From ads5ads5 at 163.com Sat May 1 06:06:42 2010 From: ads5ads5 at 163.com (ads5ads5) Date: Sat, 1 May 2010 12:06:42 +0800 (CST) Subject: [Pw_forum] LDA+U and spin orbit couple Message-ID: <1f7eb11.1541.128520b7785.Coremail.ads5ads5@163.com> Dear all: Eerything is OK when LDA+U and spin orbit couple is added separately. But when LDA+U and spin orbit couple is both used. It runs with error: %%%%%%%%%%%%%%%%\ from vhpsi : error # 1 nstart<>counter %%%%%%%%%%%%%%%%% it seems that LDAU can not work with SO coupling. Is that true? Thanks Fang Sun East China Normal University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100501/5ec649b7/attachment.htm From sd.wang000 at gmail.com Sat May 1 09:09:07 2010 From: sd.wang000 at gmail.com (shudong wang) Date: Sat, 1 May 2010 15:09:07 +0800 Subject: [Pw_forum] regular k-point grid Message-ID: Dear all: How can I get the regular k-point grid in the complete Brillouin zone? Is anybody has a code? Thanks in advance! S D Wang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100501/95ada950/attachment.htm From baroni at sissa.it Sat May 1 09:14:57 2010 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 1 May 2010 09:14:57 +0200 Subject: [Pw_forum] regular k-point grid In-Reply-To: References: Message-ID: <649205FD-7FD0-4D54-A2C2-F6C8DD2AD3AC@sissa.it> Hi: k(i,j,k)=(i-1)*G1/N1 + (j-2)*G2/N2+(k-1)*G3/N3 SB On May 1, 2010, at 9:09 AM, shudong wang wrote: > Dear all: > > How can I get the regular k-point grid in the complete Brillouin zone? Is anybody has a code? > > Thanks in advance! > > S D Wang > _______________________________________________ > 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/20100501/0a1a50fd/attachment-0001.htm From 0930hanbin at 163.com Sat May 1 10:04:23 2010 From: 0930hanbin at 163.com (0930hanbin) Date: Sat, 1 May 2010 16:04:23 +0800 (CST) Subject: [Pw_forum] phonon dispersion relation Message-ID: Dear all, Does anyone know that when I added spin to the system, whether it costs much more time to calculate the phonon dispersion relation ? Whether there are parameters to improve the efficiency of calculating the phonon dispersion relation ? Regards, Bin Han ECNU China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100501/fb31761f/attachment.htm From giannozz at democritos.it Sat May 1 11:06:02 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 1 May 2010 11:06:02 +0200 Subject: [Pw_forum] regular k-point grid In-Reply-To: References: Message-ID: <8FA8D90C-4D62-4EF9-AF18-5E10B7BA8DB7@democritos.it> On May 1, 2010, at 9:09 , shudong wang wrote: > How can I get the regular k-point grid in the complete Brillouin zone? see the FAQ, 8.3.0.3: http://www.quantum-espresso.org/user_guide/ node75.html#SECTION00093030000000000000 > --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From davood.vahedi at yahoo.com Sat May 1 11:10:48 2010 From: davood.vahedi at yahoo.com (davood Vahedi) Date: Sat, 1 May 2010 02:10:48 -0700 (PDT) Subject: [Pw_forum] External electric field Message-ID: <887405.5201.qm@web45703.mail.sp1.yahoo.com> Dear users How can i inter external Electric field to pw calculation? Thanks alot Davod Vahedi PhD student of Solid State Physics -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100501/c7182398/attachment.htm From scandolo at ictp.it Sat May 1 12:33:47 2010 From: scandolo at ictp.it (Sandro Scandolo) Date: Sat, 01 May 2010 12:33:47 +0200 Subject: [Pw_forum] About the mean square displacement in CP output In-Reply-To: <527010.46040.qm@web26501.mail.ukl.yahoo.com> References: <527010.46040.qm@web26501.mail.ukl.yahoo.com> Message-ID: <4BDC038B.5080809@ictp.it> Dear Bernard, if it converges to a finite value, your system is a solid (a crystal or a glass), not a fluid, so it makes no sense to compute the diffusion coefficient with MD, as the time scale for diffusion in solids are dictated by defect diffusion, which takes place on a much longer time scale than a MD simulation. NB: The MSD is also printed out (together with the temperature of each species) in the standard output of cp.x, every iprint. Regards Sandro On 30/04/2010 17:28, Bertrand SITAMTZE wrote: > Dear Sandro, > > Thanks very much for giving tangible responses to my questions. > My aim was to compute the diffusion coefficient using the linear > dependence of the MDS(t). Now that it converge to a finite value, how > should I proceed? > > Your help is of great interest for me. > Thanks once again > > **************************** > Bertrand SITAMTZE YOUMBI > Laboratory of Material Sciences > Department of Physics > University of Yaounde I-Cameroon > ************************************ > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Sandro Scandolo, ICTP | http://www.ictp.it/~scandolo -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100501/a3982551/attachment.htm From siyouber at yahoo.fr Sat May 1 14:46:37 2010 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Sat, 1 May 2010 12:46:37 +0000 (GMT) Subject: [Pw_forum] About the mean square displacement in CP output In-Reply-To: <4BDC038B.5080809@ictp.it> Message-ID: <77554.76004.qm@web26508.mail.ukl.yahoo.com> Dear Sandro, Thanks very much, May be I should search for another method to compute the diffusion coefficient. Best regards. **************************** Bertrand SITAMTZE YOUMBI Laboratory of Material Sciences Department of Physics University of Yaounde I-Cameroon ************************************ --- En date de?: Sam 1.5.10, Sandro Scandolo a ?crit?: De: Sandro Scandolo Objet: Re: [Pw_forum] About the mean square displacement in CP output ?: "PWSCF Forum" Date: Samedi 1 mai 2010, 12h33 Dear Bernard, if it converges to a finite value, your system is a solid (a crystal or a glass), not a fluid, so it makes no sense to compute the diffusion coefficient with MD, as the time scale for diffusion in solids are dictated by defect diffusion, which takes place on a much longer time scale than a MD simulation. NB: The MSD is also printed out (together with the temperature of each species) in the standard output of cp.x, every iprint. Regards Sandro On 30/04/2010 17:28, Bertrand SITAMTZE wrote: Dear Sandro, Thanks very much for giving tangible responses to my questions. My aim was to compute the diffusion coefficient using the linear dependence of the MDS(t).? Now that it converge to a finite value, how should I proceed? Your help is of great interest for me. Thanks once again **************************** Bertrand SITAMTZE YOUMBI Laboratory of Material Sciences Department of Physics University of Yaounde I-Cameroon ************************************ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Sandro Scandolo, ICTP | http://www.ictp.it/~scandolo -----La pi?ce jointe associ?e suit----- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100501/fb069284/attachment.htm From parwana.habibi at cea.fr Mon May 3 09:06:04 2010 From: parwana.habibi at cea.fr (Parwana HABIBI) Date: Mon, 03 May 2010 09:06:04 +0200 Subject: [Pw_forum] band calculation:chosing a specific band In-Reply-To: <895498437.44182.1272649922096.JavaMail.root@mta.iut.ac.ir> References: <895498437.44182.1272649922096.JavaMail.root@mta.iut.ac.ir> Message-ID: <4BDE75DC.9030706@cea.fr> Dear all, I have a question about band calculation. I would like to calculate a band structure for my system, which I can do. There is a surface state, and I would like to study this particular state within the band structure. Therefore, I need to chose the specific band concerning the surface state. In PWSCF input file, there is only 'nbnd' tag that marks the nuber of bands I want to calculate. How can I chose that band among the number of bands I'm calculating? I.E among the nbnd number of bands, how can I only plot my concerned band? Thanks, Parwana Habibi Ph.D student CEA-Saclay, DSM/IRAMIS/SPCSI/LNOSC France. From giuseppe.mattioli at mlib.ism.cnr.it Mon May 3 13:12:17 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Mon, 3 May 2010 13:12:17 +0200 Subject: [Pw_forum] the potential of core electron In-Reply-To: References: <201004291317.38207.giuseppe.mattioli@mlib.ism.cnr.it> <201004301243.04497.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <201005031312.17588.giuseppe.mattioli@mlib.ism.cnr.it> > Shall I do the NSCF between the scf and projwfc.x as the DOS calculation? No, but if you need it for different purposes. > Could you tell me where I can find He 1s eigenvalue ? state #651: atom 192 (H ), wfc 1 (l=0 m= 1) state #652: atom 193 (H ), wfc 1 (l=0 m= 1) state #653: atom 194 (H ), wfc 1 (l=0 m= 1) state #654: atom 195 (H ), wfc 1 (l=0 m= 1) state #655: atom 196 (H ), wfc 1 (l=0 m= 1) state #656: atom 197 (H ), wfc 1 (l=0 m= 1) state #657: atom 198 (H ), wfc 1 (l=0 m= 1) state #658: atom 199 (He ), wfc 1 (l=0 m= 1) look for the # XXX wavefunction corresponding to your He atom at the beginning of the pdos.out file, and match it with a given eigenvalue in the bulk of the same file. Giuseppe On Friday 30 April 2010 12:19:15 wujianchun wrote: > Dear Dr Giuseppe Mattioli: > > > Thank you again! > > > > Shall I do the NSCF between the scf and projwfc.x as the DOS calculation? > > I think I should get the PDOS of He. > > Could you tell me where I can find He 1s eigenvalue ? > > There are some "e" values after each k points in the outfile:pdos.out > > > > "k = 0.0000000000 0.0000000000 0.0000000000 > > e = -7.05254 eV > > psi = 0.022*[# 1]+0.022*[# 5]+0.022*[# 9]+0.022*[# 13]+0.022*[# 17]+ > > +0.022*[# 21]+0.022*[# 25]+0.022*[# 29]+0.022*[# 33]+0.022*[# 37]+ > > +0.022*[# 41]+0.022*[# 45]+0.022*[# 49]+0.022*[# 53]+0.022*[# 57]+ > > +0.022*[# 61]+0.022*[# 65]+0.022*[# 69]+0.022*[# 73]+0.022*[# 77]+ > > +0.022*[# 81]+0.022*[# 85]+0.022*[# 89]+0.022*[# 93]+0.022*[# 97]+ > > +0.022*[# 101]+0.022*[# 105]+0.022*[# 109]+0.022*[# 113]+0.022*[# 117]+ > > +0.022*[# 121]+0.022*[# 125]+0.009*[# 134]+0.009*[# 143]+0.009*[# 152]+ > > +0.009*[# 161]+0.009*[# 170]+0.009*[# 179]+0.009*[# 188]+0.009*[# 197]+ > > +0.009*[# 206]+0.009*[# 215]+0.009*[# 224]+0.009*[# 233]+0.009*[# 242]+ > > +0.009*[# 251]+0.009*[# 260]+0.009*[# 269]+0.009*[# 278]+0.009*[# 287]+ > > +0.009*[# 296]+0.009*[# 305]+0.009*[# 314]+0.009*[# 323]+0.009*[# 332]+ > > +0.009*[# 341]+0.009*[# 350]+0.009*[# 359]+0.009*[# 368]+0.009*[# 377]+ > > +0.009*[# 386]+0.009*[# 395]+0.009*[# 404]+0.009*[# 413]+ > > |psi|^2 = 0.998 > > e = -6.79505 eV" > > > > I guess they are the eigenvalues, and the lowest is He 1s eigenvalue in our > CdS system, > > am I right? > > > > > > > > RgdS > > Jianchun > Department of physics > Soochow university China.215006 > > > From: giuseppe.mattioli at mlib.ism.cnr.it > > To: pw_forum at pwscf.org > > Date: Fri, 30 Apr 2010 12:43:04 +0200 > > Subject: Re: [Pw_forum] the potential of core electron > > > > And, sorry, make a projwfc.x calculation after the scf one to find the He > > 1s eigenvalue if it does not stand alone by comparing scf and scf+He > > calculations > > > > Giuseppe > > > > On Friday 30 April 2010 03:17:41 wujianchun wrote: > > > Dear Dr Giuseppe Mattioli: > > > > > > > > > > > > Could you tell me the details on using the 1s level of a He atom to > > > align the potential. > > > > > > > > > My system is 64 atoms CdS supercell. Need we replace the Cd with He at > > > the corner?How to get the 1S level of He in the output file? > > > > > > > > > > > > Thanks a lot! > > > > > > > > > > > > Regdards > > > > > > Jianchun > > > > > > Department of physics > > > Soochow university China.215006 > > > > > > > > > > > > > > > > > > > > > > > > From: jcwu.suda at hotmail.com > > > To: pw_forum at pwscf.org > > > Date: Thu, 29 Apr 2010 18:57:26 +0800 > > > Subject: Re: [Pw_forum] the potential of core electron > > > > > > > > > > > > Dear Dr Giuseppe Mattioli: > > > > > > Many thanks! > > > I'll try the method. > > > > > > Rgds > > > Jianchun > > > > > > > To: pw_forum at pwscf.org > > > > From: giuseppe.mattioli at mlib.ism.cnr.it > > > > Date: Thu, 29 Apr 2010 13:17:38 +0200 > > > > Subject: Re: [Pw_forum] the potential of core electron > > > > > > > > Dear Jianchun > > > > You cannot get the core levels in pseudopotential calculations. At > > > > least, you cannot get such levels in a straightforward way. And you > > > > don't need! If your host matrix is not close packed, try to use the > > > > 1s level of a He atom to align the potential. The results can be > > > > often quite good... > > > > > > > > Giuseppe > > > > > > > > On Wednesday 28 April 2010 03:29:25 wujianchun wrote: > > > > > Dear All, > > > > > > > > > > > > > > > In order to align the potential between the defect supercell and > > > > > perfect supercell. > > > > > > > > > > > > > > > > > > > > I want to know the potential of core electrons(core-level). > > > > > > > > > > Could you tell me whether the PWSCF can provide the value of the > > > > > potential of core electrons? > > > > > > > > > > > > > > > Who knows how to get the core level of each atom after the scf > > > > > calculation? > > > > > > > > > > > > > > > Thanks in advance! > > > > > > > > > > Rgds > > > > > Jianchun > > > > > Department of physics > > > > > Soochow university China.215006 > > > > > > > > > > _________________________________________________________________ > > > > > MSN????????????????25???????????2010????????? > > > > > http://kaba.msn.com.cn/?k=1 > > > > > > > > -- > > > > ******************************************************** > > > > - 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 > > > > > > ????????,???????????-??,????????! ????? > > > _________________________________________________________________ > > > SkyDrive????????????????????????! > > > http://www.windowslive.cn/campaigns/e-magazine/ngmchina/?a=c > > > > -- > > ******************************************************** > > - 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 > > _________________________________________________________________ > ?????????????????msn????? > http://ditu.live.com/?form=TL&swm=1 -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00016 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From marsamos at democritos.it Mon May 3 11:33:17 2010 From: marsamos at democritos.it (marsamos at democritos.it) Date: Mon, 03 May 2010 11:33:17 +0200 Subject: [Pw_forum] workshop reminder Message-ID: <20100503113317.mrmz7u20yswc0ssk@mail.democritos.it> Dear students, researchers, This is a reminder that ICHEC and Tyndall are organising a workshop from 14th to 18th June in the Tyndall National Institute on the use of Quantum ESPRESSO. Full details of the workshop can be found on the ICHEC web site (http://www.ichec.ie/education_training/qe_workshop). The registration deadline has been extended to 16th May as the method of payment for the registration fee is still being finalized but will be in place shortly. The registration fee has been set at EUR40 for students and EUR70 for everyone else. Please note that registrants are responsible for all costs involved in attending this workshop (e.g. registration fee, travel, subsistence and accommodation); funding is not available for attendees of this event. For accommodation, please refer to http://www.tyndall.ie/contact/accommodation/ for a list of suitable hotels/guest houses. The full program for this event, along with abstracts for the topics to be covered, has also been updated and available on the web site (http://www.ichec.ie/education_training/qe_workshop/qe_workshop_programme). The series of lectures/tutorials will be delivered by a world-class scientist team of QE experts and developers. Topics at the workshop cover a range of contemporary QE applications, from simple electronic structure calculations, equilibrium structure and reaction paths search, to the most sophisticated theoretical spectroscopies such as nuclear magnetic resonance (NMR), electron paramagnetic resonance (EPR), optical absorption, Raman and scanning tunnel microscopy, etc. If you have any other queries with regards to this workshop, please contact Ivan Girotto (ivan.girotto at ichec.ie). The workshop is supported by INSPIRE, NVIDIA and CAPS Enterprise. Ivan Girotto ICHEC, Ireland ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From uccaati at ucl.ac.uk Mon May 3 11:45:28 2010 From: uccaati at ucl.ac.uk (Antonio Tilocca) Date: Mon, 3 May 2010 10:45:28 +0100 (BST) Subject: [Pw_forum] About the mean square displacement in CP output In-Reply-To: References: Message-ID: Dear Bertrand, the way you are obtaining the MSD(t) is not the best: in that way, every time point is only averaged using a single time origin, whereas it is advisable, for a better statistics, to perform an extended average over a large number of non-correlated time origins, as described (with examples of codes) in the Allen-Tildesley book, for instance. However, the trend that you obtain with your approximate approach is qualitatively correct. As for your other question, as Sandro has already pointed out, the zero slope of your (constant) MSD(t) shows the absence of diffusion, as expected for a solid, on your short observation time. Antonio Tilocca UCL > Message: 2 > Date: Fri, 30 Apr 2010 15:15:36 +0000 (GMT) > From: Bertrand SITAMTZE > Subject: Re: [Pw_forum] About the mean square displacement in CP > output > To: PWSCF Forum > Message-ID: <414847.4559.qm at web26504.mail.ukl.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Antonio, > > Thanks very much for responding. To plot MSD(t) I just go through the > standard? output file and collect all the calculated MSDs fo each atoms. > The time is computed using each "nfi"(the first column of the output > file). I will be gratefull if you indicate a postprocessing code. How to > used an oscillating MDS to compute the diffusion coefficient as usually > done? > > **************************** > Bertrand SITAMTZE YOUMBI > Laboratory of Material Sciences > Department of Physics > University of Yaounde I-Cameroon > ************************************ > > > > --- En date de?: Ven 30.4.10, Antonio Tilocca a ?crit?: > > De: Antonio Tilocca > Objet: Re: [Pw_forum] About the mean square displacement in CP output > ?: pw_forum at pwscf.org > Date: Vendredi 30 avril 2010, 16h09 > > > Dear Bertrand: > > I am not sure I understand how you are extracting the MSD(t) from the CP > trajectory: are you just plotting the final values shown in the standard > output file, or (as it would be recommended) calculating them by > post-processing the trajectory file? In any event, a flat, oscillating > MSD(t), after an initial increase, is exactly what you would > expect for a solid. > > Antonio Tilocca > UCL > > > From fratesi at mater.unimib.it Mon May 3 12:11:17 2010 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Mon, 3 May 2010 12:11:17 +0200 (CEST) Subject: [Pw_forum] Implementation of DOS in real space Message-ID: Dear Q-E (especially pwscf) developers, I was needing an evaluation of the density of states (DOS) as function of energy, integrated in a volume, rather than projected on the atomic orbitals as done by projwfc.x. The purpose was to highlight electronic states which have significant weight right outside a surface. I have implemented its calculation, for the norm-conserving part of the charge, in projwfc.x (really, I have re-adapted to the CVS version my previous implementation, with refence to previous discussion on this forum: http://www.democritos.it/pipermail/pw_forum/2008-September/010005.html ). The use of the norm-conserving part only was because the augmentation part does not contribute far from the atoms (the same is done when plotting STM images by pp.x). Conversely, near the atoms, the projection on atomic orbitals as currently implemented is probably more suited. It would be nice, in my opinion, to have this feature embedded in the espresso release. Yet I don't know if this opinion is shared among the users/developers, and the details of its best incorporation. I can provide the source code (only projwfc.f90 was modified) and a working example if that is of common interest. Maybe, the easiest way is that I get contacted by some of the developers for the details, directly or via the forum. Please let me know. Best regards, Guido Fratesi -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca From marzari at MIT.EDU Mon May 3 12:09:50 2010 From: marzari at MIT.EDU (Nicola Marzari) Date: Mon, 03 May 2010 11:09:50 +0100 Subject: [Pw_forum] band calculation:chosing a specific band In-Reply-To: <4BDE75DC.9030706@cea.fr> References: <895498437.44182.1272649922096.JavaMail.root@mta.iut.ac.ir> <4BDE75DC.9030706@cea.fr> Message-ID: <4BDEA0EE.1020006@mit.edu> Parwana HABIBI wrote: > Dear all, > > I have a question about band calculation. I would like to calculate a > band structure for my system, which I can do. There is a surface state, > and I would like to study this particular state within the band > structure. Therefore, I need to chose the specific band concerning the > surface state. In PWSCF input file, there is only 'nbnd' tag that marks > the nuber of bands I want to calculate. > How can I chose that band among the number of bands I'm calculating? I.E > among the nbnd number of bands, how can I only plot my concerned band? > > Thanks, > Dear Parwana, 1) in the calculation, you need to include all the occupied bands (plus some, for a metal). You cannot "calculate" only one band. 2) After you have finished a successful calculation, the plotting subroutines allow you to choose which band you want to plot (the second, the seventh, etc...) at which k-point. 3) if your surface state is not isolated (i.e. if anywhere in the Brillouin zone it crosses other bands), then you have no other choice than to "disentangle" it. See e.g. this http://arxiv.org/abs/0910.1748 from the SIESTA group. 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 kazempoor at ph.iut.ac.ir Mon May 3 15:26:35 2010 From: kazempoor at ph.iut.ac.ir (kazempoor at ph.iut.ac.ir) Date: Mon, 3 May 2010 17:56:35 +0430 (IRDT) Subject: [Pw_forum] add or remove electron energy In-Reply-To: <1943169952.60789.1272893036281.JavaMail.root@mta.iut.ac.ir> Message-ID: <276964397.60815.1272893195061.JavaMail.root@mta.iut.ac.ir> Dear All I add one electron to an isolated atom and the difference in E(n+1)-E(n)=-0.09 Ryd but when I remove an electron from this atom I got E(n)-E(n-1)=-0.349 Ryd. what is the reason for this difference? I think that this behavior is same for every system. Thanks a lot Ali Kazempour Physics Department, Isfahan University of Technology From degironc at sissa.it Mon May 3 15:40:25 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 03 May 2010 15:40:25 +0200 Subject: [Pw_forum] add or remove electron energy In-Reply-To: <276964397.60815.1272893195061.JavaMail.root@mta.iut.ac.ir> References: <276964397.60815.1272893195061.JavaMail.root@mta.iut.ac.ir> Message-ID: <4BDED249.7080508@sissa.it> it is the difference between electron affinity and ionization potential. stefano kazempoor at ph.iut.ac.ir wrote: > Dear All > I add one electron to an isolated atom and the difference in E(n+1)-E(n)=-0.09 Ryd but when I remove an electron from this atom > I got E(n)-E(n-1)=-0.349 Ryd. > what is the reason for this difference? I think that this behavior is same for every system. > Thanks a lot > Ali Kazempour > Physics Department, Isfahan University of Technology > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at democritos.it Mon May 3 15:42:04 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 03 May 2010 15:42:04 +0200 Subject: [Pw_forum] Implementation of DOS in real space In-Reply-To: References: Message-ID: <4BDED2AC.6080600@democritos.it> Guido Fratesi wrote: > Maybe, the easiest way is that I get contacted by some of the developers > for the details, directly or via the forum. Please let me know. Hi Guido, a general remark: one can use the address listed in http://www.quantum-espresso.org/contacts.php to contact developers P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From matteo at umn.edu Mon May 3 15:36:35 2010 From: matteo at umn.edu (Matteo Cococcioni) Date: Mon, 03 May 2010 08:36:35 -0500 Subject: [Pw_forum] LDA+U and spin orbit couple In-Reply-To: <1f7eb11.1541.128520b7785.Coremail.ads5ads5@163.com> References: <1f7eb11.1541.128520b7785.Coremail.ads5ads5@163.com> Message-ID: <4BDED163.7090709@umn.edu> Dear Fang, to the best of my knowledge LDA+U has not been implemented in the non-collinear case yet and cannot work with spin-orbit. I am not sure what the error exactly means though. probably vhpsi has more KS wavefunction than it was expecting to construct the Hubbard potential and so gives an error. but this is just my guess. regards, Matteo ads5ads5 wrote: > Dear all: > Eerything is OK when LDA+U and spin orbit couple is added separately. > But when LDA+U and spin orbit couple is both used. > It runs with error: > %%%%%%%%%%%%%%%%\ > from vhpsi : error # 1 > nstart<>counter > %%%%%%%%%%%%%%%%% > it seems that LDAU can not work with SO coupling. Is that true? > Thanks > Fang Sun > East China Normal University > > > ?????????????????????????????????????????? > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 Fax +1 612 626 7246 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From giannozz at democritos.it Mon May 3 15:59:12 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 03 May 2010 15:59:12 +0200 Subject: [Pw_forum] External electric field In-Reply-To: <887405.5201.qm@web45703.mail.sp1.yahoo.com> References: <887405.5201.qm@web45703.mail.sp1.yahoo.com> Message-ID: <4BDED6B0.5020207@democritos.it> davood Vahedi wrote: > How can i inter external Electric field to pw calculation? "inter external" ? documentation for electric field in PWscf as a sawtooth: examples/dipole_example for electric field in PWscf from modern theory of polarization: examples/example31: as above, for CP: examples/example30 plus input documentation P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From siyouber at yahoo.fr Mon May 3 16:06:30 2010 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Mon, 3 May 2010 14:06:30 +0000 (GMT) Subject: [Pw_forum] About the mean square displacement in CP output In-Reply-To: Message-ID: <743317.79665.qm@web26507.mail.ukl.yahoo.com> Dear Antonio and all users, Thanks for responses you have given until now. But I am a bit confused. Please could sombody tels me how to compute the diffusion coefficient in a solid using Ab-initio Molecular dynamics? Best regards **************************** Bertrand SITAMTZE YOUMBI Laboratory of Material Sciences Department of Physics University of Yaounde I-Cameroon *********************************** --- En date de?: Lun 3.5.10, Antonio Tilocca a ?crit?: De: Antonio Tilocca Objet: Re: [Pw_forum] About the mean square displacement in CP output ?: pw_forum at pwscf.org Date: Lundi 3 mai 2010, 11h45 Dear Bertrand, the way you are obtaining the MSD(t) is not the best: in that way, every time point is only averaged using a single time origin, whereas it is advisable, for a better statistics, to perform an extended average over a large number of non-correlated time origins, as described (with examples of codes) in the Allen-Tildesley book, for instance. However, the trend that you obtain with your approximate approach is qualitatively correct. As for your other question, as Sandro has already pointed out, the zero slope of your (constant) MSD(t) shows the absence of diffusion, as expected for a solid, on your short observation time. Antonio Tilocca UCL > Message: 2 > Date: Fri, 30 Apr 2010 15:15:36 +0000 (GMT) > From: Bertrand SITAMTZE > Subject: Re: [Pw_forum] About the mean square displacement in CP > ??? output > To: PWSCF Forum > Message-ID: <414847.4559.qm at web26504.mail.ukl.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Antonio, > > Thanks very much for responding. To plot MSD(t) I just go through the > standard? output file and collect all the calculated MSDs fo each atoms. > The time is computed using each "nfi"(the first column of the output > file). I will be gratefull if you indicate a postprocessing code. How to > used an oscillating MDS to compute the diffusion coefficient as usually > done? > > **************************** > Bertrand SITAMTZE YOUMBI > Laboratory of Material Sciences > Department of Physics > University of Yaounde I-Cameroon > ************************************ > > > > --- En date de?: Ven 30.4.10, Antonio Tilocca a ?crit?: > > De: Antonio Tilocca > Objet: Re: [Pw_forum] About the mean square displacement in CP output > ?: pw_forum at pwscf.org > Date: Vendredi 30 avril 2010, 16h09 > > > Dear Bertrand: > > I am not sure I understand how you are extracting the MSD(t) from the CP > trajectory: are you just plotting the final values shown in the standard > output file, or (as it would be recommended) calculating them by > post-processing the trajectory file? In any event, a flat, oscillating > MSD(t), after an initial increase, is exactly what you would > expect for a solid. > > Antonio Tilocca > UCL > > > _______________________________________________ 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/20100503/bd6ed916/attachment.htm From kazempoor at ph.iut.ac.ir Mon May 3 16:05:41 2010 From: kazempoor at ph.iut.ac.ir (kazempoor at ph.iut.ac.ir) Date: Mon, 3 May 2010 18:35:41 +0430 (IRDT) Subject: [Pw_forum] add or remove electron energy In-Reply-To: <4BDED249.7080508@sissa.it> Message-ID: <1302832878.61051.1272895541244.JavaMail.root@mta.iut.ac.ir> Dear Stefano I now that these are affinity and ionization, But I don't understand why ionization always is grater than affinity? I just want to know the physical reason. Thanks a lot Ali Kazempour Physics Department, Isfahn University of Technology ----- Original Message ----- From: "Stefano de Gironcoli" To: "PWSCF Forum" Sent: Monday, May 3, 2010 6:10:25 PM Subject: Re: [Pw_forum] add or remove electron energy it is the difference between electron affinity and ionization potential. stefano kazempoor at ph.iut.ac.ir wrote: > Dear All > I add one electron to an isolated atom and the difference in E(n+1)-E(n)=-0.09 Ryd but when I remove an electron from this atom > I got E(n)-E(n-1)=-0.349 Ryd. > what is the reason for this difference? I think that this behavior is same for every system. > Thanks a lot > Ali Kazempour > Physics Department, Isfahan University of Technology > _______________________________________________ > 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 nazari at iasbs.ac.ir Mon May 3 19:43:03 2010 From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir) Date: Mon, 3 May 2010 18:43:03 +0100 (BST) Subject: [Pw_forum] add or remove electron energy In-Reply-To: <276964397.60815.1272893195061.JavaMail.root@mta.iut.ac.ir> References: <276964397.60815.1272893195061.JavaMail.root@mta.iut.ac.ir> Message-ID: <58531.217.218.226.57.1272908583.squirrel@mail.iasbs.ac.ir> > Please study about the definition of Ionization energy and Electron affinity. You can find your answer. > Dear All > I add one electron to an isolated atom and the difference in > E(n+1)-E(n)=-0.09 Ryd but when I remove an electron from this atom > I got E(n)-E(n-1)=-0.349 Ryd. > what is the reason for this difference? I think that this behavior is same > for every system. > Thanks a lot > Ali Kazempour > Physics Department, Isfahan University of Technology > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From matteo at umn.edu Mon May 3 16:24:40 2010 From: matteo at umn.edu (Matteo Cococcioni) Date: Mon, 03 May 2010 09:24:40 -0500 Subject: [Pw_forum] add or remove electron energy In-Reply-To: <1302832878.61051.1272895541244.JavaMail.root@mta.iut.ac.ir> References: <1302832878.61051.1272895541244.JavaMail.root@mta.iut.ac.ir> Message-ID: <4BDEDCA8.7020803@umn.edu> Dear Ali, I think this is a good reference on this topic: J. P. Perdew, R. G. Parr, M. Levy, and J. L. Balduz, Phys. Rev. Lett. 49, 1691 (1982) Matteo kazempoor at ph.iut.ac.ir wrote: > Dear Stefano > > I now that these are affinity and ionization, But I don't understand why ionization always is grater than affinity? I just want to know the physical reason. > > > > Thanks a lot > > > > > Ali Kazempour > Physics Department, Isfahn University of Technology > > ----- Original Message ----- > From: "Stefano de Gironcoli" > To: "PWSCF Forum" > Sent: Monday, May 3, 2010 6:10:25 PM > Subject: Re: [Pw_forum] add or remove electron energy > > it is the difference between electron affinity and ionization potential. > stefano > > kazempoor at ph.iut.ac.ir wrote: > >> Dear All >> I add one electron to an isolated atom and the difference in E(n+1)-E(n)=-0.09 Ryd but when I remove an electron from this atom >> I got E(n)-E(n-1)=-0.349 Ryd. >> what is the reason for this difference? I think that this behavior is same for every system. >> Thanks a lot >> Ali Kazempour >> Physics Department, Isfahan University of Technology >> _______________________________________________ >> 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 degironc at sissa.it Mon May 3 16:35:11 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 03 May 2010 16:35:11 +0200 Subject: [Pw_forum] add or remove electron energy In-Reply-To: <1302832878.61051.1272895541244.JavaMail.root@mta.iut.ac.ir> References: <1302832878.61051.1272895541244.JavaMail.root@mta.iut.ac.ir> Message-ID: <4BDEDF1F.9030701@sissa.it> The electron affinity is the ionization potential of the negative ion. The fact that it is smaller than the ionization potential of the neutral ion is in the end due to the fact that it feels the el-el repulsion of one additional electron. Or if you prefer, in Hartree-Fock theory, Koopmans theorems say that I is - E_HOMO and A is -E_LUMO and since, by definition, E_LUMO > E_HOMO => I > A stefano kazempoor at ph.iut.ac.ir wrote: > Dear Stefano > > I now that these are affinity and ionization, But I don't understand why ionization always is grater than affinity? I just want to know the physical reason. > > > > Thanks a lot > > > > > Ali Kazempour > Physics Department, Isfahn University of Technology > > ----- Original Message ----- > From: "Stefano de Gironcoli" > To: "PWSCF Forum" > Sent: Monday, May 3, 2010 6:10:25 PM > Subject: Re: [Pw_forum] add or remove electron energy > > it is the difference between electron affinity and ionization potential. > stefano > > kazempoor at ph.iut.ac.ir wrote: > >> Dear All >> I add one electron to an isolated atom and the difference in E(n+1)-E(n)=-0.09 Ryd but when I remove an electron from this atom >> I got E(n)-E(n-1)=-0.349 Ryd. >> what is the reason for this difference? I think that this behavior is same for every system. >> Thanks a lot >> Ali Kazempour >> Physics Department, Isfahan University of Technology >> _______________________________________________ >> 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 Mon May 3 16:45:29 2010 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 3 May 2010 16:45:29 +0200 Subject: [Pw_forum] add or remove electron energy In-Reply-To: <4BDEDCA8.7020803@umn.edu> References: <1302832878.61051.1272895541244.JavaMail.root@mta.iut.ac.ir> <4BDEDCA8.7020803@umn.edu> Message-ID: <50B65CB8-958B-46BD-B7F0-EB80FA788827@sissa.it> Ali: studying and reading is always a good idea. In this case, though, trying to figure out by yourself the "physical reason" could be even more instructive. Hint(s): 1) distinguish first the case of an open-shell atom/molecule from that of a closed-shell one. 2) The simpler case is that of a closed shell. The ionization potential is the energy necessary to remove an electron from a system which has N of them, all paired into atomic/molecular orbitals. The electron affinity is the energy necessary to remove an electron from a system with the same external potential, but one electron more. In the independent-electron (or mean-field) approximation, the extra electron will necessarily be accomodated into an orbital of higher energy (all the available orbitals of equal or lower energy are occupied by the hypothesis of closed shells) ... can you complete the argument? 3) In the case of closed shells, the argument is a bit more sophisticated, because the independent-electron approximation would predict the electron affinity to be equal to the ionization potential. Can you tell why? If you can, then it should not be difficult to figure out how to refine the argument. Compare the effective potential (external-plus-electronic) of two systems with the same external potential, but differing in the number of electrons ... which one of the two is more attractive? Give yourself 1-2 days of hard thinking, and if you fail to find an answer revert to us ... Stefano B On May 3, 2010, at 4:24 PM, Matteo Cococcioni wrote: > > > Dear Ali, > > I think this is a good reference on this topic: > > J. P. Perdew, R. G. Parr, M. Levy, and J. L. Balduz, Phys. Rev. > Lett. 49, 1691 (1982) > > Matteo > > > > > kazempoor at ph.iut.ac.ir wrote: >> Dear Stefano >> >> I now that these are affinity and ionization, But I don't understand why ionization always is grater than affinity? I just want to know the physical reason. >> >> >> >> Thanks a lot >> >> >> >> >> Ali Kazempour >> Physics Department, Isfahn University of Technology >> >> ----- Original Message ----- >> From: "Stefano de Gironcoli" >> To: "PWSCF Forum" >> Sent: Monday, May 3, 2010 6:10:25 PM >> Subject: Re: [Pw_forum] add or remove electron energy >> >> it is the difference between electron affinity and ionization potential. >> stefano >> >> kazempoor at ph.iut.ac.ir wrote: >> >>> Dear All >>> I add one electron to an isolated atom and the difference in E(n+1)-E(n)=-0.09 Ryd but when I remove an electron from this atom >>> I got E(n)-E(n-1)=-0.349 Ryd. >>> what is the reason for this difference? I think that this behavior is same for every system. >>> Thanks a lot >>> Ali Kazempour >>> Physics Department, Isfahan University of Technology >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- 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/20100503/55e74089/attachment-0001.htm From giannozz at democritos.it Mon May 3 16:53:14 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 03 May 2010 16:53:14 +0200 Subject: [Pw_forum] add or remove electron energy In-Reply-To: <50B65CB8-958B-46BD-B7F0-EB80FA788827@sissa.it> References: <1302832878.61051.1272895541244.JavaMail.root@mta.iut.ac.ir> <4BDEDCA8.7020803@umn.edu> <50B65CB8-958B-46BD-B7F0-EB80FA788827@sissa.it> Message-ID: <4BDEE35A.90500@democritos.it> Stefano Baroni wrote: > 3) In the case of closed shells you mean: open, I guess P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From daniel.forrer at unipd.it Mon May 3 17:12:26 2010 From: daniel.forrer at unipd.it (Daniel Forrer) Date: Mon, 3 May 2010 17:12:26 +0200 Subject: [Pw_forum] autopilot-example Message-ID: Dear all, I'm trying to run the autopilot-example using espresso-4.1.3, but the calculation stops after 102 iterations with the message: "MAIN: convergence achieved for system relaxation". I think that the "problem" is just here. Indeed, by setting ekin_conv_thr to the (crazy) value 1e-30 Ry everything works fine. Best regards daniel -- ---------------------------------- Daniel Forrer Dipartimento di Scienze Chimiche Universit? degli Studi di Padova V. Marzolo 1, Padova mail daniel.forrer at unipd.it tel. +39 049 8275166 ---------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100503/a055239b/attachment.htm From baroni at sissa.it Mon May 3 17:13:36 2010 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 3 May 2010 17:13:36 +0200 Subject: [Pw_forum] add or remove electron energy In-Reply-To: <4BDEE35A.90500@democritos.it> References: <1302832878.61051.1272895541244.JavaMail.root@mta.iut.ac.ir> <4BDEDCA8.7020803@umn.edu> <50B65CB8-958B-46BD-B7F0-EB80FA788827@sissa.it> <4BDEE35A.90500@democritos.it> Message-ID: <700681F3-6FB4-47B4-8B85-511F4AE0FB3C@sissa.it> On May 3, 2010, at 4:53 PM, Paolo Giannozzi wrote: > Stefano Baroni wrote: > >> 3) In the case of closed shells > > you mean: open, I guess you guessed right - sorry about that Stefano > > 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 --- 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/20100503/f2c015c8/attachment.htm From giannozz at democritos.it Mon May 3 17:19:34 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 03 May 2010 17:19:34 +0200 Subject: [Pw_forum] phonon dispersion relation In-Reply-To: References: Message-ID: <4BDEE986.2090403@democritos.it> 0930hanbin wrote: > Does anyone know that when I added spin to the system, whether it costs > much more time to calculate the phonon dispersion relation ? at least twice as much P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From masoudnahali at live.com Mon May 3 23:48:21 2010 From: masoudnahali at live.com (Masoud Nahali) Date: Mon, 3 May 2010 21:48:21 +0000 Subject: [Pw_forum] Occupations Message-ID: Dear QE users Is "Occupations" variable necessary for Metals? It seems that the "tetrahedra" along with occupations variable is not suitable for optimization calculations ! my studing sample is Graphite and I do not know that the specifying of the metallicity is needed or not? a simple physical definition of "occupations" should be useful for me. I could not find a clear one in the forum. Is this variable related to the how should one select the K-POINTS !? Masoud Nahali SUT _________________________________________________________________ Hotmail: Trusted email with Microsoft?s powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100503/a65bab67/attachment.htm From marzari at MIT.EDU Tue May 4 00:13:10 2010 From: marzari at MIT.EDU (Nicola Marzari) Date: Mon, 03 May 2010 23:13:10 +0100 Subject: [Pw_forum] Occupations In-Reply-To: References: Message-ID: <4BDF4A76.8050905@mit.edu> Dear Masoud, have a look at Shobhana Narasimhan lectures from the QE summer school: http://media.quantum-espresso.org/santa_barbara_2009_07/index.php#20090719 but in short, yes, it is necessary for metals. For graphite it is probably less important, you could try with and without, and see what happens. nicola Masoud Nahali wrote: > Dear QE users > > Is "Occupations" variable necessary for Metals? It seems that the > "tetrahedra" along with occupations variable is not suitable for > optimization calculations ! > my studing sample is Graphite and I do not know that the specifying of > the metallicity is needed or not? a simple physical definition of > "occupations" should be useful for me. I could not find a clear one in > the forum. Is this variable related to the how should one select the > K-POINTS !? > > > Masoud Nahali > SUT > > > > ------------------------------------------------------------------------ > Hotmail: Trusted email with Microsoft?s powerful SPAM protection. Sign > up now. > ------------------------------------------------------------------------ > > _______________________________________________ > 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 jcwu.suda at hotmail.com Tue May 4 03:44:17 2010 From: jcwu.suda at hotmail.com (wujianchun) Date: Tue, 4 May 2010 09:44:17 +0800 Subject: [Pw_forum] the potential of core electron In-Reply-To: <201005031312.17588.giuseppe.mattioli@mlib.ism.cnr.it> References: <201004291317.38207.giuseppe.mattioli@mlib.ism.cnr.it>, <201004301243.04497.giuseppe.mattioli@mlib.ism.cnr.it>, , <201005031312.17588.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: Dear Dr Giuseppe Mattioli: Many thanks! You mean I should adopt the e = -5.55656 eV, because the # 408 wavefunction is the largest part of wavefunction psi? The eigenvalue is slightly different in different k points, should I average them and get the mean value as the He 1S eigenvalue? My pdos.out is as follows: ...... state # 397: atom 62 (Cd ), wfc 3 (l=1 m= 2) state # 398: atom 62 (Cd ), wfc 3 (l=1 m= 3) state # 399: atom 63 (Cd ), wfc 1 (l=2 m= 1) state # 400: atom 63 (Cd ), wfc 1 (l=2 m= 2) state # 401: atom 63 (Cd ), wfc 1 (l=2 m= 3) state # 402: atom 63 (Cd ), wfc 1 (l=2 m= 4) state # 403: atom 63 (Cd ), wfc 1 (l=2 m= 5) state # 404: atom 63 (Cd ), wfc 2 (l=0 m= 1) state # 405: atom 63 (Cd ), wfc 3 (l=1 m= 1) state # 406: atom 63 (Cd ), wfc 3 (l=1 m= 2) state # 407: atom 63 (Cd ), wfc 3 (l=1 m= 3) state # 408: atom 64 (He ), wfc 1 (l=0 m= 1) ..... k = 0.0000000000 0.0000000000 0.0000000000 ..... e = -5.55656 eV psi = 0.696*[# 408]+0.052*[# 105]+0.051*[# 5]+0.050*[# 77]+0.040*[# 33]+ +0.003*[# 203]+0.003*[# 223]+0.004*[# 229]+0.003*[# 157]+0.003*[# 239]+ +0.003*[# 358]+0.003*[# 6]+0.003*[# 108]+0.003*[# 7]+0.003*[# 8]+ ...... k = 0.0000000000 0.0000000000 -0.5000000000 ...... Lowdin Charges: ...... Thanks ! Rgds Jianchun Wu Department of physics Soochow university China.215006 > From: giuseppe.mattioli at mlib.ism.cnr.it > To: pw_forum at pwscf.org > Date: Mon, 3 May 2010 13:12:17 +0200 > Subject: Re: [Pw_forum] the potential of core electron > > > Shall I do the NSCF between the scf and projwfc.x as the DOS calculation? > > No, but if you need it for different purposes. > > > Could you tell me where I can find He 1s eigenvalue ? > > state #651: atom 192 (H ), wfc 1 (l=0 m= 1) > state #652: atom 193 (H ), wfc 1 (l=0 m= 1) > state #653: atom 194 (H ), wfc 1 (l=0 m= 1) > state #654: atom 195 (H ), wfc 1 (l=0 m= 1) > state #655: atom 196 (H ), wfc 1 (l=0 m= 1) > state #656: atom 197 (H ), wfc 1 (l=0 m= 1) > state #657: atom 198 (H ), wfc 1 (l=0 m= 1) > state #658: atom 199 (He ), wfc 1 (l=0 m= 1) > > look for the # XXX wavefunction corresponding to your He atom at the beginning > of the pdos.out file, and match it with a given eigenvalue in the bulk of the > same file. > > Giuseppe > > > > On Friday 30 April 2010 12:19:15 wujianchun wrote: > > Dear Dr Giuseppe Mattioli: > > > > > > Thank you again! > > > > > > > > Shall I do the NSCF between the scf and projwfc.x as the DOS calculation? > > > > I think I should get the PDOS of He. > > > > Could you tell me where I can find He 1s eigenvalue ? > > > > There are some "e" values after each k points in the outfile:pdos.out > > > > > > > > "k = 0.0000000000 0.0000000000 0.0000000000 > > > > e = -7.05254 eV > > > > psi = 0.022*[# 1]+0.022*[# 5]+0.022*[# 9]+0.022*[# 13]+0.022*[# 17]+ > > > > +0.022*[# 21]+0.022*[# 25]+0.022*[# 29]+0.022*[# 33]+0.022*[# 37]+ > > > > +0.022*[# 41]+0.022*[# 45]+0.022*[# 49]+0.022*[# 53]+0.022*[# 57]+ > > > > +0.022*[# 61]+0.022*[# 65]+0.022*[# 69]+0.022*[# 73]+0.022*[# 77]+ > > > > +0.022*[# 81]+0.022*[# 85]+0.022*[# 89]+0.022*[# 93]+0.022*[# 97]+ > > > > +0.022*[# 101]+0.022*[# 105]+0.022*[# 109]+0.022*[# 113]+0.022*[# 117]+ > > > > +0.022*[# 121]+0.022*[# 125]+0.009*[# 134]+0.009*[# 143]+0.009*[# 152]+ > > > > +0.009*[# 161]+0.009*[# 170]+0.009*[# 179]+0.009*[# 188]+0.009*[# 197]+ > > > > +0.009*[# 206]+0.009*[# 215]+0.009*[# 224]+0.009*[# 233]+0.009*[# 242]+ > > > > +0.009*[# 251]+0.009*[# 260]+0.009*[# 269]+0.009*[# 278]+0.009*[# 287]+ > > > > +0.009*[# 296]+0.009*[# 305]+0.009*[# 314]+0.009*[# 323]+0.009*[# 332]+ > > > > +0.009*[# 341]+0.009*[# 350]+0.009*[# 359]+0.009*[# 368]+0.009*[# 377]+ > > > > +0.009*[# 386]+0.009*[# 395]+0.009*[# 404]+0.009*[# 413]+ > > > > |psi|^2 = 0.998 > > > > e = -6.79505 eV" > > > > > > > > I guess they are the eigenvalues, and the lowest is He 1s eigenvalue in our > > CdS system, > > > > am I right? > > > > > > > > > > > > > > > > RgdS > > > > Jianchun > > Department of physics > > Soochow university China.215006 > > > > > From: giuseppe.mattioli at mlib.ism.cnr.it > > > To: pw_forum at pwscf.org > > > Date: Fri, 30 Apr 2010 12:43:04 +0200 > > > Subject: Re: [Pw_forum] the potential of core electron > > > > > > And, sorry, make a projwfc.x calculation after the scf one to find the He > > > 1s eigenvalue if it does not stand alone by comparing scf and scf+He > > > calculations > > > > > > Giuseppe > > > > > > On Friday 30 April 2010 03:17:41 wujianchun wrote: > > > > Dear Dr Giuseppe Mattioli: > > > > > > > > > > > > > > > > Could you tell me the details on using the 1s level of a He atom to > > > > align the potential. > > > > > > > > > > > > My system is 64 atoms CdS supercell. Need we replace the Cd with He at > > > > the corner?How to get the 1S level of He in the output file? > > > > > > > > > > > > > > > > Thanks a lot! > > > > > > > > > > > > > > > > Regdards > > > > > > > > Jianchun > > > > > > > > Department of physics > > > > Soochow university China.215006 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > From: jcwu.suda at hotmail.com > > > > To: pw_forum at pwscf.org > > > > Date: Thu, 29 Apr 2010 18:57:26 +0800 > > > > Subject: Re: [Pw_forum] the potential of core electron > > > > > > > > > > > > > > > > Dear Dr Giuseppe Mattioli: > > > > > > > > Many thanks! > > > > I'll try the method. > > > > > > > > Rgds > > > > Jianchun > > > > > > > > > To: pw_forum at pwscf.org > > > > > From: giuseppe.mattioli at mlib.ism.cnr.it > > > > > Date: Thu, 29 Apr 2010 13:17:38 +0200 > > > > > Subject: Re: [Pw_forum] the potential of core electron > > > > > > > > > > Dear Jianchun > > > > > You cannot get the core levels in pseudopotential calculations. At > > > > > least, you cannot get such levels in a straightforward way. And you > > > > > don't need! If your host matrix is not close packed, try to use the > > > > > 1s level of a He atom to align the potential. The results can be > > > > > often quite good... > > > > > > > > > > Giuseppe > > > > > > > > > > On Wednesday 28 April 2010 03:29:25 wujianchun wrote: > > > > > > Dear All, > > > > > > > > > > > > > > > > > > In order to align the potential between the defect supercell and > > > > > > perfect supercell. > > > > > > > > > > > > > > > > > > > > > > > > I want to know the potential of core electrons(core-level). > > > > > > > > > > > > Could you tell me whether the PWSCF can provide the value of the > > > > > > potential of core electrons? > > > > > > > > > > > > > > > > > > Who knows how to get the core level of each atom after the scf > > > > > > calculation? > > > > > > > > > > > > > > > > > > Thanks in advance! > > > > > > > > > > > > Rgds > > > > > > Jianchun > > > > > > Department of physics > > > > > > Soochow university China.215006 > > > > > > > > > > > > _________________________________________________________________ > > > > > > MSN????????????????25???????????2010????????? > > > > > > http://kaba.msn.com.cn/?k=1 > > > > > > > > > > -- > > > > > ******************************************************** > > > > > - 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 > > > > > > > > ????????,???????????-??,????????! ????? > > > > _________________________________________________________________ > > > > SkyDrive????????????????????????! > > > > http://www.windowslive.cn/campaigns/e-magazine/ngmchina/?a=c > > > > > > -- > > > ******************************************************** > > > - 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 > > > > _________________________________________________________________ > > ?????????????????msn????? > > http://ditu.live.com/?form=TL&swm=1 > > > > -- > ******************************************************** > - 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 _________________________________________________________________ ???????????????? http://cn.bing.com/search?q=%E5%A4%A9%E6%B0%94%E9%A2%84%E6%8A%A5&form=MICHJ2 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100504/d6d91137/attachment-0001.htm From hqzhou at nju.edu.cn Tue May 4 10:23:45 2010 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Tue, 4 May 2010 16:23:45 +0800 Subject: [Pw_forum] About q point parallelization Message-ID: dear developers, Just want someone clarifies that it's not neccessary to execute the "final run of ph.x" if I only split q points (not irr) to different machines because the *.dyn# file has been generated on each machine. Thanks! Huiqun Zhou @Nanjing University, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100504/39e5c65c/attachment.htm From lfhuang at theory.issp.ac.cn Tue May 4 10:11:27 2010 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Tue, 04 May 2010 16:11:27 +0800 Subject: [Pw_forum] =?utf-8?q?a_question_about_the_name_ESPRESSO?= Message-ID: <20100504081127.16388.qmail@ms.hfcas.ac.cn> Dear QE developers: ? ? ?As we know, you have created the acronym "ESPRESSO" for "opEn Source Package for Research in Electronic Structure, Simulation, and Optimization". Interestingly, recently I found accidentally that the word "Espresso" means an italian coffee. I am curious about how could you give the name of the code so creatively? Does the coffee "Espresso" have a special meaning to Italian people?? Best Wishes! Yours Sincerely L. F. Huang?------ ====================================================================== L.F.Huang(???) 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/20100504/34c2e277/attachment.htm From nnlinh at sissa.it Tue May 4 11:25:33 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Tue, 04 May 2010 11:25:33 +0200 Subject: [Pw_forum] a question about the name ESPRESSO In-Reply-To: <20100504081127.16388.qmail@ms.hfcas.ac.cn> References: <20100504081127.16388.qmail@ms.hfcas.ac.cn> Message-ID: <4BDFE80D.1020503@sissa.it> lfhuang wrote: > > Does the coffee "Espresso" have a special meaning to Italian people? > Yes, it is > > Best Wishes! > > Yours Sincerely > > L. F. Huang > > ------ > > ====================================================================== > L.F.Huang(???) 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 > -- ----------------------------------------------------- Nguyen Ngoc Linh, PhD Student c/o: SISSA & CNR-INFM Democritos, via Beirut 2-4, 34014 Trieste (Italy) email: nnlinh at sissa.it phone: +39 04 03787 319 skype: ngoclinh84phys ----------------------------------------------------- "The physics is theoretical but the fun is real" From giannozz at democritos.it Tue May 4 11:28:34 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 04 May 2010 11:28:34 +0200 Subject: [Pw_forum] About q point parallelization In-Reply-To: References: Message-ID: <4BDFE8C2.6030408@democritos.it> Huiqun Zhou wrote: > Just want someone clarifies that it's not necessary to execute the > "final run of ph.x" if I only split q points (not irr) to different >machines because the *.dyn# file has been generated on each machine. is this a question, or is it a statement? P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From marzari at MIT.EDU Tue May 4 11:50:43 2010 From: marzari at MIT.EDU (Nicola Marzari) Date: Tue, 04 May 2010 10:50:43 +0100 Subject: [Pw_forum] a question about the name ESPRESSO In-Reply-To: <4BDFE80D.1020503@sissa.it> References: <20100504081127.16388.qmail@ms.hfcas.ac.cn> <4BDFE80D.1020503@sissa.it> Message-ID: <4BDFEDF3.1040805@mit.edu> Dear L F Huang, Trieste (where the code originates) is the main shipping port in Italy for coffee imports, and the city has a long tradition of coffee houses and of coffee producers (the beans themselves are grown elsewhere). The most famous of these companies is "Illy", that is extremely tech savy - this below is an article that the company founder wrote a few years ago for "Scientific American": http://www.podmerchant.com/coffee/complexity-of-coffee.pdf What might intrigue you is that we invented the name while waiting in Beijing airport a flight to Xi'an - we were in Beijing for a summer school at the institute of physics (2004), and we decided to spend the weekend in the old capital. Here is the team at work - I believe Shobhana, Ralph and Carlo are missing, among those that were there : http://quasiamore.mit.edu/personal/xian/espresso.jpg 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 dalcorso at sissa.it Tue May 4 11:51:57 2010 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Tue, 04 May 2010 11:51:57 +0200 Subject: [Pw_forum] About q point parallelization In-Reply-To: References: Message-ID: <1272966717.3249.12.camel@dhcp-5-36.sissa.it> On Tue, 2010-05-04 at 16:23 +0800, Huiqun Zhou wrote: > dear developers, > > Just want someone clarifies that it's not neccessary to execute the > "final run of ph.x" > if I only split q points (not irr) to different machines because the > *.dyn# file has been > generated on each machine. > If you have the dynamical matrix files you do not need anything else. You can run q2r.x. HTH Andrea > Thanks! > > Huiqun Zhou > @Nanjing University, China > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Beirut 2/4 Fax. 0039-040-3787528 34151 Trieste (Italy) e-mail: dalcorso at sissa.it From giannozz at democritos.it Tue May 4 12:01:11 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 04 May 2010 12:01:11 +0200 Subject: [Pw_forum] a question about the name ESPRESSO In-Reply-To: <20100504081127.16388.qmail@ms.hfcas.ac.cn> References: <20100504081127.16388.qmail@ms.hfcas.ac.cn> Message-ID: <4BDFF067.7050300@democritos.it> lfhuang wrote: > you have created the acronym "ESPRESSO" just a remark: the complete name of the distribution is "Quantum ESPRESSO". The first word is important to prevent confusion with another package in the field of condensed matter physics: "ESPResSo", Extensible Simulation Package for Research on Soft matter, http://www.espresso.mpg.de/ Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From himadri.soni at gmail.com Tue May 4 12:18:21 2010 From: himadri.soni at gmail.com (Himadri Soni) Date: Tue, 4 May 2010 15:48:21 +0530 Subject: [Pw_forum] error with FeN phonon Message-ID: Hi all, I am using PWSCF code for phonon of FeN. But while doing ph.x for fen.ph.in, I am getting error like from solve_linter : error # 1 reading igk I dont understand why such error is coming. Send some suggestion. -- Himadri R. Soni Junior Research Fellow Department of Physics, Bhavnagar University, Bhavnagar 364022 From giuseppe.mattioli at mlib.ism.cnr.it Tue May 4 14:35:28 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Tue, 4 May 2010 14:35:28 +0200 Subject: [Pw_forum] the potential of core electron In-Reply-To: References: <201004291317.38207.giuseppe.mattioli@mlib.ism.cnr.it> <201005031312.17588.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <201005041435.28216.giuseppe.mattioli@mlib.ism.cnr.it> > You mean I should adopt the e = -5.55656 eV, because the # 408 > wavefunction is the largest part of wavefunction psi? Yes! > The eigenvalue is slightly different in different k points The dispersion should be (hopefully) very low... As all the procedure is quite rough, you can take the Gamma value, the average... It should not make any significant difference. Giuseppe On Tuesday 04 May 2010 03:44:17 wujianchun wrote: > Dear Dr Giuseppe Mattioli: > > Many thanks! > > > > You mean I should adopt the e = -5.55656 eV, because the # 408 > wavefunction is the largest part of wavefunction psi? > > > > The eigenvalue is slightly different in different k points, should I > average them and get the mean value as the He 1S eigenvalue? > > > > > My pdos.out is as follows: > > ...... > > state # 397: atom 62 (Cd ), wfc 3 (l=1 m= 2) > > state # 398: atom 62 (Cd ), wfc 3 (l=1 m= 3) > > state # 399: atom 63 (Cd ), wfc 1 (l=2 m= 1) > > state # 400: atom 63 (Cd ), wfc 1 (l=2 m= 2) > > state # 401: atom 63 (Cd ), wfc 1 (l=2 m= 3) > > state # 402: atom 63 (Cd ), wfc 1 (l=2 m= 4) > > state # 403: atom 63 (Cd ), wfc 1 (l=2 m= 5) > > state # 404: atom 63 (Cd ), wfc 2 (l=0 m= 1) > > state # 405: atom 63 (Cd ), wfc 3 (l=1 m= 1) > > state # 406: atom 63 (Cd ), wfc 3 (l=1 m= 2) > > state # 407: atom 63 (Cd ), wfc 3 (l=1 m= 3) > > state # 408: atom 64 (He ), wfc 1 (l=0 m= 1) > > ..... > > k = 0.0000000000 0.0000000000 0.0000000000 > > ..... > > e = -5.55656 eV > > psi = 0.696*[# 408]+0.052*[# 105]+0.051*[# 5]+0.050*[# 77]+0.040*[# 33]+ > > +0.003*[# 203]+0.003*[# 223]+0.004*[# 229]+0.003*[# 157]+0.003*[# 239]+ > > +0.003*[# 358]+0.003*[# 6]+0.003*[# 108]+0.003*[# 7]+0.003*[# 8]+ > > ...... > > k = 0.0000000000 0.0000000000 -0.5000000000 > > ...... > > Lowdin Charges: > > ...... > > > > > > > > Thanks ! > > > > > > Rgds > Jianchun Wu > Department of physics > Soochow university China.215006 > > > From: giuseppe.mattioli at mlib.ism.cnr.it > > To: pw_forum at pwscf.org > > Date: Mon, 3 May 2010 13:12:17 +0200 > > Subject: Re: [Pw_forum] the potential of core electron > > > > > Shall I do the NSCF between the scf and projwfc.x as the DOS > > > calculation? > > > > No, but if you need it for different purposes. > > > > > Could you tell me where I can find He 1s eigenvalue ? > > > > state #651: atom 192 (H ), wfc 1 (l=0 m= 1) > > state #652: atom 193 (H ), wfc 1 (l=0 m= 1) > > state #653: atom 194 (H ), wfc 1 (l=0 m= 1) > > state #654: atom 195 (H ), wfc 1 (l=0 m= 1) > > state #655: atom 196 (H ), wfc 1 (l=0 m= 1) > > state #656: atom 197 (H ), wfc 1 (l=0 m= 1) > > state #657: atom 198 (H ), wfc 1 (l=0 m= 1) > > state #658: atom 199 (He ), wfc 1 (l=0 m= 1) > > > > look for the # XXX wavefunction corresponding to your He atom at the > > beginning of the pdos.out file, and match it with a given eigenvalue in > > the bulk of the same file. > > > > Giuseppe > > > > On Friday 30 April 2010 12:19:15 wujianchun wrote: > > > Dear Dr Giuseppe Mattioli: > > > > > > > > > Thank you again! > > > > > > > > > > > > Shall I do the NSCF between the scf and projwfc.x as the DOS > > > calculation? > > > > > > I think I should get the PDOS of He. > > > > > > Could you tell me where I can find He 1s eigenvalue ? > > > > > > There are some "e" values after each k points in the outfile:pdos.out > > > > > > > > > > > > "k = 0.0000000000 0.0000000000 0.0000000000 > > > > > > e = -7.05254 eV > > > > > > psi = 0.022*[# 1]+0.022*[# 5]+0.022*[# 9]+0.022*[# 13]+0.022*[# 17]+ > > > > > > +0.022*[# 21]+0.022*[# 25]+0.022*[# 29]+0.022*[# 33]+0.022*[# 37]+ > > > > > > +0.022*[# 41]+0.022*[# 45]+0.022*[# 49]+0.022*[# 53]+0.022*[# 57]+ > > > > > > +0.022*[# 61]+0.022*[# 65]+0.022*[# 69]+0.022*[# 73]+0.022*[# 77]+ > > > > > > +0.022*[# 81]+0.022*[# 85]+0.022*[# 89]+0.022*[# 93]+0.022*[# 97]+ > > > > > > +0.022*[# 101]+0.022*[# 105]+0.022*[# 109]+0.022*[# 113]+0.022*[# 117]+ > > > > > > +0.022*[# 121]+0.022*[# 125]+0.009*[# 134]+0.009*[# 143]+0.009*[# 152]+ > > > > > > +0.009*[# 161]+0.009*[# 170]+0.009*[# 179]+0.009*[# 188]+0.009*[# 197]+ > > > > > > +0.009*[# 206]+0.009*[# 215]+0.009*[# 224]+0.009*[# 233]+0.009*[# 242]+ > > > > > > +0.009*[# 251]+0.009*[# 260]+0.009*[# 269]+0.009*[# 278]+0.009*[# 287]+ > > > > > > +0.009*[# 296]+0.009*[# 305]+0.009*[# 314]+0.009*[# 323]+0.009*[# 332]+ > > > > > > +0.009*[# 341]+0.009*[# 350]+0.009*[# 359]+0.009*[# 368]+0.009*[# 377]+ > > > > > > +0.009*[# 386]+0.009*[# 395]+0.009*[# 404]+0.009*[# 413]+ > > > > > > |psi|^2 = 0.998 > > > > > > e = -6.79505 eV" > > > > > > > > > > > > I guess they are the eigenvalues, and the lowest is He 1s eigenvalue in > > > our CdS system, > > > > > > am I right? > > > > > > > > > > > > > > > > > > > > > > > > RgdS > > > > > > Jianchun > > > Department of physics > > > Soochow university China.215006 > > > > > > > From: giuseppe.mattioli at mlib.ism.cnr.it > > > > To: pw_forum at pwscf.org > > > > Date: Fri, 30 Apr 2010 12:43:04 +0200 > > > > Subject: Re: [Pw_forum] the potential of core electron > > > > > > > > And, sorry, make a projwfc.x calculation after the scf one to find > > > > the He 1s eigenvalue if it does not stand alone by comparing scf and > > > > scf+He calculations > > > > > > > > Giuseppe > > > > > > > > On Friday 30 April 2010 03:17:41 wujianchun wrote: > > > > > Dear Dr Giuseppe Mattioli: > > > > > > > > > > > > > > > > > > > > Could you tell me the details on using the 1s level of a He atom to > > > > > align the potential. > > > > > > > > > > > > > > > My system is 64 atoms CdS supercell. Need we replace the Cd with He > > > > > at the corner?How to get the 1S level of He in the output file? > > > > > > > > > > > > > > > > > > > > Thanks a lot! > > > > > > > > > > > > > > > > > > > > Regdards > > > > > > > > > > Jianchun > > > > > > > > > > Department of physics > > > > > Soochow university China.215006 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > From: jcwu.suda at hotmail.com > > > > > To: pw_forum at pwscf.org > > > > > Date: Thu, 29 Apr 2010 18:57:26 +0800 > > > > > Subject: Re: [Pw_forum] the potential of core electron > > > > > > > > > > > > > > > > > > > > Dear Dr Giuseppe Mattioli: > > > > > > > > > > Many thanks! > > > > > I'll try the method. > > > > > > > > > > Rgds > > > > > Jianchun > > > > > > > > > > > To: pw_forum at pwscf.org > > > > > > From: giuseppe.mattioli at mlib.ism.cnr.it > > > > > > Date: Thu, 29 Apr 2010 13:17:38 +0200 > > > > > > Subject: Re: [Pw_forum] the potential of core electron > > > > > > > > > > > > Dear Jianchun > > > > > > You cannot get the core levels in pseudopotential calculations. > > > > > > At least, you cannot get such levels in a straightforward way. > > > > > > And you don't need! If your host matrix is not close packed, try > > > > > > to use the 1s level of a He atom to align the potential. The > > > > > > results can be often quite good... > > > > > > > > > > > > Giuseppe > > > > > > > > > > > > On Wednesday 28 April 2010 03:29:25 wujianchun wrote: > > > > > > > Dear All, > > > > > > > > > > > > > > > > > > > > > In order to align the potential between the defect supercell > > > > > > > and perfect supercell. > > > > > > > > > > > > > > > > > > > > > > > > > > > > I want to know the potential of core electrons(core-level). > > > > > > > > > > > > > > Could you tell me whether the PWSCF can provide the value of > > > > > > > the potential of core electrons? > > > > > > > > > > > > > > > > > > > > > Who knows how to get the core level of each atom after the scf > > > > > > > calculation? > > > > > > > > > > > > > > > > > > > > > Thanks in advance! > > > > > > > > > > > > > > Rgds > > > > > > > Jianchun > > > > > > > Department of physics > > > > > > > Soochow university China.215006 > > > > > > > > > > > > > > _______________________________________________________________ > > > > > > >__ MSN????????????????25???????????2010????????? > > > > > > > http://kaba.msn.com.cn/?k=1 > > > > > > > > > > > > -- > > > > > > ******************************************************** > > > > > > - 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 > > > > > > > > > > ????????,???????????-??,????????! ????? > > > > > _________________________________________________________________ > > > > > SkyDrive????????????????????????! > > > > > http://www.windowslive.cn/campaigns/e-magazine/ngmchina/?a=c > > > > > > > > -- > > > > ******************************************************** > > > > - 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 > > > > > > _________________________________________________________________ > > > ?????????????????msn????? > > > http://ditu.live.com/?form=TL&swm=1 > > > > -- > > ******************************************************** > > - 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 > > _________________________________________________________________ > ???????????????? > http://cn.bing.com/search?q=%E5%A4%A9%E6%B0%94%E9%A2%84%E6%8A%A5&form=MICHJ >2 -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00016 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From mahkameh_va at yahoo.com Tue May 4 13:10:32 2010 From: mahkameh_va at yahoo.com (raheleh vaziri) Date: Tue, 4 May 2010 04:10:32 -0700 (PDT) Subject: [Pw_forum] degauss Message-ID: <959138.71825.qm@web32904.mail.mud.yahoo.com> Dear All, ?I don't know?that my molecule is metal, insulator or semiconductor , thus, what is suitable value for degauss and mixing_beta? thank you for any help Raheleh Vaziri. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100504/33edc514/attachment.htm From jcwu.suda at hotmail.com Tue May 4 13:15:33 2010 From: jcwu.suda at hotmail.com (wujianchun) Date: Tue, 4 May 2010 19:15:33 +0800 Subject: [Pw_forum] the potential of core electron In-Reply-To: <201005041435.28216.giuseppe.mattioli@mlib.ism.cnr.it> References: <201004291317.38207.giuseppe.mattioli@mlib.ism.cnr.it>, <201005031312.17588.giuseppe.mattioli@mlib.ism.cnr.it>, , <201005041435.28216.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: Dear Dr Dr Giuseppe Mattioli, Thank you for your patient reply. I can manage the correction now. Rgds Jianchun Wu Department of physics Soochow university China.215006 > From: giuseppe.mattioli at mlib.ism.cnr.it > To: pw_forum at pwscf.org > Date: Tue, 4 May 2010 14:35:28 +0200 > Subject: Re: [Pw_forum] the potential of core electron > > > You mean I should adopt the e = -5.55656 eV, because the # 408 > > wavefunction is the largest part of wavefunction psi? > Yes! > > > The eigenvalue is slightly different in different k points > The dispersion should be (hopefully) very low... As all the procedure is quite > rough, you can take the Gamma value, the average... It should not make any > significant difference. > > Giuseppe > > > On Tuesday 04 May 2010 03:44:17 wujianchun wrote: > > Dear Dr Giuseppe Mattioli: > > > > Many thanks! > > > > > > > > You mean I should adopt the e = -5.55656 eV, because the # 408 > > wavefunction is the largest part of wavefunction psi? > > > > > > > > The eigenvalue is slightly different in different k points, should I > > average them and get the mean value as the He 1S eigenvalue? > > > > > > > > > > My pdos.out is as follows: > > > > ...... > > > > state # 397: atom 62 (Cd ), wfc 3 (l=1 m= 2) > > > > state # 398: atom 62 (Cd ), wfc 3 (l=1 m= 3) > > > > state # 399: atom 63 (Cd ), wfc 1 (l=2 m= 1) > > > > state # 400: atom 63 (Cd ), wfc 1 (l=2 m= 2) > > > > state # 401: atom 63 (Cd ), wfc 1 (l=2 m= 3) > > > > state # 402: atom 63 (Cd ), wfc 1 (l=2 m= 4) > > > > state # 403: atom 63 (Cd ), wfc 1 (l=2 m= 5) > > > > state # 404: atom 63 (Cd ), wfc 2 (l=0 m= 1) > > > > state # 405: atom 63 (Cd ), wfc 3 (l=1 m= 1) > > > > state # 406: atom 63 (Cd ), wfc 3 (l=1 m= 2) > > > > state # 407: atom 63 (Cd ), wfc 3 (l=1 m= 3) > > > > state # 408: atom 64 (He ), wfc 1 (l=0 m= 1) > > > > ..... > > > > k = 0.0000000000 0.0000000000 0.0000000000 > > > > ..... > > > > e = -5.55656 eV > > > > psi = 0.696*[# 408]+0.052*[# 105]+0.051*[# 5]+0.050*[# 77]+0.040*[# 33]+ > > > > +0.003*[# 203]+0.003*[# 223]+0.004*[# 229]+0.003*[# 157]+0.003*[# 239]+ > > > > +0.003*[# 358]+0.003*[# 6]+0.003*[# 108]+0.003*[# 7]+0.003*[# 8]+ > > > > ...... > > > > k = 0.0000000000 0.0000000000 -0.5000000000 > > > > ...... > > > > Lowdin Charges: > > > > ...... > > > > > > > > > > > > > > > > Thanks ! > > > > > > > > > > > > Rgds > > Jianchun Wu > > Department of physics > > Soochow university China.215006 > > > > > From: giuseppe.mattioli at mlib.ism.cnr.it > > > To: pw_forum at pwscf.org > > > Date: Mon, 3 May 2010 13:12:17 +0200 > > > Subject: Re: [Pw_forum] the potential of core electron > > > > > > > Shall I do the NSCF between the scf and projwfc.x as the DOS > > > > calculation? > > > > > > No, but if you need it for different purposes. > > > > > > > Could you tell me where I can find He 1s eigenvalue ? > > > > > > state #651: atom 192 (H ), wfc 1 (l=0 m= 1) > > > state #652: atom 193 (H ), wfc 1 (l=0 m= 1) > > > state #653: atom 194 (H ), wfc 1 (l=0 m= 1) > > > state #654: atom 195 (H ), wfc 1 (l=0 m= 1) > > > state #655: atom 196 (H ), wfc 1 (l=0 m= 1) > > > state #656: atom 197 (H ), wfc 1 (l=0 m= 1) > > > state #657: atom 198 (H ), wfc 1 (l=0 m= 1) > > > state #658: atom 199 (He ), wfc 1 (l=0 m= 1) > > > > > > look for the # XXX wavefunction corresponding to your He atom at the > > > beginning of the pdos.out file, and match it with a given eigenvalue in > > > the bulk of the same file. > > > > > > Giuseppe > > > > > > On Friday 30 April 2010 12:19:15 wujianchun wrote: > > > > Dear Dr Giuseppe Mattioli: > > > > > > > > > > > > Thank you again! > > > > > > > > > > > > > > > > Shall I do the NSCF between the scf and projwfc.x as the DOS > > > > calculation? > > > > > > > > I think I should get the PDOS of He. > > > > > > > > Could you tell me where I can find He 1s eigenvalue ? > > > > > > > > There are some "e" values after each k points in the outfile:pdos.out > > > > > > > > > > > > > > > > "k = 0.0000000000 0.0000000000 0.0000000000 > > > > > > > > e = -7.05254 eV > > > > > > > > psi = 0.022*[# 1]+0.022*[# 5]+0.022*[# 9]+0.022*[# 13]+0.022*[# 17]+ > > > > > > > > +0.022*[# 21]+0.022*[# 25]+0.022*[# 29]+0.022*[# 33]+0.022*[# 37]+ > > > > > > > > +0.022*[# 41]+0.022*[# 45]+0.022*[# 49]+0.022*[# 53]+0.022*[# 57]+ > > > > > > > > +0.022*[# 61]+0.022*[# 65]+0.022*[# 69]+0.022*[# 73]+0.022*[# 77]+ > > > > > > > > +0.022*[# 81]+0.022*[# 85]+0.022*[# 89]+0.022*[# 93]+0.022*[# 97]+ > > > > > > > > +0.022*[# 101]+0.022*[# 105]+0.022*[# 109]+0.022*[# 113]+0.022*[# 117]+ > > > > > > > > +0.022*[# 121]+0.022*[# 125]+0.009*[# 134]+0.009*[# 143]+0.009*[# 152]+ > > > > > > > > +0.009*[# 161]+0.009*[# 170]+0.009*[# 179]+0.009*[# 188]+0.009*[# 197]+ > > > > > > > > +0.009*[# 206]+0.009*[# 215]+0.009*[# 224]+0.009*[# 233]+0.009*[# 242]+ > > > > > > > > +0.009*[# 251]+0.009*[# 260]+0.009*[# 269]+0.009*[# 278]+0.009*[# 287]+ > > > > > > > > +0.009*[# 296]+0.009*[# 305]+0.009*[# 314]+0.009*[# 323]+0.009*[# 332]+ > > > > > > > > +0.009*[# 341]+0.009*[# 350]+0.009*[# 359]+0.009*[# 368]+0.009*[# 377]+ > > > > > > > > +0.009*[# 386]+0.009*[# 395]+0.009*[# 404]+0.009*[# 413]+ > > > > > > > > |psi|^2 = 0.998 > > > > > > > > e = -6.79505 eV" > > > > > > > > > > > > > > > > I guess they are the eigenvalues, and the lowest is He 1s eigenvalue in > > > > our CdS system, > > > > > > > > am I right? > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > RgdS > > > > > > > > Jianchun > > > > Department of physics > > > > Soochow university China.215006 > > > > > > > > > From: giuseppe.mattioli at mlib.ism.cnr.it > > > > > To: pw_forum at pwscf.org > > > > > Date: Fri, 30 Apr 2010 12:43:04 +0200 > > > > > Subject: Re: [Pw_forum] the potential of core electron > > > > > > > > > > And, sorry, make a projwfc.x calculation after the scf one to find > > > > > the He 1s eigenvalue if it does not stand alone by comparing scf and > > > > > scf+He calculations > > > > > > > > > > Giuseppe > > > > > > > > > > On Friday 30 April 2010 03:17:41 wujianchun wrote: > > > > > > Dear Dr Giuseppe Mattioli: > > > > > > > > > > > > > > > > > > > > > > > > Could you tell me the details on using the 1s level of a He atom to > > > > > > align the potential. > > > > > > > > > > > > > > > > > > My system is 64 atoms CdS supercell. Need we replace the Cd with He > > > > > > at the corner?How to get the 1S level of He in the output file? > > > > > > > > > > > > > > > > > > > > > > > > Thanks a lot! > > > > > > > > > > > > > > > > > > > > > > > > Regdards > > > > > > > > > > > > Jianchun > > > > > > > > > > > > Department of physics > > > > > > Soochow university China.215006 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > From: jcwu.suda at hotmail.com > > > > > > To: pw_forum at pwscf.org > > > > > > Date: Thu, 29 Apr 2010 18:57:26 +0800 > > > > > > Subject: Re: [Pw_forum] the potential of core electron > > > > > > > > > > > > > > > > > > > > > > > > Dear Dr Giuseppe Mattioli: > > > > > > > > > > > > Many thanks! > > > > > > I'll try the method. > > > > > > > > > > > > Rgds > > > > > > Jianchun > > > > > > > > > > > > > To: pw_forum at pwscf.org > > > > > > > From: giuseppe.mattioli at mlib.ism.cnr.it > > > > > > > Date: Thu, 29 Apr 2010 13:17:38 +0200 > > > > > > > Subject: Re: [Pw_forum] the potential of core electron > > > > > > > > > > > > > > Dear Jianchun > > > > > > > You cannot get the core levels in pseudopotential calculations. > > > > > > > At least, you cannot get such levels in a straightforward way. > > > > > > > And you don't need! If your host matrix is not close packed, try > > > > > > > to use the 1s level of a He atom to align the potential. The > > > > > > > results can be often quite good... > > > > > > > > > > > > > > Giuseppe > > > > > > > > > > > > > > On Wednesday 28 April 2010 03:29:25 wujianchun wrote: > > > > > > > > Dear All, > > > > > > > > > > > > > > > > > > > > > > > > In order to align the potential between the defect supercell > > > > > > > > and perfect supercell. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > I want to know the potential of core electrons(core-level). > > > > > > > > > > > > > > > > Could you tell me whether the PWSCF can provide the value of > > > > > > > > the potential of core electrons? > > > > > > > > > > > > > > > > > > > > > > > > Who knows how to get the core level of each atom after the scf > > > > > > > > calculation? > > > > > > > > > > > > > > > > > > > > > > > > Thanks in advance! > > > > > > > > > > > > > > > > Rgds > > > > > > > > Jianchun > > > > > > > > Department of physics > > > > > > > > Soochow university China.215006 > > > > > > > > > > > > > > > > _______________________________________________________________ > > > > > > > >__ MSN????????????????25???????????2010????????? > > > > > > > > http://kaba.msn.com.cn/?k=1 > > > > > > > > > > > > > > -- > > > > > > > ******************************************************** > > > > > > > - 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 > > > > > > > > > > > > ????????,???????????-??,????????! ????? > > > > > > _________________________________________________________________ > > > > > > SkyDrive????????????????????????! > > > > > > http://www.windowslive.cn/campaigns/e-magazine/ngmchina/?a=c > > > > > > > > > > -- > > > > > ******************************************************** > > > > > - 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 > > > > > > > > _________________________________________________________________ > > > > ?????????????????msn????? > > > > http://ditu.live.com/?form=TL&swm=1 > > > > > > -- > > > ******************************************************** > > > - 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 > > > > _________________________________________________________________ > > ???????????????? > > http://cn.bing.com/search?q=%E5%A4%A9%E6%B0%94%E9%A2%84%E6%8A%A5&form=MICHJ > >2 > > > > -- > ******************************************************** > - 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 _________________________________________________________________ ?????????????????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/20100504/844676a1/attachment-0001.htm From lfhuang at theory.issp.ac.cn Tue May 4 13:19:04 2010 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Tue, 04 May 2010 19:19:04 +0800 Subject: [Pw_forum] =?utf-8?q?a_question_about_the_name_ESPRESSO?= Message-ID: <20100504111904.22365.qmail@ms.hfcas.ac.cn> prof. N. Marzari: Thanks very much for your interesting story about the espresso coffee and the origination of the code name! The picture you have given is so lively. prof. P. Giannozzi and Mr N. L. Nguyen: thanks very much for your attention! Best Wishes! Yours Sincerely L. F. Huang ------ ====================================================================== L.F.Huang(???) 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/20100504/6eb71638/attachment.htm From josepht at chips.ncsu.edu Tue May 4 17:15:47 2010 From: josepht at chips.ncsu.edu (josepht at chips.ncsu.edu) Date: Tue, 4 May 2010 11:15:47 -0400 (EDT) Subject: [Pw_forum] Error with Xcryden for view input and output of pwscf file Message-ID: <58446.152.14.192.32.1272986147.squirrel@chips.ncsu.edu> Hello, I am resurrecting this thread - through spring cleaning, I observed the same behavior of xcrysden reported last year by Loc Duong Dinh. The source of the error, at least for my case, was actually unrelated to the format/content of the pwscf input/output file one attempts to read into xcrysden. Instead, the error occurs when any parent directory containing the input file has been given a name with spaces. e.g. load attempt of output file located in: /HOME/JT/QE/QUANTUM\ ESPRESSO\ TESTING/postproc/uroporphyrinogen3/scf1p2r3.out vs /HOME/JT/QE/QUANTUM__ESPRESSO__TESTING/postproc/uroporphyrinogen3/scf1p2r3.out where the first case leads to load failure, and the second is successful. This occurs with the xc-1.5.17-linux_x86-semishared.tar.gz package; untested for others. Joe Turnbull North Carolina State University On Sun, 2009-02-02 at 16:08 -0800, Tone Kokalj wrote: >You will need to provide more info! >How did you load the file (i.e. sequence of steps), what is the actual file (mail it as attachement)? Only then there is a change to help. 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 >On Sun, 2009-02-01 at 18:53 -0800, loc duong ding wrote: >> Dear all user, >> >>I have a problem when using Xcrysden to view input and output file of pwscf. The error i got was: >>wrong # args: should be "pwInputPreset file" >>wrong # args: should be "pwInputPreset file" >> while executing >>"pwInputPreset /cygdrive/g/Research/MODELLING/output_model2" >> ("eval" body line 1) >> invoked from within >>"eval $preset $file" >> (procedure "openExtStruct" line 106) >> invoked from within >>"openExtStruct 3 crystal external {sh >>/home/cuteo/XCrySDen-1.5.18-bin-shared/scripts/pwi2xsf.sh} pwi2xsf.xsf_out {PWSCF Input File} ANGS -preset pwInpu..." >> (menu invoke) >> >>I did not see this error before. >>I great appreciate all your instructions. >>----------------------------------------------- >>Loc Duong Dinh >>Ms-Ph.D Student >>Sungkyunkwan Advanced Institute of Nanotechnology, >>Sungkyunkwan University, >>Suwon, 440-746, Korea >>Email: mambom1902 at yahoo.com From giuseppe.mattioli at mlib.ism.cnr.it Tue May 4 20:36:20 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Tue, 4 May 2010 20:36:20 +0200 Subject: [Pw_forum] spin-polarized projwf option in cp.x Message-ID: <201005042036.20293.giuseppe.mattioli@mlib.ism.cnr.it> Dear all I'm trying to collect some post-processing data from a CP.x calculation, namely, I need the projection of KS wfc on atomic wfc. For example, in the case of an O2 molecule, my inpfile looks like: export FILE="o2-pbe-lsd" export INPFILE=$FILE-gs-1.inp export OUTFILE=$FILE-gs-1.out echo " $FILE" echo " $INPFILE" echo " $OUTFILE" cat > $INPFILE << EOF &control calculation = 'cp' restart_mode='from_scratch', prefix='$FILE', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/', dt=2.0, iprint=200, isave=200, disk_io='high', verbosity='default+projwfc' ndr=90, ndw=91, nstep=1000, / &system ibrav= 1, celldm(1)=15.000000, nat=2, ntyp=1, ecutwfc =25.0, ecutrho =200.0, nr1b=20, nr2b=20, nr3b=20, nspin=2, multiplicity=3, / &electrons electron_dynamics='damp', electron_damping=0.05, emass=400., emass_cutoff=3., electron_maxstep=200, electron_temperature='not_controlled', orthogonalization='ortho' ortho_max=100, / &ions ion_dynamics='none', ion_radius(1)=1.0, / ATOMIC_SPECIES O 15.999 O_pbe.van.UPF ATOMIC_POSITIONS {angstrom} O 3.522950002 3.595655772 3.312983484 O 3.873672936 4.513761776 4.065541307 EOF $PARA_PREFIX $ESPRESSO/cp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE At the end of such an scf calculation, wfc projections are printed in my outfile only for spin up electrons. Projection on atomic states atomic state atom specie wfc l m 1 - 2 2 1 1 0 0 3 - 4 2 1 2 1 -1 5 - 6 2 1 2 1 0 7 - 8 2 1 2 1 1 state # 1 sum c^2 = 0.9758 eV = -32.47 0.6212 0.6212 0.1942 0.1942 0.0905 0.0905 0.2369 0.2369 state # 2 sum c^2 = 0.9994 eV = -20.67 0.6432 0.6432 0.1783 0.1783 0.0831 0.0831 0.2175 0.2175 state # 3 sum c^2 = 0.9707 eV = -13.37 0.3215 0.3215 0.3746 0.3770 0.1749 0.1754 0.4594 0.4573 state # 4 sum c^2 = 0.9906 eV = -13.30 0.0001 0.0002 0.0954 0.0956 0.6741 0.6737 0.1789 0.1794 state # 5 sum c^2 = 0.9906 eV = -13.30 0.0007 0.0007 0.5513 0.5497 0.0377 0.0384 0.4357 0.4378 state # 6 sum c^2 = 0.9989 eV = -7.07 0.0000 0.0000 0.5263 0.5262 0.0852 0.0850 0.4640 0.4639 state # 7 sum c^2 = 0.9989 eV = -7.07 0.0001 0.0001 0.1945 0.1947 0.6723 0.6725 0.0974 0.0974 First question: how can I print spin down projections? Second question: let us look at the first eigenvalue row 0.6212 (contribution of the 2s orbital of atom 1 of species 1?) 0.6212 (contribution of the 2s orbital of atom 2 of species 1?) 0.1942 (contribution of the 2p(m1) orbital of atom 1 of species 1?) 0.1942 (contribution of the 2p(m1) orbital of atom 2 of species 1?) 0.0905 ... 0.0905 ... 0.2369 ... 0.2369 ... Is my guess correct? Thanks Giuseppe -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00016 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From baroni at sissa.it Tue May 4 21:32:49 2010 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 4 May 2010 21:32:49 +0200 Subject: [Pw_forum] a question about the name ESPRESSO In-Reply-To: <4BDFEDF3.1040805@mit.edu> References: <20100504081127.16388.qmail@ms.hfcas.ac.cn> <4BDFE80D.1020503@sissa.it> <4BDFEDF3.1040805@mit.edu> Message-ID: <04C0E821-38D3-494D-A6FC-4B5773EB308E@sissa.it> PS: the one hiding himself behind the camera is Roberto Car On May 4, 2010, at 11:50 AM, Nicola Marzari wrote: > > > Dear L F Huang, > > Trieste (where the code originates) is the main shipping port in Italy > for coffee > imports, and the city has a long tradition of coffee houses and of > coffee producers > (the beans themselves are grown elsewhere). > > The most famous of these companies is "Illy", that is extremely tech savy - > this below is an article that the company founder wrote a few years ago > for "Scientific > American": http://www.podmerchant.com/coffee/complexity-of-coffee.pdf > > What might intrigue you is that we invented the name while waiting in > Beijing airport a flight to Xi'an - we were in Beijing for a summer school > at the institute of physics (2004), and we decided to spend the weekend in > the old capital. > > Here is the team at work - I believe Shobhana, Ralph and Carlo are > missing, among those that were there : > http://quasiamore.mit.edu/personal/xian/espresso.jpg > > 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 --- 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/20100504/5894ddcb/attachment.htm From baroni at sissa.it Tue May 4 22:02:40 2010 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 4 May 2010 22:02:40 +0200 Subject: [Pw_forum] a question about the name ESPRESSO In-Reply-To: <04C0E821-38D3-494D-A6FC-4B5773EB308E@sissa.it> References: <20100504081127.16388.qmail@ms.hfcas.ac.cn> <4BDFE80D.1020503@sissa.it> <4BDFEDF3.1040805@mit.edu> <04C0E821-38D3-494D-A6FC-4B5773EB308E@sissa.it> Message-ID: <0319BAAE-1F35-4381-9A50-09E3F919BF31@sissa.it> PPS: although a bit outdated, "espresso" is actually an adjective. It used to mean "made on purpose" or "made on demand". This is the origin of the expression (note the common root of the words!) "espresso coffee", which is made on demand, rather than filtered and kept hot in a kettle. I think that it is because of its association with "coffee on demand" that at some pointthe word "espresso" came to mean "swift", or "quick" (because brewing espresso coffee is much faster than making filter coffee). As a matter of fact, the fastest Italian trains when I was a kid were named "espresso". So, "Quantum ESPRESSO" alludes to a blend of all these meanings: tasty (as good coffee), fashionable (as many Italian goods), user friendly (ready on demand), swift and powerful (as espresso trains), tech savy (as Illy coffee), a bit understating (you don't drink espresso coffee in very elegant cafes, but you can find small coffee places with a great reputation for their espresso), keeping awake/alive (as strong coffee should: please, notice the contrast with "siesta"). SB On May 4, 2010, at 9:32 PM, Stefano Baroni wrote: > PS: the one hiding himself behind the camera is Roberto Car > > On May 4, 2010, at 11:50 AM, Nicola Marzari wrote: > >> >> >> Dear L F Huang, >> >> Trieste (where the code originates) is the main shipping port in Italy >> for coffee >> imports, and the city has a long tradition of coffee houses and of >> coffee producers >> (the beans themselves are grown elsewhere). >> >> The most famous of these companies is "Illy", that is extremely tech savy - >> this below is an article that the company founder wrote a few years ago >> for "Scientific >> American": http://www.podmerchant.com/coffee/complexity-of-coffee.pdf >> >> What might intrigue you is that we invented the name while waiting in >> Beijing airport a flight to Xi'an - we were in Beijing for a summer school >> at the institute of physics (2004), and we decided to spend the weekend in >> the old capital. >> >> Here is the team at work - I believe Shobhana, Ralph and Carlo are >> missing, among those that were there : >> http://quasiamore.mit.edu/personal/xian/espresso.jpg >> >> 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 > > --- > 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 --- 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/20100504/9b90b97a/attachment-0001.htm From hqzhou at nju.edu.cn Wed May 5 04:45:05 2010 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Wed, 5 May 2010 10:45:05 +0800 Subject: [Pw_forum] a question about the name ESPRESSO References: <20100504081127.16388.qmail@ms.hfcas.ac.cn><4BDFE80D.1020503@sissa.it> <4BDFEDF3.1040805@mit.edu><04C0E821-38D3-494D-A6FC-4B5773EB308E@sissa.it> <0319BAAE-1F35-4381-9A50-09E3F919BF31@sissa.it> Message-ID: Although most chinese used to drink green tea, now we have vending machine that serves espresso on every floor of our teachoing building and Starbucks is spreading in the city, too. Let's further enjoy "espresso" in a coffee house or on our super computer! Huiqun Zhou @Earth Sciences, Nanjing University, China ----- Original Message ----- From: Stefano Baroni To: PWSCF Forum Sent: Wednesday, May 05, 2010 4:02 AM Subject: Re: [Pw_forum] a question about the name ESPRESSO PPS: although a bit outdated, "espresso" is actually an adjective. It used to mean "made on purpose" or "made on demand". This is the origin of the expression (note the common root of the words!) "espresso coffee", which is made on demand, rather than filtered and kept hot in a kettle. I think that it is because of its association with "coffee on demand" that at some pointthe word "espresso" came to mean "swift", or "quick" (because brewing espresso coffee is much faster than making filter coffee). As a matter of fact, the fastest Italian trains when I was a kid were named "espresso". So, "Quantum ESPRESSO" alludes to a blend of all these meanings: tasty (as good coffee), fashionable (as many Italian goods), user friendly (ready on demand), swift and powerful (as espresso trains), tech savy (as Illy coffee), a bit understating (you don't drink espresso coffee in very elegant cafes, but you can find small coffee places with a great reputation for their espresso), keeping awake/alive (as strong coffee should: please, notice the contrast with "siesta"). SB On May 4, 2010, at 9:32 PM, Stefano Baroni wrote: PS: the one hiding himself behind the camera is Roberto Car On May 4, 2010, at 11:50 AM, Nicola Marzari wrote: Dear L F Huang, Trieste (where the code originates) is the main shipping port in Italy for coffee imports, and the city has a long tradition of coffee houses and of coffee producers (the beans themselves are grown elsewhere). The most famous of these companies is "Illy", that is extremely tech savy - this below is an article that the company founder wrote a few years ago for "Scientific American": http://www.podmerchant.com/coffee/complexity-of-coffee.pdf What might intrigue you is that we invented the name while waiting in Beijing airport a flight to Xi'an - we were in Beijing for a summer school at the institute of physics (2004), and we decided to spend the weekend in the old capital. Here is the team at work - I believe Shobhana, Ralph and Carlo are missing, among those that were there : http://quasiamore.mit.edu/personal/xian/espresso.jpg 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 --- 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 --- 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/20100505/eb385e3b/attachment.htm From lfhuang at theory.issp.ac.cn Wed May 5 04:56:32 2010 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Wed, 05 May 2010 10:56:32 +0800 Subject: [Pw_forum] =?utf-8?q?a_question_about_the_name_ESPRESSO?