From colonel.sreekar at gmail.com Tue Apr 1 08:48:21 2008 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Tue, 1 Apr 2008 12:18:21 +0530 Subject: [Pw_forum] atomic nanocluster band calculation Message-ID: Dear users, I want to do finite system(metal cluster N~2-20) band calculation. Could anyone tell me how to do this ?Any link to a tutorial would also helpful. Thanks in advance, Sreekar Guddeti -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080401/f93ebd8c/attachment.htm From lanhaiping at gmail.com Tue Apr 1 09:08:26 2008 From: lanhaiping at gmail.com (lan haiping) Date: Tue, 1 Apr 2008 15:08:26 +0800 Subject: [Pw_forum] atomic nanocluster band calculation In-Reply-To: References: Message-ID: you can find many related tutorials in url below: http://www.quantum-espresso.org/wiki/index.php/Tutorials_and_Examples On Tue, Apr 1, 2008 at 2:48 PM, sreekar guddeti wrote: > Dear users, > I want to do finite system(metal cluster N~2-20) band calculation. Could > anyone tell me how to do this ?Any link to a tutorial would also helpful. > Thanks in advance, > Sreekar Guddeti > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080401/c092ff2d/attachment.htm From njuxuyuehua at gmail.com Tue Apr 1 09:21:55 2008 From: njuxuyuehua at gmail.com (xu yuehua) Date: Tue, 1 Apr 2008 15:21:55 +0800 Subject: [Pw_forum] something was not well in the outfile of elph calculation Message-ID: hi all i am now trying to calculate el-ph but something was not well. anyone can give some advice ? i will be grateful the el-ph input : el-ph calculation &inputph tr2_ph=1.0d-10, prefix='cnt-6-0', fildvscf='cnt60dv', amass(1)=12.011, outdir='/home/xyh/home2/pwscf/tmp/', fildyn='cnt60.dyn', elph=.true., trans=.true., ldisp=.true. nq1=1,nq2=1,nq3=1 / the part of outfile is : Pert. # 1: Fermi energy shift (Ry) = 0.0000 0.0000 iter # 83 total cpu time : 41448.8 secs av.it.: 40.6 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.718E+20 kpoint 5 ibnd 49 solve_linter: root not converged 0.147E+03 Pert. # 1: Fermi energy shift (Ry) = 0.0000 0.0000 -- Xu Yuehua physics Department of Nanjing university China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080401/1de65e05/attachment.htm From giannozz at nest.sns.it Tue Apr 1 09:22:09 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 01 Apr 2008 09:22:09 +0200 Subject: [Pw_forum] Exceptionally large charge density cut-off In-Reply-To: <1148.172.16.109.56.1206810997.squirrel@webmail.iitg.ernet.in> References: <1148.172.16.109.56.1206810997.squirrel@webmail.iitg.ernet.in> Message-ID: <47F1E2A1.8030608@nest.sns.it> Subhradip Ghosh wrote: > [..] I find that phonon frequencies at Gamma and [1/2 1/2 1/2] points > do not converge even after a large charge density cut-off although with > respect to k-mesh size and kinetic energy cut-off, > the convergence was achieved with reaonable values of these parameters. > [...] The lowest lying acoustic mode is not yet converged to within 1% > while the other modes have converged. > > This is very surprising because when I looked into the archive and the > relevent literature I didn't find any reference to such a behavior. you are using ultrasoft pseudopotentials, right? the calculation of phonon frequencies - especially acoustic phonons - with USPP is quite tricky. Large cutoffs for the charge density are needed, sometimes so large to make the calculation impractical. Unfortunately I am not aware of any remedy. Last time I tried to use USPP in a phonon calculation, I gave up. I am trying again right now... Acoustic modes are sensitive to small violations of the Acoustic Sum Rule (i.e. of translational invariance), and this is well known (even in the case of norm-conserving PP, where the violation of the ASR comes from the discretization on a grid of the exchange correlation potential). At Gamma this is typically fixed by imposing the ASR on the dynamical matrix, but this may not be sufficient. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From subhra at iitg.ernet.in Tue Apr 1 09:54:41 2008 From: subhra at iitg.ernet.in (Subhradip Ghosh) Date: Tue, 1 Apr 2008 13:24:41 +0530 (IST) Subject: [Pw_forum] Exceptionally large charge density cut-off In-Reply-To: <47F1E2A1.8030608@nest.sns.it> References: <1148.172.16.109.56.1206810997.squirrel@webmail.iitg.ernet.in> <47F1E2A1.8030608@nest.sns.it> Message-ID: <36683.202.141.81.5.1207036481.squirrel@webmail.iitg.ernet.in> Thanks Paolo. Does that mean one should not use USPP for phonon calcs at all? I guess it varies from case to case. I have seen people using USPP for phonon calculations though. For example, Dal Carso and Gironcoli, PRB 62, 273 (2000) has calculated phonons in Fe and Ni with USPP. Bungaro, Rabe and Dal Carso used USPP for Ni and Mn in Ni2MnGa phonons (PRB 68, 134104 (2003)). This is bit strange as to why USPP would fail for phonons. In that case, the applicability of USPP would be really limited. > Subhradip Ghosh wrote: > >> [..] I find that phonon frequencies at Gamma and [1/2 1/2 1/2] points > > do not converge even after a large charge density cut-off although with >> respect to k-mesh size and kinetic energy cut-off, >> the convergence was achieved with reaonable values of these parameters. >> [...] The lowest lying acoustic mode is not yet converged to within 1% >> while the other modes have converged. >> >> This is very surprising because when I looked into the archive and the >> relevent literature I didn't find any reference to such a behavior. > > you are using ultrasoft pseudopotentials, right? the calculation of > phonon frequencies - especially acoustic phonons - with USPP is quite > tricky. Large cutoffs for the charge density are needed, sometimes > so large to make the calculation impractical. Unfortunately I am not > aware of any remedy. Last time I tried to use USPP in a phonon > calculation, I gave up. I am trying again right now... > > Acoustic modes are sensitive to small violations of the Acoustic Sum > Rule (i.e. of translational invariance), and this is well known (even > in the case of norm-conserving PP, where the violation of the ASR comes > from the discretization on a grid of the exchange correlation > potential). At Gamma this is typically fixed by imposing the ASR on > the dynamical matrix, but this may not be sufficient. > > Paolo > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > ************************************************************************ Dr. Subhradip Ghosh Assistant Professor Department of Physics Indian Institute of Technology Guwahati,Assam-781039 India E-mail:subhra at iitg.ernet.in Phone: +91 361 2582717(O) +91 361 2584717(R) Fax: +91 361 2582749 (Physics) +91 361 2690762 (General) ************************************************************************ From ezadshojaee at hotmail.com Tue Apr 1 10:09:57 2008 From: ezadshojaee at hotmail.com (Ezad Shojaee) Date: Tue, 1 Apr 2008 08:09:57 +0000 Subject: [Pw_forum] Error in vc-relax Message-ID: Hi performing vc-relaxation, I have got this error: from checkallsym : error # 5 not orthogonal operation I wonder if anyone could tell me the reason and how to deal with it? thanx _________________________________________________________________ News, entertainment and everything you care about at Live.com. Get it now! http://www.live.com/getstarted.aspx -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080401/ec29c4bb/attachment.htm From colonel.sreekar at gmail.com Tue Apr 1 10:35:40 2008 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Tue, 1 Apr 2008 14:05:40 +0530 Subject: [Pw_forum] pain with bands.x Message-ID: Dear users, To create bands.dat so as to use for plotting bands i ran ./bands.x < ni_bands.in > ni_bands.out at the command prompt . The error message is STOP 2 could anyone help me out... i also have a running pwgui and XCrysden. If anyone could suggest how to output in gui mode that would be helpful. Thanks in advance, sreekar guddeti -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080401/4f364781/attachment.htm From giannozz at nest.sns.it Tue Apr 1 13:21:52 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 01 Apr 2008 13:21:52 +0200 Subject: [Pw_forum] Error in vc-relax In-Reply-To: References: Message-ID: <47F21AD0.4020109@nest.sns.it> Ezad Shojaee wrote: > from checkallsym : error # 5 > not orthogonal operation see the User Guide, Troubleshooting section, point 1.30 of the wiki version Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Tue Apr 1 13:24:09 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 01 Apr 2008 13:24:09 +0200 Subject: [Pw_forum] pain with bands.x In-Reply-To: References: Message-ID: <47F21B59.2030008@nest.sns.it> sreekar guddeti wrote: > To create bands.dat so as to use for plotting bands i ran > ./bands.x < ni_bands.in > ni_bands.out at the command prompt . > The error message is > > STOP 2 > > could anyone help me out... if you do not know how to find the true error message issued by the code: no, nobody can help you Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From nemeth at anl.gov Tue Apr 1 21:21:59 2008 From: nemeth at anl.gov (Karoly Nemeth) Date: Tue, 1 Apr 2008 14:21:59 -0500 (CDT) Subject: [Pw_forum] from projwfc : error # 90 (fwd) In-Reply-To: References: Message-ID: Guys, about two weeks ago we discussed an error message related to projwfc, namely "from projwfc : error # 90". It turned out that it was due to the use of the xlf compiler. More details ca be found below. Just in case anybody else would be wondering on this error message on some platforms and compilers. Karoly --------------------------------------------------------------- From giannozz at nest.sns.it Tue Apr 1 22:46:24 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 1 Apr 2008 22:46:24 +0200 Subject: [Pw_forum] from projwfc : error # 90 (fwd) In-Reply-To: References: Message-ID: <172CE237-A143-4DB6-B8A2-CA94858FBDD6@nest.sns.it> On Apr 1, 2008, at 21:21 , Karoly Nemeth wrote: > about two weeks ago we discussed an error message related to projwfc, > namely "from projwfc : error # 90". > It turned out that it was due to the use of the xlf compiler. maybe the xlf compiler is right: the "official" f90 syntax for namelist is &namelist ... / . The syntax &namelist ... &end was widely accepted but it was never meant to be a standard. The documentation should be fixed. Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From polynmr at physics.unc.edu Tue Apr 1 23:01:27 2008 From: polynmr at physics.unc.edu (Charles Chen) Date: Tue, 01 Apr 2008 17:01:27 -0400 Subject: [Pw_forum] MPI work via LSF Message-ID: <47F2A2A7.1010502@physics.unc.edu> Dear PWSCF users Recently, I compiled the V4.0cvs on our ITS machine, IA64 with Linux. When I run the examples from the package, e.g. example01 on Si crystal. The calculation can easily get the LSF overload and I got the warning message from the admin: > Your job on cypress (JobID 114850) is causing the load average to get very high again. Whatever you are doing is giving the system problems. Please help me on tuning the configuration and make our system admin a little happier when he see me. There is another problem which actually I have sent to the maillist but got no reply yet. Has it been answered somewhere else many times, if so, please let me know. I am not sure this is a problem originated from MPICH and LSF. I now can finish the example with Si, from SCF calculation to bands calculation, to band post-processing. However, I am still not lucky on trying the GIPAW example. Since our ITS machines do not allow interactive job, I submit job through bsub. I successfully finished si.scf.in, which is extracted from the GIPAW example. When I continued to run the nmr part, it failed. The error message is like this when I submitted the job: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from gipaw_readin : error # 1 reading inputgipaw namelist %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% The MPI error message is like this: MPI: On host cypress, Program /netscr/polynmr/espresso4.0cvs2/GIPAW/gipaw.x, Rank 0, Process 4934 called MPI_Abort(, 0) MPI: --------stack traceback------- line: 2 Unable to parse input as legal command or C expression. The "backtrace" command has failed because there is no running program. MPI: Intel(R) Debugger for applications running on IA-64, Version 10.1-32 , Build 20070829 MPI: -----stack traceback ends----- MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize() MPI: aborting job It looks the -in option does not work with GIPAW code, am I right? In case this is the configure problem, I have may config.log attached. Thanks! Charles Chen -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: sinmr.