at phy.cuhk.edu.hk Fri Nov 20 04:34:59 2009 From: jwan at phy.cuhk.edu.hk (Jones Tsz-Kai Wan) Date: Fri, 20 Nov 2009 11:34:59 +0800 Subject: [Pw_forum] GIPAW potential for C and N Message-ID: Dear pwscf/gipaw users I'm trying to calculate the magnetic response of nitrogen vacancy in diamond. The PPs available at the GIPAW page "http://www-int.impmc.upmc.fr/~software/gipaw/index.html" are norn-conserving but I require ultrasoft PPs. I'm trying to generate US GIPAW potential myself but there is no GIPAW example under the "atomic_doc" library. Can anyone send me his/her GIPAW PP input (preferably of C and N, of course) so that I can generate it myself? Regards, Jones Wan From aschauer at princeton.edu Fri Nov 20 04:55:06 2009 From: aschauer at princeton.edu (Uli Aschauer) Date: Thu, 19 Nov 2009 22:55:06 -0500 Subject: [Pw_forum] how to set nr1b, nr2b, nr3b for cp.x when using ultrasoft pseudopotential In-Reply-To: <412f6c680911191926g4bd8e5a5xf41fb5c794e3c671@mail.gmail.com> References: <4B0422C2.80005@princeton.edu> <412f6c680911191926g4bd8e5a5xf41fb5c794e3c671@mail.gmail.com> Message-ID: <4B06131A.2030108@princeton.edu> Dear Vega, the dt2bye is not in the input file but you rather have to modify the CPV/cpr.f90 file and recompile cp.x. Locate the line "dt2bye = dt2 / emass" in the file and move it somewhere below "main_loop: DO" (i.e. after "CALL start_clock( 'total_time' )"). I reckon this is something that should be put in the CVS. As for the sequence towards running cp dynamics (reaching the electronic groundstate, relaxing the system, randomizing the positions to "insert some temperature" and finally run dynamics) may i suggest you to follow the following tutorial: http://www.quantum-espresso.org/user_guide/node24.html. I would not script the whole sequence with AUTOPILOT unless you know your system really well. Best regards, -uli _________________________________________________________ Uli Aschauer Princeton University Chemistry Department Frick Laboratory, Room 213 Princeton, NJ 08544 Tel: +1-609-258-0116 Email: aschauer at princeton.edu _________________________________________________________ vega lew wrote: > Dear Uli and all the friends in the forum, > > thank you very much for your reply. > could you please tell me how to move the calculation dt2bye inside the > main loop? > I just lean from the autopilot example in the package of QE 4.0.3 > version. In that example, > the dt2bye is at the very beginning of the input file. Should I follow > that way? > > Following you last suggestion, I engage more steps to make the system > to coverge, and keep > more attention on the total energy of the system. > But this time when I add thermostat to the system, the temparature > never goes up? > could you please tell me why the thermostat never take effect? > my input files is listed as follows, > > &CONTROL > > title = 'CPMD' > , > calculation = 'cp' > , > restart_mode = 'from_scratch' > , > outdir = '/disk5/nanjing/vega/cpmd/' , > wfcdir = '/tmp/' > , > pseudo_dir = > '/home/software/nanjing/vega/espresso-4.0.1/pseudo/' , > prefix = 'cp_molecular' , > nstep = 99999 , > dt = 3, > iprint = > 50, > / > > &SYSTEM > > ibrav = > 8, > celldm(1) =24.8624, > celldm(2) = 0.8520, > celldm(3) = 1.6964, > nat = > 147, > ntyp = 3, > nr1b = 20, > nr2b = 20, > nr3b = 20, > nbnd = 630, > # my system has 1160 electrons and I add a few more empty bands to the > system. > ecutwfc = 30, > ecutrho = 300, > / > > > &ELECTRONS > mixing_mode ='local-TF', > electron_dynamics = 'damp', > / > > &IONS > > ion_dynamics = 'none', > ion_temperature = > 'not_controlled', > / > AUTOPILOT > on_step = 80 : ion_dynamics = 'damp' > on_step = 160 : ion_temperature = 'nose' > on_step = 160 : tempw =50 > on_step = 240 : tempw =100 > on_step = 540 : tempw =150 > on_step = 1000 : tempw =200 > on_step = 10000 : tempw =250 > ENDRULES > > ATOMIC_SPECIES > to output is as follows, > ............. > ............. > in while: event_index 4 > > ======================================== > EMPLOY RULES: > CURRENT_NFI= 540 > event_index= 4 > event_step== 540 > ======================================== > > RULE EVENT: tempw 150.000000000000 > in while after: event_index 5 > ............ > ............ > ATOMIC_VELOCITIES > O 0.470823E-05 0.561221E-06 0.356130E-05 > O -0.222964E-05 0.686844E-06 0.565589E-05 > O 0.245059E-07 0.368266E-05 -0.646064E-06 > O 0.340472E-06 -0.104069E-05 -0.267787E-05 > O -0.141504E-05 0.140458E-05 0.176310E-05 > O -0.138272E-05 -0.690043E-06 -0.113648E-05 > O 0.173462E-05 0.778397E-07 -0.304404E-05 > O -0.390145E-05 0.144215E-06 -0.145382E-05 > O 0.000000E+00 0.000000E+00 0.000000E+00 > O 0.000000E+00 0.000000E+00 0.000000E+00 > O 0.000000E+00 0.000000E+00 0.000000E+00 > O 0.000000E+00 0.000000E+00 0.000000E+00 > O 0.000000E+00 0.000000E+00 0.000000E+00 > O 0.000000E+00 0.000000E+00 0.000000E+00 > O 0.000000E+00 0.000000E+00 0.000000E+00 > O 0.000000E+00 0.000000E+00 0.000000E+00 > .......... > .......... > .......... > nfi ekinc temph tempp etot enthal econs > econt vnhh xnhh0 vnhp xnhp0 > 550 0.00000 0.0 0.0 -4369.56798 -4369.56798 -4369.56796 > -4369.56796 0.0000 0.0000 0.0000 0.0000 > and we found the velocities of atoms is zore. that is because some of > atoms is fixed in the system. > the velocities of atoms with is free to move is about in range of > 1E10-4~1E10-6. Do you think it is rether small? > > By the way, the initial geometry is from the optimized structure of > pw.x. This initial geometry is a local mimima > of the system, and coveged very well in the relax calculation of pw.x. > So this may be the trapped geometry. > Do you think this is the main cause of the system temparature never > goes up? > > thank you very much for reading. > any hints will be deeply appreciated > > best wishes, > > vega > > On Thu, Nov 19, 2009 at 12:37 AM, Uli Aschauer > wrote: > > Dear Vega, > > it seems that you're mixing pw.x input in your cp.x input. There is no > such such thing as mixing_beta and nosym in cp.x (check the manual). > Also your system is way too large to converge the wavefunction in 80 > steps, which is needed to get reasonable forces on the ions. There are > other I suggest you start from a cp.x example to understand how to > perform a sequence of cp.x runs. > > Also please not the changing the dt in AUTOPILOT does not work as the > dt2bye variable is calculated outside the main loop in cpr.f90 and is > thus never updated upon AUTOPILOT events. You will have to move the > calculation of dt2bye inside to make it work. > > Best regards, > -uli > > _________________________________________________________ > Uli Aschauer > Princeton University > Chemistry Department > Frick Laboratory, Room 213 > Princeton, NJ 08544 > Tel: +1-609-258-0116 > Email: aschauer at princeton.edu > _________________________________________________________ > > > > > Dear all, > > > > Sorry for last arbitrary question. I found there was a code > called cppp.x. > > > > But now I encounter another serious problem with the information > from > > pp.x of "ortho went bananas", when I try to add nose thermostat > to the > > system at 150th step. > > > > the process as follows, > > First, I get the optimized geometry from the pw.x. Then I use that > > geometry as the initial input to pp.x. > > During the first 19 of cp calculation, I did a few electronic steps > > with ions fixed and dt=1 > > From 20th step to 79th step, I enlarge the dt to 3; > > From 80th step to 149th step, I allow the ions to move and set dt to > > 5, with no thermostat. > > When I tried to add nose thermostat, the "econt" of the system > became > > to NaN and the vnhp became to Inf. > > And then the program crashed with the information that "ortho went > > bananas" > > > > here is a part of my input files, > > &CONTROL > > > > title = 'CPMD' > > , > > calculation = 'cp' > > , > > restart_mode = 'from_scratch' > > , > > outdir = '/tmp/' , > > wfcdir = '/tmp/' > > , > > pseudo_dir = '/home/vega/espresso-4.0/pseudo/' , > > prefix = 'cp_dissociation1' , > > nstep = 99999 , > > dt = > > 1, > > / > > > > &SYSTEM > > > > ibrav = > > 8, > > celldm(1) =24.8624, > > celldm(2) = 0.8520, > > celldm(3) = 1.6964, > > nat = > > 147, > > ntyp = 3, > > nr1b = 20, > > nr2b = 20, > > nr3b = > > 20, > > nosym = .true. > > , > > ecutwfc = 30, > > ecutrho = 300, > > / > > > > > > &ELECTRONS > > mixing_mode ='local-TF', > > mixing_beta = 0.4, > > electron_dynamics = 'damp', > > / > > > > &IONS > > > > ion_dynamics = 'none', > > ion_temperature = > > 'not_controlled', > > / > > AUTOPILOT > > on_step = 20 : dt=3 > > on_step = 20 : electron_dynamics = 'damp' > > on_step = 80 : dt=5 > > on_step = 80 : ion_dynamics = 'damp' > > on_step = 150 : ion_temperature = 'nose' > > ENDRULES > > > > ATOMIC_SPECIES > > > > ...... > > ...... > > ...... > > > > could you please do me a favor to tell me what is going wrong. > > > > best wishes, > > > > vega > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > ================================================================================== > Vega Lew ( weijia liu) > Graduate student > 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 > From ismotochi at gmail.com Fri Nov 20 05:29:31 2009 From: ismotochi at gmail.com (isaac motochi) Date: Fri, 20 Nov 2009 07:29:31 +0300 Subject: [Pw_forum] surface band structure and dos In-Reply-To: <9d6ea92e0907290027q28bd9c75w4a828c47234d4df9@mail.gmail.com> References: <9d6ea92e0907262324x7374a0b3o4579c84803a589fb@mail.gmail.com> <21fbc4790907262333u777c7e16hf7f0c5f004850879@mail.gmail.com> <9d6ea92e0907290027q28bd9c75w4a828c47234d4df9@mail.gmail.com> Message-ID: <9d6ea92e0911192029r216eb88by1315bd295cf806ab@mail.gmail.com> > > > > Hi forum users. I would wish to calculate projected density of states for >> diamond surface adsorbed with some elements. Can anyone help me with an >> input script to run pdos. >> > > Motochi > Moi Unversity-Kenya > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091120/9da8d3b3/attachment.htm From mtt_turion at hotmail.com Fri Nov 20 06:28:02 2009 From: mtt_turion at hotmail.com (mtt physics) Date: Fri, 20 Nov 2009 12:28:02 +0700 Subject: [Pw_forum] The piezoelectric calculated from First-principles In-Reply-To: References: Message-ID: Dear Lorenzo Paulatto and all I want to calculated piezoelectric constant from when atom displaced in the perfect tetragonal it shown polarization calculate with Berry phase method. The piezoelectric calculated from First-principles. Are there the code for calculate piezoelectric in QE regard Abdulmutta Thatribud > From: pw_forum-request at pwscf.org > Subject: Pw_forum Digest, Vol 29, Issue 53 > To: pw_forum at pwscf.org > Date: Fri, 20 Nov 2009 04:26:22 +0100 > > 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: ee potential (Nicholas E. Singh-Miller) > 2. Re: GIPAW, write tensor field, xsf (Davide Ceresoli) > 3. Re: GIPAW, write tensor field, xsf (Goranka Bilalbegovic) > 4. Re: how to set nr1b, nr2b, nr3b for cp.x when using > ultrasoft pseudopotential (vega lew) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 19 Nov 2009 15:52:27 -0500 (EST) > From: "Nicholas E. Singh-Miller" > Subject: Re: [Pw_forum] ee potential > To: PWSCF Forum > Message-ID: > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > Hi Ali, > > > vloc1.dat > > vloc2.dat > > It looks like these are the realspace ionic potentials used to calculate > the correction. Thus, 1 and 2 would be the two atom types in your > system. They are printed radially where the first column is r, the second > is the psedo-potential, and the thrid is a gaussian approximation of the > pseudo potential. As far as I can tell, these were just printed for > testing and verifying. You probably will not have much use for them. > > > vcorrz.dat > > > > My version (older) does not print this, but again it was probably for > testing and is likely the corrective potential averaged to the z axis. > > hope that helps, > > Nick > > > ***************************************** > Nicholas E. Singh-Miller > Prof. Marzari Group (quasiamore.mit.edu) > Materials Science and Engineering > Massachusetts Institute of Technology > 13-4066 > (617)324-0372 > ***************************************** > > > ------------------------------ > > Message: 2 > Date: Thu, 19 Nov 2009 15:59:30 -0500 > From: Davide Ceresoli > Subject: Re: [Pw_forum] GIPAW, write tensor field, xsf > To: PWSCF Forum > Message-ID: <4B05B1B2.80901 at mit.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Goranka Bilalbegovic wrote: > > > > Hello, > > > > I have tested two systems: my example of a cluster and the GIPAW CH4 > > molecule example. > > > > The error is: > > --- > > ERROR: while executing exec > > .../bin/gengeom 0 1 11 1 1 1 1 > > XC_gengeom.1684 > > /home/.../xcrys_tmp/xc_1684/FigFillcurr.xsf_UP_X.xsf.raw > The problem could be that xcrysden cannot handle such an > amount of "atoms". In fact, on my machine, gengeom crashed > with a "segmentation violation" error. > > > Davide > > > > ------------------------------ > > Message: 3 > Date: Fri, 20 Nov 2009 00:07:29 +0100 > From: Goranka Bilalbegovic > Subject: Re: [Pw_forum] GIPAW, write tensor field, xsf > To: PWSCF Forum > Message-ID: > <7332fead0911191507g48a17f5fhdc0cea4bd739a22e at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > On Thu, Nov 19, 2009 at 9:59 PM, Davide Ceresoli wrote: > > > > > The problem could be that xcrysden cannot handle such an > > amount of "atoms". In fact, on my machine, gengeom crashed > > with a "segmentation violation" error. > > > > > I have looked at Tone's examples and found one vector_field.xsf. It is for > N_2H_4CO and some arrows, but *.xsf is: > ------ > ATOMS > 6 0.0000000000 0.0000000000 0.0000000000 > 8 0.0000000000 0.0000000000 1.2614009982 > 7 0.0000000000 1.1482466623 -0.6997899990 > 7 0.0000000000 -1.1482466623 -0.6997899990 > 1 0.0000000000 2.0265496485 -0.2028169999 > 1 0.0000000000 -2.0265496485 -0.2028169999 > 1 0.0000000000 1.1340804828 -1.7049749982 > 1 0.0000000000 -1.1340804828 -1.7049749982 > X 2.000 0.000 2.000 0.010 0.000 0.000 > X 1.902 0.618 2.000 0.010 0.003 0.000 > ... > ------ > > I edited FigFillcurr.xsf_UP_X.xsf for the GIPAW CH4 example, deleted first 7 > lines and put "ATOMS" as the first line. Now my XCrySDen opens this file, > but it looks funny and definitely it takes a lot of memory. I am not able to > rotate it on my home PC Cygwin. Tone's example is "is merely an "artistic" > example". I wanted to get something similar to figures in Chapter 4 of > Jonathan Yates's thesis. My cluster has 18 atoms. Will try tomorrow to > decrease size of arrows, or something similar. > > Best regards, > Goranka Bilalbegovic > Department of Physics, > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091120/4595bae4/attachment-0001.htm > > ------------------------------ > > Message: 4 > Date: Fri, 20 Nov 2009 11:26:10 +0800 > From: vega lew > Subject: Re: [Pw_forum] how to set nr1b, nr2b, nr3b for cp.x when > using ultrasoft pseudopotential > To: PWSCF Forum > Message-ID: > <412f6c680911191926g4bd8e5a5xf41fb5c794e3c671 at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Uli and all the friends in the forum, > > thank you very much for your reply. > could you please tell me how to move the calculation dt2bye inside the main > loop? > I just lean from the autopilot example in the package of QE 4.0.3 version. > In that example, > the dt2bye is at the very beginning of the input file. Should I follow that > way? > > Following you last suggestion, I engage more steps to make the system to > coverge, and keep > more attention on the total energy of the system. > But this time when I add thermostat to the system, the temparature never > goes up? > could you please tell me why the thermostat never take effect? > my input files is listed as follows, > > &CONTROL > > title = 'CPMD' > , > calculation = 'cp' > , > restart_mode = 'from_scratch' > , > outdir = '/disk5/nanjing/vega/cpmd/' , > wfcdir = '/tmp/' > , > pseudo_dir = > '/home/software/nanjing/vega/espresso-4.0.1/pseudo/' , > prefix = 'cp_molecular' , > nstep = 99999 , > dt = 3, > iprint = > 50, > / > > &SYSTEM > > ibrav = > 8, > celldm(1) =24.8624, > celldm(2) = 0.8520, > celldm(3) = 1.6964, > nat = > 147, > ntyp = 3, > nr1b = 20, > nr2b = 20, > nr3b = 20, > nbnd = 630, > # my system has 1160 electrons and I add a few more empty bands to the > system. > ecutwfc = 30, > ecutrho = 300, > / > > > &ELECTRONS > mixing_mode ='local-TF', > electron_dynamics = 'damp', > / > > &IONS > > ion_dynamics = 'none', > ion_temperature = > 'not_controlled', > / > AUTOPILOT > on_step = 80 : ion_dynamics = 'damp' > on_step = 160 : ion_temperature = 'nose' > on_step = 160 : tempw =50 > on_step = 240 : tempw =100 > on_step = 540 : tempw =150 > on_step = 1000 : tempw =200 > on_step = 10000 : tempw =250 > ENDRULES > > ATOMIC_SPECIES > to output is as follows, > ............. > ............. > in while: event_index 4 > > ======================================== > EMPLOY RULES: > CURRENT_NFI= 540 > event_index= 4 > event_step== 540 > ======================================== > > RULE EVENT: tempw 150.000000000000 > in while after: event_index 5 > ............ > ............ > ATOMIC_VELOCITIES > O 0.470823E-05 0.561221E-06 0.356130E-05 > O -0.222964E-05 0.686844E-06 0.565589E-05 > O 0.245059E-07 0.368266E-05 -0.646064E-06 > O 0.340472E-06 -0.104069E-05 -0.267787E-05 > O -0.141504E-05 0.140458E-05 0.176310E-05 > O -0.138272E-05 -0.690043E-06 -0.113648E-05 > O 0.173462E-05 0.778397E-07 -0.304404E-05 > O -0.390145E-05 0.144215E-06 -0.145382E-05 > O 0.000000E+00 0.000000E+00 0.000000E+00 > O 0.000000E+00 0.000000E+00 0.000000E+00 > O 0.000000E+00 0.000000E+00 0.000000E+00 > O 0.000000E+00 0.000000E+00 0.000000E+00 > O 0.000000E+00 0.000000E+00 0.000000E+00 > O 0.000000E+00 0.000000E+00 0.000000E+00 > O 0.000000E+00 0.000000E+00 0.000000E+00 > O 0.000000E+00 0.000000E+00 0.000000E+00 > .......... > .......... > .......... > nfi ekinc temph tempp etot enthal econs > econt vnhh xnhh0 vnhp xnhp0 > 550 0.00000 0.0 0.0 -4369.56798 -4369.56798 -4369.56796 > -4369.56796 0.0000 0.0000 0.0000 0.0000 > and we found the velocities of atoms is zore. that is because some of atoms > is fixed in the system. > the velocities of atoms with is free to move is about in range of > 1E10-4~1E10-6. Do you think it is rether small? > > By the way, the initial geometry is from the optimized structure of > pw.x. This initial geometry is a local mimima > of the system, and coveged very well in the relax calculation of pw.x. So > this may be the trapped geometry. > Do you think this is the main cause of the system temparature never goes up? > > thank you very much for reading. > any hints will be deeply appreciated > > best wishes, > > vega > > On Thu, Nov 19, 2009 at 12:37 AM, Uli Aschauer wrote: > > > Dear Vega, > > > > it seems that you're mixing pw.x input in your cp.x input. There is no > > such such thing as mixing_beta and nosym in cp.x (check the manual). > > Also your system is way too large to converge the wavefunction in 80 > > steps, which is needed to get reasonable forces on the ions. There are > > other I suggest you start from a cp.x example to understand how to > > perform a sequence of cp.x runs. > > > > Also please not the changing the dt in AUTOPILOT does not work as the > > dt2bye variable is calculated outside the main loop in cpr.f90 and is > > thus never updated upon AUTOPILOT events. You will have to move the > > calculation of dt2bye inside to make it work. > > > > Best regards, > > -uli > > > > _________________________________________________________ > > Uli Aschauer > > Princeton University > > Chemistry Department > > Frick Laboratory, Room 213 > > Princeton, NJ 08544 > > Tel: +1-609-258-0116 > > Email: aschauer at princeton.edu > > _________________________________________________________ > > > > > > > > Dear all, > > > > > > Sorry for last arbitrary question. I found there was a code called > > cppp.x. > > > > > > But now I encounter another serious problem with the information from > > > pp.x of "ortho went bananas", when I try to add nose thermostat to the > > > system at 150th step. > > > > > > the process as follows, > > > First, I get the optimized geometry from the pw.x. Then I use that > > > geometry as the initial input to pp.x. > > > During the first 19 of cp calculation, I did a few electronic steps > > > with ions fixed and dt=1 > > > From 20th step to 79th step, I enlarge the dt to 3; > > > From 80th step to 149th step, I allow the ions to move and set dt to > > > 5, with no thermostat. > > > When I tried to add nose thermostat, the "econt" of the system became > > > to NaN and the vnhp became to Inf. > > > And then the program crashed with the information that "ortho went > > > bananas" > > > > > > here is a part of my input files, > > > &CONTROL > > > > > > title = 'CPMD' > > > , > > > calculation = 'cp' > > > , > > > restart_mode = 'from_scratch' > > > , > > > outdir = '/tmp/' , > > > wfcdir = '/tmp/' > > > , > > > pseudo_dir = '/home/vega/espresso-4.0/pseudo/' , > > > prefix = 'cp_dissociation1' , > > > nstep = 99999 , > > > dt = > > > 1, > > > / > > > > > > &SYSTEM > > > > > > ibrav = > > > 8, > > > celldm(1) =24.8624, > > > celldm(2) = 0.8520, > > > celldm(3) = 1.6964, > > > nat = > > > 147, > > > ntyp = 3, > > > nr1b = 20, > > > nr2b = 20, > > > nr3b = > > > 20, > > > nosym = .true. > > > , > > > ecutwfc = 30, > > > ecutrho = 300, > > > / > > > > > > > > > &ELECTRONS > > > mixing_mode ='local-TF', > > > mixing_beta = 0.4, > > > electron_dynamics = 'damp', > > > / > > > > > > &IONS > > > > > > ion_dynamics = 'none', > > > ion_temperature = > > > 'not_controlled', > > > / > > > AUTOPILOT > > > on_step = 20 : dt=3 > > > on_step = 20 : electron_dynamics = 'damp' > > > on_step = 80 : dt=5 > > > on_step = 80 : ion_dynamics = 'damp' > > > on_step = 150 : ion_temperature = 'nose' > > > ENDRULES > > > > > > ATOMIC_SPECIES > > > > > > ...... > > > ...... > > > ...... > > > > > > could you please do me a favor to tell me what is going wrong. > > > > > > best wishes, > > > > > > vega > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > ================================================================================== > Vega Lew ( weijia liu) > Graduate student > 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/20091120/cc665c86/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 29, Issue 53 > **************************************** _________________________________________________________________ Windows 7 ????: ????????????????????????????????????? ????????????????????????? http://windows.microsoft.com/shop -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091120/a910cfba/attachment-0001.htm From tone.kokalj at ijs.si Fri Nov 20 07:44:17 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 20 Nov 2009 07:44:17 +0100 Subject: [Pw_forum] GIPAW, write tensor field, xsf In-Reply-To: <4B05B1B2.80901@mit.edu> References: <7332fead0911182217l608f3651v86e565873cc8df6d@mail.gmail.com> <4B05B1B2.80901@mit.edu> Message-ID: <1258699457.13342.9.camel@walk.ijs.si> On Thu, 2009-11-19 at 15:59 -0500, Davide Ceresoli wrote: > Goranka Bilalbegovic wrote: > > > > Hello, > > > > I have tested two systems: my example of a cluster and the GIPAW CH4 > > molecule example. > > > > The error is: > > --- > > ERROR: while executing exec > > .../bin/gengeom 0 1 11 1 1 1 1 > > XC_gengeom.1684 > > /home/.../xcrys_tmp/xc_1684/FigFillcurr.xsf_UP_X.xsf.raw > The problem could be that xcrysden cannot handle such an > amount of "atoms". In fact, on my machine, gengeom crashed > with a "segmentation violation" error. This is precisely the case! Due to some awkward reasons parts of xcrysden are written in plain fortran-77, and therein the current limits for the number of atoms in the unit cell are 50000 and the total number of atoms of 200000 !!! Goranka, this is the reason why it crashed when you loaded "crystal" XSF and not for the "molecular" XSF. It is very easy to fix this problem. You need to recompile the fortran part of xcrysden, that is located in the F/ subdirectory. Since it is a plain fortran-77 the compilation is very straightforward. Make sure to increase the maximum number of atoms in file F/param.inc (variable "nac"). It is also true that 100.000 field arrows (& dummy atoms X) is a huge number of objects. Make sure you open a file on a powerful computer with good graphics card, or else xcrysden's behavior will be stalled-like. 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 gregor.mali at ki.si Fri Nov 20 08:02:41 2009 From: gregor.mali at ki.si (Gregor Mali) Date: Fri, 20 Nov 2009 08:02:41 +0100 Subject: [Pw_forum] GIPAW potential for C and N In-Reply-To: References: Message-ID: <8C0B47760A05FB4AB504C9BCAD32D256016CB894@postar.ki.si> Dear Jones, as far as I know, GIPAW module within Quantum Espresso currently works only with norm-conserving pseudopotentials. Best regards. Gregor Mali National Institute of Chemistry Ljubljana > -----Original Message----- > From: pw_forum-bounces at pwscf.org > [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Jones Tsz-Kai Wan > Sent: 20. november 2009 4:35 > To: PWSCF Forum > Subject: [Pw_forum] GIPAW potential for C and N > > Dear pwscf/gipaw users > > I'm trying to calculate the magnetic response of nitrogen > vacancy in diamond. The PPs available at the GIPAW page > "http://www-int.impmc.upmc.fr/~software/gipaw/index.html" are > norn-conserving but I require ultrasoft PPs. I'm trying to > generate US GIPAW potential myself but there is no GIPAW > example under the "atomic_doc" library. Can anyone send me > his/her GIPAW PP input (preferably of C and N, of course) so > that I can generate it myself? > > Regards, > > Jones Wan > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From sclauzer at sissa.it Fri Nov 20 08:48:27 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 20 Nov 2009 08:48:27 +0100 Subject: [Pw_forum] surface band structure and dos In-Reply-To: <9d6ea92e0911192029r216eb88by1315bd295cf806ab@mail.gmail.com> References: <9d6ea92e0907262324x7374a0b3o4579c84803a589fb@mail.gmail.com> <21fbc4790907262333u777c7e16hf7f0c5f004850879@mail.gmail.com> <9d6ea92e0907290027q28bd9c75w4a828c47234d4df9@mail.gmail.com> <9d6ea92e0911192029r216eb88by1315bd295cf806ab@mail.gmail.com> Message-ID: <4B0649CB.7060506@sissa.it> Dear Isaac, isaac motochi wrote: > > > Hi forum users. I would wish to calculate projected density of > states for diamond surface adsorbed with some elements. Can > anyone help me with an input script to run pdos. I think that running example08 and examining its input files will make clear to you how to do it. Also reading Doc/INPUT_PROJWFC.txt will help you. Regards GS > > > Motochi > Moi Unversity-Kenya > > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 xomiakk at gmail.com Fri Nov 20 09:17:48 2009 From: xomiakk at gmail.com (Olga Sedelnikova) Date: Fri, 20 Nov 2009 14:17:48 +0600 Subject: [Pw_forum] Mulliken charges Message-ID: Dear all! How can I get the Mulliken charges using PWcsf code? Thank you -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091120/775a2a71/attachment.htm From nkxirainbow at gmail.com Fri Nov 20 09:25:57 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Fri, 20 Nov 2009 16:25:57 +0800 Subject: [Pw_forum] Mulliken charges In-Reply-To: References: Message-ID: <21fbc4790911200025o7d01b585k2efaa1e8113e8ea3@mail.gmail.com> I hope this can help you?? [Pw_forum] Mulliken population http://www.democritos.it/pipermail/pw_forum/2008-January/008148.html PS: Please always sign your mails with your name and affiliation. Thanks On Fri, Nov 20, 2009 at 4:17 PM, Olga Sedelnikova wrote: > Dear all! > How can I get the Mulliken charges using PWcsf code? > > Thank you > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091120/aa92c9a0/attachment.htm From giannozz at democritos.it Fri Nov 20 09:48:33 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 20 Nov 2009 09:48:33 +0100 Subject: [Pw_forum] Mulliken charges In-Reply-To: References: Message-ID: <0C2FD24A-F413-4BA9-B2F4-3D9069C62FC8@democritos.it> On Nov 20, 2009, at 9:17 , Olga Sedelnikova wrote: > How can I get the Mulliken charges using PWcsf code? you have to adapt the code "projwfc.f90". Presently it calculates Lowdin charges. See the many messages in the mailing list about this subject, in particular this one: http://www.democritos.it/pipermail/pw_forum/2008-January/008142.html P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From jwan at phy.cuhk.edu.hk Fri Nov 20 10:10:58 2009 From: jwan at phy.cuhk.edu.hk (Jones Tsz-Kai Wan) Date: Fri, 20 Nov 2009 17:10:58 +0800 Subject: [Pw_forum] GIPAW potential for C and N In-Reply-To: <8C0B47760A05FB4AB504C9BCAD32D256016CB894@postar.ki.si> References: <8C0B47760A05FB4AB504C9BCAD32D256016CB894@postar.ki.si> Message-ID: Dear Ljubljana, Thanks. Then I guess I have to use different sets of PPs to perform structural relaxation (use US PAW PPs) and magnetic response calculation (use NG GIPAW PP). Regards, Jones On Fri, Nov 20, 2009 at 3:02 PM, Gregor Mali wrote: > Dear Jones, > > as far as I know, GIPAW module within Quantum Espresso currently works > only with norm-conserving pseudopotentials. > > Best regards. > > Gregor Mali > > National Institute of Chemistry > Ljubljana > > >> -----Original Message----- >> From: pw_forum-bounces at pwscf.org >> [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Jones Tsz-Kai Wan >> Sent: 20. november 2009 4:35 >> To: PWSCF Forum >> Subject: [Pw_forum] GIPAW potential for C and N >> >> Dear pwscf/gipaw users >> >> I'm trying to calculate the magnetic response of nitrogen >> vacancy in diamond. The PPs available at the GIPAW page >> "http://www-int.impmc.upmc.fr/~software/gipaw/index.html" are >> norn-conserving but I require ultrasoft PPs. I'm trying to >> generate US GIPAW potential myself but there is no GIPAW >> example under the "atomic_doc" library. Can anyone send me >> his/her GIPAW PP input (preferably of C and N, of course) so >> that I can generate it myself? >> >> Regards, >> >> Jones Wan >> _______________________________________________ >> 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 Ari.P.Seitsonen at iki.fi Fri Nov 20 10:16:07 2009 From: Ari.P.Seitsonen at iki.fi (Ari P Seitsonen) Date: Fri, 20 Nov 2009 10:16:07 +0100 (CET) Subject: [Pw_forum] GIPAW potential for C and N In-Reply-To: <8C0B47760A05FB4AB504C9BCAD32D256016CB894@postar.ki.si> References: <8C0B47760A05FB4AB504C9BCAD32D256016CB894@postar.ki.si> Message-ID: Dear Gregor and Jones Wan, This is indeed the case: Currently the GIPAW code is implemented only for norm-conserving pseudo potentials. The extension to ultra-soft/Vanderbilt pp's is planned but not yet performed. Greetings, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Physikalisch-Chemisches Institut der Universitaet Zuerich Tel: +41 44 63 54 497 / Mobile: +41 79 71 90 935 On Fri, 20 Nov 2009, Gregor Mali wrote: > Dear Jones, > > as far as I know, GIPAW module within Quantum Espresso currently works > only with norm-conserving pseudopotentials. > > Best regards. > > Gregor Mali > > National Institute of Chemistry > Ljubljana > > >> -----Original Message----- >> From: pw_forum-bounces at pwscf.org >> [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Jones Tsz-Kai Wan >> Sent: 20. november 2009 4:35 >> To: PWSCF Forum >> Subject: [Pw_forum] GIPAW potential for C and N >> >> Dear pwscf/gipaw users >> >> I'm trying to calculate the magnetic response of nitrogen >> vacancy in diamond. The PPs available at the GIPAW page >> "http://www-int.impmc.upmc.fr/~software/gipaw/index.html" are >> norn-conserving but I require ultrasoft PPs. I'm trying to >> generate US GIPAW potential myself but there is no GIPAW >> example under the "atomic_doc" library. Can anyone send me >> his/her GIPAW PP input (preferably of C and N, of course) so >> that I can generate it myself? >> >> Regards, >> >> Jones Wan >> _______________________________________________ >> 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 kazempoor2000 at yahoo.com Fri Nov 20 11:18:24 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Fri, 20 Nov 2009 02:18:24 -0800 (PST) Subject: [Pw_forum] Ti GIPAW Message-ID: <772222.65526.qm@web112515.mail.gq1.yahoo.com> Hi All Does anyone has GIPAW pseudopotential for Titanium? thanks a lot Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091120/8fc71de2/attachment.htm From paulatto at sissa.it Fri Nov 20 12:38:30 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 20 Nov 2009 12:38:30 +0100 Subject: [Pw_forum] piezoelectric tensor in Pb(ZrxTi1-x)O3 In-Reply-To: References: Message-ID: Replying to message "Re: [Pw_forum] piezoelectric tensor in Pb(ZrxTi1-x)O3" from mtt physics (18/11/09): > I want to calculated piezoelectric constant from when atom displaced in > the perfect tetragonal it shown polarization calculate with Berry phase > method. The piezoelectric calculated from First-principles. Dear Abdulmutta, please have a look at example10. 