= Message-ID: <20100505025632.4895.qmail@ms.hfcas.ac.cn> Dear prof. S. Baroni: Thank you very much for your interesting and complete description! It is so creative! And it is also interesting that you mentioned SIESTA, which has a different meaning in spanish. Best Wishes! Yours Sincerely L. F. Huang > From: Stefano Baroni > Subject: Re: [Pw_forum] a question about the name ESPRESSO > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > PPS: although a bit outdated, "espresso" is actually an adjective. It used to mean "made on purpose" or "made on demand". This is the origin of the expression (note the common root of the words!) "espresso coffee", which is made on demand, rather than filtered and kept hot in a kettle. I think that it is because of its association with "coffee on demand" that at some pointthe word "espresso" came to mean "swift", or "quick" (because brewing espresso coffee is much faster than making filter coffee). As a matter of fact, the fastest Italian trains when I was a kid were named "espresso". So, "Quantum ESPRESSO" alludes to a blend of all these meanings: tasty (as good coffee), fashionable (as many Italian goods), user friendly (ready on demand), swift and powerful (as espresso trains), tech savy (as Illy coffee), a bit understating (you don't drink espresso coffee in very elegant cafes, but you can find small coffee places with a great reputation for their espresso), keeping awake/alive (as strong coffee should: please, notice the contrast with "siesta"). SB > ------ ====================================================================== L.F.Huang(???) 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/20100505/402c0b63/attachment-0001.htm From baroni at sissa.it Wed May 5 08:03:06 2010 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 5 May 2010 08:03:06 +0200 Subject: [Pw_forum] a question about the name ESPRESSO In-Reply-To: References: <20100504081127.16388.qmail@ms.hfcas.ac.cn><4BDFE80D.1020503@sissa.it> <4BDFEDF3.1040805@mit.edu><04C0E821-38D3-494D-A6FC-4B5773EB308E@sissa.it> <0319BAAE-1F35-4381-9A50-09E3F919BF31@sissa.it> Message-ID: <7A514C4D-A333-404B-83A7-34D1892FE3BC@sissa.it> it's a small world! many of us (including myself) start enjoying drinking green tea ... S. On May 5, 2010, at 4:45 AM, Huiqun Zhou wrote: > Although most chinese used to drink green tea, now we have vending machine that serves > espresso on every floor of our teachoing building and Starbucks is spreading in the city, too. > > Let's further enjoy "espresso" in a coffee house or on our super computer! > > > Huiqun Zhou > @Earth Sciences, Nanjing University, China > ----- Original Message ----- > From: Stefano Baroni > To: PWSCF Forum > Sent: Wednesday, May 05, 2010 4:02 AM > Subject: Re: [Pw_forum] a question about the name ESPRESSO > > PPS: although a bit outdated, "espresso" is actually an adjective. It used to mean "made on purpose" or "made on demand". This is the origin of the expression (note the common root of the words!) "espresso coffee", which is made on demand, rather than filtered and kept hot in a kettle. I think that it is because of its association with "coffee on demand" that at some pointthe word "espresso" came to mean "swift", or "quick" (because brewing espresso coffee is much faster than making filter coffee). As a matter of fact, the fastest Italian trains when I was a kid were named "espresso". So, "Quantum ESPRESSO" alludes to a blend of all these meanings: tasty (as good coffee), fashionable (as many Italian goods), user friendly (ready on demand), swift and powerful (as espresso trains), tech savy (as Illy coffee), a bit understating (you don't drink espresso coffee in very elegant cafes, but you can find small coffee places with a great reputation for their espresso), keeping awake/alive (as strong coffee should: please, notice the contrast with "siesta"). SB > > On May 4, 2010, at 9:32 PM, Stefano Baroni wrote: > >> PS: the one hiding himself behind the camera is Roberto Car >> >> On May 4, 2010, at 11:50 AM, Nicola Marzari wrote: >> >>> >>> >>> Dear L F Huang, >>> >>> Trieste (where the code originates) is the main shipping port in Italy >>> for coffee >>> imports, and the city has a long tradition of coffee houses and of >>> coffee producers >>> (the beans themselves are grown elsewhere). >>> >>> The most famous of these companies is "Illy", that is extremely tech savy - >>> this below is an article that the company founder wrote a few years ago >>> for "Scientific >>> American": http://www.podmerchant.com/coffee/complexity-of-coffee.pdf >>> >>> What might intrigue you is that we invented the name while waiting in >>> Beijing airport a flight to Xi'an - we were in Beijing for a summer school >>> at the institute of physics (2004), and we decided to spend the weekend in >>> the old capital. >>> >>> Here is the team at work - I believe Shobhana, Ralph and Carlo are >>> missing, among those that were there : >>> http://quasiamore.mit.edu/personal/xian/espresso.jpg >>> >>> 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 >> >> --- >> 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 > > --- > 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 > _______________________________________________ > 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/20100505/f4c9ecdf/attachment-0001.htm From parthasarathi13 at gmail.com Wed May 5 08:21:03 2010 From: parthasarathi13 at gmail.com (partha sarathi ghosh) Date: Wed, 5 May 2010 11:51:03 +0530 Subject: [Pw_forum] Phonon_quarry Message-ID: Dear all, I want to do phonon calculations using PWSCF. How to calculate phonon dispersion curve using ph.x that I know ,but I want to displace a particular atom in a particular direction with adjustable displacement. I want to know is it possible to control ?? P S Ghosh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100505/f837114f/attachment.htm From tone.kokalj at ijs.si Wed May 5 10:31:54 2010 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 05 May 2010 10:31:54 +0200 Subject: [Pw_forum] Error with Xcryden for view input and output of pwscf file In-Reply-To: <58446.152.14.192.32.1272986147.squirrel@chips.ncsu.edu> References: <58446.152.14.192.32.1272986147.squirrel@chips.ncsu.edu> Message-ID: <1273048314.9405.60.camel@walk.ijs.si> On Tue, 2010-05-04 at 11:15 -0400, josepht at chips.ncsu.edu wrote: > Instead, the error occurs > when any parent directory containing the input file has been given a name with > spaces. > > e.g. load attempt of output file located in: > > /HOME/JT/QE/QUANTUM\ ESPRESSO\ TESTING/postproc/uroporphyrinogen3/scf1p2r3.out > vs > /HOME/JT/QE/QUANTUM__ESPRESSO__TESTING/postproc/uroporphyrinogen3/scf1p2r3.out > > where the first case leads to load failure, and the second is successful. This > occurs with the xc-1.5.17-linux_x86-semishared.tar.gz package; untested for others. I believe having a whitespace in directory name is not a very smart idea under Unix. It may break many scripts. Nevertheless I adapted xcrysden script, and now it seems to be able to deal with it (at least it works on my computer). You may try it yourself. The script is attached to this email, you need to copy it to your $XCRYSDEN_TOPDIR. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- A non-text attachment was scrubbed... Name: xcrysden Type: application/x-shellscript Size: 7623 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100505/c6208797/attachment.bin From tone.kokalj at ijs.si Wed May 5 10:41:43 2010 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 05 May 2010 10:41:43 +0200 Subject: [Pw_forum] Error with Xcryden for view input and output of pwscf file In-Reply-To: <1273048314.9405.60.camel@walk.ijs.si> References: <58446.152.14.192.32.1272986147.squirrel@chips.ncsu.edu> <1273048314.9405.60.camel@walk.ijs.si> Message-ID: <1273048903.9405.63.camel@walk.ijs.si> On Wed, 2010-05-05 at 10:31 +0200, Tone Kokalj wrote: > I believe having a whitespace in directory name is not a very smart idea > under Unix. It may break many scripts. > > Nevertheless I adapted xcrysden script, and now it seems to be able to > deal with it (at least it works on my computer). You may try it > yourself. The script is attached to this email, you need to copy it to > your $XCRYSDEN_TOPDIR. Well, actually I just realized that the patch works for XSF files, but not for the PWscf files. The latter is too much involved to be adapted (and it would become a mass). Hence may recommendation is: don't use the spaces in the directory names. 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 sclauzer at sissa.it Wed May 5 10:57:37 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 05 May 2010 10:57:37 +0200 Subject: [Pw_forum] LDA+U and spin orbit couple In-Reply-To: <4BDED163.7090709@umn.edu> References: <1f7eb11.1541.128520b7785.Coremail.ads5ads5@163.com> <4BDED163.7090709@umn.edu> Message-ID: <4BE13301.1000900@sissa.it> On 05/03/2010 03:36 PM, Matteo Cococcioni wrote: > > Dear Fang, > > to the best of my knowledge LDA+U has not been implemented in the > non-collinear case yet and cannot work > with spin-orbit. I am not sure what the error exactly means though. > probably vhpsi has more KS wavefunction > than it was expecting to construct the Hubbard potential and so gives > an error. but this is just my guess. It is indeed the case. In the noncollinear case the number of atomic wavefunctions is the double than in that of the collinear case. I can confirm that LDA+U and noncollinear (and hence also LDA+U and spin-orbit) do not work together at the moment. Regards, Gabriele Sclauzero (EPFL) > > regards, > > Matteo > > > > > ads5ads5 wrote: >> Dear all: >> Eerything is OK when LDA+U and spin orbit couple is added separately. >> But when LDA+U and spin orbit couple is both used. >> It runs with error: >> %%%%%%%%%%%%%%%%\ >> from vhpsi : error # 1 >> nstart<>counter >> %%%%%%%%%%%%%%%%% >> it seems that LDAU can not work with SO coupling. Is that true? >> Thanks >> Fang Sun >> East China Normal University >> >> >> ?????????????????????????????????????????? >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100505/8bcfec0f/attachment.htm From lfhuang at theory.issp.ac.cn Wed May 5 10:47:55 2010 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Wed, 05 May 2010 16:47:55 +0800 Subject: [Pw_forum] =?utf-8?q?one_question_about_the_hybrid_calculation?= Message-ID: <20100505084755.30117.qmail@ms.hfcas.ac.cn> Dear everyone: ? ? ? I am doing calculations using B3LYP pseudopotential. I found that the iteration scheme for hybrid functionals seems different for LDA and GGA. For the hybrid calculation, the code always go back to refine the hybrid calculation, which does not occur in other kinds of calculations (LDA&GGA). Why is the iteration scheme for hybrid calculations different? And I found that the total energy converges quite well in the first set of iterations, while the Fermi energy convergence needs several refinement.? Thanks very much for any kind attention and help! Best Wishes! Yours Sincerely L. F. Huang?------ ====================================================================== L.F.Huang(???) 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/20100505/c5079258/attachment.htm From masoudnahali at live.com Wed May 5 16:39:50 2010 From: masoudnahali at live.com (Masoud Nahali) Date: Wed, 5 May 2010 14:39:50 +0000 Subject: [Pw_forum] Re : Occupations Message-ID: Dear QE users Until now I have not found a clear cut explanation about occupations ! the reference that is suggested by Nicola is short. Many Thanks Masoud Nahali SUT >Dear Masoud, >http://media.quantum-espresso.org/santa_barbara_2009_07/index.php#20090719 >but in short, yes, it is necessary for metals. For graphite it is >probably less important, >you could try with and without, and see what happens. nicola >Masoud Nahali wrote: > Dear QE users > > Is "Occupations" variable necessary for Metals? It seems that the > "tetrahedra" along with occupations variable is not suitable for > optimization calculations ! > my studing sample is Graphite and I do not know that the specifying of > the metallicity is needed or not? a simple physical definition of > "occupations" should be useful for me. I could not find a clear one in > the forum. Is this variable related to the how should one select the > K-POINTS !? > > > Masoud Nahali > SUT > _________________________________________________________________ Hotmail: Free, trusted and rich email service. https://signup.live.com/signup.aspx?id=60969 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100505/ec492fa9/attachment.htm From gryko at jsu.edu Wed May 5 16:31:49 2010 From: gryko at jsu.edu (Jan Gryko) Date: Wed, 5 May 2010 09:31:49 -0500 (CDT) Subject: [Pw_forum] ABINIT-QE conversion In-Reply-To: <1978750931.8367891273069548072.JavaMail.root@mbs1.jsu.edu> Message-ID: <365484956.8370101273069909687.JavaMail.root@mbs1.jsu.edu> Hello, I am trying to convert ABINIT files into QE using QE-ABINIT Perl script. Attached are: Abinit input (Na6Si34.inp) and converted QE file Na6Si34.pw.in. I had to modify Na6Si34.pw.in by adding Na and Si symbols, as the Perl script does not recognize atom types. However, inspecting Na6Si34.pw.in with xcrysden file I see that atomic positions are incorrect. Even correcting CELL_PARAMETERS (last line should be probably 0.5 0.5 0, instead of 0.5 0 0, am I correct?) results in an incorrect structure. I also tried to directly specify trigonal lattice, ibrav = 5 celldm(1) = 19.536 celldm(4) = 0.5 but the resulting atomic positions are also incorrect. The cell coordinates in the ABINIT file are obtained using PowderCell free program, by transforming space group 227,setting 1 into trigonal group 166, setting 2, i.e. transforming cubic a,b,c, axes into A=1/2(b+c), B=1/2(a+c) C=1/2(a+b) and shifting origin by (-1/8, -1/8, -1/8). Reading INPUT_PW Doc file I see that trigonal axes used by QE are v1 = a(tx,-ty,tz), v2 = a(0,2ty,tz), v3 = a(-tx,-ty,tz). Shall I transform my coordinates into the (v1, v2, v3) axes? Thank you for your advice, Jan Gryko Jacksonville State University 232-C Martin Hall Jacksonville, Al 36265 256-782-5218 256-782-5336 fax From marzari at MIT.EDU Wed May 5 16:52:26 2010 From: marzari at MIT.EDU (Nicola Marzari) Date: Wed, 05 May 2010 15:52:26 +0100 Subject: [Pw_forum] Re : Occupations In-Reply-To: References: Message-ID: <4BE1862A.3090802@mit.edu> Masoud Nahali wrote: > Dear QE users > > Until now I have not found a clear cut explanation about occupations ! > the reference that is suggested by Nicola is short. Chap 4 of http://quasiamore.mit.edu/phd . Look also at e.g. the paper by De Gironcoli (single author) cited in there. 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 julen.azpiroz at gmail.com Wed May 5 17:52:02 2010 From: julen.azpiroz at gmail.com (Julen Ibanez Azpiroz) Date: Wed, 5 May 2010 17:52:02 +0200 Subject: [Pw_forum] General question about occupations Message-ID: Hello I have had a problem related to the Fermi level of a system of Silicon and Thallium. I was trying to compute a scf calculation of a Silicon slab made of 24 layers in the (1,1,1) direction with one thallium on top of it (the total length is about 45 Angstrom), with 10.41 Angstrom of vacuum in the same direction; this is my unit cell which tries to be a surface (fully relativistic noncollinear calculation with spin orbit coupling). First, I have used the choice occupations='smearing', smearing='methfessel-paxton', degauss=0.05d0 In this way I have let the system relax with the 'bfgs' method, and I have checked the convergence with respect to the cutoff energy (45 Ry) and the k_point mesh (16*16*1). As a result the system has ended up relaxed with negligible forces and I have calculated the bands using the results of the .save file, there was no problem when reading it and the bands fit well with the bulk background bands (calculated in bulk Si in 1 1 1 direction). Then I have increased the length of the vacuum to 30 Angstroms, I have relaxed the system, the atoms moved a little bit and I have checked all the convergences again. However, when I tried to use the results from the .save file to compute again the bands, the program has stopped with an error from setup : error # 3 problem reading ef from file /lscratch/azpiroz/scf/scf.save Also, when I have tried to perform a 'nscf' calculation using the results from the scf run, the program stops with task # 5 from efermig : error # 1 internal error, cannot braket Ef I have looked for possible explanations about this last error, and I have found that in the Users Guide from Espresso there is a place where it says 7.16 pw.x stops with "internal error: cannot braket Ef " in efermig Possible reasons: - serious error in data, such as bad number of electrons, insufficient number of bands, absurd value of broadening; - the Fermi energy is found by bisection assuming that the integrated DOS N(E ) is an increasing function of the energy. This is not guaranteed for Methfessel-Paxton smearing of order 1 and can give problems when very few k-points are used. Use some other smearing function: simple Gaussian broadening or, better, Marzari-Vanderbilt 'cold smearing'. I have tried many times the scf calculation and it never gives any error, the number of electrons is correct and I have used different values of the broadening and number of bands, and the error still persists in the nscf calculation. I dont have any clue about how to change 'correctly' the value of the broadening so that its not absurd, or the number of bands, any suggestion to this respect will be appreciated. Also, I have tried with Marzari-Vanderbilt smearing and many k points, but the error still persists. The error seems to be related with the Fermi level and the type of occupation. The question is, why does it appear when the vacuum is 30 Angstrom but not when the vacuum is 10 Angstrom long? Finally, I have seen that there is an option for the occupations called 'fixed', for 'insulators with a gap'. Even though this system is not an insulator (there is a band crossing the Fermi surface), I have tried this option and it works well, and even more it does not give any problem neither when computing the band structure nor with the 'nscf' calculation. The band structure obtained in this way coincides with the one obtained with 'methfessel-paxton' smearing (in the case of 10 Angstroms of vacuum), and as I said it works well for 30 Angstrom of vacuum. I think that the point is that with occupations='fixed' the program does not return any Fermi level, but I would really appreciate any help to this respect. Thank you very much in advance Julen Iba?ez Azpiroz University of the Basque Country -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100505/671f730f/attachment.htm From gryko at jsu.edu Wed May 5 19:14:41 2010 From: gryko at jsu.edu (Jan Gryko) Date: Wed, 5 May 2010 12:14:41 -0500 (CDT) Subject: [Pw_forum] ABINIT-QE conversion In-Reply-To: <98505844.8433661273079657224.JavaMail.root@mbs1.jsu.edu> Message-ID: <655426322.8433861273079681783.JavaMail.root@mbs1.jsu.edu> I am sorry, I did not attach abinit and QE files with my previous msg. Here they are. Hello, I am trying to convert ABINIT files into QE using QE-ABINIT Perl script. Attached are: Abinit input (Na6Si34.inp) and converted QE file Na6Si34.pw.in. I had to modify Na6Si34.pw.in by adding Na and Si symbols, as the Perl script does not recognize atom types. However, inspecting Na6Si34.pw.in with xcrysden file I see that atomic positions are incorrect. Even correcting CELL_PARAMETERS (last line should be probably 0.5 0.5 0, instead of 0.5 0 0, am I correct?) results in an incorrect structure. I also tried to directly specify trigonal lattice, ibrav = 5 celldm(1) = 19.536 celldm(4) = 0.5 but the resulting atomic positions are also incorrect. The cell coordinates in the ABINIT file are obtained using PowderCell free program, by transforming space group 227,setting 1 into trigonal group 166, setting 2, i.e. transforming cubic a,b,c, axes into A=1/2(b+c), B=1/2(a+c) C=1/2(a+b) and shifting origin by (-1/8, -1/8, -1/8). Reading INPUT_PW Doc file I see that trigonal axes used by QE are v1 = a(tx,-ty,tz), v2 = a(0,2ty,tz), v3 = a(-tx,-ty,tz). Shall I transform my coordinates into the (v1, v2, v3) axes? Thank you for your advice, Jan Gryko Jacksonville State University 232-C Martin Hall Jacksonville, Al 36265 256-782-5218 256-782-5336 fax _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- A non-text attachment was scrubbed... Name: Na6Si34.inp Type: application/octet-stream Size: 3669 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100505/0dbc1f3d/attachment-0002.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: Na6Si34.pw.in Type: application/octet-stream Size: 1307 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100505/0dbc1f3d/attachment-0003.obj From giannozz at democritos.it Wed May 5 21:08:35 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 5 May 2010 21:08:35 +0200 Subject: [Pw_forum] General question about occupations In-Reply-To: References: Message-ID: <5077B850-D41F-4EAB-8DC5-8698C61DB643@democritos.it> On May 5, 2010, at 17:52 , Julen Ibanez Azpiroz wrote: > from setup : error # 3 > problem reading ef from file /lscratch/azpiroz/scf/scf.save go into /lscratch/azpiroz/scf/scf.save/data-file.xml, look if there is a tag and whether it has anything anomalous 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 May 5 21:11:01 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 5 May 2010 21:11:01 +0200 Subject: [Pw_forum] one question about the hybrid calculation In-Reply-To: <20100505084755.30117.qmail@ms.hfcas.ac.cn> References: <20100505084755.30117.qmail@ms.hfcas.ac.cn> Message-ID: On May 5, 2010, at 10:47 , lfhuang wrote: > Why is the iteration scheme for hybrid calculations different? > please have a look at examples/EXX_example/README 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 sd.wang000 at gmail.com Thu May 6 04:37:52 2010 From: sd.wang000 at gmail.com (shudong wang) Date: Thu, 6 May 2010 10:37:52 +0800 Subject: [Pw_forum] About example07 Message-ID: Dear all: I want to calculate el-ph coulpling but I do not kwon what in the example07 means: The fourth column represents the el-ph coulpling constant lamda??? And the "dos_el" means what? Is it the Eliashberg function??? If I want to get the phonon energy-Eliashberg function plot,what should I do??? Thanks in advance! S.D.Wang Electron-phonon coupling constant, lambda Broadening 0.0050 lambda 0.2057 dos_el 1.3387 Broadening 0.0100 lambda 0.3844 dos_el 1.8818 Broadening 0.0150 lambda 0.3957 dos_el 2.1232 Broadening 0.0200 lambda 0.3742 dos_el 2.2498 Broadening 0.0250 lambda 0.3545 dos_el 2.3298 Broadening 0.0300 lambda 0.3445 dos_el 2.3960 Broadening 0.0350 lambda 0.3422 dos_el 2.4552 Broadening 0.0400 lambda 0.3442 dos_el 2.5079 Broadening 0.0450 lambda 0.3476 dos_el 2.5530 Broadening 0.0500 lambda 0.3510 dos_el 2.5896 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100506/bc8a43d1/attachment.htm From lfhuang at theory.issp.ac.cn Thu May 6 10:27:07 2010 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Thu, 06 May 2010 16:27:07 +0800 Subject: [Pw_forum] =?utf-8?q?one_question_about_the_hybrid_calculation?= Message-ID: <20100506082707.13687.qmail@ms.hfcas.ac.cn> Dear prof. P. Giannozzi: Thank you very much for your kind help! Best Wishes! Yours Sincerely L. F. Huang > From: Paolo Giannozzi > Subject: Re: [Pw_forum] one question about the hybrid calculation > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset=US-ASCII; format=flowed > > On May 5, 2010, at 10:47 , lfhuang wrote: > > Why is the iteration scheme for hybrid calculations different? > > > please have a look at examples/EXX_example/README > > P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 ------ ====================================================================== L.F.Huang(???) 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/20100506/8b99b805/attachment.htm From giannozz at democritos.it Thu May 6 11:10:15 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 06 May 2010 11:10:15 +0200 Subject: [Pw_forum] spin-polarized projwf option in cp.x In-Reply-To: <201005042036.20293.giuseppe.mattioli@mlib.ism.cnr.it> References: <201005042036.20293.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <4BE28777.5010608@democritos.it> Giuseppe Mattioli wrote: > At the end of such an scf calculation, wfc projections are printed in my > outfile only for spin up electrons. > > Projection on atomic states > atomic state atom specie wfc l m > 1 - 2 2 1 1 0 0 > 3 - 4 2 1 2 1 -1 > 5 - 6 2 1 2 1 0 > 7 - 8 2 1 2 1 1 printed by which code and for which version? In any case, you can process files produced by cp.x (use option "disk_io='high'") with "projwfc.x" P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Thu May 6 11:52:58 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 06 May 2010 11:52:58 +0200 Subject: [Pw_forum] spin-polarized projwf option in cp.x In-Reply-To: <201005042036.20293.giuseppe.mattioli@mlib.ism.cnr.it> References: <201005042036.20293.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <4BE2917A.4060207@democritos.it> I see, cp.x can calculate projections over atomic wavefunctions but it doesn't do it proeprly for the spin-polarized case > Second question: let us look at the first eigenvalue row > > 0.6212 (contribution of the 2s orbital of atom 1 of species 1?) > 0.6212 (contribution of the 2s orbital of atom 2 of species 1?) > 0.1942 (contribution of the 2p(m1) orbital of atom 1 of species 1?) > 0.1942 (contribution of the 2p(m1) orbital of atom 2 of species 1?) > 0.0905 ... > 0.0905 ... > 0.2369 ... > 0.2369 ... > > Is my guess correct? it is. "Projwfc.x" uses a more explicit format P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Thu May 6 11:59:27 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 06 May 2010 11:59:27 +0200 Subject: [Pw_forum] About example07 In-Reply-To: References: Message-ID: <4BE292FF.8050305@democritos.it> shudong wang wrote: > The fourth column represents the el-ph coulpling constant lamda??? in your opinion, what does the following line mean? > Electron-phonon coupling constant, lambda > And the "dos_el" means what? DOS at the Fermi energy P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From julen.azpiroz at gmail.com Thu May 6 15:26:08 2010 From: julen.azpiroz at gmail.com (Julen Ibanez Azpiroz) Date: Thu, 6 May 2010 15:26:08 +0200 Subject: [Pw_forum] General question about occupations In-Reply-To: <5077B850-D41F-4EAB-8DC5-8698C61DB643@democritos.it> References: <5077B850-D41F-4EAB-8DC5-8698C61DB643@democritos.it> Message-ID: Hello First of all thanks for answering. The word FERMI_ENERGY appears two times in /lscratch/azpiroz/scf/scf.save/data-file.xml, First F and second 3.130244659417582E-002 I dont know if the first has anything to do with the problem. The second one, I have no clue to say if this number is reasonable, but at least its a number in the sense that it has not any strange letter or sign which the program could not read. It seems that its not the Fermi energy of the scf calculation, which was 2.0857 eV (even if the units of were Rydbergs it would be 0.75 eV). The rest of the file seems in good conditions, at first glance I havent found any anomalous data. I have looked in the file data-file.xml given by the calculation of exactly the same system but with the choice occupations='fixed', and there it says 2.360818145117281E-001 I cannot compare this value with any Fermi energy because the output of the scf run with occupations='fixed' does not return any Fermi value (I had verbosity='high'). Using the results of this last scf run the program does not give any problem related to the Fermi level when computing the bands or a nscf calculation. Hope this information helps you to help me, thank you very much in advance Julen University of the Basque Country -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100506/78c0a2c4/attachment.htm From marsamos at democritos.it Thu May 6 16:21:54 2010 From: marsamos at democritos.it (marsamos at democritos.it) Date: Thu, 06 May 2010 16:21:54 +0200 Subject: [Pw_forum] ABINIT-QE conversion In-Reply-To: <655426322.8433861273079681783.JavaMail.root@mbs1.jsu.edu> References: <655426322.8433861273079681783.JavaMail.root@mbs1.jsu.edu> Message-ID: <20100506162154.7kx0vvob4co8c0sw@mail.democritos.it> Dear Jan, Looking at your input files it seems that you have a normal Fd-3m, with the atomic positions writen in crystal units. Anyway, for runing pw is better to change the cell with v1 = (a/2)(-1,0,1), v2 = (a/2)(0,1,1), v3 = (a/2)(-1,1,0) (invertible) that is: CELL_PARAMETERS cubic -0.5 0.0 0.5 0.0 0.5 0.5 -0.5 0.5 0.0 but this not a problem of the converter, i think, is more related to the convention chosen. Moh! Why you need to transform to hexagonal 166? bests Layla Quoting Jan Gryko : > > I am sorry, I did not attach abinit and QE files with my previous > msg. Here they are. > > Hello, > > I am trying to convert ABINIT files into QE using QE-ABINIT Perl > script. Attached are: Abinit input (Na6Si34.inp) > and converted QE file Na6Si34.pw.in. I had to modify Na6Si34.pw.in > by adding Na and Si symbols, as the Perl > script does not recognize atom types. However, inspecting > Na6Si34.pw.in with xcrysden file I see that > atomic positions are incorrect. > Even correcting CELL_PARAMETERS (last line should be probably 0.5 0.5 > 0, instead of 0.5 0 0, am I > correct?) results in an incorrect structure. I also tried to > directly specify trigonal lattice, > ibrav = 5 > celldm(1) = 19.536 > celldm(4) = 0.5 > > but the resulting atomic positions are also incorrect. The cell > coordinates in the ABINIT file are > obtained using PowderCell free program, by transforming space group > 227,setting 1 into trigonal > group 166, setting 2, i.e. transforming cubic a,b,c, axes into > A=1/2(b+c), B=1/2(a+c) C=1/2(a+b) and > shifting origin by (-1/8, -1/8, -1/8). > > Reading INPUT_PW Doc file I see that trigonal axes used by QE are > v1 = a(tx,-ty,tz), v2 = a(0,2ty,tz), v3 = a(-tx,-ty,tz). Shall I > transform my coordinates into > the (v1, v2, v3) axes? > > Thank you for your advice, > > Jan Gryko > Jacksonville State University > 232-C Martin Hall > Jacksonville, Al 36265 > 256-782-5218 > 256-782-5336 fax > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. L. Martin-Samos tel. +39 040 3787 429 CNR-DEMOCRITOS and International School for Advanced Studies (ISAS-SISSA) via Beirut 2-4 34151 Trieste Italy ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From naylin.nll at gmail.com Thu May 6 17:13:43 2010 From: naylin.nll at gmail.com (Nay Lin) Date: Thu, 6 May 2010 23:13:43 +0800 Subject: [Pw_forum] NEB calculation Message-ID: Dear all, I am using NEB to calculate the adatom diffusion barrier on metallic surface. Do I need to relax the first and last image in separate calculations before writing the input file for NEB calculation with intermediate images? Or can be done automatically in single NEB file? What is the criteria for convergence? (i.e. is it the third column of output file (image energy(eV) *error(eV/A)* fronze) ? regards Richard Lin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100506/6e67fbd6/attachment.htm From nnlinh at sissa.it Thu May 6 17:20:13 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Thu, 06 May 2010 17:20:13 +0200 Subject: [Pw_forum] NEB calculation In-Reply-To: References: Message-ID: <4BE2DE2D.9060708@sissa.it> Nay Lin wrote: > Dear all, > > I am using NEB to calculate the adatom diffusion barrier on metallic > surface. > > Do I need to relax the first and last image in separate calculations > before writing the input file for NEB calculation with intermediate > images? Yes, because the first and last images will be frozen during NEB optimization. > Or can be done automatically in single NEB file? What is the criteria > for convergence? It is "path_thr", see in PW input to know more about it. > (i.e. is it the third column of output file (image energy(eV) > *error(eV/A)* fronze) ? Yes, it is Good luck Linh > > regards > Richard Lin > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ----------------------------------------------------- Nguyen Ngoc Linh, PhD Student c/o: SISSA & CNR-INFM Democritos, via Beirut 2-4, 34014 Trieste (Italy) email: nnlinh at sissa.it phone: +39 04 03787 319 skype: ngoclinh84phys ----------------------------------------------------- "The physics is theoretical but the fun is real" From degironc at sissa.it Thu May 6 17:22:08 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 06 May 2010 17:22:08 +0200 Subject: [Pw_forum] NEB calculation In-Reply-To: References: Message-ID: <4BE2DEA0.9020609@sissa.it> There is a variable in the &ions namelist called first_last_opt that if set .true. makes the minimization of the first and last images along with the NEB optimization... I think that usually it is more convenient to optimize these two images separately and then keep them fixed because the NEB optimization itself is not very efficient, but if you already have a rather good estimate of them it may be convenient. stefano Nay Lin wrote: > Dear all, > > I am using NEB to calculate the adatom diffusion barrier on metallic > surface. > > Do I need to relax the first and last image in separate calculations before > writing the input file for NEB calculation with intermediate images? Or can > be done automatically in single NEB file? What is the criteria for > convergence? (i.e. is it the third column of output file (image > energy(eV) *error(eV/A)* fronze) ? > > regards > Richard Lin > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From izaakw89 at yahoo.com Thu May 6 19:51:18 2010 From: izaakw89 at yahoo.com (Izaak Williamson) Date: Thu, 6 May 2010 10:51:18 -0700 (PDT) Subject: [Pw_forum] Point Group from phonon calculation Message-ID: <842363.75103.qm@web44801.mail.sp1.yahoo.com> After running the phonon calculation for ZnO at gamma point, the frequencies were displayed as: ************************************************************************** Mode symmetry, C_3v (3m) point group: omega( 1 - 1) = -26.3 [cm-1] --> A_1 L_1 I+R omega( 2 - 3) = 101.8 [cm-1] --> E L_3 I+R omega( 4 - 5) = 110.3 [cm-1] --> E L_3 I+R omega( 6 - 6) = 253.3 [cm-1] --> A_1 L_1 I+R omega( 7 - 7) = 379.8 [cm-1] --> A_1 L_1 I+R omega( 8 - 9) = 398.5 [cm-1] --> E L_3 I+R omega( 10 - 11) = 426.6 [cm-1] --> E L_3 I+R omega( 12 - 12) = 540.6 [cm-1] --> A_1 L_1 I+R ************************************************************************** I understand that A means the frequency is not degenerate and E means there is a degeneracy of 2. I just do not know what the L_1 and L_3 characters represent? Also, what does I+R mean? Thanks, Izaak Williamson Physics Dept. Boise State University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100506/7ca2f4c1/attachment.htm From giannozz at democritos.it Thu May 6 21:25:46 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 6 May 2010 21:25:46 +0200 Subject: [Pw_forum] General question about occupations In-Reply-To: References: <5077B850-D41F-4EAB-8DC5-8698C61DB643@democritos.it> Message-ID: <1C79A37D-8D0F-4715-8A71-425066CC9ECD@democritos.it> On May 6, 2010, at 15:26 , Julen Ibanez Azpiroz wrote: > > First of all thanks for answering. The word FERMI_ENERGY appears > two times in /lscratch/azpiroz/scf/scf.save/data-file.xml > [...] > > 3.130244659417582E-002 > ok, the file looks good. Try to reproduce the same problem on a different machine, or with a different compiler (and maybe as a first step on the same machine and same compiler but differemt number of procesors). Just copy the data directory and perform the same operation that gave you "error reading Efermi" or whatever it was. If it is a real problem, it should be reproducible. 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 Thu May 6 21:28:01 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 6 May 2010 21:28:01 +0200 Subject: [Pw_forum] Point Group from phonon calculation In-Reply-To: <842363.75103.qm@web44801.mail.sp1.yahoo.com> References: <842363.75103.qm@web44801.mail.sp1.yahoo.com> Message-ID: <0A625EBF-3DBC-4A2C-A90B-44DD0A1CB76D@democritos.it> On May 6, 2010, at 19:51 , Izaak Williamson wrote: > Also, what does I+R mean? Infrared- and Raman-active 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 Thu May 6 21:29:52 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 6 May 2010 21:29:52 +0200 Subject: [Pw_forum] error with FeN phonon In-Reply-To: References: Message-ID: <300300EC-A758-401E-B4C7-0DEADC8E7BF2@democritos.it> On May 4, 2010, at 12:18 , Himadri Soni wrote: > from solve_linter : error # 1 > reading igk you aren't executing other executables at the same time working in the same directory, are you? 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 xomiakk at gmail.com Fri May 7 05:28:48 2010 From: xomiakk at gmail.com (Olga Sedelnikova) Date: Fri, 7 May 2010 10:28:48 +0700 Subject: [Pw_forum] relax Message-ID: Dear All, I am trying to optimize NH3 molecul. The error was: from readpp : error # 2 inconsistene DFT read My input file was: &control calculation='relax', restart_mode='from_scratch', prefix='nh3', disk_io='low', wf_collect=.TRUE., pseudo_dir='', outdir='' / &system ibrav = 0, celldm(1)= 1.0 nat = 4, ntyp = 2, ecutwfc = 16.0, nbnd = 128, ecutrho=200.0, occupations='smearing', degauss=0.02 / &electrons mixing_mode='local-TF' mixing_beta = 0.7, conv_thr = 1.0d-6 / &ions ion_dynamics='bfgs' ion_positions='default' / ATOMIC_SPECIES H 1.0d0 H.vbc.UPF N 16.0d0 N.BLYP.UPF CELL_PARAMETERS {cubic} 30.00000 0.000000 0.000000 0.000000 30.000000 0.000000 0.000000 0.000000 30.000000 ATOMIC_POSITIONS {angstrom} N -1.111 0.001 -1.058 H -0.900 -0.555 -1.882 H -1.939 -0.397 -0.623 H -1.349 0.938 -1.372 K_POINTS {automatic} 1 1 1 0 0 0 The error was: from readpp : error # 2 inconsistene DFT read I did not see this error before. I great appreciate all your instructions. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100507/66c42b8f/attachment.htm From xomiakk at gmail.com Fri May 7 05:31:39 2010 From: xomiakk at gmail.com (Olga Sedelnikova) Date: Fri, 7 May 2010 10:31:39 +0700 Subject: [Pw_forum] relax Message-ID: Dear All, I am trying to optimize NH3 molecul. The error was: from readpp : error # 2 inconsistene DFT read My input file was: &control calculation='relax', restart_mode='from_scratch', prefix='nh3', disk_io='low', wf_collect=.TRUE., pseudo_dir='', outdir='' / &system ibrav = 0, celldm(1)= 1.0 nat = 4, ntyp = 2, ecutwfc = 16.0, nbnd = 128, ecutrho=200.0, occupations='smearing', degauss=0.02 / &electrons mixing_mode='local-TF' mixing_beta = 0.7, conv_thr = 1.0d-6 / &ions ion_dynamics='bfgs' ion_positions='default' / ATOMIC_SPECIES H 1.0d0 H.vbc.UPF N 16.0d0 N.BLYP.UPF CELL_PARAMETERS {cubic} 30.00000 0.000000 0.000000 0.000000 30.000000 0.000000 0.000000 0.000000 30.000000 ATOMIC_POSITIONS {angstrom} N -1.111 0.001 -1.058 H -0.900 -0.555 -1.882 H -1.939 -0.397 -0.623 H -1.349 0.938 -1.372 K_POINTS {automatic} 1 1 1 0 0 0 I did not see this error before. I great appreciate all your instructions. Best regards, Olga Sedelnikova Nikolaev Institute of Inorganic Chemistry SB RAS Novosibirsk, Russia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100507/16959f44/attachment.htm From sclauzer at sissa.it Fri May 7 09:50:48 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 07 May 2010 09:50:48 +0200 Subject: [Pw_forum] relax In-Reply-To: References: Message-ID: <4BE3C658.100@sissa.it> Probably you are trying to use at the same time PPs that have been built for different XC functionals. This is a FAQ, so please take some time to search in the forum archives and in the user guide. For instance you can have a look here: http://www.quantum-espresso.org/user_guide/node42.html GS On 05/07/2010 05:28 AM, Olga Sedelnikova wrote: > Dear All, > > I am trying to optimize NH3 molecul. > The error was: > from readpp : error # 2 > inconsistene DFT read > > My input file was: > &control > calculation='relax', > restart_mode='from_scratch', > prefix='nh3', > disk_io='low', > wf_collect=.TRUE., > pseudo_dir='', > outdir='' > / > &system > ibrav = 0, > celldm(1)= 1.0 > nat = 4, > ntyp = 2, > ecutwfc = 16.0, > nbnd = 128, > ecutrho=200.0, > occupations='smearing', > degauss=0.02 > / > &electrons > mixing_mode='local-TF' > mixing_beta = 0.7, > conv_thr = 1.0d-6 > / > &ions > ion_dynamics='bfgs' > ion_positions='default' > / > ATOMIC_SPECIES > H 1.0d0 H.vbc.UPF > N 16.0d0 N.BLYP.UPF > CELL_PARAMETERS {cubic} > 30.00000 0.000000 0.000000 > 0.000000 30.000000 0.000000 > 0.000000 0.000000 30.000000 > ATOMIC_POSITIONS {angstrom} > N -1.111 0.001 -1.058 > H -0.900 -0.555 -1.882 > H -1.939 -0.397 -0.623 > H -1.349 0.938 -1.372 > K_POINTS {automatic} > 1 1 1 0 0 0 > > The error was: > from readpp : error # 2 > inconsistene DFT read > > I did not see this error before. > I great appreciate all your instructions. > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100507/b537c877/attachment.htm From nnlinh at sissa.it Fri May 7 10:09:43 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Fri, 07 May 2010 10:09:43 +0200 Subject: [Pw_forum] relax In-Reply-To: References: Message-ID: <4BE3CAC7.9090001@sissa.it> The problem comes from Pseudo Potential files. Their formats are old ones. You should download the new Pseudo Potential files of N and H from http://www.quantum-espresso.org/pseudo.php, then rerun your problem. I checked for new ones, and it works well Good lucks, Linh Olga Sedelnikova wrote: > Dear All, > > I am trying to optimize NH3 molecul. > The error was: > from readpp : error # 2 > inconsistene DFT read > > My input file was: > &control > calculation='relax', > restart_mode='from_scratch', > prefix='nh3', > disk_io='low', > wf_collect=.TRUE., > pseudo_dir='', > outdir='' > / > &system > ibrav = 0, > celldm(1)= 1.0 > nat = 4, > ntyp = 2, > ecutwfc = 16.0, > nbnd = 128, > ecutrho=200.0, > occupations='smearing', > degauss=0.02 > / > &electrons > mixing_mode='local-TF' > mixing_beta = 0.7, > conv_thr = 1.0d-6 > / > &ions > ion_dynamics='bfgs' > ion_positions='default' > / > ATOMIC_SPECIES > H 1.0d0 H.vbc.UPF > N 16.0d0 N.BLYP.UPF > CELL_PARAMETERS {cubic} > 30.00000 0.000000 0.000000 > 0.000000 30.000000 0.000000 > 0.000000 0.000000 30.000000 > ATOMIC_POSITIONS {angstrom} > N -1.111 0.001 -1.058 > H -0.900 -0.555 -1.882 > H -1.939 -0.397 -0.623 > H -1.349 0.938 -1.372 > K_POINTS {automatic} > 1 1 1 0 0 0 > > The error was: > from readpp : error # 2 > inconsistene DFT read > > I did not see this error before. > I great appreciate all your instructions. > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ----------------------------------------------------- Nguyen Ngoc Linh, PhD Student c/o: SISSA & CNR-INFM Democritos, via Beirut 2-4, 34014 Trieste (Italy) email: nnlinh at sissa.it phone: +39 04 03787 319 skype: ngoclinh84phys ----------------------------------------------------- "The physics is theoretical but the fun is real" From giannozz at democritos.it Fri May 7 10:14:08 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 07 May 2010 10:14:08 +0200 Subject: [Pw_forum] relax In-Reply-To: <4BE3CAC7.9090001@sissa.it> References: <4BE3CAC7.9090001@sissa.it> Message-ID: <4BE3CBD0.6000005@democritos.it> Ngoc Linh Nguyen wrote: > The problem comes from Pseudo Potential files. Their formats are old ones. > You should download the new Pseudo Potential files of N and H from > http://www.quantum-espresso.org/pseudo.php, then rerun your problem. it's not a problem of new or old format. The problem is that one PP is generated with Perdew-Zunger LDA, the other with BLYP P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From xomiakk at gmail.com Fri May 7 10:37:24 2010 From: xomiakk at gmail.com (Olga Sedelnikova) Date: Fri, 7 May 2010 15:37:24 +0700 Subject: [Pw_forum] relax Message-ID: Dear Gabriele, Thank you for helping over my problem! Best regards, Olga Sedelnikova Nikolaev Institute of Inorganic Chemistry SB RAS Novosibirsk, Russia > Probably you are trying to use at the same time PPs that have been built > for different XC functionals. > > This is a FAQ, so please take some time to search in the forum archives > and in the user guide. For instance you can have a look here: > > http://www.quantum-espresso.org/user_guide/node42.html > > GS > > Gabriele Sclauzero, EPFL SB ITP CSEA > PH H2 462, Station 3, CH-1015 Lausanne > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100507/b3cfd9e2/attachment.htm From chenweiguang82 at gmail.com Fri May 7 15:13:57 2010 From: chenweiguang82 at gmail.com (Weiguang Chen) Date: Fri, 7 May 2010 21:13:57 +0800 Subject: [Pw_forum] Installation Problems: Can not found MKL Message-ID: Hi, All I am installing espresso-4.1.3 in intel cluster. I have installed the latest intel compiler(v11.069) and MKL(the same as compiler). I compiled with configure like this: ./configure -enable-shared LIBDIRS="/home/software/intel/Compiler/11.1/069/lib/intel64 /home/software/intel/Compiler/11.1/069/mkl/lib/em64t" --prefix=/home/software/espresso F77=ifort CC=icc But shows as follow: checking whether Fortran files must be preprocessed... no checking how to get verbose linking output from ifort... -v checking for Fortran libraries of ifort... -L/home/software/intel/Compiler/11.1/069/lib/intel64 -L/home/software/intel/Compiler/11.1/069/ipp/em64t/lib -L/home/software/intel/Compiler/11.1/069/mkl/lib/em64t -L/home/software/intel/Compiler/11.1/069/tbb/intel64/cc4.1.0_libc2.4_kernel2.6.16.21/lib -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../.. -L/lib64 -L/lib -L/usr/lib64 -L/usr/lib -lifport -lifcore -limf -lsvml -lm -lipgo -lirc -lpthread -lgcc_s -lirc_s -ldl checking for dummy main to link with Fortran libraries... none checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore checking for library containing dgemm... no in /opt/intel/mkl/*/lib/em64t: checking for library containing dgemm... no in /opt/intel/mkl*/lib/em64t: checking for library containing dgemm... no checking for library containing dgemm... no in /usr/local/lib: checking for library containing dgemm... no checking for library containing dgemm... no in /usr/local/lib: checking for library containing dgemm... no checking for library containing dspev... no in /usr/local/lib: checking for library containing dspev... no setting BLAS_LIBS... ../flib/blas.a setting LAPACK_LIBS... ../flib/lapack.a checking for library containing dfftw_execute_dft... -lfftw3 setting FFT_LIBS... -lfftw3 setting MASS_LIBS... checking for library containing mpi_init... none required setting MPI_LIBS... checking for library containing mpi_init... (cached) none required setting DFLAGS... -D__INTEL -D__FFTW3 -D__MPI -D__PARA setting IFLAGS... -I../include setting FDFLAGS... $(DFLAGS) checking for ranlib... ranlib setting RANLIB... ranlib configure: creating ./config.status config.status: creating include/fft_defs.h config.status: creating make.sys config.status: creating configure.msg config.status: creating include/c_defs.h config.status: include/c_defs.h is unchanged -------------------------------------------------------------------- ESPRESSO can take advantage of several optimized numerical libraries (essl, fftw, mkl...). This configure script attempts to find them, but may fail if they have been installed in non-standard locations. If a required library is not found, the local copy will be compiled. The following libraries have been found: BLAS_LIBS=../flib/blas.a LAPACK_LIBS=../flib/lapack.a FFT_LIBS= -lfftw3 Please check if this is what you expect. If any libraries are missing, you may specify a list of directories to search and retry, as follows: ./configure LIBDIRS="list of directories, separated by spaces" Parallel environment detected successfully. Configured for compilation of parallel executables. For more info, read the ESPRESSO User's Guide (Doc/users-guide.tex). -------------------------------------------------------------------- configure: success It seems not found the MKL. What's the problem? How to solve it? Thanks Weiguang - ***************************************************************************** * Chen, Weiguang (PhD Student) * Laboratory of Condensed Matter Theory and Computatational Materials & * School of Physics and Engineering * 75 North University Road, Physics Building Rm#202 * Zhengzhou University, Zhengzhou, 450052 Henan, China * * Tel: 86-13203730117? 86-13783677861; Fax: 86-371-67767758; * Email: chenweiguang82 at gmail.com **************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100507/57a50a7a/attachment.htm From julen.azpiroz at gmail.com Fri May 7 15:20:27 2010 From: julen.azpiroz at gmail.com (Julen Ibanez Azpiroz) Date: Fri, 7 May 2010 15:20:27 +0200 Subject: [Pw_forum] General question about occupations In-Reply-To: <1C79A37D-8D0F-4715-8A71-425066CC9ECD@democritos.it> References: <5077B850-D41F-4EAB-8DC5-8698C61DB643@democritos.it> <1C79A37D-8D0F-4715-8A71-425066CC9ECD@democritos.it> Message-ID: Dear Paolo You were right, changing the number of processors has worked, no matter the option of occupations I choose and the length of the vacuum. Even more, trying with the same script than before, the same numbers of processors, the same machine, etc. has worked. Thus, I guess there is not any real problem and that the machines where I sent the scripts were having some kind of problem those days and have been fixed, I should ask. Sorry for that and thank you very much for your help Julen University of the Basque Country -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100507/43092fe8/attachment.htm From giovanni.cantele at na.infn.it Fri May 7 16:24:15 2010 From: giovanni.cantele at na.infn.it (Giovanni Cantele) Date: Fri, 7 May 2010 16:24:15 +0200 (CEST) Subject: [Pw_forum] Installation Problems: Can not found MKL In-Reply-To: References: Message-ID: <49777.93.150.96.197.1273242255.squirrel@imap-ac.na.infn.it> > Hi, All > I am installing espresso-4.1.3 in intel cluster. I have installed the > latest > intel compiler(v11.069) and MKL(the same as compiler). > I compiled with configure like this: ./configure -enable-shared > LIBDIRS="/home/software/intel/Compiler/11.1/069/lib/intel64 > /home/software/intel/Compiler/11.1/069/mkl/lib/em64t" > --prefix=/home/software/espresso F77=ifort CC=icc > It seems not found the MKL. What's the problem? How to solve it? > Thanks > Weiguang try linking as follows: LDFLAGS="-L$MKL_PATH $MKL_PATH/libmkl_solver_lp64_sequential.a -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -lpthread" also have a look here: http://www.quantum-espresso.org/user_guide/node13.html#SECTION00036350000000000000 Finally, here http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/ you can get hel on the correct way of linking to mkl. Giovanni -- Giovanni Cantele, PhD CNR-SPIN and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario M. S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 - Fax: +39 081 676346 Skype contact: giocan74 ResearcherID: http://www.researcherid.com/rid/A-1951-2009 Web page: http://people.na.infn.it/~cantele http://www.nanomat.unina.it From stenuit at sissa.it Fri May 7 17:03:05 2010 From: stenuit at sissa.it (Geoffrey Stenuit) Date: Fri, 7 May 2010 17:03:05 +0200 Subject: [Pw_forum] GWW+U In-Reply-To: <1190877259.25470.1272265315937.JavaMail.root@mta.iut.ac.ir> References: <1057440677.25459.1272265277910.JavaMail.root@mta.iut.ac.ir> <1190877259.25470.1272265315937.JavaMail.root@mta.iut.ac.ir> Message-ID: <20100507150304.GA6097@sissa.it> Dear Ali Kazempour, The CVS version of the GWW code is implemented to work also with the LDA or GGA+U w.f. and energies as a starting guess for the G0W0 calculations. The way to use the code is similar than without the U, excepted that in the initial scf input file, you have to add all the "espresso input flags" performing the U calculations. The other files "*.pw4gww.in" and "inputgww" are unchanged (see http://gww.qe-forge.org) ... Good work, Joe On Mon, Apr 26, 2010 at 11:31:55AM +0430, kazempoor at ph.iut.ac.ir wrote: > Dear Gabriele > > I want to investigate the GW sensitivity to range of U. > Moreover there are some publication that GW at GGA+U work well for (f-electron oxides). > Thanks > > Ali Kazempour > Physics Department, Isfahn University of Technology > > ----- Original Message ----- > From: "Gabriele Sclauzero" > To: "PWSCF Forum" > Sent: Monday, April 26, 2010 10:31:41 AM > Subject: Re: [Pw_forum] GWW+U > > > > kazempoor at ph.iut.ac.ir wrote: > > Dear all I want to do GW at GGA+U, But as far as I know the authers said that the phonon > > calculation with U has not been implemented yet? is it implemented right now or not > > yet? > > DFPT+U is not implemented in QE and I'w not aware of any plan to do it. Moreover, I think > that the DFT+U theory has not yet been extended to DFPT. > > Anyway, why would you apply GW to DFT+U? People who uses GW corrections usually believe > that these are more precise than +U corrections. > > GS > > > thanks a lot Ali Kazempour Physics Department, Isfahan University of Technology > > _______________________________________________ Pw_forum mailing list > > Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at democritos.it Fri May 7 19:07:55 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 07 May 2010 19:07:55 +0200 Subject: [Pw_forum] Phonon_quarry In-Reply-To: References: Message-ID: <4BE448EB.5010201@democritos.it> partha sarathi ghosh wrote: > How to calculate phonon dispersion curve using ph.x that I know > but I want to displace a particular atom in a particular direction > with adjustable displacement. doesn't make sense to me. There is no "real" dispacement in the phonon code (unlike in "frozen phonon" method): the linear response to a displacement is calculated instead P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From saqib.javaid at ipcms.u-strasbg.fr Fri May 7 19:42:35 2010 From: saqib.javaid at ipcms.u-strasbg.fr (saqib.javaid at ipcms.u-strasbg.fr) Date: Fri, 07 May 2010 19:42:35 +0200 Subject: [Pw_forum] Question about slow speed of version 4.1.3 In-Reply-To: <20100507150304.GA6097@sissa.it> References: <1057440677.25459.1272265277910.JavaMail.root@mta.iut.ac.ir> <1190877259.25470.1272265315937.JavaMail.root@mta.iut.ac.ir> <20100507150304.GA6097@sissa.it> Message-ID: <1273254155.4be4510b88852@ipcms.u-strasbg.fr> Dear PWSCF users, I have a question regarding newer PWSCF version 4.1.3. I have been using 4.0.3 version for a while. I have recently complied 4.1.3 (which is done successfully) but surprised to see that it is a lot slower than 4.0.3. Installation has been done in the same envirement. I have been using Intell-cc-10, intell_fc_10, mkl10 and openmpi Apparently i am stuck somewhere in compatability. I would appreciate if you could help me solve this problem with best regards saqib javaid University of strasbourg ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From giannozz at democritos.it Fri May 7 22:07:08 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 7 May 2010 22:07:08 +0200 Subject: [Pw_forum] Question about slow speed of version 4.1.3 In-Reply-To: <1273254155.4be4510b88852@ipcms.u-strasbg.fr> References: <1057440677.25459.1272265277910.JavaMail.root@mta.iut.ac.ir> <1190877259.25470.1272265315937.JavaMail.root@mta.iut.ac.ir> <20100507150304.GA6097@sissa.it> <1273254155.4be4510b88852@ipcms.u-strasbg.fr> Message-ID: <03182314-6987-4E9A-B3CB-5E26D8F5A477@democritos.it> On May 7, 2010, at 19:42 , saqib.javaid at ipcms.u-strasbg.fr wrote: > I have recently complied 4.1.3 (...) but surprised to see that it > is a lot > slower than 4.0.3. Installation has been done in the same envirement. are you sure? make a "diff" of both make.sys and of the output 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 baroni at sissa.it Sat May 8 08:50:23 2010 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 8 May 2010 08:50:23 +0200 Subject: [Pw_forum] Phonon_quarry In-Reply-To: <4BE448EB.5010201@democritos.it> References: <4BE448EB.5010201@democritos.it> Message-ID: <98AB66D6-3D74-4D45-9154-17D228C41FEB@sissa.it> To be more precise: it does not make any sense to "displace" any atom by any specific amount. Forces on any other atoms will be linear in the amplitude of the displacement by construction (they are calculated in the linear-response regime), and energy difference quadratic therein. It can make sense to ask what it is the force linear responce to the displacement of any specific atom in any specific direction, though: this is obtained by calculating the interatomic force constants, by using a procedure that you certainly know. If you don't, it may be worthwhile to take a glance at how this is done, starting from google, or, even better, from some good old fashioned bibliographic search ... SB On May 7, 2010, at 7:07 PM, Paolo Giannozzi wrote: > partha sarathi ghosh wrote: > >> How to calculate phonon dispersion curve using ph.x that I know >> but I want to displace a particular atom in a particular direction >> with adjustable displacement. > > doesn't make sense to me. There is no "real" dispacement in the > phonon code (unlike in "frozen phonon" method): the linear response > to a displacement is calculated instead > > 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 --- 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/20100508/9132ca87/attachment.htm From mahkameh_va at yahoo.com Sat May 8 10:04:55 2010 From: mahkameh_va at yahoo.com (raheleh vaziri) Date: Sat, 8 May 2010 01:04:55 -0700 (PDT) Subject: [Pw_forum] degauss Message-ID: <222411.13830.qm@web32902.mail.mud.yahoo.com> Dear All, ?I don't know?that my molecule is metal, insulator or semiconductor , thus, what is suitable value for degauss and mixing_beta? thank you for any help Raheleh Vaziri. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100508/e689ae6c/attachment.htm From archygu at gmail.com Sat May 8 11:41:49 2010 From: archygu at gmail.com (archygu) Date: Sat, 8 May 2010 17:41:49 +0800 Subject: [Pw_forum] relax References: Message-ID: <201005081741462651272@gmail.com> hi olga Sedelnikova, maybe you use different psudopotential, normal conserving psudopotential mix with ultrasoft psudoptential together. that is wrong. regards, archer GU 2010-05-08 archygu ???? Olga Sedelnikova ????? 2010-05-07 11:32:00 ???? pw_forum ??? ??? [Pw_forum] relax Dear All, I am trying to optimize NH3 molecul. The error was: from readpp : error # 2 inconsistene DFT read My input file was: &control calculation='relax', restart_mode='from_scratch', prefix='nh3', disk_io='low', wf_collect=.TRUE., pseudo_dir='', outdir='' / &system ibrav = 0, celldm(1)= 1.0 nat = 4, ntyp = 2, ecutwfc = 16.0, nbnd = 128, ecutrho=200.0, occupations='smearing', degauss=0.02 / &electrons mixing_mode='local-TF' mixing_beta = 0.7, conv_thr = 1.0d-6 / &ions ion_dynamics='bfgs' ion_positions='default' / ATOMIC_SPECIES H 1.0d0 H.vbc.UPF N 16.0d0 N.BLYP.UPF CELL_PARAMETERS {cubic} 30.00000 0.000000 0.000000 0.000000 30.000000 0.000000 0.000000 0.000000 30.000000 ATOMIC_POSITIONS {angstrom} N -1.111 0.001 -1.058 H -0.900 -0.555 -1.882 H -1.939 -0.397 -0.623 H -1.349 0.938 -1.372 K_POINTS {automatic} 1 1 1 0 0 0 I did not see this error before. I great appreciate all your instructions. Best regards, Olga Sedelnikova Nikolaev Institute of Inorganic Chemistry SB RAS Novosibirsk, Russia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100508/ba940189/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Sat May 8 14:05:28 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Sat, 8 May 2010 14:05:28 +0200 Subject: [Pw_forum] degauss In-Reply-To: <222411.13830.qm@web32902.mail.mud.yahoo.com> References: <222411.13830.qm@web32902.mail.mud.yahoo.com> Message-ID: <201005081405.28133.giuseppe.mattioli@mlib.ism.cnr.it> Dear Raheleh In the case of degauss, you should use the smallest value at which your calculation does not struggle to converge. Try, e.g., 0.01 Ry. Look in the output at the smearing contribution to total energy smearing contrib. (-TS) = 0.00081361 Ry and make some tests to ensure that your total energy values are quite unaffected by different smearing values. If your system is an insulator, you should face no particular problems. In the case of mixing beta, you can start with a quite high value, e.g., 0.5, in a davidson diagonalization scheme. If your scf calculation does not converge you could try to reduce the mixing value down to 0.1 or 0.05 (this will slow your calculation...) or to use the robust cg diagonalization scheme (this will slow very much your calculation...). Hope this helps Giuseppe On Saturday 08 May 2010 10:04:55 raheleh vaziri wrote: > Dear All, > > > ?I don't know?that my molecule is metal, insulator or semiconductor , thus, > what is suitable value for degauss and mixing_beta? > > thank you for any help > > Raheleh Vaziri. -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00016 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From giannozz at democritos.it Sat May 8 12:19:19 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 8 May 2010 12:19:19 +0200 Subject: [Pw_forum] relax In-Reply-To: <201005081741462651272@gmail.com> References: <201005081741462651272@gmail.com> Message-ID: <788F6D56-418F-433C-8EE3-18A60CE71EBE@democritos.it> On May 8, 2010, at 11:41 , archygu wrote: > hi olga Sedelnikova, maybe you use different psudopotential, normal > conserving psudopotential mix with ultrasoft psudoptential together. > that is wrong. no, that is correct --- 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 Sat May 8 18:35:58 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Sat, 8 May 2010 18:35:58 +0200 Subject: [Pw_forum] Question about slow speed of version 4.1.3 In-Reply-To: <1273254155.4be4510b88852@ipcms.u-strasbg.fr> References: <1057440677.25459.1272265277910.JavaMail.root@mta.iut.ac.ir> <1190877259.25470.1272265315937.JavaMail.root@mta.iut.ac.ir> <20100507150304.GA6097@sissa.it> <1273254155.4be4510b88852@ipcms.u-strasbg.fr> Message-ID: <1B331A03-D469-477F-B8EC-3A8F84341F7B@sissa.it> It may be that in order to link to the new version of MKL the -openmp flag has been added to the LDFLAGS variable (see make.sys) . If you are running on a multicore or HT system, the OS may select automatically a number of threads greater than one and this is not efficient in your case perhaps. To see if this is the case you should monitor the number of running pw.x threads (these are usually hidden in the process list from the top command, you should press H in order to visualize all threads), or set export OMP_NUM_THREADS=1 and rerun the job. HTH GS Il giorno 07/mag/10, alle ore 19:42, saqib.javaid at ipcms.u-strasbg.fr ha scritto: > Dear PWSCF users, > > I have a question regarding newer PWSCF version 4.1.3. I have been > using 4.0.3 > version for a while. I have recently complied 4.1.3 (which is done > successfully) but surprised to see that it is a lot slower than 4.0.3. > Installation has been done in the same envirement. I have been using > Intell-cc-10, intell_fc_10, mkl10 and openmpi > Apparently i am stuck somewhere in compatability. I would appreciate > if you > could help me solve this problem > with best regards > saqib javaid > University of strasbourg > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100508/b7df11a1/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 1753 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100508/b7df11a1/attachment.bin From baroni at sissa.it Sat May 8 19:02:12 2010 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 8 May 2010 19:02:12 +0200 Subject: [Pw_forum] degauss In-Reply-To: <222411.13830.qm@web32902.mail.mud.yahoo.com> References: <222411.13830.qm@web32902.mail.mud.yahoo.com> Message-ID: <3C400B8F-93B4-47F3-BB6C-F6500C5A9043@sissa.it> wait, wait, wait: please, wait! being a metal/ insulator / semiconductor (which is the same as being an insulator) is a property of infinite systems, NOT of isolated molecules. Please, be sure to understand this concept before proceeding. If you don't, take some time to revert to some basic solid-state textbook. If you do not know where to start from, ask our advice. (exercise #1) this being said, the same *trick* is used by QE (as well as by many other codes) to deal with metallicity in infinite systems and quasi-degeneracy in finite ones. I think that this issue has been discussed many times in this mailing list. Please, search its archive and try to retrieve the relevant info (exercice #2). in a nutshell, convergence to self-consistency may be slowed down (or even hindered) if the ground state is quasi-degenerate with one of the excited states. during the self-consistent cycle, the algorithm may jump from one state to the other quite easily, thus hindering convergence. the use os a ghaussian spearing (or of a smearing whatsoever) allows the code to average between the ground- and the quasi-degegenerate excited-state, thus easing the convergence. try to understand this (exercise #3). if you fail, revert to us with further questions as focused as possible. SB PS: do not forget that we all expect to know something about the identity of our internet-pals (please, provide your affiliation) On May 8, 2010, at 10:04 AM, raheleh vaziri wrote: > Dear All, > > I don't know that my molecule is metal, insulator or semiconductor , thus, what is suitable value for degauss and mixing_beta? > > thank you for any help > > Raheleh Vaziri. > > > > > _______________________________________________ > 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/20100508/56f4bda3/attachment-0001.htm From kazempoor at ph.iut.ac.ir Mon May 10 09:03:24 2010 From: kazempoor at ph.iut.ac.ir (kazempoor at ph.iut.ac.ir) Date: Mon, 10 May 2010 11:33:24 +0430 (IRDT) Subject: [Pw_forum] Hybridization In-Reply-To: <636554074.90983.1273474978463.JavaMail.root@mta.iut.ac.ir> Message-ID: <1781867119.90991.1273475004181.JavaMail.root@mta.iut.ac.ir> Dear All It is not clear for me if the orbitals of one atom hybridyze with each other? I mean for example for Mn isolated atoms does the s and p and d hybridyze? How does the situation change when go from isolated atom to crystal ? In general when does the overlap between orbitals lead to hybridization? Thanks a lot Ali Kazempour Physics Department, Isfahn University of Technology From degironc at sissa.it Mon May 10 09:24:01 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 10 May 2010 09:24:01 +0200 Subject: [Pw_forum] Hybridization In-Reply-To: <1781867119.90991.1273475004181.JavaMail.root@mta.iut.ac.ir> References: <1781867119.90991.1273475004181.JavaMail.root@mta.iut.ac.ir> Message-ID: <4BE7B491.9090702@sissa.it> kazempoor at ph.iut.ac.ir wrote: > Dear All > It is not clear for me if the orbitals of one atom hybridyze with each other? I mean for example for Mn isolated atoms does the s and > p and d hybridyze? How does the situation change when go from isolated atom to crystal ? > In general when does the overlap between orbitals lead to hybridization? > always unless they belong to different symmetry representations. Hence s, p and d orbitals of a system with spherical symmetry do not hybridize, while in a solid or in a molecule they usually do. Stefano de Gironcoli SISSA and DEMOCRITOS > Thanks a lot > > Ali Kazempour > Physics Department, Isfahn University of Technology > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From siyouber at yahoo.fr Mon May 10 10:54:23 2010 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Mon, 10 May 2010 08:54:23 +0000 (GMT) Subject: [Pw_forum] Postprocessing code Message-ID: <88038.11921.qm@web26501.mail.ukl.yahoo.com> Dear all, Please could somebody indicates a postprocessing code for extracting the mean square displacement(MSD) of atoms from QE, cp.x? ouput? Thank for your help *********************** Bertrand SITAMTZE YOUMBI Laboratory of Material Sciences Department of Physics University of Yaounde I-Cameroon ********************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100510/de0b0696/attachment.htm From siyouber at yahoo.fr Tue May 11 15:17:21 2010 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Tue, 11 May 2010 13:17:21 +0000 (GMT) Subject: [Pw_forum] Fw : Postprocessing code Message-ID: <914086.25060.qm@web26507.mail.ukl.yahoo.com> --- En date de?: Lun 10.5.10, Bertrand SITAMTZE a ?crit?: De: Bertrand SITAMTZE Objet: Postprocessing code ?: "pw code" Date: Lundi 10 mai 2010, 10h54 Dear all, Please could somebody indicates a postprocessing code for extracting the mean square displacement(MSD) of atoms from QE, cp.x? ouput? Thank for your help *********************** Bertrand SITAMTZE YOUMBI Laboratory of Material Sciences Department of Physics University of Yaounde I-Cameroon ********************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100511/9f4c02c1/attachment.htm From mohnish.iitk at gmail.com Tue May 11 07:35:00 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Tue, 11 May 2010 11:05:00 +0530 Subject: [Pw_forum] Bader and LOwdin analysis Message-ID: Dear QE users, I want to do Bader and Lowdin analysis for thin films of some materials. I was searching for some module in QE for the same but I did'nt get it. Can somebody please tell me how can I do that analysis using QE. Thanks a lot in advance, -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100511/85f9ba0c/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Tue May 11 20:36:31 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Tue, 11 May 2010 20:36:31 +0200 Subject: [Pw_forum] Bader and LOwdin analysis In-Reply-To: References: Message-ID: <201005112036.32079.giuseppe.mattioli@mlib.ism.cnr.it> dear Mohnish projwfc.x performs Lowdin analysis Giuseppe On Tuesday 11 May 2010 07:35:00 mohnish pandey wrote: > Dear QE users, > I want to do Bader and Lowdin analysis for thin > films of some materials. I was searching for some module in QE for the same > but I did'nt get it. Can somebody please tell me how can I do that analysis > using QE. > Thanks a lot in advance, -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00016 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From aryjunior at gmail.com Tue May 11 18:43:33 2010 From: aryjunior at gmail.com (Ary Junior) Date: Tue, 11 May 2010 13:43:33 -0300 Subject: [Pw_forum] Bader and LOwdin analysis In-Reply-To: <201005112036.32079.giuseppe.mattioli@mlib.ism.cnr.it> References: <201005112036.32079.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: Hi, for Bader Analysis take a look at http://theory.cm.utexas.edu/bader/ ... Before you need run pp.x to generate a .cube file... []s Ary Junior On Tue, May 11, 2010 at 3:36 PM, Giuseppe Mattioli < giuseppe.mattioli at mlib.ism.cnr.it> wrote: > dear Mohnish > projwfc.x performs Lowdin analysis > > Giuseppe > > On Tuesday 11 May 2010 07:35:00 mohnish pandey wrote: > > Dear QE users, > > I want to do Bader and Lowdin analysis for > thin > > films of some materials. I was searching for some module in QE for the > same > > but I did'nt get it. Can somebody please tell me how can I do that > analysis > > using QE. > > Thanks a lot in advance, > > > > -- > ******************************************************** > - 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 > -- Ary Rodrigues Ferreira Junior Grupo de F?sico-Qu?mica de S?lidos e Interfaces Departamento de Qu?mica Universidade Federal de Juiz de Fora CEP 36036-330 Juiz de Fora - MG -Brazil -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100511/de50b150/attachment.htm From giannozz at democritos.it Tue May 11 18:54:42 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 11 May 2010 18:54:42 +0200 Subject: [Pw_forum] Bader and LOwdin analysis In-Reply-To: References: Message-ID: On May 11, 2010, at 7:35 , mohnish pandey wrote: > I want to do Bader and Lowdin analysis for Lowdin, see prevous answer. For Bader, see this remark in the user guide (new version): Note about Bader's analysis: on \texttt{http://theory.cm.utexas.edu/bader/} one can find a software that performs Bader's analysis starting from charge on a regular grid. The required "cube" format can be produced by \qe\ using \texttt{pp.x} (info by G. Lapenna who has successfully used this technique). This code should perform decomposition into Voronoi polyhedra as well, in place of obsolete code \texttt{voronoy.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 Tue May 11 13:25:14 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Tue, 11 May 2010 16:55:14 +0530 Subject: [Pw_forum] Lowdin and Bader analysis Message-ID: Dear QE users, I want to do Bader and Lowdin analysis for thin films of some materials. I was searching for some module in QE for the same but I did'nt get it. Can somebody please tell me how can I do that analysis using QE. Thanks a lot in advance, -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100511/f2249a93/attachment.htm From giannozz at democritos.it Wed May 12 11:47:07 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 12 May 2010 11:47:07 +0200 Subject: [Pw_forum] Quantum ESPRESSO v.4.2 Message-ID: <4A524761-0950-4A05-9590-10F0A4B8AA25@democritos.it> Version 4.2 of the Quantum ESPRESSO distribution is available for download from the website http://www.quantum-espresso.org . This release contains the following improvements over previous versions: * HSE exchange-correlation functionals (courtesy of Hannu-Pekka Komsa) * New package GWW for GW calculations with Wannier functions (courtesy of Geoffrey Stenuit and Paolo Umari) * Grid parallelization for the phonon code * Improved mixed openMP-MPI parallelization * Martyna-Tuckerman algorithm for isolated systems plus other minor improvements and bug fixes (see file Doc/release- notes). Everybody who is using the Quantum-ESPRESSO distribution is encouraged to upgrade and to report problems to the mailing list. The Quantum ESPRESSO group --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Wed May 12 13:58:57 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 12 May 2010 13:58:57 +0200 Subject: [Pw_forum] Fw : Postprocessing code In-Reply-To: <914086.25060.qm@web26507.mail.ukl.yahoo.com> References: <914086.25060.qm@web26507.mail.ukl.yahoo.com> Message-ID: <0928D35C-DFB9-4FAA-A247-0C806BB034AA@democritos.it> On May 11, 2010, at 15:17 , Bertrand SITAMTZE wrote: > Please could somebody indicates a postprocessing code > for extracting the mean square displacement(MSD) of > atoms from QE, cp.x ouput? you might try to modify cppp.x (in CP/fpmdpp.f90, documentation in Doc/INPUT_CPPP*) to ehat you need 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 elie.moujaes at hotmail.co.uk Wed May 12 17:37:06 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Wed, 12 May 2010 16:37:06 +0100 Subject: [Pw_forum] jagged phonon dispersion in graphene Message-ID: Dear all, Hope you are all doing fine. I am computing the phono dispersion in graphene. I am using 1000 points in the matdyn.in file and I used an 8x 8 x 1 grid but I get a jagged dispersion spectrum. I tried even using a 16 x16 x1 grid but almost got the same jagged results..I am not sure why this happening. You will find attached the ps graph of the dispersion. Below are all the input files. Thanks for your help in advance. SCF calculation: control prefix='phmonog', calculation='scf', restart_mode='from_scratch', pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.1.3/pseudo/', outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/' / &system ibrav= 4, celldm(1) =4.608737, celldm(3)=4.53666, nat=2, ntyp= 1, ecutwfc = 60.D0, nosym=.true.,occupations='smearing', smearing='XYZ', degauss=0.01, nelec=8 / &electrons conv_thr=1.D-8, mixing_beta=0.1D0, mixing_mode='local-TF' / ATOMIC_SPECIES C 12.00000 C.pz-rrkjus.UPF ATOMIC_POSITIONS crystal C 0.000000 0.000000 0.000000 1 1 1 C 0.333333 -0.33333 0.000000 1 1 1 K_POINTS automatic 25 25 1 0 0 0 Ph.in file: Phonon dispersion for monographene &inputph tr2_ph=1.0d-12, prefix='phmonog', ldisp=.true., lnscf=.true., nq1=16, nq2=16, nq3=1 amass(1)=12.00, outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', fildyn='phmgraphene.dyn', / q2r file: &input fildyn = 'phmgraphene.dyn', zasr = 'crystal' , flfrc = 'mgraph16160.fc' / matdyn.in file : &input asr = 'crystal', amass(1) = 12.00 , flfrc = 'mgraph16160.fc', flfrq = 'mgraph16160.freq', / 1000 0.00000000 0.00000000 0.00000000 1.000000e-03 0.00000000 0.00000000 0.10000000 1.000000e-03 0.00000000 0.00000000 0.20000000 1.000000e-03 0.00000000 0.00000000 0.30000000 1.000000e-03 0.00000000 0.00000000 0.40000000 1.000000e-03 0.00000000 0.00000000 0.50000000 1.000000e-03 0.00000000 0.00000000 0.60000000 1.000000e-03 0.00000000 0.00000000 0.70000000 1.000000e-03 ......................... _________________________________________________________________ http://clk.atdmt.com/UKM/go/195013117/direct/01/ We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100512/813fecad/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: mgraph16160.bands.ps Type: application/postscript Size: 19751 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100512/813fecad/attachment-0001.ps From modaresi.mohsen at gmail.com Wed May 12 21:07:38 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Wed, 12 May 2010 23:37:38 +0430 Subject: [Pw_forum] Low speed Message-ID: Dear Developers and users, I run a SCF calculation with 71 atoms on a camputer with 8 cpu and 8GB RAM, i expect it run in some minutes, But it take 3 hours to run. Is it regular? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100512/26abd41a/attachment.htm From nnlinh at sissa.it Wed May 12 21:23:34 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Wed, 12 May 2010 21:23:34 +0200 Subject: [Pw_forum] Low speed In-Reply-To: References: Message-ID: <4BEB0036.9050900@sissa.it> mohsen modaresi wrote: > Dear Developers and users, > I run a SCF calculation with 71 atoms on a camputer with 8 cpu and 8GB > RAM, i expect it run in some minutes, But it take 3 hours to run. Is > it regular? I thinks we don't have any reference table for time calculation of QE. With this kind of question I think, basing on my experience, with your model and your computer system it is regular. However, a scf calculation estimated right or wrong should be depended on if it converges or not, it does not depend mainly on calculating time Hope this help. Linh > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ----------------------------------------------------- Nguyen Ngoc Linh, PhD Student c/o: SISSA & CNR-INFM Democritos, via Beirut 2-4, 34014 Trieste (Italy) email: nnlinh at sissa.it phone: +39 04 03787 319 skype: ngoclinh84phys ----------------------------------------------------- "The physics is theoretical but the fun is real" From modaresi.mohsen at gmail.com Wed May 12 21:39:03 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Thu, 13 May 2010 00:09:03 +0430 Subject: [Pw_forum] Low speed In-Reply-To: <4BEB0036.9050900@sissa.it> References: <4BEB0036.9050900@sissa.it> Message-ID: Daer Ngoc, Thanks for your answer. This is "make.sys", Do any body have any suggestion for increasing speed? Thanks again for your answers, Mohsen Modaresi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100513/2eef66ba/attachment.htm From modaresi.mohsen at gmail.com Wed May 12 21:40:14 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Thu, 13 May 2010 00:10:14 +0430 Subject: [Pw_forum] Low speed In-Reply-To: References: <4BEB0036.9050900@sissa.it> Message-ID: Excuse me this is make.sys # make.sys. Generated from make.sys.in by configure. # compilation rules .SUFFIXES : .SUFFIXES : .o .c .f .f90 # most fortran compilers can directly preprocess c-like directives: use # $(MPIF90) $(F90FLAGS) -c $< # if explicit preprocessing by the C preprocessor is needed, use: # $(CPP) $(CPPFLAGS) $< -o $*.F90 # $(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o # remember the tabulator in the first column !!! .f90.o: $(MPIF90) $(F90FLAGS) -c $< # .f.o and .c.o: do not modify .f.o: $(F77) $(FFLAGS) -c $< .c.o: $(CC) $(CFLAGS) -c $< # DFLAGS = precompilation options (possible arguments to -D and -U) # used by the C compiler and preprocessor # FDFLAGS = as DFLAGS, for the f90 compiler # See include/defs.h.README for a list of options and their meaning # With the exception of IBM xlf, FDFLAGS = $(DFLAGS) # For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas DFLAGS = -D__GFORTRAN -D__FFTW -D__MPI -D__PARA FDFLAGS = $(DFLAGS) # IFLAGS = how to locate directories where files to be included are # In most cases, IFLAGS = -I../include IFLAGS = -I../include # MODFLAGS = flag used by f90 compiler to locate modules # You need to search for modules in ./, in ../iotk/src, in ../Modules # Some applications also need modules in ../PW and ../PH MODFLAGS = -I./ -I../Modules -I../iotk/src \ -I../PW -I../PH -I../EE -I../GIPAW # Compilers: fortran-90, fortran-77, C # If a parallel compilation is desired, MPIF90 should be a fortran-90 # compiler that produces executables for parallel execution using MPI # (such as for instance mpif90, mpf90, mpxlf90,...); # otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90, ifort,...) # If you have a parallel machine but no suitable candidate for MPIF90, # try to specify the directory containing "mpif.h" in IFLAGS # and to specify the location of MPI libraries in MPI_LIBS MPIF90 = mpif90 #F90 = gfortran CC = cc F77 = gfortran # C preprocessor and preprocessing flags - for explicit preprocessing, # if needed (see the compilation rules above) # preprocessing flags must include DFLAGS and IFLAGS CPP = cpp CPPFLAGS = -P -traditional $(DFLAGS) $(IFLAGS) # compiler flags: C, F90, F77 # C flags must include DFLAGS and IFLAGS # F90 flags must include MODFLAGS, IFLAGS, and FDFLAGS with appropriate syntax CFLAGS = -O3 $(DFLAGS) $(IFLAGS) F90FLAGS = $(FFLAGS) -x f95-cpp-input $(FDFLAGS) $(IFLAGS) $(MODFLAGS) FFLAGS = -O3 # compiler flags without optimization for fortran-77 # the latter is NEEDED to properly compile dlamch.f, used by lapack FFLAGS_NOOPT = -O0 # Linker, linker-specific flags (if any) # Typically LD coincides with F90 or MPIF90, LD_LIBS is empty LD = mpif90 LDFLAGS = LD_LIBS = # External Libraries (if any) : blas, lapack, fft, MPI # If you have nothing better, use the local copy : ../flib/blas.a BLAS_LIBS = ../flib/blas.a # The following lapack libraries will be available in flib/ : # ../flib/lapack.a : contains all needed routines # ../flib/lapack_atlas.a: only routines not present in the Atlas library # For IBM machines with essl (-D__ESSL): load essl BEFORE lapack ! # remember that LAPACK_LIBS precedes BLAS_LIBS in loading order LAPACK_LIBS = ../flib/lapack.a # nothing needed here if the the internal copy of FFTW is compiled # (needs -D__FFTW in DFLAGS) FFT_LIBS = # For parallel execution, the correct path to MPI libraries must # be specified in MPI_LIBS (except for IBM if you use mpxlf) MPI_LIBS = # IBM-specific: MASS libraries, if available and if -D__MASS is defined in FDFLAGS MASS_LIBS = # pgplot libraries (used by some post-processing tools) PGPLOT_LIBS = # ar command and flags - for most architectures: AR = ar, ARFLAGS = ruv # ARFLAGS_DYNAMIC is used in iotk to produce a dynamical library, # for Mac OS-X with PowerPC and xlf compiler. In all other cases # ARFLAGS_DYNAMIC = $(ARFLAGS) AR = ar ARFLAGS = ruv ARFLAGS_DYNAMIC= ruv # ranlib command. If ranlib is not needed (it isn't in most cases) use # RANLIB = echo RANLIB = ranlib # all internal and external libraries - do not modify LIBOBJS = ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a ../Multigrid/mglib.a LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FFT_LIBS) $(MPI_LIBS) $(MASS_LIBS) $(PGPLOT_LIBS) $(LD_LIBS) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100513/8a260bd1/attachment.htm From elbuesta at icqmail.com Wed May 12 22:47:00 2010 From: elbuesta at icqmail.com (elbuesta at icqmail.com) Date: Wed, 12 May 2010 16:47:00 -0400 Subject: [Pw_forum] Low speed In-Reply-To: References: Message-ID: <8CCC02B67105B3E-1144-48F6@webmail-d020.sysops.aol.com> It seems to me that the mkl libraries were not found. From my experience, something like ? "BLAS_LIBS????? = -L/opt/intel/mkl/9.0/lib/em64t -lmkl_em64t" and LAPACK_LIBS??? = -lmkl_lapack? -L/opt/intel/mkl/9.0/lib/em64t -lmkl_em64t ? should be written on the make.sys. In your case, the code is not using?the mkl?math optimization libraries. So that is why it is slow, since these libraries make a considerable difference. I would try this: ? > ./configure LIBDIRS="/home/fabionr/intel/mkl/10.x.x.xxx/lib/em64t /home/fabionr/intel/mkl/10.x.x.xxx/lib/em64t" replacing the x with the mkl version you have. ? I hope it helps, ? Fabio Negreiros Ribeiro Departamento de F?sica, Universidade Federal de Minas Gerais, MG, Brazil -----Original Message----- From: mohsen modaresi <modaresi.mohsen at gmail.com> To: PWSCF Forum <pw_forum at pwscf.org> Sent: Wed, May 12, 2010 4:40 pm Subject: Re: [Pw_forum] Low speed Excuse me this is make.sys # make.sys.? Generated from make.sys.in by configure. # compilation rules .SUFFIXES : .SUFFIXES : .o .c .f .f90 # most fortran compilers can directly preprocess c-like directives: use # ??? $(MPIF90) $(F90FLAGS) -c $< # if explicit preprocessing by the C preprocessor is needed, use: # ??? $(CPP) $(CPPFLAGS) $< -o $*.F90 #???? $(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o # remember the tabulator in the first column !!! .f90.o: ????? $(MPIF90) $(F90FLAGS) -c $< # .f.o and .c.o: do not modify .f.o: ????? $(F77) $(FFLAGS) -c $< .c.o: ????? $(CC) $(CFLAGS)? -c $< # DFLAGS? = precompilation options (possible arguments to -D and -U) #?????????? used by the C compiler and preprocessor # FDFLAGS = as DFLAGS, for the f90 compiler # See include/defs.h.README for a list of options and their meaning # With the exception of IBM xlf, FDFLAGS = $(DFLAGS) # For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas DFLAGS???????? =? -D__GFORTRAN -D__FFTW -D__MPI -D__PARA FDFLAGS??????? = $(DFLAGS) # IFLAGS = how to locate directories where files to be included are # In most cases, IFLAGS = -I../include IFLAGS???????? = -I../include # MODFLAGS = flag used by f90 compiler to locate modules # You need to search for modules in ./, in ../iotk/src, in ../Modules # Some applications also need modules in ../PW and ../PH MODFLAGS?????? = -I./? -I../Modules? -I../iotk/src ???????????????? -I../PW? -I../PH? -I../EE -I../GIPAW # Compilers: fortran-90, fortran-77, C # If a parallel compilation is desired, MPIF90 should be a fortran-90 # compiler that produces executables for parallel execution using MPI # (such as for instance mpif90, mpf90, mpxlf90,...); # otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90, ifort,...) # If you have a parallel machine but no suitable candidate for MPIF90, # try to specify the directory containing "mpif.h" in IFLAGS # and to specify the location of MPI libraries in MPI_LIBS MPIF90???????? = mpif90 #F90?????????? = gfortran CC???????????? = cc F77??????????? = gfortran # C preprocessor and preprocessing flags - for explicit preprocessing, # if needed (see the compilation rules above) # preprocessing flags must include DFLAGS and IFLAGS CPP??????????? = cpp CPPFLAGS?????? = -P -traditional $(DFLAGS) $(IFLAGS) # compiler flags: C, F90, F77 # C flags must include DFLAGS and IFLAGS # F90 flags must include MODFLAGS, IFLAGS, and FDFLAGS with appropriate syntax CFLAGS???????? = -O3 $(DFLAGS) $(IFLAGS) F90FLAGS?????? = $(FFLAGS) -x f95-cpp-input $(FDFLAGS) $(IFLAGS) $(MODFLAGS) FFLAGS???????? = -O3 # compiler flags without optimization for fortran-77 # the latter is NEEDED to properly compile dlamch.f, used by lapack FFLAGS_NOOPT?? = -O0 # Linker, linker-specific flags (if any) # Typically LD coincides with F90 or MPIF90, LD_LIBS is empty LD???????????? = mpif90 LDFLAGS??????? = LD_LIBS??????? = # External Libraries (if any) : blas, lapack, fft, MPI # If you have nothing better, use the local copy : ../flib/blas.a BLAS_LIBS????? = ../flib/blas.a # The following lapack libraries will be available in flib/ : # ../flib/lapack.a : contains all needed routines # ../flib/lapack_atlas.a: only routines not present in the Atlas library # For IBM machines with essl (-D__ESSL): load essl BEFORE lapack ! # remember that LAPACK_LIBS precedes BLAS_LIBS in loading order LAPACK_LIBS??? = ../flib/lapack.a # nothing needed here if the the internal copy of FFTW is compiled # (needs -D__FFTW in DFLAGS) FFT_LIBS?????? = # For parallel execution, the correct path to MPI libraries must # be specified in MPI_LIBS (except for IBM if you use mpxlf) MPI_LIBS?????? = # IBM-specific: MASS libraries, if available and if -D__MASS is defined in FDFLAGS MASS_LIBS????? = # pgplot libraries (used by some post-processing tools) PGPLOT_LIBS??? = # ar command and flags - for most architectures: AR = ar, ARFLAGS = ruv # ARFLAGS_DYNAMIC is used in iotk to produce a dynamical library, # for Mac OS-X with PowerPC and xlf compiler. In all other cases # ARFLAGS_DYNAMIC = $(ARFLAGS) AR???????????? = ar ARFLAGS??????? = ruv ARFLAGS_DYNAMIC= ruv # ranlib command. If ranlib is not needed (it isn't in most cases) use # RANLIB = echo RANLIB???????? = ranlib # all internal and external libraries - do not modify LIBOBJS??????? = ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a ../Multigrid/mglib.a LIBS?????????? = $(LAPACK_LIBS) $(BLAS_LIBS) $(FFT_LIBS) $(MPI_LIBS) $(MASS_LIBS) $(PGPLOT_LIBS) $(LD_LIBS) ? _______________________________________________ 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/20100512/791f194d/attachment-0001.htm From hqzhou at nju.edu.cn Thu May 13 04:09:29 2010 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Thu, 13 May 2010 10:09:29 +0800 Subject: [Pw_forum] Low speed References: <4BEB0036.9050900@sissa.it> Message-ID: mohsen, Increasing speed is a difficult task unless you could find better algorithms and write better programs. Anyway, first thing is first, my recommendation is to change your compiler to Intel FORTRAN and use Intel MKL instead of your self-compiled BLAS and LAPACK. Huiqun Zhou @Earth Sciences, Nanjing University, China ----- Original Message ----- From: mohsen modaresi To: PWSCF Forum Sent: Thursday, May 13, 2010 3:39 AM Subject: Re: [Pw_forum] Low speed Daer Ngoc, Thanks for your answer. This is "make.sys", Do any body have any suggestion for increasing speed? Thanks again for your answers, Mohsen Modaresi ------------------------------------------------------------------------------ _______________________________________________ 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/20100513/259e1cb4/attachment.htm From giannozz at democritos.it Thu May 13 08:28:02 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 13 May 2010 08:28:02 +0200 Subject: [Pw_forum] Low speed In-Reply-To: References: Message-ID: <453D946C-A9B5-4F5A-81EE-0DFC089012B6@democritos.it> On May 12, 2010, at 21:07 , mohsen modaresi wrote: > I run a SCF calculation with 71 atoms on a camputer > with 8 cpu and 8GB RAM, i expect it run in some minutes, > But it take 3 hours to run. Is it regular? it depends. There are two separate issues to be considered: - serial speed, i.e. the speed of a single processors, and - effectiveness of parallelization. For the former, you need fast mathematical libraries and a decent compiler. For the latter, you need to have an idea of how parallelism in QE works, then to perform some tests. QE is carefully parallelized, but don't assume that running on 8 processors (especially of multicore machines) guarantees running in 1/8 of the time. 