From yukihiro_okuno at fujifilm.co.jp Thu Apr 1 02:47:12 2010 From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp) Date: Thu, 1 Apr 2010 09:47:12 +0900 Subject: [Pw_forum] GW code with Ultra-soft pseudo potential Message-ID: Dear PWSCF users and developers. I'm now try to calculate the quasi-particle spectra of some materials. and I want to use ultrasoft pseudopotential in the calculation. There are some GW codes with interface of PWSCF, Yambo http://www.yambo-code.org/ Sax http://www.sax-project.org/ these code seems it does not correspond the ultra-soft pseudo potential. GWW seems under development and the program of large scale system with complex procedures. Are there GW codes in which we can use ultra-soft pseudo potential with the interface of PWSCF? Sincerely. From baroni at sissa.it Thu Apr 1 07:42:25 2010 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 1 Apr 2010 07:42:25 +0200 Subject: [Pw_forum] phonon dispersion for graphene In-Reply-To: References: , , , <4BB36769.4060507@sissa.it>, , , , , , Message-ID: <22946977-5709-4DA4-BECB-6F36B95D27BE@sissa.it> Dear Elie, may I respectfully ask how much time do you allow yourself to think how to solve a problem between the time you encounter it and the time you hit "return" on a request to this mailing list? May I suggest that a reasonable time could be something in between a few hours and a day? (well a few days may well be worth of it for an important problem, up to several weeks or months, when this requires attending a course). Regards, SB On Mar 31, 2010, at 10:46 PM, Elie Moujaes wrote: > Dear Prof. Gianozzi and all, > > Actually the "&" was there but I missed it when i copied the file. The missing title was the problem. This is sorted but when I started running the ph.x I got another error: > > > > Atomic displacements: > There are 6 irreducible representations > > Representation 1 1 modes -A To be done > > Representation 2 1 modes -A To be done > > Representation 3 1 modes -A To be done > > Representation 4 1 modes -A To be done > > Representation 5 1 modes - To be done > > Representation 6 1 modes - To be done > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from davcio : error # 20 > error while reading from file > > > Well, I found that some people on the forum have got such an error but with I/O error than "reading from file". The error probably means that something was wrong while reading the previous file...I ran a scf calculation (pw.x) followed by the ph.x. I would appreciate it if you can suggest how to fic this problem..I repeated the calculations several times but in vain.. > > Regards > > > > > > From: giannozz at democritos.it > > Date: Wed, 31 Mar 2010 21:30:58 +0200 > > To: pw_forum at pwscf.org > > Subject: Re: [Pw_forum] phonon dispersion for graphene > > > > > > On Mar 31, 2010, at 21:26 , Elie Moujaes wrote: > > > > > reading inputph namelist > > > > if the code says that your namelist is wrong: it is wrong. > > > > > inputph > > > > Missing: a title line; a & before inputph > > --- > > 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 > > Do you have a story that started on Hotmail? Tell us now_______________________________________________ > 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/20100401/211652c7/attachment-0001.htm From lfhuang at theory.issp.ac.cn Thu Apr 1 07:37:48 2010 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Thu, 01 Apr 2010 13:37:48 +0800 Subject: [Pw_forum] =?utf-8?q?phonon_dispersion_for_graphene?= Message-ID: <20100401053748.2071.qmail@ms.hfcas.ac.cn> Dear prof. S. Baroni's: Your previous email for Elie has also enlightened me a lot. Thank you very much! Best Wishes! Yours Sincerely L.F.Huang > From: Stefano Baroni > Subject: Re: [Pw_forum] phonon dispersion for graphene > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > Dear Elie, > > may I respectfully ask how much time do you allow yourself to think how to solve a problem between the time you encounter it and the time you hit "return" on a request to this mailing list? May I suggest that a reasonable time could be something in between a few hours and a day? (well a few days may well be worth of it for an important problem, up to several weeks or months, when this requires attending a course). > > Regards, > SB > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html ------ ====================================================================== 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/20100401/039cd18d/attachment.htm From giannozz at democritos.it Thu Apr 1 08:22:11 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 1 Apr 2010 08:22:11 +0200 Subject: [Pw_forum] Symmetry problem in Ge and phonon calculation problem in InP In-Reply-To: <6D7E0C0F56302745BD0EC910BF4FF30813FB0247@BL2PRD0103MB037.prod.exchangelabs.com> References: <6D7E0C0F56302745BD0EC910BF4FF30813FB0247@BL2PRD0103MB037.prod.exchangelabs.com> Message-ID: On Mar 31, 2010, at 22:41 , Ashutosh Kumar wrote: > Extremely sorry for writing again the symmetry problem in Ge. > I searched the forum about germanium it is not a problem, it is not specific tp germanium, you should have searched "symmetry" and not "germanium", and please do not quote an entire digest http://www.quantum-espresso.org/user_guide/node56.html http://www.quantum-espresso.org/user_guide/node57.html --- 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 Apr 1 08:44:02 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 01 Apr 2010 08:44:02 +0200 Subject: [Pw_forum] Error of GWW in running head.x In-Reply-To: References: Message-ID: <4BB440B2.9010404@democritos.it> yukihiro_okuno at fujifilm.co.jp wrote: > I began to use GWW code, and run the simple examples. > But, I met the error in running head.x > for GWW calculation. > [...] > from seqopn : error # 1 > wrong unit. I tried the current development (cvs) version and didn't get any error. Which version did you use? P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From marsamos at democritos.it Thu Apr 1 11:17:40 2010 From: marsamos at democritos.it (marsamos at democritos.it) Date: Thu, 01 Apr 2010 11:17:40 +0200 Subject: [Pw_forum] GW code with Ultra-soft pseudo potential In-Reply-To: References: Message-ID: <20100401111740.nkbaxdhxws400woc@mail.democritos.it> Dear user, at the moment there is no GW code with ultrasoft pseudo. I think that VASP (not GPL, nor interfaced with espresso) does have PAW (but maybe only in the development version). Anyway One of my collaborators try the GW in VASP and told me that it was very slow. boh! There is in july a CECAM tutorial for GWW, maybe you can try to apply. bests Layla Quoting yukihiro_okuno at fujifilm.co.jp: > > Dear PWSCF users and developers. > > I'm now try to calculate the quasi-particle spectra of some materials. > and I want to use ultrasoft pseudopotential in the calculation. > > There are some GW codes with interface of PWSCF, > > Yambo > http://www.yambo-code.org/ > > Sax > http://www.sax-project.org/ > > these code seems it does not correspond the ultra-soft pseudo potential. > > GWW > > seems under development and the program of large scale system with complex > > procedures. > > Are there GW codes in which we can use ultra-soft pseudo potential with > > the interface of PWSCF? > > Sincerely. > > _______________________________________________ > 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 yukihiro_okuno at fujifilm.co.jp Thu Apr 1 12:06:18 2010 From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp) Date: Thu, 1 Apr 2010 19:06:18 +0900 Subject: [Pw_forum] Re2: Error of GWW in running head.x Message-ID: Dear Prof. Giannozzi. Thank you for your reply. I tried the current development (cvs) version which was downloaded by cvs cvs -d :pserver:anonymous at scm.qe-forge.org:/cvsroot/q-e checkout espresso. Then try GWW_examples/example02 and in the process of HEAD calculation still give same error, the contents of "CRASH" file are %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 0 from seqopn : error # 1 wrong unit %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% my condition of configure is ./configure F90=mpif90 F77=mpif90 CC=mpicc FFLAGS=-O3 CFLAGS=-O3 with intel ifort Fortran compiler Version 10.1 in Linux machine. Compile is succeeded. I think error come from the parts of the program I previously wrote in this forum. ( I think , but it may be wrong.) Sincerely, Yukihiro Okuno. From marsamos at democritos.it Thu Apr 1 15:11:12 2010 From: marsamos at democritos.it (marsamos at democritos.it) Date: Thu, 01 Apr 2010 15:11:12 +0200 Subject: [Pw_forum] workshop announcement Message-ID: <20100401151112.edkjzsqf50kksc0s@mail.democritos.it> Dear all, from june 14th and june 18th of 2010 will be held a Quantum ESPRESSO workshop in Ireland. Please find as attachement the official announcement. Best Layla -- 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. -------------- next part -------------- A non-text attachment was scrubbed... Name: workshop_announcement.pdf Type: application/pdf Size: 47961 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100401/e4526407/attachment-0001.pdf From sd.wang000 at gmail.com Thu Apr 1 15:16:35 2010 From: sd.wang000 at gmail.com (shudong wang) Date: Thu, 1 Apr 2010 21:16:35 +0800 Subject: [Pw_forum] disentangle.x Message-ID: Dear developers: I confused what is the input file of disentangle.x code? S.D.Wang Southeast Universy in Nanjing , China Tel:+86 15050597535 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100401/47652c3c/attachment.htm From giannozz at democritos.it Thu Apr 1 15:17:48 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 1 Apr 2010 15:17:48 +0200 Subject: [Pw_forum] disentangle.x In-Reply-To: References: Message-ID: <9D8BF967-1AD8-41E3-B3E2-F164C87222F2@democritos.it> On Apr 1, 2010, at 15:16 , shudong wang wrote: > I confused what is the input file of disentangle.x code? I am confused too: what is disentangle.x code? --- 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 Apr 1 16:05:39 2010 From: sd.wang000 at gmail.com (shudong wang) Date: Thu, 1 Apr 2010 22:05:39 +0800 Subject: [Pw_forum] About midpoint.x Message-ID: Dear all: I use the midpoint.x to get the wannier centers in WanT code, but I have some problem as following in output file: ====================================================================== = = = *** WanT *** Wannier Transport Code = = (www.wannier-transport.org) = = Ultra Soft Pseudopotential Implem. = = = ====================================================================== Program v. 2.1.0 starts ... Date 1Apr2010 at 21:59:41 Serial run. BUILT : Thu Apr 1 20:30:37 2010 HOST : x86_64-unknown-linux-gnu ARCH : amd64 CC : icc CPP : cpp F90 : mpif90 F77 : ifort DFLAGS : -D__INTEL -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA BLAS LIBS : -L/usr/local/intel/cmkl/8.0/lib/em64t -lmkl_em64t -lguide -lpthread LAPACK LIBS : -lmkl_lapack FFT LIBS : MASS LIBS : *** from PE : 0 *** in routine : io_init *** error msg. : invalid dftdata_fmt = *** error code : 1 *** aborting *** My input file is : &INPUT prefix = 'pt_h2_pt', work_dir = '/home/sdwang/WanT/tmp/test11/pt_h2_pt.export/index.xml', output_fmt = "crystal" rcut = 5.0 toll = 0.10 / What is my problem? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100401/d205c9d6/attachment.htm From ferretti at mit.edu Thu Apr 1 16:35:09 2010 From: ferretti at mit.edu (Andrea Ferretti) Date: Thu, 1 Apr 2010 15:35:09 +0100 (BST) Subject: [Pw_forum] disentangle.x Message-ID: Hi everyone, I guess you are using the disentangle.x code of the WanT package. If you want to have any help, please provide more information (eg the piece of input file that you do not understand, including the reasons of that). Andrea BTW: hopefully, there is going to be soon a WanT-specific mailing list implemented through the qe-forge portal. > > On Apr 1, 2010, at 15:16 , shudong wang wrote: > >> I confused what is the input file of disentangle.x code? > > I am confused too: what is disentangle.x code? > --- > 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 > -- 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 dalcorso at sissa.it Thu Apr 1 16:49:50 2010 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Thu, 01 Apr 2010 16:49:50 +0200 Subject: [Pw_forum] Re2: Error of GWW in running head.x In-Reply-To: References: Message-ID: <1270133390.3281.30.camel@dhcp-5-36.sissa.it> On Thu, 2010-04-01 at 19:06 +0900, yukihiro_okuno at fujifilm.co.jp wrote: > Dear Prof. Giannozzi. > > Thank you for your reply. > > I tried the current development (cvs) version > > which was downloaded by cvs > > cvs -d :pserver:anonymous at scm.qe-forge.org:/cvsroot/q-e checkout espresso. > > Then try GWW_examples/example02 > > and in the process of HEAD calculation still give same error, > > the contents of "CRASH" file are > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > task # 0 > from seqopn : error # 1 > wrong unit > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > my condition of configure is > > ./configure F90=mpif90 F77=mpif90 CC=mpicc FFLAGS=-O3 CFLAGS=-O3 > > with intel ifort Fortran compiler Version 10.1 in Linux machine. Compile is > succeeded. > > I think error come from the parts of the program I previously wrote in this > forum. > ( I think , but it may be wrong.) > Thank you again for your patience and insistence. You are right. There is another incompatibility between GWW and the recent changes to the phonon code. Just set iunrec=99 at the beginning of GWW/head/close_phq.f90. This variable is no more set by the phonon code. Now I will update also the cvs version. HTH Andrea > Sincerely, > > Yukihiro Okuno. > > > _______________________________________________ > 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 ferretti at mit.edu Thu Apr 1 16:36:53 2010 From: ferretti at mit.edu (Andrea Ferretti) Date: Thu, 1 Apr 2010 15:36:53 +0100 (BST) Subject: [Pw_forum] About midpoint.x In-Reply-To: References: Message-ID: prefix looks correct, but work_dir must be work_dir='/home/sdwang/WanT/tmp/test11' what is inside the directories .export or .save written by espresso is managed internally. The user should just point out the position of the above dirs. Andrea > ? > ?*** from PE??? :???? 0 > ?*** in routine : io_init > ?*** error msg. : invalid dftdata_fmt = > ?*** error code :???? 1 > ?*** aborting *** > > My input file is : > &INPUT > ?? prefix? = 'pt_h2_pt', > ?? work_dir = '/home/sdwang/WanT/tmp/test11/pt_h2_pt.export/index.xml',?????? > ?? output_fmt? =? "crystal"??? > ?? rcut? =? 5.0???????? > ?? toll? =? 0.10???????? > / > What is my problem? > > -- 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 kumar.198 at buckeyemail.osu.edu Thu Apr 1 19:39:28 2010 From: kumar.198 at buckeyemail.osu.edu (Ashutosh Kumar) Date: Thu, 1 Apr 2010 17:39:28 +0000 Subject: [Pw_forum] Symmetry problem in Ge and phonon calculation problem in InP Message-ID: <6D7E0C0F56302745BD0EC910BF4FF30813FB02D5@BL2PRD0103MB037.prod.exchangelabs.com> I tried by removing the occupations='smearing'. It writes the dynamic matrix file for q=0. Then i was trying to execute q2r.x. I used q2r.in as 1) &input zasr='simple', fildyn='inp_1.dyn', flfrc='inp_1.fc', la2F=.true. / 1 1 1 1 2) &input zasr='simple', fildyn='inp_1.dyn', flfrc='inp_1.fc', la2F=.true. nr1=0, nr2=0, nr3=0, nfile=1, filin ='inp_1.dyn' (and also tried using various combinations of nrs=1 and 0) / In 1st case it kept on saying, "inp_1.dyn0 file not found" and in the latter it was saying, "invalid reference to variable in namelist". I actually wanted to calculate the dynamic matrix at different q-points and then q2r.x to read these dynamic marix to write coefficients file. I tried using a q mesh in input file for ph.x, but in that case it crashes for epsil=.true. So i was trying to create the dynamic matrix separately for all the q points and let q2r.x to read these. My input for ph.x was: Electron-phonon coefficients &inputph tr2_ph=1.0d-15, prefix='inp_1', epsil=.true., amass(1)=30.974, amass(2)=114.82, outdir='$/tmp/', fildyn='inp_1.dyn', / 0.0 0.0 0.0 Could you please guide me what should be the correct procedure to be able to do the same? Sincere thanks-- Ashutosh Kumar Grad Student The Ohio State University From samolyuk at gmail.com Thu Apr 1 22:19:06 2010 From: samolyuk at gmail.com (German Samolyuk) Date: Thu, 1 Apr 2010 16:19:06 -0400 Subject: [Pw_forum] how to specify initial ion velocities in pw.x In-Reply-To: <5da157840912160746k253c5af9ld620c33be3cf5a3a@mail.gmail.com> References: <5da157840912031047u68819036qe08177d40b46cbfd@mail.gmail.com> <4B18D5C0.1040101@democritos.it> <5da157840912041042w3598170chdf33892d9b0770ff@mail.gmail.com> <48151239-97C5-467C-B9B1-FC03B901AE05@democritos.it> <5da157840912160746k253c5af9ld620c33be3cf5a3a@mail.gmail.com> Message-ID: Dear all, I'm trying to optimize structure correspondent to quadrupole of dislocation in bcc Fe. The electronic system did not converge after 50 iterations. Attached please find input and output files. I run this task on cray xt4 as "aprun -n 288 pw.x -npool 8 -ndiag 36 < fe.scf.in > fe.scf.out" Any help would be appreciated Sincerely, German Samolyuk On Wed, Dec 16, 2009 at 10:46 AM, German Samolyuk wrote: > Thank you! It works. > German. > > German Samolyuk, > Oak Ridge National Laboratory, > USA > > On Sat, Dec 12, 2009 at 9:03 AM, Paolo Giannozzi > wrote: > > > > On Dec 4, 2009, at 19:42 , German Samolyuk wrote: > > > >> does it mean that if I add after line number 466 of > >> dynamics_module.f90 > >> something like > >> > >> tau_old(1,100) = tau(1,100) - v_x*dt/alat > >> tau_old(2,100) = tau(2,100) - v_y*dt/alat > >> tau_old(3,100) = tau(3,100) - v_z*dt/alat > >> > >> it should be equivalent to set up initial velocity (v_x,v_y,v_z) to > >> particle number 100? > > > > quite likely. Unfortunately the way dynamics_mofdule is written makes > > the seting of initial velocities not straoghtforward > > > >> What units is used for dt? Is it atomic Hartree or atomic Rydberg? > > > > atomic Rydberg (in PWscf; in CP, atomic Hartree...) > > > > Paolo > > --- > > Paolo Giannozzi, Dept of Physics, University of Udine > > via delle Scienze 208, 33100 Udine, Italy > > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100401/ba45b0ae/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: fe.scf.in Type: application/octet-stream Size: 14455 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100401/ba45b0ae/attachment-0002.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: fe.scf.out Type: application/octet-stream Size: 51358 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100401/ba45b0ae/attachment-0003.obj From jiachen at princeton.edu Thu Apr 1 22:26:31 2010 From: jiachen at princeton.edu (jia chen) Date: Thu, 1 Apr 2010 16:26:31 -0400 Subject: [Pw_forum] starting_magnetization and magnetization optimization in pwscf Message-ID: Dear All, Pwscf has a very nice feature that can set initial magnetism of a certain kind of atom by starting_magnetization. It is working very well for me. But I would like to know more about how this is really working in cp code, during magnetization optimization calculations. It is too much for me to read the code to get the answer. So I would like to give a guess of basic idea of this process. When we start a calculation with initial atomic wave functions. Pwscf code can give atomic occupations of spin up and down whose ratio satisfy the value of starting_magnetization. During the calculation, pwscf can adjust the occupation number after each diagonal step according to orbitals energies because pwscf goes with a bunch of empty states. Then there can be "electron flow" between spin up and down. Basically, that's I guess how pwscf does magnetization optimization. Can you tell me what is the actual process pwscf goes though in this kind of magnetization optimizations? Any comments are very welcome. Thank you in advance. Best Wishes -- Jia Chen Dept of Chemistry Princeton University Princeton, NJ 08544 From degironc at sissa.it Thu Apr 1 23:17:50 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 01 Apr 2010 23:17:50 +0200 Subject: [Pw_forum] starting_magnetization and magnetization optimization in pwscf In-Reply-To: References: Message-ID: <4BB50D7E.6000905@sissa.it> Dear Jia Chen, the starting magnetization variable is used to define the initial charge density in a scf run in pwscf. This density is used to build the first KS potential which thus results to have a magnetically broken symmetry. The resulting spin-up and spin-down hamiltonians are diagonalized and the Fermi energy located from the constraint on the total number of electrons (the system must be treated as a metal and a number of empty states are present). This determines the output density and since the potential is "magnetically ordered" the density also is if the system likes so. Then the code mixes in and out densities and builds a new guess for the input density and hence the new KS potential and so on... So starting magnetization really enters only in PW/atomic_rho.f90 which is used to build the starting guess for the input charge density as rho_up = sum_s (1.0+starting_magnetization_atom_s)/2 * unpolarized_rho_atom_s rho_dw = sum_s (1.0-starting_magnetization_atom_s)/2 * unpolarized_rho_atom_s Hope this helps, stefano jia chen wrote: > Dear All, > > Pwscf has a very nice feature that can set initial magnetism of a > certain kind of atom by starting_magnetization. It is working very > well for me. But I would like to know more about how this is really > working in cp code, during magnetization optimization calculations. It > is too much for me to read the code to get the answer. So I would like > to give a guess of basic idea of this process. > > When we start a calculation with initial atomic wave functions. Pwscf > code can give atomic occupations of spin up and down whose ratio > satisfy the value of starting_magnetization. During the calculation, > pwscf can adjust the occupation number after each diagonal step > according to orbitals energies because pwscf goes with a bunch of > empty states. Then there can be "electron flow" between spin up and > down. Basically, that's I guess how pwscf does magnetization > optimization. > > Can you tell me what is the actual process pwscf goes though in this > kind of magnetization optimizations? Any comments are very welcome. > Thank you in advance. > > Best Wishes > From anna.ferrari at unito.it Fri Apr 2 14:15:27 2010 From: anna.ferrari at unito.it (Anna Maria Ferrari) Date: Fri, 2 Apr 2010 13:15:27 +0100 Subject: [Pw_forum] HSE Message-ID: <00f601cad25e$2f0c1440$2376c082@desdemona> Dear All I would be interested in the use of HSE functional. I know that for the moment the suggestion is to use usual PBE, PW91 pseudopotentail since HSE pseudo are not available. Am I right? Anyway I would like to know if there is an example in the PWSCF list of examples or a documentation that i should know in order to prepare a correct input for this long-range scheme? thanks anna *********************************** Anna Maria Ferrari Dipartimento Chimica IFM Universit? di Torino via P. Giuria 5 10125 Torino ITALY phone ++39 +11 6707563 fax ++39 +11 670 7855 *********************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100402/4688b6e8/attachment.htm From carlo.nervi at unito.it Fri Apr 2 13:55:04 2010 From: carlo.nervi at unito.it (Carlo Nervi) Date: Fri, 02 Apr 2010 13:55:04 +0200 Subject: [Pw_forum] HSE In-Reply-To: <00f601cad25e$2f0c1440$2376c082@desdemona> References: <00f601cad25e$2f0c1440$2376c082@desdemona> Message-ID: <4BB5DB18.7030403@unito.it> Anna, as far as I know (perhaps others should confirm what I'm writing) the HSE functional can be employed, provided that you compile QE with -DEXX. A different problem is the generation of PP by ld1.x with the desired functional. Carlo Anna Maria Ferrari ha scritto: > Dear All > I would be interested in the use of HSE functional. > I know that for the moment the suggestion is to use usual PBE, PW91 > pseudopotentail > since HSE pseudo are not available. Am I right? > Anyway I would like to know if there is an example in the PWSCF list of > examples > or a documentation that i should know in order > to prepare a correct input for this long-range scheme? > > thanks > anna > > *********************************** > Anna Maria Ferrari > Dipartimento Chimica IFM > Universit? di Torino > via P. Giuria 5 > 10125 Torino ITALY > > phone ++39 +11 6707563 > fax ++39 +11 670 7855 > *********************************** > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ------------------------------------------------------ Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 Fax: +39 011 6707855 - Dipartimento di Chimica IFM via P. Giuria 7, 10125 Torino, Italy http://lem.ch.unito.it/ From daijiayu at nudt.edu.cn Fri Apr 2 18:23:27 2010 From: daijiayu at nudt.edu.cn (Jiayu Dai) Date: Sat, 03 Apr 2010 00:23:27 +0800 Subject: [Pw_forum] LDA+U in md calculations Message-ID: Dear developers, I have some doubts about the molecular dynamics calculations using LDA+U. First, is LDA+U performed in MD calculations? Because i did not find the Hubbard energy in the output file of MD. Second, i think the value of U be dependent on the temperature and density, also on the ionic structures. Therefore, since ionic positions are different in each time step, is U different at each time step? If so, the performance of LDA+U should be very difficult in MD. I did not know if what i said is right. Hope experts comment on this problem. Thanks a lot. Jiayu ------------------------------------------- Jiayu Dai Department of Physics National University of Defense Technology, Changsha, 410073, P R China ----------------------------------------- From matteo at umn.edu Fri Apr 2 18:56:46 2010 From: matteo at umn.edu (Matteo Cococcioni) Date: Fri, 02 Apr 2010 11:56:46 -0500 Subject: [Pw_forum] LDA+U in md calculations In-Reply-To: References: Message-ID: <4BB621CE.8000203@umn.edu> Dear Jiayu, are you talking about Car-Parrinello MD or Born-Oppenheimer MD (run with pwscf)? In any case lda+U MD is implemented in the sense that the code computes the forces and the stress as derivatives of the lda+U energy functional. However it is not able to account for the variation of U with atomic position or with the cell. So it is a dynamics at fixed U. To account for this variation one would need to evaluate dU/dR or dU/d\epsilon (R and \epsilon being atomic positions and strains). Some work in this direction has been recently done (not sure it's published yet) by Kulik and Marzari. If the structure you are interested in doesn't change dramatically during the MD run I would expect that keeping the same U is not too bad. but this is just my guess. regards, Matteo Jiayu Dai wrote: > Dear developers, > > I have some doubts about the molecular dynamics calculations using LDA+U. First, is LDA+U performed in MD calculations? Because i did not find the Hubbard energy in the output file of MD. Second, i think the value of U be dependent on the temperature and density, also on the ionic structures. Therefore, since ionic positions are different in each time step, is U different at each time step? If so, the performance of LDA+U should be very difficult in MD. > > I did not know if what i said is right. Hope experts comment on this problem. > > Thanks a lot. > > Jiayu > ------------------------------------------- > Jiayu Dai > Department of Physics > National University of Defense Technology, > Changsha, 410073, P R China > ----------------------------------------- > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From junkermeier at yahoo.com Fri Apr 2 19:34:02 2010 From: junkermeier at yahoo.com (Chad Junkermeier) Date: Fri, 2 Apr 2010 10:34:02 -0700 (PDT) Subject: [Pw_forum] iflag=1, output_format=0 Message-ID: <299665.57237.qm@web111014.mail.gq1.yahoo.com> Hi, I am trying to produce a plot of the potential along some vector. As far as I can tell I am using all of the proper commands to do this. But the output ends up being the same as the output for a 3D plot. I have looked at INPUT_PP.html and previous forum messages but I don't see anything that tells me where I am going wrong. I include a listing of the file that I am using to run pp.x as well as the first 20 odd lines from the output file that was produced by pp.x. Chad Junkermeier, Ph.D. NRC Post-Doctoral Associate Naval Research Laboratory 4555 Overlook Ave, S.W. Washington DC 20375 --------------------------------------File used to run PP-------------------------------------- &inputPP outdir='/somedirectory/', plot_num=11 filplot = 'system.pot' prefix='system' / &plot iflag=1, output_format=0 e1(1) = 0.1666666667, e1(2) = 0.3333333333, e1(3) = 1.0, x0(1) = 0.1666666667, x0(2) = 0.3333333333, x0(3) = 0.0, nx = 30, / --------------------------------------OUTPUT------------------------------------------- 120 120 540 120 120 540 4 2 4 9.80000000 0.00000000 4.74489796 0.00000000 0.00000000 0.00000000 2919.2659431030 4.0000000000 300.0000000000 11 1 C 4.00 2 F 7.00 1 0.000000000 0.000000000 0.046638636 1 2 0.000000000 0.577350269 -0.046638636 1 3 0.000000000 0.000000000 0.314784179 2 4 0.000000000 0.577350269 -0.314784179 2 -9.096756667E+00 -8.995541503E+00 -8.698802996E+00 -8.228148056E+00 -7.617132192E+00 -6.899775019E+00 -6.105117728E+00 -5.266900369E+00 -4.426489702E+00 -3.631924483E+00 -2.950202255E+00 -2.425718709E+00 -2.020466228E+00 -1.681320250E+00 -1.398244426E+00 -1.162559046E+00 -9.650982679E-01 -8.010643304E-01 -6.634409389E-01 -5.490599505E-01 -4.532133969E-01 -3.730915748E-01 -3.061221943E-01 -2.498868814E-01 -2.029587705E-01 -1.634065045E-01 -1.304753941E-01 -1.026662013E-01 -7.951487978E-02 -6.014058861E-02 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100402/9a20663e/attachment.htm From wparker at mps.ohio-state.edu Fri Apr 2 19:12:10 2010 From: wparker at mps.ohio-state.edu (William Parker) Date: Fri, 2 Apr 2010 13:12:10 -0400 (EDT) Subject: [Pw_forum] HSE In-Reply-To: <4BB5DB18.7030403@unito.it> References: <00f601cad25e$2f0c1440$2376c082@desdemona> <4BB5DB18.7030403@unito.it> Message-ID: Anna, Carlo, other interested QE users, QE does not have HSE (at least, as of version 4.1.2). Hybrid functionals such as B3LYP and PBE0 that use exact exchange without screening are implemented (activated, as Carlo mentioned, by putting -DEXX in the DFLAGS of the make.sys file before compiling). Is anyone working on adding screened exchange? It's on my list of things to do but not too near the top. --William ====================================================================== William Parker Tel : +1 (614) 292-2887 Graduate Research Associate Fax : +1 (614) 292-7557 Ohio State University Department of Physics 191 West Woodruff Avenue email: wparker at mps.ohio-state.edu Columbus, OH 43210-1117 http://www.physics.ohio-state.edu/~wparker U.S.A. Office: 2025 Physics Research Building ====================================================================== On Fri, 2 Apr 2010, Carlo Nervi wrote: > Anna, > as far as I know (perhaps others should confirm what I'm writing) the > HSE functional can be employed, provided that you compile QE with -DEXX. > > A different problem is the generation of PP by ld1.x with the desired > functional. > Carlo > > Anna Maria Ferrari ha scritto: > > Dear All > > I would be interested in the use of HSE functional. > > I know that for the moment the suggestion is to use usual PBE, PW91 > > pseudopotentail > > since HSE pseudo are not available. Am I right? > > Anyway I would like to know if there is an example in the PWSCF list of > > examples > > or a documentation that i should know in order > > to prepare a correct input for this long-range scheme? > > > > thanks > > anna > > > > *********************************** > > Anna Maria Ferrari > > Dipartimento Chimica IFM > > Universit? di Torino > > via P. Giuria 5 > > 10125 Torino ITALY > > > > phone ++39 +11 6707563 > > fax ++39 +11 670 7855 > > *********************************** > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > -- > ------------------------------------------------------ > Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 > Fax: +39 011 6707855 - Dipartimento di Chimica IFM > via P. Giuria 7, 10125 Torino, Italy > http://lem.ch.unito.it/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From ceresoli at MIT.EDU Fri Apr 2 20:14:24 2010 From: ceresoli at MIT.EDU (Davide Ceresoli) Date: Fri, 02 Apr 2010 14:14:24 -0400 Subject: [Pw_forum] HSE In-Reply-To: References: <00f601cad25e$2f0c1440$2376c082@desdemona> <4BB5DB18.7030403@unito.it> Message-ID: <4BB63400.1000102@mit.edu> William Parker wrote: > Anna, Carlo, other interested QE users, > > QE does not have HSE (at least, as of version 4.1.2). Hybrid functionals > such as B3LYP and PBE0 that use exact exchange without screening are > implemented (activated, as Carlo mentioned, by putting -DEXX in the DFLAGS > of the make.sys file before compiling). Is anyone working on adding > screened exchange? It's on my list of things to do but not too near the > top. HSE has been implemented recently and it's in the CVS version. D. From wparker at mps.ohio-state.edu Fri Apr 2 20:38:10 2010 From: wparker at mps.ohio-state.edu (William Parker) Date: Fri, 2 Apr 2010 14:38:10 -0400 (EDT) Subject: [Pw_forum] HSE In-Reply-To: <4BB63400.1000102@mit.edu> References: <00f601cad25e$2f0c1440$2376c082@desdemona> <4BB5DB18.7030403@unito.it> <4BB63400.1000102@mit.edu> Message-ID: Thanks for the heads up, Davide. I just updated my CVS version. Do you know what tests have been done on the HSE implementation? --William On Fri, 2 Apr 2010, Davide Ceresoli wrote: > William Parker wrote: > > Anna, Carlo, other interested QE users, > > > > QE does not have HSE (at least, as of version 4.1.2). Hybrid functionals > > such as B3LYP and PBE0 that use exact exchange without screening are > > implemented (activated, as Carlo mentioned, by putting -DEXX in the DFLAGS > > of the make.sys file before compiling). Is anyone working on adding > > screened exchange? It's on my list of things to do but not too near the > > top. > HSE has been implemented recently and it's in the CVS version. > > D. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From jiachen at princeton.edu Fri Apr 2 22:44:47 2010 From: jiachen at princeton.edu (jia chen) Date: Fri, 2 Apr 2010 16:44:47 -0400 Subject: [Pw_forum] Pw_forum Digest, Vol 34, Issue 5 In-Reply-To: References: Message-ID: Dear Prof Stefano de Gironcoli, Thank you for your explanation. It is really helpful. I have been using Quantum Espresso for a while. I like this project very much and I hope I can do a little contribution to this community. Since QE4.0, empty states feature in CP code didn't work anymore. I added about ten lines to emptystartes.f90 module and it works in 4.1.1 and 4.1.2. I know people have other methods to do it, but this feather may be handy, so I attached the code which may be useful, just in case, for someone. I am not a good programmer, I can do nothing more than making it work... Best Regards jia On Fri, Apr 2, 2010 at 3:17 AM, wrote: > Send Pw_forum mailing list submissions to > ? ? ? ?pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > ? ? ? ?http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > ? ? ? ?pw_forum-request at pwscf.org > > You can reach the person managing the list at > ? ? ? ?pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > ? 1. starting_magnetization and magnetization optimization in > ? ? ?pwscf (jia chen) > ? 2. Re: starting_magnetization and magnetization optimization in > ? ? ?pwscf (Stefano de Gironcoli) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 1 Apr 2010 16:26:31 -0400 > From: jia chen > Subject: [Pw_forum] starting_magnetization and magnetization > ? ? ? ?optimization in pwscf > To: pw_forum at pwscf.org > Message-ID: > ? ? ? ? > Content-Type: text/plain; charset=ISO-8859-1 > > Dear All, > > Pwscf has a very nice feature that can set initial magnetism of a > certain kind of atom by starting_magnetization. It is working very > well for me. But I would like to know more about how this is really > working in cp code, during magnetization optimization calculations. It > is too much for me to read the code to get the answer. So I would like > to give a guess of basic idea of this process. > > When we start a calculation with initial atomic wave functions. Pwscf > code can give atomic occupations of spin up and down whose ratio > satisfy the value of starting_magnetization. During the calculation, > pwscf can adjust the occupation number after each diagonal step > according to orbitals energies because pwscf goes with a bunch of > empty states. Then there can be "electron flow" between spin up and > down. Basically, that's I guess how pwscf does magnetization > optimization. > > Can you tell me what is the actual process pwscf goes though in this > kind of magnetization optimizations? Any comments are very welcome. > Thank you in advance. > > Best Wishes > -- > Jia Chen > > Dept of Chemistry > Princeton University > Princeton, NJ 08544 > > > ------------------------------ > > Message: 2 > Date: Thu, 01 Apr 2010 23:17:50 +0200 > From: Stefano de Gironcoli > Subject: Re: [Pw_forum] starting_magnetization and magnetization > ? ? ? ?optimization in pwscf > To: PWSCF Forum > Message-ID: <4BB50D7E.6000905 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Jia Chen, > ?the starting magnetization variable is used to define the initial > charge density in a scf run in pwscf. > ?This density is used to build the first KS potential which thus > results to have a magnetically broken symmetry. > ?The resulting spin-up and spin-down hamiltonians are diagonalized and > the Fermi energy located from the constraint on the total number of > electrons (the system must be treated as a metal and a number of empty > states are present). > ?This determines the output density and since the potential is > "magnetically ordered" the density also is if the system likes so. > ?Then the code mixes in and out densities and builds a new guess for > the input density and hence the new KS potential and so on... > ? So starting magnetization really enters only in PW/atomic_rho.f90 > which ?is used to build the starting guess for the ?input charge density as > > ? rho_up = ?sum_s ?(1.0+starting_magnetization_atom_s)/2 * > unpolarized_rho_atom_s > ? rho_dw = sum_s ?(1.0-starting_magnetization_atom_s)/2 * > unpolarized_rho_atom_s > > Hope this helps, > > stefano > > > jia chen wrote: >> Dear All, >> >> Pwscf has a very nice feature that can set initial magnetism of a >> certain kind of atom by starting_magnetization. It is working very >> well for me. But I would like to know more about how this is really >> working in cp code, during magnetization optimization calculations. It >> is too much for me to read the code to get the answer. So I would like >> to give a guess of basic idea of this process. >> >> When we start a calculation with initial atomic wave functions. Pwscf >> code can give atomic occupations of spin up and down whose ratio >> satisfy the value of starting_magnetization. During the calculation, >> pwscf can adjust the occupation number after each diagonal step >> according to orbitals energies because pwscf goes with a bunch of >> empty states. Then there can be "electron flow" between spin up and >> down. Basically, that's I guess how pwscf does magnetization >> optimization. >> >> Can you tell me what is the actual process pwscf goes though in this >> kind of magnetization optimizations? Any comments are very welcome. >> Thank you in advance. >> >> Best Wishes >> > > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 34, Issue 5 > *************************************** > -- Jia Chen Dept of Chemistry Princeton University Princeton, NJ 08544 -------------- next part -------------- A non-text attachment was scrubbed... Name: emptystates.f90 Type: text/x-fortran Size: 21444 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100402/81b82b79/attachment-0001.bin From daijiayu at nudt.edu.cn Sat Apr 3 13:08:40 2010 From: daijiayu at nudt.edu.cn (Jiayu Dai) Date: Sat, 03 Apr 2010 19:08:40 +0800 Subject: [Pw_forum] LDA+U in md calculations Message-ID: Dear Matteo, Thanks for your comments. I am using the BOMD (pwscf). In my case, at high density, i would expect the U should be different with the change of ionic structures. In particular, i am concerning about the pressure. I found a strange thing: the pressure with LDA+U is lower than the pressure without U adding. As my experience, th pressure should be larger when we added the U parameter, is it right? Besides, all the cases using LDA+U is about the transition metals, which has the d or f electrons. How about the s or p electrons? Thanks. Jiayu > Dear Jiayu, are you talking about Car-Parrinello MD or Born-Oppenheimer MD (run with pwscf)? In any case lda+U MD is implemented in the sense that the code computes the forces and the stress as derivatives of the lda+U energy functional. However it is not able to account for the variation of U with atomic position or with the cell. So it is a dynamics at fixed U. To account for this variation one would need to evaluate dU/dR or dU/d\epsilon (R and \epsilon being atomic positions and strains). Some work in this direction has been recently done (not sure it's published yet) by Kulik and Marzari. If the structure you are interested in doesn't change dramatically during the MD run I would expect that keeping the same U is not too bad. but this is just my guess. regards, Matteo Jiayu Dai wrote: > Dear developers, > > I have some doubts about the molecular dynamics calculations using LDA+U. First, is LDA+U performed in MD calculations? Because i did not find the Hubbard energy in the output file of MD. Second, i think the value of U be dependent on the temperature and density, also on the ionic structures. Therefore, since ionic positions are different in each time step, is U different at each time step? If so, the performance of LDA+U should be very difficult in MD. > > I did not know if what i said is right. Hope experts comment on this problem. > > Thanks a lot. > > Jiayu > ------------------------------------------- > Jiayu Dai > Department of Physics > National University of Defense Technology, > Changsha, 410073, P R China > ----------------------------------------- > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From baroni at sissa.it Sat Apr 3 21:13:31 2010 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 3 Apr 2010 21:13:31 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 34, Issue 5 In-Reply-To: References: Message-ID: <7E2C6F76-9595-4EFD-87BB-E6AE75561431@sissa.it> thank you - we really appreciate SB On Apr 2, 2010, at 10:44 PM, jia chen wrote: > Dear Prof Stefano de Gironcoli, > > Thank you for your explanation. It is really helpful. > I have been using Quantum Espresso for a while. I like this project > very much and I hope I can do a little contribution to this community. > Since QE4.0, empty states feature in CP code didn't work anymore. I > added about ten lines to emptystartes.f90 module and it works in 4.1.1 > and 4.1.2. I know people have other methods to do it, but this feather > may be handy, so I attached the code which may be useful, just in > case, for someone. I am not a good programmer, I can do nothing more > than making it work... > > Best Regards > jia > On Fri, Apr 2, 2010 at 3:17 AM, wrote: >> Send Pw_forum mailing list submissions to >> pw_forum at pwscf.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://www.democritos.it/mailman/listinfo/pw_forum >> or, via email, send a message with subject or body 'help' to >> pw_forum-request at pwscf.org >> >> You can reach the person managing the list at >> pw_forum-owner at pwscf.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Pw_forum digest..." >> >> >> Today's Topics: >> >> 1. starting_magnetization and magnetization optimization in >> pwscf (jia chen) >> 2. Re: starting_magnetization and magnetization optimization in >> pwscf (Stefano de Gironcoli) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Thu, 1 Apr 2010 16:26:31 -0400 >> From: jia chen >> Subject: [Pw_forum] starting_magnetization and magnetization >> optimization in pwscf >> To: pw_forum at pwscf.org >> Message-ID: >> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> Dear All, >> >> Pwscf has a very nice feature that can set initial magnetism of a >> certain kind of atom by starting_magnetization. It is working very >> well for me. But I would like to know more about how this is really >> working in cp code, during magnetization optimization calculations. It >> is too much for me to read the code to get the answer. So I would like >> to give a guess of basic idea of this process. >> >> When we start a calculation with initial atomic wave functions. Pwscf >> code can give atomic occupations of spin up and down whose ratio >> satisfy the value of starting_magnetization. During the calculation, >> pwscf can adjust the occupation number after each diagonal step >> according to orbitals energies because pwscf goes with a bunch of >> empty states. Then there can be "electron flow" between spin up and >> down. Basically, that's I guess how pwscf does magnetization >> optimization. >> >> Can you tell me what is the actual process pwscf goes though in this >> kind of magnetization optimizations? Any comments are very welcome. >> Thank you in advance. >> >> Best Wishes >> -- >> Jia Chen >> >> Dept of Chemistry >> Princeton University >> Princeton, NJ 08544 >> >> >> ------------------------------ >> >> Message: 2 >> Date: Thu, 01 Apr 2010 23:17:50 +0200 >> From: Stefano de Gironcoli >> Subject: Re: [Pw_forum] starting_magnetization and magnetization >> optimization in pwscf >> To: PWSCF Forum >> Message-ID: <4BB50D7E.6000905 at sissa.it> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Dear Jia Chen, >> the starting magnetization variable is used to define the initial >> charge density in a scf run in pwscf. >> This density is used to build the first KS potential which thus >> results to have a magnetically broken symmetry. >> The resulting spin-up and spin-down hamiltonians are diagonalized and >> the Fermi energy located from the constraint on the total number of >> electrons (the system must be treated as a metal and a number of empty >> states are present). >> This determines the output density and since the potential is >> "magnetically ordered" the density also is if the system likes so. >> Then the code mixes in and out densities and builds a new guess for >> the input density and hence the new KS potential and so on... >> So starting magnetization really enters only in PW/atomic_rho.f90 >> which is used to build the starting guess for the input charge density as >> >> rho_up = sum_s (1.0+starting_magnetization_atom_s)/2 * >> unpolarized_rho_atom_s >> rho_dw = sum_s (1.0-starting_magnetization_atom_s)/2 * >> unpolarized_rho_atom_s >> >> Hope this helps, >> >> stefano >> >> >> jia chen wrote: >>> Dear All, >>> >>> Pwscf has a very nice feature that can set initial magnetism of a >>> certain kind of atom by starting_magnetization. It is working very >>> well for me. But I would like to know more about how this is really >>> working in cp code, during magnetization optimization calculations. It >>> is too much for me to read the code to get the answer. So I would like >>> to give a guess of basic idea of this process. >>> >>> When we start a calculation with initial atomic wave functions. Pwscf >>> code can give atomic occupations of spin up and down whose ratio >>> satisfy the value of starting_magnetization. During the calculation, >>> pwscf can adjust the occupation number after each diagonal step >>> according to orbitals energies because pwscf goes with a bunch of >>> empty states. Then there can be "electron flow" between spin up and >>> down. Basically, that's I guess how pwscf does magnetization >>> optimization. >>> >>> Can you tell me what is the actual process pwscf goes though in this >>> kind of magnetization optimizations? Any comments are very welcome. >>> Thank you in advance. >>> >>> Best Wishes >>> >> >> >> >> ------------------------------ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> End of Pw_forum Digest, Vol 34, Issue 5 >> *************************************** >> > > > > -- > Jia Chen > > Dept of Chemistry > Princeton University > Princeton, NJ 08544 > _______________________________________________ > 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/20100403/ce99e178/attachment-0001.htm From dimpy.sharma at tyndall.ie Sun Apr 4 15:18:23 2010 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Sun, 4 Apr 2010 14:18:23 +0100 Subject: [Pw_forum] Plane waves parallelization Message-ID: Hi Quantum espresso users, I was trying to run a scf calculation for my system (518 atoms), I used 100 nodes to simulate the system however it crashed after 3 iterations without any error message (consumed 883MB).I used K_Points 2x1x1. From the user guide , I was reading the parallelism in quantum espresso,I could not follow "pools" and plane wave parallelization, and how to do the K_Point sampling in mpi parallelization for my system. Thanks and regards! Dimpy Msc(Nanotechnology) PhD UCC,Ireland -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100404/6d587d56/attachment.htm From ouuing at gmail.com Mon Apr 5 03:53:14 2010 From: ouuing at gmail.com (Hanyu) Date: Mon, 5 Apr 2010 09:53:14 +0800 Subject: [Pw_forum] Plane waves parallelization In-Reply-To: References: Message-ID: Generally, it is not necessary to use many k point for so many atoms. I think it is enough to use K_points 1x1x1. On Sun, Apr 4, 2010 at 9:18 PM, Dimpy Sharma wrote: > Hi Quantum espresso users, > > I was trying to run a scf calculation for my system (518 atoms), I used 100 > nodes to simulate the system however it crashed after 3 iterations without > any error message (consumed 883MB).I used K_Points 2x1x1. > > ?From the user guide , I was reading the parallelism in quantum espresso,I > could not follow "pools" and plane wave parallelization, and how to do the > K_Point sampling in mpi parallelization for my system. > > Thanks and regards! > > Dimpy > Msc(Nanotechnology) > PhD > UCC,Ireland > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=**=-=**=-=**=-=*=-=*=-=*=-=*=-=*=- Hanyu Liu(???), MS. State key Laboratory of Superhard Materials, Jilin University, China Email: liuhanyu08 at mails.jlu.edu.cn ouuing at gmail.com From matteo at umn.edu Mon Apr 5 05:36:35 2010 From: matteo at umn.edu (Matteo Cococcioni) Date: Sun, 04 Apr 2010 22:36:35 -0500 Subject: [Pw_forum] LDA+U in md calculations In-Reply-To: References: Message-ID: <4BB95AC3.4060003@umn.edu> Dear Jiayu in order to fully account the effects of the +U correction on pressure one should include a contribution from dU/dV too. you may find this reference useful: Phys. Rev. B 12, 125124 (2009) regards, Matteo Jiayu Dai wrote: > Dear Matteo, > > Thanks for your comments. I am using the BOMD (pwscf). In my case, at high density, i would expect the U should be different with the change of ionic structures. In particular, i am concerning about the pressure. I found a strange thing: the pressure with LDA+U is lower than the pressure without U adding. As my experience, th pressure should be larger when we added the U parameter, is it right? > > Besides, all the cases using LDA+U is about the transition metals, which has the d or f electrons. How about the s or p electrons? > > Thanks. > > Jiayu > > > > > Dear Jiayu, > > are you talking about Car-Parrinello MD or Born-Oppenheimer MD (run with > pwscf)? > In any case lda+U MD is implemented in the sense that the code computes > the forces and the stress > as derivatives of the lda+U energy functional. However it is not able > to account for the variation > of U with atomic position or with the cell. So it is a dynamics at fixed U. > To account for this variation one would need to evaluate dU/dR or > dU/d\epsilon (R and \epsilon being atomic > positions and strains). Some work in this direction has been recently > done (not sure it's > published yet) by Kulik and Marzari. > If the structure you are interested in doesn't change dramatically > during the MD run I would expect > that keeping the same U is not too bad. but this is just my guess. > > regards, > > Matteo > > > Jiayu Dai wrote: > >> Dear developers, >> >> I have some doubts about the molecular dynamics calculations using LDA+U. First, is LDA+U performed in MD calculations? Because i did not find the Hubbard energy in the output file of MD. Second, i think the value of U be dependent on the temperature and density, also on the ionic structures. Therefore, since ionic positions are different in each time step, is U different at each time step? If so, the performance of LDA+U should be very difficult in MD. >> >> I did not know if what i said is right. Hope experts comment on this problem. >> >> Thanks a lot. >> >> Jiayu >> ------------------------------------------- >> Jiayu Dai >> Department of Physics >> National University of Defense Technology, >> Changsha, 410073, P R China >> ----------------------------------------- >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > > _______________________________________________ > 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 hsuhan at cems.umn.edu Mon Apr 5 07:35:10 2010 From: hsuhan at cems.umn.edu (Han Hsu) Date: Mon, 5 Apr 2010 00:35:10 -0500 (CDT) Subject: [Pw_forum] LDA+U in md calculations In-Reply-To: <4BB95AC3.4060003@umn.edu> References: <4BB95AC3.4060003@umn.edu> Message-ID: <2117.71.195.59.176.1270445710.squirrel@webmail.cems.umn.edu> Jiayu and Matteo, PRB volume 12 was published in 1975. The paper discussing the contribution of dU/dV is actually: Phys. Rev. B 79, 125124 (2009). Regards, Han On Sun, April 4, 2010 10:36 pm, Matteo Cococcioni wrote: > > Dear Jiayu > > in order to fully account the effects of the +U correction on pressure > one should include a contribution from dU/dV too. > you may find this reference useful: > > Phys. Rev. B 12, 125124 (2009) > > regards, > > Matteo > > > Jiayu Dai wrote: >> Dear Matteo, >> >> Thanks for your comments. I am using the BOMD (pwscf). In my case, at >> high density, i would expect the U should be different with the change >> of ionic structures. In particular, i am concerning about the pressure. >> I found a strange thing: the pressure with LDA+U is lower than the >> pressure without U adding. As my experience, th pressure should be >> larger when we added the U parameter, is it right? >> >> Besides, all the cases using LDA+U is about the transition metals, which >> has the d or f electrons. How about the s or p electrons? >> >> Thanks. >> >> Jiayu >> >> >> >> >> Dear Jiayu, >> >> are you talking about Car-Parrinello MD or Born-Oppenheimer MD (run with >> pwscf)? >> In any case lda+U MD is implemented in the sense that the code computes >> the forces and the stress >> as derivatives of the lda+U energy functional. However it is not able >> to account for the variation >> of U with atomic position or with the cell. So it is a dynamics at fixed >> U. >> To account for this variation one would need to evaluate dU/dR or >> dU/d\epsilon (R and \epsilon being atomic >> positions and strains). Some work in this direction has been recently >> done (not sure it's >> published yet) by Kulik and Marzari. >> If the structure you are interested in doesn't change dramatically >> during the MD run I would expect >> that keeping the same U is not too bad. but this is just my guess. >> >> regards, >> >> Matteo >> >> >> Jiayu Dai wrote: >> >>> Dear developers, >>> >>> I have some doubts about the molecular dynamics calculations using >>> LDA+U. First, is LDA+U performed in MD calculations? Because i did not >>> find the Hubbard energy in the output file of MD. Second, i think the >>> value of U be dependent on the temperature and density, also on the >>> ionic structures. Therefore, since ionic positions are different in >>> each time step, is U different at each time step? If so, the >>> performance of LDA+U should be very difficult in MD. >>> >>> I did not know if what i said is right. Hope experts comment on this >>> problem. >>> >>> Thanks a lot. >>> >>> Jiayu >>> ------------------------------------------- >>> Jiayu Dai >>> Department of Physics >>> National University of Defense Technology, >>> Changsha, 410073, P R China >>> ----------------------------------------- >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> >> >> _______________________________________________ >> 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 > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From mahasinalam at yahoo.co.uk Mon Apr 5 08:48:08 2010 From: mahasinalam at yahoo.co.uk (MAHASIN ALAM) Date: Mon, 5 Apr 2010 06:48:08 +0000 (GMT) Subject: [Pw_forum] Band Structures Calculations Message-ID: <324257.91595.qm@web24106.mail.ird.yahoo.com> Dear Friends, ? I am trying to calculate the band structure of GeNW using PWScf. My input file is below when I submit this job I got the error message ?can?t read the k-points?. Can anyone please help me to overcome this problem and also how to get the Fermi Energy? Thanks a lot. ? ? &CONTROL ???????????????? calculation = 'bands', ??????????????? restart_mode = 'from_scratch', ????????????????????? prefix = 'h-genw' ????????????????????? outdir = '/Scratch/ihpcalam/h-genw/', ????????????????? pseudo_dir = '/Scratch/ihpcalam/pseudo/' ?