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 quantumdft at gmail.com Fri Nov 20 14:51:52 2009 From: quantumdft at gmail.com (vega lew) Date: Fri, 20 Nov 2009 21:51:52 +0800 Subject: [Pw_forum] a question about cppp.x Message-ID: <412f6c680911200551x7eba31eamd624b7c7bdfe7589@mail.gmail.com> Dear all, thank you for all the help from the friends in the forum. I could perform calculations with cp.x but now I found something wrong with using cppp.x to extract useful information from the output of cp.x when I try to run cppp.x, the error warned like this, ######################################################################################################################## # FROM IOTK LIBRARY, VERSION 1.1.0development # UNRECOVERABLE ERROR (ierr=1) # ERROR IN: iotk_open_read (iotk_files.spp:487) # CVS Revision: 1.3 # unit file=/disk5/nanjing/vega/cpmd//cp_molecular_51.save/data-file.xml binary=F iostat=29 ######################################################################################################################## [cn151:17091] MPI_ABORT invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1 I think the code try to find /disk5/nanjing/vega/cpmd//cp_molecular_51.save folders. But I only have /disk5/nanjing/vega/cpmd//cp_molecular_50.save How could I deal with this? thank you for reading. many thanks best wishes, vega -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091120/21996b24/attachment.htm From paulatto at sissa.it Fri Nov 20 15:24:15 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 20 Nov 2009 15:24:15 +0100 Subject: [Pw_forum] a question about cppp.x In-Reply-To: <412f6c680911200551x7eba31eamd624b7c7bdfe7589@mail.gmail.com> References: <412f6c680911200551x7eba31eamd624b7c7bdfe7589@mail.gmail.com> Message-ID: Replying to message "[Pw_forum] a question about cppp.x" from vega lew (20/11/09): > I think the code try to find > /disk5/nanjing/vega/cpmd//cp_molecular_51.save > folders. But I only have /disk5/nanjing/vega/cpmd//cp_molecular_50.save > How could I deal with this? I don't know the detail of cp post-processing, but the input manual says: Variable: ndr Type: INTEGER Default: 51 Description: CP restart file number to post process 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 quantumdft at gmail.com Fri Nov 20 15:28:22 2009 From: quantumdft at gmail.com (vega lew) Date: Fri, 20 Nov 2009 22:28:22 +0800 Subject: [Pw_forum] a question about cppp.x In-Reply-To: References: <412f6c680911200551x7eba31eamd624b7c7bdfe7589@mail.gmail.com> Message-ID: <412f6c680911200628l758f3c44w4172331ab5950dfb@mail.gmail.com> Dear friend, thank you. I got it. Sorry for my careless and so hurry. best wishes, vega On Fri, Nov 20, 2009 at 10:24 PM, Lorenzo Paulatto wrote: > Replying to message "[Pw_forum] a question about cppp.x" from vega lew > (20/11/09): > > I think the code try to find > > /disk5/nanjing/vega/cpmd//cp_molecular_51.save > > folders. But I only have /disk5/nanjing/vega/cpmd//cp_molecular_50.save > > How could I deal with this? > > I don't know the detail of cp post-processing, but the input manual says: > > Variable: ndr > > Type: INTEGER > Default: 51 > Description: CP restart file number to post process > > 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 > -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091120/72ecb26d/attachment-0001.htm From jwan at phy.cuhk.edu.hk Fri Nov 20 17:06:35 2009 From: jwan at phy.cuhk.edu.hk (Jones Tsz-Kai Wan) Date: Sat, 21 Nov 2009 00:06:35 +0800 Subject: [Pw_forum] GIPAW potential for C and N In-Reply-To: References: <8C0B47760A05FB4AB504C9BCAD32D256016CB894@postar.ki.si> Message-ID: Dear Ari, Thanks for the information. Regarding this, I want to generate NC GIPAW potential myself, but I can't see any example/doc in the atomic_doc directory. Do you (all any user) know how I can generate GIPAW PP using the atomic code? Regards, Jones On Fri, Nov 20, 2009 at 5:16 PM, Ari P Seitsonen wrote: > > Dear Gregor and Jones Wan, > > ? This is indeed the case: Currently the GIPAW code is implemented only > for norm-conserving pseudo potentials. The extension to > ultra-soft/Vanderbilt pp's is planned but not yet performed. > > ? ? Greetings, > > ? ? ? ?apsi > > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- > ? Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ > ? Physikalisch-Chemisches Institut der Universitaet Zuerich > ? Tel: +41 44 63 54 497 ?/ ?Mobile: +41 79 71 90 935 > > On Fri, 20 Nov 2009, Gregor Mali wrote: > >> Dear Jones, >> >> as far as I know, GIPAW module within Quantum Espresso currently works >> only with norm-conserving pseudopotentials. >> >> Best regards. >> >> Gregor Mali >> >> National Institute of Chemistry >> Ljubljana >> >> >>> -----Original Message----- >>> From: pw_forum-bounces at pwscf.org >>> [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Jones Tsz-Kai Wan >>> Sent: 20. november 2009 4:35 >>> To: PWSCF Forum >>> Subject: [Pw_forum] GIPAW potential for C and N >>> >>> Dear pwscf/gipaw users >>> >>> I'm trying to calculate the magnetic response of nitrogen >>> vacancy in diamond. The PPs available at the GIPAW page >>> "http://www-int.impmc.upmc.fr/~software/gipaw/index.html" are >>> norn-conserving but I require ultrasoft PPs. I'm trying to >>> generate US GIPAW potential myself but there is no GIPAW >>> example under the "atomic_doc" library. Can anyone send me >>> his/her GIPAW PP input (preferably of C and N, of course) so >>> that I can generate it myself? >>> >>> Regards, >>> >>> Jones Wan >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From Ari.P.Seitsonen at iki.fi Fri Nov 20 17:09:28 2009 From: Ari.P.Seitsonen at iki.fi (Ari P Seitsonen) Date: Fri, 20 Nov 2009 17:09:28 +0100 (CET) Subject: [Pw_forum] GIPAW potential for C and N In-Reply-To: References: <8C0B47760A05FB4AB504C9BCAD32D256016CB894@postar.ki.si> Message-ID: Dear Jones et al, VERY short summary at the bottom of: http://www-int.impmc.upmc.fr/~software/gipaw/instructions.html Greetings from Zurich, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Physikalisch-Chemisches Institut der Universitaet Zuerich Tel: +41 44 63 54 497 / Mobile: +41 79 71 90 935 On Sat, 21 Nov 2009, Jones Tsz-Kai Wan wrote: > Dear Ari, > > Thanks for the information. Regarding this, I want to generate NC > GIPAW potential myself, but I can't see any example/doc in the > atomic_doc directory. Do you (all any user) know how I can generate > GIPAW PP using the atomic code? > > Regards, > > Jones > > > On Fri, Nov 20, 2009 at 5:16 PM, Ari P Seitsonen wrote: >> >> Dear Gregor and Jones Wan, >> >> ? This is indeed the case: Currently the GIPAW code is implemented only >> for norm-conserving pseudo potentials. The extension to >> ultra-soft/Vanderbilt pp's is planned but not yet performed. >> >> ? ? Greetings, >> >> ? ? ? ?apsi >> >> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- >> ? Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ >> ? Physikalisch-Chemisches Institut der Universitaet Zuerich >> ? Tel: +41 44 63 54 497 ?/ ?Mobile: +41 79 71 90 935 >> >> On Fri, 20 Nov 2009, Gregor Mali wrote: >> >>> Dear Jones, >>> >>> as far as I know, GIPAW module within Quantum Espresso currently works >>> only with norm-conserving pseudopotentials. >>> >>> Best regards. >>> >>> Gregor Mali >>> >>> National Institute of Chemistry >>> Ljubljana >>> >>> >>>> -----Original Message----- >>>> From: pw_forum-bounces at pwscf.org >>>> [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Jones Tsz-Kai Wan >>>> Sent: 20. november 2009 4:35 >>>> To: PWSCF Forum >>>> Subject: [Pw_forum] GIPAW potential for C and N >>>> >>>> Dear pwscf/gipaw users >>>> >>>> I'm trying to calculate the magnetic response of nitrogen >>>> vacancy in diamond. The PPs available at the GIPAW page >>>> "http://www-int.impmc.upmc.fr/~software/gipaw/index.html" are >>>> norn-conserving but I require ultrasoft PPs. I'm trying to >>>> generate US GIPAW potential myself but there is no GIPAW >>>> example under the "atomic_doc" library. Can anyone send me >>>> his/her GIPAW PP input (preferably of C and N, of course) so >>>> that I can generate it myself? >>>> >>>> Regards, >>>> >>>> Jones Wan >>>> _______________________________________________ >>>> Pw_forum mailing list >>>> Pw_forum at pwscf.org >>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > From baroni at sissa.it Fri Nov 20 17:13:31 2009 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 20 Nov 2009 17:13:31 +0100 Subject: [Pw_forum] a question about cppp.x In-Reply-To: <412f6c680911200628l758f3c44w4172331ab5950dfb@mail.gmail.com> References: <412f6c680911200551x7eba31eamd624b7c7bdfe7589@mail.gmail.com> <412f6c680911200628l758f3c44w4172331ab5950dfb@mail.gmail.com> Message-ID: <68C2AC9A-68D8-4F18-B430-C0F33432C7C5@sissa.it> the response of this mailing list is notoriously excellent at times, too much so ;-) SB On Nov 20, 2009, at 3:28 PM, vega lew wrote: > Dear friend, > > thank you. I got it. > > Sorry for my careless and so hurry. > > best wishes, > > vega > > On Fri, Nov 20, 2009 at 10:24 PM, Lorenzo Paulatto > wrote: > Replying to message "[Pw_forum] a question about cppp.x" from vega lew > (20/11/09): > > I think the code try to find > > /disk5/nanjing/vega/cpmd//cp_molecular_51.save > > folders. But I only have /disk5/nanjing/vega/cpmd// > cp_molecular_50.save > > How could I deal with this? > > I don't know the detail of cp post-processing, but the input manual > says: > > Variable: ndr > > Type: INTEGER > Default: 51 > Description: CP restart file number to post process > > 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 > > > > -- > = > = > = > = > = > = > = > = > = > = > = > = > ====================================================================== > Vega Lew ( weijia liu) > Graduate student > 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 --- 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/20091120/5c7e9435/attachment.htm From giannozz at democritos.it Fri Nov 20 18:57:50 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 20 Nov 2009 18:57:50 +0100 Subject: [Pw_forum] a question about cppp.x In-Reply-To: <412f6c680911200628l758f3c44w4172331ab5950dfb@mail.gmail.com> References: <412f6c680911200551x7eba31eamd624b7c7bdfe7589@mail.gmail.com> <412f6c680911200628l758f3c44w4172331ab5950dfb@mail.gmail.com> Message-ID: On Nov 20, 2009, at 15:28 , vega lew wrote: > Sorry for my careless but not useless: the code should issue a more meaningful error message in this case P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From quantumdft at gmail.com Sat Nov 21 04:41:38 2009 From: quantumdft at gmail.com (vega lew) Date: Sat, 21 Nov 2009 11:41:38 +0800 Subject: [Pw_forum] a question about cppp.x In-Reply-To: References: <412f6c680911200551x7eba31eamd624b7c7bdfe7589@mail.gmail.com> <412f6c680911200628l758f3c44w4172331ab5950dfb@mail.gmail.com> Message-ID: <412f6c680911201941h67e96ce7yf64b77a5db081b93@mail.gmail.com> Dear sir, I got another question about cppp.x. when I want extract the trajectory from the cp.x, I find there is something wrong. here is my input file of cppp.inp, prefix = 'cp_molecular' , fileout = cppp.out outdir = '/disk5/nanjing/vega/cpmd/150/' ndr = 50, ldynamics = .true., when I use "ldynamics = .true.," to the input, the error was warning like this. "Error: dynamics requested, but only one frame" but there is some trajectories written by cp.x. from the dynamics process of 600 steps to 800 steps. (iprint = 100,isave= default, steps before 600 is used for reaching the GS and make random to the unfixed atoms and further reaching the GS and several steps for verlet dynamcis both electronic and ionic without temparature) could you tell me how to cope with this? thank you for your attention. best wishes, vega On Sat, Nov 21, 2009 at 1:57 AM, Paolo Giannozzi wrote: > > On Nov 20, 2009, at 15:28 , vega lew wrote: > > > Sorry for my careless > > but not useless: the code should issue a more meaningful > error message in this case > > P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091121/739e8e74/attachment-0001.htm From jwan at phy.cuhk.edu.hk Sat Nov 21 07:26:26 2009 From: jwan at phy.cuhk.edu.hk (Jones Tsz-Kai Wan) Date: Sat, 21 Nov 2009 14:26:26 +0800 Subject: [Pw_forum] calculations of hyperfine tensor Message-ID: Dear pwscf/gipaw users, Does anyone have experience on hyperfine tensor calculation using QE? I'm trying to calculate the hyperfine tensor in diamond defects, and I heard that the hyperfine tensor is given during gipaw calculation as a by-product. Regards, Jones Wan From Ari.P.Seitsonen at iki.fi Sat Nov 21 10:09:22 2009 From: Ari.P.Seitsonen at iki.fi (Ari P Seitsonen) Date: Sat, 21 Nov 2009 10:09:22 +0100 (CET) Subject: [Pw_forum] calculations of hyperfine tensor In-Reply-To: References: Message-ID: Dear Jones, Well, by-product in the sense that it is the hyperfine tensor is very cheap to calculate, but still you have to use the module GIPAW (gipaw.x) to get it. Greetings, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Physikalisch-Chemisches Institut der Universitaet Zuerich Tel: +41 44 63 54 497 / Mobile: +41 79 71 90 935 On Sat, 21 Nov 2009, Jones Tsz-Kai Wan wrote: > Dear pwscf/gipaw users, > > Does anyone have experience on hyperfine tensor calculation using QE? > I'm trying to calculate the hyperfine tensor in diamond defects, and I > heard that the hyperfine tensor is given during gipaw calculation as a > by-product. > > Regards, > > Jones Wan > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From wangqj1 at 126.com Sat Nov 21 12:56:17 2009 From: wangqj1 at 126.com (Q.J.Wang) Date: Sat, 21 Nov 2009 19:56:17 +0800 (CST) Subject: [Pw_forum] about pbs Message-ID: <23650494.129291258804577221.JavaMail.coremail@bj126app52.126.com> Dear all Sometimes when I use PBS to submit the task ,it turn up the error as following : :%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 3 from potinit : error # 1 starting and expected charges differ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% when I not use PBS ,it runs well ,I don't why .Anybody who encounter the same problem ? Any help will be appreciated . -- Best regards Q.J.Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091121/3563b182/attachment.htm From ceresoli at MIT.EDU Sat Nov 21 17:16:50 2009 From: ceresoli at MIT.EDU (Davide Ceresoli) Date: Sat, 21 Nov 2009 11:16:50 -0500 Subject: [Pw_forum] calculations of hyperfine tensor In-Reply-To: References: Message-ID: <4B081272.7040200@mit.edu> Jones Tsz-Kai Wan wrote: > Dear pwscf/gipaw users, > > Does anyone have experience on hyperfine tensor calculation using QE? > I'm trying to calculate the hyperfine tensor in diamond defects, and I > heard that the hyperfine tensor is given during gipaw calculation as a > by-product. > > Regards, > > Jones Wan A brief description of the input file, for hyperfine calculations, is given in this message: http://www.democritos.it/pipermail/pw_forum/2009-September/014475.html Best, Davide From gbilalbegovic at gmail.com Sat Nov 21 22:39:01 2009 From: gbilalbegovic at gmail.com (Goranka Bilalbegovic) Date: Sat, 21 Nov 2009 22:39:01 +0100 Subject: [Pw_forum] GIPAW, write tensor field, xsf Message-ID: <7332fead0911211339of1f243dkb00b758a48a6f19e@mail.gmail.com> Tone Kokalj wrote: > It is also true that 100.000 field arrows (& dummy atoms X) is a > huge number of objects. Make sure you open a file on a powerful computer > with good graphics card, or else xcrysden's behavior will be > stalled-like. 91132 ~ 100.000 field arrows is only for a small GIPAW CH_4 example where "README: In production calculation one would need: higher cutoff, larger supercells for molecules...". My 18 atoms cluster produces 13.824.000 dummy X atoms. Not only that I do not have a such powerful computer, but in general write_tensor_fields produces too many arrows, and too dense colored area on the screen. I also looked at these arrows with gOpenMol where exist: "flat formatted text file containing the vector information" and "Vectors are shown as a line drawing. This is the fastest display mode". Davide, what do you think about decreasing number of X atoms by writing in the subroutine xsf_vector_3d: do i1 = 1, nr1, scalef do i2 = 1, nr2, scalef do i3 = 1, nr3, scalef where scalef is (perhaps system dependent) scaling factor ? I tried for the CH4 example and with scalef=100 obtained 130 X atoms. Of course, *.xsf is small and easy to work with. Regards, Goranka --- Goranka Bilalbegovic Department of Physics, Faculty of Science University of Zagreb, Croatia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091121/a70cc3ee/attachment.htm From somesh.kb at gmail.com Sat Nov 21 22:48:15 2009 From: somesh.kb at gmail.com (Somesh Kumar Bhattacharya) Date: Sat, 21 Nov 2009 22:48:15 +0100 Subject: [Pw_forum] a question about cppp.x In-Reply-To: <412f6c680911201941h67e96ce7yf64b77a5db081b93@mail.gmail.com> References: <412f6c680911200551x7eba31eamd624b7c7bdfe7589@mail.gmail.com> <412f6c680911200628l758f3c44w4172331ab5950dfb@mail.gmail.com> <412f6c680911201941h67e96ce7yf64b77a5db081b93@mail.gmail.com> Message-ID: Hi Vega, One has to provide the number of frames in the input file. Please use : nframes = If you don't provide this, then by default it is 1. Also specify the atomic species. Kindly take a look at the INPUT_CPPP for details. Cheers, Somesh On Sat, Nov 21, 2009 at 4:41 AM, vega lew wrote: > Dear sir, > > I got another question about cppp.x. > > when I want extract the trajectory from the cp.x, I find there > is something wrong. > > here is my input file of cppp.inp, > prefix = 'cp_molecular' , > fileout = cppp.out > outdir = '/disk5/nanjing/vega/cpmd/150/' > ndr = 50, > ldynamics = .true., > > when I use "ldynamics = .true.," to the input, the error was warning like > this. > "Error: dynamics requested, but only one frame" > > but there is some trajectories written by cp.x. from the dynamics > process of 600 steps to 800 steps. (iprint = 100,isave= default, steps > before 600 is used for reaching the GS and make random to the unfixed atoms > and further reaching the GS and several steps for verlet dynamcis both > electronic and ionic without temparature) could you tell me how to cope with > this? > > thank you for your attention. > > best wishes, > > vega > On Sat, Nov 21, 2009 at 1:57 AM, Paolo Giannozzi wrote: > >> >> On Nov 20, 2009, at 15:28 , vega lew wrote: >> >> > Sorry for my careless >> >> but not useless: the code should issue a more meaningful >> error message in this case >> >> P. >> --- >> Paolo Giannozzi, Dept of Physics, University of Udine >> via delle Scienze 208, 33100 Udine, Italy >> Phone +39-0432-558216, fax +39-0432-558222 >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > > ================================================================================== > Vega Lew ( weijia liu) > Graduate student > 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 > > -- Somesh Kr. Bhattacharya Post Doctoral Fellow Room No. 263, Leonardo Building, The Abdus Salam International Centre for Theoretical Physics Strada Costiera, 11 I-34014 Trieste Italy Phone: +39-040-2240399 http://portal.ictp.it/cmsp/members/postdoctoral-fellows/somesh-kumar-bhattacharya/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091121/186c176f/attachment.htm From quantumdft at gmail.com Sun Nov 22 16:22:59 2009 From: quantumdft at gmail.com (vega lew) Date: Sun, 22 Nov 2009 07:22:59 -0800 Subject: [Pw_forum] a question about cppp.x In-Reply-To: References: <412f6c680911200551x7eba31eamd624b7c7bdfe7589@mail.gmail.com> <412f6c680911200628l758f3c44w4172331ab5950dfb@mail.gmail.com> <412f6c680911201941h67e96ce7yf64b77a5db081b93@mail.gmail.com> Message-ID: <412f6c680911220722i732f4ab4ya554c73d0ef36860@mail.gmail.com> Dear Somesh Kr. Bhattacharya, thank you for you help. with your help I could extract the trajectories. thank you so much. best, vega On Sat, Nov 21, 2009 at 1:48 PM, Somesh Kumar Bhattacharya < somesh.kb at gmail.com> wrote: > Hi Vega, > > One has to provide the number of frames in the input file. > Please use : > > nframes = > > If you don't provide this, then by default it is 1. > > Also specify the atomic species. Kindly take a look at the INPUT_CPPP for > details. > > Cheers, > > Somesh > > > > On Sat, Nov 21, 2009 at 4:41 AM, vega lew wrote: > >> Dear sir, >> >> I got another question about cppp.x. >> >> when I want extract the trajectory from the cp.x, I find there >> is something wrong. >> >> here is my input file of cppp.inp, >> prefix = 'cp_molecular' , >> fileout = cppp.out >> outdir = '/disk5/nanjing/vega/cpmd/150/' >> ndr = 50, >> ldynamics = .true., >> >> when I use "ldynamics = .true.," to the input, the error was warning like >> this. >> "Error: dynamics requested, but only one frame" >> >> but there is some trajectories written by cp.x. from the dynamics >> process of 600 steps to 800 steps. (iprint = 100,isave= default, steps >> before 600 is used for reaching the GS and make random to the unfixed atoms >> and further reaching the GS and several steps for verlet dynamcis both >> electronic and ionic without temparature) could you tell me how to cope with >> this? >> >> thank you for your attention. >> >> best wishes, >> >> vega >> On Sat, Nov 21, 2009 at 1:57 AM, Paolo Giannozzi < >> giannozz at democritos.it> wrote: >> >>> >>> On Nov 20, 2009, at 15:28 , vega lew wrote: >>> >>> > Sorry for my careless >>> >>> but not useless: the code should issue a more meaningful >>> error message in this case >>> >>> P. >>> --- >>> Paolo Giannozzi, Dept of Physics, University of Udine >>> via delle Scienze 208, 33100 Udine, Italy >>> Phone +39-0432-558216, fax +39-0432-558222 >>> >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >> >> >> >> -- >> >> ================================================================================== >> Vega Lew ( weijia liu) >> Graduate student >> 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 >> >> > > > -- > Somesh Kr. Bhattacharya > Post Doctoral Fellow > Room No. 263, > Leonardo Building, > The Abdus Salam International Centre for Theoretical Physics > Strada Costiera, 11 > I-34014 Trieste > Italy > Phone: +39-040-2240399 > > http://portal.ictp.it/cmsp/members/postdoctoral-fellows/somesh-kumar-bhattacharya/ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091122/7da78d92/attachment.htm From brad.malone at gmail.com Sun Nov 22 20:36:16 2009 From: brad.malone at gmail.com (Brad Malone) Date: Sun, 22 Nov 2009 11:36:16 -0800 Subject: [Pw_forum] Calculation of Raman tensor/intensity for material with indirect band overlap Message-ID: Hi, I'm interested in calculating the Raman intensity for a material with a small indirect band overlap within LDA (~0.3 eV). As has been mentioned many times on this forum, Raman intensities cannot be calculated for a pure metal. But should I expect to be able to calculate the intensity for a material with a small, indirect band overlap? When I attempted to do so (using lraman=.true. in the ph.x calculation) I received the following messages: Computing Pc [DH,Drho] |psi> > > Derivative coefficient: 0.001000 Threshold: 1.00E-12 > ik 1 ibnd 17 linter: root not converged 0.578E+08 > kpoint 1 ibnd 17 pcgreen: root not converged 0.763E+05 > ik 1 ibnd 17 linter: root not converged 0.193E+11 > kpoint 1 ibnd 17 pcgreen: root not converged 0.119E+05 > ik 1 ibnd 17 linter: root not converged 0.595E+09 > kpoint 1 ibnd 17 pcgreen: root not converged 0.182E+05 > ik 1 ibnd 17 linter: root not converged 0.142E+31 > kpoint 1 ibnd 17 pcgreen: root not converged 0.224E+24 > ik 1 ibnd 17 linter: root not converged 0.143E+30 > kpoint 1 ibnd 17 pcgreen: root not converged 0.170E+25 > ik 1 ibnd 17 linter: root not converged 0.765E+28 > kpoint 1 ibnd 17 pcgreen: root not converged 0.151E+25 > ik 1 ibnd 17 linter: root not converged 0.643E+09 > kpoint 1 ibnd 17 pcgreen: root not converged 0.460E+05 > ik 1 ibnd 17 linter: root not converged 0.619E+10 > kpoint 1 ibnd 17 pcgreen: root not converged 0.547E+07 > ik 1 ibnd 17 linter: root not converged 0.685E+09 > kpoint 1 ibnd 17 pcgreen: root not converged 0.810E+04 > ik 1 ibnd 17 linter: root not converged 0.290E+34 > kpoint 1 ibnd 17 pcgreen: root not converged 0.848E+19 > ik 1 ibnd 17 linter: root not converged 0.132E+33 > kpoint 1 ibnd 17 pcgreen: root not converged 0.333E+18 > ik 1 ibnd 17 linter: root not converged 0.155E+34 > kpoint 1 ibnd 17 pcgreen: root not converged 0.133E+20 > ik 1 ibnd 17 linter: root not converged 0.146E+06 > kpoint 1 ibnd 17 pcgreen: root not converged 0.442E+05 > ik 1 ibnd 17 linter: root not converged 0.135E+07 > kpoint 1 ibnd 17 pcgreen: root not converged 0.169E+06 > ik 1 ibnd 17 linter: root not converged 0.567E+08 > kpoint 1 ibnd 17 pcgreen: root not converged 0.493E+06 > ik 1 ibnd 17 linter: root not converged 0.292E+27 > kpoint 1 ibnd 17 pcgreen: root not converged 0.518E+23 > ik 1 ibnd 17 linter: root not converged 0.882E+28 > kpoint 1 ibnd 17 pcgreen: root not converged 0.215E+24 > ik 1 ibnd 17 linter: root not converged 0.104E+29 > kpoint 1 ibnd 17 pcgreen: root not converged 0.328E+23 > ik 2 ibnd 17 linter: root not converged 0.585E+21 > kpoint 2 ibnd 17 pcgreen: root not converged 0.363E+23 > ik 2 ibnd 17 linter: root not converged 0.505E+21 > kpoint 2 ibnd 17 pcgreen: root not converged 0.119E+22 > ik 2 ibnd 17 linter: root not converged 0.117E+21 > kpoint 2 ibnd 17 pcgreen: root not converged 0.267E+22 > ik 2 ibnd 17 linter: root not converged 0.159E+33 > kpoint 2 ibnd 17 pcgreen: root not converged 0.283E+27 > ik 2 ibnd 17 linter: root not converged 0.367E+32 > kpoint 2 ibnd 17 pcgreen: root not converged 0.660E+27 > ik 2 ibnd 17 linter: root not converged 0.876E+32 > kpoint 2 ibnd 17 pcgreen: root not converged 0.670E+28 > ik 2 ibnd 17 linter: root not converged 0.249E+32 > kpoint 2 ibnd 17 pcgreen: root not converged 0.125E+28 > ik 2 ibnd 17 linter: root not converged 0.348E+31 > kpoint 2 ibnd 17 pcgreen: root not converged 0.206E+26 > ik 2 ibnd 17 linter: root not converged 0.141E+30 > kpoint 2 ibnd 17 pcgreen: root not converged 0.561E+25 > ik 2 ibnd 17 linter: root not converged 0.520E+36 > kpoint 2 ibnd 17 pcgreen: root not converged 0.990E+24 > ik 2 ibnd 17 linter: root not converged 0.140E+37 > kpoint 2 ibnd 17 pcgreen: root not converged 0.721E+24 > ik 2 ibnd 17 linter: root not converged 0.836E+35 > kpoint 2 ibnd 17 pcgreen: root not converged 0.690E+25 > ik 2 ibnd 17 linter: root not converged 0.246E+30 > kpoint 2 ibnd 17 pcgreen: root not converged 0.540E+24 > ik 2 ibnd 17 linter: root not converged 0.517E+29 > kpoint 2 ibnd 17 pcgreen: root not converged 0.415E+25 > ik 2 ibnd 17 linter: root not converged 0.133E+30 > kpoint 2 ibnd 17 pcgreen: root not converged 0.202E+26 > ik 2 ibnd 17 linter: root not converged 0.570E+27 > kpoint 2 ibnd 17 pcgreen: root not converged 0.103E+21 > ik 2 ibnd 17 linter: root not converged 0.270E+29 > kpoint 2 ibnd 17 pcgreen: root not converged 0.451E+22 > ik 2 ibnd 17 linter: root not converged 0.381E+29 > kpoint 2 ibnd 17 pcgreen: root not converged 0.346E+22 > ik 3 ibnd 17 linter: root not converged 0.118E+34 > and so on for each ik in the calculation. The code never crashed and I stopped it prematurely due to concern about these messages (seeing values on the order of 1E+34 is never calming). The code was also taking a very long time to calculate each ik. From what I've read in the Lazzeri and Mauri paper (PRL 90, 036401, 2003) some of the methods used to calculate the Raman tensor can take a lot of linear response calculations and so maybe I shouldn't expect it to go extremely fast. However, this root convergence worries me. The 17th band, which is the only band that this problem occurs for that I've seen, is the first conduction band of the system and is the band that indirectly overlaps with the top of the valence band. Any help or comments would be greatly appreciated! Thanks, Brad Malone UC Berkeley P.S. I used 'fixed' occupancies in the SCF run to avoid the 'elec. field' error in the ph.x calculation. The fixed occupancy is what I would expect for this material in experiment, as the GW bandstructure for this material predicts it to be semiconducting. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091122/f8966fc2/attachment.htm From wangqj1 at 126.com Mon Nov 23 04:15:37 2009 From: wangqj1 at 126.com (Q.J.Wang) Date: Mon, 23 Nov 2009 11:15:37 +0800 (CST) Subject: [Pw_forum] relax with lelfield Message-ID: <15332264.175101258946137492.JavaMail.coremail@bj126app26.126.com> Dear pwscf developers I want to relax with lelfield ,but in the example31 it said that :"To perform a calculations with an electric field, an estimate of the optimized wavefunctions is needed to build the electric field operator." So I want to know whether I should optimize wavefunctions before relax with lelfield or not ? -- Best regards Q.J.Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091123/fc5af10e/attachment-0001.htm From quantumdft at gmail.com Mon Nov 23 08:16:34 2009 From: quantumdft at gmail.com (vega lew) Date: Sun, 22 Nov 2009 23:16:34 -0800 Subject: [Pw_forum] one more question about NEB and CP Message-ID: <412f6c680911222316t6dd98468l6d0dc6779432b1f8@mail.gmail.com> Dear all, I used to perform NEB calculations to estimate the energy barrier for certain chemical reaction. The calculated activation barrier is about 0.2 eV. I want the see the reaction process during some pico-second of CP calculations. Do you think the reaction could happen in such a short time? and what temperature is suitable for jumping over the saddle point? thank you for reading best wishes, vega -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091122/f869793a/attachment.htm From lfhuang at theory.issp.ac.cn Mon Nov 23 09:23:57 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Mon, 23 Nov 2009 16:23:57 +0800 Subject: [Pw_forum] =?utf-8?q?one_more_question_about_NEB_and_CP?= Message-ID: <20091123082357.29977.qmail@ms.hfcas.ac.cn> It seems my email is held by the email system of PW_FORUM due to the body of my email is too large, so I convert the picture in the attachement from eps form to pdf form. And now I send the same picture again. May it be OK this time. L.F.Huang ------ ====================================================================== L.F.Huang(???) ph.D candidate, DFT and phonon physics ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(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/20091123/e35984d3/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: reaction_rate.pdf Type: application/octet-stream Size: 40398 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091123/e35984d3/attachment-0001.obj From anvari_meh at physics.iust.ac.ir Mon Nov 23 09:35:57 2009 From: anvari_meh at physics.iust.ac.ir (Mehrnaz Anvari) Date: Mon, 23 Nov 2009 12:05:57 +0330 Subject: [Pw_forum] a2F.dos Message-ID: Hi When I run matdyn.x code to calculate a2F(w), I have 7 columns in output instead of 5 columns. these two columns present zero values. What is the reason of this happening? Mehrnaz Iran University of science & technology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091123/cf2b21b9/attachment.htm From lfhuang at theory.issp.ac.cn Mon Nov 23 09:30:18 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Mon, 23 Nov 2009 16:30:18 +0800 Subject: [Pw_forum] =?utf-8?q?one_more_question_about_NEB_and_CP?