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20080401/1cecc16b/attachment.txt From herofather at 163.com Wed Apr 2 09:52:38 2008 From: herofather at 163.com (herofather) Date: Wed, 2 Apr 2008 15:52:38 +0800 (CST) Subject: [Pw_forum] is there a tool for the IR curve from .vib.analysis file? Message-ID: <4918468.959121207122758507.JavaMail.coremail@bj163app110.163.com> hello everybody, i have got a .vib.analysis file now, and i want to get the IR absorption curve, i know i can extract the data from the file. but i don't know whether there is a tool in the pwscf for curve direactly? thanking for your reply. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080402/a2f5a0a0/attachment.htm From giannozz at nest.sns.it Wed Apr 2 10:57:28 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 02 Apr 2008 10:57:28 +0200 Subject: [Pw_forum] MPI work via LSF In-Reply-To: <47F2A2A7.1010502@physics.unc.edu> References: <47F2A2A7.1010502@physics.unc.edu> Message-ID: <47F34A78.5090203@nest.sns.it> Charles Chen wrote: > When I run the examples from the package, e.g. example01 on Si crystal. > The calculation can easily get the LSF overload and I got the warning > message from the admin: > >> Your job on cypress (JobID 114850) is causing the load average to get >> very high again. Whatever you are doing is giving the system problems. > > Please help me on tuning the configuration and make our system admin a > little happier when he see me. on the basis of the confused info (or lack of it) contained in your message, the only conclusions I can draw are that 1) you need to learn how to use a parallel machine 2) you need a better system manager > from gipaw_readin : error # 1 > reading inputgipaw namelist the code is not reading anything > It looks the -in option does not work with GIPAW code, am I right? it works -- Paolo Giannozzi, Democritos and University of Udine, Italy From ezadshojaee at hotmail.com Wed Apr 2 12:09:40 2008 From: ezadshojaee at hotmail.com (Ezad Shojaee) Date: Wed, 2 Apr 2008 10:09:40 +0000 Subject: [Pw_forum] phonons by LDA+U Message-ID: Hi I have performed an LDA+U calculation for my case, seems to be OK(with a noticable improvement in the band gap). But when i tried to perform phonon calculation, it converged to meaningless figures(containing a lot of minus ones) that are not comparable to the LDA. The structure is relatively relaxed due to the forces and stresses(that should be reasonable, as I have used U_Progection_type=atomic) Is there anything i should concern? sorry for the basic question! _________________________________________________________________ Discover the new Windows Vista http://search.msn.com/results.aspx?q=windows+vista&mkt=en-US&form=QBRE -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080402/0fe2aa5a/attachment.htm From giannozz at nest.sns.it Wed Apr 2 12:17:43 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 02 Apr 2008 12:17:43 +0200 Subject: [Pw_forum] Exceptionally large charge density cut-off In-Reply-To: <36683.202.141.81.5.1207036481.squirrel@webmail.iitg.ernet.in> References: <1148.172.16.109.56.1206810997.squirrel@webmail.iitg.ernet.in> <47F1E2A1.8030608@nest.sns.it> <36683.202.141.81.5.1207036481.squirrel@webmail.iitg.ernet.in> Message-ID: <47F35D47.7010801@nest.sns.it> Subhradip Ghosh wrote: > Thanks Paolo. Does that mean one should not use USPP for phonon calcs at > all? I guess it varies from case to case. this is also my guess. For sure it works in some cases, but in other cases USPP (especially those produced by Vanderbilt's code, according to my limited experience) are so difficult to use in phonon calculations that you do not gain anything with respect to ordinary PPs > This is bit strange as to why USPP would fail for phonons. In that case, > the applicability of USPP would be really limited. unfortunately it is. Ideas welcome. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Wed Apr 2 12:25:04 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 02 Apr 2008 12:25:04 +0200 Subject: [Pw_forum] difference between P63 and P63/mmc space groups In-Reply-To: <609118.875641206862606966.JavaMail.coremail@bj163app128.163.com> References: <609118.875641206862606966.JavaMail.coremail@bj163app128.163.com> Message-ID: <47F35F00.7040709@nest.sns.it> wangjunjie1981_0 wrote: > Recently, i encounter a structure with space group P63,but when i > build this structure by corresponding P63 informations it finds > the space group P63/mmc WHO finds the space group P63/mmc ? > numbers of symmetry operators is changed from 6 to 24 "is changed" by WHAT? > I want to know whether these results are correct or not at this time. then please reformulate your query in a form that is understandable Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From glaweh at physik.fu-berlin.de Wed Apr 2 12:12:42 2008 From: glaweh at physik.fu-berlin.de (Henning Glawe) Date: Wed, 2 Apr 2008 12:12:42 +0200 Subject: [Pw_forum] phonons by LDA+U In-Reply-To: References: Message-ID: <20080402101242.GA16130@physik.fu-berlin.de> On Wed, Apr 02, 2008 at 10:09:40AM +0000, Ezad Shojaee wrote: > I have performed an LDA+U calculation for my case, seems to be OK(with a noticable improvement in the band gap). But when i tried to perform phonon calculation, it converged to meaningless figures(containing a lot of minus ones) that are not comparable to the LDA. The structure is relatively relaxed due to the forces and stresses(that should be reasonable, as I have used U_Progection_type=atomic) > Is there anything i should concern? > sorry for the basic question! AFAIK there is no support for LDA+U in the phonon code. -- c u henning From wangjunjie1981_0 at 163.com Wed Apr 2 13:10:02 2008 From: wangjunjie1981_0 at 163.com (wangjunjie1981_0) Date: Wed, 2 Apr 2008 19:10:02 +0800 (CST) Subject: [Pw_forum] fix lattice constants Message-ID: <12127872.1645371207134602956.JavaMail.coremail@bj163app127.163.com> Dear All, I want to fix the lattice parameters to optimize the structure, but i don't know how to achieve. What should be added in input file. Best regards, Junjie Wang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080402/d0398353/attachment.htm From paulatto at sissa.it Wed Apr 2 13:49:41 2008 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 2 Apr 2008 13:49:41 +0200 (CEST) Subject: [Pw_forum] fix lattice constants In-Reply-To: <12127872.1645371207134602956.JavaMail.coremail@bj163app127.163.com> References: <12127872.1645371207134602956.JavaMail.coremail@bj163app127.163.com> Message-ID: <11605.147.122.5.182.1207136981.squirrel@webmail.sissa.it> On Mer, Aprile 2, 2008 13:10, wangjunjie1981_0 wrote: > > Dear All, > I want to fix the lattice parameters to optimize the structure, but i > don't know how to achieve. What should be added in input file. If calculation type is 'relax' than the cell will remain constant, if it is 'vc-relax' than the cell can change; no other setting is necessary. You will find more information in the manual. ragards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) +39 040 3787 511 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From matteo at umn.edu Wed Apr 2 16:52:32 2008 From: matteo at umn.edu (Matteo Cococcioni) Date: Wed, 02 Apr 2008 09:52:32 -0500 Subject: [Pw_forum] phonons by LDA+U In-Reply-To: <20080402101242.GA16130@physik.fu-berlin.de> References: <20080402101242.GA16130@physik.fu-berlin.de> Message-ID: <47F39DB0.6020406@umn.edu> Dear Ezad, yes, the extension of LDA+U to the phonon code is not ready yet. as far as I understand you have relaxed the structure with LDA+U, but that structure won't be stable in LDA. That's why the phonon code is giving you meaningless results. Matteo Henning Glawe wrote: > On Wed, Apr 02, 2008 at 10:09:40AM +0000, Ezad Shojaee wrote: > >> I have performed an LDA+U calculation for my case, seems to be OK(with a noticable improvement in the band gap). But when i tried to perform phonon calculation, it converged to meaningless figures(containing