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 alex968873 at yahoo.com.cn Thu May 13 13:19:00 2010 From: alex968873 at yahoo.com.cn (=?gb2312?B?wO6x8w==?=) Date: Thu, 13 May 2010 19:19:00 +0800 (CST) Subject: [Pw_forum] Is there PBE UPF for K element ? Message-ID: <861337.29167.qm@web15108.mail.cnb.yahoo.com> Dear all, I need a UPF using PBE Exchange-Correlation for K element, because other elements in my material don't have PZ Exchange-Correlation UPF, and using inconsistent DFT is forbidden. Unfortunately, I can't find any K.pbe...UPF file in pseudo folder or QE website. So who can provide it to me? Or give me some suggestion? Thank a lot in advance! ************************** Li Bin Department of Physics, Southeast University, PRC. *********************************************** From eyvaz_isaev at yahoo.com Thu May 13 15:31:39 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 13 May 2010 06:31:39 -0700 (PDT) Subject: [Pw_forum] jagged phonon dispersion in graphene Message-ID: <810587.42975.qm@web65710.mail.ac4.yahoo.com> Dear Elie, Have you tried PlotPhon utility from QE 4.2? Any troubles, please contact me. 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 isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Wed, 5/12/10, Elie Moujaes wrote: From: Elie Moujaes Subject: [Pw_forum] jagged phonon dispersion in graphene To: pw_forum at pwscf.org Date: Wednesday, May 12, 2010, 7:37 PM Dear all, ? Hope you are all doing fine.? I am computing the phono dispersion in graphene. I am using 1000 points in the matdyn.in file and I used an 8x?8 x 1 grid but I get a jagged dispersion spectrum. I tried even using a 16 x16 x1 grid but almost got the same jagged results..I am not sure why this happening. You will find attached the ps graph of the dispersion. Below are all the input files. Thanks for your help in advance. ? SCF calculation: ? control ??? prefix='phmonog', ??? calculation='scf', ??? restart_mode='from_scratch', ??? pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.1.3/pseudo/', ??? outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/' ?/ ?&system??? ??? ibrav=? 4, celldm(1) =4.608737, celldm(3)=4.53666, nat=2, ntyp= 1, ??? ecutwfc = 60.D0, nosym=.true.,occupations='smearing', smearing='XYZ', degauss=0.01, nelec=8 / ?&electrons ??? conv_thr=1.D-8,???? ??? mixing_beta=0.1D0, ??? mixing_mode='local-TF' ?/ ATOMIC_SPECIES ?C? 12.00000? C.pz-rrkjus.UPF ATOMIC_POSITIONS crystal ?C 0.000000? 0.000000 0.000000 1 1 1 ?C 0.333333? -0.33333 0.000000 1 1 1 K_POINTS automatic 25 25 1 0 0 0 ? Ph.in file: ? Phonon dispersion for monographene ?&inputph ? tr2_ph=1.0d-12, ? prefix='phmonog', ? ldisp=.true., ? lnscf=.true., ? nq1=16, nq2=16, nq3=1 ? amass(1)=12.00, ? outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', ? fildyn='phmgraphene.dyn', / ? q2r file: ? ?&input ?fildyn = 'phmgraphene.dyn', ?zasr = 'crystal' , ?flfrc = 'mgraph16160.fc' / ? matdyn.in file : ? &input ?asr = 'crystal', ?amass(1) = 12.00 , ?flfrc = 'mgraph16160.fc', ?flfrq = 'mgraph16160.freq', / 1000 ? 0.00000000? 0.00000000? 0.00000000? 1.000000e-03 ? 0.00000000? 0.00000000? 0.10000000? 1.000000e-03 ? 0.00000000? 0.00000000? 0.20000000? 1.000000e-03 ? 0.00000000? 0.00000000? 0.30000000? 1.000000e-03 ? 0.00000000? 0.00000000? 0.40000000? 1.000000e-03 ? 0.00000000? 0.00000000? 0.50000000? 1.000000e-03 ? 0.00000000? 0.00000000? 0.60000000? 1.000000e-03 ? 0.00000000? 0.00000000 ?0.70000000? 1.000000e-03 ?? ......................... ? Get a new e-mail account with Hotmail - Free. Sign-up now. -----Inline Attachment Follows----- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100513/fc8503cb/attachment.htm From fratesi at mater.unimib.it Thu May 13 18:20:19 2010 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Thu, 13 May 2010 18:20:19 +0200 (CEST) Subject: [Pw_forum] Is there PBE UPF for K element ? In-Reply-To: <861337.29167.qm@web15108.mail.cnb.yahoo.com> References: <861337.29167.qm@web15108.mail.cnb.yahoo.com> Message-ID: Dear Li Bin, There is an extensive discussion on this subject in the forum: see http://www.democritos.it/pipermail/pw_forum/2007-September/007155.html and following messages. If you like the PZ pseudo for K which is available on the Q-E website, you could adapt it to PBE, as a starting point. See: http://www.quantum-espresso.org/pseudo/upfdetails.php?upf=K.pz-sp-van.UPF That pseudo was generated by the Vanderbilt code "uspp". You can find the input for its generation in in http://www.physics.rutgers.edu/~dhv/uspp/uspp-cur/Work/019-K/019-K-ca-sp-vgrp/ In the file k_ae_s1.adat change the variable exfact 0 -> 5 (PBE). You might have to change ifqopt 2 -> 3 (different augfun pseudiz; 2 not allowed for GGA, if I remember correctly) in the file k_ps.adat. Finally, convert the resulting pseudopotential file to UPF format with uspp2upf.x (in espresso/upftools). I was doing this sometimes ago, and I was satisfied by further enlarging the parmeter of rinner to 0.95 (in the file k_ps.adat), which enabled a better convergence with respect to ecutrho. As always, tests are recommended... Hope this helps, Guido On Thu, 13 May 2010, ?? wrote: > Dear all, > > I need a UPF using PBE Exchange-Correlation for K element, because other elements in my material don't have PZ Exchange-Correlation UPF, and using inconsistent DFT is forbidden. Unfortunately, I can't find any K.pbe...UPF file in pseudo folder or QE website. So who can provide it to me? Or give me some suggestion? Thank a lot in advance! > > > ************************** > > Li Bin > Department of Physics, Southeast University, PRC. > > *********************************************** > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca From modaresi.mohsen at gmail.com Thu May 13 18:40:05 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Thu, 13 May 2010 21:10:05 +0430 Subject: [Pw_forum] 2 question about parallel computing and Imaginary part of dielectric Message-ID: Dear users, 1) I want to calculate imaginary part of dielectric function which can be done with WIEN2k (for Ex. "Practical aspects of running the WIEN2k code for electron spectroscopy, *Micron*Volume 38, Issue 1, January 2007, Pages 12-28"), Can Q.E do this kind of calculation? 2) For parallel computing the input file must be modified? (in other word if we run a program with 1CPU and then we want to run it with N CPUs, we must modify the input file) Mohsen Modaresi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100513/8dcd1ebd/attachment-0001.htm From elie.moujaes at hotmail.co.uk Thu May 13 19:44:23 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Thu, 13 May 2010 18:44:23 +0100 Subject: [Pw_forum] jagged phonon dispersion in graphene In-Reply-To: <810587.42975.qm@web65710.mail.ac4.yahoo.com> References: <810587.42975.qm@web65710.mail.ac4.yahoo.com> Message-ID: Dear Prof. Isaev, Thanks very much for the information. I downloaded the attachment from one of the e-mails in the forum as a .BIN file. I am not sure though how to use it. Is it possible to explain me a bit more about this utility and how it can be used. I could not find it within the QE 4.2 package. This is why i downloaded it from forum. Many thanks Elie Mouajes University of nottingham NF7 2RD UK Date: Thu, 13 May 2010 06:31:39 -0700 From: eyvaz_isaev at yahoo.com To: pw_forum at pwscf.org Subject: Re: [Pw_forum] jagged phonon dispersion in graphene Dear Elie, Have you tried PlotPhon utility from QE 4.2? Any troubles, please contact me. 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 isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Wed, 5/12/10, Elie Moujaes wrote: From: Elie Moujaes Subject: [Pw_forum] jagged phonon dispersion in graphene To: pw_forum at pwscf.org Date: Wednesday, May 12, 2010, 7:37 PM Dear all, Hope you are all doing fine. I am computing the phono dispersion in graphene. I am using 1000 points in the matdyn.in file and I used an 8x 8 x 1 grid but I get a jagged dispersion spectrum. I tried even using a 16 x16 x1 grid but almost got the same jagged results..I am not sure why this happening. You will find attached the ps graph of the dispersion. Below are all the input files. Thanks for your help in advance. SCF calculation: control prefix='phmonog', calculation='scf', restart_mode='from_scratch', pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.1.3/pseudo/', outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/' / &system ibrav= 4, celldm(1) =4.608737, celldm(3)=4.53666, nat=2, ntyp= 1, ecutwfc = 60.D0, nosym=.true.,occupations='smearing', smearing='XYZ', degauss=0.01, nelec=8 / &electrons conv_thr=1.D-8, mixing_beta=0.1D0, mixing_mode='local-TF' / ATOMIC_SPECIES C 12.00000 C.pz-rrkjus.UPF ATOMIC_POSITIONS crystal C 0.000000 0.000000 0.000000 1 1 1 C 0.333333 -0.33333 0.000000 1 1 1 K_POINTS automatic 25 25 1 0 0 0 Ph.in file: Phonon dispersion for monographene &inputph tr2_ph=1.0d-12, prefix='phmonog', ldisp=.true., lnscf=.true., nq1=16, nq2=16, nq3=1 amass(1)=12.00, outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', fildyn='phmgraphene.dyn', / q2r file: &input fildyn = 'phmgraphene.dyn', zasr = 'crystal' , flfrc = 'mgraph16160.fc' / matdyn.in file : &input asr = 'crystal', amass(1) = 12.00 , flfrc = 'mgraph16160.fc', flfrq = 'mgraph16160.freq', / 1000 0.00000000 0.00000000 0.00000000 1.000000e-03 0.00000000 0.00000000 0.10000000 1.000000e-03 0.00000000 0.00000000 0.20000000 1.000000e-03 0.00000000 0.00000000 0.30000000 1.000000e-03 0.00000000 0.00000000 0.40000000 1.000000e-03 0.00000000 0.00000000 0.50000000 1.000000e-03 0.00000000 0.00000000 0.60000000 1.000000e-03 0.00000000 0.00000000 0.70000000 1.000000e-03 ......................... Get a new e-mail account with Hotmail - Free. Sign-up now. -----Inline Attachment Follows----- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum _________________________________________________________________ http://clk.atdmt.com/UKM/go/197222280/direct/01/ We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100513/05eac753/attachment.htm From giannozz at democritos.it Thu May 13 19:56:51 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 13 May 2010 19:56:51 +0200 Subject: [Pw_forum] jagged phonon dispersion in graphene In-Reply-To: References: <810587.42975.qm@web65710.mail.ac4.yahoo.com> Message-ID: <08DFF0B2-0DE0-4A7A-827E-BF94B87EAB93@democritos.it> On May 13, 2010, at 19:44 , Elie Moujaes wrote: > I could not find it within the QE 4.2 package in PlotPhon/ --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From alex968873 at yahoo.com.cn Fri May 14 09:27:49 2010 From: alex968873 at yahoo.com.cn (=?utf-8?B?5p2O5paM?=) Date: Fri, 14 May 2010 15:27:49 +0800 (CST) Subject: [Pw_forum] =?utf-8?b?5Zue5aSN77yaIFB3X2ZvcnVtIERpZ2VzdCwgVm9sIDM1?= =?utf-8?q?=2C_Issue_25?= In-Reply-To: Message-ID: <505740.9233.qm@web15108.mail.cnb.yahoo.com> Thank you very much, Prof. Fratesi ! --- 10?5?14????, pw_forum-request at pwscf.org ??? > ???: pw_forum-request at pwscf.org > ??: Pw_forum Digest, Vol 35, Issue 25 > ???: pw_forum at pwscf.org > ??: 2010?5?14?,??,??12:40 > 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. Is there PBE UPF for K element ? (??) > ???2. Re: jagged phonon dispersion in > graphene (Eyvaz Isaev) > ???3. Re: Is there PBE UPF for K element ? > (Guido Fratesi) > ???4. 2 question about parallel computing > and Imaginary part??? of > ? ? ? dielectric (mohsen modaresi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 13 May 2010 19:19:00 +0800 (CST) > From: ?? > Subject: [Pw_forum] Is there PBE UPF for K element ? > To: pw_forum at pwscf.org > Message-ID: <861337.29167.qm at web15108.mail.cnb.yahoo.com> > Content-Type: text/plain; charset=gb2312 > > Dear all, > > I need a UPF using PBE Exchange-Correlation for K element, > because other elements in my material don't have PZ > Exchange-Correlation UPF, and using inconsistent DFT is > forbidden. Unfortunately, I can't find? any K.pbe...UPF > file in pseudo folder or QE website. So who can provide it > to me? Or give me some suggestion? Thank a lot in advance! > > > ************************** > > Li Bin > Department of Physics, Southeast University, PRC. > > *********************************************** > > > ? ? ? > > > > ------------------------------ > > Message: 2 > Date: Thu, 13 May 2010 06:31:39 -0700 (PDT) > From: Eyvaz Isaev > Subject: Re: [Pw_forum] jagged phonon dispersion in > graphene > To: PWSCF Forum > Message-ID: <810587.42975.qm at web65710.mail.ac4.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Elie, > > Have you tried PlotPhon utility from QE 4.2? Any troubles, > please contact me. > > 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 > > isaev at ifm.liu.se, > eyvaz_isaev at yahoo.com > > --- On Wed, 5/12/10, Elie Moujaes > wrote: > > From: Elie Moujaes > Subject: [Pw_forum] jagged phonon dispersion in graphene > To: pw_forum at pwscf.org > Date: Wednesday, May 12, 2010, 7:37 PM > > > > > Dear all, > > ? > > Hope you are all doing fine.? I am computing the phono > dispersion in graphene. I am using 1000 points in the > matdyn.in file and I used an 8x?8 x 1 grid but I get a > jagged dispersion spectrum. I tried even using a 16 x16 x1 > grid but almost got the same jagged results..I am not sure > why this happening. You will find attached the ps graph of > the dispersion. Below are all the input files. Thanks for > your help in advance. > > ? > > SCF calculation: > > ? > > control > ??? prefix='phmonog', > ??? calculation='scf', > ??? restart_mode='from_scratch', > ??? pseudo_dir = > '/exp/home/caiapo/emoujaes/espresso/espresso-4.1.3/pseudo/', > > ??? > outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/' > > ?/ > ?&system???? > ??? ibrav=? 4, celldm(1) =4.608737, celldm(3)=4.53666, > nat=2, ntyp= 1, > ??? ecutwfc = 60.D0, nosym=.true.,occupations='smearing', > smearing='XYZ', degauss=0.01, nelec=8 > / > ?&electrons > ??? conv_thr=1.D-8,????? > ??? mixing_beta=0.1D0, > ??? mixing_mode='local-TF' > ?/ > ATOMIC_SPECIES > ?C? 12.00000? C.pz-rrkjus.UPF > ATOMIC_POSITIONS crystal > ?C 0.000000? 0.000000 0.000000 1 1 1? > ?C 0.333333? -0.33333 0.000000 1 1 1? > K_POINTS automatic > 25 25 1 0 0 0 > ? > > Ph.in file: > > ? > > Phonon dispersion for monographene > ?&inputph > ? tr2_ph=1.0d-12, > ? prefix='phmonog', > ? ldisp=.true., > ? lnscf=.true., > ? nq1=16, nq2=16, nq3=1 > ? amass(1)=12.00, > ? > outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', > > ? fildyn='phmgraphene.dyn', > / > ? > q2r file: > ? > ?&input > ?fildyn = 'phmgraphene.dyn', > ?zasr = 'crystal' , > ?flfrc = 'mgraph16160.fc' > / > ? > matdyn.in file : > ? > &input > ?asr = 'crystal', > ?amass(1) = 12.00 , > ?flfrc = 'mgraph16160.fc', > ?flfrq = 'mgraph16160.freq', > / > 1000 > ? 0.00000000? 0.00000000? 0.00000000? 1.000000e-03? > ? 0.00000000? 0.00000000? 0.10000000? 1.000000e-03? > ? 0.00000000? 0.00000000? 0.20000000? 1.000000e-03? > ? 0.00000000? 0.00000000? 0.30000000? 1.000000e-03? > ? 0.00000000? 0.00000000? 0.40000000? 1.000000e-03? > ? 0.00000000? 0.00000000? 0.50000000? 1.000000e-03? > ? 0.00000000? 0.00000000? 0.60000000? 1.000000e-03? > ? 0.00000000? 0.00000000 ?0.70000000? 1.000000e-03? > ?? ......................... > ? > ??? > ???????? > ?????? ??? > ? > Get a new e-mail account with Hotmail - Free. Sign-up now. > > > -----Inline Attachment Follows----- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > ? ? ? > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100513/fc8503cb/attachment-0001.htm > > > ------------------------------ > > Message: 3 > Date: Thu, 13 May 2010 18:20:19 +0200 (CEST) > From: Guido Fratesi > Subject: Re: [Pw_forum] Is there PBE UPF for K element ? > To: PWSCF Forum > Message-ID: > ??? > Content-Type: text/plain; charset="iso-2022-jp" > > Dear Li Bin, > > > There is an extensive discussion on this subject in the > forum: see > http://www.democritos.it/pipermail/pw_forum/2007-September/007155.html > and following messages. > > > If you like the PZ pseudo for K which is available on the > Q-E website, you > could adapt it to PBE, as a starting point. See: > http://www.quantum-espresso.org/pseudo/upfdetails.php?upf=K.pz-sp-van.UPF > > That pseudo was generated by the Vanderbilt code "uspp". > You can find the > input for its generation in in > http://www.physics.rutgers.edu/~dhv/uspp/uspp-cur/Work/019-K/019-K-ca-sp-vgrp/ > > In the file k_ae_s1.adat change the variable exfact 0 -> > 5 (PBE). > You might have to change ifqopt 2 -> 3 (different augfun > pseudiz; 2 not > allowed for GGA, if I remember correctly) in the file > k_ps.adat. > > Finally, convert the resulting pseudopotential file to UPF > format with > uspp2upf.x (in espresso/upftools). > > I was doing this sometimes ago, and I was satisfied by > further enlarging > the parmeter of rinner to 0.95 (in the file k_ps.adat), > which enabled a > better convergence with respect to ecutrho. > > As always, tests are recommended... > > Hope this helps, > Guido > > > On Thu, 13 May 2010, ?? wrote: > > > Dear all, > > > > I need a UPF using PBE Exchange-Correlation for K > element, because other elements in my material don't have PZ > Exchange-Correlation UPF, and using inconsistent DFT is > forbidden. Unfortunately, I can't find? any K.pbe...UPF > file in pseudo folder or QE website. So who can provide it > to me? Or give me some suggestion? Thank a lot in advance! > > > > > > ************************** > > > > Li Bin > > Department of Physics, Southeast University, PRC. > > > > *********************************************** > > > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > Guido Fratesi > > Dipartimento di Scienza dei Materiali > Universita` degli Studi di Milano-Bicocca > > ------------------------------ > > Message: 4 > Date: Thu, 13 May 2010 21:10:05 +0430 > From: mohsen modaresi > Subject: [Pw_forum] 2 question about parallel computing and > Imaginary > ??? part??? of dielectric > To: PWSCF Forum > Message-ID: > ??? > Content-Type: text/plain; charset="iso-8859-1" > > Dear users, > 1) I want to calculate imaginary part of dielectric > function which can be > done with WIEN2k (for Ex. "Practical aspects of running the > WIEN2k code for > electron spectroscopy, > *Micron*Volume > 38, Issue 1, > January 2007, Pages 12-28"), Can Q.E do this kind of > calculation? > 2) For parallel computing the input file must be modified? > (in other word if > we run a program with 1CPU and then we want to run it with > N CPUs, we must > modify the input file) > Mohsen Modaresi > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100513/8dcd1ebd/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 35, Issue 25 > **************************************** > From giannozz at democritos.it Fri May 14 09:45:21 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 14 May 2010 09:45:21 +0200 Subject: [Pw_forum] 2 question about parallel computing and Imaginary part of dielectric In-Reply-To: References: Message-ID: <4BECFF91.6020201@democritos.it> mohsen modaresi wrote: > 1) I want to calculate imaginary part of dielectric function try code "epsilon.x", documentation in Doc/eps_man.tex > 2) For parallel computing the input file must be modified? no, you need only to specify appropriate command-line options P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From modaresi.mohsen at gmail.com Fri May 14 09:50:52 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Fri, 14 May 2010 12:20:52 +0430 Subject: [Pw_forum] 2 question about parallel computing and Imaginary part of dielectric In-Reply-To: <4BECFF91.6020201@democritos.it> References: <4BECFF91.6020201@democritos.it> Message-ID: Dear Paolo Thanks for your answer, It is helpful. Mohsen -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100514/611f7e89/attachment.htm From sd.wang000 at gmail.com Fri May 14 12:21:54 2010 From: sd.wang000 at gmail.com (shudong wang) Date: Fri, 14 May 2010 18:21:54 +0800 Subject: [Pw_forum] phonon lifetime Message-ID: Dear all: Can I get the phonon lifetime with pwscf code? Is anybody have some advice? Thanks in advance! S D Wang Southeast University,Nanjing,China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100514/e5ff82ea/attachment.htm From condmatter at gmail.com Fri May 14 12:57:18 2010 From: condmatter at gmail.com (shiningstar) Date: Fri, 14 May 2010 12:57:18 +0200 Subject: [Pw_forum] phonon lifetime In-Reply-To: References: Message-ID: Of course you can. SCF calculations and then phonon calculations fowlling by Anharmonic calculation. Using the calculated third-order energy derivative of potential to calculate the phonon lifetime for Umklapp phonon scattering. Read code please. 2010/5/14 shudong wang > Dear all: > Can I get the phonon lifetime with pwscf code? Is anybody have some advice? > > Thanks in advance! > > S D Wang > > Southeast University,Nanjing,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/20100514/876986eb/attachment.htm From jonathan.breeze at imperial.ac.uk Fri May 14 13:57:37 2010 From: jonathan.breeze at imperial.ac.uk (Jonathan Breeze) Date: Fri, 14 May 2010 12:57:37 +0100 Subject: [Pw_forum] phonon lifetime In-Reply-To: References: Message-ID: <1273838257.8855.22.camel@m65-precision> Dear S D Wang, Actually, as far as I am aware the d3.x code (part of espresso) calculates D3(q,-q,0), the 3rd-order anharmonic dynamical tensor that couples a zone centre (q=0) phonon to a pair of phonons with equal and opposite momentum (+/- q). Calculating the phonon lifetime requires an integration over the Brillouin zone. See the Debernardi paper for details: http://prl.aps.org/abstract/PRL/v75/i9/p1819_1 Also see: http://prb.aps.org/abstract/PRB/v76/i5/e054116 http://prb.aps.org/abstract/PRB/v69/i1/e014304 http://prb.aps.org/abstract/PRB/v69/i4/e045205 ? Regards, ?Jonathan Breeze Research Fellow Department of Materials Imperial College London On Fri, 2010-05-14 at 11:57 +0100, shiningstar wrote: > Of course you can. SCF calculations and then phonon calculations > fowlling by Anharmonic calculation. Using the calculated third-order > energy derivative of potential to calculate the phonon lifetime for > Umklapp phonon scattering. Read code please. > > 2010/5/14 shudong wang > Dear all: > Can I get the phonon lifetime with pwscf code? Is anybody have > some advice? > > Thanks in advance! > > S D Wang > > Southeast University,Nanjing,China > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From snd2mra at yahoo.com Fri May 14 15:49:27 2010 From: snd2mra at yahoo.com (Madan Mithra. L. M) Date: Fri, 14 May 2010 06:49:27 -0700 (PDT) Subject: [Pw_forum] Quantum ESPRESSO v.4.2 - Examples -results Message-ID: <260458.82374.qm@web53306.mail.re2.yahoo.com> Dear All, Giving feed back of the test run of Quantum ESPRESSO v.4.2. I compiled Quantum ESPRESSO v.4.2 in IBM 720 Cluster (XLF compiler, Linux, 64 bit, power5 processor), but when I ran the examples, a number of examples fail. I reduced the optimization level to -O0 and used the built- in lapack, Blas and FFTW routines, but there was no channge in the results - many of them failed dumping the core. On another machine (Dell Cluster, multicore, intel ifort 11.1 64 bit, Linux) I ran my test that uses EXX (PBE0), it showed segmentation fault. Same error was found with IBM XLF compiler too, on another machine when the EXX was tried. In all case both the built-in libraries as well as the architecture specific libraries were tried with no success. No code optimization was enabled. Here is the list of errors from the code compiled in IBM 02 :: running the phonon calculation at X for Si...Error condition encountered during test: exit status = 139 (CORE Dump) 06 :: running the phonon calculation ...Error condition encountered 07 :: running the el-ph calculation...Error condition encountered (CORE Dump) 09 :: running normal mode calculation for CH4...Error condition encountered (CORE Dump) 14 :: running the phonon calculation for Si at Gamma...Error condition encountered (CORE Dump) 15 :: running the response calculation...Error condition encountered (CORE Dump) 22 :: running the phonon calculation for Pt with spin-orbit coupling...Error condition (CORE Dump) 24 :: running ph.x at Gamma for Pt with gga-pbe and spin-orbit coupling...Error condition (CORE Dump) 32 :: running the phonon calculation for C at Gamma...Error condition encountered (CORE Dump) 33 :: running the dynamic polarizability calculation ...Error condition encountered (CORE Dump) 35 :: running ph.x at Gamma for Si with gga-pbe and spin-orbit coupling...Error condition (CORE Dump) - Madan Madan Mithra .L.M Senior Research Fellow Dept.of Physics Indian Institute of Science Bangalore - 560 012 INDIA ......................................... e-mail : mit at physics.iisc.ernet.in : snd2mra at yahoo.com Phone : 91-80-22932313 (Lab) FAX : (080) 360 2602 ......................................... --- On Wed, 5/12/10, Paolo Giannozzi wrote: > From: Paolo Giannozzi > Subject: [Pw_users] Quantum ESPRESSO v.4.2 > To: "pw_users" , "PWSCF Forum" > Date: Wednesday, May 12, 2010, 3:17 PM > Version 4.2 of the Quantum ESPRESSO > distribution is available for > download from the website http://www.quantum-espresso.org . This > release contains the following improvements over previous > versions: > > * HSE exchange-correlation functionals > (courtesy of Hannu-Pekka > Komsa) > * New package GWW for GW calculations with > Wannier functions > (courtesy of Geoffrey Stenuit and > Paolo Umari) > * Grid parallelization for the phonon code > * Improved mixed openMP-MPI parallelization > * Martyna-Tuckerman algorithm for isolated > systems > > plus other minor improvements and bug fixes (see file > Doc/release- > notes). > > Everybody who is using the Quantum-ESPRESSO distribution is > encouraged > to upgrade and to report problems to the mailing list. > > The Quantum ESPRESSO group > --- > Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Fri May 14 16:16:03 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 14 May 2010 16:16:03 +0200 Subject: [Pw_forum] Quantum ESPRESSO v.4.2 - Examples -results In-Reply-To: <260458.82374.qm@web53306.mail.re2.yahoo.com> References: <260458.82374.qm@web53306.mail.re2.yahoo.com> Message-ID: <4BED5B23.9080409@democritos.it> Madan Mithra. L. M wrote: > a number of examples fail it looks like the phonon code is miscompiled. If you do not find where and why (and a workaround), you should complain with IBM > I ran my test that uses EXX (PBE0), it showed segmentation fault what about the examples in in examples/EXX_examples? do they work? P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From sd.wang000 at gmail.com Sat May 15 09:50:42 2010 From: sd.wang000 at gmail.com (shudong wang) Date: Sat, 15 May 2010 15:50:42 +0800 Subject: [Pw_forum] ESPRESSO-4.2 Message-ID: Dear developers: I use v4.2 do relax calculation,but it appears: Message from routine iosys: pot_extrapolation='second_order' not available, using 'atomic' Message from routine iosys: wfc_extrapolation='second_order' not available, using 'atomic' my input file is : &control title='go' calculation='relax', restart_mode='from_scratch', prefix='go' pseudo_dir = '/home/sdwang/espresso-4.1.2/pseudo', outdir='/home/sdwang/GO/go/tmp' tprnfor=.true. tstress=.true. / &system ibrav = 8, celldm(1)=4.650,celldm(2)=1.7317, celldm(3)=7.3170 ,nat=6, ntyp=2, ecutwfc = 40.0,occupations='smearing',degauss=0.01,smearing='gaussian' / &electrons mixing_beta = 0.7 conv_thr = 1.0d-8 / &ions ion_dynamics='bfgs', bfgs_ndim=1, pot_extrapolation="second_order", wfc_extrapolation="second_order", / ATOMIC_SPECIES C 12.0 C.pz-vbc.UPF O 16.0 O.pz-mt.UPF ATOMIC_POSITIONS (crystal) C 0.24680 0.16962 0.07944 C 0.74680 0.33632 0.07944 C 0.24680 0.83642 0.07944 C 0.74680 0.66972 0.07944 O 0.77674 0.49750 0.15405 O 0.23131 0.98180 0.00297 K_POINTS (automatic) 7 7 1 0 00 What is the problem? Thanks! S D Wang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100515/200daf85/attachment.htm From giannozz at democritos.it Sat May 15 12:53:53 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 15 May 2010 12:53:53 +0200 Subject: [Pw_forum] ESPRESSO-4.2 In-Reply-To: References: Message-ID: On May 15, 2010, at 9:50 , shudong wang wrote: > What is the problem? there is no problem. Extrapolation should be used only for molecular dynamics. 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 nkxirainbow at gmail.com Sat May 15 16:21:47 2010 From: nkxirainbow at gmail.com (xirainbow) Date: Sat, 15 May 2010 14:21:47 +0000 Subject: [Pw_forum] What is the unit of q point in ph.x output file? Message-ID: Dear all: I have *four* little question about q point in ph.x and I use quantum espresso 4.0.4. *Question one: *How to write the input file of ph.x to get phonon dispersion along a special line. For example, 10 q-points from Gama(0 0 0) to M(0.5 0 0) in graphene? In the output file of ph.x for only one q point, it write : " * ...........* * Diagonalizing the dynamical matrix* * q = ( 0.501273548 0.501273548 0.501273548 ) * * ...........* " *Question two:* What is the unit of q point? I tried two kinds to specify the q point in input file. One is : " * ............* * ldisp = .true.,* * nq1 = 4 ,* * nq2 = 4 ,* * nq3 = 4 ,* * iq1 = 4 ,* * iq2 = 2 ,* * iq3 = 2 ,* * ............* " Then I get the following output: " * Dynamical matrices for ( 4, 4, 4,) uniform grid of q-points* * with only ( 4, 2, 2,) point requested* * ( 1q-points):* * N xq(1) xq(2) xq(3) * * 1 0.50000 0.50000 0.50000 "* * Calculation of q = 0.5000 0.5000 0.5000* * * * reciprocal axes: (cart. coord. in units 2 pi/a_0)* * b(1) = ( 1.000000 -1.000000 0.000000 ) * * b(2) = ( 0.000000 1.000000 1.742637 ) * * b(3) = ( -1.000000 0.000000 1.742637 ) * " *Question three:* Why *q= 0.5 0.5 0.5?* I think it should be *q= -0.5 0.5 0.8713185.* The other method to specify q point in input file is as below: " * .......* * ldisp = .false.,* * .......* * /* * 0.5000000 -0.5000000 0.8713186 * " Then I get the following result: " * reciprocal axes: (cart. coord. in units 2 pi/a_0)* * b(1) = ( 1.000000 -1.000000 0.000000 ) * * b(2) = ( 0.000000 1.000000 1.742637 ) * * b(3) = ( -1.000000 0.000000 1.742637 ) * * * * Diagonalizing the dynamical matrix* * q = ( 0.500000000 -0.500000000 0.871318600 ) * " *Question four: Is unit of q point for "ldisp = .true." and "ldisp = .false." the same? * * * *Thanks in advance??* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100515/4bc868d4/attachment.htm From vparkash at mtu.edu Sun May 16 01:23:55 2010 From: vparkash at mtu.edu (Vidur Parkash) Date: Sat, 15 May 2010 16:23:55 -0700 (PDT) Subject: [Pw_forum] Question on epsilon.x Message-ID: <94938.10910.qm@web33005.mail.mud.yahoo.com> Hi everybody I was doing some computations on dielectric functions, and noticed a 'shift' parameter that offsets the imaginary part of the dielectric function by some value. I wanted to know why is the parameter needed anyway, and how do we decide what value is used Vidur Vidur Parkash, Ph.D Candidate Electrical & Computer Engineering Michigan Technological University 716 EERC, 1400 Townsend Drive Houghton, MI-49931, USA Tel: 1-906-487-0023 From padmaja_patnaik at yahoo.co.uk Sun May 16 04:31:49 2010 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Sun, 16 May 2010 02:31:49 +0000 (GMT) Subject: [Pw_forum] Doubt in starting magnetization value Message-ID: <133173.17118.qm@web26102.mail.ukl.yahoo.com> Dear all I have the following doubt. Is it possible that in a non magnetic sample, when i perform the scf calculations with a small value of starting magnetization (starting_magnetization=0.5) for each type of atom in the sample, then the final value of 'total magnetization' obtained will be some positive value? I expect that 'total magnetization' to be zero irrespective is the starting magnetization value as the sample is non-magnetic. 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/20100516/31aa2908/attachment.htm From nkxirainbow at gmail.com Sun May 16 05:17:59 2010 From: nkxirainbow at gmail.com (xirainbow) Date: Sun, 16 May 2010 03:17:59 +0000 Subject: [Pw_forum] What is the unit of q point in ph.x output file? In-Reply-To: References: Message-ID: Dear developers: I found a confusing thing. *Maybe it is a bug.* I try ph.x in quantum espresso 4.2. input file: " * &INPUTPH* * ............* * ldisp = .true.,* * nq1 = 4 ,* * nq2 = 4 ,* * nq3 = 4 ,* * ............* " output file: " * reciprocal axes: (cart. coord. in units 2 pi/a_0)* * b(1) = ( 1.0000 -1.0000 0.0000 ) * * b(2) = ( 0.0000 1.0000 1.7426 ) * * b(3) = ( -1.0000 0.0000 1.7426 ) * * Dynamical matrices for ( 4, 4, 4,) uniform grid of q-points* * ( 13q-points):* * N xq(1) xq(2) xq(3) * * 1 0.000000000 0.000000000 0.000000000* * 2 -0.250000000 0.000000000 0.435659282* * 3 0.500000000 0.000000000 -0.871318563* * 4 -0.250000000 0.250000000 0.871318563* * 5 0.500000000 0.250000000 -0.435659282* * 6 0.250000000 0.250000000 0.000000000* * 7 0.500000000 -0.500000000 -1.742637127* * 8 0.000000000 0.000000000 0.871318563* * 9 0.750000000 0.000000000 -0.435659282* * 10 0.500000000 0.000000000 0.000000000* * 11 0.750000000 -0.750000000 -1.742637127* * 12 0.500000000 -0.500000000 -0.871318563* * 13 0.000000000 0.000000000 -1.742637127* " I can understand the above output information. And I try another input method: " * &INPUTPH* * ............* * ldisp = .true.,* * nq1 = 4 ,* * nq2 = 4 ,* * nq3 = 4 ,* * iq1 = 4 ,* * iq2 = 2 ,* * iq3 = 2 ,* * ............* " output file: " * reciprocal axes: (cart. coord. in units 2 pi/a_0)* * b(1) = ( 1.0000 -1.0000 0.0000 ) * * b(2) = ( 0.0000 1.0000 1.7426 ) * * b(3) = ( -1.0000 0.0000 1.7426 ) * * * * Computing dynamical matrix for * * q = ( 0.5000000 0.5000000 0.5000000 )* " Howver, I failed to understand the * q = ( 0.5000000 0.5000000 0.5000000 )*. * * *"q = ( 0.5000000 0.5000000 0.5000000 )" *does not appear in the 13 q points: * Dynamical matrices for ( 4, 4, 4,) uniform grid of q-points ( 13q-points): N xq(1) xq(2) xq(3) 1 0.000000000 0.000000000 0.000000000 2 -0.250000000 0.000000000 0.435659282 3 0.500000000 0.000000000 -0.871318563 4 -0.250000000 0.250000000 0.871318563 5 0.500000000 0.250000000 -0.435659282 6 0.250000000 0.250000000 0.000000000 7 0.500000000 -0.500000000 -1.742637127 8 0.000000000 0.000000000 0.871318563 9 0.750000000 0.000000000 -0.435659282 10 0.500000000 0.000000000 0.000000000 11 0.750000000 -0.750000000 -1.742637127 12 0.500000000 -0.500000000 -0.871318563 13 0.000000000 0.000000000 -1.742637127 * *Does is a bug?* Bye the way, do all these q points are given in the *(cart. coord. in units 2 pi/a_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/20100516/559f83ff/attachment-0001.htm From ferretti at mit.edu Sun May 16 14:40:54 2010 From: ferretti at mit.edu (Andrea Ferretti) Date: Sun, 16 May 2010 13:40:54 +0100 (BST) Subject: [Pw_forum] Question on epsilon.x In-Reply-To: <94938.10910.qm@web33005.mail.mud.yahoo.com> References: <94938.10910.qm@web33005.mail.mud.yahoo.com> Message-ID: Dear Vidur, the "shift" parameter is used in epsilon.x to shift the transition energies (computed as differences of eigenvalues, thus "shift" works as a scissor operator). Imposing a non-zero shift value basically changes the origin of the frequency axis in the spectra. If you do not have any special reason to use it (eg set empirically the DFT kohn-sham gap close to the experimental one, etc), just set it to zero (or leave it out of the namelist) Andrea > > I was doing some computations on dielectric functions, and noticed a > 'shift' parameter that offsets the imaginary part of the dielectric function by some value. > > I wanted to know why is the parameter needed anyway, and how do we decide what value is used > > Vidur > > Vidur Parkash, Ph.D Candidate > Electrical & Computer Engineering > Michigan Technological University > 716 EERC, 1400 Townsend Drive > Houghton, MI-49931, USA > Tel: 1-906-487-0023 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Andrea Ferretti Oxford University, Department of Materials Parks Road, Oxford OX1 3PH, UK Tel: +44 (0)1865 612796; 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 baroni at sissa.it Sun May 16 18:22:14 2010 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 16 May 2010 18:22:14 +0200 Subject: [Pw_forum] Doubt in starting magnetization value In-Reply-To: <133173.17118.qm@web26102.mail.ukl.yahoo.com> References: <133173.17118.qm@web26102.mail.ukl.yahoo.com> Message-ID: may be your allegedly "non-magnetic" material is actually magnetic? (or at least predicted to be so by the XC functional you are using ...) SB On May 16, 2010, at 4:31 AM, Padmaja Patnaik wrote: > Dear all > > I have the following doubt. Is it possible that in a non magnetic sample, when i perform the scf calculations with a small value of starting magnetization (starting_magnetization=0.5) for each type of atom in the sample, then the final value of 'total magnetization' obtained will be some positive value? I expect that 'total magnetization' to be zero irrespective is the starting magnetization value as the sample is non-magnetic. > > 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/20100516/762adc56/attachment.htm From bipulrr at gmail.com Mon May 17 08:40:23 2010 From: bipulrr at gmail.com (Bipul Rakshit) Date: Mon, 17 May 2010 12:10:23 +0530 Subject: [Pw_forum] How to specify spin for individual atoms Message-ID: Dear Users, I am doing a system in which i have 8 Mn. Following is the atomic positions in fractional co-ordinate. Mn1 0.12500000000 0.25000000000 0.27940000000 + Mn1 0.37500000000 0.75000000000 0.72060000000 + Mn2 0.12500000000 0.25000000000 0.74860000000 - Mn2 0.37500000000 0.75000000000 0.25140000000 - Mn1 0.62500000000 0.25000000000 0.27940000000 - Mn1 0.87500000000 0.75000000000 0.72060000000 - Mn2 0.62500000000 0.25000000000 0.74860000000 + Mn2 0.87500000000 0.75000000000 0.25140000000 + Now i want to specify the spin as shown by the last column, (with + & - signs). So can you please tell me what flags i have to use to specify the magnetic spin for particular atom. -- 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/20100517/87eed91b/attachment.htm From baris.malcioglu at gmail.com Mon May 17 09:51:04 2010 From: baris.malcioglu at gmail.com (O. Baris Malcioglu) Date: Mon, 17 May 2010 10:51:04 +0300 Subject: [Pw_forum] How to specify spin for individual atoms In-Reply-To: References: Message-ID: Dear Bipul Rakshit, Please take a glance at "starting_magnetization" under the system namelist. You can find the relevant information in the supplied documentation directory. Best, Baris 2010/5/17 Bipul Rakshit : > Dear Users, > I am doing a system in which i have 8 Mn. > Following is the atomic positions in fractional co-ordinate. > > Mn1????? 0.12500000000????? 0.25000000000????? 0.27940000000??? + > Mn1????? 0.37500000000????? 0.75000000000????? 0.72060000000??? + > Mn2????? 0.12500000000????? 0.25000000000????? 0.74860000000??? - > Mn2????? 0.37500000000????? 0.75000000000????? 0.25140000000??? - > Mn1????? 0.62500000000????? 0.25000000000????? 0.27940000000??? - > Mn1????? 0.87500000000????? 0.75000000000????? 0.72060000000??? - > Mn2????? 0.62500000000????? 0.25000000000????? 0.74860000000??? + > Mn2????? 0.87500000000????? 0.75000000000????? 0.25140000000??? + > > > Now i want to specify the spin as shown by the last column, (with + & - > signs). > So can? you please tell me what flags i have to use to specify the magnetic > spin for particular atom. > -- > ?Bipul Rakshit > Research Fellow, > 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 > > From bipulrr at gmail.com Mon May 17 10:11:12 2010 From: bipulrr at gmail.com (Bipul Rakshit) Date: Mon, 17 May 2010 13:41:12 +0530 Subject: [Pw_forum] How to specify spin for individual atoms In-Reply-To: References: Message-ID: Dear Baris, thanks for your kind reply. I go through the "starting_magnetization" and the related documents. But with the help of that flag, we can specify the magnetic moment to particular type. But if u see the atomic co-ordinate i gave there i require the Mn1 spin up & down, and Mn2 spin up & down. So that's i didnt understand how do i specify the spins for particular atoms not with particular type. On Mon, May 17, 2010 at 1:21 PM, O. Baris Malcioglu < baris.malcioglu at gmail.com> wrote: > Dear Bipul Rakshit, > > Please take a glance at "starting_magnetization" under the system > namelist. You can find the relevant information in the supplied > documentation directory. > > Best, > Baris > > > 2010/5/17 Bipul Rakshit : > > Dear Users, > > I am doing a system in which i have 8 Mn. > > Following is the atomic positions in fractional co-ordinate. > > > > Mn1 0.12500000000 0.25000000000 0.27940000000 + > > Mn1 0.37500000000 0.75000000000 0.72060000000 + > > Mn2 0.12500000000 0.25000000000 0.74860000000 - > > Mn2 0.37500000000 0.75000000000 0.25140000000 - > > Mn1 0.62500000000 0.25000000000 0.27940000000 - > > Mn1 0.87500000000 0.75000000000 0.72060000000 - > > Mn2 0.62500000000 0.25000000000 0.74860000000 + > > Mn2 0.87500000000 0.75000000000 0.25140000000 + > > > > > > Now i want to specify the spin as shown by the last column, (with + & - > > signs). > > So can you please tell me what flags i have to use to specify the > magnetic > > spin for particular atom. > > -- > > Bipul Rakshit > > Research Fellow, > > 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 > > > > > _______________________________________________ > 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/20100517/1bcafbf6/attachment.htm From paulatto at sissa.it Mon May 17 10:13:47 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 17 May 2010 10:13:47 +0200 Subject: [Pw_forum] How to specify spin for individual atoms In-Reply-To: References: Message-ID: On Mon, 17 May 2010 10:11:12 +0200, Bipul Rakshit wrote: > But if u see the atomic co-ordinate i gave there i require the Mn1 spin > up & down, and Mn2 spin up & down. Dear Bipul, all the point of defining two different fake types for a single element is to give them different magnetization. Can't you just call Mn1 all the ones with spin up and Mn2 all the ones with spin down? Otherwise, you'll have to do Mn1, Mn2, Mn3, Mn4... regards -- Lorenzo Paulatto *** Note: my affiliation has changed! please send future correspondence to: *** post-doc @ IMPMC/UPMC - Universit? Paris 6 phone: +33 (0)1 44 27 74 89 www: http://www-int.impmc.upmc.fr/~paulatto/ previously: phd student @ SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 www: http://people.sissa.it/~paulatto/ From paulatto at sissa.it Mon May 17 10:26:20 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 17 May 2010 10:26:20 +0200 Subject: [Pw_forum] What is the unit of q point in ph.x output file? In-Reply-To: References: Message-ID: On Sat, 15 May 2010 16:21:47 +0200, xirainbow wrote: > *Question one: *How to write the input file of ph.x to get phonon > dispersion along a special line. There is a set of scripts from Eyvaz Isaev that does that, I think. They should be included in the most recent version of QE. However, the standard way to do it is compute phonons on a regular grid and then use Fourier interpolation to have a nice smooth curve along the path of your choice. See example06 for details. > *Question two:* What is the unit of q point? It is 2 pi/alat, where alat is the lattice parameter (i.e. what you specified as celldm(1), or as "a" in the pw.x calcualtion) > * Dynamical matrices for ( 4, 4, 4,) uniform grid of q-points* > * with only ( 4, 2, 2,) point requested* > * ( 1q-points):* > * N xq(1) xq(2) xq(3) * > * 1 0.50000 0.50000 0.50000 "* > * Calculation of q = 0.5000 0.5000 0.5000* > *Question three:* Why *q= 0.5 0.5 0.5?* > I think it should be *q= -0.5 0.5 0.8713185.* I think you are right, well actually it would be 0.5 -0.5 0.8713185. But I've noticed that the subroutine computing the value of the q-point is actually called *after* the one the prints it; I guess the calculation is probably done at the correct point, it is the output on screen that is wrong. At the end of the calculation you can check inside the dynamical matrix file (matdyn) to be sure. > *Question four: Is unit of q point for "ldisp = .true." and "ldisp = > .false." the same? * Yes, I think it is just the problem is the one I was stating above. > *Thanks in advance??* you're welcome, thank you for reporting -- Lorenzo Paulatto *** Note: my affiliation has changed! please send future correspondence to: *** post-doc @ IMPMC/UPMC - Universit? Paris 6 phone: +33 (0)1 44 27 74 89 www: http://www-int.impmc.upmc.fr/~paulatto/ previously: phd student @ SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 www: http://people.sissa.it/~paulatto/ From baris.malcioglu at gmail.com Mon May 17 10:37:33 2010 From: baris.malcioglu at gmail.com (Osman Baris Malcioglu) Date: Mon, 17 May 2010 11:37:33 +0300 Subject: [Pw_forum] How to specify spin for individual atoms In-Reply-To: References: Message-ID: <311ABD67-4D63-40D7-8C68-906551572520@gmail.com> Dear Bipul, Please also read the section "atomic species" in the documentation. You can have several different types that all use the same pp. On 17.May.2010, at 11:11, Bipul Rakshit wrote: > Dear Baris, > thanks for your kind reply. I go through the "starting_magnetization" and the related documents. But with the help of that flag, we can specify the magnetic moment to particular type. But if u see the atomic co-ordinate i gave there i require the Mn1 spin up & down, and Mn2 spin up & down. > > So that's i didnt understand how do i specify the spins for particular atoms not with particular type. > > On Mon, May 17, 2010 at 1:21 PM, O. Baris Malcioglu wrote: > Dear Bipul Rakshit, > > Please take a glance at "starting_magnetization" under the system > namelist. You can find the relevant information in the supplied > documentation directory. > > Best, > Baris > > > 2010/5/17 Bipul Rakshit : > > Dear Users, > > I am doing a system in which i have 8 Mn. > > Following is the atomic positions in fractional co-ordinate. > > > > Mn1 0.12500000000 0.25000000000 0.27940000000 + > > Mn1 0.37500000000 0.75000000000 0.72060000000 + > > Mn2 0.12500000000 0.25000000000 0.74860000000 - > > Mn2 0.37500000000 0.75000000000 0.25140000000 - > > Mn1 0.62500000000 0.25000000000 0.27940000000 - > > Mn1 0.87500000000 0.75000000000 0.72060000000 - > > Mn2 0.62500000000 0.25000000000 0.74860000000 + > > Mn2 0.87500000000 0.75000000000 0.25140000000 + > > > > > > Now i want to specify the spin as shown by the last column, (with + & - > > signs). > > So can you please tell me what flags i have to use to specify the magnetic > > spin for particular atom. > > -- > > Bipul Rakshit > > Research Fellow, > > 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 > > > > > _______________________________________________ > 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 > _______________________________________________ > 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/20100517/3a44cec4/attachment-0001.htm From nkxirainbow at gmail.com Mon May 17 10:58:10 2010 From: nkxirainbow at gmail.com (xirainbow) Date: Mon, 17 May 2010 08:58:10 +0000 Subject: [Pw_forum] What is the unit of q point in ph.x output file? In-Reply-To: References: Message-ID: Dear Lorenzo Paulatto: On Mon, May 17, 2010 at 8:26 AM, Lorenzo Paulatto wrote: > On Sat, 15 May 2010 16:21:47 +0200, xirainbow > > > * Dynamical matrices for ( 4, 4, 4,) uniform grid of q-points* > > * with only ( 4, 2, 2,) point requested* > > * ( 1q-points):* > > * N xq(1) xq(2) xq(3) * > > * 1 0.50000 0.50000 0.50000 "* > > * Calculation of q = 0.5000 0.5000 0.5000* > > *Question three:* Why *q= 0.5 0.5 0.5?* > > I think it should be *q= -0.5 0.5 0.8713185.* > > I think you are right, well actually it would be 0.5 -0.5 0.8713185. > But I've noticed that the subroutine computing the value of the q-point is > actually called *after* the one the prints it; I guess the calculation is > probably done at the correct point, it is the output on screen that is > wrong. At the end of the calculation you can check inside the dynamical > matrix file (matdyn) to be sure. > > *Firstly?thank you for your patient reply??** * Secondly, in my output file, the frequency, degeneracy and symmetry of the phonon * Dynamical matrices for ( 4, 4, 4,) uniform grid of q-points** * with only ( 4, 2, 2,) point requested** * ( 1q-points):** * N xq(1) xq(2) xq(3) ** * 1 0.50000 0.50000 0.50000 "** are absolutely different from " * .......* * ldisp = .false.,* * .......* * /* * 0.5000000 -0.5000000 0.8713186 * " Unfortunately, I have deleted these output files. If you need, I will recalculate them and send it to you. -- ____________________________________ 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/20100517/a83a2560/attachment.htm From giannozz at democritos.it Mon May 17 12:50:45 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 17 May 2010 12:50:45 +0200 Subject: [Pw_forum] What is the unit of q point in ph.x output file? In-Reply-To: References: Message-ID: <4BF11F85.1080500@democritos.it> If you need to calculate dispersions running one q-point at the time, please use start_q and last_q. The alternative way with iq1,iq2,iq3 is clumsy and obsolete P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From sd.wang000 at gmail.com Mon May 17 14:59:40 2010 From: sd.wang000 at gmail.com (shudong wang) Date: Mon, 17 May 2010 20:59:40 +0800 Subject: [Pw_forum] band jagged Message-ID: Dear developers; I used v4.2 to calculate band structures of graphene,but the structures have a jagged behaviour in high energy region. Why it is ? Thanks! S D Wang Southeast University ,Nanjing,China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100517/8e37d854/attachment.htm From marzari at MIT.EDU Mon May 17 15:01:26 2010 From: marzari at MIT.EDU (Nicola Marzari) Date: Mon, 17 May 2010 14:01:26 +0100 Subject: [Pw_forum] band jagged In-Reply-To: References: Message-ID: <4BF13E26.3040905@mit.edu> shudong wang wrote: > Dear developers; > I used v4.2 to calculate band structures of graphene,but the > structures have a jagged behaviour in high energy region. Why it is ? > > Thanks! > > S D Wang > > Southeast University ,Nanjing,China Hi, can you try redoing the calculation using option "atomic+random" as a start point for the wavefunction, and report back to us (do you still get the jagged behavior, or not). Thanks, 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 giannozz at democritos.it Mon May 17 16:31:20 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 17 May 2010 16:31:20 +0200 Subject: [Pw_forum] band jagged In-Reply-To: <4BF13E26.3040905@mit.edu> References: <4BF13E26.3040905@mit.edu> Message-ID: <4BF15338.7090008@democritos.it> Nicola Marzari wrote: > can you try redoing the calculation using option "atomic+random" as a > start point it should already be the default Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From modaresi.mohsen at gmail.com Mon May 17 16:34:25 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Mon, 17 May 2010 19:04:25 +0430 Subject: [Pw_forum] Question on epsilon.x In-Reply-To: References: <94938.10910.qm@web33005.mail.mud.yahoo.com> Message-ID: Dear all, I have not any answer for this question, Actually I have a problem about eps.x, I can't understand this two parameters (intersmear, intrasmear). How can i determine (intersmear, intrasmear). Thanks for your answers From ferretti at mit.edu Mon May 17 17:07:29 2010 From: ferretti at mit.edu (Andrea Ferretti) Date: Mon, 17 May 2010 16:07:29 +0100 (BST) Subject: [Pw_forum] Question on epsilon.x In-Reply-To: References: <94938.10910.qm@web33005.mail.mud.yahoo.com> Message-ID: Dear Mohsen, the meaning of these parameters (smearing for inter and intra band transitions) is somehow explained in the epsilon.x manual, ~espresso/Doc/eps_man.pdf Andrea > Dear all, > I have not any answer for this question, Actually I have a problem > about eps.x, I can't understand this two parameters (intersmear, > intrasmear). > How can i determine (intersmear, intrasmear). > Thanks for your answers > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Andrea Ferretti Oxford University, Department of Materials Parks Road, Oxford OX1 3PH, UK Tel: +44 (0)1865 612796; 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 Mon May 17 17:37:33 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Mon, 17 May 2010 20:07:33 +0430 Subject: [Pw_forum] Question on epsilon.x In-Reply-To: References: <94938.10910.qm@web33005.mail.mud.yahoo.com> Message-ID: Dear Andrea, Thanks for your answer, I know the meaning of these parameters, I want to know how can i determine these parameters for a system (Like a CNT (6,0))? Thanks for your answers. Mohsen On Mon, May 17, 2010 at 7:37 PM, Andrea Ferretti wrote: > > > Dear Mohsen, > > the meaning of these parameters (smearing for inter and intra band > transitions) is somehow explained in the epsilon.x manual, > ~espresso/Doc/eps_man.pdf > > Andrea > > > > Dear all, > > I have not any answer for this question, Actually I have a problem > > about eps.x, I can't understand this two parameters (intersmear, > > intrasmear). > > How can i determine (intersmear, intrasmear). > > Thanks for your answers > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > Andrea Ferretti > Oxford University, Department of Materials > Parks Road, Oxford OX1 3PH, UK > Tel: +44 (0)1865 612796; 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 > _______________________________________________ > 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/20100517/ec708d1f/attachment.htm From ferretti at mit.edu Mon May 17 18:01:52 2010 From: ferretti at mit.edu (Andrea Ferretti) Date: Mon, 17 May 2010 17:01:52 +0100 (BST) Subject: [Pw_forum] Question on epsilon.x Message-ID: Hi Mohsen, the smearing technique is meant to be a numerical tool to perform the thermodynamic limit (# of kpts going to infinity, i.e. size of the system going from being finite to extended). The actual value of the smearing parameters thus depends on how far the evaluation of the limit is, i.e. on how many kpts you are using in the calculation. Generally, the bigger the # of kpts, the smaller the smearing can be. The smaller the smearing, the higher the accuracy of the final limit. But smearings that are too small (relative to the # of kpts) lead to unphysical features, especially in the spectra (due to the finiteness of the systems studied)... After all, the value of the smearing (and the number of kpts) depend on the accuracy you want to reach. (if you want eg to describe the 1/sqrt(E) divergences of a nanotube DOS and JDOS you probably need a lot of kpts). A rule of thumb to avoid spurious features is the following: given a finite mesh of kpts, the bands of the systems are discretized. The smearing parameter should be of the order of the difference in the eigenvalues (transition energies in your case) corresponding to nearby kpts (i.e., the smearing should be of the order of the discretization induced on the eigenvalues, or transition energies in the case of epsilon.x) practically, I would start with the default value of the smearing, and then check a posteriori. hope it helps Andrea > Dear Andrea, > Thanks for your answer, I know the meaning of these parameters, > I want to know how can i determine these parameters for a system > (Like a CNT (6,0))? > Thanks for your answers. > Mohsen > > On Mon, May 17, 2010 at 7:37 PM, Andrea Ferretti wrote: > > > Dear Mohsen, > > the meaning of these parameters (smearing for inter and intra band > transitions) is somehow explained in the epsilon.x manual, > ~espresso/Doc/eps_man.pdf > > Andrea > > > > Dear all, > > I have not any answer for this question, Actually I have a problem > > about eps.x, I can't understand this two parameters (intersmear, > > intrasmear). > > How can i determine (intersmear, intrasmear). > > Thanks for your answers > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > Andrea Ferretti > Oxford University, Department of Materials > Parks Road, Oxford OX1 3PH, UK > Tel: +44 (0)1865 612796; ?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 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- Andrea Ferretti Oxford University, Department of Materials Parks Road, Oxford OX1 3PH, UK Tel: +44 (0)1865 612796; 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 kopinjol at gmail.com Tue May 18 01:40:50 2010 From: kopinjol at gmail.com (Kopinjol Baishya) Date: Mon, 17 May 2010 18:40:50 -0500 Subject: [Pw_forum] parallel compilation Message-ID: Hi, I am trying to compile quantum espresso on our linux cluster. But every time i do configure i get the following message "Parallel environment not detected (is this a parallel machine?). Configured for compilation of serial executables." I have been able to compile other programs in parallel, VASP etc. and they are all compiled using "FC=mpif77". I tried the same with espresso, but i still get the same message! I have tried the last three versions all have failed to compile in parallel. I am little confused and not sure what may be going wrong. Any help will be greatly appreciated. Thanks in advance, kopinjol -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100517/838a03fd/attachment.htm From sd.wang000 at gmail.com Tue May 18 04:53:36 2010 From: sd.wang000 at gmail.com (shudong wang) Date: Tue, 18 May 2010 10:53:36 +0800 Subject: [Pw_forum] band jagged Message-ID: Dear developers: I used v4.1.2 recalculate it, it is well.My unit cell has 4C and 2O.Is there something different between v4.1.2 and v4.2? Why the v4.2 has a jagged band?Is it a bug? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100518/448c37c4/attachment.htm From jiachen at princeton.edu Tue May 18 05:49:48 2010 From: jiachen at princeton.edu (jia chen) Date: Mon, 17 May 2010 23:49:48 -0400 Subject: [Pw_forum] failure to restart a cp calculation from pwscf restart files in spin polarized cases Message-ID: Dear All, I am trying to restart cp calculations from pwscf restart files. It works very well in spin-unpolarized cases but fails when I need spin polarization. Actually, I tried version 3.2, 4.1.1, 4.2, they all suffer the same problem. I think it is a very nice feature. So, I will be greatly appreciate if anyone can fix this problem or give me some hint about how to make it work. Following is error message from 4.2, hope it is helpful. Thank you in advance ############################# # FROM IOTK LIBRARY, VERSION 1.2.0 # UNRECOVERABLE ERROR (ierr=-1) # ERROR IN: iotk_scan_attr (iotk_attr.spp:453) # CVS Revision: 1.21 # Attribute not found name=UP ############################# Regards -- Jia Chen Dept of Chemistry Princeton University Princeton, NJ 08544 From padmaja_patnaik at yahoo.co.uk Tue May 18 06:51:22 2010 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Tue, 18 May 2010 04:51:22 +0000 (GMT) Subject: [Pw_forum] Pw_forum Digest, Vol 35, Issue 29 In-Reply-To: Message-ID: <405043.26623.qm@web26105.mail.ukl.yahoo.com> Thank you for your response. Will check as per your advise. Padmaja Patnaik Research Scholar Dept of Physics IIT Bombay Mumbai, India Message: 2 Date: Sun, 16 May 2010 18:22:14 +0200 From: Stefano Baroni Subject: Re: [Pw_forum] Doubt in starting magnetization value To: PWSCF Forum Message-ID: Content-Type: text/plain; charset="iso-8859-1" may be your allegedly "non-magnetic" material is actually magnetic? (or at least predicted to be so by the XC functional you are using ...) SB On May 16, 2010, at 4:31 AM, Padmaja Patnaik wrote: > Dear all > > I have the following doubt. Is it possible that in a non magnetic sample, when i perform the scf calculations with a small value of starting magnetization (starting_magnetization=0.5) for each type of atom in the sample, then the final value of 'total magnetization' obtained will be some positive value? I expect that 'total magnetization' to be zero irrespective is the starting magnetization value as the sample is non-magnetic. > > 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/20100516/762adc56/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 35, Issue 29 **************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100518/f1e2fd13/attachment.htm From baris.malcioglu at gmail.com Tue May 18 07:08:33 2010 From: baris.malcioglu at gmail.com (Osman Baris Malcioglu) Date: Tue, 18 May 2010 08:08:33 +0300 Subject: [Pw_forum] parallel compilation In-Reply-To: References: Message-ID: <2B2DA8A6-F1FA-4373-ACB2-D98E6546BE5F@gmail.com> Dear Kopinjol, What does mpif77 wrap? Quantum Espresso requires a fortran90 compiler (or above), which is usually wrapped as mpif90 not mpif77. Since configure does not return an error, you probably have a fortran 90 compiler in your path, but your mpi environment is not configured properly. Consult your system admin. Tip : just type configure, without setting any environment flags, if you have everything listed in PATH, configure should find the proper ones for you. Best, Baris On 18.May.2010, at 02:40, Kopinjol Baishya wrote: > Hi, > > I am trying to compile quantum espresso on our linux cluster. But every time i do configure i get the following message > > "Parallel environment not detected (is this a parallel machine?). > Configured for compilation of serial executables." > > I have been able to compile other programs in parallel, VASP etc. and they are all compiled using "FC=mpif77". I tried the same with espresso, but i still get the same message! I have tried the last three versions all have failed to compile in parallel. > > I am little confused and not sure what may be going wrong. Any help will be greatly appreciated. > > Thanks in advance, > kopinjol > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at democritos.it Tue May 18 08:07:50 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 18 May 2010 08:07:50 +0200 Subject: [Pw_forum] band jagged In-Reply-To: References: Message-ID: <202543B5-F20E-4AFF-99A9-06E7C8D4A37B@democritos.it> On May 18, 2010, at 4:53 , shudong wang wrote: > I used v4.1.2 recalculate it, it is well.My unit cell has 4C and 2O. > Is there something different between v4.1.2 and v4.2? Why the > v4.2 has a jagged band?Is it a bug? please file a bug report on qe-forge.org, or provide a test job 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 May 18 14:07:24 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 18 May 2010 14:07:24 +0200 Subject: [Pw_forum] band jagged In-Reply-To: References: Message-ID: Il giorno 18/mag/10, alle ore 04:53, shudong wang ha scritto: > Dear developers: > > I used v4.1.2 recalculate it, it is well.My unit cell has 4C and 2O. In your first email you were speaking of graphene... are you comparing the same system? GS > Is there something different between v4.1.2 and v4.2? Why the v4.2 > has a jagged band?Is it a bug? > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100518/f0b7df7f/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 1753 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100518/f0b7df7f/attachment.bin From pc229 at kent.ac.uk Tue May 18 14:30:00 2010 From: pc229 at kent.ac.uk (P.Canepa) Date: Tue, 18 May 2010 13:30:00 +0100 Subject: [Pw_forum] PAW pseudopotentials in QE Message-ID: <42054E10C02CD44D81EF510077A30A073829ED4976@MAPI.ad.kent.ac.uk> Dear all, on the web-page of Quantum Espresso is claimed that PWscf can use projector augmented pseudo-potentials (PAW). Is there any label which marks those at the http://www.quantum-espresso.org/pseudo.php . For instance if I look at one common elements like O I cannot find any PAW pseudopotentials. Thanks, Piero -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc229 at kent.ac.uk mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- From mambom1902 at yahoo.com Tue May 18 18:02:07 2010 From: mambom1902 at yahoo.com (loc duong ding) Date: Tue, 18 May 2010 09:02:07 -0700 (PDT) Subject: [Pw_forum] Stress contraint Message-ID: <383969.29789.qm@web38801.mail.mud.yahoo.com> Dear PWscf users, I would like to calculate the cell parameter under pressure (along z axis). I read in the manual, it can be use press option to get the target pressure but it looks along z-axis. How can I make a pressure target along z-axis? I appreciate all your helps. Sincerely, ----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com, ddloc at skku.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100518/c40f5e4c/attachment.htm From nnlinh at sissa.it Tue May 18 18:17:07 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Tue, 18 May 2010 18:17:07 +0200 Subject: [Pw_forum] PAW pseudopotentials in QE In-Reply-To: <42054E10C02CD44D81EF510077A30A073829ED4976@MAPI.ad.kent.ac.uk> References: <42054E10C02CD44D81EF510077A30A073829ED4976@MAPI.ad.kent.ac.uk> Message-ID: <4BF2BD83.5010704@sissa.it> P.Canepa wrote: > Dear all, > > on the web-page of Quantum Espresso is claimed that PWscf can use projector augmented pseudo-potentials (PAW). Is there any label which marks those at the http://www.quantum-espresso.org/pseudo.php . For instance if I look at one common elements like O I cannot find any PAW pseudopotentials. > I don't think you can find any PAW pseudo potentials in QE website, because they are in testing. You can create by yourself a PAW PP, see example in atomic_doc/paw_library/input and check if it work or not. See in previous archivers of Pw_forum to find an example for Ti also. Hope this help. Linh > Thanks, Piero > > > -- ----------------------------------------------------- Nguyen Ngoc Linh, PhD Student c/o: SISSA, via Beirut 2-4, 34014 Trieste (Italy) email: nnlinh at sissa.it phone: +39 04 03787 319 skype: ngoclinh84phys ----------------------------------------------------- "The physics is theoretical but the fun is real" From marsamos at democritos.it Tue May 18 18:35:11 2010 From: marsamos at democritos.it (marsamos at democritos.it) Date: Tue, 18 May 2010 18:35:11 +0200 Subject: [Pw_forum] wyckoff position builder Message-ID: <20100518183511.hg63ezpzy8csc04k@mail.democritos.it> Dear all, we are testing a new atomic position builder (including Wyckoff groups), consistent with Quantum ESPRESSO. We would like to test it with some "realistic" systems that you have found during your research (in particular orthorhombic C, trigonal R and monoclinic C). We would need Wychoff group, atom types, multiplicity, wyckoff letter, cell parameters, etc ... and the corresponding file xyz. Thank you very much for your contribution Layla & Riccardo Sabatini -- Dr. L. Martin-Samos tel. +39 040 3787 429 CNR-DEMOCRITOS and International School for Advanced Studies (ISAS-SISSA) via Beirut 2-4 34151 Trieste Italy ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From gryko at jsu.edu Tue May 18 18:52:08 2010 From: gryko at jsu.edu (Jan Gryko) Date: Tue, 18 May 2010 11:52:08 -0500 (CDT) Subject: [Pw_forum] wyckoff position builder In-Reply-To: <1249418532.10419511274201453906.JavaMail.root@mbs1.jsu.edu> Message-ID: <1842338377.10419971274201528265.JavaMail.root@mbs1.jsu.edu> Hello, Excellent idea - it will be very nice if Espresso could read crystallographic files, such as .cif or .cel files. Attached are several .cel files that are used by the PowderCell. Download free PowderCell program and run it. PowderCell will read the attached files and display structures and X-ray powder spectra (to load the attached file, click File --> Load). To examine the input file, click Structure --> Edit initial data. You can see all generated positions by clicking Structure-->Info-->Generated positions. Jan Gryko Jacksonville State University 232-C Martin Hall Jacksonville, Al 36265 256-782-5218 256-782-5336 fax ----- Original Message ----- From: marsamos at democritos.it To: "pw forum" , "pw users" Sent: Tuesday, May 18, 2010 11:35:11 AM GMT -06:00 US/Canada Central Subject: [Pw_forum] wyckoff position builder Dear all, we are testing a new atomic position builder (including Wyckoff groups), consistent with Quantum ESPRESSO. We would like to test it with some "realistic" systems that you have found during your research (in particular orthorhombic C, trigonal R and monoclinic C). We would need Wychoff group, atom types, multiplicity, wyckoff letter, cell parameters, etc ... and the corresponding file xyz. Thank you very much for your contribution Layla & Riccardo Sabatini -- Dr. L. Martin-Samos tel. +39 040 3787 429 CNR-DEMOCRITOS and International School for Advanced Studies (ISAS-SISSA) via Beirut 2-4 34151 Trieste Italy ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: AL2O3-HEX.cel Url: http://www.democritos.it/pipermail/pw_forum/attachments/20100518/8421031a/attachment.asc -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... 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Name: Na6Si34-166_2_from_227_2.cel Url: http://www.democritos.it/pipermail/pw_forum/attachments/20100518/8421031a/attachment-0001.txt From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: ------=_Part_282329_1738535771.1274201528261 Content-Type: text/plain; name=FULLERENE.cel Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename=FULLERENE.cel CELL 14.1600 14.1600 14.1600 90.000 90.000 90.000 C 6 0.0000 0.0490 0.2450 C 6 0.2170 0.0800 0.0940 C 6 0.1840 0.1510 0.0520 RGNR 202 ------=_Part_282329_1738535771.1274201528261 Content-Type: text/plain; name=LI13SI4.cel Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename=LI13SI4.cel CELL 7.9900 15.2100 4.4300 90.000 90.000 90.000 Si1 14 0.4165 0.1601 0.0000 Si2 14 0.4263 0.4321 0.5000 Li1 3 0.0000 0.5000 0.0000 Li 3 0.0940 0.1950 0.0000 Li 3 0.7700 0.1550 0.0000 Li 3 0.6550 0.4740 0.0000 Li 3 0.7590 0.4040 0.5000 Li 3 0.9110 0.2450 0.5000 Li 3 0.5940 0.1050 0.5000 RGNR 55 ------=_Part_282329_1738535771.1274201528261 Content-Type: text/plain; name=MGAL2O4.cel Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename=MGAL2O4.cel CELL 8.0800 8.0800 8.0800 90.000 90.000 90.000 Mg 12 0.0000 0.0000 0.0000 Al 13 0.6250 0.6250 0.6250 O 8 0.8630 0.8630 0.8630 RGNR 227 ------=_Part_282329_1738535771.1274201528261-- From Trinh.Vo at jpl.nasa.gov Tue May 18 21:49:13 2010 From: Trinh.Vo at jpl.nasa.gov (Vo, Trinh (388C)) Date: Tue, 18 May 2010 12:49:13 -0700 Subject: [Pw_forum] MKL libraries Message-ID: Dear PWSCF Users, I am compiling QE 4.1.2 with Intel compiler 11.1.038. I go to the following link to find which libraries for my system. I am not sure which of the following is the better choice for compiling with QE: sequential or multi-threaded version of Intel? MKL. If any of you have experience with this, could you give me some advise. Thank you very much in advance, Trinh Vo Computing Group JPL/CalTech -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100518/67da5f8c/attachment.htm From masoudnahali at live.com Tue May 18 22:45:42 2010 From: masoudnahali at live.com (Masoud Nahali) Date: Tue, 18 May 2010 20:45:42 +0000 Subject: [Pw_forum] error # 800 Message-ID: Dear Quantum Espresso Users I have a simulation system with 72 Au atoms in a slab form. My OS is Ubuntu and the used compiler is gfortran. The k-points are 2*1*1. Position of Atoms : Cartesian axes site n. atom positions (a_0 units) 1 Au tau( 1) = ( 0.0000000 0.0000000 0.0000000 ) 2 Au tau( 2) = ( 0.1666180 0.1666180 0.0000000 ) 3 Au tau( 3) = ( 0.0000000 0.1666180 0.1666180 ) 4 Au tau( 4) = ( 0.1666180 0.0000000 0.1666180 ) 5 Au tau( 5) = ( 0.3332361 0.0000000 0.0000000 ) 6 Au tau( 6) = ( 0.4998541 0.1666180 0.0000000 ) 7 Au tau( 7) = ( 0.3332361 0.1666180 0.1666180 ) 8 Au tau( 8) = ( 0.4998541 0.0000000 0.1666180 ) 9 Au tau( 9) = ( 0.6664721 0.0000000 0.0000000 ) 10 Au tau( 10) = ( 0.8330901 0.1666180 0.0000000 ) 11 Au tau( 11) = ( 0.6664721 0.1666180 0.1666180 ) 12 Au tau( 12) = ( 0.8330901 0.0000000 0.1666180 ) 13 Au tau( 13) = ( 0.0000000 0.3332361 0.0000000 ) 14 Au tau( 14) = ( 0.1666180 0.4998541 0.0000000 ) 15 Au tau( 15) = ( 0.0000000 0.4998541 0.1666180 ) 16 Au tau( 16) = ( 0.1666180 0.3332361 0.1666180 ) 17 Au tau( 17) = ( 0.3332361 0.3332361 0.0000000 ) 18 Au tau( 18) = ( 0.4998541 0.4998541 0.0000000 ) 19 Au tau( 19) = ( 0.3332361 0.4998541 0.1666180 ) 20 Au tau( 20) = ( 0.4998541 0.3332361 0.1666180 ) 21 Au tau( 21) = ( 0.6664721 0.3332361 0.0000000 ) 22 Au tau( 22) = ( 0.8330901 0.4998541 0.0000000 ) 23 Au tau( 23) = ( 0.6664721 0.4998541 0.1666180 ) 24 Au tau( 24) = ( 0.8330901 0.3332361 0.1666180 ) 25 Au tau( 25) = ( 0.0000000 0.6664721 0.0000000 ) 26 Au tau( 26) = ( 0.1666180 0.8330901 0.0000000 ) 27 Au tau( 27) = ( 0.0000000 0.8330901 0.1666180 ) 28 Au tau( 28) = ( 0.1666180 0.6664721 0.1666180 ) 29 Pd tau( 29) = ( 0.3332361 0.6664721 0.0000000 ) 30 Au tau( 30) = ( 0.4998541 0.8330901 0.0000000 ) 31 Au tau( 31) = ( 0.3332361 0.8330901 0.1666180 ) 32 Au tau( 32) = ( 0.4998541 0.6664721 0.1666180 ) 33 Pd tau( 33) = ( 0.6664721 0.6664721 0.0000000 ) 34 Au tau( 34) = ( 0.8330901 0.8330901 0.0000000 ) 35 Au tau( 35) = ( 0.6664721 0.8330901 0.1666180 ) 36 Au tau( 36) = ( 0.8330901 0.6664721 0.1666180 ) 37 Au tau( 37) = ( 0.0000000 0.0000000 0.3332361 ) 38 Au tau( 38) = ( 0.1666180 0.1666180 0.3332361 ) 39 Au tau( 39) = ( 0.0000000 0.1666180 0.4998541 ) 40 Au tau( 40) = ( 0.1666180 0.0000000 0.4998541 ) 41 Au tau( 41) = ( 0.3332361 0.0000000 0.3332361 ) 42 Au tau( 42) = ( 0.4998541 0.1666180 0.3332361 ) 43 Au tau( 43) = ( 0.3332361 0.1666180 0.4998541 ) 44 Au tau( 44) = ( 0.4998541 0.0000000 0.4998541 ) 45 Au tau( 45) = ( 0.6664721 0.0000000 0.3332361 ) 46 Au tau( 46) = ( 0.8330901 0.1666180 0.3332361 ) 47 Au tau( 47) = ( 0.6664721 0.1666180 0.4998541 ) 48 Au tau( 48) = ( 0.8330901 0.0000000 0.4998541 ) 49 Au tau( 49) = ( 0.0000000 0.3332361 0.3332361 ) 50 Au tau( 50) = ( 0.1666180 0.4998541 0.3332361 ) 51 Au tau( 51) = ( 0.0000000 0.4998541 0.4998541 ) 52 Au tau( 52) = ( 0.1666180 0.3332361 0.4998541 ) 53 Au tau( 53) = ( 0.3332361 0.3332361 0.3332361 ) 54 Au tau( 54) = ( 0.4998541 0.4998541 0.3332361 ) 55 Au tau( 55) = ( 0.3332361 0.4998541 0.4998541 ) 56 Au tau( 56) = ( 0.4998541 0.3332361 0.4998541 ) 57 Au tau( 57) = ( 0.6664721 0.3332361 0.3332361 ) 58 Au tau( 58) = ( 0.8330901 0.4998541 0.3332361 ) 59 Au tau( 59) = ( 0.6664721 0.4998541 0.4998541 ) 60 Au tau( 60) = ( 0.8330901 0.3332361 0.4998541 ) 61 Au tau( 61) = ( 0.0000000 0.6664721 0.3332361 ) 62 Au tau( 62) = ( 0.1666180 0.8330901 0.3332361 ) 63 Au tau( 63) = ( 0.0000000 0.8330901 0.4998541 ) 64 Au tau( 64) = ( 0.1666180 0.6664721 0.4998541 ) 65 Au tau( 65) = ( 0.3332361 0.6664721 0.3332361 ) 66 Au tau( 66) = ( 0.4998541 0.8330901 0.3332361 ) 67 Au tau( 67) = ( 0.3332361 0.8330901 0.4998541 ) 68 Au tau( 68) = ( 0.4998541 0.6664721 0.4998541 ) 69 Au tau( 69) = ( 0.6664721 0.6664721 0.3332361 ) 70 Au tau( 70) = ( 0.8330901 0.8330901 0.3332361 ) 71 Au tau( 71) = ( 0.6664721 0.8330901 0.4998541 ) 72 Au tau( 72) = ( 0.8330901 0.6664721 0.4998541 ) Out put file : number of k points= 4 gaussian broad. (Ry)= 0.0100 ngauss = 1 cart. coord. in units 2pi/a_0 k( 1) = ( 0.2500000 0.2500000 -0.2500000), wk = 0.5000000 k( 2) = ( -0.2500000 0.2500000 0.2500000), wk = 0.5000000 k( 3) = ( 0.2500000 0.2500000 -0.2500000), wk = 0.5000000 k( 4) = ( -0.2500000 0.2500000 0.2500000), wk = 0.5000000 G cutoff = 4067.9500 (2173519 G-vectors) FFT grid: (128,128,256) G cutoff = 2169.5734 ( 846635 G-vectors) smooth grid: ( 96, 96,192) Largest allocated arrays est. size (Mb) dimensions Kohn-Sham Wavefunctions 765.64 Mb ( 105858, 474) NL pseudopotentials 1511.89 Mb ( 105858, 936) Each V/rho on FFT grid 128.00 Mb (4194304, 2) Each G-vector array 16.58 Mb (2173519) G-vector shells 0.06 Mb ( 7460) Largest temporary arrays est. size (Mb) dimensions Auxiliary wavefunctions -1033.46 Mb ( 105858,1896) Each subspace H/S matrix 54.85 Mb ( 1896,1896) Each matrix 6.77 Mb ( 936, 474) Arrays for rho mixing 512.00 Mb (4194304, 8) Check: negative/imaginary core charge= -0.000019 0.000000 Initial potential from superposition of free atoms Check: negative starting charge=(component1): -0.000220 Check: negative starting charge=(component2): -0.000216 starting charge 789.99136, renormalised to 790.00000 negative rho (up, down): 0.220E-03 0.216E-03 Starting wfc are 642 atomic wfcs %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from cdiaghg : error # 800 diagonalization (ZHEGV*) failed %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... I have checked all of points in user guide except compiling of LAPACK , ATLAS. Would you please help me about this error ? Many Thanks Masoud _________________________________________________________________ Hotmail: Trusted email with Microsoft?s powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100518/76edf6a8/attachment-0001.htm From sd.wang000 at gmail.com Wed May 19 03:20:17 2010 From: sd.wang000 at gmail.com (shudong wang) Date: Wed, 19 May 2010 09:20:17 +0800 Subject: [Pw_forum] band jagged Message-ID: Yes, I have tested with the same system.But v4.1.2 are OK. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100519/981b56ae/attachment.htm From vitruss at gmail.com Wed May 19 04:30:35 2010 From: vitruss at gmail.com (Vit) Date: Wed, 19 May 2010 09:30:35 +0700 Subject: [Pw_forum] MKL libraries In-Reply-To: References: Message-ID: Dear Trinh Vo! Here is some info from user guide http://quantum-espresso.org/user_guide/node7.html http://quantum-espresso.org/user_guide/node15.html WIth best regards, Koroteev Victor PhD student NIIC SB RAS On Wed, May 19, 2010 at 2:49 AM, Vo, Trinh (388C) wrote: > Dear PWSCF Users, > > I am compiling QE 4.1.2 with Intel compiler 11.1.038. ??I go to the > following link to find which libraries for my system. ?I am not sure which > of the following is the better choice for compiling with QE: sequential or > multi-threaded version of Intel? MKL. If any of you have ?experience with > this, could you give me some advise. > > Thank you very much in advance, > > Trinh Vo > Computing Group > JPL/CalTech > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From hqzhou at nju.edu.cn Wed May 19 05:45:32 2010 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Wed, 19 May 2010 11:45:32 +0800 Subject: [Pw_forum] MKL libraries References: Message-ID: <2A58092E23C24BE6BE89EB2D4B754578@solarflare> MKL librariesHi, You'd better use sequential version of MKL for MPI parallelization. For example, when you configure qe-espresso, ./configure ...... ...... BLAS_LIBS="-L$(MKLROOT)/lib/em64t -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" LAPACK_LIBS="" ...... Huiqun Zhou @Earth Sciences, Nanjing University ----- Original Message ----- From: Vo, Trinh (388C) To: PWSCF Forum Sent: Wednesday, May 19, 2010 3:49 AM Subject: [Pw_forum] MKL libraries Dear PWSCF Users, I am compiling QE 4.1.2 with Intel compiler 11.1.038. I go to the following link to find which libraries for my system. I am not sure which of the following is the better choice for compiling with QE: sequential or multi-threaded version of Intel? MKL. If any of you have experience with this, could you give me some advise. Thank you very much in advance, Trinh Vo Computing Group JPL/CalTech ------------------------------------------------------------------------------ _______________________________________________ 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/20100519/96e98e72/attachment.htm From hqzhou at nju.edu.cn Wed May 19 05:56:17 2010 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Wed, 19 May 2010 11:56:17 +0800 Subject: [Pw_forum] How to specify spin for individual atoms References: Message-ID: <975630A64AF040A4BF348FADEBC0634F@solarflare> Hi, Something look like below ....... starting_magnetization(1) = 0.5 starting_magnetization(2) = -0.5 ...... ATOM_SPECIES Mn1 mass_of_mn Mn.gga.upf Mn2 mass_of_mn Mn.gga.upf ........ Huiqun Zhou @Earth Sciences, Nanjing University, China ----- Original Message ----- From: Bipul Rakshit To: PWSCF Forum Sent: Monday, May 17, 2010 4:11 PM Subject: Re: [Pw_forum] How to specify spin for individual atoms Dear Baris, thanks for your kind reply. I go through the "starting_magnetization" and the related documents. But with the help of that flag, we can specify the magnetic moment to particular type. But if u see the atomic co-ordinate i gave there i require the Mn1 spin up & down, and Mn2 spin up & down. So that's i didnt understand how do i specify the spins for particular atoms not with particular type. On Mon, May 17, 2010 at 1:21 PM, O. Baris Malcioglu wrote: Dear Bipul Rakshit, Please take a glance at "starting_magnetization" under the system namelist. You can find the relevant information in the supplied documentation directory. Best, Baris 2010/5/17 Bipul Rakshit : > Dear Users, > I am doing a system in which i have 8 Mn. > Following is the atomic positions in fractional co-ordinate. > > Mn1 0.12500000000 0.25000000000 0.27940000000 + > Mn1 0.37500000000 0.75000000000 0.72060000000 + > Mn2 0.12500000000 0.25000000000 0.74860000000 - > Mn2 0.37500000000 0.75000000000 0.25140000000 - > Mn1 0.62500000000 0.25000000000 0.27940000000 - > Mn1 0.87500000000 0.75000000000 0.72060000000 - > Mn2 0.62500000000 0.25000000000 0.74860000000 + > Mn2 0.87500000000 0.75000000000 0.25140000000 + > > > Now i want to specify the spin as shown by the last column, (with + & - > signs). > So can you please tell me what flags i have to use to specify the magnetic > spin for particular atom. > -- > Bipul Rakshit > Research Fellow, > 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 > > _______________________________________________ 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 ------------------------------------------------------------------------------ _______________________________________________ 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/20100519/243c3742/attachment.htm From nnlinh at sissa.it Wed May 19 08:56:55 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Wed, 19 May 2010 08:56:55 +0200 Subject: [Pw_forum] error # 800 In-Reply-To: References: Message-ID: <4BF38BB7.5030609@sissa.it> This question related to "cdiaghg" have been asked many times, See in: http://www.quantum-espresso.org/user_guide/node50.html#SECTION000111070000000000000 or previous archives of Pw_forum. Good luck, Linh Masoud Nahali wrote: > Dear Quantum Espresso Users > > I have a simulation system with 72 Au atoms in a slab form. My OS is > Ubuntu and the used compiler is gfortran. > The k-points are 2*1*1. > Position of Atoms : > Cartesian axes > > site n. atom positions (a_0 units) > / 1 Au tau( 1) = ( 0.0000000 0.0000000 0.0000000 ) > 2 Au tau( 2) = ( 0.1666180 0.1666180 0.0000000 ) > 3 Au tau( 3) = ( 0.0000000 0.1666180 0.1666180 ) > 4 Au tau( 4) = ( 0.1666180 0.0000000 0.1666180 ) > 5 Au tau( 5) = ( 0.3332361 0.0000000 0.0000000 ) > 6 Au tau( 6) = ( 0.4998541 0.1666180 0.0000000 ) > 7 Au tau( 7) = ( 0.3332361 0.1666180 0.1666180 ) > 8 Au tau( 8) = ( 0.4998541 0.0000000 0.1666180 ) > 9 Au tau( 9) = ( 0.6664721 0.0000000 0.0000000 ) > 10 Au tau( 10) = ( 0.8330901 0.1666180 0.0000000 ) > 11 Au tau( 11) = ( 0.6664721 0.1666180 0.1666180 ) > 12 Au tau( 12) = ( 0.8330901 0.0000000 0.1666180 ) > 13 Au tau( 13) = ( 0.0000000 0.3332361 0.0000000 ) > 14 Au tau( 14) = ( 0.1666180 0.4998541 0.0000000 ) > 15 Au tau( 15) = ( 0.0000000 0.4998541 0.1666180 ) > 16 Au tau( 16) = ( 0.1666180 0.3332361 0.1666180 ) > 17 Au tau( 17) = ( 0.3332361 0.3332361 0.0000000 ) > 18 Au tau( 18) = ( 0.4998541 0.4998541 0.0000000 ) > 19 Au tau( 19) = ( 0.3332361 0.4998541 0.1666180 ) > 20 Au tau( 20) = ( 0.4998541 0.3332361 0.1666180 ) > 21 Au tau( 21) = ( 0.6664721 0.3332361 0.0000000 ) > 22 Au tau( 22) = ( 0.8330901 0.4998541 0.0000000 ) > 23 Au tau( 23) = ( 0.6664721 0.4998541 0.1666180 ) > 24 Au tau( 24) = ( 0.8330901 0.3332361 0.1666180 ) > 25 Au tau( 25) = ( 0.0000000 0.6664721 0.0000000 ) > 26 Au tau( 26) = ( 0.1666180 0.8330901 0.0000000 ) > 27 Au tau( 27) = ( 0.0000000 0.8330901 0.1666180 ) > 28 Au tau( 28) = ( 0.1666180 0.6664721 0.1666180 ) > 29 Pd tau( 29) = ( 0.3332361 0.6664721 0.0000000 ) > 30 Au tau( 30) = ( 0.4998541 0.8330901 0.0000000 ) > 31 Au tau( 31) = ( 0.3332361 0.8330901 0.1666180 ) > 32 Au tau( 32) = ( 0.4998541 0.6664721 0.1666180 ) > 33 Pd tau( 33) = ( 0.6664721 0.6664721 0.0000000 ) > 34 Au tau( 34) = ( 0.8330901 0.8330901 0.0000000 ) > 35 Au tau( 35) = ( 0.6664721 0.8330901 0.1666180 ) > 36 Au tau( 36) = ( 0.8330901 0.6664721 0.1666180 ) > 37 Au tau( 37) = ( 0.0000000 0.0000000 0.3332361 ) > 38 Au tau( 38) = ( 0.1666180 0.1666180 0.3332361 ) > 39 Au tau( 39) = ( 0.0000000 0.1666180 0.4998541 ) > 40 Au tau( 40) = ( 0.1666180 0.0000000 0.4998541 ) > 41 Au tau( 41) = ( 0.3332361 0.0000000 0.3332361 ) > 42 Au tau( 42) = ( 0.4998541 0.1666180 0.3332361 ) > 43 Au tau( 43) = ( 0.3332361 0.1666180 0.4998541 ) > 44 Au tau( 44) = ( 0.4998541 0.0000000 0.4998541 ) > 45 Au tau( 45) = ( 0.6664721 0.0000000 0.3332361 ) > 46 Au tau( 46) = ( 0.8330901 0.1666180 0.3332361 ) > 47 Au tau( 47) = ( 0.6664721 0.1666180 0.4998541 ) > 48 Au tau( 48) = ( 0.8330901 0.0000000 0.4998541 ) > 49 Au tau( 49) = ( 0.0000000 0.3332361 0.3332361 ) > 50 Au tau( 50) = ( 0.1666180 0.4998541 0.3332361 ) > 51 Au tau( 51) = ( 0.0000000 0.4998541 0.4998541 ) > 52 Au tau( 52) = ( 0.1666180 0.3332361 0.4998541 ) > 53 Au tau( 53) = ( 0.3332361 0.3332361 0.3332361 ) > 54 Au tau( 54) = ( 0.4998541 0.4998541 0.3332361 ) > 55 Au tau( 55) = ( 0.3332361 0.4998541 0.4998541 ) > 56 Au tau( 56) = ( 0.4998541 0.3332361 0.4998541 ) > 57 Au tau( 57) = ( 0.6664721 0.3332361 0.3332361 ) > 58 Au tau( 58) = ( 0.8330901 0.4998541 0.3332361 ) > 59 Au tau( 59) = ( 0.6664721 0.4998541 0.4998541 ) > 60 Au tau( 60) = ( 0.8330901 0.3332361 0.4998541 ) > 61 Au tau( 61) = ( 0.0000000 0.6664721 0.3332361 ) > 62 Au tau( 62) = ( 0.1666180 0.8330901 0.3332361 ) > 63 Au tau( 63) = ( 0.0000000 0.8330901 0.4998541 ) > 64 Au tau( 64) = ( 0.1666180 0.6664721 0.4998541 ) > 65 Au tau( 65) = ( 0.3332361 0.6664721 0.3332361 ) > 66 Au tau( 66) = ( 0.4998541 0.8330901 0.3332361 ) > 67 Au tau( 67) = ( 0.3332361 0.8330901 0.4998541 ) > 68 Au tau( 68) = ( 0.4998541 0.6664721 0.4998541 ) > 69 Au tau( 69) = ( 0.6664721 0.6664721 0.3332361 ) > 70 Au tau( 70) = ( 0.8330901 0.8330901 0.3332361 ) > 71 Au tau( 71) = ( 0.6664721 0.8330901 0.4998541 ) > 72 Au tau( 72) = ( 0.8330901 0.6664721 0.4998541 )/ > > > Out put file : > > /number of k points= 4 gaussian broad. (Ry)= 0.0100 ngauss = 1 > cart. coord. in units 2pi/a_0 > k( 1) = ( 0.2500000 0.2500000 -0.2500000), wk = 0.5000000 > k( 2) = ( -0.2500000 0.2500000 0.2500000), wk = 0.5000000 > k( 3) = ( 0.2500000 0.2500000 -0.2500000), wk = 0.5000000 > k( 4) = ( -0.2500000 0.2500000 0.2500000), wk = 0.5000000 > > G cutoff = 4067.9500 (2173519 G-vectors) FFT grid: (128,128,256) > G cutoff = 2169.5734 ( 846635 G-vectors) smooth grid: ( 96, 96,192) > > Largest allocated arrays est. size (Mb) dimensions > Kohn-Sham Wavefunctions 765.64 Mb ( 105858, 474) > NL pseudopotentials 1511.89 Mb ( 105858, 936) > Each V/rho on FFT grid 128.00 Mb (4194304, 2) > Each G-vector array 16.58 Mb (2173519) > G-vector shells 0.06 Mb ( 7460) > Largest temporary arrays est. size (Mb) dimensions > Auxiliary wavefunctions -1033.46 Mb ( 105858,1896) > Each subspace H/S matrix 54.85 Mb ( 1896,1896) > Each matrix 6.77 Mb ( 936, 474) > Arrays for rho mixing 512.00 Mb (4194304, 8) > > Check: negative/imaginary core charge= -0.000019 0.000000 > > Initial potential from superposition of free atoms > Check: negative starting charge=(component1): -0.000220 > Check: negative starting charge=(component2): -0.000216 > > starting charge 789.99136, renormalised to 790.00000 > > negative rho (up, down): 0.220E-03 0.216E-03 > Starting wfc are 642 atomic wfcs > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from cdiaghg : error # 800 > diagonalization (ZHEGV*) failed > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > stopping .../ > > > I have checked all of points in user guide except compiling of LAPACK > , ATLAS. > > Would you please help me about this error ? > > Many Thanks > Masoud > > > > ------------------------------------------------------------------------ > Hotmail: Trusted email with Microsoft?s powerful SPAM protection. Sign > up now. > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ----------------------------------------------------- Nguyen Ngoc Linh, PhD Student c/o: SISSA & CNR-INFM Democritos, via Beirut 2-4, 34014 Trieste (Italy) email: nnlinh at sissa.it phone: +39 04 03787 319 skype: ngoclinh84phys ----------------------------------------------------- "The physics is theoretical but the fun is real" From parthasarathi13 at gmail.com Wed May 19 14:11:28 2010 From: parthasarathi13 at gmail.com (partha sarathi ghosh) Date: Wed, 19 May 2010 17:41:28 +0530 Subject: [Pw_forum] negative frequency Message-ID: Dear all, I am trying to do phonon calculation of bcc-Zr from (0,0,0) to (1,1,1) in q-space.But I am getting negative frequencies in several q-points, also my curve is very different from experimental one. I optimized the system w.r.t ecutwf, ecutrho ,conv_thr, k-point sampling .I also tried the same calculation by changing potential also.I am new fellow in this field so I am unable to understand what is happening wrong !! My input files are : 1) zr.scf.in &control calculation='scf' restart_mode='from_scratch', tstress = .true. tprnfor = .true. prefix='zr', pseudo_dir = '/home/general/Desktop/espresso-4.0.5/pseudo/', outdir='./' / &system ibrav= 0, celldm(1) =6.7, nat= 1, ntyp= 1, degauss=0.04, smearing='mp', occupations='smearing', ecutwfc =35.0 ecutrho = 350.0 / &electrons conv_thr = 1.0d-8 mixing_beta = 0.7 / ATOMIC_SPECIES Zr 91.22 Zr.pbe-nsp-van.UPF ATOMIC_POSITIONS Zr 0.00 0.00 0.00 K_POINTS AUTOMATIC 16 16 16 0 0 0 CELL_PARAMETERS { cubic } -0.500000000000000 0.500000000000000 0.500000000000000 0.500000000000000 -0.500000000000000 0.500000000000000 0.500000000000000 0.500000000000000 -0.500000000000000 ########################################## 2) zr.ph.in phonons of Zr &inputph tr2_ph=1.0d-10, prefix='zr', ldisp=.true., nq1=8, nq2=8, nq3=8 amass(1)=91.22, outdir='./', fildyn='zr.dyn', / Any one can help me please . Thanks in advance. P S Ghosh B.A.R.C. India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100519/3002766b/attachment.htm From nkxirainbow at gmail.com Wed May 19 15:08:56 2010 From: nkxirainbow at gmail.com (xirainbow) Date: Wed, 19 May 2010 21:08:56 +0800 Subject: [Pw_forum] negative frequency In-Reply-To: References: Message-ID: Dear P S Ghosh? Do you relax the crystal ? Firstly, relax crystal with "*calculation = 'vc-relax' *". Phonon should be calculated after vc-relax, On Wed, May 19, 2010 at 8:11 PM, partha sarathi ghosh < parthasarathi13 at gmail.com> wrote: > Dear all, > I am trying to do phonon calculation of bcc-Zr from (0,0,0) to > (1,1,1) in q-space.But I am getting negative frequencies in several > q-points, also my curve is very different from experimental one. I optimized > the system w.r.t ecutwf, ecutrho ,conv_thr, k-point sampling .I also tried > the same calculation by changing potential also.I am new fellow in this > field so I am unable to understand what is happening wrong !! > My input files are : > 1) zr.scf.in > &control > calculation='scf' > restart_mode='from_scratch', > tstress = .true. > tprnfor = .true. > prefix='zr', > pseudo_dir = '/home/general/Desktop/espresso-4.0.5/pseudo/', > outdir='./' > / > &system > ibrav= 0, celldm(1) =6.7, nat= 1, ntyp= 1, > degauss=0.04, > smearing='mp', > occupations='smearing', > ecutwfc =35.0 > ecutrho = 350.0 > / > &electrons > conv_thr = 1.0d-8 > mixing_beta = 0.7 > / > ATOMIC_SPECIES > Zr 91.22 Zr.pbe-nsp-van.UPF > ATOMIC_POSITIONS > Zr 0.00 0.00 0.00 > K_POINTS AUTOMATIC > 16 16 16 0 0 0 > CELL_PARAMETERS { cubic } > -0.500000000000000 0.500000000000000 0.500000000000000 > 0.500000000000000 -0.500000000000000 0.500000000000000 > 0.500000000000000 0.500000000000000 -0.500000000000000 > ########################################## > 2) zr.ph.in > phonons of Zr > &inputph > tr2_ph=1.0d-10, > prefix='zr', > ldisp=.true., > nq1=8, nq2=8, nq3=8 > amass(1)=91.22, > outdir='./', > fildyn='zr.dyn', > / > Any one can help me please . > Thanks in advance. > P S Ghosh > B.A.R.C. > India > > _______________________________________________ > 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/20100519/e648c90a/attachment.htm From rezaebraahimi at yahoo.com Wed May 19 15:27:06 2010 From: rezaebraahimi at yahoo.com (Reza Ebraahimi) Date: Wed, 19 May 2010 06:27:06 -0700 (PDT) Subject: [Pw_forum] About the "pseudo-gen.txt" file Message-ID: <62682.26703.qm@web59411.mail.ac4.yahoo.com> Hello everyone I found the file "pseudo-gen.tex" (in the atomic_doc folder of the code) very usefull, but i have problem with following it's strange notation (in the formula sections).?Is there any pdf format of this file? Could anyone refer me to an easy-to-read-version of it? Thank You? R. Ebraahimi Grad. Student- Tehran University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100519/5320fe44/attachment.htm From nedward at MIT.EDU Wed May 19 15:56:34 2010 From: nedward at MIT.EDU (Nicholas E. Singh-Miller) Date: Wed, 19 May 2010 09:56:34 -0400 (EDT) Subject: [Pw_forum] About the "pseudo-gen.txt" file In-Reply-To: <62682.26703.qm@web59411.mail.ac4.yahoo.com> References: <62682.26703.qm@web59411.mail.ac4.yahoo.com> Message-ID: Hi R. Ebraahimi, This is a .tex file in a markup language called latex. You can create a .pdf with the command (from the linux commandline if you have the latex program installed): pdflatex pseudo-gen.tex There are also ways to compile such .tex in windows, but I am not sure of them. If you are unable to do either, I have attached the .pdf. Latex is quite a nice way to write documents, and many journals accept (maybe prefer) submission in .tex form. hope that helps, Nicholas On Wed, 19 May 2010, Reza Ebraahimi wrote: > Hello everyone > I found the file "pseudo-gen.tex" (in the atomic_doc folder of the code) > very usefull, but i have problem with following it's strange notation (in > the formula sections).?Is there any pdf format of this file? Could anyone > refer me to an easy-to-read-version of it? > Thank You? > ? > R. Ebraahimi > Grad. Student- Tehran University > > > ***************************************** Nicholas E. Singh-Miller Prof. Marzari Group (quasiamore.mit.edu) Materials Science and Engineering Massachusetts Institute of Technology 13-4066 (617)324-0372 ***************************************** -------------- next part -------------- A non-text attachment was scrubbed... Name: pseudo-gen.pdf Type: application/pdf Size: 130887 bytes Desc: Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100519/bd26ef8e/attachment-0001.pdf From paulatto at sissa.it Wed May 19 16:04:25 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 19 May 2010 16:04:25 +0200 Subject: [Pw_forum] About the "pseudo-gen.txt" file In-Reply-To: References: <62682.26703.qm@web59411.mail.ac4.yahoo.com> Message-ID: On Wed, 19 May 2010 15:56:34 +0200, Nicholas E. Singh-Miller wrote: > There are also ways to compile such .tex in windows, but I am not sure of > them. It's called miktex, you can just google it. regards -- Lorenzo Paulatto *** Note: my affiliation has changed! please send future correspondence to: *** post-doc @ IMPMC/UPMC - Universit? Paris 6 phone: +33 (0)1 44 27 74 89 www: http://www-int.impmc.upmc.fr/~paulatto/ previously: phd student @ SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 www: http://people.sissa.it/~paulatto/ From glapenna at iccom.cnr.it Wed May 19 16:12:52 2010 From: glapenna at iccom.cnr.it (Giovanni La Penna) Date: Wed, 19 May 2010 16:12:52 +0200 (CEST) Subject: [Pw_forum] negative frequency In-Reply-To: References: Message-ID: In user_guide.pdf (page 75 of qe-4.1.2) I read that tr2_ph may be too large. Actually, I tested benzene and the imaginary frequency disappeared with tr2_ph = 1.d-12 (as suggested in example02). Giovanni La Penna ============================================================ Giovanni La Penna - National research council (Cnr) Institute for chemistry of organo-metallic compounds (Iccom) via Madonna del Piano 10, I-50019 Sesto Fiorentino, Firenze, Italy tel.: +39 055 522-5264, fax: +39 055 522-5203 e-mail: glapenna at iccom.cnr.it - http://www.iccom.cnr.it/lapenna skype: giovannilapenna ============================================================ From rezaebraahimi at yahoo.com Wed May 19 17:50:11 2010 From: rezaebraahimi at yahoo.com (Reza Ebraahimi) Date: Wed, 19 May 2010 08:50:11 -0700 (PDT) Subject: [Pw_forum] About the "pseudo-gen.txt" file Message-ID: <192577.57435.qm@web59409.mail.ac4.yahoo.com> Hello Thanks a lot for your comments And specially to You Nicholas for providing the .pdf file. R. Ebraahimi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100519/e8f38a41/attachment.htm From Michael.Mehl at nrl.navy.mil Wed May 19 18:11:32 2010 From: Michael.Mehl at nrl.navy.mil (Mike Mehl) Date: Wed, 19 May 2010 12:11:32 -0400 Subject: [Pw_forum] negative frequency In-Reply-To: References: Message-ID: <4BF40DB4.7040804@nrl.navy.mil> On 05/19/2010 08:11 AM, partha sarathi ghosh wrote: > Dear all, > I am trying to do phonon calculation of bcc-Zr from > (0,0,0) to (1,1,1) in q-space.But I am getting negative frequencies in > several q-points, also my curve is very different from experimental one. > I optimized the system w.r.t ecutwf, ecutrho ,conv_thr, k-point sampling > .I also tried the same calculation by changing potential also.I am new > fellow in this field so I am unable to understand what is happening wrong !! First, the ground state of Zr is HCP, not BCC, so you shouldn't expect being able to match the HCP phonon spectrum. With a bcc calculation. Second, the high-temperature hcp-bcc transition is driven by an unstable bcc phonon, so, yes, you'd expect "negative" (actually imaginary) frequencies at some k-points. See below. It's written about Mg, but it will apply to Zr as well. @Article{wentzcovitch88:hcp_to_bcc, author = {Renata M. Wentzcovitch and Marvin L. Cohen}, title = {Theoretical model for the hcp-bcc transition in Mg}, journal = {Phys. Rev. B}, year = 1988, volume = 37, number = 10, pages = {5571-5576}, month = {April}, url = {http://link.aps.org/abstract/PRB/v37/p5571}, doi = {10.1103/PhysRevB.37.5571}, keywords = {structure}, abstract = {Using a first-principles total-energy pseudopotential method, we investigate the transition mechanism for a pressure-induced martensitic transformation hcp-->bcc which occurs in Mg at pressures around 50 GPa. Two internal structural degrees of freedom are selected and one lattice is transformed into the other by relaxing these two parameters continuously. One of the parameters characterizes the relative displacement of the hexagonal layers and corresponds to a transverse phonon at the Brillouin-zone edge A in the hexagonal structure. The other characterizes the distortion of the internal hexagonal angles and corresponds to uniform strain along one of the [0010][hcp] directions. The interaction between these two distortion modes causes important anharmonic effects in the zone-edge phonon a nd provides a low-energy path for the structural transition. The small activation barrier at the transition indicates that quantum fluctuations between the two structures could be taking place.} -- Michael J. Mehl Head, Center for Computational Materials Science Naval Research Laboratory Code 6390 Washington DC From vv0210 at gmail.com Wed May 19 20:09:21 2010 From: vv0210 at gmail.com (Vikas Varshney) Date: Wed, 19 May 2010 14:09:21 -0400 Subject: [Pw_forum] Visualization of Results Message-ID: Dear Developers, I am a new user of QE and currently going through various examples (along with tutorials) to understand the software. I have few questions regarding how I can visualize some results. I have VMD installed on my machine but do not have XCrySDen. Is it possible to input the output files (.out format as outputted from the calculations) directly somehow to VMD to visualize molecular relaxation (like example03). Or do I need to install XCrySDen? I also tried to visualize the output of example02 (phonon spectra) using PP/pp.x but was totally unsuccessful. Any help will be highly appreciated Thanks in advance. Best Regards, Vikas -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100519/e91ea6db/attachment.htm From Trinh.Vo at jpl.nasa.gov Wed May 19 20:30:45 2010 From: Trinh.Vo at jpl.nasa.gov (Vo, Trinh (388C)) Date: Wed, 19 May 2010 11:30:45 -0700 Subject: [Pw_forum] MKL libraries In-Reply-To: <2A58092E23C24BE6BE89EB2D4B754578@solarflare> Message-ID: Hi Vit and Huiqun, Thanks a lot for your help. Trinh On 5/18/10 8:45 PM, "Huiqun Zhou" wrote: Hi, You'd better use sequential version of MKL for MPI parallelization. For example, when you configure qe-espresso, ./configure ...... ...... BLAS_LIBS="-L$(MKLROOT)/lib/em64t -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" LAPACK_LIBS="" ...... Huiqun Zhou @Earth Sciences, Nanjing University ----- Original Message ----- From: Vo, Trinh (388C) To: PWSCF Forum Sent: Wednesday, May 19, 2010 3:49 AM Subject: [Pw_forum] MKL libraries Dear PWSCF Users, I am compiling QE 4.1.2 with Intel compiler 11.1.038. I go to the following link to find which libraries for my system. I am not sure which of the following is the better choice for compiling with QE: sequential or multi-threaded version of Intel? MKL. If any of you have experience with this, could you give me some advise. Thank you very much in advance, Trinh Vo Computing Group JPL/CalTech ________________________________ _______________________________________________ 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/20100519/722ad06d/attachment.htm From giannozz at democritos.it Wed May 19 20:34:58 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 19 May 2010 20:34:58 +0200 Subject: [Pw_forum] band jagged In-Reply-To: References: Message-ID: On May 19, 2010, at 3:20 , shudong wang wrote: > Yes, I have tested with the same system please provide a test job ... --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From baris.malcioglu at gmail.com Wed May 19 20:59:54 2010 From: baris.malcioglu at gmail.com (Osman Baris Malcioglu) Date: Wed, 19 May 2010 21:59:54 +0300 Subject: [Pw_forum] Visualization of Results In-Reply-To: References: Message-ID: <4EB77F6D-8FC9-4D92-BC4D-B503D3170B11@gmail.com> Dear Vikas, With a simple script you can extract the coordinates from the stdout and convert it to animated xyz format which VMD (and many other programs) support. Please find an example I have written for the espresso 3.2 below. Feel free to modify it if it is not working. Best, Baris -------------- next part -------------- A non-text attachment was scrubbed... Name: pwo2xyz.tcl Type: application/octet-stream Size: 3343 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100519/53ebf0f6/attachment-0001.obj -------------- next part -------------- On 19.May.2010, at 21:09, Vikas Varshney wrote: > Dear Developers, > I am a new user of QE and currently going through various examples (along with tutorials) to understand the software. I have few questions regarding how I can visualize some results. > > I have VMD installed on my machine but do not have XCrySDen. Is it possible to input the output files (.out format as outputted from the calculations) directly somehow to VMD to visualize molecular relaxation (like example03). Or do I need to install XCrySDen? > > I also tried to visualize the output of example02 (phonon spectra) using PP/pp.x but was totally unsuccessful. Any help will be highly appreciated > > Thanks in advance. > > Best Regards, > Vikas > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From vv0210 at gmail.com Wed May 19 21:08:16 2010 From: vv0210 at gmail.com (Vikas Varshney) Date: Wed, 19 May 2010 15:08:16 -0400 Subject: [Pw_forum] Visualization of Results In-Reply-To: <4EB77F6D-8FC9-4D92-BC4D-B503D3170B11@gmail.com> References: <4EB77F6D-8FC9-4D92-BC4D-B503D3170B11@gmail.com> Message-ID: Dear Osman, Thanks, for the Tcl script. I will try it out for sure. Best Regards, Vikas On Wed, May 19, 2010 at 2:59 PM, Osman Baris Malcioglu < baris.malcioglu at gmail.com> wrote: > Dear Vikas, > > With a simple script you can extract the coordinates from the stdout and > convert it to animated xyz format which VMD (and many other programs) > support. > > Please find an example I have written for the espresso 3.2 below. Feel free > to modify it if it is not working. > > Best, > Baris > > > > On 19.May.2010, at 21:09, Vikas Varshney wrote: > > > Dear Developers, > > I am a new user of QE and currently going through various examples (along > with tutorials) to understand the software. I have few questions regarding > how I can visualize some results. > > > > I have VMD installed on my machine but do not have XCrySDen. Is it > possible to input the output files (.out format as outputted from the > calculations) directly somehow to VMD to visualize molecular relaxation > (like example03). Or do I need to install XCrySDen? > > > > I also tried to visualize the output of example02 (phonon spectra) using > PP/pp.x but was totally unsuccessful. Any help will be highly appreciated > > > > Thanks in advance. > > > > Best Regards, > > Vikas > > _______________________________________________ > > 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/20100519/329e8091/attachment.htm From javier.fuhr at gmail.com Wed May 19 22:47:23 2010 From: javier.fuhr at gmail.com (Javier Fuhr) Date: Wed, 19 May 2010 17:47:23 -0300 Subject: [Pw_forum] missing cell_dofree options Message-ID: Dear all, I found that the options 'xyt', 'xys' and 'xyzt' for 'cell_dofree' have been removed in QE versions 4.1 and 4.2 (they were available in 4.0.5). Were they not working as expected? I'm tempted to copy the corresponding options from input.f90 of v4.0.5 to cell_base.f90 in v4.2, but I would like to know if there has been any problem reported for these options. Regards, Javier -- Dr. Javier Daniel Fuhr Surface Physics Group Centro At?mico Bariloche Bariloche - Argentina From srix at princeton.edu Thu May 20 00:10:34 2010 From: srix at princeton.edu (Stephan Rix) Date: Wed, 19 May 2010 18:10:34 -0400 Subject: [Pw_forum] phonon modes for transition state Message-ID: Dear all, I am trying to calculate the phonon modes for a transition state using ph.x. I am expecting to find one negative/imaginary mode, but all resulting phonon modes are positive. The transition state was optimized using pw.x with nudged elastic band and climbing image. Before running ph.x for the transition state I tested it with respect to necessary thresholds on a fully relaxed equilibrium state and the results were fine. Question: Is ph.x in principle capable of calculating transition state phonon modes, i.e. returning negative/imaginary modes? If so, I would appreciate any ideas or advice on how to obtain the desired negative phonon mode. Thanks for your help. Stephan Stephan Rix Dept. of Chemistry Princeton University Princeton, NJ 08540 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100519/cce6a85b/attachment.htm From pnyawere at gmail.com Thu May 20 08:43:14 2010 From: pnyawere at gmail.com (Phillip Nyawere) Date: Thu, 20 May 2010 09:43:14 +0300 Subject: [Pw_forum] Visualization of Results In-Reply-To: References: Message-ID: To visualize you need to use XCrysDen which you can install in your computer. I have not used pp.x but I shall check and see if I can offer any meaningful help. On Wed, May 19, 2010 at 9:09 PM, Vikas Varshney wrote: > Dear Developers, > I am a new user of QE and currently going through various examples (along > with tutorials) to understand the software. I have few questions regarding > how I can visualize some results. > > I have VMD installed on my machine but do not have XCrySDen. Is it possible > to input the output files (.out format as outputted from the calculations) > directly somehow to VMD to visualize molecular relaxation (like example03). > Or do I need to install XCrySDen? > > I also tried to visualize the output of example02 (phonon spectra) using > PP/pp.x but was totally unsuccessful. Any help will be highly appreciated > > Thanks in advance. > > Best Regards, > Vikas > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Phillip W. Otieno Nyawere, Kabarak University, Dept of Physics & Mathematics, P.O Box Private Bag - 20157, Kabarak, Kenya. Tel +254728342054 pnyawere at gmail.com, potieno at kabarak.ac.ke The battle belongs to the Lord. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100520/ae5b1600/attachment.htm From pnyawere at gmail.com Thu May 20 08:50:07 2010 From: pnyawere at gmail.com (Phillip Nyawere) Date: Thu, 20 May 2010 09:50:07 +0300 Subject: [Pw_forum] Low speed In-Reply-To: References: Message-ID: You need high speed computer. I tried with 96 atoms and it was taking even longer. Success. On Wed, May 12, 2010 at 10:07 PM, mohsen modaresi wrote: > Dear Developers and users, > I run a SCF calculation with 71 atoms on a camputer with 8 cpu and 8GB RAM, > i expect it run in some minutes, But it take 3 hours to run. > Is it regular? > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Phillip W. Otieno Nyawere, Kabarak University, Dept of Physics & Mathematics, P.O Box Private Bag - 20157, Kabarak, Kenya. Tel +254728342054 pnyawere at gmail.com, potieno at kabarak.ac.ke The battle belongs to the Lord. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100520/02cb657e/attachment.htm From lfhuang at theory.issp.ac.cn Thu May 20 09:33:25 2010 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Thu, 20 May 2010 15:33:25 +0800 Subject: [Pw_forum] =?utf-8?q?phonon_modes_for_transition_state?= Message-ID: <20100520073325.15439.qmail@ms.hfcas.ac.cn> Dear Stephan Rix: Apart from some convergence problems sometimes when the structure is far away from equilibrium, PWSCF can calculate the phonons for any structure in principle. Are you sure you have the very transition-state structure in your calculation of phonons? Are you sure there is a transition state in the reaction path specified by you? Transition state is also a saddle-point state, in which there is an imaginary vibrational mode along the migration coordinate with other modes being real. Thus, there should be an imaginary mode if the structure is in/close to the transition state. Best Wishes! Yours Sincerely L. F. Huang > From: Stephan Rix > Subject: [Pw_forum] phonon modes for transition state > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > > I am trying to calculate the phonon modes for a transition state using ph.x. > > I am expecting to find one negative/imaginary mode, but all resulting phonon > modes are positive. > > The transition state was optimized using pw.x with nudged elastic band and > climbing image. > Before running ph.x for the transition state I tested it with respect to > necessary thresholds on a fully relaxed equilibrium state and the results > were fine. > > Question: Is ph.x in principle capable of calculating transition state > phonon modes, i.e. returning negative/imaginary modes? > If so, I would appreciate any ideas or advice on how to obtain the desired > negative phonon mode. > > Thanks for your help. > Stephan > > > Stephan Rix > Dept. of Chemistry > Princeton University > Princeton, NJ 08540 ------ ====================================================================== L.F.Huang(???) 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/20100520/e9402b0f/attachment.htm From baris.malcioglu at gmail.com Thu May 20 10:03:33 2010 From: baris.malcioglu at gmail.com (O. Baris Malcioglu) Date: Thu, 20 May 2010 11:03:33 +0300 Subject: [Pw_forum] Low speed In-Reply-To: References: Message-ID: Dear Mohsen, Please notice that you have asked a rather vague question regarding performance, First of all, please notice that since PW is a plane wave code, it is not just the number of atoms that determine the "size" of the system. You have to take into account the number of plane waves you are using. This depends on your cutoffs and simulation supercell. Exaggerating the situation unnecessarily, for example putting only an ethane molecule in a 500x500x500 Bohr box (even with modest cutoff) will result in a system size that will certainly give a hard time to the computer you are describing. In the same sense, using very high cutoffs will lead to same problem. Secondly, "3 hours" is not a good enough criteria, how many scf steps do you perform in these 3 hours? Does your system have some convergence problems? Finally, 8 cpu is not a good enough identification nowadays, if the "cpu" you are mentioning is due to hyper-threading, it is usually better if you use only 4, since you waste your precious memory bandwidth. This is especially important if you are using a low memory bandwidth architecture. Some general guidelines : -Make sure that your computer is not using swap, -Use architecture dependent acceleration libraries such as MKL. For example you can setup fftw 3.x to utilize instruction sets such as sse2. -If this is a parallel compiler check wall times, how much do you loose communicating? Best, Baris 2010/5/20 Phillip Nyawere : > You need high speed computer. I tried with 96 atoms and it was taking even > longer. > Success. > > On Wed, May 12, 2010 at 10:07 PM, mohsen modaresi > wrote: >> >> Dear Developers and users, >> I run a SCF calculation with 71 atoms on a camputer with 8 cpu and 8GB >> RAM, i expect it run in some minutes, But it take 3 hours to run. >> Is it regular? >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > Phillip W. Otieno Nyawere, > Kabarak University, > Dept of Physics & Mathematics, > P.O Box Private Bag - 20157, > Kabarak, Kenya. > Tel +254728342054 > pnyawere at gmail.com, potieno at kabarak.ac.ke > > The battle belongs to the Lord. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From giannozz at democritos.it Thu May 20 10:54:54 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 20 May 2010 10:54:54 +0200 Subject: [Pw_forum] phonon modes for transition state In-Reply-To: References: Message-ID: <4BF4F8DE.70707@democritos.it> Stephan Rix wrote: > Question: Is ph.x in principle capable of calculating transition state > phonon modes, i.e. returning negative/imaginary modes? it is P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Thu May 20 10:58:49 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 20 May 2010 10:58:49 +0200 Subject: [Pw_forum] Visualization of Results In-Reply-To: References: Message-ID: <4BF4F9C9.7060000@democritos.it> Vikas Varshney wrote: > I also tried to visualize the output of example02 (phonon spectra) using > PP/pp.x but was totally unsuccessful. you can't visualize phonons with a postprocessing code that is meant to visualize the charge density, potentials, etc P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Thu May 20 11:01:48 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 20 May 2010 11:01:48 +0200 Subject: [Pw_forum] missing cell_dofree options In-Reply-To: References: Message-ID: <4BF4FA7C.5020203@democritos.it> Javier Fuhr wrote: > I would like to know if there has been > any problem reported for these options. I don't know, but you can follow the story here: http://qe-forge.org/cgi-bin/cvstrac/q-e/rlog?f=espresso/Modules/cell_base.f90 P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From baroni at sissa.it Thu May 20 12:45:31 2010 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 20 May 2010 12:45:31 +0200 Subject: [Pw_forum] About the "pseudo-gen.txt" file In-Reply-To: <192577.57435.qm@web59409.mail.ac4.yahoo.com> References: <192577.57435.qm@web59409.mail.ac4.yahoo.com> Message-ID: <307F1EE3-6E3E-4F31-9585-4B85170237E5@sissa.it> Ebraahimi: you should rather thank "specially" Lorenzo, who taught you how to produce the pdf file by yourself ... ;-) SB On May 19, 2010, at 5:50 PM, Reza Ebraahimi wrote: > Hello > Thanks a lot for your comments > And specially to You Nicholas for providing the .pdf file. > > R. Ebraahimi > > _______________________________________________ > 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/20100520/2c6dbb6f/attachment-0001.htm From vv0210 at gmail.com Thu May 20 14:00:16 2010 From: vv0210 at gmail.com (Vikas Varshney) Date: Thu, 20 May 2010 08:00:16 -0400 Subject: [Pw_forum] Visualization of Results In-Reply-To: <4BF4F9C9.7060000@democritos.it> References: <4BF4F9C9.7060000@democritos.it> Message-ID: Dear developers, Thanks for all the answers. Dear Paolo, I did not intend to visualize the phonons. I wanted to see the phonon dispersion relation. Which postprocessing code should I use for that. In general, where I can find the information where the output of all the executables in PP/ directory is mentioned and what information I would have to provide for each of them, if I want to use them. Best Regards, Vikas On Thu, May 20, 2010 at 4:58 AM, Paolo Giannozzi wrote: > Vikas Varshney wrote: > > > I also tried to visualize the output of example02 (phonon spectra) using > > PP/pp.x but was totally unsuccessful. > > you can't visualize phonons with a postprocessing code that is meant to > visualize the charge density, potentials, etc > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100520/591369f0/attachment.htm From miguel.martinez at ehu.es Thu May 20 14:14:28 2010 From: miguel.martinez at ehu.es (Miguel =?ISO-8859-1?B?TWFydO1uZXo=?=) Date: Thu, 20 May 2010 13:14:28 +0100 Subject: [Pw_forum] Visualization of Results In-Reply-To: References: <4BF4F9C9.7060000@democritos.it> Message-ID: <20100520131428.0274081c@mark> plotband.x should help with that. Both postscript and xmgrace output. Regards, Miguel On Thu, 20 May 2010 08:00:16 -0400 Vikas Varshney wrote: > Dear developers, > Thanks for all the answers. > > Dear Paolo, > I did not intend to visualize the phonons. I wanted to see the phonon > dispersion relation. Which postprocessing code should I use for that. > In general, where I can find the information where the output of all > the executables in PP/ directory is mentioned and what information I > would have to provide for each of them, if I want to use them. > > Best Regards, > Vikas > > On Thu, May 20, 2010 at 4:58 AM, Paolo Giannozzi > wrote: > > > Vikas Varshney wrote: > > > > > I also tried to visualize the output of example02 (phonon > > > spectra) using PP/pp.x but was totally unsuccessful. > > > > you can't visualize phonons with a postprocessing code that is > > meant to visualize the charge density, potentials, etc > > > > 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 > > -- ---------------------------------------- Dr. Miguel Martinez Canales Department of Physics & Astronomy University College London Gower Street, London, WC1E 6BT (UK) Fax: +44 207 679 0595 Tlf: +44 207 678 3476 ---------------------------------------- "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 elbuesta at icqmail.com Thu May 20 15:19:59 2010 From: elbuesta at icqmail.com (elbuesta at icqmail.com) Date: Thu, 20 May 2010 09:19:59 -0400 Subject: [Pw_forum] phonon modes for transition state In-Reply-To: References: Message-ID: <8CCC63647C2A9BF-4848-F704@Webmail-m112.sysops.aol.com> From my experience with phonons (that is not big), yes it can and very well. I performed a few phonon calculations on noble metals on transition states generated from NEB optimizations, like you did, and the results obtained were good, one negative frequency corresponding to the exchange path and the all the others positive. All I can say is what is mostly written on the manuals and examples, you have to be really carefull with the thresholds. The energy cutoff must be significant, the charge cutoff very big specially if there is vacuum, a good number of k points are required if the cell is small, the convergence for sel-consistency must be really strict (I would say conv_thr=10-12) and the phonon convergence also (tr2_ph<10-16). I hope it helps. Fabio Negreiros Ribeiro Departamento de Fisica, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil -----Original Message----- From: Stephan Rix <srix at princeton.edu> To: pw_forum at pwscf.org Sent: Wed, May 19, 2010 7:10 pm Subject: [Pw_forum] phonon modes for transition state Dear all, I am trying to calculate the phonon modes for a transition state using ph.x. I am expecting to find one negative/imaginary mode, but all resulting phonon modes are positive. The transition state was optimized using pw.x with nudged elastic band and climbing image. Before running ph.x for the transition state I tested it with respect to necessary thresholds on a fully relaxed equilibrium state and the results were fine. Question: Is ph.x in principle capable of calculating transition state phonon modes, i.e. returning negative/imaginary modes? If so, I would appreciate any ideas or advice on how to obtain the desired negative phonon mode. Thanks for your help. Stephan Stephan Rix Dept. of Chemistry Princeton University Princeton, NJ 08540 _______________________________________________ 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/20100520/902c7866/attachment.htm From sclauzer at sissa.it Thu May 20 15:45:14 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 20 May 2010 15:45:14 +0200 Subject: [Pw_forum] Visualization of Results In-Reply-To: References: <4BF4F9C9.7060000@democritos.it> Message-ID: <4BF53CEA.2070106@sissa.it> This should help: cat espresso-4.2/PlotPhon/Examples/Al_SC/Run_Plot_phonons #!/bin/bash echo 'Plot Phonon Dispersion Relations' echo 'Eyvaz Isaev' echo 'IFM, Linkoping University, Sweden' echo 'Moscow State Institute of Steel and Alloys, Russia' echo 'eyvaz_isaev at yahoo.com, isaev at ifm.liu.se' ... GS On 05/20/2010 02:00 PM, Vikas Varshney wrote: > Dear developers, > Thanks for all the answers. > > Dear Paolo, > I did not intend to visualize the phonons. I wanted to see the phonon > dispersion relation. Which postprocessing code should I use for that. > In general, where I can find the information where the output of all > the executables in PP/ directory is mentioned and what information I > would have to provide for each of them, if I want to use them. > > Best Regards, > Vikas > > On Thu, May 20, 2010 at 4:58 AM, Paolo Giannozzi > > wrote: > > Vikas Varshney wrote: > > > I also tried to visualize the output of example02 (phonon > spectra) using > > PP/pp.x but was totally unsuccessful. > > you can't visualize phonons with a postprocessing code that is > meant to > visualize the charge density, potentials, etc > > 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 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100520/035de5aa/attachment.htm From modaresi.mohsen at gmail.com Thu May 20 19:43:31 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Thu, 20 May 2010 22:13:31 +0430 Subject: [Pw_forum] Low speed In-Reply-To: References: Message-ID: Dear Baris Thanks a lot for your answer. how many scf steps "do you perform in these 3 hours? Does your system have some convergence problems?", It take 12 iteration to perform, And there is no convergence problem "This is especially important if you are using a low memory bandwidth architecture.", I can not understand your hint, We use a P4 machine with 8 core, I think you say we must use Half of them, Is it true? And finally thanks for your answer Moshen Modaresi On 5/20/10, O. Baris Malcioglu wrote: > Dear Mohsen, > Please notice that you have asked a rather vague question regarding > performance, > > First of all, please notice that since PW is a plane wave code, it is > not just the number of atoms that determine the "size" of the system. > You have to take into account the number of plane waves you are using. > This depends on your cutoffs and simulation supercell. Exaggerating > the situation unnecessarily, for example putting only an ethane > molecule in a 500x500x500 Bohr box (even with modest cutoff) will > result in a system size that will certainly give a hard time to the > computer you are describing. In the same sense, using very high > cutoffs will lead to same problem. > > Secondly, "3 hours" is not a good enough criteria, how many scf steps > do you perform in these 3 hours? Does your system have some > convergence problems? > > Finally, 8 cpu is not a good enough identification nowadays, if the > "cpu" you are mentioning is due to hyper-threading, it is usually > better if you use only 4, since you waste your precious memory > bandwidth. This is especially important if you are using a low memory > bandwidth architecture. > > Some general guidelines : > > -Make sure that your computer is not using swap, > -Use architecture dependent acceleration libraries such as MKL. For > example you can setup fftw 3.x to utilize instruction sets such as > sse2. > -If this is a parallel compiler check wall times, how much do you > loose communicating? > > Best, > Baris > > 2010/5/20 Phillip Nyawere : >> You need high speed computer. I tried with 96 atoms and it was taking even >> longer. >> Success. >> >> On Wed, May 12, 2010 at 10:07 PM, mohsen modaresi >> wrote: >>> >>> Dear Developers and users, >>> I run a SCF calculation with 71 atoms on a camputer with 8 cpu and 8GB >>> RAM, i expect it run in some minutes, But it take 3 hours to run. >>> Is it regular? >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >> >> >> >> -- >> Phillip W. Otieno Nyawere, >> Kabarak University, >> Dept of Physics & Mathematics, >> P.O Box Private Bag - 20157, >> Kabarak, Kenya. >> Tel +254728342054 >> pnyawere at gmail.com, potieno at kabarak.ac.ke >> >> The battle belongs to the Lord. >> >> _______________________________________________ >> 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 modaresi.mohsen at gmail.com Thu May 20 19:49:13 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Thu, 20 May 2010 22:19:13 +0430 Subject: [Pw_forum] Low speed In-Reply-To: References: Message-ID: PS, We increased speed with install some external libraries (BLAS, LAPACK, and MPI Lib.), I hope it help to other users. Mohsen On 5/20/10, mohsen modaresi wrote: > Dear Baris > Thanks a lot for your answer. > how many scf steps > "do you perform in these 3 hours? Does your system have some > convergence problems?", It take 12 iteration to perform, And there is > no convergence problem > "This is especially important if you are using a low memory > bandwidth architecture.", I can not understand your hint, We use a P4 > machine with 8 core, I think you say we must use Half of them, Is it > true? > And finally thanks for your answer > Moshen Modaresi > > > On 5/20/10, O. Baris Malcioglu wrote: >> Dear Mohsen, >> Please notice that you have asked a rather vague question regarding >> performance, >> >> First of all, please notice that since PW is a plane wave code, it is >> not just the number of atoms that determine the "size" of the system. >> You have to take into account the number of plane waves you are using. >> This depends on your cutoffs and simulation supercell. Exaggerating >> the situation unnecessarily, for example putting only an ethane >> molecule in a 500x500x500 Bohr box (even with modest cutoff) will >> result in a system size that will certainly give a hard time to the >> computer you are describing. In the same sense, using very high >> cutoffs will lead to same problem. >> >> Secondly, "3 hours" is not a good enough criteria, how many scf steps >> do you perform in these 3 hours? Does your system have some >> convergence problems? >> >> Finally, 8 cpu is not a good enough identification nowadays, if the >> "cpu" you are mentioning is due to hyper-threading, it is usually >> better if you use only 4, since you waste your precious memory >> bandwidth. This is especially important if you are using a low memory >> bandwidth architecture. >> >> Some general guidelines : >> >> -Make sure that your computer is not using swap, >> -Use architecture dependent acceleration libraries such as MKL. For >> example you can setup fftw 3.x to utilize instruction sets such as >> sse2. >> -If this is a parallel compiler check wall times, how much do you >> loose communicating? >> >> Best, >> Baris >> >> 2010/5/20 Phillip Nyawere : >>> You need high speed computer. I tried with 96 atoms and it was taking >>> even >>> longer. >>> Success. >>> >>> On Wed, May 12, 2010 at 10:07 PM, mohsen modaresi >>> wrote: >>>> >>>> Dear Developers and users, >>>> I run a SCF calculation with 71 atoms on a camputer with 8 cpu and 8GB >>>> RAM, i expect it run in some minutes, But it take 3 hours to run. >>>> Is it regular? >>>> >>>> >>>> _______________________________________________ >>>> Pw_forum mailing list >>>> Pw_forum at pwscf.org >>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>> >>> >>> >>> >>> -- >>> Phillip W. Otieno Nyawere, >>> Kabarak University, >>> Dept of Physics & Mathematics, >>> P.O Box Private Bag - 20157, >>> Kabarak, Kenya. >>> Tel +254728342054 >>> pnyawere at gmail.com, potieno at kabarak.ac.ke >>> >>> The battle belongs to the Lord. >>> >>> _______________________________________________ >>> 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 marsamos at democritos.it Fri May 21 11:34:51 2010 From: marsamos at democritos.it (marsamos at democritos.it) Date: Fri, 21 May 2010 11:34:51 +0200 Subject: [Pw_forum] thank you for your contributions to Wyckoff builder Message-ID: <20100521113451.06zo26nfkg8csww0@mail.democritos.it> Dear users, Thank you very much for contributing to the improvement of QE/MOKA. Bug caught in base centered cells!! bests Layla and Riccardo ------------------------- Dr. L. Martin-Samos tel. +39 040 3787 429 CNR-DEMOCRITOS and International School for Advanced Studies (ISAS-SISSA) via Beirut 2-4 34151 Trieste Italy ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From parthasarathi13 at gmail.com Fri May 21 11:41:18 2010 From: parthasarathi13 at gmail.com (partha sarathi ghosh) Date: Fri, 21 May 2010 15:11:18 +0530 Subject: [Pw_forum] negative frequency Message-ID: Dear all, Thank you xirainbow and Michael J. Mehlfor for your reply & suggestion . I was trying to calculate longitudinal phonon dispersion of Zr along [111] direction. I wanted to validate my calculation with experimental results for bcc-Zr (not hcp) given in the paper :Phy.Rev.B,vol-29,page 1575-1587(1984). But I am getting negative frequencies near q=2/3(1 1 1) and the over all appearance of the curve is different from the experimental one. I optimized the system w.r.t ecutwf, ecutrho , k-point sampling , volume ,degauss, conv_thr. I have also tried with different q-point sampling in ph.in file (like 4 4 4, 8 8 8) with tr2_ph=1.0d-12. My questions are : 1. Is DFTP suitable for studying particular phonon mode like in Zr ?? 2. If yes then how to make my calculations efficient ?? 3. If not then any suggestion of other methods ?? Any one can please help me. Thanks in advance. P. S. Ghosh B.A.R.C. INDIA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100521/2ff212cf/attachment.htm From kajalmh18 at gmail.com Fri May 21 12:12:07 2010 From: kajalmh18 at gmail.com (kajal jindal) Date: Fri, 21 May 2010 15:42:07 +0530 Subject: [Pw_forum] Question about plotting DOS Message-ID: Hi, I am working on 3*3*3 supercell of ZnO...and I am replacing two Zn atoms by 2 Co atoms in it...Using the input file projwfc.x, I have calculated the projected DOS.. Firstly I want to know, what is clearly the difference between PDOS and LDOS.??? Also, Since I have 108 atom supercell, So Corresponding to every atom I have a output file containing its DOS.....So, when i want to plot partial DOS for the whole system,shall I take an average of DOS over all Zn atoms and all O atoms and so on????? I am really confused that PDOS for which atom should I consider while plotting PDOS for the whole system???? Thanks in advance, sincerely, Miss Kajal (UTA)(University of Delhi) Junior Research Fellow -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100521/e3e86390/attachment.htm From prasenjit.jnc at gmail.com Fri May 21 12:40:54 2010 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Fri, 21 May 2010 12:40:54 +0200 Subject: [Pw_forum] negative frequency In-Reply-To: References: Message-ID: Dear Partha Sarathi, I am not an expert on phonon calculation and I am also not familiar with your system; however, an imaginary (negative) phonon mode at a non zero q-vector usually indicates that the cell parameters (crystal lattice vectors) which your determined, does not correspond to the equilibrium one. Have you checked how the stresses are with your equilibrium geometry? Also at gamma point, are you getting 3 zero modes and rest non-zero modes? With regards, Prasenjit On 21 May 2010 11:41, partha sarathi ghosh wrote: > Dear all, > ?????????????????????????? Thank you xirainbow and Michael J. Mehlfor for > your reply & suggestion . > ?I was trying to calculate longitudinal phonon dispersion of Zr along [111] > direction. > I wanted to validate my calculation with experimental results for bcc-Zr > (not hcp) given in the paper :Phy.Rev.B,vol-29,page 1575-1587(1984). > But I am getting negative frequencies near q=2/3(1 1 1) and the over all > appearance of the curve is different from the experimental one.? I optimized > the system w.r.t? ecutwf, ecutrho , k-point sampling , volume ,degauss, > conv_thr. I have also tried with different q-point sampling in ph.in file > (like 4 4 4, 8 8 8) with tr2_ph=1.0d-12. > My questions are : > 1. Is DFTP suitable for studying particular phonon mode like in Zr ?? > 2. If yes then how to make my calculations efficient ?? > 3. If not then any suggestion of other methods ?? > ?Any one can please help me. > Thanks in advance. > P. S. Ghosh > B.A.R.C. > INDIA > > _______________________________________________ > 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 From degironc at sissa.it Fri May 21 13:10:47 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 21 May 2010 13:10:47 +0200 Subject: [Pw_forum] negative frequency In-Reply-To: References: Message-ID: <4BF66A37.7020102@sissa.it> If a negative (i.e. imaginary ) frequency is present at a non-zero q point this means that the system is unstable w.r.t a displacement at that q vector and therefore the unit cell for the (static) equilibrium geometry should actually be larger than the one you have chosen and should such that the unstable q-vector folds into the Gamma point of the super-cell. This is indeed the case for bcc Zr where if I remember correctly the bcc phase is stable only at high temperature due to anharmonic effects [see for instance PRB 31 6775-6778 (1985) and PRL 58, 1769-1772 (1987) by Chen, Fu, Ho, and Harmon] Stefano de Gironcoli - SISSA and DEMOCRITOS Prasenjit Ghosh wrote: > Dear Partha Sarathi, > > I am not an expert on phonon calculation and I am also not familiar > with your system; however, an imaginary (negative) phonon mode at a > non zero q-vector usually indicates that the cell parameters (crystal > lattice vectors) which your determined, does not correspond to the > equilibrium one. Have you checked how the stresses are with your > equilibrium geometry? > > Also at gamma point, are you getting 3 zero modes and rest non-zero modes? > > With regards, > Prasenjit > > On 21 May 2010 11:41, partha sarathi ghosh wrote: > >> Dear all, >> Thank you xirainbow and Michael J. Mehlfor for >> your reply & suggestion . >> I was trying to calculate longitudinal phonon dispersion of Zr along [111] >> direction. >> I wanted to validate my calculation with experimental results for bcc-Zr >> (not hcp) given in the paper :Phy.Rev.B,vol-29,page 1575-1587(1984). >> But I am getting negative frequencies near q=2/3(1 1 1) and the over all >> appearance of the curve is different from the experimental one. I optimized >> the system w.r.t ecutwf, ecutrho , k-point sampling , volume ,degauss, >> conv_thr. I have also tried with different q-point sampling in ph.in file >> (like 4 4 4, 8 8 8) with tr2_ph=1.0d-12. >> My questions are : >> 1. Is DFTP suitable for studying particular phonon mode like in Zr ?? >> 2. If yes then how to make my calculations efficient ?? >> 3. If not then any suggestion of other methods ?? >> Any one can please help me. >> Thanks in advance. >> P. S. Ghosh >> B.A.R.C. >> INDIA >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> > > > > From lhe.oum at gmail.com Fri May 21 13:18:16 2010 From: lhe.oum at gmail.com (chaou oum) Date: Fri, 21 May 2010 12:18:16 +0100 Subject: [Pw_forum] input graphene Message-ID: I would like to ask you some questions about DOS of graphene. I have some results, I have not found a good results . Could you please given to me the input file for graphene (scf) and (dos) Many thanks oum.chou PhD student at UFR-PHE Rabat -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100521/8e456d41/attachment.htm From siyouber at yahoo.fr Fri May 21 13:23:12 2010 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Fri, 21 May 2010 11:23:12 +0000 (GMT) Subject: [Pw_forum] Supercells Message-ID: <95897.78788.qm@web26502.mail.ukl.yahoo.com> Dear all, I wanted to built a supercell for my system in QE. I went through the forum and saw some procedures. I followed this: 1. Upload the unit cell in XcrySDen, display the asymmetric unit, modify the number of unit drawn to fit the shape of the desired supercell (2*2*2) and then save the XSF file. 2. From the XSF file, the coordinates of atoms in the supercell are obtained, in angstrom. But the problem is with the CELL. How should I built the CELL parameters and read the final structure with XCrySDen? Note: I choosed the same ibrav as for the unit cell, then multiply the celldm by 2, but the structure does'nt look fine in XCrySDen. Thans for your help ************************* Bertrand SITAMTZE YOUMBI Laboratory of Material Sciences Department of Physics University of Yaounde I-Cameroon ************************************ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100521/e5e1125d/attachment.htm From suza.rri at gmail.com Fri May 21 13:43:36 2010 From: suza.rri at gmail.com (Suza W) Date: Fri, 21 May 2010 13:43:36 +0200 Subject: [Pw_forum] pseudo Message-ID: Dear all, Does anyone have a PZ LDA ultrasoft pseudo potential for Strontium ? Thanking you all, Suza W PhD RRI, Bangalore -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100521/4bc49398/attachment.htm From eyvaz_isaev at yahoo.com Fri May 21 13:46:33 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 21 May 2010 04:46:33 -0700 (PDT) Subject: [Pw_forum] negative frequency In-Reply-To: Message-ID: <971586.32583.qm@web65708.mail.ac4.yahoo.com> Dear Ghosh, Well, first of all, negative modes near q=2/3(111)? means QE works correctly!!! As bcc Zr is a high temperature phase, but DFT deals with T=0K, so, there is no direct way to get stable modes for bcc Zr (Ti, Hf). Instability near q=2/3(111) means the possiblity to transform to \omega phase. At high temperatures phonon-phonon interaction (anharmonicity) becomes important, but it is quite difficult to implement it directly. In the paper you mentioned they do account anharmonic terms (see the papar).? What you can do? Of course, you can perform MD calculations at high temerature and even get? Phonon DOS, but in this way you can not calculate phonon dispersions. Not sure, D3 code can do this (phonon dispersions). The only code that deals with phonons at high temperature is so called SCAILD code. But it is not linear response method, it is based on direct (supercell) method.? I am thinking about is it possible to implement it in QE (sure, it will take time). For reference see PRL 100, 095901 (2008). Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, ? DeTheoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia,partment of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Fri, 5/21/10, partha sarathi ghosh wrote: From: partha sarathi ghosh Subject: [Pw_forum] negative frequency To: pw_forum at pwscf.org Date: Friday, May 21, 2010, 1:41 PM Dear all, ?????????????????????????? Thank you xirainbow and Michael J. Mehlfor for your reply & suggestion . ?I was trying to calculate longitudinal phonon dispersion of Zr along [111] direction. I wanted to validate my calculation with experimental results for bcc-Zr (not hcp) given in the paper :Phy.Rev.B,vol-29,page 1575-1587(1984). But I am getting negative frequencies near q=2/3(1 1 1) and the over all appearance of the curve is different from the experimental one.? I optimized the system w.r.t? ecutwf, ecutrho , k-point sampling , volume ,degauss, conv_thr. I have also tried with different q-point sampling in ph.in file (like 4 4 4, 8 8 8) with tr2_ph=1.0d-12. My questions are : 1. Is DFTP suitable for studying particular phonon mode like in Zr ?? 2. If yes then how to make my calculations efficient ?? 3. If not then any suggestion of other methods ?? ?Any one can please help me. Thanks in advance. P. S. Ghosh B.A.R.C. INDIA? -----Inline Attachment Follows----- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100521/cf37c600/attachment-0001.htm From mohnish.iitk at gmail.com Fri May 21 14:10:02 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Fri, 21 May 2010 17:40:02 +0530 Subject: [Pw_forum] dipole moment of thin film Message-ID: Dear users, I want to calculate the dipole moment of some thin polar films. Does QE has any module for doing the same? And if it does have then that dipole moment is per unit volume (volume of the supercell ) or it is total dipole moment? I am really stuck in this. Thanks a lot in advance, -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100521/cc13f6f2/attachment.htm From amit99266 at rediffmail.com Fri May 21 15:33:51 2010 From: amit99266 at rediffmail.com (Yamit ) Date: 21 May 2010 13:33:51 -0000 Subject: [Pw_forum] =?utf-8?q?input_graphene?= In-Reply-To: Message-ID: <1274442574.S.3561.32882.H.WWNoYW91IG91bQBbUHdfZm9ydW1dIGlucHV0IGdyYXBoZW5l.f4-235-139.old.1274448831.23779@webmail.rediffmail.com> Dear Mr. Oum Chou The input files for graphene is as follows, SCF calculation: &CONTROL calculation = 'scf' restart_mode='from_scratch' prefix='graphene' pseudo_dir = $PSEUDO_DIR outdir = $TMP_DIR / &SYSTEM ibrav=4 celldm(1)=4.6595 celldm(3)=4.0571 ##(Lattice parameters,a=2.465 A (4.6595 a.u.= experimental value of graphite in-plane lattice constant),and c~10.00A as it is 2D material, do put large vacuum region in z direction to minimize interaction between graphene layers.) nat=2 ntyp=1 ecutwfc=40.0 ecutrho=200.0 (#modify ecut according to you psp.) occupations='smearing' #(Provide small amount of smearing, as graphene is semi-metallic system.) smearing='gaussian' nbnd = 8 degauss=0.02 / &ELECTRONS electron_maxstep = 100 conv_thr = 1.0e-8 / ATOMIC_SPECIES C 12.011 C.#your psp file#.UPF ATOMIC_POSITIONS (angstrom) C 0.000000000 0.000000000 0.000000000 C 1.232850116 0.706423116 0.000000000 #Do fix C atoms, to obtain C-C bond length ~1.42A K_POINTS {automatic} 16 16 1 0 0 0 #(1 k-point is Z-direction, as large vacuum is there.) (For DOS calculations use a dense grid of k-points e.g. 32x32x1 or better ) Run, nscf calculation (by changing calculation = 'nscf' in scf file). #################################################################### For DOS calcualtions: dos.in: ============================ &inputpp prefix='graphene' outdir=$TMP_DIR fildos='graphene.dos' Emin=-25.0, Emax=20.0, DeltaE=0.1 / ============================ Get Emin & Emax from band structure values. Just check: "$PATH/espresso-ver/Doc/INPUT_PW.txt" and "$PATH/espresso-ver/Doc/INPUT_DOS.txt" and for details. You can analyse the data in 'graphene.dos', using gnuplot or xmgrace . Warm Regards Amit N. Harode Applications Group : Computational Materials Simulations Computational Research Laboratories Ltd.,(CRL INDIA) Pune - 411004, India. On Fri, 21 May 2010 17:19:34 +0530 wrote > I would like to ask you some questions about DOS of graphene. I have some results, I have not found a good results . Could you please given to me the input file for graphene (scf) and (dos) Many thanks oum.chou PhD student at UFR-PHE Rabat _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum On Fri, 21 May 2010 17:19:34 +0530 wrote >?I would ?like to ask you some questions about ?DOS ?of ?graphene. I have ?some results, ?I ?have not found a good results . ? Could you please? given to me the input file for graphene? (scf) and (dos) Many thanks oum.chou PhD student at UFR-PHE Rabat _______________________________________________ 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/20100521/3d2ebdb0/attachment.htm From amit99266 at rediffmail.com Fri May 21 15:37:12 2010 From: amit99266 at rediffmail.com (Yamit ) Date: 21 May 2010 13:37:12 -0000 Subject: [Pw_forum] =?utf-8?q?input_graphene?= In-Reply-To: Message-ID: <1274442574.S.3561.32882.H.WWNoYW91IG91bQBbUHdfZm9ydW1dIGlucHV0IGdyYXBoZW5l.f4-235-139.old.replied.1274449032.41348@webmail.rediffmail.com> Dear Mr. Oum Chou The input files for graphene is as follows, SCF calculation: &CONTROL calculation = 'scf' restart_mode='from_scratch' prefix='graphene' pseudo_dir = $PSEUDO_DIR outdir = $TMP_DIR / &SYSTEM ibrav=4 celldm(1)=4.6595 celldm(3)=4.0571 ##(Lattice parameters,a=2.465 A (4.6595 a.u.= experimental value of graphite in-plane lattice constant),and c~10.00A as it is 2D material, do put large vacuum region in z direction to minimize interaction between graphene layers.) nat=2 ntyp=1 ecutwfc=40.0 ecutrho=200.0 (#modify ecut according to you psp.) occupations='smearing' #(Provide small amount of smearing, as graphene is semi-metallic system.) smearing='gaussian' nbnd = 8 degauss=0.02 / &ELECTRONS electron_maxstep = 100 conv_thr = 1.0e-8 / ATOMIC_SPECIES C 12.011 C.#your psp file#.UPF ATOMIC_POSITIONS (angstrom) C 0.000000000 0.000000000 0.000000000 C 1.232850116 0.706423116 0.000000000 #Do fix C atoms, to obtain C-C bond length ~1.42A K_POINTS {automatic} 16 16 1 0 0 0 #(1 k-point is Z-direction, as large vacuum is there.) (For DOS calculations use a dense grid of k-points e.g. 32x32x1 or better ) Run, nscf calculation (by changing calculation = 'nscf' in scf file). #################################################################### For DOS calcualtions: dos.in: ============================ &inputpp prefix='graphene' outdir=$TMP_DIR fildos='graphene.dos' Emin=-25.0, Emax=20.0, DeltaE=0.1 / ============================ Get Emin & Emax from band structure values. Just check: "$PATH/espresso-ver/Doc/INPUT_PW.txt" and "$PATH/espresso-ver/Doc/INPUT_DOS.txt" and for details. You can analyse the data in 'graphene.dos', using gnuplot or xmgrace . Warm Regards Amit N. Harode Applications Group : Computational Materials Simulations Computational Research Laboratories Ltd.,(CRL INDIA) Pune - 411004, India. On Fri, 21 May 2010 17:19:34 +0530 wrote > I would like to ask you some questions about DOS of graphene. I have some results, I have not found a good results . Could you please given to me the input file for graphene (scf) and (dos) Many thanks oum.chou PhD student at UFR-PHE Rabat _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum On Fri, 21 May 2010 17:19:34 +0530 wrote >?I would ?like to ask you some questions about ?DOS ?of ?graphene. I have ?some results, ?I ?have not found a good results . ? Could you please? given to me the input file for graphene? (scf) and (dos) Many thanks oum.chou PhD student at UFR-PHE Rabat _______________________________________________ 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/20100521/93e887ad/attachment.htm From Michael.Mehl at nrl.navy.mil Fri May 21 16:39:44 2010 From: Michael.Mehl at nrl.navy.mil (Mike Mehl) Date: Fri, 21 May 2010 10:39:44 -0400 Subject: [Pw_forum] negative frequency In-Reply-To: References: Message-ID: <4BF69B30.3040006@nrl.navy.mil> Dear Ghosh, If I've read the paper correctly, the paper you are looking at is entirely computational, not experimental, so basically you are trying to decide if pseudopotentials used in that paper and in your calculation are going to give the same result. You're not comparing with experiment, which, as has been pointed out by others, is at a high temperature. You want to compare your calculations to Ho's. So have you tried to duplicate the frozen phonon calculations described in the paper? Or, possibly better, Figure 3? On 05/21/2010 05:41 AM, partha sarathi ghosh wrote: > Dear all, > Thank you xirainbow and Michael J. Mehlfor > for your reply & suggestion . > I was trying to calculate longitudinal phonon dispersion of Zr along > [111] direction. > I wanted to validate my calculation with experimental results for bcc-Zr > (not hcp) given in the paper :Phy.Rev.B,vol-29,page 1575-1587(1984). > But I am getting negative frequencies near q=2/3(1 1 1) and the over all > appearance of the curve is different from the experimental one. I > optimized the system w.r.t ecutwf, ecutrho , k-point sampling , volume > ,degauss, conv_thr. I have also tried with different q-point sampling in > ph.in file (like 4 4 4, 8 8 8) with tr2_ph=1.0d-12. > My questions are : > 1. Is DFTP suitable for studying particular phonon mode like in Zr ?? > 2. If yes then how to make my calculations efficient ?? > 3. If not then any suggestion of other methods ?? > Any one can please help me. > Thanks in advance. > P. S. Ghosh > B.A.R.C. > INDIA > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Michael J. Mehl Head, Center for Computational Materials Science Naval Research Laboratory Code 6390 Washington DC From nnlinh at sissa.it Fri May 21 18:02:18 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Fri, 21 May 2010 18:02:18 +0200 Subject: [Pw_forum] Question about plotting DOS In-Reply-To: References: Message-ID: <4BF6AE8A.8030600@sissa.it> kajal jindal wrote: > Hi, > > I am working on 3*3*3 supercell of ZnO...and I am replacing two Zn > atoms by 2 Co atoms in it...Using the input file projwfc.x, I have > calculated the projected DOS.. > Firstly I want to know, what is clearly the difference between PDOS > and LDOS.??? See in: http://www.quantum-espresso.org/input-syntax/INPUT_PROJWFC.html you will have definition of LDOS. > Also, Since I have 108 atom supercell, So Corresponding to every atom > I have a output file containing its DOS.....So, when i want to plot > partial DOS for the whole system,shall I take an average of DOS over > all Zn atoms and all O atoms and so on????? I do not think taking average of PDOS (not DOS) partially over all atom of each species will help you learn somethings, because they are not correlates all each other. Anyway, if you still want to do that, you just do partially linear combination each projected DOS of the same kind atoms. > I am really confused that PDOS for which atom should I consider while > plotting PDOS for the whole system???? > Again, you should specify what you want to do (in my opinion), for example, you want to see the hybridization of Oxygen atom and Zn atom , you just consider only for Oxygen and for Zn that Oxygen binds to. Hope this help. Linh > Thanks in advance, > > sincerely, > Miss Kajal > (UTA)(University of Delhi) > Junior Research Fellow > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ----------------------------------------------------- Nguyen Ngoc Linh, PhD Student c/o: SISSA & CNR-INFM Democritos, via Beirut 2-4, 34014 Trieste (Italy) email: nnlinh at sissa.it phone: +39 04 03787 319 skype: ngoclinh84phys ----------------------------------------------------- "The physics is theoretical but the fun is real" From mohnish.iitk at gmail.com Fri May 21 18:08:22 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Fri, 21 May 2010 21:38:22 +0530 Subject: [Pw_forum] dipole moment of thin polar films Message-ID: Dear users, I want to calculate the dipole moment of some thin polar films. Does QE has any module for doing the same? And if it does have then that dipole moment is per unit volume (volume of the supercell ) or it is total dipole moment? I am really stuck in this. Thanks a lot in advance, -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100521/f08e46a3/attachment-0001.htm From nnlinh at sissa.it Fri May 21 18:12:58 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Fri, 21 May 2010 18:12:58 +0200 Subject: [Pw_forum] Supercells In-Reply-To: <95897.78788.qm@web26502.mail.ukl.yahoo.com> References: <95897.78788.qm@web26502.mail.ukl.yahoo.com> Message-ID: <4BF6B10A.2000408@sissa.it> Bertrand SITAMTZE wrote: > Dear all, > > I wanted to built a supercell for my system in QE. I went through the > forum and saw some procedures. I followed this: > > 1. Upload the unit cell in XcrySDen, display the asymmetric unit, > modify the number of unit drawn to fit the shape of the desired > supercell (2*2*2) and then save the XSF file. > > 2. From the XSF file, the coordinates of atoms in the supercell are > obtained, in angstrom. > > But the problem is with the CELL. How should I built the CELL parameters > I think the CELL parameters should be calculated agree with lattice constants. > and read the final structure with XCrySDen? > I don't understand "final structure". > > Note: I choosed the same ibrav as for the unit cell, then multiply the > celldm by 2, but the structure does'nt look fine in XCrySDen. > Why don't you post the input files that you have on forum, and everyone can help you fix it. Best regards, Linh > Thans for your help > > > > ************************* > Bertrand SITAMTZE YOUMBI > Laboratory of Material Sciences > Department of Physics > University of Yaounde I-Cameroon > ************************************ > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ----------------------------------------------------- Nguyen Ngoc Linh, PhD Student c/o: SISSA & CNR-INFM Democritos, via Beirut 2-4, 34014 Trieste (Italy) email: nnlinh at sissa.it phone: +39 04 03787 319 skype: ngoclinh84phys ----------------------------------------------------- "The physics is theoretical but the fun is real" From nnlinh at sissa.it Fri May 21 18:22:53 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Fri, 21 May 2010 18:22:53 +0200 Subject: [Pw_forum] dipole moment of thin polar films In-Reply-To: References: Message-ID: <4BF6B35D.3060205@sissa.it> mohnish pandey wrote: > Dear users, > I want to calculate the dipole moment of some thin > polar films. Does QE has any module for doing the same? You should read this archives that's related to turning on dipole correction. http://www.democritos.it/pipermail/pw_forum/2009-March/011935.html Then read in http://www.quantum-espresso.org/input-syntax/INPUT_PW.html#id3900364 about the input of "dipfield" and others related. > And if it does have then that dipole moment is per unit volume (volume > of the supercell ) or it is total dipole moment? I am really stuck in > this. Can you define "total dipole moment"?, In my opinion , if you consider a space, you will have dipole moment only in that space. Hope this help Linh > > Thanks a lot in advance, > > -- > Regards, > MOHNISH, > ----------------------------------------------------------------- > Mohnish Pandey > Y6927262,4th Year dual degree student, > Department of Chemical Engineering, > IIT KANPUR, UP, INDIA > +919235721300 > ----------------------------------------------------------------- > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ----------------------------------------------------- Nguyen Ngoc Linh, PhD Student c/o: SISSA & CNR-INFM Democritos, via Beirut 2-4, 34014 Trieste (Italy) email: nnlinh at sissa.it phone: +39 04 03787 319 skype: ngoclinh84phys ----------------------------------------------------- "The physics is theoretical but the fun is real" From giannozz at democritos.it Fri May 21 18:41:20 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 21 May 2010 18:41:20 +0200 Subject: [Pw_forum] dipole moment of thin polar films In-Reply-To: References: Message-ID: <4BF6B7B0.4@democritos.it> mohnish pandey wrote: > I want to calculate the dipole moment of some thin polar films. for a thin polar film, you can try to make a planar average of the charge density (code average.x, doc in the header of PP/average.f90) and then calculate the dipole by integrating along z. P -- Paolo Giannozzi, Democritos and University of Udine, Italy From mohnish.iitk at gmail.com Fri May 21 18:43:35 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Fri, 21 May 2010 22:13:35 +0530 Subject: [Pw_forum] dipole moment of thin polar films In-Reply-To: <4BF6B7B0.4@democritos.it> References: <4BF6B7B0.4@democritos.it> Message-ID: Thanks a lot Dr. Paolo and dear Linh. On Fri, May 21, 2010 at 10:11 PM, Paolo Giannozzi wrote: > mohnish pandey wrote: > > > I want to calculate the dipole moment of some thin polar films. > > for a thin polar film, you can try to make a planar average > of the charge density (code average.x, doc in the header of > PP/average.f90) and then calculate the dipole by integrating > along z. > > 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 > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100521/bf3d441a/attachment.htm From kechang.nju at gmail.com Sat May 22 11:22:02 2010 From: kechang.nju at gmail.com (=?GB2312?B?v8Kzow==?=) Date: Sat, 22 May 2010 17:22:02 +0800 Subject: [Pw_forum] Pseudopotential for "hydrogen-like atoms" or "pseudo hydrogens" Message-ID: Dear all I'm working on the modeling of semiconductor nanostructure and want to cap the surface with H with fractional charge in order to eliminate the surface state. Is there anyone has the pseudopotentials for these so call "hydrogen-like atoms" or "pseudo hydrogens". I need the H(Z=4/3) and H(Z=2/3). For the literature, it seems these pseudo hydrogens are used a lot in VASP. Thanks in advance, sincerely, Ke chang NTU, Sg PHD student -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100522/308b47af/attachment.htm From siyouber at yahoo.fr Sat May 22 13:22:16 2010 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Sat, 22 May 2010 11:22:16 +0000 (GMT) Subject: [Pw_forum] Re : Supercells In-Reply-To: <95897.78788.qm@web26502.mail.ukl.yahoo.com> Message-ID: <317478.35461.qm@web26503.mail.ukl.yahoo.com> Dear all, My problem with the supercell has been solved and I wanted to share it with you. I would like to thank P.Canepa for the useful supercell program. To solve the problem, one could use one of the following methods: 1) Use XCrySDen as I mentioned previously, but once has to modify the number of atoms in the SYSTEM input list according to the total number of atoms in the supercell. Otherwise it will not work. Then the atoms coordinates are in angstrom. 2) Use the Canepa's supercell program to generate the coordinate in crystal units. Here also, the number of atoms in the SYSTEM input list should fit the supercell Both methods have been successfull for me Thanks once again for your help Both --- En date de?: Ven 21.5.10, Bertrand SITAMTZE a ?crit?: De: Bertrand SITAMTZE Objet: [Pw_forum] Supercells ?: "pw code" Date: Vendredi 21 mai 2010, 13h23 Dear all, I wanted to built a supercell for my system in QE. I went through the forum and saw some procedures. I followed this: 1. Upload the unit cell in XcrySDen, display the asymmetric unit, modify the number of unit drawn to fit the shape of the desired supercell (2*2*2) and then save the XSF file. 2. From the XSF file, the coordinates of atoms in the supercell are obtained, in angstrom. But the problem is with the CELL. How should I built the CELL parameters and read the final structure with XCrySDen? Note: I choosed the same ibrav as for the unit cell, then multiply the celldm by 2, but the structure does'nt look fine in XCrySDen. Thans for your help ************************* Bertrand SITAMTZE YOUMBI Laboratory of Material Sciences Department of Physics University of Yaounde I-Cameroon ************************************ -----La pi?ce jointe associ?e suit----- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100522/a6e5c44e/attachment.htm From ttduyle at gmail.com Sat May 22 16:53:56 2010 From: ttduyle at gmail.com (Duy Le) Date: Sat, 22 May 2010 10:53:56 -0400 Subject: [Pw_forum] Pseudopotential for "hydrogen-like atoms" or "pseudo hydrogens" In-Reply-To: References: Message-ID: I don't think VASP provides potential for Z=X/3. Other than Z/3, you might find them in quantum expresso website. -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Sat, May 22, 2010 at 5:22 AM, ?? wrote: > Dear all > > I'm working on the modeling of semiconductor nanostructure and want to cap > the surface with H with fractional charge in order to eliminate the surface > state. Is there anyone has the pseudopotentials for these so call > "hydrogen-like atoms" or "pseudo hydrogens". I need the H(Z=4/3) and > H(Z=2/3). For the literature, it seems these pseudo hydrogens are used a lot > in VASP. > > > Thanks in advance, > > sincerely, > Ke chang > NTU, Sg > PHD student > > _______________________________________________ > 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/20100522/eb946e04/attachment.htm From lhe.oum at gmail.com Sat May 22 18:22:11 2010 From: lhe.oum at gmail.com (chaou oum) Date: Sat, 22 May 2010 17:22:11 +0100 Subject: [Pw_forum] input graphene In-Reply-To: <1274442574.S.3561.32882.H.WWNoYW91IG91bQBbUHdfZm9ydW1dIGlucHV0IGdyYXBoZW5l.f4-235-139.old.replied.1274449032.41348@webmail.rediffmail.com> References: <1274442574.S.3561.32882.H.WWNoYW91IG91bQBbUHdfZm9ydW1dIGlucHV0IGdyYXBoZW5l.f4-235-139.old.replied.1274449032.41348@webmail.rediffmail.com> Message-ID: Many thanks for your replay 2010/5/21 Yamit > > > Dear Mr. Oum Chou > > The input files for graphene is as follows, > > SCF calculation: > > &CONTROL > calculation = 'scf' > restart_mode='from_scratch' > prefix='graphene' > pseudo_dir = $PSEUDO_DIR > outdir = $TMP_DIR > / > &SYSTEM > ibrav=4 > celldm(1)=4.6595 > celldm(3)=4.0571 > ##(Lattice parameters,a=2.465 A (4.6595 a.u.= experimental value of > graphite in-plane lattice constant),and c~10.00A as it is 2D material, do > put large vacuum region in z direction to minimize interaction between > graphene layers.) > > nat=2 > ntyp=1 > ecutwfc=40.0 > ecutrho=200.0 > (#modify ecut according to you psp.) > occupations='smearing' > #(Provide small amount of smearing, as graphene is semi-metallic system.) > smearing='gaussian' > nbnd = 8 > degauss=0.02 > / > &ELECTRONS > electron_maxstep = 100 > conv_thr = 1.0e-8 > / > ATOMIC_SPECIES > C 12.011 C.#your psp file#.UPF > > > ATOMIC_POSITIONS (angstrom) > C 0.000000000 0.000000000 0.000000000 > C 1.232850116 0.706423116 0.000000000 > > #Do fix C atoms, to obtain C-C bond length ~1.42A > > K_POINTS {automatic} > 16 16 1 0 0 0 > > #(1 k-point is Z-direction, as large vacuum is there.) > (For DOS calculations use a dense grid of k-points e.g. 32x32x1 or better ) > > Run, nscf calculation (by changing calculation = 'nscf' in scf file). > > #################################################################### > For DOS calcualtions: > > dos.in: > ============================ > &inputpp > prefix='graphene' > outdir=$TMP_DIR > fildos='graphene.dos' > Emin=-25.0, Emax=20.0, DeltaE=0.1 > / > ============================ > Get Emin & Emax from band structure values. > Just check: "$PATH/espresso-ver/Doc/INPUT_PW.txt" and > "$PATH/espresso-ver/Doc/INPUT_DOS.txt" and for details. You can analyse the > data in 'graphene.dos', using gnuplot or xmgrace . > > Warm Regards > Amit N. Harode > Applications Group : Computational Materials Simulations > Computational Research Laboratories Ltd.,(CRL INDIA) > Pune - 411004, India. > > On Fri, 21 May 2010 17:19:34 +0530 wrote > > I would like > > to ask you some questions about DOS of graphene. I have some results, I > have not found a good results . Could you please given to me the input file > for graphene (scf) and (dos) > > > > Many thanks > > > > oum.chou > PhD student at UFR-PHE Rabat > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > On Fri, 21 May 2010 17:19:34 +0530 wrote > > I would like > > to ask you some questions about DOS of graphene. I have some results, > I have not found a good results . Could you please given to me the > input file for graphene (scf) and (dos) > > > > Many thanks > > > > oum.chou > PhD student at UFR-PHE Rabat > > _______________________________________________ > > 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/20100522/43d5bae3/attachment.htm From 1009ukumar at gmail.com Sat May 22 19:12:44 2010 From: 1009ukumar at gmail.com (sonu kumar) Date: Sat, 22 May 2010 22:42:44 +0530 Subject: [Pw_forum] generation of pseudopotential for Ho? Message-ID: Dear all QE users, I have troubles with generations of pp for Ho. I did many changes in input file( Ho.ps.in)...but no success. 1) i am generating Pseudopotential taking into 6s and 4f states as valence with no semicore. Input file and error are as follows. input file:--------- &input iswitch=3, rlderiv=2.8, eminld=-13.0, emaxld=2.5, deld=0.01d0, nld=2, #4 rel=0, zed=67.0, config="[Xe] 4f10 6s0 " #+3 state dft='LDA', / &inputp lloc=3,#2 pseudotype=1, file_pseudopw='Ho.rrkj3.UPF', zval=10.0, / 2 6S 1 0 0.00 0.00 3.0 3.0 4F 2 3 10.0 0.00 1.30 1.30 error is:--------- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 0 from read_psconfig : error # 2 ps-label wrong? %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 2) i, also, want to take into account semicore states. For that, do i need to just add 5s and 5p into valence? I need your help. I am new to Quantum Espresso. With Regards, Sonu Kumar Phd Student Physics Department Indian Institute of Technology Delhi Delhi-110016 web:-http://www.iitd.ac.in/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100522/9aab6d3e/attachment-0001.htm From maradaki at gmail.com Sun May 23 15:45:50 2010 From: maradaki at gmail.com (moi moi) Date: Sun, 23 May 2010 15:45:50 +0200 Subject: [Pw_forum] cd tests Message-ID: I am new in rhe usage of lunix and to install QE I folow the tutorial. However, in the last step, when I make the quick test to verify that things look good cd tests No files found Could someone help me Thank you -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100523/55bbd988/attachment.htm From ttduyle at gmail.com Sun May 23 22:53:04 2010 From: ttduyle at gmail.com (Duy Le) Date: Sun, 23 May 2010 16:53:04 -0400 Subject: [Pw_forum] cd tests In-Reply-To: References: Message-ID: well, You should start to learn basic commands in unix/linux first. Spend one day or so to go over any unix/linux tutorial for beginner (e.x. http://www.ee.surrey.ac.uk/Teaching/Unix/, tutorial one and two). When you have enough confident with unix/liux, you can start thinking about compiling QE. You might have someone compile it for you. -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Sun, May 23, 2010 at 9:45 AM, moi moi wrote: > I am new in rhe usage of lunix and to install QE I folow the tutorial. > However, in the last step, when I make the quick test to verify that things > look good > > cd tests > > No files found > > Could someone help me > > Thank you > > _______________________________________________ > 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/20100523/106e8169/attachment.htm From modaresi.mohsen at gmail.com Mon May 24 12:53:25 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Mon, 24 May 2010 06:53:25 -0400 Subject: [Pw_forum] Question on epsilon.x In-Reply-To: References: <94938.10910.qm@web33005.mail.mud.yahoo.com> Message-ID: Dear Andrea thanks for your answers, they were helpful for me. I faced with a new question, can any one help me, please?: I run a PW.X with this input file &control calculation = 'scf' restart_mode='from_scratch', prefix='silicon', tstress = .true. tprnfor = .true. pseudo_dir = '/home/nano/Desktop/esp/psudo' outdir='/home/nano/Desktop/esp/out/si' / &system ibrav= 2, celldm(1) =10.20, nat= 2, ntyp= 1, ecutwfc =70.0, / &electrons mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES Si 28.086 Si.pz-vbc.UPF ATOMIC_POSITIONS Si 0.00 0.00 0.00 Si 0.25 0.25 0.25 K_POINTS 10 0.1250000 0.1250000 0.1250000 1.00 0.1250000 0.1250000 0.3750000 3.00 0.1250000 0.1250000 0.6250000 3.00 0.1250000 0.1250000 0.8750000 3.00 0.1250000 0.3750000 0.3750000 3.00 0.1250000 0.3750000 0.6250000 6.00 0.1250000 0.3750000 0.8750000 6.00 0.1250000 0.6250000 0.6250000 3.00 0.3750000 0.3750000 0.3750000 1.00 0.3750000 0.3750000 0.6250000 3.00 Every things done well, But when i run epsilon.x with this input file: &inputpp outdir= '/home/nano/Desktop/esp/out/si' prefix='silicon', calculation= 'eps', / &energy_grid smeartype='gauss' intersmear=0.1 intrasmear=0.1 wmax=30.0d0 wmin=0.0d0 nw=100 shift=0.0d0 / I get this eror: Program POST-PROC v.4.1.2 starts ... Today is 24May2010 at 15:22:14 Parallel version (MPI) Number of processors in use: 1 Reading input file... Broadcasting variables... Reading PW restart file... Planes per process (thick) : nr3 = 40 npp = 40 ncplane = 1600 Proc/ planes cols G planes cols G columns G Pool (dense grid) (smooth grid) (wavefct grid) 1 40 1003 20875 40 1003 20875 295 3215 Fermi energy [eV] is: 5.93574 The system is a dielectric... Performing eps calculation... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from epsilon : error # 1 bad band number %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... and in the command prompt it print: "application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0" Where is the problem? Thanks for your reply. Mohsen Modaresi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100524/8076498e/attachment.htm From ferretti at mit.edu Mon May 24 13:39:41 2010 From: ferretti at mit.edu (Andrea Ferretti) Date: Mon, 24 May 2010 12:39:41 +0100 (BST) Subject: [Pw_forum] Question on epsilon.x In-Reply-To: References: <94938.10910.qm@web33005.mail.mud.yahoo.com> Message-ID: Dear Mohsen, according to the error you get (try always to locate it into the sources) > ???? from epsilon : error #???????? 1 > ???? bad band number your problem is that you didn't compute any empty state. silicon has a gap, you are working with fixed occupations (no smearing, which is the standard choice here), but you are also not specifying the number of bands to be computed, so the code computes just the valence. Note also that during a scf calculation, unoccupied bands are computed with a lowered accuracy. Use diago_full_acc = .TRUE. to lift this optimization and use the full accuracy. (this is not the case of nscf or bands calculations, where diago_full_acc = .TRUE. is the default) Anyway, I would run are the following calculations instead: * scf, only valence bands, just compute the charge density * nscf, compute a certain number of empty states as well (to be checked as a convergence parameter on the epsilon results) * epsilon hope it helps Andrea >> Dear Andrea thanks for your answers, they were helpful for me. >> I faced with a new question, can any one help me, please?: >> I run a PW.X with this input file >> ?&control >> ??? calculation = 'scf' >> ??? restart_mode='from_scratch', >> ??? prefix='silicon', >> ??? tstress = .true. >> ??? tprnfor = .true. >> ??? pseudo_dir = '/home/nano/Desktop/esp/psudo' >> ??? outdir='/home/nano/Desktop/esp/out/si' >> ?/ >> ?&system??? >> ??? ibrav=? 2, celldm(1) =10.20, nat=? 2, ntyp= 1, >> ??? ecutwfc =70.0, >> ?/ >> ?&electrons >> ??? mixing_mode = 'plain' >> ??? mixing_beta = 0.7 >> ??? conv_thr =? 1.0d-8 >> ?/ >> ATOMIC_SPECIES >> ?Si? 28.086? Si.pz-vbc.UPF >> ATOMIC_POSITIONS >> ?Si 0.00 0.00 0.00 >> ?Si 0.25 0.25 0.25 >> K_POINTS >> ?? 10 >> ??? 0.1250000? 0.1250000? 0.1250000?? 1.00 >> ??? 0.1250000? 0.1250000? 0.3750000?? 3.00 >> ??? 0.1250000? 0.1250000? 0.6250000?? 3.00 >> ??? 0.1250000? 0.1250000? 0.8750000?? 3.00 >> ??? 0.1250000? 0.3750000? 0.3750000?? 3.00 >> ??? 0.1250000? 0.3750000? 0.6250000?? 6.00 >> ??? 0.1250000? 0.3750000? 0.8750000?? 6.00 >> ??? 0.1250000? 0.6250000? 0.6250000?? 3.00 >> ??? 0.3750000? 0.3750000? 0.3750000?? 1.00 >> ??? 0.3750000? 0.3750000? 0.6250000?? 3.00 >> Every things done well, But when i run epsilon.x with this input file: >> &inputpp >> ??? outdir= '/home/nano/Desktop/esp/out/si' >> ?? prefix='silicon', >> ?? calculation= 'eps', >> ?/ >> ?&energy_grid >> ??? smeartype='gauss' >> ??? intersmear=0.1 >> ??? intrasmear=0.1 >> ??? wmax=30.0d0 >> ??? wmin=0.0d0 >> ??? nw=100 >> ??? shift=0.0d0 >> ?/ >> >> I get this eror: >> ? Program POST-PROC v.4.1.2? starts ... >> ???? Today is 24May2010 at 15:22:14 >> >> ???? Parallel version (MPI) >> >> ???? Number of processors in use:?????? 1 >> >> >> ???? Reading input file... >> ???? Broadcasting variables... >> ???? Reading PW restart file... >> >> ???? Planes per process (thick) : nr3 = 40 npp =? 40 ncplane = 1600 >> >> ???? Proc/? planes cols???? G??? planes cols??? G????? columns? G >> ???? Pool?????? (dense grid)?????? (smooth grid)????? (wavefct grid) >> ??????? 1??? 40?? 1003??? 20875?? 40?? 1003??? 20875??? 295???? 3215 >> >> >> >> ???? Fermi energy [eV] is:? 5.93574 >> ???? The system is a dielectric... >> >> ???? Performing eps calculation... >> >> ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> ???? from epsilon : error #???????? 1 >> ???? bad band number >> ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> ???? stopping ... >> >> and in the command prompt it print: "application called >> MPI_Abort(MPI_COMM_WORLD, 0) - process 0" >> Where is the problem? >> Thanks for your reply. >> Mohsen Modaresi >> ? >> -- Andrea Ferretti Oxford University, Department of Materials Parks Road, Oxford OX1 3PH, UK Tel: +44 (0)1865 612796; 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 amit99266 at rediffmail.com Mon May 24 15:01:11 2010 From: amit99266 at rediffmail.com (Yamit ) Date: 24 May 2010 13:01:11 -0000 Subject: [Pw_forum] =?utf-8?q?About_F=5FQHA=2Ex?= Message-ID: <20100524130111.37406.qmail@f4mail-235-147.rediffmail.com> Dear All I have attempted to calculate the specific heat of Si using "F_QHA.x", and the calculated Silicon phonon dos as an input. (The calculated Si phonon frequencies are in excellent agreement with available experimental data. ) As the output of "F_QHA.x", I have obtained the following results, (in QHA.out file) ############################################################################################################ # T in K, F_vib in Ry/cell, C_v in R (the universal gas constant by 3N modes), S in k_B ############################################################################################################ # T E_internal F_vibration Specific heat (C_v) Entropy ############################################################################################################ : : 295.00 0.0139740852 0.0055747646 4.6621714979 4.4956255367 300.00 0.0141222695 0.0054311560 4.6966380876 4.5742737931 305.00 0.0142715257 0.0052850687 4.7298757363 4.6521815403 310.00 0.0144218157 0.0051365259 4.7619351485 4.7293532915 : : : ############################################################################################################ From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: 4.6966380876 * 8.314 = 39.048 (where, Gas constant, R = 8.314 J/(mol K) ) and for Silicon N = 2, so 3N=6 modes So, Specific heat, C_v= 38.761 / 3N = 6.5080 J/(mol K) Experimentally the Specific heat, C_v of Si at 25 ??C (~298) is found equal to 9.789 J??mol???1??K???1. Can anybody could explain the reason behind this huge error in the calculation of specific heat ? Warm Regards Amit N. Harode C R Labs INDIA --=_4a06efe62f7e490c411d1ac6750ade1f Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="UTF-8" Dear All