= Message-ID: <20091123083018.31469.qmail@ms.hfcas.ac.cn> (Because of the mistake I made due to not knowing the limitation of the size of the attachement, the previous emails are not complete. Now, the below one is complete.) Dear Vega Lew: From the reaction rate theory, you can estimate with the Arrhenius equation, with your activation energy value (0.2eV), I have made an estimation for you (please see the attachment). From my estimation, if you want to the reaction to occur within several pico-seconds, the temperature should be above about 1000 Kelvin (reaction time is proportional to the inverse of the reaction/jump frequency). (if the Zero point energy correction can not omitted, please add it in to the activation energy: E_ac=delta_E_p - E_ZPE). Best Wishes! Yours Sincerely L.F.Huang > > Message: 1 > Date: Sun, 22 Nov 2009 23:16:34 -0800 > From: vega lew > Subject: [Pw_forum] one more question about NEB and CP > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > > I used to perform NEB calculations to estimate the energy barrier for > certain chemical reaction. > The calculated activation barrier is about 0.2 eV. I want the see the > reaction process during some pico-second of CP calculations. > Do you think the reaction could happen in such a short time? and what > temperature is suitable for jumping over the saddle point? > > thank you for reading > > best wishes, > > vega > > -- > ================================================================================== > Vega Lew ( weijia liu) > Graduate student > 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 > ------ ====================================================================== L.F.Huang(???) ph.D candidate, DFT and phonon physics ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(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/20091123/10804ea4/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: reaction_rate.pdf Type: application/octet-stream Size: 40398 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091123/10804ea4/attachment-0001.obj From sclauzer at sissa.it Mon Nov 23 10:20:09 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 23 Nov 2009 10:20:09 +0100 Subject: [Pw_forum] about pbs In-Reply-To: <23650494.129291258804577221.JavaMail.coremail@bj126app52.126.com> References: <23650494.129291258804577221.JavaMail.coremail@bj126app52.126.com> Message-ID: <4B0A53C9.2070005@sissa.it> Dear Wang, Q.J.Wang wrote: > Dear all > Sometimes when I use PBS to submit the task ,it turn up the error > as following : > :%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > task # 3 > from potinit : error # 1 > starting and expected charges differ > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% This problem has been reported many times in this forum and in many different contexts. In the majority of cases it is due to a wrong input file. If you don't specify something more (for instance the input file...) it will be difficult to help you. First try a search about this problem on the forum archives or on google: "starting and expected charges differ" site:democritos.it > > when I not use PBS ,it runs well ,I don't why .Anybody who encounter the > same problem ? Does it mean that you find this problem only when running in parallel and not in serial mode? Which fft libraries are you linking your program to? regards, GS > Any help will be appreciated . > > -- > Best regards > > Q.J.Wang > > XiangTan University > > > ------------------------------------------------------------------------ > ?????????????????3D????????? > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 helen at fh.huji.ac.il Mon Nov 23 11:48:42 2009 From: helen at fh.huji.ac.il (Helen) Date: Mon, 23 Nov 2009 12:48:42 +0200 Subject: [Pw_forum] EXX in espresso4.1.1 Message-ID: <00d401ca6c2a$8b927d20$cd604084@fh.huji.ac.il> I've managed to install and compile espresso4.1.1 and it works with example01 but when I try to run EXX_example (I changed the make.sys file in exactly the same way as I did for version 3.2 which worked fine) it doesn't compile fortcom: Error: input.f90, line 240: Name in only-list does not exist. [X_GAMMA_EXTRAPOLATION] x_gamma_extrapolation, nqx1, nqx2, nqx3, & -------------------------------^ fortcom: Error: input.f90, line 240: Name in only-list does not exist. [NQX1] x_gamma_extrapolation, nqx1, nqx2, nqx3, & ------------------------------------------------------^ fortcom: Error: input.f90, line 240: Name in only-list does not exist. [NQX2] x_gamma_extrapolation, nqx1, nqx2, nqx3, & ------------------------------------------------------------^ fortcom: Error: input.f90, line 240: Name in only-list does not exist. [NQX3] x_gamma_extrapolation, nqx1, nqx2, nqx3, & ------------------------------------------------------------------^ fortcom: Severe: Too many errors, exiting compilation aborted for input.f90 (code 1) make[1]: *** [input.o] Error 1 make[1]: Leaving directory `/home2/helen/pwscf4.1_bnl/espresso-4.1.1/PW' make: *** [pw] Error 2 Is the EXX routine working in version 4.1.1 ? Thank you, Dr. Helen Eisenberg Hebrew University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091123/579982d9/attachment.htm From physik.shyam at gmail.com Mon Nov 23 12:29:57 2009 From: physik.shyam at gmail.com (Shyam Khambholja) Date: Mon, 23 Nov 2009 16:59:57 +0530 Subject: [Pw_forum] Contents of Pw_forum digest Message-ID: <9b382fa70911230329j736741fco3a46710956ff716b@mail.gmail.com> Dear Sir, I am a new user of pwscf. I need some general instructions regarding use of pwscf. I am trying to work out some simple examples given in the package. I want to understand the basic rule to work with pwscf. Please give me hints for this. thanks. -- Shyam G Khambholja Reseach student, Depratment of Physics, Sardar Patel University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091123/ebdb9c70/attachment.htm From giannozz at democritos.it Mon Nov 23 12:36:07 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 23 Nov 2009 12:36:07 +0100 Subject: [Pw_forum] EXX in espresso4.1.1 In-Reply-To: <00d401ca6c2a$8b927d20$cd604084@fh.huji.ac.il> References: <00d401ca6c2a$8b927d20$cd604084@fh.huji.ac.il> Message-ID: <4B0A73A7.4000708@democritos.it> Helen wrote: > Is the EXX routine working in version 4.1.1 ? it is. "make clean" first, or else: /bin/rm Modules/*.o PW/*.o Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From nkxirainbow at gmail.com Mon Nov 23 13:21:05 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Mon, 23 Nov 2009 12:21:05 +0000 Subject: [Pw_forum] Contents of Pw_forum digest In-Reply-To: <9b382fa70911230329j736741fco3a46710956ff716b@mail.gmail.com> References: <9b382fa70911230329j736741fco3a46710956ff716b@mail.gmail.com> Message-ID: <21fbc4790911230421xa56c7ebu9e685165df759775@mail.gmail.com> Dear Khambholja? The following website gives all the lecture of 2009 QE summer school. http://www.quantum-espresso.org/wiki/index.php/QESB09 The school cover basic concepts and recent advances and developments of QE. I hope it can help you?? On Mon, Nov 23, 2009 at 11:29 AM, Shyam Khambholja wrote: > Dear Sir, > I am a new user of pwscf. I need some general instructions regarding > use of pwscf. I am trying to work out some simple examples given in the > package. I want to understand the basic rule to work with pwscf. Please give > me hints for this. thanks. > > -- > Shyam G Khambholja > Reseach student, > Depratment of Physics, > Sardar Patel University > -- ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091123/7dc06a6a/attachment.htm From marzari at MIT.EDU Mon Nov 23 15:23:00 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Mon, 23 Nov 2009 09:23:00 -0500 Subject: [Pw_forum] one more question about NEB and CP In-Reply-To: <412f6c680911222316t6dd98468l6d0dc6779432b1f8@mail.gmail.com> References: <412f6c680911222316t6dd98468l6d0dc6779432b1f8@mail.gmail.com> Message-ID: <4B0A9AC4.9090803@mit.edu> vega lew wrote: > Dear all, > > I used to perform NEB calculations to estimate the energy barrier for > certain chemical reaction. > The calculated activation barrier is about 0.2 eV. I want the see the > reaction process during some pico-second of CP calculations. > Do you think the reaction could happen in such a short time? and what > temperature is suitable for jumping over the saddle point? > > thank you for reading > > best wishes, > > vega Hi Vega, try to work this out by yourself, looking at the arrhenius formula ; put an attempt rate comparable to say an optical phonon. But the answer is probably yes, especially if you are a bit over room temperature (500-600K). 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 kazempoor2000 at yahoo.com Mon Nov 23 15:45:45 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Mon, 23 Nov 2009 06:45:45 -0800 (PST) Subject: [Pw_forum] ee potential In-Reply-To: References: <79307.36495.qm@web112512.mail.gq1.yahoo.com> Message-ID: <357980.47370.qm@web112509.mail.gq1.yahoo.com> Daer Nick thanks a lot for reply. I want to correct my charged supercell to compare with makov-payne correction. but how can I set the parameter to detect more tiny range. I other word which set up lead to correct results? thanks a lot Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German ________________________________ From: Nicholas E. Singh-Miller To: PWSCF Forum Sent: Thu, November 19, 2009 9:52:27 PM Subject: Re: [Pw_forum] ee potential Hi Ali, > vloc1.dat > vloc2.dat It looks like these are the realspace ionic potentials used to calculate the correction. Thus, 1 and 2 would be the two atom types in your system. They are printed radially where the first column is r, the second is the psedo-potential, and the thrid is a gaussian approximation of the pseudo potential. As far as I can tell, these were just printed for testing and verifying. You probably will not have much use for them. > vcorrz.dat > My version (older) does not print this, but again it was probably for testing and is likely the corrective potential averaged to the z axis. hope that helps, Nick ***************************************** Nicholas E. Singh-Miller Prof. Marzari Group (quasiamore.mit.edu) Materials Science and Engineering Massachusetts Institute of Technology 13-4066 (617)324-0372 ***************************************** _______________________________________________ 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/20091123/0620b66b/attachment.htm From kazempoor2000 at yahoo.com Mon Nov 23 16:04:13 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Mon, 23 Nov 2009 07:04:13 -0800 (PST) Subject: [Pw_forum] average Message-ID: <901056.50680.qm@web112520.mail.gq1.yahoo.com> Hi ALL I am doing defect charged calculation and to compute the correct defect formation energy we need to also enter (delta-V) that is the difference between VBM in defect and perfect supercell. I calculte the average of potential in one unit cell of perfect , neutral and charged defect and saw that the microscopic average of potential in Z direction shift in these case smoothly . My question is how can I use such kind of observation in average of these potentials to correct the formation energy? thanks a lot Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091123/ea3b7982/attachment-0001.htm From jwan at phy.cuhk.edu.hk Mon Nov 23 17:58:58 2009 From: jwan at phy.cuhk.edu.hk (Jones Tsz-Kai Wan) Date: Tue, 24 Nov 2009 00:58:58 +0800 Subject: [Pw_forum] problem in nmr calculation Message-ID: Dear gipaw users, I encountered the following error during nmr calculation: ------------------------------------------------------------------------ Computing the magnetic susceptibility isolve=0 ethr=0.1000E-09 k-point # 1 of 26 pool # 1 k-point # 2 of 26 pool # 1 k-point # 3 of 26 pool # 1 k-point # 4 of 26 pool # 1 k-point # 5 of 26 pool # 1 k-point # 6 of 26 pool # 1 k-point # 7 of 26 pool # 1 k-point # 8 of 26 pool # 1 k-point # 9 of 26 pool # 1 k-point # 10 of 26 pool # 1 ATTENTION: ik= 10 ibnd= 20 eigenvalues differ too much! 19.9838 19.4785 ATTENTION: ik= 10 ibnd= 20 eigenvalues differ too much! 19.9838 19.4793 ATTENTION: ik= 10 ibnd= 20 eigenvalues differ too much! 19.9838 19.4793 ATTENTION: ik= 10 ibnd= 20 eigenvalues differ too much! 19.9838 19.4793 ATTENTION: ik= 10 ibnd= 20 eigenvalues differ too much! 19.9838 19.4793 ATTENTION: ik= 10 ibnd= 20 eigenvalues differ too much! 19.9838 19.4793 ATTENTION: ik= 10 ibnd= 20 eigenvalues differ too much! 19.9838 19.4793 ------------------------------------------------------------------------ What is the reason of this and how can I avoid this? -- Best regards, Jones ------------------------------------------- All work and no play makes Jones a dull boy From ceresoli at MIT.EDU Mon Nov 23 18:34:42 2009 From: ceresoli at MIT.EDU (Davide Ceresoli) Date: Mon, 23 Nov 2009 12:34:42 -0500 Subject: [Pw_forum] problem in nmr calculation In-Reply-To: References: Message-ID: <4B0AC7B2.7070501@mit.edu> Jones Tsz-Kai Wan wrote: > Dear gipaw users, > > I encountered the following error during nmr calculation: > > ------------------------------------------------------------------------ > Computing the magnetic susceptibility isolve=0 ethr=0.1000E-09 > k-point # 1 of 26 pool # 1 > k-point # 2 of 26 pool # 1 > k-point # 3 of 26 pool # 1 > k-point # 4 of 26 pool # 1 > k-point # 5 of 26 pool # 1 > k-point # 6 of 26 pool # 1 > k-point # 7 of 26 pool # 1 > k-point # 8 of 26 pool # 1 > k-point # 9 of 26 pool # 1 > k-point # 10 of 26 pool # 1 > ATTENTION: ik= 10 ibnd= 20 eigenvalues differ too much! > 19.9838 19.4785 > ATTENTION: ik= 10 ibnd= 20 eigenvalues differ too much! > 19.9838 19.4793 > ATTENTION: ik= 10 ibnd= 20 eigenvalues differ too much! > 19.9838 19.4793 > ATTENTION: ik= 10 ibnd= 20 eigenvalues differ too much! > 19.9838 19.4793 > ATTENTION: ik= 10 ibnd= 20 eigenvalues differ too much! > 19.9838 19.4793 > ATTENTION: ik= 10 ibnd= 20 eigenvalues differ too much! > 19.9838 19.4793 > ATTENTION: ik= 10 ibnd= 20 eigenvalues differ too much! > 19.9838 19.4793 > ------------------------------------------------------------------------ > > What is the reason of this and how can I avoid this? Dear Jones Tsz-Kai Wan, this is not really an error, it's more a warning. Most of the times, it signals a problem with the diagonalization at k+q. You can try to change the value of isolve (0 or 1) in the gipaw input. Sometimes, everything works out ok. In any event, do the results look reasonable to you? Davide From modaresi.mohsen at gmail.com Mon Nov 23 21:16:37 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Mon, 23 Nov 2009 23:16:37 +0300 Subject: [Pw_forum] Contents of Pw_forum digest In-Reply-To: <9b382fa70911230329j736741fco3a46710956ff716b@mail.gmail.com> References: <9b382fa70911230329j736741fco3a46710956ff716b@mail.gmail.com> Message-ID: Dear Khambholja There are some useful example which distributed with Q.esperesso, at first start with them. On Mon, Nov 23, 2009 at 2:29 PM, Shyam Khambholja wrote: > Dear Sir, > I am a new user of pwscf. I need some general instructions regarding > use of pwscf. I am trying to work out some simple examples given in the > package. I want to understand the basic rule to work with pwscf. Please give > me hints for this. thanks. > > -- > Shyam G Khambholja > Reseach student, > Depratment of Physics, > Sardar Patel 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/20091123/326f3bc1/attachment.htm From wangqj1 at 126.com Tue Nov 24 02:04:23 2009 From: wangqj1 at 126.com (Q.J.Wang) Date: Tue, 24 Nov 2009 09:04:23 +0800 (CST) Subject: [Pw_forum] about pbs (Gabriele Sclauzero) In-Reply-To: References: Message-ID: <24124660.678521259024663915.JavaMail.coremail@bj126app29.126.com> Dear Gabriele Thank you very much for your advice ,I have found the problem in forum archives ,but no problem as mine . You said that it is the problem of input file ,but when I use "mpirun -np 8 pw.xout 'instead of pbs to submit the job ,it runs well .This puzzled me . >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: about pbs (Gabriele Sclauzero) > 2. EXX in espresso4.1.1 (Helen) > 3. Contents of Pw_forum digest (Shyam Khambholja) > 4. Re: EXX in espresso4.1.1 (Paolo Giannozzi) > 5. Re: Contents of Pw_forum digest (xirainbow) > 6. Re: one more question about NEB and CP (Nicola Marzari) > 7. Re: ee potential (ali kazempour) > 8. average (ali kazempour) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Mon, 23 Nov 2009 10:20:09 +0100 >From: Gabriele Sclauzero >Subject: Re: [Pw_forum] about pbs >To: PWSCF Forum >Message-ID: <4B0A53C9.2070005 at sissa.it> >Content-Type: text/plain; charset=UTF-8; format=flowed > >Dear Wang, > >Q.J.Wang wrote: >> Dear all >> Sometimes when I use PBS to submit the task ,it turn up the error >> as following : >> :%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> task # 3 >> from potinit : error # 1 >> starting and expected charges differ >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > >This problem has been reported many times in this forum and in many different contexts. In >the majority of cases it is due to a wrong input file. If you don't specify something more >(for instance the input file...) it will be difficult to help you. First try a search >about this problem on the forum archives or on google: >"starting and expected charges differ" site:democritos.it > >> >> when I not use PBS ,it runs well ,I don't why .Anybody who encounter the >> same problem ? > >Does it mean that you find this problem only when running in parallel and not in serial >mode? Which fft libraries are you linking your program to? > >regards, > >GS > >> Any help will be appreciated . Best regards Q.J.Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091124/6e194f9a/attachment.htm From jwan at phy.cuhk.edu.hk Tue Nov 24 04:01:52 2009 From: jwan at phy.cuhk.edu.hk (Jones Tsz-Kai Wan) Date: Tue, 24 Nov 2009 11:01:52 +0800 Subject: [Pw_forum] problem in nmr calculation In-Reply-To: References: <20091123184225.pgf3n0mjmg4w0s8w@webmail.sissa.it> Message-ID: Dear Davide and Emine, The problem was fixed after I set q_gipaw to 0.05, but I have another error now, nmr calculation stopped and said: from grid_gather : error # 46592 f_out too small I guess it's because I'm using to less k-points, I'm increasing the k-points to see if that happen again. Regards, Jones On Tue, Nov 24, 2009 at 10:26 AM, Jones Tsz-Kai Wan wrote: > Dear Davide and Emine, > > The problem was fixed after I set q_gipaw to 0.05, but I have another > error now, nmr calculation stopped and said: > > ? ? from ?grid_gather ?: error # ? ? 46592 > ? ? ?f_out too small > > I guess it's because I'm using to less k-points, I'm increasing the > k-points to see if that happen again. > > Regards, > > Jones > > On Tue, Nov 24, 2009 at 1:42 AM, Emine Kucukbenli wrote: >> Dear John, >>> >>> ? ? ATTENTION: ik= ?10 ?ibnd= 20 ?eigenvalues differ too much! >>> ? ? ? ?19.9838 ? ? 19.4785 >>> What is the reason of this and how can I avoid this? >> >> Not an expert on the issue yet, but cheking the code what I see is that: >> eigenvalues at k and k+q differ more than 0.2eV (from compute_u_kq >> subroutine) This violates the small q approximations I suppose. Have you >> tried with a smaller q? >> emine kucukbenli, phd student, sissa, italy >> >> >> >> >> >> ---------------------------------------------------------------- >> ?SISSA Webmail https://webmail.sissa.it/ >> ?Powered by Horde http://www.horde.org/ From jwan at phy.cuhk.edu.hk Tue Nov 24 04:02:44 2009 From: jwan at phy.cuhk.edu.hk (Jones Tsz-Kai Wan) Date: Tue, 24 Nov 2009 11:02:44 +0800 Subject: [Pw_forum] problem in nmr calculation In-Reply-To: References: <20091123184225.pgf3n0mjmg4w0s8w@webmail.sissa.it> Message-ID: Typo -- I was using q_gipaw = 0.005 instead. -- Jones On Tue, Nov 24, 2009 at 11:01 AM, Jones Tsz-Kai Wan wrote: > Dear Davide and Emine, > > The problem was fixed after I set q_gipaw to 0.05, but I have another > error now, nmr calculation stopped and said: > > ? ?from ?grid_gather ?: error # ? ? 46592 > ? ? f_out too small > > I guess it's because I'm using to less k-points, I'm increasing the > k-points to see if that happen again. > > Regards, > > Jones > > On Tue, Nov 24, 2009 at 10:26 AM, Jones Tsz-Kai ?Wan > wrote: >> Dear Davide and Emine, >> >> The problem was fixed after I set q_gipaw to 0.05, but I have another >> error now, nmr calculation stopped and said: >> >> ? ? from ?grid_gather ?: error # ? ? 46592 >> ? ? ?f_out too small >> >> I guess it's because I'm using to less k-points, I'm increasing the >> k-points to see if that happen again. >> >> Regards, >> >> Jones >> >> On Tue, Nov 24, 2009 at 1:42 AM, Emine Kucukbenli wrote: >>> Dear John, >>>> >>>> ? ? ATTENTION: ik= ?10 ?ibnd= 20 ?eigenvalues differ too much! >>>> ? ? ? ?19.9838 ? ? 19.4785 >>>> What is the reason of this and how can I avoid this? >>> >>> Not an expert on the issue yet, but cheking the code what I see is that: >>> eigenvalues at k and k+q differ more than 0.2eV (from compute_u_kq >>> subroutine) This violates the small q approximations I suppose. Have you >>> tried with a smaller q? >>> emine kucukbenli, phd student, sissa, italy >>> >>> >>> >>> >>> >>> ---------------------------------------------------------------- >>> ?SISSA Webmail https://webmail.sissa.it/ >>> ?Powered by Horde http://www.horde.org/ From quantumdft at gmail.com Tue Nov 24 05:55:57 2009 From: quantumdft at gmail.com (vega lew) Date: Mon, 23 Nov 2009 20:55:57 -0800 Subject: [Pw_forum] one more question about NEB and CP In-Reply-To: <4B0A9AC4.9090803@mit.edu> References: <412f6c680911222316t6dd98468l6d0dc6779432b1f8@mail.gmail.com> <4B0A9AC4.9090803@mit.edu> Message-ID: <412f6c680911232055m647d68d6qe07e408ced21cd22@mail.gmail.com> Dear friends, thank you for all the help. I see arrhenius formula is suitable for my question. But I am wondering how to determine the attempt rate for specific system? Do you think 300K is suitable for the reaction with activation energy of 0.2 eV? And in my case, the product state is lower than reactant state for about 0.4 eV, i.e. if the reaction happens, there is 0.6 eV barrier for the product state to go back to the reactant state. Do you think the dynamical equilibria of the reaction could see in some ps simulation of pw.x? best wishes, vega On Mon, Nov 23, 2009 at 6:23 AM, Nicola Marzari wrote: > vega lew wrote: > > Dear all, > > > > I used to perform NEB calculations to estimate the energy barrier for > > certain chemical reaction. > > The calculated activation barrier is about 0.2 eV. I want the see the > > reaction process during some pico-second of CP calculations. > > Do you think the reaction could happen in such a short time? and what > > temperature is suitable for jumping over the saddle point? > > > > thank you for reading > > > > best wishes, > > > > vega > > > Hi Vega, > > try to work this out by yourself, looking at the arrhenius formula ; put an > attempt rate comparable to say an optical phonon. But the answer is > probably yes, > especially if you are a bit over room temperature (500-600K). > > 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 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091123/be7315ac/attachment.htm From yuminqian at gmail.com Tue Nov 24 06:05:38 2009 From: yuminqian at gmail.com (Y.M.Qian) Date: Tue, 24 Nov 2009 13:05:38 +0800 Subject: [Pw_forum] problems on spin polarized lowdin charges References: , <20091123184225.pgf3n0mjmg4w0s8w@webmail.sissa.it>, , Message-ID: <200911241305353599177@gmail.com> Dear PWSCF user Recently I am doing calculation to get the magnetic moment of each atom of a given crystal SrCrO3 . I follow the steps of previous mail about " Magnetic moment on each atom " . 1 SCF 2 nscf 3 projwfc and get the information from the output file Lowdin Charges: Atom # 1: total charge = 9.5544, s = 1.9621, p = 6.3724, d = 1.2199, spin up = 4.7911, s = 0.9832, p = 3.1883, d = 0.6196, spin down = 4.7633, s = 0.9789, p = 3.1841, d = 0.6003, polarization = 0.0277, s = 0.0043, p = 0.0042, d = 0.0192, Atom # 2: total charge = 13.4411, s = 2.1863, p = 6.8075, d = 4.4473, spin up = 7.6579, s = 1.0967, p = 3.4108, d = 3.1504, spin down = 5.7832, s = 1.0896, p = 3.3967, d = 1.2968, polarization = 1.8748, s = 0.0070, p = 0.0141, d = 1.8536, Atom # 3: total charge = 6.3147, s = 1.5461, p = 4.7686, d = 0.0000, spin up = 3.1680, s = 0.7732, p = 2.3948, d = 0.0000, spin down = 3.1466, s = 0.7729, p = 2.3738, d = 0.0000, polarization = 0.0214, s = 0.0003, p = 0.0210, d = 0.0000, Atom # 4: total charge = 6.3147, s = 1.5461, p = 4.7686, d = 0.0000, spin up = 3.1680, s = 0.7732, p = 2.3948, d = 0.0000, spin down = 3.1466, s = 0.7729, p = 2.3738, d = 0.0000, polarization = 0.0214, s = 0.0003, p = 0.0210, d = 0.0000, Atom # 5: total charge = 6.3147, s = 1.5461, p = 4.7686, d = 0.0000, spin up = 3.1680, s = 0.7732, p = 2.3948, d = 0.0000, spin down = 3.1466, s = 0.7729, p = 2.3738, d = 0.0000, polarization = 0.0214, s = 0.0003, p = 0.0210, d = 0.0000, Spilling Parameter: 0.0014 The second atom is transition metal Cr , large magnetic moment appears . But according to the chemical composition of the compound SrCrO3 , there should be two electrons that occupy the d orbitals . But here the results shows there are 4.4473 electrons that occupy d orbitals . 1 Why is so large number of electrons that occupy d orbitals ? Is there any one know how to explain this discrepancy ? I also read the tips from Frequently Asked Questions (FAQ) and the correspond reference Sanchez-Portal et al., Sol. State Commun. 95, 685 (1995). Though absolute number of charge that projected to the d orbitals lack clear physical meaning ,currently , but the absolute value of difference of spin-up and spin-down charge have clear physical meaning : magnetic moment . So if the charge on atoms can't be calcualted accurately 2 how to determine the magnetic moment accurately? your sincerely Yumin Qian -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091124/305f81ad/attachment.htm From charlary at 126.com Tue Nov 24 05:41:59 2009 From: charlary at 126.com (charlary) Date: Tue, 24 Nov 2009 12:41:59 +0800 (CST) Subject: [Pw_forum] one more question about NEB and CP In-Reply-To: <4B0A9AC4.9090803@mit.edu> References: <4B0A9AC4.9090803@mit.edu> <412f6c680911222316t6dd98468l6d0dc6779432b1f8@mail.gmail.com> Message-ID: <22843091.723481259037719210.JavaMail.coremail@bj126app93.126.com> Dear all, In vega's email below, he talk about the variable t(time). How should I put this variable into the equation or algorithm of NEB? and how should I calculate the image changing with time? Thank you for guidance. charlary Nicola?Marzari"?? >vega?lew?wrote: >>?Dear?all, >> >>?I?used?to?perform?NEB?calculations?to?estimate?the?energy?barrier?for? >>?certain?chemical?reaction. >>?The?calculated?activation?barrier?is?about?0.2?eV.?I?want?the?see?the? >>?reaction?process?during?some?pico-second?of?CP?calculations. >>?Do?you?think?the?reaction?could?happen?in?such?a?short?time???and?what? >>?temperature?is?suitable?for?jumping?over?the?saddle?point? >> >>?thank?you?for?reading >> >>?best?wishes, >> >>?vega > > >Hi?Vega, > >try?to?work?this?out?by?yourself,?looking?at?the?arrhenius?formula?;?put?an >attempt?rate?comparable?to?say?an?optical?phonon.?But?the?answer?is? >probably?yes, >especially?if?you?are?a?bit?over?room?temperature?(500-600K). > >????????????????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? > >_______________________________________________ >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/20091124/a9a59258/attachment-0001.htm From lfhuang at theory.issp.ac.cn Tue Nov 24 06:46:36 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Tue, 24 Nov 2009 13:46:36 +0800 Subject: [Pw_forum] =?utf-8?q?one_more_question_about_NEB_and_CP?= Message-ID: <20091124054636.25663.qmail@ms.hfcas.ac.cn> Dear vega lew: Harmonic Transition State Theory (hTST) can help you to calculate the attempt frequency which can be obtained if the vibrational frequencies of the reactant and saddle-point states are known. Reference: H.Eyring, J.Chem.Phys. 3,107 (1935) (Or you can call it "quantum mechanically modified TST"). Its classical limit is the Vineyard form: G.H.Vineyard, J.Phys.Chem.Solids 3,121 (1957) However, the calculation of phonons maybe time consuming, so empirical values for attempt frequency should be prefered if you just want to make an estimation. The usually used attempt frequency range from 1.0*10^12 to 5.0*10^12 (or the optical mode frequency as prof. N. Marzari said). This should yield quite reasonable results because the jump frequency is just linearly proportional to the attempt frequency, and the jump frequency is exponentially dependent on the activation energy and temperature. And from the Arrhenius formula, an reaction event should not happen within several pico-seconds under 1000 K with E_ac=0.6 eV, and T>800 K should be required for the reaction with 0.2 eV. In order to estimate, you need just plot the Arrhenius formula in Gnuplot or Origin: v=v_attemp*exp(-11594E_ac/T) with E_ac in eV unit. Best Wishes! Yours Sincerely L.F.Huang > From: vega lew > Subject: Re: [Pw_forum] one more question about NEB and CP > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear friends, > > thank you for all the help. > > I see arrhenius formula is suitable for my question. But I am wondering how > to determine the attempt rate for specific system? > > Do you think 300K is suitable for the reaction with activation energy of 0.2 > eV? > > And in my case, the product state is lower than reactant state for about 0.4 > eV, i.e. if the reaction happens, there is 0.6 eV barrier for > the product state to go back to the reactant state. Do you think the > dynamical equilibria of the reaction could see in some ps simulation > of pw.x? > > best wishes, > > vega > > On Mon, Nov 23, 2009 at 6:23 AM, Nicola Marzari wrote: > > > vega lew wrote: > > > Dear all, > > > > > > I used to perform NEB calculations to estimate the energy barrier for > > > certain chemical reaction. > > > The calculated activation barrier is about 0.2 eV. I want the see the > > > reaction process during some pico-second of CP calculations. > > > Do you think the reaction could happen in such a short time? and what > > > temperature is suitable for jumping over the saddle point? > > > > > > thank you for reading > > > > > > best wishes, > > > > > > vega > > > > > > Hi Vega, > > > > try to work this out by yourself, looking at the arrhenius formula ; put an > > attempt rate comparable to say an optical phonon. But the answer is > > probably yes, > > especially if you are a bit over room temperature (500-600K). > > > > 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 > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > ================================================================================== > Vega Lew ( weijia liu) > Graduate student > 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 > ------ ====================================================================== L.F.Huang(???) ph.D candidate, DFT and phonon physics ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(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/20091124/e61962fe/attachment.htm From giannozz at democritos.it Tue Nov 24 07:58:08 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 24 Nov 2009 07:58:08 +0100 Subject: [Pw_forum] about pbs (Gabriele Sclauzero) In-Reply-To: <24124660.678521259024663915.JavaMail.coremail@bj126app29.126.com> References: <24124660.678521259024663915.JavaMail.coremail@bj126app29.126.com> Message-ID: <9CF0CCC9-7FE9-42C3-8CC7-1982851EABAD@democritos.it> On Nov 24, 2009, at 2:04 , Q.J.Wang wrote: > when I use "mpirun -np 8 pw.xout 'instead > of pbs to submit the job ,it runs well batch queue environment differs from the environment for interactive execution. You are reading data from a different data file in the two cases. P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From sclauzer at sissa.it Tue Nov 24 09:12:20 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 24 Nov 2009 09:12:20 +0100 Subject: [Pw_forum] about pbs (Gabriele Sclauzero) In-Reply-To: <24124660.678521259024663915.JavaMail.coremail@bj126app29.126.com> References: <24124660.678521259024663915.JavaMail.coremail@bj126app29.126.com> Message-ID: <4B0B9564.1050209@sissa.it> Q.J.Wang wrote: > Dear Gabriele > Thank you very much for your advice ,I have found the problem in > forum archives ,but no problem as mine . > You said that it is the problem of input file ,but when I use > "mpirun -np 8 pw.xout 'instead of pbs to submit the job ,it runs > well .This puzzled me . > Sorry, I don't understand well what you are doing. When you speak of PBS I suppose that you run your job with mpirun as well, but using a batch scheduler which does not need human interaction (i.e. you submit a script to the queuing system of your cluster). So, if your job runs with mpirun in interactive mode and not in batch mode, it could be a problem in your batch environment setup: you have to check environment variables, libraries, disk access and space, etc. etc. and maybe contact your system administrators... 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 wangqj1 at 126.com Tue Nov 24 10:42:03 2009 From: wangqj1 at 126.com (Q.J.Wang) Date: Tue, 24 Nov 2009 17:42:03 +0800 (CST) Subject: [Pw_forum] about pbs In-Reply-To: References: Message-ID: <23429577.1103331259055723256.JavaMail.coremail@bj126app29.126.com> Dear Paolo Thank you very much ,but I still have some puzzled problem as following. >From: Paolo Giannozzi >Subject: Re: [Pw_forum] about pbs (Gabriele Sclauzero) >To: PWSCF Forum >Message-ID: <9CF0CCC9-7FE9-42C3-8CC7-1982851EABAD at democritos.it> >Content-Type: text/plain; charset=US-ASCII; format=flowed > > >On Nov 24, 2009, at 2:04 , Q.J.Wang wrote: > >> when I use "mpirun -np 8 pw.xout 'instead >> of pbs to submit the job ,it runs well > >batch queue environment differs from the environment >for interactive execution. You are reading data from a >different data file in the two cases. Yes,the former read from pbs date ,the latter read from the input file . But why the error will turm up use pbs ? How can I solve this problem ? Can you give me specific illustration about this ,I am not understand about this .Thank you very much ! Best regards ? Q.J.Wang ? XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091124/b3759b25/attachment.htm From giannozz at democritos.it Tue Nov 24 10:47:44 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 24 Nov 2009 10:47:44 +0100 Subject: [Pw_forum] about pbs In-Reply-To: <23429577.1103331259055723256.JavaMail.coremail@bj126app29.126.com> References: <23429577.1103331259055723256.JavaMail.coremail@bj126app29.126.com> Message-ID: <4B0BABC0.4080509@democritos.it> Q.J.Wang wrote: > How can I solve this problem ? exactly in the same way as all problems are solved: observe, experiment, think, make an hypothesis, verify...computer problems are infinitely simpler than physics problems -- Paolo Giannozzi, Democritos and University of Udine, Italy From lanhaiping at gmail.com Tue Nov 24 10:48:27 2009 From: lanhaiping at gmail.com (lan haiping) Date: Tue, 24 Nov 2009 17:48:27 +0800 Subject: [Pw_forum] about pbs In-Reply-To: <23429577.1103331259055723256.JavaMail.coremail@bj126app29.126.com> References: <23429577.1103331259055723256.JavaMail.coremail@bj126app29.126.com> Message-ID: Why not to get a userguide for a PBS ? Different environmental settings will give rise to different behaviors of your scripts. Best 2009/11/24 Q.J.Wang > Dear Paolo > Thank you very much ,but I still have some puzzled problem as > following. > > >From: Paolo Giannozzi > >Subject: Re: [Pw_forum] about pbs (Gabriele Sclauzero) > >To: PWSCF Forum > >Message-ID: <9CF0CCC9-7FE9-42C3-8CC7-1982851EABAD at democritos.it> > >Content-Type: text/plain; charset=US-ASCII; format=flowed > > > > > >On Nov 24, 2009, at 2:04 , Q.J.Wang wrote: > > > >> when I use "mpirun -np 8 pw.xout 'instead > >> of pbs to submit the job ,it runs well > > > >batch queue environment differs from the environment > >for interactive execution. You are reading data from a > >different data file in the two cases. > Yes,the former read from pbs date ,the latter read from the input file . > But why the error will turm up use pbs ? How can I solve this problem ? Can > you give me specific illustration about this ,I am not understand about this > .Thank you very much ! > > Best regards > > Q.J.Wang > > XiangTan University > > > > ------------------------------ > 09???3D?????????????????? > _______________________________________________ > 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/20091124/8fac9f84/attachment.htm From physik.shyam at gmail.com Tue Nov 24 12:10:50 2009 From: physik.shyam at gmail.com (Shyam Khambholja) Date: Tue, 24 Nov 2009 16:40:50 +0530 Subject: [Pw_forum] Thanks Message-ID: <9b382fa70911240310s65a1ed37j261cae8085899248@mail.gmail.com> Dear friends, Thank you all fro your help and suggestions. -- Shyam G Khambholja Reseach student, Depratment of Physics, Sardar Patel University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091124/53a32126/attachment.htm From wangqj1 at 126.com Tue Nov 24 15:47:35 2009 From: wangqj1 at 126.com (Q.J.Wang) Date: Tue, 24 Nov 2009 22:47:35 +0800 (CST) Subject: [Pw_forum] about relax in electric field Message-ID: <26724746.1247551259074055444.JavaMail.coremail@bj126app104.126.com> Dear all When I add external electric field to optimize the structure .It runs very very slower than not add the electric field , after 2 days ,the output file is still as following : iteration # 1 ecut= 30.00 Ry beta=0.20 Davidson diagonalization with overlap ethr = 1.00E-02, avg # of iterations = 4.4 PAY ATTENTION: EL FIELD AND OCCUPATIONS Expectation value of exp(iGx): (2.751012649613009E-016,-3.679346535033460E-017) 0.866025403784439 Electronic Dipole per cell (a.u.) -0.482785724081663 Ionic Dipole per cell (a.u.) 3794.73195575151 PAY ATTENTION: EL FIELD AND OCCUPATIONS My input file adhere here: &CONTROL calculation = 'relax' , restart_mode = 'from_scratch' , pseudo_dir = './' , prefix = 'ZnO' , nstep = 250 , tprnfor = .true. , lelfield = .true. , nberrycyc = 1 , gdir = 3 , / &SYSTEM ibrav = 14, celldm(1) = 18.6286, celldm(2) = 0.6666667, celldm(3) = 1.0733333, celldm(4) = 0, celldm(5) = 0, celldm(6) = -0.5, nat = 48, ntyp = 3, ecutwfc = 30 , ecutrho = 300 , nosym = .true. , occupations = 'smearing' , degauss = 0.008 , smearing = 'gaussian' , nspin = 2 , starting_magnetization(1) = 0.5, starting_magnetization(2) = 0.5, starting_magnetization(3) = 0.5, lda_plus_u = .false. , / &ELECTRONS conv_thr = 1.D-7 , mixing_mode = 'plain' , mixing_beta = 0.2 , startingwfc = 'random' , efield = 0 , / &IONS ion_dynamics = 'bfgs' , phase_space = 'full' , / ATOMIC_SPECIES O 15.00000 O.pbe-rrkjus.UPF Zn 65.00000 Zn.pbe-van.UPF Mn 54.94000 Mn.pbe-sp-van.UPF ATOMIC_POSITIONS angstrom Zn 0.000000000 1.875966909 0.000000000 1 1 1 O 0.000000000 1.875966909 1.991601344 1 1 1 .................................................... K_POINTS automatic 3 3 3 1 1 1 I don't know why after I add the electric field ,the speed of relax is so slow ? Any advice will be appreciated ! -- Best regards Q.J.Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091124/c751ca32/attachment-0001.htm From paulatto at sissa.it Tue Nov 24 16:26:13 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 24 Nov 2009 16:26:13 +0100 Subject: [Pw_forum] about relax in electric field In-Reply-To: <26724746.1247551259074055444.JavaMail.coremail@bj126app104.126.com> References: <26724746.1247551259074055444.JavaMail.coremail@bj126app104.126.com> Message-ID: Replying to message "[Pw_forum] about relax in electric field" from Q.J.Wang (24/11/09): > PAY ATTENTION: EL FIELD AND OCCUPATIONS Dear Q.J. Wang, this message is not very explicative, but it means that Berry-phase electric field is not really well defined with smearing and can cause problems. In particular, it is not defined for metals, or any system that have fractional band occupations. If you have a band gap and your smearing is much smaller than that, then dipfield may work, but if some fractional occupation arises, the system may never converge, or converge to some meaningless state. In practice, if your system has a band gap, albeit small, you should try to use fixed occupations. Otherwise, you cannot use dipfield. 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 johnsondr at ornl.gov Tue Nov 24 16:31:40 2009 From: johnsondr at ornl.gov (Johnson, D. Ray) Date: Tue, 24 Nov 2009 10:31:40 -0500 Subject: [Pw_forum] Pw_forum Digest, Vol 29, Issue 68 In-Reply-To: Message-ID: Lisa, I will likely be at USCAR on Dec 9. Regards, Ray On 11/24/09 10:19 AM, "pw_forum-request at pwscf.org" wrote: Send Pw_forum mailing list submissions to pw_forum at pwscf.org To subscribe or unsubscribe via the World Wide Web, visit http://www.democritos.it/mailman/listinfo/pw_forum or, via email, send a message with subject or body 'help' to pw_forum-request at pwscf.org You can reach the person managing the list at pw_forum-owner at pwscf.org When replying, please edit your Subject line so it is more specific than "Re: Contents of Pw_forum digest..." Today's Topics: 1. Re: about pbs (Gabriele Sclauzero) (Gabriele Sclauzero) 2. Re: about pbs (Q.J.Wang) 3. Re: about pbs (Paolo Giannozzi) 4. Re: about pbs (lan haiping) 5. Thanks (Shyam Khambholja) 6. about relax in electric field (Q.J.Wang) ---------------------------------------------------------------------- Message: 1 Date: Tue, 24 Nov 2009 09:12:20 +0100 From: Gabriele Sclauzero Subject: Re: [Pw_forum] about pbs (Gabriele Sclauzero) To: PWSCF Forum Message-ID: <4B0B9564.1050209 at sissa.it> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Q.J.Wang wrote: > Dear Gabriele > Thank you very much for your advice ,I have found the problem in > forum archives ,but no problem as mine . > You said that it is the problem of input file ,but when I use > "mpirun -np 8 pw.xout 'instead of pbs to submit the job ,it runs > well .This puzzled me . > Sorry, I don't understand well what you are doing. When you speak of PBS I suppose that you run your job with mpirun as well, but using a batch scheduler which does not need human interaction (i.e. you submit a script to the queuing system of your cluster). So, if your job runs with mpirun in interactive mode and not in batch mode, it could be a problem in your batch environment setup: you have to check environment variables, libraries, disk access and space, etc. etc. and maybe contact your system administrators... 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 ------------------------------ Message: 2 Date: Tue, 24 Nov 2009 17:42:03 +0800 (CST) From: "Q.J.Wang" Subject: Re: [Pw_forum] about pbs To: pw_forum Message-ID: <23429577.1103331259055723256.JavaMail.coremail at bj126app29.126.com> Content-Type: text/plain; charset="gbk" Dear Paolo Thank you very much ,but I still have some puzzled problem as following. >From: Paolo Giannozzi >Subject: Re: [Pw_forum] about pbs (Gabriele Sclauzero) >To: PWSCF Forum >Message-ID: <9CF0CCC9-7FE9-42C3-8CC7-1982851EABAD at democritos.it> >Content-Type: text/plain; charset=US-ASCII; format=flowed > > >On Nov 24, 2009, at 2:04 , Q.J.Wang wrote: > >> when I use "mpirun -np 8 pw.xout 'instead >> of pbs to submit the job ,it runs well > >batch queue environment differs from the environment >for interactive execution. You are reading data from a >different data file in the two cases. Yes,the former read from pbs date ,the latter read from the input file . But why the error will turm up use pbs ? How can I solve this problem ? Can you give me specific illustration about this ,I am not understand about this .Thank you very much ! Best regards ? Q.J.Wang ? XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091124/b3759b25/attachment-0001.htm ------------------------------ Message: 3 Date: Tue, 24 Nov 2009 10:47:44 +0100 From: Paolo Giannozzi Subject: Re: [Pw_forum] about pbs To: PWSCF Forum Message-ID: <4B0BABC0.4080509 at democritos.it> Content-Type: text/plain; charset=x-gbk; format=flowed Q.J.Wang wrote: > How can I solve this problem ? exactly in the same way as all problems are solved: observe, experiment, think, make an hypothesis, verify...computer problems are infinitely simpler than physics problems -- Paolo Giannozzi, Democritos and University of Udine, Italy ------------------------------ Message: 4 Date: Tue, 24 Nov 2009 17:48:27 +0800 From: lan haiping Subject: Re: [Pw_forum] about pbs To: PWSCF Forum Message-ID: Content-Type: text/plain; charset="gb2312" Why not to get a userguide for a PBS ? Different environmental settings will give rise to different behaviors of your scripts. Best 2009/11/24 Q.J.Wang > Dear Paolo > Thank you very much ,but I still have some puzzled problem as > following. > > >From: Paolo Giannozzi > >Subject: Re: [Pw_forum] about pbs (Gabriele Sclauzero) > >To: PWSCF Forum > >Message-ID: <9CF0CCC9-7FE9-42C3-8CC7-1982851EABAD at democritos.it> > >Content-Type: text/plain; charset=US-ASCII; format=flowed > > > > > >On Nov 24, 2009, at 2:04 , Q.J.Wang wrote: > > > >> when I use "mpirun -np 8 pw.xout 'instead > >> of pbs to submit the job ,it runs well > > > >batch queue environment differs from the environment > >for interactive execution. You are reading data from a > >different data file in the two cases. > Yes,the former read from pbs date ,the latter read from the input file . > But why the error will turm up use pbs ? How can I solve this problem ? Can > you give me specific illustration about this ,I am not understand about this > .Thank you very much ! > > Best regards > > Q.J.Wang > > XiangTan University > > > > ------------------------------ > 09???3D?????????????????? > _______________________________________________ > 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/20091124/8fac9f84/attachment-0001.htm ------------------------------ Message: 5 Date: Tue, 24 Nov 2009 16:40:50 +0530 From: Shyam Khambholja Subject: [Pw_forum] Thanks To: pw_forum at pwscf.org Message-ID: <9b382fa70911240310s65a1ed37j261cae8085899248 at mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Dear friends, Thank you all fro your help and suggestions. -- Shyam G Khambholja Reseach student, Depratment of Physics, Sardar Patel University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091124/53a32126/attachment-0001.htm ------------------------------ Message: 6 Date: Tue, 24 Nov 2009 22:47:35 +0800 (CST) From: "Q.J.Wang" Subject: [Pw_forum] about relax in electric field To: pw_forum Message-ID: <26724746.1247551259074055444.JavaMail.coremail at bj126app104.126.com> Content-Type: text/plain; charset="gbk" Dear all When I add external electric field to optimize the structure .It runs very very slower than not add the electric field , after 2 days ,the output file is still as following : iteration # 1 ecut= 30.00 Ry beta=0.20 Davidson diagonalization with overlap ethr = 1.00E-02, avg # of iterations = 4.4 PAY ATTENTION: EL FIELD AND OCCUPATIONS Expectation value of exp(iGx): (2.751012649613009E-016,-3.679346535033460E-017) 0.866025403784439 Electronic Dipole per cell (a.u.) -0.482785724081663 Ionic Dipole per cell (a.u.) 3794.73195575151 PAY ATTENTION: EL FIELD AND OCCUPATIONS My input file adhere here: &CONTROL calculation = 'relax' , restart_mode = 'from_scratch' , pseudo_dir = './' , prefix = 'ZnO' , nstep = 250 , tprnfor = .true. , lelfield = .true. , nberrycyc = 1 , gdir = 3 , / &SYSTEM ibrav = 14, celldm(1) = 18.6286, celldm(2) = 0.6666667, celldm(3) = 1.0733333, celldm(4) = 0, celldm(5) = 0, celldm(6) = -0.5, nat = 48, ntyp = 3, ecutwfc = 30 , ecutrho = 300 , nosym = .true. , occupations = 'smearing' , degauss = 0.008 , smearing = 'gaussian' , nspin = 2 , starting_magnetization(1) = 0.5, starting_magnetization(2) = 0.5, starting_magnetization(3) = 0.5, lda_plus_u = .false. , / &ELECTRONS conv_thr = 1.D-7 , mixing_mode = 'plain' , mixing_beta = 0.2 , startingwfc = 'random' , efield = 0 , / &IONS ion_dynamics = 'bfgs' , phase_space = 'full' , / ATOMIC_SPECIES O 15.00000 O.pbe-rrkjus.UPF Zn 65.00000 Zn.pbe-van.UPF Mn 54.94000 Mn.pbe-sp-van.UPF ATOMIC_POSITIONS angstrom Zn 0.000000000 1.875966909 0.000000000 1 1 1 O 0.000000000 1.875966909 1.991601344 1 1 1 .................................................... K_POINTS automatic 3 3 3 1 1 1 I don't know why after I add the electric field ,the speed of relax is so slow ? Any advice will be appreciated ! -- Best regards Q.J.Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091124/c751ca32/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 29, Issue 68 **************************************** From dimpy.sharma at tyndall.ie Tue Nov 24 18:39:39 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Tue, 24 Nov 2009 17:39:39 -0000 Subject: [Pw_forum] Calculation of projected density of states for individual atoms in chain Message-ID: Hi Quantum espresso users, I have calculated projected density of states (PDOS) for my system which contains 2 silicon atoms and 4 hydrogen atoms. Now I would like to calculate the PDOS for my individual atoms (i,e for Si1 , Si2 ) . I would like to know for calculating the PDOS for individual atom, which atomic coordinate shall I need to give in my input file , as I cannot give atomic coordinate for only one atom of Silicon ( as that would mean PDOS for single Silicon), what is the correct way of approaching ? Thanks a million Dimpy UCC Ireland -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091124/033345c5/attachment.htm From paulatto at sissa.it Tue Nov 24 18:48:42 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 24 Nov 2009 18:48:42 +0100 Subject: [Pw_forum] Calculation of projected density of states for individual atoms in chain In-Reply-To: References: Message-ID: Replying to message "[Pw_forum] Calculation of projected density of states for individual atoms in chain" from Dimpy Sharma (24/11/09): > I would like to know for calculating the PDOS for individual atom Dear Dimpy, pdos always computes the projected density of states for each individual atom. In the directory where you have executed projwfc.x you will have a bunch of file with names like this: prefix.pdos_atm#4(Pd)_wfc#3(p) This file does include projection on the 3rd wavefunction (which is of type p) belonging to the 4th atom (of type Pd). Inside the file itself you can find several columns that belong to the p_z, p_x and p_y orbitals and the total. It is all explained in Doc/INPUT_PROJWFC.txt, together with many more details. 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 jhouska at kfy.zcu.cz Tue Nov 24 20:04:28 2009 From: jhouska at kfy.zcu.cz (Jiri Houska) Date: Tue, 24 Nov 2009 20:04:28 +0100 Subject: [Pw_forum] cp.x code Message-ID: <20091124200428.9ipx2zys00ws0wsc@webmail.zcu.cz> Hello, please I am quite confused about the cp.x code which I an going to use: (I) is there a difference between (1) scf calculation using cp.x and (3) scf calculation using pw.x ? (II) is there a difference between (1) scf calculation using cp.x and (2) cp calculation using cp.x with electron_dynamics = (say) 'sd' and ion_dynamics = 'none' ? (III) how critical is the "ion_radius" choice ... e.g. is it clever to make it equal to (known) covalent radius? Thanks a lot, Jiri Houska University of West Bohemia From giannozz at democritos.it Tue Nov 24 21:37:53 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 24 Nov 2009 21:37:53 +0100 Subject: [Pw_forum] cp.x code In-Reply-To: <20091124200428.9ipx2zys00ws0wsc@webmail.zcu.cz> References: <20091124200428.9ipx2zys00ws0wsc@webmail.zcu.cz> Message-ID: <48987221-D34A-4B3C-95CB-D79ED30AC32A@democritos.it> On Nov 24, 2009, at 20:04 , Jiri Houska wrote: > (I) is there a difference between (1) scf calculation using cp.x and > (3) scf calculation using pw.x ? one is performed with damped (fictitious) dynamics on electrons, another with traditional self-consistency on the charge density > (II) is there a difference between (1) scf calculation using cp.x and > (2) cp calculation using cp.x with electron_dynamics = (say) 'sd' and > ion_dynamics = 'none' ? no, but steepest descent should be used only to start the calculation: it is very inefficient > (III) how critical is the "ion_radius" choice ... e.g. is it clever to > make it equal to (known) covalent radius? the defaults should be ok. The so called ion radius is used to broaden the point charges of the nuclei into a gaussian distribution of charges. It is a convenient computational trick. P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From apv544 at phys.tsu.ru Wed Nov 25 03:52:43 2009 From: apv544 at phys.tsu.ru (Pavel A. Akulov) Date: Wed, 25 Nov 2009 08:52:43 +0600 Subject: [Pw_forum] Trouble with parallel running ld1.x Message-ID: <20091125025207.M9749@phys.tsu.ru> Dear PWSCF users and developers! I've faced a problem of parallel running ld1.x program. Stand-alone version works well (i've tried examples in atomic_doc), but parallel version gets me error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from ld1_readin : error # 1 reading input namelist %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% (even in examples). I run it with string(for example 2 procs h.in in /atomic_doc/all-electron) "mpirun -np 2 /path/ld1.x -in h.in > h.out" For pw.x this works well. But for ld1.x i don't know what's wrong. Help me please. -- Akulov P. Student, Dept. of Physics Tomsk State University From jwan at phy.cuhk.edu.hk Wed Nov 25 06:15:47 2009 From: jwan at phy.cuhk.edu.hk (Jones Tsz-Kai Wan) Date: Wed, 25 Nov 2009 13:15:47 +0800 Subject: [Pw_forum] problem in nmr calculation In-Reply-To: <20091124134039.csjggq480kssswo0@webmail.sissa.it> References: <20091123184225.pgf3n0mjmg4w0s8w@webmail.sissa.it> <20091124134039.csjggq480kssswo0@webmail.sissa.it> Message-ID: Dear Emine, I tried and I discover that I need more k-points to do the calculation. Regards, Jones On Tue, Nov 24, 2009 at 8:40 PM, Emine Kucukbenli wrote: > Hi Jones, > >>> ? from ?grid_gather ?: error # ? ? 46592 >>> ? ?f_out too small >>> > Just guessing: > this may mean that you are asking for too many pools. If it is so, > increasing k mesh may help(?) but also you can try decreasing the number of > pools i suppose. I wonder, have you tried changing isolve for your previous > problem? I'm just a newbie so if I were you, I'd take Davide's suggestions > more seriously than mine :) > > emine kucukbenli, phd student, sissa, italy > > ps: I'm writing you in private because i'm not sure and don't want to > clutter the mailing list and misinform others. But if it works, feel free to > report your solutions to the list. > > > > > ---------------------------------------------------------------- > ?SISSA Webmail https://webmail.sissa.it/ > ?Powered by Horde http://www.horde.org/ From giannozz at democritos.it Wed Nov 25 07:31:52 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 25 Nov 2009 07:31:52 +0100 Subject: [Pw_forum] Trouble with parallel running ld1.x In-Reply-To: <20091125025207.M9749@phys.tsu.ru> References: <20091125025207.M9749@phys.tsu.ru> Message-ID: <27D55C8A-64BF-4ECD-B308-65650B58D9AF@democritos.it> On Nov 25, 2009, at 3:52 , Pavel A. Akulov wrote: > I've faced a problem of parallel running ld1.x program. > Stand-alone version works well (i've tried examples in atomic_doc), > but parallel version gets me error: there is no such thing as a "parallel version" of ld1.x : it always runs on a single processor. It can be compiled and run in the same way as all other codes for the user's convenience. > I run it with string "mpirun -np 2 /path/ld1.x -in h.in > h.out" there must be something wrong with input redirection. "mpirun -np 2 /path/ld1.x < h.in > h.out" works. In any case, don't run it in parallel: you gain nothing P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed Nov 25 07:40:58 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 25 Nov 2009 07:40:58 +0100 Subject: [Pw_forum] Trouble with parallel running ld1.x In-Reply-To: <20091125025207.M9749@phys.tsu.ru> References: <20091125025207.M9749@phys.tsu.ru> Message-ID: <77242CB7-C3E0-4505-B8C5-5E3A60021FF6@democritos.it> On Nov 25, 2009, at 3:52 , Pavel A. Akulov wrote: > "mpirun -np 2 /path/ld1.x -in h.in > h.out" actually redirection with "-in file" is simply not implemented in ld1.x. P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From mohnish.iitk at gmail.com Wed Nov 25 08:02:27 2009 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Wed, 25 Nov 2009 12:32:27 +0530 Subject: [Pw_forum] difference in energy calculated by "gaussian" and "m-v" smearing Message-ID: Dear users, I have calculated the energy of zinc oxide thin film having nine layers. But the energy calculated by "m-v" and "gaussian" smearing is coming out to be very different. The difference is around 0.1 Rydberg. I have used used "degauss" to be .05 and 10^-3 respectively for "m-v" and "gaussain smearing". Can anybody please tell me why the energy is coming out to be very different. I have gone through the sections of book by Martin and Sholl also but I couldnt find that. Sincere thanks in advance. Mohnish Pandey -- Mohnish Pandey Y6262,4th Year Undergraduate, Department of Chemical Engineering, IIT KANPUR -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091125/621b3505/attachment.htm From modaresi.mohsen at gmail.com Wed Nov 25 10:08:12 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Wed, 25 Nov 2009 12:38:12 +0330 Subject: [Pw_forum] a question about Want package Message-ID: Hi dear users Is there any body who worked with Want package before? Mohsen Modaresi Msc. Student of Solid State Physics, Department of Physics,Ferdowsi University of Mashhad, Iran. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091125/f3dea4ed/attachment.htm From paulatto at sissa.it Wed Nov 25 10:24:40 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 25 Nov 2009 10:24:40 +0100 Subject: [Pw_forum] Trouble with parallel running ld1.x In-Reply-To: <27D55C8A-64BF-4ECD-B308-65650B58D9AF@democritos.it> References: <20091125025207.M9749@phys.tsu.ru> <27D55C8A-64BF-4ECD-B308-65650B58D9AF@democritos.it> Message-ID: Replying to message "Re: [Pw_forum] Trouble with parallel running ld1.x" from Paolo Giannozzi (25/11/09): > there is no such thing as a "parallel version" of ld1.x : it always runs > on a single processor. It can be compiled and run in the same way > as all other codes for the user's convenience. Some part of ld1 *are* actually parallel. However you can still run ld1 drectly (i.e. ithout mpirun) which should give no problem with input. 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 paulatto at sissa.it Wed Nov 25 10:27:43 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 25 Nov 2009 10:27:43 +0100 Subject: [Pw_forum] difference in energy calculated by "gaussian" and "m-v" smearing In-Reply-To: References: Message-ID: Replying to message "[Pw_forum] difference in energy calculated by "gaussian" and "m-v" smearing" from mohnish pandey (25/11/09): > Can anybody please tell me why the energy is coming out to be very > different. Dear Mohnish, it depends on how muche is "very" for you. In general, gaussian smearing is much slower to converge than mp or mv, at the point that it should not really be used for scf calculation. You gaussina.smearing calculation may just not be converged (with respect to the number of k-points). Furthermore, at the end of self-consistency the code prints the total energy along with the smearing contribution; if you *removre* the smearing contribution from the total energy, what do you get? 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 paulatto at sissa.it Wed Nov 25 10:28:26 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 25 Nov 2009 10:28:26 +0100 Subject: [Pw_forum] a question about Want package In-Reply-To: References: Message-ID: Replying to message "[Pw_forum] a question about Want package" from mohsen modaresi (25/11/09): > Is there any body who worked with Want package before? Yes, about 3 years ago and very superficially. What puzzles you? -- 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 modaresi.mohsen at gmail.com Wed Nov 25 10:34:22 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Wed, 25 Nov 2009 13:04:22 +0330 Subject: [Pw_forum] a question about Want package In-Reply-To: References: Message-ID: Dear Lorenzo I start working with Want, and I also see 'wannier.x' in Esp. package Is There any resemblance bwtween them? On Wed, Nov 25, 2009 at 12:58 PM, Lorenzo Paulatto wrote: > Replying to message "[Pw_forum] a question about Want package" from mohsen > modaresi (25/11/09): > > Is there any body who worked with Want package before? > > Yes, about 3 years ago and very superficially. What puzzles you? > > -- > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091125/219d241b/attachment.htm From paulatto at sissa.it Wed Nov 25 10:39:09 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 25 Nov 2009 10:39:09 +0100 Subject: [Pw_forum] a question about Want package In-Reply-To: References: Message-ID: Replying to message "Re: [Pw_forum] a question about Want package" from mohsen modaresi (25/11/09): > I start working with Want, and I also see 'wannier.x' in Esp. package > Is There any resemblance bwtween them? The package included in (some versions of) QE is Wannier90; which I've never used. They are similar to some extent, as they do mostly the same thing; but I really cannot say more. 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 modaresi.mohsen at gmail.com Wed Nov 25 10:46:17 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Wed, 25 Nov 2009 13:16:17 +0330 Subject: [Pw_forum] a question about Want package In-Reply-To: References: Message-ID: Dear Lorenzo Thanks for your answers Take care Mohsen Modaresi On Wed, Nov 25, 2009 at 1:09 PM, Lorenzo Paulatto wrote: > Replying to message "Re: [Pw_forum] a question about Want package" from > mohsen modaresi (25/11/09): > > I start working with Want, and I also see 'wannier.x' in Esp. package > > Is There any resemblance bwtween them? > > > The package included in (some versions of) QE is Wannier90; which I've > never used. They are similar to some extent, as they do mostly the same > thing; but I really cannot say more. > > 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/ > _______________________________________________ > 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/20091125/2918743a/attachment.htm From marzari at MIT.EDU Wed Nov 25 13:31:49 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Wed, 25 Nov 2009 07:31:49 -0500 Subject: [Pw_forum] difference in energy calculated by "gaussian" and "m-v" smearing In-Reply-To: References: Message-ID: <4B0D23B5.3060205@mit.edu> Dear Mohnish, roughly speaking you should use a similar degauss for m-v and gaussian. .05 Ry is fairly large, I'd stick with .02 Ry or so. Try this - study a bulk system (i.e. as small as possible) and plot for 3 or 4 k-point meshes the free energy (E-TS) as a function of smearing. At very small smearings the free energy will not be converged with respect to k-points; at high smearings it will, but will also be very dependent on smearing. You want the sweet spot in between. nicola mohnish pandey wrote: > Dear users, > I have calculated the energy of zinc oxide thin > film having nine layers. But the energy calculated by "m-v" and > "gaussian" smearing is coming out to be very different. The difference > is around 0.1 Rydberg. I have used used "degauss" to be .05 and 10^-3 > respectively for "m-v" and "gaussain smearing". Can anybody please > tell me why the energy is coming out to be very different. I have gone > through the sections of book by Martin and Sholl also but I couldnt > find that. > > Sincere thanks in advance. > Mohnish Pandey > > > -- > Mohnish Pandey > Y6262,4th Year Undergraduate, > Department of Chemical Engineering, > IIT KANPUR > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- --------------------------------------------------------------------- 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 kazempoor2000 at yahoo.com Wed Nov 25 14:43:21 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Wed, 25 Nov 2009 05:43:21 -0800 (PST) Subject: [Pw_forum] EE Message-ID: <991629.93630.qm@web112514.mail.gq1.yahoo.com> I have one extra charge in supercell, and I did a calculation to get total energy with(DCC correction) and without EE correction , but both of them are same. How can I put threshold on these parameter to include the ee correction.? How can I trust the results come from ee correction? I mean how can I optimize the ee total energies? Second question is : when I plot the average of total potential in a supercell for neutral defect and charge defect (for example in Z direction) I observe that the potential has constant shift w.r.t to each other. Is it the potential allignment(Delta_V) that people use in defect formation energy for charge systems or not? thanks a lot Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091125/da020547/attachment.htm From mohnish.iitk at gmail.com Wed Nov 25 15:18:50 2009 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Wed, 25 Nov 2009 19:48:50 +0530 Subject: [Pw_forum] difference in energy calculated by "gaussian" and "m-v" smearing In-Reply-To: <4B0D23B5.3060205@mit.edu> References: <4B0D23B5.3060205@mit.edu> Message-ID: Thank you so much Dr. Marzari and Lorenzo.... On Wed, Nov 25, 2009 at 6:01 PM, Nicola Marzari wrote: > > Dear Mohnish, > > roughly speaking you should use a similar degauss for m-v and gaussian. > .05 Ry is fairly large, I'd stick with > .02 Ry or so. > > Try this - study a bulk system (i.e. as small as possible) and plot for > 3 or 4 k-point meshes the free energy (E-TS) > as a function of smearing. At very small smearings the free energy will > not be converged with respect to k-points; > at high smearings it will, but will also be very dependent on smearing. > > You want the sweet spot in between. > > nicola > > > mohnish pandey wrote: > > Dear users, > > I have calculated the energy of zinc oxide thin > > film having nine layers. But the energy calculated by "m-v" and > > "gaussian" smearing is coming out to be very different. The difference > > is around 0.1 Rydberg. I have used used "degauss" to be .05 and 10^-3 > > respectively for "m-v" and "gaussain smearing". Can anybody please > > tell me why the energy is coming out to be very different. I have gone > > through the sections of book by Martin and Sholl also but I couldnt > > find that. > > > > Sincere thanks in advance. > > Mohnish Pandey > > > > > > -- > > Mohnish Pandey > > Y6262,4th Year Undergraduate, > > Department of Chemical Engineering, > > IIT KANPUR > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > --------------------------------------------------------------------- > 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 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Mohnish Pandey Y6262,4th Year Undergraduate, Department of Chemical Engineering, IIT KANPUR -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091125/eff89210/attachment-0001.htm From rhouyang at dicp.ac.cn Wed Nov 25 15:46:50 2009 From: rhouyang at dicp.ac.cn (runhai ouyang) Date: Wed, 25 Nov 2009 22:46:50 +0800 Subject: [Pw_forum] non-relativistic calculation Message-ID: <200911252246499530314@dicp.ac.cn> pw_forum,Hi! Can PWscf perform non-relativistic calulation? and how to do it ? Thanks very much!! runhai ouyang rhouyang at dicp.ac.cn 2009-11-25 From ferretti at MIT.EDU Wed Nov 25 17:21:01 2009 From: ferretti at MIT.EDU (Andrea Ferretti) Date: Wed, 25 Nov 2009 11:21:01 -0500 (EST) Subject: [Pw_forum] a question about Want package In-Reply-To: Message-ID: Hi Mohsen, I think the two codes are meant to do similar jobs for the hardcore part of the calculation (such as the localization of wannier functions), while then probably differ more in terms of the final applications, postproc tools, user interface, etc... you can find more details looking directly at the websites: wannier90: http://www.wannier.org want: http://www.wannier-transport.org cheers Andrea > Replying to message "Re: [Pw_forum] a question about Want package" from > mohsen modaresi (25/11/09): > > I start working with Want, and I also see 'wannier.x' in Esp. package > > Is There any resemblance bwtween them? > > > The package included in (some versions of) QE is Wannier90; which I've > never used. They are similar to some extent, as they do mostly the same > thing; but I really cannot say more. > > cheers > > > -- Andrea Ferretti MIT, Dept Material Science & Engineering bldg 13-4078, 77, Massachusetts Ave, Cambridge, MA Tel: +1 617-452-2455; Skype: andrea_ferretti URL: http://quasiamore.mit.edu Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html From modaresi.mohsen at gmail.com Wed Nov 25 21:34:11 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Wed, 25 Nov 2009 23:34:11 +0300 Subject: [Pw_forum] request help for gaas band structure Message-ID: Dear Q.E users I try to plot GaAs band structure, I follow this procedure 1) I run pw.x with gaasspw.in 2) I run pw.x with gaassnpw.in 3) I run pw.x with gaasban.in 4) I run bands.x with bands.in 5) i run plotband.x ( attached files) And at final step i get (gaasbandstructure), Which have some important deferent with gaas.jpg (which i get from internet). Can any body help me to correct my result? With thankks Mohsen Modaresi Msc. Student of Solid State Physics, Department of Physics,Ferdowsi University of Mashhad, Iran. -------------- next part -------------- An HTML attachment was scrubbed... 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Name: GaAs.jpg Type: image/jpeg Size: 53540 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091125/919beb61/attachment-0001.jpg From ceresoli at MIT.EDU Wed Nov 25 22:07:56 2009 From: ceresoli at MIT.EDU (Davide Ceresoli) Date: Wed, 25 Nov 2009 16:07:56 -0500 Subject: [Pw_forum] request help for gaas band structure In-Reply-To: References: Message-ID: <4B0D9CAC.70603@mit.edu> mohsen modaresi wrote: > Dear Q.E users > I try to plot GaAs band structure, I follow this procedure > 1) I run pw.x with gaasspw.in It's always a good idea to look at your structure with XCrysden. GaAs is diamond, not rock-salt. Also check your lattice spacing. Davide From modaresi.mohsen at gmail.com Thu Nov 26 00:42:32 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Thu, 26 Nov 2009 02:42:32 +0300 Subject: [Pw_forum] request help for gaas band structure In-Reply-To: <4B0D9CAC.70603@mit.edu> References: <4B0D9CAC.70603@mit.edu> Message-ID: Hi I do this again with another input files, and gain this band structure, the dereference are omited but energy scale is not true, I there any problem in my calculations? Thanks Mohsen Modaresi On Thu, Nov 26, 2009 at 12:07 AM, Davide Ceresoli wrote: > mohsen modaresi wrote: > > Dear Q.E users > > I try to plot GaAs band structure, I follow this procedure > > 1) I run pw.x with gaasspw.in > It's always a good idea to look at your structure with XCrysden. > GaAs is diamond, not rock-salt. Also check your lattice spacing. > > > > Davide > > _______________________________________________ > 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/20091126/29dcf1e5/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: GaAs.jpg Type: image/jpeg Size: 53540 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091126/29dcf1e5/attachment-0001.jpg -------------- next part -------------- A non-text attachment was scrubbed... Name: 8 Type: application/octet-stream Size: 25343 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091126/29dcf1e5/attachment-0001.obj From yccheng.nju at gmail.com Thu Nov 26 01:52:44 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Thu, 26 Nov 2009 08:52:44 +0800 Subject: [Pw_forum] request help for gaas band structure In-Reply-To: References: <4B0D9CAC.70603@mit.edu> Message-ID: Please check the unit of the k point! K_POINTS 36 You can try to use the crystal unit of the k point in your gaasban.in file. K_POINTS crystal 36 ....... 