/ ?&SYSTEM ?????????????????????? ibrav = 0, ?????????????????????????? A = 31.00 , ?????????????????????????? B = 31.00 , ?????????????????????????? C = 11.55 , ?????????????????????? cosAB = 0 , ?????????????????????? cosAC = 0 , ?????????????????????? cosBC = 0 , ???????????????????????? nat = 112, ??????????????????????? ntyp = 2, ???????????????????? ecutwfc = 30.00, ???????????????? occupations = 'smearing' , ?/ ?&ELECTRONS ??????????????????? conv_thr = 1.0d-6 ???????????????? mixing_mode = 'plain' ???????????????? mixing_beta = 0.7 ???????????? diagonalization = 'david' ?/ &IONS ? ion_dynamics = 'damp', ? pot_extrapolation = "second_order", ? wfc_extrapolation = "second_order", / &CELL cell_dynamics = 'damp-pr' , press_conv_thr = 0.1 , / CELL_PARAMETERS cubic ?? 0.999364983?? 0.000000228?? 0.000000624 ?? 0.000000228?? 0.999363704? -0.000000544 ?? 0.000000232? -0.000000202?? 0.371528245 ATOMIC_SPECIES ?? Ge?? 72.61000? Ge.pbe-paw_kj.UPF ??? H??? 1.00794? H.pbe-paw_kj.UPF ATOMIC_POSITIONS angstrom Ge????? 12.801794970? 12.801763793?? 1.439416230 Ge????? 12.877095227? 10.747187971?? 2.816319487 Ge???????????? ??????????? ?????????????????????????? ?????????????????????????? ? K_POINTS 28 ?? 0.0 0.0 0.0 1.0 ?? 0.0 0.0 0.1 1.0 ?? 0.0 0.0 0.2 1.0 ?? 0.0 0.0 0.3 1.0 ?? 0.0 0.0 0.4 1.0 ?? 0.0 0.0 0.5 1.0 ?? 0.0 0.0 0.6 1.0 ?? 0.0 0.0 0.7 1.0 ?? 0.0 0.0 0.8 1.0 ?? 0.0 0.0 0.9 1.0 ?? 0.0 0.0 1.0 1.0 ?? 0.0 0.0 0.0 1.0 ?? 0.0 0.1 0.1 1.0 ?? 0.0 0.2 0.2 1.0 ?? 0.0 0.3 0.3 1.0 ?? 0.0 0.4 0.4 1.0 ?? 0.0 0.5 0.5 1.0 ?? 0.0 0.6 0.6 1.0 ?? 0.0 0.7 0.7 1.0 ?? 0.0 0.8 0.8 1.0 ?? 0.0 0.9 0.9 1.0 ?? 0.0 1.0 1.0 1.0 ?? 0.0 0.0 0.0 1.0 ?? 0.1 0.1 0.1 1.0 ?? 0.2 0.2 0.2 1.0 ?? 0.3 0.3 0.3 1.0 ?? 0.4 0.4 0.4 1.0 ?? 0.5 0.5 0.5 1.0 ? ? Warm regardsSk Mahasin Alam M. Pharm (JU) PhD student School of Chemical and Biomedical Engineering Nanyang Technological University Sinpapore -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100405/bd96f7ab/attachment-0001.htm From shekoufe.khosravi at gmail.com Mon Apr 5 10:00:24 2010 From: shekoufe.khosravi at gmail.com (shekoufe khosravi) Date: Mon, 5 Apr 2010 12:30:24 +0430 Subject: [Pw_forum] Hessian of charge density Message-ID: Dear All I would like to know if PWscf will calculate Hessian of charge density? Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100405/d144eb1e/attachment.htm From ceresoli at MIT.EDU Mon Apr 5 09:59:48 2010 From: ceresoli at MIT.EDU (Davide Ceresoli) Date: Mon, 05 Apr 2010 03:59:48 -0400 Subject: [Pw_forum] HSE In-Reply-To: References: <00f601cad25e$2f0c1440$2376c082@desdemona> <4BB5DB18.7030403@unito.it> <4BB63400.1000102@mit.edu> Message-ID: <4BB99874.6000406@mit.edu> William Parker wrote: > Thanks for the heads up, Davide. I just updated my CVS version. Do you > know what tests have been done on the HSE implementation? > Dear William, silicon for sure ;-) Seriously, I don't know. HSE has been implemented mainly by Hannu-Pekka Komsa at EPFL, with the help from Layla Martin-Samos, Andrea Ferretti, and small contributions from other people. You might ask these people. Best, Davide From nnlinh at sissa.it Mon Apr 5 10:08:36 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Mon, 5 Apr 2010 10:08:36 +0200 (CEST) Subject: [Pw_forum] Band Structures Calculations In-Reply-To: <324257.91595.qm@web24106.mail.ird.yahoo.com> References: <324257.91595.qm@web24106.mail.ird.yahoo.com> Message-ID: <5909.62.2.168.58.1270454916.squirrel@webmail.sissa.it> Overview the K_POINTS in input file, I don't see any problem in it. But I have 2 wondering points: 1. Have you run scf for your system yet? If yes, you can find Fermi energy level for the metal system. 2. You are consider ibrav =0, why you put cosAB, cosAC or cosBC So, the solution is run with "scf" first, then run with "bands", More detail let see in example01. Good luck, Linh > Dear Friends, > ?? > I am trying to calculate the band structure of GeNW using PWScf. My input > file is below when I submit this job I got the error message ???can???t > read the k-points???. Can anyone please help me to overcome this problem > and also how to get the Fermi Energy? Thanks a lot. > ?? > ?? > &CONTROL > ???????????????????????????????? calculation = 'bands', > ?????????????????????????????? restart_mode = 'from_scratch', > ?????????????????????????????????????????? prefix = 'h-genw' > ?????????????????????????????????????????? outdir = > '/Scratch/ihpcalam/h-genw/', > ?????????????????????????????????? pseudo_dir = > '/Scratch/ihpcalam/pseudo/' > ??/ > ??&SYSTEM > ???????????????????????????????????????????? ibrav = 0, > ???????????????????????????????????????????????????? A = 31.00 , > ???????????????????????????????????????????????????? B = 31.00 , > ???????????????????????????????????????????????????? C = 11.55 , > ???????????????????????????????????????????? cosAB = 0 , > ???????????????????????????????????????????? cosAC = 0 , > ???????????????????????????????????????????? cosBC = 0 , > ???????????????????????????????????????????????? nat = 112, > ?????????????????????????????????????????????? ntyp = 2, > ???????????????????????????????????????? ecutwfc = 30.00, > ???????????????????????????????? occupations = 'smearing' , > ??/ > ??&ELECTRONS > ?????????????????????????????????????? conv_thr = 1.0d-6 > ???????????????????????????????? mixing_mode = 'plain' > ???????????????????????????????? mixing_beta = 0.7 > ???????????????????????? diagonalization = 'david' > ??/ > &IONS > ?? ion_dynamics = 'damp', > ?? pot_extrapolation = "second_order", > ?? wfc_extrapolation = "second_order", > / > &CELL > cell_dynamics = 'damp-pr' , > press_conv_thr = 0.1 , > / > CELL_PARAMETERS cubic > ???? 0.999364983???? 0.000000228???? 0.000000624 > ???? 0.000000228???? 0.999363704?? -0.000000544 > ???? 0.000000232?? -0.000000202???? 0.371528245 > ATOMIC_SPECIES > ???? Ge???? 72.61000?? Ge.pbe-paw_kj.UPF > ?????? H?????? 1.00794?? H.pbe-paw_kj.UPF > ATOMIC_POSITIONS angstrom > Ge?????????? 12.801794970?? 12.801763793???? 1.439416230 > Ge?????????? 12.877095227?? 10.747187971???? 2.816319487 > Ge???????????????????????? ????????????????????????????????? > ?????????????????????????????????????????????????????????????????????????????? > ?????????????????????????????????????????????????????????????????????????????? > ?? > K_POINTS > 28 > ???? 0.0 0.0 0.0 1.0 > ???? 0.0 0.0 0.1 1.0 > ???? 0.0 0.0 0.2 1.0 > ???? 0.0 0.0 0.3 1.0 > ???? 0.0 0.0 0.4 1.0 > ???? 0.0 0.0 0.5 1.0 > ???? 0.0 0.0 0.6 1.0 > ???? 0.0 0.0 0.7 1.0 > ???? 0.0 0.0 0.8 1.0 > ???? 0.0 0.0 0.9 1.0 > ???? 0.0 0.0 1.0 1.0 > ???? 0.0 0.0 0.0 1.0 > ???? 0.0 0.1 0.1 1.0 > ???? 0.0 0.2 0.2 1.0 > ???? 0.0 0.3 0.3 1.0 > ???? 0.0 0.4 0.4 1.0 > ???? 0.0 0.5 0.5 1.0 > ???? 0.0 0.6 0.6 1.0 > ???? 0.0 0.7 0.7 1.0 > ???? 0.0 0.8 0.8 1.0 > ???? 0.0 0.9 0.9 1.0 > ???? 0.0 1.0 1.0 1.0 > ???? 0.0 0.0 0.0 1.0 > ???? 0.1 0.1 0.1 1.0 > ???? 0.2 0.2 0.2 1.0 > ???? 0.3 0.3 0.3 1.0 > ???? 0.4 0.4 0.4 1.0 > ???? 0.5 0.5 0.5 1.0 > ?? > ?? > Warm regardsSk Mahasin Alam > > M. Pharm (JU) > PhD student > School of Chemical and Biomedical Engineering > Nanyang Technological University > Sinpapore > > > _______________________________________________ > 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" ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From sd.wang000 at gmail.com Mon Apr 5 11:53:15 2010 From: sd.wang000 at gmail.com (shudong wang) Date: Mon, 5 Apr 2010 17:53:15 +0800 Subject: [Pw_forum] About wannier center Message-ID: dear all: When I use the disentangle.x code in WanT package, the output file is : ====================================================================== = = = *** WanT *** Wannier Transport Code = = (www.wannier-transport.org) = = Ultra Soft Pseudopotential Implem. = = = ====================================================================== Program v. 2.1.0 starts ... Date 5Apr2010 at 17:39:53 Parallel run, # proc: 8 BUILT : Thu Apr 1 20:30:37 2010 HOST : x86_64-unknown-linux-gnu ARCH : amd64 CC : icc CPP : cpp F90 : mpif90 F77 : ifort DFLAGS : -D__INTEL -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA BLAS LIBS : -L/usr/local/intel/cmkl/8.0/lib/em64t -lmkl_em64t -lguide -lpthread LAPACK LIBS : -lmkl_lapack FFT LIBS : MASS LIBS : DFT-data fmt automaticaly detected: qexml ----------------------------------------------------------------------- ---------------------------------------------------------------------- it stop here have not any other information,and my input file for disentangle is : &CONTROL prefix = '33' postfix = '_WanT' work_dir = '/home/sdwang/33/' verbosity = 'medium' wantdata_fmt = 'binary' / &SUBSPACE dimwann = 50 win_max = 10.0 win_min=-15.0 maxiter_dis = 3000 / &LOCALIZATION a_condmin = 20.0 maxiter0_wan = 1000, alpha0_wan = 0.5 maxiter1_wan = 3000, alpha1_wan = 0.5 ncg = 9 / WANNIER_CENTERS {crystal} 1gauss 0.000000000 0.087520000 0.101960000 0 0 0.5 1.0 1gauss 0.101960000 0.087520000 0.000000000 0 0 0.5 1.0 1gauss 0.203920000 0.087520000 0.101960000 0 0 0.5 1.0 1gauss 0.101960000 0.175030000 0.101960000 0 0 0.5 1.0 1gauss 0.000000000 0.000000000 0.203920000 0 0 0.5 1.0 1gauss 0.000000000 0.087520000 0.305870000 0 0 0.5 1.0 1gauss 0.101960000 0.000000000 0.305870000 0 0 0.5 1.0 1gauss 0.101960000 0.087520000 0.203920000 0 0 0.5 1.0 1gauss 0.203920000 0.000000000 0.203920000 0 0 0.5 1.0 1gauss 0.203920000 0.087520000 0.305870000 0 0 0.5 1.0 1gauss 0.305870000 0.087520000 0.203920000 0 0 0.5 1.0 1gauss 0.000000000 0.175030000 0.203920000 0 0 0.5 1.0 1gauss 0.101960000 0.175030000 0.305870000 0 0 0.5 1.0 1gauss 0.101960000 0.262550000 0.203920000 0 0 0.5 1.0 1gauss 0.000000000 0.820710000 0.101960000 0 0 0.5 1.0 1gauss 0.101960000 0.733200000 0.101960000 0 0 0.5 1.0 1gauss 0.101960000 0.820710000 0.000000000 0 0 0.5 1.0 1gauss 0.203920000 0.820710000 0.101960000 0 0 0.5 1.0 1gauss 0.101960000 0.645680000 0.203920000 0 0 0.5 1.0 1gauss 0.000000000 0.820710000 0.305870000 0 0 0.5 1.0 1gauss 0.101960000 0.733200000 0.305870000 0 0 0.5 1.0 1gauss 0.101960000 0.820710000 0.203910000 0 0 0.5 1.0 1gauss 0.203920000 0.733200000 0.203910000 0 0 0.5 1.0 1gauss 0.203920000 0.820710000 0.305870000 0 0 0.5 1.0 1gauss 0.305870000 0.820710000 0.203910000 0 0 0.5 1.0 1gauss 0.101960000 0.909530000 0.101960000 0 0 0.5 1.0 1gauss 0.000000000 0.909530000 0.203920000 0 0 0.5 1.0 1gauss 0.203920000 0.909530000 0.203920000 0 0 0.5 1.0 1gauss 0.104560000 0.561910000 0.203540000 0 0 0.5 1.0 1gauss 0.104560000 0.346290000 0.203540000 0 0 0.5 1.0 1gauss 0.104560000 0.510410000 0.203540000 0 0 0.5 1.0 1gauss 0.104560000 0.454100000 0.203540000 0 0 0.5 1.0 1gauss 0.104560000 0.397790000 0.203540000 0 0 0.5 1.0 the atoms are 28 Au,2N,3C What is my problem? Thanks in advance! S.D. Wang Southeast University in Nanjing China. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100405/08cc9d24/attachment.htm From duchl06 at 163.com Mon Apr 5 14:29:22 2010 From: duchl06 at 163.com (duchl06) Date: Mon, 5 Apr 2010 20:29:22 +0800 (CST) Subject: [Pw_forum] how to determine the value of U in a lda+U calculation Message-ID: <1510843.2f57.127cdf2542f.Coremail.duchl06@163.com> dear pw users i want to do a calculation of V chain absorb on a plane with DFT+U, but i donot know how to determine the value of U. i found a PPT on the pwscf's media site, they said the value of U could be decised by a linear response approach. but i really donot understand that like the input file resp_mat.in &input_mat ntyp = 1 # number of types of atoms na(1) = 2 # number of atoms per type if we have different type atoms with different number, how we set these? nalfa = 5 # number of perturbations (alpha) filepos = 'pos_sc1' # file containing the atomic positions and the vectors of the unit cell back = 'neutral' # to add a neutralizing ?background?. see PRB 71 35105 (2005) what does this mean filednda = 'file_sc1' # file containing the names of the files dn*dat n1 = 4 n2 = 4 # number of unit cells in each direction to construct the supercell for n3 = 4 # extrapolation (in this case a 4x4x4 supercell of the SC one) &end and they get the U is about 2.4ev for the iron, and they use 4.3ev for the FeO calculation, we always need a linear response approach to get the U for every system or just a U for a certain pseudopotential (i mean if we get a U for V bulk, then if i could use this value for another system with V atom, like V2O3 etc.) any suggestions or comment would be OK. thanks Du xiaguanying university -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100405/e47eadbf/attachment-0001.htm From matteo at umn.edu Mon Apr 5 15:48:59 2010 From: matteo at umn.edu (Matteo Cococcioni) Date: Mon, 05 Apr 2010 08:48:59 -0500 Subject: [Pw_forum] how to determine the value of U in a lda+U calculation In-Reply-To: <1510843.2f57.127cdf2542f.Coremail.duchl06@163.com> References: <1510843.2f57.127cdf2542f.Coremail.duchl06@163.com> Message-ID: <4BB9EA4B.3040108@umn.edu> Dear Du, the input you found below is to extract the U values from a series of scf calculations. You can give a look (besides the reference cited below) to the tutorials you find in this webpage: http://www.quantum-espresso.org/wiki/index.php/QESB09. Unfrtunately the value of U is generally not portable and changes depending on the invironment of the atom in the specific crystal you are considering. the one you cite is a good example: Fe in bulk Fe and in FeO. So in principles we need to recompute it each time. hope this helps. Matteo duchl06 wrote: > dear pw users > i want to do a calculation of V chain absorb on a plane with DFT+U, > but i donot know how to determine the value of U. > i found a PPT on the pwscf's media site, they said the value of U > could be decised by a linear response approach. > but i really donot understand that like the input file resp_mat.in > > &input_mat > ntyp = 1 # number of types of atoms > na(1) = 2 # number of atoms per type > if we have different type atoms with different number, how we set these? > > nalfa = 5 # number of perturbations (alpha) > filepos = 'pos_sc1' # file containing the atomic positions and the > vectors of the unit cell > back = 'neutral' # to add a neutralizing ??background??. see PRB 71 > 35105 (2005) > what does this mean > filednda = 'file_sc1' # file containing the names of the files dn*dat > n1 = 4 > n2 = 4 # number of unit cells in each direction to construct the > supercell for > n3 = 4 # extrapolation (in this case a 4x4x4 supercell of the SC one) > &end > > and they get the U is about 2.4ev for the iron, and they use 4.3ev for > the FeO calculation, > we always need a linear response approach to get the U for every system > or just a U for a certain pseudopotential (i mean if we get a U for V > bulk, then if i could use this value for another system with V atom, > like V2O3 etc.) > any suggestions or comment would be OK. > thanks > > Du > xiaguanying university > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From physolde at yahoo.fr Mon Apr 5 16:42:58 2010 From: physolde at yahoo.fr (kada galami) Date: Mon, 5 Apr 2010 14:42:58 +0000 (GMT) Subject: [Pw_forum] cp.x not existent or not executable Message-ID: <457702.61328.qm@web26607.mail.ukl.yahoo.com> dear users when i try to run the example 20, i found this : /espresso-4.0.5/examples/example20> ./run_example usr/local/espresso-4.0.5/examples/example20 : starting This example shows how to use cp.x to perform molecular dynamicssimulation of NH3. ??executables directory: /usr/local/espresso-4.0.5/bin??pseudo directory: ? ? ?/usr/local/espresso-4.0.5/pseudo??temporary directory: ??/usr/local/tmp??checking that needed directories and files exist...ERROR:?/usr/local/espresso-4.0.5/bin/cp.x not existent or not executableAborting what is the probleme -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100405/7b4dd966/attachment.htm From baroni at sissa.it Mon Apr 5 16:49:52 2010 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 5 Apr 2010 16:49:52 +0200 Subject: [Pw_forum] Hessian of charge density In-Reply-To: References: Message-ID: <74AE8405-11B6-471C-B3FE-B59ECD09AF0D@sissa.it> Dear Mr. X: would you please explain to us what is the "Hessian of charge density", and take the time of signing your posts? Many thanks - SB On Apr 5, 2010, at 10:00 AM, shekoufe khosravi wrote: > Dear All > I would like to know if PWscf will calculate Hessian of charge density? > > Thanks > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100405/f90165ba/attachment.htm From baroni at sissa.it Mon Apr 5 16:54:44 2010 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 5 Apr 2010 16:54:44 +0200 Subject: [Pw_forum] cp.x not existent or not executable In-Reply-To: <457702.61328.qm@web26607.mail.ukl.yahoo.com> References: <457702.61328.qm@web26607.mail.ukl.yahoo.com> Message-ID: <8CD84ED2-F3BE-4CB5-A951-DE7765B192A8@sissa.it> most probably, you forgot to compile cp.x, or else the executable is misplaced, or it does not have execute permissions ... try "ls -l /usr/local/espresso-4.0.5/bin" and verify that cp.x is there, with execute permissions (a number of "x" should appear on the left of the filename) SB On Apr 5, 2010, at 4:42 PM, kada galami wrote: > dear users > > when i try to run the example 20, i found this : > > /espresso-4.0.5/examples/example20> ./run_example > > usr/local/espresso-4.0.5/examples/example20 : starting > > This example shows how to use cp.x to perform molecular dynamics > simulation of NH3. > > executables directory: /usr/local/espresso-4.0.5/bin > pseudo directory: /usr/local/espresso-4.0.5/pseudo > temporary directory: /usr/local/tmp > checking that needed directories and files exist... > ERROR: /usr/local/espresso-4.0.5/bin/cp.x not existent or not executable > Aborting > > what is the probleme > > > > _______________________________________________ > 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/20100405/89c95520/attachment-0001.htm From duchl06 at 163.com Mon Apr 5 17:09:08 2010 From: duchl06 at 163.com (duchl06) Date: Mon, 5 Apr 2010 23:09:08 +0800 (CST) Subject: [Pw_forum] how to determine the value of U in a lda+U calculation In-Reply-To: <4BB9EA4B.3040108@umn.edu> References: <4BB9EA4B.3040108@umn.edu> <1510843.2f57.127cdf2542f.Coremail.duchl06@163.com> Message-ID: <10e9897.3d3e.127ce8498d8.Coremail.duchl06@163.com> Dear Matteo thanks for your quick reply, so another question as i mentioned in the former email. if we have different atoms with different number, how we set the value of the keyword below >> ntyp = 1 # number of types of atoms >> na(1) = 2 # number of atoms per type or is it only relate to the atom with a nonzero U value. best regards! du ?2010-04-05 21:48:59?"Matteo Cococcioni" ??? > >Dear Du, > >the input you found below is to extract the U values from a series of >scf calculations. >You can give a look (besides the reference cited below) to the tutorials >you find in this webpage: >http://www.quantum-espresso.org/wiki/index.php/QESB09. >Unfrtunately the value of U is generally not portable and changes >depending on the invironment of the atom in the >specific crystal you are considering. the one you cite is a good >example: Fe in bulk Fe and in FeO. >So in principles we need to recompute it each time. > >hope this helps. > >Matteo > > >duchl06 wrote: >> dear pw users >> i want to do a calculation of V chain absorb on a plane with DFT+U, >> but i donot know how to determine the value of U. >> i found a PPT on the pwscf's media site, they said the value of U >> could be decised by a linear response approach. >> but i really donot understand that like the input file resp_mat.in >> >> &input_mat >> ntyp = 1 # number of types of atoms >> na(1) = 2 # number of atoms per type >> if we have different type atoms with different number, how we set these? >> >> nalfa = 5 # number of perturbations (alpha) >> filepos = 'pos_sc1' # file containing the atomic positions and the >> vectors of the unit cell >> back = 'neutral' # to add a neutralizing ?background?. see PRB 71 >> 35105 (2005) >> what does this mean >> filednda = 'file_sc1' # file containing the names of the files dn*dat >> n1 = 4 >> n2 = 4 # number of unit cells in each direction to construct the >> supercell for >> n3 = 4 # extrapolation (in this case a 4x4x4 supercell of the SC one) >> &end >> >> and they get the U is about 2.4ev for the iron, and they use 4.3ev for >> the FeO calculation, >> we always need a linear response approach to get the U for every system >> or just a U for a certain pseudopotential (i mean if we get a U for V >> bulk, then if i could use this value for another system with V atom, >> like V2O3 etc.) >> any suggestions or comment would be OK. >> thanks >> >> Du >> xiaguanying university >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100405/53ae7787/attachment.htm From physolde at yahoo.fr Mon Apr 5 17:26:50 2010 From: physolde at yahoo.fr (kada galami) Date: Mon, 5 Apr 2010 15:26:50 +0000 (GMT) Subject: [Pw_forum] cp.x not existent or not executable Message-ID: <101393.77658.qm@web26608.mail.ukl.yahoo.com> hiwhen i try make alla found this: :~/espresso-4.0.5> make alltest -d bin || mkdir binif test -d iotk ; then \ ( cd iotk ; if test "make" = "" ; then make ?TLDEPS= lib+util ; \ else make ?TLDEPS= lib+util ; fi ) ; fimake[1]: entrant dans le r?pertoire ??/usr/local/espresso-4.0.5/iotk ?cd src ; make lib+utilmake[2]: entrant dans le r?pertoire ? /usr/local/espresso-4.0.5/iotk/src ?( cd ../../bin ; ln -sf ../iotk/src/iotk_print_kinds.x . )( cd ../../bin ; ln -sf ../iotk/src/iotk.x . )( cd ../../bin ; ln -sf ../iotk/tools/iotk . )make[2]: quittant le r?pertoire ? /usr/local/espresso-4.0.5/iotk/src ?make[1]: quittant le r?pertoire ? /usr/local/espresso-4.0.5/iotk ?( cd Modules ; if test "make" = "" ; then make ?TLDEPS= all ; \ else make ?TLDEPS= all ; fi )make[1]: entrant dans le r?pertoire ? /usr/locale/espresso-4.0.5/Modules ?make[1]: Rien ? faire pour ? all ?.make[1]: quittant le r?pertoire ? /usr/local/espresso-4.0.5/Modules ?( cd clib ; if test "make" = "" ; then make ?TLDEPS= all ; \ else make ?TLDEPS= all ; fi )make[1]: entrant dans le r?pertoire ? /usr/local/espresso-4.0.5/clib ?cc -O3 -D__GFORTRAN -D__FFTW -D__USE_INTERNAL_FFTW -I../include ? -c memstat.cIn file included from /usr/include/stdio.h:909,?? ? ? ? ? ? ? ? from /usr/include/malloc.h:26,?? ? ? ? ? ? ? ? from memstat.c:20:/usr/include/bits/stdio.h: In function ?memstat_?:/usr/include/bits/stdio.h:38: error: nested function ?vprintf? declared ?extern?/usr/include/bits/stdio.h:37: error: static declaration of ?vprintf? follows non-static declaration/usr/include/bits/stdio.h:46: error: nested function ?getchar? declared ?extern?/usr/include/bits/stdio.h:45: error: static declaration of ?getchar? follows non-static declaration/usr/include/stdio.h:522: note: previous declaration of ?getchar? was here/usr/include/bits/stdio.h:55: error: nested function ?fgetc_unlocked? declared ?extern?/usr/include/bits/stdio.h:54: error: static declaration of ?fgetc_unlocked? follows non-static declaration/usr/include/stdio.h:545: note: previous declaration of ?fgetc_unlocked? was here/usr/include/bits/stdio.h:65: error: nested function ?getc_unlocked? declared ?extern?/usr/include/bits/stdio.h:64: error: static declaration of ?getc_unlocked? follows non-static declaration/usr/include/stdio.h:534: note: previous declaration of ?getc_unlocked? was here/usr/include/bits/stdio.h:72: error: nested function ?getchar_unlocked? declared ?extern?/usr/include/bits/stdio.h:71: error: static declaration of ?getchar_unlocked? follows non-static declaration/usr/include/stdio.h:535: note: previous declaration of ?getchar_unlocked? was here/usr/include/bits/stdio.h:81: error: nested function ?putchar? declared ?extern?/usr/include/bits/stdio.h:80: error: static declaration of ?putchar? follows non-static declaration/usr/include/bits/stdio.h:90: error: nested function ?fputc_unlocked? declared ?extern?/usr/include/bits/stdio.h:89: error: static declaration of ?fputc_unlocked? follows non-static declaration/usr/include/bits/stdio.h:100: error: nested function ?putc_unlocked? declared ?extern?/usr/include/bits/stdio.h:99: error: static declaration of ?putc_unlocked? follows non-static declaration/usr/include/bits/stdio.h:107: error: nested function ?putchar_unlocked? declared ?extern?/usr/include/bits/stdio.h:106: error: static declaration of ?putchar_unlocked? follows non-static declaration/usr/include/bits/stdio.h:127: error: nested function ?feof_unlocked? declared ?extern?/usr/include/bits/stdio.h:126: error: static declaration of ?feof_unlocked? follows non-static declaration/usr/include/stdio.h:811: note: previous declaration of ?feof_unlocked? was here/usr/include/bits/stdio.h:134: error: nested function ?ferror_unlocked? declared ?extern?/usr/include/bits/stdio.h:133: error: static declaration of ?ferror_unlocked? follows non-static declaration/usr/include/stdio.h:812: note: previous declaration of ?ferror_unlocked? was heremake[1]: *** [memstat.o] Erreur 1make[1]: quittant le r?pertoire ? /usr/local/espresso-4.0.5/clib ?make: *** [libs] Erreur 2 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100405/754c359b/attachment.htm From ferretti at mit.edu Mon Apr 5 19:14:05 2010 From: ferretti at mit.edu (Andrea Ferretti) Date: Mon, 5 Apr 2010 18:14:05 +0100 (BST) Subject: [Pw_forum] About wannier center In-Reply-To: References: Message-ID: Hi, tha code seems to be stuck. You are running on 8 cpus, but the version of the want you are running (2.1.0) is parallel only in the transport part. Try to run serial. BTW: the WanT-2.3.0 (which is fully parallel) is going to be released soon. Andrea > ? > When I use the disentangle.x code in WanT package, the output file is : > > ? ====================================================================== > ????????????? =??????????????????????????????????????????? = > ????????????? =???? *** WanT *** Wannier Transport Code??? = > ????????????? =??????? (www.wannier-transport.org)???????? = > ????????????? =????? Ultra Soft Pseudopotential Implem.??? = > ????????????? =??????????????????????????????????????????? = > ? ====================================================================== > > ? Program ? v. 2.1.0? starts ... > ? Date? 5Apr2010 at 17:39:53 > ???? Parallel run, # proc:??? 8 > ????????? BUILT :??? Thu Apr? 1 20:30:37 2010 > ?????????? HOST :??? x86_64-unknown-linux-gnu > ?????????? ARCH :??? amd64 > ???????????? CC :??? icc > ??????????? CPP :??? cpp > ??????????? F90 :??? mpif90 > ??????????? F77 :??? ifort > ???????? DFLAGS :??? -D__INTEL -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA > ????? BLAS LIBS :??? -L/usr/local/intel/cmkl/8.0/lib/em64t -lmkl_em64t -lguide -lpthread > ??? LAPACK LIBS :??? -lmkl_lapack > ?????? FFT LIBS :??? > ????? MASS LIBS :??? > > ? DFT-data fmt automaticaly detected: qexml > ----------------------------------------------------------------------- > ----------------------------------------------------------------------? > ? > it stop here have not any other information,and my input file for disentangle is : > ? > > &CONTROL > ?? prefix = '33' > ?? postfix = '_WanT' > ?? work_dir = '/home/sdwang/33/' > ?? verbosity = 'medium' > ?? wantdata_fmt = 'binary' > / > &SUBSPACE > ?? dimwann = 50???? > ?? win_max = 10.0 > ?? win_min=-15.0 > ?? maxiter_dis = 3000 > / > &LOCALIZATION > ?? a_condmin = 20.0 > ?? maxiter0_wan = 1000, > ?? alpha0_wan = 0.5 > ?? maxiter1_wan = 3000, > ?? alpha1_wan = 0.5 > ?? ncg = 9????? > / > WANNIER_CENTERS {crystal} > 1gauss????? 0.000000000??? 0.087520000??? 0.101960000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.101960000??? 0.087520000??? 0.000000000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.203920000??? 0.087520000??? 0.101960000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.101960000??? 0.175030000??? 0.101960000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.000000000??? 0.000000000??? 0.203920000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.000000000??? 0.087520000??? 0.305870000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.101960000??? 0.000000000??? 0.305870000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.101960000??? 0.087520000??? 0.203920000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.203920000??? 0.000000000??? 0.203920000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.203920000??? 0.087520000??? 0.305870000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.305870000??? 0.087520000??? 0.203920000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.000000000??? 0.175030000??? 0.203920000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.101960000??? 0.175030000??? 0.305870000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.101960000??? 0.262550000??? 0.203920000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.000000000??? 0.820710000??? 0.101960000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.101960000??? 0.733200000??? 0.101960000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.101960000??? 0.820710000??? 0.000000000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.203920000??? 0.820710000??? 0.101960000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.101960000??? 0.645680000??? 0.203920000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.000000000??? 0.820710000??? 0.305870000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.101960000??? 0.733200000??? 0.305870000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.101960000??? 0.820710000??? 0.203910000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.203920000??? 0.733200000??? 0.203910000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.203920000??? 0.820710000??? 0.305870000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.305870000??? 0.820710000??? 0.203910000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.101960000??? 0.909530000??? 0.101960000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.000000000??? 0.909530000??? 0.203920000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.203920000??? 0.909530000??? 0.203920000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.104560000??? 0.561910000??? 0.203540000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.104560000??? 0.346290000??? 0.203540000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.104560000??? 0.510410000??? 0.203540000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.104560000??? 0.454100000??? 0.203540000??? 0? 0?? 0.5? 1.0 > 1gauss????? 0.104560000??? 0.397790000??? 0.203540000??? 0? 0?? 0.5? 1.0 > the atoms are 28 Au,2N,3C > ? > What is my problem? > ? > Thanks in advance! > ? > S.D. Wang? > ? > Southeast University in Nanjing China. > > -- 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 elie.moujaes at hotmail.co.uk Mon Apr 5 20:10:16 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Mon, 5 Apr 2010 19:10:16 +0100 Subject: [Pw_forum] ph.x taking a lot of time to run! Message-ID: Dear PWSCF users, Hope you all had a happy Easter. I am running the ph.x code for graphene(and Thankfully no errors are encountered). it is just that it IS taking a really long time to produce the dynamical matrices on the q grid I specified which is: nq1= 2, nq2=2, nq3=2 (a total of 8 points).. It is taking like an our to produce the .dyn files for every q point. I do not think it should require that much time. Is there something I might be missing? Thank you Elie Moujaes University of Nottingham NG7 2RD UK _________________________________________________________________ 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/20100405/cc13d510/attachment.htm From matteo at umn.edu Mon Apr 5 23:52:51 2010 From: matteo at umn.edu (Matteo Cococcioni) Date: Mon, 05 Apr 2010 16:52:51 -0500 Subject: [Pw_forum] how to determine the value of U in a lda+U calculation In-Reply-To: <10e9897.3d3e.127ce8498d8.Coremail.duchl06@163.com> References: <4BB9EA4B.3040108@umn.edu> <1510843.2f57.127cdf2542f.Coremail.duchl06@163.com> <10e9897.3d3e.127ce8498d8.Coremail.duchl06@163.com> Message-ID: <4BBA5BB3.5080108@umn.edu> Only atoms for which you want to compute U should be listed. same thing in the file of positions. Matteo duchl06 wrote: > Dear Matteo > thanks for your quick reply, so another question as i mentioned in the > former email. > if we have different atoms with different number, how we set the value > of the keyword below > >> ntyp = 1 # number of types of atoms > >> na(1) = 2 # number of atoms per type > or is it only relate to the atom with a nonzero U value. > best regards! > du > > ??2010-04-05 21:48:59??"Matteo Cococcioni" ?????? > > > >Dear Du, > > > >the input you found below is to extract the U values from a series of > >scf calculations. > >You can give a look (besides the reference cited below) to the tutorials > >you find in this webpage: > >http://www.quantum-espresso.org/wiki/index.php/QESB09. > >Unfrtunately the value of U is generally not portable and changes > >depending on the invironment of the atom in the > >specific crystal you are considering. the one you cite is a good > >example: Fe in bulk Fe and in FeO. > >So in principles we need to recompute it each time. > > > >hope this helps. > > > >Matteo > > > > > >duchl06 wrote: > >> dear pw users > >> i want to do a calculation of V chain absorb on a plane with DFT+U, > >> but i donot know how to determine the value of U. > >> i found a PPT on the pwscf's media site, they said the value of U > >> could be decised by a linear response approach. > >> but i really donot understand that like the input file resp_mat.in > >> > >> &input_mat > >> ntyp = 1 # number of types of atoms > >> na(1) = 2 # number of atoms per type > >> if we have different type atoms with different number, how we set these? > >> > >> nalfa = 5 # number of perturbations (alpha) > >> filepos = 'pos_sc1' # file containing the atomic positions and the > >> vectors of the unit cell > >> back = 'neutral' # to add a neutralizing ??background??. see PRB 71 > >> 35105 (2005) > >> what does this mean > >> filednda = 'file_sc1' # file containing the names of the files dn*dat > >> n1 = 4 > >> n2 = 4 # number of unit cells in each direction to construct the > >> supercell for > >> n3 = 4 # extrapolation (in this case a 4x4x4 supercell of the SC one) > >> &end > >> > >> and they get the U is about 2.4ev for the iron, and they use 4.3ev for > >> the FeO calculation, > >> we always need a linear response approach to get the U for every system > >> or just a U for a certain pseudopotential (i mean if we get a U for V > >> bulk, then if i could use this value for another system with V atom, > >> like V2O3 etc.) > >> any suggestions or comment would be OK. > >> thanks > >> > >> Du > >> xiaguanying 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 > -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 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 ouuing at gmail.com Tue Apr 6 06:45:17 2010 From: ouuing at gmail.com (Hanyu) Date: Tue, 6 Apr 2010 12:45:17 +0800 Subject: [Pw_forum] ph.x taking a lot of time to run! In-Reply-To: References: Message-ID: Generally, the dynamics calculation will cost a long time. so you need much better claculation source. I think 8 points perhaps are not enough. nq1=4,nq2=4,na3=4, perhaps more is better. best regards. On Tue, Apr 6, 2010 at 2:10 AM, Elie Moujaes wrote: > Dear PWSCF users, > > Hope you all had a happy Easter. I am running the ph.x code for graphene(and > Thankfully no errors are encountered). it is just that it IS taking a really > long time to produce the dynamical matrices on the q grid I specified which > is: > > nq1= 2, nq2=2, nq3=2 (a total of 8 points).. It is taking like an our to > produce the .dyn files for every?q?point. I do not think it should require > that much time. Is there something I might be missing? > > > Thank you > > Elie Moujaes > University of Nottingham > NG7 2RD > UK > > ________________________________ > 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 > > -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=**=-=**=-=**=-=*=-=*=-=*=-=*=-=*=- Hanyu Liu(???), MS. State key Laboratory of Superhard Materials, Jilin University, China Email: liuhanyu08 at mails.jlu.edu.cn ouuing at gmail.com From duchl06 at 163.com Tue Apr 6 06:49:59 2010 From: duchl06 at 163.com (duchl06) Date: Tue, 6 Apr 2010 12:49:59 +0800 (CST) Subject: [Pw_forum] how to determine the value of U in a lda+U calculation In-Reply-To: <4BBA5BB3.5080108@umn.edu> References: <4BBA5BB3.5080108@umn.edu> <4BB9EA4B.3040108@umn.edu> <1510843.2f57.127cdf2542f.Coremail.duchl06@163.com> <10e9897.3d3e.127ce8498d8.Coremail.duchl06@163.com> Message-ID: <4dc17c.7d5b.127d1741c1c.Coremail.duchl06@163.com> could you tell me what does the first three rows mean i saw they are all 10.d0 0.d0 0.d0 0.d0 10.d0 0.d0 0.d0 0.d0 10.d0 in your example. and the others must be in internal crystal coordinates? Thanks! Du ?2010-04-06 05:52:51?"Matteo Cococcioni" ??? > >Only atoms for which you want to compute U should be listed. >same thing in the file of positions. > >Matteo > >duchl06 wrote: >> Dear Matteo >> thanks for your quick reply, so another question as i mentioned in the >> former email. >> if we have different atoms with different number, how we set the value >> of the keyword below >> >> ntyp = 1 # number of types of atoms >> >> na(1) = 2 # number of atoms per type >> or is it only relate to the atom with a nonzero U value. >> best regards! >> du >> >> ?2010-04-05 21:48:59?"Matteo Cococcioni" ??? >> > >> >Dear Du, >> > >> >the input you found below is to extract the U values from a series of >> >scf calculations. >> >You can give a look (besides the reference cited below) to the tutorials >> >you find in this webpage: >> >http://www.quantum-espresso.org/wiki/index.php/QESB09. >> >Unfrtunately the value of U is generally not portable and changes >> >depending on the invironment of the atom in the >> >specific crystal you are considering. the one you cite is a good >> >example: Fe in bulk Fe and in FeO. >> >So in principles we need to recompute it each time. >> > >> >hope this helps. >> > >> >Matteo >> > >> > >> >duchl06 wrote: >> >> dear pw users >> >> i want to do a calculation of V chain absorb on a plane with DFT+U, >> >> but i donot know how to determine the value of U. >> >> i found a PPT on the pwscf's media site, they said the value of U >> >> could be decised by a linear response approach. >> >> but i really donot understand that like the input file resp_mat.in >> >> >> >> &input_mat >> >> ntyp = 1 # number of types of atoms >> >> na(1) = 2 # number of atoms per type >> >> if we have different type atoms with different number, how we set these? >> >> >> >> nalfa = 5 # number of perturbations (alpha) >> >> filepos = 'pos_sc1' # file containing the atomic positions and the >> >> vectors of the unit cell >> >> back = 'neutral' # to add a neutralizing ?background?. see PRB 71 >> >> 35105 (2005) >> >> what does this mean >> >> filednda = 'file_sc1' # file containing the names of the files dn*dat >> >> n1 = 4 >> >> n2 = 4 # number of unit cells in each direction to construct the >> >> supercell for >> >> n3 = 4 # extrapolation (in this case a 4x4x4 supercell of the SC one) >> >> &end >> >> >> >> and they get the U is about 2.4ev for the iron, and they use 4.3ev for >> >> the FeO calculation, >> >> we always need a linear response approach to get the U for every system >> >> or just a U for a certain pseudopotential (i mean if we get a U for V >> >> bulk, then if i could use this value for another system with V atom, >> >> like V2O3 etc.) >> >> any suggestions or comment would be OK. >> >> thanks >> >> >> >> Du >> >> xiaguanying 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 >> > > >-- >%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >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 >%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100406/a98a6e20/attachment.htm From lfhuang at theory.issp.ac.cn Tue Apr 6 13:24:26 2010 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Tue, 06 Apr 2010 19:24:26 +0800 Subject: [Pw_forum] =?utf-8?q?ph=2Ex_taking_a__lot_of_time_to_run!?= Message-ID: <20100406112426.17086.qmail@ms.hfcas.ac.cn> Dear Elie Moujaes: The time cost for the calculation of dynamical matrix in your case is reasonable. Because DFPT needs to solve the perturbation KS equation iteratively for each reciprocal vector. In addition, why did not you specify the value of nq3 to be 1? Graphene is a monolayer of carbon atoms, nq3=1 is enough. To obtain decent phonon dispersion, maybe denser q grid be needed. And to calculate some thermodynamic functions accurately, maybe q grid denser than 9*9*1 is needed. May these be somewhat helpful. Best Wishes! Yours Sincerely L. F. Huang > From: Elie Moujaes > Subject: [Pw_forum] ph.x taking a lot of time to run! > To: > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > > Dear PWSCF users, > > > > Hope you all had a happy Easter. I am running the ph.x code for graphene(and Thankfully no errors are encountered). it is just that it IS taking a really long time to produce the dynamical matrices on the q grid I specified which is: > > > > nq1= 2, nq2=2, nq3=2 (a total of 8 points).. It is taking like an our to produce the .dyn files for every q point. I do not think it should require that much time. Is there something I might be missing? > > Thank you > > Elie Moujaes > > University of Nottingham > > NG7 2RD > > UK ------ ====================================================================== 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/20100406/709eee83/attachment.htm From shekoufe.khosravi at gmail.com Tue Apr 6 14:35:33 2010 From: shekoufe.khosravi at gmail.com (shekoufe khosravi) Date: Tue, 6 Apr 2010 17:05:33 +0430 Subject: [Pw_forum] Hessian of the charge density Message-ID: Dear Prof. Baroni Excuse me if I was hasty. I mean the Hessian matrix(second-order partial derivatives) of the charge density (as a scalar field) in the unit cell (at FFT points). Thanks for your attention (Mrs.) shekoufe Khosravi PhD student Isfahan University of Technology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100406/1642eb23/attachment.htm From elie.moujaes at hotmail.co.uk Tue Apr 6 15:04:16 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Tue, 6 Apr 2010 14:04:16 +0100 Subject: [Pw_forum] ph.x taking a lot of time to run! In-Reply-To: References: , Message-ID: Thanks very much for the reply. It kind of made me relax. I knew that 8 points are not enough but I just wanted to check if I do get results or not after of course running q2r.x and matdyn.x later. Thank you again Elie > Date: Tue, 6 Apr 2010 12:45:17 +0800 > From: ouuing at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] ph.x taking a lot of time to run! > > Generally, the dynamics calculation will cost a long time. so you need > much better claculation source. I think 8 points perhaps are not > enough. nq1=4,nq2=4,na3=4, perhaps more is better. > > best regards. > > On Tue, Apr 6, 2010 at 2:10 AM, Elie Moujaes wrote: > > Dear PWSCF users, > > > > Hope you all had a happy Easter. I am running the ph.x code for graphene(and > > Thankfully no errors are encountered). it is just that it IS taking a really > > long time to produce the dynamical matrices on the q grid I specified which > > is: > > > > nq1= 2, nq2=2, nq3=2 (a total of 8 points).. It is taking like an our to > > produce the .dyn files for every q point. I do not think it should require > > that much time. Is there something I might be missing? > > > > > > Thank you > > > > Elie Moujaes > > University of Nottingham > > NG7 2RD > > UK > > > > ________________________________ > > 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 > > > > > > > > -- > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=**=-=**=-=**=-=*=-=*=-=*=-=*=-=*=- > Hanyu Liu(???), > MS. > State key Laboratory of Superhard Materials, Jilin University, China > Email: liuhanyu08 at mails.jlu.edu.cn ouuing at gmail.com > _______________________________________________ > 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/20100406/9eb9701e/attachment.htm From baroni at sissa.it Tue Apr 6 16:43:53 2010 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 6 Apr 2010 16:43:53 +0200 Subject: [Pw_forum] Hessian of the charge density In-Reply-To: References: Message-ID: <0626F402-080E-4D62-9D6E-3916A174508A@sissa.it> Not that I know, but it should be simple to implement numerically, through FFT. SB On Apr 6, 2010, at 2:35 PM, shekoufe khosravi wrote: > Dear Prof. Baroni > Excuse me if I was hasty. > I mean the Hessian matrix(second-order partial derivatives) of the charge density > (as a scalar field) in the unit cell (at FFT points). > > Thanks for your attention > > (Mrs.) shekoufe Khosravi > PhD student > Isfahan University of Technology > _______________________________________________ > 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/20100406/521d88b0/attachment.htm From elie.moujaes at hotmail.co.uk Tue Apr 6 16:48:05 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Tue, 6 Apr 2010 15:48:05 +0100 Subject: [Pw_forum] Traceback not available error! Message-ID: Dear all, I am sorry to disturb you each now and then. I am at the last step of calculating the phonon dispresion spectrum for graphene mainly applying matdyn.x whne I got ther following error: At line 285 of file matdyn.f90 (Unit 5) Traceback not available, compile with -ftrace=frame or -ftrace=full Fortran runtime error: End of File Well, yes it is clear that something is wrong at line 285 of the fortran file code matdyn but i am not much of a fortran expert so even looking at the line 285 might not help much. My question is did anyone else got this specific error or is it just a problem with my compiler (which maybe is most certainly the case). Any suggestions of a solution or where I can find one.. P.S: I looked to several resources but I could not find any general solution to tackle the problem. Thanks Elie Moujaes University of Nottingham NG7 2RD Nottingham UK _________________________________________________________________ http://clk.atdmt.com/UKM/go/197222280/direct/01/ Do you have a story that started on Hotmail? Tell us now -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100406/68abd13f/attachment-0001.htm From giannozz at democritos.it Tue Apr 6 17:21:26 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 6 Apr 2010 17:21:26 +0200 Subject: [Pw_forum] HSE In-Reply-To: References: <00f601cad25e$2f0c1440$2376c082@desdemona> <4BB5DB18.7030403@unito.it> <4BB63400.1000102@mit.edu> Message-ID: On Apr 2, 2010, at 20:38 , William Parker wrote: > Do you know what tests have been done on the HSE implementation? there are a few examples in examples/EXX_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 giannozz at democritos.it Tue Apr 6 17:32:56 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 6 Apr 2010 17:32:56 +0200 Subject: [Pw_forum] cp.x not existent or not executable In-Reply-To: <101393.77658.qm@web26608.mail.ukl.yahoo.com> References: <101393.77658.qm@web26608.mail.ukl.yahoo.com> Message-ID: On Apr 5, 2010, at 17:26 , kada galami wrote: > > /usr/include/bits/stdio.h: In function ?memstat_?: > /usr/include/bits/stdio.h:38: error: nested function ?vprintf? > declared ?extern? > /usr/include/bits/stdio.h:37: error: static declaration of > ?vprintf? follows non-static declaration > ... fixed in more recent versions (later than oct. 2009): http://qe-forge.org/cgi-bin/cvstrac/q-e/chngview?cn=6952 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 Apr 6 17:54:49 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 6 Apr 2010 17:54:49 +0200 Subject: [Pw_forum] Traceback not available error! In-Reply-To: References: Message-ID: <065DA9A2-2B10-4495-AF15-E870B8EB7B92@democritos.it> On Apr 6, 2010, at 16:48 , Elie Moujaes wrote: > Fortran runtime error: End of File this is the error: you are trying to read past the end of file. --- 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 Apr 6 19:16:27 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 6 Apr 2010 19:16:27 +0200 Subject: [Pw_forum] iflag=1, output_format=0 In-Reply-To: <299665.57237.qm@web111014.mail.gq1.yahoo.com> References: <299665.57237.qm@web111014.mail.gq1.yahoo.com> Message-ID: <72BA1EF6-017A-40C6-8DF3-6FCADB04EA5D@democritos.it> On Apr 2, 2010, at 19:34 , Chad Junkermeier wrote: > I include a listing of the file that I am using to run pp.x as well > as the first 20 odd > lines from the output file that was produced by pp.x. what you call the "output file" is in fact an intermediate data file that you do not need except in some special cases. The name of the "true" output file name - the one with data to be plotted - should be provided in variable "fileout" in the second namelist. 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 Apr 6 19:19:17 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 6 Apr 2010 19:19:17 +0200 Subject: [Pw_forum] Band Structures Calculations In-Reply-To: <324257.91595.qm@web24106.mail.ird.yahoo.com> References: <324257.91595.qm@web24106.mail.ird.yahoo.com> Message-ID: <8B26F1CC-D036-44B2-B1C7-3EC6617F23F7@democritos.it> On Apr 5, 2010, at 8:48 , MAHASIN ALAM wrote: > when I submit this job I got the error message ?can?t read the k- > points? if the code says so, it must be right. Either the format of the K_POINTS card is incorrect, or the preceding card, ATOMIC_SPECIES, does not contain all the needed atoms 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 Apr 6 19:21:12 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 6 Apr 2010 19:21:12 +0200 Subject: [Pw_forum] Plane waves parallelization In-Reply-To: References: Message-ID: <820A6900-334B-4B48-B937-C355A10A1EFC@democritos.it> On Apr 4, 2010, at 15:18 , Dimpy Sharma wrote: > From the user guide , I was reading the parallelism in quantum > espresso, I could not follow "pools" and plane wave > parallelization, and how to do the K_Point sampling in mpi > parallelization for my system. > what is your question here? I cannot follow what you are asking for. 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 Apr 6 22:02:01 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 6 Apr 2010 22:02:01 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 34, Issue 5 In-Reply-To: References: Message-ID: <123AB98F-AAE7-48D4-A264-273B9942786B@democritos.it> On Apr 2, 2010, at 22:44 , jia chen wrote: > Since QE4.0, empty states feature in CP code didn't work anymore. it works in a different way: you can use the charge density produced using CP to start a conventional non-selfconsistent calculation 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 Wed Apr 7 04:31:05 2010 From: sd.wang000 at gmail.com (shudong wang) Date: Wed, 7 Apr 2010 10:31:05 +0800 Subject: [Pw_forum] disentangle.x Message-ID: Dear developers. I used disentangle.x code in WanT package do some calculation, but it stops here ====================================================================== = Starting Iteration loop = ====================================================================== Initial trial subspace: projected localized orbitals p0_13395: p4_error: interrupt SIGx: 6 what is the problem? I run it serial. Thanks in advance! S.D.Wang Southeast University in Nanjing,China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100407/db6f5801/attachment.htm From mohnish.iitk at gmail.com Wed Apr 7 05:11:18 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Wed, 7 Apr 2010 08:41:18 +0530 Subject: [Pw_forum] how to plot phonon phonon modes after calculation Message-ID: Dear users , I have followed the example 06 to calculate phonon modes for ZnO. I have gone through the paper by Dr. Baroni on DFPT to get insight of the calculations, but after getting all the dynamical matrix files seperately for all the the q-points I am unable to plot the phonon modes. Can anybody please tell me how to integrate all those informations and plot it.(Is there any plotting module for phonon modes especially?) Thanks alot in advance, Sincerely, MOHNISH -- Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR 09235721300 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100407/3853bec6/attachment.htm From nnlinh at sissa.it Wed Apr 7 09:51:26 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Wed, 07 Apr 2010 09:51:26 +0200 Subject: [Pw_forum] how to plot phonon phonon modes after calculation In-Reply-To: References: Message-ID: <4BBC397E.5020407@sissa.it> mohnish pandey wrote: > Dear users , > I have followed the example 06 to calculate phonon > modes for ZnO. I have gone through the paper by Dr. Baroni on DFPT to > get insight of the calculations, but after getting all the dynamical > matrix files seperately for all the the q-points I am unable to plot > the phonon modes. Can anybody please tell me how to integrate all > those informations and plot it.