I have attempted to calculate the specific heat of Si using "F_QHA.x", and = the calculated Silicon phonon dos as an input.
(The calculated Si phonon frequencies are in excellent agreement with avail= able experimental data. )

As the output of "F_QHA.x", I have obtained the following results, (in QHA.= out file)

###########################################################################= #################################

# T in K, F_vib in Ry/cell, C_v in R (the universal gas constant by 3N mode= s), S in k_B
###########################################################################= #################################
# T E_internal F_vibration Specific heat (C_v) = Entropy
###########################################################################= #################################
:
:
295.00 0.0139740852 0.0055747646 4.6621714979 = 4.4956255367
300.00 0.0141222695 0.0054311560 4.6966380876 = 4.5742737931
305.00 0.0142715257 0.0052850687 4.7298757363 = 4.6521815403
310.00 0.0144218157 0.0051365259 4.7619351485 = 4.7293532915
:
:
:
###########################################################################= #################################

From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID:
4.6966380876 * 8.314 =3D 39.048
(where, Gas constant, R =3D 8.314 J/(mol K) ) and for Silicon N =3D 2, so 3= N=3D6 modes

So, Specific heat, C_v=3D 38.761 / 3N =3D 6.5080 J/(mol K)

Experimentally the Specific heat, C_v of Si at 25 =C2=B0C (~298) is found e= qual to 9.789 J=C2=B7mol=E2=88=921=C2=B7K=E2=88=921.

Can anybody could explain the reason behind this huge error in the calculat= ion of specific heat ?

Warm Regards
Amit N. Harode
C R Labs INDIA

--=_4a06efe62f7e490c411d1ac6750ade1f-- From marzari at MIT.EDU Mon May 24 15:16:11 2010 From: marzari at MIT.EDU (Nicola Marzari) Date: Mon, 24 May 2010 14:16:11 +0100 Subject: [Pw_forum] About F_QHA.x In-Reply-To: <20100524130111.37406.qmail@f4mail-235-147.rediffmail.com> References: <20100524130111.37406.qmail@f4mail-235-147.rediffmail.com> Message-ID: <4BFA7C1B.50903@mit.edu> Yamit wrote: > Dear All > > I have attempted to calculate the specific heat of Si using "F_QHA.x", > and the calculated Silicon phonon dos as an input. > (The calculated Si phonon frequencies are in excellent agreement with > available experimental data. ) > > As the output of "F_QHA.x", I have obtained the following results, (in > QHA.out file) Try to compare your calculated phonons and phonon DOS for Si first - do they come out as obtained e.g. by Giannozzi/De Gironcoli/Pavone/Baroni PRB 1991 ? 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 eyvaz_isaev at yahoo.com Mon May 24 16:38:16 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 24 May 2010 07:38:16 -0700 (PDT) Subject: [Pw_forum] About F_QHA.x In-Reply-To: <20100524130111.37406.qmail@f4mail-235-147.rediffmail.com> Message-ID: <646254.55091.qm@web65703.mail.ac4.yahoo.com> Dear Amit, Can you please send me your IFC file so I can test it? Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Mon, 5/24/10, Yamit wrote: From: Yamit Subject: [Pw_forum] About F_QHA.x To: pw_forum at pwscf.org Date: Monday, May 24, 2010, 5:01 PM Dear All I have attempted to calculate the specific heat of Si using "F_QHA.x", and the calculated Silicon phonon dos as an input. (The calculated Si phonon frequencies are in excellent agreement with available experimental data. ) As the output of "F_QHA.x", I have obtained the following results, (in QHA.out file) ############################################################################################################ # T in K, F_vib in Ry/cell, C_v in R (the universal gas constant by 3N modes), S in k_B ############################################################################################################ # T E_internal F_vibration Specific heat (C_v) Entropy ############################################################################################################ : : 295.00 0.0139740852 0.0055747646 4.6621714979 4.4956255367 300.00 0.0141222695 0.0054311560 4.6966380876 4.5742737931 305.00 0.0142715257 0.0052850687 4.7298757363 4.6521815403 310.00 0.0144218157 0.0051365259 4.7619351485 4.7293532915 : : : ############################################################################################################ From the above results, at 300 K: 4.6966380876 * 8.314 = 39.048 (where, Gas constant, R = 8.314 J/(mol K) ) and for Silicon N = 2, so 3N=6 modes So, Specific heat, C_v= 38.761 / 3N = 6.5080 J/(mol K) Experimentally the Specific heat, C_v of Si at 25 ?C (~298) is found equal to 9.789 J?mol?1?K?1. Can anybody could explain the reason behind this huge error in the calculation of specific heat ? Warm Regards Amit N. Harode C R Labs INDIA -----Inline Attachment Follows----- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100524/cd04a50e/attachment-0001.htm From amit99266 at rediffmail.com Mon May 24 16:28:21 2010 From: amit99266 at rediffmail.com (Yamit ) Date: 24 May 2010 14:28:21 -0000 Subject: [Pw_forum] =?utf-8?q?About_F=5FQHA=2Ex?= In-Reply-To: <20100524130111.37406.qmail@f4mail-235-147.rediffmail.com> Message-ID: <1274706511.S.7414.43599.H.WVlhbWl0IABbUHdfZm9ydW1dIEFib3V0IEZfUUhBLng_.f4-235-129.old.replied.1274711301.63473@webmail.rediffmail.com> Dear Prof Nicola Marzari Thank you for your reply! The phonon values from this work are in good agreement (with error of ~1-2 %) with the values reported in Giannozzi, PRB 43-7231-1991. ===================================================== Table : (Frequency in cm^{-1},) - & Current work & PRB 43-7231-1991 \ Gamma_{TO/LO} & 525.350461 & 517 \ L_{TA} & 109 & 111 \ L_{LA} & 379 & 378 \ ========================================================= As the output of "F_QHA.x", I have obtained the following results, (in QHA.out file) ############################################################################################################ # T in K, F_vib in Ry/cell, C_v in R (the universal gas constant by 3N modes), S in k_B ############################################################################################################ # T E_internal F_vibration Specific heat (C_v) Entropy ############################################################################################################ : : 295.00 0.0139740852 0.0055747646 4.6621714979 4.4956255367 300.00 0.0141222695 0.0054311560 4.6966380876 4.5742737931 305.00 0.0142715257 0.0052850687 4.7298757363 4.6521815403 310.00 0.0144218157 0.0051365259 4.7619351485 4.7293532915 : : : ############################################################################################################ From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: 4.6966380876 * 8.314 = 39.048 (where, Gas constant, R = 8.314 J/(mol K) ) and for Silicon N = 2, so 3N=6 modes So, Specific heat, C_v= 38.761 / 3N = 6.5080 J/(mol K) Experimentally the Specific heat, C_v of Si at 25 ??C (~298) is found equal to 9.789 J??mol???1??K???1. Can anybody could explain the reason behind this huge error in the calculation of specific heat ? Regards Amit N.Harode CR Labs INDIA > Try to compare your calculated phonons and phonon DOS for Si first - > do they > come out as obtained e.g. by Giannozzi/De Gironcoli/Pavone/Baroni > PRB 1991 ? > nicola On Mon, 24 May 2010 18:38:31 +0530 wrote >Dear All > > I have attempted to calculate the specific heat of Si using "F_QHA.x", and the calculated Silicon phonon dos as an input. > (The calculated Si phonon frequencies are in excellent agreement with available experimental data. ) > > As the output of "F_QHA.x", I have obtained the following results, (in QHA.out file) > > ############################################################################################################ > > # T in K, F_vib in Ry/cell, C_v in R (the universal gas constant by 3N modes), S in k_B > ############################################################################################################ > # T E_internal F_vibration Specific heat (C_v) Entropy > ############################################################################################################ > : > : > 295.00 0.0139740852 0.0055747646 4.6621714979 4.4956255367 > 300.00 0.0141222695 0.0054311560 4.6966380876 4.5742737931 > 305.00 0.0142715257 0.0052850687 4.7298757363 4.6521815403 > 310.00 0.0144218157 0.0051365259 4.7619351485 4.7293532915 > : > : > : > ############################################################################################################ > > From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: > > 4.6966380876 * 8.314 = 39.048 > (where, Gas constant, R = 8.314 J/(mol K) ) and for Silicon N = 2, so 3N=6 modes > > So, Specific heat, C_v= 38.761 / 3N = 6.5080 J/(mol K) > > Experimentally the Specific heat, C_v of Si at 25 ??C (~298) is found equal to 9.789 J??mol???1??K???1. > > Can anybody could explain the reason behind this huge error in the calculation of specific heat ? > > Warm Regards > Amit N. Harode > C R Labs INDIA > _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum --=_376bbf633a2cfff03e99b121171615e6 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="UTF-8"
Dear Prof Nicola Marzari

Thank you for your reply! The phonon values from this work are in good agre= ement (with error of ~1-2 %) with the values reported in Giannozzi, PRB 43-= 7231-1991.

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D
Table : (Frequency in cm^{-1},)

- & Current work & PRB 43-7231-1991

Gamma_{TO/LO} & 525.350461 & 517

L_{TA} & 109 & 111
L_{LA} & 379 & 378
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D


As the output of "F_QHA.x", I have obtained the following results, (in QHA.= out file)

###########################################################################= #################################

# T in K, F_vib in Ry/cell, C_v in R (the universal gas constant by 3N mode= s), S in k_B
###########################################################################= #################################
# T E_internal F_vibration Specific heat (C_v) Entropy
###########################################################################= #################################
:
:
295.00 0.0139740852 0.0055747646 4.6621714979 4.4956255367
300.00 0.0141222695 0.0054311560 4.6966380876 4.5742737931
305.00 0.0142715257 0.0052850687 4.7298757363 4.6521815403
310.00 0.0144218157 0.0051365259 4.7619351485 4.7293532915
:
:
:
###########################################################################= #################################

From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID:
4.6966380876 * 8.314 =3D 39.048
(where, Gas constant, R =3D 8.314 J/(mol K) ) and for Silicon N =3D 2, so 3= N=3D6 modes

So, Specific heat, C_v=3D 38.761 / 3N =3D 6.5080 J/(mol K)

Experimentally the Specific heat, C_v of Si at 25 =C2=B0C (~298) is found e= qual to 9.789 J=C2=B7mol=E2=88=921=C2=B7K=E2=88=921.

Can anybody could explain the reason behind this huge error in the calculat= ion of specific heat ?
Regards
Amit N.Harode
CR Labs INDIA


> Try to compare your calculated phonons and phonon DOS for Si first - > do= they
> come out as obtained e.g. by Giannozzi/De Gironcoli/Pavone/Baroni > PRB 1= 991 ?

> nicola
On Mon, 24 May 2010 18:38:31 +0530 wrote
>Dear All
>

>
I have attempted to calculate the specific heat of Si using "F_QHA.x", and = the calculated Silicon phonon dos as an input.
>
(The calculated Si phonon frequencies are in excellent agreement with avail= able experimental data. )
>

>
As the output of "F_QHA.x", I have obtained the following results, (in QHA.= out file)
>

>
###########################################################################= #################################
>

>
# T in K, F_vib in Ry/cell, C_v in R (the universal gas constant by 3N mode= s), S in k_B
>
###########################################################################= #################################
>
# T E_internal F_vibration Specific heat (C_v) = Entropy
>
###########################################################################= #################################
>
:
>
:
>
295.00 0.0139740852 0.0055747646 4.6621714979 = 4.4956255367
>
300.00 0.0141222695 0.0054311560 4.6966380876 = 4.5742737931
>
305.00 0.0142715257 0.0052850687 4.7298757363 = 4.6521815403
>
310.00 0.0144218157 0.0051365259 4.7619351485 = 4.7293532915
>
:
>
:
>
:
>
###########################################################################= #################################
>

>
From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: >

>
4.6966380876 * 8.314 =3D 39.048
>
(where, Gas constant, R =3D 8.314 J/(mol K) ) and for Silicon N =3D 2, so 3= N=3D6 modes
>

>
So, Specific heat, C_v=3D 38.761 / 3N =3D 6.5080 J/(mol K)
>

>
Experimentally the Specific heat, C_v of Si at 25 =C2=B0C (~298) is found e= qual to 9.789 J=C2=B7mol=E2=88=921=C2=B7K=E2=88=921.
>

>
Can anybody could explain the reason behind this huge error in the calculat= ion of specific heat ?
>

>
Warm Regards
>
Amit N. Harode
>
C R Labs INDIA
>


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--=_376bbf633a2cfff03e99b121171615e6-- From modaresi.mohsen at gmail.com Mon May 24 19:23:15 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Mon, 24 May 2010 21:53:15 +0430 Subject: [Pw_forum] Question on epsilon.x In-Reply-To: References: <94938.10910.qm@web33005.mail.mud.yahoo.com> Message-ID: Thanks Andrea, Your answers are complete and helpful. Thanks again Mohsen From sxu2 at ncsu.edu Mon May 24 20:33:47 2010 From: sxu2 at ncsu.edu (shu xu) Date: Mon, 24 May 2010 14:33:47 -0400 Subject: [Pw_forum] internal error, cannot braket Ef In-Reply-To: References: Message-ID: > > hi, I am doing relaxation of graphene on SiC with tpss pseudopotential and > received the following error message. > I did the relaxation with GGA pseudopotentials and there was no problem. > Why it could not get through with tpss PP? > > > > iteration # 8 ecut= 40.00 Ry beta=0.30 > Davidson diagonalization with overlap > ethr = 1.00E-02, avg # of iterations = 1.0 > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from efermig : error # 1 > > > internal error, cannot braket Ef > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > part of the input file is : > > > > > forc_conv_thr = 1.0D-3, > etot_conv_thr = 1.0D-4, > tstress = .true. , > tprnfor = .true. , > dipfield = .true. , > tefield = .true. , > / > &SYSTEM > > ecutwfc = 40 , > ecutrho = 320 , > occupations = 'smearing' , > degauss = 0.01D0 , > smearing = 'mp' , > edir = 3, > eamp = 0, > eopreg = 0.01, > emaxpos = 0.6302, > / > &ELECTRONS > mixing_mode = 'plain' , > mixing_beta = 0.3 , > diagonalization = 'david' , > > / > &IONS > pot_extrapolation = 'first_order', > wfc_extrapolation = 'first_order' > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100524/a36dd3c3/attachment.htm From ttduyle at gmail.com Mon May 24 21:37:06 2010 From: ttduyle at gmail.com (Duy Le) Date: Mon, 24 May 2010 15:37:06 -0400 Subject: [Pw_forum] internal error, cannot braket Ef In-Reply-To: References: Message-ID: It sounds like you got some problems with smearing. I would try other smearing methods. -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Mon, May 24, 2010 at 2:33 PM, shu xu wrote: > hi, I am doing relaxation of graphene on SiC with tpss pseudopotential and >> received the following error message. >> I did the relaxation with GGA pseudopotentials and there was no problem. >> Why it could not get through with tpss PP? >> >> >> >> iteration # 8 ecut= 40.00 Ry beta=0.30 >> Davidson diagonalization with overlap >> ethr = 1.00E-02, avg # of iterations = 1.0 >> >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> from efermig : error # 1 >> >> >> internal error, cannot braket Ef >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> part of the input file is : >> >> >> >> >> forc_conv_thr = 1.0D-3, >> etot_conv_thr = 1.0D-4, >> tstress = .true. , >> tprnfor = .true. , >> dipfield = .true. , >> tefield = .true. , >> / >> &SYSTEM >> >> ecutwfc = 40 , >> ecutrho = 320 , >> occupations = 'smearing' , >> degauss = 0.01D0 , >> smearing = 'mp' , >> edir = 3, >> eamp = 0, >> eopreg = 0.01, >> emaxpos = 0.6302, >> / >> &ELECTRONS >> mixing_mode = 'plain' , >> mixing_beta = 0.3 , >> diagonalization = 'david' , >> >> / >> &IONS >> pot_extrapolation = 'first_order', >> wfc_extrapolation = 'first_order' >> >> > > _______________________________________________ > 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/20100524/e8fd7897/attachment.htm From eyvaz_isaev at yahoo.com Tue May 25 01:01:57 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 24 May 2010 16:01:57 -0700 (PDT) Subject: [Pw_forum] About F_QHA.x Message-ID: <622427.30746.qm@web65711.mail.ac4.yahoo.com> Hi, Well, let me add that I have found experimental C_v for Al (Phys. Rev. 162, 549). From Table II CV(300K)=22.91(J/mol/K) and C_v(500K)=24.23(J/mol/K) From phonon calculations: C_v(300K)=2.7491(R)? and C_v(500K)=2.9065 (R) From F_QHA.f90: from R to J/(mol K) multiply C_v by 8.314 Doing this, one gets (from calculated): C_v(300K)=2.7491*8.314=22.856 J/mol/K, C_v(500K)=24.164 J/mol/K One can see there is excellent agreement with the experimental data. So, the conversion prescribed in F_QHA.f90 is correct. Please check again experimental data for Si (may be it is in cal/mol/K?). You can note that 4.6966*1.985=9.32 cal/mol/K, not too far from experimental data you provided C_v(300K)=9.789. Besides, may be experimental value is C_p, but not C_v. By the way, you have mistaken. 3N in F_QHA.f90 refers to the total number of phonon modes and has no commons with "mol" unit. Bests, Eyvaz. P.S. In Kittel's textbook provided C_p is about 4.7 cal/mol/K (most likely per atom) Introduction to solid state physics (1996); Fig.5.8 ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Mon, 5/24/10, Yamit wrote: From: Yamit Subject: Re: [Pw_forum] About F_QHA.x To: pw_forum at pwscf.org Date: Monday, May 24, 2010, 6:28 PM Dear Prof Nicola Marzari Thank you for your reply! The phonon values from this work are in good agreement (with error of ~1-2 %) with the values reported in Giannozzi, PRB 43-7231-1991. ===================================================== Table : (Frequency in cm^{-1},) - & Current work & PRB 43-7231-1991 Gamma_{TO/LO} & 525.350461 & 517 L_{TA} & 109 & 111 L_{LA} & 379 & 378 ========================================================= As the output of "F_QHA.x", I have obtained the following results, (in QHA.out file) ############################################################################################################ # T in K, F_vib in Ry/cell, C_v in R (the universal gas constant by 3N modes), S in k_B ############################################################################################################ # T E_internal F_vibration Specific heat (C_v) Entropy ############################################################################################################ : : 295.00 0.0139740852 0.0055747646 4.6621714979 4.4956255367 300.00 0.0141222695 0.0054311560 4.6966380876 4.5742737931 305.00 0.0142715257 0.0052850687 4.7298757363 4.6521815403 310.00 0.0144218157 0.0051365259 4.7619351485 4.7293532915 : : : ############################################################################################################ From the above results, at 300 K: 4.6966380876 * 8.314 = 39.048 (where, Gas constant, R = 8.314 J/(mol K) ) and for Silicon N = 2, so 3N=6 modes So, Specific heat, C_v= 38.761 / 3N = 6.5080 J/(mol K) Experimentally the Specific heat, C_v of Si at 25 ?C (~298) is found equal to 9.789 J?mol?1?K?1. Can anybody could explain the reason behind this huge error in the calculation of specific heat ? Regards Amit N.Harode CR Labs INDIA > Try to compare your calculated phonons and phonon DOS for Si first - > do they > come out as obtained e.g. by Giannozzi/De Gironcoli/Pavone/Baroni > PRB 1991 ? > nicola On Mon, 24 May 2010 18:38:31 +0530? wrote >Dear All > > I have attempted to calculate the specific heat of Si using "F_QHA.x", and the calculated Silicon phonon dos? as an input. > (The calculated Si phonon frequencies are in excellent agreement with available experimental data. ) > > As the output of "F_QHA.x", I have obtained the following results, (in QHA.out file) > > ############################################################################################################ > > # T in K, F_vib in Ry/cell, C_v in R (the universal gas constant by 3N modes), S in k_B > ############################################################################################################ > #???T? ? ? ???E_internal? ? ? ? F_vibration? ? ? ? ? Specific heat (C_v)? ? ???Entropy > ############################################################################################################ > : > : > ? 295.00? ? ? 0.0139740852? ? ? 0.0055747646? ? ? ? ???4.6621714979? ? ? ? ? 4.4956255367 > 300.00? ? ? 0.0141222695? ? ? 0.0054311560? ? ? ? ???4.6966380876? ? ? ? ? 4.5742737931 > 305.00? ? ? 0.0142715257? ? ? 0.0052850687? ? ? ? ???4.7298757363? ? ? ? ? 4.6521815403 > 310.00? ? ? 0.0144218157? ? ? 0.0051365259? ? ? ? ???4.7619351485? ? ? ? ? 4.7293532915 > : > : > : > ############################################################################################################ > > From the above results, at 300 K: > > 4.6966380876? * 8.314 = 39.048 > (where, Gas constant, R = 8.314 J/(mol K) ) and for Silicon N = 2, so 3N=6 modes > > So, Specific heat, C_v= 38.761 / 3N = 6.5080? J/(mol K) > > Experimentally the Specific heat, C_v of Si at 25 ?C (~298) is found equal to 9.789 J?mol?1?K?1. > > Can anybody could explain the reason behind this huge error in the calculation of specific heat ? > > Warm Regards > Amit N. Harode > C R Labs INDIA > _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -----Inline Attachment Follows----- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at democritos.it Tue May 25 10:02:55 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 25 May 2010 10:02:55 +0200 Subject: [Pw_forum] cd tests In-Reply-To: References: Message-ID: On May 23, 2010, at 15:45 , moi moi wrote: > cd tests > > No files found did you download and unpack espresso-4.*-examples.tar.gz ? The subdirectory tests/ is there 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 costanzo at ms.fci.unibo.it Tue May 25 10:16:12 2010 From: costanzo at ms.fci.unibo.it (Francesca Costanzo) Date: Tue, 25 May 2010 10:16:12 +0200 (CEST) Subject: [Pw_forum] 'how to plot the sawtooth potential' Message-ID: Dear Users, After applying the dipole correction to my system, that you clearly explained in various examples ( like dipole examples ), I didn't find how to plot ONLY the sawtooth potential. May be is already explained somewhere and I have just missed this information... Thank you a lot, Ps.your forum is really helpful:) Francesca Costanzo -- Francesca Costanzo, Ph.D. Dipartimento di Chimica Fisica ed Inorganica Viale Risorgimento 4 40136 Bologna tel.0039-051-2093710 fax 0039-051-2093690 From giannozz at democritos.it Tue May 25 12:28:36 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 25 May 2010 12:28:36 +0200 Subject: [Pw_forum] Pseudopotential for "hydrogen-like atoms" or "pseudo hydrogens" In-Reply-To: References: Message-ID: On May 22, 2010, at 11:22 , ?? wrote: > I need the H(Z=4/3) and H(Z=2/3) never heard about such values. Some time ago, upon popular request, I put on the web site these fake H PPs : Z=0.50 http://www.quantum-espresso.org/pseudo/1.3/UPF/H.pz- vbc_050.UPF Z=0.75 http://www.quantum-espresso.org/pseudo/1.3/UPF/H.pz- vbc_075.UPF Z=1.25 http://www.quantum-espresso.org/pseudo/1.3/UPF/H.pz- vbc_125.UPF > Z=1.50 http://www.quantum-espresso.org/pseudo/1.3/UPF/H.pz- vbc_150.UPF 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 Tue May 25 12:30:32 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 25 May 2010 12:30:32 +0200 Subject: [Pw_forum] 'how to plot the sawtooth potential' In-Reply-To: References: Message-ID: <05D78674-42D8-4B8F-BE9C-8ABB56B8C203@democritos.it> On May 25, 2010, at 10:16 , Francesca Costanzo wrote: > I didn't find how to plot ONLY the sawtooth potential. should be pp.x with option plot_num=12 (see Doc/INPUT_PP.*) 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 elahe_afrodit at yahoo.com Tue May 25 13:17:02 2010 From: elahe_afrodit at yahoo.com (eli) Date: Tue, 25 May 2010 04:17:02 -0700 (PDT) Subject: [Pw_forum] (no subject) Message-ID: <675169.74987.qm@web32505.mail.mud.yahoo.com> Dear All I have attempted to calculate the specific heat? from phonon dos as an input. how do i calculate C-v with out deby model?? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100525/727ac4f3/attachment.htm From lhe.oum at gmail.com Tue May 25 14:19:54 2010 From: lhe.oum at gmail.com (chaou oum) Date: Tue, 25 May 2010 13:19:54 +0100 Subject: [Pw_forum] input graphene In-Reply-To: References: <1274442574.S.3561.32882.H.WWNoYW91IG91bQBbUHdfZm9ydW1dIGlucHV0IGdyYXBoZW5l.f4-235-139.old.replied.1274449032.41348@webmail.rediffmail.com> Message-ID: Dear all I would like to ask you about input of bands d'energie ' fermi suface' plot spin-polarized of graphene i would like to do the same work like exemple n8 many thanks oum 2010/5/22 chaou oum > Many thanks for your replay > > 2010/5/21 Yamit > > >> >> Dear Mr. Oum Chou >> >> The input files for graphene is as follows, >> >> SCF calculation: >> >> &CONTROL >> calculation = 'scf' >> restart_mode='from_scratch' >> prefix='graphene' >> pseudo_dir = $PSEUDO_DIR >> outdir = $TMP_DIR >> / >> &SYSTEM >> ibrav=4 >> celldm(1)=4.6595 >> celldm(3)=4.0571 >> ##(Lattice parameters,a=2.465 A (4.6595 a.u.= experimental value of >> graphite in-plane lattice constant),and c~10.00A as it is 2D material, do >> put large vacuum region in z direction to minimize interaction between >> graphene layers.) >> >> nat=2 >> ntyp=1 >> ecutwfc=40.0 >> ecutrho=200.0 >> (#modify ecut according to you psp.) >> occupations='smearing' >> #(Provide small amount of smearing, as graphene is semi-metallic system.) >> smearing='gaussian' >> nbnd = 8 >> degauss=0.02 >> / >> &ELECTRONS >> electron_maxstep = 100 >> conv_thr = 1.0e-8 >> / >> ATOMIC_SPECIES >> C 12.011 C.#your psp file#.UPF >> >> >> ATOMIC_POSITIONS (angstrom) >> C 0.000000000 0.000000000 0.000000000 >> C 1.232850116 0.706423116 0.000000000 >> >> #Do fix C atoms, to obtain C-C bond length ~1.42A >> >> K_POINTS {automatic} >> 16 16 1 0 0 0 >> >> #(1 k-point is Z-direction, as large vacuum is there.) >> (For DOS calculations use a dense grid of k-points e.g. 32x32x1 or better >> ) >> >> Run, nscf calculation (by changing calculation = 'nscf' in scf file). >> >> #################################################################### >> For DOS calcualtions: >> >> dos.in: >> ============================ >> &inputpp >> prefix='graphene' >> outdir=$TMP_DIR >> fildos='graphene.dos' >> Emin=-25.0, Emax=20.0, DeltaE=0.1 >> / >> ============================ >> Get Emin & Emax from band structure values. >> Just check: "$PATH/espresso-ver/Doc/INPUT_PW.txt" and >> "$PATH/espresso-ver/Doc/INPUT_DOS.txt" and for details. You can analyse the >> data in 'graphene.dos', using gnuplot or xmgrace . >> >> Warm Regards >> Amit N. Harode >> Applications Group : Computational Materials Simulations >> Computational Research Laboratories Ltd.,(CRL INDIA) >> Pune - 411004, India. >> >> On Fri, 21 May 2010 17:19:34 +0530 wrote >> > I would like >> >> to ask you some questions about DOS of graphene. I have some results, I >> have not found a good results . Could you please given to me the input file >> for graphene (scf) and (dos) >> >> >> >> Many thanks >> >> >> >> oum.chou >> PhD student at UFR-PHE Rabat >> >> _______________________________________________ >> >> Pw_forum mailing list >> >> Pw_forum at pwscf.org >> >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> On Fri, 21 May 2010 17:19:34 +0530 wrote >> > I would like >> >> to ask you some questions about DOS of graphene. I have some results, >> I have not found a good results . Could you please given to me the >> input file for graphene (scf) and (dos) >> >> >> >> Many thanks >> >> >> >> oum.chou >> PhD student at UFR-PHE Rabat >> >> _______________________________________________ >> >> 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/20100525/c1a9b120/attachment.htm From amit99266 at rediffmail.com Tue May 25 14:58:01 2010 From: amit99266 at rediffmail.com (Yamit ) Date: 25 May 2010 12:58:01 -0000 Subject: [Pw_forum] =?utf-8?q?=28no_subject=29?= In-Reply-To: <675169.74987.qm@web32505.mail.mud.yahoo.com> Message-ID: <1274785896.S.3872.61922.H.WWVsaQBbUHdfZm9ydW1dIChubyBzdWJqZWN0KQ__.f4-235-207.1274792281.36417@webmail.rediffmail.com> Dear Mr. Eli You can use F_QHA.x (or fqha.x, as per your Quantum ESPRESSO distribution). It calculates the specific heat using Quasi-Harmonic Approximation (QHA). The output file is pretty much self-explanatory. About QHA you can get more information from the following reference, S. Baroni, P. Giannozzi, and Eyvaz Isaev "Density-Functional Perturbation Theory for Quasi-Harmonic Calculations,"Reviews in Mineralogy and Geochemistry 2010 71: 39-57. Warm Regards Amit N. Harode Applications Group : Computational Materials Simulations Computational Research Laboratories (CRL INDIA) On Tue, 25 May 2010 16:41:36 +0530 wrote >Dear All I have attempted to calculate the specific heat from phonon dos as an input. how do i calculate C-v with out deby model? _______________________________________________ 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/20100525/fe692d69/attachment.htm From dimeo at democritos.it Tue May 25 15:11:38 2010 From: dimeo at democritos.it (Riccardo Di Meo) Date: Tue, 25 May 2010 15:11:38 +0200 Subject: [Pw_forum] ATLAS DSYGVX problem + mailing list question Message-ID: <4BFBCC8A.9060703@democritos.it> Dear all, I have compiled pw.x and linked it against the last version of the ATLAS/LAPACK packages from netlib. On a specific system, PW (Atlas actually...) complains: ** On entry to DSYGVX parameter number 20 had an illegal value This is quite strange however, since with another input (showing the same &CONTROL/&SYSTEM/&ELECTRONS cards but a different molecule) the executable worked fine for hours without any significant difference between the output of the ATLAS executable and the vanilla one. As you will notice, the offending system is quite tame. Is this a known problem? I found a warning about a similar issue in the QE user_guide for the AIX architecture, but I don't think it applies to my case very well. The code was compiled with gcc4.4 on a 64bit AMD system, and linked against: atlas3.6.0 lapack-3.2.1 fftw-2.1.5 openmpi-1.4.2 Uname reports: Linux hostname 2.6.18-194.el5 #1 SMP Fri Apr 2 14:58:14 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux The offending input and resulting output are in attachment. Thank you for you attention, Best regards, Riccardo Di Meo PS: is there a way to search in the content of the pw_forum archive? I found just one page with the backed up traffic of the archive, but no mean to look into the files online. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: water.input Url: http://www.democritos.it/pipermail/pw_forum/attachments/20100525/94e51310/attachment-0001.asc -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: water.output Url: http://www.democritos.it/pipermail/pw_forum/attachments/20100525/94e51310/attachment-0001.txt From dimeo at democritos.it Tue May 25 15:12:01 2010 From: dimeo at democritos.it (Riccardo Di Meo) Date: Tue, 25 May 2010 15:12:01 +0200 Subject: [Pw_forum] ATLAS DSYGVX problem + mailing list question Message-ID: <4BFBCCA1.30809@democritos.it> Dear all, I have compiled pw.x and linked it against the last version of the ATLAS/LAPACK packages from netlib. On a specific system, PW (Atlas actually...) complains: ** On entry to DSYGVX parameter number 20 had an illegal value This is quite strange however, since with another input (showing the same &CONTROL/&SYSTEM/&ELECTRONS cards but a different molecule) the executable worked fine for hours without any significant difference between the output of the ATLAS executable and the vanilla one. As you will notice, the offending system is quite tame. Is this a known problem? I found a warning about a similar issue in the QE user_guide for the AIX architecture, but I don't think it applies to my case very well. The code was compiled with gcc4.4 on a 64bit AMD system, and linked against: atlas3.6.0 lapack-3.2.1 fftw-2.1.5 openmpi-1.4.2 Uname reports: Linux hostname 2.6.18-194.el5 #1 SMP Fri Apr 2 14:58:14 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux The offending input and resulting output are in attachment. Thank you for you attention, Best regards, Riccardo Di Meo PS: is there a way to search in the content of the pw_forum archive? I found just one page with the backed up traffic of the archive, but no mean to look into the files online. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: water.input Url: http://www.democritos.it/pipermail/pw_forum/attachments/20100525/06d5b688/attachment.asc -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: water.output Url: http://www.democritos.it/pipermail/pw_forum/attachments/20100525/06d5b688/attachment.txt From amit99266 at rediffmail.com Tue May 25 15:29:55 2010 From: amit99266 at rediffmail.com (Yamit ) Date: 25 May 2010 13:29:55 -0000 Subject: [Pw_forum] =?utf-8?q?About_F=5FQHA=2Ex?= In-Reply-To: <622427.30746.qm@web65711.mail.ac4.yahoo.com> Message-ID: <1274741793.S.11278.14637.H.TkV5dmF6IElzYWV2AFJlOiBbUHdfZm9ydW1dIEFib3V0IEZfUUhBLng_.f4-234-202.old.1274794195.29396@webmail.rediffmail.com> Dear Prof. Eyvaz Isaev Thank your explanations! On Tue, 25 May 2010 04:26:33 +0530 wrote >Hi, > One can see there is excellent agreement with the experimental data. >So, the conversion prescribed in F_QHA.f90 is correct. Please check >again experimental data for Si (may be it is in cal/mol/K?). > You can note that 4.6966*1.985=9.32 cal/mol/K, not too far from >experimental data you provided C_v(300K)=9.789. Besides, may be >experimental value is C_p, but not C_v. I would like to correct a mistake in last post, for Si, C (298 K) = 19.789 J.mol^{-1}.K^{-1} (and not 9.789 J.mol^{-1}.K^{-1} ) (Sorry for it.) For Si, C_p - C_v < 0.004 (Ref.:Flubacher et.al, Phil Mag, 4: 39, 273 ? 294) Also, from PRB, 50, 14587, C_v {~300} ~ 20 J.mol^{-1}.K^{-1} Regards Amit N. Harode Well, let me add that I have found experimental C_v for Al (Phys. Rev. 162, 549). From Table II CV(300K)=22.91(J/mol/K) and C_v(500K)=24.23(J/mol/K) From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: Doing this, one gets (from calculated): C_v(300K)=2.7491*8.314=22.856 J/mol/K, C_v(500K)=24.164 J/mol/K By the way, you have mistaken. 3N in F_QHA.f90 refers to the total number of phonon modes and has no commons with "mol" unit. Bests, Eyvaz. P.S. In Kittel's textbook provided C_p is about 4.7 cal/mol/K (most likely per atom) Introduction to solid state physics (1996); Fig.5.8 ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Mon, 5/24/10, Yamit wrote: From: Yamit Subject: Re: [Pw_forum] About F_QHA.x To: pw_forum at pwscf.org Date: Monday, May 24, 2010, 6:28 PM Dear Prof Nicola Marzari Thank you for your reply! The phonon values from this work are in good agreement (with error of ~1-2 %) with the values reported in Giannozzi, PRB 43-7231-1991. ===================================================== Table :(Frequency in cm^{-1},) - & Current work & PRB 43-7231-1991 Gamma_{TO/LO} & 525.350461 & 517 L_{TA} & 109 & 111 L_{LA} & 379 & 378 ========================================================= As the output of "F_QHA.x", I have obtained the following results, (in QHA.out file) ############################################################################################################ # T in K, F_vib in Ry/cell, C_v in R (the universal gas constant by 3N modes), S in k_B ############################################################################################################ # T E_internal F_vibration Specific heat (C_v) Entropy ############################################################################################################ : : 295.00 0.0139740852 0.0055747646 4.6621714979 4.4956255367 300.00 0.0141222695 0.0054311560 4.6966380876 4.5742737931 305.00 0.0142715257 0.0052850687 4.7298757363 4.6521815403 310.00 0.0144218157 0.0051365259 4.7619351485 4.7293532915 : : : ############################################################################################################ From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: 4.6966380876 * 8.314 = 39.048 (where, Gas constant, R = 8.314 J/(mol K) ) and for Silicon N = 2, so 3N=6 modes So, Specific heat, C_v= 38.761 / 3N = 6.5080 J/(mol K) Experimentally the Specific heat, C_v of Si at 25 ??C (~298) is found equal to 9.789 J??mol???1??K???1. Can anybody could explain the reason behind this huge error in the calculation of specific heat ? Regards Amit N.Harode CR Labs INDIA > Try to compare your calculated phonons and phonon DOS for Si first - > do they > come out as obtained e.g. by Giannozzi/De Gironcoli/Pavone/Baroni > PRB 1991 ? > nicola On Mon, 24 May 2010 18:38:31 +0530??? wrote >Dear All > > I have attempted to calculate the specific heat of Si using "F_QHA.x", and the calculated Silicon phonon dos??? as an input. > (The calculated Si phonon frequencies are in excellent agreement with available experimental data. ) > > As the output of "F_QHA.x", I have obtained the following results, (in QHA.out file) > > ############################################################################################################ > > # T in K, F_vib in Ry/cell, C_v in R (the universal gas constant by 3N modes), S in k_B > ############################################################################################################ > #??? ?????? T??? ??? ??? ??? ?????? E_internal??? ??? ??? ??? F_vibration??? ??? ??? ??? ??? Specific heat (C_v)??? ??? ??? ?????? Entropy > ############################################################################################################ > : > : > ??? 295.00??? ??? ??? 0.0139740852??? ??? ??? 0.0055747646??? ??? ??? ??? ??? ?????? 4.6621714979??? ??? ??? ??? ??? 4.4956255367 > 300.00??? ??? ??? 0.0141222695??? ??? ??? 0.0054311560??? ??? ??? ??? ??? ?????? 4.6966380876??? ??? ??? ??? ??? 4.5742737931 > 305.00??? ??? ??? 0.0142715257??? ??? ??? 0.0052850687??? ??? ??? ??? ??? ?????? 4.7298757363??? ??? ??? ??? ??? 4.6521815403 > 310.00??? ??? ??? 0.0144218157??? ??? ??? 0.0051365259??? ??? ??? ??? ??? ?????? 4.7619351485??? ??? ??? ??? ??? 4.7293532915 > : > : > : > ############################################################################################################ > > From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: > > 4.6966380876??? * 8.314 = 39.048 > (where, Gas constant, R = 8.314 J/(mol K) ) and for Silicon N = 2, so 3N=6 modes > > So, Specific heat, C_v= 38.761 / 3N = 6.5080??? J/(mol K) > > Experimentally the Specific heat, C_v of Si at 25 ??C (~298) is found equal to 9.789 J??mol???1??K???1. > > Can anybody could explain the reason behind this huge error in the calculation of specific heat ? > > Warm Regards > Amit N. Harode > C R Labs INDIA > _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -----Inline Attachment Follows----- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum --=_3c2bcaaa63db7e8f797f418158be1bfe Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="UTF-8"
Dear Prof. Eyvaz Isaev

Thank your explanations!

On Tue, 25 May 2010 04:26:33 +0530 wrote
>Hi,
> One can see there is excellent agreement with the experimental data. >So,= the conversion prescribed in F_QHA.f90 is correct. Please check >again exp= erimental data for Si (may be it is in cal/mol/K?).

> You can note that 4.6966*1.985=3D9.32 cal/mol/K, not too far from >experi= mental data you provided C_v(300K)=3D9.789. Besides, may be >experimental v= alue is C_p, but not C_v.

I would like to correct a mistake in last post, for Si, C (298 K) =3D 19.7= 89 J.mol^{-1}.K^{-1} (and not 9.789 J.mol^{-1}.K^{-1} ) (Sorry for it.)

For Si, C_p - C_v < 0.004 (Ref.:Flubacher et.al, Phil Mag, 4: 39, 273 =E2= =80=94 294)

Also, from PRB, 50, 14587, C_v {~300} ~ 20 J.mol^{-1}.K^{-1}


Regards
Amit N. Harode




Well, let me add that I have found experimental C_v for Al (Phys. Rev. 162,= 549). From Table II CV(300K)=3D22.91(J/mol/K) and C_v(500K)=3D24.23(J/mol/= K)



From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: 9065 (R)



From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID:


Doing this, one gets (from calculated):

C_v(300K)=3D2.7491*8.314=3D22.856 J/mol/K, C_v(500K)=3D24.164 J/mol/K





By the way, you have mistaken. 3N in F_QHA.f90 refers to the total number o= f phonon modes and has no commons with "mol" unit.



Bests,

Eyvaz.

P.S. In Kittel's textbook provided C_p is about 4.7 cal/mol/K (most likely = per atom) Introduction to solid state physics (1996); Fig.5.8



-------------------------------------------------------------------

Prof. Eyvaz Isaev,

Department of Physics, Chemistry, and Biology (IFM), Linkoping University, = Sweden

Theoretical Physics Department, Moscow State Institute of Steel & Alloys, R= ussia,

isaev at ifm.liu.se, eyvaz_isaev at yahoo.com



--- On Mon, 5/24/10, Yamit wrote:



From: Yamit

Subject: Re: [Pw_forum] About F_QHA.x

To: pw_forum at pwscf.org

Date: Monday, May 24, 2010, 6:28 PM







Dear Prof Nicola Marzari







Thank you for your reply! The phonon values from this work are in good agre= ement (with error of ~1-2 %) with the values reported in Giannozzi, PRB 43-= 7231-1991.







=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D



Table :(Frequency in cm^{-1},)







- & Current work & PRB 43-7231-1991







Gamma_{TO/LO} & 525.350461 & 517







L_{TA} & 109 & 111



L_{LA} & 379 & 378



=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D











As the output of "F_QHA.x", I have obtained the following results, (in QHA.= out file)







###########################################################################= #################################







# T in K, F_vib in Ry/cell, C_v in R (the universal gas constant by 3N mode= s), S in k_B



###########################################################################= #################################



# T E_internal F_vibration Specific heat (C_v) Entropy



###########################################################################= #################################



:



:



295.00 0.0139740852 0.0055747646 4.6621714979 4.4956255367



300.00 0.0141222695 0.0054311560 4.6966380876 4.5742737931



305.00 0.0142715257 0.0052850687 4.7298757363 4.6521815403



310.00 0.0144218157 0.0051365259 4.7619351485 4.7293532915



:



:



:



###########################################################################= #################################







From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID:






4.6966380876 * 8.314 =3D 39.048



(where, Gas constant, R =3D 8.314 J/(mol K) ) and for Silicon N =3D 2, so 3= N=3D6 modes







So, Specific heat, C_v=3D 38.761 / 3N =3D 6.5080 J/(mol K)







Experimentally the Specific heat, C_v of Si at 25 =C2=B0C (~298) is found e= qual to 9.789 J=C2=B7mol=E2=88=921=C2=B7K=E2=88=921.







Can anybody could explain the reason behind this huge error in the calculat= ion of specific heat ?



Regards



Amit N.Harode



CR Labs INDIA











> Try to compare your calculated phonons and phonon DOS for Si first - > do= they



> come out as obtained e.g. by Giannozzi/De Gironcoli/Pavone/Baroni > PRB 1= 991 ?







> nicola



On Mon, 24 May 2010 18:38:31 +0530=EF=BF=BD wrote



>Dear All



>







>



I have attempted to calculate the specific heat of Si using "F_QHA.x", and = the calculated Silicon phonon dos=EF=BF=BD as an input.