2009/11/26 mohsen modaresi : > Hi > I do this again with another input files, and gain this band structure, the > dereference are omited but energy scale is not true, I there any problem in > my calculations? > Thanks > > Mohsen Modaresi > > On Thu, Nov 26, 2009 at 12:07 AM, Davide Ceresoli wrote: >> >> mohsen modaresi wrote: >> > Dear Q.E users >> > I try to plot GaAs band structure, I follow this procedure >> > 1) I run pw.x with gaasspw.in >> It's always a good idea to look at your structure with XCrysden. >> GaAs is diamond, not rock-salt. Also check your lattice spacing. > > >> >> Davide >> >> _______________________________________________ >> 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 > > -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com From eyvaz_isaev at yahoo.com Thu Nov 26 02:34:27 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 25 Nov 2009 17:34:27 -0800 (PST) Subject: [Pw_forum] request help for gaas band structure In-Reply-To: Message-ID: <130685.19005.qm@web65712.mail.ac4.yahoo.com> Hi, --- On Thu, 11/26/09, ??? wrote: > You can try to use the crystal unit of the k point in your > gaasban.in file. > > K_POINTS? crystal > 36 This, most likely, will not affect, as K_POINTS provided are in 2\pi/a and cartesian, and look correct. > > 2009/11/26 mohsen modaresi : > I do this again with another input files, and gain > this band structure, the dereference are omited but energy > scale is not true, I there any problem in my calculations? Hopefully you mean results obtained by correct atomic positions (Ga(0,0,0), As(0.25,0.25,0.25)) [as it was reported by Davide C] and correct lattice parameter that is 5.65 Angstrom, but not 4.551Ang as you specified (8.6 a.u). This huge difference can induce big changes in the band structure (in energy scale, as example). But looking at your band structure it seems you deal with spin-relativistic band structure for GaAs. To compare see PRL 94, 226601 (2005). How about your PsP files, are they fully-relativistic or not? 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 From eyvaz_isaev at yahoo.com Thu Nov 26 03:20:23 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 25 Nov 2009 18:20:23 -0800 (PST) Subject: [Pw_forum] request help for gaas band structure In-Reply-To: <130685.19005.qm@web65712.mail.ac4.yahoo.com> Message-ID: <145848.73984.qm@web65713.mail.ac4.yahoo.com> > > But looking at your band structure it seems you deal with > spin-relativistic band structure for GaAs. Sorry, relativistic band structure, of course. I have misprinted. 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 From bipulrr at gmail.com Thu Nov 26 08:53:31 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Thu, 26 Nov 2009 13:23:31 +0530 Subject: [Pw_forum] CVS version of espresso Message-ID: <3a749910911252353y7247e0e4s4eac49a74be469e0@mail.gmail.com> Dear PWSCF users, I try to get the cvs version of espresso, with the following commands *export CVS_RSH=ssh export CVSROOT=:pserver:cvsanon at democritos.sissa.it:/home/cvs Then: cvs login and enter password: /cvsanon/* But it is showing some connection error *cvs [login aborted]: connect to [democritos.sissa.it]:2401 failed: Connection refused* Please help me in this matter. -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091126/22406c11/attachment.htm From modaresi.mohsen at gmail.com Thu Nov 26 09:04:52 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Thu, 26 Nov 2009 11:04:52 +0300 Subject: [Pw_forum] request help for gaas band structure In-Reply-To: <145848.73984.qm@web65713.mail.ac4.yahoo.com> References: <130685.19005.qm@web65712.mail.ac4.yahoo.com> <145848.73984.qm@web65713.mail.ac4.yahoo.com> Message-ID: Dear Eyvaz Thanks for your answers I changed lattice parameter to 10.68 Bohr, and i attach again results, after this the results improved, but energy scale is not match. I used this kind of pseudopotentials 'Scalar-Relativistic Calculation'. Is there any mistake? Another question : Where i can change 'spin-relativistic band structure', i did not inter relativistic feature in my pw input file. Thanks Mohsen Modaresi Where i can change relativistic calculation for On Thu, Nov 26, 2009 at 5:20 AM, Eyvaz Isaev wrote: > > > > > But looking at your band structure it seems you deal with > > spin-relativistic band structure for GaAs. > > Sorry, relativistic band structure, of course. I have misprinted. > > > 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 > > > > > > _______________________________________________ > 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/20091126/50523752/attachment.htm From marsamos at democritos.it Thu Nov 26 11:27:54 2009 From: marsamos at democritos.it (marsamos at democritos.it) Date: Thu, 26 Nov 2009 11:27:54 +0100 Subject: [Pw_forum] CVS version of espresso In-Reply-To: <3a749910911252353y7247e0e4s4eac49a74be469e0@mail.gmail.com> References: <3a749910911252353y7247e0e4s4eac49a74be469e0@mail.gmail.com> Message-ID: <20091126112754.bab7tsjtwwk84koc@mail.democritos.it> Dear Bipul, you have to use the commands: cvs -d :pserver:anonymous at scm.qe-forge.org:/cvsroot/q-e login cvs -d :pserver:anonymous at scm.qe-forge.org:/cvsroot/q-e checkout espresso see http://qe-forge.org/scm/?group_id=10 for detailed instruction best Layla Quoting Bipul Rakshit : > Dear PWSCF users, > I try to get the cvs version of espresso, with the following commands > > *export CVS_RSH=ssh > export CVSROOT=:pserver:cvsanon at democritos.sissa.it:/home/cvs > > Then: > > cvs login > > and enter password: /cvsanon/* > > But it is showing some connection error > > *cvs [login aborted]: connect to [democritos.sissa.it]:2401 failed: > Connection refused* > > Please help me in this matter. > -- > Dr. Bipul Rakshit > Research Associate, > S N Bose Centre for Basic Sciences, > Salt Lake, > Kolkata 700 098 > India > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From eyvaz_isaev at yahoo.com Thu Nov 26 11:42:11 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 26 Nov 2009 02:42:11 -0800 (PST) Subject: [Pw_forum] request help for gaas band structure In-Reply-To: Message-ID: <295025.82394.qm@web65704.mail.ac4.yahoo.com> Dear Mohsen, --- On Thu, 11/26/09, mohsen modaresi wrote: > Thanks for your answers Welcome! > I changed lattice parameter to 10.68 Bohr, and i attach > again results, after this the results improved, but energy > scale is not match. As you did not attach any figure I can not give any comment. > I used this kind of pseudopotentials > 'Scalar-Relativistic Calculation'. > Is there any mistake? Definitley not! > Another question : > Where i can change 'spin-relativistic band > structure', i did not inter relativistic feature in my > pw input file. Not spin-relativistic, but relativistic (or fully-relativistic). Hopefully you found the paper I mentioned. How to setup additional parameters for fully-relativistic (instead of scalar-relativistic) pseudopotentials please see example22. For this purpose you will need properly generated pseudopotentials, too. Bests, Eyvaz. From kazempoor2000 at yahoo.com Thu Nov 26 11:50:03 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Thu, 26 Nov 2009 02:50:03 -0800 (PST) Subject: [Pw_forum] regular kmesh Message-ID: <698927.35907.qm@web112511.mail.gq1.yahoo.com> I am doing GW calculation with sax code. For this I need REGULAR K-POINT GRID IN THE COMPLETE BRILLOUIN ZONE. By kpoint.x we can generate the set of kpoint that some of them are grater than 1.0. Do I change these values to first BZ or not? How can I make kmesh in complete BZ? thanks a lot Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091126/4d444c13/attachment.htm From paulatto at sissa.it Thu Nov 26 11:54:34 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 26 Nov 2009 11:54:34 +0100 Subject: [Pw_forum] regular kmesh In-Reply-To: <698927.35907.qm@web112511.mail.gq1.yahoo.com> References: <698927.35907.qm@web112511.mail.gq1.yahoo.com> Message-ID: Replying to message "[Pw_forum] regular kmesh" from ali kazempour (26/11/09): > Do I change these values to first BZ or not? How can I make kmesh in > complete BZ? It only means (I think) that the code cannot (yet?) use symmetry to reduce the number of kpoints. You just press "f" when kpoint.x asks you if you want to "write all k". I think you can have the same effect by setting nosym=.true. in pw.x. I would advise you to check the mailing list archive before believing me, as it is a bit complicated (it has already been discussed several times). 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 dimpy.sharma at tyndall.ie Thu Nov 26 13:33:05 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Thu, 26 Nov 2009 12:33:05 -0000 Subject: [Pw_forum] Suggested book for projected density of states Message-ID: Hi Friends, can any one please suggest me some reference book getting Proejected density of states. Thanks and regards Dimpy Dimpy Sharma UCC Ireland -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091126/7da6e1a2/attachment.htm From giannozz at democritos.it Thu Nov 26 14:30:38 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 26 Nov 2009 14:30:38 +0100 Subject: [Pw_forum] non-relativistic calculation In-Reply-To: <200911252246499530314@dicp.ac.cn> References: <200911252246499530314@dicp.ac.cn> Message-ID: <4B0E82FE.4060804@democritos.it> runhai ouyang wrote: > Can PWscf perform non-relativistic calulation? and how to do it ? it can perform ONLY non-relativistic calculations! pseudopotentials can be relativistic, though P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From modaresi.mohsen at gmail.com Thu Nov 26 15:58:32 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Thu, 26 Nov 2009 17:58:32 +0300 Subject: [Pw_forum] A problem about Ex.12 Message-ID: Hi dear users I read Ex.12 and run it, In the input file for Al (al.scf.in ) i see this part ibrav = 6, celldm(1) =5.3, celldm(3) =1.414, But we konw that Al has F.CC structure, Why they set ibarav=6 not 2, I faced with this problem in example 11 in the Want package. Thanks for answers Mohsen Modaresi Msc. Student of Solid State Physics, Department of Physics,Ferdowsi University of Mashhad, Iran. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091126/2deaf3fa/attachment.htm From degironc at sissa.it Thu Nov 26 16:26:42 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 26 Nov 2009 16:26:42 +0100 Subject: [Pw_forum] A problem about Ex.12 In-Reply-To: References: Message-ID: <4B0E9E32.7010801@sissa.it> Dear mohsen modaresi you can describe an fcc crystal in an FCC bravais lattice with one atom per cell or in a Simple Cubic cell with 4 atoms per cell or in a tetragonal cell with 2 atoms per cell or in many other equivalent ways. Why it is done using tetragonal lattice in that particular example I don't know but it may be due to the need of using some particular orientation or orthonormal Bravais vectors or some other reason. Hope this helps, stefano. mohsen modaresi wrote: > Hi dear users > I read Ex.12 and run it, In the input file for Al (al.scf.in > ) i see this part > ibrav = 6, > celldm(1) =5.3, > celldm(3) =1.414, > But we konw that Al has F.CC structure, Why they set ibarav=6 not 2, I > faced with this problem in example 11 in the Want package. > Thanks for answers > > Mohsen Modaresi > Msc. Student of Solid State Physics, > Department of Physics,Ferdowsi University of Mashhad, > Iran. > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From jwan at phy.cuhk.edu.hk Thu Nov 26 16:56:34 2009 From: jwan at phy.cuhk.edu.hk (Jones Tsz-Kai Wan) Date: Thu, 26 Nov 2009 23:56:34 +0800 Subject: [Pw_forum] Hybrid functional Message-ID: Dear QE users, I found that hybrid functionals are implemented in QE (http://www.quantum-espresso.org/whatcanqedo.php#01). Does anyone know where I can get examples/documents of hybrid functionals in QE? Regards, Jones From marsamos at democritos.it Thu Nov 26 17:02:32 2009 From: marsamos at democritos.it (marsamos at democritos.it) Date: Thu, 26 Nov 2009 17:02:32 +0100 Subject: [Pw_forum] Hybrid functional In-Reply-To: References: Message-ID: <20091126170232.sngiyc8q8oo0os4o@mail.democritos.it> Dear user take a look to EXX_examples within the QE examples directory. bests Layla Quoting Jones Tsz-Kai Wan : > Dear QE users, > > I found that hybrid functionals are implemented in QE > (http://www.quantum-espresso.org/whatcanqedo.php#01). Does anyone know > where I can get examples/documents of hybrid functionals in QE? > > Regards, > > Jones > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From quantumdft at gmail.com Thu Nov 26 18:23:36 2009 From: quantumdft at gmail.com (vega lew) Date: Thu, 26 Nov 2009 09:23:36 -0800 Subject: [Pw_forum] Do you think QE could benefit from the Hyper-Threading Tech of XEON 5500 series? Message-ID: <412f6c680911260923s7cd75b6er3d06dbc9f19a855b@mail.gmail.com> Dear all, I got 5 computers with two XEON 5520 and 24G memory. I find the Hyper-Threading is switched on by default. I wonder if QE could benefit from Hyper-Threading Tech. of Xeon CPUs? Should I switch it off and trigger one process for each core to promote the QE performance? Or remain the Hyper-Threading on and trigger two processes for each core? best vega -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091126/959345f9/attachment-0001.htm From modaresi.mohsen at gmail.com Thu Nov 26 19:17:30 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Thu, 26 Nov 2009 21:17:30 +0300 Subject: [Pw_forum] A problem about Ex.12 In-Reply-To: <4B0E9E32.7010801@sissa.it> References: <4B0E9E32.7010801@sissa.it> Message-ID: Dear Stefano Thanks for your answer Why they used this kind of lattice? there are many another example like this. Mohsen Modaresi On Thu, Nov 26, 2009 at 6:26 PM, Stefano de Gironcoli wrote: > Dear mohsen modaresi > > you can describe an fcc crystal in an FCC bravais lattice with one atom > per cell or in a Simple Cubic cell with 4 atoms per cell or in a > tetragonal cell with 2 atoms per cell or in many other equivalent ways. > Why it is done using tetragonal lattice in that particular example I > don't know but it may be due to the need of using some particular > orientation or orthonormal Bravais vectors or some other reason. > Hope this helps, > > stefano. > > mohsen modaresi wrote: > > Hi dear users > > I read Ex.12 and run it, In the input file for Al (al.scf.in > > ) i see this part > > ibrav = 6, > > celldm(1) =5.3, > > celldm(3) =1.414, > > But we konw that Al has F.CC structure, Why they set ibarav=6 not 2, I > > faced with this problem in example 11 in the Want package. > > Thanks for answers > > > > Mohsen Modaresi > > Msc. Student of Solid State Physics, > > Department of Physics,Ferdowsi University of Mashhad, > > Iran. > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091126/08b1c551/attachment.htm From ferretti at MIT.EDU Thu Nov 26 19:49:55 2009 From: ferretti at MIT.EDU (Andrea Ferretti) Date: Thu, 26 Nov 2009 13:49:55 -0500 (EST) Subject: [Pw_forum] A problem about Ex.12 In-Reply-To: Message-ID: Dear Mohsen, actually test11 in WanT is using ibrav=8 (orthorombic cell). The reason is the supercell approximation used to simulate the 1D chains of the example. Andrea > > > > mohsen modaresi wrote: > > > Hi dear users > > > I read Ex.12 and run it, In the input file for Al (al.scf.in > > > ) i see this part > > > ibrav = 6, > > > celldm(1) =5.3, > > > celldm(3) =1.414, > > > But we konw that Al has F.CC structure, Why they set ibarav=6 not 2, I > > > faced with this problem in example 11 in the Want package. > > > Thanks for answers > > > > > > Mohsen Modaresi > > > Msc. Student of Solid State Physics, > > > Department of Physics,Ferdowsi University of Mashhad, > > > Iran. > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > 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 > > > -- Andrea Ferretti MIT, Dept Material Science & Engineering bldg 13-4078, 77, Massachusetts Ave, Cambridge, MA Tel: +1 617-452-2455; Skype: andrea_ferretti URL: http://quasiamore.mit.edu Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html From sh.shapt at gmail.com Thu Nov 26 19:56:18 2009 From: sh.shapt at gmail.com (Shaptrishi Sharma) Date: Thu, 26 Nov 2009 18:56:18 +0000 Subject: [Pw_forum] Number of processor and the size of system Message-ID: Hi QEs users, why do we need more number of processors for some systems ( with less number of atoms ), compared to other systems which have less number of atoms , otheriwse the job crashes and says 'cholesky decompostion' however it runs at high number of processors. Thanks SS Msc (Physics) Pune India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091126/ac264915/attachment.htm From paulatto at sissa.it Thu Nov 26 20:03:07 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 26 Nov 2009 20:03:07 +0100 Subject: [Pw_forum] Number of processor and the size of system In-Reply-To: References: Message-ID: Replying to message "[Pw_forum] Number of processor and the size of system" from Shaptrishi Sharma (26/11/09): > why do we need more number of processors for some systems ( with less > number of atoms ), compared to other systems which have less number of > atoms , > otheriwse the job crashes and says 'cholesky decompostion' however it > runs at high number of processors. Dear Shaptrishi, it depends on the details. Please provide more information on you job: how many processors do you use in both cases? How many pools? The usual stuff... 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 asafis at yahoo.com.br Thu Nov 26 20:54:19 2009 From: asafis at yahoo.com.br (=?iso-8859-1?Q?=C1lvaro_Alves?=) Date: Thu, 26 Nov 2009 11:54:19 -0800 (PST) Subject: [Pw_forum] magnetic coupling X pressure Message-ID: <496028.88374.qm@web52305.mail.re2.yahoo.com> Users PWscf Hello, I'm willing to investigate how the magnetic coupling in a solid varies with the pressure. The unit cell is triclinic. What better way to do this in PWscf .. ? A. S. Santos Universidade Federal Fluminense Niter?i - Rio de Janeiro - Brasil ____________________________________________________________________________________ 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/20091126/656b3f2b/attachment.htm From vamsi.iisc at gmail.com Fri Nov 27 06:53:02 2009 From: vamsi.iisc at gmail.com (vamsi kv) Date: Fri, 27 Nov 2009 11:23:02 +0530 Subject: [Pw_forum] validation of energy values Message-ID: <84ff69170911262153y68ff2365h6c4b65506b345638@mail.gmail.com> Dear PWScf users, I want to study the interaction of H2O with Fe surfaces. I have choosen the potential and cutoffs for Fe by validating with experimental vaues like lattice parameter and cohesive energy. My question is when it comes to gas or liquid molecules how can i validate the output values of the simulations. I am getting the bond length and bond angle correctly within 1% error on relaxing the structure in a supercell of 20 bohrs . But I was trying to validate with heat of formation of H2O and i am not successful. Can any one help me in resolving my problem Thanks & Regards K V Vamsi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091127/3423fe2b/attachment.htm From physik.shyam at gmail.com Fri Nov 27 08:38:17 2009 From: physik.shyam at gmail.com (Shyam Khambholja) Date: Fri, 27 Nov 2009 13:08:17 +0530 Subject: [Pw_forum] contents of Pw_forum digest Message-ID: <9b382fa70911262338qcef66ces62d696ad43c6109d@mail.gmail.com> Hi, friends, I am a new user of pwscf. I am trying to generate k-points using kpoints.x. can you tell me the significance of mesh : n1 n2 n3 and mesh : k1 k2 k3 [ 0 no shift, 1 shifted ] Thanks -- Shyam G Khambholja Reseach student, Depratment of Physics, Sardar Patel University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091127/bb04bb1e/attachment.htm From nkxirainbow at gmail.com Fri Nov 27 08:54:03 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Fri, 27 Nov 2009 07:54:03 +0000 Subject: [Pw_forum] contents of Pw_forum digest In-Reply-To: <9b382fa70911262338qcef66ces62d696ad43c6109d@mail.gmail.com> References: <9b382fa70911262338qcef66ces62d696ad43c6109d@mail.gmail.com> Message-ID: <21fbc4790911262354w713da2eek3bb85ea340a1b7c6@mail.gmail.com> Dear Khambholja: When calculating the total energy, QE performs integration in the first Brillioun zone to account the energy of electrons. But this integration can not be fulfilled analytically. Instead, it must be performed by numerical integration. Therefore, the k-mesh is used in this numerical integration. The k-shift may be used to avoid special high symmetry points, for example gama point. However, I am also a little confused with the significance of k-shift. Can any one give a explanation about k-shift?? Thanks in advance?? numerical integration On Fri, Nov 27, 2009 at 7:38 AM, Shyam Khambholja wrote: > Hi, friends, > > I am a new user of pwscf. I am trying to generate > k-points using kpoints.x. can you tell me the significance of > > mesh : n1 n2 n3 and > > mesh : k1 k2 k3 [ 0 no shift, 1 shifted ] > > Thanks > > > -- > Shyam G Khambholja > Reseach student, > Depratment of Physics, > Sardar Patel University > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091127/dde4b7b7/attachment.htm From quantumdft at gmail.com Fri Nov 27 10:10:27 2009 From: quantumdft at gmail.com (vega lew) Date: Fri, 27 Nov 2009 01:10:27 -0800 Subject: [Pw_forum] Temperature continuously going down in cp.x run Message-ID: <412f6c680911270110p365d8d5cvcb7f0048afc398d@mail.gmail.com> dear all, I want to calculate certain heterogeneous reaction on a solid surface. First input the initial structure from previous pw.x relaxations. Second I fixed ions and let electron damping calculation run; Then un-fixed the ions and let both electron and ions damping calculations run. Third I gave a random motion to the atoms in the system with amprp(1)~(3) = 0.01 and then repeated second step to bring the system to the ground state. Fourth I added temperature (300K) to the system, using verlet schedule. But the temperature continuously going down, from 1000K to 150K during the fisrt 3000 steps. I think there might be something wrong with my cp.x calcuation. Do you think the amprp(1)~(3) = 0.01 of random motion is too small? Here is the input of my dynamics process, &CONTROL title = 'CP' , calculation = 'cp' , restart_mode = 'restart' , outdir = '/disk5/nanjing/vega/cp/300/' , wfcdir = '/tmp/' , pseudo_dir = '/home/software/nanjing/vega/espresso-4.0.1/pseudo/' , prefix = 'cp_molecular' , nstep = 99999 , dt = 10, iprint = 5, isave = 150, / &SYSTEM ibrav = 8, celldm(1) =24.8624, celldm(2) = 0.8520, celldm(3) = 1.6964, nat = 147, ntyp = 3, nr1b = 20, nr2b = 20, nr3b = 20, nbnd = 630, ecutwfc = 30, ecutrho = 300, / &ELECTRONS electron_dynamics = 'verlet', / &IONS ion_dynamics = 'verlet' ion_temperature = 'nose', tempw = 300, / .................. .................. best wishes, vega -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091127/2d63cd14/attachment.htm From degironc at sissa.it Fri Nov 27 11:02:15 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 27 Nov 2009 11:02:15 +0100 Subject: [Pw_forum] Temperature continuously going down in cp.x run In-Reply-To: <412f6c680911270110p365d8d5cvcb7f0048afc398d@mail.gmail.com> References: <412f6c680911270110p365d8d5cvcb7f0048afc398d@mail.gmail.com> Message-ID: <4B0FA3A7.8060408@sissa.it> is the total (kinetic + potential) energy conserved ? stefano vega lew wrote: > dear all, > > I want to calculate certain heterogeneous reaction on a solid surface. > First input the initial structure from previous pw.x relaxations. > Second I fixed ions and let electron damping calculation run; > Then un-fixed the ions and let both electron and ions damping > calculations run. > Third I gave a random motion to the atoms in the system with > amprp(1)~(3) = 0.01 > and then repeated second step to bring the system to the ground state. > Fourth I added temperature (300K) to the system, using verlet schedule. > > But the temperature continuously going down, from 1000K to 150K during > the fisrt 3000 steps. > I think there might be something wrong with my cp.x calcuation. > Do you think the amprp(1)~(3) = 0.01 of random motion is too small? > > Here is the input of my dynamics process, > &CONTROL > > title = 'CP' > , > calculation = 'cp' > , > restart_mode = 'restart' > , > outdir = '/disk5/nanjing/vega/cp/300/' , > wfcdir = '/tmp/' > , > pseudo_dir = > '/home/software/nanjing/vega/espresso-4.0.1/pseudo/' , > prefix = 'cp_molecular' , > nstep = 99999 , > dt = 10, > iprint = 5, > isave = > 150, > / > > &SYSTEM > > ibrav = > 8, > celldm(1) =24.8624, > celldm(2) = 0.8520, > celldm(3) = 1.6964, > nat = > 147, > ntyp = 3, > nr1b = 20, > nr2b = 20, > nr3b = 20, > nbnd = > 630, > ecutwfc = 30, > ecutrho = 300, > / > > > &ELECTRONS > electron_dynamics = 'verlet', > / > > &IONS > > ion_dynamics = 'verlet' > ion_temperature = 'nose', > tempw = 300, > / > .................. > .................. > > best wishes, > > vega > > -- > ================================================================================== > Vega Lew ( weijia liu) > Graduate student > 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 > From quantumdft at gmail.com Fri Nov 27 12:42:47 2009 From: quantumdft at gmail.com (vega lew) Date: Fri, 27 Nov 2009 03:42:47 -0800 Subject: [Pw_forum] Temperature continuously going down in cp.x run In-Reply-To: <4B0FA3A7.8060408@sissa.it> References: <412f6c680911270110p365d8d5cvcb7f0048afc398d@mail.gmail.com> <4B0FA3A7.8060408@sissa.it> Message-ID: <412f6c680911270342o3676ebe1ucd37f7969c03c411@mail.gmail.com> Dear sir, Did you ask whether the (etot+ekinc) conserve during the dynamic process? I sum the corresponding columns. I found it is not changing very much. For example, the (ekinc+ etot) is -4369.40879 (-4369.44669+0.0379) at 2200 step. Then it changes to -4369.41514 (-4369.45479+0.03965) at 2300 step. And it sometimes goes a little up and sometimes a little down. But the value is in range of -4369.41 and -4369.45. thank you for reading. vega On Fri, Nov 27, 2009 at 2:02 AM, Stefano de Gironcoli wrote: > is the total (kinetic + potential) energy conserved ? > stefano > > vega lew wrote: > > dear all, > > > > I want to calculate certain heterogeneous reaction on a solid surface. > > First input the initial structure from previous pw.x relaxations. > > Second I fixed ions and let electron damping calculation run; > > Then un-fixed the ions and let both electron and ions damping > > calculations run. > > Third I gave a random motion to the atoms in the system with > > amprp(1)~(3) = 0.01 > > and then repeated second step to bring the system to the ground state. > > Fourth I added temperature (300K) to the system, using verlet schedule. > > > > But the temperature continuously going down, from 1000K to 150K during > > the fisrt 3000 steps. > > I think there might be something wrong with my cp.x calcuation. > > Do you think the amprp(1)~(3) = 0.01 of random motion is too small? > > > > Here is the input of my dynamics process, > > &CONTROL > > > > title = 'CP' > > , > > calculation = 'cp' > > , > > restart_mode = 'restart' > > , > > outdir = '/disk5/nanjing/vega/cp/300/' , > > wfcdir = '/tmp/' > > , > > pseudo_dir = > > '/home/software/nanjing/vega/espresso-4.0.1/pseudo/' , > > prefix = 'cp_molecular' , > > nstep = 99999 , > > dt = 10, > > iprint = 5, > > isave = > > 150, > > / > > > > &SYSTEM > > > > ibrav = > > 8, > > celldm(1) =24.8624, > > celldm(2) = 0.8520, > > celldm(3) = 1.6964, > > nat = > > 147, > > ntyp = 3, > > nr1b = 20, > > nr2b = 20, > > nr3b = 20, > > nbnd = > > 630, > > ecutwfc = 30, > > ecutrho = 300, > > / > > > > > > &ELECTRONS > > electron_dynamics = 'verlet', > > / > > > > &IONS > > > > ion_dynamics = 'verlet' > > ion_temperature = 'nose', > > tempw = 300, > > / > > .................. > > .................. > > > > best wishes, > > > > vega > > > > -- > > > ================================================================================== > > Vega Lew ( weijia liu) > > Graduate student > > 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 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091127/4e439b4e/attachment.htm From dimpy.sharma at tyndall.ie Fri Nov 27 13:05:30 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Fri, 27 Nov 2009 12:05:30 -0000 Subject: [Pw_forum] Books related to Projected density of states Message-ID: Hi there, My question has not been answered, I would like to know some reference books for studying Projected density of states. Thanks and regards Dimpy Dimpy Sharma PhD ( Nanotechnology) UCC Cork Ireland -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091127/55ce08d8/attachment-0001.htm From somesh.kb at gmail.com Fri Nov 27 13:04:45 2009 From: somesh.kb at gmail.com (Somesh Kumar Bhattacharya) Date: Fri, 27 Nov 2009 13:04:45 +0100 Subject: [Pw_forum] Temperature continuously going down in cp.x run In-Reply-To: <412f6c680911270342o3676ebe1ucd37f7969c03c411@mail.gmail.com> References: <412f6c680911270110p365d8d5cvcb7f0048afc398d@mail.gmail.com> <4B0FA3A7.8060408@sissa.it> <412f6c680911270342o3676ebe1ucd37f7969c03c411@mail.gmail.com> Message-ID: Dear Vega, The CP program prints different energy in the output file *.evp. In this file the eighth column is the constant of motion which should remain a constant. Plot this eighth column vs the timesteps and see what fluctuations are you getting in the plot. This is I guess what Stefano asked you. Regards, Somesh On Fri, Nov 27, 2009 at 12:42 PM, vega lew wrote: > Dear sir, > > Did you ask whether the (etot+ekinc) conserve during the dynamic process? > > I sum the corresponding columns. I found it is not changing very much. > > For example, the (ekinc+ etot) is -4369.40879 (-4369.44669+0.0379) at 2200 > step. > Then it changes to -4369.41514 (-4369.45479+0.03965) at 2300 step. > And it sometimes goes a little up and sometimes a little down. But the > value is in range of > -4369.41 and -4369.45. > > thank you for reading. > > vega > > > > On Fri, Nov 27, 2009 at 2:02 AM, Stefano de Gironcoli wrote: > >> is the total (kinetic + potential) energy conserved ? >> stefano >> >> vega lew wrote: >> > dear all, >> > >> > I want to calculate certain heterogeneous reaction on a solid surface. >> > First input the initial structure from previous pw.x relaxations. >> > Second I fixed ions and let electron damping calculation run; >> > Then un-fixed the ions and let both electron and ions damping >> > calculations run. >> > Third I gave a random motion to the atoms in the system with >> > amprp(1)~(3) = 0.01 >> > and then repeated second step to bring the system to the ground state. >> > Fourth I added temperature (300K) to the system, using verlet schedule. >> > >> > But the temperature continuously going down, from 1000K to 150K during >> > the fisrt 3000 steps. >> > I think there might be something wrong with my cp.x calcuation. >> > Do you think the amprp(1)~(3) = 0.01 of random motion is too small? >> > >> > Here is the input of my dynamics process, >> > &CONTROL >> > >> > title = 'CP' >> > , >> > calculation = 'cp' >> > , >> > restart_mode = 'restart' >> > , >> > outdir = '/disk5/nanjing/vega/cp/300/' , >> > wfcdir = '/tmp/' >> > , >> > pseudo_dir = >> > '/home/software/nanjing/vega/espresso-4.0.1/pseudo/' , >> > prefix = 'cp_molecular' , >> > nstep = 99999 , >> > dt = 10, >> > iprint = 5, >> > isave = >> > 150, >> > / >> > >> > &SYSTEM >> > >> > ibrav = >> > 8, >> > celldm(1) =24.8624, >> > celldm(2) = 0.8520, >> > celldm(3) = 1.6964, >> > nat = >> > 147, >> > ntyp = 3, >> > nr1b = 20, >> > nr2b = 20, >> > nr3b = 20, >> > nbnd = >> > 630, >> > ecutwfc = 30, >> > ecutrho = 300, >> > / >> > >> > >> > &ELECTRONS >> > electron_dynamics = 'verlet', >> > / >> > >> > &IONS >> > >> > ion_dynamics = 'verlet' >> > ion_temperature = 'nose', >> > tempw = 300, >> > / >> > .................. >> > .................. >> > >> > best wishes, >> > >> > vega >> > >> > -- >> > >> ================================================================================== >> > Vega Lew ( weijia liu) >> > Graduate student >> > 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 >> > >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > > ================================================================================== > Vega Lew ( weijia liu) > Graduate student > 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 > > -- Somesh Kr. Bhattacharya Post Doctoral Fellow Room No. 263, Leonardo Building, The Abdus Salam International Centre for Theoretical Physics Strada Costiera, 11 I-34014 Trieste Italy Phone: +39-040-2240399 http://portal.ictp.it/cmsp/members/postdoctoral-fellows/somesh-kumar-bhattacharya/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091127/e629a11b/attachment.htm From quantumdft at gmail.com Fri Nov 27 13:26:03 2009 From: quantumdft at gmail.com (vega lew) Date: Fri, 27 Nov 2009 04:26:03 -0800 Subject: [Pw_forum] Temperature continuously going down in cp.x run In-Reply-To: References: <412f6c680911270110p365d8d5cvcb7f0048afc398d@mail.gmail.com> <4B0FA3A7.8060408@sissa.it> <412f6c680911270342o3676ebe1ucd37f7969c03c411@mail.gmail.com> Message-ID: <412f6c680911270426q7ab8893bxab9bb3aae53e55bc@mail.gmail.com> Dear friend, thank you for you information. I