(Is there any plotting module for > phonon modes especially?) Normally, we can draw by Gnuplot or by Xmgrace with some tricks, such as by defining the finite q_points (Gamma, X ,... ) then presenting the intermediate q_points for 1 dimension (Ox), then you can draw 3 modes for each q_point (Oy1, Oy2, Oy3) Anyway, if you want you some think more formal, you should find on "Google.com" Linh > > Thanks alot in advance, > Sincerely, > MOHNISH > > -- > Mohnish Pandey > Y6927262,4th Year dual degree student, > Department of Chemical Engineering, > IIT KANPUR > 09235721300 > ------------------------------------------------------------------------ > > _______________________________________________ > 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 eyvaz_isaev at yahoo.com Wed Apr 7 12:14:07 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 7 Apr 2010 03:14:07 -0700 (PDT) Subject: [Pw_forum] how to plot phonon phonon modes after calculation Message-ID: <242074.83787.qm@web65709.mail.ac4.yahoo.com> Dear Mohnish and QE users, --- On Wed, 4/7/10, mohnish pandey wrote: Is there any plotting module for phonon modes especially? YES, it is. Theres is plot_phonon_dispersions utility released approximately a month ago via QE forum. Please follow the next link http://www.democritos.it/pipermail/pw_forum/2010-March/016176.html Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From ferretti at mit.edu Wed Apr 7 12:16:57 2010 From: ferretti at mit.edu (Andrea Ferretti) Date: Wed, 7 Apr 2010 11:16:57 +0100 (BST) Subject: [Pw_forum] disentangle.x Message-ID: Hi, please note this forum is about quantum-espresso, so please make sure that what you post here is relevant to the forum. (otherwise post it directly to me, eg when specifically related to WanT compilation etc etc) Anyway: it is actually difficult to guess what's going on here without any information about the hardware, configuration (make.sys file) and the input file you are using. close to "starting iteration loop" (assuming this means anything), nothing weird is done, the big part of the memory is already deallocated, and just some mild use of linear algebra routines is done.. some ideas: - try to compile the code using the internal blas and lapack libraries and check if the error is still there. In particular, I remember I got some run-time problems when linking some optimized version of the lapack lib (eg acml). The problems where related to calls to ZGESVD (singular value decompositon). In that case, linking acml as blas, but the internal version for the lapack lib solved the problem. - are you sure the code is compiled serially ?? (the p4_error below, when googled, leads to a lot of issues related to MPI) even if this should be perfectly legal, messing around with libraries may make things harder to understand Andrea > ? > I used disentangle.x code in WanT package do some calculation, but it stops > here > ? > ? ====================================================================== > ? =? Starting Iteration loop?????????????????????????????????????????? = > ? ====================================================================== > ? Initial trial subspace: projected localized orbitals > p0_13395:? p4_error: interrupt SIGx: 6 > ? > what is the problem? > ? > I run it serial. > Thanks in advance! > ? > S.D.Wang > ? > Southeast University in Nanjing,China > -- 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 skgupta.physics at gmail.com Wed Apr 7 12:20:23 2010 From: skgupta.physics at gmail.com (Sanjeev Kumar Gupta) Date: Wed, 7 Apr 2010 12:20:23 +0200 Subject: [Pw_forum] how to plot phonon phonon modes after calculation In-Reply-To: <242074.83787.qm@web65709.mail.ac4.yahoo.com> References: <242074.83787.qm@web65709.mail.ac4.yahoo.com> Message-ID: Please find in attachment. Really Prof. Eyvaz had done nice work, Please thank to Prof. Eyvaz. Best Sanjeev On 7 April 2010 12:14, Eyvaz Isaev wrote: > Dear Mohnish and QE users, > > --- On Wed, 4/7/10, mohnish pandey wrote: > Is there any plotting module for phonon modes especially? > > YES, it is. Theres is plot_phonon_dispersions utility released > approximately a month ago via QE forum. > > Please follow the next link > http://www.democritos.it/pipermail/pw_forum/2010-March/016176.html > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > 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 > -- S. K. Gupta PhD Student, Dept. of Physics, Bhavnagar University. Bhavnagar, 364 022., Gujarat, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100407/68924db6/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: Plot_phonon_dispersions.tar.bz2 Type: application/x-bzip2 Size: 30151 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100407/68924db6/attachment-0001.bin From mohnish.iitk at gmail.com Wed Apr 7 13:57:06 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Wed, 7 Apr 2010 17:27:06 +0530 Subject: [Pw_forum] how to plot phonon phonon modes after calculation In-Reply-To: <242074.83787.qm@web65709.mail.ac4.yahoo.com> References: <242074.83787.qm@web65709.mail.ac4.yahoo.com> Message-ID: Thank you so much Dr. Eyvaz for your help Regards, MOHNISH On Wed, Apr 7, 2010 at 3:44 PM, Eyvaz Isaev wrote: > Dear Mohnish and QE users, > > --- On Wed, 4/7/10, mohnish pandey wrote: > Is there any plotting module for phonon modes especially? > > YES, it is. Theres is plot_phonon_dispersions utility released > approximately a month ago via QE forum. > > Please follow the next link > http://www.democritos.it/pipermail/pw_forum/2010-March/016176.html > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > 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 > -- Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR 09235721300 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100407/6de6a452/attachment.htm From elie.moujaes at hotmail.co.uk Wed Apr 7 16:36:54 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Wed, 7 Apr 2010 15:36:54 +0100 Subject: [Pw_forum] Traceback not available error! In-Reply-To: <065DA9A2-2B10-4495-AF15-E870B8EB7B92@democritos.it> References: , <065DA9A2-2B10-4495-AF15-E870B8EB7B92@democritos.it> Message-ID: Thank you. Problem was sorted. Regards Elie > From: giannozz at democritos.it > Date: Tue, 6 Apr 2010 17:54:49 +0200 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] Traceback not available error! > > > On Apr 6, 2010, at 16:48 , Elie Moujaes wrote: > > > Fortran runtime error: End of File > > this is the error: you are trying to read past the > end of file. > --- > 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 _________________________________________________________________ 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/20100407/bf5c6294/attachment.htm From eariel99 at gmail.com Wed Apr 7 20:20:59 2010 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Wed, 7 Apr 2010 15:20:59 -0300 Subject: [Pw_forum] generating pseudopotential for Ti Message-ID: Hello, I am trying to make an alternative pseudopotential for Ti, and I have the following wanrings and errors, that I have not been able to avoid changing parameters --------------------- Generating NC pseudopotential --------------------- Generating local potential from pseudized AE potential: Matching radius rcloc = 1.1000 Local pseudo, rcloc= 1.088 Estimated cut-off energy= 20.72 Ry Wfc 3S rcut= 1.088 Estimated cut-off energy= 40.68 Ry Using 4 Bessel functions for this wfc, rho(0) = 0.010 This function has 0 nodes for 0 < r < 1.088 Wfc 3P rcut= 1.088 Estimated cut-off energy= 149.03 Ry This function has 0 nodes for 0 < r < 1.088 Wfc 3D rcut= 1.088 Estimated cut-off energy= 194.63 Ry This function has 0 nodes for 0 < r < 1.088 Wfc 4S rcut= 3.031 Estimated cut-off energy= 4.89 Ry Using 4 Bessel functions for this wfc, rho(0) = 0.010 This function has 0 nodes for 0 < r < 3.031 ............ WARNING! Expected number of nodes: 0= 1- 0- 1, number of nodes found: 2. Setting wfc to zero for this iteration. (This warning will only be printed once per wavefunction) WARNING! Expected number of nodes: 1= 2- 0- 1, number of nodes found: 2. Setting wfc to zero for this iteration. (This warning will only be printed once per wavefunction) ............. ------------------------ End of All-electron run ------------------------ WARNING! Expected number of nodes: 0= 2- 1- 1, number of nodes found: 1. Setting wfc to zero for this iteration. (This warning will only be printed once per wavefunction) WARNING! Expected number of nodes: 0= 3- 2- 1, number of nodes found: 1. Setting wfc to zero for this iteration. (This warning will only be printed once per wavefunction) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from run_pseudo : error # 1 Errors in PS-KS equation %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% The input is the following &input title='Ti ultrasofts pp', zed=22.0, iswitch=3, rel=1, dft='PBE' config='[Ne] 3s2 3p6 3d2 4s2 4p0', ! nld=2, / &inputp pseudotype=2, upf_v1_format=.true., file_pseudopw='Ti-pbe-rrkjus.UPF', lloc=-1, rcloc=1.10, nlcc=.false., rho0=0.01, author='EMP', / 4 3S 1 0 2.00 0.00 1.10 1.10 3P 2 1 6.00 0.00 1.10 1.10 3D 3 2 2.00 0.00 1.10 1.10 4S 2 0 2.00 0.00 3.00 3.00 &TEST nconf=1, ecutmin=20.0, ecutmax=100.0, configts(1)='[Ne] 3s2 3p6 3d2 4s2 4p0', In fact, I want to make an ultrasoft, this input is for norm conserving hust ti isolate the source of the error. thanks -- Eduardo Menendez Departamento de Fisica Facultad de Ciencias Universidad de Chile Phone: (56)(2)9787439 URL: http://fisica.ciencias.uchile.cl/~emenendez -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100407/9d82326f/attachment.htm From hsuhan at cems.umn.edu Wed Apr 7 23:37:47 2010 From: hsuhan at cems.umn.edu (Han Hsu) Date: Wed, 7 Apr 2010 16:37:47 -0500 (CDT) Subject: [Pw_forum] bfgs : error # 1 Message-ID: <43956.129.186.252.240.1270676267.squirrel@webmail.cems.umn.edu> Dear PWscf users/developers, I was performing an atomic-relaxation (calculation= 'relax') on a spin-polarized system. It went well at the first 19 atomic steps. Then it stopped with an error message "from bfgs : error # 1". The last few lines of the output file is shown below. I have successfully performed bfgs on the same system at different pressures (volumes). The difference in the input file is only celldm(1). For other volumes, this error message was not showing and the atomic relaxations were completed. I would appreciate any hint. I am using espresso-4.1 compiled with ompi with mkl library. Hope this information would be helpful. --------------------------------------------------------- number of scf cycles = 17 number of bfgs steps = 8 energy old = -1350.7860624581 Ry energy new = -1350.7860605130 Ry CASE: energy _new > energy _old new trust radius = 0.0000499345 bohr trust_radius < trust_radius_min resetting bfgs history %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from bfgs : error # 1 bfgs history already reset at previous step %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ------------------------------------------------------------------ ******************************************************* Han Hsu, Ph.D. Postdoctoral Associate Department of Chemical Engineering & Materials Science University of Minnesota http://www.cems.umn.edu/~hsuhan ******************************************************* From duchl06 at 163.com Thu Apr 8 04:25:59 2010 From: duchl06 at 163.com (duchl06) Date: Thu, 8 Apr 2010 10:25:59 +0800 (CST) Subject: [Pw_forum] could pwscf do a Geometry Optimization calculation in LDA+U Scheme Message-ID: <39b807d1.11793.127db3cfc61.Coremail.duchl06@163.com> dear pw users could any one tell me which method is right? 1)relax in GGA scheme, then use the Geometry do a GGA+U scf calculation or 2) relax in GGA+U scheme, got the Geometry, then a GGA+U scf calculation I ask this question because i did a Geometry Optimization GGA scheme and GGA+U (other parameters are almost the same), and i got a very pwdifferent Geometry with the two method, why does this happen? best regards! Du xiaguanying university -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100408/1cb8b282/attachment.htm From padmaja_patnaik at yahoo.co.uk Thu Apr 8 06:16:32 2010 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Thu, 8 Apr 2010 04:16:32 +0000 (GMT) Subject: [Pw_forum] Error while running nscf Message-ID: <538508.22545.qm@web26103.mail.ukl.yahoo.com> Dear All While running for density of states of a super cell the scf calculation is complete but the nscf calculations stops with the following message. ? running DOS calculation for Ni...*** glibc detected *** /home/padmaja/espresso-4.0.5/bin/pw.x: corrupted double-linked list: 0x0000000002dd1580 *** ======= Backtrace: ========= /lib/libc.so.6[0x7f56e251a322] /lib/libc.so.6(cfree+0x8c)[0x7f56e251dc1c] /home/padmaja/espresso-4.0.5/bin/pw.x[0xef7d28] /home/padmaja/espresso-4.0.5/bin/pw.x[0x5c1d2d] /home/padmaja/espresso-4.0.5/bin/pw.x[0x5cea6d] /home/padmaja/espresso-4.0.5/bin/pw.x[0x5cdb92] /home/padmaja/espresso-4.0.5/bin/pw.x[0x53ba9b] /home/padmaja/espresso-4.0.5/bin/pw.x[0x50b4a1] /home/padmaja/espresso-4.0.5/bin/pw.x(realloc+0x473)[0x40fdcb] /home/padmaja/espresso-4.0.5/bin/pw.x(realloc+0x264)[0x40fbbc] /lib/libc.so.6(__libc_start_main+0xf4)[0x7f56e24c41c4] /home/padmaja/espresso-4.0.5/bin/pw.x(realloc+0x191)[0x40fae9] ======= Memory map: ======== 00400000-01140000 r-xp 00000000 08:07 10773669?????????????????????????? /home/padmaja/espresso-4.0.5/PW/pw.x 01340000-0138b000 rwxp 00d40000 08:07 10773669?????????????????????????? /home/padmaja/espresso-4.0.5/PW/pw.x 0138b000-087e7000 rwxp 0138b000 00:00 0????????????????????????????????? [heap] 403be000-403bf000 ---p 403be000 00:00 0 403bf000-407bf000 rwxp 403bf000 00:00 0 407bf000-407c0000 ---p 407bf000 00:00 0 407c0000-40bc0000 rwxp 407c0000 00:00 0 40dc5000-40dc6000 ---p 40dc5000 00:00 0 40dc6000-40dd6000 rwxp 40dc6000 00:00 0 40dd6000-40dd7000 ---p 40dd6000 00:00 0 40dd7000-411d7000 rwxp 40dd7000 00:00 0 7f56a0000000-7f56a0ea0000 rwxp 7f56a0000000 00:00 0 7f56a0ea0000-7f56a4000000 ---p 7f56a0ea0000 00:00 0 7f56a8000000-7f56a965d000 rwxp 7f56a8000000 00:00 0 7f56a965d000-7f56ac000000 ---p 7f56a965d000 00:00 0 7f56c73d4000-7f56e2094000 rwxp 7f56c73d4000 00:00 0 7f56e2094000-7f56e2096000 r-xp 00000000 08:05 229575???????????????????? /lib/libdl-2.7.so 7f56e2096000-7f56e2296000 ---p 00002000 08:05 229575???????????????????? /lib/libdl-2.7.so 7f56e2296000-7f56e2298000 rwxp 00002000 08:05 229575???????????????????? /lib/libdl-2.7.so 7f56e2298000-7f56e22a5000 r-xp 00000000 08:05 229439???????????????????? /lib/libgcc_s.so.1 7f56e22a5000-7f56e24a5000 ---p 0000d000 08:05 229439???????????????????? /lib/libgcc_s.so.1 7f56e24a5000-7f56e24a6000 rwxp 0000d000 08:05 229439???????????????????? /lib/libgcc_s.so.1 7f56e24a6000-7f56e25fe000 r-xp 00000000 08:05 229572???????????????????? /lib/libc-2.7.so 7f56e25fe000-7f56e27fe000 ---p 00158000 08:05 229572???????????????????? /lib/libc-2.7.so 7f56e27fe000-7f56e2801000 r-xp 00158000 08:05 229572???????????????????? /lib/libc-2.7.so 7f56e2801000-7f56e2803000 rwxp 0015b000 08:05 229572???????????????????? /lib/libc-2.7.so 7f56e2803000-7f56e2808000 rwxp 7f56e2803000 00:00 0 7f56e2808000-7f56e281e000 r-xp 00000000 08:05 229586???????????????????? /lib/libpthread-2.7.so 7f56e281e000-7f56e2a1e000 ---p 00016000 08:05 229586???????????????????? /lib/libpthread-2.7.so 7f56e2a1e000-7f56e2a20000 rwxp 00016000 08:05 229586???????????????????? /lib/libpthread-2.7.so 7f56e2a20000-7f56e2a24000 rwxp 7f56e2a20000 00:00 0 7f56e2a24000-7f56e2aa4000 r-xp 00000000 08:05 229576???????????????????? /lib/libm-2.7.so 7f56e2aa4000-7f56e2ca3000 ---p 00080000 08:05 229576???????????????????? /lib/libm-2.7.so 7f56e2ca3000-7f56e2ca5000 rwxp 0007f000 08:05 229576???????????????????? /lib/libm-2.7.so 7f56e2ca5000-7f56e2cc2000 r-xp 00000000 08:05 229569???????????????????? /lib/ld-2.7.so 7f56e2ea7000-7f56e2eab000 rwxp 7f56e2ea7000 00:00 0 7f56e2ebf000-7f56e2ec2000 rwxp 7f56e2ebf000 00:00 0 7f56e2ec2000-7f56e2ec4000 rwxp 0001d000 08:05 229569???????????????????? /lib/ld-2.7.so 7fff3ce67000-7fff3ceac000 rwxp 7ffffffba000 00:00 0????????????????????? [stack] 7fff3cffe000-7fff3d000000 r-xp 7fff3cffe000 00:00 0????????????????????? [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0????????????????? [vsyscall] Aborted ?done Whats the problem, please suggest. 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/20100408/b21df04a/attachment-0001.htm From hx35 at cornell.edu Thu Apr 8 06:42:28 2010 From: hx35 at cornell.edu (Huolin Xin) Date: Thu, 8 Apr 2010 00:42:28 -0400 Subject: [Pw_forum] How to get unfilled orbitals from ld1.x? Message-ID: Dear all, Is it possible to let ld1.x calculate a few more unfilled orbitals and output them without hacking the code? Below is an input for a Si all electron calculation. &input title = 'all-electron calculation for Si atom' zed = 14.0 iswitch = 1 dft = 'LDA' prefix = 'Si-output-neutral' config = '[Ne] 3s2 3p2' latt = 1 rmax = 950 dx = 0.005 / Huolin From giannozz at democritos.it Thu Apr 8 08:42:12 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 8 Apr 2010 08:42:12 +0200 Subject: [Pw_forum] How to get unfilled orbitals from ld1.x? In-Reply-To: References: Message-ID: On Apr 8, 2010, at 6:42 , Huolin Xin wrote: > Is it possible to let ld1.x calculate a few more unfilled orbitals and > output them without hacking the code? > config = '[Ne] 3s2 3p2' use "config = '[Ne] 3s2 3p2 3d0 4p0 4s0 ...' . Note that unfilled orbitals are often unbound (for instance, 3d0 is unbound in Si) 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 Apr 8 08:43:56 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 8 Apr 2010 08:43:56 +0200 Subject: [Pw_forum] Error while running nscf In-Reply-To: <538508.22545.qm@web26103.mail.ukl.yahoo.com> References: <538508.22545.qm@web26103.mail.ukl.yahoo.com> Message-ID: <76B2F42B-27E5-41E1-B5D3-B258946DED0F@democritos.it> On Apr 8, 2010, at 6:16 , Padmaja Patnaik wrote: > While running for density of states of a super cell the scf > calculation > is complete but the nscf calculations stops with the following > message. > > running DOS calculation for Ni...*** glibc detected *** /home/ > padmaja/espresso-4.0.5/bin/pw.x: corrupted double-linked list: > 0x0000000002dd1580 *** is this one of the examples provided with the code? then your compiler is buggy. 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 degironc at sissa.it Thu Apr 8 08:55:06 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 08 Apr 2010 08:55:06 +0200 Subject: [Pw_forum] could pwscf do a Geometry Optimization calculation in LDA+U Scheme In-Reply-To: <39b807d1.11793.127db3cfc61.Coremail.duchl06@163.com> References: <39b807d1.11793.127db3cfc61.Coremail.duchl06@163.com> Message-ID: <4BBD7DCA.5040208@sissa.it> Dear Du, duchl06 wrote: > dear pw users > could any one tell me which method is right? > 1)relax in GGA scheme, then use the Geometry do a GGA+U scf calculation > or > 2) relax in GGA+U scheme, got the Geometry, then a GGA+U scf calculation > The consistent way of proceeding is 2). consider however that structural minimization may suffer from the problem of having many local minima and typically one is interested in the lowest energy one. the two different results may therefore represent two different minima in your system landscape, reached because the history of the relaxation has been different for some random reasons. To check on that you might start a new GGA+U relaxation from the converged GGA geometry and see whether the system evolves toward the geometry you have found in the GGA+U relaxation, suggesting a real difference between the minima of the two methods, or remains in the neighborhood of the GGA minimum, suggesting that both minima are actually local ones for GGA+U. The ultimate decision on which minimum is better would then be taken on the basis of their energy .. paying attention to compare apples with apples, that is comparing GGA+U OR GGA energies among them and NEVER a GGA energy with a GGA+U one ... hope this helps, stefano > > I ask this question because i did a Geometry Optimization GGA scheme and GGA+U (other parameters are almost the same), and i got a very pwdifferent Geometry with the two method, why does this happen? > > best regards! > > Du > xiaguanying university > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at democritos.it Thu Apr 8 09:20:05 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 08 Apr 2010 09:20:05 +0200 Subject: [Pw_forum] bfgs : error # 1 In-Reply-To: <43956.129.186.252.240.1270676267.squirrel@webmail.cems.umn.edu> References: <43956.129.186.252.240.1270676267.squirrel@webmail.cems.umn.edu> Message-ID: <4BBD83A5.20106@democritos.it> Han Hsu wrote: > energy old = -1350.7860624581 Ry > energy new = -1350.7860605130 Ry sometimes, very close to convergence, numerical noise on forces confuses the bfgs algorithm. You are at almost perfect convergence anyway. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From science35 at gmail.com Thu Apr 8 09:29:12 2010 From: science35 at gmail.com (patriot pershing) Date: Thu, 8 Apr 2010 09:29:12 +0200 Subject: [Pw_forum] error message in pw.x running Message-ID: dear anyone: i have installed espresso4.1 version under fedora core2 succefuly and i have check tests files without any problem but when i would excute my input file using pw.x the next error message appear: From degironc at sissa.it Thu Apr 8 09:53:57 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 08 Apr 2010 09:53:57 +0200 Subject: [Pw_forum] error message in pw.x running In-Reply-To: References: Message-ID: <4BBD8B95.4020509@sissa.it> the error says that there is some unrecognized or mis-typed variable or value in the control namelist are you sure that no control-character slipped in your input file ? without seeing your input file it's difficult to tell more. stefano patriot pershing wrote: > dear anyone: > i have installed espresso4.1 version under fedora core2 succefuly and i have > check tests files without any problem but when i would excute my input file > using pw.x the next error message appear: > From read_namelists : error # 17 > reading namelist control > > we add, that the input file was prepared by pwgui4.1 separetly and excute in > terminal using: > /home/espresso/bin/pw.x file.pw.out > and the same file was excute and running succefuly by espresso4.1.2 under > cygwin > best regards > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at democritos.it Thu Apr 8 11:45:24 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 08 Apr 2010 11:45:24 +0200 Subject: [Pw_forum] generating pseudopotential for Ti In-Reply-To: References: Message-ID: <4BBDA5B4.5060203@democritos.it> Eduardo Ariel Menendez Proupin wrote: > I am trying to make an alternative pseudopotential for Ti not an easy task. The problem is that the current way of generating US-PP does not allow to use the most obvious choice of pseudization energies: those corresponding to bound states. You have to choose the lowest state (3s in this case) and one unbound state at an energy not too far away from E(3s). The pseudization radii shouldn't differ too much either, I would say. Some time ago I had a student who was supposed to produce a PAW Ti. Not sure what he managed to produce, though. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From naylin.nll at gmail.com Thu Apr 8 18:06:12 2010 From: naylin.nll at gmail.com (Nay Lin) Date: Fri, 9 Apr 2010 00:06:12 +0800 Subject: [Pw_forum] Copper pseudopotential Message-ID: Dear all I am testing Cu.pbe-d-rrkjus.UPF for equilibrium lattice constant. with the k grid of 30x30x30 0 0 0 (automatic), Ecut 30, rhocut 120, occupation='smearing', smearing='mp', degauss=0.02 i am getting the lattice constant around 6.93 where experimental value is 6.82 bohr. Is this accuracy enough for supercell copper surface calculations? Please help Thanks Lin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100409/1c2b873b/attachment.htm From sks.jnc at gmail.com Thu Apr 8 19:23:39 2010 From: sks.jnc at gmail.com (S. K. S.) Date: Thu, 8 Apr 2010 22:53:39 +0530 Subject: [Pw_forum] flow-chart in PWSCF In-Reply-To: <4BACC081.8030504@sissa.it> References: <4BA0E2B4.7020401@democritos.it> <4BACC081.8030504@sissa.it> Message-ID: Dear All, First, let me thank Ngoc Linh Nguyen for his helpful reply. A part of his reply is as follows: In general, the scf processes are similar, but in QE a density convergence check is applied to accelerate convergence in scf caculation, i.e. see in PRB 38, 12807 (1988). This reference is indeed helpful. I have still one confusion: what, in fact, QE starts with as an initial density n(r) at the 0th iteration, i.e. what is n_0(r) ???? Is that simply constant or r dependent or both r and R dependent???? Then, n0(r, R) = what ????? Here, r and R are electronic and nuclei co-ordinates, respectively. Thanking you and with my best regards, Saha SK R&D assistant JNCASR Bangalore -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100408/218f0cb4/attachment.htm From naromero at gmail.com Thu Apr 8 21:37:15 2010 From: naromero at gmail.com (Nichols A. Romero) Date: Thu, 8 Apr 2010 14:37:15 -0500 Subject: [Pw_forum] flow-chart in PWSCF In-Reply-To: References: <4BA0E2B4.7020401@democritos.it> <4BACC081.8030504@sissa.it> Message-ID: I believe the initial density is constructed from the atomic densities. On Thu, Apr 8, 2010 at 12:23 PM, S. K. S. wrote: > > ?Dear All, > > ?First, let me thank Ngoc Linh Nguyen for his helpful reply. > ?A part of his reply is as follows: > In general, the scf processes are similar, but in QE a density > convergence check is applied to accelerate convergence in scf > caculation, i.e. see in PRB 38, ?12807 (1988). > > This reference is indeed helpful. > I have still one confusion: what, in fact, QE starts with? as > an initial density n(r)? at the 0th iteration, i.e. what is n_0(r) ???? > Is that simply constant or r dependent or both r and R dependent???? > Then,? n0(r, R) = what ????? > Here, r and R are electronic and nuclei co-ordinates, respectively. > > Thanking you and with my best regards, > ?Saha SK > ?R&D assistant > ?JNCASR > ?Bangalore > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Nichols A. Romero, Ph.D. Argonne Leadership Computing Facility Argonne, IL 60490 (630) 252-3441 (O) (630) 470-0462 (C) From giannozz at democritos.it Thu Apr 8 21:58:38 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 8 Apr 2010 21:58:38 +0200 Subject: [Pw_forum] flow-chart in PWSCF In-Reply-To: References: <4BA0E2B4.7020401@democritos.it> <4BACC081.8030504@sissa.it> Message-ID: <6F2225ED-C5B5-4FF8-B8BA-D796F4B6C205@democritos.it> On Apr 8, 2010, at 19:23 , S. K. S. wrote: > what, in fact, QE starts with as an initial density n(r) at the > 0th iteration, > i.e. what is n_0(r) ???? the answer is printed at the beginning of the scf calculation: Initial potential from superposition of free atoms 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 ouuing at gmail.com Fri Apr 9 04:41:35 2010 From: ouuing at gmail.com (Hanyu) Date: Fri, 9 Apr 2010 10:41:35 +0800 Subject: [Pw_forum] Copper pseudopotential In-Reply-To: References: Message-ID: dear Lin in fact, it need to test. perhaps, your k grid is enough. I think the value of the lattic constant is enough close to the experimental value. best regards. Hanyu On Fri, Apr 9, 2010 at 12:06 AM, Nay Lin wrote: > Dear all > > I am testing Cu.pbe-d-rrkjus.UPF for equilibrium lattice constant. > > with the k grid of 30x30x30 0 0 0 (automatic), Ecut 30, rhocut 120, > occupation='smearing', smearing='mp', degauss=0.02 > > i am getting the lattice constant around 6.93 where experimental value is > 6.82 bohr. > > Is this accuracy enough for supercell copper surface calculations? > > Please help > Thanks > Lin > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=**=-=**=-=**=-=*=-=*=-=*=-=*=-=*=- Hanyu Liu(???), MS. State key Laboratory of Superhard Materials, Jilin University, China Email: liuhanyu08 at mails.jlu.edu.cn ouuing at gmail.com From sivaramakrishnaj at gmail.com Fri Apr 9 06:38:50 2010 From: sivaramakrishnaj at gmail.com (siva rama krishna) Date: Fri, 9 Apr 2010 10:08:50 +0530 Subject: [Pw_forum] Constraint on centre of mass of a molecule Message-ID: Dear Users, Could anyone please let me know how to write a new constraint on the centre of mass of a molecule. I want to allow an approaching molecule onto a substrate to move along XY plane while its Z-component of centre of mass is arrested. One can arrest the Z-component of an atom by setting ' if_pos(nat)(3)=0 ' for the atom with index number 'nat'. Similarly, can we arrest the Z-component of the centre of mass of a molecule ? Thanks and Regards, Sivaramakrishna J Member of Technical Staff Computational Research Labs, Pune. India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100409/f066ad38/attachment.htm From hsuhan at cems.umn.edu Fri Apr 9 08:08:38 2010 From: hsuhan at cems.umn.edu (Han Hsu) Date: Fri, 9 Apr 2010 01:08:38 -0500 (CDT) Subject: [Pw_forum] bfgs : error # 1 In-Reply-To: <4BBD83A5.20106@democritos.it> References: <43956.129.186.252.240.1270676267.squirrel@webmail.cems.umn.edu> <4BBD83A5.20106@democritos.it> Message-ID: <2433.71.195.59.176.1270793318.squirrel@webmail.cems.umn.edu> Thank you very much. Han On Thu, April 8, 2010 2:20 am, Paolo Giannozzi wrote: > Han Hsu wrote: > >> energy old = -1350.7860624581 Ry >> energy new = -1350.7860605130 Ry > > sometimes, very close to convergence, numerical noise > on forces confuses the bfgs algorithm. You are at almost > perfect convergence anyway. > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From nnlinh at sissa.it Fri Apr 9 10:04:12 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Fri, 09 Apr 2010 10:04:12 +0200 Subject: [Pw_forum] Constraint on centre of mass of a molecule In-Reply-To: References: Message-ID: <4BBEDF7C.30805@sissa.it> siva rama krishna wrote: > Dear Users, > > Could anyone please let me know how to write a new constraint on the > centre of mass of a molecule. > I want to allow an approaching molecule onto a substrate to move along > XY plane while its Z-component of centre of mass is arrested. > One can arrest the Z-component of an atom by setting ' > if_pos(nat)(3)=0 ' for the atom with index number 'nat'. > Similarly, can we arrest the Z-component of the centre of mass of a > molecule ? Yes, you can. By put "if_pos(nat)(3) = 0" for all atoms in the molecule the Z-component of the center of mass of the molecule will be unchanged Linh > > Thanks and Regards, > > Sivaramakrishna J > Member of Technical Staff > Computational Research Labs, Pune. > India > ------------------------------------------------------------------------ > > _______________________________________________ > 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 paulatto at sissa.it Fri Apr 9 10:43:13 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 09 Apr 2010 10:43:13 +0200 Subject: [Pw_forum] Constraint on centre of mass of a molecule In-Reply-To: References: Message-ID: On Fri, 09 Apr 2010 06:38:50 +0200, siva rama krishna wrote: > Similarly, can we arrest the Z-component of the centre of mass of a > molecule > ? No, you cannot. pw.x does not have the concept of molecule at all. Furthermore, if you put the molecule on teh substrate and it just breaks, than the centre of mass would pretty much loose any meaning. This does not mean that it is impossible to implement, actually it should be quite easy; have a look at Module/constraints_module.f90. 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 giannozz at democritos.it Fri Apr 9 10:47:56 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 09 Apr 2010 10:47:56 +0200 Subject: [Pw_forum] Copper pseudopotential In-Reply-To: References: Message-ID: <4BBEE9BC.5080905@democritos.it> Nay Lin wrote: > i am getting the lattice constant around 6.93 where experimental value > is 6.82 bohr. 1.5% overestimate; quite typical for gradient-corrected functionals P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From nnlinh at sissa.it Fri Apr 9 11:33:00 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Fri, 09 Apr 2010 11:33:00 +0200 Subject: [Pw_forum] Constraint on centre of mass of a molecule In-Reply-To: References: Message-ID: <4BBEF44C.1030505@sissa.it> Lorenzo Paulatto wrote: > On Fri, 09 Apr 2010 06:38:50 +0200, siva rama krishna > wrote: > >> Similarly, can we arrest the Z-component of the centre of mass of a >> molecule >> ? >> > Furthermore, if you put the molecule on teh substrate and it just breaks, > than the centre of mass would pretty much loose any meaning. Sometime, the molecules is physisorbed, only weak binding, to the substrate, and the molecule's dissociation has not happened yet. In that case, the diffusion of molecules will be presented, and it can be seen as a picture that the molecules are moving parallelly to the plane's substrate to find out the activate sites. And of course, the center of mass is not changed at all belong to Oz component. Anyway, in the realistic case the mechanism of molecules is more complicated. regards, Linh -- ----------------------------------------------------- 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 paulatto at sissa.it Fri Apr 9 11:40:03 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 09 Apr 2010 11:40:03 +0200 Subject: [Pw_forum] Constraint on centre of mass of a molecule In-Reply-To: <4BBEF44C.1030505@sissa.it> References: <4BBEF44C.1030505@sissa.it> Message-ID: On Fri, 09 Apr 2010 11:33:00 +0200, Ngoc Linh Nguyen wrote: > In that > case, the diffusion of molecules will be presented, and it can be seen > as a picture that the molecules are moving parallelly to the plane's > substrate to find out the activate sites. And of course, the center of > mass is not changed at all belong to Oz component. yes, but the molecule cannot rotate if you fix the z components of all its atoms: it is a condition sufficient to fix the center of mass, but not necessary. cheers -- 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 elbuesta at icqmail.com Fri Apr 9 13:49:46 2010 From: elbuesta at icqmail.com (elbuesta at icqmail.com) Date: Fri, 09 Apr 2010 07:49:46 -0400 Subject: [Pw_forum] Copper pseudopotential In-Reply-To: References: Message-ID: <8CCA5F1E2B88A2A-1D08-ED25@webmail-d050.sysops.aol.com> Just one thing, the "Cu.pbe-d-rrkjus.UPF" is an Ultrasoft pseudopotential, so I might check if higher "rhocut' values (up to 10*Ecut) do not change considerably your results, if you didn't yet. All best. Fabio Negreiros Ribeiro Departamento de Fiica de Minas Gerais. Brazil -----Original Message----- From: Nay Lin <naylin.nll at gmail.com> To: pw_forum at pwscf.org Sent: Thu, Apr 8, 2010 1:06 pm Subject: [Pw_forum] Copper pseudopotential Dear all ? I am testing Cu.pbe-d-rrkjus.UPF for equilibrium lattice constant. ? with the k grid of 30x30x30 0 0 0 (automatic), Ecut 30, rhocut 120, occupation='smearing', smearing='mp', degauss=0.02 ? i am getting the lattice constant around 6.93 where experimental value is 6.82 bohr. ? Is this accuracy enough for supercell copper surface calculations? ? Please help Thanks Lin _______________________________________________ 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/20100409/1925b0a0/attachment.htm From physik.shyam at gmail.com Sat Apr 10 10:22:06 2010 From: physik.shyam at gmail.com (Shyam Khambholja) Date: Sat, 10 Apr 2010 13:52:06 +0530 Subject: [Pw_forum] regarding bulk modulus Message-ID: Hi all, I have performed total energy calculation for Al as a function of lattice parameter. then i fit those data to murnaghan equation of state and got bulk modulus. when i use method of hydrostatic strain and got bulk modulus, it is much smaller than the one obtained by fitting E-a curve to murnaghan eos. So, which one is more reliable, since, bulk modulus obtained by fitting to mur. eos is quite near to experimental data. and which one should be used to determine other elastic stiffness constant ? Thanks in advance -- Mr. Shyam G Khambholja Reseach student, Depratment of Physics, Sardar Patel University India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100410/54864074/attachment.htm From mohnish.iitk at gmail.com Sat Apr 10 15:47:05 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Sat, 10 Apr 2010 19:17:05 +0530 Subject: [Pw_forum] negative phonon frequency in GaN bulk Message-ID: Dear PWSCF users, I am trying to get phonon dispersion relation of Gallium Nitride. First I have done the vc-relax calculation for GaN to get equilibrium lattice parameter. Then using that equilibrium lattice parameter I have done 'scf' calculation after which I have to do phonon calculation, but the problem is after doing the 'scf' calculation there is some pressure (greater than the threshold pressure for vc-relax) calculation. My input, output f for *vc-relax* and input, output for *'scf'*calculation are *respectively* *INPUT FOR VC-RELAX* &control calculation = 'vc-relax', restart_mode='restart', nstep=200 outdir='/home/rajpala/Desktop/gan_wur', pseudo_dir='/home/rajpala/Desktop/gan_wur' prefix='gan', tstress = .true., tprnfor = .true., / &system ibrav= 4, a = 3.3, c = 5.3,nat= 4, ntyp= 2, ecutwfc = 30,ecutrho=240,occupations='smearing',degauss=0.01,smearing='gaussian' / &electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-7 / &IONS ion_dynamics='bfgs' trust_radius_min=1.D-7 / &CELL cell_dynamics='bfgs' / ATOMIC_SPECIES Ga 69.723 Ga.pbe-nsp-van.UPF N 14.0067 N.pbe-rrkjus.UPF ATOMIC_POSITIONS (crystal) Ga 0.00 0.00 0.00 Ga 1/3 2/3 1/2 N 0.0 0.0 69/200 N 1/3 2/3 169/200 K_POINTS (automatic) 6 6 4 0 0 0 *SEGMENT OF OUTPUT* *OF VC-RELAX* ! total energy = -395.68385837 Ry Harris-Foulkes estimate = -395.68385837 Ry estimated scf accuracy < 6.2E-10 Ry The total energy is the sum of the following terms: one-electron contribution = -190.48989791 Ry hartree contribution = 134.51657806 Ry xc contribution = -108.33929602 Ry ewald contribution = -231.37124250 Ry smearing contrib. (-TS) = -0.00000000 Ry convergence has been achieved in 3 iterations Forces acting on atoms (Ry/au): atom 1 type 1 force = -0.00000000 0.00000000 0.00003463 atom 2 type 1 force = 0.00000000 -0.00000000 -0.00003656 atom 3 type 2 force = -0.00000000 -0.00000000 0.00000483 atom 4 type 2 force = 0.00000000 0.00000000 -0.00000291 Total force = 0.000051 Total SCF correction = 0.000052 SCF correction compared to forces is too large, reduce conv_thr entering subroutine stress ... total stress (Ry/bohr**3) (kbar) P= -0.20 -0.00000138 -0.00000000 -0.00000000 -0.20 -0.00 -0.00 -0.00000000 -0.00000138 -0.00000000 -0.00 -0.20 -0.00 -0.00000000 -0.00000000 -0.00000124 -0.00 -0.00 -0.18 bfgs converged in 24 scf cycles and 13 bfgs steps (criteria: energy < 0.10E-03, force < 0.10E-02, cell < 0.50E+00) End of BFGS Geometry Optimization Final enthalpy = -395.6838583715 Ry new unit-cell volume = 315.86297 a.u.^3 ( 46.80606 Ang^3 ) CELL_PARAMETERS (alat) 0.973879690 0.000000000 0.000000000 -0.486939845 0.843404552 -0.000000000 -0.000000000 -0.000000000 1.585692727 ATOMIC_POSITIONS (crystal) Ga -0.000000000 -0.000000000 -0.015912479 Ga 0.333333333 0.666666667 0.484088029 N 0.000000000 0.000000000 0.360941274 N 0.333333333 0.666666667 0.860883176 *INPUT FOR SCF *&control calculation = 'scf', restart_mode='restart', outdir='/home/rajpala/Desktop/gan', pseudo_dir='/home/rajpala/Desktop/gan' prefix='gan', tstress = .true., tprnfor = .true., / &system ibrav= 4, a = 3.213802977, c = 5.232785999,nat= 4, ntyp= 2, ecutwfc = 30,ecutrho=240,occupations='smearing',degauss=0.01,smearing='gaussian' / &electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-7 / ATOMIC_SPECIES Ga 69.723 Ga.pbe-nsp-van.UPF N 14.0067 N.pbe-rrkjus.UPF ATOMIC_POSITIONS (crystal) Ga -0.000000000 -0.000000000 -0.015912479 Ga 0.333333333 0.666666667 0.484088029 N 0.000000000 0.000000000 0.360941274 N 0.333333333 0.666666667 0.860883176 K_POINTS (automatic) 6 6 4 0 0 0* * *OUTPUT FOR SCF* ! total energy = -395.68329166 Ry Harris-Foulkes estimate = -395.68329169 Ry estimated scf accuracy < 0.00000005 Ry The total energy is the sum of the following terms: one-electron contribution = -190.48963216 Ry hartree contribution = 134.51703338 Ry xc contribution = -108.33945035 Ry ewald contribution = -231.37124253 Ry smearing contrib. (-TS) = -0.00000000 Ry convergence has been achieved in 8 iterations Forces acting on atoms (Ry/au): atom 1 type 1 force = 0.00000000 0.00000000 -0.00006952 atom 2 type 1 force = 0.00000000 0.00000000 -0.00008099 atom 3 type 2 force = 0.00000000 0.00000000 -0.00003004 atom 4 type 2 force = 0.00000000 0.00000000 0.00018054 Total force = 0.000212 Total SCF correction = 0.000060 entering subroutine stress ... total stress (Ry/bohr**3) (kbar) P= -1.64 -0.00001229 0.00000000 0.00000000 -1.81 0.00 0.00 0.00000000 -0.00001229 0.00000000 0.00 -1.81 0.00 0.00000000 0.00000000 -0.00000878 0.00 0.00 -1.29 *As you can see there is perssure is different in final vc-relax and scf calculation. After that I am doing phonon calculation and I am getting some frequencies to be negative. Can anybody please tell me where I am going wrong.* Thanks in advance, Sincerely, mohnish -- Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR 09235721300 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100410/b907bf02/attachment.htm From giannozz at democritos.it Sat Apr 10 18:24:14 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 10 Apr 2010 18:24:14 +0200 Subject: [Pw_forum] negative phonon frequency in GaN bulk In-Reply-To: References: Message-ID: On Apr 10, 2010, at 15:47 , mohnish pandey wrote: > As you can see there is perssure is different in final vc-relax and > scf calculation. this has been explained no less than 36000 times: the number of plane waves depends upon the starting cell volume of a vc-relax calculation, so it may differ from the number of plane waves used in a scf calculation with the same final geometry. In your case the difference in presure is so ridicolously small that it doesn't deserve to be called a difference. > After that I am doing phonon calculation and I am getting some > frequencies to be negative. and this has been explained a litle bit more than 72000 times: http://www.quantum-espresso.org/user_guide/ node79.html#SECTION00097030000000000000 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 Sat Apr 10 18:27:14 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 10 Apr 2010 18:27:14 +0200 Subject: [Pw_forum] regarding bulk modulus In-Reply-To: References: Message-ID: <35454291-366C-4D0A-940B-516D09014C4B@democritos.it> On Apr 10, 2010, at 10:22 , Shyam Khambholja wrote: > I have performed total energy calculation for Al as a function of > lattice parameter. > then i fit those data to murnaghan equation of state and got bulk > modulus. when i > use method of hydrostatic strain and got bulk modulus, it is much > smaller than the > one obtained by fitting E-a curve to murnaghan eos. So, which one > is more reliable, > since, bulk modulus obtained by fitting to mur. eos is quite near > to experimental data. > and which one should be used to determine other elastic stiffness > constant ? this is one of the first thing anybody involved in calculations in solids should know. Fitting to an equation of state converges more quickly with the plane- wave basis set. If however you find large differences between the various methods, either you did something wrong, or you are very fare from convergence wrt PW 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 Sat Apr 10 18:38:55 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 10 Apr 2010 18:38:55 +0200 Subject: [Pw_forum] scf not converging (was: how to specify initial ion velocities in pw.x) In-Reply-To: References: <5da157840912031047u68819036qe08177d40b46cbfd@mail.gmail.com> <4B18D5C0.1040101@democritos.it> <5da157840912041042w3598170chdf33892d9b0770ff@mail.gmail.com> <48151239-97C5-467C-B9B1-FC03B901AE05@democritos.it> <5da157840912160746k253c5af9ld620c33be3cf5a3a@mail.gmail.com> Message-ID: On Apr 1, 2010, at 22:19 , German Samolyuk wrote: > I'm trying to optimize structure correspondent to quadrupole of > dislocation in bcc Fe. > The electronic system did not converge after 50 iterations. there isn't anything obviously wrong in your input, apart from a cutoff (20Ry) that looks to me a little bit too small. You should try first a smaller supercell and experiment a bit with that: it is easier to spot problems and to find solutions without extensive damage to your computer budget 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 Sat Apr 10 18:42:31 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 10 Apr 2010 18:42:31 +0200 Subject: [Pw_forum] Symmetry problem in Ge and phonon calculation problem in InP In-Reply-To: <6D7E0C0F56302745BD0EC910BF4FF30813FB02D5@BL2PRD0103MB037.prod.exchangelabs.com> References: <6D7E0C0F56302745BD0EC910BF4FF30813FB02D5@BL2PRD0103MB037.prod.exchangelabs.com> Message-ID: <2BAC86B6-B531-461E-A889-F748C390797B@democritos.it> On Apr 1, 2010, at 19:39 , Ashutosh Kumar wrote: > Could you please guide me what should be the correct > procedure to be able to do the same? why don't you follow the provided examples? --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From xinhuolin at gmail.com Sat Apr 10 19:17:02 2010 From: xinhuolin at gmail.com (Huolin Xin) Date: Sat, 10 Apr 2010 13:17:02 -0400 Subject: [Pw_forum] How to get unfilled orbitals from ld1.x? In-Reply-To: References: Message-ID: Hi Paolo, Thank you very much! I tried this out, it works. However, is it possible to trick ld1.x to calculate unbound states for me, i.e. u_l(r,E>0). Huolin On Thu, Apr 8, 2010 at 2:42 AM, Paolo Giannozzi wrote: > > On Apr 8, 2010, at 6:42 , Huolin Xin wrote: > >> Is it possible to let ld1.x calculate a few more unfilled orbitals and >> output them without hacking the code? > >> config = '[Ne] 3s2 3p2' > > use "config = '[Ne] 3s2 3p2 3d0 4p0 4s0 ...' . Note that > unfilled orbitals are often unbound (for instance, 3d0 is > unbound in Si) > > 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 mohnish.iitk at gmail.com Sun Apr 11 13:48:00 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Sun, 11 Apr 2010 17:18:00 +0530 Subject: [Pw_forum] "epsil" for GaN and ZnO (0001) surface Message-ID: Dear users, I am doing phonon calculation for GaN and ZnO (0001) surface. As you all know this has non-zero electric field in in as per Taker type 3 instability. But when I am setting epsil = true in the calculation it is giving error as *%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%* *from phq+readin : error # 1* *no elec. field with metals %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%* * * *Can anybody please help me out.* * * *Thanks in advance,* *MOHNISH -- * Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR 09235721300 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100411/08a3de1b/attachment.htm From paulatto at sissa.it Sun Apr 11 16:47:58 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sun, 11 Apr 2010 16:47:58 +0200 Subject: [Pw_forum] "epsil" for GaN and ZnO (0001) surface In-Reply-To: References: Message-ID: Replying to message "[Pw_forum] "epsil" for GaN and ZnO (0001) surface" from mohnish pandey (11/04/10): > *%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%* > *from phq+readin : error # 1* > *no elec. field with metals > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%* Dear Mohnish, in the phonon code a metal is anything with smearing > zero. see this discussion for details: http://www.democritos.it/pipermail/pw_forum/2007-May/006573.html regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From jcwu.suda at hotmail.com Mon Apr 12 12:57:08 2010 From: jcwu.suda at hotmail.com (wujianchun) Date: Mon, 12 Apr 2010 18:57:08 +0800 Subject: [Pw_forum] Cadmium psudo potential Message-ID: Dear users, I am trying to calculate the total energy of CdS by use of hybrid-functionals. In the official web site of QE, the psudopotential of Cd is Vanderbilt ultrasoft which has not been implemented in the hybrid-functionals calculation. Where can I find the NORM-CONSERVING pseudopotential of Cd? or could someone kindly provide me the NORM-CONSERVING pseudopotential of Cd. Thanks a lot! Rgds Jianchun Wu Department of Physics Soochow university China.215006 _________________________________________________________________ SkyDrive????????????????????????! http://www.windowslive.cn/campaigns/e-magazine/ngmchina/?a=c -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100412/fe46272e/attachment.htm From giannozz at democritos.it Mon Apr 12 13:05:20 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 12 Apr 2010 13:05:20 +0200 Subject: [Pw_forum] How to get unfilled orbitals from ld1.x? In-Reply-To: References: Message-ID: <4BC2FE70.9010604@democritos.it> Huolin Xin wrote: > is it possible to trick ld1.x to calculate unbound states for me, > i.e. u_l(r,E>0) ld1.x calculates unbound states when they are needed, e.g in the calculation of logarithmic derivatives. If you want them calculated "for you", I am afrais that you need to modify the code P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From junkermeier at yahoo.com Mon Apr 12 15:31:28 2010 From: junkermeier at yahoo.com (Chad Junkermeier) Date: Mon, 12 Apr 2010 06:31:28 -0700 (PDT) Subject: [Pw_forum] graphene workfunction Message-ID: <353709.66042.qm@web111011.mail.gq1.yahoo.com> Hi, I am trying to compute the workfunction of graphene. I saw that someone else has been able to compute it and get reliable numbers (). After looking at the examples and what has been written in the forums my best guess as to the general form of the file to run pp.x (before running average.x) is given here. &inputPP outdir='/workspace/junky/WFC_2/tmp', plot_num=11 filplot = 'WFC_2.2.pot' prefix='WFC_2' / &plot iflag=3, output_format=3, nx=10, ny=10, nz =5, / My problem is that this is taking a really long time to run; much, much longer than the corresponding singlepoint SCF calculation ran using the same number of processors. At this point, the pp.x has been running for 43 hours. I can't believe that this is normal. Here are the last couple of lines from the pp.x output file: Writing data to file WFC_2.2.pot Reading data from file WFC_2.2.pot What is a normal length of time for this to run (I am running on 48 processors)? Is my input for pp.x really screwed up? Is pp.x just sitting there eating up computer time and not computing anything? Thank you for your help. Chad Junkermeier, Ph.D. NRC Post-Doctoral Associate Naval Research Laboratory &CONTROL calculation = "scf", prefix='WFC' restart_mode='from_scratch', pseudo_dir = "/app/espresso/pseudo", outdir = "/workspace/junky/WFC/tmp", / &SYSTEM ibrav = 4, celldm(1) = 9.300, celldm(3) = 5.00000000000000000000, nat = 8, ntyp = 1, ecutwfc = 300.0, occupations = "smearing", smearing = "methfessel-paxton", degauss = 0.05, / &ELECTRONS conv_thr = 1.D-6, mixing_beta = 0.3, / ATOMIC_SPECIES C 6.0 C.pbe-van_ak.UPF ATOMIC_POSITIONS crystal C 0.0 0.0 0.0 C 0.1666666666666667 0.3333333333333333 0.0 C 0.0 0.5 0.0 C 0.1666666666666667 0.8333333333333333 0.0 C 0.5 0.0 0.0 C 0.6666666666666667 0.3333333333333333 0.0 C 0.5 0.5 0.0 C 0.6666666666666667 0.8333333333333333 0.0 K_POINTS automatic 4 4 1 0 0 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100412/54e9545b/attachment.htm From nnlinh at sissa.it Mon Apr 12 15:45:28 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Mon, 12 Apr 2010 15:45:28 +0200 Subject: [Pw_forum] graphene workfunction In-Reply-To: <353709.66042.qm@web111011.mail.gq1.yahoo.com> References: <353709.66042.qm@web111011.mail.gq1.yahoo.com> Message-ID: <4BC323F8.3090507@sissa.it> > > Writing data to file WFC_2.2.pot > Reading data from file WFC_2.2.pot It does not run at al. > What is a normal length of time for this to run (I am running on 48 > processors)? Is my input for pp.x really screwed up? Is pp.x just > sitting there eating up computer time and not computing anything? Comparing 2 input files (for pw.x (below) and pp.x), they are different in ./outdir. Pls check it. Good luck Linh > > Thank you for your help. > > > Chad Junkermeier, Ph.D. > NRC Post-Doctoral Associate > Naval Research Laboratory > > > > > &CONTROL > calculation = "scf", > prefix='WFC' > restart_mode='from_scratch', > pseudo_dir = "/app/espresso/pseudo", > outdir = "/workspace/junky/WFC/tmp", > / > &SYSTEM > ibrav = 4, > celldm(1) = 9.300, > celldm(3) = 5.00000000000000000000, > nat = 8, > ntyp = 1, > ecutwfc = 300.0, > occupations = "smearing", > smearing = "methfessel-paxton", > degauss = 0.05, > / > &ELECTRONS > conv_thr = 1.D-6, > mixing_beta = 0.3, > / > ATOMIC_SPECIES > C 6.0 C.pbe-van_ak.UPF > ATOMIC_POSITIONS crystal > C 0.0 0.0 0.0 > C 0.1666666666666667 0.3333333333333333 0.0 > C 0.0 0.5 0.0 > C 0.1666666666666667 0.8333333333333333 0.0 > C 0.5 0.0 0.0 > C 0.6666666666666667 0.3333333333333333 0.0 > C 0.5 0.5 0.0 > C 0.6666666666666667 0.8333333333333333 0.0 > K_POINTS automatic > 4 4 1 0 0 0 > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 junkermeier at yahoo.com Mon Apr 12 16:11:33 2010 From: junkermeier at yahoo.com (Chad Junkermeier) Date: Mon, 12 Apr 2010 07:11:33 -0700 (PDT) Subject: [Pw_forum] graphene workfunction Message-ID: <856355.69115.qm@web111002.mail.gq1.yahoo.com> Earlier I sent an email where the output directory was different for the two files. The directories where erroneous in only the email, in my calculations the output directories are the same. The problem came from starting the original email a few days ago, and then repurposing it to ask the questions I wrote this morning. Sorry about the confusion. I made the proper changes to the two files. Chad Junkermeier, Ph.D. NRC Post-Doctoral Associate Naval Research Laboratory ________________________________ From: Chad Junkermeier To: pw_forum at pwscf.org Sent: Mon, April 12, 2010 9:31:28 AM Subject: graphene workfunction Hi, I am trying to compute the workfunction of graphene. I saw that someone else has been able to compute it and get reliable numbers (http://www.democritos.it/pipermail/pw_forum/2009-September/014336.html). After looking at the examples and what has been written in the forums my best guess as to the general form of the file to run pp.x (before running average.x) is given here. &inputPP outdir='/workspace/junky/WFC_2/tmp', plot_num=11 filplot = 'WFC_2.2.pot' prefix='WFC_2' / &plot iflag=3, output_format=3, nx=10, ny=10, nz =5, / My problem is that this is taking a really long time to run; much, much longer than the corresponding singlepoint SCF calculation ran using the same number of processors. At this point, the pp.x has been running for 43 hours. I can't believe that this is normal. Here are the last couple of lines from the pp.x output file: Writing data to file WFC_2.2.pot Reading data from file WFC_2.2.pot What is a normal length of time for this to run (I am running on 48 processors)? Is my input for pp.x really screwed up? Is pp.x just sitting there eating up computer time and not computing anything? Thank you for your help. Chad Junkermeier, Ph.D. NRC Post-Doctoral Associate Naval Research Laboratory &CONTROL calculation = "scf", prefix='WFC' restart_mode='from_scratch', pseudo_dir = "/app/espresso/pseudo", outdir = "/workspace/junky/WFC_2/tmp", / &SYSTEM ibrav = 4, celldm(1) = 9.300, celldm(3) = 5.00000000000000000000, nat = 8, ntyp = 1, ecutwfc = 300.0, occupations = "smearing", smearing = "methfessel-paxton", degauss = 0.05, / &ELECTRONS conv_thr = 1.D-6, mixing_beta = 0.3, / ATOMIC_SPECIES C 6.0 C.pbe-van_ak.UPF ATOMIC_POSITIONS crystal C 0.0 0.0 0.0 C 0.1666666666666667 0.3333333333333333 0.0 C 0.0 0.5 0.0 C 0.1666666666666667 0.8333333333333333 0.0 C 0.5 0.0 0.0 C 0.6666666666666667 0.3333333333333333 0.0 C 0.5 0.5 0.0 C 0.6666666666666667 0.8333333333333333 0.0 K_POINTS automatic 4 4 1 0 0 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100412/369917ee/attachment.htm From giovanni.cantele at na.infn.it Mon Apr 12 16:26:56 2010 From: giovanni.cantele at na.infn.it (Giovanni Cantele) Date: Mon, 12 Apr 2010 16:26:56 +0200 Subject: [Pw_forum] graphene workfunction In-Reply-To: <856355.69115.qm@web111002.mail.gq1.yahoo.com> References: <856355.69115.qm@web111002.mail.gq1.yahoo.com> Message-ID: > &inputPP > outdir='/workspace/junky/WFC_2/tmp', > plot_num=11 > filplot = 'WFC_2.2.pot' > prefix='WFC_2' > / > &plot > iflag=3, > output_format=3, > nx=10, > ny=10, > nz =5, > / > > My problem is that this is taking a really long time to run; much, much longer than the corresponding singlepoint SCF calculation ran using the same number of processors. At this point, the pp.x has been running for 43 hours. I can't believe that this is normal. Here are the last couple of lines from the pp.x output file: I'm not very sure about that, but it could be that if you specify the nx, ny, nz variables, the pp.x makes an interpolation using the original FFT grid. This can be very slow, as also (if I well remember) specified in Doc/INPUT_PP*. Try to specify x0, e1, e2, e3 or else nothing, and maybe the original FFT grid (or a subset of it) will be used instead, this should make your calculation much faster. 