>



(The calculated Si phonon frequencies are in excellent agreement with avail= able experimental data. )



>







>



As the output of "F_QHA.x", I have obtained the following results, (in QHA.= out file)



>







>



###########################################################################= #################################



>







>



# T in K, F_vib in Ry/cell, C_v in R (the universal gas constant by 3N mode= s), S in k_B



>



###########################################################################= #################################



>



#=EF=BF=BD =EF=BF=BD=EF=BF=BD T=EF=BF=BD =EF=BF=BD =EF=BF=BD =EF=BF=BD =EF= =BF=BD=EF=BF=BD E_internal=EF=BF=BD =EF=BF=BD =EF=BF=BD =EF=BF=BD F_vibrati= on=EF=BF=BD =EF=BF=BD =EF=BF=BD =EF=BF=BD =EF=BF=BD Specific heat (C_v)=EF= =BF=BD =EF=BF=BD =EF=BF=BD =EF=BF=BD=EF=BF=BD Entropy



>



###########################################################################= #################################



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:



>



:



>



=EF=BF=BD 295.00=EF=BF=BD =EF=BF=BD =EF=BF=BD 0.0139740852=EF=BF=BD =EF=BF= =BD =EF=BF=BD 0.0055747646=EF=BF=BD =EF=BF=BD =EF=BF=BD =EF=BF=BD =EF=BF=BD= =EF=BF=BD=EF=BF=BD 4.6621714979=EF=BF=BD =EF=BF=BD =EF=BF=BD =EF=BF=BD =EF= =BF=BD 4.4956255367



>



300.00=EF=BF=BD =EF=BF=BD =EF=BF=BD 0.0141222695=EF=BF=BD =EF=BF=BD =EF=BF= =BD 0.0054311560=EF=BF=BD =EF=BF=BD =EF=BF=BD =EF=BF=BD =EF=BF=BD =EF=BF=BD= =EF=BF=BD 4.6966380876=EF=BF=BD =EF=BF=BD =EF=BF=BD =EF=BF=BD =EF=BF=BD 4.5= 742737931



>



305.00=EF=BF=BD =EF=BF=BD =EF=BF=BD 0.0142715257=EF=BF=BD =EF=BF=BD =EF=BF= =BD 0.0052850687=EF=BF=BD =EF=BF=BD =EF=BF=BD =EF=BF=BD =EF=BF=BD =EF=BF=BD= =EF=BF=BD 4.7298757363=EF=BF=BD =EF=BF=BD =EF=BF=BD =EF=BF=BD =EF=BF=BD 4.6= 521815403



>



310.00=EF=BF=BD =EF=BF=BD =EF=BF=BD 0.0144218157=EF=BF=BD =EF=BF=BD =EF=BF= =BD 0.0051365259=EF=BF=BD =EF=BF=BD =EF=BF=BD =EF=BF=BD =EF=BF=BD =EF=BF=BD= =EF=BF=BD 4.7619351485=EF=BF=BD =EF=BF=BD =EF=BF=BD =EF=BF=BD =EF=BF=BD 4.7= 293532915



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:



>



:



>



:



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>



From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID:


>







>



4.6966380876=EF=BF=BD * 8.314 =3D 39.048



>



(where, Gas constant, R =3D 8.314 J/(mol K) ) and for Silicon N =3D 2, so 3= N=3D6 modes



>







>



So, Specific heat, C_v=3D 38.761 / 3N =3D 6.5080=EF=BF=BD J/(mol K)



>







>



Experimentally the Specific heat, C_v of Si at 25 =C2=B0C (~298) is found e= qual to 9.789 J=C2=B7mol=E2=88=921=C2=B7K=E2=88=921.



>







>



Can anybody could explain the reason behind this huge error in the calculat= ion of specific heat ?



>







>



Warm Regards



>



Amit N. Harode



>



C R Labs INDIA



>











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Pw_forum mailing list







Pw_forum at pwscf.org







http://www.democritos.it/mailman/listinfo/pw_forum











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Pw_forum mailing list

Pw_forum at pwscf.org

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Pw_forum mailing list

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--=_3c2bcaaa63db7e8f797f418158be1bfe-- From lhe.oum at gmail.com Tue May 25 15:49:57 2010 From: lhe.oum at gmail.com (chaou oum) Date: Tue, 25 May 2010 14:49:57 +0100 Subject: [Pw_forum] input bands energie graphene Fermi Suface Message-ID: Dear all I would like to ask you about input of bands d'energie ' fermi suface' plot spin-polarized of graphene a have find DOS for graphene i would like to do the same work like exemple n8 'Ni' many thanks oum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100525/aa7cb094/attachment.htm From sxu2 at ncsu.edu Tue May 25 16:57:19 2010 From: sxu2 at ncsu.edu (shu xu) Date: Tue, 25 May 2010 10:57:19 -0400 Subject: [Pw_forum] problems with tpss pseudopotential In-Reply-To: References: Message-ID: Hi, > I am doing a test of scf of ideal graphene with tpss pseudopotential. > it crashed with the error > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > task # 6 > from pzpotrf : error # 14 > problems computing cholesky decomposition > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > you can see from the output that the total energy changed from -22 to > -2863. > > > iteration # 5 ecut= 40.00 Ry beta=0.30 > Davidson diagonalization with overlap > ethr = 1.00E-02, avg # of iterations = 1.1 > Warning: cannot save meta-gga kinetic terms: not implemented. > > total cpu time spent up to now is 3.41 secs > > total energy = -22.63457069 Ry > Harris-Foulkes estimate = -22.97866955 Ry > estimated scf accuracy < 2.78503926 Ry > > iteration # 6 ecut= 40.00 Ry beta=0.30 > Davidson diagonalization with overlap > ethr = 1.00E-02, avg # of iterations = 3.6 > Warning: cannot save meta-gga kinetic terms: not implemented. > > total cpu time spent up to now is 3.68 secs > > total energy = -2863.69961690 Ry > Harris-Foulkes estimate = -22.67770863 Ry > estimated scf accuracy < 0.06270506 Ry > > iteration # 7 ecut= 40.00 Ry beta=0.30 > Davidson diagonalization with overlap > c_bands: 4 eigenvalues not converged > c_bands: 4 eigenvalues not converged > > > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > pseudo_dir = '../pseudo' , > outdir = './', > prefix = 'GR' , > wf_collect=.true., > forc_conv_thr = 1.0D-3, > etot_conv_thr = 1.0D-4, > tstress = .true. , > tprnfor = .true. , > / > &SYSTEM > ibrav = 4, > celldm(1) = 4.601, > celldm(3) = 5.0, > nat = 2, > ntyp = 1, > ecutwfc = 40 , > ecutrho = 320 , > occupations = 'smearing' , > degauss = 0.03D0 , > smearing = 'cold' , > / > &ELECTRONS > mixing_mode = 'plain' , > mixing_beta = 0.3 , > diagonalization = 'david', > > / > ATOMIC_SPECIES > C 12.0107 C.tpss-mt.UPF > ATOMIC_POSITIONS alat > C 0.000000000 0.000000000 0.000000000 > C 0.000000000 0.577350269 0.000000000 > K_POINTS automatic > 16 16 1 0 0 0 > > so what is wrong? > Shu Xu phD of Dept. of Physics NCSU USA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100525/97d4ba35/attachment.htm From ttduyle at gmail.com Tue May 25 17:30:38 2010 From: ttduyle at gmail.com (Duy Le) Date: Tue, 25 May 2010 11:30:38 -0400 Subject: [Pw_forum] input bands energie graphene Fermi Suface In-Reply-To: References: Message-ID: I don't know what the example n8 is about, but if you want to do the same thing, you just need to replace all the parameters of Ni system to those of graphene system. -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Tue, May 25, 2010 at 9:49 AM, chaou oum wrote: > Dear all > I would like to ask you about input of bands d'energie ' fermi suface' > plot spin-polarized of graphene > a have find DOS for graphene i would like to do the same work like exemple > n8 'Ni' > many thanks > oum > > _______________________________________________ > 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/20100525/fdee925f/attachment.htm From lhe.oum at gmail.com Tue May 25 17:47:06 2010 From: lhe.oum at gmail.com (chaou oum) Date: Tue, 25 May 2010 16:47:06 +0100 Subject: [Pw_forum] input bands energie graphene Fermi Suface In-Reply-To: References: Message-ID: but a need same input as :starting_magnetization for graphene (starting_magnetization(1)=0.8 for Ni) 2010/5/25 Duy Le > I don't know what the example n8 is about, but if you want to do the same > thing, you just need to replace all the parameters of Ni system to those of > graphene system. > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > > "Men don't need hand to do things" > > > On Tue, May 25, 2010 at 9:49 AM, chaou oum wrote: > >> Dear all >> I would like to ask you about input of bands d'energie ' fermi suface' >> plot spin-polarized of graphene >> a have find DOS for graphene i would like to do the same work like >> exemple n8 'Ni' >> many thanks >> oum >> >> _______________________________________________ >> 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/20100525/66fce2d4/attachment.htm From giannozz at democritos.it Tue May 25 19:10:06 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 25 May 2010 19:10:06 +0200 Subject: [Pw_forum] ATLAS DSYGVX problem + mailing list question In-Reply-To: <4BFBCCA1.30809@democritos.it> References: <4BFBCCA1.30809@democritos.it> Message-ID: <69498ADC-497D-4F48-8B3E-EFDA641F3E38@democritos.it> On May 25, 2010, at 15:12 , Riccardo Di Meo wrote: > PS: is there a way to search in the content of the pw_forum archive? there are two (none of which is good, IMHO, or at least, I never find anything when I search for something). See: http://www.quantum-espresso.org/ => contacts 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 Tue May 25 19:14:49 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 25 May 2010 19:14:49 +0200 Subject: [Pw_forum] ATLAS DSYGVX problem + mailing list question In-Reply-To: <4BFBCCA1.30809@democritos.it> References: <4BFBCCA1.30809@democritos.it> Message-ID: <68887660-2E98-44B0-AE37-D67C5D2FD1AC@democritos.it> On May 25, 2010, at 15:12 , Riccardo Di Meo wrote: > ** On entry to DSYGVX parameter number 20 had an illegal value called by PW/rdiaghg.f90, parameter number 20 is lwork. It is set according to what the lapack manual says it should be set to. Please print its value and see if there is something obviously wrong Paolo PS: do not compile with 64-bit integers as default. It produces all sort of funny problems. --- 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 Tue May 25 19:17:21 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 25 May 2010 19:17:21 +0200 Subject: [Pw_forum] problems with tpss pseudopotential In-Reply-To: References: Message-ID: On May 25, 2010, at 16:57 , shu xu wrote: > I am doing a test of scf of ideal graphene with tpss pseudopotential. tpss meta-gga is 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 modaresi.mohsen at gmail.com Tue May 25 19:18:06 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Tue, 25 May 2010 21:48:06 +0430 Subject: [Pw_forum] Question on epsilon.x In-Reply-To: References: <94938.10910.qm@web33005.mail.mud.yahoo.com> Message-ID: Dear users, at first, i am so sorry that i asked many question about "epsilon.x". But i faced with "USPP are not implemented", Which means i can not use ultrasoft pseudopotentials but i want work with Ba and Ti, is there any another Ref. for pseudopotentials or can i solve this problem in some way? Thanks for your reply Mohsen Modaresi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100525/b48fde98/attachment-0001.htm From giannozz at democritos.it Tue May 25 19:21:15 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 25 May 2010 19:21:15 +0200 Subject: [Pw_forum] problems with tpss pseudopotential In-Reply-To: References: Message-ID: <4FEBB3C6-57A9-4985-95DA-0A2A67BBFB67@democritos.it> On May 25, 2010, at 16:57 , shu xu wrote: > ecutwfc = 40 , > ecutrho = 320 , I don't think meta-gga is implemented together with double grid. In any case, you do not need the double grid, since meta-gga is not implemenetd for ultrasoft PPs. Do not specify ecutrho. 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 sh.shapt at gmail.com Tue May 25 19:32:22 2010 From: sh.shapt at gmail.com (Shaptrishi Sharma) Date: Tue, 25 May 2010 18:32:22 +0100 Subject: [Pw_forum] Cannot converge a calculation Message-ID: Hi all, I would like to converge my system but I acn se that if I vary a single parameter also there is a huge variation in result. For example, when I kept the cell _parameter as 1 0 0 1 1.5 0 1 0 1.5 the total energy seems to change from 0.087 eV to 0.601 eV . Can anybody please advice me ? Thanks Shapt Pune University Pune India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100525/7ae6da21/attachment.htm From dimeo at democritos.it Tue May 25 20:31:23 2010 From: dimeo at democritos.it (Riccardo Di Meo) Date: Tue, 25 May 2010 20:31:23 +0200 Subject: [Pw_forum] ATLAS DSYGVX problem + mailing list question In-Reply-To: <69498ADC-497D-4F48-8B3E-EFDA641F3E38@democritos.it> References: <4BFBCCA1.30809@democritos.it> <69498ADC-497D-4F48-8B3E-EFDA641F3E38@democritos.it> Message-ID: <4BFC177B.2040102@democritos.it> Paolo Giannozzi wrote: > On May 25, 2010, at 15:12 , Riccardo Di Meo wrote: > > >> PS: is there a way to search in the content of the pw_forum archive? >> > > there are two (none of which is good, IMHO, or at least, I never find > anything when I search for something). See: > http://www.quantum-espresso.org/ => contacts > I'll try it next time, before searching help in the list, Thank you, Riccardo > 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 eyvaz_isaev at yahoo.com Tue May 25 22:51:53 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 25 May 2010 13:51:53 -0700 (PDT) Subject: [Pw_forum] C_v calculations In-Reply-To: <675169.74987.qm@web32505.mail.mud.yahoo.com> Message-ID: <9410.46563.qm@web65702.mail.ac4.yahoo.com> Dear Eli, See QHA in QuantumESPRESSO v.4.2. More questions, please let me know. Please provide your affiliation, too. Bests, Eyvaz. P.S. I have noticed many times that people who submits a question is not worried about the Subject or? mail content is completely different from the subject. Evidently, this may cause not responding to a? message or late respond. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Tue, 5/25/10, eli wrote: From: eli Subject: [Pw_forum] (no subject) To: pw_forum at pwscf.org Date: Tuesday, May 25, 2010, 3:17 PM Dear All I have attempted to calculate the specific heat? from phonon dos as an input. how do i calculate C-v with out deby model?? -----Inline Attachment Follows----- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100525/2de16b5b/attachment.htm From eyvaz_isaev at yahoo.com Tue May 25 23:26:22 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 25 May 2010 14:26:22 -0700 (PDT) Subject: [Pw_forum] About F_QHA.x Message-ID: <786553.4282.qm@web65714.mail.ac4.yahoo.com> Hi, Let me finish this discussion about? the heat capacity conversion. Well, I have calculated C_v for graphite with 4 atoms in the unit cell (hexagonal). Calculated C_v(295K)= 4.0758 (R).? Now converting it to J/mol/K we get 4.0758*8.3145/4=8.472 J/mol/K which is very good agreement with? 8.517 J/mol/K. Please pay attention that in this case C_v is per atom, not for the unit cell. Applying the same procedure for Si we get: 4.6966*8.314/2 = 39.048/2 = 19.524 J/mpl/K that matches very well 19.789 you updated (see below). > I would like to correct a mistake in last post, for Si, C (298 K) = > 19.789 J.mol^{-1}.K^{-1} (and not 9.789 J.mol^{-1}.K^{-1} ) (Sorry for > it.) > Also, from PRB, 50, 14587, C_v {~300} ~ 20 J.mol^{-1}.K^{-1} > For Si, C_p - C_v < 0.004 (Ref.:Flubacher et.al, Phil Mag, 4: 39, 273 > ? 294) Yes, sure there will be not too much difference in between C_p and C_v at room temperature. > Can anybody could explain the reason behind this huge error in the > calculation of specific heat ? Hopefully, now it is explained. Just be sure in comparison with an experimental data whether C_v(Exp) is for per atom or per cell or formula unit, etc. Bests, Eyvaz ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From njuxuyuehua at gmail.com Wed May 26 06:13:26 2010 From: njuxuyuehua at gmail.com (xu yuehua) Date: Wed, 26 May 2010 12:13:26 +0800 Subject: [Pw_forum] how to deal with the IR calculation for a metal--no smearing option in scf can not convergence Message-ID: Dear all: i want to calculate the IR intensity for metal. now, i have deleted the occupation option and so on in SCF file base upon the suggestion in this forum, but the scf can not convergence, so it is serious, i have changed other parameters, such as mix_beta.mix_mode. still not convergence, so i am thinking about how to deal with this problem?/ anyone who experience the same question, please give me some ideas. i would be appreciated -- Yuehua Xu Group of Computational Condensed Matter Physics, National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, P. R. China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100526/6b7c956f/attachment.htm From amit99266 at rediffmail.com Wed May 26 08:52:33 2010 From: amit99266 at rediffmail.com (Yamit ) Date: 26 May 2010 06:52:33 -0000 Subject: [Pw_forum] =?utf-8?q?input_bands_energie_graphene_Fermi_Suface?= In-Reply-To: Message-ID: <1274802112.S.7205.41252.H.WWNoYW91IG91bQBSZTogW1B3X2ZvcnVtXSBpbnB1dCBiYW5kcyBlbmVyZ2llIGdyYXBoZW5lIEZlcm1pIFM_.f4-235-216.1274856753.7809@webmail.rediffmail.com> Dear Mr. Chaou Oum The values for starting_magnetization between -1 (completely down magnetized) and 1 (completely up magnetized).(Default value is equal to zero.)(Refer: $ESPRESSO_DIR/DOC/INPUT_PW.txt) Just test for this range (by performing series of scf runs) and you can work with the value at which you can get minimum total energy. Warm Regards Amit N. Harode CRL INDIA On Tue, 25 May 2010 21:11:52 +0530 wrote >but a need same input as :starting_magnetization for graphene (starting_magnetization(1)=0.8 for Ni) 2010/5/25 Duy Le I don't know what the example n8 is about, but if you want to do the same thing, you just need to replace all the?parameters?of Ni system to those of graphene system.-------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Tue, May 25, 2010 at 9:49 AM, chaou oum wrote: Dear all I would like to? ask you? about input of bands d'energie ' fermi suface'? plot spin-polarized of graphene a have find DOS for graphene i would like to do the same work like? exemple n8 'Ni' many thanks oum _______________________________________________ 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/20100526/d2b74b00/attachment.htm From giannozz at democritos.it Wed May 26 09:10:20 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 26 May 2010 09:10:20 +0200 Subject: [Pw_forum] how to deal with the IR calculation for a metal--no smearing option in scf can not convergence In-Reply-To: References: Message-ID: <4BFCC95C.1000403@democritos.it> xu yuehua wrote: > i want to calculate the IR intensity for metal. zero P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From sclauzer at sissa.it Tue May 25 11:52:15 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 25 May 2010 11:52:15 +0200 Subject: [Pw_forum] 'how to plot the sawtooth potential' In-Reply-To: References: Message-ID: <9621DEF5-ABBD-469F-B25C-9AC805F16B77@sissa.it> From Doc/INPUT_PP.txt I guess that you should call pp.x with plot_num=12. 12 = the electric field potential Not completely sure that's what you want, though. HTH GS Il giorno 25/mag/10, alle ore 10:16, Francesca Costanzo ha scritto: > Dear Users, > > After applying the dipole correction to my system, that you clearly > explained in various examples ( like dipole examples ), > I didn't find how to plot ONLY the sawtooth potential. > May be is already explained somewhere and I have just missed this > information... > Thank you a lot, > > Ps.your forum is really helpful:) > > Francesca Costanzo > > -- > Francesca Costanzo, Ph.D. > Dipartimento di Chimica Fisica ed Inorganica > Viale Risorgimento 4 > 40136 Bologna > tel.0039-051-2093710 > fax 0039-051-2093690 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100525/cd7c36ef/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 1753 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100525/cd7c36ef/attachment.bin From pnyawere at gmail.com Wed May 26 09:39:16 2010 From: pnyawere at gmail.com (Phillip Nyawere) Date: Wed, 26 May 2010 10:39:16 +0300 Subject: [Pw_forum] Supercells In-Reply-To: <95897.78788.qm@web26502.mail.ukl.yahoo.com> References: <95897.78788.qm@web26502.mail.ukl.yahoo.com> Message-ID: If the cell spacing was 1 unit for the unit cell then divide it by two for 2 unit cells. Place the atoms manually at this new spacing and then view in the xcrysden. It requires a lot of practice but after sometime you will be used to it. Cheers On Fri, May 21, 2010 at 2:23 PM, Bertrand SITAMTZE wrote: > Dear all, > > I wanted to built a supercell for my system in QE. I went through the forum > and saw some procedures. I followed this: > > 1. Upload the unit cell in XcrySDen, display the asymmetric unit, modify > the number of unit drawn to fit the shape of the desired supercell (2*2*2) > and then save the XSF file. > > 2. From the XSF file, the coordinates of atoms in the supercell are > obtained, in angstrom. > > But the problem is with the CELL. How should I built the CELL parameters > and read the final structure with XCrySDen? > > > Note: I choosed the same ibrav as for the unit cell, then multiply the > celldm by 2, but the structure does'nt look fine in XCrySDen. > > Thans for your help > > > > ************************* > Bertrand SITAMTZE YOUMBI > Laboratory of Material Sciences > Department of Physics > University of Yaounde I-Cameroon > ************************************ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Phillip W. Otieno Nyawere, Kabarak University, Dept of Physics & Mathematics, P.O Box Private Bag - 20157, Kabarak, Kenya. Tel +254728342054 pnyawere at gmail.com, potieno at kabarak.ac.ke The battle belongs to the Lord. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100526/7105f923/attachment.htm From lfhuang at theory.issp.ac.cn Wed May 26 12:03:48 2010 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Wed, 26 May 2010 18:03:48 +0800 Subject: [Pw_forum] =?utf-8?q?how_to_deal_with_the_IR_calculation_for_a_me?= =?utf-8?q?tal--no_smearing_option_in_scf_can_not_convergence?= Message-ID: <20100526100348.29340.qmail@ms.hfcas.ac.cn> Dear Y. H. Xu: In physics, any electromagnetic wave can not transmit in the infinite bulk of a metal, which has been shown by Maxwell's equations by many books. In computation, the calculation method for the IR&Raman spectroscopy that PWSCF provided is feasible to insulators or semiconductors. However, maybe in some experiments, very thin metal films can be characterized by optical methods. But the process behind may be somewhat a little complicated, especially the effect of electrons. Some physic models and analytic derivation may be needed here. May these have some help. Best Wishes! Yours Sincerely L. F. Huang > Date: Wed, 26 May 2010 12:13:26 +0800 > From: xu yuehua > Subject: [Pw_forum] how to deal with the IR calculation for a > metal--no smearing option in scf can not convergence > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear all: > > i want to calculate the IR intensity for metal. > > now, i have deleted the occupation option and so on in SCF file base upon > the suggestion in this forum, > > but the scf can not convergence, so it is serious, i have changed other > parameters, such as mix_beta.mix_mode. > > still not convergence, > > so i am thinking about how to deal with this problem?/ > > anyone who experience the same question, please give me some ideas. > > i would be appreciated > > -- > Yuehua Xu > Group of Computational Condensed Matter Physics, > National Laboratory of Solid State Microstructures and Department of > Physics, > Nanjing University, > Nanjing 210093, > P. R. China ------ ====================================================================== L.F.Huang(???) 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/20100526/30251226/attachment.htm From 1009ukumar at gmail.com Wed May 26 16:03:53 2010 From: 1009ukumar at gmail.com (sonu kumar) Date: Wed, 26 May 2010 19:33:53 +0530 Subject: [Pw_forum] Help regarding the generation of Pseudopotentials for rare earths? Message-ID: Dear all QE users, I am new user of Quantum Espresso. Can anybody tell/give me PP generation files/links etc., to generate "PP" for rare earth elements using *ld1.x* ? http://www.quantum-espresso.org/pseudo.php doesn't contain pp for rare earths. With kind regards, Sonu Kumar -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100526/18ae704b/attachment.htm From nnlinh at sissa.it Wed May 26 17:08:47 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Wed, 26 May 2010 17:08:47 +0200 Subject: [Pw_forum] Help regarding the generation of Pseudopotentials for rare earths? In-Reply-To: References: Message-ID: <4BFD397F.6090606@sissa.it> sonu kumar wrote: > Dear all QE users, > > I am new user of Quantum Espresso. > Can anybody tell/give me PP generation files/links etc., to generate > "PP" for rare earth elements using *ld1.x* ? Let use: http://www.quantum-espresso.org/input-syntax/INPUT_LD1.html to understand the input file of ld1.x Also in ./atomic_doc directory, you can find some example of input file. Hope this help, Linh > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ----------------------------------------------------- Nguyen Ngoc Linh, PhD Student c/o: SISSA & CNR-INFM Democritos, via Beirut 2-4, 34014 Trieste (Italy) email: nnlinh at sissa.it phone: +39 04 03787 319 skype: ngoclinh84phys ----------------------------------------------------- "The physics is theoretical but the fun is real" From dimeo at democritos.it Wed May 26 17:47:40 2010 From: dimeo at democritos.it (Riccardo Di Meo) Date: Wed, 26 May 2010 17:47:40 +0200 Subject: [Pw_forum] ATLAS DSYGVX problem + mailing list question In-Reply-To: <68887660-2E98-44B0-AE37-D67C5D2FD1AC@democritos.it> References: <4BFBCCA1.30809@democritos.it> <68887660-2E98-44B0-AE37-D67C5D2FD1AC@democritos.it> Message-ID: <4BFD429C.5030306@democritos.it> Paolo Giannozzi wrote: > On May 25, 2010, at 15:12 , Riccardo Di Meo wrote: > > >> ** On entry to DSYGVX parameter number 20 had an illegal value >> > > called by PW/rdiaghg.f90, parameter number 20 is lwork. It is set > according > to what the lapack manual says it should be set to. Please print its > value and > see if there is something obviously wrong > well, I don't know why the value is wrong, but it's clear something fishy is going on: using a "print *," the plain version reports lwork to be 48 (N = 6, NB = 32), where the atlas one reports lwork to be 24 (N = 6, NB = 1). It seems therefore that the culprit is the line: nb = ILAENV( 1, 'DSYTRD', 'U', n, -1, -1, -1 ) which produces two different results with the same input, although I don't know why. > Paolo > > PS: do not compile with 64-bit integers as default. It produces all > sort of > funny problem I used the default flags for compilation (which, I assume, produce 64 bit integers, if gfortran works as gcc does), however I didn't found a way to downgrade the integer size to 4 (besides the obvious, and wrong way, of -m32), or at least the manpages for gcc and gfortran doesn't seem to mention the possibility. Am I missing something? Hope this helps, let me know if more info are needed Thank you, Riccardo From giannozz at democritos.it Wed May 26 18:05:42 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 26 May 2010 18:05:42 +0200 Subject: [Pw_forum] ATLAS DSYGVX problem + mailing list question In-Reply-To: <4BFD429C.5030306@democritos.it> References: <4BFBCCA1.30809@democritos.it> <68887660-2E98-44B0-AE37-D67C5D2FD1AC@democritos.it> <4BFD429C.5030306@democritos.it> Message-ID: <4BFD46D6.2050806@democritos.it> Riccardo Di Meo wrote: > It seems therefore that the culprit is the line: > > nb = ILAENV( 1, 'DSYTRD', 'U', n, -1, -1, -1 ) > > which produces two different results with the same input, although I > don't know why. ILAENV is a Lapack auxiliary routine. The Atlas version of ILAENV should return the value of nb that is most suited to the Atlas version of Lapack. Apparently it doesn't even return a correct value. Not a QE problem, apparently. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Wed May 26 18:07:35 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 26 May 2010 18:07:35 +0200 Subject: [Pw_forum] Help regarding the generation of Pseudopotentials for rare earths? In-Reply-To: References: Message-ID: <4BFD4747.7050309@democritos.it> sonu kumar wrote: > Can anybody tell/give me PP generation files/links etc., to generate > "PP" for rare earth elements using *ld1.x* ? > http://www.quantum-espresso.org/pseudo.php doesn't contain pp for rare > earths. there is a good reason for this: http://www.quantum-espresso.org/user_guide/node56.html P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From dimeo at democritos.it Wed May 26 18:13:58 2010 From: dimeo at democritos.it (Riccardo Di Meo) Date: Wed, 26 May 2010 18:13:58 +0200 Subject: [Pw_forum] ATLAS DSYGVX problem + mailing list question In-Reply-To: <4BFD46D6.2050806@democritos.it> References: <4BFBCCA1.30809@democritos.it> <68887660-2E98-44B0-AE37-D67C5D2FD1AC@democritos.it> <4BFD429C.5030306@democritos.it> <4BFD46D6.2050806@democritos.it> Message-ID: <4BFD48C6.3020702@democritos.it> Paolo Giannozzi wrote: > Riccardo Di Meo wrote: > > >> It seems therefore that the culprit is the line: >> >> nb = ILAENV( 1, 'DSYTRD', 'U', n, -1, -1, -1 ) >> >> which produces two different results with the same input, although I >> don't know why. >> > > ILAENV is a Lapack auxiliary routine. The Atlas version of ILAENV > should return the value of nb that is most suited to the Atlas > version of Lapack. Apparently it doesn't even return a correct > value. Not a QE problem, apparently. > > P. > Thank you for the explanation: it seems indeed a lapack/atlas problem. I'll look a bit into it, and post if I'll find something of some use. Best regards, Riccardo From gbilalbegovic at gmail.com Wed May 26 18:14:33 2010 From: gbilalbegovic at gmail.com (Goranka Bilalbegovic) Date: Wed, 26 May 2010 18:14:33 +0200 Subject: [Pw_forum] Help regarding the generation of Pseudopotentials for rare earths? In-Reply-To: <4BFD4747.7050309@democritos.it> References: <4BFD4747.7050309@democritos.it> Message-ID: On Wed, May 26, 2010 at 6:07 PM, Paolo Giannozzi wrote: > sonu kumar wrote: > > > Can anybody tell/give me PP generation files/links etc., to generate > > "PP" for rare earth elements using *ld1.x* ? > > http://www.quantum-espresso.org/pseudo.php doesn't contain pp for rare > > earths. > > there is a good reason for this: > http://www.quantum-espresso.org/user_guide/node56.html > > > However, last year there was a message about PAW for rare earths (without details): http://www.democritos.it/pipermail/pw_forum/2009-May/012897.html (this was found by internal search facility of QE) -- 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/20100526/3259c26b/attachment.htm From dimeo at democritos.it Wed May 26 19:12:43 2010 From: dimeo at democritos.it (Riccardo Di Meo) Date: Wed, 26 May 2010 19:12:43 +0200 Subject: [Pw_forum] ATLAS DSYGVX problem + mailing list question In-Reply-To: <4BFD48C6.3020702@democritos.it> References: <4BFBCCA1.30809@democritos.it> <68887660-2E98-44B0-AE37-D67C5D2FD1AC@democritos.it> <4BFD429C.5030306@democritos.it> <4BFD46D6.2050806@democritos.it> <4BFD48C6.3020702@democritos.it> Message-ID: <4BFD568B.3040305@democritos.it> Riccardo Di Meo wrote: > Paolo Giannozzi wrote: > >> Riccardo Di Meo wrote: >> >> >> >>> It seems therefore that the culprit is the line: >>> >>> nb = ILAENV( 1, 'DSYTRD', 'U', n, -1, -1, -1 ) >>> >>> which produces two different results with the same input, although I >>> don't know why. >>> >>> >> ILAENV is a Lapack auxiliary routine. The Atlas version of ILAENV >> should return the value of nb that is most suited to the Atlas >> version of Lapack. Apparently it doesn't even return a correct >> value. Not a QE problem, apparently. >> >> P. >> >> > Thank you for the explanation: it seems indeed a lapack/atlas problem. > > I'll look a bit into it, and post if I'll find something of some use. > > Best regards, > Riccardo > Dear all, I digged a bit in the LAPACK documentation/source http://www.netlib.org/lapack/util/ilaenv.f http://www.netlib.org/lapack/double/dsygvx.f and wheter this is an Espresso problem or a Lapack one, depends on how the said docs are read. For the way *I* understand it, the ILAENV routine returns the optimal nb value for DSYGVX, but it's responsability of the application (QE) to check if said number satisfies the constraints set by DSYGVX itself. This also makes sense, since as far as I understand, the results of ILAENV with a specific 'NAME' argument, fits multiple LAPACK routines, and therefore couldn't be possibly checked in advance by ILAENV. This interpretation is also reinforced by the trailing comment to DSYGVX, in which it's required: LWORK >= max(1,8*N) Not much point in writing it explicitly, if the value returned by ILAENV (which should be the optimal one) would produce the correct lwork anyway... That said, inserting: IF (lwork < 8 * n) THEN lwork = 8 * n ENDIF before the ALLOCATE(work(lwork)) line fixes the problem (and doesn't hurt anyway). So the bug is neither in QE or lapack, but in the lapack documentation IMO. Best Regards, RDM From vv0210 at gmail.com Wed May 26 20:59:40 2010 From: vv0210 at gmail.com (Vikas Varshney) Date: Wed, 26 May 2010 14:59:40 -0400 Subject: [Pw_forum] Parallel installation MPIF90 issue Message-ID: Dear all, I have a very simple question. I have 2 mpif90 installed on my machine one in /usr/local/bin which does not have fortran support. It says "Unfortunately, this installation of Open MPU was not compiled with Fortran 90 support ..." other one is in my local directory which was installed by me. It does have fortran compiler (ifort). When, I try to run configure script to genarate makefile, it assumes mpif90 to be the first one and results in unsuccessful configure. So, my question is that how can I direct the configure script to look for other mpif90 and the assciated libraries and header files. Where do I need to make necessary changes? Or do I need to ask my admin to update mpif90 in /usr/local/bin (where I dont have writable access)? Thanks in advance. Best Regards, Vikas -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100526/6b31a5aa/attachment.htm From dimeo at democritos.it Wed May 26 21:11:22 2010 From: dimeo at democritos.it (Riccardo Di Meo) Date: Wed, 26 May 2010 21:11:22 +0200 Subject: [Pw_forum] Parallel installation MPIF90 issue In-Reply-To: References: Message-ID: <4BFD725A.20600@democritos.it> Vikas Varshney wrote: > Dear all, > I have a very simple question. > > I have 2 mpif90 installed on my machine > one in /usr/local/bin which does not have fortran support. It says > "Unfortunately, this installation of Open MPU was not compiled with > Fortran 90 support ..." > other one is in my local directory which was installed by me. It does > have fortran compiler (ifort). > > When, I try to run configure script to genarate makefile, it assumes > mpif90 to be the first one and results in unsuccessful configure. So, > my question is that how can I direct the configure script to look for > other mpif90 and the assciated libraries and header files. Where do I > need to make necessary changes? Or do I need to ask my admin to update > mpif90 in /usr/local/bin (where I dont have writable access)? Two solutions: There's a MPIF90 environment variable, which can be set to the mpif90 compiler of your choice. Just point it to your mpif90 binary in your home before configuring QE. This is the standard/correct solution. A "one size fits all" solution, which you can use also for other similar cases ,would be to make your PATH environment variable give precedence to the location of the mpif90 compiler you want to use: export PATH=:$PATH [bash] Hope this helps, RDM > > Thanks in advance. > > Best Regards, > Vikas > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From vv0210 at gmail.com Wed May 26 21:19:22 2010 From: vv0210 at gmail.com (Vikas Varshney) Date: Wed, 26 May 2010 15:19:22 -0400 Subject: [Pw_forum] Parallel installation MPIF90 issue In-Reply-To: <4BFD725A.20600@democritos.it> References: <4BFD725A.20600@democritos.it> Message-ID: Dear Riccardo, Thanks, I tried first one just before I saw your email. I got into some other problem now. When I tried make all, I got some compilation errors in the first fortran program itself iotl_base.f90 The error seems to be "Lead underscore not allowed". This is coming repeatedly and there a a repeated warning "Bad #preprocessor line". I am using ifort compiler. I am going to do some search to see what this is about. If you have any insight, help will be highly appreciated. Best Regards, Vikas On Wed, May 26, 2010 at 3:11 PM, Riccardo Di Meo wrote: > Vikas Varshney wrote: > > Dear all, > > I have a very simple question. > > > > I have 2 mpif90 installed on my machine > > one in /usr/local/bin which does not have fortran support. It says > > "Unfortunately, this installation of Open MPU was not compiled with > > Fortran 90 support ..." > > other one is in my local directory which was installed by me. It does > > have fortran compiler (ifort). > > > > When, I try to run configure script to genarate makefile, it assumes > > mpif90 to be the first one and results in unsuccessful configure. So, > > my question is that how can I direct the configure script to look for > > other mpif90 and the assciated libraries and header files. Where do I > > need to make necessary changes? Or do I need to ask my admin to update > > mpif90 in /usr/local/bin (where I dont have writable access)? > > Two solutions: > > There's a MPIF90 environment variable, which can be set to the mpif90 > compiler of your choice. Just point it to your mpif90 binary in your > home before configuring QE. This is the standard/correct solution. > > A "one size fits all" solution, which you can use also for other similar > cases ,would be to make your PATH environment variable give precedence > to the location of the mpif90 compiler you want to use: > > export PATH=:$PATH [bash] > > Hope this helps, > RDM > > > > > Thanks in advance. > > > > Best Regards, > > Vikas > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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/20100526/e25ee276/attachment.htm From dimeo at democritos.it Wed May 26 21:25:23 2010 From: dimeo at democritos.it (Riccardo Di Meo) Date: Wed, 26 May 2010 21:25:23 +0200 Subject: [Pw_forum] Parallel installation MPIF90 issue In-Reply-To: References: <4BFD725A.20600@democritos.it> Message-ID: <4BFD75A3.1040805@democritos.it> Vikas Varshney wrote: > Dear Riccardo, > > Thanks, I tried first one just before I saw your email. > I got into some other problem now. When I tried make all, I got some > compilation errors in the first fortran program itself iotl_base.f90 > The error seems to be "Lead underscore not allowed". This is coming > repeatedly and there a a repeated warning "Bad #preprocessor line". I > am using ifort compiler. I am going to do some search to see what this > is about. If you have any insight, help will be highly appreciated. > > Best Regards, > Vikas I do remember having similar problems, and although not sure, maybe the issue came from mixing different compilers. Is maybe configure picking your mpif90 compiler (which uses intel) as the fortran parallel compiler, and gfortran as the serial one? If so, you might want to use the FC env variable and point it to the intel compiler manually. Just guessing anyway... Cheers, RDM From soumyajyoti.haldar at gmail.com Wed May 26 21:39:35 2010 From: soumyajyoti.haldar at gmail.com (soumyajyoti haldar) Date: Wed, 26 May 2010 21:39:35 +0200 Subject: [Pw_forum] Parallel installation MPIF90 issue In-Reply-To: <4BFD725A.20600@democritos.it> References: <4BFD725A.20600@democritos.it> Message-ID: Hi, On Wed, May 26, 2010 at 9:11 PM, Riccardo Di Meo wrote: > Vikas Varshney wrote: > > Dear all, > > I have a very simple question. > > > > I have 2 mpif90 installed on my machine > > one in /usr/local/bin which does not have fortran support. It says > > "Unfortunately, this installation of Open MPU was not compiled with > > Fortran 90 support ..." > > other one is in my local directory which was installed by me. It does > > have fortran compiler (ifort). > > > > When, I try to run configure script to genarate makefile, it assumes > > mpif90 to be the first one and results in unsuccessful configure. So, > > my question is that how can I direct the configure script to look for > > other mpif90 and the assciated libraries and header files. Where do I > > need to make necessary changes? Or do I need to ask my admin to update > > mpif90 in /usr/local/bin (where I dont have writable access)? > > Two solutions: > > There's a MPIF90 environment variable, which can be set to the mpif90 > compiler of your choice. Just point it to your mpif90 binary in your > home before configuring QE. This is the standard/correct solution. > > A "one size fits all" solution, which you can use also for other similar > cases ,would be to make your PATH environment variable give precedence > to the location of the mpif90 compiler you want to use: > > export PATH=:$PATH [bash] > you need to set correct LD_LIBRARY_PATH also. Otherwise during compilation and run time it may pickup the wrong library and give you error. set this as follows export LD_LIBRARY_PATH=/lib:$LD_LIBRARY_PATH [bash] and one personal experience ,by default /usr/bin and /usr/local/bin are set as path when u boot up the system. and now if you your current mpif90 directory to PATH, it may not pick up the correct one. bcoz u have 2 mpif90, one is in /usr/bin , other is in some directory in you home. the search order for the mpif90 depends on which folder path is loaded to your path variable first . So if your PATH variable contains the entry of /usr/bin first then it'll not pick up the mpif90 from ur home. I made some changes in my .bash_profile as follows line 1 : unset PATH line 2 : export PATH="${PATH}:" line 3: export PATH="${PATH}:/bin:/usr/bin:/usr/local/bin" and finally load "/etc/profile" again line 4: source /etc/profile use it with extreme caution ... > Hope this helps, > RDM > > > > > Thanks in advance. > > > > Best Regards, > > Vikas > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 > Hope this helps .... SJH -- Junior Research Fellow Advance Computing Laboratory Department of Physics, University of Pune Ganeshkhind, Pune - 411007; INDIA Tel : (+91 20) 25692678; Extn# 408 ~~~***~~~***~~~***~~~***~~~***~~~***~~~***~~~ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100526/2c26ab4a/attachment.htm From giannozz at democritos.it Wed May 26 21:50:11 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 26 May 2010 21:50:11 +0200 Subject: [Pw_forum] ATLAS DSYGVX problem + mailing list question In-Reply-To: <4BFD568B.3040305@democritos.it> References: <4BFBCCA1.30809@democritos.it> <68887660-2E98-44B0-AE37-D67C5D2FD1AC@democritos.it> <4BFD429C.5030306@democritos.it> <4BFD46D6.2050806@democritos.it> <4BFD48C6.3020702@democritos.it> <4BFD568B.3040305@democritos.it> Message-ID: <69E965CB-9C74-428A-8CD8-F4536849CB46@democritos.it> On May 26, 2010, at 19:12 , Riccardo Di Meo wrote: > For the way *I* understand it, the ILAENV routine returns the > optimal nb > value for DSYGVX, but it's responsability of the application (QE) to > check if said number satisfies the constraints set by DSYGVX itself. ok, I see: the check was actualy there, but it wasn't the good one. Now it should be fixed 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 vv0210 at gmail.com Wed May 26 22:46:10 2010 From: vv0210 at gmail.com (Vikas Varshney) Date: Wed, 26 May 2010 16:46:10 -0400 Subject: [Pw_forum] Parallel installation MPIF90 issue In-Reply-To: References: <4BFD725A.20600@democritos.it> Message-ID: Dear Soumyajyoti, Riccardo, Thanks for your input. I successfully finished the installation (it seems). I also included LD_LIBRARY_PATH as Soumya mentioned. When I tried to run examples through run_example (example01), it seems it is running in serial on single processor. I looked around a little bit and found that I need to put the path to mpiexec and no of processors in enviromental_variable files in PARA_PREFIX and PARA_POSTFIX options. When I tried that, this is what I got. PARA_PREFIX = ~/local/openmpi/bin/mpiexec -n 4 PARA_POSTFIX = What I got was "No executable was specified on the mpiexec command line". I though the run_example script will take care of the executable as it contain of the following lines PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX" I tried searching it in archive but did not get a satisfactory answer. Best Wishes, Vikas Varshney On Wed, May 26, 2010 at 3:39 PM, soumyajyoti haldar < soumyajyoti.haldar at gmail.com> wrote: > Hi, > > On Wed, May 26, 2010 at 9:11 PM, Riccardo Di Meo wrote: > >> Vikas Varshney wrote: >> > Dear all, >> > I have a very simple question. >> > >> > I have 2 mpif90 installed on my machine >> > one in /usr/local/bin which does not have fortran support. It says >> > "Unfortunately, this installation of Open MPU was not compiled with >> > Fortran 90 support ..." >> > other one is in my local directory which was installed by me. It does >> > have fortran compiler (ifort). >> > >> > When, I try to run configure script to genarate makefile, it assumes >> > mpif90 to be the first one and results in unsuccessful configure. So, >> > my question is that how can I direct the configure script to look for >> > other mpif90 and the assciated libraries and header files. Where do I >> > need to make necessary changes? Or do I need to ask my admin to update >> > mpif90 in /usr/local/bin (where I dont have writable access)? >> >> Two solutions: >> >> There's a MPIF90 environment variable, which can be set to the mpif90 >> compiler of your choice. Just point it to your mpif90 binary in your >> home before configuring QE. This is the standard/correct solution. >> >> A "one size fits all" solution, which you can use also for other similar >> cases ,would be to make your PATH environment variable give precedence >> to the location of the mpif90 compiler you want to use: >> >> export PATH=:$PATH [bash] >> > > you need to set correct LD_LIBRARY_PATH also. Otherwise during compilation > and run time it may pickup the wrong library and give you error. set this as > follows > export LD_LIBRARY_PATH= directory>/lib:$LD_LIBRARY_PATH [bash] > > and one personal experience ,by default /usr/bin and /usr/local/bin are > set as path when u boot up the system. > and now if you your current mpif90 directory to PATH, it may not pick up > the correct one. bcoz u have 2 mpif90, one is in /usr/bin , other is in some > directory in you home. the search order for the mpif90 depends on which > folder path is loaded to your path variable first . So if your PATH > variable contains the entry of /usr/bin first then it'll not pick up the > mpif90 from ur home. > > I made some changes in my .bash_profile as follows > > line 1 : unset PATH > line 2 : export PATH="${PATH}:" > line 3: export PATH="${PATH}:/bin:/usr/bin:/usr/local/bin" and finally load > "/etc/profile" again > line 4: source /etc/profile > > use it with extreme caution ... > > > >> Hope this helps, >> RDM >> >> > >> > Thanks in advance. >> > >> > Best Regards, >> > Vikas >> > ------------------------------------------------------------------------ >> > >> > _______________________________________________ >> > 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 >> > > > Hope this helps .... > > > SJH > > -- > Junior Research Fellow > Advance Computing Laboratory > Department of Physics, University of Pune > Ganeshkhind, Pune - 411007; INDIA > > Tel : (+91 20) 25692678; Extn# 408 > > ~~~***~~~***~~~***~~~***~~~***~~~***~~~***~~~ > > _______________________________________________ > 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/20100526/9bad9c42/attachment.htm From giannozz at democritos.it Wed May 26 22:57:36 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 26 May 2010 22:57:36 +0200 Subject: [Pw_forum] Parallel installation MPIF90 issue In-Reply-To: References: <4BFD725A.20600@democritos.it> Message-ID: On May 26, 2010, at 22:46 , Vikas Varshney wrote: > PARA_PREFIX = ~/local/openmpi/bin/mpiexec -n 4 you mean: PARA_PREFIX = "~/local/openmpi/bin/mpiexec -n 4" ? 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 dimeo at democritos.it Wed May 26 23:48:08 2010 From: dimeo at democritos.it (Riccardo Di Meo) Date: Wed, 26 May 2010 23:48:08 +0200 Subject: [Pw_forum] Parallel installation MPIF90 issue In-Reply-To: References: <4BFD725A.20600@democritos.it> Message-ID: <4BFD9718.8020607@democritos.it> soumyajyoti haldar wrote: > Hi, > > On Wed, May 26, 2010 at 9:11 PM, Riccardo Di Meo > wrote: > > Vikas Varshney wrote: > > Dear all, > > I have a very simple question. > > > > I have 2 mpif90 installed on my machine > > one in /usr/local/bin which does not have fortran support. It says > > "Unfortunately, this installation of Open MPU was not compiled with > > Fortran 90 support ..." > > other one is in my local directory which was installed by me. It > does > > have fortran compiler (ifort). > > > > When, I try to run configure script to genarate makefile, it assumes > > mpif90 to be the first one and results in unsuccessful > configure. So, > > my question is that how can I direct the configure script to > look for > > other mpif90 and the assciated libraries and header files. Where > do I > > need to make necessary changes? Or do I need to ask my admin to > update > > mpif90 in /usr/local/bin (where I dont have writable access)? > > Two solutions: > > There's a MPIF90 environment variable, which can be set to the mpif90 > compiler of your choice. Just point it to your mpif90 binary in your > home before configuring QE. This is the standard/correct solution. > > A "one size fits all" solution, which you can use also for other > similar > cases ,would be to make your PATH environment variable give precedence > to the location of the mpif90 compiler you want to use: > > export PATH=:$PATH [bash] > > > you need to set correct LD_LIBRARY_PATH also. Otherwise during > compilation and run time it may pickup the wrong LD_LIBRARY_PATH it's a variable used only at runtime and has nothing to do withbcompilation (man ld.so for details). Btw if the MPI implementation is openmpi, LD_LIBRARY_PATH doesn't need to be changed , as mpirun/mpiexec will set the correct environment automatically (not to mention implementations like mpich v1, which link statically by default)... > > and one personal experience ,by default /usr/bin and /usr/local/bin > are set as path when u boot up the system. > and now if you your current mpif90 directory to PATH, it may not pick > up the correct one. bcoz u have 2 mpif90, one is in /usr/bin , other > is in some directory in you home. the search order for the mpif90 > depends on which folder path is loaded to your path variable first . > So if your PATH variable contains the entry of /usr/bin first then > it'll not pick up the mpif90 from ur home. > > I made some changes in my .bash_profile as follows > > line 1 : unset PATH > line 2 : export PATH="${PATH}:" > line 3: export PATH="${PATH}:/bin:/usr/bin:/usr/local/bin" and finally > load "/etc/profile" again > line 4: source /etc/profile Maybe I'm missing something, but besides from using 4 instructions instead of one, and from adding a stylish ":" in front of your PATH, what's the added benefit of your suggestion over the compact form export PATH=:$PATH in my reply? Besides, your suggestion assumes that the definition of PATH comes only from /etc/profile, which would prevent people accepting it from using software installed by the administrator in non standard ways (e.g. by modifying /etc/skel/.bashrc) Cheers, RDM From soumyajyoti.haldar at gmail.com Thu May 27 00:49:51 2010 From: soumyajyoti.haldar at gmail.com (soumyajyoti haldar) Date: Thu, 27 May 2010 00:49:51 +0200 Subject: [Pw_forum] Parallel installation MPIF90 issue In-Reply-To: <4BFD9718.8020607@democritos.it> References: <4BFD725A.20600@democritos.it> <4BFD9718.8020607@democritos.it> Message-ID: Hi Riccardo and all, I am extremely sorry if I offended someone. My purpose was definitely not that. On Wed, May 26, 2010 at 11:48 PM, Riccardo Di Meo wrote: > soumyajyoti haldar wrote: > > Hi, > > > > On Wed, May 26, 2010 at 9:11 PM, Riccardo Di Meo > > wrote: > > > > Vikas Varshney wrote: > > > Dear all, > > > I have a very simple question. > > > > > > I have 2 mpif90 installed on my machine > > > one in /usr/local/bin which does not have fortran support. It says > > > "Unfortunately, this installation of Open MPU was not compiled with > > > Fortran 90 support ..." > > > other one is in my local directory which was installed by me. It > > does > > > have fortran compiler (ifort). > > > > > > When, I try to run configure script to genarate makefile, it > assumes > > > mpif90 to be the first one and results in unsuccessful > > configure. So, > > > my question is that how can I direct the configure script to > > look for > > > other mpif90 and the assciated libraries and header files. Where > > do I > > > need to make necessary changes? Or do I need to ask my admin to > > update > > > mpif90 in /usr/local/bin (where I dont have writable access)? > > > > Two solutions: > > > > There's a MPIF90 environment variable, which can be set to the mpif90 > > compiler of your choice. Just point it to your mpif90 binary in your > > home before configuring QE. This is the standard/correct solution. > > > > A "one size fits all" solution, which you can use also for other > > similar > > cases ,would be to make your PATH environment variable give > precedence > > to the location of the mpif90 compiler you want to use: > > > > export PATH=:$PATH [bash] > > > > > > you need to set correct LD_LIBRARY_PATH also. Otherwise during > > compilation and run time it may pickup the wrong > LD_LIBRARY_PATH it's a variable used only at runtime and has nothing to > do withbcompilation (man ld.so for details). > Yes I know that LD_LIBRARY_PATH variable used only at runtime. ' compilation ' was just by mistake I wrote. > Btw if the MPI implementation is openmpi, LD_LIBRARY_PATH doesn't need > to be changed , as mpirun/mpiexec will set the correct environment > automatically (not to mention implementations like mpich v1, which link > statically by default)... > Well , that was the impression I had earlier, that it can set the correct environment. But if the system contains both gcc compiled openmpi ( most common location is /usr/lib/openmpi , iff installed by the OS !!! ) and intel compiled MPI ( installed by user ) then my personal experience tells me to better set the LD_LIBRARY_PATH. openmpi faq's are also telling same thing, ( I found it during the trouble shooting of my problem ). However openmpi can be run without setting the LD_LIBRARY_PATH, provided you always mention the full path . My understanding from the following faqs tails me these. Pls correct me if I am wrong. http://www.open-mpi.org/faq/?category=running#adding-ompi-to-path But again it's my personal experience . > > > > > and one personal experience ,by default /usr/bin and /usr/local/bin > > are set as path when u boot up the system. > > and now if you your current mpif90 directory to PATH, it may not pick > > up the correct one. bcoz u have 2 mpif90, one is in /usr/bin , other > > is in some directory in you home. the search order for the mpif90 > > depends on which folder path is loaded to your path variable first . > > So if your PATH variable contains the entry of /usr/bin first then > > it'll not pick up the mpif90 from ur home. > > > > I made some changes in my .bash_profile as follows > > > > line 1 : unset PATH > > line 2 : export PATH="${PATH}:" > > line 3: export PATH="${PATH}:/bin:/usr/bin:/usr/local/bin" and finally > > load "/etc/profile" again > > line 4: source /etc/profile > > Maybe I'm missing something, but besides from using 4 instructions > instead of one, and from adding a stylish ":" in front of your PATH, > what's the added benefit of your suggestion over the compact form > > export PATH=:$PATH > > in my reply? > Nothing wrong in your reply. > Besides, your suggestion assumes that the definition of PATH comes only > from /etc/profile, which would prevent people accepting it from using > software installed by the administrator in non standard ways (e.g. by > modifying /etc/skel/.bashrc) > > Cheers, > RDM > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Soumyajyoti Haldar, M.Sc Junior Research Fellow Advance Computing Laboratory Department of Physics, University of Pune Ganeshkhind, Pune - 411007; INDIA Tel : (+91 20) 25692678; Extn# 408 ~~~***~~~***~~~***~~~***~~~***~~~***~~~***~~~ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100527/94cf11dd/attachment.htm From arebol2 at uic.edu Thu May 27 01:52:56 2010 From: arebol2 at uic.edu (Alejandro =?iso-8859-1?Q?R=E9bola?=) Date: Wed, 26 May 2010 18:52:56 -0500 Subject: [Pw_forum] Question about qexml.f90 in PP sudirectory Message-ID: Hello everybody, I'm trying to compile the qexml file (make qexml.x) contained in ~/espresso/PP and I'm getting an error message: undefined reference to errore. Checking qexml.f90 I found that the subroutine errore is not defined and that commenting that line (1052) the compilation is normal. Does anybody have the same problem? Thank you in advance, Alejandro From dimeo at democritos.it Thu May 27 02:34:55 2010 From: dimeo at democritos.it (Riccardo Di Meo) Date: Thu, 27 May 2010 02:34:55 +0200 Subject: [Pw_forum] Parallel installation MPIF90 issue In-Reply-To: References: <4BFD725A.20600@democritos.it> <4BFD9718.8020607@democritos.it> Message-ID: <4BFDBE2F.2090709@democritos.it> [...] > > > Btw if the MPI implementation is openmpi, LD_LIBRARY_PATH doesn't need > to be changed , as mpirun/mpiexec will set the correct environment > automatically (not to mention implementations like mpich v1, which > link > statically by default)... > > > Well , that was the impression I had earlier, that it can set the > correct environment. But if the system contains both gcc compiled > openmpi ( most common location is /usr/lib/openmpi , iff installed by > the OS !!! ) and intel compiled MPI ( installed by user ) then my > personal experience tells me to better set the LD_LIBRARY_PATH. > openmpi faq's are also I agree with you that setting the LD_LIBRARY_PATH is a good idea, since if the binary is executed directly instead of using mpirun/mpiexec (which is a common practice, e.g. for debugging) afaik there is no other way to let it work without admin privileges (and it woulnd't hurt in all other cases anyway). And it's a good thing you suggested it in your mail, since I completely forgot about that. As far as how much I liked the suggestion about the PATH variable, that's the only reason why I have put politeness aside in my reply. If you correct somebody by pushing for a solution that's far worse than the original one, being bashed is the physiological reaction and not a personal matter. This is just the way the dialectic process works as far as the hacking community is concerned: no hard feelings (you should lurk a bit in the ##C channel on freenode or sample a couple of mail in the kernel mailing list and you'll see what I mean: man, the things you'll see there... :-| ). Anyway, we are both here to help, and you had a point about LD_LIBRARY_PATH, so thank you for your contribution Best Regards, Riccardo From giannozz at democritos.it Thu May 27 09:32:40 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 27 May 2010 09:32:40 +0200 Subject: [Pw_forum] Question about qexml.f90 in PP sudirectory In-Reply-To: References: Message-ID: <4BFE2018.300@democritos.it> Alejandro R?bola wrote: > I'm trying to compile the qexml file (make qexml.x) contained in > ~/espresso/PP and I'm getting an error message it's a bug. Edit PP/makefile, locate the following lines: qexml.x: qexml.o qexml_example.o $(LD) $(LDFLAGS) -o $@ qexml_example.o qexml.o $(LIBOBJS) insert $(QEOBJS) before $(LIBOBJS). Thank you for the report P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Thu May 27 09:33:27 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 27 May 2010 09:33:27 +0200 Subject: [Pw_forum] Parallel installation MPIF90 issue In-Reply-To: References: <4BFD725A.20600@democritos.it> <4BFD9718.8020607@democritos.it> Message-ID: <4BFE2047.602@democritos.it> soumyajyoti haldar wrote: > I am extremely sorry if I offended someone you didn't offend anybody P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From 1009ukumar at gmail.com Thu May 27 12:17:53 2010 From: 1009ukumar at gmail.com (sonu kumar) Date: Thu, 27 May 2010 15:47:53 +0530 Subject: [Pw_forum] Help regarding the generation of Pseudopotentials for rare earths? Message-ID: Dear Paolo,Goranka, and all QE users, I want to generate nonrelativistic and relativistic USPP/NCPP with/without spin-orbit interaction for rare eaths. It seems, after reading the "espresso-4.1.2/atomic_doc" that pp for rare-earths can be generated. By the way http://www.quantum-espresso.org/user_guide/node56.html, question-11.3.0.2, tells about code "atomic". where can i find it? is it "ld1.x" or different? Thanks for your kind help !! With Kind Regards Sonu Kumar Phd Student Physics Department Indian Institute of Technology Delhi-110016, India web:-http://www.iitd.ac.in/ > > Can anybody tell/give me PP generation files/links etc., to generate > > "PP" for rare earth elements using *ld1.x* ? > > http://www.quantum-espresso.org/pseudo.php doesn't contain pp for rare > > earths. > > there is a good reason for this: > http://www.quantum-espresso.org/user_guide/node56.html > > > >However, last year there was a message about PAW for rare earths (without >details): >http://www.democritos.it/pipermail/pw_forum/2009-May/012897.html -- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100527/52f7e12d/attachment.htm From ierrea001 at ikasle.ehu.es Thu May 27 12:36:24 2010 From: ierrea001 at ikasle.ehu.es (Ion Errea Lope) Date: Thu, 27 May 2010 12:36:24 +0200 Subject: [Pw_forum] something wrong D_2h Message-ID: <1274956584.1604.37.camel@montblanc> Dear all, I am calculating with espresso-4.1 the dynamical matrix of a supercell containing 32 atoms of Ca. The scf calculation runs without problems, but when computing the dynamical matrix of that system with ph.x the program stops with the following error message: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%% from divide_class : error # 1 something wrong D_2h %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%% It seems there is a problem with the irreps emerging from the subroutines divide_class.f90 and divide_class_so.f90 that I do not understand well. Looking into the forum archive I found a similar problem discussed in 2007 that was solved modifying the subroutines mentioned above. Here is the link to that post: http://www.democritos.it/pipermail/pw_forum/2007-August/007054.html I wonder whether a similar modification of the subroutines may solve this issue or the problem is different. I would be very grateful if someone could help me with this issue. Below I include the input files of the pw.x and ph.x calculations: -> pw.x &control calculation='scf' prefix='ca' pseudo_dir='/scratch/ionerrea/pseudo' outdir='/lscratch/ionerrea/results-supercell_7_pol2-lscratch' / &system ibrav = 8 celldm(1) =19.371149508 celldm(2) = 1.000000000 celldm(3) = 0.500000000 nat = 32 ntyp = 1 nbnd = 416 ecutwfc = 30.0 ecutrho = 300.0 occupations='smearing' smearing='marzari-vanderbilt' degauss=0.02 / &electrons conv_thr = 1.0e-8 mixing_beta = 0.7 / ATOMIC_SPECIES Ca 40.078 Ca.pbe-nsp-van.UPF ATOMIC_POSITIONS {crystal} Ca 0.000000000 0.000000000 0.000000000 Ca 0.000000000 0.000000000 0.500000000 Ca 0.003535534 0.253535534 0.000000000 Ca -0.003535534 0.246464466 0.500000000 Ca 0.000000000 0.500000000 0.000000000 Ca 0.000000000 0.500000000 0.500000000 Ca -0.003535534 0.746464466 0.000000000 Ca 0.003535534 0.753535534 0.500000000 Ca 0.253535534 0.003535534 0.000000000 Ca 0.246464466 -0.003535534 0.500000000 Ca 0.250000000 0.250000000 0.000000000 Ca 0.250000000 0.250000000 0.500000000 Ca 0.246464466 0.496464466 0.000000000 Ca 0.253535534 0.503535534 0.500000000 Ca 0.250000000 0.750000000 0.000000000 Ca 0.250000000 0.750000000 0.500000000 Ca 0.500000000 0.000000000 0.000000000 Ca 0.500000000 0.000000000 0.500000000 Ca 0.496464466 0.246464466 0.000000000 Ca 0.503535534 0.253535534 0.500000000 Ca 0.500000000 0.500000000 0.000000000 Ca 0.500000000 0.500000000 0.500000000 Ca 0.503535534 0.753535534 0.000000000 Ca 0.496464466 0.746464466 0.500000000 Ca 0.746464466 -0.003535534 0.000000000 Ca 0.753535534 0.003535534 0.500000000 Ca 0.750000000 0.250000000 0.000000000 Ca 0.750000000 0.250000000 0.500000000 Ca 0.753535534 0.503535534 0.000000000 Ca 0.746464466 0.496464466 0.500000000 Ca 0.750000000 0.750000000 0.000000000 Ca 0.750000000 0.750000000 0.500000000 K_POINTS {automatic} 4 4 8 1 1 1 -> ph.x &inputph tr2_ph=1.0d-16 prefix='ca' amass(1)=40.078 outdir='/lscratch/ionerrea/results-supercell_7_pol2-lscratch ' fildyn='dyn_B_plus_0.02_1' alpha_mix(1)=0.4 lnscf=.true. / 0.00000 0.00000 0.00000 Thank you very much for your help. Kind regards, Ion -- ?======================================== Ion Errea Lope *Donostia International Physics Center (DIPC) *Materia Kondentsatuaren Fisika Saila Zientzia eta Teknologia Fakultatea Euskal Herriko Unibertsitatea 644 Posta Kutxatila, 48080 Bilbo, Spain Telefonoa: +34 946015322 Mail: ion.errea at ehu.es ======================================== From dalcorso at sissa.it Thu May 27 14:02:26 2010 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Thu, 27 May 2010 14:02:26 +0200 Subject: [Pw_forum] something wrong D_2h In-Reply-To: <1274956584.1604.37.camel@montblanc> References: <1274956584.1604.37.camel@montblanc> Message-ID: <1274961746.3280.12.camel@dhcp-098.cm.sissa.it> Which version of QE are you using? If it is an old one, please update. On QE 4.2 your input seems to work (at least pw.x with verbosity='high' finds the correct group and representations). Andrea On Thu, 2010-05-27 at 12:36 +0200, Ion Errea Lope wrote: > Dear all, > > I am calculating with espresso-4.1 the dynamical matrix of a supercell > containing 32 atoms of Ca. The scf calculation runs without problems, > but when computing the dynamical matrix of that system with ph.x the > program stops with the following error message: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%% > from divide_class : error # 1 > something wrong D_2h > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%% > > It seems there is a problem with the irreps emerging from the > subroutines divide_class.f90 and divide_class_so.f90 that I do not > understand well. Looking into the forum archive I found a similar > problem discussed in 2007 that was solved modifying the subroutines > mentioned above. Here is the link to that post: > > http://www.democritos.it/pipermail/pw_forum/2007-August/007054.html > > I wonder whether a similar modification of the subroutines may solve > this issue or the problem is different. I would be very grateful if > someone could help me with this issue. > > Below I include the input files of the pw.x and ph.x calculations: > > -> pw.x > > &control > calculation='scf' > prefix='ca' > pseudo_dir='/scratch/ionerrea/pseudo' > outdir='/lscratch/ionerrea/results-supercell_7_pol2-lscratch' > / > &system > ibrav = 8 > celldm(1) =19.371149508 > celldm(2) = 1.000000000 > celldm(3) = 0.500000000 > nat = 32 > ntyp = 1 > nbnd = 416 > ecutwfc = 30.0 > ecutrho = 300.0 > occupations='smearing' > smearing='marzari-vanderbilt' > degauss=0.02 > / > &electrons > conv_thr = 1.0e-8 > mixing_beta = 0.7 > / > ATOMIC_SPECIES > Ca 40.078 Ca.pbe-nsp-van.UPF > ATOMIC_POSITIONS {crystal} > Ca 0.000000000 0.000000000 0.000000000 > Ca 0.000000000 0.000000000 0.500000000 > Ca 0.003535534 0.253535534 0.000000000 > Ca -0.003535534 0.246464466 0.500000000 > Ca 0.000000000 0.500000000 0.000000000 > Ca 0.000000000 0.500000000 0.500000000 > Ca -0.003535534 0.746464466 0.000000000 > Ca 0.003535534 0.753535534 0.500000000 > Ca 0.253535534 0.003535534 0.000000000 > Ca 0.246464466 -0.003535534 0.500000000 > Ca 0.250000000 0.250000000 0.000000000 > Ca 0.250000000 0.250000000 0.500000000 > Ca 0.246464466 0.496464466 0.000000000 > Ca 0.253535534 0.503535534 0.500000000 > Ca 0.250000000 0.750000000 0.000000000 > Ca 0.250000000 0.750000000 0.500000000 > Ca 0.500000000 0.000000000 0.000000000 > Ca 0.500000000 0.000000000 0.500000000 > Ca 0.496464466 0.246464466 0.000000000 > Ca 0.503535534 0.253535534 0.500000000 > Ca 0.500000000 0.500000000 0.000000000 > Ca 0.500000000 0.500000000 0.500000000 > Ca 0.503535534 0.753535534 0.000000000 > Ca 0.496464466 0.746464466 0.500000000 > Ca 0.746464466 -0.003535534 0.000000000 > Ca 0.753535534 0.003535534 0.500000000 > Ca 0.750000000 0.250000000 0.000000000 > Ca 0.750000000 0.250000000 0.500000000 > Ca 0.753535534 0.503535534 0.000000000 > Ca 0.746464466 0.496464466 0.500000000 > Ca 0.750000000 0.750000000 0.000000000 > Ca 0.750000000 0.750000000 0.500000000 > K_POINTS {automatic} > 4 4 8 1 1 1 > > -> ph.x > > &inputph > tr2_ph=1.0d-16 > prefix='ca' > amass(1)=40.078 > outdir='/lscratch/ionerrea/results-supercell_7_pol2-lscratch > ' > fildyn='dyn_B_plus_0.02_1' > alpha_mix(1)=0.4 > lnscf=.true. > / > 0.00000 0.00000 0.00000 > > Thank you very much for your help. > > Kind regards, > > Ion > > -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Beirut 2/4 Fax. 0039-040-3787528 34151 Trieste (Italy) e-mail: dalcorso at sissa.it From ierrea001 at ikasle.ehu.es Thu May 27 14:28:27 2010 From: ierrea001 at ikasle.ehu.es (Ion Errea Lope) Date: Thu, 27 May 2010 14:28:27 +0200 Subject: [Pw_forum] something wrong D_2h In-Reply-To: <1274961746.3280.12.camel@dhcp-098.cm.sissa.it> References: <1274956584.1604.37.camel@montblanc> <1274961746.3280.12.camel@dhcp-098.cm.sissa.it> Message-ID: <1274963307.1604.40.camel@montblanc> Dear Andrea, Thank you very much for your quick answer. Actually I'm using version 4.1. I will update to 4.2, use verbosity='high' and check whether it works. If it does not I will report it. Thanks again, Ion Jatorrizko mezua: og., 2010-05-27 14:02 +0200, egilea: Dal Corso Andrea > Which version of QE are you using? > If it is an old one, please update. On QE 4.2 your input seems to work > (at least pw.x with verbosity='high' finds the correct group and > representations). > > Andrea > > > On Thu, 2010-05-27 at 12:36 +0200, Ion Errea Lope wrote: > > Dear all, > > > > I am calculating with espresso-4.1 the dynamical matrix of a supercell > > containing 32 atoms of Ca. The scf calculation runs without problems, > > but when computing the dynamical matrix of that system with ph.x the > > program stops with the following error message: > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > %%%%%% > > from divide_class : error # 1 > > something wrong D_2h > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > %%%%%%% > > > > It seems there is a problem with the irreps emerging from the > > subroutines divide_class.f90 and divide_class_so.f90 that I do not > > understand well. Looking into the forum archive I found a similar > > problem discussed in 2007 that was solved modifying the subroutines > > mentioned above. Here is the link to that post: > > > > http://www.democritos.it/pipermail/pw_forum/2007-August/007054.html > > > > I wonder whether a similar modification of the subroutines may solve > > this issue or the problem is different. I would be very grateful if > > someone could help me with this issue. > > > > Below I include the input files of the pw.x and ph.x calculations: > > > > -> pw.x > > > > &control > > calculation='scf' > > prefix='ca' > > pseudo_dir='/scratch/ionerrea/pseudo' > > outdir='/lscratch/ionerrea/results-supercell_7_pol2-lscratch' > > / > > &system > > ibrav = 8 > > celldm(1) =19.371149508 > > celldm(2) = 1.000000000 > > celldm(3) = 0.500000000 > > nat = 32 > > ntyp = 1 > > nbnd = 416 > > ecutwfc = 30.0 > > ecutrho = 300.0 > > occupations='smearing' > > smearing='marzari-vanderbilt' > > degauss=0.02 > > / > > &electrons > > conv_thr = 1.0e-8 > > mixing_beta = 0.7 > > / > > ATOMIC_SPECIES > > Ca 40.078 Ca.pbe-nsp-van.UPF > > ATOMIC_POSITIONS {crystal} > > Ca 0.000000000 0.000000000 0.000000000 > > Ca 0.000000000 0.000000000 0.500000000 > > Ca 0.003535534 0.253535534 0.000000000 > > Ca -0.003535534 0.246464466 0.500000000 > > Ca 0.000000000 0.500000000 0.000000000 > > Ca 0.000000000 0.500000000 0.500000000 > > Ca -0.003535534 0.746464466 0.000000000 > > Ca 0.003535534 0.753535534 0.500000000 > > Ca 0.253535534 0.003535534 0.000000000 > > Ca 0.246464466 -0.003535534 0.500000000 > > Ca 0.250000000 0.250000000 0.000000000 > > Ca 0.250000000 0.250000000 0.500000000 > > Ca 0.246464466 0.496464466 0.000000000 > > Ca 0.253535534 0.503535534 0.500000000 > > Ca 0.250000000 0.750000000 0.000000000 > > Ca 0.250000000 0.750000000 0.500000000 > > Ca 0.500000000 0.000000000 0.000000000 > > Ca 0.500000000 0.000000000 0.500000000 > > Ca 0.496464466 0.246464466 0.000000000 > > Ca 0.503535534 0.253535534 0.500000000 > > Ca 0.500000000 0.500000000 0.000000000 > > Ca 0.500000000 0.500000000 0.500000000 > > Ca 0.503535534 0.753535534 0.000000000 > > Ca 0.496464466 0.746464466 0.500000000 > > Ca 0.746464466 -0.003535534 0.000000000 > > Ca 0.753535534 0.003535534 0.500000000 > > Ca 0.750000000 0.250000000 0.000000000 > > Ca 0.750000000 0.250000000 0.500000000 > > Ca 0.753535534 0.503535534 0.000000000 > > Ca 0.746464466 0.496464466 0.500000000 > > Ca 0.750000000 0.750000000 0.000000000 > > Ca 0.750000000 0.750000000 0.500000000 > > K_POINTS {automatic} > > 4 4 8 1 1 1 > > > > -> ph.x > > > > &inputph > > tr2_ph=1.0d-16 > > prefix='ca' > > amass(1)=40.078 > > outdir='/lscratch/ionerrea/results-supercell_7_pol2-lscratch > > ' > > fildyn='dyn_B_plus_0.02_1' > > alpha_mix(1)=0.4 > > lnscf=.true. > > / > > 0.00000 0.00000 0.00000 > > > > Thank you very much for your help. > > > > Kind regards, > > > > Ion > > > > > -- > Andrea Dal Corso Tel. 0039-040-3787428 > SISSA, Via Beirut 2/4 Fax. 0039-040-3787528 > 34151 Trieste (Italy) e-mail: dalcorso at sissa.it > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ?======================================== Ion Errea Lope *Donostia International Physics Center (DIPC) *Materia Kondentsatuaren Fisika Saila Zientzia eta Teknologia Fakultatea Euskal Herriko Unibertsitatea 644 Posta Kutxatila, 48080 Bilbo, Spain Telefonoa: +34 946015322 Mail: ion.errea at ehu.es ======================================== From giannozz at democritos.it Thu May 27 14:51:43 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 27 May 2010 14:51:43 +0200 Subject: [Pw_forum] Help regarding the generation of Pseudopotentials for rare earths? In-Reply-To: References: Message-ID: <4BFE6ADF.60906@democritos.it> sonu kumar wrote: > It seems, after reading the "espresso-4.1.2/atomic_doc" that pp for > rare-earths can be generated. of course they can: the problem is how usable they are in practise > question-11.3.0.2, tells about code "atomic". where can i find it? is it > "ld1.x" or different? the package is called "atomic", the executable is called "ld1.x" P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From vv0210 at gmail.com Thu May 27 18:24:08 2010 From: vv0210 at gmail.com (Vikas Varshney) Date: Thu, 27 May 2010 12:24:08 -0400 Subject: [Pw_forum] Parallel installation MPIF90 issue In-Reply-To: <4BFE2047.602@democritos.it> References: <4BFD725A.20600@democritos.it> <4BFD9718.8020607@democritos.it> <4BFE2047.602@democritos.it> Message-ID: Dear Pablo, Thanks, your suggestion worked. I could successfully run the first example (as well as few others) in serial as well as parallel. Best Regards, Vikas On Thu, May 27, 2010 at 3:33 AM, Paolo Giannozzi wrote: > soumyajyoti haldar wrote: > > > I am extremely sorry if I offended someone > > you didn't offend anybody > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100527/b2ec41e2/attachment.htm From sclauzer at sissa.it Thu May 27 18:35:18 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 27 May 2010 18:35:18 +0200 Subject: [Pw_forum] Cannot converge a calculation In-Reply-To: References: Message-ID: <3E24C455-AE3C-4C65-8BC6-4ECE639F0A2C@sissa.it> Dear Shapt, I'm sorry, but your problem is far from clear to me. Il giorno 25/mag/10, alle ore 19:32, Shaptrishi Sharma ha scritto: > Hi all, > > I would like to converge my system but I acn se that if I vary a > single parameter also there is a huge variation in result. Of course if you change a parameter of the calculation, for instance the lattice constant of a bulk system, you could see huge variations of the total energy. That said, it depends on which parameter you are speaking of. > For example, when I kept the cell _parameter as > 1 0 0 > 1 1.5 0 > 1 0 1.5 > > the total energy seems to change from 0.087 eV to 0.601 eV . And so, what are you changing? And how? Please try to be more clear and provide some sample of the input file you are using, just to understand if we are speaking of apples or bananas... Regards, GS > Can anybody please advice me ? > > Thanks > > Shapt > > Pune University > Pune > India > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100527/843ec611/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 1753 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100527/843ec611/attachment-0001.bin From ferretti at mit.edu Thu May 27 18:43:17 2010 From: ferretti at mit.edu (Andrea Ferretti) Date: Thu, 27 May 2010 17:43:17 +0100 (BST) Subject: [Pw_forum] Question on epsilon.x Message-ID: Hi Mohsen, epsilon.x computes the matrix elements of the momentum p, which is not easy to augment in a ultrasoft-pp fashion (at variance with operators which are functions of r, i.e. local). According to the size of system you want to study, you may want to generate your own norm-conserving pseudopotentials for Ba and Ti. The other possibility is instead to use the PAW formalism, where the augmentation of p matrix elements is as easy as for r. (of course this would require the generation of the PAW dataset, and some implementation) Related to the program epsilon.x: optical response can be also calculated through the matrix elements of the operator e^(iqr), which can be augmented easily with USPP. Unfortunately, using this solution would require to re-write the program almost from scratch (not recommended). Anyway if you want to follow this possibility, I would then start from a working norm-conserving implementation of it, as the ones in Sax or Yambo hope it helps Andrea BTW: in future posts please remember to add your affilication, according to the "politeness policy" of this forum > Dear users, > at first, i am so sorry that i asked many question about "epsilon.x". > But i faced with "USPP are not implemented", Which means i can not use > ultrasoft pseudopotentials but i want work with Ba and Ti, > is there any another Ref. for pseudopotentials or can i solve this problem in > some way? > Thanks for your reply > Mohsen Modaresi > -- Andrea Ferretti Oxford University, Department of Materials Parks Road, Oxford OX1 3PH, UK Tel: +44 (0)1865 612796; 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 hrhee at ucdavis.edu Thu May 27 23:51:25 2010 From: hrhee at ucdavis.edu (Hahnbidt Rhee) Date: Thu, 27 May 2010 14:51:25 -0700 Subject: [Pw_forum] a2Fq2r.* Message-ID: Hello. What exactly are in the files a2Fq2r.* (the suffix ranging from 51 to 60), which are generated during an el-ph calculation? The format of these files are like those of the dynamical matrices, but they are not the same. How are they related to the dynamical matrices? Why are there 10 of them, and how are these related to each other? Thank you! HB -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100527/ebd310ac/attachment.htm From eyvaz_isaev at yahoo.com Fri May 28 01:49:23 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 27 May 2010 16:49:23 -0700 (PDT) Subject: [Pw_forum] a2Fq2r.* Message-ID: <159492.5916.qm@web65709.mail.ac4.yahoo.com> Dear Rhee, --- On Fri, 5/28/10, Hahnbidt Rhee wrote: > What exactly are in the files a2Fq2r.* (the suffix ranging from 51 to > 60), which are generated during an el-ph calculation? The format of > these files are like those of the dynamical matrices, but they are not > the same. They are Eliashberg function (\alpha^2F(\omega)) calculated for 10 degauss (ranging from 0.005 till 0.05 by default) which are then used to evaluate lambda. > How are they related to the dynamical matrices? Not sure they are related. > Why are there 10 of them, and how are these related to each other? This one is due to double delta in the \gamma function which enters to the Eliashberg function. As integration of double delta is a hard problem, the summation in the BZ is performed by special points and broadening techniques. Different values for delta (10 by default) is used to find converged (w.r.t. delta) lambda. So, they are not related. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From hrhee at ucdavis.edu Fri May 28 07:00:43 2010 From: hrhee at ucdavis.edu (Hahnbidt Rhee) Date: Thu, 27 May 2010 22:00:43 -0700 Subject: [Pw_forum] a2Fq2r.* In-Reply-To: <159492.5916.qm@web65709.mail.ac4.yahoo.com> References: <159492.5916.qm@web65709.mail.ac4.yahoo.com> Message-ID: Prof Isaev, Thank you for your response. I am still confused, though. a2F is a function of omega only, but the a2Fq2r.* files hold matrices, in the exact format of the dynamical matrices. But these are not the dyn mats; separate files called matdyn* (* ranging from 1 to number of q-points) are created, which are the dyn mats. Another issue is that these a2Fq2r.* files are created BEFORE the q2r calculation. q2r.x actually uses these files and creates the files a2Fmatdyn.* (* ranging from 61 to 70). It seems to me like the a2Fmatdyn.* are used for matdyn.x to get a2F(omega), so the a2Fq2r.* files--and the a2Fmatdyn.* files, for that matter--couldn't possibly be the spectral function data. Am I incorrect? Thank you for your time. HB On Thu, May 27, 2010 at 4:49 PM, Eyvaz Isaev wrote: > Dear Rhee, > > --- On Fri, 5/28/10, Hahnbidt Rhee wrote: > > > What exactly are in the files a2Fq2r.* (the suffix ranging from 51 to > > 60), which are generated during an el-ph calculation? The format of > > these files are like those of the dynamical matrices, but they are not > > the same. > > They are Eliashberg function (\alpha^2F(\omega)) calculated for 10 degauss > (ranging from 0.005 till 0.05 by default) which are then used to evaluate > lambda. > > > How are they related to the dynamical matrices? > > Not sure they are related. > > > Why are there 10 of them, and how are these related to each other? > > This one is due to double delta in the \gamma function which enters to the > Eliashberg function. As integration of double delta is a hard problem, the > summation in the BZ is performed by special points and broadening > techniques. Different values for delta (10 by default) is used to find > converged (w.r.t. delta) lambda. > > So, they are not related. > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > > > > _______________________________________________ > 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/20100527/de002dc7/attachment.htm From vovi47 at yahoo.com Fri May 28 07:34:43 2010 From: vovi47 at yahoo.com (Vi Vo) Date: Thu, 27 May 2010 22:34:43 -0700 (PDT) Subject: [Pw_forum] Spin polarized option for tetragonal Message-ID: <708561.18465.qm@web114510.mail.gq1.yahoo.com> Dear PWSCF users, I set up an input to run a scf calculation for a body center tetragonal (BCT) system (ibrav=7), with nspin=2 (spin-polarized). However, I kept having the following errors: task # 5 from read_namelists : error # 19 reading namelist system I am not sure if the spin polarized option is implemented for BCT case or my input is wrong. Could you help me with this. Below is a section of my input (I have error in the system namelist): &system ibrav= 7 celldm(1) = 31.535747297405 celldm(3) = 1.3342521572387 nat=104, ntyp= 3 nbnd= 840 nelec = 840 npsin = 2 starting_magnetization(1)=0.7, occupations='smearing', smearing='marzari-vanderbilt', degauss=0.008 ecutwfc = 30.0 / &electrons diagonalization='cg' mixing_beta = 0.30 conv_thr = 1.0d-7 / ATOMIC_SPECIES Sb 121.757 Sb.rel-pbe-rrkj.UPF Mn 54.93805 Mn.pbe-sp-van.UPF Ca 40.078 Ca.pbe-nsp-van.UPF ATOMIC_POSITIONS crystal Sb 0.7500 0.5105 0.9895 Sb 0.7500 0.2395 0.2605 Sb 0.9790 0.2605 0.5105 ........................... Mn ............... Thank you very much, Vi Vo Chemical Engineering, University of Houston -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100527/bf4af4b7/attachment.htm From giannozz at democritos.it Fri May 28 08:42:00 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 28 May 2010 08:42:00 +0200 Subject: [Pw_forum] Spin polarized option for tetragonal In-Reply-To: <708561.18465.qm@web114510.mail.gq1.yahoo.com> References: <708561.18465.qm@web114510.mail.gq1.yahoo.com> Message-ID: <284C7AE6-481B-46C5-9196-5E5E2335106D@democritos.it> On May 28, 2010, at 7:34 , Vi Vo wrote: > nelec = 840 no longer present since v.4.2 (see Doc/release-notes) > npsin = 2 npsin != nspin --- 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 Fri May 28 08:49:23 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 28 May 2010 08:49:23 +0200 Subject: [Pw_forum] a2Fq2r.* In-Reply-To: References: Message-ID: <430CFD0D-0405-42F8-8DA4-06C7CA612491@democritos.it> On May 27, 2010, at 23:51 , Hahnbidt Rhee wrote: > What exactly are in the files a2Fq2r.* electron-phonon matrix elements, calculated for ten different values of boardening, for subsequent interpolation by q2r.x. Why do you want to know? internal files are, well, internal. 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 Fri May 28 09:10:53 2010 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 28 May 2010 09:10:53 +0200 Subject: [Pw_forum] a2Fq2r.* In-Reply-To: <430CFD0D-0405-42F8-8DA4-06C7CA612491@democritos.it> References: <430CFD0D-0405-42F8-8DA4-06C7CA612491@democritos.it> Message-ID: <749698BC-665A-4384-960A-3F731454C21C@sissa.it> On May 28, 2010, at 8:49 AM, Paolo Giannozzi wrote: > > On May 27, 2010, at 23:51 , Hahnbidt Rhee wrote: > >> What exactly are in the files a2Fq2r.* > > electron-phonon matrix elements, calculated for ten different > values of boardening, for subsequent interpolation by q2r.x. > Why do you want to know? internal files are, well, internal. I do appreciate, though, that some people get interested in the guts of the code. Hope that some of them get interested enough to join the efforts of the developers ... Stefano B > > 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/20100528/2690bf3a/attachment-0001.htm From modaresi.mohsen at gmail.com Fri May 28 10:51:16 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Fri, 28 May 2010 13:21:16 +0430 Subject: [Pw_forum] comparsion of Rusult with reported one (Imaginary part of dielectric function) Message-ID: Dear all I compute imaginary part of dielectric function for (h-BN) and i get this result but there is some remarkable difference between my result and reported one. Where is my problem? (SCF, NSCF, result and reported dielectric funtion (Ref: Camputatioal Materials Science 22 (2001) 78-80) are attached). I used the SCF and NSCF input file from test3 of WANT package. Thanks a lot Mohsen Modarsei M.Sc Student of Solid State Physics, Ferdowsi University of Mashhad, Iran. -------------- next part -------------- A non-text attachment was scrubbed... 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Name: reported..JPG Type: image/jpeg Size: 23266 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100528/88a3f35a/attachment-0001.jpeg From kazempoor2000 at yahoo.com Fri May 28 10:29:30 2010 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Fri, 28 May 2010 01:29:30 -0700 (PDT) Subject: [Pw_forum] Hse & PBE0 Message-ID: <119946.94847.qm@web114417.mail.gq1.yahoo.com> Dear all In general which hybrid functional (Hse or Pbe0) is faster? 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/20100528/b7266f5d/attachment.htm From marsamos at democritos.it Fri May 28 14:12:02 2010 From: marsamos at democritos.it (marsamos at democritos.it) Date: Fri, 28 May 2010 14:12:02 +0200 Subject: [Pw_forum] Hse & PBE0 In-Reply-To: <119946.94847.qm@web114417.mail.gq1.yahoo.com> References: <119946.94847.qm@web114417.mail.gq1.yahoo.com> Message-ID: <20100528141202.6zmk5pww04kwgg8c@mail.democritos.it> Dear Ali, it is very recently that HSE and PBE0 have been implemented. We do not have any benchmark! However if you perform some calculations with both it would very useful for all of us. bests Layla Quoting ali kazempour : > Dear all > In general which hybrid functional (Hse or Pbe0) is faster? > 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 > > > -- Dr. L. Martin-Samos tel. +39 040 3787 429 CNR-DEMOCRITOS and International School for Advanced Studies (ISAS-SISSA) via Beirut 2-4 34151 Trieste Italy ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From giuseppe.mattioli at mlib.ism.cnr.it Fri May 28 16:39:14 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Fri, 28 May 2010 16:39:14 +0200 Subject: [Pw_forum] Hse & PBE0 In-Reply-To: <20100528141202.6zmk5pww04kwgg8c@mail.democritos.it> References: <119946.94847.qm@web114417.mail.gq1.yahoo.com> <20100528141202.6zmk5pww04kwgg8c@mail.democritos.it> Message-ID: <201005281639.14600.giuseppe.mattioli@mlib.ism.cnr.it> Dear Ali and Layla I performed some calculations by using PBE0 and HSE on the same (molecular) systems, with same cutoffs, pseudopotentials, etc. There was not any (computational) difference between the two functional. Paolo (Giannozzi) suggested that FFT routines dominate the calculation weight, so that you do not find any benefit in the HSE screening wrt PBE0. Hope this helps Giuseppe On Friday 28 May 2010 14:12:02 marsamos at democritos.it wrote: > Dear Ali, it is very recently that HSE and PBE0 have been implemented. > We do not have any benchmark! However if you perform some calculations > with both it would very useful for all of us. > > bests > > Layla > > Quoting ali kazempour : > > Dear all > > In general which hybrid functional (Hse or Pbe0) is faster? > > 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 -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00016 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From hx35 at cornell.edu Fri May 28 17:07:28 2010 From: hx35 at cornell.edu (Huolin Xin) Date: Fri, 28 May 2010 11:07:28 -0400 Subject: [Pw_forum] Hse & PBE0 In-Reply-To: <201005281639.14600.giuseppe.mattioli@mlib.ism.cnr.it> References: <119946.94847.qm@web114417.mail.gq1.yahoo.com> <20100528141202.6zmk5pww04kwgg8c@mail.democritos.it> <201005281639.14600.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: Dear Giuseppe, Is there a depository of HSE/PBE0 pseudopotentials for PWscf? On Fri, May 28, 2010 at 10:39 AM, Giuseppe Mattioli < giuseppe.mattioli at mlib.ism.cnr.it> wrote: > Dear Ali and Layla > I performed some calculations by using PBE0 and HSE on the same (molecular) > systems, with same cutoffs, pseudopotentials, etc. > There was not any (computational) difference between the two functional. > Paolo (Giannozzi) suggested that FFT routines dominate the calculation > weight, > so that you do not find any benefit in the HSE screening wrt PBE0. > Hope this helps > Giuseppe > > On Friday 28 May 2010 14:12:02 marsamos at democritos.it wrote: > > Dear Ali, it is very recently that HSE and PBE0 have been implemented. > > We do not have any benchmark! However if you perform some calculations > > with both it would very useful for all of us. > > > > bests > > > > Layla > > > > Quoting ali kazempour : > > > Dear all > > > In general which hybrid functional (Hse or Pbe0) is faster? > > > 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 > > > > -- > ******************************************************** > - 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/20100528/5cf5836c/attachment.htm From giannozz at democritos.it Fri May 28 18:28:38 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 28 May 2010 18:28:38 +0200 Subject: [Pw_forum] Hse & PBE0 In-Reply-To: References: <119946.94847.qm@web114417.mail.gq1.yahoo.com> <20100528141202.6zmk5pww04kwgg8c@mail.democritos.it> <201005281639.14600.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <4BFFEF36.3030202@democritos.it> Huolin Xin wrote: > Is there a depository of HSE/PBE0 pseudopotentials for PWscf? short answer: no. Right now, the nly way is to use a PBE pseudopotential and input_dft='PBE0' or 'HSE' P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From davood.vahedi at yahoo.com Sat May 29 13:18:15 2010 From: davood.vahedi at yahoo.com (davood Vahedi) Date: Sat, 29 May 2010 04:18:15 -0700 (PDT) Subject: [Pw_forum] number of k-point Message-ID: <46921.99674.qm@web45703.mail.sp1.yahoo.com> Dear all I want to generate many?uniform K-point?for?NSCf calculation ?How?can i generate such a kpoint grid? Davoud Vahedi Ferdowsi University of Mashhad -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100529/0a5eeeac/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Sat May 29 21:54:08 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Sat, 29 May 2010 21:54:08 +0200 Subject: [Pw_forum] number of k-point In-Reply-To: <46921.99674.qm@web45703.mail.sp1.yahoo.com> References: <46921.99674.qm@web45703.mail.sp1.yahoo.com> Message-ID: <201005292154.08814.giuseppe.mattioli@mlib.ism.cnr.it> Dear Davoud Use K_POINTS {automatic} 4, 4, 4, 1, 1, 1 for a grid of, e.g., 4*4*4 k points (shifted wrt gamma, this is the meaning of the 1,1,1 cards). If you want to include gamma, your six numbers will be 4, 4, 4, 0, 0, 0. Notice that the generated k-points could be replicated (or deleted) depending upon the symmetry of your system. Read (more carefully) the /yourespresso/Doc/INPUT_PW.txt file for further insight... Yours Giuseppe On Saturday 29 May 2010 13:18:15 davood Vahedi wrote: > Dear all > I want to generate many?uniform K-point?for?NSCf calculation > ?How?can i generate such a kpoint grid? > > Davoud Vahedi > Ferdowsi University of Mashhad -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00016 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From condmatter at gmail.com Sun May 30 01:20:19 2010 From: condmatter at gmail.com (shiningstar) Date: Sun, 30 May 2010 01:20:19 +0200 Subject: [Pw_forum] Phonon calculations on the Grid Message-ID: Dear pwscf users, I am trying to calculate phonons by GRID method for which GRID_example has been given. I followed the procedure suggested by user guide, SCF by pw.x and then ph.x for separated q points ... (the second approach of "Calculation of Phonon Dispersions on the Grid Using Quantum ESPRESSO" by Riccardo di Meo). My problem is that when I was doing calculations for each individual q points I got an error GAMA point in file output1: from davcio : error # 20 error while reading from file and I got a empty file.dyn1! However, for the rest of q points I did't have such problem. I checked the problem, it occurs at the reading of wave function. But this problem still comes when I copy the wavefunction file file.wfc1 to the tmp directory. My input files like this: phonons of AlAs &inputph tr2_ph=1.0d-12, prefix='alas', ldisp=.true., nq1=4, nq2=4, nq3=4 start_q=1 last_q=1 recover=.true., amass(1)=26.98, amass(2)=74.92, outdir="/home/test/AlAs/1", fildyn='alas.dyn', / What is the possible reason? Any suggestion would be appreciated. Thanks. shiningstar -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100530/db9d1970/attachment.htm From suza.rri at gmail.com Sun May 30 03:16:22 2010 From: suza.rri at gmail.com (Suza W) Date: Sat, 29 May 2010 21:16:22 -0400 Subject: [Pw_forum] Orthorhombic Message-ID: Dear all, I am getting following error in the Simple Orthorhombic case when using Prof. Eyvaz's PlotPhon scripts: At line 47 of file K_for_bands.f90 (unit = 5, file = 'stdin') Fortran runtime error: Bad real number in item 1 of list input However, other cases such as simple cubic, FCC or hexagonal do not encounter the above error. Any suggestions? Thanking you, Suza W. Student RRI Bangalore -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100529/ce3db4ab/attachment.htm From giannozz at democritos.it Sun May 30 09:59:18 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 30 May 2010 09:59:18 +0200 Subject: [Pw_forum] Orthorhombic In-Reply-To: References: Message-ID: <6DC741B6-D44C-491C-BACF-79C597040D69@democritos.it> On May 30, 2010, at 3:16 , Suza W wrote: > At line 47 of file K_for_bands.f90 (unit = 5, file = 'stdin') > Fortran runtime error: Bad real number in item 1 of list input > [...] > Any suggestions? go to lne 47 of file K_for_bands.f90 and look at what is read from input. The first number read is wrong. 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 sagduk82 at hotmail.com Sun May 30 10:49:49 2010 From: sagduk82 at hotmail.com (=?windows-1254?B?c2F2Yf4gYfBkdWs=?=) Date: Sun, 30 May 2010 11:49:49 +0300 Subject: [Pw_forum] Strain Tensor Message-ID: Hi , I 'm new in Quantum Espresso and I don't know how to apply strain tensor to primitive vectors. In fact, I have read some articles to learn how to calculate elastic modulus but they don't help for quantum espresso way. Any help is much appreciated ! Thanks . _________________________________________________________________ Yeni Windows 7: Size en uygun bilgisayar? bulun. Daha fazla bilgi edinin. http://windows.microsoft.com/shop -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100530/6c4e3962/attachment.htm From baroni at sissa.it Sun May 30 12:12:09 2010 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 30 May 2010 12:12:09 +0200 Subject: [Pw_forum] Strain Tensor In-Reply-To: References: Message-ID: Hi! Welcome to this forum. As you will learn staying with us, we all much appreciate our forum-pals to sign their posts, and also provide their affiliation. Please, do the same in the future. This being said, your question has nothing to do with Quantum ESPRESSO. You have first to understand what the strain tensor is supposed to represent: it is nothing but the linear relation describing a scale transformation of the tipe r'=(1+e)r, where r' are the scaled variables of a pont in real space, r the unscaled ones, "1" the 3x3 identity matrix, and "e" the 3x3 infinitesimal (symmetric) strain tensor. The above matrix relation trivially holds for the primitive vectors of a lattice, but not for the internally coordinates of individual atoms, if the lattice is not primitive (i.e. if it has a basis). In the latter case, internal coordinates have to be optimized upon application of the strain. Hope this helps Stefano Baroni On May 30, 2010, at 10:49 AM, sava? a?duk wrote: > > Hi , > > I 'm new in Quantum Espresso and I don't know how to apply strain tensor to > primitive vectors. In fact, I have read some articles to learn how to calculate elastic > modulus but they don't help for quantum espresso way. Any help is much appreciated ! > > Thanks . > > ; > > > Windows 7: Size en uygun bilgisayar? bulun. Daha fazla bilgi edinin. _______________________________________________ > 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/20100530/12281abf/attachment.htm From niuli1978 at yahoo.com.cn Sun May 30 13:51:07 2010 From: niuli1978 at yahoo.com.cn (li niu) Date: Sun, 30 May 2010 19:51:07 +0800 (CST) Subject: [Pw_forum] Norm-conserving Zn/In/Ga pseudopotential Message-ID: <590394.65154.qm@web15005.mail.cnb.yahoo.com> Dear users and developers,I want to calculate vibrational properties of InGaO3(ZnO)n compounds.However,there are not norm-conserving pseudopotential for Zn, In and Ga atoms at http://www.quantum-espresso.org/pseudo.php.?I would be very grateful if someone that has generated such a pseudocould send it to me. My email: niuli1978 at yahoo.com.cnThanks in advance and kind regards,?Li Niu School of Physics and Electronic Engineering, Harbin Normal University, Harbin 150025, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100530/bc8a87cf/attachment.htm From baroni at sissa.it Sun May 30 14:22:07 2010 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 30 May 2010 14:22:07 +0200 Subject: [Pw_forum] corporate usage of Quantum ESPRESSO Message-ID: Dear All (especially users doing research in industrial laboratories), QE developers are extremely glad and proud of the growing favor that their software is gaining worldwide among researchers in the academia and in the industry alike: the latest release of QE (4.2) has been downloaded more than 800 times since May 10, 2010; this mailing list has more than 1100 subscribers and is a very lively discussion forum (~10 posts/day); the QE manifesto, appeared last fall on J Phys: Condens Matter, is gathering 16-17 citations per month in 2010; Quantum ESPRESSO is used as a benchmark in the European supercomputing initiatives DEISA and PRACE. Thanks to all (developers and users alike) for making all this possible! As you know, Quantum ESPRESSO is, and will continue to be, free software. This does not mean that it is easy for QE developers to get from their institutions and from the funding agencies in their countries the continuous support that such a large-scale project requires. We are working hard to obtain such support, and we will work harder in the future, but we need a little help from all of you. In a time where research funds are shrinking in many countries (including Italy, where much of the QE development, and most of its maintenance, take place), the ability to claim and document an impact on applied research can make a difference between getting or loosing a grant. That's why it would be extremely useful if we could avail ourselves of an up-to-date list of industrial users / groups of users. I would be extremely grateful if scientists active in industrial and national laboratories that use Quantum ESPRESSO for their research were kind enough so as to send *me* (not this forum) a line of email, authorizing me to insert their identity in a *private* list of non-academic users and the name of their laboratory in a list that could be used in public presentations. (no info on such sensitive issues as the actual content of their research is obviously required). I thank in advance those who can help, and wish all of you much fun and success using Quantum ESPRESSO. Stefano Baroni --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100530/5a188fd4/attachment-0001.htm From kyin.cn at gmail.com Sun May 30 14:42:02 2010 From: kyin.cn at gmail.com (Kun Yin) Date: Sun, 30 May 2010 20:42:02 +0800 Subject: [Pw_forum] how to do fixed volume optimization Message-ID: <201005302041597969466@gmail.com> Dear All, Does anyone have the experience to do volume fixed optimization with QE, which means the structure is optimized allowing all cell parameters and atomic positions to vary while keeping the volume fixed? Kun Yin Najing University, China 2010-05-30 From mohnish.iitk at gmail.com Sun May 30 14:46:29 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Sun, 30 May 2010 18:16:29 +0530 Subject: [Pw_forum] how to do fixed volume optimization In-Reply-To: <201005302041597969466@gmail.com> References: <201005302041597969466@gmail.com> Message-ID: Dear Yin 'vc-relax' calculation optimizes the structures by the lattice parameters also but if you set the calculation 'relax' then it optimizes the geometry within the given fixed volume constraints. This calculation moves the atom keeping the volume constant within the given symmetry constraint. hope this helps :) On Sun, May 30, 2010 at 6:12 PM, Kun Yin wrote: > Dear All, > > Does anyone have the experience to do volume fixed optimization with QE, > which means the structure is optimized allowing all cell parameters and > atomic positions to vary while keeping the volume fixed? > > Kun Yin > Najing University, China > 2010-05-30 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100530/7e7a28aa/attachment.htm From kyin.cn at gmail.com Sun May 30 15:09:34 2010 From: kyin.cn at gmail.com (Kun Yin) Date: Sun, 30 May 2010 21:09:34 +0800 Subject: [Pw_forum] how to do fixed volume optimization References: <201005302041597969466@gmail.com> Message-ID: <201005302109318285369@gmail.com> Thanks for your reply, Mohnish. The 'relax' calculation will keep the volume constant but it will fix the cell parameters, too. For example, if I optimize a tetragonal cell, I want the c and a axis to change but the volume unchanged. I know this could be done by varing c/a ratio manually with a series of relax calculation. My question is, can this be done automatically in QE? ------------------ Kun Yin 2010-05-30 Dear Yin 'vc-relax' calculation optimizes the structures by the lattice parameters also but if you set the calculation 'relax' then it optimizes the geometry within the given fixed volume constraints. This calculation moves the atom keeping the volume constant within the given symmetry constraint. hope this helps :) On Sun, May 30, 2010 at 6:12 PM, Kun Yin wrote: > Dear All, > > Does anyone have the experience to do volume fixed optimization with QE, > which means the structure is optimized allowing all cell parameters and > atomic positions to vary while keeping the volume fixed? > > Kun Yin > Najing University, China > 2010-05-30 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 ----------------------------------------------------------------- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From tkaloni at gmail.com Sun May 30 15:22:10 2010 From: tkaloni at gmail.com (Thaneshwor Kaloni) Date: Sun, 30 May 2010 18:52:10 +0530 Subject: [Pw_forum] Pw_forum Digest, Vol 35, Issue 61 In-Reply-To: References: Message-ID: Dear all, I am using quantum Espresso, I am facing problem to get accurate band structure of Graphene, it will be appreciated if anyone resolve my problem. With Best Regards!! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100530/2611619f/attachment.htm From giannozz at democritos.it Sun May 30 15:47:26 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 30 May 2010 15:47:26 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 35, Issue 61 In-Reply-To: References: Message-ID: <055BFCC3-2653-48A0-B172-74A7EFD6AC8F@democritos.it> On May 30, 2010, at 15:22 , Thaneshwor Kaloni wrote: > I am facing problem to get accurate band structure of Graphene again...please search the mailing list archives, there are questions about graphene every week 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 May 30 15:50:08 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 30 May 2010 15:50:08 +0200 Subject: [Pw_forum] Norm-conserving Zn/In/Ga pseudopotential In-Reply-To: <590394.65154.qm@web15005.mail.cnb.yahoo.com> References: <590394.65154.qm@web15005.mail.cnb.yahoo.com> Message-ID: On May 30, 2010, at 13:51 , li niu wrote: > there are not norm-conserving pseudopotential for Zn, In and Ga atoms for In and Ga, there are lda norm-conserving pseudopotentials 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 May 30 16:43:37 2010 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 30 May 2010 16:43:37 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 35, Issue 61 In-Reply-To: <055BFCC3-2653-48A0-B172-74A7EFD6AC8F@democritos.it> References: <055BFCC3-2653-48A0-B172-74A7EFD6AC8F@democritos.it> Message-ID: Also, if after searching and reading the mailing list archive (but only *after* making a serious effort to find a solution to your problems), you feel that you still need some help, please: 1) describe what your problem is, possibly providing an input and an output of a calculation. (how can anybody help if nobody knows what the problem is?) 2) Sign your posts, including your academic affiliation. Thanks - Stefano B On May 30, 2010, at 3:47 PM, Paolo Giannozzi wrote: > > On May 30, 2010, at 15:22 , Thaneshwor Kaloni wrote: > >> I am facing problem to get accurate band structure of Graphene > > again...please search the mailing list archives, there are > questions about graphene every week > > 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/20100530/b6a6dcf2/attachment.htm From payam.norouzzadeh at gmail.com Sun May 30 16:55:04 2010 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Sun, 30 May 2010 19:25:04 +0430 Subject: [Pw_forum] merging results of individual k points phonon calculation Message-ID: Hello all Because of restriction on running time I want to do phonon calculations for each k point individually and then merge the results to have one file for force constants,... Is there any utility available to do that?what is the procedure? Breg, Payam Kiel University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100530/14e28b1c/attachment-0001.htm From giannozz at democritos.it Sun May 30 16:59:02 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 30 May 2010 16:59:02 +0200 Subject: [Pw_forum] merging results of individual k points phonon calculation In-Reply-To: References: Message-ID: On May 30, 2010, at 16:55 , Payam Norouzzadeh wrote: > Because of restriction on running time I want to do phonon > calculations for each k point individually and then merge the > results to have one file for force constants,... > Is there any utility available to do that?what is the procedure? in recent versions, see examples/GRID_example/ 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 mambom1902 at yahoo.com Mon May 31 02:03:39 2010 From: mambom1902 at yahoo.com (loc duong ding) Date: Sun, 30 May 2010 17:03:39 -0700 (PDT) Subject: [Pw_forum] IR-Raman calcualtion Message-ID: <566838.25329.qm@web38801.mail.mud.yahoo.com> Dear all, I tried to calculation the Ir-Raman cross-section of nanoribbon. I saw in some topics in the forum that showed that occupations is not used for calculation IR-Raman cross section. However, I can not get the convergence of scf calculation if smearing is not used. Can you give me some instructions to overcome this problem? I appreciate all your helps. Sincerely, ----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com, ddloc at skku.edu From archygu at gmail.com Mon May 31 03:03:07 2010 From: archygu at gmail.com (chenjie gu) Date: Mon, 31 May 2010 09:03:07 +0800 Subject: [Pw_forum] quenching input file example Message-ID: Dear Pwscf Users, recently I want to simulate the quench procedure using BOMD, however I am not very clear how to set the input parameters, so is there any one has the input examples for my reference, it will be a big kindness of you. many thanks. -- Yours Regards, chenjie GU EEE,Nanyang Technoligical University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100531/e1300f26/attachment.htm From seung43210 at yahoo.com Mon May 31 05:27:06 2010 From: seung43210 at yahoo.com (seunghwan lee) Date: Sun, 30 May 2010 20:27:06 -0700 (PDT) Subject: [Pw_forum] plotting orbital Message-ID: <417413.19541.qm@web50506.mail.re2.yahoo.com> Hi All, I am trying to plot some orbitals of my system (CNT with metal). I see the option plot_num=7 for pp.x to plot |psi|^2, but is there any way to plot the orbital itself, not the square of orbital? Thanks for your help. Seunghwan Lee University of North Carolina From baroni at sissa.it Mon May 31 07:19:11 2010 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 31 May 2010 07:19:11 +0200 Subject: [Pw_forum] IR-Raman calcualtion In-Reply-To: <566838.25329.qm@web38801.mail.mud.yahoo.com> References: <566838.25329.qm@web38801.mail.mud.yahoo.com> Message-ID: <5186C6A0-FEA5-4D17-B8E7-1CF991DFAC7C@sissa.it> Try to reduce the smearing down to zero after achieving convergence. (swindling ph.x by setting the weights to zero by hands may also work, but I am not sure). SB On May 31, 2010, at 2:03 AM, loc duong ding wrote: > Dear all, > > I tried to calculation the Ir-Raman cross-section of nanoribbon. > > I saw in some topics in the forum that showed that occupations is not used for calculation IR-Raman cross section. > However, I can not get the convergence of scf calculation if smearing is not used. > > Can you give me some instructions to overcome this problem? > > I appreciate all your helps. > > > Sincerely, > ----------------------------------------------- > Loc Duong Dinh > Ms-Ph.D Student > Sungkyunkwan Advanced Institute of Nanotechnology, > Sungkyunkwan University, > Suwon, 440-746, Korea > Email: mambom1902 at yahoo.com, ddloc at skku.edu > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- 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/20100531/5ce34f77/attachment.htm From soumyajyoti.haldar at gmail.com Mon May 31 07:46:29 2010 From: soumyajyoti.haldar at gmail.com (soumyajyoti haldar) Date: Mon, 31 May 2010 07:46:29 +0200 Subject: [Pw_forum] quenching input file example In-Reply-To: References: Message-ID: Hi, you have to set ion_temperature = 'reduce-T' it reduce the ionic temperature every "nraise" steps by the (negative) value "delta_t" so you need to set those also. For more details on the parameter pls refer to you /Doc/INPUT_PW.txt , Name List IONS. Reagards, -- Soumyajyoti Haldar Junior Research Fellow Advance Computing Laboratory Department of Physics, University of Pune Ganeshkhind, Pune - 411007; INDIA Tel : (+91 20) 25692678; Extn # 408 ~~~***~~~***~~~***~~~***~~~***~~~***~~~***~~~ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100531/5d60468d/attachment.htm From nnlinh at sissa.it Mon May 31 09:41:55 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Mon, 31 May 2010 09:41:55 +0200 Subject: [Pw_forum] how to do fixed volume optimization In-Reply-To: <201005302109318285369@gmail.com> References: <201005302041597969466@gmail.com> <201005302109318285369@gmail.com> Message-ID: <4C036843.3090902@sissa.it> Kun Yin wrote: > Thanks for your reply, Mohnish. > The 'relax' calculation will keep the volume constant but it will fix the cell parameters, too. For example, if I optimize a tetragonal cell, I want the c and a axis to change but the volume unchanged. I know this could be done by varing c/a ratio manually with a series of relax calculation. My question is, can this be done automatically in QE > Why don't you build a supercell that stores the considering structure. When you do optimization, the volume of supercell will be fixed , but the structure is still optimized. Hope this help. Linh > ------------------ > Kun Yin > 2010-05-30 > > Dear Yin 'vc-relax' calculation optimizes the structures by the lattice > parameters also but if you set the calculation 'relax' then it optimizes the > geometry within the given fixed volume constraints. This calculation moves > the atom keeping the volume constant within the given symmetry constraint. > hope this helps :) > > On Sun, May 30, 2010 at 6:12 PM, Kun Yin wrote: > > >> Dear All, >> >> Does anyone have the experience to do volume fixed optimization with QE, >> which means the structure is optimized allowing all cell parameters and >> atomic positions to vary while keeping the volume fixed? >> >> Kun Yin >> Najing University, China >> 2010-05-30 >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > > -- ----------------------------------------------------- Nguyen Ngoc Linh, PhD Student c/o: SISSA & CNR-INFM Democritos, via Beirut 2-4, 34014 Trieste (Italy) email: nnlinh at sissa.it phone: +39 04 03787 319 skype: ngoclinh84phys ----------------------------------------------------- "The physics is theoretical but the fun is real" From gehricht at googlemail.com Mon May 31 09:53:51 2010 From: gehricht at googlemail.com (Wolfgang Gehricht) Date: Mon, 31 May 2010 09:53:51 +0200 Subject: [Pw_forum] Job crashes on multiple nodes Message-ID: Dear group! I am experiencing the following problem with pw.x. When I run a job on a single core with 8 processors, the calculation does not exceed the available RAM, i.e. it works. When I run the same job on two cores, the calculation crashes (mpierun: Forwarding signal 12 to job) [relevant log-parts see below]. However, I can compute this job on two cores with a smaller k-point sampling, hence I suspect that it has to do somehow with the memory demands/distribution. I am using the "Davidson iterative diagonalization" as a minimizer, with just settings for the thresholds (convergence, 1st iterative diagonalization). Can you please point me into the right direction? With thanks Yours Wolfgang --- Parallel version (MPI) Number of processors in use: 16 R & G space division: proc/pool = 16 ... Subspace diagonalization in iterative solution of the eigenvalue problem: a parallel distributed memory algorithm will be used, eigenstates matrixes will be distributed block like on ortho sub-group = 4* 4 procs ... Planes per process (thick) : nr3 = 90 npp = 6 ncplane = 8100 Proc/ planes cols G planes cols G columns G Pool (dense grid) (smooth grid) (wavefct grid) 1 6 339 18817 6 339 18817 92 2668 2 6 339 18817 6 339 18817 92 2668 3 6 339 18817 6 339 18817 92 2668 4 6 338 18812 6 338 18812 92 2668 5 6 338 18812 6 338 18812 93 2669 6 6 338 18812 6 338 18812 93 2669 7 6 338 18812 6 338 18812 93 2669 8 6 338 18812 6 338 18812 93 2669 9 6 338 18812 6 338 18812 93 2669 10 6 338 18812 6 338 18812 93 2669 11 5 339 18817 5 339 18817 93 2669 12 5 339 18815 5 339 18815 93 2669 13 5 339 18815 5 339 18815 93 2669 14 5 339 18815 5 339 18815 92 2666 15 5 339 18815 5 339 18815 92 2666 16 5 339 18815 5 339 18815 92 2666 tot 90 5417 301027 90 5417 301027 1481 42691 ... G cutoff = 1729.8995 ( 301027 G-vectors) FFT grid: ( 90, 90, 90) Largest allocated arrays est. size (Mb) dimensions Kohn-Sham Wavefunctions 4.63 Mb ( 2373, 128) NL pseudopotentials 9.12 Mb ( 2373, 252) Each V/rho on FFT grid 1.48 Mb ( 48600, 2) Each G-vector array 0.14 Mb ( 18817) G-vector shells 0.01 Mb ( 1370) Largest temporary arrays est. size (Mb) dimensions Auxiliary wavefunctions 18.54 Mb ( 2373, 512) Each subspace H/S matrix 4.00 Mb ( 512, 512) Each matrix 0.49 Mb ( 252, 128) Arrays for rho mixing 5.93 Mb ( 48600, 8) Initial potential from superposition of free atoms 16 total processes killed (some possibly by mpirun during cleanup) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100531/7c9a054e/attachment.htm From sclauzer at sissa.it Mon May 31 09:57:06 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 31 May 2010 09:57:06 +0200 Subject: [Pw_forum] plotting orbital In-Reply-To: <417413.19541.qm@web50506.mail.re2.yahoo.com> References: <417413.19541.qm@web50506.mail.re2.yahoo.com> Message-ID: <77445795-C70E-47CA-9B52-C7BDD315734B@sissa.it> Since there is an arbitrariness in the choice of the phase of the wavefunction, one usually visualizes its squared modulus. At k=(0,0,0) the wavefunctions can be chosen real, so that you can plot sign(psi)*| psi|^2 by setting lsign=.TRUE. Anyway, for some purpose you may want to visualize both the modulus and the complex phase of the wavefunction. I think this is not implemented in pp.x, but I remember some posts about that dating roughly 1 year ago, or so. You may try a search in the archives (something like: 'wavefunction phase plot site:democritos.it' on google). Moreover, some other postprocessing utility may already be implementing this feature (perhaps pw2casino, just a guess), since the .wfc files in principle should store all the necessary information. Regards, GS Il giorno 31/mag/10, alle ore 05:27, seunghwan lee ha scritto: > Hi All, > > I am trying to plot some orbitals of my system (CNT with metal). I > see the > option plot_num=7 for pp.x to plot |psi|^2, but is there any way to > plot > the orbital itself, not the square of orbital? > > Thanks for your help. > > Seunghwan Lee > University of North Carolina > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100531/432cbecc/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 1753 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100531/432cbecc/attachment.bin From sclauzer at sissa.it Mon May 31 10:12:25 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 31 May 2010 10:12:25 +0200 Subject: [Pw_forum] Job crashes on multiple nodes In-Reply-To: References: Message-ID: Dear Wolfgang, Il giorno 31/mag/10, alle ore 09:53, Wolfgang Gehricht ha scritto: > Dear group! > > I am experiencing the following problem with pw.x. When I run a job > on a single core with 8 processors, the calculation does not exceed > the available RAM, i.e. it works. When I run the same job on two > cores, the calculation crashes (mpierun: Forwarding signal 12 to > job) [relevant log-parts see below]. However, I can compute this job > on two cores with a smaller k-point sampling, hence I suspect that > it has to do somehow with the memory demands/distribution. I am > using the "Davidson iterative diagonalization" as a minimizer, with > just settings for the thresholds (convergence, 1st iterative > diagonalization). > Can you please point me into the right direction? > With thanks > Yours Wolfgang > --- > Parallel version (MPI) > > Number of processors in use: 16 > R & G space division: proc/pool = 16 It's not a good idea to run 16 processes on 8 cores... even worst on 2 cores! The data is distributed among the processes, so the more processes in the R&G pool, the smaller amount of memory needed per processes. Anyway, if you run all processes on the same core, you are not distributing the data *physically*. Moreover these processes will tend to stomp on each other's feet. About the k-point sampling (assuming that you don't use parallelization over k-points, i.e. npool=1): the largest data arrays are present in the main memory only for one k-point at a time (unless you use options like disk_io='none' or so), so that incresing the number of k-points will increase the computation time almost linearly, but will leave the memory consumption almost unchanged. If the problem is with the parallel Davidson diagonalization, you may try to disable it with ndiag=1. All that said, from the memory usage estimate reported below, it looks like you're not running such a big system... nothing that couldn't be run on a laptop with 2GB of memory. HTH GS > ... > Subspace diagonalization in iterative solution of the eigenvalue > problem: > a parallel distributed memory algorithm will be used, > eigenstates matrixes will be distributed block like on > ortho sub-group = 4* 4 procs > ... > Planes per process (thick) : nr3 = 90 npp = 6 ncplane = 8100 > > Proc/ planes cols G planes cols G columns G > Pool (dense grid) (smooth grid) (wavefct grid) > 1 6 339 18817 6 339 18817 92 2668 > 2 6 339 18817 6 339 18817 92 2668 > 3 6 339 18817 6 339 18817 92 2668 > 4 6 338 18812 6 338 18812 92 2668 > 5 6 338 18812 6 338 18812 93 2669 > 6 6 338 18812 6 338 18812 93 2669 > 7 6 338 18812 6 338 18812 93 2669 > 8 6 338 18812 6 338 18812 93 2669 > 9 6 338 18812 6 338 18812 93 2669 > 10 6 338 18812 6 338 18812 93 2669 > 11 5 339 18817 5 339 18817 93 2669 > 12 5 339 18815 5 339 18815 93 2669 > 13 5 339 18815 5 339 18815 93 2669 > 14 5 339 18815 5 339 18815 92 2666 > 15 5 339 18815 5 339 18815 92 2666 > 16 5 339 18815 5 339 18815 92 2666 > tot 90 5417 301027 90 5417 301027 1481 42691 > ... > G cutoff = 1729.8995 ( 301027 G-vectors) FFT grid: ( 90, 90, 90) > > Largest allocated arrays est. size (Mb) dimensions > Kohn-Sham Wavefunctions 4.63 Mb ( 2373, 128) > NL pseudopotentials 9.12 Mb ( 2373, 252) > Each V/rho on FFT grid 1.48 Mb ( 48600, 2) > Each G-vector array 0.14 Mb ( 18817) > G-vector shells 0.01 Mb ( 1370) > Largest temporary arrays est. size (Mb) dimensions > Auxiliary wavefunctions 18.54 Mb ( 2373, 512) > Each subspace H/S matrix 4.00 Mb ( 512, 512) > Each matrix 0.49 Mb ( 252, 128) > Arrays for rho mixing 5.93 Mb ( 48600, 8) > > Initial potential from superposition of free atoms > 16 total processes killed (some possibly by mpirun during cleanup) > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100531/7727cab4/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 1753 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100531/7727cab4/attachment-0001.bin From kyin.cn at gmail.com Mon May 31 10:14:05 2010 From: kyin.cn at gmail.com (Kun Yin) Date: Mon, 31 May 2010 16:14:05 +0800 Subject: [Pw_forum] how to do fixed volume optimization References: <201005302041597969466@gmail.com>, <201005302109318285369@gmail.com> Message-ID: <201005311614027962613@gmail.com> Thanks Linh. I doubt that if I don't break the crystal symmetry, the 'relax' optimization of a supercell will have the same effect as the primitive cell. Even if not, there are two side effects of this idea: (1) more time to spend for computing a supercell, (2) difficulty to extract a primitive cell back from the supercell and appreciate its symmetry. The 'vc-relax' calculation optimzes both the shape of the cell and atomic positions while keeping the symmetry at a target pressure. It takes the pressure as convergence criterion. The 'relax' calculation optimizes the atomic positions while keeping the shape of the cell. It takes the force on atoms as convergence criterion. I want to optimize the both the cell parameters and atomic positions while keeping the symmetry and volume constant. It will take energy as convergence criterion. I don't know if QE has the options in input to do this easily. This can be done by performing a series of 'relax' calculation to optimize all degrees of freedom in cell parameters and find the minimum value. But this is labrious especially for low symmetry structure such as monoclinic cell. ------------------ Kun Yin 2010-05-31 Kun Yin wrote: > Thanks for your reply, Mohnish. > The 'relax' calculation will keep the volume constant but it will fix the cell parameters, too. For example, if I optimize a tetragonal cell, I want the c and a axis to change but the volume unchanged. I know this could be done by varing c/a ratio manually with a series of relax calculation. My question is, can this be done automatically in QE > Why don't you build a supercell that stores the considering structure. When you do optimization, the volume of supercell will be fixed , but the structure is still optimized. Hope this help. Linh > ------------------ > Kun Yin > 2010-05-30 > > Dear Yin 'vc-relax' calculation optimizes the structures by the lattice > parameters also but if you set the calculation 'relax' then it optimizes the > geometry within the given fixed volume constraints. This calculation moves > the atom keeping the volume constant within the given symmetry constraint. > hope this helps :) > > On Sun, May 30, 2010 at 6:12 PM, Kun Yin wrote: > > >> Dear All, >> >> Does anyone have the experience to do volume fixed optimization with QE, >> which means the structure is optimized allowing all cell parameters and >> atomic positions to vary while keeping the volume fixed? >> >> Kun Yin >> Najing University, China >> 2010-05-30 >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > > -- ----------------------------------------------------- Nguyen Ngoc Linh, PhD Student c/o: SISSA & CNR-INFM Democritos, via Beirut 2-4, 34014 Trieste (Italy) email: nnlinh at sissa.it phone: +39 04 03787 319 skype: ngoclinh84phys ----------------------------------------------------- "The physics is theoretical but the fun is real" _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From giacsport at libero.it Mon May 31 12:40:01 2010 From: giacsport at libero.it (giacsport at libero.it) Date: Mon, 31 May 2010 12:40:01 +0200 (CEST) Subject: [Pw_forum] DFT+U AND GW Message-ID: <13705387.1375591275302401134.JavaMail.defaultUser@defaultHost> Dear All, I am definitely new in PWscf so maybe my question could seem strange. I want to calculate ZnO bandgap. Now, DFT gives a starting bad description of the 3d orbitals of Zn. At least a DFT+U calculation seems to be mandatory in order to align these 3d orbitals to the experimental level (around -7 eV below the top of the VB). Now, once I have aligned these orbitals, is it possible to calculate the GW correction on this previously calculated DFT+U band structure? In other words, 1. a DFT+U calculation for aligning the 3d orbitals of Zn 2. a GW correction for consistently opening the band gap (trying to reproduce the experimental one) Thanks in advance. Best regards, Giacomo From giannozz at democritos.it Mon May 31 13:15:39 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 31 May 2010 13:15:39 +0200 Subject: [Pw_forum] how to do fixed volume optimization In-Reply-To: <201005311614027962613@gmail.com> References: <201005302041597969466@gmail.com>, <201005302109318285369@gmail.com> <201005311614027962613@gmail.com> Message-ID: <4C039A5B.1080903@democritos.it> Kun Yin wrote: > I want to optimize the both the cell parameters and atomic > positions while keeping the symmetry and volume constant. > I don't know if QE has the options in input to do this easily. short answer: no. It should be relatively easy to implement but it has never been done, to the best of my knowledge. You can use 'vc-relax' at costant pressure, though, and vary the pressure, if I remember correctly P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From kyin.cn at gmail.com Mon May 31 14:28:54 2010 From: kyin.cn at gmail.com (Kun Yin) Date: Mon, 31 May 2010 20:28:54 +0800 Subject: [Pw_forum] how to do fixed volume optimization References: <201005302041597969466@gmail.com>, <201005302109318285369@gmail.com>, <201005311614027962613@gmail.com> Message-ID: <201005312028518289019@gmail.com> I see. Thanks for giving the answer, Paolo. I hope this easy-to-implement functionality, doing 'vc-relax' at constant volume, will be done by some enthusiastic guy, since it is very useful in some research such as the study of high-pressure materials. ------------------ Kun Yin 2010-05-31 Kun Yin wrote: > I want to optimize the both the cell parameters and atomic > positions while keeping the symmetry and volume constant. > I don't know if QE has the options in input to do this easily. short answer: no. It should be relatively easy to implement but it has never been done, to the best of my knowledge. You can use 'vc-relax' at costant pressure, though, and vary the pressure, if I remember correctly P. -- Paolo Giannozzi, Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From mambom1902 at yahoo.com Mon May 31 14:43:25 2010 From: mambom1902 at yahoo.com (loc duong ding) Date: Mon, 31 May 2010 05:43:25 -0700 (PDT) Subject: [Pw_forum] Pw_forum Digest, Vol 35, Issue 63 In-Reply-To: References: Message-ID: <873220.10394.qm@web38803.mail.mud.yahoo.com> Dear Prof. Stefano Baroni, It works well by this method. At first, I try to get the convergence with the smearing and later, drop down this options. Thank you to your helpful instructions. >Try to reduce the smearing down to zero > after achieving convergence. (swindling ph.x by setting the weights to zero by > hands may also work, but I am not sure). SB ----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com, ddloc at skku.edu From amit99266 at rediffmail.com Mon May 31 14:52:31 2010 From: amit99266 at rediffmail.com (Yamit ) Date: 31 May 2010 12:52:31 -0000 Subject: [Pw_forum] =?utf-8?q?Is_it_possible_to_calculate_the_phonon_dos_f?= =?utf-8?q?or_each_branch=3F?= Message-ID: <20100531125231.17148.qmail@f4mail-235-230.rediffmail.com> Dear All Is it possible to calculate the phonon dos(density of states) for each Phonon Branch separately using "matdyn.x"? Warm Regards Amit N. Harode C.R .Labs INDIA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100531/9467a432/attachment.htm From wangqj1 at 126.com Mon May 31 14:39:20 2010 From: wangqj1 at 126.com (Q.J.Wang) Date: Mon, 31 May 2010 20:39:20 +0800 (CST) Subject: [Pw_forum] USPP and Raman Message-ID: <453fe33.a806.128ee5f949c.Coremail.wangqj1@126.com> Dear pwscf developers I want to know whether the US PsPs are implemented in Raman calculations or not now ? I want to calculate the Raman intensity, and there is little NCPP in the official website, what should I do if US PsPs are not implemented in Raman calculations ? Thanks for your selfless contribution? -- Best regards Q.J.Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100531/a37c4030/attachment.htm From nkxirainbow at gmail.com Mon May 31 15:38:38 2010 From: nkxirainbow at gmail.com (xirainbow) Date: Mon, 31 May 2010 21:38:38 +0800 Subject: [Pw_forum] USPP and Raman In-Reply-To: <453fe33.a806.128ee5f949c.Coremail.wangqj1@126.com> References: <453fe33.a806.128ee5f949c.Coremail.wangqj1@126.com> Message-ID: Dear Wang: USPP can not be used to calculate Raman intensity. 2010/5/31 Q.J.Wang > *Dear pwscf developers* > * I want to know whether the US PsPs are implemented in Raman** calculations > or not now ? I want to calculate the Raman intensity, and there is little > NCPP in the official website, what should I do if US PsPs are not > implemented in Raman calculations ?* > *Thanks for your selfless contribution?* > > -- > Best regards > > Q.J.Wang > > XiangTan 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/20100531/3e0aefc7/attachment.htm From arvifis at gmail.com Mon May 31 15:58:56 2010 From: arvifis at gmail.com (Arles V. Gil Rebaza) Date: Mon, 31 May 2010 10:58:56 -0300 Subject: [Pw_forum] Magnetic Field Message-ID: Hi QE user, i would like calculate magnetic properties of Fe alloys with a magnetic field applied... I can do this using QE..?? Best Regards. Arles V. Gil Rebaza Instituto de F?sica de La Plata La Plata - Argentina -- ###---------> Arles V. <---------### -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100531/c96ce2b5/attachment.htm From sclauzer at sissa.it Mon May 31 16:05:14 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 31 May 2010 16:05:14 +0200 Subject: [Pw_forum] DFT+U AND GW In-Reply-To: <13705387.1375591275302401134.JavaMail.defaultUser@defaultHost> References: <13705387.1375591275302401134.JavaMail.defaultUser@defaultHost> Message-ID: <63F32ECC-E47B-4E31-B47D-1888F5865A2C@sissa.it> Dear Giacomo, welcome to the QE community and to the users' forum. On your next post please give your full name and affiliation, so that everyone understands better to whom is talking to. if I remember correctly, a thread about DFT+U +GW has appeared on this forum not so long ago (from weeks to a couple of months). Please try a search on the forum archives. I think the reply was "yes", but I don't remember the details, sorry. Regards, GS Il giorno 31/mag/10, alle ore 12:40, giacsport at libero.it ha scritto: > Dear All, > I am definitely new in PWscf so maybe my question could > seem > strange. > > I want to calculate ZnO bandgap. > > Now, DFT gives a starting bad description of the 3d orbitals of Zn. > > At least a DFT+U calculation seems to be mandatory in order to align > these 3d > orbitals to the experimental level (around -7 eV below the top of > the VB). > > Now, once I have aligned these orbitals, is it possible to calculate > the GW > correction on this previously calculated DFT+U band structure? > > In other words, 1. a DFT+U calculation for aligning the 3d orbitals > of Zn > 2. a GW correction for consistently > opening the > band gap (trying to reproduce the experimental one) > > Thanks in advance. > > Best regards, > Giacomo > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100531/a8cae1ad/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 1753 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100531/a8cae1ad/attachment-0001.bin From eyvaz_isaev at yahoo.com Mon May 31 16:15:58 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 31 May 2010 07:15:58 -0700 (PDT) Subject: [Pw_forum] Is it possible to calculate the phonon dos for each branch? Message-ID: <473806.454.qm@web65708.mail.ac4.yahoo.com> Dear Amit, --- On Mon, 5/31/10, Yamit wrote: > Is it possible to calculate the phonon dos(density of states) for each > Phonon Branch separately using "matdyn.x"? No. But, in fact, it can be done using QHA, though it is not included in its current version. Just to note "branch" in the program is a band from e_min(band) to e_max(band). Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From giannozz at democritos.it Mon May 31 16:26:37 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 31 May 2010 16:26:37 +0200 Subject: [Pw_forum] Is it possible to calculate the phonon dos for each branch? In-Reply-To: <473806.454.qm@web65708.mail.ac4.yahoo.com> References: <473806.454.qm@web65708.mail.ac4.yahoo.com> Message-ID: <4C03C71D.2070103@democritos.it> Eyvaz Isaev wrote: > No. But, in fact, it can be done using QHA, though it is not included > in its current version. v.4.2 of QE includes QHA, as far as I know P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From arvifis at gmail.com Mon May 31 16:58:39 2010 From: arvifis at gmail.com (Arles V. Gil Rebaza) Date: Mon, 31 May 2010 11:58:39 -0300 Subject: [Pw_forum] calculation with magnetic field Message-ID: Hi QE user's, I would like calculate magnetic properties of Fe alloys with a magnetic field applied... I can do this using QE..?? Best Regards. Arles V. Gil Rebaza Instituto de F?sica de La Plata La Plata - Argentina -- ###---------> Arles V. <---------### -- ###---------> Arles V. <---------### -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100531/dc8847a3/attachment.htm From giannozz at democritos.it Mon May 31 17:05:21 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 31 May 2010 17:05:21 +0200 Subject: [Pw_forum] calculation with magnetic field In-Reply-To: References: Message-ID: <4C03D031.5090007@democritos.it> Arles V. Gil Rebaza wrote: > Hi QE user's, I would like calculate magnetic properties of Fe alloys > with a magnetic field applied... I can do this using QE..?? no, and I don't think it is easy P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From arvifis at gmail.com Mon May 31 17:20:36 2010 From: arvifis at gmail.com (Arles V. Gil Rebaza) Date: Mon, 31 May 2010 12:20:36 -0300 Subject: [Pw_forum] calculation with magnetic field In-Reply-To: <4C03D031.5090007@democritos.it> References: <4C03D031.5090007@democritos.it> Message-ID: Hi Paolo.. what about B_field(3) variable in input_parameters.f90 of QE 4.1.1 ..?? Best 2010/5/31 Paolo Giannozzi > Arles V. Gil Rebaza wrote: > > > Hi QE user's, I would like calculate magnetic properties of Fe alloys > > with a magnetic field applied... I can do this using QE..?? > > no, and I don't think it is easy > > 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 > -- ###---------> Arles V. <---------### -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100531/e5230d27/attachment.htm From sd.wang000 at gmail.com Mon May 31 18:00:53 2010 From: sd.wang000 at gmail.com (shudong wang) Date: Tue, 1 Jun 2010 00:00:53 +0800 Subject: [Pw_forum] About GWW Message-ID: Dear developers: I kown the V4.2 pwscf can have performed GW calculation. Does it can deal with various system?For example, cluster, molecule, or quantum dot and extended system like periodic solids? Thanks! SDWang Southeast University , Nanjing ,China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100601/a1ee1c5a/attachment.htm From mambom1902 at yahoo.com Mon May 31 18:10:19 2010 From: mambom1902 at yahoo.com (loc duong ding) Date: Mon, 31 May 2010 09:10:19 -0700 (PDT) Subject: [Pw_forum] Computing Second order response Message-ID: <894050.23278.qm@web38803.mail.mud.yahoo.com> Dear all, I want calculated IR and Raman of nanoribbon. The problem is when the code calcualtion second order response, it is not convergence. This is the output: Calling punch_plot_e Writing on file drho Computing Pc [DH,Drho] |psi> Derivative coefficient: 0.001000 Threshold: 1.00E-12 Non-scf u_k: avg # of iterations = 23.5 Non-scf Du_k: avg # of iterations = 37.6 Dielectric constant from finite-differences ( 1.626169126 -0.012354543 0.000000672 ) ( -0.012354543 1.773889718 -0.001492007 ) ( 0.000000672 -0.001492007 1.106263603 ) Computing Second order response iter # 1 av.it.: 10.8 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.194E+04 iter # 2 av.it.: 15.7 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.509E+09 iter # 3 av.it.: 15.2 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.134E+07 iter # 4 av.it.: 12.7 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.986E+03 iter # 5 av.it.: 11.2 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.693E+01 iter # 6 av.it.: 14.3 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.269E+04 iter # 7 av.it.: 13.7 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.154E+02 iter # 8 av.it.: 12.8 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.631E+01 iter # 9 av.it.: 11.5 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.136E+00 iter # 10 av.it.: 10.8 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.116E+02 iter # 11 av.it.: 10.0 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.598E+00 iter # 12 av.it.: 9.3 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.220E+00 iter # 13 av.it.: 10.2 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.416E+01 iter # 14 av.it.: 10.7 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.340E+00 iter # 15 av.it.: 10.0 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.648E+01 iter # 16 av.it.: 11.0 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.214E+02 iter # 17 av.it.: 12.3 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.152E+03 iter # 18 av.it.: 12.2 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.314E-01 iter # 19 av.it.: 12.2 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.538E+02 iter # 20 av.it.: 11.2 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.744E+01 iter # 21 av.it.: 13.0 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.150E+04 iter # 22 av.it.: 13.7 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.426E+03 iter # 23 av.it.: 12.7 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.238E+03 iter # 24 av.it.: 17.2 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.143E+07 iter # 25 av.it.: 15.8 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.118E+06 iter # 26 av.it.: 18.8 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.122E+08 iter # 27 av.it.: 19.3 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.361E+07 iter # 28 av.it.: 19.5 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.447E+08 iter # 29 av.it.: 22.5 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.186E+11 iter # 30 av.it.: 23.2 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.390E+10 iter # 31 av.it.: 25.7 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.538E+12 iter # 32 av.it.: 25.8 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.231E+12 iter # 33 av.it.: 27.2 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.105E+14 iter # 34 av.it.: 30.5 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.700E+15 iter # 35 av.it.: 31.2 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.228E+15 iter # 36 av.it.: 31.8 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.362E+17 iter # 37 av.it.: 34.0 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.201E+17 iter # 38 av.it.: 35.8 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.245E+19 iter # 39 av.it.: 38.2 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.370E+20 iter # 40 av.it.: 37.7 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.172E+20 iter # 41 av.it.: 41.2 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.300E+22 Could you give me some instructions to overcome this problem? I appreciate to all your helps. sincerely, ----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com, ddloc at skku.edu From eyvaz_isaev at yahoo.com Mon May 31 18:13:48 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 31 May 2010 09:13:48 -0700 (PDT) Subject: [Pw_forum] Is it possible to calculate the phonon dos for each branch? In-Reply-To: <4C03C71D.2070103@democritos.it> Message-ID: <904455.56019.qm@web65709.mail.ac4.yahoo.com> Hi Paolo, Sorry for the confusing note I have written. You are right, now QHA in QE v.4.2. In fact, I was talking about the possibility for branch-resolved phonon DOS, that is not included in the current version of QHA. But you know I am going top upgrade it (QHA), so i will include it, too. One reason for not including of this option was that I had no data (and do not have) to compare. Bests, Eyvaz. --- On Mon, 5/31/10, Paolo Giannozzi wrote: > From: Paolo Giannozzi > Subject: Re: [Pw_forum] Is it possible to calculate the phonon dos for each branch? > To: "PWSCF Forum" > Date: Monday, May 31, 2010, 6:26 PM > Eyvaz Isaev wrote: > > > No. But, in fact, it can be done using QHA, though it > is not included > > in its current version. > > v.4.2 of QE includes QHA, as far as I know > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From gbilalbegovic at gmail.com Mon May 31 18:34:41 2010 From: gbilalbegovic at gmail.com (Goranka Bilalbegovic) Date: Mon, 31 May 2010 18:34:41 +0200 Subject: [Pw_forum] About GWW In-Reply-To: References: Message-ID: On Mon, May 31, 2010 at 6:00 PM, shudong wang wrote: > > I kown the V4.2 pwscf can have performed GW calculation. Does it can deal > with various system?For example, cluster, molecule, or quantum dot and > extended system like periodic solids? > > Dear SDWang, The answer is yes for all your questions above. You may find very useful: http://gww.qe-forge.org/index.php?page=intro Examples (for benzene molecule and Si bulk) are on: http://gww.qe-forge.org/index.php?page=tutorial 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/20100531/af75e0ed/attachment.htm From giannozz at democritos.it Mon May 31 18:38:59 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 31 May 2010 18:38:59 +0200 Subject: [Pw_forum] Computing Second order response In-Reply-To: <894050.23278.qm@web38803.mail.mud.yahoo.com> References: <894050.23278.qm@web38803.mail.mud.yahoo.com> Message-ID: On May 31, 2010, at 18:10 , loc duong ding wrote: > The problem is when the code calcualtion second order response, > it is not convergence. try to reduce "alpha_mix" to a smaller value, 0.3 or 0.1 or whatever is appropriate (default is 0.7) 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 gbilalbegovic at gmail.com Mon May 31 18:54:27 2010 From: gbilalbegovic at gmail.com (Goranka Bilalbegovic) Date: Mon, 31 May 2010 18:54:27 +0200 Subject: [Pw_forum] About GWW In-Reply-To: References: Message-ID: On Mon, May 31, 2010 at 6:34 PM, Goranka Bilalbegovic < gbilalbegovic at gmail.com> wrote: > > > On Mon, May 31, 2010 at 6:00 PM, shudong wang wrote: > >> >> I kown the V4.2 pwscf can have performed GW calculation. Does it can deal >> with various system?For example, cluster, molecule, or quantum dot and >> extended system like periodic solids? >> >> > Dear SDWang, > > The answer is yes for all your questions above. You may find very useful: > http://gww.qe-forge.org/index.php?page=intro > Examples (for benzene molecule and Si bulk) are on: > http://gww.qe-forge.org/index.php?page=tutorial > > > In addition, there is a "GWW_examples" directory in "examples": http://qe-forge.org/frs/download.php/95/espresso-4.2-examples.tar.gz There you may find: example01 computes the GW quasi-particle energies in C6H6 (Benzene molecule) example02 computes the GW quasi-particle energies in bulk Si (extended system) example03 computes the orbital decomposition of the total GWW density of states in C6H6 (Benzene molecule) -- 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/20100531/05c3e704/attachment.htm From baroni at sissa.it Mon May 31 21:27:26 2010 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 31 May 2010 21:27:26 +0200 Subject: [Pw_forum] About GWW In-Reply-To: References: Message-ID: For periodic systems, GWW may not be the best choice, though. (it requires supercells to perform BZ sampling) For periodic systems, you may want to check SAX or YAMBO, which also have a noce QE interface SB On May 31, 2010, at 6:34 PM, Goranka Bilalbegovic wrote: > > > On Mon, May 31, 2010 at 6:00 PM, shudong wang wrote: > > I kown the V4.2 pwscf can have performed GW calculation. Does it can deal with various system?For example, cluster, molecule, or quantum dot and extended system like periodic solids? > > > Dear SDWang, > > The answer is yes for all your questions above. You may find very useful: http://gww.qe-forge.org/index.php?page=intro > Examples (for benzene molecule and Si bulk) are on: http://gww.qe-forge.org/index.php?page=tutorial > > Best regards, > > > > -- > Goranka Bilalbegovic, > Department of Physics, Faculty of Science, > University of Zagreb, Croatia > _______________________________________________ > 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/20100531/02b4efa5/attachment.htm From hsuhan at cems.umn.edu Mon May 31 22:09:50 2010 From: hsuhan at cems.umn.edu (Han Hsu) Date: Mon, 31 May 2010 15:09:50 -0500 (CDT) Subject: [Pw_forum] how to do fixed volume optimization In-Reply-To: <201005312028518289019@gmail.com> References: <201005302041597969466@gmail.com>, <201005302109318285369@gmail.com>, <201005311614027962613@gmail.com> <201005312028518289019@gmail.com> Message-ID: <1503.71.195.59.176.1275336590.squirrel@webmail.cems.umn.edu> Hello Kun Yin, I'd appreciate if you would let me know why constant-volume vc-relax is "very useful" in high-pressure physics. Here is my response to your question. Do you really need to perform vc-relax at a "constant" volume, or do you just need the final volume to be very close to the initial volume? If the latter, you can do so by properly setting the target pressure (press), usually through good guessing, in your input file. Han > I see. Thanks for giving the answer, Paolo. I hope this easy-to-implement > functionality, doing 'vc-relax' at constant volume, will be done by some > enthusiastic guy, since it is very useful in some research such as the > study of high-pressure materials. > Kun Yin > 2010-05-31 > > > > short answer: no. It should be relatively easy to implement but > it has never been done, to the best of my knowledge. You can > use 'vc-relax' at costant pressure, though, and vary the > pressure, if I remember correctly > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy ******************************************************* Han Hsu, Ph.D. Postdoctoral Associate Department of Chemical Engineering & Materials Science University of Minnesota http://www.cems.umn.edu/~hsuhan ******************************************************* From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: reading namelist cell.... =20 I have checked that the input is missing and that &ions precedes &cell in t= he input. Part of the input is below..Thanks =20 / &system =20 ibrav=3D 0=2C celldm(1) =3D1.88972=2C nat=3D60=2C ntyp=3D 1=2C ecutwfc= =3D 110D0 =2Coccupations=3D'smearing'=2C smearing=3D'methfessel-paxton'=2C= degauss=3D0.01 / &electrons conv_thr=3D1.D-8=2C =20 mixing_beta=3D0.05D0=2C mixing_mode=3D'local-TF'=2C diagonalization=3D'david'=20 / &ions ion_dynamics =3D 'bfgs'=2C pot_extrapolation =3D 'second-order'=2C wfc_extrapolation =3D 'second-order' / &cell cell_dynamics =3D 'bfgs'=2C press_conv_thr =3D 0.1 =20 CELL_PARAMETERS hexagonal =20 24.527679 0.000000 0.000000 0.000003 6.614491 0.000000 0.000000 0.000000 10.000000 =20 ATOMIC_SPECIES C 12.0107 C.pz-vbc.UPF ATOMIC_POSITIONS angstrom C -11.737980 -3.561278 0.000000 C -11.057718 -1.211571 0.000000 ....... .............. =20 Elie Moujaes University of Nottingham NG7 2RD UK =20 =20 _________________________________________________________________ http://clk.atdmt.com/UKM/go/195013117/direct/01/ We want to hear all your funny=2C exciting and crazy Hotmail stories. Tell = us now= --_85e88d03-f247-435c-8dea-c71601b47010_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear All=2C
 =3B
I am trying to relax a =3Bsystem using vc-relax and I am getting the fo= llowing error:
 =3B
From read_namelists : error # 1
reading namelist cell....
 =3B
I have checked that the input is missing and that &=3Bions precedes &= =3Bcell in the input. Part of the input is below..Thanks
 =3B