attach the file in the list. In the file, I find the 8th column is not remain the same. thank you again. vega On Fri, Nov 27, 2009 at 4:04 AM, Somesh Kumar Bhattacharya < somesh.kb at gmail.com> wrote: > Dear Vega, > > The CP program prints different energy in the output file *.evp. In this > file the eighth column is the constant of motion which should remain a > constant. Plot this eighth column vs the timesteps and see what fluctuations > are you getting in the plot. > > This is I guess what Stefano asked you. > > Regards, > > Somesh > > > On Fri, Nov 27, 2009 at 12:42 PM, vega lew wrote: > >> Dear sir, >> >> Did you ask whether the (etot+ekinc) conserve during the dynamic process? >> >> I sum the corresponding columns. I found it is not changing very much. >> >> For example, the (ekinc+ etot) is -4369.40879 (-4369.44669+0.0379) at 2200 >> step. >> Then it changes to -4369.41514 (-4369.45479+0.03965) at 2300 step. >> And it sometimes goes a little up and sometimes a little down. But the >> value is in range of >> -4369.41 and -4369.45. >> >> thank you for reading. >> >> vega >> >> >> >> On Fri, Nov 27, 2009 at 2:02 AM, Stefano de Gironcoli wrote: >> >>> is the total (kinetic + potential) energy conserved ? >>> stefano >>> >>> vega lew wrote: >>> > dear all, >>> > >>> > I want to calculate certain heterogeneous reaction on a solid surface. >>> > First input the initial structure from previous pw.x relaxations. >>> > Second I fixed ions and let electron damping calculation run; >>> > Then un-fixed the ions and let both electron and ions damping >>> > calculations run. >>> > Third I gave a random motion to the atoms in the system with >>> > amprp(1)~(3) = 0.01 >>> > and then repeated second step to bring the system to the ground state. >>> > Fourth I added temperature (300K) to the system, using verlet schedule. >>> > >>> > But the temperature continuously going down, from 1000K to 150K during >>> > the fisrt 3000 steps. >>> > I think there might be something wrong with my cp.x calcuation. >>> > Do you think the amprp(1)~(3) = 0.01 of random motion is too small? >>> > >>> > Here is the input of my dynamics process, >>> > &CONTROL >>> > >>> > title = 'CP' >>> > , >>> > calculation = 'cp' >>> > , >>> > restart_mode = 'restart' >>> > , >>> > outdir = '/disk5/nanjing/vega/cp/300/' , >>> > wfcdir = '/tmp/' >>> > , >>> > pseudo_dir = >>> > '/home/software/nanjing/vega/espresso-4.0.1/pseudo/' , >>> > prefix = 'cp_molecular' , >>> > nstep = 99999 , >>> > dt = 10, >>> > iprint = 5, >>> > isave = >>> > 150, >>> > / >>> > >>> > &SYSTEM >>> > >>> > ibrav = >>> > 8, >>> > celldm(1) =24.8624, >>> > celldm(2) = 0.8520, >>> > celldm(3) = 1.6964, >>> > nat = >>> > 147, >>> > ntyp = 3, >>> > nr1b = 20, >>> > nr2b = 20, >>> > nr3b = 20, >>> > nbnd = >>> > 630, >>> > ecutwfc = 30, >>> > ecutrho = 300, >>> > / >>> > >>> > >>> > &ELECTRONS >>> > electron_dynamics = 'verlet', >>> > / >>> > >>> > &IONS >>> > >>> > ion_dynamics = 'verlet' >>> > ion_temperature = 'nose', >>> > tempw = 300, >>> > / >>> > .................. >>> > .................. >>> > >>> > best wishes, >>> > >>> > vega >>> > >>> > -- >>> > >>> ================================================================================== >>> > Vega Lew ( weijia liu) >>> > Graduate student >>> > 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 >>> > >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >> >> >> >> -- >> >> ================================================================================== >> Vega Lew ( weijia liu) >> Graduate student >> 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 >> >> > > > -- > Somesh Kr. Bhattacharya > Post Doctoral Fellow > Room No. 263, > Leonardo Building, > The Abdus Salam International Centre for Theoretical Physics > Strada Costiera, 11 > I-34014 Trieste > Italy > Phone: +39-040-2240399 > > http://portal.ictp.it/cmsp/members/postdoctoral-fellows/somesh-kumar-bhattacharya/ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091127/dea97c06/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: cp_molecular.evp Type: application/octet-stream Size: 45551 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20091127/dea97c06/attachment-0001.obj From nkxirainbow at gmail.com Fri Nov 27 13:27:24 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Fri, 27 Nov 2009 12:27:24 +0000 Subject: [Pw_forum] Books related to Projected density of states In-Reply-To: References: Message-ID: <21fbc4790911270427g3663f170x2f3f6e38359356b3@mail.gmail.com> Dear Dimpy I can not give your any reference books. But ,I hope the following website can give you some help?? https://wiki.fysik.dtu.dk/gpaw/documentation/pdos/pdos.html On Fri, Nov 27, 2009 at 12:05 PM, Dimpy Sharma wrote: > > Hi there, > > My question has not been answered, I would like to know some reference > books for studying Projected density of states. > > Thanks and regards > > Dimpy > > Dimpy Sharma > PhD ( Nanotechnology) > UCC > Cork > Ireland > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091127/4465cce1/attachment.htm From degironc at sissa.it Fri Nov 27 13:27:42 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 27 Nov 2009 13:27:42 +0100 Subject: [Pw_forum] Books related to Projected density of states In-Reply-To: References: Message-ID: <4B0FC5BE.3000000@sissa.it> Solids and Surfaces: A chemist's view of bonding in extended systems by Roald Hoffman I don't know if this can be called a reference book but it explains things in a simple terms. Stefano de Gironcoli Dimpy Sharma wrote: > > Hi there, > > My question has not been answered, I would like to know some reference > books for studying Projected density of states. > > Thanks and regards > > Dimpy > > Dimpy Sharma > PhD ( Nanotechnology) > UCC > Cork > Ireland > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From somesh.kb at gmail.com Fri Nov 27 13:33:39 2009 From: somesh.kb at gmail.com (Somesh Kumar Bhattacharya) Date: Fri, 27 Nov 2009 13:33:39 +0100 Subject: [Pw_forum] Temperature continuously going down in cp.x run In-Reply-To: <412f6c680911270426q7ab8893bxab9bb3aae53e55bc@mail.gmail.com> References: <412f6c680911270110p365d8d5cvcb7f0048afc398d@mail.gmail.com> <4B0FA3A7.8060408@sissa.it> <412f6c680911270342o3676ebe1ucd37f7969c03c411@mail.gmail.com> <412f6c680911270426q7ab8893bxab9bb3aae53e55bc@mail.gmail.com> Message-ID: Dear Vega, something is wrong in your simulation. I don't know exactly what. The constant of motion is changing by 0.01 hartree which is quite significant. Regards, Somesh On Fri, Nov 27, 2009 at 1:26 PM, vega lew wrote: > Dear friend, > > thank you for you information. > I attach the file in the list. In the file, I find the 8th column is not > remain the same. > > thank you again. > > vega > > > On Fri, Nov 27, 2009 at 4:04 AM, Somesh Kumar Bhattacharya < > somesh.kb at gmail.com> wrote: > >> Dear Vega, >> >> The CP program prints different energy in the output file *.evp. In this >> file the eighth column is the constant of motion which should remain a >> constant. Plot this eighth column vs the timesteps and see what fluctuations >> are you getting in the plot. >> >> This is I guess what Stefano asked you. >> >> Regards, >> >> Somesh >> >> >> On Fri, Nov 27, 2009 at 12:42 PM, vega lew wrote: >> >>> Dear sir, >>> >>> Did you ask whether the (etot+ekinc) conserve during the dynamic process? >>> >>> I sum the corresponding columns. I found it is not changing very much. >>> >>> For example, the (ekinc+ etot) is -4369.40879 (-4369.44669+0.0379) at >>> 2200 step. >>> Then it changes to -4369.41514 (-4369.45479+0.03965) at 2300 step. >>> And it sometimes goes a little up and sometimes a little down. But the >>> value is in range of >>> -4369.41 and -4369.45. >>> >>> thank you for reading. >>> >>> vega >>> >>> >>> >>> On Fri, Nov 27, 2009 at 2:02 AM, Stefano de Gironcoli >> > wrote: >>> >>>> is the total (kinetic + potential) energy conserved ? >>>> stefano >>>> >>>> vega lew wrote: >>>> > dear all, >>>> > >>>> > I want to calculate certain heterogeneous reaction on a solid surface. >>>> > First input the initial structure from previous pw.x relaxations. >>>> > Second I fixed ions and let electron damping calculation run; >>>> > Then un-fixed the ions and let both electron and ions damping >>>> > calculations run. >>>> > Third I gave a random motion to the atoms in the system with >>>> > amprp(1)~(3) = 0.01 >>>> > and then repeated second step to bring the system to the ground state. >>>> > Fourth I added temperature (300K) to the system, using verlet >>>> schedule. >>>> > >>>> > But the temperature continuously going down, from 1000K to 150K during >>>> > the fisrt 3000 steps. >>>> > I think there might be something wrong with my cp.x calcuation. >>>> > Do you think the amprp(1)~(3) = 0.01 of random motion is too small? >>>> > >>>> > Here is the input of my dynamics process, >>>> > &CONTROL >>>> > >>>> > title = 'CP' >>>> > , >>>> > calculation = 'cp' >>>> > , >>>> > restart_mode = 'restart' >>>> > , >>>> > outdir = '/disk5/nanjing/vega/cp/300/' , >>>> > wfcdir = '/tmp/' >>>> > , >>>> > pseudo_dir = >>>> > '/home/software/nanjing/vega/espresso-4.0.1/pseudo/' , >>>> > prefix = 'cp_molecular' , >>>> > nstep = 99999 , >>>> > dt = 10, >>>> > iprint = 5, >>>> > isave = >>>> > 150, >>>> > / >>>> > >>>> > &SYSTEM >>>> > >>>> > ibrav = >>>> > 8, >>>> > celldm(1) =24.8624, >>>> > celldm(2) = 0.8520, >>>> > celldm(3) = 1.6964, >>>> > nat = >>>> > 147, >>>> > ntyp = 3, >>>> > nr1b = 20, >>>> > nr2b = 20, >>>> > nr3b = 20, >>>> > nbnd = >>>> > 630, >>>> > ecutwfc = 30, >>>> > ecutrho = 300, >>>> > / >>>> > >>>> > >>>> > &ELECTRONS >>>> > electron_dynamics = 'verlet', >>>> > / >>>> > >>>> > &IONS >>>> > >>>> > ion_dynamics = 'verlet' >>>> > ion_temperature = 'nose', >>>> > tempw = 300, >>>> > / >>>> > .................. >>>> > .................. >>>> > >>>> > best wishes, >>>> > >>>> > vega >>>> > >>>> > -- >>>> > >>>> ================================================================================== >>>> > Vega Lew ( weijia liu) >>>> > Graduate student >>>> > 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 >>>> > >>>> >>>> _______________________________________________ >>>> Pw_forum mailing list >>>> Pw_forum at pwscf.org >>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>> >>> >>> >>> >>> -- >>> >>> ================================================================================== >>> Vega Lew ( weijia liu) >>> Graduate student >>> 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 >>> >>> >> >> >> -- >> Somesh Kr. Bhattacharya >> Post Doctoral Fellow >> Room No. 263, >> Leonardo Building, >> The Abdus Salam International Centre for Theoretical Physics >> Strada Costiera, 11 >> I-34014 Trieste >> Italy >> Phone: +39-040-2240399 >> >> http://portal.ictp.it/cmsp/members/postdoctoral-fellows/somesh-kumar-bhattacharya/ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > > ================================================================================== > Vega Lew ( weijia liu) > Graduate student > 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 > > -- Somesh Kr. Bhattacharya Post Doctoral Fellow Room No. 263, Leonardo Building, The Abdus Salam International Centre for Theoretical Physics Strada Costiera, 11 I-34014 Trieste Italy Phone: +39-040-2240399 http://portal.ictp.it/cmsp/members/postdoctoral-fellows/somesh-kumar-bhattacharya/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091127/e5f22c95/attachment.htm From giannozz at democritos.it Fri Nov 27 13:50:17 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 27 Nov 2009 13:50:17 +0100 Subject: [Pw_forum] Temperature continuously going down in cp.x run In-Reply-To: <412f6c680911270110p365d8d5cvcb7f0048afc398d@mail.gmail.com> References: <412f6c680911270110p365d8d5cvcb7f0048afc398d@mail.gmail.com> Message-ID: <4B0FCB09.7020405@democritos.it> vega lew wrote: > But the temperature continuously going down, from 1000K to 150K during > the fisrt 3000 steps. you are using the Nose' thermostat. It is quite normal that the temperature makes wide oscillation around the required value. Do you know how to use it? if not, please stop computing and start reading some documentation and literature P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From quantumdft at gmail.com Fri Nov 27 13:53:42 2009 From: quantumdft at gmail.com (vega lew) Date: Fri, 27 Nov 2009 04:53:42 -0800 Subject: [Pw_forum] Temperature continuously going down in cp.x run In-Reply-To: <4B0FCB09.7020405@democritos.it> References: <412f6c680911270110p365d8d5cvcb7f0048afc398d@mail.gmail.com> <4B0FCB09.7020405@democritos.it> Message-ID: <412f6c680911270453o30228687wf63623cd185af16a@mail.gmail.com> Dear sir, The temperature is not oscillation around the required value. But it is always decreasing. thank you for reading vega On Fri, Nov 27, 2009 at 4:50 AM, Paolo Giannozzi wrote: > vega lew wrote: > > > But the temperature continuously going down, from 1000K to 150K during > > the fisrt 3000 steps. > > you are using the Nose' thermostat. It is quite normal that the > temperature makes wide oscillation around the required value. > Do you know how to use it? if not, please stop computing and > start reading some documentation and literature > > 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 > -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091127/0429edce/attachment.htm From quantumdft at gmail.com Fri Nov 27 14:02:56 2009 From: quantumdft at gmail.com (vega lew) Date: Fri, 27 Nov 2009 05:02:56 -0800 Subject: [Pw_forum] Temperature continuously going down in cp.x run In-Reply-To: References: <412f6c680911270110p365d8d5cvcb7f0048afc398d@mail.gmail.com> <4B0FA3A7.8060408@sissa.it> <412f6c680911270342o3676ebe1ucd37f7969c03c411@mail.gmail.com> <412f6c680911270426q7ab8893bxab9bb3aae53e55bc@mail.gmail.com> Message-ID: <412f6c680911270502kc6f276ckda7816ab65c49517@mail.gmail.com> Dear Somesh, do you think this is reasonable when all the atoms in my system is at their equilibrium position? vega On Fri, Nov 27, 2009 at 4:33 AM, Somesh Kumar Bhattacharya < somesh.kb at gmail.com> wrote: > Dear Vega, > > something is wrong in your simulation. I don't know exactly what. The > constant of motion is changing by 0.01 hartree which is quite significant. > > Regards, > > Somesh > > > On Fri, Nov 27, 2009 at 1:26 PM, vega lew wrote: > >> Dear friend, >> >> thank you for you information. >> I attach the file in the list. In the file, I find the 8th column is not >> remain the same. >> >> thank you again. >> >> vega >> >> >> On Fri, Nov 27, 2009 at 4:04 AM, Somesh Kumar Bhattacharya < >> somesh.kb at gmail.com> wrote: >> >>> Dear Vega, >>> >>> The CP program prints different energy in the output file *.evp. In this >>> file the eighth column is the constant of motion which should remain a >>> constant. Plot this eighth column vs the timesteps and see what fluctuations >>> are you getting in the plot. >>> >>> This is I guess what Stefano asked you. >>> >>> Regards, >>> >>> Somesh >>> >>> >>> On Fri, Nov 27, 2009 at 12:42 PM, vega lew wrote: >>> >>>> Dear sir, >>>> >>>> Did you ask whether the (etot+ekinc) conserve during the dynamic >>>> process? >>>> >>>> I sum the corresponding columns. I found it is not changing very much. >>>> >>>> For example, the (ekinc+ etot) is -4369.40879 (-4369.44669+0.0379) at >>>> 2200 step. >>>> Then it changes to -4369.41514 (-4369.45479+0.03965) at 2300 step. >>>> And it sometimes goes a little up and sometimes a little down. But the >>>> value is in range of >>>> -4369.41 and -4369.45. >>>> >>>> thank you for reading. >>>> >>>> vega >>>> >>>> >>>> >>>> On Fri, Nov 27, 2009 at 2:02 AM, Stefano de Gironcoli < >>>> degironc at sissa.it> wrote: >>>> >>>>> is the total (kinetic + potential) energy conserved ? >>>>> stefano >>>>> >>>>> vega lew wrote: >>>>> > dear all, >>>>> > >>>>> > I want to calculate certain heterogeneous reaction on a solid >>>>> surface. >>>>> > First input the initial structure from previous pw.x relaxations. >>>>> > Second I fixed ions and let electron damping calculation run; >>>>> > Then un-fixed the ions and let both electron and ions damping >>>>> > calculations run. >>>>> > Third I gave a random motion to the atoms in the system with >>>>> > amprp(1)~(3) = 0.01 >>>>> > and then repeated second step to bring the system to the ground >>>>> state. >>>>> > Fourth I added temperature (300K) to the system, using verlet >>>>> schedule. >>>>> > >>>>> > But the temperature continuously going down, from 1000K to 150K >>>>> during >>>>> > the fisrt 3000 steps. >>>>> > I think there might be something wrong with my cp.x calcuation. >>>>> > Do you think the amprp(1)~(3) = 0.01 of random motion is too small? >>>>> > >>>>> > Here is the input of my dynamics process, >>>>> > &CONTROL >>>>> > >>>>> > title = 'CP' >>>>> > , >>>>> > calculation = 'cp' >>>>> > , >>>>> > restart_mode = 'restart' >>>>> > , >>>>> > outdir = '/disk5/nanjing/vega/cp/300/' , >>>>> > wfcdir = '/tmp/' >>>>> > , >>>>> > pseudo_dir = >>>>> > '/home/software/nanjing/vega/espresso-4.0.1/pseudo/' , >>>>> > prefix = 'cp_molecular' , >>>>> > nstep = 99999 , >>>>> > dt = 10, >>>>> > iprint = 5, >>>>> > isave = >>>>> > 150, >>>>> > / >>>>> > >>>>> > &SYSTEM >>>>> > >>>>> > ibrav = >>>>> > 8, >>>>> > celldm(1) =24.8624, >>>>> > celldm(2) = 0.8520, >>>>> > celldm(3) = 1.6964, >>>>> > nat = >>>>> > 147, >>>>> > ntyp = 3, >>>>> > nr1b = 20, >>>>> > nr2b = 20, >>>>> > nr3b = 20, >>>>> > nbnd = >>>>> > 630, >>>>> > ecutwfc = 30, >>>>> > ecutrho = 300, >>>>> > / >>>>> > >>>>> > >>>>> > &ELECTRONS >>>>> > electron_dynamics = 'verlet', >>>>> > / >>>>> > >>>>> > &IONS >>>>> > >>>>> > ion_dynamics = 'verlet' >>>>> > ion_temperature = 'nose', >>>>> > tempw = 300, >>>>> > / >>>>> > .................. >>>>> > .................. >>>>> > >>>>> > best wishes, >>>>> > >>>>> > vega >>>>> > >>>>> > -- >>>>> > >>>>> ================================================================================== >>>>> > Vega Lew ( weijia liu) >>>>> > Graduate student >>>>> > 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 >>>>> > >>>>> >>>>> _______________________________________________ >>>>> Pw_forum mailing list >>>>> Pw_forum at pwscf.org >>>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>>> >>>> >>>> >>>> >>>> -- >>>> >>>> ================================================================================== >>>> Vega Lew ( weijia liu) >>>> Graduate student >>>> 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 >>>> >>>> >>> >>> >>> -- >>> Somesh Kr. Bhattacharya >>> Post Doctoral Fellow >>> Room No. 263, >>> Leonardo Building, >>> The Abdus Salam International Centre for Theoretical Physics >>> Strada Costiera, 11 >>> I-34014 Trieste >>> Italy >>> Phone: +39-040-2240399 >>> >>> http://portal.ictp.it/cmsp/members/postdoctoral-fellows/somesh-kumar-bhattacharya/ >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> >> -- >> >> ================================================================================== >> Vega Lew ( weijia liu) >> Graduate student >> 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 >> >> > > > -- > Somesh Kr. Bhattacharya > Post Doctoral Fellow > Room No. 263, > Leonardo Building, > The Abdus Salam International Centre for Theoretical Physics > Strada Costiera, 11 > I-34014 Trieste > Italy > Phone: +39-040-2240399 > > http://portal.ictp.it/cmsp/members/postdoctoral-fellows/somesh-kumar-bhattacharya/ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091127/c5a52515/attachment-0001.htm From duchl06 at 163.com Fri Nov 27 15:16:24 2009 From: duchl06 at 163.com (duchl06) Date: Fri, 27 Nov 2009 22:16:24 +0800 (CST) Subject: [Pw_forum] request help for gaas band structure In-Reply-To: References: <130685.19005.qm@web65712.mail.ac4.yahoo.com> <145848.73984.qm@web65713.mail.ac4.yahoo.com> Message-ID: <26415054.401841259331384277.JavaMail.coremail@app151.163.com> Hi Mohsen Modaresi you can set the energy zero point in the plotbands.x input file. best regards! du ?2009-11-26?"mohsen modaresi" ??? Dear Eyvaz Thanks for your answers I changed lattice parameter to 10.68 Bohr, and i attach again results, after this the results improved, but energy scale is not match. I used this kind of pseudopotentials 'Scalar-Relativistic Calculation'. Is there any mistake? Another question : Where i can change 'spin-relativistic band structure', i did not inter relativistic feature in my pw input file. Thanks Mohsen Modaresi Where i can change relativistic calculation for On Thu, Nov 26, 2009 at 5:20 AM, Eyvaz Isaev wrote: > > But looking at your band structure it seems you deal with > spin-relativistic band structure for GaAs. Sorry, relativistic band structure, of course. I have misprinted. 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 _______________________________________________ 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/20091127/b09808aa/attachment.htm From modaresi.mohsen at gmail.com Fri Nov 27 15:56:41 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Fri, 27 Nov 2009 17:56:41 +0300 Subject: [Pw_forum] request help for gaas band structure In-Reply-To: <26415054.401841259331384277.JavaMail.coremail@app151.163.com> References: <130685.19005.qm@web65712.mail.ac4.yahoo.com> <145848.73984.qm@web65713.mail.ac4.yahoo.com> <26415054.401841259331384277.JavaMail.coremail@app151.163.com> Message-ID: Dear duchl Thanks, It worked properly. Thank for your helpful advise. Mohsen Mosaresi 2009/11/27 duchl06 > Hi Mohsen Modaresi > you can set the energy zero point in the plotbands.x input file. > best regards! > > > du > > ?2009-11-26?"mohsen modaresi" ??? > > Dear Eyvaz > Thanks for your answers > I changed lattice parameter to 10.68 Bohr, and i attach again results, > after this the results improved, but energy scale is not match. > I used this kind of pseudopotentials 'Scalar-Relativistic Calculation'. > Is there any mistake? > Another question : > Where i can change 'spin-relativistic band structure', i did not inter > relativistic feature in my pw input file. > Thanks > Mohsen Modaresi > Where i can change relativistic calculation for > On Thu, Nov 26, 2009 at 5:20 AM, Eyvaz Isaev wrote: > >> >> > >> > But looking at your band structure it seems you deal with >> > spin-relativistic band structure for GaAs. >> >> Sorry, relativistic band structure, of course. I have misprinted. >> >> >> 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 >> >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > ------------------------------ > 09???3D?????????????????? > _______________________________________________ > 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/20091127/e4e415ea/attachment.htm From aschauer at princeton.edu Fri Nov 27 16:32:11 2009 From: aschauer at princeton.edu (Uli Aschauer) Date: Fri, 27 Nov 2009 10:32:11 -0500 Subject: [Pw_forum] Temperature continuously going down in cp.x run In-Reply-To: <412f6c680911270110p365d8d5cvcb7f0048afc398d@mail.gmail.com> References: <412f6c680911270110p365d8d5cvcb7f0048afc398d@mail.gmail.com> Message-ID: <91556257-88ED-4854-95E3-EF349E52F611@princeton.edu> Dear Vega, Your choice of dt=10 seems a bit large to me for dynamics. You will have to find a good value of dt combined with emass (for which you take the default value of 400) to conserve the energy in your system. To understand what this is all about I would suggest you to read at least the relevant section (2.4.4) herein: http://www.fz-juelich.de/nic-series/Volume1/marx.pdf For the Nose thermostat you not only set the target temperature but also the frequency. The default may be completely out of the range of the frequencies you try to excite in your system. As Paolo suggested, you will almost certainly have to tune the Nose parameters to get effective thermostatting. As for the amplitude of the randomization it does not really matter all that much. You will just spend a lot less computer time if you choose a value to give you something close to the temperature you want. You can randomize a few different amplitudes and then run dynamics without thermostat to see what temperature you converge to after a few hundred steps (given your dynamics is setup correctly). This allows you to make sort of a calibration of the temperature as a function of the randomization amplitude for your system. Best regards, -uli _________________________________________________________ Uli Aschauer Princeton University Chemistry Department Frick Laboratory, Room 213 Princeton, NJ 08544 Tel: +1-609-258-0116 Email: aschauer at princeton.edu _________________________________________________________ On 27.11.2009, at 04:10, vega lew wrote: > dear all, > > I want to calculate certain heterogeneous reaction on a solid surface. > First input the initial structure from previous pw.x relaxations. > Second I fixed ions and let electron damping calculation run; > Then un-fixed the ions and let both electron and ions damping calculations run. > Third I gave a random motion to the atoms in the system with amprp(1)~(3) = 0.01 > and then repeated second step to bring the system to the ground state. > Fourth I added temperature (300K) to the system, using verlet schedule. > > But the temperature continuously going down, from 1000K to 150K during the fisrt 3000 steps. > I think there might be something wrong with my cp.x calcuation. > Do you think the amprp(1)~(3) = 0.01 of random motion is too small? > > Here is the input of my dynamics process, > &CONTROL > title = 'CP' , > calculation = 'cp' , > restart_mode = 'restart' , > outdir = '/disk5/nanjing/vega/cp/300/' , > wfcdir = '/tmp/' , > pseudo_dir = '/home/software/nanjing/vega/espresso-4.0.1/pseudo/' , > prefix = 'cp_molecular' , > nstep = 99999 , > dt = 10, > iprint = 5, > isave = 150, > / > &SYSTEM > ibrav = 8, > celldm(1) =24.8624, > celldm(2) = 0.8520, > celldm(3) = 1.6964, > nat = 147, > ntyp = 3, > nr1b = 20, > nr2b = 20, > nr3b = 20, > nbnd = 630, > ecutwfc = 30, > ecutrho = 300, > / > > &ELECTRONS > electron_dynamics = 'verlet', > / > &IONS > ion_dynamics = 'verlet' > ion_temperature = 'nose', > tempw = 300, > / > .................. > .................. > > best wishes, > > vega > > -- > ================================================================================== > Vega Lew ( weijia liu) > Graduate student > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091127/7f7dffdb/attachment-0001.htm From quantumdft at gmail.com Fri Nov 27 16:52:58 2009 From: quantumdft at gmail.com (vega lew) Date: Fri, 27 Nov 2009 07:52:58 -0800 Subject: [Pw_forum] Temperature continuously going down in cp.x run In-Reply-To: <91556257-88ED-4854-95E3-EF349E52F611@princeton.edu> References: <412f6c680911270110p365d8d5cvcb7f0048afc398d@mail.gmail.com> <91556257-88ED-4854-95E3-EF349E52F611@princeton.edu> Message-ID: <412f6c680911270752m6c8359ceyb28482155babc95@mail.gmail.com> Dear Uli, Thank you for your time. I'll read it and try to find more reasonable dt and emass. Could you please tell me more about how to choose a suitable frequencies for thermostat? best, vega On Fri, Nov 27, 2009 at 7:32 AM, Uli Aschauer wrote: > Dear Vega, > > Your choice of dt=10 seems a bit large to me for dynamics. You will have to > find a good value of dt combined with emass (for which you take the default > value of 400) to conserve the energy in your system. To understand what this > is all about I would suggest you to read at least the relevant section > (2.4.4) herein: http://www.fz-juelich.de/nic-series/Volume1/marx.pdf > > For the Nose thermostat you not only set the target temperature but also > the frequency. The default may be completely out of the range of the > frequencies you try to excite in your system. As Paolo suggested, you will > almost certainly have to tune the Nose parameters to get effective > thermostatting. > > As for the amplitude of the randomization it does not really matter all > that much. You will just spend a lot less computer time if you choose a > value to give you something close to the temperature you want. You can > randomize a few different amplitudes and then run dynamics without > thermostat to see what temperature you converge to after a few hundred steps > (given your dynamics is setup correctly). This allows you to make sort of a > calibration of the temperature as a function of the randomization amplitude > for your system. > > Best regards, > -uli > > _________________________________________________________ > Uli Aschauer > Princeton University > Chemistry Department > Frick Laboratory, Room 213 > Princeton, NJ 08544 > Tel: +1-609-258-0116 > Email: aschauer at princeton.edu > _________________________________________________________ > > On 27.11.2009, at 04:10, vega lew wrote: > > dear all, > > I want to calculate certain heterogeneous reaction on a solid surface. > First input the initial structure from previous pw.x relaxations. > Second I fixed ions and let electron damping calculation run; > Then un-fixed the ions and let both electron and ions damping calculations > run. > Third I gave a random motion to the atoms in the system with amprp(1)~(3) = > 0.01 > and then repeated second step to bring the system to the ground state. > Fourth I added temperature (300K) to the system, using verlet schedule. > > But the temperature continuously going down, from 1000K to 150K during the > fisrt 3000 steps. > I think there might be something wrong with my cp.x calcuation. > Do you think the amprp(1)~(3) = 0.01 of random motion is too small? > > Here is the input of my dynamics process, > &CONTROL > > title = 'CP' > , > calculation = 'cp' > , > restart_mode = 'restart' > , > outdir = '/disk5/nanjing/vega/cp/300/' , > wfcdir = '/tmp/' > , > pseudo_dir = > '/home/software/nanjing/vega/espresso-4.0.1/pseudo/' , > prefix = 'cp_molecular' , > nstep = 99999 , > dt = 10, > iprint = 5, > isave = > 150, > / > > &SYSTEM > > ibrav = > 8, > celldm(1) =24.8624, > celldm(2) = 0.8520, > celldm(3) = 1.6964, > nat = > 147, > ntyp = 3, > nr1b = 20, > nr2b = 20, > nr3b = 20, > nbnd = > 630, > ecutwfc = 30, > ecutrho = 300, > / > > > &ELECTRONS > electron_dynamics = 'verlet', > / > > &IONS > > ion_dynamics = 'verlet' > ion_temperature = 'nose', > tempw = 300, > / > .................. > .................. > > best wishes, > > vega > > -- > > ================================================================================== > Vega Lew ( weijia liu) > Graduate student > 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 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091127/60e983f2/attachment.htm From prasenjit.jnc at gmail.com Fri Nov 27 18:49:00 2009 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Fri, 27 Nov 2009 18:49:00 +0100 Subject: [Pw_forum] validation of energy values In-Reply-To: <84ff69170911262153y68ff2365h6c4b65506b345638@mail.gmail.com> References: <84ff69170911262153y68ff2365h6c4b65506b345638@mail.gmail.com> Message-ID: <627e0ffa0911270949u7491907dwc9a31ae5efeab18f@mail.gmail.com> Dear Vamsi, H2O is a polar molecule. The long range dipole moment interaction between the periodic images will result in a fictitious electric field acting on the molecule. I think 20 bohrs is probably not enough to reduce the interaction between the periodic images. You can check this either by varying the box size & check the convergence in total energy wrt the box size or else you can use pp.x and plot the electrostatic potential (plot_num=11) along the direction in which the distance between the molecules are minimum. In the vacuum region, the potential should be flat if there is no interaction between the periodic charges. Hope this helps, With regards, Prasenjit. 2009/11/27 vamsi kv > Dear PWScf users, > > I want to study the interaction of H2O with Fe surfaces. I have choosen the > potential and cutoffs for Fe by validating with experimental vaues like > lattice parameter and cohesive energy. My question is when it comes to gas > or liquid molecules how can i validate the output values of the simulations. > I am getting the bond length and bond angle correctly within 1% error on > relaxing the structure in a supercell of 20 bohrs . But I was trying to > validate with heat of formation of H2O and i am not successful. > Can any one help me in resolving my problem > > > Thanks & Regards > K V Vamsi > > _______________________________________________ > 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) URL: http://portal.ictp.it/cmsp/members/postdoctoral-fellows/prasenjit-ghosh/prasenjit_ghosh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091127/cde02c25/attachment.htm From marzari at MIT.EDU Fri Nov 27 19:17:45 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Fri, 27 Nov 2009 13:17:45 -0500 Subject: [Pw_forum] Temperature continuously going down in cp.x run In-Reply-To: <412f6c680911270110p365d8d5cvcb7f0048afc398d@mail.gmail.com> References: <412f6c680911270110p365d8d5cvcb7f0048afc398d@mail.gmail.com> Message-ID: <4B1017C9.2050801@mit.edu> One more suggestion - before ever using any thermostat, make sure your microcanonical run runs fine - total constant of motion absolutely flat, constant, and a ficitituious kinetic energy for the electrons at least 10 times smaller than the ionic kinetic energy. Make sure this happens, before doing anything else. 