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100412/ac7fbbcb/attachment-0001.htm From nnlinh at sissa.it Mon Apr 12 16:40:52 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Mon, 12 Apr 2010 16:40:52 +0200 Subject: [Pw_forum] graphene workfunction In-Reply-To: References: <856355.69115.qm@web111002.mail.gq1.yahoo.com> Message-ID: <4BC330F4.7070601@sissa.it> Giovanni Cantele wrote: >> &inputPP >> outdir='/workspace/junky/WFC_2/tmp', >> plot_num=11 >> filplot = 'WFC_2.2.pot' >> prefix='WFC_2' >> / >> &plot >> iflag=3, >> output_format=3, >> nx=10, >> ny=10, >> nz =5, >> / >> >> My problem is that this is taking a really long time to run; much, >> much longer than the corresponding singlepoint SCF calculation ran >> using the same number of processors. At this point, the pp.x has >> been running for 43 hours. I can't believe that this is normal. >> Here are the last couple of lines from the pp.x output file: > > > I'm not very sure about that, but it could be that if you specify the > nx, ny, nz variables, the pp.x makes an interpolation using the > original FFT grid. This can be very slow, as also (if I well remember) > specified in Doc/INPUT_PP*. Try to specify x0, e1, e2, e3 or else > nothing, and maybe the original FFT grid (or a subset of it) will be > used instead, this should make your calculation much faster. I think that nx=10, ny=10, and nz =5 are alright, even you can increase them higher for a finer mesh. The problem could relate to that the plane wave grid is too large, with ecutwfc = 300 as shown in scf input files. It, for sure, make not only your scf run very long, but also make the grid of V very large, and pp.x almost stops at reading data from file. So, you should reduce the ecutwfc value. good luck Linh > > 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 > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 kumar.198 at buckeyemail.osu.edu Mon Apr 12 17:42:47 2010 From: kumar.198 at buckeyemail.osu.edu (Ashutosh Kumar) Date: Mon, 12 Apr 2010 15:42:47 +0000 Subject: [Pw_forum] Symmetry problem in Ge and phonon calculation problem in InP Message-ID: <6D7E0C0F56302745BD0EC910BF4FF30813FBFCD3@BL2PRD0103MB037.prod.exchangelabs.com> Dear Sir Thank you for your reply. I did dynamic matrix calculation and e-p coefficient calculation separately and it worked. Since epsil=.true. and elph=.true. are not compatible(it kept on saying that Electron-phonon only for metals if i used both), so I did separate calculations for electron phonon coefficients and dynamic matrix separately. I was wondering if the dynamic matrix written by ph.x is used by this command to write other files too, like eph_wql_out and if changing dynamic matrix by a different calculation would affect heavily the phonon calculations. Ashutosh Kumar Grad Student The Ohio State University From chinafuentes2000 at yahoo.com Mon Apr 12 18:44:40 2010 From: chinafuentes2000 at yahoo.com (Maria Elena Fuentes) Date: Mon, 12 Apr 2010 09:44:40 -0700 (PDT) Subject: [Pw_forum] generating pseudopotential for Ti In-Reply-To: References: Message-ID: <717658.45378.qm@web111414.mail.gq1.yahoo.com> [message deleted] From idoldog at gmail.com Mon Apr 12 19:30:51 2010 From: idoldog at gmail.com (idoldog) Date: Tue, 13 Apr 2010 01:30:51 +0800 Subject: [Pw_forum] Alignment Procedure of Energy level in Different Systems Message-ID: <201004130130473759173@gmail.com> Dear PWSCF users, recently, i was puzzled by an issue about energy level of different systems. what i studied was doped perovskite-type crystal. because there were two elements i used to dope, i got some different systems. For example, in La-doped system, it must contain the element La, however, in Mo-doped system, there is Mo dopant atoms instead of La impurity. Some scientists say its zero energy is arbitrariness, so one must preform some alignment procedure. so my question is: 1. what is meaning about the Fermi level given by PWSCF code directly? in the output file, it might look like this: ---------------------------------------------------------------------- the Fermi energy is 12.3654 ev ! total energy = -2320.88829157 Ry Harris-Foulkes estimate = -2320.88829157 Ry estimated scf accuracy < 7.7E-10 Ry --------------------------------------------------------------------- 2. i have got a lot of Fermi level with different systems. Can they compare with each other? or should i preform some alignment procedure? how to do? Someone tell me that one usually treat the top of valence band each systems as zero energy. is that right? Look forward to your reply and ANY SUGGESTION IS APPRECIATED. Li Fei 2010-04-13 -- ????? ?? ?????????????? ----------------------------------------------- ???http://icm.nankai.edu.cn/sxliu/cn ???022-23509005 Email?lifei_job at yeah.net MSN?lifei.chn at hotmail.com ???????????????????????????????????300071) ? ?????????????????????????????????????????????????????????????????????????????? From taebumlee at gmail.com Mon Apr 12 21:59:25 2010 From: taebumlee at gmail.com (TAE BUM LEE) Date: Mon, 12 Apr 2010 14:59:25 -0500 Subject: [Pw_forum] Fortran runtime error Message-ID: Hi, I am trying to calculate slab model of ZnO crystal using quantum-espresso on my PC (ubuntu 9.0) For small size (1x1x1 or 2x2x1) slab cell doesn't have any problem to finish typical scf calculation while 3x3x1 slab model generates following odd error message. Does anybody has same problem before? Any suggestion will be helpful too. Regards, TaeBum taebum at Aubie:~/Documents/QE/ZNO$ pw.x < large.in > large.out & [1] 2808 taebum at Aubie:~/Documents/QE/ZNO$ At line 556 of file read_cards.f90 Fortran runtime error: Bad real number in item 1 of list input [1]+ Exit 2 /usr/local/bin/espresso-4.0.5/bin/pw.x < large.in > large.out F.Y.I, here is my input. &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , wf_collect = .true. , outdir = '.' , pseudo_dir = '/home/taebum/espresso/pseudo' , prefix = 'large' , forc_conv_thr = 0.0001 , nstep = 5000 , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 4, A = 9.7482 , B = 9.7482 , C = 15.6114 , cosAB = -0.5 , cosAC = 0.0 , cosBC = 0.0 , nat = 36, ntyp = 2, ecutwfc = 40.0 , ecutrho = 320 , occupations = 'smearing' , degauss = 0.02 , smearing = 'methfessel-paxton' , / &ELECTRONS conv_thr = 1.0d-8 , mixing_beta = 0.7 , / ATOMIC_SPECIES Zn 65.41000 Zn.pbe-van.UPF O 16.00000 O.pbe-van_ak.UPF ATOMIC_POSITIONS {angstrom} Zn -0.0000162470 1.8760513450 0.0000000000 O -0.0000162470 1.8760513450 1.9883719800 Zn 1.6244887890 0.9380116020 2.6019000000 O 1.6244887890 0.9380116020 4.3972110000 Zn -1.6247162470 4.6901142920 0.0000000000 O -1.6247162470 4.6901142920 1.9883719800 Zn -0.0002112110 3.7520745490 2.6019000000 O -0.0002112110 3.7520745490 4.3972110000 Zn -3.2494162470 7.5041772390 0.0000000000 O -3.2494162470 7.5041772390 1.9883719800 Zn -1.6249112110 6.5661374960 2.6019000000 O -1.6249112110 6.5661374960 4.3972110000 Zn 3.2493837530 1.8760513450 0.0000000000 O 3.24938375Zn 1.8760513450 1.9883719800 Zn 4.8738887890 0.9380116020 2.6019000000 O 4.8738887890 0.9380116020 4.3972110000 Zn 1.6246837530 4.6901142920 0.0000000000 O 1.62468375Zn 4.6901142920 1.9883719800 Zn 3.2491887890 3.7520745490 2.6019000000 O 3.2491887890 3.7520745490 4.3972110000 Zn -0.0000162470 7.5041772390 0.0000000000 O -0.0000162470 7.5041772390 1.9883719800 Zn 1.6244887890 6.5661374960 2.6019000000 O 1.6244887890 6.5661374960 4.3972110000 Zn 6.4987837530 1.8760513450 0.0000000000 O 6.49878375Zn 1.8760513450 1.9883719800 Zn 8.1232887890 0.9380116020 2.6019000000 O 8.1232887890 0.9380116020 4.3972110000 Zn 4.8740837530 4.6901142920 0.0000000000 O 4.87408375Zn 4.6901142920 1.9883719800 Zn 6.4985887890 3.7520745490 2.6019000000 O 6.4985887890 3.7520745490 4.3972110000 Zn 3.2493837530 7.5041772390 0.0000000000 O 3.24938375Zn 7.5041772390 1.9883719800 Zn 4.8738887890 6.5661374960 2.6019000000 O 4.8738887890 6.5661374960 4.3972110000 K_POINTS automatic 1 1 1 1 1 1 -- ######################################## TAE BUM LEE Dept. Chem. & Biochem Auburn Univ. AL. 36849 TEL.: 334-844-6912 e-mail: taebumlee at gmail.com ######################################## -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100412/12c3d9d0/attachment-0001.htm From giannozz at democritos.it Mon Apr 12 22:11:30 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 12 Apr 2010 22:11:30 +0200 Subject: [Pw_forum] Fortran runtime error In-Reply-To: References: Message-ID: On Apr 12, 2010, at 21:59 , TAE BUM LEE wrote: > taebum at Aubie:~/Documents/QE/ZNO$ At line 556 of file read_cards.f90 > Fortran runtime error: Bad real number in item 1 of list input as clear as it can be: what and where > F.Y.I, here is my input. > O 3.24938375Zn 1.8760513450 1.9883719800 how nice! > O 1.62468375Zn 4.6901142920 1.9883719800 ...and there are a few more of them --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From izaakw89 at yahoo.com Tue Apr 13 00:59:12 2010 From: izaakw89 at yahoo.com (Izaak Williamson) Date: Mon, 12 Apr 2010 15:59:12 -0700 (PDT) Subject: [Pw_forum] Computer Server Configurations Message-ID: <690931.45476.qm@web44815.mail.sp1.yahoo.com> I am trying to buy a computer server and have to decide between the following two configurations: configuration L2 cache Main Memory A 6MBx2 64GB B 12MBx2 48GB Both cost the same amount. Question: which one will be the best to buy? Izaak Williamson -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100412/ba806913/attachment.htm From jcwu.suda at hotmail.com Tue Apr 13 04:18:55 2010 From: jcwu.suda at hotmail.com (wujianchun) Date: Tue, 13 Apr 2010 10:18:55 +0800 Subject: [Pw_forum] How to calculate DOS by Hybrid functionals. Message-ID: Dear All, I want to get the DOS of Si by use of Hybrid functionals. The first step scf calculation can be run normally and the result is same as the EXX_example. but the nscf calculation reports error. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_namelists : error # 1 reading namelist control %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Below is my input file. Could someone help me to deal with DOS calculation? Thanks in advance! Rgds Jianchun Wu Departmant of Physics Soochow Univ. China 215006 _____________________________________________________________________________ cat > CdS-0-o.pw.inp << EOF &CONTROL title = 'Si-0', calculation = 'scf', prefix = 'Si-0.pw', outdir = './Si-0', ! Need to create this directory wf_collect=.true., ! restart_mode='from_scratch', ! Change to restart if you want to restart max_seconds=255000 ! Just under 259200 == 72 hours / &system ibrav= 2, celldm(1) =10.20, nat= 2, ntyp= 1, ecutwfc =12.0, nbnd = 8, input_dft='pbe0', nqx1 = 1, nqx2 = 1, nqx3 = 1, / &electrons mixing_beta = 0.7 / 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 EOF cd $QSUB_WORKDIR tot_cores=$(($QSUB_VNODES*$QSUB_CPUS)) time mpirun -perhost $QSUB_CPUS -n $tot_cores /apps/Espresso/espresso-4.1.2-i11scaEXX/bin/pw.x -in CdS-0-o.pw.inp >> CdS-0-o.pw.out #Create this file when done touch CdS-0-o.pw.done #DOS calculation for VCd cat > ni.dos.in << EOF &CONTROL title = 'Si-0', calculation = 'nscf', prefix = 'Si-0.pw', outdir = './Si-0', ! Need to create this directory wf_collect=.true., ! Collect data all in one place restart_mode='from_scratch', ! Change to restart if you want to restart max_seconds=255000 ! Just under 259200 == 72 hours / / &system ibrav= 2, celldm(1) =10.20, nat= 2, ntyp= 1, ecutwfc =12.0, nbnd = 8, input_dft='pbe0', nqx1 = 1, nqx2 = 1, nqx3 = 1, / &electrons mixing_beta = 0.7 / 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 EOF cat > ni.dos2.in << EOF &inputpp prefix = 'Si-0.pw', outdir = './Si-0', fildos='Si.dos', Emin=-8.0, Emax=12.0, DeltaE=0.01 / EOF cd $QSUB_WORKDIR tot_cores=$(($QSUB_VNODES*$QSUB_CPUS)) time mpirun -perhost $QSUB_CPUS -n $tot_cores /apps/Espresso/espresso-4.1.2-i11scaEXX/bin/pw.x < ni.dos.in > ni.dos.out time mpirun -perhost $QSUB_CPUS -n $tot_cores /apps/Espresso/espresso-4.1.2-i11scaEXX/bin/dos.x < ni.dos2.in > ni.dos2.out touch dos.done _________________________________________________________________ SkyDrive????????????????????????! http://www.windowslive.cn/campaigns/e-magazine/ngmchina/?a=c -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100413/38b0cbe6/attachment.htm From giannozz at democritos.it Tue Apr 13 09:49:03 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 13 Apr 2010 09:49:03 +0200 Subject: [Pw_forum] Symmetry problem in Ge and phonon calculation problem in InP In-Reply-To: <6D7E0C0F56302745BD0EC910BF4FF30813FBFCD3@BL2PRD0103MB037.prod.exchangelabs.com> References: <6D7E0C0F56302745BD0EC910BF4FF30813FBFCD3@BL2PRD0103MB037.prod.exchangelabs.com> Message-ID: <4BC421EF.2090503@democritos.it> Ashutosh Kumar wrote: > Since epsil=.true. and elph=.true. are not compatible in a metal, macroscopic electric fields are zero. In an insulator, tha electron-phonon coefficient "lambda" is zero. Why do you want to calculate both? P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From nnlinh at sissa.it Tue Apr 13 10:25:09 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Tue, 13 Apr 2010 10:25:09 +0200 Subject: [Pw_forum] How to calculate DOS by Hybrid functionals. In-Reply-To: References: Message-ID: <4BC42A65.4090309@sissa.it> I rerun your calculations basing on your input files with a modify for pseudo directory, and they work well. So, pls check carefully the input file before starting calculations. Good luck, Linh wujianchun wrote: > Dear All, > > I want to get the DOS of Si by use of /Hybrid functionals. /The first > step scf calculation can be run normally and the result is same as the > EXX_example. but the nscf calculation reports error. > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_namelists : error # 1 > reading namelist control > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > Below is my input file. Could someone help me to deal with DOS > calculation? > > Thanks in advance! > > Rgds > Jianchun Wu > > Departmant of Physics > Soochow Univ. China > 215006 > > _____________________________________________________________________________ > cat > CdS-0-o.pw.inp << EOF > &CONTROL > title = 'Si-0', > calculation = 'scf', > prefix = 'Si-0.pw', > outdir = './Si-0', ! Need to create this directory > wf_collect=.true., ! > restart_mode='from_scratch', ! Change to restart if you want to restart > max_seconds=255000 ! Just under 259200 == 72 hours > / > &system > ibrav= 2, celldm(1) =10.20, nat= 2, ntyp= 1, > ecutwfc =12.0, nbnd = 8, > input_dft='pbe0', nqx1 = 1, nqx2 = 1, nqx3 = 1, > / > &electrons > mixing_beta = 0.7 > / > 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 > EOF > cd $QSUB_WORKDIR > tot_cores=$(($QSUB_VNODES*$QSUB_CPUS)) > time mpirun -perhost $QSUB_CPUS -n $tot_cores > /apps/Espresso/espresso-4.1.2-i11scaEXX/bin/pw.x -in CdS-0-o.pw.inp >> > CdS-0-o.pw.out > #Create this file when done > touch CdS-0-o.pw.done > > #DOS calculation for VCd > cat > ni.dos.in << EOF > &CONTROL > title = 'Si-0', > calculation = 'nscf', > prefix = 'Si-0.pw', > outdir = './Si-0', ! Need to create this directory > wf_collect=.true., ! Collect data all in one place > restart_mode='from_scratch', ! Change to restart if you want to restart > max_seconds=255000 ! Just under 259200 == 72 hours > / > / > &system > ibrav= 2, celldm(1) =10.20, nat= 2, ntyp= 1, > ecutwfc =12.0, nbnd = 8, > input_dft='pbe0', nqx1 = 1, nqx2 = 1, nqx3 = 1, > / > &electrons > mixing_beta = 0.7 > / > 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 > EOF > > cat > ni.dos2.in << EOF > &inputpp > prefix = 'Si-0.pw', > outdir = './Si-0', > fildos='Si.dos', > Emin=-8.0, Emax=12.0, DeltaE=0.01 > / > EOF > > cd $QSUB_WORKDIR > tot_cores=$(($QSUB_VNODES*$QSUB_CPUS)) > time mpirun -perhost $QSUB_CPUS -n $tot_cores > /apps/Espresso/espresso-4.1.2-i11scaEXX/bin/pw.x < ni.dos.in > ni.dos.out > time mpirun -perhost $QSUB_CPUS -n $tot_cores > /apps/Espresso/espresso-4.1.2-i11scaEXX/bin/dos.x < ni.dos2.in > > ni.dos2.out > > touch dos.done > > > ------------------------------------------------------------------------ > ??+??+?? ??????,??MSN????! ????! > ------------------------------------------------------------------------ > > _______________________________________________ > 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 Tue Apr 13 10:40:32 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Tue, 13 Apr 2010 10:40:32 +0200 Subject: [Pw_forum] Alignment Procedure of Energy level in Different Systems In-Reply-To: <201004130130473759173@gmail.com> References: <201004130130473759173@gmail.com> Message-ID: <4BC42E00.90707@sissa.it> idoldog wrote: > Dear PWSCF users, > > recently, i was puzzled by an issue about energy level of different systems. what i studied was doped perovskite-type crystal. because there were two elements i used to dope, i got some different systems. For example, in La-doped system, it must contain the element La, however, in Mo-doped system, there is Mo dopant atoms instead of La impurity. Some scientists say its zero energy is arbitrariness, so one must preform some alignment procedure. > > so my question is: > > 1. what is meaning about the Fermi level given by PWSCF code directly? in the output file, it might look like this: > ---------------------------------------------------------------------- > the Fermi energy is 12.3654 ev > > ! total energy = -2320.88829157 Ry > Harris-Foulkes estimate = -2320.88829157 Ry > estimated scf accuracy < 7.7E-10 Ry > --------------------------------------------------------------------- > The question about Fermi energy is asked by many times, here is one explanation as example: http://www.democritos.it/pipermail/pw_forum/2009-April/012396.html > 2. i have got a lot of Fermi level with different systems. Can they compare with each other? Depend on what do you want to obtain. For example, it is interesting if we consider the change of Ef as impurity's adoption. Best regards, Linh > Look forward to your reply and ANY SUGGESTION IS APPRECIATED. > > > > Li Fei > 2010-04-13 > > > -- > > ????? ?? > ?????????????? > ----------------------------------------------- > ???http://icm.nankai.edu.cn/sxliu/cn > ???022-23509005 > Email?lifei_job at yeah.net > MSN?lifei.chn at hotmail.com > ???????????????????????????????????300071) > ? ?????????????????????????????????????????????????????????????????????????????? > _______________________________________________ > 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 jcwu.suda at hotmail.com Tue Apr 13 11:04:05 2010 From: jcwu.suda at hotmail.com (wujianchun) Date: Tue, 13 Apr 2010 17:04:05 +0800 Subject: [Pw_forum] How to calculate DOS by Hybrid functionals. In-Reply-To: <4BC42A65.4090309@sissa.it> References: , <4BC42A65.4090309@sissa.it> Message-ID: Dear Linh, Thanks a lot! Could you tell me how to get the NORM-CONSERVING pseudopotential of Cd (Cadmium) which can be used in hybrid-functionals calculation? I only find the ultrosoft pseudopotential of Cd which has not been implemented in the hybrid-functionals calculation. Thank you again! Rgds Jianchun Wu Departmant of Physics Soochow Univ. China 215006 > Date: Tue, 13 Apr 2010 10:25:09 +0200 > From: nnlinh at sissa.it > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] How to calculate DOS by Hybrid functionals. > > > I rerun your calculations basing on your input files with a modify for > pseudo directory, and they work well. > > So, pls check carefully the input file before starting calculations. > > Good luck, > > Linh > > wujianchun wrote: > > Dear All, > > > > I want to get the DOS of Si by use of /Hybrid functionals. /The first > > step scf calculation can be run normally and the result is same as the > > EXX_example. but the nscf calculation reports error. > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > from read_namelists : error # 1 > > reading namelist control > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > Below is my input file. Could someone help me to deal with DOS > > calculation? > > > > Thanks in advance! > > > > Rgds > > Jianchun Wu > > > > Departmant of Physics > > Soochow Univ. China > > 215006 > > > > _____________________________________________________________________________ > > cat > CdS-0-o.pw.inp << EOF > > &CONTROL > > title = 'Si-0', > > calculation = 'scf', > > prefix = 'Si-0.pw', > > outdir = './Si-0', ! Need to create this directory > > wf_collect=.true., ! > > restart_mode='from_scratch', ! Change to restart if you want to restart > > max_seconds=255000 ! Just under 259200 == 72 hours > > / > > &system > > ibrav= 2, celldm(1) =10.20, nat= 2, ntyp= 1, > > ecutwfc =12.0, nbnd = 8, > > input_dft='pbe0', nqx1 = 1, nqx2 = 1, nqx3 = 1, > > / > > &electrons > > mixing_beta = 0.7 > > / > > 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 > > EOF > > cd $QSUB_WORKDIR > > tot_cores=$(($QSUB_VNODES*$QSUB_CPUS)) > > time mpirun -perhost $QSUB_CPUS -n $tot_cores > > /apps/Espresso/espresso-4.1.2-i11scaEXX/bin/pw.x -in CdS-0-o.pw.inp >> > > CdS-0-o.pw.out > > #Create this file when done > > touch CdS-0-o.pw.done > > > > #DOS calculation for VCd > > cat > ni.dos.in << EOF > > &CONTROL > > title = 'Si-0', > > calculation = 'nscf', > > prefix = 'Si-0.pw', > > outdir = './Si-0', ! Need to create this directory > > wf_collect=.true., ! Collect data all in one place > > restart_mode='from_scratch', ! Change to restart if you want to restart > > max_seconds=255000 ! Just under 259200 == 72 hours > > / > > / > > &system > > ibrav= 2, celldm(1) =10.20, nat= 2, ntyp= 1, > > ecutwfc =12.0, nbnd = 8, > > input_dft='pbe0', nqx1 = 1, nqx2 = 1, nqx3 = 1, > > / > > &electrons > > mixing_beta = 0.7 > > / > > 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 > > EOF > > > > cat > ni.dos2.in << EOF > > &inputpp > > prefix = 'Si-0.pw', > > outdir = './Si-0', > > fildos='Si.dos', > > Emin=-8.0, Emax=12.0, DeltaE=0.01 > > / > > EOF > > > > cd $QSUB_WORKDIR > > tot_cores=$(($QSUB_VNODES*$QSUB_CPUS)) > > time mpirun -perhost $QSUB_CPUS -n $tot_cores > > /apps/Espresso/espresso-4.1.2-i11scaEXX/bin/pw.x < ni.dos.in > ni.dos.out > > time mpirun -perhost $QSUB_CPUS -n $tot_cores > > /apps/Espresso/espresso-4.1.2-i11scaEXX/bin/dos.x < ni.dos2.in > > > ni.dos2.out > > > > touch dos.done > > > > > > ------------------------------------------------------------------------ > > ??+??+?? ??????,??MSN????! ????! > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 _________________________________________________________________ ???????????????? 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/20100413/767e8569/attachment.htm From giannozz at democritos.it Tue Apr 13 11:14:52 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 13 Apr 2010 11:14:52 +0200 Subject: [Pw_forum] How to calculate DOS by Hybrid functionals. In-Reply-To: References: , <4BC42A65.4090309@sissa.it> Message-ID: <4BC4360C.7030608@democritos.it> wujianchun wrote: > Could you tell me how to get the NORM-CONSERVING pseudopotential of Cd Yesterday I wasted some time updating the FAQs: the list of Frequently Asked Questions that everybody should read (but nobody does) before asking. This is what I was writing: ================ \paragraph{Where can I find pseudopotentials for atom X?} If you do not find anything suitable in the ``pseudo'' page of the web site links, we have bad news for you: you have to produce it by yourself. You can use the \texttt{atomic} code, or else any other code for which a converter to the UPF format exists. New contributions to the PP table are very appreciated (and very scarce). If X is one of the rare earths: please consider first if DFT is suitable for your system! In many cases, it isn't (at least ``plain'' DFT: GGA and the like). \paragraph{Is there a converter from format XYZ to UPF?} What is available (no warranty) is in directory \texttt{upftools/}. You are most welcome to contribute a new converter. ================ Bu the way, your previous question is also in the FAQ list: ================ \paragraph{Why is my parallel job crashing when reading input data / doing nothing?} If the same data work in serial execution, use \texttt{code -inp input\_file} instead of \texttt{code $<$ input\_file}. Some MPI libraries do not properly handle input redirection. \paragraph{The code stops with an "error reading namelist xxxx"} Most likely there is a misspelled variable in namelist xxxx. If there isn't any (have you looked carefully? really?? REALLY???), beware control characters like DOS control-M: they can confuse the namelist-reading code. If this happens to the first namelist to be read (usually "\&control") in parallel execution, see above. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Tue Apr 13 11:23:23 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 13 Apr 2010 11:23:23 +0200 Subject: [Pw_forum] Alignment Procedure of Energy level in Different Systems In-Reply-To: <201004130130473759173@gmail.com> References: <201004130130473759173@gmail.com> Message-ID: <4BC4380B.5050500@democritos.it> idoldog wrote: > Some scientists say its zero energy is arbitrary, so one must perform some alignment procedure. these "some scientists" are right. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From fedainanir at yahoo.com Tue Apr 13 11:32:05 2010 From: fedainanir at yahoo.com (Fedai Inanir) Date: Tue, 13 Apr 2010 02:32:05 -0700 (PDT) Subject: [Pw_forum] Invitation to connect on LinkedIn Message-ID: <1204323709.554216.1271151125417.JavaMail.app@ech3-cdn12.prod> LinkedIn ------------Fedai Inanir requested to add you as a connection on LinkedIn: ------------------------------------------ veronica, I'd like to add you to my professional network on LinkedIn. - Fedai Accept invitation from Fedai Inanir http://www.linkedin.com/e/XAAkmOm8d3sw5mZYSULFbcFqV9UKwx/blk/I70182103_5/6lColZJrmZznQNdhjRQnOpBtn9QfmhBt71BoSd1p65Lr6lOfPlvcP0NczwNc3t9bPtzp51AjmNUbPAMejcOcj0Ocz4LrCBxbOYWrSlI/EML_comm_afe/ View invitation from Fedai Inanir http://www.linkedin.com/e/XAAkmOm8d3sw5mZYSULFbcFqV9UKwx/blk/I70182103_5/dlYPc34Oe34MdQALqnpPbOYWrSlI/svi/ ------------------------------------------ DID YOU KNOW you can showcase your professional knowledge on LinkedIn to receive job/consulting offers and enhance your professional reputation? Posting replies to questions on LinkedIn Answers puts you in front of the world's professional community. http://www.linkedin.com/e/abq/inv-24/ ------ (c) 2010, LinkedIn Corporation -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100413/1a2c8fe1/attachment.htm From jcwu.suda at hotmail.com Tue Apr 13 11:47:54 2010 From: jcwu.suda at hotmail.com (wujianchun) Date: Tue, 13 Apr 2010 17:47:54 +0800 Subject: [Pw_forum] How to calculate DOS by Hybrid functionals. In-Reply-To: <4BC4360C.7030608@democritos.it> References: , , <4BC42A65.4090309@sissa.it>, , <4BC4360C.7030608@democritos.it> Message-ID: Dear Paolo and Linh, Thanks a lot! Rgds Jianchu Wu > Date: Tue, 13 Apr 2010 11:14:52 +0200 > From: giannozz at democritos.it > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] How to calculate DOS by Hybrid functionals. > > wujianchun wrote: > > > Could you tell me how to get the NORM-CONSERVING pseudopotential of Cd > > Yesterday I wasted some time updating the FAQs: the list of Frequently Asked > Questions that everybody should read (but nobody does) before asking. > This is what I was writing: > > ================ > \paragraph{Where can I find pseudopotentials for atom X?} > > If you do not find anything suitable in the ``pseudo'' page of the web > site links, we have bad news for you: you have to produce it by yourself. > You can use the \texttt{atomic} code, or else any other code for which > a converter to the UPF format exists. > New contributions to the PP table are very appreciated (and very scarce). > If X is one of the rare earths: please consider first if DFT is > suitable for your system! In many cases, it isn't (at least ``plain'' > DFT: GGA and the like). > > \paragraph{Is there a converter from format XYZ to UPF?} > > What is available (no warranty) is in directory \texttt{upftools/}. > You are most welcome to contribute a new converter. > ================ > > Bu the way, your previous question is also in the FAQ list: > > ================ > \paragraph{Why is my parallel job crashing when reading input data / > doing nothing?} > > If the same data work in serial execution, use > \texttt{code -inp input\_file} instead of \texttt{code $<$ input\_file}. > Some MPI libraries do not properly handle input redirection. > > \paragraph{The code stops with an "error reading namelist xxxx"} > > Most likely there is a misspelled variable in namelist xxxx. > If there isn't any (have you looked carefully? really?? REALLY???), > beware control characters like DOS control-M: they can confuse > the namelist-reading code. If this happens to the first namelist > to be read (usually "\&control") in parallel execution, see above. > > -- > 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 _________________________________________________________________ MSN????????????????25???????????2010????????? http://kaba.msn.com.cn/?k=1 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100413/8dd5bcd7/attachment-0001.htm From sclauzer at sissa.it Tue Apr 13 14:35:48 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 13 Apr 2010 14:35:48 +0200 Subject: [Pw_forum] Alignment Procedure of Energy level in Different Systems In-Reply-To: <201004130130473759173@gmail.com> References: <201004130130473759173@gmail.com> Message-ID: <4BC46524.5040000@sissa.it> idoldog wrote: > recently, i was puzzled by an issue about energy level of different systems. what i studied was doped perovskite-type crystal. because there were two elements i used to dope, i got some different systems. For example, in La-doped system, it must contain the element La, however, in Mo-doped system, there is Mo dopant atoms instead of La impurity. Some scientists say its zero energy is arbitrariness, so one must preform some alignment procedure. > so my question is: > 2. i have got a lot of Fermi level with different systems. Can they compare with each other? or should i preform some alignment procedure? how to do? > Someone tell me that one usually treat the top of valence band each systems as zero energy. is that right? Some work about alignment of band structures has been done by Pasquarello's group recently. You may have a look at this paper and similar ones: A. Alkauskas, P. Broqvist, and A. Pasquarello, Defect Energy Levels in Density Functional Calculations: Alignment and Band Gap Problem, Phys. Rev. Lett. 101, 046405 (2008). You may find useful this link as well http://www.cecam.org/workshop-291.html HTH GS > Li Fei > 2010-04-13 > > > -- > > ????? ?? > ?????????????? Could you please include your affiliation in non-Chinese characters? Unfortunately many of us cannot understand Chinese alphabeth... o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Tue Apr 13 14:41:31 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 13 Apr 2010 14:41:31 +0200 Subject: [Pw_forum] graphene workfunction In-Reply-To: <856355.69115.qm@web111002.mail.gq1.yahoo.com> References: <856355.69115.qm@web111002.mail.gq1.yahoo.com> Message-ID: <4BC4667B.7020105@sissa.it> Chad Junkermeier wrote: > After looking at the examples and what has been written in the forums > my best guess as to the general form of the file to run pp.x (before > running average.x) is given here. > > > &inputPP > outdir='/workspace/junky/WFC_2/tmp', > plot_num=11 > filplot = 'WFC_2.2.pot' > prefix='WFC_2' > / > &plot > iflag=3, > output_format=3, > nx=10, > ny=10, > nz =5, > / > > My problem is that this is taking a really long time to run; much, much > longer than the corresponding singlepoint SCF calculation ran using the > same number of processors. At this point, the pp.x has been running for > 43 hours. I can't believe that this is normal. Here are the last > couple of lines from the pp.x output file: > > > Writing data to file WFC_2.2.pot > Reading data from file WFC_2.2.pot > > > What is a normal length of time for this to run (I am running on 48 > processors)? Is my input for pp.x really screwed up? Is pp.x just > sitting there eating up computer time and not computing anything? Has the WFC_2.2.pot file been produced? If so, maybe the problem is that the second part of the pp run (that corresponding to the &plot namelist) should be performed on a single processor and in the past it used to get stuck when it was run in parallel (maybe this has been fixed in the meanwhile...) I suggest to first run pp.x in parallel leaving the &plot namelist blank, and then run again pp.x in serial specifying the plot part. HTH GS > > Thank you for your help. > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Tue Apr 13 14:52:31 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 13 Apr 2010 14:52:31 +0200 Subject: [Pw_forum] Computer Server Configurations In-Reply-To: <690931.45476.qm@web44815.mail.sp1.yahoo.com> References: <690931.45476.qm@web44815.mail.sp1.yahoo.com> Message-ID: <4BC4690F.7090102@sissa.it> Izaak Williamson wrote: > I am trying to buy a computer server and have to decide between the > following two configurations: > > configuration L2 cache Main Memory > A 6MBx2 64GB > B 12MBx2 48GB > Both cost the same amount. > Question: which one will be the best to buy? If everything else is the same, I would buy the second. Cache memory is integrated in the chip or motherboard and are more difficult/expensive to upgrade, while the main memory should be easier (and the cost of a memory bank is going to decrease with time, for sure). Then, it depends on your applications, since you may actually need that much RAM or not. GS > > Izaak Williamson Plz., append affiliation. Thanks. > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From elie.moujaes at hotmail.co.uk Tue Apr 13 16:36:43 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Tue, 13 Apr 2010 15:36:43 +0100 Subject: [Pw_forum] pw.x: command not found Message-ID: Dear PWSCF users, I have downloaded the latest version of espresso (espresso-4.1.3) and I have placed that on the server (as I am working on the server for more space). The system's configuration is x86_64. The configuration ends with a success..However when I compile each package alone (say PW, or PP, pr PH) using make...I get a warning-at the end- of the type: "Clock skew detected : your build maybe incomplete"..All commands pw.x, pp.x and ph.x are in the bin folder but when i try to compile: /espresso-4.1.3/bin/pw.xfilename.out I get : "pw.x :command not found".. I do not really understand the source of this error Is it related to the above warning? Thank you Elie Moujaes University of Nottingham NG7 2RD UK _________________________________________________________________ http://clk.atdmt.com/UKM/go/197222280/direct/01/ Do you have a story that started on Hotmail? Tell us now -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100413/d758b8e1/attachment.htm From giannozz at democritos.it Tue Apr 13 16:41:10 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 13 Apr 2010 16:41:10 +0200 Subject: [Pw_forum] pw.x: command not found In-Reply-To: References: Message-ID: <4BC48286.8060108@democritos.it> ..and while wasting more of my time updating the user guide (another document nobody ever reads), I added a note at the beginning that may be of interest for you: ====== This guide assume that you know the basic Unix concepts (shell, execution path, directories etc.) and utilities. If you don't, you will have a hard time running \qe. ==== -- Paolo Giannozzi, Democritos and University of Udine, Italy From carlo.nervi at unito.it Wed Apr 14 09:29:25 2010 From: carlo.nervi at unito.it (Carlo Nervi) Date: Wed, 14 Apr 2010 09:29:25 +0200 Subject: [Pw_forum] a brief and (maybe) stupid question Message-ID: <4BC56ED5.4000503@unito.it> Dear all, when doing calculations (I'm interested in PW, CP and GIPAW) using PP build with PBE functional (for example), QE compiled with -DEXX flag produces the same results of the version compiled without this flag? I mean comparing the results using functionals that are available in both (with and without -DEXX) of the QE compiled versions. I apologize if this will sound as a dumb question... Carlo -- ------------------------------------------------------ Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 Fax: +39 011 6707855 - Dipartimento di Chimica IFM via P. Giuria 7, 10125 Torino, Italy http://lem.ch.unito.it/ From degironc at sissa.it Wed Apr 14 09:30:24 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 14 Apr 2010 09:30:24 +0200 Subject: [Pw_forum] a brief and (maybe) stupid question In-Reply-To: <4BC56ED5.4000503@unito.it> References: <4BC56ED5.4000503@unito.it> Message-ID: <4BC56F10.20709@sissa.it> Yes ! this is the correct and expected behavior. Please report to the list and the developers if you have any evidence that this is not the case... thank you, Stefano de Gironcoli Carlo Nervi wrote: > Dear all, > when doing calculations (I'm interested in PW, CP and GIPAW) using PP > build with PBE functional (for example), QE compiled with -DEXX flag > produces the same results of the version compiled without this flag? > I mean comparing the results using functionals that are available in > both (with and without -DEXX) of the QE compiled versions. > I apologize if this will sound as a dumb question... > Carlo > From daijiayu at nudt.edu.cn Wed Apr 14 10:00:08 2010 From: daijiayu at nudt.edu.cn (Jiayu Dai) Date: Wed, 14 Apr 2010 16:00:08 +0800 Subject: [Pw_forum] core-hole states in PPs of GIPAW-UPF files. Message-ID: Dear users, Recently, i am generating the PPs of Li with one core-hole in 1s state, for the usage of x-ray calculation. As a test, i firstly generated the GIPAW-UPF files of O according to the example: http://www-int.impmc.upmc.fr/~software/gipaw/instructions.html, and modified it as following: &input title = 'O' prefix = 'O' zed = 8.0 rel = 1 rlderiv = 2.0 beta = 0.5 eminld = -4.0 emaxld = +4.0 deld = 0.02 nld = 3 config = '1s1 2s2 2p4 3s-1 3p-1 3d-1' iswitch = 3 dft = 'PBE' / &inputp pseudotype = 3 lloc = 2 file_pseudopw = 'O_pbe.UPF' file_recon = 'O_pbe.recon' lgipaw_reconstruction = .true. tm = .true. / 5 2S 1 0 2.00 0.00 1.40000000000 1.60000000000 2S 1 0 0.00 0.05 1.20000000000 1.60000000000 2P 2 1 4.00 0.00 1.40000000000 1.60000000000 2P 2 1 0.00 0.05 1.20000000000 1.60000000000 3D 3 2 -2.00 0.15 1.40000000000 1.60000000000 &test / 4 2S 1 0 2.00 0.00 1.40 1.60 2P 2 1 4.00 0.00 1.40 1.60 3S 2 0 0.00 0.00 1.40 1.60 3P 3 1 0.00 -0.05 1.40 1.60 Then, i got the file of O_pbe.UPF successfully. As we can see, there is one hole in 1s state, and the number of valence electrons is also 7. However, when i used the command "upf2plotcore.sh" in XSpectra directory, there is no core states: "#number of core states 0 = " Since the x-ray calculation needs the file of *.wfc, i can not continue to do the calculation. So, is there anything i forgot? Besides, i also found the same problem for the GIPAW file of Be(Be.star1s-pz-n-vbc.UPF). What's the problem? I think there should be a lot of people having the experiences for generating the PPs with core-hole, so please give me some suggestions. Thanks a lot. Jiayu ---------------- ------------------------------------------- Jiayu Dai Department of Physics National University of Defense Technology, Changsha, 410073, P R China ----------------------------------------- From daijiayu at nudt.edu.cn Wed Apr 14 14:03:40 2010 From: daijiayu at nudt.edu.cn (Jiayu Dai) Date: Wed, 14 Apr 2010 20:03:40 +0800 Subject: [Pw_forum] core-hole states in PPs of GIPAW-UPF files. Message-ID: ok, i think i found the problem here. The old script "upf2plotcore.sh" can only be used for the GIPAW version 1. Now, we are using the version 2 and the data type is a little different. Therefore, the script can not recongize the key works in new version. Besides, i found that in the *.wfc file, the data for 1s state is included. What i want to know is that if this file is the same as the one from "upf2plotcore.sh" script? That is to say, we can use this data in *.wfc when we generated the PPs with GIPAW to calculate the X ray absorption? Thanks a lot. Jiayu Dear users, Recently, i am generating the PPs of Li with one core-hole in 1s state, for the usage of x-ray calculation. As a test, i firstly generated the GIPAW-UPF files of O according to the example: http://www-int.impmc.upmc.fr/~software/gipaw/instructions.html, and modified it as following: &input title = 'O' prefix = 'O' zed = 8.0 rel = 1 rlderiv = 2.0 beta = 0.5 eminld = -4.0 emaxld = +4.0 deld = 0.02 nld = 3 config = '1s1 2s2 2p4 3s-1 3p-1 3d-1' iswitch = 3 dft = 'PBE' / &inputp pseudotype = 3 lloc = 2 file_pseudopw = 'O_pbe.UPF' file_recon = 'O_pbe.recon' lgipaw_reconstruction = .true. tm = .true. / 5 2S 1 0 2.00 0.00 1.40000000000 1.60000000000 2S 1 0 0.00 0.05 1.20000000000 1.60000000000 2P 2 1 4.00 0.00 1.40000000000 1.60000000000 2P 2 1 0.00 0.05 1.20000000000 1.60000000000 3D 3 2 -2.00 0.15 1.40000000000 1.60000000000 &test / 4 2S 1 0 2.00 0.00 1.40 1.60 2P 2 1 4.00 0.00 1.40 1.60 3S 2 0 0.00 0.00 1.40 1.60 3P 3 1 0.00 -0.05 1.40 1.60 Then, i got the file of O_pbe.UPF successfully. As we can see, there is one hole in 1s state, and the number of valence electrons is also 7. However, when i used the command "upf2plotcore.sh" in XSpectra directory, there is no core states: "#number of core states 0 = " Since the x-ray calculation needs the file of *.wfc, i can not continue to do the calculation. So, is there anything i forgot? Besides, i also found the same problem for the GIPAW file of Be(Be.star1s-pz-n-vbc.UPF). What's the problem? I think there should be a lot of people having the experiences for generating the PPs with core-hole, so please give me some suggestions. Thanks a lot. Jiayu ---------------- ------------------------------------------- Jiayu Dai Department of Physics National University of Defense Technology, Changsha, 410073, P R China ----------------------------------------- From amiri_physics at yahoo.com Wed Apr 14 15:42:17 2010 From: amiri_physics at yahoo.com (peyman amiri) Date: Wed, 14 Apr 2010 06:42:17 -0700 (PDT) Subject: [Pw_forum] passivation Message-ID: <464102.20324.qm@web58006.mail.re3.yahoo.com> Dear all ?I am working on (100) and (110) free surfaces of cubic?NaCl?type MnSe (alpha-MnSe) with aniferromagnetic order in 111 direction. Since alpha-MnSe is a semiconductor, I like to passivate the Mn and Se dangling bonds at the free surfaces by using Hydrogen atoms. Unfortunately it is not clear to me which type of H pseudopotential has to be used for passivation of surface Mn and Se atoms. Should I use (positive/negative) charged hydrogen atoms or neutral H atoms are enough for passivation. Moreover, how many Hydrogen atoms are needed for the passivation of surface Mn and Se dangling bonds? Your kind explanations and comments on these questions are highly apprecaited. With best regards Peiman ====================================== Peiman Amiri Computational Condensed Matter Research Lab Physics Department, Isfahan University of Technology, Iran Tel lab: +98 311 391 3733 Fax Office: +98311 391 3746 ------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100414/986c885a/attachment.htm From nnlinh at sissa.it Wed Apr 14 16:03:29 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Wed, 14 Apr 2010 16:03:29 +0200 Subject: [Pw_forum] passivation In-Reply-To: <464102.20324.qm@web58006.mail.re3.yahoo.com> References: <464102.20324.qm@web58006.mail.re3.yahoo.com> Message-ID: <4BC5CB31.4080008@sissa.it> peyman amiri wrote: > Dear all > I am working on (100) and (110) free surfaces of cubic NaCl type MnSe > (alpha-MnSe) with aniferromagnetic order in 111 direction. Since > alpha-MnSe is a semiconductor, I like to passivate the Mn and Se > dangling bonds at the free surfaces by using Hydrogen atoms. > Unfortunately it is not clear to me which type of H pseudopotential > has to be used for passivation of surface Mn and Se atoms. > You should estimate it by yourself what is the best PP for your model, but in my opinion I often use ultrasolf PP for surface models than others because it results close experiment's one. If you use Ultrasolf PP, you should find also Ultrasolf PP for other kinds of atom. > Should I use (positive/negative) charged hydrogen atoms or neutral H > atoms are enough for passivation. Moreover, how many Hydrogen atoms > are needed for the passivation of surface Mn and Se dangling bonds? > Again, it is a question that you have to figure it out by yourself. As far as I know the passivation depends not only on kind of adopted atoms but also on positions of the absorbates. Finding out the optimum parameters is as the first step of your problem. Good luck, Linh > > Your kind explanations and comments on these questions are highly > apprecaited. > > With best regards > Peiman > ====================================== > Peiman Amiri > Computational Condensed Matter Research Lab > Physics Department, Isfahan University of Technology, Iran > > Tel lab: +98 311 391 3733 Fax Office: +98311 391 3746 > ------------------------------ > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 prasenjit.jnc at gmail.com Wed Apr 14 17:19:09 2010 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Wed, 14 Apr 2010 17:19:09 +0200 Subject: [Pw_forum] passivation In-Reply-To: <4BC5CB31.4080008@sissa.it> References: <464102.20324.qm@web58006.mail.re3.yahoo.com> <4BC5CB31.4080008@sissa.it> Message-ID: On 14 April 2010 16:03, Ngoc Linh Nguyen wrote: > peyman amiri wrote: > > Dear all > > I am working on (100) and (110) free surfaces of cubic NaCl type MnSe > > (alpha-MnSe) with aniferromagnetic order in 111 direction. Since > > alpha-MnSe is a semiconductor, I like to passivate the Mn and Se > > dangling bonds at the free surfaces by using Hydrogen atoms. > > Unfortunately it is not clear to me which type of H pseudopotential > > has to be used for passivation of surface Mn and Se atoms. > > > You should estimate it by yourself what is the best PP for your model, > but in my opinion I often use ultrasolf PP for surface models than > others because it results close experiment's one. > If you use Ultrasolf PP, you should find also Ultrasolf PP for other > kinds of atom. > > I don't think it is the question of ultrasoft vs norm conserving. Rather it is which exchange correlation functional one should use.....I don't have any experience regarding MnSe passivated with H, however only for Se I found GGA works quite well at least for predicting structural properties you should make sure that for all the elements you should use the same exchange correlation functional......u can mix ultrasoft PP with a norm conserving one. With regards, Prasenjit. -- PRASENJIT GHOSH, POST-DOC, ROOM NO: 265, MAIN BUILDING, CM SECTION, ICTP, STRADA COSTERIA 11, TRIESTE, 34104, ITALY PHONE: +39 040 2240 369 (O) +39 3807528672 (M) URL: http://portal.ictp.it/cmsp/members/postdoctoral-fellows/prasenjit-ghosh/prasenjit_ghosh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100414/d248228b/attachment.htm From modaresi.mohsen at gmail.com Wed Apr 14 17:48:25 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Wed, 14 Apr 2010 20:18:25 +0430 Subject: [Pw_forum] How can i use my processors? Message-ID: Dear PW users, When i run PW on my computer, one of the processors is in rest. How can i use both of them simultaneously ? Thanks Mohsen Modaresi M. Sc student of Solid State Physics Ferdowsi University of Mashhad, Iran -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100414/672c6ac7/attachment.htm From nnlinh at sissa.it Wed Apr 14 17:50:20 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Wed, 14 Apr 2010 17:50:20 +0200 Subject: [Pw_forum] How can i use my processors? In-Reply-To: References: Message-ID: <4BC5E43C.2070801@sissa.it> mohsen modaresi wrote: > Dear PW users, > When i run PW on my computer, one of the processors is in rest. > How can i use both of them simultaneously ? You have to compile parallel compilers for your computer (see previous archives to know how to do that or search in google) Good luck Linh > Thanks > > Mohsen Modaresi > M. Sc student of Solid State Physics > Ferdowsi University of Mashhad, Iran > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 daijiayu at nudt.edu.cn Thu Apr 15 07:55:49 2010 From: daijiayu at nudt.edu.cn (Jiayu Dai) Date: Thu, 15 Apr 2010 13:55:49 +0800 Subject: [Pw_forum] core-hole states in PPs of GIPAW-UPF files. Message-ID: >Is this for XAS? Yes, do you have any suggestions? On Wed, Apr 14, 2010 at 4:00 AM, Jiayu Dai wrote: Dear users, Recently, i am generating the PPs of Li with one core-hole in 1s state, for the usage of x-ray calculation. As a test, i firstly generated the GIPAW-UPF files of O according to the example: http://www-int.impmc.upmc.fr/~software/gipaw/instructions.html, and modified it as following: &input title = 'O' prefix = 'O' zed = 8.0 rel = 1 rlderiv = 2.0 beta = 0.5 eminld = -4.0 emaxld = +4.0 deld = 0.02 nld = 3 config = '1s1 2s2 2p4 3s-1 3p-1 3d-1' iswitch = 3 dft = 'PBE' / &inputp pseudotype = 3 lloc = 2 file_pseudopw = 'O_pbe.UPF' file_recon = 'O_pbe.recon' lgipaw_reconstruction = .true. tm = .true. / 5 2S 1 0 2.00 0.00 1.40000000000 1.60000000000 2S 1 0 0.00 0.05 1.20000000000 1.60000000000 2P 2 1 4.00 0.00 1.40000000000 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100415/31247dc2/attachment-0001.htm From sd.wang000 at gmail.com Thu Apr 15 10:48:40 2010 From: sd.wang000 at gmail.com (shudong wang) Date: Thu, 15 Apr 2010 16:48:40 +0800 Subject: [Pw_forum] phonon dispersion Message-ID: Dear developers: I performed phonon dispersion of two-dimensional Si with two layer silicon atoms passivated by H atom (Si4H2) ,and there are two branches have frequncy higher than others(in red), and the result is : &plot nbnd= 18, nks= 61 / 0.000000 0.000000 0.000000 -16.5775 -7.8790 -3.1558 97.8351 105.6592 222.2850 390.0047 474.5206 478.3406 482.2919 494.0081 502.5633 602.3562 620.0962 648.4555 660.1258 2110.7548 2116.3744 0.016667 0.016667 0.000000 -16.1481 4.8616 17.1698 98.9575 107.0761 222.1388 389.3945 474.3367 478.1513 482.3187 493.1097 502.8504 602.4038 620.8876 648.1560 660.0547 2110.3105 2116.3290 0.033333 0.033333 0.000000 -14.9035 13.0400 36.1211 102.1200 111.2414 221.7379 387.5912 473.7711 477.6237 482.2742 490.9342 503.3493 602.4055 623.2746 647.2722 659.9022 2109.0949 2116.0984 ........ ........ ........ ........ my input files are: &inputph tr2_ph=1.0d-10, prefix='s2', fildvscf='s2dv', amass(1)=28.0855, amass(2)=1.0 outdir='/home/sdwang/aa/tmp/', fildyn='s2.dyn', elph=.false., trans=.true., ldisp=.true. nq1=4, nq2=4, nq3=1 / &input asr='simple',amass(1)=28.0855,amass(2)=1.0, flfrc='s2444.fc',flfrq='s2444.freq',la2f=.false.,dos=.false., / 61 0.000000 0.000000 0.000000 1.00 0.016667 0.016667 0.000000 1.00 0.033333 0.033333 0.000000 1.00 0.050000 0.050000 0.000000 1.00 ....... &input zasr='simple', fildyn='s2.dyn', flfrc='s2444.fc', la2F=.false. / What's the matter? Thanks! S.D.Wang Southeast University in Nanjing ,China. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100415/9a9d866a/attachment.htm From giannozz at democritos.it Thu Apr 15 11:16:10 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 15 Apr 2010 11:16:10 +0200 Subject: [Pw_forum] phonon dispersion In-Reply-To: References: Message-ID: <4BC6D95A.5060605@democritos.it> shudong wang wrote: > What's the matter? the matter is "Condensed Matter Physics", in particular "Phonon Physics". Study it and you will discover that typical H-Si stretching frequencies are in the order of 1500-2000 cm(-1) P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Thu Apr 15 11:19:09 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 15 Apr 2010 11:19:09 +0200 Subject: [Pw_forum] passivation In-Reply-To: <464102.20324.qm@web58006.mail.re3.yahoo.com> References: <464102.20324.qm@web58006.mail.re3.yahoo.com> Message-ID: <4BC6DA0D.7060303@democritos.it> peyman amiri wrote: > Unfortunately it is not clear to me which type of H pseudopotential has > to be used for passivation of surface Mn and Se atoms. nor is it to me, but I would try to find out which kind of saturation produces an electonic configuration that resembles the most to that of bulk MnSe P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From matteo.calandra at impmc.jussieu.fr Thu Apr 15 18:46:51 2010 From: matteo.calandra at impmc.jussieu.fr (Matteo Calandra) Date: Thu, 15 Apr 2010 18:46:51 +0200 Subject: [Pw_forum] core-hole states in PPs of GIPAW-UPF files. Message-ID: <4BC742FB.3000907@impmc.jussieu.fr> Dear Jiayu-Day, The script upf2plotcore.sh extract the core wavefunction from pseudopotentials upf version one. Soon we will include a script to use with version 2. In the meantime you can generate your pseudopotential as you did before and simply add: upf_v1_format=.true., in the namelist &inputp. Your inputp namelist will be something like &inputp pseudotype = 3 lloc = 2 file_pseudopw = 'O_pbe.UPF' file_recon = 'O_pbe.recon' lgipaw_reconstruction = .true. tm = .true. upf_v1_format=.true., / ant then use upf2plotcore.sh script. Concerning the pseudo Be.star1s-pz-n-vbc.UPF , this is not a GIPAW pseudo so it does not include informations about core states. You should use the pseudos with the suffix _gipaw.UPF. Finally remember that the 1s wavefunction you need is not the one with the core-hole but without the core-hole. Indeed this is used in the initial state and not in the final state. Thus you should extract the 1s wavefunction from a _gipaw pseudo without core-hole. I hope it helps, Matteo -- * * * * Matteo Calandra, Charge de Recherche (CR1) Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris Universit? Pierre et Marie Curie, tour 16, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra From Michael.Mehl at nrl.navy.mil Thu Apr 15 22:16:44 2010 From: Michael.Mehl at nrl.navy.mil (Mike Mehl) Date: Thu, 15 Apr 2010 16:16:44 -0400 Subject: [Pw_forum] (Slightly) different energies based on ordering of atomic positions Message-ID: <4BC7742C.8010608@nrl.navy.mil> I've been doing frozen phonon calculations with pwscf, and found a difference in the output of the code based on how I ordered the list of atomic positions. Specifically: Both of the attached runs compute the energy of an 8 atom supercell of IrV in the L1_0 structure with no displacements away from the equilibrium positions, so they should give the same energy. They don't. The difference between the runs is that the atomic positions were generated from two different irreducible representations from Harold Stokes's FINDSYM program, and the input differs slightly. That is, the atomic positions for the run "m000.U1.in" are Ir 0.00000000000000 0.00000000000000 0.00000000000000 Ir 0.00000000000000 5.21947856004048 0.00000000000000 Ir 0.00000000000000 15.65843568012144 0.00000000000000 Ir 0.00000000000000 10.43895712008096 0.00000000000000 V 2.60973928002024 13.04869640010120 -3.46622752200000 V 2.60973928002024 13.04869640010120 3.46622752200000 V 2.60973928002024 7.82921784006072 -3.46622752200000 V 2.60973928002024 7.82921784006072 3.46622752200000 and for "m000.U2.in" we have Ir 0.00000000000000 10.43895712008096 0.00000000000000 Ir 0.00000000000000 0.00000000000000 0.00000000000000 Ir 0.00000000000000 5.21947856004048 0.00000000000000 Ir 0.00000000000000 15.65843568012144 0.00000000000000 V 2.60973928002024 13.04869640010120 -3.46622752200000 V 2.60973928002024 13.04869640010120 3.46622752200000 V 2.60973928002024 7.82921784006072 -3.46622752200000 V 2.60973928002024 7.82921784006072 3.46622752200000 e.g., the Ir atoms are arranged in a different order. As I said, I get different results. The relevant differences in the outputs seem to be: $ diff m000.U1.out m000.U2.out < Found symmetry operation: I + ( 0.0000 0.2500 0.2500) This is a supercell, fractional translation are disabled --- > Found symmetry operation: I + ( 0.0000 0.5000 0.5000) This is a supercell, fractional translation are disabled < < the Fermi energy is 14.9323 ev < < ! total energy = -346.21707104 Ry < Harris-Foulkes estimate = -346.21707104 Ry < estimated scf accuracy < 9.2E-11 Ry --- > > the Fermi energy is 14.9317 ev > > ! total energy = -346.21709373 Ry > Harris-Foulkes estimate = -346.21709373 Ry > estimated scf accuracy < 6.2E-11 Ry Of course, the eigenvalues are different as well. I suspect that the problem is that the first non-symmorphic symmetry operation found is different in the two runs, so different space group operations are thrown out of the two calculations. Admittedly, this is a contrived situation (displacing the atoms away from equilibrium consistent with the symmetry of the phonon mode removes the problem), and the energy difference is inconsequential, so I'm hesitant to label it as a bug. Nevertheless I find it a bit disconcerting to get two different answers from what should be identical input. -- Michael J. Mehl Head, Center for Computational Materials Science Naval Research Laboratory Code 6390 Washington DC -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: m000.U1.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20100415/550c3323/attachment-0002.asc -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: m000.U2.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20100415/550c3323/attachment-0002.txt -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... 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Name: m000.U2.out Url: http://www.democritos.it/pipermail/pw_forum/attachments/20100415/550c3323/attachment-0003.txt From chenweiguang82 at gmail.com Fri Apr 16 02:27:10 2010 From: chenweiguang82 at gmail.com (Weiguang Chen) Date: Thu, 15 Apr 2010 17:27:10 -0700 (PDT) Subject: [Pw_forum] Invitation to connect on LinkedIn Message-ID: <186288928.2118862.1271377630430.JavaMail.app@ech3-cdn06.prod> LinkedIn ------------Weiguang Chen requested to add you as a connection on LinkedIn: ------------------------------------------ veronica, I'd like to add you to my professional network on LinkedIn. - Weiguang Accept invitation from Weiguang Chen http://www.linkedin.com/e/XOi1HZwtMe9Ipae3GXPJ40oAN5nddd/blk/I70856151_5/6lColZJrmZznQNdhjRQnOpBtn9QfmhBt71BoSd1p65Lr6lOfPlvcjkNdzkUc3t9bQVam55lcndqbPcSc3ASdjwOcz4LrCBxbOYWrSlI/EML_comm_afe/ View invitation from Weiguang Chen http://www.linkedin.com/e/XOi1HZwtMe9Ipae3GXPJ40oAN5nddd/blk/I70856151_5/dlYNdj4SdjwMdQALqnpPbOYWrSlI/svi/ ------------------------------------------ DID YOU KNOW you can use your LinkedIn profile as your website? Select a vanity URL and then promote this address on your business cards, email signatures, website, etc http://www.linkedin.com/e/ewp/inv-21/ ------ (c) 2010, LinkedIn Corporation -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100415/b6627a1f/attachment.htm From giannozz at democritos.it Fri Apr 16 10:03:21 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 16 Apr 2010 10:03:21 +0200 Subject: [Pw_forum] (Slightly) different energies based on ordering of atomic positions In-Reply-To: <4BC7742C.8010608@nrl.navy.mil> References: <4BC7742C.8010608@nrl.navy.mil> Message-ID: <4BC819C9.4010806@democritos.it> Mike Mehl wrote: > I suspect that the problem is that the first non-symmorphic symmetry > operation found is different in the two runs, so different space group > operations are thrown out of the two calculations. no, I don't think this is the problem. In both cases the code just discards fractional translations. It should find the same symmetry operations (this can be verified using "verbosity='high'"). Note that the first scf iterations give exactly the same results, then a small difference starts to build up. Why? hard to say. > I find it a bit disconcerting to get two different answers > from what should be identical input. me too. However, once you have spent several days chasing a bug that turns out to be due to different processors producing different results from the same operations on the same data (it happened to me some time ago on a BlueGene), you abandon any hope to get reproducible numbers with more than a few significant digits. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From daijiayu at nudt.edu.cn Fri Apr 16 10:46:26 2010 From: daijiayu at nudt.edu.cn (Jiayu Dai) Date: Fri, 16 Apr 2010 16:46:26 +0800 Subject: [Pw_forum] core-hole states in PPs of GIPAW-UPF files Message-ID: Dear Matteo Calandra Thank you for your explanation, it is very clear to use this script. I will study the examples more carefully. Thanks again. Jiayu From: Matteo Calandra Subject: [Pw_forum] core-hole states in PPs of GIPAW-UPF files. To: pw_forum at pwscf.org Message-ID: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Dear Jiayu-Day, The script upf2plotcore.sh extract the core wavefunction from pseudopotentials upf version one. Soon we will include a script to use with version 2. In the meantime you can generate your pseudopotential as you did before and simply add: upf_v1_format=.true., in the namelist &inputp. Your inputp namelist will be something like &inputp pseudotype = 3 lloc = 2 file_pseudopw = 'O_pbe.UPF' file_recon = 'O_pbe.recon' lgipaw_reconstruction = .true. tm = .true. upf_v1_format=.true., / ant then use upf2plotcore.sh script. Concerning the pseudo Be.star1s-pz-n-vbc.UPF , this is not a GIPAW pseudo so it does not include informations about core states. You should use the pseudos with the suffix _gipaw.UPF. Finally remember that the 1s wavefunction you need is not the one with the core-hole but without the core-hole. Indeed this is used in the initial state and not in the final state. Thus you should extract the 1s wavefunction from a _gipaw pseudo without core-hole. I hope it helps, Matteo -- * * * * Matteo Calandra, Charge de Recherche (CR1) Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris Universit? Pierre et Marie Curie, tour 16, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra From sclauzer at sissa.it Fri Apr 16 11:53:28 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 16 Apr 2010 11:53:28 +0200 Subject: [Pw_forum] projector for local channel in ultrasoft pseudopotential In-Reply-To: <532cb13c1003301627q75dc8729i3c9df4c697d5599d@mail.gmail.com> References: <532cb13c1003301627q75dc8729i3c9df4c697d5599d@mail.gmail.com> Message-ID: <4BC83398.4070408@sissa.it> Dear Alaska, asubedi wrote: > Dear all, > > I am a complete newbie trying to create an ultrasoft pseudopotential > for bismuth. I would like to use l=1 for the local part and I also > want projectors for it. So I have (excluding other valence electrons) Why do you want to do this? Do you understand the difference (theoretical and practical) between local part and non-local part of the pseudopotential? Given an electronic shell, for instance 6p, either you describe it with projectors or you include it in the local part. The last option is a reasonable choice only for some shells as far as I know (either s electrons or empty shells). Not sure for the 6p shell of Bi, which is in valence and partially occupied. Maybe someone else can give a more correct explanation than mine. HTH GS > > 6P 2 1 2.00 0.00 3.10 3.20 0.5 > 6P 2 1 0.00 -0.50 3.10 3.20 0.5 > 6P 2 1 1.00 0.00 3.10 3.20 1.5 > 6P 2 1 0.00 -0.50 3.10 3.20 1.5 > > However, the code gives an error: > > from ld1_readin : error # 1 > only one local channel > > Am I right in concluding that ld1.x cannot make ultasoft > pseudopotential for the local channel? I checked the formula for > decomposition of pseudopotential to local plus nonlocal part. For the > nonlocal part, summation is over l=0 to lmax and does not exclude > l_local. > > Thanks, > Alaska > UTK and ORNL -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Fri Apr 16 12:04:36 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 16 Apr 2010 12:04:36 +0200 Subject: [Pw_forum] magnesium diboride In-Reply-To: <875430.54644.qm@web112314.mail.gq1.yahoo.com> References: <875430.54644.qm@web112314.mail.gq1.yahoo.com> Message-ID: <4BC83634.7070808@sissa.it> If none of the equations of state implemented in ev.x is suitable for your system, you may find out which one should be used and implement it in the code and, after testing, contribute it to the QE project. Such a contribution from you would be very welcome! GS P.S. Please always remember to take a few second to sign your posts and put your affiliation, thanks. Nicholas Muthaka wrote: > hi.am working on properties of magnesium diboride and wish to run the > equation of state but have problems on how to insert the c lattice > constant in the script since the one i have come across seems to be the > one for cubics systems. please help. > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From matteo.calandra at impmc.jussieu.fr Fri Apr 16 16:55:31 2010 From: matteo.calandra at impmc.jussieu.fr (Matteo Calandra) Date: Fri, 16 Apr 2010 16:55:31 +0200 Subject: [Pw_forum] upf2plotcore.sh new version (Jiayu-Day) Message-ID: <4BC87A63.30507@impmc.jussieu.fr> Dear Jiayu-Day I have just committed a new version of the upf2plotcore.sh script that extracts core-wavefunctions from upf version 1 and upf version 2. Thanks to Ari Seitsonen providing the script. Matteo. -- * * * * Matteo Calandra, Charge de Recherche (CR1) Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris Universit? Pierre et Marie Curie, tour 16, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra From daijiayu at nudt.edu.cn Sat Apr 17 13:45:02 2010 From: daijiayu at nudt.edu.cn (Jiayu Dai) Date: Sat, 17 Apr 2010 19:45:02 +0800 Subject: [Pw_forum] upf2plotcore.sh new version Message-ID: Dear Matteo, Thanks for your new script, but where can we get it? Is it in the cvs version? By the way, i have a problem for the GIPAW PPs. If we want to use a PPs with all electrons in the valence, for example, for He with 2 elelctrons, or Li with 3 electrons in the valence, the GIPAW PPs are then without core orbitals. In this case, we can not get the wave functions anyway, therefore we can not did the calculation of XSpectra. How can we solve this problem? For example, for Li, we can get the NCPPs with GIPAW as follows: &input title = 'Li' prefix = 'li' zed = 3.0 rel = 1 beta = 0.5 rlderiv = 2.5 eminld = -4.0 emaxld = 4.0 deld = 0.01 nld = 2 iswitch = 3 config = '1s1.0 2s1.00 2p-2.0' dft = 'PBE' / &inputp pseudotype = 2 lloc = 1 tm = .true. file_pseudopw = 'Li.pbe.gipaw.UPF' file_recon = 'Li.pbe.gipaw.rec' lgipaw_reconstruction = .true. upf_v1_format = .true. / 5 1S 1 0 1.00 0.00 0.75 0.75 1S 1 0 0.00 0.05 0.75 0.75 2S 1 0 1.00 0.00 0.75 0.75 2S 1 0 0.00 0.05 0.75 0.75 2P 2 1 -2.00 0.15 0.75 0.75 &test / 3 1S 1 0 1.00 0.00 0.75 0.75 2S 1 0 1.00 0.00 0.75 0.75 2P 2 1 -2.00 0.15 0.75 0.75 In the cases of high pressure and high temperature, we have to consider all electrons. It gives me a lot of puzzle. Thank you very much. Jiayu Date: Fri, 16 Apr 2010 16:55:31 +0200 From: Matteo Calandra Subject: [Pw_forum] upf2plotcore.sh new version (Jiayu-Day) To: pw_forum at pwscf.org Message-ID: <4BC87A63.30507 at impmc.jussieu.fr> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Dear Jiayu-Day I have just committed a new version of the upf2plotcore.sh script that extracts core-wavefunctions from upf version 1 and upf version 2. Thanks to Ari Seitsonen providing the script. Matteo. -- ---------------- ------------------------------------------- Jiayu Dai Department of Physics National University of Defense Technology, Changsha, 410073, P R China ----------------------------------------- From eariel99 at gmail.com Sat Apr 17 14:19:31 2010 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Sat, 17 Apr 2010 09:19:31 -0300 Subject: [Pw_forum] projector for local channel in ultrasoft pseudopotential Message-ID: Hi Alaska, I recently made a norm conserving Bi pseudo without the 5d semicore states. This can be used with low cutoffs as the ultrasofts. The 5d states has energy of -2.58 Ry, I have seen a recipe in the manual of other code, that states over -3 Ry need to be included in the valence. Hence, this pseudo does not fulfill this recipe and the transferibility must be checked. You can check the transferibility making tests and comparisons with the other norm conserving pseudos that are on the web site. You may also modify the input to generate an ultrasoft that includes the 5d states. Change the line "6D 3 2 0.00 0.00 2.60 2.6" by "5D , etc ". &input title='Bi ultrasofts pp', zed=83.0, iswitch=3, rel=1, dft='PBE' config='[Xe] 4f14 5d10 5f0 6s2 6p2 6d0', / &inputp pseudotype=2, upf_v1_format=.true., file_pseudopw='Bi.UPF', lloc=1, nlcc=.true., rho0=0.01, author='EMP', / 4 6S 1 0 2.00 0.00 2.40 2.40 6D 3 2 0.00 0.00 2.60 2.60 5F 4 3 0.00 0.00 2.40 2.40 6P 2 1 2.00 0.00 2.40 2.40 &TEST nconf=1, ecutmin=20.0, ecutmax=100.0, configts(1)='[Xe] 4f14 5d10 5f0 6s2 6p3 6d0', Below is a summary of the cutoff study made with a ficticious BiO structure bcc-like (Bi at a corner and O at the center of a cubic cell). You must make your own study. I think it is safe to use a cutoff of 30 Ry, or 35 Ry if you need to do variable cell relaxations or dynamics. #alat vol(a.u.) ecut(Ry) total_E(Ry) P(kbar) 5.9995 215.9460 25 -50.64005577 -40.42 5.9995 215.9460 30 -50.65420993 21.02 5.9995 215.9460 35 -50.65484781 27.84 5.9995 215.9460 40 -50.65563353 27.21 5.9995 215.9460 45 -50.65607150 26.15 5.9995 215.9460 50 -50.65655203 26.54 5.9995 215.9460 60 -50.65685079 27.84 5.9995 215.9460 70 -50.65691919 28.3 5.9995 215.9460 80 -50.65703269 28.14 5.9995 215.9460 100 -50.65709652 28.48 5.9995 215.9460 110 -50.65709881 28.18 5.9995 215.9460 120 -50.65710837 28.33 Best regards, -- Eduardo Menendez Departamento de Fisica Facultad de Ciencias Universidad de Chile Phone: (56)(2)9787439 URL: http://fisica.ciencias.uchile.cl/~emenendez -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100417/9ed3fd98/attachment.htm From giannozz at democritos.it Sat Apr 17 14:37:31 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 17 Apr 2010 14:37:31 +0200 Subject: [Pw_forum] (Slightly) different energies based on ordering of atomic positions In-Reply-To: <4BC7742C.8010608@nrl.navy.mil> References: <4BC7742C.8010608@nrl.navy.mil> Message-ID: This is what I got on a sp6 (FFT grids are slghtly different, the rest should be the same; I used the most recent version). The final steps of self- consistency are slightly different in the two cases, but the final results are the same (and the same as your second output) Paolo -------------- next part -------------- A non-text attachment was scrubbed... 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Or can I doing phonon calculation along with relax or vc-relax calculation.? Thanks a lot in advance, -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR 09235721300 ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100417/98f93058/attachment.htm From skgupta.physics at gmail.com Sat Apr 17 16:43:50 2010 From: skgupta.physics at gmail.com (Sanjeev Kumar Gupta) Date: Sat, 17 Apr 2010 20:13:50 +0530 Subject: [Pw_forum] pseudopotential for Ce and Pr Message-ID: Dear Quantum-Espresso users, Greetings Does anyone have the pseudopotential for Ce and Pr ? Any information would be appreciated. Thank you very much. Best Regards Sanjeev GUPTA -- S. K. Gupta PhD Student, Dept. of Physics, Bhavnagar University. Bhavnagar, 364 022., Gujarat, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100417/0275124d/attachment.htm From mohnish.iitk at gmail.com Sun Apr 18 05:16:09 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Sun, 18 Apr 2010 08:46:09 +0530 Subject: [Pw_forum] phonon calculation for optimized geometry Message-ID: Dear users, I want to do phonon calculation for some structures, but after geometry optimization when I am using optimized geometry parameters for scf calculation there is difference in stress of scf calculation and vc-relax calculation which is changing phonon dispersion. Can anybody please tell me if there is any option to use the data of relax or vc-relax calculation for phonon dispersion.. Or can I doing phonon calculation along with relax or vc-relax calculation.? Thanks a lot in advance, -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR 09235721300 ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100418/d814100a/attachment.htm From ouuing at gmail.com Sun Apr 18 11:30:08 2010 From: ouuing at gmail.com (Hanyu) Date: Sun, 18 Apr 2010 17:30:08 +0800 Subject: [Pw_forum] phonon calculation for optimized geometry In-Reply-To: References: Message-ID: dear mohnish : I think you should check it carefully again. I don't think it should be happen. In fact, the stress of scf and vc-relax should be the same. but if the stress is not the hydrostatic pressure, the result is not be believed. you have to relax the structure until the stress of the phase is what you want. best regards. Hanyu On Sun, Apr 18, 2010 at 11:16 AM, mohnish pandey wrote: > Dear users, > ?? ? ? ? ? ? ? ? ?I want to do phonon calculation for some structures, but > after geometry optimization when I am using optimized geometry parameters > for scf calculation there is difference in stress of scf calculation and > vc-relax calculation which is changing phonon dispersion. Can anybody please > tell me if there is any option to use the data of relax or vc-relax > calculation for phonon dispersion.. Or can I doing phonon calculation along > with relax or vc-relax calculation.? > Thanks a lot in advance, > > -- > Regards, > MOHNISH, > ----------------------------------------------------------------- > Mohnish Pandey > Y6927262,4th Year dual degree student, > Department of Chemical Engineering, > IIT KANPUR > 09235721300 > ----------------------------------------------------------------- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=**=-=**=-=**=-=*=-=*=-=*=-=*=-=*=- Hanyu Liu(???), MS. State key Laboratory of Superhard Materials, Jilin University, China Email: liuhanyu08 at mails.jlu.edu.cn ouuing at gmail.com From moronaphtaly84 at gmail.com Sun Apr 18 11:39:36 2010 From: moronaphtaly84 at gmail.com (naphtaly moro) Date: Sun, 18 Apr 2010 12:39:36 +0300 Subject: [Pw_forum] Phase Transition Pressures Message-ID: Dear all, I am working on the pressure induced phase transitions of GaAs, I have already obtained, the respective EV data for the structures and want to get the transition pressures for the structures, Any advice on how this can be done in Espresso? Thanks Cecil Naphtaly Moro, Mphil. Student, Department of Physics, Moi University, Chepkoilel Campus, Kenya -- Cecil Naphtaly Moro From mohnish.iitk at gmail.com Sun Apr 18 13:30:46 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Sun, 18 Apr 2010 17:00:46 +0530 Subject: [Pw_forum] phonon calculation for optimized geometry -one subtle confusion Message-ID: Dear Hanyu ! Thanks for your reply. As you now the default value for the pressure in PWSCF is 0.5. I am using that value as convergence threshold but when I am doing scf calculation with the geometrical parameters value obtained from the vc-relax calculation the pressure value is different from vc-relax final run. And as you know pressure will effect the phonon dispresion relation..Can you please give me any suggestion, Thanks alot, MOHNISH On Sun, Apr 18, 2010 at 3:00 PM, Hanyu wrote: > dear mohnish : > I think you should check it carefully again. I don't think it should > be happen. In fact, the stress of scf and vc-relax should be the same. > but if the stress is not the hydrostatic pressure, the result is not > be believed. you have to relax the structure until the stress of the > phase is what you want. > > best regards. > > Hanyu > > On Sun, Apr 18, 2010 at 11:16 AM, mohnish pandey > wrote: > > Dear users, > > I want to do phonon calculation for some structures, > but > > after geometry optimization when I am using optimized geometry parameters > > for scf calculation there is difference in stress of scf calculation and > > vc-relax calculation which is changing phonon dispersion. Can anybody > please > > tell me if there is any option to use the data of relax or vc-relax > > calculation for phonon dispersion.. Or can I doing phonon calculation > along > > with relax or vc-relax calculation.? > > Thanks a lot in advance, > > > > -- > > Regards, > > MOHNISH, > > ----------------------------------------------------------------- > > Mohnish Pandey > > Y6927262,4th Year dual degree student, > > Department of Chemical Engineering, > > IIT KANPUR > > 09235721300 > > ----------------------------------------------------------------- > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=**=-=**=-=**=-=*=-=*=-=*=-=*=-=*=- > Hanyu Liu(???), > MS. > State key Laboratory of Superhard Materials, Jilin University, China > Email: liuhanyu08 at mails.jlu.edu.cn ouuing at gmail.com > _______________________________________________ > 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 09235721300 ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100418/33c1d112/attachment.htm From xinhuolin at gmail.com Sun Apr 18 15:04:09 2010 From: xinhuolin at gmail.com (Huolin Xin) Date: Sun, 18 Apr 2010 09:04:09 -0400 Subject: [Pw_forum] Phase Transition Pressures In-Reply-To: References: Message-ID: You'll need phonon entropy and electronic entropy as well. Free energy is E-TS. The transition pressure is where the free energy of the two structures are the same. On Sun, Apr 18, 2010 at 5:39 AM, naphtaly moro wrote: > Dear all, > > I am working on the pressure induced phase transitions of GaAs, I have > already obtained, the respective EV data for the structures and want > to get the transition pressures for the structures, Any advice on how > this can be done in Espresso? > > Thanks > Cecil Naphtaly Moro, > Mphil. Student, > Department of Physics, > Moi University, Chepkoilel Campus, > Kenya > > -- > Cecil Naphtaly Moro > _______________________________________________ > 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/20100418/760267f5/attachment.htm From baroni at sissa.it Sun Apr 18 15:18:53 2010 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 18 Apr 2010 15:18:53 +0200 Subject: [Pw_forum] Phase Transition Pressures In-Reply-To: References: Message-ID: <3B09F403-6C17-49E5-9371-DA31DF9A7DB8@sissa.it> On Apr 18, 2010, at 11:39 AM, naphtaly moro wrote: > Dear all, > > I am working on the pressure induced phase transitions of GaAs, I have > already obtained, the respective EV data for the structures and want > to get the transition pressures for the structures, Any advice on how > this can be done in Espresso? As with any other code: using the Maxwell construction (if you have never heard about this concept, browse any book in classical thermodynamics / elementary statistical mechanics and/or google). In a nutshell: you plot the two E(V) curves for the two structures, and you look for a straight line that is tangent to both curves: the slope of the straight line is the transition pressure. If you want to understand why this construction works, remember that at any given pressure the stable structure is the one that minimizes the enthalpy of the system (E+PV) or the Giibbs free energy (E-TS+PV). In both these expressione remember that the volume is a *dependent* variable that has to be expressed in terms of the pressure (the independent variable). Start from this, and try to work out the Maxwell construction by yourself ... Cecil: one thing that every student has to learn is how to grade different methods and concepts. In the present case, you will see that the concepts needed to solve your problem are rather general and have little (if anything) to do with the specific code you use to obtain the E(V) data. I am saying this not to suggest that you shouldn't have asked this question on this mailing list: you did well, and you are most welcome to ask similar questions in the future. Only, I would like to make sure that you see the difference between what is general and what is specific. Good luck - Stefano B > > Thanks > Cecil Naphtaly Moro, > Mphil. Student, > Department of Physics, > Moi University, Chepkoilel Campus, > Kenya > > -- > Cecil Naphtaly Moro > _______________________________________________ > 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/20100418/3dd8fec8/attachment-0001.htm From baroni at sissa.it Sun Apr 18 15:25:01 2010 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 18 Apr 2010 15:25:01 +0200 Subject: [Pw_forum] Phase Transition Pressures In-Reply-To: References: Message-ID: <2AD31070-1ECA-4C42-9790-F97C0AA2FDA5@sissa.it> Dear Huolin: as explained in my previous post, I beg to differ. Phonons have nothing to do with the question asked by Cecil, as long as the temperature is low enough. Even less, the electronic entropy, as long as the the system insulating (even in metals, the electronic entropy play a very little role, below the Farmi temperature which is typically several thousands degrees ...). Even considering temperature effects, it is not the "free energy" that has to be made equal (usually, one indicates with this term the Helmholts free energy, E-TS), but the "Gibbs free energy" (E-TS+PV). Hope this clarifies a bit ... SB On Apr 18, 2010, at 3:04 PM, Huolin Xin wrote: > You'll need phonon entropy and electronic entropy as well. Free energy is E-TS. The transition pressure is where the free energy of the two structures are the same. > > On Sun, Apr 18, 2010 at 5:39 AM, naphtaly moro wrote: > Dear all, > > I am working on the pressure induced phase transitions of GaAs, I have > already obtained, the respective EV data for the structures and want > to get the transition pressures for the structures, Any advice on how > this can be done in Espresso? > > Thanks > Cecil Naphtaly Moro, > Mphil. Student, > Department of Physics, > Moi University, Chepkoilel Campus, > Kenya > > -- > Cecil Naphtaly Moro > _______________________________________________ > 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/20100418/2f5c07f1/attachment.htm From xinhuolin at gmail.com Sun Apr 18 15:35:27 2010 From: xinhuolin at gmail.com (Huolin Xin) Date: Sun, 18 Apr 2010 09:35:27 -0400 Subject: [Pw_forum] Phase Transition Pressures In-Reply-To: <2AD31070-1ECA-4C42-9790-F97C0AA2FDA5@sissa.it> References: <2AD31070-1ECA-4C42-9790-F97C0AA2FDA5@sissa.it> Message-ID: Stefano, thanks a lot for pointing my mistake out. In the entropy term, besides phonon and electronic entropy, how to calculate the structural entropy? On Sun, Apr 18, 2010 at 9:25 AM, Stefano Baroni wrote: > Dear Huolin: as explained in my previous post, I beg to differ. Phonons > have nothing to do with the question asked by Cecil, as long as the > temperature is low enough. Even less, the electronic entropy, as long as the > the system insulating (even in metals, the electronic entropy play a very > little role, below the Farmi temperature which is typically several > thousands degrees ...). Even considering temperature effects, it is not the > "free energy" that has to be made equal (usually, one indicates with this > term the Helmholts free energy, E-TS), but the "Gibbs free energy" > (E-TS+PV). Hope this clarifies a bit ... SB > > On Apr 18, 2010, at 3:04 PM, Huolin Xin wrote: > > You'll need phonon entropy and electronic entropy as well. Free energy is > E-TS. The transition pressure is where the free energy of the two structures > are the same. > > On Sun, Apr 18, 2010 at 5:39 AM, naphtaly moro wrote: > >> Dear all, >> >> I am working on the pressure induced phase transitions of GaAs, I have >> already obtained, the respective EV data for the structures and want >> to get the transition pressures for the structures, Any advice on how >> this can be done in Espresso? >> >> Thanks >> Cecil Naphtaly Moro, >> Mphil. Student, >> Department of Physics, >> Moi University, Chepkoilel Campus, >> Kenya >> >> -- >> Cecil Naphtaly Moro >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de la > pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100418/4fe1ff76/attachment.htm From nnlinh at sissa.it Sun Apr 18 17:03:23 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Sun, 18 Apr 2010 17:03:23 +0200 (CEST) Subject: [Pw_forum] phonon calculation for optimized geometry -one subtle confusion In-Reply-To: References: Message-ID: <45090.93.149.238.193.1271603003.squirrel@webmail.sissa.it> > Dear Hanyu ! > Thanks for your reply. As you now the default value > for > the pressure in PWSCF is 0.5. This value should be 0.0 as the default value (see in input PW website) > I am using that value as convergence > threshold > but when I am doing scf calculation with the geometrical parameters value > obtained from the vc-relax calculation the pressure value is different > from > vc-relax final run. And as you know pressure will effect the phonon > dispresion relation..Can you please give me any suggestion, Before doing scf calculations, have you changed the cell-parameters in scf input file as same as the converged cell-parameters from vc-relax? Best regards, Linh > > Thanks alot, > MOHNISH > > On Sun, Apr 18, 2010 at 3:00 PM, Hanyu wrote: > >> dear mohnish : >> I think you should check it carefully again. I don't think it should >> be happen. In fact, the stress of scf and vc-relax should be the same. >> but if the stress is not the hydrostatic pressure, the result is not >> be believed. you have to relax the structure until the stress of the >> phase is what you want. >> >> best regards. >> >> Hanyu >> >> On Sun, Apr 18, 2010 at 11:16 AM, mohnish pandey >> >> wrote: >> > Dear users, >> > I want to do phonon calculation for some structures, >> but >> > after geometry optimization when I am using optimized geometry >> parameters >> > for scf calculation there is difference in stress of scf calculation >> and >> > vc-relax calculation which is changing phonon dispersion. Can anybody >> please >> > tell me if there is any option to use the data of relax or vc-relax >> > calculation for phonon dispersion.. Or can I doing phonon calculation >> along >> > with relax or vc-relax calculation.? >> > Thanks a lot in advance, >> > >> > -- >> > Regards, >> > MOHNISH, >> > ----------------------------------------------------------------- >> > Mohnish Pandey >> > Y6927262,4th Year dual degree student, >> > Department of Chemical Engineering, >> > IIT KANPUR >> > 09235721300 >> > ----------------------------------------------------------------- >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> > >> >> >> >> -- >> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=**=-=**=-=**=-=*=-=*=-=*=-=*=-=*=- >> Hanyu Liu(?????????), >> MS. >> State key Laboratory of Superhard Materials, Jilin University, China >> Email: liuhanyu08 at mails.jlu.edu.cn ouuing at gmail.com >> _______________________________________________ >> 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 > 09235721300 > ----------------------------------------------------------------- > _______________________________________________ > 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" ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From baroni at sissa.it Sun Apr 18 19:19:22 2010 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 18 Apr 2010 19:19:22 +0200 Subject: [Pw_forum] Phase Transition Pressures In-Reply-To: References: <2AD31070-1ECA-4C42-9790-F97C0AA2FDA5@sissa.it> Message-ID: there are no other relevant contributions to the entropy than phonons and (to a much lesser extent) electrons. my only point was that they are both irrelevant in the low-temperature regime which I presume cecil is mostly interested in. what is instead far from being irrelevant is the difference between different thermodynamical potential, which may be an obvious concept to an experimented researcher, not necessarily so to a student. the important thing to remember is that at finite pressuer the most stable structure is that which minimizes the enthalpy (or Gibbs free energy), and NOT the energy (or Helmholtz free energy). Hope this helps. Stefano On Apr 18, 2010, at 3:35 PM, Huolin Xin wrote: > Stefano, thanks a lot for pointing my mistake out. In the entropy term, besides phonon and electronic entropy, how to calculate the structural entropy? > > On Sun, Apr 18, 2010 at 9:25 AM, Stefano Baroni wrote: > Dear Huolin: as explained in my previous post, I beg to differ. Phonons have nothing to do with the question asked by Cecil, as long as the temperature is low enough. Even less, the electronic entropy, as long as the the system insulating (even in metals, the electronic entropy play a very little role, below the Farmi temperature which is typically several thousands degrees ...). Even considering temperature effects, it is not the "free energy" that has to be made equal (usually, one indicates with this term the Helmholts free energy, E-TS), but the "Gibbs free energy" (E-TS+PV). Hope this clarifies a bit ... SB > > On Apr 18, 2010, at 3:04 PM, Huolin Xin wrote: > >> You'll need phonon entropy and electronic entropy as well. Free energy is E-TS. The transition pressure is where the free energy of the two structures are the same. >> >> On Sun, Apr 18, 2010 at 5:39 AM, naphtaly moro wrote: >> Dear all, >> >> I am working on the pressure induced phase transitions of GaAs, I have >> already obtained, the respective EV data for the structures and want >> to get the transition pressures for the structures, Any advice on how >> this can be done in Espresso? >> >> Thanks >> Cecil Naphtaly Moro, >> Mphil. Student, >> Department of Physics, >> Moi University, Chepkoilel Campus, >> Kenya >> >> -- >> Cecil Naphtaly Moro >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > _______________________________________________ > 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/20100418/c46e86bc/attachment.htm From giannozz at democritos.it Sun Apr 18 19:29:09 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 18 Apr 2010 19:29:09 +0200 Subject: [Pw_forum] phonon calculation for optimized geometry -one subtle confusion In-Reply-To: References: Message-ID: On Apr 18, 2010, at 13:30 , mohnish pandey wrote: > when I am doing scf calculation with the geometrical parameters > value obtained from the vc-relax calculation the pressure value is > different from vc-relax final run. as explained a diverging number of times (even recently): the plane-wave basis set used during variable-cell calculations is determined by the given cutoff and the INITIAL cell. If you make a calculation with the final geometry at the same cutoff, you may get slightly different results. The difference should be small, though. P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From modaresi.mohsen at gmail.com Sun Apr 18 22:28:30 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Sun, 18 Apr 2010 23:28:30 +0300 Subject: [Pw_forum] A question about MPICH Message-ID: Hello Q.E. users Excuse me for this silly question!!! My computer has a dual-core processor, I installed MPICH, This is the part of 'make.sys' DFLAGS = -D__GFORTRAN -D__FFTW -D__MPI -D__PARA and MPIF90 = mpif90 #F90 = gfortran CC = cc F77 = gfortran but when i run "mpirun -np 2 pw.x -nimage 1 -inp gaaspw.out", I get This massage: connect to address ::1: Connection refused Trying 127.0.0.1... Permission denied. Where is the problem? Thanks Mohsen Modaresi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100418/09dee851/attachment.htm From idoldog at gmail.com Mon Apr 19 03:46:58 2010 From: idoldog at gmail.com (=?UTF-8?B?5p2O6aOe?=) Date: Mon, 19 Apr 2010 09:46:58 +0800 Subject: [Pw_forum] Alignment Procedure of Energy level in Different Systems In-Reply-To: <4BC42E00.90707@sissa.it> References: <201004130130473759173@gmail.com> <4BC42E00.90707@sissa.it> Message-ID: Thank you, i have known about that. Li Fei ? 2010?4?13? ??4:40?Ngoc Linh Nguyen ??? > idoldog wrote: > > Dear PWSCF users, > > > > recently, i was puzzled by an issue about energy level of different > systems. what i studied was doped perovskite-type crystal. because there > were two elements i used to dope, i got some different systems. For example, > in La-doped system, it must contain the element La, however, in Mo-doped > system, there is Mo dopant atoms instead of La impurity. Some scientists say > its zero energy is arbitrariness, so one must preform some alignment > procedure. > > > > so my question is: > > > > 1. what is meaning about the Fermi level given by PWSCF code directly? > in the output file, it might look like this: > > ---------------------------------------------------------------------- > > the Fermi energy is 12.3654 ev > > > > ! total energy = -2320.88829157 Ry > > Harris-Foulkes estimate = -2320.88829157 Ry > > estimated scf accuracy < 7.7E-10 Ry > > --------------------------------------------------------------------- > > > The question about Fermi energy is asked by many times, here is one > explanation as example: > > http://www.democritos.it/pipermail/pw_forum/2009-April/012396.html > > 2. i have got a lot of Fermi level with different systems. Can they > compare with each other? > Depend on what do you want to obtain. For example, it is interesting if > we consider the change of Ef as impurity's adoption. > > Best regards, > > > Linh > > > Look forward to your reply and ANY SUGGESTION IS APPRECIATED. > > > > > > > > Li Fei > > 2010-04-13 > > > > > > -- > > > > ????? ?? > > ?????????????? > > ----------------------------------------------- > > ???http://icm.nankai.edu.cn/sxliu/cn > > ???022-23509005 > > Email?lifei_job at yeah.net > > MSN?lifei.chn at hotmail.com > > ???????????????????????????????????300071) > > ? > ?????????????????????????????????????????????????????????????????????????????? > > _______________________________________________ > > 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 > -- ????????????? ?????????94? ??????? Email:lifei.job at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100419/9c9f1597/attachment-0001.htm From mohnish.iitk at gmail.com Mon Apr 19 05:48:55 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Mon, 19 Apr 2010 09:18:55 +0530 Subject: [Pw_forum] phonon calculation for optimized geometry -one subtle confusion In-Reply-To: <45090.93.149.238.193.1271603003.squirrel@webmail.sissa.it> References: <45090.93.149.238.193.1271603003.squirrel@webmail.sissa.it> Message-ID: Yea dear Linh, I have used the converged cell parameter from vc-relax calculation for scf run, Thnaks, mohnish On Sun, Apr 18, 2010 at 8:33 PM, Ngoc Linh Nguyen wrote: > > > Dear Hanyu ! > > Thanks for your reply. As you now the default value > > for > > the pressure in PWSCF is 0.5. > > This value should be 0.0 as the default value (see in input PW website) > > > I am using that value as convergence > > threshold > > but when I am doing scf calculation with the geometrical parameters value > > obtained from the vc-relax calculation the pressure value is different > > from > > vc-relax final run. And as you know pressure will effect the phonon > > dispresion relation..Can you please give me any suggestion, > > Before doing scf calculations, have you changed the cell-parameters in scf > input file as same as the converged cell-parameters from vc-relax? > > Best regards, > > Linh > > > > > > > Thanks alot, > > MOHNISH > > > > On Sun, Apr 18, 2010 at 3:00 PM, Hanyu wrote: > > > >> dear mohnish : > >> I think you should check it carefully again. I don't think it should > >> be happen. In fact, the stress of scf and vc-relax should be the same. > >> but if the stress is not the hydrostatic pressure, the result is not > >> be believed. you have to relax the structure until the stress of the > >> phase is what you want. > >> > >> best regards. > >> > >> Hanyu > >> > >> On Sun, Apr 18, 2010 at 11:16 AM, mohnish pandey > >> > >> wrote: > >> > Dear users, > >> > I want to do phonon calculation for some structures, > >> but > >> > after geometry optimization when I am using optimized geometry > >> parameters > >> > for scf calculation there is difference in stress of scf calculation > >> and > >> > vc-relax calculation which is changing phonon dispersion. Can anybody > >> please > >> > tell me if there is any option to use the data of relax or vc-relax > >> > calculation for phonon dispersion.. Or can I doing phonon calculation > >> along > >> > with relax or vc-relax calculation.? > >> > Thanks a lot in advance, > >> > > >> > -- > >> > Regards, > >> > MOHNISH, > >> > ----------------------------------------------------------------- > >> > Mohnish Pandey > >> > Y6927262,4th Year dual degree student, > >> > Department of Chemical Engineering, > >> > IIT KANPUR > >> > 09235721300 > >> > ----------------------------------------------------------------- > >> > > >> > _______________________________________________ > >> > Pw_forum mailing list > >> > Pw_forum at pwscf.org > >> > http://www.democritos.it/mailman/listinfo/pw_forum > >> > > >> > > >> > >> > >> > >> -- > >> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=**=-=**=-=**=-=*=-=*=-=*=-=*=-=*=- > >> Hanyu Liu(?????????), > >> MS. > >> State key Laboratory of Superhard Materials, Jilin University, China > >> Email: liuhanyu08 at mails.jlu.edu.cn ouuing at gmail.com > >> _______________________________________________ > >> 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 > > 09235721300 > > ----------------------------------------------------------------- > > _______________________________________________ > > 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" > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by SquirrelMail http://www.squirrelmail.org/ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR 09235721300 ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100419/69117321/attachment.htm From paulatto at sissa.it Mon Apr 19 11:07:46 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 19 Apr 2010 11:07:46 +0200 Subject: [Pw_forum] A question about MPICH In-Reply-To: References: Message-ID: Replying to message "[Pw_forum] A question about MPICH" from mohsen modaresi (18/04/10): > but when i run "mpirun -np 2 pw.x -nimage 1 -inp gaaspw.out", When you use "-inp" you don't have to use "<" (input redirector); I don't know if this is the cause of your problem, but for sure it does not help. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From parwana.habibi at cea.fr Mon Apr 19 15:49:37 2010 From: parwana.habibi at cea.fr (Parwana HABIBI) Date: Mon, 19 Apr 2010 15:49:37 +0200 Subject: [Pw_forum] question about projwfc.x Message-ID: <4BCC5F71.4080001@cea.fr> Hi, I would like to study the character of a surface state in chromium (is it more dz2 or dxy or .. ?), and for that, I've done a projwfc calculation. It gives me on each kpt, each band and the total weight of all the orbitals. What I would like to get is the contribution for each orbital separate. Is that possible? Or should I change a piece of the code? and if so? how do I know the right place? Thanks, Parwana From Michael.Mehl at nrl.navy.mil Mon Apr 19 16:03:14 2010 From: Michael.Mehl at nrl.navy.mil (Mike Mehl) Date: Mon, 19 Apr 2010 10:03:14 -0400 Subject: [Pw_forum] (Slightly) different energies based on ordering of atomic positions In-Reply-To: References: <4BC7742C.8010608@nrl.navy.mil> Message-ID: <4BCC62A2.6060904@nrl.navy.mil> Ah. A glitch in the computer architecture, then. Thanks Paolo. On 04/17/2010 08:37 AM, Paolo Giannozzi wrote: > This is what I got on a sp6 (FFT grids are slghtly different, the rest > should be > the same; I used the most recent version). The final steps of > self-consistency > are slightly different in the two cases, but the final results are the > same (and > the same as your second output) > > Paolo > > > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Michael J. Mehl Head, Center for Computational Materials Science Naval Research Laboratory Code 6390 Washington DC From nnlinh at sissa.it Mon Apr 19 16:10:50 2010 From: nnlinh at sissa.it (NgocLinh Nguyen) Date: Mon, 19 Apr 2010 16:10:50 +0200 Subject: [Pw_forum] question about projwfc.x In-Reply-To: <4BCC5F71.4080001@cea.fr> References: <4BCC5F71.4080001@cea.fr> Message-ID: <4BCC646A.9050405@sissa.it> Parwana HABIBI wrote: > Hi, > > I would like to study the character of a surface state in chromium (is > it more dz2 or dxy or .. ?), and for that, I've done a projwfc calculation. > It gives me on each kpt, each band and the total weight of all the orbitals. > Here, I am not clear about what you meant as kpt ??? > What I would like to get is the contribution for each orbital separate. > The fact that what you get from projwfc calculation are not only for all orbitals of each atom but also Projected DOS on each valence orbital of the each atom. Is it right ? If so, see more in http://www.quantum-espresso.org/input-syntax/INPUT_PROJWFC.html Good luck, Linh > Is that possible? Or should I change a piece of the code? and if so? how > p/s: Pls enclose your affiliation 's name in next discusses. > do I know the right place? > > Thanks, > > Parwana > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From parwana.habibi at cea.fr Mon Apr 19 16:15:57 2010 From: parwana.habibi at cea.fr (Parwana HABIBI) Date: Mon, 19 Apr 2010 16:15:57 +0200 Subject: [Pw_forum] question about projwfc.x In-Reply-To: <4BCC646A.9050405@sissa.it> References: <4BCC5F71.4080001@cea.fr> <4BCC646A.9050405@sissa.it> Message-ID: <4BCC659D.5040307@cea.fr> Hi, what I mean is this : 1 1Cr1 1 2 1 1 1 0.0000239456 1 2 0.0000330427 1 3 0.0000002564 1 4 0.0002903697 1 5 0.0022361365 1 6 0.0091035384 1 7 0.0255469182 1 8 0.0353335072 1 9 0.0000000000 1 10 0.0078272056 1 11 0.0000000000 1 12 0.0308578770 1 13 0.0591287408 1 14 0.0000000000 1 15 0.0634927971 1 16 0.0891558543 1 17 0.0000000000 1 18 0.0668713027 1 19 0.0609816494 .... For each atom considered, I have in the output the k-point, then the band number and then the total weight of all the orbitals projected of the corresponding band. I would like to see the different contributions of each orbital listed exactly as this, but for each orbital. THanks again, NgocLinh Nguyen wrote: > Parwana HABIBI wrote: > >> Hi, >> >> I would like to study the character of a surface state in chromium (is >> it more dz2 or dxy or .. ?), and for that, I've done a projwfc calculation. >> It gives me on each kpt, each band and the total weight of all the orbitals. >> >> > Here, I am not clear about what you meant as kpt ??? > >> What I would like to get is the contribution for each orbital separate. >> >> > The fact that what you get from projwfc calculation are not only for all > orbitals of each atom but also Projected DOS on each valence orbital of > the each atom. > Is it right ? If so, see more in > http://www.quantum-espresso.org/input-syntax/INPUT_PROJWFC.html > > > Good luck, > Linh > > >> Is that possible? Or should I change a piece of the code? and if so? how >> >> > > p/s: Pls enclose your affiliation 's name in next discusses. > >> do I know the right place? >> >> Thanks, >> >> Parwana >> _______________________________________________ >> 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 Mon Apr 19 16:24:50 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 19 Apr 2010 16:24:50 +0200 Subject: [Pw_forum] question about projwfc.x In-Reply-To: <4BCC659D.5040307@cea.fr> References: <4BCC5F71.4080001@cea.fr> <4BCC646A.9050405@sissa.it> <4BCC659D.5040307@cea.fr> Message-ID: <4BCC67B2.40608@democritos.it> Parwana HABIBI wrote: > I would like to see the different contributions > of each orbital listed exactly as this, but for each orbital. the output file contains the decomposition of each Kohn-Sham orbital into atomic orbitals P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Mon Apr 19 16:28:46 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 19 Apr 2010 16:28:46 +0200 Subject: [Pw_forum] (Slightly) different energies based on ordering of atomic positions In-Reply-To: <4BCC62A2.6060904@nrl.navy.mil> References: <4BC7742C.8010608@nrl.navy.mil> <4BCC62A2.6060904@nrl.navy.mil> Message-ID: <4BCC689E.4000307@democritos.it> Mike Mehl wrote: > Ah. A glitch in the computer architecture, then. maybe, or maybe not: hard to say. Sometimes highly optimized mathematical libraries are also a source of loss of accuracy. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From deyulu at yahoo.com Mon Apr 19 17:27:44 2010 From: deyulu at yahoo.com (Lu Deyu) Date: Mon, 19 Apr 2010 08:27:44 -0700 (PDT) Subject: [Pw_forum] Invitation to connect on LinkedIn Message-ID: <12751169.5781724.1271690864246.JavaMail.app@ech3-cdn10.prod> LinkedIn ------------Lu Deyu requested to add you as a connection on LinkedIn: ------------------------------------------ veronica, I'd like to add you to my professional network on LinkedIn. - Lu Accept invitation from Lu Deyu http://www.linkedin.com/e/XAAkmOm8d3sw5mZYSULFbcFqV9UKwx/blk/I71438744_5/6lColZJrmZznQNdhjRQnOpBtn9QfmhBt71BoSd1p65Lr6lOfPlvd3gTe3cQcjt9bR94m4dcmn92bPoQd3ANcjkPcz4LrCBxbOYWrSlI/EML_comm_afe/ View invitation from Lu Deyu http://www.linkedin.com/e/XAAkmOm8d3sw5mZYSULFbcFqV9UKwx/blk/I71438744_5/dlYQd3sUcPgNdQALqnpPbOYWrSlI/svi/ ------------------------------------------ DID YOU KNOW LinkedIn can help you find the right service providers using recommendations from your trusted network? Using LinkedIn Services, you can take the risky guesswork out of selecting service providers by reading the recommendations of credible, trustworthy members of your network. http://www.linkedin.com/e/svp/inv-25/ ------ (c) 2010, LinkedIn Corporation -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100419/d9ab684f/attachment.htm From modaresi.mohsen at gmail.com Mon Apr 19 19:18:39 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Mon, 19 Apr 2010 20:18:39 +0300 Subject: [Pw_forum] A question about MPICH In-Reply-To: References: Message-ID: Dear Lorenzo Thanks for your reply, But it did'nt work. any sugtion appreciated, Best regards, Mohsen Modarsei On Mon, Apr 19, 2010 at 12:07 PM, Lorenzo Paulatto wrote: > Replying to message "[Pw_forum] A question about MPICH" from mohsen > modaresi (18/04/10): > > but when i run "mpirun -np 2 pw.x -nimage 1 -inp > gaaspw.out", > > When you use "-inp" you don't have to use "<" (input redirector); I don't > know if this is the cause of your problem, but for sure it does not help. > > regards > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100419/e0dd232d/attachment.htm From paulatto at sissa.it Mon Apr 19 19:40:14 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 19 Apr 2010 19:40:14 +0200 Subject: [Pw_forum] A question about MPICH In-Reply-To: References: Message-ID: Replying to message "Re: [Pw_forum] A question about MPICH" from mohsen modaresi (19/04/10): > Thanks for your reply, But it did'nt work. Have you tried this? http://www.mcs.anl.gov/research/projects/mpi/mpich1/docs/faq.htm#permdenied -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From rmaezono at mac.com Tue Apr 20 05:54:04 2010 From: rmaezono at mac.com (=?ISO-2022-JP?B?GyRCQTAxYBsoQiAbJEJOQxsoQg==?