 =3B/

 =3B&=3Bsystem&nbs= p=3B =3B =3B

 =3B =3B =3B ibrav=3D =3B 0=2C celldm(1) =3D1.88972=2C nat=3D60=2C ntyp=3D 1= =2C ecutwfc =3D 110D0 =2Coccupations=3D'smearing'=2C smearing=3D'methfessel= -paxton'=2C degauss=3D0.01

/

 =3B&=3Belectrons

 =3B =3B =3B conv_thr=3D1.D-8=2C =3B =3B =3B =3B

 =3B  =3B =3B= mixing_beta=3D0.05D0=2C

 =3B =3B =3B mixing_mode=3D'local-TF'=2C

 =3B =3B =3B diagonalization=3D'david'

 =3B/

 =3B &=3Bions

 =3B =3B =3B ion_dynamics =3D 'bfgs'=2C

 =3B =3B =3B pot_extrapolation =3D 'second-orde= r'=2C

 =3B =3B =3B wfc_extrapolation =3D 'second-orde= r'

/

 =3B &=3Bcell

 =3B =3B =3B cell_dynamics =3D 'bfgs'=2C

 =3B =3B =3B press_conv_thr =3D 0.1<= /FONT>

 =3B

CELL_PARAMETERS hexagonal=

 =3B

24.527679 =3B =3B 0.000000 =3B =3B =3B 0.000000<= /P>

0.000003 =3B =3B =3B 6.614491 =3B =3B =3B 0.000000<= /SPAN>

0.000000 =3B =3B =  =3B0.000000 =3B =3B <= /SPAN>10.000000

 =3B

ATOMIC_SPECIES=

 =3BC =3B = 12.0107 =3B C.pz-vbc.UPF<= /o:p>

ATOMIC_POSITIONS angstrom=

 =3BC =3B =3B= -11.737980 =3B =3B = =3B -3.561278 =3B =3B = =3B =3B 0.000000

 =3BC =3B =3B= -11.057718 =3B =3B = =3B -1.211571 =3B =3B = =3B =3B 0.000000

.......
..............
 =3B
Elie Moujaes
University of Nottingham
NG7 2RD
UK
 =3B

Get a new e-mail account with Hotmail -= Free. Sign-up now. = --_85e88d03-f247-435c-8dea-c71601b47010_-- From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: reading namelist cell.... =20 I have checked that the input is missing and that &ions precedes &cell in t= he input. Part of the input is below..Thanks =20 / &system =20 ibrav=3D 0=2C celldm(1) =3D1.88972=2C nat=3D60=2C ntyp=3D 1=2C ecutwfc= =3D 110D0 =2Coccupations=3D'smearing'=2C smearing=3D'methfessel-paxton'=2C= degauss=3D0.01 / &electrons conv_thr=3D1.D-8=2C =20 mixing_beta=3D0.05D0=2C mixing_mode=3D'local-TF'=2C diagonalization=3D'david' / &ions ion_dynamics =3D 'bfgs'=2C pot_extrapolation =3D 'second-order'=2C wfc_extrapolation =3D 'second-order' / &cell cell_dynamics =3D 'bfgs'=2C press_conv_thr =3D 0.1 =20 CELL_PARAMETERS hexagonal =20 24.527679 0.000000 0.000000 0.000003 6.614491 0.000000 0.000000 0.000000 10.000000 =20 ATOMIC_SPECIES C 12.0107 C.pz-vbc.UPF ATOMIC_POSITIONS angstrom C -11.737980 -3.561278 0.000000 C -11.057718 -1.211571 0.000000....... .............. =20 Elie Moujaes University of Nottingham NG7 2RD UK =20 Get a new e-mail account with Hotmail - Free. Sign-up now. ________________= _______________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum =A7 Gabriele Sclauzero=2C EPFL SB ITP CSEA PH H2 462=2C Station 3=2C CH-1015 Lausanne =20 _________________________________________________________________ http://clk.atdmt.com/UKM/go/195013117/direct/01/ --_1ba34787-0f28-469a-9712-86ac4a421252_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Thanks very much..That was a stupid mistake to do.
 =3B
Regards
 =3B
Elie
 =3B
From: sclauzer at sissa.it
To: pw_forum at pwscf.org
Date: Fri=2C 4 Jun 201= 0 15:34:45 +0200
Subject: Re: [Pw_forum] error 208=2C reading namelist c= ell

Dear Elie=2C

 =3B =3B the / should go at the end of each namelist=2C not at= the beginning. The F90 standard prescribes that a namelist named=2C for in= stance=2C TEST=2C can be accessed with

&=3BTEST
...
/ =3B

or

&=3BTEST
...
&=3BEND

The namelist "cell" has not been closed in your example.


HTH


GS


Il giorno 04/giu/10=2C alle ore 15:25=2C Elie Moujaes ha scritto:
Dear All=2C
 =3B
I am trying to relax a =3Bsystem using vc-r= elax and I am getting the following error:
 =3B
Fr= om read_namelists : error # 1
reading namelist cel= l....
 =3B
I have checked that the input is missing and th= at &=3Bions precedes &=3Bcell in the input. Part of the input is belo= w..Thanks
 =3B
 =3B/
 =3B&=3Bsystem =3B =3B =3B
 =3B =3B =3B =3Bibrav=3D =3B =3B0=2C celldm(1) =3D1.88972=2C nat=3D60=2C nty= p=3D 1=2C ecutwfc =3D 110D0 =2Coccupations=3D'smearing'=2C smearing=3D'meth= fessel-paxton'=2C degauss=3D0.01
/
 =3B&=3Belectrons
 =3B =3B =3B =3Bconv_thr=3D1.D-8=2C =3B =3B =3B&nb= sp=3B
 =3B =3B=  =3B =3Bmixing_beta=3D0.05D0=2C
 =3B =3B =3B =3Bmixing_mode=3D'local-TF'=2C
 =3B =3B =3B =3Bdiagonalization=3D'david'
 =3B/
 =3B =3B= &=3Bions
 =3B =3B =3B =3Bion_dynamics =3D 'bfgs'=2C
 =3B =3B =3B =3Bpot_extrapolation =3D 'second-order'=2C
 =3B =3B =3B =3Bwfc_extrapolation =3D 'second-order'
/
 =3B =3B= &=3Bcell
 =3B =3B =3B =3Bcell_dynamics =3D 'bfgs'=2C
 =3B =3B =3B =3Bpress_conv_thr =3D 0.1
 =3B
CELL_PARAMETERS hexagonal
 =3B
24.527679 =3B =3B =3B0.000000 =3B =3B =3B =3B0.000000
0.000003 =3B =3B =3B =3B6.614491 =3B =3B =3B =3B0.000000
0.000000 =3B =3B =3B =3B0.000000 =3B =3B<= SPAN class=3DecxApple-converted-space> =3B10.000000
 =3B
ATOMIC_SPECIES
 =3BC =3B =3B12.0107 =3B =3BC.pz-vbc.UPF
ATOMIC_POSITIONS angstrom
 =3BC =3B =3B =3B-11.737980 =3B =3B = =3B =3B-3.561278 =3B =3B =3B =3B=  =3B0.000000
 =3BC =3B =3B =3B-11.057718 =3B =3B = =3B =3B-1.211571 =3B =3B =3B =3B=  =3B0.000000
.......
..............=
 =3B
Elie Moujaes
University of Nottingham
NG7 2RD
UK =3B

Get a new e-mail account with Hotmail - Free. =3BSign-up now. =3B_______________________________________________
Pw_forum mailing li= st
Pw_forum at pwscf.org
http://www.democr= itos.it/mailman/listinfo/pw_forum

=A7 Gabriele Sclauzero=2C =3BEPFL SB ITP CSEA
 =3B =3B = PH H2 462=2C Station 3=2C =3BCH-1015 Lausanne


Get a free e-mail account with Hotmai= l. Sign-up now. = --_1ba34787-0f28-469a-9712-86ac4a421252_-- From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: and your Al slab extends from z=0 to z=82 bohr. Based on this data, a good choice of emaxpos & eopreg would be: emaxpos=0.77 eopreg=0.05 An important thing when applying strong electric fields (which is your case) is to check against the electron field emission (i.e. that a fraction of electrons doesn't spill to a dipole layer). This can be verified by inspecting a charge density in the vacuum region (or even better a charge density difference between a slab under electric field and no field). Best 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 bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: > and your Al slab extends from z=3D0 to z=3D82 bohr. Based on this data, a > good choice of emaxpos & eopreg would be: > > Sorry, I have now a slab put in the middle of the cell in the Z axis, fr= om z=3D32 to z=3D50 (maximum). An important thing when applying strong electric fields (which is your > case) is to check against the electron field emission (i.e. that a > fraction of electrons doesn't spill to a dipole layer). This can be > verified by inspecting a charge density in the vacuum region (or even > better a charge density difference between a slab under electric field > and no field). > Really thanks, I will check this when I obtain some results, using E-Field. Regards Joaquin Peralta --=20 ---------------------------------------------------- Group of NanoMaterials ---------------------------------------------------- http://www.gnm.cl ---------------------------------------------------- Joaqu=EDn Andr=E9s Peralta Camposano ---------------------------------------------------- http://www.lpmd.cl/jperalta In a world without frontiers, who needs Gates and Win. --0016363b906c3b1df1048f0fb26d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Tone

Thanks you so much for the answer.


> =A0 =A0edir =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0=3D 3
> =A0 =A0emaxpos =A0 =A0 =A0 =A0 =A0 =A0 =A0 =3D 0.9
> =A0 =A0eopreg =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=3D 0.2
> =A0 =A0eamp =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=3D 0.019447
> /

This input explains why you face SCF problems: they are inevitable wi= th
your dipole-layer specification. You have placed your dipole layer
from 0.9 to 0.9+0.2=3D1.1. Note that position of emaxpos/eopreg is in
internal units, in range [0,1].

Now I'm a litt= le bit confused, because i use a previous thread about that

= http://www.democritos.it/pipermail/pw_forum/2009-December/015430.html
What I have to do?

From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: and your Al slab extends from z=3D0 to z=3D82 bohr. Based on this data, a good choice of emaxpos & eopreg would be:

Sorry, I have now a slab put in the middle of the cel= l in the Z axis,=A0 from z=3D32 to z=3D50 (maximum).

An important thing when applying strong electric fields (which is your
case) is to check against the electron field emission (i.e. that a
fraction of electrons doesn't spill to a dipole layer). This can be
verified by inspecting a charge density in the vacuum region (or even
better a charge density difference between a slab under electric field
and no field).

Really thanks, I will check this wh= en I obtain some results, using E-Field.

Regards
Joa= quin Peralta


--
------------------------------= ----------------------
Group of NanoMaterials
-------------------------------------------------= ---
http://www.gnm.cl
----------------------------------------------------
Joaqu=EDn Andr= =E9s Peralta Camposano
----------------------------------------------------
http://www.lpmd.cl/jperalta
<= br>In a world without frontiers,
who needs Gates and Win.
--0016363b906c3b1df1048f0fb26d-- From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: > and your Al slab extends from z=3D0 to z=3D82 bohr. Based on this data, a > good choice of emaxpos & eopreg would be: > > Sorry, I have now a slab put in the middle of the cell in the Z axis, fr= om z=3D32 to z=3D50 (maximum). An important thing when applying strong electric fields (which is your > case) is to check against the electron field emission (i.e. that a > fraction of electrons doesn't spill to a dipole layer). This can be > verified by inspecting a charge density in the vacuum region (or even > better a charge density difference between a slab under electric field > and no field). > Really thanks, I will check this when I obtain some results, using E-Field. Regards Joaquin Peralta --=20 ---------------------------------------------------- Group of NanoMaterials ---------------------------------------------------- http://www.gnm.cl ---------------------------------------------------- Joaqu=EDn Andr=E9s Peralta Camposano ---------------------------------------------------- http://www.lpmd.cl/jperalta In a world without frontiers, who needs Gates and Win. --00163630f2b971a7be048f0fb0bd Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Tone

Thanks you so much for the answer.


> =A0 =A0edir =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0=3D 3
> =A0 =A0emaxpos =A0 =A0 =A0 =A0 =A0 =A0 =A0 =3D 0.9
> =A0 =A0eopreg =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=3D 0.2
> =A0 =A0eamp =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=3D 0.019447
> /

This input explains why you face SCF problems: they are inevitable wi= th
your dipole-layer specification. You have placed your dipole layer
from 0.9 to 0.9+0.2=3D1.1. Note that position of emaxpos/eopreg is in
internal units, in range [0,1].

Now I'm a litt= le bit confused, because i use a previous thread about that

= http://www.democritos.it/pipermail/pw_forum/2009-December/015430.html
What I have to do?

From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: and your Al slab extends from z=3D0 to z=3D82 bohr. Based on this data, a good choice of emaxpos & eopreg would be:

Sorry, I have now a slab put in the middle of the cel= l in the Z axis,=A0 from z=3D32 to z=3D50 (maximum).

An important thing when applying strong electric fields (which is your
case) is to check against the electron field emission (i.e. that a
fraction of electrons doesn't spill to a dipole layer). This can be
verified by inspecting a charge density in the vacuum region (or even
better a charge density difference between a slab under electric field
and no field).

Really thanks, I will check this wh= en I obtain some results, using E-Field.

Regards
Joa= quin Peralta


--
------------------------------= ----------------------
Group of NanoMaterials
-------------------------------------------------= ---
http://www.gnm.cl
----------------------------------------------------
Joaqu=EDn Andr= =E9s Peralta Camposano
----------------------------------------------------
http://www.lpmd.cl/jperalta
<= br>In a world without frontiers,
who needs Gates and Win.
--00163630f2b971a7be048f0fb0bd-- From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: K-point is included also in the 9x9x1 and 12x12x1 meshes (without shift, at least that's what your have written in the picture and in the input files), so this may explain why you get strange results for those meshes without smearing.

As a result, problem should be related with K-special-point.

If you include the shift I think that the K-point will never be included (excepting the 3x3x1 grid perhaps). I suggest you to study the convergence of the frequencies separately for the shifted and unshifted grids (both with smearing) and see if they converge to the same result. Some people believe that including the K-point in the BZ sampling is of vital importance, even with dense meshes. I'm not sure of that.


BUT. Still I cannot understand why inclusion of a point in BZ corresponds to such a HUGE difference in phonon frequencies.
Maybe someone in this list gives a better explanation for that....

I cannot explain this, sorry. Let's wait for an answer from a graphene or phonon expert (or both).


Regards


GS


All of the files are available at http://db.tt/xK2Jtu1

Ragards.


On Thu, Sep 30, 2010 at 4:47 PM, Gabriele Sclauzero <sclauzer at sissa.it> wrote:
Dear Mehmet,

   graphene has zero gap, hence you probably need to include smearing of the occupations in the scf calculations.


HTH

GS


On 09/29/2010 04:54 PM, Mehmet Topsakal wrote:
Dear all,

For graphene structure, I noticed that I get completely wrong phonon frequencies when I use KPOINTS such as 9 9 1, 12 12 1, 15 15 1

For example:

K_POINTS {automatic}
11 11 1    0 0 0 

gives realistic frequencies as in 11.phonon.out file 

BUT

K_POINTS {automatic}
12 12 1    0 0 0 

gives "omega( 1) =    -149.592762 [THz] =   -4989.910586 [cm-1]" as in 12.phonon.out


What should be the reason ????

Thanks.

--

Mehmet Topsakal  (Ph.D. Student)
UNAM-Institute of Materials Science and Nanotechnology.
Bilkent University. 06800 Bilkent, Ankara/Türkiye
Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365
UNAM-web  : www.nano.org.tr


_______________________________________________
Pw_forum mailing list

Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum
  


-- 

Gabriele Sclauzero, EPFL SB ITP CSEA
PH H2 462, Station 3, CH-1015 Lausanne

_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum




--

Mehmet Topsakal  (Ph.D. Student)
UNAM-Institute of Materials Science and Nanotechnology.
Bilkent University. 06800 Bilkent, Ankara/Türkiye
Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365
UNAM-web  : www.nano.org.tr


_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum
  


-- 

Gabriele Sclauzero, EPFL SB ITP CSEA
PH H2 462, Station 3, CH-1015 Lausanne
--------------010408010104000906030208-- From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: http://www.democritos.it/pipermail/pw_forum/2008-September/010123.html http://www.democritos.it/pipermail/pw_forum/2010-February.txt I understand that the third derivatives were never implemented and that only the LDA part was calculated, for the Perdew Zunger parameterization. Is this third derivative the third derivative that is mentioned in the routine PH/raman_mat.f90 (i.e, the third derivative of the energy with respect to the atomic displacements and with respect to two electric fields, as described in Lazzeri and Mauri, PRL 90,036401)? I am interested in getting a feel for what would be needed to implement the third derivatives with GGA into the code, as well as what sort of errors one might expect when using the third-order term as currently coded with LDA pseudopotentials (comments in the forums have hinted that the errors are likely small). The shift in the Raman spectra for cd-Si is pretty minor when using a GGA pseudo compared to that of an LDA calculation, but I wanted to be able to quantify the error better for other systems where comparing the GGA raman spectra to one calculated within LDA was not possible (e.g., when the system doesn't exhibit a gap in LDA). Thanks for the help! Best, Brad UC Berkeley From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: http://www.democritos.it/pipermail/pw_forum/2008-September/010123.html http://www.democritos.it/pipermail/pw_forum/2010-February.txt I understand that the third derivatives were never implemented and that only the LDA part was calculated, for the Perdew Zunger parameterization. Is this third derivative the third derivative that is mentioned in the routine PH/raman_mat.f90 (i.e, the third derivative of the energy with respect to the atomic displacements and with respect to two electric fields, as described in Lazzeri and Mauri, PRL 90,036401)? I am interested in getting a feel for what would be needed to implement the third derivatives with GGA into the code, as well as what sort of errors one might expect when using the third-order term as currently coded with LDA pseudopotentials (comments in the forums have hinted that the errors are likely small). The shift in the Raman spectra for cd-Si is pretty minor when using a GGA pseudo compared to that of an LDA calculation, but I wanted to be able to quantify the error better for other systems where comparing the GGA raman spectra to one calculated within LDA was not possible (e.g., when the system doesn't exhibit a gap in LDA). Thanks for the help! Best, Brad UC Berkeley On Tue, Nov 9, 2010 at 5:00 PM, Brad Malone wrote: > Hi, I am seeking more information on the error > > > from phq_setup : error # 1 > > third order derivatives not implemented with GGA > > From the forums: > > http://www.democritos.it/pipermail/pw_forum/2008-September/010123.html > http://www.democritos.it/pipermail/pw_forum/2010-February.txt > > I understand that the third derivatives were never implemented and > that only the LDA part was calculated, for the Perdew Zunger > parameterization. Is this third derivative the third derivative that > is mentioned in the routine PH/raman_mat.f90 (i.e, the third > derivative of the energy with respect to the atomic displacements and > with respect to two electric fields, as described in Lazzeri and > Mauri, PRL 90,036401)? > > I am interested in getting a feel for what would be needed to > implement the third derivatives with GGA into the code, as well as > what sort of errors one might expect when using the third-order term > as currently coded with LDA pseudopotentials (comments in the forums > have hinted that the errors are likely small). The shift in the Raman > spectra for cd-Si is pretty minor when using a GGA pseudo compared to > that of an LDA calculation, but I wanted to be able to quantify the > error better for other systems where comparing the GGA raman spectra > to one calculated within LDA was not possible (e.g., when the system > doesn't exhibit a gap in LDA). > > Thanks for the help! > > Best, > Brad > UC Berkeley > --000e0cd1e7da1a89630494a936f2 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable It appears that my last email was severely truncated on the mailing list (e= ven though it looks fine in my outbox). Below is what is should have been:<= div>-----------------------
Hi, I am seeking more information on the err= or

> from phq_setup : error # 1
> third order derivatives not imp= lemented with GGA

From the forums:

http://www.democritos.it/pipermail/pw_fo= rum/2008-September/010123.html
http://www.democritos.i= t/pipermail/pw_forum/2010-February.txt

I understand that the thi= rd derivatives were never implemented and
that only the LDA part was calculated, for the Perdew Zunger
parameteriz= ation. Is this third derivative the third derivative that
is mentioned i= n the routine PH/raman_mat.f90 (i.e, the third
derivative of the energy = with respect to the atomic displacements and
with respect to two electric fields, as described in Lazzeri and
Mauri, = PRL 90,036401)?