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 quantumdft at gmail.com Sat Nov 28 03:36:59 2009 From: quantumdft at gmail.com (vega lew) Date: Fri, 27 Nov 2009 18:36:59 -0800 Subject: [Pw_forum] Temperature continuously going down in cp.x run In-Reply-To: <4B1017C9.2050801@mit.edu> References: <412f6c680911270110p365d8d5cvcb7f0048afc398d@mail.gmail.com> <4B1017C9.2050801@mit.edu> Message-ID: <412f6c680911271836u32c18932yda20f07bf06b3447@mail.gmail.com> Dear nicola, thank you suggestion. I'll make the NVE calculation after random the ions. I wonder what temperature is demand for the NVE? if the temperature is too high than the demanded temperature, should I make the smaller random again? For example, if the temperature is ~1000K after NVE, but the demanded is 300K, should I make the random process again using smaller amprp(1~3)? thank you vega On Fri, Nov 27, 2009 at 10:17 AM, Nicola Marzari wrote: > > > One more suggestion - before ever using any thermostat, make sure your > microcanonical run runs fine - total constant of motion absolutely flat, > constant, > and a ficitituious kinetic energy for the electrons at least 10 times > smaller than > the ionic kinetic energy. Make sure this happens, before doing anything > else. > > 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 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091127/8310aaf1/attachment-0001.htm From quantumdft at gmail.com Sat Nov 28 03:58:07 2009 From: quantumdft at gmail.com (vega lew) Date: Fri, 27 Nov 2009 18:58:07 -0800 Subject: [Pw_forum] How to decide fnosep for slab model describing the heterogeneous reaction Message-ID: <412f6c680911271858x60792c5cn9e43a65d27f256e4@mail.gmail.com> Dear all, I wonder how to decide the fnosep for the slab model describing the heterogeneous reaction. Should I using the IR vibrational spectrum tested by the experiment? if there are two or three character peak, should I average the three by relative intensity? best vega -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091127/565479e3/attachment.htm From marzari at MIT.EDU Sat Nov 28 15:47:04 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Sat, 28 Nov 2009 09:47:04 -0500 Subject: [Pw_forum] Temperature continuously going down in cp.x run In-Reply-To: <412f6c680911271836u32c18932yda20f07bf06b3447@mail.gmail.com> References: <412f6c680911270110p365d8d5cvcb7f0048afc398d@mail.gmail.com> <4B1017C9.2050801@mit.edu> <412f6c680911271836u32c18932yda20f07bf06b3447@mail.gmail.com> Message-ID: <4B1137E8.8070206@mit.edu> vega lew wrote: > Dear nicola, > > thank you suggestion. > I'll make the NVE calculation after random the ions. > > I wonder what temperature is demand for the NVE? > if the temperature is too high than the demanded temperature, should I > make the smaller random again? > For example, if the temperature is ~1000K after NVE, but the demanded > is 300K, should I make the random process again using smaller amprp(1~3)? > > thank you > > vega Correct. In NVE yuo have no option (of course) to set the temperature - you start froma distorted configuration, and the higher the potential energy of this inital configuration, the higher the average kinetic energy (i.e. temperature) of the equilibrated system. Very much worth experimenting with this, before moving on. 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 quantumdft at gmail.com Sat Nov 28 16:08:05 2009 From: quantumdft at gmail.com (vega lew) Date: Sat, 28 Nov 2009 07:08:05 -0800 Subject: [Pw_forum] Temperature continuously going down in cp.x run In-Reply-To: <4B1137E8.8070206@mit.edu> References: <412f6c680911270110p365d8d5cvcb7f0048afc398d@mail.gmail.com> <4B1017C9.2050801@mit.edu> <412f6c680911271836u32c18932yda20f07bf06b3447@mail.gmail.com> <4B1137E8.8070206@mit.edu> Message-ID: <412f6c680911280708q4784fec5sf72f5c486de581ab@mail.gmail.com> Dear nicola, thank you for you reply. I got another question after reading you repy. I random all the atoms that allowed to move during the simulation including the upper half of the slab and the adsorbate on the surface. I think what I want to see is the reaction on the surface. So should I only random the adsorbate with the all the atoms in slab fixed? Do you think this method will be more easy to achieve the desired temperature? By the way, during the NVE calculation, is there a command to keep the energy of the system? best vega On Sat, Nov 28, 2009 at 6:47 AM, Nicola Marzari wrote: > vega lew wrote: > > Dear nicola, > > > > thank you suggestion. > > I'll make the NVE calculation after random the ions. > > > > I wonder what temperature is demand for the NVE? > > if the temperature is too high than the demanded temperature, should I > > make the smaller random again? > > For example, if the temperature is ~1000K after NVE, but the demanded > > is 300K, should I make the random process again using smaller amprp(1~3)? > > > > thank you > > > > vega > > > Correct. In NVE yuo have no option (of course) to set the temperature - you > start froma distorted configuration, and the higher the potential energy > of this inital > configuration, the higher the average kinetic energy (i.e. temperature) > of the > equilibrated system. > > Very much worth experimenting with this, before moving on. > > 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 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091128/857fa749/attachment.htm From ppzang at gmail.com Sun Nov 29 07:57:00 2009 From: ppzang at gmail.com (Chenpeng Zang) Date: Sun, 29 Nov 2009 14:57:00 +0800 Subject: [Pw_forum] How to select plane? Message-ID: I want to display the contours of charge density on certain plane with XCrysDen. While it is quite successful to display that on the three basal planes, I cannot find a way to display charge density on other planes. For example, if I am interested in charge density on the plane [1,1,1], what can I do? I got my data from vasp with CHGCAR file, and use v2xsf to translate it into the xsf form. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091129/dce81e4d/attachment.htm From modaresi.mohsen at gmail.com Sun Nov 29 09:39:55 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Sun, 29 Nov 2009 12:09:55 +0330 Subject: [Pw_forum] a question about magnetization Message-ID: Dear users Suppose we have an orthorhombic structure which its unit cell contain (AAAABBCCCC), A and C are ferromagnet, we have 2 situation 1) A and B have parallel magnetization direction 2) A and C have anti parallel magnetization direction could i inter this deference in calculation (actually A and C are the same matter)? (This situation happened in GMR calculation in magnetic multi-layers) Thanks for your answers Mohsen Modaresi Msc. Student of Solid State Physics, Department of Physics,Ferdowsi University of Mashhad, Iran. ** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091129/ada36b56/attachment.htm From baris.malcioglu at gmail.com Sun Nov 29 09:59:39 2009 From: baris.malcioglu at gmail.com (O. Baris Malcioglu) Date: Sun, 29 Nov 2009 09:59:39 +0100 Subject: [Pw_forum] Do you think QE could benefit from the Hyper-Threading Tech of XEON 5500 series? In-Reply-To: <412f6c680911260923s7cd75b6er3d06dbc9f19a855b@mail.gmail.com> References: <412f6c680911260923s7cd75b6er3d06dbc9f19a855b@mail.gmail.com> Message-ID: Dear Vega, I am afraid what you are asking is a bit technical question that is not strictly related to Quantum Espresso. Perhaps the many discussions and benchmarks in the forums regarding the benefits/losses of hyper-threading in HPC environments may be of more use to you. If it will really help my "enthusiast" level, maybe outdated viewpoint on the matter is this. The cores enabled by Hyper-threading are not as performing as a "real" core, thus you obtain two somewhat crippled cores instead of one performing core. Now, if your memory bandwith is enough, and your program can take care of parallelization effectively this is a nice thing, it really makes things faster. But if your memory bandwith is not so high, you are wasting it for some crippled cores. If the program you are using is intensive on the memory, this is quite a bad thing no matter how well parallelized it is. Most of the server architectures like XEON are optimized for relialibility, and you will notice that most boards out there offer significantly less memory bandwith, especially if there are error correction measures, compared to their desktop equivalents. Adding this the fact that this already low bandwith is shared by many other cores, the memory bandwith becomes a very very precious resource in a server used in number crunching. Now, the performance of QE in such an environment will depend on how you use and compile it. In my experience using the "standart" parallelization with lapack/blas the QE is intensive on the memory of the cores, but somewhat light on the inter-core communication. In this case, the hyperthrading will probably slow things down on the single job level (Remember, HPCs are multi-user environments, if you have many users, although somewhat slow on the job level, hyperthreading might still be beneficial due to higher number of jobs accepted per unit time) Although I have not yet tested myself, threading instead of spawning processes like the openMP parallelization should work much better on the per job level in a hyper-threading environment, of course, provided you have proper threaded libraries installed and configured. For example MKL has threading support. So in short, if you are the single user of that machine, try OpenMP + threaded libraries. If it doesn't help try switching hyper threading off and compare your benchmarks. If you have many users, it is probably better to leave it on. I hope this helps, Best, Baris 2009/11/26 vega lew : > Dear all, > > I got 5 computers with two XEON 5520 and 24G memory. I find the > Hyper-Threading is switched on by default. I wonder if QE could benefit from > Hyper-Threading Tech. of Xeon CPUs? > Should I switch it off and trigger one process for each core to promote the > QE performance? > Or remain the Hyper-Threading on and trigger two processes for each core? > > best > > vega > > -- > ================================================================================== > Vega Lew ( weijia liu) > Graduate student > 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 > > From giannozz at democritos.it Sun Nov 29 10:41:54 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 29 Nov 2009 10:41:54 +0100 Subject: [Pw_forum] How to select plane? In-Reply-To: References: Message-ID: <293A8541-3906-42D5-9F24-E24550E68829@democritos.it> On Nov 29, 2009, at 7:57 , Chenpeng Zang wrote: > I want to display the contours of charge density on certain > plane with XCrysDen. the proper place where to ask questions on XCrySDen is the mailing list for XCrySDen. P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sun Nov 29 10:46:36 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 29 Nov 2009 10:46:36 +0100 Subject: [Pw_forum] Temperature continuously going down in cp.x run In-Reply-To: <412f6c680911280708q4784fec5sf72f5c486de581ab@mail.gmail.com> References: <412f6c680911270110p365d8d5cvcb7f0048afc398d@mail.gmail.com> <4B1017C9.2050801@mit.edu> <412f6c680911271836u32c18932yda20f07bf06b3447@mail.gmail.com> <4B1137E8.8070206@mit.edu> <412f6c680911280708q4784fec5sf72f5c486de581ab@mail.gmail.com> Message-ID: <0EFD92B3-B0D5-432B-9D35-47044AC028A4@democritos.it> On Nov 28, 2009, at 16:08 , vega lew wrote: > By the way, during the NVE calculation, is there a command > to keep the energy of the system? what do you mean? the total (kinetic+potential) energy is conserved during a (well-executed) NVE calculation. If you keep the kinetic energy constant (which you can do using velocity rescaling) it is no longer NVE Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sun Nov 29 10:49:10 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 29 Nov 2009 10:49:10 +0100 Subject: [Pw_forum] a question about magnetization In-Reply-To: References: Message-ID: <68343251-8628-437C-A20B-75003279A191@democritos.it> On Nov 29, 2009, at 9:39 , mohsen modaresi wrote: > 1) A and B have parallel magnetization direction > 2) A and C have anti parallel magnetization direction > could i inter this deference in calculation with an appropriate usage of "starting_magnetization" you should be able to select between a final state of type 1) or 2). Energy differences may turn out to be VERY small, though Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From quantumdft at gmail.com Sun Nov 29 19:31:32 2009 From: quantumdft at gmail.com (vega lew) Date: Mon, 30 Nov 2009 02:31:32 +0800 Subject: [Pw_forum] Temperature continuously going down in cp.x run In-Reply-To: <0EFD92B3-B0D5-432B-9D35-47044AC028A4@democritos.it> References: <412f6c680911270110p365d8d5cvcb7f0048afc398d@mail.gmail.com> <4B1017C9.2050801@mit.edu> <412f6c680911271836u32c18932yda20f07bf06b3447@mail.gmail.com> <4B1137E8.8070206@mit.edu> <412f6c680911280708q4784fec5sf72f5c486de581ab@mail.gmail.com> <0EFD92B3-B0D5-432B-9D35-47044AC028A4@democritos.it> Message-ID: <412f6c680911291031j673394b4yab5020a15fea3165@mail.gmail.com> Dear Paolo, Thank you for your reply. Now I realize the importance of NVE and make the total energy conserve. thank you again vega On Sun, Nov 29, 2009 at 5:46 PM, Paolo Giannozzi wrote: > > On Nov 28, 2009, at 16:08 , vega lew wrote: > > > By the way, during the NVE calculation, is there a command > > to keep the energy of the system? > > what do you mean? the total (kinetic+potential) energy is > conserved during a (well-executed) NVE calculation. If you > keep the kinetic energy constant (which you can do using > velocity rescaling) it is no longer NVE > > Paolo > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091130/d012e8f9/attachment.htm From quantumdft at gmail.com Sun Nov 29 19:45:13 2009 From: quantumdft at gmail.com (vega lew) Date: Mon, 30 Nov 2009 02:45:13 +0800 Subject: [Pw_forum] Do you think QE could benefit from the Hyper-Threading Tech of XEON 5500 series? In-Reply-To: References: <412f6c680911260923s7cd75b6er3d06dbc9f19a855b@mail.gmail.com> Message-ID: <412f6c680911291045s420e4d41g1c8292b43ee1bdd6@mail.gmail.com> Dear friend, thank you for your reply in detail. I also tested my servers using cp.x code with 5 steps running. The conclusion is Hyper-threading of Xeon E5520 will result in a small decrease of the performance. When the Hyper-threading is switched on in BIOS, two nodes with 32 process parallelly calculating the task will consume 2m19.41s CPU time, 6m37.24s wall time two nodes with 16 process parallelly calculating the task will consume 3m 7.28s CPU time, 7m 0.30s wall time one node with 16 process parallelly calculating the task will consume 5m30.79s CPU time, 6m18.88s wall time one node with 8 process parallelly calculating the task will consume 5m 2.42s CPU time, 8m50.53s wall time But when we switched off the Hyper-threading in BIOS, one node with 8 process parallelly calculating the task will consume 5m28.05s CPU time, 5m58.40s wall time two nodes with 16 process parallelly calculating the task will consume 2m32.28s CPU time, 6m16.31s wall tim thank you again for your time. best, vega On Sun, Nov 29, 2009 at 4:59 PM, O. Baris Malcioglu < baris.malcioglu at gmail.com> wrote: > Dear Vega, > > I am afraid what you are asking is a bit technical question that is > not strictly related to Quantum Espresso. Perhaps the many discussions > and benchmarks in the forums regarding the benefits/losses of > hyper-threading in HPC environments may be of more use to you. > > If it will really help my "enthusiast" level, maybe outdated viewpoint > on the matter is this. > > The cores enabled by Hyper-threading are not as performing as a "real" > core, thus you obtain two somewhat crippled cores instead of one > performing core. > > Now, if your memory bandwith is enough, and your program can take care > of parallelization effectively this is a nice thing, it really makes > things faster. > > But if your memory bandwith is not so high, you are wasting it for > some crippled cores. If the program you are using is intensive on the > memory, this is quite a bad thing no matter how well parallelized it > is. > > Most of the server architectures like XEON are optimized for > relialibility, and you will notice that most boards out there offer > significantly less memory bandwith, especially if there are error > correction measures, compared to their desktop equivalents. > > Adding this the fact that this already low bandwith is shared by many > other cores, the memory bandwith becomes a very very precious resource > in a server used in number crunching. > > Now, the performance of QE in such an environment will depend on how > you use and compile it. > > In my experience using the "standart" parallelization with lapack/blas > the QE is intensive on the memory of the cores, but somewhat light on > the inter-core communication. In this case, the hyperthrading will > probably slow things down on the single job level (Remember, HPCs are > multi-user environments, if you have many users, although somewhat > slow on the job level, hyperthreading might still be beneficial due to > higher number of jobs accepted per unit time) > > Although I have not yet tested myself, threading instead of spawning > processes like the openMP parallelization should work much better on > the per job level in a hyper-threading environment, of course, > provided you have proper threaded libraries installed and configured. > For example MKL has threading support. > > So in short, if you are the single user of that machine, try OpenMP + > threaded libraries. If it doesn't help try switching hyper threading > off and compare your benchmarks. If you have many users, it is > probably better to leave it on. > > I hope this helps, > > Best, > Baris > > > 2009/11/26 vega lew : > > Dear all, > > > > I got 5 computers with two XEON 5520 and 24G memory. I find the > > Hyper-Threading is switched on by default. I wonder if QE could benefit > from > > Hyper-Threading Tech. of Xeon CPUs? > > Should I switch it off and trigger one process for each core to promote > the > > QE performance? > > Or remain the Hyper-Threading on and trigger two processes for each core? > > > > best > > > > vega > > > > -- > > > ================================================================================== > > Vega Lew ( weijia liu) > > Graduate student > > 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 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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/20091130/3bfc1ef7/attachment-0001.htm From hqzhou at nju.edu.cn Mon Nov 30 03:47:34 2009 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Mon, 30 Nov 2009 10:47:34 +0800 Subject: [Pw_forum] Do you think QE could benefit from the Hyper-ThreadingTech of XEON 5500 series? References: <412f6c680911260923s7cd75b6er3d06dbc9f19a855b@mail.gmail.com> Message-ID: <642EDF3414CD46C5B9378ADABAA8878D@solarflare> Hyper-threading usually lowers the performance by 5-15% in HPC environment, you'd better turn it off. HT benefits applications in enterprise environment where the CPU usage is about 15-25% so that a physical CPU core can handle two threads effectively in a time-sharing way. Huiqun Zhou @Earth Sciences, Nanjing University, China ----- Original Message ----- From: vega lew To: PWSCF Forum Sent: Friday, November 27, 2009 1:23 AM Subject: [Pw_forum] Do you think QE could benefit from the Hyper-ThreadingTech of XEON 5500 series? Dear all, I got 5 computers with two XEON 5520 and 24G memory. I find the Hyper-Threading is switched on by default. I wonder if QE could benefit from Hyper-Threading Tech. of Xeon CPUs? Should I switch it off and trigger one process for each core to promote the QE performance? Or remain the Hyper-Threading on and trigger two processes for each core? best vega -- ================================================================================== Vega Lew ( weijia liu) Graduate student 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091130/b1449ba2/attachment.htm From modaresi.mohsen at gmail.com Mon Nov 30 07:32:16 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Mon, 30 Nov 2009 10:02:16 +0330 Subject: [Pw_forum] a question about magnetization In-Reply-To: <68343251-8628-437C-A20B-75003279A191@democritos.it> References: <68343251-8628-437C-A20B-75003279A191@democritos.it> Message-ID: Dear Paolo Thanks for your answer But I want a situation which atoms have different magnetization at the final, is there any suggestion? Thanks Mohsen Modaresi On Sun, Nov 29, 2009 at 1:19 PM, Paolo Giannozzi wrote: > > On Nov 29, 2009, at 9:39 , mohsen modaresi wrote: > > > 1) A and B have parallel magnetization direction > > 2) A and C have anti parallel magnetization direction > > could i inter this deference in calculation > > with an appropriate usage of "starting_magnetization" > you should be able to select between a final state of > type 1) or 2). Energy differences may turn out to be > VERY small, though > > Paolo > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091130/947192e2/attachment.htm From limch at ihpc.a-star.edu.sg Mon Nov 30 07:26:48 2009 From: limch at ihpc.a-star.edu.sg (Lim Chiang Huay, Freda) Date: Mon, 30 Nov 2009 14:26:48 +0800 Subject: [Pw_forum] from invmat : error #1 singular matrix Message-ID: Dear all, I am trying to run NEB to find out the activation energy required to transform one configuration (sandwiched) of a sandwich-molecular wire to another configuration (zigged-zagged). And I get this error msg: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 3 from invmat : error # 1 singular matrix %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I can't find any clue as to what's wrong with my job from previous forum postings. Can anyone help? Thanks, Rgds Freda Lim Institute of High Performance Computing 1 Fusionopolis Way, #16-16 Connexis Singapore 138632 Email: limch at ihpc.a-star.edu.sg ________________________________ This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091130/066b8240/attachment.htm From baroni at sissa.it Mon Nov 30 08:02:12 2009 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 30 Nov 2009 08:02:12 +0100 Subject: [Pw_forum] a question about magnetization In-Reply-To: References: <68343251-8628-437C-A20B-75003279A191@democritos.it> Message-ID: <9FB34024-0C72-4BB5-A870-83973ABF6E21@sissa.it> If what you want is different from what Mother Nature wants (or, rather from the caricature of Mother Nature's willings given by DFT/ GGA/etc.) the only way is to use magnetic constraints. They used to be implemented. Don't know what the current situation of the implemenattion is. You can try without constraints to start with ... SB On Nov 30, 2009, at 7:32 AM, mohsen modaresi wrote: > Dear Paolo > Thanks for your answer > But I want a situation which atoms have different magnetization at > the final, > is there any suggestion? > Thanks > > Mohsen Modaresi > > On Sun, Nov 29, 2009 at 1:19 PM, Paolo Giannozzi > wrote: > > On Nov 29, 2009, at 9:39 , mohsen modaresi wrote: > > > 1) A and B have parallel magnetization direction > > 2) A and C have anti parallel magnetization direction > > could i inter this deference in calculation > > with an appropriate usage of "starting_magnetization" > you should be able to select between a final state of > type 1) or 2). Energy differences may turn out to be > VERY small, though > > Paolo > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > _______________________________________________ > Pw_forum 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/20091130/9bf3635e/attachment-0001.htm From modaresi.mohsen at gmail.com Mon Nov 30 08:12:32 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Mon, 30 Nov 2009 10:42:32 +0330 Subject: [Pw_forum] a question about magnetization In-Reply-To: <9FB34024-0C72-4BB5-A870-83973ABF6E21@sissa.it> References: <68343251-8628-437C-A20B-75003279A191@democritos.it> <9FB34024-0C72-4BB5-A870-83973ABF6E21@sissa.it> Message-ID: Dear Stefano Thanks Ih has dont want any things whic conflict with nature, I want to calculate GMR (in the situation with out any magnetic field there is an exchange coupling which leads to different magnetization, But this kind of exchange coupling do'nt colculated in Q.E so it must be intered artifically) Thanks for your answers Mohsen Modarersi On Mon, Nov 30, 2009 at 10:32 AM, Stefano Baroni wrote: > If what you want is different from what Mother Nature wants (or, rather > from the caricature of Mother Nature's willings given by DFT/GGA/etc.) the > only way is to use magnetic constraints. They used to be implemented. Don't > know what the current situation of the implemenattion is. You can try > without constraints to start with ... SB > > On Nov 30, 2009, at 7:32 AM, mohsen modaresi wrote: > > Dear Paolo > Thanks for your answer > But I want a situation which atoms have different magnetization at the > final, > is there any suggestion? > Thanks > > Mohsen Modaresi > > On Sun, Nov 29, 2009 at 1:19 PM, Paolo Giannozzi wrote: > >> >> On Nov 29, 2009, at 9:39 , mohsen modaresi wrote: >> >> > 1) A and B have parallel magnetization direction >> > 2) A and C have anti parallel magnetization direction >> > could i inter this deference in calculation >> >> with an appropriate usage of "starting_magnetization" >> you should be able to select between a final state of >> type 1) or 2). Energy differences may turn out to be >> VERY small, though >> >> Paolo >> --- >> Paolo Giannozzi, Dept of Physics, University of Udine >> via delle Scienze 208, 33100 Udine, Italy >> Phone +39-0432-558216, fax +39-0432-558222 >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > _______________________________________________ > Pw_forum 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/20091130/6e8197c9/attachment.htm From baroni at sissa.it Mon Nov 30 08:14:57 2009 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 30 Nov 2009 08:14:57 +0100 Subject: [Pw_forum] from invmat : error #1 singular matrix In-Reply-To: References: Message-ID: Difficult to say, without any knowledge of you input data, etc. Can you locate the region of the code where the error occur? Among the many things that may give such an error (others may know much more than me) is two parallel primitive vectors for the Bravais lattice ... SB On Nov 30, 2009, at 7:26 AM, Lim Chiang Huay, Freda wrote: > Dear all, > > I am trying to run NEB to find out the activation energy required to > transform one configuration (sandwiched) of a sandwich-molecular > wire to another configuration (zigged-zagged). > > And I get this error msg: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%% > task # 3 > from invmat : error # 1 > singular matrix > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%%% > > I can?t find any clue as to what?s wrong with my job from previous > forum postings. > > Can anyone help? > > Thanks, > Rgds > > Freda Lim > Institute of High Performance Computing > 1 Fusionopolis Way, #16-16 Connexis > Singapore 138632 > Email: limch at ihpc.a-star.edu.sg > > > > > This email is confidential and may be privileged. If you are not the > intended recipient, please delete it and notify us immediately. > Please do not copy or use it for any purpose, or disclose its > contents to any other person. Thank you. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- 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/20091130/19721921/attachment-0001.htm From modaresi.mohsen at gmail.com Mon Nov 30 08:16:11 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Mon, 30 Nov 2009 10:46:11 +0330 Subject: [Pw_forum] a question about magnetization In-Reply-To: References: <68343251-8628-437C-A20B-75003279A191@democritos.it> <9FB34024-0C72-4BB5-A870-83973ABF6E21@sissa.it> Message-ID: Dear users Excuse me for 'Ih has dont want any things whic conflict with nature' It Means ' I dont want any thing Which has conflict with nature' It is for my keybopard. Mohsen Modaresi On Mon, Nov 30, 2009 at 10:42 AM, mohsen modaresi wrote: > Dear Stefano > Thanks > Ih has dont want any things whic conflict with nature, I want to calculate > GMR (in the situation with out any magnetic field there is an exchange > coupling which leads to different magnetization, But this kind of exchange > coupling do'nt colculated in Q.E so it must be intered artifically) > Thanks for your answers > > Mohsen Modarersi > > > > > > > On Mon, Nov 30, 2009 at 10:32 AM, Stefano Baroni wrote: > >> If what you want is different from what Mother Nature wants (or, rather >> from the caricature of Mother Nature's willings given by DFT/GGA/etc.) the >> only way is to use magnetic constraints. They used to be implemented. Don't >> know what the current situation of the implemenattion is. You can try >> without constraints to start with ... SB >> >> On Nov 30, 2009, at 7:32 AM, mohsen modaresi wrote: >> >> Dear Paolo >> Thanks for your answer >> But I want a situation which atoms have different magnetization at the >> final, >> is there any suggestion? >> Thanks >> >> Mohsen Modaresi >> >> On Sun, Nov 29, 2009 at 1:19 PM, Paolo Giannozzi wrote: >> >>> >>> On Nov 29, 2009, at 9:39 , mohsen modaresi wrote: >>> >>> > 1) A and B have parallel magnetization direction >>> > 2) A and C have anti parallel magnetization direction >>> > could i inter this deference in calculation >>> >>> with an appropriate usage of "starting_magnetization" >>> you should be able to select between a final state of >>> type 1) or 2). Energy differences may turn out to be >>> VERY small, though >>> >>> Paolo >>> --- >>> Paolo Giannozzi, Dept of Physics, University of Udine >>> via delle Scienze 208, 33100 Udine, Italy >>> Phone +39-0432-558216, fax +39-0432-558222 >>> >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >> >> _______________________________________________ >> Pw_forum 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/20091130/0ff0c04f/attachment.htm From limch at ihpc.a-star.edu.sg Mon Nov 30 08:23:36 2009 From: limch at ihpc.a-star.edu.sg (Lim Chiang Huay, Freda) Date: Mon, 30 Nov 2009 15:23:36 +0800 Subject: [Pw_forum] from invmat : error #1 singular matrix In-Reply-To: References: Message-ID: Hi there, Thanks for your reply, I've included my input and output. INPUT FILE looks like this: &CONTROL title = '2VB_ecl-sta_NEB', prefix = '2VB_ecl-sta_NEB', calculation = 'neb', restart_mode = 'from_scratch', forc_conv_thr = 0.007, etot_conv_thr = 0.0004, tprnfor = .true., nstep = 1000, / &SYSTEM nosym = .true., ibrav = 0, celldm(1) = 1 nat = 25, ntyp = 4, ecutwfc = 50, ecutrho = 600, occupations = 'smearing', degauss = 0.00735, smearing = 'methfessel-paxton', nspin = 2, starting_magnetization = 0.5, / &ELECTRONS conv_thr = 0.000001, electron_maxstep = 250, startingpot = 'atomic' startingwfc = 'atomic' mixing_mode ='local-TF', mixing_beta = 0.3, mixing_ndim = 8, diagonalization = 'david', diago_david_ndim = 8, / &IONS ion_dynamics = 'bfgs', path_thr = 0.05D0, num_of_images = 3, CI_scheme = 'auto', first_last_opt = .FALSE., opt_scheme = 'quick-min', / ATOMIC_SPECIES V 50.940 V.pbe-n-van.UPF N 14.010 N.pbe-van_ak.UPF H 1.008 H.pbe-van_ak.UPF B 10.810 B.pbe-n-van_ak.UPF ATOMIC_POSITIONS (angstrom) first_image V 0.000000 0.000000 0.000000 0 0 0 N -0.825867 1.302892 4.613177 N 1.517559 0.151978 4.618972 N -0.650980 -1.302130 4.639378 N 0.640393 1.280360 -4.681705 N -1.528057 -0.174206 -4.657982 N 0.814850 -1.324864 -4.652189 H -2.864377 -0.132769 4.655665 H 2.617434 0.226766 4.630213 H -1.439116 2.219037 4.620181 H 1.283285 2.635363 4.450732 H 1.627465 -2.338822 4.666773 H -1.136941 -2.291553 4.652012 H 2.853590 0.111039 -4.690857 H -2.627921 -0.248899 -4.670122 H 1.126337 2.269734 -4.697005 H -1.637927 2.316932 -4.701964 H -1.290642 -2.650174 -4.417053 H 1.428171 -2.240944 -4.660091 B -1.568944 -0.055825 4.631763 B 0.713167 1.475191 4.583787 B 0.896512 -1.266670 4.637860 B 1.557996 0.033737 -4.671921 B -0.907138 1.244425 -4.678017 B -0.724177 -1.497770 -4.615617 last_image V 0.000000 0.000000 0.000000 N -2.788484 1.130175 2.132116 N -0.667261 -0.008607 2.137975 N -2.714116 -1.276193 2.145638 N 2.714116 1.276193 -2.145638 N 0.667261 0.008607 -2.137975 N 2.788484 -1.130175 -2.132116 H -4.539330 -0.128263 2.139650 H 0.426089 0.025180 2.137502 H -3.364421 2.060119 2.127031 H -0.881711 2.136841 2.125957 H -0.748820 -2.163203 2.150121 H -3.231530 -2.239924 2.151195 H 4.539330 0.128263 -2.139650 H -0.426089 -0.025180 -2.137502 H 3.231530 2.239924 -2.151195 H 0.748820 2.163203 -2.150121 H 0.881711 -2.136841 -2.125957 H 3.364421 -2.060119 -2.127031 B -3.445980 -0.094476 2.139177 B -1.399125 1.173109 2.131514 B -1.324757 -1.233258 2.145037 B 3.445980 0.094476 -2.139177 B 1.324757 1.233258 -2.145037 B 1.399125 -1.173109 -2.131514 K_POINTS ( gamma ) CELL_PARAMETERS { cubic } 50.00000 0.00000 0.00000 0.00000 50.00000 0.00000 0.00000 0.00000 50.00000 OUTPUT FILE looks like this: Program PWSCF v.4.1.1 starts ... Today is 30Nov2009 at 14:46: 1 Parallel version (MPI) Number of processors in use: 4 R & G space division: proc/pool = 4 For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW Current dimensions of program pwscf are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 Waiting for input... gamma-point specific algorithms are used initial path length = 30.1576 bohr initial inter-image distance = 15.0788 bohr calculation = neb restart_mode = from_scratch opt_scheme = quick-min num_of_images = 3 nstep = 1000 CI_scheme = auto first_last_opt = F coarse-grained phase-space = F use_freezing = F ds = 1.0000 a.u. k_max = 0.1000 a.u. k_min = 0.1000 a.u. suggested k_max = 0.6169 a.u. suggested k_min = 0.6169 a.u. path_thr = 0.0500 eV / A ------------------------------ iteration 1 ------------------------------ tcpu = 0.5 self-consistency for image 1 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from invmat : error # 1 singular matrix %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... ________________________________ From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Stefano Baroni Sent: Monday, November 30, 2009 3:15 PM To: PWSCF Forum Subject: Re: [Pw_forum] from invmat : error #1 singular matrix Difficult to say, without any knowledge of you input data, etc. Can you locate the region of the code where the error occur? Among the many things that may give such an error (others may know much more than me) is two parallel primitive vectors for the Bravais lattice ... SB On Nov 30, 2009, at 7:26 AM, Lim Chiang Huay, Freda wrote: Dear all, I am trying to run NEB to find out the activation energy required to transform one configuration (sandwiched) of a sandwich-molecular wire to another configuration (zigged-zagged). And I get this error msg: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 3 from invmat : error # 1 singular matrix %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I can't find any clue as to what's wrong with my job from previous forum postings. Can anyone help? Thanks, Rgds Freda Lim Institute of High Performance Computing 1 Fusionopolis Way, #16-16 Connexis Singapore 138632 Email: limch at ihpc.a-star.edu.sg ________________________________ This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum --- 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 ________________________________ This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091130/14e2c003/attachment-0001.htm From modaresi.mohsen at gmail.com Mon Nov 30 09:35:42 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Mon, 30 Nov 2009 12:05:42 +0330 Subject: [Pw_forum] Minimum requirement system Message-ID: Dear users I want buy a new computer for my PWscf calculation what is your suggestion? (minimum requirement please) Thanks for your answers Mohsen Modaresi Msc. Student of Solid State Physics, Department of Physics,Ferdowsi University of Mashhad, Iran. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091130/bc9e236f/attachment.htm From paulatto at sissa.it Mon Nov 30 09:47:35 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 30 Nov 2009 09:47:35 +0100 Subject: [Pw_forum] Minimum requirement system In-Reply-To: References: Message-ID: Replying to message "[Pw_forum] Minimum requirement system" from mohsen modaresi (30/11/09): > I want buy a new computer for my PWscf calculation > what is your suggestion? (minimum requirement please) > Thanks for your answers Dear Mohsen, it depends on the size of the system you are going to study, and on what you want to study. I usually run small molecules (less than 20 electrons) on my laptop, systems with about 100 electrons on at least 32 processors (with dedicated high-speed network connection and filesystem), systems with about 1000 electron require at the very least 128 processors. 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 paulatto at sissa.it Mon Nov 30 09:55:18 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 30 Nov 2009 09:55:18 +0100 Subject: [Pw_forum] from invmat : error #1 singular matrix In-Reply-To: References: Message-ID: Replying to message "Re: [Pw_forum] from invmat : error #1 singular matrix" from Lim Chiang Huay, Freda (30/11/09): > ibrav = 0, > celldm(1) = 1 Dear Fread, if you use ibrav=0 you have to manually specify the unit cell, using the CELL cards list, in units of celldm(1) bohrs(see the input manual). You have not done it, which causes the unit cell to be of size zero. The error you are experiencing happens when atomic positions are converted to the internal unit of measure. 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 Mon Nov 30 09:55:27 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 30 Nov 2009 09:55:27 +0100 Subject: [Pw_forum] A problem about Ex.12 In-Reply-To: <4B0E9E32.7010801@sissa.it> References: <4B0E9E32.7010801@sissa.it> Message-ID: <4B13887F.3030308@sissa.it> Dear mohsen modaresi, Stefano de Gironcoli wrote: > Dear mohsen modaresi > > you can describe an fcc crystal in an FCC bravais lattice with one atom > per cell or in a Simple Cubic cell with 4 atoms per cell or in a > tetragonal cell with 2 atoms per cell or in many other equivalent ways. > Why it is done using tetragonal lattice in that particular example I > don't know but it may be due to the need of using some particular > orientation or orthonormal Bravais vectors or some other reason. What Stefano says is true. In that specific example, a tetragonal superell has been used in order to postprocess the charge density with pwcond.x and obtain the complex band structure of FCC Al along the (001) direction, as it is written in the README file which explains the example. Since the pwcond code is built such that the transport direction has to be along z, you have to rotate your crystal according to the real desired transport direction. Also notice that the basal plane of the supercell has to be orthogonal to this direction. HTH GS > Hope this helps, > > stefano. > > mohsen modaresi wrote: >> Hi dear users >> I read Ex.12 and run it, In the input file for Al (al.scf.in >> ) i see this part >> ibrav = 6, >> celldm(1) =5.3, >> celldm(3) =1.414, >> But we konw that Al has F.CC structure, Why they set ibarav=6 not 2, I >> faced with this problem in example 11 in the Want package. >> Thanks for answers >> >> Mohsen Modaresi >> Msc. Student of Solid State Physics, >> Department of Physics,Ferdowsi University of Mashhad, >> Iran. >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 sclauzer at sissa.it Mon Nov 30 10:13:18 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 30 Nov 2009 10:13:18 +0100 Subject: [Pw_forum] a question about magnetization In-Reply-To: <9FB34024-0C72-4BB5-A870-83973ABF6E21@sissa.it> References: <68343251-8628-437C-A20B-75003279A191@democritos.it> <9FB34024-0C72-4BB5-A870-83973ABF6E21@sissa.it> Message-ID: <4B138CAE.2030701@sissa.it> Dear Mohsen Modaresi (and Stefano), Stefano Baroni wrote: > If what you want is different from what Mother Nature wants (or, rather > from the caricature of Mother Nature's willings given by DFT/GGA/etc.) > the only way is to use magnetic constraints. They used to be > implemented. Don't know what the current situation of the implemenattion > is. You can try without constraints to start with ... SB I can confirm that they are still implemented, though I never explored the functionality of all the possible magnetic constraints. The costraints are implemented by adding a "penalty" magnetic field (see appendix of the PhD thesis of Gabriele Cipriani, downloadable from http://www.sissa.it/cm/phd.php), which means that you have to chose a parameter lambda to which the penalty energy is proportional. When you are exactly at the target magnetization the penalty energy (and field) are zero, so that the resulting total energy should not depend on lambda. choosing lambda may be tricky: if it is too small the final magnetization may be far from the target one. If too big, the scf cycle might not converge. If you want to experiment this method on your system please search for "constrained_magnetization" in Doc/INPUT_PW.txt and have a look to PW/add_bfield.f90. HTH GS > > On Nov 30, 2009, at 7:32 AM, mohsen modaresi wrote: > >> Dear Paolo >> Thanks for your answer >> But I want a situation which atoms have different magnetization at the >> final, >> is there any suggestion? >> Thanks >> >> Mohsen Modaresi >> >> On Sun, Nov 29, 2009 at 1:19 PM, Paolo Giannozzi >> > wrote: >> >> >> On Nov 29, 2009, at 9:39 , mohsen modaresi wrote: >> >> > 1) A and B have parallel magnetization direction >> > 2) A and C have anti parallel magnetization direction >> > could i inter this deference in calculation >> >> with an appropriate usage of "starting_magnetization" >> you should be able to select between a final state of >> type 1) or 2). Energy differences may turn out to be >> VERY small, though >> >> Paolo >> --- >> Paolo Giannozzi, Dept of Physics, University of Udine >> via delle Scienze 208, 33100 Udine, Italy >> Phone +39-0432-558216, fax +39-0432-558222 >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> _______________________________________________ >> Pw_forum 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 -- 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 Mon Nov 30 10:16:44 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 30 Nov 2009 10:16:44 +0100 Subject: [Pw_forum] from invmat : error #1 singular matrix In-Reply-To: References: Message-ID: <4B138D7C.3010200@democritos.it> Lorenzo Paulatto wrote: >> ibrav = 0, >> celldm(1) = 1 > if you use ibrav=0 you have to manually specify the unit cell, using the > CELL cards list, in units of celldm(1) bohrs(see the input manual). I think it is correct as it is now. One can - specify the kind of lattice (ibrav) and the lattice parameters (celldm, or else a,b,c ...) - specify lattice vectors (ibrav=0 + CELL card); the lattice parameter is assumed to be the length of lattice vector 1 - specify lattice vectors and lattice parameter (ibrav=0 + celldm(1), or else a + CELL card); the lattice vectors are in units of the lattice parameter I think that the third option is a very bad idea, but it shouldn't be wrong. All these cases are checked for consistency in input anyway. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From paulatto at sissa.it Mon Nov 30 10:24:23 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 30 Nov 2009 10:24:23 +0100 Subject: [Pw_forum] from invmat : error #1 singular matrix In-Reply-To: <4B138D7C.3010200@democritos.it> References: <4B138D7C.3010200@democritos.it> Message-ID: Replying to message "Re: [Pw_forum] from invmat : error #1 singular matrix" from Paolo Giannozzi (30/11/09): > - specify lattice vectors and lattice parameter (ibrav=0 + > celldm(1), or else a + CELL card); the lattice vectors are > in units of the lattice parameter Oh, yes, I'm sorry. I missed the CELL card at the end of the input and assumed it was not specified. Well, so I'm at loss on the possible cause of the problem... 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 mtt_turion at hotmail.com Mon Nov 30 10:28:51 2009 From: mtt_turion at hotmail.com (mtt physics) Date: Mon, 30 Nov 2009 16:28:51 +0700 Subject: [Pw_forum] How to set atomic position with Pb(Zr_xTi_1-x)O3 In-Reply-To: References: Message-ID: Dear all I want to determine the position of an atom in the structure PZT(Pb(Zr_xTi_1-x)O3). > From: pw_forum-request at pwscf.org > Subject: Pw_forum Digest, Vol 29, Issue 88 > To: pw_forum at pwscf.org > Date: Mon, 30 Nov 2009 08:25:39 +0100 > > 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: a question about magnetization (mohsen modaresi) > 2. Re: from invmat : error #1 singular matrix > (Lim Chiang Huay, Freda) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 30 Nov 2009 10:46:11 +0330 > From: mohsen modaresi > Subject: Re: [Pw_forum] a question about magnetization > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear users > Excuse me for 'Ih has dont want any things whic conflict with nature' > It Means ' I dont want any thing Which has conflict with nature' > It is for my keybopard. > > Mohsen Modaresi > > On Mon, Nov 30, 2009 at 10:42 AM, mohsen modaresi > wrote: > > > Dear Stefano > > Thanks > > Ih has dont want any things whic conflict with nature, I want to calculate > > GMR (in the situation with out any magnetic field there is an exchange > > coupling which leads to different magnetization, But this kind of exchange > > coupling do'nt colculated in Q.E so it must be intered artifically) > > Thanks for your answers > > > > Mohsen Modarersi > > > > > > > > > > > > > > On Mon, Nov 30, 2009 at 10:32 AM, Stefano Baroni wrote: > > > >> If what you want is different from what Mother Nature wants (or, rather > >> from the caricature of Mother Nature's willings given by DFT/GGA/etc.) the > >> only way is to use magnetic constraints. They used to be implemented. Don't > >> know what the current situation of the implemenattion is. You can try > >> without constraints to start with ... SB > >> > >> On Nov 30, 2009, at 7:32 AM, mohsen modaresi wrote: > >> > >> Dear Paolo > >> Thanks for your answer > >> But I want a situation which atoms have different magnetization at the > >> final, > >> is there any suggestion? > >> Thanks > >> > >> Mohsen Modaresi > >> > >> On Sun, Nov 29, 2009 at 1:19 PM, Paolo Giannozzi wrote: > >> > >>> > >>> On Nov 29, 2009, at 9:39 , mohsen modaresi wrote: > >>> > >>> > 1) A and B have parallel magnetization direction > >>> > 2) A and C have anti parallel magnetization direction > >>> > could i inter this deference in calculation > >>> > >>> with an appropriate usage of "starting_magnetization" > >>> you should be able to select between a final state of > >>> type 1) or 2). Energy differences may turn out to be > >>> VERY small, though > >>> > >>> Paolo > >>> --- > >>> Paolo Giannozzi, Dept of Physics, University of Udine > >>> via delle Scienze 208, 33100 Udine, Italy > >>> Phone +39-0432-558216, fax +39-0432-558222 > >>> > >>> > >>> > >>> _______________________________________________ > >>> Pw_forum mailing list > >>> Pw_forum at pwscf.org > >>> http://www.democritos.it/mailman/listinfo/pw_forum > >>> > >> > >> _______________________________________________ > >> Pw_forum 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/20091130/0ff0c04f/attachment-0001.htm > > ------------------------------ > > Message: 2 > Date: Mon, 30 Nov 2009 15:23:36 +0800 > From: "Lim Chiang Huay, Freda" > Subject: Re: [Pw_forum] from invmat : error #1 singular matrix > To: PWSCF Forum > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi there, > Thanks for your reply, I've included my input and output. > > INPUT FILE looks like this: > &CONTROL > title = '2VB_ecl-sta_NEB', > prefix = '2VB_ecl-sta_NEB', > calculation = 'neb', > restart_mode = 'from_scratch', > forc_conv_thr = 0.007, > etot_conv_thr = 0.0004, > tprnfor = .true., > nstep = 1000, > / > &SYSTEM > nosym = .true., > ibrav = 0, > celldm(1) = 1 > nat = 25, > ntyp = 4, > ecutwfc = 50, > ecutrho = 600, > occupations = 'smearing', > degauss = 0.00735, > smearing = 'methfessel-paxton', > nspin = 2, > starting_magnetization = 0.5, > / > &ELECTRONS > conv_thr = 0.000001, > electron_maxstep = 250, > startingpot = 'atomic' > startingwfc = 'atomic' > mixing_mode ='local-TF', > mixing_beta = 0.3, > mixing_ndim = 8, > diagonalization = 'david', > diago_david_ndim = 8, > / > &IONS > ion_dynamics = 'bfgs', > path_thr = 0.05D0, > num_of_images = 3, > CI_scheme = 'auto', > first_last_opt = .FALSE., > opt_scheme = 'quick-min', > > / > ATOMIC_SPECIES > V 50.940 V.pbe-n-van.UPF > N 14.010 N.pbe-van_ak.UPF > H 1.008 H.pbe-van_ak.UPF > B 10.810 B.pbe-n-van_ak.UPF > > ATOMIC_POSITIONS (angstrom) > first_image > V 0.000000 0.000000 0.000000 0 0 0 > N -0.825867 1.302892 4.613177 > N 1.517559 0.151978 4.618972 > N -0.650980 -1.302130 4.639378 > N 0.640393 1.280360 -4.681705 > N -1.528057 -0.174206 -4.657982 > N 0.814850 -1.324864 -4.652189 > H -2.864377 -0.132769 4.655665 > H 2.617434 0.226766 4.630213 > H -1.439116 2.219037 4.620181 > H 1.283285 2.635363 4.450732 > H 1.627465 -2.338822 4.666773 > H -1.136941 -2.291553 4.652012 > H 2.853590 0.111039 -4.690857 > H -2.627921 -0.248899 -4.670122 > H 1.126337 2.269734 -4.697005 > H -1.637927 2.316932 -4.701964 > H -1.290642 -2.650174 -4.417053 > H 1.428171 -2.240944 -4.660091 > B -1.568944 -0.055825 4.631763 > B 0.713167 1.475191 4.583787 > B 0.896512 -1.266670 4.637860 > B 1.557996 0.033737 -4.671921 > B -0.907138 1.244425 -4.678017 > B -0.724177 -1.497770 -4.615617 > > last_image > V 0.000000 0.000000 0.000000 > N -2.788484 1.130175 2.132116 > N -0.667261 -0.008607 2.137975 > N -2.714116 -1.276193 2.145638 > N 2.714116 1.276193 -2.145638 > N 0.667261 0.008607 -2.137975 > N 2.788484 -1.130175 -2.132116 > H -4.539330 -0.128263 2.139650 > H 0.426089 0.025180 2.137502 > H -3.364421 2.060119 2.127031 > H -0.881711 2.136841 2.125957 > H -0.748820 -2.163203 2.150121 > H -3.231530 -2.239924 2.151195 > H 4.539330 0.128263 -2.139650 > H -0.426089 -0.025180 -2.137502 > H 3.231530 2.239924 -2.151195 > H 0.748820 2.163203 -2.150121 > H 0.881711 -2.136841 -2.125957 > H 3.364421 -2.060119 -2.127031 > B -3.445980 -0.094476 2.139177 > B -1.399125 1.173109 2.131514 > B -1.324757 -1.233258 2.145037 > B 3.445980 0.094476 -2.139177 > B 1.324757 1.233258 -2.145037 > B 1.399125 -1.173109 -2.131514 > > K_POINTS ( gamma ) > > CELL_PARAMETERS { cubic } > 50.00000 0.00000 0.00000 > 0.00000 50.00000 0.00000 > 0.00000 0.00000 50.00000 > > OUTPUT FILE looks like this: > > Program PWSCF v.4.1.1 starts ... > Today is 30Nov2009 at 14:46: 1 > > Parallel version (MPI) > > Number of processors in use: 4 > R & G space division: proc/pool = 4 > > For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW > > Current dimensions of program pwscf are: > Max number of different atomic species (ntypx) = 10 > Max number of k-points (npk) = 40000 > Max angular momentum in pseudopotentials (lmaxx) = 3 > Waiting for input... > > gamma-point specific algorithms are used > > > initial path length = 30.1576 bohr > initial inter-image distance = 15.0788 bohr > > calculation = neb > restart_mode = from_scratch > opt_scheme = quick-min > num_of_images = 3 > nstep = 1000 > CI_scheme = auto > first_last_opt = F > coarse-grained phase-space = F > use_freezing = F > ds = 1.0000 a.u. > k_max = 0.1000 a.u. > k_min = 0.1000 a.u. > suggested k_max = 0.6169 a.u. > suggested k_min = 0.6169 a.u. > path_thr = 0.0500 eV / A > > ------------------------------ iteration 1 ------------------------------ > > tcpu = 0.5 self-consistency for image 1 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from invmat : error # 1 > singular matrix > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > ________________________________ > From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Stefano Baroni > Sent: Monday, November 30, 2009 3:15 PM > To: PWSCF Forum > Subject: Re: [Pw_forum] from invmat : error #1 singular matrix > > Difficult to say, without any knowledge of you input data, etc. Can you locate the region of the code where the error occur? > Among the many things that may give such an error (others may know much more than me) is two parallel primitive vectors for the Bravais lattice ... > SB > > On Nov 30, 2009, at 7:26 AM, Lim Chiang Huay, Freda wrote: > > > Dear all, > > I am trying to run NEB to find out the activation energy required to transform one configuration (sandwiched) of a sandwich-molecular wire to another configuration (zigged-zagged). > > And I get this error msg: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > task # 3 > from invmat : error # 1 > singular matrix > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > I can't find any clue as to what's wrong with my job from previous forum postings. > > Can anyone help? > > Thanks, > Rgds > > Freda Lim > Institute of High Performance Computing > 1 Fusionopolis Way, #16-16 Connexis > Singapore 138632 > Email: limch at ihpc.a-star.edu.sg > > > > > ________________________________ > This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > --- > 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 > > > > > > > > > ________________________________ > This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091130/14e2c003/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 29, Issue 88 > **************************************** _________________________________________________________________ Windows Live: ??????? ?????????????????????????? Flickr, Yelp ??? Digg ????????????????????????????? http://www.microsoft.com/windows/windowslive/see-it-in-action/social-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:th-th:SI_SB_3:092010 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091130/2ae1aae5/attachment-0001.htm From modaresi.mohsen at gmail.com Mon Nov 30 10:35:34 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Mon, 30 Nov 2009 13:05:34 +0330 Subject: [Pw_forum] Minimum requirement system In-Reply-To: References: Message-ID: Dear Lorenzo Thanks for your answer Mohsen Modaresi On Mon, Nov 30, 2009 at 12:17 PM, Lorenzo Paulatto wrote: > Replying to message "[Pw_forum] Minimum requirement system" from mohsen > modaresi (30/11/09): > > I want buy a new computer for my PWscf calculation > > what is your suggestion? (minimum requirement please) > > Thanks for your answers > > Dear Mohsen, > it depends on the size of the system you are going to study, and on what > you want to study. > > I usually run small molecules (less than 20 electrons) on my laptop, > systems with about 100 electrons on at least 32 processors (with dedicated > high-speed network connection and filesystem), systems with about 1000 > electron require at the very least 128 processors. > > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091130/1b9a07e8/attachment.htm From sclauzer at sissa.it Mon Nov 30 10:49:49 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 30 Nov 2009 10:49:49 +0100 Subject: [Pw_forum] How to set atomic position with Pb(Zr_xTi_1-x)O3 In-Reply-To: References: Message-ID: <4B13953D.6010507@sissa.it> mtt physics wrote: > Dear all > I want to determine the position of an atom in the structure > PZT(Pb(Zr_xTi_1-x)O3). Good luck! 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 sclauzer at sissa.it Mon Nov 30 10:57:09 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 30 Nov 2009 10:57:09 +0100 Subject: [Pw_forum] magnetic coupling X pressure In-Reply-To: <496028.88374.qm@web52305.mail.re2.yahoo.com> References: <496028.88374.qm@web52305.mail.re2.yahoo.com> Message-ID: <4B1396F5.1090807@sissa.it> Dear Alvaro, ?lvaro Alves wrote: > Users PWscf Hello, I'm willing to investigate how the magnetic coupling > in a solid varies with the pressure. The unit cell is triclinic. What Can you explain better what do you mean by magnetic coupling? Which units of measure has this? > better way to do this in PWscf .. ? If you know how to measure that quantity, you may let pwscf compute the pressure by enabling the tstress flag and repeat the calculations at different values of the lattice parameter. Though, since I don't know much about what you want to compute, my solution might be too much simplistic... GS > > A. S. Santos > Universidade Federal Fluminense > Niter?i - Rio de Janeiro - Brasil > > ------------------------------------------------------------------------ > Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 > > - Celebridades > > - M?sica > > - Esportes > > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 Mon Nov 30 11:05:02 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 30 Nov 2009 11:05:02 +0100 Subject: [Pw_forum] from invmat : error #1 singular matrix In-Reply-To: References: Message-ID: <4B1398CE.5080204@democritos.it> Lim Chiang Huay, Freda wrote: > from invmat : error # 1 > singular matrix quick & dirty fix: edit flib/invmat.f90, remove the line IF (ABS(da) < 1.d-10) CALL errore(' invmat ',' singular matrix ',1) P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From Michael at ihpc.a-star.edu.sg Mon Nov 30 10:38:10 2009 From: Michael at ihpc.a-star.edu.sg (Michael Sullivan) Date: Mon, 30 Nov 2009 17:38:10 +0800 Subject: [Pw_forum] from invmat : error #1 singular matrix In-Reply-To: <4B138D7C.3010200@democritos.it> References: <4B138D7C.3010200@democritos.it> Message-ID: Paolo: I think you are right. Seems there might be a bug but in any case, using the third method is bad and crashes while the first two methods work. Mike Institute of High Performance Computing, Singapore http://www.sullivan.sg/ -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi Sent: Monday, November 30, 2009 5:17 PM To: PWSCF Forum Subject: Re: [Pw_forum] from invmat : error #1 singular matrix Lorenzo Paulatto wrote: >> ibrav = 0, >> celldm(1) = 1 > if you use ibrav=0 you have to manually specify the unit cell, using the > CELL cards list, in units of celldm(1) bohrs(see the input manual). I think it is correct as it is now. One can - specify the kind of lattice (ibrav) and the lattice parameters (celldm, or else a,b,c ...) - specify lattice vectors (ibrav=0 + CELL card); the lattice parameter is assumed to be the length of lattice vector 1 - specify lattice vectors and lattice parameter (ibrav=0 + celldm(1), or else a + CELL card); the lattice vectors are in units of the lattice parameter I think that the third option is a very bad idea, but it shouldn't be wrong. All these cases are checked for consistency in input anyway. 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 This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. From sclauzer at sissa.it Mon Nov 30 11:10:19 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 30 Nov 2009 11:10:19 +0100 Subject: [Pw_forum] contents of Pw_forum digest In-Reply-To: <9b382fa70911262338qcef66ces62d696ad43c6109d@mail.gmail.com> References: <9b382fa70911262338qcef66ces62d696ad43c6109d@mail.gmail.com> Message-ID: <4B139A0B.3020303@sissa.it> Shyam Khambholja wrote: > Hi, friends, > > I am a new user of pwscf. I am trying to generate > k-points using kpoints.x. can you tell me the significance of > > mesh : n1 n2 n3 and > > mesh : k1 k2 k3 [ 0 no shift, 1 shifted ] n1,n2,n3 are the size of the regular k-point grid in each direction, while k1,k2,k3 tells the code if the grid as to be shifted from the origin in the corresponding direction. It has the same significance that it has for the pwscf input keyword (please look in Doc/INPUT_PW.txt). Is has been discussed many times in the forum, so you can find plenty of discussions in the archives. For instance: http://www.democritos.it/pipermail/pw_forum/2006-May/004299.html but there are many other similar topics for sure. If you still don't understand what these number mean, please have a look at the first lecture of Prof. Narasimhan from the 2009 QE summer school: http://media.quantum-espresso.org/santa_barbara_2009_07/index.php HTH GS > > Thanks > > > -- > Shyam G Khambholja > Reseach student, > Depratment of Physics, > Sardar Patel University > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 siyouber at yahoo.fr Mon Nov 30 14:35:56 2009 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Mon, 30 Nov 2009 13:35:56 +0000 (GMT) Subject: [Pw_forum] CP.x and adiabaticity Message-ID: <763455.28430.qm@web26501.mail.ukl.yahoo.com> Dear all, I performed several molecular dynamic runs but I? still facing some difficulties in choosing the time step and fictitious electron mass that help to control the adiabaticity. I search the web and read some documents, but I still lack a good paper that takes the problem in its practical aspect (how to know if the time step should be increase or not, how to manage the electrons mass after the .evp file, etc). Can somebody give me a hint? ********************************** Bertrand SITAMTZE YOUMBI Research and Teaching Assistant Laboratory of Material Sciences Department of Physics University of Yaound? I-Cameroon ************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091130/681404af/attachment.htm From modaresi.mohsen at gmail.com Mon Nov 30 17:08:54 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Mon, 30 Nov 2009 19:38:54 +0330 Subject: [Pw_forum] Minimum requirement system In-Reply-To: References: Message-ID: Dear users These are my choices, System with 4cores and 4MB RAM and 8cores with 4MB RAM, Is there many deferences between this two system for runing Q.E? Thanks On Mon, Nov 30, 2009 at 1:05 PM, mohsen modaresi wrote: > Dear Lorenzo > Thanks for your answer > > Mohsen Modaresi > > > > On Mon, Nov 30, 2009 at 12:17 PM, Lorenzo Paulatto wrote: > >> Replying to message "[Pw_forum] Minimum requirement system" from mohsen >> modaresi (30/11/09): >> > I want buy a new computer for my PWscf calculation >> > what is your suggestion? (minimum requirement please) >> > Thanks for your answers >> >> Dear Mohsen, >> it depends on the size of the system you are going to study, and on what >> you want to study. >> >> I usually run small molecules (less than 20 electrons) on my laptop, >> systems with about 100 electrons on at least 32 processors (with dedicated >> high-speed network connection and filesystem), systems with about 1000 >> electron require at the very least 128 processors. >> >> 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 >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091130/e27845ee/attachment-0001.htm From giuseppe.mattioli at mlib.ism.cnr.it Mon Nov 30 17:45:20 2009 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Mon, 30 Nov 2009 17:45:20 +0100 Subject: [Pw_forum] Minimum requirement system In-Reply-To: References: Message-ID: <200911301745.21542.giuseppe.mattioli@mlib.ism.cnr.it> I hope that 4MB RAM are actually 4GB RAM...:-) Anyway, in my opinion you need at least 8GB, or you will miss systems containing more than about 500 electrons. If you can afford it, the best choice would be 8 cores and 16 GB... Hope this help Giuseppe On Monday 30 November 2009 17:08:54 mohsen modaresi wrote: > Dear users > These are my choices, System with 4cores and 4MB RAM and 8cores with 4MB > RAM, Is there many deferences between this two system for runing Q.E? > Thanks > > > On Mon, Nov 30, 2009 at 1:05 PM, mohsen modaresi > > wrote: > > Dear Lorenzo > > Thanks for your answer > > > > Mohsen Modaresi > > > > On Mon, Nov 30, 2009 at 12:17 PM, Lorenzo Paulatto wrote: > >> Replying to message "[Pw_forum] Minimum requirement system" from mohsen > >> > >> modaresi (30/11/09): > >> > I want buy a new computer for my PWscf calculation > >> > what is your suggestion? (minimum requirement please) > >> > Thanks for your answers > >> > >> Dear Mohsen, > >> it depends on the size of the system you are going to study, and on what > >> you want to study. > >> > >> I usually run small molecules (less than 20 electrons) on my laptop, > >> systems with about 100 electrons on at least 32 processors (with > >> dedicated high-speed network connection and filesystem), systems with > >> about 1000 electron require at the very least 128 processors. > >> > >> 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 -- ******************************************************** - 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/20091130/69742f19/attachment.htm From modaresi.mohsen at gmail.com Mon Nov 30 17:47:37 2009 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Mon, 30 Nov 2009 20:17:37 +0330 Subject: [Pw_forum] Minimum requirement system In-Reply-To: <200911301745.21542.giuseppe.mattioli@mlib.ism.cnr.it> References: <200911301745.21542.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: Dear Yes of course Thanks On Mon, Nov 30, 2009 at 8:15 PM, Giuseppe Mattioli < giuseppe.mattioli at mlib.ism.cnr.it> wrote: > I hope that 4MB RAM are actually 4GB RAM...:-) > Anyway, in my opinion you need at least 8GB, or you will miss systems > containing more than about 500 electrons. If you can afford it, the best > choice would be 8 cores and 16 GB... > Hope this help > > > Giuseppe > > > On Monday 30 November 2009 17:08:54 mohsen modaresi wrote: > > Dear users > > These are my choices, System with 4cores and 4MB RAM and 8cores with 4MB > > RAM, Is there many deferences between this two system for runing Q.E? > > Thanks > > > > > > On Mon, Nov 30, 2009 at 1:05 PM, mohsen modaresi > > > > wrote: > > > Dear Lorenzo > > > Thanks for your answer > > > > > > Mohsen Modaresi > > > > > > On Mon, Nov 30, 2009 at 12:17 PM, Lorenzo Paulatto >wrote: > > >> Replying to message "[Pw_forum] Minimum requirement system" from > mohsen > > >> > > >> modaresi (30/11/09): > > >> > I want buy a new computer for my PWscf calculation > > >> > what is your suggestion? (minimum requirement please) > > >> > Thanks for your answers > > >> > > >> Dear Mohsen, > > >> it depends on the size of the system you are going to study, and on > what > > >> you want to study. > > >> > > >> I usually run small molecules (less than 20 electrons) on my laptop, > > >> systems with about 100 electrons on at least 32 processors (with > > >> dedicated high-speed network connection and filesystem), systems with > > >> about 1000 electron require at the very least 128 processors. > > >> > > >> 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 > > > -- > ******************************************************** > - 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: > > _______________________________________________ > 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/20091130/48ac9a0e/attachment.htm From antonio.pwscf at gmail.com Mon Nov 30 17:47:57 2009 From: antonio.pwscf at gmail.com (Antonio MSJ) Date: Mon, 30 Nov 2009 14:47:57 -0200 Subject: [Pw_forum] Finite Electric field Message-ID: <8a14f9e0911300847g7b535a20p44707f0a37461138@mail.gmail.com> Hi, I used Gaussian code to apply a finite electric field to a molecule, now I'm trying to do the same with a periodic system with PWscf. I found in PWscf manual the 'lelfield' amd 'gdir' variables and I understood that I can define the direction of the field to be only the axis direction on reciprocal lattice. Is there any way to define the electric field direction with components of a*, b* and c*? In another words, a diagonal electric field through the cell? Thank you very much. Ant?nio -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091130/9543d6e9/attachment.htm From paulatto at sissa.it Mon Nov 30 18:30:41 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 30 Nov 2009 18:30:41 +0100 Subject: [Pw_forum] Finite Electric field In-Reply-To: <8a14f9e0911300847g7b535a20p44707f0a37461138@mail.gmail.com> References: <8a14f9e0911300847g7b535a20p44707f0a37461138@mail.gmail.com> Message-ID: Replying to message "[Pw_forum] Finite Electric field" from Antonio MSJ (30/11/09): > I'm trying to do the same with a periodic system with PWscf. I found in > PWscf manual the 'lelfield' amd 'gdir' variables and I understood that I > can define the direction of the field to be only the axis direction on > reciprocal lattice. Is there any way to define the electric field > direction with components of a*, b* and c*? In another words, a diagonal > electric > field through the cell? Dear Antonio, It is possible, but it is not programmed. As you are studying an isolated system, cannot you just turn the molecule? Alternatively, you can use the dipfield Berry-phase electric field, but I would suggest a bit of mailing-list digging, before, because it is a bit more complicated to use. 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/