=) Date: Tue, 20 Apr 2010 12:54:04 +0900 Subject: [Pw_forum] pw2casino for Gamma point molecular calculation Message-ID: <6A14A9F2-BD0C-4BD9-9901-EC17ED48F04B@mac.com> Dear colleagues, I calculated CO by Gamma point treatment, getting a reasonable result (all below are by single CPU calculation): linux10as03% cat co-mol.scf.in &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , prefix ='co-mol.scf' outdir = './' pseudo_dir = './' wf_collect = .true., tstress = .true., tprnfor = .true., / &SYSTEM ibrav = 0, nat = 2, ntyp = 2, ecutwfc = 500.0D0 , nosym = .true. , / &ELECTRONS conv_thr = 1.D-8 , mixing_beta = 0.3D0 , / CELL_PARAMETERS {hexagonal} 8.484874 0.000000 0.000000 4.242437 7.348108 0.000000 0.000000 0.000000 40.345668 ATOMIC_SPECIES C 12.0101 C-ppot-d.gon O 15.9994 O-ppot-d.gon ATOMIC_POSITIONS (angstrom) C 0.000047119 -0.000175620 8.307212730 0 0 0 O 0.000047176 -0.000175829 9.441855461 K_POINTS {Gamma} linux10as03% grep ene co co-mol.scf.in co-mol.scf.o co-mol.scf.save/ co-mol.scf.wfc1 linux10as03% grep ene co-mol.scf.o kinetic-energy cutoff = 500.0000 Ry Generated by old ld1 code (numerical format) Generated by old ld1 code (numerical format) total energy = -43.34077817 Ry total energy = -43.36187379 Ry total energy = -43.36056407 Ry total energy = -43.36197220 Ry total energy = -43.36207955 Ry total energy = -43.36212499 Ry total energy = -43.36218362 Ry total energy = -43.36216663 Ry total energy = -43.36217616 Ry total energy = -43.36217644 Ry total energy = -43.36217634 Ry total energy = -43.36217637 Ry total energy = -43.36217636 Ry ! total energy = -43.36217636 Ry The total energy is the sum of the following terms: General routines After this I used pw2casino, getting weird positive value of Total energy: linux10as03% cp inp_conv cp: missing destination file operand after `inp_conv' Try `cp --help' for more information. linux10as03% cat inp_conv &inputpp prefix='co-mol.scf', outdir='./' / linux10as03% ./pw2casino.x < inp_conv Program POST-PROC v.4.1.2 starts ... Today is 20Apr2010 at 12:21:17 Parallel version (MPI) Number of processors in use: 1 file O-ppot-d.gon: wavefunction(s) nX renormalized Planes per process (thick) : nr3 =576 npp = 576 ncplane =15625 Proc/ planes cols G planes cols G columns G Pool (dense grid) (smooth grid) (wavefct grid) 1 576 9925 3799907 576 9925 3799907 2479 475049 Writing file pwfn.data for program CASINO Kinetic energy 7.91267629151064 Local energy -45.0168438953591 Non-Local energy 1.60731128964544 Ewald energy 19.5535179884070 xc contribution -5.06908484728056 hartree energy 37.2571507178923 Total energy 16.2447275448156 For normal periodic X'tals, pw2casino works well in my computational environment. Is this a bug or something wrong in my operation? -------- Ryo Maezono Lecturer, Ph.D. Japan Advanced Institute of Science and Technology (JAIST) School of Information Science 1-1, Asahidai, Nomi, Ishikawa 923-1292 Japan rmaezono at mac.com From sclauzer at sissa.it Tue Apr 20 09:26:28 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 20 Apr 2010 09:26:28 +0200 Subject: [Pw_forum] question about projwfc.x In-Reply-To: <4BCC659D.5040307@cea.fr> References: <4BCC5F71.4080001@cea.fr> <4BCC646A.9050405@sissa.it> <4BCC659D.5040307@cea.fr> Message-ID: <4BCD5724.2020904@sissa.it> Parwana HABIBI wrote: > .... > I would like to see the different contributions > of each orbital listed exactly as this, but for each orbital. Given that this question is far from being clear, I hope I can guess what you want. If you specify filpdos in the inputpp namelist you will get, for each of the possible atomic orbitals in your system (given by the number of atoms and by the number of projectors in each PP file), a file containing the PDOS (the DOS projected onto that atomic orbital). In principle, given the projections in the filproj file (those you were showing previously), the k-point weights and a smearing function you could build by yourself the same quantity without any difficulty (have a look inside PP/projwfc.f90). You can select the orbitals centered on surface atoms and visualize their PDOS. You can even sum several PDOS, for instance those of certain surface layers, by using the utility sumpdos.x. HTH GS P.S. please append your affiliation, thanks. > > THanks again, > > > > NgocLinh Nguyen wrote: >> Parwana HABIBI wrote: >> >>> Hi, >>> >>> I would like to study the character of a surface state in chromium (is >>> it more dz2 or dxy or .. ?), and for that, I've done a projwfc calculation. >>> It gives me on each kpt, each band and the total weight of all the orbitals. >>> >>> >> Here, I am not clear about what you meant as kpt ??? >> >>> What I would like to get is the contribution for each orbital separate. >>> >>> >> The fact that what you get from projwfc calculation are not only for all >> orbitals of each atom but also Projected DOS on each valence orbital of >> the each atom. >> Is it right ? If so, see more in >> http://www.quantum-espresso.org/input-syntax/INPUT_PROJWFC.html >> >> >> Good luck, >> Linh >> >> >>> Is that possible? Or should I change a piece of the code? and if so? how >>> >>> >> p/s: Pls enclose your affiliation 's name in next discusses. >> >>> do I know the right place? >>> >>> Thanks, >>> >>> Parwana > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Tue Apr 20 09:53:33 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 20 Apr 2010 09:53:33 +0200 Subject: [Pw_forum] question about projwfc.x In-Reply-To: <4BCD5911.5040808@cea.fr> References: <4BCD5911.5040808@cea.fr> Message-ID: <4BCD5D7D.5020508@sissa.it> Parwana HABIBI wrote: > Hi, > > My question is not about the PDOS, because PDOS are integration of the > population on each energy level. This definition of PDOS does not make sense, to me at least, sorry. > What I meant in my question, is I would like to have the population (so > to say the weight) of each orbital on each band. Then, it is what you have shown previously in the filproj file. An electronic band extends in the BZ, so that you have also a dependency on the k-point. > The purpose of that, is that I would like to visualize the components of > a surface state in chromium, is it more dz2, or dxy... How do you identify the surface state? This depends a lot on the system, on the geometry... It seems to me that your task is not a general purpose one, those that can be done automagically by some utility. > > Do you understand my question now? Not much more than before, sorry. GS > Thanks, > > Parwana. > > PS: Ph.D student at CEA Saclay, France. -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Tue Apr 20 10:19:40 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 20 Apr 2010 10:19:40 +0200 Subject: [Pw_forum] question about projwfc.x In-Reply-To: <4BCD600B.8090800@cea.fr> References: <4BCD5911.5040808@cea.fr> <4BCD5D7D.5020508@sissa.it> <4BCD600B.8090800@cea.fr> Message-ID: <4BCD639C.7040808@sissa.it> Parwana HABIBI wrote: > Hi again, > > This is what I've shown, but the weight is the weight of ALL the orbitals. Yes, for each KS state (fixed by k-point and band) the code computes the square modulus of the projection on each atomic orbital (identified by an index). > Basically a DOS is an integration from -infinity to Fermi Level of a > dirac(E-Ef). for a projected dos it is the same multiplied by a certain > weight. OK, I agree. > It is that weight that I want to have. That weight depends on k-point, band and index of the atomic orbital, and it exactly what is shown on output in the filproj file. If you want the weights on the specific atomic orbital i, let's say, then you can use grep on that file (once you have identified the correct i). HTH GS > > > > Gabriele Sclauzero wrote: >> >> Parwana HABIBI wrote: >>> Hi, >>> >>> My question is not about the PDOS, because PDOS are integration of >>> the population on each energy level. >> >> This definition of PDOS does not make sense, to me at least, sorry. >> >> >>> What I meant in my question, is I would like to have the population >>> (so to say the weight) of each orbital on each band. >> >> Then, it is what you have shown previously in the filproj file. An >> electronic band extends in the BZ, so that you have also a dependency >> on the k-point. >> >>> The purpose of that, is that I would like to visualize the components >>> of a surface state in chromium, is it more dz2, or dxy... >> >> How do you identify the surface state? This depends a lot on the >> system, on the geometry... It seems to me that your task is not a >> general purpose one, those that can be done automagically by some >> utility. >> >>> >>> Do you understand my question now? >> >> Not much more than before, sorry. >> >> GS >> >>> Thanks, >>> >>> Parwana. >>> >>> PS: Ph.D student at CEA Saclay, France. >> > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Tue Apr 20 10:21:32 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 20 Apr 2010 10:21:32 +0200 Subject: [Pw_forum] question about projwfc.x In-Reply-To: <4BCD639C.7040808@sissa.it> References: <4BCD5911.5040808@cea.fr> <4BCD5D7D.5020508@sissa.it> <4BCD600B.8090800@cea.fr> <4BCD639C.7040808@sissa.it> Message-ID: <4BCD640C.6000805@sissa.it> Gabriele Sclauzero wrote: > > Parwana HABIBI wrote: >> Hi again, >> >> This is what I've shown, but the weight is the weight of ALL the orbitals. > > Yes, for each KS state (fixed by k-point and band) the code computes the square modulus of > the projection on each atomic orbital (identified by an index). > >> Basically a DOS is an integration from -infinity to Fermi Level of a >> dirac(E-Ef). for a projected dos it is the same multiplied by a certain >> weight. > > OK, I agree. > >> It is that weight that I want to have. > > That weight depends on k-point, band and index of the atomic orbital, and it exactly what Maybe this could be misinterpreted... I meant: k-point and band index of the KS state AND index of the atomic orbital GS > is shown on output in the filproj file. If you want the weights on the specific atomic > orbital i, let's say, then you can use grep on that file (once you have identified the > correct i). > > > HTH > > GS > > >> >> >> Gabriele Sclauzero wrote: >>> Parwana HABIBI wrote: >>>> Hi, >>>> >>>> My question is not about the PDOS, because PDOS are integration of >>>> the population on each energy level. >>> This definition of PDOS does not make sense, to me at least, sorry. >>> >>> >>>> What I meant in my question, is I would like to have the population >>>> (so to say the weight) of each orbital on each band. >>> Then, it is what you have shown previously in the filproj file. An >>> electronic band extends in the BZ, so that you have also a dependency >>> on the k-point. >>> >>>> The purpose of that, is that I would like to visualize the components >>>> of a surface state in chromium, is it more dz2, or dxy... >>> How do you identify the surface state? This depends a lot on the >>> system, on the geometry... It seems to me that your task is not a >>> general purpose one, those that can be done automagically by some >>> utility. >>> >>>> Do you understand my question now? >>> Not much more than before, sorry. >>> >>> GS >>> >>>> Thanks, >>>> >>>> Parwana. >>>> >>>> PS: Ph.D student at CEA Saclay, France. > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From merlin.meheut at lmtg.obs-mip.fr Tue Apr 20 12:03:01 2010 From: merlin.meheut at lmtg.obs-mip.fr (Merlin Meheut) Date: Tue, 20 Apr 2010 12:03:01 +0200 Subject: [Pw_forum] RRKJ pseudopotentials and raman calculations Message-ID: <4BCD7BD5.4040202@lmtg.obs-mip.fr> Dear PWSCF users, To be simple, I would like to know if there is a fundamental difference between rrkj pseudopotentials generated with the opium software and rrkj"us" pseudopotentials, such as the carbon pseudopotential C.pbe-rrkjus.UPF present on your website. Apparently, the former work for Raman calculations, on the same level as trouillier-martins, whereas the latter is considered as "ultrasoft" and therefore the calculation crashes. For my use, these rrkj pseudopotentials are perfect, since they seem sufficiently accurate and soft, and permit (if it is not a trick) to make Raman calculations. Pure Trouillier-Martins are usually very hard if high-precision is needed. Thanks in advance, Merlin (University of Toulouse, France) -- Merlin M?heut Maitre de conf?rences LMTG- Universit? Paul Sabatier Toulouse 3 14 avenue Edoaurd Belin 31400 Toulouse tel: (+33)5 61 33 26 21 Fax: (+33) 5 61 33 25 60 Mobile: (+33) 6 34 67 57 02 From marsamos at democritos.it Tue Apr 20 15:40:42 2010 From: marsamos at democritos.it (marsamos at democritos.it) Date: Tue, 20 Apr 2010 15:40:42 +0200 Subject: [Pw_forum] Fwd: new sax release Message-ID: <20100420154042.jy5qbl9iscso88ow@mail.democritos.it> New SAX (Self-energies And eXcitations) release sax-1.1.beta available at http://qe-forge.org/frs/?group_id=17). New improvements are: -Implementation of Martyna-Tuckerman trick for isolated systems (see example2) -1D (chains, wires, ....) systems affordable in a theoretically coherent way (see example4) -Excitons: for human readable analysis of bse and plot of the excitonic wave functions (beta version) Please inform the developers of any miss function or doubt. You can subscribe to the users mailing list at: http://qe-forge.org/mailman/listinfo/sax-project-users GOOD WORK bests sax developer team -- 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. ----- End forwarded message ----- -- 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 modaresi.mohsen at gmail.com Tue Apr 20 15:45:17 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Tue, 20 Apr 2010 18:15:17 +0430 Subject: [Pw_forum] A question about MPICH In-Reply-To: References: Message-ID: Dear Lorenzo I am so grateful, But this page is old and this not updated. But i could solve my problem with 'rsh 127.0.0.1' Mohsen Modaresi On Mon, Apr 19, 2010 at 10:10 PM, Lorenzo Paulatto wrote: > Replying to message "Re: [Pw_forum] A question about MPICH" from mohsen > modaresi (19/04/10): > > Thanks for your reply, But it did'nt work. > > Have you tried this? > http://www.mcs.anl.gov/research/projects/mpi/mpich1/docs/faq.htm#permdenied > > > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100420/f19c34a6/attachment.htm From paulatto at sissa.it Tue Apr 20 15:51:09 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 20 Apr 2010 15:51:09 +0200 Subject: [Pw_forum] A question about MPICH In-Reply-To: References: Message-ID: On Tue, 20 Apr 2010 15:45:17 +0200, mohsen modaresi wrote: > I am so grateful, But this page is old and this not updated. mpich itself is old, not updated since 2005 > But i could solve my problem with 'rsh 127.0.0.1' I'm happy to hear that, good luck with your work > Mohsen Modaresi -- 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 giannozz at democritos.it Tue Apr 20 17:13:13 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 20 Apr 2010 17:13:13 +0200 Subject: [Pw_forum] RRKJ pseudopotentials and raman calculations In-Reply-To: <4BCD7BD5.4040202@lmtg.obs-mip.fr> References: <4BCD7BD5.4040202@lmtg.obs-mip.fr> Message-ID: <4BCDC489.8020107@democritos.it> Merlin Meheut wrote: > I would like to know if there is a fundamental difference between > rrkj pseudopotentials generated with the opium software and rrkj"us" > pseudopotentials, such as the carbon pseudopotential C.pbe-rrkjus.UPF > present on your website. Apparently, the former work for Raman > calculations, on the same level as trouillier-martins, whereas the > latter is considered as "ultrasoft" and therefore the calculation crashes the calculation doesn't "crash", it stops with an error message. C.pbe-rrkjus.UPF is not "considered" ultrasoft: it "is" ultrasoft, obtained by ultrasoft pseudization of a hard norm-conserving pseudopotential. The latter is (usually but not necessarily) generated using the RRKJ (Rabe-Rappe-Kaxiras-Joanoupoulos) algorithm. This is why they are called "rrkjus". Norm conserving PP generated by ld1.x using the RRKJ pseudization should be more or less the same as those generated by OPIUM (just a guess, I never tried to compare them) > For my use, these rrkj pseudopotentials are perfect No problem, use them P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From merlin.meheut at lmtg.obs-mip.fr Tue Apr 20 17:25:45 2010 From: merlin.meheut at lmtg.obs-mip.fr (Merlin Meheut) Date: Tue, 20 Apr 2010 17:25:45 +0200 Subject: [Pw_forum] RRKJ pseudopotentials and raman calculations In-Reply-To: <4BCDC489.8020107@democritos.it> References: <4BCD7BD5.4040202@lmtg.obs-mip.fr> <4BCDC489.8020107@democritos.it> Message-ID: <4BCDC779.5020208@lmtg.obs-mip.fr> Paolo Giannozzi a ?crit : > Merlin Meheut wrote: > > >> I would like to know if there is a fundamental difference between >> rrkj pseudopotentials generated with the opium software and rrkj"us" >> pseudopotentials, such as the carbon pseudopotential C.pbe-rrkjus.UPF >> present on your website. Apparently, the former work for Raman >> calculations, on the same level as trouillier-martins, whereas the >> latter is considered as "ultrasoft" and therefore the calculation crashes >> > > the calculation doesn't "crash", it stops with an error message. > C.pbe-rrkjus.UPF is not "considered" ultrasoft: it "is" ultrasoft, > obtained by ultrasoft pseudization of a hard norm-conserving > pseudopotential. The latter is (usually but not necessarily) > generated using the RRKJ (Rabe-Rappe-Kaxiras-Joanoupoulos) > algorithm. This is why they are called "rrkjus". Norm conserving > PP generated by ld1.x using the RRKJ pseudization should be more > or less the same as those generated by OPIUM (just a guess, I never > tried to compare them) > > >> For my use, these rrkj pseudopotentials are perfect >> > > No problem, use them > > P. > Dear Paolo, If I have well understood what you said, rrkj ("optimized") pseudopotentials generated with opium are also ultrasoft. In this case, I would like to understand why pwscf does not stop with an error message when doing raman calculations with these pseudopotentials. Sincerely, Merlin -- Merlin M?heut Maitre de conf?rences LMTG- Universit? Paul Sabatier Toulouse 3 14 avenue Edoaurd Belin 31400 Toulouse tel: (+33)5 61 33 26 21 Fax: (+33) 5 61 33 25 60 Mobile: (+33) 6 34 67 57 02 From giannozz at democritos.it Tue Apr 20 17:35:02 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 20 Apr 2010 17:35:02 +0200 Subject: [Pw_forum] RRKJ pseudopotentials and raman calculations In-Reply-To: <4BCDC779.5020208@lmtg.obs-mip.fr> References: <4BCD7BD5.4040202@lmtg.obs-mip.fr> <4BCDC489.8020107@democritos.it> <4BCDC779.5020208@lmtg.obs-mip.fr> Message-ID: <4BCDC9A6.70902@democritos.it> Merlin Meheut wrote: > If I have well understood what you said, rrkj ("optimized") > pseudopotentials generated with opium are also ultrasoft. I don't think so. DO you have any evidence of this? P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From ejwalt at wm.edu Tue Apr 20 17:38:10 2010 From: ejwalt at wm.edu (Eric J. Walter) Date: Tue, 20 Apr 2010 11:38:10 -0400 Subject: [Pw_forum] RRKJ pseudopotentials and raman calculations In-Reply-To: <4BCDC9A6.70902@democritos.it> References: <4BCD7BD5.4040202@lmtg.obs-mip.fr> <4BCDC489.8020107@democritos.it> <4BCDC779.5020208@lmtg.obs-mip.fr> <4BCDC9A6.70902@democritos.it> Message-ID: <4BCDCA62.2030700@wm.edu> Paolo Giannozzi wrote: > Merlin Meheut wrote: > > >> If I have well understood what you said, rrkj ("optimized") >> pseudopotentials generated with opium are also ultrasoft. >> > > I don't think so. DO you have any evidence of this? > > P. > OPIUM makes norm conserving pseudopotentials only. No ultrasoft. Eric From merlin.meheut at lmtg.obs-mip.fr Tue Apr 20 17:53:29 2010 From: merlin.meheut at lmtg.obs-mip.fr (Merlin Meheut) Date: Tue, 20 Apr 2010 17:53:29 +0200 Subject: [Pw_forum] RRKJ pseudopotentials and raman calculations In-Reply-To: <4BCDCA62.2030700@wm.edu> References: <4BCD7BD5.4040202@lmtg.obs-mip.fr> <4BCDC489.8020107@democritos.it> <4BCDC779.5020208@lmtg.obs-mip.fr> <4BCDC9A6.70902@democritos.it> <4BCDCA62.2030700@wm.edu> Message-ID: <4BCDCDF9.3020703@lmtg.obs-mip.fr> Eric J. Walter a ?crit : > Paolo Giannozzi wrote: > >> Merlin Meheut wrote: >> >> >> >>> If I have well understood what you said, rrkj ("optimized") >>> pseudopotentials generated with opium are also ultrasoft. >>> >>> >> I don't think so. DO you have any evidence of this? >> >> P. >> >> > > > OPIUM makes norm conserving pseudopotentials only. No ultrasoft. > > Eric > > > I understand now. My confusion comes from the fact that, to my knowledge, there is no norm-conserving pseudopotentials generated using the RRKJ algorithm on the official website. Is there a reason for this? Merlin > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Merlin M?heut Maitre de conf?rences LMTG- Universit? Paul Sabatier Toulouse 3 14 avenue Edoaurd Belin 31400 Toulouse tel: (+33)5 61 33 26 21 Fax: (+33) 5 61 33 25 60 Mobile: (+33) 6 34 67 57 02 From ejwalt at wm.edu Tue Apr 20 17:59:04 2010 From: ejwalt at wm.edu (Eric J. Walter) Date: Tue, 20 Apr 2010 11:59:04 -0400 Subject: [Pw_forum] RRKJ pseudopotentials and raman calculations In-Reply-To: <4BCDCDF9.3020703@lmtg.obs-mip.fr> References: <4BCD7BD5.4040202@lmtg.obs-mip.fr> <4BCDC489.8020107@democritos.it> <4BCDC779.5020208@lmtg.obs-mip.fr> <4BCDC9A6.70902@democritos.it> <4BCDCA62.2030700@wm.edu> <4BCDCDF9.3020703@lmtg.obs-mip.fr> Message-ID: <4BCDCF48.2000406@wm.edu> Merlin Meheut wrote: > Eric J. Walter a ?crit : > >> Paolo Giannozzi wrote: >> >> >>> Merlin Meheut wrote: >>> >>> >>> >>> >>>> If I have well understood what you said, rrkj ("optimized") >>>> pseudopotentials generated with opium are also ultrasoft. >>>> >>>> >>>> >>> I don't think so. DO you have any evidence of this? >>> >>> P. >>> >>> >>> >> OPIUM makes norm conserving pseudopotentials only. No ultrasoft. >> >> Eric >> >> >> >> > > I understand now. My confusion comes from the fact that, to my knowledge, > there is no norm-conserving pseudopotentials generated using the RRKJ > algorithm > on the official website. Is there a reason for this? > > Merlin > > > >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> > > > Both ld1 and opium generate norm-conserving psps using the RRKJ method. The RRKJ method (also called "optimized") is standard norm-conserving psp generation method, just like Troullier-Martins. The RRKJ method can also be used as a starting point for generating an ultrasoft psp, in which case is sometimes referred to as RRKJ-US. Only the ld1 code can do this, however. Eric From giannozz at democritos.it Tue Apr 20 18:00:16 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 20 Apr 2010 18:00:16 +0200 Subject: [Pw_forum] RRKJ pseudopotentials and raman calculations In-Reply-To: <4BCDCDF9.3020703@lmtg.obs-mip.fr> References: <4BCD7BD5.4040202@lmtg.obs-mip.fr> <4BCDC489.8020107@democritos.it> <4BCDC779.5020208@lmtg.obs-mip.fr> <4BCDC9A6.70902@democritos.it> <4BCDCA62.2030700@wm.edu> <4BCDCDF9.3020703@lmtg.obs-mip.fr> Message-ID: <4BCDCF90.30303@democritos.it> Merlin Meheut wrote: > My confusion comes from the fact that, to my knowledge, there is no > norm-conserving pseudopotentials generated using the RRKJ algorithm > on the official website there are a few: Al.pbe-rrkj.UPF Ar.pz-rrkj.UPF Si.pbe-rrkj.UPF Te.pbe-rrkj.UPF P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Tue Apr 20 22:46:32 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 20 Apr 2010 22:46:32 +0200 Subject: [Pw_forum] pw2casino for Gamma point molecular calculation In-Reply-To: <6A14A9F2-BD0C-4BD9-9901-EC17ED48F04B@mac.com> References: <6A14A9F2-BD0C-4BD9-9901-EC17ED48F04B@mac.com> Message-ID: <0CA223B6-EC57-436F-BB1F-924B799D6465@democritos.it> On Apr 20, 2010, at 5:54 , ?? ? wrote: > After this I used pw2casino, getting weird positive value of Total > energy I am not sure pw2casino is supposed to work for gamma-only calculations. You can easily check this by performing the same scf calculation with K_POINTS {tpiba} 1 0.0 0.0 0.0 1.0 (no Gamma-point tricks) instead of K_POINTS {Gamma} I made a quick test and it looks like the local energy in pw2casino is not the same 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 udayagiri3 at gmail.com Wed Apr 21 06:38:51 2010 From: udayagiri3 at gmail.com (udayagiri sai babu) Date: Wed, 21 Apr 2010 10:08:51 +0530 Subject: [Pw_forum] bands calculation Message-ID: Dear all i am calculating electronic band structure of LaoFeP superconductor. I have two questions regarding this. As I have understood from the example01, I need to perform an "scf" calculation followed by "bands" calculation. My question is 1) Why cant we do bands calculation alone, as all we need is energy eigen values at different k_points for all available bands. This can be done by solving Kohn-Sham equations at those k points for all bands. 2) what data from scf calculation is used by bands calculation. 3)when I did scf calculation for the following input file fermienergy is not written in the output file. can somebody tell me if something is wrong? &control calculation ='scf' restart_mode='from_scratch', outdir='/home/sai/laofep/', prefix='laofep' pseudo_dir='/home/sai/softwares/espresso-4.1.2/pseudo' / &system ibrav=0, celldm(1)=7.487, celldm(3)=16.083, nat=8, ntyp=4, ecutwfc=50, ecutrho=500, occupations='fixed', nbnd=38, / &electrons conv_thr=1.D-8, diagonalization='david', mixing_mode='plain', mixing_beta= 0.7 / ATOMIC_SPECIES La 138.905 La.pw91-nsp-van.UPF O 15.999 O.pw91-van_ak.UPF P 30.973 P.pw91-van_ak.UPF Fe 55.845 Fe.pw91-sp-van_ak.UPF ATOMIC_POSITIONS (bohr) La 0.000234206 3.687761102 10.487650296 La 3.687732709 0.000277249 5.739475052 O 0.000215849 0.000260237 8.115083977 O 3.687739522 3.687788174 8.115072590 Fe 0.000245844 0.000231960 0.091985046 Fe 3.687778452 3.687741841 0.091985975 P 3.687720269 0.000225890 14.089592313 P 0.000266430 3.687752524 2.133535171 K_POINTS {automatic} 10 10 5 0 0 0 CELL_PARAMETERS 0.985045304 0.000000280 -0.000002934 0.000000280 0.985045750 0.000000396 -0.000004795 -0.000000455 2.142143981 -- U.Saibabu PhD student, Deformation mechanisms modeling group, Materials engineering department, IISc Bangalore, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100421/9ec0f87f/attachment.htm From mahasinalam at yahoo.co.uk Wed Apr 21 07:46:06 2010 From: mahasinalam at yahoo.co.uk (MAHASIN ALAM) Date: Wed, 21 Apr 2010 05:46:06 +0000 (GMT) Subject: [Pw_forum] How to run jobs in PWScf? Message-ID: <617789.3272.qm@web24104.mail.ird.yahoo.com> Dear Friends, ? I have compiled the esspresso-4.0.5 in linux cluster. I have run some examples using command ./run_example. All the jobs finished successfuly. Can any one help me how to run my own jobs in PWScf. I mean how to create the input file and how to run it in PWScf. Thanks a lot. ? Warm regards ? Mahasin M. Pharm (JU) PhD student School of Chemical and Biomedical Engineering Nanyang Technological University Sinpapore -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100421/d10e26cd/attachment.htm From nnlinh at sissa.it Wed Apr 21 09:55:06 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Wed, 21 Apr 2010 09:55:06 +0200 Subject: [Pw_forum] How to run jobs in PWScf? In-Reply-To: <617789.3272.qm@web24104.mail.ird.yahoo.com> References: <617789.3272.qm@web24104.mail.ird.yahoo.com> Message-ID: <4BCEAF5A.3060001@sissa.it> MAHASIN ALAM wrote: > Dear Friends, > > I have compiled the esspresso-4.0.5 in linux cluster. I have run some > examples using command ./run_example. All the jobs finished > successfuly. Can any one help me how to run my own jobs in PWScf. > > I mean how to create the input file > To create an input file, you should see in the examples to refer and see in http://www.quantum-espresso.org/input-syntax/INPUT_PW.html#id3668692 to understand the parameters in input file. > and how to run it in PWScf. Thanks a lot. > to run PWScf, you see in user guider: http://www.quantum-espresso.org/user_guide/user_guide.html and it just need you have some background about Unix environment. Also, see in the run_example script in the examples to learn more. Good luck, Linh > > Warm regards > > Mahasin > > M. Pharm (JU) > PhD student > School of Chemical and Biomedical Engineering > Nanyang Technological University > Sinpapore > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 Wed Apr 21 10:06:56 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Wed, 21 Apr 2010 10:06:56 +0200 Subject: [Pw_forum] bands calculation In-Reply-To: References: Message-ID: <4BCEB220.5080900@sissa.it> udayagiri sai babu wrote: > Dear all i am calculating electronic band structure of LaoFeP > superconductor. I have two questions regarding this. > As I have understood from the example01, I need to perform an "scf" > calculation followed by "bands" calculation. > My question is > 1) Why cant we do bands calculation alone, as all we need is energy > eigen values at different k_points for all available bands. This can > be done by solving Kohn-Sham equations at those k points for all bands. Because "scf" run will do solving Kohn-Sham equations, and "bands" does some things else. > 2) what data from scf calculation is used by bands calculation. that are mainly the eigenvalues at each K_point and also some other relevant data. > > 3)when I did scf calculation for the following input file fermienergy > is not written in the output file. can somebody tell me if something > is wrong? Fermi_energy in isolators is not written out, but in metals. You can see in previous archives to see how to estimate the Fermi_energy of isolator. It is not so difficult. Good luck, Linh > > &control > calculation ='scf' > restart_mode='from_scratch', > outdir='/home/sai/laofep/', > prefix='laofep' > pseudo_dir='/home/sai/softwares/espresso-4.1.2/pseudo' > / > &system > ibrav=0, > celldm(1)=7.487, > celldm(3)=16.083, > nat=8, > ntyp=4, > ecutwfc=50, > ecutrho=500, > occupations='fixed', > nbnd=38, > / > &electrons > conv_thr=1.D-8, > diagonalization='david', > mixing_mode='plain', > mixing_beta= 0.7 > / > ATOMIC_SPECIES > La 138.905 La.pw91-nsp-van.UPF > O 15.999 O.pw91-van_ak.UPF > P 30.973 P.pw91-van_ak.UPF > Fe 55.845 Fe.pw91-sp-van_ak.UPF > ATOMIC_POSITIONS (bohr) > La 0.000234206 3.687761102 10.487650296 > La 3.687732709 0.000277249 5.739475052 > O 0.000215849 0.000260237 8.115083977 > O 3.687739522 3.687788174 8.115072590 > Fe 0.000245844 0.000231960 0.091985046 > Fe 3.687778452 3.687741841 0.091985975 > P 3.687720269 0.000225890 14.089592313 > P 0.000266430 3.687752524 2.133535171 > K_POINTS {automatic} > 10 10 5 0 0 0 > CELL_PARAMETERS > 0.985045304 0.000000280 -0.000002934 > 0.000000280 0.985045750 0.000000396 > -0.000004795 -0.000000455 2.142143981 > > -- > U.Saibabu > PhD student, > Deformation mechanisms modeling group, > Materials engineering department, > IISc Bangalore, > India. > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ----------------------------------------------------- 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 Wed Apr 21 10:14:50 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 21 Apr 2010 10:14:50 +0200 Subject: [Pw_forum] bands calculation In-Reply-To: <4BCEB220.5080900@sissa.it> References: <4BCEB220.5080900@sissa.it> Message-ID: <4BCEB3FA.9090002@democritos.it> Ngoc Linh Nguyen wrote: >> 2) what data from scf calculation is used by bands calculation. > that are mainly the eigenvalues at each K_point and also some other > relevant data. not true. A band calculation uses the charge density from a scf calculation. -- Paolo Giannozzi, Democritos and University of Udine, Italy From mahkameh_va at yahoo.com Wed Apr 21 12:37:53 2010 From: mahkameh_va at yahoo.com (raheleh vaziri) Date: Wed, 21 Apr 2010 03:37:53 -0700 (PDT) Subject: [Pw_forum] isosurface of wave functions Message-ID: <297714.43579.qm@web32901.mail.mud.yahoo.com> Dear All, How can obtain or compute isosurfaces of? wafe functions at fermi state or gama state? thank you so much for any help! R.Vaziri -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100421/dcdf2fe9/attachment.htm From sclauzer at sissa.it Wed Apr 21 13:47:37 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 21 Apr 2010 13:47:37 +0200 Subject: [Pw_forum] bands calculation In-Reply-To: References: Message-ID: <4BCEE5D9.8020009@sissa.it> udayagiri sai babu wrote: > Dear all i am calculating electronic band structure of LaoFeP > superconductor. I have two questions regarding this. > As I have understood from the example01, I need to perform an "scf" > calculation followed by "bands" calculation. That's right. > My question is > 1) Why cant we do bands calculation alone, as all we need is energy > eigen values at different k_points for all available bands. This can be > done by solving Kohn-Sham equations at those k points for all bands. Because DFT is a self-consistent field (SCF) method! I hope this is clear to you, with all that this implies. Essentially, to get the self-consistent KS Hamiltonian you need the self-consistent charge density, which is defined as an integral in the 3D BZ. This integral is approximated with a sum over an appropriate set of k-points in the BZ (PWscf uses uniformly spaced regular grids, possibly shifted from the origin). Since you have to perform this kind of summation many times in a self consistent cycle (until converge is reached), you choose the minimal set of k-points which gives you the desired accuracy. Once you have the SCF Hamiltonian (only AFTER you got the SCF charge density), you can diagonalize it at any desired k-point to get the band structure along a path in reciprocal space. This path is not chosen in order to give a good sampling of the BZ (as instead the regular grid of above), but usually follows some high symmetry lines of the crystal. > 2) what data from scf calculation is used by bands calculation. The self-consistent charge density is the key quantity. See also the replies from other people. > > 3)when I did scf calculation for the following input file fermienergy is > not written in the output file. can somebody tell me if something is wrong? Nothing wrong. The Fermi energy is not well defined for an insulator. HTH GS > > &control > calculation ='scf' > restart_mode='from_scratch', > outdir='/home/sai/laofep/', > prefix='laofep' > pseudo_dir='/home/sai/softwares/espresso-4.1.2/pseudo' > / > &system > ibrav=0, > celldm(1)=7.487, > celldm(3)=16.083, > nat=8, > ntyp=4, > ecutwfc=50, > ecutrho=500, > occupations='fixed', > nbnd=38, > / > &electrons > conv_thr=1.D-8, > diagonalization='david', > mixing_mode='plain', > mixing_beta= 0.7 > / > ATOMIC_SPECIES > La 138.905 La.pw91-nsp-van.UPF > O 15.999 O.pw91-van_ak.UPF > P 30.973 P.pw91-van_ak.UPF > Fe 55.845 Fe.pw91-sp-van_ak.UPF > ATOMIC_POSITIONS (bohr) > La 0.000234206 3.687761102 10.487650296 > La 3.687732709 0.000277249 5.739475052 > O 0.000215849 0.000260237 8.115083977 > O 3.687739522 3.687788174 8.115072590 > Fe 0.000245844 0.000231960 0.091985046 > Fe 3.687778452 3.687741841 0.091985975 > P 3.687720269 0.000225890 14.089592313 > P 0.000266430 3.687752524 2.133535171 > K_POINTS {automatic} > 10 10 5 0 0 0 > CELL_PARAMETERS > 0.985045304 0.000000280 -0.000002934 > 0.000000280 0.985045750 0.000000396 > -0.000004795 -0.000000455 2.142143981 > > -- > U.Saibabu > PhD student, > Deformation mechanisms modeling group, > Materials engineering department, > IISc Bangalore, > India. > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Wed Apr 21 14:41:49 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 21 Apr 2010 14:41:49 +0200 Subject: [Pw_forum] isosurface of wave functions In-Reply-To: <297714.43579.qm@web32901.mail.mud.yahoo.com> References: <297714.43579.qm@web32901.mail.mud.yahoo.com> Message-ID: <4BCEF28D.5060301@sissa.it> Dear R. Vaziri, raheleh vaziri wrote: > Dear All, > > How can obtain or compute isosurfaces of wafe functions at fermi state > or gama state? The procedure is similar to that for obtaining a charge density contour plot (see example05 and http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_postproc.pdf). In the pp.x run you have to tell the program that you want to extract the electronic wavefunction (see Doc/INPUT_PP) and select the k-point and band index corresponding to the state that you want to visualize (see k-point list at the beginning of the output of pw.x and the band eigenvalues at the end). Instead of using plotrho.x, you can use, for instance, xcrysden or gnuplot to generate the contour plots once you have extracted the quantity (3D or 2D in the first case, only 2D on the second). HTH GS > > thank you so much for any help! > > R.Vaziri Please be so kind to supply your affiliation next time. Thanks! > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From wangqj1 at 126.com Wed Apr 21 16:19:47 2010 From: wangqj1 at 126.com (Q.J.Wang) Date: Wed, 21 Apr 2010 22:19:47 +0800 (CST) Subject: [Pw_forum] relax not converge Message-ID: Dear all When I optimized the structure of two Mn atoms doped 2*2*2 supercell, the scf not converge at the eighth cycle and it stops after 100 iterations. So I want to know the reson of this problem, is it the structural distortion ? Hwo to solve this problem ? Any advice will be appreciated . -- Best regards Q.J.Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100421/91a39bad/attachment.htm From nnlinh at sissa.it Wed Apr 21 17:14:30 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Wed, 21 Apr 2010 17:14:30 +0200 Subject: [Pw_forum] relax not converge In-Reply-To: References: Message-ID: <4BCF1656.30808@sissa.it> Q.J.Wang wrote: > Dear all > When I optimized the structure of two Mn atoms doped 2*2*2 > supercell, the scf not converge at the eighth cycle and it stops after > 100 iterations. So I want to know the reson of this problem, is it the > structural distortion ? The problem has been considered many times and also become "Frequently Asked Questions" > Hwo to solve this problem ? See in previous archives of Pw_forum or in http://www.quantum-espresso.org/user_guide/node78.html#SECTION00096020000000000000 Good luck, Linh > Any advice will be appreciated . > -- > Best regards > > Q.J.Wang > > XiangTan University > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 amiri_physics at yahoo.com Thu Apr 22 12:23:39 2010 From: amiri_physics at yahoo.com (peyman amiri) Date: Thu, 22 Apr 2010 03:23:39 -0700 (PDT) Subject: [Pw_forum] (no subject) Message-ID: <191684.32245.qm@web58002.mail.re3.yahoo.com> Dear all I am working on a (100) free surface of cubic NaCl MnSe, In an optimization stage i have a problem with a below fault message: ? ? ? ? ? ?? from n_plane_waves : error #???????? 1 ???????????????????????????????? No PWs ! What is a reason of this problem? It should be mentioned that program was performed on a cluster.? Any kind advice will be appreciated, Regards Peiman ====================================== Peiman Amiri Computational Condensed Matter Research Lab Physics Department, Isfahan University of Technology, Iran Tel lab: +98 311 391 3733 Fax Office: +98311 391 3746 ------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100422/69ce295e/attachment.htm From giannozz at democritos.it Thu Apr 22 12:45:00 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 22 Apr 2010 12:45:00 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: <191684.32245.qm@web58002.mail.re3.yahoo.com> References: <191684.32245.qm@web58002.mail.re3.yahoo.com> Message-ID: On Apr 22, 2010, at 12:23 , peyman amiri wrote: > from n_plane_waves : error # 1 > No PWs ! this is very strange: you should never get such a message unless you are using more processors than plane waves. 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 udayagiri3 at gmail.com Fri Apr 23 06:32:02 2010 From: udayagiri3 at gmail.com (udayagiri sai babu) Date: Fri, 23 Apr 2010 10:02:02 +0530 Subject: [Pw_forum] bands calculation In-Reply-To: <4BCEE5D9.8020009@sissa.it> References: <4BCEE5D9.8020009@sissa.it> Message-ID: Thank you very much Gabriele Sclauzero for your clear explanation. Now I understand what is happening in the band structure calculation. On Wed, Apr 21, 2010 at 5:17 PM, Gabriele Sclauzero wrote: > > udayagiri sai babu wrote: > > Dear all i am calculating electronic band structure of LaoFeP > > superconductor. I have two questions regarding this. > > As I have understood from the example01, I need to perform an "scf" > > calculation followed by "bands" calculation. > > That's right. > > > My question is > > 1) Why cant we do bands calculation alone, as all we need is energy > > eigen values at different k_points for all available bands. This can be > > done by solving Kohn-Sham equations at those k points for all bands. > > Because DFT is a self-consistent field (SCF) method! I hope this is clear > to you, with all > that this implies. > > Essentially, to get the self-consistent KS Hamiltonian you need the > self-consistent charge > density, which is defined as an integral in the 3D BZ. This integral is > approximated with > a sum over an appropriate set of k-points in the BZ (PWscf uses uniformly > spaced regular > grids, possibly shifted from the origin). Since you have to perform this > kind of summation > many times in a self consistent cycle (until converge is reached), you > choose the minimal > set of k-points which gives you the desired accuracy. > > Once you have the SCF Hamiltonian (only AFTER you got the SCF charge > density), you can > diagonalize it at any desired k-point to get the band structure along a > path in reciprocal > space. This path is not chosen in order to give a good sampling of the BZ > (as instead the > regular grid of above), but usually follows some high symmetry lines of the > crystal. > > > > 2) what data from scf calculation is used by bands calculation. > > The self-consistent charge density is the key quantity. See also the > replies from other > people. > > > > > 3)when I did scf calculation for the following input file fermienergy is > > not written in the output file. can somebody tell me if something is > wrong? > > Nothing wrong. The Fermi energy is not well defined for an insulator. > > HTH > > GS > > > > > &control > > calculation ='scf' > > restart_mode='from_scratch', > > outdir='/home/sai/laofep/', > > prefix='laofep' > > pseudo_dir='/home/sai/softwares/espresso-4.1.2/pseudo' > > / > > &system > > ibrav=0, > > celldm(1)=7.487, > > celldm(3)=16.083, > > nat=8, > > ntyp=4, > > ecutwfc=50, > > ecutrho=500, > > occupations='fixed', > > nbnd=38, > > / > > &electrons > > conv_thr=1.D-8, > > diagonalization='david', > > mixing_mode='plain', > > mixing_beta= 0.7 > > / > > ATOMIC_SPECIES > > La 138.905 La.pw91-nsp-van.UPF > > O 15.999 O.pw91-van_ak.UPF > > P 30.973 P.pw91-van_ak.UPF > > Fe 55.845 Fe.pw91-sp-van_ak.UPF > > ATOMIC_POSITIONS (bohr) > > La 0.000234206 3.687761102 10.487650296 > > La 3.687732709 0.000277249 5.739475052 > > O 0.000215849 0.000260237 8.115083977 > > O 3.687739522 3.687788174 8.115072590 > > Fe 0.000245844 0.000231960 0.091985046 > > Fe 3.687778452 3.687741841 0.091985975 > > P 3.687720269 0.000225890 14.089592313 > > P 0.000266430 3.687752524 2.133535171 > > K_POINTS {automatic} > > 10 10 5 0 0 0 > > CELL_PARAMETERS > > 0.985045304 0.000000280 -0.000002934 > > 0.000000280 0.985045750 0.000000396 > > -0.000004795 -0.000000455 2.142143981 > > > > -- > > U.Saibabu > > PhD student, > > Deformation mechanisms modeling group, > > Materials engineering department, > > IISc Bangalore, > > India. > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- U.Saibabu PhD student, Deformation mechanisms modeling group, Materials engineering department, IISc Bangalore, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100423/7a7ace87/attachment.htm From xomiakk at gmail.com Fri Apr 23 07:34:02 2010 From: xomiakk at gmail.com (Olga Sedelnikova) Date: Fri, 23 Apr 2010 12:34:02 +0700 Subject: [Pw_forum] intraband transitions in eps.x code Message-ID: Dear All, The equation for complex dielectric function used in eps.x code contains intra and interband transitions. From the other hand, the matrix elemt acconts only for interband transitions. My question is Wither will the intraband transitions affect on the results of eps.x calculations? Thank you Olga Sedelnikova -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100423/1de1a45e/attachment.htm From vitruss at gmail.com Fri Apr 23 08:46:14 2010 From: vitruss at gmail.com (Vit) Date: Fri, 23 Apr 2010 14:46:14 +0800 Subject: [Pw_forum] MoS2 - reproducing papers Message-ID: Dear, all! I'm trying to reproduce MoS2 band structure from [1], but it seems to be really different! I've double checked all the input, but nothing helps. Could you please point me where am I wrong? Band file, reference band structure and my computations are attached. With best regards, Koroteev Victor PhD student, NIIC SB RAS -- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100423/52c96b3f/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: MoS2-reference.png Type: image/png Size: 77151 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100423/52c96b3f/attachment-0002.png -------------- next part -------------- A non-text attachment was scrubbed... Name: MoS2-mine.png Type: image/png Size: 40666 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100423/52c96b3f/attachment-0003.png -------------- next part -------------- A non-text attachment was scrubbed... Name: MoS2.band.in Type: application/octet-stream Size: 3429 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100423/52c96b3f/attachment-0001.obj From modaresi.mohsen at gmail.com Fri Apr 23 10:25:20 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Fri, 23 Apr 2010 12:55:20 +0430 Subject: [Pw_forum] MoS2 - reproducing papers In-Reply-To: References: Message-ID: Hi Vit Have you done NSCF calculation in given direction? Mohsen Modaresi On Fri, Apr 23, 2010 at 11:16 AM, Vit wrote: > Dear, all! > I'm trying to reproduce MoS2 band structure from [1], but it seems to be > really different! > I've double checked all the input, but nothing helps. Could you please > point me where am I wrong? > Band file, reference band structure and my computations are attached. > With best regards, > Koroteev Victor > PhD student, > NIIC SB RAS > > > -- > > > _______________________________________________ > 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/20100423/c022ce8f/attachment.htm From vitruss at gmail.com Fri Apr 23 10:32:15 2010 From: vitruss at gmail.com (Vit) Date: Fri, 23 Apr 2010 16:32:15 +0800 Subject: [Pw_forum] MoS2 - reproducing papers In-Reply-To: References: Message-ID: Dear Mohsen, Actually, I'm doing NSCF calculation (I'm running pw.x MoS2.bands.in). I've tried to change "calculation='bands'" to "calculation='nscf'" and it doesn't affect band structure. Regards, Koroteev Victor > Hi Vit > Have you done NSCF calculation in given direction? > Mohsen Modaresi > On Fri, Apr 23, 2010 at 11:16 AM, Vit wrote: >> Dear, all! >> I'm trying to reproduce MoS2 band structure from [1], but it seems to be really different! >> I've double checked all the input, but nothing helps. Could you please point me where am I wrong? >> Band file, reference band structure and my computations are attached. >> With best regards,Koroteev Victor >> PhD student, >> NIIC SB RAS >> -- >> _______________________________________________ >> 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/20100423/64539a65/attachment.htm From giannozz at democritos.it Fri Apr 23 12:14:35 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 23 Apr 2010 12:14:35 +0200 Subject: [Pw_forum] MoS2 - reproducing papers In-Reply-To: References: Message-ID: <4BD1730B.5090409@democritos.it> Vit wrote: > I've double checked all the input, but nothing helps. did you visualized your structure with xcrysden? are you sure it is the correct one? P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From vitruss at gmail.com Fri Apr 23 11:56:06 2010 From: vitruss at gmail.com (Vit) Date: Fri, 23 Apr 2010 17:56:06 +0800 Subject: [Pw_forum] MoS2 - reproducing papers In-Reply-To: <4BD1730B.5090409@democritos.it> References: <4BD1730B.5090409@democritos.it> Message-ID: Dear Paolo, Yes. I've done it. It looks good. Regards, Koroteev Victor On Fri, 23 Apr 2010 18:14:35 +0800, Paolo Giannozzi wrote: > Vit wrote: > >> I've double checked all the input, but nothing helps. > > did you visualized your structure with xcrysden? are you > sure it is the correct one? > > P. -- From baroni at sissa.it Fri Apr 23 13:01:13 2010 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 23 Apr 2010 13:01:13 +0200 Subject: [Pw_forum] intraband transitions in eps.x code In-Reply-To: References: Message-ID: <3E9A1381-BBC7-4F7C-BD24-C5207EA698F6@sissa.it> Olga: I know nothing about eps.x, but my solid-state textbook says that only inter-band transitions contribute to the optical absorption coefficient (because of selection rules, electromagnetic radiation only couples electronic states with a same wavevector). Maybe, part of the code (or of its documentation) refers to the general dielectric function, eps(q,omega), whereas some other parts only calculate eps(q=0,omega). The latter is relevant for optical transitions (and, as said, does not contain contributions from intra-band transitions). The former does have contributions from intraband transition (only in metals, though), but it is not relevant for optical transitions (it is for other spectroscopies, such as eels). The former note on the relevance of interband transitions (if any) only for metals is due to the Pauli principle which forbids transition to an accupied state. Hope this helps - Stefano PS: would you mind completeing your signature with your current scientific affiliation? thanks On Apr 23, 2010, at 7:34 AM, Olga Sedelnikova wrote: > Dear All, > The equation for complex dielectric function used in eps.x code contains intra and interband transitions. From the other hand, the matrix elemt acconts only for interband transitions. > My question is > Wither will the intraband transitions affect on the results of eps.x calculations? > > Thank you > > Olga Sedelnikova > > _______________________________________________ > 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/20100423/5f6ef686/attachment.htm From modaresi.mohsen at gmail.com Fri Apr 23 14:10:03 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Fri, 23 Apr 2010 16:40:03 +0430 Subject: [Pw_forum] MoS2 - reproducing papers In-Reply-To: References: <4BD1730B.5090409@democritos.it> Message-ID: Dear Via I am not sure, But i think you have not done "nscf" calculation before your bond structure calculation. My suggestion: 1) Do scf calculation with automatic option for K-points. 2) Do nscf calculation in given direction 3) Plot bond structure. Mohsen Modaresi On Fri, Apr 23, 2010 at 2:26 PM, Vit wrote: > Dear Paolo, > Yes. I've done it. It looks good. > Regards, > Koroteev Victor > > On Fri, 23 Apr 2010 18:14:35 +0800, Paolo Giannozzi < > giannozz at democritos.it> wrote: > > > Vit wrote: > > > >> I've double checked all the input, but nothing helps. > > > > did you visualized your structure with xcrysden? are you > > sure it is the correct one? > > > > P. > > > -- > _______________________________________________ > 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/20100423/4e78c0f2/attachment.htm From nnlinh at sissa.it Fri Apr 23 14:23:47 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Fri, 23 Apr 2010 14:23:47 +0200 Subject: [Pw_forum] MoS2 - reproducing papers In-Reply-To: References: Message-ID: <4BD19153.5000704@sissa.it> Vit wrote: > Dear, all! > I'm trying to reproduce MoS2 band structure from [1], but it seems to > be really different! > I've double checked all the input, but nothing helps. Could you please > point me where am I wrong? > Band file, reference band structure and my computations are attached. By visualizing configuration, I find that your input file has a "strange" structure of MoS2. I search on google and find that the MoS2 structure is analogous graphene structure, see in http://www.tribology-abc.com/abc/solidlub.htm , but your model is not the same at al. It for sure induces a different band structure. Try checking it again . Good luck, Linh > With best regards, > Koroteev Victor > PhD student, > NIIC SB RAS > > > -- > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 paulatto at sissa.it Fri Apr 23 14:38:19 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 23 Apr 2010 14:38:19 +0200 Subject: [Pw_forum] MoS2 - reproducing papers In-Reply-To: References: <4BD1730B.5090409@democritos.it> Message-ID: On Fri, 23 Apr 2010 14:10:03 +0200, mohsen modaresi wrote: > I am not sure, But i think you have not done "nscf" calculation before > your bond structure calculation. A band (not bond) calculation and a ncsf calculation are almost exactly the same thing. In particular, they produce the same band structure. 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 vitruss at gmail.com Fri Apr 23 14:39:41 2010 From: vitruss at gmail.com (Vit) Date: Fri, 23 Apr 2010 19:39:41 +0700 Subject: [Pw_forum] MoS2 - reproducing papers In-Reply-To: <4BD19153.5000704@sissa.it> References: <4BD19153.5000704@sissa.it> Message-ID: Dear Ngoc! The structure you are giving is not the same. But it's not 2H-MoS2, which is in paper. 2H-MoS2 looks like here http://www.ems.psu.edu/~ryba/coursework/492W/MoS2.jpg you can compare it to mine. It's the same. I can send you cif file in case. Best regards, Victor Koroteev On Fri, Apr 23, 2010 at 7:23 PM, Ngoc Linh Nguyen wrote: > Vit wrote: >> Dear, all! >> I'm trying to reproduce MoS2 band structure from [1], but it seems to >> be really different! >> I've double checked all the input, but nothing helps. Could you please >> point me where am I wrong? >> Band file, reference band structure and my computations are attached. > By visualizing configuration, I find that your input file has a > "strange" structure of MoS2. > I search on google and find that the MoS2 structure is analogous > graphene structure, > see in http://www.tribology-abc.com/abc/solidlub.htm , but your model is > not the same at al. It for sure induces a different band structure. > > Try checking it again . > > Good luck, > > Linh >> With best regards, >> Koroteev Victor >> PhD student, >> NIIC SB RAS >> >> >> -- >> >> >> ------------------------------------------------------------------------ >> >> >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 nnlinh at sissa.it Fri Apr 23 15:18:11 2010 From: nnlinh at sissa.it (Ngoc Linh Nguyen) Date: Fri, 23 Apr 2010 15:18:11 +0200 Subject: [Pw_forum] MoS2 - reproducing papers In-Reply-To: References: <4BD19153.5000704@sissa.it> Message-ID: <4BD19E13.8060900@sissa.it> Vit wrote: > Dear Ngoc! > The structure you are giving is not the same. But it's not 2H-MoS2, > which is in paper. 2H-MoS2 looks like here > http://www.ems.psu.edu/~ryba/coursework/492W/MoS2.jpg you can compare > it to mine. It's the same. I can send you cif file in case. > Using Xcryden and visualizing your input file, I see that they are different in periodic structure. Here, I send to you an example change, in which I reduced the cell's values a bit, and you can see the structure is closer to reference one in periodic structure. Of course, you should recalculate the cell's parameters to get better configurations. Anyway, I suggest to use supercell for this kind of structure. Good luck, Linh > Best regards, > Victor Koroteev > > On Fri, Apr 23, 2010 at 7:23 PM, Ngoc Linh Nguyen wrote: > >> Vit wrote: >> >>> Dear, all! >>> I'm trying to reproduce MoS2 band structure from [1], but it seems to >>> be really different! >>> I've double checked all the input, but nothing helps. Could you please >>> point me where am I wrong? >>> Band file, reference band structure and my computations are attached. >>> >> By visualizing configuration, I find that your input file has a >> "strange" structure of MoS2. >> I search on google and find that the MoS2 structure is analogous >> graphene structure, >> see in http://www.tribology-abc.com/abc/solidlub.htm , but your model is >> not the same at al. It for sure induces a different band structure. >> >> Try checking it again . >> >> Good luck, >> >> Linh >> >>> With best regards, >>> Koroteev Victor >>> PhD student, >>> NIIC SB RAS >>> >>> >>> -- >>> >>> >>> ------------------------------------------------------------------------ >>> >>> >>> ------------------------------------------------------------------------ >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> 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 >> >> > _______________________________________________ > 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" -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: aa.