I am interested in getting a feel for what would be = needed to
implement the third derivatives with GGA into the code, as wel= l as
what sort of errors one might expect when using the third-order term
as = currently coded with LDA pseudopotentials (comments in the forums
have h= inted that the errors are likely small). =A0The shift in the Raman
spect= ra for cd-Si is pretty minor when using a GGA pseudo compared to
that of an LDA calculation, but I wanted to be able to quantify the
erro= r better for other systems where comparing the GGA raman spectra
to one = calculated within LDA was not possible (e.g., when the system
doesn'= t exhibit a gap in LDA).

Thanks for the help!

Best,
Brad
UC Berkeley

=
On Tue, Nov 9, 2010 at 5:00 PM, Brad Malone <brad.malone at gmai= l.com> wrote:
Hi, I am seeking more information on the er= ror

> from phq_setup : error # 1
> third order derivatives not implemented with GGA

From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID:
http://www.democritos.it/pipermail/pw_forum/2008-= September/010123.html
http://www.democritos.it/pipermail/pw_forum/2010-February.= txt

I understand that the third derivatives were never implemented and
that only the LDA part was calculated, for the Perdew Zunger
parameterization. Is this third derivative the third derivative that
is mentioned in the routine PH/raman_mat.f90 (i.e, the third
derivative of the energy with respect to the atomic displacements and
with respect to two electric fields, as described in Lazzeri and
Mauri, PRL 90,036401)?

I am interested in getting a feel for what would be needed to
implement the third derivatives with GGA into the code, as well as
what sort of errors one might expect when using the third-order term
as currently coded with LDA pseudopotentials (comments in the forums
have hinted that the errors are likely small). =A0The shift in the Raman spectra for cd-Si is pretty minor when using a GGA pseudo compared to
that of an LDA calculation, but I wanted to be able to quantify the
error better for other systems where comparing the GGA raman spectra
to one calculated within LDA was not possible (e.g., when the system
doesn't exhibit a gap in LDA).

Thanks for the help!

Best,
Brad
UC Berkeley

--000e0cd1e7da1a89630494a936f2-- From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: http://www.democritos.it/pipermail/pw_forum/2008-September/010123.html http://www.democritos.it/pipermail/pw_forum/2010-February.txt I understand that the third derivatives were never implemented and that only the LDA part was calculated, for the Perdew Zunger parameterization. Is this third derivative the third derivative that is mentioned in the routine PH/raman_mat.f90 (i.e, the third derivative of the energy with respect to the atomic displacements and with respect to two electric fields, as described in Lazzeri and Mauri, PRL 90,036401)? I am interested in getting a feel for what would be needed to implement the third derivatives with GGA into the code, as well as what sort of errors one might expect when using the third-order term as currently coded with LDA pseudopotentials (comments in the forums have hinted that the errors are likely small). The shift in the Raman spectra for cd-Si is pretty minor when using a GGA pseudo compared to that of an LDA calculation, but I wanted to be able to quantify the error better for other systems where comparing the GGA raman spectra to one calculated within LDA was not possible (e.g., when the system doesn't exhibit a gap in LDA). Thanks for the help! Best, Brad UC Berkeley On Tue, Nov 9, 2010 at 5:59 PM, Brad Malone wrote: > It appears that my last email was severely truncated on the mailing list > (even though it looks fine in my outbox). Below is what is should have been: > ----------------------- > Hi, I am seeking more information on the error > > > from phq_setup : error # 1 > > third order derivatives not implemented with GGA > > From the forums: > > http://www.democritos.it/pipermail/pw_forum/2008-September/010123.html > http://www.democritos.it/pipermail/pw_forum/2010-February.txt > > I understand that the third derivatives were never implemented and > that only the LDA part was calculated, for the Perdew Zunger > parameterization. Is this third derivative the third derivative that > is mentioned in the routine PH/raman_mat.f90 (i.e, the third > derivative of the energy with respect to the atomic displacements and > with respect to two electric fields, as described in Lazzeri and > Mauri, PRL 90,036401)? > > I am interested in getting a feel for what would be needed to > implement the third derivatives with GGA into the code, as well as > what sort of errors one might expect when using the third-order term > as currently coded with LDA pseudopotentials (comments in the forums > have hinted that the errors are likely small). The shift in the Raman > spectra for cd-Si is pretty minor when using a GGA pseudo compared to > that of an LDA calculation, but I wanted to be able to quantify the > error better for other systems where comparing the GGA raman spectra > to one calculated within LDA was not possible (e.g., when the system > doesn't exhibit a gap in LDA). > > Thanks for the help! > > Best, > Brad > UC Berkeley > > On Tue, Nov 9, 2010 at 5:00 PM, Brad Malone wrote: > >> Hi, I am seeking more information on the error >> >> > from phq_setup : error # 1 >> > third order derivatives not implemented with GGA >> >> From the forums: >> >> http://www.democritos.it/pipermail/pw_forum/2008-September/010123.html >> http://www.democritos.it/pipermail/pw_forum/2010-February.txt >> >> I understand that the third derivatives were never implemented and >> that only the LDA part was calculated, for the Perdew Zunger >> parameterization. Is this third derivative the third derivative that >> is mentioned in the routine PH/raman_mat.f90 (i.e, the third >> derivative of the energy with respect to the atomic displacements and >> with respect to two electric fields, as described in Lazzeri and >> Mauri, PRL 90,036401)? >> >> I am interested in getting a feel for what would be needed to >> implement the third derivatives with GGA into the code, as well as >> what sort of errors one might expect when using the third-order term >> as currently coded with LDA pseudopotentials (comments in the forums >> have hinted that the errors are likely small). The shift in the Raman >> spectra for cd-Si is pretty minor when using a GGA pseudo compared to >> that of an LDA calculation, but I wanted to be able to quantify the >> error better for other systems where comparing the GGA raman spectra >> to one calculated within LDA was not possible (e.g., when the system >> doesn't exhibit a gap in LDA). >> >> Thanks for the help! >> >> Best, >> Brad >> UC Berkeley >> > > --000e0cd1e7da89ad9c0494a93ee2 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable No idea why it is being truncated, so this time I'll start the email af= ter the error message
---------------
From the forums:

=

I understand that the third derivatives were never impl= emented and
that only the LDA part was calculated, for the Perdew Zunger
parameterization. Is this third derivative the third derivative that
=
is mentioned in the routine PH/raman_mat.f90 (i.e, the third
derivative of the energy with respect to the atomic displacements and<= /div>
with respect to two electric fields, as described in Lazzeri and<= /div>
Mauri, PRL 90,036401)?

I am interested i= n getting a feel for what would be needed to
implement the third derivatives with GGA into the code, as well as
what sort of errors one might expect when using the third-order term=
as currently coded with LDA pseudopotentials (comments in the fo= rums
have hinted that the errors are likely small). =A0The shift in the Ram= an
spectra for cd-Si is pretty minor when using a GGA pseudo comp= ared to
that of an LDA calculation, but I wanted to be able to qu= antify the
error better for other systems where comparing the GGA raman spectra
to one calculated within LDA was not possible (e.g., when the syst= em
doesn't exhibit a gap in LDA).

Thanks for the help!

Best,
Brad
UC Berkeley


On Tue, Nov 9, 2010 at 5:59 PM, Brad Malone <brad.malone at gmail.com> wrot= e:
It appears that my last email was severely = truncated on the mailing list (even though it looks fine in my outbox). Bel= ow is what is should have been:
-----------------------
Hi, I am seeking more information on the error
> from phq_setup : error # 1
> third order derivatives not imp= lemented with GGA

From the forums:

http://www.democritos.it/pipermail/pw_forum= /2008-September/010123.html
http://www.democritos.it/p= ipermail/pw_forum/2010-February.txt

I understand that the third = derivatives were never implemented and
that only the LDA part was calculated, for the Perdew Zunger
parameteriz= ation. Is this third derivative the third derivative that
is mentioned i= n the routine PH/raman_mat.f90 (i.e, the third
derivative of the energy = with respect to the atomic displacements and
with respect to two electric fields, as described in Lazzeri and
Mauri, = PRL 90,036401)?

I am interested in getting a feel for what would be = needed to
implement the third derivatives with GGA into the code, as wel= l as
what sort of errors one might expect when using the third-order term
as = currently coded with LDA pseudopotentials (comments in the forums
have h= inted that the errors are likely small). =A0The shift in the Raman
spect= ra for cd-Si is pretty minor when using a GGA pseudo compared to
that of an LDA calculation, but I wanted to be able to quantify the
erro= r better for other systems where comparing the GGA raman spectra
to one = calculated within LDA was not possible (e.g., when the system
doesn'= t exhibit a gap in LDA).

Thanks for the help!

Best,
Brad
UC Berkeley

=
On= Tue, Nov 9, 2010 at 5:00 PM, Brad Malone <brad.malone at gmail.com&g= t; wrote:
Hi, I am seeking more information on the err= or

> from phq_setup : error # 1
> third order derivatives not implemented with GGA

From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID:
http://www.democritos.it/pipermail/pw_forum/2008-= September/010123.html
http://www.democritos.it/pipermail/pw_forum/2010-February.= txt

I understand that the third derivatives were never implemented and
that only the LDA part was calculated, for the Perdew Zunger
parameterization. Is this third derivative the third derivative that
is mentioned in the routine PH/raman_mat.f90 (i.e, the third
derivative of the energy with respect to the atomic displacements and
with respect to two electric fields, as described in Lazzeri and
Mauri, PRL 90,036401)?

I am interested in getting a feel for what would be needed to
implement the third derivatives with GGA into the code, as well as
what sort of errors one might expect when using the third-order term
as currently coded with LDA pseudopotentials (comments in the forums
have hinted that the errors are likely small). =A0The shift in the Raman spectra for cd-Si is pretty minor when using a GGA pseudo compared to
that of an LDA calculation, but I wanted to be able to quantify the
error better for other systems where comparing the GGA raman spectra
to one calculated within LDA was not possible (e.g., when the system
doesn't exhibit a gap in LDA).

Thanks for the help!

Best,
Brad
UC Berkeley


--000e0cd1e7da89ad9c0494a93ee2-- From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: www.democritos.it/pipermail/pw_forum/2008-September/010123.html

I understand that the third derivativ= es were never implemented and
that only the LDA part was calculated, for the Perdew Zunger
parameterization. Is this third derivative the third derivative that
=
is mentioned in the routine PH/raman_mat.f90 (i.e, the third
derivative of the energy with respect to the atomic displacements and<= /div>
with respect to two electric fields, as described in Lazzeri and<= /div>
Mauri, PRL 90,036401)?

I am interested i= n getting a feel for what would be needed to
implement the third derivatives with GGA into the code, as well as
what sort of errors one might expect when using the third-order term=
as currently coded with LDA pseudopotentials (comments in the fo= rums
have hinted that the errors are likely small). =A0The shift in the Ram= an
spectra for cd-Si is pretty minor when using a GGA pseudo comp= ared to
that of an LDA calculation, but I wanted to be able to qu= antify the
error better for other systems where comparing the GGA raman spectra
to one calculated within LDA was not possible (e.g., when the syst= em
doesn't exhibit a gap in LDA).

Thanks for the help!

Best,
Brad
UC Berkeley
=

On Tue, Nov 9, 2010 at 5:59 PM, Br= ad Malone <brad.malone at gmail.com> wrote:
It appears that my last email was severely t= runcated on the mailing list (even though it looks fine in my outbox). Belo= w is what is should have been:
-----------------------
Hi, I am seeking more information on the error

> from phq_setup : error # 1
> third order derivatives not imp= lemented with GGA

From the forums:

http://www.democritos.it/pipermail/pw_forum= /2008-September/010123.html
http://www.democritos.it/p= ipermail/pw_forum/2010-February.txt

I understand that the third = derivatives were never implemented and
that only the LDA part was calculated, for the Perdew Zunger
parameteriz= ation. Is this third derivative the third derivative that
is mentioned i= n the routine PH/raman_mat.f90 (i.e, the third
derivative of the energy = with respect to the atomic displacements and
with respect to two electric fields, as described in Lazzeri and
Mauri, = PRL 90,036401)?

I am interested in getting a feel for what would be = needed to
implement the third derivatives with GGA into the code, as wel= l as
what sort of errors one might expect when using the third-order term
as = currently coded with LDA pseudopotentials (comments in the forums
have h= inted that the errors are likely small). =A0The shift in the Raman
spect= ra for cd-Si is pretty minor when using a GGA pseudo compared to
that of an LDA calculation, but I wanted to be able to quantify the
erro= r better for other systems where comparing the GGA raman spectra
to one = calculated within LDA was not possible (e.g., when the system
doesn'= t exhibit a gap in LDA).

Thanks for the help!

Best,
Brad
UC Berkeley

=
On Tue, Nov 9, = 2010 at 5:00 PM, Brad Malone <brad.malone at gmail.com> wro= te:
Hi, I am seeking more information on the err= or

> from phq_setup : error # 1
> third order derivatives not implemented with GGA

From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID:
http://www.democritos.it/pipermail/pw_forum/2008-= September/010123.html
http://www.democritos.it/pipermail/pw_forum/2010-February.= txt

I understand that the third derivatives were never implemented and
that only the LDA part was calculated, for the Perdew Zunger
parameterization. Is this third derivative the third derivative that
is mentioned in the routine PH/raman_mat.f90 (i.e, the third
derivative of the energy with respect to the atomic displacements and
with respect to two electric fields, as described in Lazzeri and
Mauri, PRL 90,036401)?

I am interested in getting a feel for what would be needed to
implement the third derivatives with GGA into the code, as well as
what sort of errors one might expect when using the third-order term
as currently coded with LDA pseudopotentials (comments in the forums
have hinted that the errors are likely small). =A0The shift in the Raman spectra for cd-Si is pretty minor when using a GGA pseudo compared to
that of an LDA calculation, but I wanted to be able to quantify the
error better for other systems where comparing the GGA raman spectra
to one calculated within LDA was not possible (e.g., when the system
doesn't exhibit a gap in LDA).

Thanks for the help!

Best,
Brad
UC Berkeley



_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum


--90e6ba18183a3cb3ec0494aa1df4-- From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: ............ running pwcond.x to calculate transmission of a perfect Al wire ...STOP 2 Error condition encountered during test: exit status = 2 Aborting ............ From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: ........... E-Ef(ev), T(x2 spins) = 1.5500000 6.0000000 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% from gep_x : error # 38 error on zggev %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% stopping ... ......... I vaguely remember problems with zggev being reported in the Fora one or two years ago. Now, running QE 4.2.1 example 12 under an Ubuntu 8.04.4 umbrella goes just fine. So...I smell a fortran compiler problem here. 8.04.4 comes with gfortran-4.2, whilst 10.04.1 has "upgraded" to gfortran-4.4. Anyone else run into gfortran problems with QE 4.2.1? A few months ago, Eyvaz solved a gfortran problem I was having with lambda.f90. On the general issue of fortran compilers, I've noticed over the years whenever a discussion ensues between advocates (zealots) of one particular edition over another, the collective IQ can descend to 30. I've heard both good and bad things about gfortran, but there does seem to be some agreement that it produces reasonably optimized code. And it's free...cheap at twice the price. Paul Grant www.w2agz.com ------=_NextPart_000_0192_01CB832A.A8ADAB10 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

To = All...

 

Running example 12 from QE 4.2.1 within an Ubuntu = 10.04.1 distro results in the following abend messages:

 

From the = terminal...

............

running pwcond.x to calculate transmission of a = perfect Al wire ...STOP 2

Error = condition encountered during test: exit status =3D 2

Aborting

............

 

From = AlWireAl.cond.out......

...........

E-Ef(ev), T(x2 spins) =3D    = 1.5500000   6.0000000

 

= %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%= %%%%%

     from = gep_x : error #        = 38

     error on = zggev

= %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%= %%%%%

 

     stopping ...

.........

I vaguely = remember problems with zggev being reported in the Fora one or two years = ago.  Now, running QE 4.2.1 example 12 under an Ubuntu 8.04.4 = umbrella goes just fine.  So...I smell a fortran compiler problem = here.  8.04.4 comes with gfortran-4.2, whilst 10.04.1 has = “upgraded” to gfortran-4.4.  Anyone else run into = gfortran problems with QE 4.2.1?  A few months ago, Eyvaz solved a = gfortran problem I was having with lambda.f90.

 

On the = general issue of fortran compilers, I’ve noticed over the years = whenever a discussion ensues between advocates (zealots) of one = particular edition over another, the collective IQ can descend to = 30.  I’ve heard both good and bad things about gfortran, but = there does seem to be some agreement that it produces reasonably = optimized code.  And it’s free...cheap at twice the = price.

 

Paul Grant

www.w2agz.com

 

------=_NextPart_000_0192_01CB832A.A8ADAB10-- From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: 'Iam using xcrysden both on Linux and on Mac and that feature works for me. I understood that one can generate k-pont path in linux version of xcrysden too. I will see to that once again. Thanku once again for your reply. Priyanka Ph.D student IICT India. From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: This module calculates the non-local correlation contribution to the energy !! and potential. This method is based on the method of Guillermo Roman-P= erez !! and Jose M. Soler described in: !! !! G. Roman-Perez and J. M. Soler, PRL 103, 096101 (2009) !! henceforth referred to as SOLER. That method is a new implementation !! of the method found in: !! !! M. Dion, H. Rydberg, E. Schroeder, D. C. Langreth, and !! B. I. Lundqvist, Phys. Rev. Lett. 92, 246401 (2004). !! !! henceforth referred to as DION. Further information about the !! functional and its corresponding potential can be found in: !! !! T. Thonhauser, V.R. Cooper, S. Li, A. Puzder, P. Hyldgaard, !! and D.C. Langreth, Phys. Rev. B 76, 125112 (2007). !! !! A review article that shows many of the applications vdW-DF has been !! applied to so far can be found at: !! !! D. C. Langreth et al., J. Phys.: Condens. Matter 21, 084203 (2009). If you want to try JuNoLo, it interfaces with Quantum ESPRESSO and can be f= ound here: http://www.fz-juelich.de/iff/src/th1/JuNoLo/ As this is CVS code, you might want to do a bit of testing until you feel c= omfortable that there aren't any issues with this part or one of the other = parts the developers have changed or added. Hope that helps. Mike Sullivan Institute of High Performance Computing, Singapore michael at ihpc.a-star.edu.sg http://www.sullivan.sg/ http://www.ihpc.a-star.edu.sg/ From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Beh= alf Of WANG Wei Sent: Thursday, January 13, 2011 9:47 PM To: PWSCF Forum Subject: Re: [Pw_forum] van der Waals density functional Dear Giuseppe Mattioli, Thank you for your reply. I mean that the vdW is calculated from first prin= ciples [vdW-DF M. Dion et al., PRL 92, 246401 (2004)]. It will seem to be = implemented in QE 4.3 and no example yet. Thank you! see QE/Module/funct.f90 ! Special cases (dft_shortname): ! "vdw-df"=3D "sla+pw+rpb+vdw" =3D vdW-DF ! "bp" =3D "b88+p86" =3D Becke-Perdew grad.corr= . ! "pw91" =3D "pw +ggx+ggc" =3D PW91 (aka GGA) ! "blyp" =3D "sla+b88+lyp+blyp" =3D BLYP ! "pbe" =3D "sla+pw+pbx+pbc" =3D PBE ! "revpbe"=3D"sla+pw+rpb+pbc" =3D revPBE (Zhang-Yang) ! "pbesol"=3D"sla+pw+psx+psc" =3D PBEsol ! "hcth" =3D "nox+noc+hcth+hcth" =3D HCTH/120 ! "olyp" =3D "nox+lyp+optx+blyp" =3D OLYP ! "tpss" =3D "sla+pw+meta+meta" =3D TPSS Meta-GGA ! "wc" =3D "sla+pw+wcx+pbc" =3D Wu-Cohen ! "pbe0" =3D "pb0x+pw+pb0x+pbc" =3D PBE0 ! "hse" =3D "nox+pw+hse+pbc" =3D Heyd-Scuseria-Ernzerho= f HSE 06 ! "b3lyp" =3D "b3lp+vwn+b3lp+b3lp"=3D B3LYP ! ! References: ! vdW-DF M. Dion et al., PRL 92, 246401 (2004) Best, WANG IHPC Values :: Impact :: Honesty :: Performance :: Co-operati= on This email is confidential and may be privileged. If you are not the intend= ed recipient, please delete it and notify us immediately. Please do not cop= y or use it for any purpose, or disclose its contents to any other person. = Thank you. From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: This module calculates the non-local correlation contribution to the energy=
=A0!! and potential. This method is based on the method of Guillermo Roman= -Perez
=A0!! and Jose M. Soler described in:
=A0!!
=A0!! =A0 =A0G. Roman-Perez and J. M. Soler, PRL 103, 096101 (2009)

=A0!! henceforth referred to as SOLER. That method is a new implementation=
=A0!! of the method found in:
=A0!!
=A0!! =A0 =A0M. Dion, H. Rydberg, E. Schroeder, D. C. Langreth, and
=A0!! =A0 =A0B. I. Lundqvist, Phys. Rev. Lett. 92, 246401 (2004).
=A0!!
=A0!! henceforth referred to as DION. Further information about the
=A0!! functional and its corresponding potential can be found in:
=A0!!
=A0!! =A0 =A0T. Thonhauser, V.R. Cooper, S. Li, A. Puzder, P. Hyldgaard, =A0!! =A0 =A0and D.C. Langreth, Phys. Rev. B 76, 125112 (2007).
=A0!!
=A0!! A review article that shows many of the applications vdW-DF has been=
=A0!! applied to so far can be found at:
=A0!!
=A0!! =A0 =A0D. C. Langreth et al., J. Phys.: Condens. Matter 21, 084203 (= 2009).

If you want to try JuNoLo, it interfaces with Quantum ESPRESSO and can be f= ound here:
= http://www.fz-juelich.de/iff/src/th1/JuNoLo/

As this is CVS code, you might want to do a bit of testing until you feel c= omfortable that there aren't any issues with this part or one of the ot= her parts the developers have changed or added.

Hope that helps.

Mike Sullivan
Institute of High Performance Computing, Singapore
michael at ihpc.a-star.edu.sg
http://www.sullivan.s= g/
http://www.ihp= c.a-star.edu.sg/

From: pw_forum-bounces at pwscf.= org [mailto:pw_forum-boun= ces at pwscf.org] On Behalf Of WANG Wei
Sent: Thursday, January 13, 2011 9:47 PM
To: PWSCF Forum
Subject: Re: [Pw_forum] van der Waals density functional

Dear Giuseppe Mattioli,

Thank you for your reply. I mean that the vdW is calculated from first prin= ciples [vdW-DF =A0M. Dion et al., PRL 92, 246401 (2004)]. It will seem to b= e =A0implemented in QE 4.3 and no example yet. Thank you!

see QE/Module/funct.f90
=A0! Special cases (dft_shortname):

=A0! =A0 =A0 =A0 =A0 =A0 =A0 =A0"vdw-df"=3D "sla+pw+rpb+vdw= " =A0 =A0=3D vdW-DF
=A0! =A0 =A0 =A0 =A0 =A0 =A0 =A0"bp" =A0 =A0=3D "b88+p86&qu= ot; =A0 =A0 =A0 =A0 =A0 =3D Becke-Perdew grad.corr.
=A0! =A0 =A0 =A0 =A0 =A0 =A0 =A0"pw91" =A0=3D "pw +ggx+ggc&= quot; =A0 =A0 =A0 =3D PW91 (aka GGA)
=A0! =A0 =A0 =A0 =A0 =A0 =A0 =A0"blyp" =A0=3D "sla+b88+lyp+= blyp" =A0=3D BLYP
=A0! =A0 =A0 =A0 =A0 =A0 =A0 =A0"pbe" =A0 =3D "sla+pw+pbx+p= bc" =A0 =A0=3D PBE
=A0! =A0 =A0 =A0 =A0 =A0 =A0 =A0"revpbe"=3D"sla+pw+rpb+pbc&= quot; =A0 =A0 =3D revPBE (Zhang-Yang)
=A0! =A0 =A0 =A0 =A0 =A0 =A0 =A0"pbesol"=3D"sla+pw+psx+psc&= quot; =A0 =A0 =3D PBEsol
=A0! =A0 =A0 =A0 =A0 =A0 =A0 =A0"hcth" =A0=3D "nox+noc+hcth= +hcth" =3D HCTH/120
=A0! =A0 =A0 =A0 =A0 =A0 =A0 =A0"olyp" =A0=3D "nox+lyp+optx= +blyp" =3D OLYP
=A0! =A0 =A0 =A0 =A0 =A0 =A0 =A0"tpss" =A0=3D "sla+pw+meta+= meta" =A0=3D TPSS Meta-GGA
=A0! =A0 =A0 =A0 =A0 =A0 =A0 =A0"wc" =A0 =A0=3D "sla+pw+wcx= +pbc" =A0 =A0=3D Wu-Cohen
=A0! =A0 =A0 =A0 =A0 =A0 =A0 =A0"pbe0" =A0=3D "pb0x+pw+pb0x= +pbc" =A0=3D PBE0
=A0! =A0 =A0 =A0 =A0 =A0 =A0 =A0"hse" =A0 =3D "nox+pw+hse+p= bc" =A0 =A0=3D Heyd-Scuseria-Ernzerhof HSE 06
=A0! =A0 =A0 =A0 =A0 =A0 =A0 =A0"b3lyp" =3D "b3lp+vwn+b3lp+= b3lp"=3D B3LYP
=A0!
=A0! References:
=A0! =A0 =A0 =A0 =A0 =A0 =A0 =A0vdW-DF =A0M. Dion et al., PRL 92, 246401 (= 2004)

Best,
WANG


IHPC Values =A0:: =A0Impact =A0 :: =A0 Honesty =A0 :: =A0 Performance= =A0 :: =A0 Co-operation
This email is confidential and may be privileged. If you are not the intend= ed recipient, please delete it and notify us immediately. Please do not cop= y 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

--0016e6de00ee20a5620499c3d7d1-- From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: point. I was just confused because the scf calculation does not output a zero gap. I mean the line "highest occupied, lowest unoccupied level" shows two different values and I expected them to be equal. 
This was just explained by Mehmet. Check it again

So, it seems I did not too bad in fact.
But how to experimentally get a zero gap then?
Thanks,

??????????????????? Eric.


--------------------------------------------------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"

On 03/09/2011 07:02 AM, Mehmet Topsakal wrote:

Dear?Eric,
In addition,?if you select 18x18x1 kpoints, your mesh should include both K
and M points.
But for a band-structure calculation, you should arrange a kpoints list
along special directions, such as from GAMMA-to-M-to-K-to-GAMMA, and do a
nscf calculation....


On Wed, Mar 9, 2011 at 11:28 AM, xirainbow <nkxirainbow at gmail.com> wrote:

Dear?Eric:
The occupied and unoccupied bands touch each other only at M point(or K
point, I forget it).
You must include this point in you k-mesh.
Furthermore, if you include spin-orbital coupling, the band gap will be
opened at this point.

On Thu, Mar 10, 2011 at 1:30 AM, Eric Germaneau <germaneau at gucas.ac.cn>
wrote:

Dear all,

I'm trying to compute graphene's band gap but get stuck.

From bogus@does.not.exist.com  Tue May 11 17:31:48 2010
From: bogus@does.not.exist.com ()
Date: Tue, 11 May 2010 15:31:48 -0000
Subject: No subject
Message-ID: 

for the highest occupied and lowest occupied level which means a zero gap.
I played with the number a kpoints a finally got a band gap of 0.57 which
is not null.
The scf convergence looks good.
I'm not (yet) an expert in DFT calculation so may did something wrong or
misunderstood something here.
So, I wonder if someone has already successfully performed such
calculation.
I have attached my input file.
Thanks in advance,

??????????????????????????????? Eric.

--
Be the change you wish to see in the world
? Mahatma Gandhi ?

Dr. ?ric Germaneau

College of Physical Sciences
Graduate University of Chinese Academy of Sciences
Yuquan Road 19A
Beijing 100049
China

Please consider the environment before printing this email.
Consid?rez svp l'environnement avant d'imprimer cet email.
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--
____________________________________
Hui Wang
School of physics, Fudan University, Shanghai, China

_______________________________________________
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--

Mehmet Topsakal? (Ph.D. Student)
UNAM-Institute of Materials Science and Nanotechnology.
Bilkent University. 06800 Bilkent, Ankara/Turkey
Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365
http://www.researcherid.com/rid/A-5015-2010


_______________________________________________
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--
Be the change you wish to see in the world
? Mahatma Gandhi ?

Dr. ?ric Germaneau

College of Physical Sciences
Graduate University of Chinese Academy of Sciences
Yuquan Road 19A
Beijing 100049
China

Please consider the environment before printing this email.
Consid?rez svp l'environnement avant d'imprimer cet email.
_______________________________________________
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

--
Be the change you wish to see in the world
 ? Mahatma Gandhi ?
Dr. ?ric Germaneau

College of Physical Sciences
Graduate University of Chinese Academy of Sciences
Yuquan Road 19A
Beijing 100049
China

Please consider the environment before printing this email.
Consid?rez svp l'environnement avant d'imprimer cet email.
--------------070406090406060909020207-- From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: structure calculation of several materials using VASP and SIESTA and obtained the band gaps in excellent agreement with experiments. So my guess is that they are propagating the "LDA-1/2" pseudo in the extended system as is. Hi Layla, Thanks a lot. I am looking forward to hear from you about the details of LDA-1/2 in QE-4.3a. Thanks, and regards, Rajan Rajan K. Pandey, Ph.D. Advisory Research Engineer, Semiconductor Research & Development Center India Systems & Technology Engineering Lab IBM India Pvt. Ltd. MD3 1F B354 Manyata Embassy Business Park Nagawara, Outer Ring Road Bangalore - 560045, India Phone: +91-80-28061262 Mobile: +91-9901850981 Email: rajapand at in.ibm.com rajanpandey at gmail.com On Tue, Mar 29, 2011 at 9:17 PM, Layla Martin-Samos wrote: > H, > sometime ago LDA-1/2 in pwscf was working. I saw some numbers for TiO2 > anatase, But I do not remember the details. > > i'll ask around > > bests regards > > Layla > > > > > 2011/3/29 Nicola Marzari > >> >> >> Hi, >> >> If I understand correctly, you generated a lda-1/2 pseudo >> with the atomic code, but did a lda calculation on silicon >> with pwscf - so you will have gotten very similar but not perfectly >> identical results, of lda bulk silicon done with a consistent >> pseudo (lda) or an inconsistent pseudo . >> >> 2) not sure if lda-1/2 is in pwscf (I think not) or if it >> can be applied to solids. >> >> nicola >> >> >> >> On 3/29/11 3:28 PM, Rajan Pandey wrote: >> > Dear Quantum Espresso Community, >> > >> > I built the latest release (perhaps alpha) of QE-4.3a. Tried to look >> > into the latest LDA -1/2 (assumed to be similar to SIC) in atomic code >> > (ld1), and from the available test case of Silicon, >> > I decided to check if I get a corrected band gap of bulk Si (from >> > example05). First I generated LDA - 0.5 pseudo (input deck for the same >> > is supplied with the distribution). Subsequently, >> > to run a band structure calculation of Si, I used the template in >> > example05. First I did band structure calculation with Si.pz-vbc.UPF, >> > and then another calculation with the LDA - 0.5 pseudo (Si.LDA.0.5.UPF). >> > I checked the output of scf calculation of the latter (I am copying the >> > portion from output): >> > >> > >> > PseudoPot. # 1 for Si read from file Si.LDA.0.5.UPF >> > MD5 check sum: ac6493edff0fd6b486246c8fa11d17dc >> > Pseudo is Norm-conserving, Zval = 4.0 >> > Generated using LDA-1/2 implemented by Leonardo Matheus Marion >> Jorge >> > Using radial grid of 431 points, 2 beta functions with: >> > l(1) = 0 >> > l(2) = 1 >> > >> > atomic species valence mass pseudopotential >> > Si 4.00 28.08600 Si( 1.00) >> > >> > 48 Sym.Ops. (with inversion) >> > >> > However, the end results of the two calculations are the same. That is >> > the band structure and hence the band gap in two cases are same - nearly >> > 50% underestimated. >> > Not sure if I am missing something. I have attached the two scripts: >> > run_example-0 ==> uses LDA pseudo, and run_example ==> uses LDA - 1/2 >> > pseudo. >> > I shall appreciate any suggestion. >> > >> > Thanks, and regards, >> > >> > Rajan >> > >> -- >> ---------------------------------------------------------------------- >> Prof Nicola Marzari Department of Materials University of Oxford >> Chair of Materials Modelling Director, Materials Modelling Laboratory >> nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM >> _______________________________________________ >> 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 > > --000325557c86cafc59049fa1b5d8 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Nicola,

Your comment prompted me to get the reference [ L. G. Fer= reira, M. Marques
and L. K. Teles, Phys. Rev. B 78 125116 (2008) ] and t= ry to figure out the way authors worked out LDA - 1/2 method, in general. From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: ure calculation of several materials using VASP
and SIESTA and obtained = the band gaps in excellent agreement with experiments. So my guess is that = they are propagating
the "LDA-1/2" pseudo in the extended system as is.

Hi Lay= la,

Thanks a lot. I am looking forward to hear from you about the d= etails of LDA-1/2 in QE-4.3a.

Thanks, and regards,

Rajan

Rajan K. Pandey, Ph.D.

Advisory Research Engineer,
Semiconduc= tor Research & Development Center
India Systems & Technology En= gineering Lab
IBM India Pvt. Ltd.
MD3 1F B354
Manyata Embassy=A0 Business Park
N= agawara, Outer Ring Road
Bangalore - 560045, India
Phone: +91-80-2806= 1262
Mobile: +91-9901850981
Email: rajapand at in.ibm.com
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 rajanpandey at gmail.com

On Tue, Mar 29, 2011 at 9:17 PM, Layla Martin-Samos &l= t;lmartinsamos at gmail.com><= /span> wrote:
H,
sometime ag= o LDA-1/2 in pwscf was working. I saw some numbers for TiO2 anatase, But I = do not remember the details.

i'll ask around

bests regards
Layla




2011/3/29 Nicola Marzari <nicola.marzari at materials.ox.ac.u= k>


Hi,

If I understand correctly, you generated a lda-1/2 pseudo
with the atomic code, but did a lda calculation on silicon
with pwscf - so you will have gotten very similar but not perfectly
identical results, of lda bulk silicon done with a consistent
pseudo (lda) or an inconsistent pseudo .

2) not sure if lda-1/2 is in pwscf (I think not) or if it
can be applied to solids.

=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0nicola



On 3/29/11 3:28 PM, Rajan Pandey wrote:
> Dear Quantum Espresso Community,
>
> I built the latest release (perhaps alpha) of QE-4.3a. Tried to look > into the latest LDA -1/2 (assumed to be similar to SIC) in atomic code=
> (ld1), and from the available test case of Silicon,
> I decided to check if I get a corrected band gap of bulk Si (from
> example05). First I generated LDA - 0.5 pseudo (input deck for the sam= e
> is supplied with the distribution). Subsequently,
> to run a band structure calculation of Si, I used the template in
> example05. First I did band structure calculation with Si.pz-vbc.UPF,<= br> > and then another calculation with the LDA - 0.5 pseudo (Si.LDA.0.5.UPF= ).
> I checked the output of scf calculation of the latter (I am copying th= e
> portion from output):
>
>
> =A0 =A0 =A0 PseudoPot. # 1 for Si read from file Si.LDA.0.5.UPF
> =A0 =A0 =A0 MD5 check sum: ac6493edff0fd6b486246c8fa11d17dc
> =A0 =A0 =A0 Pseudo is Norm-conserving, Zval =3D =A04.0
> =A0 =A0 =A0 Generated using LDA-1/2 implemented by Leonardo Matheus Ma= rion Jorge
> =A0 =A0 =A0 Using radial grid of =A0431 points, =A02 beta functions wi= th:
> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0l(1) =3D =A0 0
> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0l(2) =3D =A0 1
>
> =A0 =A0 =A0 atomic species =A0 valence =A0 =A0mass =A0 =A0 pseudopoten= tial
> =A0 =A0 =A0 =A0 =A0Si =A0 =A0 =A0 =A0 =A0 =A0 4.00 =A0 =A028.08600 =A0= =A0 Si( 1.00)
>
> =A0 =A0 =A0 48 Sym.Ops. (with inversion)
>
> However, the end results of the two calculations are the same. That is=
> the band structure and hence the band gap in two cases are same - near= ly
> 50% underestimated.
> Not sure if I am missing something. I have attached the two scripts: > run_example-0 =3D=3D> uses LDA pseudo, and run_example =3D=3D> u= ses LDA - 1/2
> pseudo.
> I shall appreciate any suggestion.
>
> Thanks, and regards,
>
> Rajan
>
--
----------------------------------------------------------------------
Prof Nicola Marzari =A0 =A0Department of Materials =A0 =A0University of Oxf= ord
Chair of Materials Modelling =A0Director, Materials Modelling Laboratory nico= la.marzari at materials.ox.ac.uk =A0 =A0 http://mml.materials.ox.ac.uk/NM
_______________________________________________=
Pw_forum mailing list
Pw_forum at pwscf.org<= /a>
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


--000325557c86cafc59049fa1b5d8-- From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: Variable: input_dft Type: CHARACTER Default: read from pseudopotential files Description: Exchange-correlation functional: eg 'PBE', 'BLYP' etc See Modules/functionals.f90 for allowed values. Overrides the value read from pseudopotential files. Use with care and if you know what you are doing! But as far as I remember this works (at least, worked) for norm-conserving pseudopotentials only. > Is it important that pseudo potentials matches to the DFT functional? Yes, all pseudopotentials you apply should have the same DFT if you do not use input_dft keyword. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: Bernd Doser To: pw_forum at pwscf.org Sent: Mon, April 18, 2011 5:27:42 PM Subject: [Pw_forum] Pseudo potentials for hybrid DFT Dear QuantumEspresso Community, I am interested in calculating organic molecules using hybrid DFT functionals like PBE0 or B3LYP. Therefore I searching pseudo potentials mainly for the elements H, C, O, N, S, Cl, Br, and I. In the database of QuantumEspresso I don't have found a consistent PP set for all these elements. So, what is the best way to select pseudo potentials? Is it important that pseudo potentials matches to the DFT functional? Thank yo in advance, Sincerely, -- Dr Bernd Doser Scientific Software Engineer Avant-garde Materials Simulation Merzhauser Strasse 177 79100 Freiburg im Breisgau, Germany Phone: +49 761 479984-23 Homepage: http://www.avmatsim.de _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum --0-1196003776-1303143950=:73975 Content-Type: text/html; charset=us-ascii
Dear Brend,

From /Doc/INPUT_PW.txt

 Variable:       input_dft

   Type:           CHARACTER
   Default:        read from pseudopotential files
   Description:    Exchange-correlation functional: eg 'PBE', 'BLYP' etc
                         See Modules/functionals.f90 for allowed values.
                         Overrides the value read from pseudopotential files.
                        Use with care and if you know what you are doing!

But as far as I remember this works (at least, worked) for norm-conserving pseudopotentials only.

> Is it important that pseudo potentials matches to the DFT functional?

Yes, all pseudopotentials you apply should have the same DFT if you  do not use input_dft keyword.

Bests,
Eyvaz.

-------------------------------------------------------------------
Prof. Eyvaz Isaev,
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia,
isaev at ifm.liu.se, eyvaz_isaev at yahoo.com


From: Bernd Doser <doser at avmatsim.de>
To: pw_forum at pwscf.org
Sent: Mon, April 18, 2011 5:27:42 PM
Subject: [Pw_forum] Pseudo potentials for hybrid DFT

Dear QuantumEspresso Community,

I am interested in calculating organic molecules using hybrid DFT
functionals like PBE0 or B3LYP. Therefore I searching pseudo potentials
mainly for the elements H, C, O, N, S, Cl, Br, and I. In the database of
QuantumEspresso I don't have found a consistent PP set for all these
elements. So, what is the best way to select pseudo potentials? Is it
important that pseudo potentials matches to the DFT functional?

Thank yo in advance,

Sincerely,

--
Dr Bernd Doser
Scientific Software Engineer

Avant-garde Materials Simulation
Merzhauser Strasse 177
79100 Freiburg im Breisgau, Germany

Phone: +49 761 479984-23
Homepage: http://www.avmatsim.de

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--0-1196003776-1303143950=:73975-- From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: the curvature trap was activated so it must be something else (and I do not know QE well enough to start guessing, so wont). As a double check, according to the SVN (which I just checked out), in Module/bfgs_mod.f90 the addition starts at line 738 and is ! Now the trap itself if ( sdoty < 0.20D0*sBs ) then ! Conventional damping Theta =3D 0.8D0*sBs/(sBs-sdoty) WRITE( stdout, '(/,5X,"WARNING: bfgs curvature condition ",= & & "failed, Theta=3D",F6.3)' )theta y =3D Theta*y + (1.D0 - Theta)*yH endif If the write statement is not there, then the trap could not be showing up, about a 1% chance. Sorry to not be very helpful. 2011/4/18 =D0=9C=D0=B0=D0=BA=D1=81=D0=B8=D0=BC =D0=9F=D0=BE=D0=BF=D0=BE=D0= =B2 : > Dear Prof. Marks, > > I've sent the whole output file to your private e-mail as you suggested. > Here I just put the result of grep command: > > CVS version: > !=C2=A0=C2=A0=C2=A0 total energy=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 =3D=C2=A0=C2=A0=C2=A0 -242.65271405= Ry > =C2=A0=C2=A0=C2=A0=C2=A0 number of bfgs steps=C2=A0=C2=A0=C2=A0 =3D=C2=A0= =C2=A0 0 > !=C2=A0=C2=A0=C2=A0 total energy=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 =3D=C2=A0=C2=A0=C2=A0 -242.66331605= Ry > =C2=A0=C2=A0=C2=A0=C2=A0 number of bfgs steps=C2=A0=C2=A0=C2=A0 =3D=C2=A0= =C2=A0 1 > !=C2=A0=C2=A0=C2=A0 total energy=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 =3D=C2=A0=C2=A0=C2=A0 -242.66341971= Ry > =C2=A0=C2=A0=C2=A0=C2=A0 number of bfgs steps=C2=A0=C2=A0=C2=A0 =3D=C2=A0= =C2=A0 2 > !=C2=A0=C2=A0=C2=A0 total energy=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 =3D=C2=A0=C2=A0=C2=A0 -242.66342267= Ry > =C2=A0=C2=A0=C2=A0=C2=A0 bfgs converged in=C2=A0=C2=A0 4 scf cycles and= =C2=A0=C2=A0 3 bfgs steps > !=C2=A0=C2=A0=C2=A0 total energy=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 =3D=C2=A0=C2=A0=C2=A0 -242.66284562= Ry > > v.4.2.1 > !=C2=A0=C2=A0=C2=A0 total energy=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 =3D=C2=A0=C2=A0=C2=A0 -242.65271405= Ry > =C2=A0=C2=A0=C2=A0=C2=A0 number of bfgs steps=C2=A0=C2=A0=C2=A0 =3D=C2=A0= =C2=A0 0 > !=C2=A0=C2=A0=C2=A0 total energy=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 =3D=C2=A0=C2=A0=C2=A0 -242.64460983= Ry > =C2=A0=C2=A0=C2=A0=C2=A0 number of bfgs steps=C2=A0=C2=A0=C2=A0 =3D=C2=A0= =C2=A0 1 > !=C2=A0=C2=A0=C2=A0 total energy=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 =3D=C2=A0=C2=A0=C2=A0 -242.66331847= Ry > =C2=A0=C2=A0=C2=A0=C2=A0 number of bfgs steps=C2=A0=C2=A0=C2=A0 =3D=C2=A0= =C2=A0 1 > !=C2=A0=C2=A0=C2=A0 total energy=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 =3D=C2=A0=C2=A0=C2=A0 -242.66341565= Ry > =C2=A0=C2=A0=C2=A0=C2=A0 number of bfgs steps=C2=A0=C2=A0=C2=A0 =3D=C2=A0= =C2=A0 2 > !=C2=A0=C2=A0=C2=A0 total energy=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 =3D=C2=A0=C2=A0=C2=A0 -242.66342170= Ry > =C2=A0=C2=A0=C2=A0=C2=A0 number of bfgs steps=C2=A0=C2=A0=C2=A0 =3D=C2=A0= =C2=A0 3 > !=C2=A0=C2=A0=C2=A0 total energy=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 =3D=C2=A0=C2=A0=C2=A0 -242.66342336= Ry > =C2=A0=C2=A0=C2=A0=C2=A0 bfgs converged in=C2=A0=C2=A0 6 scf cycles and= =C2=A0=C2=A0 4 bfgs steps > > Best regards, > Maxim. > > > 2011/4/18 Laurence Marks >> >> The latest BFGS has a curvature trap which can change the behavior >> particularly if you have too few k-points. Can you please do >> >> grep -e "! =C2=A0 =C2=A0tot" -e bfgs WHATEVER.out >> >> (where WHATEVER is relevant) and send it to me, perhaps at my private >> email (or the full .out file). I am not an expert with QE, but might >> be able to say something. >> >> 2011/4/18 =D0=9C=D0=B0=D0=BA=D1=81=D0=B8=D0=BC =D0=9F=D0=BE=D0=BF=D0=BE= =D0=B2 : >> > Dear QE developers, >> > >> > comparing vc-relax calculations between BFGS(4.2.1) and the latest >> > BFGS(from >> > CVS) I faced=C2=A0 with a following problem: >> > the newest QE calculates one extra point after achieving convergence >> > criteria (etot_conv_thr,force_conv_thr,press_conv_thr), >> > which leads to slightly higher total energy. >> > >> > Here are the two latest energies from outputs: >> > =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 v.4.2.1=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0=C2= =A0 CVS(18.04.2011) >> > >> > -242.66342170 Ry=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 -242.66342267 Ry >> > -242.66342336 Ry=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 -242.66284562 Ry >> > >> > One can see that there is a good agreement between the last energy by >> > v.4.2.1 and next to the last by CVS-version, whereas >> > the last energy by CVS is higher by ~ 0.5 mRy. >> > >> > I tried relax (cell shape fixed) also - it works fine, no extra point >> > calculation. >> > >> > -- >> > Best regards, Max Popov >> > Ph.D. student >> > Materials center Leoben (MCL), Leoben, Austria. >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> > >> >> >> >> -- >> Laurence Marks >> Department of Materials Science and Engineering >> MSE Rm 2036 Cook Hall >> 2220 N Campus Drive >> Northwestern University >> Evanston, IL 60208, USA >> Tel: (847) 491-3996 Fax: (847) 491-7820 >> email: L-marks at northwestern dot edu >> Web: www.numis.northwestern.edu >> Chair, Commission on Electron Crystallography of IUCR >> www.numis.northwestern.edu/ >> Research is to see what everybody else has seen, and to think what >> nobody else has thought >> Albert Szent-Gyorgi >> _______________________________________________ >> 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 > > --=20 Laurence Marks Department of Materials Science and Engineering MSE Rm 2036 Cook Hall 2220 N Campus Drive Northwestern University Evanston, IL 60208, USA Tel: (847) 491-3996 Fax: (847) 491-7820 email: L-marks at northwestern dot edu Web: www.numis.northwestern.edu Chair, Commission on Electron Crystallography of IUCR www.numis.northwestern.edu/ Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: Please suggest me. Thanks in advance. Best Regards Sanjay D. Gupta ~Best Regards ........................................................... Sanjay D. Gupta Research Fellow Department of Physics, Bhavnagar University, Bhavnagar-364 022 Gujarat, Mobile-9879666643 email:guptasanjay_56 at yahoo.co.in ........................................................... --20cf30050eaa0e650304a42cfb60 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear, PWSCF users,

Greetings!!!

Here I am facing problem of = high pressure in per nitride materials. When we do scf using two different = platform such as ABINIT and PWSCF, we got different pressure like abinit gi= ve nearly 20 GPa and pwscf gives 2720.7 GPa, while I am using same geometry= and even same strcture. Two codes should not differ so much, so I am not c= lear, where i am doing mistake.
From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: suggest me. Thanks in advance.

Best Regards
Sanjay D. Gupta





~Best Regards
......................= .....................................
Sanjay D. Gupta
Research Fellow
Department of Physics,
Bhavnagar U= niversity, Bhavnagar-364 022
Gujarat, Mobile-9879666643
email:guptasanja= y_56 at yahoo.co.in
...........................................................
--20cf30050eaa0e650304a42cfb60-- From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: suggest me. Thanks in advance.

Best Regards
Sanjay D. Gupta





~Best Regards
......................= .....................................
Sanjay D. Gupta
Research Fellow
Department of Physics,
Bhavnagar U= niversity, Bhavnagar-364 022
Gujarat, Mobile-9879666643
email:guptasanja= y_56 at yahoo.co.in
...........................................................

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Pw_forum at pwscf.org
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--
Best regards, Max P= opov
Ph.D. student
Materials center Leoben (MCL), Leoben, Austria. --bcaec520f0bfe21e1404a42d305c-- From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: x Phi(i1,i2, na, nb) for pairs of atoms in the super-cell with the relative= positions given by R =3D (i-1)*a + (j-1)*b +(k-1)*c where i j and k are read from Al444.fc file. However, such a supercell does not include the pair of atoms located along= the cube axis direction i.e R =3D (a,0,0) or (0,a,0) or (0,0,a), and hence= the calculation CAN NOT give us the force-constant matrices along those pa= ir of atoms. How do we obtain the force-constant matrices for pair of atoms located alo= ng the cube axes direction. I will be VERY VERY GRATEFUL to any help in this regard. Sandeep K. Lahiri Department of Mechanical Engineering Massachusetts Institute of Technology Cambridge, MA= From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: \begin{equation} \sum_{ \k,v } \epsilon_{ \k,v } = - {\hbar^2 \over 2m} \sum_{ \k,v } \int \psi^*_{ \k,v }(\r) \nabla ^2 \psi_{ \k,v }(\r) d\r + \sum_{ \k,v,\mu,\R} \int \psi^*_{ \k,v }(\r) \hat V^\mu(\r-\d_\mu-\R) \psi_{ \k,v }(\r) + e^2 \int { n(\r) n(\r') \over \mid \r-\r' \mid } d\r d\r' + \int n(\r) V_{xc}(\r) d\r \end{equation} and we can give an alternate formula for the total energy of a crystal: \begin{equation} E_{tot} = \sum_{ \k,v } \epsilon_{ \k,v } - {e^2 \over 2} \int {n(\r) n(\r') \over \mid \r-\r' \mid} d\r d\r' + \int n(\r)\left(\epsilon_{xc}(\r) - V_{xc}(\r)\right) d\r + {e^2 \over 2} \sum'_{\mu,\nu,\R,\R'} {Z_\mu Z_\nu \over \mid \d_\mu+\R-\d_\nu-\R' \mid } \end{equation} \newpage {\bf Plane-wave -- Pseudopotential formalism} \par Let us consider the \G-space representation of the wavefunctions: \begin{equation} |\psi_\k> = \sum_\G \Psi(\k+\G) |\k+\G>, \qquad \Psi ({\bf k+G}) = <{\bf k+G} \mid \psi_\k>,\qquad \mid {\bf k+G} > = {1 \over \sqrt V} e^{i {\bf (k+G) r}},\end{equation} where $ V = N \Omega $ is the volume of the crystal. With these definitions, the normalizations are: \begin{equation} <\k+\G|\k+\G>'=\delta_{\G,\G'}, \qquad<\psi_\k |\psi_\k>=1 \quad\mbox{if}\quad\sum_\G |\Psi(\k+\G)|^2 = 1. \end{equation} Let us define the Fourier trasform for a periodic function $ F(\r)=\sum_\R f(\r-\R) $ as: \begin{eqnarray} F(\G) & = & {1\over N\Omega} \int d\r F(\r) e^{-i{\bf G r}} = {1 \over \Omega} \int d\r f(\r) e^{-i{\bf G r}} = <{\bf k+G}_1 \mid F(\r) \mid {\bf k+G}_2> ~, \qquad {\bf G = G}_1-\G_2 \\ F(\r) & = &\sum_\G F(\G) e^{i{\bf G r}}. \end{eqnarray} We assume non local pseudopotential of general form $\hat V^\mu = V_\mu(r)+\sum_i V_{\mu,i}(\r,\r')$. The total energy per unit cell in reciprocal space is: \begin{eqnarray} { E_{tot} \over N } & = & {1 \over N} {\hbar^2 \over 2m} \sum_{\k,v} \sum_\G {\mid \Psi_v({\bf k+G}) \mid}^2 ({\bf k+G})^2 + \Omega \sum_\G n^*(\G) \sum_\mu S_\mu(\G) V_\mu(\G) + {1 \over N} \sum_{\k,v} \sum_{\mu,i} \sum_{{\bf G,G'}} S_\mu({\bf G - G'}) \times \nonumber \\ & & \mbox{} \times \Psi_v^*({\bf k+G}) \Psi_v({\bf k+G'}) V_{\mu,i}({\bf k+G},{\bf k+G'}) + { \Omega \over 2} \sum_\G n^*(\G) V_{Hartree}(\G) + \Omega\sum_\G n^*(\G)\epsilon_{xc}(\G)d\r + {e^2 \over 2} \sum'_{\mu,\nu,\R} {Z_\mu Z_\nu \over \mid \d_\mu-\d_\nu-\R\mid } \end{eqnarray} where $ S_\mu(\G) = \sum_\mu e^{-i{\bf G d_\mu}}$ is the structure factor, and \begin{equation} V_{Hartree}(\G) = 4\pi e^2 { n({\bf G)} \over \G^2 }, \qquad V_\mu(\G) = {1 \over \Omega} \int V_\mu(\r) e^{-i{\bf G r}} d\r, \qquad V_{\mu,i}(\k_1,\k_2) = {1 \over \Omega} \int e^{-i\k_1\r} V_{\mu,i}(\r,\r') e^{i\k_2\r'} d\r d\r' . \end{equation} Note that we have assumed one atom of each kind. The generalization is straightforward: the structure factor becomes $ S_\mu(\G) = \sum_{i_\mu} e^{-i{\bf G d_{i\mu}}}$ where $i_\mu$ runs over atoms of the same kind $\mu$. Using eigenvalues sum, the total energy per unit cell is \begin{equation} { E_{tot} \over N } = {1 \over N} \sum_{\k,v} \epsilon_{\k,v} - { \Omega \over 2} \sum_\G n^*(\G) V_{Hartree}(\G) + \Omega \sum_\G n^*(\G) \left(\epsilon_{xc}(\G)-V_{xc}(\G)\right) + {e^2 \over 2} \sum'_{\mu,\nu,\R} {Z_\mu Z_\nu \over \mid \d_\mu-\d_\nu-\R \mid }. \end{equation} In the plane-wave representation the Kohn-Sham equation becomes \begin{equation} \sum_{\G'} <{\bf k+G} \mid H-\epsilon \mid {\bf k+G'}> \Psi ({\bf k+G'}) = 0, \qquad\mbox{or} \qquad \sum_{\G'} <{\bf k+G} \mid H \mid {\bf k+G'}> \Psi ({\bf k+G'}) = \epsilon \Psi ({\bf k+G}) \end{equation} The matrix elements of the hamiltonian are \begin{eqnarray} <{\bf k+G} \mid H-\epsilon \mid {\bf k+G'}> & = & \biggl ( - {\hbar^2 \over 2m} ({\bf k+G})^2 -\epsilon \biggr ) \delta_{\bf GG'} + \sum_\mu S_\mu(\G-\G') \biggl ( V_\mu(\G-\G') + \sum_i V_{\mu,i}({\bf k+G},{\bf k+G'}) \biggr ) \nonumber \\ & + & V_{Hartree}(\G-\G') + V_{xc}(\G-\G') . \end{eqnarray} {\em Divergent Terms in the potential} \par The Hartree term, $V_{Hartree}(0)$, and local potential term, $\sum_\mu S_\mu(0)V_\mu(0)$, are separately divergent and must be treated in a special way. Let us consider their sum $\widetilde V(\r)=V_{loc}(\r)+V_{Hartree}(\r)$. Its $\G=0$ term is not divergent: \begin{equation} \widetilde V(\G=0) ={1\over\Omega} \int d\r\left(\sum_\mu V_\mu(\r-\d_\mu) + {1\over N} e^2 \int {n(\r')\over |\r-\r'|} d\r'\right)= {1\over\Omega} \sum_\mu \int d\r \left( V_\mu(r) + {Z_\mu e^2\over r} \right ) = {1\over\Omega} \sum_\mu \alpha_\mu \end{equation} where we used \begin{equation} V_\mu(r) \sim -{Z_\mu e^2\over r}\quad\mbox{for large~} r,\qquad {1\over N} \int n(\r) = \sum_\mu Z_\mu. \end{equation} The $\alpha_\mu$ are parameters depending only on the pseudopotential. \newpage {\em Divergent Terms in the energy} \par The $\G=0$ terms of the ion-ion, Hartree, and local pseudopotential terms in the total energy are separately divergent and must be treated in a special way. Let us call $E_{div}$ the sum of all divergent terms. First Step: split $E_{div} = E_{div}^{(1)} + E_{div}^{(2)}$, with \begin{equation} E_{div}^{(1)} = \int n(\r) \sum_\mu V_\mu(\r-\d_\mu) d\r + {1\over N} e^2 \int {n(\r)n(\r')\over |\r-\r'|} d\r d\r' \end{equation} \begin{equation} E_{div}^{(2)} = {e^2\over 2} \sum'_{\mu,\nu,\R}{Z_\mu Z_\nu\over|\d_\mu-\d_\nu-\R|} - {1\over N} {e^2\over 2} \int {n(\r)n(\r')\over |\r-\r'|} d\r d\r' \end{equation} Using the previous definition of $\widetilde V(\r)$, the first divergent term can be written as \begin{equation} E_{div}^{(1)}= \int n(\r) \widetilde V(\r) d\r. \end{equation} The $\G=0$ term of $\widetilde V(\G)$ is not divergent and has been previously calculated: \begin{equation} \widetilde V(\G=0) = {1\over\Omega} \sum_\mu \alpha_\mu,\qquad n(\G=0)=\sum_\mu {Z_\mu \over \Omega}. \end{equation} We finally get for the $\G=0$ contribution what is usually called ``$\alpha Z$ term'': \begin{equation} E_{div}^{(1)} = \Omega\sum_{\G\neq 0} n^*(\G) \widetilde V(\G) + {1\over\Omega}(\sum_\mu Z_\mu)(\sum_\mu \alpha_\mu) = \Omega\sum_\G n^*(\G) \widetilde V_{loc}(\G) + 2 \widetilde E_{Hartree} \end{equation} where $\widetilde V_{loc}$ is the local potential for $\G\neq 0$, contains the $\alpha Z$ term in $\G=0$ component, and \begin{equation} \widetilde E_{Hartree} = {\Omega\over 2}\sum_{\G\neq 0} n^*(\G)V_{Hartree}(\G). \end{equation} Second step: write $E_{div}^{(2)}= E_{Ewald}^{(1)} + E_{Ewald}^{(2)}-E_{Hartree}$, with \begin{equation} E_{Ewald}^{(1)} = {e^2\over 2} \sum'_{\mu,\nu,\R}{Z_\mu Z_\nu\over|\d_\mu-\d_\nu-\R|} \mbox{erfc}(\sqrt{\eta}|\d_\mu-\d_\nu-\R|)~,\qquad E_{Ewald}^{(2)} = {e^2\over 2} \sum_{\mu,\nu,\R}{Z_\mu Z_\nu\over|\d_\mu-\d_\nu-\R|} \mbox{erf} (\sqrt{\eta}|\d_\mu-\d_\nu-\R|) - e^2 \sqrt{\eta\over\pi}\sum_\mu Z_\mu^2. \end{equation} This identity is verified for any value of $\eta$. The sum in $E_{Ewald}^{(2)}$ includes the term with $\d_\mu-\d_\nu-\R=0$ (note the missing prime), that is subtracted back in the second term of $E_{Ewald}^{(2)}$ (note that $\mbox{erf}(x)\rightarrow 2x/\sqrt\pi$ for small $x$). The first Ewald term $E_{Ewald}^{(1)}$ is rapidly convergent in real space for any reasonable values of $\eta$. The sum in $E_{Ewald}^{(2)}$ can be written as the interaction energy between point charges $n_c(\r)$ and the potential $V_g(\r)$ produced by a gaussian distribution of charges: \begin{equation} E_{Ewald}^{(2)}= {1\over 2}\int n_c(\r)V_g(\r)d\r - e^2 \sqrt{\eta\over\pi}\sum_\mu Z_\mu^2~,\qquad n_c(\r)=\sum_\mu Z_\mu\delta(\r-\d_\mu)~, \qquad V_g(\r)=e^2\sum_{\mu,\R} {Z_\mu\mbox{erf}(\sqrt{\eta}|\r-\d_\mu-\R|) \over |\r-\d_\mu-\R|} \end{equation} In reciprocal space, by using the Fourier transform \begin{equation} {1\over r'} \mbox{erf} (\sqrt{\eta}r') = \left({\eta\over \pi}\right)^{3/2} \int {e^{-\eta r^2}\over |\r-\r'|} d\r = \int {4\pi e^{-G^2/4\eta}\over G^2}e^{i\G\cdot\r'} d\G \end{equation} one obtains (forgetting for the moment the divergence of $V_g(\G=0)$): \begin{equation} E_{Ewald}^{(2)}= {\Omega\over 2}\sum_{\G} n_c^*(\G)V_g(\G) - e^2 \sqrt{\eta\over\pi}\sum_\mu Z_\mu^2~,\qquad n_c(\G)={1\over\Omega}\sum_\mu Z_\mu e^{i\G\cdot\d_\mu}~, \qquad V_g(\G) = {4\pi e^2\over\Omega} \sum_\mu Z_\mu e^{i\G\cdot\d_\mu} {e^{-G^2/4\eta}\over G^2} \end{equation} The $\G = 0$ contribution to $E_{Ewald}^{(2)}-E_{Hartree}$: \begin{equation} E_0 = {\Omega\over 2} \left(n_c(0)V_g(0)-n(0)V_{Hartree}(0)\right) \end{equation} is no longer divergent, because $n(0)=n_c(0)=\sum_\mu Z_\mu/\Omega$ due to the neutrality of the system: \begin{eqnarray} (V_g-V_{Hartree})(\G=0) & = & {e^2\over N \Omega} \int\left( \sum_{\mu,\R} Z_\mu {\mbox{erf}(\sqrt{\eta}|\r-\d_\mu-\R)|)\over |\r-\d_\mu-\R)|} - \int {n(\r')\over |\r-\r'|}d\r'\right)d\r \nonumber \\ & = & {e^2\over\Omega}\left(\sum_\mu Z_\mu\right) \int {\mbox{erf}(\sqrt{\eta}r)-1\over r}d\r = {e^2\over \Omega} \left(\sum_\mu Z_\mu\right) {\pi\over\eta} \end{eqnarray} The integral appearing in the last expression can be found in tables: \begin{equation} \int {\mbox{erf}(\sqrt{\eta}r)-1\over r}d\r = 4\pi \int (\mbox{erf}(\sqrt{\eta}r)-1)rdr = 4\pi{1 \over 4\eta}. \end{equation} Putting all pieces together, one obtains for $E^{(2)}_{div}$: \begin{eqnarray} E^{(2)}_{div} = -\widetilde E_{hartree} + E_{Ewald} & = & - {\Omega\over 2} \sum_{\G\neq0} n^*(\G)V_{Hartree}(\G) + {4\pi\over\Omega} {e^2\over 2}\sum_{\G\neq 0} \left |\sum_\mu Z_\mu e^{i\G\d_\mu}\right |^2 {e^{-G^2/4\eta}\over G^2} \nonumber \\ & & \mbox{} + {e^2\over 2} \sum'_{\mu,\nu,\R} {Z_\mu Z_\nu\over|\d_\mu-\d_\nu-\R|} \mbox{erfc}(\sqrt{\eta}|\d_\mu-\d_\nu-\R|) - e^2 \sqrt{\eta\over\pi}\sum_\mu Z_\mu^2 - {4\pi\over\Omega} {e^2\over 2} {1\over 4\eta} \left(\sum_\mu Z_\mu\right)^2 \end{eqnarray} and for the total energy: \begin{eqnarray} { E_{tot} \over N } & = & {1 \over N} {\hbar^2 \over 2m} \sum_{\k,v} \sum_\G {\mid \Psi_v({\bf k+G}) \mid}^2 ({\bf k+G})^2 + {1 \over N} \sum_{\k,v} \sum_{\mu,i} \sum_{{\bf G,G'}} S_\mu({\bf G - G'}) \Psi_v^*({\bf k+G}) \Psi_v({\bf k+G'}) V_{\mu,i}({\bf k+G},{\bf k+G'}) \nonumber \\ & & \mbox{} + \Omega \sum_\G n^*(\G) \epsilon_{xc}(\G) + \Omega \sum_\G n^*(\G) \widetilde V_{loc}(\G) + \widetilde E_{Hartree} + E_{Ewald}. \end{eqnarray} One can use the sum of the eigenvalues to calculate the total energy: the kinetic, non local, and local (including the $\alpha Z$ term) contributions disappear and the expression of the total energy becomes: \begin{eqnarray} { E_{tot} \over N } = {1 \over N} \sum_{\k,v} \epsilon_{\k,v} + \Omega \sum_\G n^*(\G)\left(\epsilon_{xc}(\G)-V_{xc}(\G)\right) - \tilde E_{Hartree} + E_{Ewald}. \end{eqnarray} {\em Calculation of energy in CP} \par Let us define $n_g$ as the sum of gaussian charges centered at atomic sites: \begin{equation} n_g(\r) = \sum_\mu Z_\mu \left ({\eta\over\pi}\right)^{3/2} e^{-\eta(\r-\d_\mu)^2}. \end{equation} The divergent terms $E_{div}$ of the energy can be rewritten as $E_{div} = E_{div}^{(1)} + E_{div}^{(2)}$, with \begin{equation} E_{div}^{(1)} = \int n(\r) \sum_\mu V_\mu(\r-\d_\mu) d\r - {1\over N} e^2 \int {n(\r)n_g(\r')\over |\r-\r'|} d\r d\r' \end{equation} \begin{equation} E_{div}^{(2)} = {e^2\over 2} \sum'_{\mu,\nu,\R}{Z_\mu Z_\nu\over|\d_\mu-\d_\nu-\R|} + {1\over N} {e^2\over 2} \int {n(\r)n(\r')\over |\r-\r'|} d\r d\r' + {1\over N} e^2 \int {n (\r)n_g(\r')\over |\r-\r'|} d\r d\r' \end{equation} $E_{div}^{(1)}$ can be rewritten as \begin{equation} E_{div}^{(1)}= \int n(\r) V_{loc+g}(\r)d\r,\qquad V_{loc+g}(\r) = \left ( \sum_\mu V_\mu(\r-\d_\mu) + V_g(\r) \right ), \end{equation} where $V_g(\r)$ is the potential generated by the gaussians. The singularity at $\G=0$ disappears : \begin{equation} V_{loc+g}(\G=0) = {1\over\Omega} \sum_\mu \int d\r \left(V_\mu(r) + {Z_\mu e^2\mbox{erf}(\sqrt{\eta}r)\over r}\right) \equiv {1\over\Omega} \sum_\mu \alpha'_\mu. \end{equation} Note that this term is similar to, but not equal to, the $\alpha Z$ term. $E_{div}^{(1)}$ can be rewritten as: \begin{equation} E_{div}^{(1)} = {1\over\Omega} \left(\sum_\mu Z_\mu\right) \left(\sum_\mu \alpha'_\mu\right) + \Omega \sum_{\G\neq 0} n^*(\G)V_{loc+g}(\G) . \end{equation} $E_{div}^{(2)}$ can be rewritten as $E_{div}^{(2)}= E_{Ewald} + E_{H+g}$, where $E_{Ewald}$ is the well-known Ewald sum, \begin{equation} E_{Ewald} = {e^2\over 2} \sum'_{\mu,\nu,\R}{Z_\mu Z_\nu\over|\d_\mu-\d_\nu-\R|} - {1\over N} {e^2\over 2} \int {n_g(\r)n_g(\r')\over |\r-\r'|} d\r d\r', \end{equation} while $E_{H+g}$ is the electrostatic energy of a system of electrons and ions with a gaussian charge distribution: \begin{equation} E_{H+g} = {1\over N} {e^2\over 2} \int {(n(\r)+n_g(\r))(n(\r')+n_g(\r'))\over |\r-\r'|} d\r d\r'. \end{equation} Both terms are regular at $\G=0$ because they are the electrostatic energy of neutral systems. $E_{H+g}$ can be directly calculated: \begin{equation} E_{H+g} = \Omega \sum_{\G\neq 0} (n^*(\G)+n_g^*(\G)) V_{H+g}(\G), \quad V_{H+g}(\G) = {4\pi e^2\over G^2} \left(n(\G)+n_g(\G) \right) . \end{equation} $E_{Ewald}$ can be easily computed using the same technique used before: \begin{equation} E_{Ewald} = E^{(1)}_{Ewald} + E^{(2)}_{Ewald}, \end{equation} where (note the sum over all vectors including $\d_\mu-\d_\nu-\R=0$): \begin{equation} E^{(1)}_{Ewald} = {e^2\over 2} \sum_{\mu,\nu,\R}{Z_\mu Z_\nu\over|\d_\mu-\d_\nu-\R|} \mbox{erf}(\sqrt{\zeta}|\d_\mu-\d_\nu-\R|) - {1\over N} {e^2\over 2} \int {n_g(\r)n_g(\r')\over |\r-\r'|} d\r d\r' \end{equation} and (note the self-interaction term compensating the $\d_\mu-\d_\nu-\R=0$ contribution of the former term): \begin{equation} E^{(2)}_{Ewald} = {e^2\over 2} \sum'_{\mu,\nu,\R}{Z_\mu Z_\nu\over|\d_\mu-\d_\nu-\R|} \mbox{erfc}(\sqrt{\zeta}|\d_\mu-\d_\nu-\R|) - e^2 \sqrt{\zeta\over\pi}\sum_\mu Z_\mu^2. \end{equation} for an arbitrary value of $\zeta$. $E^{(1)}_{Ewald}$ can be made to vanish, because both terms appearing in it can be written in reciprocal space as an Ewald sum. Leaving apart the $\G=0$ contribution, \begin{equation} {1\over N} {e^2\over 2} \int {n_g(\r)n_g(\r')\over |\r-\r'|} d\r d\r' = {\Omega \over 2}\sum_{\G\neq 0} { n_g^*(\G)V_g(\G)} = {4\pi\over\Omega}{e^2\over 2}\sum_{\G\neq 0} \left|\sum_\mu Z_\mu e^{i\G\cdot\d_\mu}\right|^2 {e^{-G^2/2\eta}\over G^2}. \end{equation} This expression comes from the Fourier transform of $n_g(\r)$ and $V_g(\r)$: \begin{equation} n_g(\G) = {1\over \Omega} \sum_\mu Z_\mu e^{i\G\cdot\d_\mu} {e^{-G^2/4\eta}},\quad V_g(\G) = {4\pi e^2 n_g(\G) \over G^2}. \end{equation} By setting $2\zeta=\eta$, one finds exactly the reciprocal space expression for the first term: \begin{equation} {e^2\over 2} \sum_{\mu,\nu,\R}{Z_\mu Z_\nu\over|\d_\mu-\d_\nu-\R|} \mbox{erf}(\sqrt{\zeta}|\d_\mu-\d_\nu-\R|) = {4\pi\over\Omega}{e^2\over 2}\sum_{\G\neq 0} \left|\sum_\mu Z_\mu e^{i\G\cdot\d_\mu}\right|^2 {e^{-G^2/4\zeta}\over G^2}. \end{equation} $E^{(2)}_{Ewald}$ is a rapidly convergent sum in real space, plus a term coming from the self-interaction of gaussians. {\em Miscellaneous} \par When a set of special points $\{ \k_i \} $, with weights $ w_i$, $ \sum_i w_i = 1$, is used to sample the Brillouin Zone, one has: \begin{equation} {1 \over N} \sum_\k f(\k) \Longrightarrow \sum_i w_i f(\k_i). \end{equation} The $\psi(\r)$ as defined above are vanishingly small in order to be normalized. What is actually calculated, and used in the Fast Fourier Transform algorithm, is $\sqrt{N} \psi(\r)$: $\Psi(\k+\G) \stackrel{FFT}{\longleftrightarrow}\sqrt{N}\psi(\r)$. 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--=-xsLS2OHo0sssv8zp0NPY-- From bogus@does.not.exist.com Tue May 11 17:31:48 2010 From: bogus@does.not.exist.com () Date: Tue, 11 May 2010 15:31:48 -0000 Subject: No subject Message-ID: web and in the Users' Guide, these values of "ecutwfc" and "ecutrho" are greatly in excess of what should be needed to achieve convergence. This raises the question of how to define convergence. One Users' Forum post said that a convenient criterion is 1 mryd/atom. Since my slab unit cell contains 91 atoms, the difference between 40/400 and 50/500 is 2.4 mryd/atom. Is it total energy or total energy per atom that I should be looking at ? What I'm actually interested in is reaction energies (or adsorption energies). The reaction energies I get for 40/400 and 60/720 are -0.316 and -0.317 eV respectively. In other words, they're identical, because the energy differences between 40/400 and 60/720 for the bare slab and for the slab+adsorbate cancel. I'm not sure whether I should be relieved by this or if I should be wary of a hidden problem. As another comment, results for 6x6x1 and 12x12x1 Monkhorst-Pack grids are virtually identical (with ecutwfc=40 and ecutrho=400 in both cases). Hence, k-point spacing doesn't appear to be an issue. I'm inserting below a typical input file here: &CONTROL calculation='scf', title='repeat energy calculation like #50400 but bigger ecutwfc and ecutrho', pseudo_dir='/lustre/cmf/scratch/b/bermudez/QE_PP/', verbosity='default' / &SYSTEM ibrav=8, a=5.860, b=7.673, c=53.00, nat=91, ntyp=5, ecutwfc=50.0, ecutrho=500.0, occupations='fixed', nosym_evc=.TRUE. / &ELECTRONS electron_maxstep=100, conv_thr=1.0D-9, mixing_beta=0.7D0, mixing_ndim=8, mixing_mode='plain' / ATOMIC_SPECIES Si 28.0855 Si_pbe-n-van_UPF N 14.0067 N_pbe-van_ak_UPF O 15.9994 O_pbe-van_ak_UPF F 18.9984032 F_pbe-n-van_UPF H 1.00794 H_pbe-van_ak_UPF ATOMIC_POSITIONS angstrom F -0.828943122 -3.842610696 10.898762889 H 2.956336746 -3.913628193 11.481740207 O 2.130945237 -3.743406775 10.990758649 Si -0.740055896 -3.727473495 9.278104350 Si 2.197736003 -3.719125735 9.357412872 O 0.733635389 -0.092404715 8.709367118 O -2.198390199 -0.092106250 8.703606145 N 0.727690134 -2.912055280 8.831492617 N -2.199510369 -2.913961388 8.797211298 N -0.730334009 2.291265533 8.708545486 N 2.200026883 2.299996238 8.715832903 Si 0.740325891 1.486240963 8.197839727 Si -2.201425602 1.487223849 8.194133645 Si 0.731520021 -1.484390893 7.805743483 Si -2.199544503 -1.481807201 7.794749488 N -0.730477119 -1.509950402 6.851115290 N 2.192766376 -1.509070971 6.850785646 N 0.734572342 1.428876787 6.443023829 N -2.196689576 1.428710465 6.440830516 Si -0.730671582 1.383061493 5.485559504 Si 2.198231920 1.383467537 5.484097670 Si -0.731571258 -1.634722031 5.102794951 Si 2.196186337 -1.634652146 5.102809652 N 0.732378551 -2.470977191 4.637802788 N -2.197580366 -2.470463034 4.640966741 N -0.731691807 2.788232427 4.443687098 N 2.197979174 2.788401786 4.442656379 N -0.731484010 -0.019627141 4.441442429 N 2.198010976 -0.019733235 4.440785365 Si 0.732965820 3.599969198 3.935485972 Si -2.196881366 3.600616053 3.936927345 Si -0.732092418 0.194969145 2.706451385 Si 2.197948022 0.194942344 2.705997893 N 0.732838523 3.815828133 2.206216987 N -2.196890255 3.816167783 2.207269314 N 0.732842940 1.010463084 2.200606165 N -2.197021884 1.010498140 2.200720312 N -0.732301333 -1.402362859 1.988160033 N 2.197752904 -1.402429612 1.987932157 Si 0.732683992 -2.247692417 1.532621948 Si -2.197244178 -2.247708827 1.532715316 Si 0.732816753 2.419773565 1.160763975 Si -2.197113870 2.420131824 1.161325553 N -0.732304509 2.385786603 0.203241957 N 2.197969280 2.385645498 0.203316922 N 0.732493393 -2.433993290 -0.207756507 N -2.197450470 -2.434258734 -0.207663162 Si -0.732495688 -2.466691676 -1.166181979 Si 2.197512928 -2.466630603 -1.166105788 Si -0.732435027 2.205350148 -1.537697562 Si 2.197675396 2.205337618 -1.537670714 N 0.732607176 1.361450666 -1.991660707 N -2.197386115 1.361482103 -1.991967809 N -0.732555455 -1.052728897 -2.197325278 N 2.197485775 -1.052686623 -2.197266201 N -0.732575216 3.812491336 -2.215973946 N 2.197423357 3.812523616 -2.215877477 Si 0.732455781 -0.237903510 -2.702429787 Si -2.197536589 -0.237927098 -2.702546727 Si -0.732782356 -3.644946429 -3.947788648 Si 2.197212071 -3.644957994 -3.947708493 N 0.732186804 -0.022261163 -4.433181470 N -2.197780158 -0.022299546 -4.433277495 N 0.732217627 -2.830367771 -4.450667073 N -2.197813068 -2.830395474 -4.450700148 N -0.732746654 2.428899633 -4.661913346 N 2.197243946 2.428854425 -4.661795907 Si 0.732252914 1.582997684 -5.112922128 Si -2.197749414 1.582996773 -5.112924046 Si 0.732131635 -1.416752401 -5.483156140 Si -2.197874184 -1.416795000 -5.483202539 N -0.732884377 -1.446757009 -6.437077490 N 2.197101491 -1.446724700 -6.437084206 N 0.732395894 1.404310755 -6.857972381 N -2.197609347 1.404357298 -6.857976982 Si -0.732500000 1.391882200 -7.807890185 0 0 0 Si 2.197500000 1.391882200 -7.807890185 0 0 0 Si -0.732500000 -1.607109850 -8.180675410 0 0 0 Si 2.197500000 -1.607109850 -8.180675410 0 0 0 N 0.732500000 -2.451907150 -8.633865291 0 0 0 N -2.197500000 -2.451907150 -8.633865291 0 0 0 N -0.732500000 2.806399750 -8.838531689 0 0 0 N 2.197500000 2.806399750 -8.838531689 0 0 0 O -0.732500000 0.000000000 -8.860017231 0 0 0 O 2.197500000 0.000000000 -8.860017231 0 0 0 Si 0.732500000 3.621272350 -9.343552671 0 0 0 Si -2.197500000 3.621272350 -9.343552671 0 0 0 O 0.823729487 3.733135449 -10.991705035 0 0 0 O -2.106270809 3.733135519 -10.991705242 0 0 0 H -0.038874881 3.812689877 -11.453270153 0 0 0 H -2.968874621 3.812689805 -11.453270009 0 0 0 K_POINTS automatic 6 6 1 0 0 0 As always, thanks in advance for whatever help and advice you can provide. Best Wishes, Vic Bermudez ************ Victor M. Bermudez Code 6876 U.S. Naval Research Laboratory 4555 Overlook Ave., S.W. Washington, DC 20375-5347 Phone: 202-767-6728 FAX: 202-767-1165 E-mail: victor.bermudez at nrl.navy.mil