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20100423/64761587/attachment.asc From vitruss at gmail.com Fri Apr 23 14:32:57 2010 From: vitruss at gmail.com (Vit) Date: Fri, 23 Apr 2010 20:32:57 +0800 Subject: [Pw_forum] MoS2 - reproducing papers In-Reply-To: <4BD19E13.8060900@sissa.it> References: <4BD19153.5000704@sissa.it> <4BD19E13.8060900@sissa.it> Message-ID: Thank you very much for your efforts. It really was structure problem, but it was in one sign of cell axis. It should be -1.57500000. I've spent full day thinking what it could be! With best regards, Koroteev Victor > Vit wrote: >> Dear Ngoc! >> The structure you are giving is not the same. But it's not 2H-MoS2, >> which is in paper. 2H-MoS2 looks like here >> http://www.ems.psu.edu/~ryba/coursework/492W/MoS2.jpg you can compare >> it to mine. It's the same. I can send you cif file in case. >> > Using Xcryden and visualizing your input file, I see that they are > different in periodic structure. > Here, I send to you an example change, in which I reduced the cell's > values a bit, and you can see the structure is closer to reference one > in periodic structure. > Of course, you should recalculate the cell's parameters to get better > configurations. Anyway, I suggest to use supercell for this kind of > structure. > > Good luck, > > Linh > > > >> Best regards, >> Victor Koroteev >> >> On Fri, Apr 23, 2010 at 7:23 PM, Ngoc Linh Nguyen wrote: >> >>> Vit wrote: >>> >>>> Dear, all! >>>> I'm trying to reproduce MoS2 band structure from [1], but it seems to >>>> be really different! >>>> I've double checked all the input, but nothing helps. Could you please >>>> point me where am I wrong? >>>> Band file, reference band structure and my computations are attached. >>>> >>> By visualizing configuration, I find that your input file has a >>> "strange" structure of MoS2. >>> I search on google and find that the MoS2 structure is analogous >>> graphene structure, >>> see in http://www.tribology-abc.com/abc/solidlub.htm , but your model is >>> not the same at al. It for sure induces a different band structure. >>> >>> Try checking it again . >>> >>> Good luck, >>> >>> Linh >>> >>>> With best regards, >>>> Koroteev Victor >>>> PhD student, >>>> NIIC SB RAS >>>> >>>> >>>> -- >>>> >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > -- From wulilixiangguo at sina.com Fri Apr 23 21:37:14 2010 From: wulilixiangguo at sina.com (wulilixiangguo at sina.com) Date: Sat, 24 Apr 2010 03:37:14 +0800 Subject: [Pw_forum] INPUT file for average.x Message-ID: <20100423193714.92437CF615F@mail3-92.sinamail.sina.com.cn>  I read below and have a question about macroscopic averages. If my system have a surface between two materials which have different lattice constant. How to set the awin?How to macroscopic it twice? Thank you! 1 filename 1.0 3000 3 2.59 The explanation is in the header of the file PP/average.f90: ! nfile ! the number of 3D-FFT files ! for each file: ! filename ! the name of the 3D-FFT file ! weight ! the weight of the quantity in this file ! . ! . ! end ! npt ! the number of points of the thick mesh ! idir ! 1,2 or 3. It is the fixed index which defines ! ! the planes of the planar average ! awin ! the size of the window for macroscopic averages. ! With the example above you'll get a 3-column output file for the quantity to average V(u): - column 1: coordinate u, defined over a mesh of npt=3000 points along the direction idir=3 - column 2: averaged quantity V - column 3: macroscopically averaged quantity V', over a windows with size awin=2.50 au If you want to average a weighted sum of different quantities V1,...,VN defined over the same FFT mesh, just set nfile to N and specify N file names with the relative weight. Regards, Giovanni -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100424/27712efa/attachment.htm From payam.norouzzadeh at gmail.com Sat Apr 24 05:28:55 2010 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Sat, 24 Apr 2010 07:58:55 +0430 Subject: [Pw_forum] Error message Message-ID: Hello All I am doing Phonon calculations for Germanium Clathrates. I have done scf calculations before and this is my Ge.ph.in file : phonons of Ge &inputph tr2_ph=1.0d-14, ldisp=.true. , nq1=6, nq2=6, nq3=6 amass(1)=72.64, prefix='PH', outdir='/lustre/work/espresso/Recover' fildyn='Ge.dyn', / I get this error messages and no where I found any explanation: from phonon : error # 1 wrong starting k Could any one help me? Breg, Payam Norouzzadeh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100424/13b21fd1/attachment-0001.htm From rmaezono at mac.com Sat Apr 24 05:35:49 2010 From: rmaezono at mac.com (=?ISO-2022-JP?B?GyRCQTAxYBsoQiAbJEJOQxsoQg==?=) Date: Sat, 24 Apr 2010 12:35:49 +0900 Subject: [Pw_forum] pw2casino for Gamma point molecular calculation (Ryo Maezono) In-Reply-To: References: Message-ID: <7A378F84-3D1B-442D-9F80-890F95FD6AEE@mac.com> Thank you, Paolo, I found that your proposed way is working solution. ------------- Ryo Maezono Lecturer, Ph.D. Japan Advanced Institute of Science and Technology (JAIST) School of Information Science 1-1, Asahidai, Nomi, Ishikawa 923-1292 Japan rmaezono at mac.com > Message: 6 > Date: Tue, 20 Apr 2010 22:46:32 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] pw2casino for Gamma point molecular > calculation > To: PWSCF Forum > Message-ID: <0CA223B6-EC57-436F-BB1F-924B799D6465 at democritos.it> > Content-Type: text/plain; charset=UTF-8; delsp=yes; format=flowed > > On Apr 20, 2010, at 5:54 , ?? ? wrote: > >> After this I used pw2casino, getting weird positive value of Total >> energy > > I am not sure pw2casino is supposed to work for gamma-only > calculations. > You can easily check this by performing the same scf calculation with > K_POINTS {tpiba} > 1 > 0.0 0.0 0.0 1.0 > (no Gamma-point tricks) instead of > K_POINTS {Gamma} > I made a quick test and it looks like the local energy in pw2casino > is not > the same 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 payam.norouzzadeh at gmail.com Sat Apr 24 05:56:40 2010 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Sat, 24 Apr 2010 08:26:40 +0430 Subject: [Pw_forum] recovering interrupted jobs Message-ID: Hello All I have time limitation in running jobs on cluster (48 hours at most) . After that time the job is not processed more and I need to learn how to recover interrupted jobs. I created prefix.EXIT in working directory to recover job for ph.x later but it does not reply at all. The version of quantum-espresso I am using is 4-0-5. Could anyone do me a favor and teach me how to recover my interrupted jobs? Breg, Payam Norouzzadeh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100424/869f9445/attachment.htm From sheena.shah at materials.ox.ac.uk Sat Apr 24 10:24:18 2010 From: sheena.shah at materials.ox.ac.uk (Sheena Shah) Date: Sat, 24 Apr 2010 09:24:18 +0100 Subject: [Pw_forum] recovering interrupted jobs In-Reply-To: References: Message-ID: I do not know your input file, but you should use the flag: recover=.true. and this should pick up from your phPREFIX.phsave directory how many modes have already been calculated and just continue from there. From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Payam Norouzzadeh Sent: 24 April 2010 04:57 To: pw_forum at pwscf.org Subject: [Pw_forum] recovering interrupted jobs Hello All I have time limitation in running jobs on cluster (48 hours at most) . After that time the job is not processed more and I need to learn how to recover interrupted jobs. I created prefix.EXIT in working directory to recover job for ph.x later but it does not reply at all. The version of quantum-espresso I am using is 4-0-5. Could anyone do me a favor and teach me how to recover my interrupted jobs? Breg, Payam Norouzzadeh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100424/169c296a/attachment.htm From mohnish.iitk at gmail.com Sat Apr 24 11:06:05 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Sat, 24 Apr 2010 14:36:05 +0530 Subject: [Pw_forum] recovering interrupted jobs In-Reply-To: References: Message-ID: For pw.x calculation you can use "restart_mode" = "restart" flag in &control to recover your jobs. On Sat, Apr 24, 2010 at 9:26 AM, Payam Norouzzadeh < payam.norouzzadeh at gmail.com> wrote: > Hello All > I have time limitation in running jobs on cluster (48 hours at most) . > After that time the job is not processed more and I need to learn how to > recover interrupted jobs. > I created prefix.EXIT in working directory to recover job for ph.x later > but it does not reply at all. > The version of quantum-espresso I am using is 4-0-5. > Could anyone do me a favor and teach me how to recover my interrupted jobs? > Breg, Payam Norouzzadeh > > _______________________________________________ > 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 09235721300 ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100424/893de6e5/attachment.htm From giannozz at democritos.it Sat Apr 24 16:22:51 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 24 Apr 2010 16:22:51 +0200 Subject: [Pw_forum] the code for pwscf to castep In-Reply-To: <3e36a8fc1003090611l6bd31774qbff3bb7344593765@mail.gmail.com> References: <3e36a8fc1003090611l6bd31774qbff3bb7344593765@mail.gmail.com> Message-ID: <3FA6D453-08FF-4085-80BD-9DF3A2C1C890@democritos.it> On Mar 9, 2010, at 15:11 , Wei Zhou wrote: > -- http://www2.tcm.phy.cam.ac.uk/onetep/Main/Utilities > there are a code which can translate the castep pseudo potential to > pwscf , > however I found the effect does not good [...] if somebody have > interests > about it ,he can inverstigate the source code and change it to more > accurate. Statements like "I will do" are much more welcome than statements like "please someone do". Anyway: I made a quick test with two pseudopotentials for C and O and the resulting CO molecule was looking good, i.e., similar to what one obtains with other 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 modaresi.mohsen at gmail.com Sat Apr 24 20:53:18 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Sat, 24 Apr 2010 23:23:18 +0430 Subject: [Pw_forum] =?windows-1252?q?A_problem_in_installation_=28nested_f?= =?windows-1252?q?unction_=91getchar=92_declared_=91extern=92=29?= Message-ID: Dear Users and Developers, I want install Q.E. on a x86_64 system, And i get this eror make[1]: Leaving directory `/home/user/Desktop/espresso411/Modules' ( cd clib ; if test "make" = "" ; then make TLDEPS= all ; \ else make TLDEPS= all ; fi ) make[1]: Entering directory `/home/user/Desktop/espresso411/clib' cc -O3 -D__GFORTRAN -D__FFTW3 -D__MPI -D__PARA -I../include -c stack.c cc -O3 -D__GFORTRAN -D__FFTW3 -D__MPI -D__PARA -I../include -c c_mkdir.c cc -O3 -D__GFORTRAN -D__FFTW3 -D__MPI -D__PARA -I../include -c cptimer.c cc -O3 -D__GFORTRAN -D__FFTW3 -D__MPI -D__PARA -I../include -c eval_infix.c cc -O3 -D__GFORTRAN -D__FFTW3 -D__MPI -D__PARA -I../include -c fft_stick.c cc -O3 -D__GFORTRAN -D__FFTW3 -D__MPI -D__PARA -I../include -c indici.c cc -O3 -D__GFORTRAN -D__FFTW3 -D__MPI -D__PARA -I../include -c memstat.c In file included from /usr/include/stdio.h:907, from /usr/include/malloc.h:26, from memstat.c:24: /usr/include/bits/stdio.h: In function ?memstat_?: /usr/include/bits/stdio.h:46: error: nested function ?getchar? declared ?extern? /usr/include/bits/stdio.h:45: error: static declaration of ?getchar? follows non-static declaration /usr/include/stdio.h:520: note: previous declaration of ?getchar? was here /usr/include/bits/stdio.h:55: error: nested function ?fgetc_unlocked? declared ?extern? /usr/include/bits/stdio.h:54: error: static declaration of ?fgetc_unlocked? follows non-static declaration /usr/include/stdio.h:543: note: previous declaration of ?fgetc_unlocked? was here /usr/include/bits/stdio.h:65: error: nested function ?getc_unlocked? declared ?extern? /usr/include/bits/stdio.h:64: error: static declaration of ?getc_unlocked? follows non-static declaration /usr/include/stdio.h:532: note: previous declaration of ?getc_unlocked? was here /usr/include/bits/stdio.h:72: error: nested function ?getchar_unlocked? declared ?extern? /usr/include/bits/stdio.h:71: error: static declaration of ?getchar_unlocked? follows non-static declaration /usr/include/stdio.h:533: note: previous declaration of ?getchar_unlocked? was here /usr/include/bits/stdio.h:81: error: nested function ?putchar? declared ?extern? /usr/include/bits/stdio.h:80: error: static declaration of ?putchar? follows non-static declaration /usr/include/bits/stdio.h:90: error: nested function ?fputc_unlocked? declared ?extern? /usr/include/bits/stdio.h:89: error: static declaration of ?fputc_unlocked? follows non-static declaration /usr/include/bits/stdio.h:100: error: nested function ?putc_unlocked? declared ?extern? /usr/include/bits/stdio.h:99: error: static declaration of ?putc_unlocked? follows non-static declaration /usr/include/bits/stdio.h:107: error: nested function ?putchar_unlocked? declared ?extern? /usr/include/bits/stdio.h:106: error: static declaration of ?putchar_unlocked? follows non-static declaration /usr/include/bits/stdio.h:127: error: nested function ?feof_unlocked? declared ?extern? /usr/include/bits/stdio.h:126: error: static declaration of ?feof_unlocked? follows non-static declaration /usr/include/stdio.h:809: note: previous declaration of ?feof_unlocked? was here /usr/include/bits/stdio.h:134: error: nested function ?ferror_unlocked? declared ?extern? /usr/include/bits/stdio.h:133: error: static declaration of ?ferror_unlocked? follows non-static declaration /usr/include/stdio.h:810: note: previous declaration of ?ferror_unlocked? was here In file included from /usr/include/stdio.h:910, from /usr/include/malloc.h:26, from memstat.c:24: /usr/include/bits/stdio2.h:33: error: nested function ?sprintf? declared ?extern? /usr/include/bits/stdio2.h:32: error: static declaration of ?sprintf? follows non-static declaration /usr/include/bits/stdio2.h:46: error: nested function ?vsprintf? declared ?extern? /usr/include/bits/stdio2.h:44: error: static declaration of ?vsprintf? follows non-static declaration /usr/include/bits/stdio2.h:64: error: nested function ?snprintf? declared ?extern? /usr/include/bits/stdio2.h:62: error: static declaration of ?snprintf? follows non-static declaration /usr/include/bits/stdio2.h:77: error: nested function ?vsnprintf? declared ?extern? /usr/include/bits/stdio2.h:75: error: static declaration of ?vsnprintf? follows non-static declaration /usr/include/bits/stdio2.h:97: error: nested function ?fprintf? declared ?extern? /usr/include/bits/stdio2.h:96: error: static declaration of ?fprintf? follows non-static declaration /usr/include/bits/stdio2.h:104: error: nested function ?printf? declared ?extern? /usr/include/bits/stdio2.h:103: error: static declaration of ?printf? follows non-static declaration /usr/include/bits/stdio2.h:116: error: nested function ?vprintf? declared ?extern? /usr/include/bits/stdio2.h:115: error: static declaration of ?vprintf? follows non-static declaration /usr/include/bits/stdio2.h:127: error: nested function ?vfprintf? declared ?extern? /usr/include/bits/stdio2.h:125: error: static declaration of ?vfprintf? follows non-static declaration /usr/include/bits/stdio2.h:227: error: nested function ?gets? declared ?extern? /usr/include/bits/stdio2.h:226: error: static declaration of ?gets? follows non-static declaration /usr/include/stdio.h:612: note: previous declaration of ?gets? was here /usr/include/bits/stdio2.h:246: error: nested function ?fgets? declared ?extern? /usr/include/bits/stdio2.h:245: error: static declaration of ?fgets? follows non-static declaration /usr/include/stdio.h:604: note: previous declaration of ?fgets? was here /usr/include/bits/stdio2.h:276: error: nested function ?fread? declared ?extern? /usr/include/bits/stdio2.h:274: error: static declaration of ?fread? follows non-static declaration /usr/include/stdio.h:682: note: previous declaration of ?fread? was here /usr/include/bits/stdio2.h:337: error: nested function ?fread_unlocked? declared ?extern? /usr/include/bits/stdio2.h:335: error: static declaration of ?fread_unlocked? follows non-static declaration /usr/include/stdio.h:710: note: previous declaration of ?fread_unlocked? was here make[1]: *** [memstat.o] Error 1 make[1]: Leaving directory `/home/user/Desktop/espresso411/clib' make: *** [libs] Error 2 Any suggestion appreciated Best regards, Mohsen Modarsei From giannozz at democritos.it Sat Apr 24 21:23:41 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 24 Apr 2010 21:23:41 +0200 Subject: [Pw_forum] =?windows-1252?q?A_problem_in_installation_=28nested_f?= =?windows-1252?q?unction_=91getchar=92_declared_=91extern=92=29?= In-Reply-To: References: Message-ID: <90BB1BB9-E8DB-44DA-A66E-066DCC7BD804@democritos.it> On Apr 24, 2010, at 20:53 , mohsen modaresi wrote: > I want install Q.E. on a x86_64 system, And i get this eror http://www.democritos.it/pipermail/pw_forum/2010-February/015757.html --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From zdw2000 at gmail.com Sun Apr 25 02:20:37 2010 From: zdw2000 at gmail.com (Wei Zhou) Date: Sun, 25 Apr 2010 08:20:37 +0800 Subject: [Pw_forum] the code for pwscf to castep In-Reply-To: <3FA6D453-08FF-4085-80BD-9DF3A2C1C890@democritos.it> References: <3e36a8fc1003090611l6bd31774qbff3bb7344593765@mail.gmail.com> <3FA6D453-08FF-4085-80BD-9DF3A2C1C890@democritos.it> Message-ID: yes ,my dear profesor, what you said is right, but in my understand the pseudo is a very complex theory,which need a long time to study it clearly, for the time being I donnot have enough time to do this. In fact I test the pseudo of Ba from castep to pwscf, but it donnot give a good result, the lattic parameter is wrong a lot of for bcc Ba. 2010/4/24 Paolo Giannozzi > > On Mar 9, 2010, at 15:11 , Wei Zhou wrote: > > > -- http://www2.tcm.phy.cam.ac.uk/onetep/Main/Utilities > > there are a code which can translate the castep pseudo potential to > > pwscf , > > however I found the effect does not good [...] if somebody have > > interests > > about it ,he can inverstigate the source code and change it to more > > accurate. > > Statements like "I will do" are much more welcome than statements like > "please someone do". Anyway: I made a quick test with two > pseudopotentials > for C and O and the resulting CO molecule was looking good, i.e., > similar to > what one obtains with other 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 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ZhouDawei JiLin Universiyt ,ChangChun ,China zdw2000 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100425/a09b02e6/attachment-0001.htm From payam.norouzzadeh at gmail.com Sun Apr 25 03:25:30 2010 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Sun, 25 Apr 2010 05:55:30 +0430 Subject: [Pw_forum] different XC functionals Message-ID: Hello All I am going to do phonon calculations for Ba, Ga, Ge semiconductor alloys but their available pseudopotentials are not of the same type. They have different exchange correlations functionals. Do I have to generate all necessary pseudopotentials myself? Are these differences between XC functionals negligible? For example can I apply Ga.pw91-n-van.UPF and Ge.pw91-n-van.UPF along with Ba.pw91-nsp-van.UPF? Are above mentioned pseudopotentials proper for phonon calculations? I don't know exactly the meaning of pw91, pbe, n,van,nsp,meta,tm ,.... abbreviations. Where can I find a comprehensive information about them? Best regards,Payam Norouzzadeh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100425/e8d26a12/attachment.htm From payam.norouzzadeh at gmail.com Sun Apr 25 04:35:44 2010 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Sun, 25 Apr 2010 07:05:44 +0430 Subject: [Pw_forum] atomic mass for virtual atom Message-ID: Hello All Does anyone know how can I calculate atomic mass for a virtual atom? For example, if I mix two atoms with atomic masses 10 and 20 with 60% and 40% contribution what will be the atomic mass for virtual atom? I need it to insert in input file in front of ATOMIC_SPECIES flag. Best regards,Payam Norouzzadeh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100425/180bf1b8/attachment.htm From kazempoor at ph.iut.ac.ir Sun Apr 25 09:07:02 2010 From: kazempoor at ph.iut.ac.ir (kazempoor at ph.iut.ac.ir) Date: Sun, 25 Apr 2010 11:37:02 +0430 (IRDT) Subject: [Pw_forum] GWW+U Message-ID: <462980679.21115.1272179222780.JavaMail.root@mta.iut.ac.ir> 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? thanks a lot Ali Kazempour Physics Department, Isfahan University of Technology From kucukben at sissa.it Sun Apr 25 09:51:50 2010 From: kucukben at sissa.it (Emine Kucukbenli) Date: Sun, 25 Apr 2010 09:51:50 +0200 Subject: [Pw_forum] different XC functionals In-Reply-To: References: Message-ID: <20100425095150.ku9u4uidj40o8kg8@webmail.sissa.it> Dear Payam, > For example can I apply Ga.pw91-n-van.UPF and Ge.pw91-n-van.UPF along with > Ba.pw91-nsp-van.UPF? They all have the same XC : pw91 Also from : "SLA PW GGX GGC PW91 Exchange-Correlation functional" The "sp" in Ba.pw91-nsp-van.UPF refers to semicore states s&p being in valance, I believe. emine kucukbenli, phd student, sissa, italy ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From sd.wang000 at gmail.com Sun Apr 25 10:05:55 2010 From: sd.wang000 at gmail.com (shudong wang) Date: Sun, 25 Apr 2010 16:05:55 +0800 Subject: [Pw_forum] band calculation Message-ID: Dear all: I calculate the band structure of some materials,but I can not find the Fermi-energy in the scf.out file?Where is it? Wy procedure are: scf, bands(nscf), bands.x, plotband.x, is it right? Thanks! S.D.Wang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100425/d765ad17/attachment.htm From kucukben at sissa.it Sun Apr 25 10:09:25 2010 From: kucukben at sissa.it (Emine Kucukbenli) Date: Sun, 25 Apr 2010 10:09:25 +0200 Subject: [Pw_forum] different XC functionals In-Reply-To: References: Message-ID: <20100425100925.bam6obl5s088k4g8@webmail.sissa.it> For the abbreviations used, you can check upf format from quantum espresso wiki, i guess. For example, XC ones are here: http://www.quantum-espresso.org/wiki/index.php/Exchange-correlation_functional emine kucukbenli, phd student, sissa, italy ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From kucukben at sissa.it Sun Apr 25 10:28:58 2010 From: kucukben at sissa.it (Emine Kucukbenli) Date: Sun, 25 Apr 2010 10:28:58 +0200 Subject: [Pw_forum] atomic mass for virtual atom In-Reply-To: References: Message-ID: <20100425102858.nhjkkjrd0k8o0wcg@webmail.sissa.it> Dear Payam, I've never used this feature but i think this may answer your question: http://www.democritos.it/pipermail/pw_forum/2007-October/007492.html it always helps to check the forum archive first. cheers, emine kucukbenli, phd student, sissa, italy ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From paulatto at sissa.it Sun Apr 25 12:17:47 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sun, 25 Apr 2010 12:17:47 +0200 Subject: [Pw_forum] atomic mass for virtual atom In-Reply-To: References: Message-ID: Replying to message "[Pw_forum] atomic mass for virtual atom" from Payam Norouzzadeh (25/04/10): > I need it to insert in input file in front of ATOMIC_SPECIES flag. Unless you are doing a molecular dynamics or a phonon calculation the mass is not used. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From modaresi.mohsen at gmail.com Sun Apr 25 14:18:58 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Sun, 25 Apr 2010 16:48:58 +0430 Subject: [Pw_forum] =?windows-1252?q?A_problem_in_installation_=28nested_f?= =?windows-1252?q?unction_=91getchar=92_declared_=91extern=92=29?= In-Reply-To: <90BB1BB9-E8DB-44DA-A66E-066DCC7BD804@democritos.it> References: <90BB1BB9-E8DB-44DA-A66E-066DCC7BD804@democritos.it> Message-ID: Thanks Paolo It works properly Mohsen Modaresi On Sat, Apr 24, 2010 at 11:53 PM, Paolo Giannozzi wrote: > > On Apr 24, 2010, at 20:53 , mohsen modaresi wrote: > > > I want install Q.E. on a x86_64 system, And i get this eror > > http://www.democritos.it/pipermail/pw_forum/2010-February/015757.html > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100425/11bd8524/attachment.htm From baroni at sissa.it Sun Apr 25 14:47:23 2010 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 25 Apr 2010 14:47:23 +0200 Subject: [Pw_forum] atomic mass for virtual atom In-Reply-To: References: Message-ID: <8B30A44E-B1B5-4D0F-9CA8-57D00C4A632B@sissa.it> On Apr 25, 2010, at 12:17 PM, Lorenzo Paulatto wrote: > Replying to message "[Pw_forum] atomic mass for virtual atom" from Payam > Norouzzadeh (25/04/10): >> I need it to insert in input file in front of ATOMIC_SPECIES flag. > > Unless you are doing a molecular dynamics or a phonon calculation the mass > is not used. and, if you do, it would not be a good idea to use the virtual-crystal approximation, but possibly for calculating long-wavelength acoustic modes. SB --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100425/1cce0ee0/attachment.htm From ttduyle at gmail.com Sun Apr 25 16:07:25 2010 From: ttduyle at gmail.com (Duy Le) Date: Sun, 25 Apr 2010 10:07:25 -0400 Subject: [Pw_forum] band calculation In-Reply-To: References: Message-ID: There are many ways to do it. One of them is: 1. count number of electrons, 2. you will know number of occupied band 3. Find the energy of the highest occupied bands 4. Find lowest energy of unoccupied bands -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Sun, Apr 25, 2010 at 4:05 AM, shudong wang wrote: > Dear all: > I calculate the band structure of some materials,but I can not find the > Fermi-energy in the scf.out file?Where is it? > Wy procedure are: scf, bands(nscf), bands.x, plotband.x, is it right? > Thanks! > S.D.Wang > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From gianluca.giovannetti at gmail.com Mon Apr 26 08:31:11 2010 From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti) Date: Mon, 26 Apr 2010 08:31:11 +0200 Subject: [Pw_forum] Hg pseudopotential Message-ID: Dear All, i need to use Hg pseudopotential to make simulation of a cuprate. However in the webpage http://www.quantum-espresso.org/pseudo.php i cannot find it. Does anyone know how and where i can get it? :-) thank you. Gianluca -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100426/fc1aac7b/attachment.htm From sclauzer at sissa.it Mon Apr 26 08:41:20 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 26 Apr 2010 08:41:20 +0200 Subject: [Pw_forum] INPUT file for average.x In-Reply-To: <20100423193714.92437CF615F@mail3-92.sinamail.sina.com.cn> References: <20100423193714.92437CF615F@mail3-92.sinamail.sina.com.cn> Message-ID: <4BD53590.9060309@sissa.it> wulilixiangguo at sina.com wrote: > I read below and have a question about macroscopic averages. If my > system have a surface between two materials which have different lattice > constant. Do you mean an interface? (I would say a "surface" only if one of the two "materials" is vacuum, but maybe I'm pedantic...) How to set the awin? Not sure of this, but I think that it is not a good idea to use macroscopic averages when there is a change in the periodicity. For instance, in a recent paper by Singh-Miller and Marzari (PRB, 2010) it has been reported that the technique is not well suited for slab geometries when you account for the relaxation of the distances between layers. How to macroscopic it twice? Maybe I don't understand this point. You could run the program twice, with two different window sizes, in order to match the two different lattice spacings, but then I don't know if there is a way to give a meaningful interpretation to the data at the interface. GS > > Thank you! > > 1 > filename > 1.0 > 3000 > 3 > 2.59 > > The explanation is in the header of the file PP/average.f90: > > ! nfile ! the number of 3D-FFT files > ! for each file: > ! filename ! the name of the 3D-FFT file > ! weight ! the weight of the quantity in this file > ! . > ! . > ! end > ! npt ! the number of points of the thick mesh > ! idir ! 1,2 or 3. It is the fixed index which defines > ! ! the planes of the planar average > ! awin ! the size of the window for macroscopic averages. > ! > > With the example above you'll get a 3-column output file for the > quantity to average > V(u): > - column 1: coordinate u, defined over a mesh of npt=3000 points along > the direction > idir=3 > - column 2: averaged quantity V > - column 3: macroscopically averaged quantity V', over a windows with size > awin=2.50 au > > If you want to average a weighted sum of different quantities V1,...,VN > defined over the same FFT mesh, just set nfile to N and specify N file names > with the relative weight. > > Regards, > Giovanni > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Mon Apr 26 08:50:14 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 26 Apr 2010 08:50:14 +0200 Subject: [Pw_forum] recovering interrupted jobs In-Reply-To: References: Message-ID: <4BD537A6.7040207@sissa.it> Dear Payam, Payam Norouzzadeh wrote: > Hello All > I have time limitation in running jobs on cluster (48 hours at most) . > After that time the job is not processed more and I need to learn how to > recover interrupted jobs. > I created prefix.EXIT in working directory to recover job for ph.x > later but it does not reply at all. That is to interrupt the job, not to restart it! Please read the manual. > The version of quantum-espresso I am using is 4-0-5. > Could anyone do me a favor and teach me how to recover my interrupted jobs? It is explained in the user guide: http://www.quantum-espresso.org/user_guide/node21.html Just follow the procedure. Best regards, GS > Breg, Payam Norouzzadeh > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Mon Apr 26 09:01:41 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 26 Apr 2010 09:01:41 +0200 Subject: [Pw_forum] GWW+U In-Reply-To: <462980679.21115.1272179222780.JavaMail.root@mta.iut.ac.ir> References: <462980679.21115.1272179222780.JavaMail.root@mta.iut.ac.ir> Message-ID: <4BD53A55.3050606@sissa.it> 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 From kazempoor at ph.iut.ac.ir Mon Apr 26 09:01:55 2010 From: kazempoor at ph.iut.ac.ir (kazempoor at ph.iut.ac.ir) Date: Mon, 26 Apr 2010 11:31:55 +0430 (IRDT) Subject: [Pw_forum] GWW+U In-Reply-To: <1057440677.25459.1272265277910.JavaMail.root@mta.iut.ac.ir> Message-ID: <1190877259.25470.1272265315937.JavaMail.root@mta.iut.ac.ir> 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 From baroni at sissa.it Mon Apr 26 10:47:17 2010 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 26 Apr 2010 10:47:17 +0200 Subject: [Pw_forum] INPUT file for average.x In-Reply-To: <4BD53590.9060309@sissa.it> References: <20100423193714.92437CF615F@mail3-92.sinamail.sina.com.cn> <4BD53590.9060309@sissa.it> Message-ID: <036B28FE-17D8-48B8-A21E-0247EA9E8961@sissa.it> On Apr 26, 2010, at 8:41 AM, Gabriele Sclauzero wrote: > > > wulilixiangguo at sina.com wrote: >> I read below and have a question about macroscopic averages. If my >> system have a surface between two materials which have different lattice >> constant. > > Do you mean an interface? (I would say a "surface" only if one of the two "materials" is > vacuum, but maybe I'm pedantic...) > > How to set the awin? > > Not sure of this, but I think that it is not a good idea to use macroscopic averages when > there is a change in the periodicity. For instance, in a recent paper by Singh-Miller and > Marzari (PRB, 2010) it has been reported that the technique is not well suited for slab > geometries when you account for the relaxation of the distances between layers. > > > How to macroscopic it twice? > > Maybe I don't understand this point. > > You could run the program twice, with two different window sizes, in order to match the > two different lattice spacings, but then I don't know if there is a way to give a > meaningful interpretation to the data at the interface. What you propose, Gabriele, is perfectly legitimate and has been done indeed af few times in the good ol' times when macroscopic averages had been invented. I do not remember by heart the reference, but somebody may want to try a bibliographic search with "resta" and "baroni" as authors and select the title(s) that may suggest the investigation of lattice mismatched interfaces. SB --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100426/b567a3fc/attachment.htm From giannozz at democritos.it Mon Apr 26 13:24:19 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 26 Apr 2010 13:24:19 +0200 Subject: [Pw_forum] band calculation In-Reply-To: References: Message-ID: <4BD577E3.9040607@democritos.it> shudong wang wrote: > I calculate the band structure of some materials,but I can not find the > Fermi-energy in the scf.out file?Where is it? it is where it should be: printed in the output. If it is not there, you did not specify the data (i.e. gaussian smearing) that allow to calculate a sensible Fermi energy. In that case, the code prints the top of the valence band (or the HOMO) and the bottom of the conduction band (or the LUMO). If it doesn't, you haven't specified the number of bands to be calculated and the code calculates occupied bands only P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Mon Apr 26 14:37:54 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 26 Apr 2010 14:37:54 +0200 Subject: [Pw_forum] Hg pseudopotential In-Reply-To: References: Message-ID: <4BD58922.5000300@democritos.it> Gianluca Giovannetti wrote: > Does anyone know how and where i can get it? :-) \paragraph{Where can I find pseudopotentials for atom X?} First, a general rule: when you ask for a pseudopotential, you should always specify which kind of pseudopotential you need (norm-conserving, ultrasoft, PAW, full- or scalar-relativistic, for which XC functional, and for many elements, with how many electrons in valence). If you do not find anything suitable in the ``pseudo'' page of the web site links, we have bad news for you: you have to produce it by yourself. You can use the \texttt{atomic} code: have a look first at the contents of the library of input data in \texttt{atomic\_doc/pseudo\_gen}. otherwise, you can use any other code producing a file format that is either recognized by \qe\ or for which a converter to the UPF format exists. New contributions to the PP table are very appreciated (and very scarce). -- Paolo Giannozzi, Democritos and University of Udine, Italy From nedward at MIT.EDU Mon Apr 26 15:24:48 2010 From: nedward at MIT.EDU (Nicholas E. Singh-Miller) Date: Mon, 26 Apr 2010 09:24:48 -0400 (EDT) Subject: [Pw_forum] INPUT file for average.x In-Reply-To: <036B28FE-17D8-48B8-A21E-0247EA9E8961@sissa.it> References: <20100423193714.92437CF615F@mail3-92.sinamail.sina.com.cn> <4BD53590.9060309@sissa.it> <036B28FE-17D8-48B8-A21E-0247EA9E8961@sissa.it> Message-ID: Hi, Alice Runi's thesis from 1997 talks about macroscopic averages at interfaces, in chapter 5. http://www.sissa.it/cm/thesis/1997/ruini.ps.gz maybe a good starting point. -Nick On Mon, 26 Apr 2010, Stefano Baroni wrote: > > On Apr 26, 2010, at 8:41 AM, Gabriele Sclauzero wrote: > > > > wulilixiangguo at sina.com wrote: > I read below and have a question about > macroscopic averages. If my > > system have a surface between two materials which > have different lattice > > constant. > > > Do you mean an interface? (I would say a "surface" only if > one of the two "materials" is > vacuum, but maybe I'm pedantic...) > > How to set the awin? > > Not sure of this, but I think that it is not a good idea to > use macroscopic averages when > there is a change in the periodicity. For instance, in a > recent paper by Singh-Miller and > Marzari (PRB, 2010) it has been reported that the technique > is not well suited for slab > geometries when you account for the relaxation of the > distances between layers. > > > How to macroscopic it twice? > > Maybe I don't understand this point. > > You could run the program twice, with two different window > sizes, in order to match the > two different lattice spacings, but then I don't know if > there is a way to give a > meaningful interpretation to the data at the interface. > > > What you propose, Gabriele, is perfectly legitimate and has been done > indeed af few times in the good ol' times when macroscopic averages had > been invented. I do not remember by heart the reference, but somebody may > want to try a bibliographic search with "resta" and "baroni" as authors > and select the title(s) that may suggest the investigation of lattice > mismatched interfaces. > > SB > > --- > Stefano Baroni - SISSA??&??DEMOCRITOS National Simulation Center - > Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de > la pens?e - Jean Piaget > > Please, if possible, don't??send me MS Word or PowerPoint attachments > Why? See:??http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > > ***************************************** Nicholas E. Singh-Miller Prof. Marzari Group (quasiamore.mit.edu) Materials Science and Engineering Massachusetts Institute of Technology 13-4066 (617)324-0372 ***************************************** From matteo at umn.edu Mon Apr 26 15:40:46 2010 From: matteo at umn.edu (Matteo Cococcioni) Date: Mon, 26 Apr 2010 08:40:46 -0500 Subject: [Pw_forum] GWW+U In-Reply-To: <4BD53A55.3050606@sissa.it> References: <462980679.21115.1272179222780.JavaMail.root@mta.iut.ac.ir> <4BD53A55.3050606@sissa.it> Message-ID: <4BD597DE.10907@umn.edu> DFPT+U is actually almost ready. hopefully it will be ported to the cvs version during the summer or in the fall (we need some more time to test the code and finilize it). regards, Matteo Gabriele Sclauzero wrote: > 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 >> >> > > From bahareh.rahmani at gmail.com Mon Apr 26 20:35:50 2010 From: bahareh.rahmani at gmail.com (bahareh rahmani) Date: Mon, 26 Apr 2010 13:35:50 -0500 Subject: [Pw_forum] breaking grid of q-points and merging resulted files Message-ID: Dear All I am doing long run phonon calculations and because of time limitation for running jobs on our cluster I am looking for a way to do calculations q-point by q-point. It is not a difficult task but I don't know how I can merge the resulted output to a unique output for next calculations. For example, instead of doing phonon calculations using ph.x for a grid of q-points like nq1=4,nq2=4,nq3=4 I am going to do calculaions for 0 0 0 , then 1 0 0 and so on. The question is how I can merge the files resulted from several applications of ph.x into a file proper for applying q2r.x in next step? Best regards,Bahareh Rahmani -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100426/8a209aff/attachment.htm From sclauzer at sissa.it Tue Apr 27 08:53:56 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 27 Apr 2010 08:53:56 +0200 Subject: [Pw_forum] breaking grid of q-points and merging resulted files In-Reply-To: References: Message-ID: <4BD68A04.1060505@sissa.it> Dear Bahareh, bahareh rahmani wrote: > Dear All > > I am doing long run phonon calculations and because of time limitation > for running jobs on our cluster I am looking for a way to do > calculations q-point by q-point. It is not a difficult task but I don't > know how I can merge the resulted output to a unique output for next > calculations. For example, instead of doing phonon calculations using > ph.x for a grid of q-points like nq1=4,nq2=4,nq3=4 I am going to do > calculaions for 0 0 0 , then 1 0 0 and so on. The question is how I can > merge the files resulted from several applications of ph.x into a file > proper for applying q2r.x in next step? This possibility (to split a phonon run over q-points and also over the irreps) has been added recently by Di Meo, Giannozzi, and Dal Corso. See here: http://users.ictp.it/~pub_off/lectures/lns024/10-giannozzi/10-giannozzi.pdf Probably you need to download the CVS version to have this functionality in full and to see the example in examples/GRID_example/ under the espresso source tree. HTH GS > > Best regards,Bahareh Rahmani Please supply your affiliation next time. Thanks! > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From jcwu.suda at hotmail.com Tue Apr 27 11:01:01 2010 From: jcwu.suda at hotmail.com (wujianchun) Date: Tue, 27 Apr 2010 17:01:01 +0800 Subject: [Pw_forum] core level Message-ID: Dear All, Who knows how to get the core level of each atom after the scf calculation? many thanks Rgds Jianchun Department of physics Soochow university China.215006 _________________________________________________________________ ?????????Windows Live????????? http://windowslivesky.spaces.live.com/blog/cns!5892B6048E2498BD!889.entry -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100427/d0372a75/attachment.htm From taebumlee at gmail.com Wed Apr 28 03:11:59 2010 From: taebumlee at gmail.com (TAE BUM LEE) Date: Tue, 27 Apr 2010 20:11:59 -0500 Subject: [Pw_forum] parallel version error in quad core Xeon Message-ID: Hi, Does anybody know the reason of following error? The same input is OK on SGI altix computer while my Intel xeon desktop generate error just after execution. Serial version is OK for both case. Which part should I check first? My system is Intel Xeon quad core with ubuntu 10.04. MPICH2 is configured with pwscf. Regards, TaeBum Program PWSCF v.4.1.3 starts ... Today is 27Apr2010 at 20: 4: 7 Parallel version (MPI) Number of processors in use: 4 R & G space division: proc/pool = 4 For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW Current dimensions of program pwscf are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 Waiting for input... 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 = 2* 2 procs warning: symmetry operation # 24 not allowed. fractional translation: 0.0001000 0.0001000 0.0000000 in crystal coordinates Planes per process (thick) : nr3 = 36 npp = 9 ncplane = 576 Planes per process (smooth): nr3s= 25 npps= 7 ncplanes= 225 Proc/ planes cols G planes cols G columns G Pool (dense grid) (smooth grid) (wavefct grid) 1 9 85 1957 7 41 699 14 146 2 9 85 1957 6 41 701 13 139 3 9 82 1954 6 40 690 14 144 4 9 85 1955 6 41 701 14 144 tot 36 337 7823 25 163 2791 55 573 bravais-lattice index = 4 lattice parameter (a_0) = 6.1404 a.u. unit-cell volume = 321.0853 (a.u.)^3 number of atoms/cell = 4 number of atomic types = 2 number of electrons = 36.00 number of Kohn-Sham states= 22 kinetic-energy cutoff = 16.0000 Ry charge density cutoff = 128.0000 Ry convergence threshold = 1.0E-08 mixing beta = 0.7000 number of iterations used = 8 plain mixing Exchange-correlation = SLA PW PBE PBE (1434) celldm(1)= 6.140400 celldm(2)= 0.000000 celldm(3)= 1.601400 celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 crystal axes: (cart. coord. in units of a_0) a(1) = ( 1.000000 0.000000 0.000000 ) a(2) = ( -0.500000 0.866025 0.000000 ) a(3) = ( 0.000000 0.000000 1.601400 ) reciprocal axes: (cart. coord. in units 2 pi/a_0) b(1) = ( 1.000000 0.577350 -0.000000 ) b(2) = ( 0.000000 1.154701 0.000000 ) b(3) = ( 0.000000 -0.000000 0.624454 ) PseudoPot. # 1 for Zn read from file Zn.pbe-van.UPF Pseudo is Ultrasoft, Zval = 12.0 Generated by new atomic code, or converted to UPF format Using radial grid of 869 points, 6 beta functions with: l(1) = 0 l(2) = 0 l(3) = 1 l(4) = 1 l(5) = 2 l(6) = 2 Q(r) pseudized with 8 coefficients, rinner = 0.800 0.800 0.800 0.800 0.800 PseudoPot. # 2 for O read from file O.pbe-van_ak.UPF Pseudo is Ultrasoft, Zval = 6.0 Generated by new atomic code, or converted to UPF format Using radial grid of 737 points, 4 beta functions with: l(1) = 0 l(2) = 0 l(3) = 1 l(4) = 1 Q(r) pseudized with 8 coefficients, rinner = 0.800 0.800 0.800 atomic species valence mass pseudopotential Zn 12.00 65.41000 Zn( 1.00) O 6.00 16.00000 O ( 1.00) No symmetry! Cartesian axes site n. atom positions (a_0 units) 1 Zn tau( 1) = ( 0.0000000 0.5772925 0.0000000 ) 2 Zn tau( 2) = ( 0.4999500 0.2886463 0.8007000 ) 3 O tau( 3) = ( 0.0000000 0.5772925 0.6118949 ) 4 O tau( 4) = ( 0.4999500 0.2886463 1.3531830 ) number of k points= 36 gaussian broad. (Ry)= 0.0200 ngauss = 1 cart. coord. in units 2pi/a_0 k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0312500 k( 2) = ( 0.0000000 0.0000000 0.1561134), wk = 0.0625000 k( 3) = ( 0.0000000 0.0000000 -0.3122268), wk = 0.0312500 k( 4) = ( 0.0000000 0.2886751 0.0000000), wk = 0.0625000 k( 5) = ( 0.0000000 0.2886751 0.1561134), wk = 0.0625000 k( 6) = ( 0.0000000 0.2886751 -0.3122268), wk = 0.0625000 k( 7) = ( 0.0000000 -0.5773503 0.0000000), wk = 0.0312500 k( 8) = ( 0.0000000 -0.5773503 0.1561134), wk = 0.0625000 k( 9) = ( 0.0000000 -0.5773503 -0.3122268), wk = 0.0312500 k( 10) = ( 0.2500000 0.4330127 0.0000000), wk = 0.0625000 k( 11) = ( 0.2500000 0.4330127 0.1561134), wk = 0.0625000 k( 12) = ( 0.2500000 0.4330127 -0.3122268), wk = 0.0625000 k( 13) = ( -0.2500000 0.1443376 0.0000000), wk = 0.0625000 k( 14) = ( 0.2500000 0.1443376 0.0000000), wk = 0.0625000 k( 15) = ( 0.0000000 -0.2886751 0.1561134), wk = 0.0625000 k( 16) = ( -0.2500000 0.1443376 0.1561134), wk = 0.0625000 k( 17) = ( 0.2500000 0.1443376 0.1561134), wk = 0.0625000 k( 18) = ( -0.2500000 -0.1443376 0.1561134), wk = 0.0625000 k( 19) = ( 0.2500000 -0.1443376 0.1561134), wk = 0.0625000 k( 20) = ( -0.2500000 0.1443376 -0.3122268), wk = 0.0625000 k( 21) = ( 0.2500000 0.1443376 -0.3122268), wk = 0.0625000 k( 22) = ( 0.5000000 -0.2886751 0.0000000), wk = 0.0312500 k( 23) = ( -0.5000000 -0.2886751 0.0000000), wk = 0.0312500 k( 24) = ( 0.5000000 -0.2886751 0.1561134), wk = 0.0625000 k( 25) = ( -0.5000000 -0.2886751 0.1561134), wk = 0.0625000 k( 26) = ( 0.5000000 -0.2886751 -0.3122268), wk = 0.0312500 k( 27) = ( -0.5000000 -0.2886751 -0.3122268), wk = 0.0312500 k( 28) = ( -0.2500000 0.4330127 0.0000000), wk = 0.0625000 k( 29) = ( 0.5000000 0.0000000 0.0000000), wk = 0.0625000 k( 30) = ( -0.2500000 -0.4330127 0.1561134), wk = 0.0625000 k( 31) = ( -0.2500000 0.4330127 -0.1561134), wk = 0.0625000 k( 32) = ( 0.2500000 -0.4330127 -0.1561134), wk = 0.0625000 k( 33) = ( 0.5000000 0.0000000 0.1561134), wk = 0.0625000 k( 34) = ( -0.5000000 0.0000000 0.1561134), wk = 0.0625000 k( 35) = ( -0.2500000 0.4330127 0.3122268), wk = 0.0625000 k( 36) = ( 0.5000000 0.0000000 -0.3122268), wk = 0.0625000 G cutoff = 122.2485 ( 7823 G-vectors) FFT grid: ( 24, 24, 36) G cutoff = 61.1243 ( 2791 G-vectors) smooth grid: ( 15, 15, 25) rank 3 in job 37 Lynx_60167 caused collective abort of all ranks exit status of rank 3: killed by signal 9 -- ######################################## TAE BUM LEE Dept. Chem. & Biochem Auburn Univ. AL. 36849 TEL.: 334-844-6912 e-mail: taebumlee at gmail.com ######################################## -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100427/a0fb4aa0/attachment.htm From jcwu.suda at hotmail.com Wed Apr 28 03:29:25 2010 From: jcwu.suda at hotmail.com (wujianchun) Date: Wed, 28 Apr 2010 09:29:25 +0800 Subject: [Pw_forum] the potential of core electron Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100428/f9a82c12/attachment.htm From archygu at gmail.com Wed Apr 28 03:31:07 2010 From: archygu at gmail.com (archygu) Date: Wed, 28 Apr 2010 09:31:07 +0800 Subject: [Pw_forum] parallel version error in quad core Xeon References: Message-ID: <201004280931050626361@gmail.com> Hi, is this your full out put file? it seams that the error happen has not been mentioned. 2010-04-28 archygu ???? TAE BUM LEE ????? 2010-04-28 09:12:14 ???? pw_forum at pwscf.org ??? ??? [Pw_forum] parallel version error in quad core Xeon Hi, Does anybody know the reason of following error? The same input is OK on SGI altix computer while my Intel xeon desktop generate error just after execution. Serial version is OK for both case. Which part should I check first? My system is Intel Xeon quad core with ubuntu 10.04. MPICH2 is configured with pwscf. Regards, TaeBum Program PWSCF v.4.1.3 starts ... Today is 27Apr2010 at 20: 4: 7 Parallel version (MPI) Number of processors in use: 4 R & G space division: proc/pool = 4 For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW Current dimensions of program pwscf are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 Waiting for input... 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 = 2* 2 procs warning: symmetry operation # 24 not allowed. fractional translation: 0.0001000 0.0001000 0.0000000 in crystal coordinates Planes per process (thick) : nr3 = 36 npp = 9 ncplane = 576 Planes per process (smooth): nr3s= 25 npps= 7 ncplanes= 225 Proc/ planes cols G planes cols G columns G Pool (dense grid) (smooth grid) (wavefct grid) 1 9 85 1957 7 41 699 14 146 2 9 85 1957 6 41 701 13 139 3 9 82 1954 6 40 690 14 144 4 9 85 1955 6 41 701 14 144 tot 36 337 7823 25 163 2791 55 573 bravais-lattice index = 4 lattice parameter (a_0) = 6.1404 a.u. unit-cell volume = 321.0853 (a.u.)^3 number of atoms/cell = 4 number of atomic types = 2 number of electrons = 36.00 number of Kohn-Sham states= 22 kinetic-energy cutoff = 16.0000 Ry charge density cutoff = 128.0000 Ry convergence threshold = 1.0E-08 mixing beta = 0.7000 number of iterations used = 8 plain mixing Exchange-correlation = SLA PW PBE PBE (1434) celldm(1)= 6.140400 celldm(2)= 0.000000 celldm(3)= 1.601400 celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 crystal axes: (cart. coord. in units of a_0) a(1) = ( 1.000000 0.000000 0.000000 ) a(2) = ( -0.500000 0.866025 0.000000 ) a(3) = ( 0.000000 0.000000 1.601400 ) reciprocal axes: (cart. coord. in units 2 pi/a_0) b(1) = ( 1.000000 0.577350 -0.000000 ) b(2) = ( 0.000000 1.154701 0.000000 ) b(3) = ( 0.000000 -0.000000 0.624454 ) PseudoPot. # 1 for Zn read from file Zn.pbe-van.UPF Pseudo is Ultrasoft, Zval = 12.0 Generated by new atomic code, or converted to UPF format Using radial grid of 869 points, 6 beta functions with: l(1) = 0 l(2) = 0 l(3) = 1 l(4) = 1 l(5) = 2 l(6) = 2 Q(r) pseudized with 8 coefficients, rinner = 0.800 0.800 0.800 0.800 0.800 PseudoPot. # 2 for O read from file O.pbe-van_ak.UPF Pseudo is Ultrasoft, Zval = 6.0 Generated by new atomic code, or converted to UPF format Using radial grid of 737 points, 4 beta functions with: l(1) = 0 l(2) = 0 l(3) = 1 l(4) = 1 Q(r) pseudized with 8 coefficients, rinner = 0.800 0.800 0.800 atomic species valence mass pseudopotential Zn 12.00 65.41000 Zn( 1.00) O 6.00 16.00000 O ( 1.00) No symmetry! Cartesian axes site n. atom positions (a_0 units) 1 Zn tau( 1) = ( 0.0000000 0.5772925 0.0000000 ) 2 Zn tau( 2) = ( 0.4999500 0.2886463 0.8007000 ) 3 O tau( 3) = ( 0.0000000 0.5772925 0.6118949 ) 4 O tau( 4) = ( 0.4999500 0.2886463 1.3531830 ) number of k points= 36 gaussian broad. (Ry)= 0.0200 ngauss = 1 cart. coord. in units 2pi/a_0 k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0312500 k( 2) = ( 0.0000000 0.0000000 0.1561134), wk = 0.0625000 k( 3) = ( 0.0000000 0.0000000 -0.3122268), wk = 0.0312500 k( 4) = ( 0.0000000 0.2886751 0.0000000), wk = 0.0625000 k( 5) = ( 0.0000000 0.2886751 0.1561134), wk = 0.0625000 k( 6) = ( 0.0000000 0.2886751 -0.3122268), wk = 0.0625000 k( 7) = ( 0.0000000 -0.5773503 0.0000000), wk = 0.0312500 k( 8) = ( 0.0000000 -0.5773503 0.1561134), wk = 0.0625000 k( 9) = ( 0.0000000 -0.5773503 -0.3122268), wk = 0.0312500 k( 10) = ( 0.2500000 0.4330127 0.0000000), wk = 0.0625000 k( 11) = ( 0.2500000 0.4330127 0.1561134), wk = 0.0625000 k( 12) = ( 0.2500000 0.4330127 -0.3122268), wk = 0.0625000 k( 13) = ( -0.2500000 0.1443376 0.0000000), wk = 0.0625000 k( 14) = ( 0.2500000 0.1443376 0.0000000), wk = 0.0625000 k( 15) = ( 0.0000000 -0.2886751 0.1561134), wk = 0.0625000 k( 16) = ( -0.2500000 0.1443376 0.1561134), wk = 0.0625000 k( 17) = ( 0.2500000 0.1443376 0.1561134), wk = 0.0625000 k( 18) = ( -0.2500000 -0.1443376 0.1561134), wk = 0.0625000 k( 19) = ( 0.2500000 -0.1443376 0.1561134), wk = 0.0625000 k( 20) = ( -0.2500000 0.1443376 -0.3122268), wk = 0.0625000 k( 21) = ( 0.2500000 0.1443376 -0.3122268), wk = 0.0625000 k( 22) = ( 0.5000000 -0.2886751 0.0000000), wk = 0.0312500 k( 23) = ( -0.5000000 -0.2886751 0.0000000), wk = 0.0312500 k( 24) = ( 0.5000000 -0.2886751 0.1561134), wk = 0.0625000 k( 25) = ( -0.5000000 -0.2886751 0.1561134), wk = 0.0625000 k( 26) = ( 0.5000000 -0.2886751 -0.3122268), wk = 0.0312500 k( 27) = ( -0.5000000 -0.2886751 -0.3122268), wk = 0.0312500 k( 28) = ( -0.2500000 0.4330127 0.0000000), wk = 0.0625000 k( 29) = ( 0.5000000 0.0000000 0.0000000), wk = 0.0625000 k( 30) = ( -0.2500000 -0.4330127 0.1561134), wk = 0.0625000 k( 31) = ( -0.2500000 0.4330127 -0.1561134), wk = 0.0625000 k( 32) = ( 0.2500000 -0.4330127 -0.1561134), wk = 0.0625000 k( 33) = ( 0.5000000 0.0000000 0.1561134), wk = 0.0625000 k( 34) = ( -0.5000000 0.0000000 0.1561134), wk = 0.0625000 k( 35) = ( -0.2500000 0.4330127 0.3122268), wk = 0.0625000 k( 36) = ( 0.5000000 0.0000000 -0.3122268), wk = 0.0625000 G cutoff = 122.2485 ( 7823 G-vectors) FFT grid: ( 24, 24, 36) G cutoff = 61.1243 ( 2791 G-vectors) smooth grid: ( 15, 15, 25) rank 3 in job 37 Lynx_60167 caused collective abort of all ranks exit status of rank 3: killed by signal 9 -- ######################################## TAE BUM LEE Dept. Chem. & Biochem Auburn Univ. AL. 36849 TEL.: 334-844-6912 e-mail: taebumlee at gmail.com ######################################## -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100428/2211ebd6/attachment-0001.htm From taebumlee at gmail.com Wed Apr 28 04:12:27 2010 From: taebumlee at gmail.com (TAE BUM LEE) Date: Tue, 27 Apr 2010 21:12:27 -0500 Subject: [Pw_forum] parallel version error in quad core Xeon In-Reply-To: <201004280931050626361@gmail.com> References: <201004280931050626361@gmail.com> Message-ID: HI, Yes it is. Please see the last two lines.... Thanks, TaeBum 2010/4/27 archygu > Hi, is this your full out put file? it seams that the error happen has > not been mentioned. > > > 2010-04-28 > ------------------------------ > archygu > ------------------------------ > *????* TAE BUM LEE > *?????* 2010-04-28 09:12:14 > *????* pw_forum at pwscf.org > *???* > *???* [Pw_forum] parallel version error in quad core Xeon > Hi, > > Does anybody know the reason of following error? The same input is OK on > SGI altix computer while my Intel xeon desktop generate error just after > execution. Serial version is OK for both case. Which part should I check > first? My system is Intel Xeon quad core with ubuntu 10.04. MPICH2 is > configured with pwscf. > > Regards, > TaeBum > > Program PWSCF v.4.1.3 starts ... > Today is 27Apr2010 at 20: 4: 7 > > Parallel version (MPI) > > Number of processors in use: 4 > R & G space division: proc/pool = 4 > > For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW > > Current dimensions of program pwscf are: > Max number of different atomic species (ntypx) = 10 > Max number of k-points (npk) = 40000 > Max angular momentum in pseudopotentials (lmaxx) = 3 > Waiting for input... > > 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 = 2* 2 procs > > warning: symmetry operation # 24 not allowed. fractional > translation: > 0.0001000 0.0001000 0.0000000 in crystal coordinates > > Planes per process (thick) : nr3 = 36 npp = 9 ncplane = 576 > Planes per process (smooth): nr3s= 25 npps= 7 ncplanes= 225 > > Proc/ planes cols G planes cols G columns G > Pool (dense grid) (smooth grid) (wavefct grid) > 1 9 85 1957 7 41 699 14 146 > 2 9 85 1957 6 41 701 13 139 > 3 9 82 1954 6 40 690 14 144 > 4 9 85 1955 6 41 701 14 144 > tot 36 337 7823 25 163 2791 55 573 > > > > bravais-lattice index = 4 > lattice parameter (a_0) = 6.1404 a.u. > unit-cell volume = 321.0853 (a.u.)^3 > number of atoms/cell = 4 > number of atomic types = 2 > number of electrons = 36.00 > number of Kohn-Sham states= 22 > kinetic-energy cutoff = 16.0000 Ry > charge density cutoff = 128.0000 Ry > convergence threshold = 1.0E-08 > mixing beta = 0.7000 > number of iterations used = 8 plain mixing > Exchange-correlation = SLA PW PBE PBE (1434) > > celldm(1)= 6.140400 celldm(2)= 0.000000 celldm(3)= 1.601400 > celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 > > crystal axes: (cart. coord. in units of a_0) > a(1) = ( 1.000000 0.000000 0.000000 ) > a(2) = ( -0.500000 0.866025 0.000000 ) > a(3) = ( 0.000000 0.000000 1.601400 ) > > reciprocal axes: (cart. coord. in units 2 pi/a_0) > b(1) = ( 1.000000 0.577350 -0.000000 ) > b(2) = ( 0.000000 1.154701 0.000000 ) > b(3) = ( 0.000000 -0.000000 0.624454 ) > > > PseudoPot. # 1 for Zn read from file Zn.pbe-van.UPF > Pseudo is Ultrasoft, Zval = 12.0 > Generated by new atomic code, or converted to UPF format > Using radial grid of 869 points, 6 beta functions with: > l(1) = 0 > l(2) = 0 > l(3) = 1 > l(4) = 1 > l(5) = 2 > l(6) = 2 > Q(r) pseudized with 8 coefficients, rinner = 0.800 0.800 > 0.800 > 0.800 0.800 > > PseudoPot. # 2 for O read from file O.pbe-van_ak.UPF > Pseudo is Ultrasoft, Zval = 6.0 > Generated by new atomic code, or converted to UPF format > Using radial grid of 737 points, 4 beta functions with: > l(1) = 0 > l(2) = 0 > l(3) = 1 > l(4) = 1 > Q(r) pseudized with 8 coefficients, rinner = 0.800 0.800 > 0.800 > > > atomic species valence mass pseudopotential > Zn 12.00 65.41000 Zn( 1.00) > O 6.00 16.00000 O ( 1.00) > > No symmetry! > > Cartesian axes > > site n. atom positions (a_0 units) > 1 Zn tau( 1) = ( 0.0000000 0.5772925 0.0000000 > ) > 2 Zn tau( 2) = ( 0.4999500 0.2886463 0.8007000 > ) > 3 O tau( 3) = ( 0.0000000 0.5772925 0.6118949 > ) > 4 O tau( 4) = ( 0.4999500 0.2886463 1.3531830 > ) > > number of k points= 36 gaussian broad. (Ry)= 0.0200 ngauss = > 1 > cart. coord. in units 2pi/a_0 > k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0312500 > k( 2) = ( 0.0000000 0.0000000 0.1561134), wk = 0.0625000 > k( 3) = ( 0.0000000 0.0000000 -0.3122268), wk = 0.0312500 > k( 4) = ( 0.0000000 0.2886751 0.0000000), wk = 0.0625000 > k( 5) = ( 0.0000000 0.2886751 0.1561134), wk = 0.0625000 > k( 6) = ( 0.0000000 0.2886751 -0.3122268), wk = 0.0625000 > k( 7) = ( 0.0000000 -0.5773503 0.0000000), wk = 0.0312500 > k( 8) = ( 0.0000000 -0.5773503 0.1561134), wk = 0.0625000 > k( 9) = ( 0.0000000 -0.5773503 -0.3122268), wk = 0.0312500 > k( 10) = ( 0.2500000 0.4330127 0.0000000), wk = 0.0625000 > k( 11) = ( 0.2500000 0.4330127 0.1561134), wk = 0.0625000 > k( 12) = ( 0.2500000 0.4330127 -0.3122268), wk = 0.0625000 > k( 13) = ( -0.2500000 0.1443376 0.0000000), wk = 0.0625000 > k( 14) = ( 0.2500000 0.1443376 0.0000000), wk = 0.0625000 > k( 15) = ( 0.0000000 -0.2886751 0.1561134), wk = 0.0625000 > k( 16) = ( -0.2500000 0.1443376 0.1561134), wk = 0.0625000 > k( 17) = ( 0.2500000 0.1443376 0.1561134), wk = 0.0625000 > k( 18) = ( -0.2500000 -0.1443376 0.1561134), wk = 0.0625000 > k( 19) = ( 0.2500000 -0.1443376 0.1561134), wk = 0.0625000 > k( 20) = ( -0.2500000 0.1443376 -0.3122268), wk = 0.0625000 > k( 21) = ( 0.2500000 0.1443376 -0.3122268), wk = 0.0625000 > k( 22) = ( 0.5000000 -0.2886751 0.0000000), wk = 0.0312500 > k( 23) = ( -0.5000000 -0.2886751 0.0000000), wk = 0.0312500 > k( 24) = ( 0.5000000 -0.2886751 0.1561134), wk = 0.0625000 > k( 25) = ( -0.5000000 -0.2886751 0.1561134), wk = 0.0625000 > k( 26) = ( 0.5000000 -0.2886751 -0.3122268), wk = 0.0312500 > k( 27) = ( -0.5000000 -0.2886751 -0.3122268), wk = 0.0312500 > k( 28) = ( -0.2500000 0.4330127 0.0000000), wk = 0.0625000 > k( 29) = ( 0.5000000 0.0000000 0.0000000), wk = 0.0625000 > k( 30) = ( -0.2500000 -0.4330127 0.1561134), wk = 0.0625000 > k( 31) = ( -0.2500000 0.4330127 -0.1561134), wk = 0.0625000 > k( 32) = ( 0.2500000 -0.4330127 -0.1561134), wk = 0.0625000 > k( 33) = ( 0.5000000 0.0000000 0.1561134), wk = 0.0625000 > k( 34) = ( -0.5000000 0.0000000 0.1561134), wk = 0.0625000 > k( 35) = ( -0.2500000 0.4330127 0.3122268), wk = 0.0625000 > k( 36) = ( 0.5000000 0.0000000 -0.3122268), wk = 0.0625000 > > G cutoff = 122.2485 ( 7823 G-vectors) FFT grid: ( 24, 24, 36) > G cutoff = 61.1243 ( 2791 G-vectors) smooth grid: ( 15, 15, 25) > rank 3 in job 37 Lynx_60167 caused collective abort of all ranks > exit status of rank 3: killed by signal 9 > > > -- > ######################################## > TAE BUM LEE > Dept. Chem. & Biochem > Auburn Univ. AL. 36849 > TEL.: 334-844-6912 > e-mail: taebumlee at gmail.com > ######################################## > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ######################################## TAE BUM LEE Dept. Chem. & Biochem Auburn Univ. AL. 36849 TEL.: 334-844-6912 e-mail: taebumlee at gmail.com ######################################## -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100427/8a3fb637/attachment-0001.htm From zfhou at fudan.edu.cn Wed Apr 28 04:25:47 2010 From: zfhou at fudan.edu.cn (Zhufeng Hou) Date: Wed, 28 Apr 2010 11:25:47 +0900 Subject: [Pw_forum] Several questions about the xspectra code in QE Message-ID: Dear all, For the usage of xspectra code, I have the following questions to be clear. 1) When one does the self-consistent calculations of system with core-hole, should the keyword "nelec" be specified explicitly with a value (N or N+1, N is the total electrons of this system without core-hole)? I did a test calculation without the keyword "nelec" in the inptu file for the system with core-hole, and found that the value of total electrons is automatically determined to be N+1. 2). In the examples provided with the distribution of QE (4.1.1 version), several cases such as NiO and SiO2 demonstrated the calculations only for the XAS spectra of systems without core-hole. Why not show the calculations with core-hole? If one wants to do exercises for reproducing the the results presented in the related papers (PRB80,075102(2009) and PRB79, 045118 (2009)), should the systems with core-hole be calculated? 3) From the formula of the dipolar cross section (e.g., eq.(27) in PRB80,075102(2009)), it seems that the angle \theta between the c axis and the polarization vector is controlled by the values of keywords "xkev(1:3)" and "xepsilon(1:3)". Is my understanding correct? Best regards Zhufeng From daijiayu at nudt.edu.cn Wed Apr 28 07:05:54 2010 From: daijiayu at nudt.edu.cn (=?gb2312?B?tPe80e7a?=) Date: Wed, 28 Apr 2010 13:05:54 +0800 Subject: [Pw_forum] x-ray spectra with "Fermi-Dirac" electronic smearing. Message-ID: Dear developers, What i want to do is to calculate the x-ray absorption (or k-edge) for a matter at high temperature. As we know, considering the contribution of electronic temperature, we should use the Fermi-Dirac distribution. However, when i want to calculate the "calculation='fermi_level'", it stopped with a hints of "metallic case". I read the code of xpectra.f90, it seems that we can not calculate the cases using a smearing of 'fermi-dirac', is it right? Another one is in the examples, how they get the fermi level for the SiO2 or NiO, since you did not perform the calculation of 'fermi_level'. If some body is interested in this field, i should be very appreciated for his/her collaborations. My input files are attached. Thanks a lot. Jiayu ------------------------------------------- Jiayu Dai Department of Physics National University of Defense Technology, Changsha, 410073, P R China -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Li128.10g.2000K.scf.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20100428/246aa375/attachment.txt -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Li128.10g.2000K.xspectra_fermi.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20100428/246aa375/attachment.asc -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Li128.10g.2000K.xspectra.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20100428/246aa375/attachment-0001.txt From kazempoor at ph.iut.ac.ir Wed Apr 28 07:22:02 2010 From: kazempoor at ph.iut.ac.ir (kazempoor at ph.iut.ac.ir) Date: Wed, 28 Apr 2010 09:52:02 +0430 (IRDT) Subject: [Pw_forum] PAW pseudopotential Message-ID: <676517887.34386.1272432122733.JavaMail.root@mta.iut.ac.ir> Dear All Is it possible to do calculation with PAW pseudopotential by espresso ? Is it possible to get PAW pseudopotentail for other code and change their format to espresso? Thanks Ali Kazempour Physics Department, Isfahn University of Technology From paulatto at sissa.it Wed Apr 28 09:23:16 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 28 Apr 2010 09:23:16 +0200 Subject: [Pw_forum] PAW pseudopotential In-Reply-To: <676517887.34386.1272432122733.JavaMail.root@mta.iut.ac.ir> References: <676517887.34386.1272432122733.JavaMail.root@mta.iut.ac.ir> Message-ID: On Wed, 28 Apr 2010 07:22:02 +0200, wrote: > Is it possible to do calculation with PAW pseudopotential by espresso ? yes > Is it possible to get PAW pseudopotentail for other code and change > their format to espresso? no that I know -- 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 matteo.calandra at impmc.jussieu.fr Wed Apr 28 12:13:39 2010 From: matteo.calandra at impmc.jussieu.fr (Matteo Calandra) Date: Wed, 28 Apr 2010 12:13:39 +0200 Subject: [Pw_forum] x-ray spectra with "Fermi-Dirac" electronic (Jayu) Message-ID: <4BD80A53.30104@impmc.jussieu.fr> Dear Jiayu, if I understand correctly you would like to calculate K-edge XAS at high temperature including the contribution of Fermi functions in the Fermi golden rule. If this is what you would like to do, this is currently not implemented in XSPECTRA, as we always assume the temperature to be negligible with respect to the energy of the electronic excitations (1 eV=11605 Kelvin). In practice we assume that the XAS spectra is temperature independent, or, better, the only temperature dependence comes from the thermal expansion of the crystal structure. This is generally true except when vibrations contribute to the XAS spectra. Increasing temperature increase atomic vibrations and it is known in some case to wakly affect the spectra in the pre-edge region. However even in this case I guess that the problem can be solved without the need of introducing Fermi functions in the XAS cross section. You will find more details on the XAS equation implemented in Christos Gougoussis, Matteo Calandra, Ari P. Seitsonen, and Francesco Mauri, Phys. Rev. B 80, 075102 (2009) http://link.aps.org/doi/10.1103/PhysRevB.80.075102 Equation 1. What the fermi_level option in XSPECTRA does is simply calculating the Fermi level with a given electronic smearing. The electronic smearing is used in the case of metals to improve the sampling of the Fermi surface when a finite grid of k-points is used. In the case of a metallic system, as your case is, then XSPECTRA does not calculate the Fermi level and stops as this quantity can be simply read from the pw.x scf output that you must have run before XSPECTRA. Finally, note that to calculate the electronic structure and the cross section, any smearing available in pw.x should also work on XSPECTRA. However this is not equivalent in adding Fermi functions to the Fermi golden rule. Matteo -- * * * * Matteo Calandra, Charge de Recherche (CR1) Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris Universit? Pierre et Marie Curie, tour 16, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra From xinhuolin at gmail.com Wed Apr 28 14:54:57 2010 From: xinhuolin at gmail.com (Huolin Xin) Date: Wed, 28 Apr 2010 08:54:57 -0400 Subject: [Pw_forum] x-ray spectra with "Fermi-Dirac" electronic smearing. In-Reply-To: References: Message-ID: Dear developers, Since when did quantum espresso start to offer XANEFS calculations? I remember I sent an email on this forum half of a hear ago to ask whether anyone is interested in developing an EELS calculation plugin. I got no response. 2010/4/28 ??? : > Dear developers, > > What i want to do is to calculate the x-ray absorption (or k-edge) for a matter at high temperature. As we know, considering the contribution of electronic temperature, we should use the Fermi-Dirac distribution. However, when i want to calculate the "calculation='fermi_level'", it stopped with a hints of "metallic case". I read the code of xpectra.f90, it seems that we can not calculate the cases using a smearing of 'fermi-dirac', is it right? > > Another one is in the examples, how they get the fermi level for the SiO2 or NiO, since you did not perform the calculation of 'fermi_level'. If some body is interested in this field, i should be very appreciated for his/her collaborations. > > My input files are attached. > > Thanks a lot. > > Jiayu > > ------------------------------------------- > Jiayu Dai > Department of Physics > National University of Defense Technology, > Changsha, 410073, P R China > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From kazempoor at ph.iut.ac.ir Wed Apr 28 15:20:45 2010 From: kazempoor at ph.iut.ac.ir (kazempoor at ph.iut.ac.ir) Date: Wed, 28 Apr 2010 17:50:45 +0430 (IRDT) Subject: [Pw_forum] PAW for Ti and O Message-ID: <891252192.37774.1272460845858.JavaMail.root@mta.iut.ac.ir> Dear All Does anyone has PAW pseudopotential for Ti and O? Thanks a lot Ali Kazempour Physics Department, Isfahn University of Technology From paulatto at sissa.it Wed Apr 28 16:07:35 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 28 Apr 2010 16:07:35 +0200 Subject: [Pw_forum] PAW for Ti and O In-Reply-To: <891252192.37774.1272460845858.JavaMail.root@mta.iut.ac.ir> References: <891252192.37774.1272460845858.JavaMail.root@mta.iut.ac.ir> Message-ID: On Wed, 28 Apr 2010 15:20:45 +0200, wrote: > Does anyone has PAW pseudopotential for Ti and O? > Thanks a lot There is an input file for the oxygen in atomic_doc/paw_library/input About titanium... I have an input (attached) but I have never tested it. I.e. the logarithmic derivatives look honest, but it may not fit properly the experimental data: cell parameter, phonons... I'm attaching it to the email so you can test it. If it works, or if you can make it work with minor modifications, please let me know. 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/ -------------- next part -------------- A non-text attachment was scrubbed... Name: Ti.in Type: application/octet-stream Size: 767 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100428/7314d47d/attachment.obj From modaresi.mohsen at gmail.com Wed Apr 28 18:54:21 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Wed, 28 Apr 2010 21:24:21 +0430 Subject: [Pw_forum] A Question About Time Message-ID: Dear all When i run parallel (With MPICH) version with 4 core, in output file i see this "total time until now 6.06 sec." but if i use my watch it take 29 sec to run. What is the problem? another problem: If i use MPICH with 1 core it takes only 17 sec (on my watch) which is smaller than 29, Why? Sincerely yours, Mohsen Modaresi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100428/9cb5b23b/attachment.htm From bahareh.rahmani at gmail.com Thu Apr 29 03:25:23 2010 From: bahareh.rahmani at gmail.com (bahareh rahmani) Date: Thu, 29 Apr 2010 05:55:23 +0430 Subject: [Pw_forum] Wyckoff sites Message-ID: Dear All I have converted Wyckoff positions to x,y,x coordinates for a Clathrate type VIII . As an example I converted 2a site to 0,0,0 and 1/2,1/2,1/2 based on literature but quantum-espresso produces an error message and says the above mentioned atoms have overlap. This happens for many other sites too. Deos anyone any idea how to solve this problem? Best regards,Bahareh Rahmani -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100429/197a923b/attachment.htm From chenhanghuipwscf at gmail.com Thu Apr 29 05:29:48 2010 From: chenhanghuipwscf at gmail.com (hanghui chen) Date: Wed, 28 Apr 2010 23:29:48 -0400 Subject: [Pw_forum] magnetization Message-ID: Dear QE developers, I have a very naive question: the variable 'tot_magnetization' is of the type INTEGER. If I understand correctly, nelup+neldw = total number of electrons nelup - neldw = total magnetization. Since both nelup and neldw are REAL type (could be fractional), why does 'tot_magnetization' have to be an integer? In many real system, the total magnetization is not an integer. Thank you. Hanghui Chen Department of Physics Yale University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100428/fb30917e/attachment.htm From mohnish.iitk at gmail.com Thu Apr 29 06:01:36 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Thu, 29 Apr 2010 09:31:36 +0530 Subject: [Pw_forum] Wyckoff sites In-Reply-To: References: Message-ID: Dear Bahareh ! You must use Xcrysden to visualize the structure first before submitting job for running. It will help you to make correct structure. Its available free at Xcrysden website. And please provide your affiliation next time. On Thu, Apr 29, 2010 at 6:55 AM, bahareh rahmani wrote: > Dear All > > I have converted Wyckoff positions to x,y,x coordinates for a Clathrate > type VIII . As an example I converted 2a site to 0,0,0 and 1/2,1/2,1/2 > based on literature but quantum-espresso produces an error message and says > the above mentioned atoms have overlap. This happens for many other sites > too. Deos anyone any idea how to solve this problem? > > Best regards,Bahareh Rahmani > > _______________________________________________ > 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/20100429/5b5c43bf/attachment-0001.htm From matteo.calandra at impmc.jussieu.fr Thu Apr 29 09:24:50 2010 From: matteo.calandra at impmc.jussieu.fr (Matteo Calandra) Date: Thu, 29 Apr 2010 09:24:50 +0200 Subject: [Pw_forum] x-ray spectra with "Fermi-Dirac" electronic smearing., (Huolin Xin) Message-ID: <4BD93442.1030101@impmc.jussieu.fr> >Dear developers, >Since when did quantum espresso start to offer XANEFS calculations? I >remember I sent an email on this forum half of a hear ago to ask >whether anyone is interested in developing an EELS calculation plugin. >I got no response. Dear Huolin Xin, I think it is roughly 1 year that the XSpectra package is included in the CVS version and maybe somewhat less (I don't quite remember) that it is included in the official distribution. However, you should be careful with EELS. XSpectra calculates K-edge XAS (both dipolar and quadrupolar terms). EELS is similar to XAS but not identical. In particular the angular dependence of EELS spectra is not purely dipolar but there is a monopole term (that usually is assumed negligible even when it is not). So using the XAS dipolar simulations to interpret EELS spectra must be done "cum grano salis". We have planned to include EELS calculation in XSpectra, however we have not yet started. M. -- * * * * Matteo Calandra, Charge de Recherche (CR1) Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris Universit? Pierre et Marie Curie, tour 16, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra From paulatto at sissa.it Thu Apr 29 09:44:24 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 29 Apr 2010 09:44:24 +0200 Subject: [Pw_forum] magnetization In-Reply-To: References: Message-ID: On Thu, 29 Apr 2010 05:29:48 +0200, hanghui chen wrote: > why does 'tot_magnetization' have to be an integer? Dear Hanghui Chen, it is not an integers, but a real. +-------------------------------------------------------------------- Variable: tot_magnetization Type: REAL <------------xx Default: -1 [unspecified] Description: total majority spin charge - minority spin charge. Used to impose a specific total electronic magnetization. If unspecified then tot_magnetization variable is ignored and the amount of electronic magnetization is determined during the self-consistent cycle. +-------------------------------------------------------------------- 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 giuseppe.mattioli at mlib.ism.cnr.it Thu Apr 29 13:17:38 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Thu, 29 Apr 2010 13:17:38 +0200 Subject: [Pw_forum] the potential of core electron Message-ID: <201004291317.38207.giuseppe.mattioli@mlib.ism.cnr.it> 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: From nkxirainbow at gmail.com Thu Apr 29 11:41:46 2010 From: nkxirainbow at gmail.com (xirainbow) Date: Thu, 29 Apr 2010 17:41:46 +0800 Subject: [Pw_forum] What's scattering geometry in Raman intensity? Message-ID: Dear developer: Can ultra-soft PP be used to calculate Raman intensity? I want to know the Raman scattering geometry in Raman intensity. Who can tell me? Thanks in advance?? -- ____________________________________ 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/20100429/067a7b41/attachment.htm From giannozz at democritos.it Thu Apr 29 11:51:16 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 29 Apr 2010 11:51:16 +0200 Subject: [Pw_forum] A Question About Time In-Reply-To: References: Message-ID: <4BD95694.7060504@democritos.it> mohsen modaresi wrote: > When i run parallel (With MPICH) version with 4 core, > in output file i see this "total time until now 6.06 sec." it take > but if i use my watch29 sec to run. What is the problem? > another problem: > If i use MPICH with 1 core it takes only 17 sec (on my watch) which is > smaller than 29, Why? See Sec.3, "Understanding parallelization", and sec.6.4, "Parallelization issues", of the user guide. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Thu Apr 29 11:52:09 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 29 Apr 2010 11:52:09 +0200 Subject: [Pw_forum] What's scattering geometry in Raman intensity? In-Reply-To: References: Message-ID: <4BD956C9.9060507@democritos.it> xirainbow wrote: > Can ultra-soft PP be used to calculate Raman intensity? no > I want to know the Raman scattering geometry in Raman intensity. > Who can tell me? the experimentalist that makes the measurement can tell you P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From daijiayu at nudt.edu.cn Thu Apr 29 11:39:34 2010 From: daijiayu at nudt.edu.cn (jydai) Date: Thu, 29 Apr 2010 17:39:34 +0800 Subject: [Pw_forum] x-ray spectra with "Fermi-Dirac" electronic smearing Message-ID: Dear Matteo, Thanks for your detailed answers. Yes, i want to consider the electronic contribution to the K-edge XAS when temperature is high, .ie., above 1 eV. This can be reached by adding the Fermi functions for the electronic distribution, i think. However, people are doing on this project without this contribution now, as said in the papers i sent to you before. So, i think it also can be solved partly by the dipolar or more detailed considerations as you said. I will try again as your suggestions, thanks a lot. Jiayu ----------------------------------------------------------------------- if I understand correctly you would like to calculate K-edge XAS at high temperature including the contribution of Fermi functions in the Fermi golden rule. If this is what you would like to do, this is currently not implemented in XSPECTRA, as we always assume the temperature to be negligible with respect to the energy of the electronic excitations (1 eV=11605 Kelvin). In practice we assume that the XAS spectra is temperature independent, or, better, the only temperature dependence comes from the thermal expansion of the crystal structure. This is generally true except when vibrations contribute to the XAS spectra. Increasing temperature increase atomic vibrations and it is known in some case to wakly affect the spectra in the pre-edge region. However even in this case I guess that the problem can be solved without the need of introducing Fermi functions in the XAS cross section. You will find more details on the XAS equation implemented in Christos Gougoussis, Matteo Calandra, Ari P. Seitsonen, and Francesco Mauri, Phys. Rev. B 80, 075102 (2009) http://link.aps.org/doi/10.1103/PhysRevB.80.075102 Equation 1. What the fermi_level option in XSPECTRA does is simply calculating the Fermi level with a given electronic smearing. The electronic smearing is used in the case of metals to improve the sampling of the Fermi surface when a finite grid of k-points is used. In the case of a metallic system, as your case is, then XSPECTRA does not calculate the Fermi level and stops as this quantity can be simply read from the pw.x scf output that you must have run before XSPECTRA. Finally, note that to calculate the electronic structure and the cross section, any smearing available in pw.x should also work on XSPECTRA. However this is not equivalent in adding Fermi functions to the Fermi golden rule. ---------------- ------------------------------------------- Jiayu Dai Department of Physics National University of Defense Technology, Changsha, 410073, P R China ----------------------------------------- From giannozz at democritos.it Thu Apr 29 12:55:07 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 29 Apr 2010 12:55:07 +0200 Subject: [Pw_forum] parallel version error in quad core Xeon In-Reply-To: References: Message-ID: <4BD9658B.3030509@democritos.it> TAE BUM LEE wrote: > Does anybody know the reason of following error? > rank 3 in job 37 Lynx_60167 caused collective abort of all ranks > exit status of rank 3: killed by signal 9 http://www.quantum-espresso.org/user_guide/node48.html or, updated version: \subsection{pw.x crashes in parallel execution with an obscure message related to MPI errors} Random crashes due to MPI errors have often been reported, typically in Linux PC clusters. We cannot rule out the possibility that bugs in \qe\ cause such behavior, but we are quite confident that the most likely explanation is a hardware problem (defective RAM for instance) or a software bug (in MPI libraries, compiler, operating system) P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From jcwu.suda at hotmail.com Thu Apr 29 12:57:26 2010 From: jcwu.suda at hotmail.com (wujianchun) Date: Thu, 29 Apr 2010 18:57:26 +0800 Subject: [Pw_forum] the potential of core electron In-Reply-To: <201004291317.38207.giuseppe.mattioli@mlib.ism.cnr.it> References: <201004291317.38207.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: 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 _________________________________________________________________ ???????????????? 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/20100429/a8bc6867/attachment.htm From kazempoor at ph.iut.ac.ir Thu Apr 29 13:25:25 2010 From: kazempoor at ph.iut.ac.ir (kazempoor at ph.iut.ac.ir) Date: Thu, 29 Apr 2010 15:55:25 +0430 (IRDT) Subject: [Pw_forum] PAW pseudopotential In-Reply-To: Message-ID: <959888781.40132.1272540325376.JavaMail.root@mta.iut.ac.ir> Dear Lorenzo Thanks for the input file.I am testing and will inform you .Is it possible to make and use norm-conserving PAW pseudopotential? I ask this since I need NCPP to do GW calculation. Thanks Ali Kazempour Physics Department, Isfahn University of Technology ----- Original Message ----- From: "Lorenzo Paulatto" To: "PWSCF Forum" Sent: Wednesday, April 28, 2010 11:53:16 AM Subject: Re: [Pw_forum] PAW pseudopotential On Wed, 28 Apr 2010 07:22:02 +0200, wrote: > Is it possible to do calculation with PAW pseudopotential by espresso ? yes > Is it possible to get PAW pseudopotentail for other code and change > their format to espresso? no that I know -- 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/ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From siyouber at yahoo.fr Thu Apr 29 15:09:27 2010 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Thu, 29 Apr 2010 13:09:27 +0000 (GMT) Subject: [Pw_forum] About the mean square displacement in CP output In-Reply-To: Message-ID: <967354.13531.qm@web26501.mail.ukl.yahoo.com> Dear QE users, I am running CP dynamic with fixed temperature for a given solid system, using cp.x. The microcanonical calculation went very well with a conserved energy.Now the energy is still conserved. But my emphasis is on the mean square displacement(MSD) of atoms. They are calculated and plotted as a function of time. At the begining, the dependence seems to be linear at after, the MSD seem to oscillate around certain values which can be taken as a mean value after a sufficiently long time. My questions are: 1) According to the litterature, the dependence at the beginning should be quadratic and became linear after a long time. But for condensed system as a solid it is, the MSD should saturate after a very long time. What is happening for my case? 2) The MSD computed with cp.x are tree dimensionnal. Please, confirm it or not. 3) In which file should I see how those MSD are computed? Thanks very much 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/20100429/1f75229d/attachment.htm From nkxirainbow at gmail.com Thu Apr 29 15:43:45 2010 From: nkxirainbow at gmail.com (xirainbow) Date: Thu, 29 Apr 2010 21:43:45 +0800 Subject: [Pw_forum] What's scattering geometry in Raman intensity? In-Reply-To: <4BD956C9.9060507@democritos.it> References: <4BD956C9.9060507@democritos.it> Message-ID: Dear Paolo: Thanks for your instant reply?? Can you tell me the scattering geometry in dynmat.f90 ? On Thu, Apr 29, 2010 at 5:52 PM, Paolo Giannozzi wrote: > xirainbow wrote: > > > Can ultra-soft PP be used to calculate Raman intensity? > > no > > > I want to know the Raman scattering geometry in Raman intensity. > > Who can tell me? > > the experimentalist that makes the measurement can tell you > > 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 > -- ____________________________________ 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/20100429/b0f4a105/attachment.htm From giannozz at democritos.it Thu Apr 29 15:51:12 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 29 Apr 2010 15:51:12 +0200 Subject: [Pw_forum] What's scattering geometry in Raman intensity? In-Reply-To: References: <4BD956C9.9060507@democritos.it> Message-ID: <4BD98ED0.8050007@democritos.it> xirainbow wrote: > Can you tell me the scattering geometry in dynmat.f90 ? had you looked inside the code, you should have noticed this line: ! alpha, beta2: see PRB 54, 7830 (1996) and refs quoted therein P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From paulatto at sissa.it Thu Apr 29 16:27:27 2010 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 29 Apr 2010 16:27:27 +0200 Subject: [Pw_forum] PAW pseudopotential In-Reply-To: <959888781.40132.1272540325376.JavaMail.root@mta.iut.ac.ir> References: <959888781.40132.1272540325376.JavaMail.root@mta.iut.ac.ir> Message-ID: On Thu, 29 Apr 2010 13:25:25 +0200, wrote: > Thanks for the input file.I am testing and will inform you .Is it > possible to make and use norm-conserving PAW pseudopotential? I ask this > since I need NCPP to do GW calculation. You can impose norm-conservation on a PAW dataset (not pseudopotential!), but you will still get something totally different from a norm-conserving pseudopotential. In brief: no. 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 iori at theory.polytechnique.fr Thu Apr 29 17:59:46 2010 From: iori at theory.polytechnique.fr (iori at theory.polytechnique.fr) Date: Thu, 29 Apr 2010 17:59:46 +0200 Subject: [Pw_forum] xc functional, again.. Message-ID: <0b63736c6f97ca381d97d7ca326622ea.squirrel@theory.polytechnique.fr> Hi all. Maybe my question have already found an answer here ( that unfortuntely I can't find at the moment), so: I know I can force pw to use some xc functional, with input_dft="somefunctional". In the Modules/functionals.f90 source files I have the list. But, which is exactly the set of flag I can use to select the functionals? and which of them are implemented among the list starting at line 75 in this source file? If some of you already replied to this kind of question, just send me corresponding link. I will look at that. Thanks a lot. federico iori. Dr. Federico Iori, PhD! Laboratoire des Solides Irradi?s, Ecole Polytechnique - CEA/DSM, CNRS 91128 Palaiseau, France www.etsf.polytechnique.fr phone: +33 (0) 1 69 33 44 85 emails: federico.iori @ polytechnique.edu iori.federico @ unimore.it http://www.pdmodena.it/ http://www.comune.mo.it From marsamos at democritos.it Thu Apr 29 18:49:41 2010 From: marsamos at democritos.it (marsamos at democritos.it) Date: Thu, 29 Apr 2010 18:49:41 +0200 Subject: [Pw_forum] xc functional, again.. In-Reply-To: <0b63736c6f97ca381d97d7ca326622ea.squirrel@theory.polytechnique.fr> References: <0b63736c6f97ca381d97d7ca326622ea.squirrel@theory.polytechnique.fr> Message-ID: <20100429184941.s7kbq24kyogkwgwg@mail.democritos.it> Dear Fefe, you can look at dft_shortname in file Modules/funct.f90. bests Layla Quoting iori at theory.polytechnique.fr: > Hi all. > Maybe my question have already found an answer here ( that unfortuntely I > can't find at the moment), so: > > I know I can force pw to use some xc functional, with > input_dft="somefunctional". > In the Modules/functionals.f90 source files I have the list. > But, which is exactly the set of flag I can use to select the functionals? > and which of them are implemented among the list starting at line 75 in > this source file? > > If some of you already replied to this kind of question, just send me > corresponding link. I will look at that. > > Thanks a lot. > federico iori. > > Dr. Federico Iori, PhD! > > Laboratoire des Solides Irradi?s, > Ecole Polytechnique - CEA/DSM, CNRS > 91128 Palaiseau, France > > www.etsf.polytechnique.fr > > phone: +33 (0) 1 69 33 44 85 > emails: federico.iori @ polytechnique.edu > iori.federico @ unimore.it > http://www.pdmodena.it/ > http://www.comune.mo.it > > > > _______________________________________________ > 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 iori at theory.polytechnique.fr Thu Apr 29 18:55:46 2010 From: iori at theory.polytechnique.fr (iori at theory.polytechnique.fr) Date: Thu, 29 Apr 2010 18:55:46 +0200 Subject: [Pw_forum] xc functional, again.. In-Reply-To: <20100429184941.s7kbq24kyogkwgwg@mail.democritos.it> References: <0b63736c6f97ca381d97d7ca326622ea.squirrel@theory.polytechnique.fr> <20100429184941.s7kbq24kyogkwgwg@mail.democritos.it> Message-ID: <394dcee725e5fe191fe6946c02dbecc5.squirrel@theory.polytechnique.fr> Thanks Layla. So, I should set input_dft with 'dft_shortname' kind, if I understand correctly. ex: input_dft='pw91' or 'pbesol' and the only cases are the ones in this list 'dft_shortname' Is it correct ? Thanks a lot, ff. > Dear Fefe, you can look at dft_shortname in file Modules/funct.f90. > > bests > > Layla > > > Quoting iori at theory.polytechnique.fr: > >> Hi all. >> Maybe my question have already found an answer here ( that unfortuntely >> I >> can't find at the moment), so: >> >> I know I can force pw to use some xc functional, with >> input_dft="somefunctional". >> In the Modules/functionals.f90 source files I have the list. >> But, which is exactly the set of flag I can use to select the >> functionals? >> and which of them are implemented among the list starting at line 75 in >> this source file? >> >> If some of you already replied to this kind of question, just send me >> corresponding link. I will look at that. >> >> Thanks a lot. >> federico iori. >> >> Dr. Federico Iori, PhD! >> >> Laboratoire des Solides Irradi?s, >> Ecole Polytechnique - CEA/DSM, CNRS >> 91128 Palaiseau, France >> >> www.etsf.polytechnique.fr >> >> phone: +33 (0) 1 69 33 44 85 >> emails: federico.iori @ polytechnique.edu >> iori.federico @ unimore.it >> http://www.pdmodena.it/ >> http://www.comune.mo.it >> >> >> >> _______________________________________________ >> 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. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > Dr. Federico Iori, PhD! Laboratoire des Solides Irradi?s, Ecole Polytechnique - CEA/DSM, CNRS 91128 Palaiseau, France www.etsf.polytechnique.fr phone: +33 (0) 1 69 33 44 85 emails: federico.iori @ polytechnique.edu iori.federico @ unimore.it http://www.pdmodena.it/ http://www.comune.mo.it From marsamos at democritos.it Thu Apr 29 19:25:21 2010 From: marsamos at democritos.it (marsamos at democritos.it) Date: Thu, 29 Apr 2010 19:25:21 +0200 Subject: [Pw_forum] xc functional, again.. In-Reply-To: <394dcee725e5fe191fe6946c02dbecc5.squirrel@theory.polytechnique.fr> References: <0b63736c6f97ca381d97d7ca326622ea.squirrel@theory.polytechnique.fr> <20100429184941.s7kbq24kyogkwgwg@mail.democritos.it> <394dcee725e5fe191fe6946c02dbecc5.squirrel@theory.polytechnique.fr> Message-ID: <20100429192521.62usi2flk2s4kg8s@mail.democritos.it> Dear Fefe, I think so. However it could be (maybe) not difficult to make a cocktail and introduce a new dft! bests Layla Quoting iori at theory.polytechnique.fr: > > Thanks Layla. > So, I should set input_dft with 'dft_shortname' kind, if I understand > correctly. > ex: input_dft='pw91' or 'pbesol' > > and the only cases are the ones in this list 'dft_shortname' > Is it correct ? > > Thanks a lot, > ff. > >> Dear Fefe, you can look at dft_shortname in file Modules/funct.f90. >> >> bests >> >> Layla >> >> >> Quoting iori at theory.polytechnique.fr: >> >>> Hi all. >>> Maybe my question have already found an answer here ( that unfortuntely >>> I >>> can't find at the moment), so: >>> >>> I know I can force pw to use some xc functional, with >>> input_dft="somefunctional". >>> In the Modules/functionals.f90 source files I have the list. >>> But, which is exactly the set of flag I can use to select the >>> functionals? >>> and which of them are implemented among the list starting at line 75 in >>> this source file? >>> >>> If some of you already replied to this kind of question, just send me >>> corresponding link. I will look at that. >>> >>> Thanks a lot. >>> federico iori. >>> >>> Dr. Federico Iori, PhD! >>> >>> Laboratoire des Solides Irradi?s, >>> Ecole Polytechnique - CEA/DSM, CNRS >>> 91128 Palaiseau, France >>> >>> www.etsf.polytechnique.fr >>> >>> phone: +33 (0) 1 69 33 44 85 >>> emails: federico.iori @ polytechnique.edu >>> iori.federico @ unimore.it >>> http://www.pdmodena.it/ >>> http://www.comune.mo.it >>> >>> >>> >>> _______________________________________________ >>> 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. >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > Dr. Federico Iori, PhD! > > Laboratoire des Solides Irradi?s, > Ecole Polytechnique - CEA/DSM, CNRS > 91128 Palaiseau, France > > www.etsf.polytechnique.fr > > phone: +33 (0) 1 69 33 44 85 > emails: federico.iori @ polytechnique.edu > iori.federico @ unimore.it > http://www.pdmodena.it/ > http://www.comune.mo.it > > > > _______________________________________________ > 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 giannozz at democritos.it Thu Apr 29 21:46:32 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 29 Apr 2010 21:46:32 +0200 Subject: [Pw_forum] xc functional, again.. In-Reply-To: <20100429192521.62usi2flk2s4kg8s@mail.democritos.it> References: <0b63736c6f97ca381d97d7ca326622ea.squirrel@theory.polytechnique.fr> <20100429184941.s7kbq24kyogkwgwg@mail.democritos.it> <394dcee725e5fe191fe6946c02dbecc5.squirrel@theory.polytechnique.fr> <20100429192521.62usi2flk2s4kg8s@mail.democritos.it> Message-ID: On Apr 29, 2010, at 19:25 , marsamos at democritos.it wrote: >> and the only cases are the ones in this list 'dft_shortname' >> Is it correct ? no, these cases are allowed: ! dft is the exchange-correlation functional, described by ! any nonconflicting combination of the following keywords (list follows) as well as these: ! Special cases (dft_shortname): (list follows) 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 Thu Apr 29 23:48:41 2010 From: modaresi.mohsen at gmail.com (mohsen modaresi) Date: Fri, 30 Apr 2010 02:18:41 +0430 Subject: [Pw_forum] A Question About Time In-Reply-To: <4BD95694.7060504@democritos.it> References: <4BD95694.7060504@democritos.it> Message-ID: Dear Paolo tahnks for your Ref. But i think there is bug in Q.E., When i run pw.x, CPUs work for 29 sec but time given in output file is 6 sec. Thanks again for your answer Mohsen Modaresi On Thu, Apr 29, 2010 at 2:21 PM, Paolo Giannozzi wrote: > mohsen modaresi wrote: > > > When i run parallel (With MPICH) version with 4 core, > > in output file i see this "total time until now 6.06 sec." it take > > but if i use my watch29 sec to run. What is the problem? > > another problem: > > If i use MPICH with 1 core it takes only 17 sec (on my watch) which is > > smaller than 29, Why? > > See Sec.3, "Understanding parallelization", and sec.6.4, > "Parallelization issues", of the user guide. > > 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/20100430/1dd6d5c5/attachment.htm From jcwu.suda at hotmail.com Fri Apr 30 03:17:41 2010 From: jcwu.suda at hotmail.com (wujianchun) Date: Fri, 30 Apr 2010 09:17:41 +0800 Subject: [Pw_forum] the potential of core electron In-Reply-To: References: <201004291317.38207.giuseppe.mattioli@mlib.ism.cnr.it>, Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100430/ca976c4a/attachment.htm From sd.wang000 at gmail.com Fri Apr 30 06:17:25 2010 From: sd.wang000 at gmail.com (shudong wang) Date: Fri, 30 Apr 2010 12:17:25 +0800 Subject: [Pw_forum] About kpoint Message-ID: Dear developers: When I perform nscf calculation, it needs generation of k-point meshes .What code can get the meshes in PWSCF? Thanks! Yours S.D.Wang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100430/d7587eba/attachment.htm From archygu at gmail.com Fri Apr 30 08:52:27 2010 From: archygu at gmail.com (archygu) Date: Fri, 30 Apr 2010 14:52:27 +0800 Subject: [Pw_forum] About kpoint References: Message-ID: <201004301452252188620@gmail.com> hi, you can use xcrysden to chose your own K path. 2010-04-30 archygu ???? shudong wang ????? 2010-04-30 12:17:54 ???? PWSCF??? ??? ??? [Pw_forum] About kpoint Dear developers: When I perform nscf calculation, it needs generation of k-point meshes .What code can get the meshes in PWSCF? Thanks! Yours S.D.Wang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100430/d16f5228/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Fri Apr 30 12:39:36 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Fri, 30 Apr 2010 12:39:36 +0200 Subject: [Pw_forum] the potential of core electron In-Reply-To: References: <201004291317.38207.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <201004301239.36639.giuseppe.mattioli@mlib.ism.cnr.it> Dear Jianchun Place one interstitial He atom where you think it can be safely placed in the bulk supercell (i.e., far from the defect site...). If you want, freeze the Cd and S atoms in their positions and optimize the He position. Look at the forces and check that they remain quite low. Then place an He atom in the same position of the supercell containing a defect. Use the He 1s value to align (it is a relative alignment...) the bulk and defect Kohn-Sham eigenvalues, or use the "Delta He" as a Delta V correction if you want to compare the eigenvalues of neutral and charged supercells. Be careful: it works better when the number of electrons is high, so that it does not matter very much if you add one... And remember that someone could not like this rough estimate... 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: From giuseppe.mattioli at mlib.ism.cnr.it Fri Apr 30 12:43:04 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Fri, 30 Apr 2010 12:43:04 +0200 Subject: [Pw_forum] the potential of core electron In-Reply-To: References: <201004291317.38207.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <201004301243.04497.giuseppe.mattioli@mlib.ism.cnr.it> 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: From jcwu.suda at hotmail.com Fri Apr 30 11:20:35 2010 From: jcwu.suda at hotmail.com (wujianchun) Date: Fri, 30 Apr 2010 17:20:35 +0800 Subject: [Pw_forum] the potential of core electron In-Reply-To: <201004301239.36639.giuseppe.mattioli@mlib.ism.cnr.it> References: <201004291317.38207.giuseppe.mattioli@mlib.ism.cnr.it>, , , <201004301239.36639.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: Dear Dr Giuseppe Mattioli; That's indeed very helpful. Thanks a lot! Rgds Jianchun > From: giuseppe.mattioli at mlib.ism.cnr.it > To: pw_forum at pwscf.org > Date: Fri, 30 Apr 2010 12:39:36 +0200 > Subject: Re: [Pw_forum] the potential of core electron > > Dear Jianchun > Place one interstitial He atom where you think it can be safely placed in the > bulk supercell (i.e., far from the defect site...). If you want, freeze the > Cd and S atoms in their positions and optimize the He position. Look at the > forces and check that they remain quite low. Then place an He atom in the > same position of the supercell containing a defect. Use the He 1s value to > align (it is a relative alignment...) the bulk and defect Kohn-Sham > eigenvalues, or use the "Delta He" as a Delta V correction if you want to > compare the eigenvalues of neutral and charged supercells. Be careful: it > works better when the number of electrons is high, so that it does not matter > very much if you add one... > > And remember that someone could not like this rough estimate... > > 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 _________________________________________________________________ ???????????????? 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/20100430/b166798d/attachment-0001.htm From jcwu.suda at hotmail.com Fri Apr 30 12:19:15 2010 From: jcwu.suda at hotmail.com (wujianchun) Date: Fri, 30 Apr 2010 18:19:15 +0800 Subject: [Pw_forum] the potential of core electron In-Reply-To: <201004301243.04497.giuseppe.mattioli@mlib.ism.cnr.it> References: <201004291317.38207.giuseppe.mattioli@mlib.ism.cnr.it>, , , <201004301243.04497.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100430/9c4dd89a/attachment.htm From uccaati at ucl.ac.uk Fri Apr 30 16:09:17 2010 From: uccaati at ucl.ac.uk (Antonio Tilocca) Date: Fri, 30 Apr 2010 15:09:17 +0100 (BST) Subject: [Pw_forum] About the mean square displacement in CP output Message-ID: 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 siyouber at yahoo.fr Thu Apr 29 15:09:27 2010 >From: siyouber at yahoo.fr (Bertrand SITAMTZE) >Date: Thu, 29 Apr 2010 13:09:27 +0000 (GMT) >Subject: [Pw_forum] About the mean square displacement in CP output >I am running CP dynamic with fixed temperature for a given solid system, >using cp.x. The microcanonical calculation went very well with a >conserved energy.Now the energy is still conserved. But my emphasis is on > the mean >square displacement(MSD) of atoms. They are calculated and plotted as a >function of time. At the begining, the dependence seems to be linear at >after, the MSD seem to oscillate around certain values which can be taken >as a mean value after a sufficiently long time. My questions are: 1) >According to the litterature, the dependence at the beginning should be >quadratic and became linear after a long time. But for condensed system >as >a solid it is, the MSD should saturate after a very long time. What is >happening for my case? 2) The MSD computed with cp.x are tree >dimensionnal. Please, confirm it or not. 3) In which file should I see >how >those MSD are computed? From scandolo at ictp.it Fri Apr 30 16:10:15 2010 From: scandolo at ictp.it (Sandro Scandolo) Date: Fri, 30 Apr 2010 16:10:15 +0200 Subject: [Pw_forum] About the mean square displacement in CP output In-Reply-To: <967354.13531.qm@web26501.mail.ukl.yahoo.com> References: <967354.13531.qm@web26501.mail.ukl.yahoo.com> Message-ID: <4BDAE4C7.1050802@ictp.it> Dear Bertrand: 1) The MSD is quadratic in time at the beginning if you start with finite velocities. If you start with zero velocities the MSD will be even slower (t**4 in principle). For a fluid, the asymptotic behavior is linear in t, for a solid it converges to a finite value (which can be connected to the Debye-Waller factor of x-ray intensities) in a time scale comparable to the vibrational time scale, so not too slow. 2) The MSD computed in cp.x are 3-D. 3) MSD's are computed in subroutine "ions_displacement" which can be found inside "ions_base.f90" in directory "Modules". Your simulation looks ok, except perhaps for the linear dependence in t at the beginning, but the quadratic (or other) initial laws are generally seen only in the first very few steps, 10-20 steps are more than enough to spoil the ideal behavior typically. Sandro > > > I am running CP dynamic with fixed temperature for a given solid > system, using cp.x. The microcanonical calculation went very well with > a conserved energy.Now the energy is still conserved. But my emphasis > is on the mean square displacement(MSD) of atoms. They are calculated > and plotted as a function of time. > At the begining, the dependence seems to be linear at after, the MSD > seem to oscillate around certain values which can be taken as a mean > value after a sufficiently long time. My questions are: > 1) According to the litterature, the dependence at the beginning > should be quadratic and became linear after a long time. But for > condensed system as a solid it is, the MSD should saturate after a > very long time. What is happening for my case? > 2) The MSD computed with cp.x are tree dimensionnal. Please, confirm > it or not. > 3) In which file should I see how those MSD are computed? > > > Thanks very much 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 > -- Sandro Scandolo, ICTP | http://www.ictp.it/~scandolo -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100430/e9bfd199/attachment.htm From giannozz at democritos.it Fri Apr 30 16:25:53 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 30 Apr 2010 16:25:53 +0200 Subject: [Pw_forum] A Question About Time In-Reply-To: References: <4BD95694.7060504@democritos.it> Message-ID: <4BDAE871.6050100@democritos.it> mohsen modaresi wrote: > When i run pw.x, CPUs work for 29 sec > but time given in output file is 6 sec. CPU time .NE. wall time P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From 0930hanbin at 163.com Fri Apr 30 16:12:58 2010 From: 0930hanbin at 163.com (0930hanbin) Date: Fri, 30 Apr 2010 22:12:58 +0800 (CST) Subject: [Pw_forum] cannot open xml_recover file for writing Message-ID: <891bf6.103c7.1284f102666.Coremail.0930hanbin@163.com> Dear all, I am trying to get the phonon dispersion relation of NbO2, but when I run the program, I get : *********************************************************************** from ph_writefile : error # 14 cannot open xml_recover file for writing *********************************************************************** My input is: phonons of NbO2 &inputph tr2_ph=1.0d-14, ldisp=.true., nq1=4, nq2=4, nq3=4 amass(1)=92.9063, amass(2)=15.9994 prefix='NbO2', fildyn='NbO2.dyn', recover=.true. / Can anyone tell me what the matter is ? Thanks a lot in asvance. Sincerely, Bin Han, ECNU China. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100430/f9fa1e81/attachment.htm From siyouber at yahoo.fr Fri Apr 30 17:15:36 2010 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Fri, 30 Apr 2010 15:15:36 +0000 (GMT) Subject: [Pw_forum] About the mean square displacement in CP output In-Reply-To: Message-ID: <414847.4559.qm@web26504.mail.ukl.yahoo.com> 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? Thanks once again **************************** 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 siyouber at yahoo.fr? Thu Apr 29 15:09:27 2010 >From: siyouber at yahoo.fr (Bertrand SITAMTZE) >Date: Thu, 29 Apr 2010 13:09:27 +0000 (GMT) >Subject: [Pw_forum] About the mean square displacement in CP output >I am running CP dynamic with fixed temperature for a given solid system, >using cp.x. The microcanonical calculation went very well with a >conserved energy.Now the energy is still conserved. But my emphasis is on > the mean >square displacement(MSD) of atoms. They are calculated and plotted as a >function of time. At the begining, the dependence seems to be linear at >after, the MSD seem to oscillate around certain values which can be taken >as a mean value after a sufficiently long time. My questions are: 1) >According to the litterature, the dependence at the beginning should be >quadratic and became linear after a long time. But for condensed system >as >a solid it is, the MSD should saturate after a very long time. What is >happening for my case? 2) The MSD computed with cp.x are tree >dimensionnal. Please, confirm it or not. 3) In which file should I see >how >those MSD are computed? _______________________________________________ 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/20100430/f76fc471/attachment.htm From siyouber at yahoo.fr Fri Apr 30 17:28:08 2010 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Fri, 30 Apr 2010 15:28:08 +0000 (GMT) Subject: [Pw_forum] About the mean square displacement in CP output In-Reply-To: <4BDAE4C7.1050802@ictp.it> Message-ID: <527010.46040.qm@web26501.mail.ukl.yahoo.com> 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 ************************************ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100430/4d90f933/attachment.htm From giannozz at democritos.it Fri Apr 30 18:56:02 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 30 Apr 2010 18:56:02 +0200 Subject: [Pw_forum] cannot open xml_recover file for writing In-Reply-To: <891bf6.103c7.1284f102666.Coremail.0930hanbin@163.com> References: <891bf6.103c7.1284f102666.Coremail.0930hanbin@163.com> Message-ID: <4BDB0BA2.6040203@democritos.it> 0930hanbin wrote: > recover=.true. do you really need to restart from an interrupted run? P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From kazempoor at ph.iut.ac.ir Fri Apr 30 19:52:02 2010 From: kazempoor at ph.iut.ac.ir (kazempoor at ph.iut.ac.ir) Date: Fri, 30 Apr 2010 22:22:02 +0430 (IRDT) Subject: [Pw_forum] convergence In-Reply-To: <720296692.44172.1272649706708.JavaMail.root@mta.iut.ac.ir> Message-ID: <895498437.44182.1272649922096.JavaMail.root@mta.iut.ac.ir> Dear All For confident calculation, which parameter is better in normal calculation( after k-point and ecut convergence),total energy or cohesive energy? Another question: how much is the enough cutoff energy for NCPP? Thanks a lot Ali Kazempour Physics Department, Isfahan University of Technology