a lot of minus ones) that are not comparable to the LDA. The structure is relatively relaxed due to the forces and stresses(that should be reasonable, as I have used U_Progection_type=atomic) >> Is there anything i should concern? >> sorry for the basic question! >> > > AFAIK there is no support for LDA+U in the phonon code. > > > -------------- next part -------------- A non-text attachment was scrubbed... Name: matteo.vcf Type: text/x-vcard Size: 294 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20080402/e213b433/attachment.vcf From colonel.sreekar at gmail.com Wed Apr 2 19:20:58 2008 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Wed, 2 Apr 2008 22:50:58 +0530 Subject: [Pw_forum] example 05 band structure calculation Message-ID: Dear Users, I run example 05 (espresso 4.0cvs)and get the output as cleaning /home/colonel/tmp... done running the scf calculation... done running pp.x to do a 2-d plot of the charge density... done running plotrho.x to generate rho.ps... done running the band-structure calculation for Si... done running the post-processing for band structure..../run_example: line 237: 15828 Segmentation fault (core dumped) $BANDS_COMMAND < si.bands.in > si.bands.out Error condition encountered during test: exit status = 139 Aborting so i try removing band structure evaluation part(post processing code) from the script and charge density profile(2D) is successfully outputted. So pain seems to be in bands. x part. This executable is there in bin directory. Could anyone guide me... Thanks, Sreekar Guddeti -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080402/78fb92b0/attachment.htm From giannozz at nest.sns.it Wed Apr 2 21:19:35 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 2 Apr 2008 21:19:35 +0200 Subject: [Pw_forum] MPI work via LSF In-Reply-To: <47F395E1.8050308@physics.unc.edu> References: <47F2A2A7.1010502@physics.unc.edu> <47F34A78.5090203@nest.sns.it> <47F395E1.8050308@physics.unc.edu> Message-ID: <6EA7766B-A320-4DDE-8B6A-38B5C29AC812@nest.sns.it> On Apr 2, 2008, at 16:19 , Charles Chen wrote: > I just followed the direction from ITS service here, submit job > through LSF, eg. > > bsub -q $queue -m $machine -n 4 -o $job.out -r $job.err -a mpichp4 > mpirun -np 4 $BIN_DIR/pw.x -in $job.in > > I have no clue what's wrong when LSF detects overload and suspends > my job, and the administrator send me warning message. inquire with your system manager what is wrong and what they are complaining about ("overload" of what? cpu? disk I/O?). This is not a quantum- espresso problem: it is related to your specific software and hardware installation. It is the responsibility of your computing center to provide the users with the needed information to run a job. All we can do is to provide a code that works and some general information on how to run it (e.g. required communication hardware and software, how to avoid large I/O load). There is in particular a section "running on parallel machine" in the user guide: did you read it? if you want to do serious calculations, you have to know the machine you are running on. > Then, any tip to figure out what's wrong? the -in option works > quite well with other codes. in the data file: verify that the terminator is / and not \ or &end . Check for spurious control characters in the input file. Leave a space before &inputgipaw. in the code: locate the part of the gipaw code that reads the namelist and check what every line does. Compare a case that work with one that doesn't. Initialize variable ios to 0. Ignore the error message and check what has been read. Extract a small program that just reads, experiment with it. Try a different compiler. Try serial execution with parallel compilation, then serial compilation. Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at nest.sns.it Wed Apr 2 21:23:50 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 2 Apr 2008 21:23:50 +0200 Subject: [Pw_forum] example 05 band structure calculation In-Reply-To: References: Message-ID: <88714C74-39A7-4272-B5A2-063BADE992FB@nest.sns.it> On Apr 2, 2008, at 19:20 , sreekar guddeti wrote: > > running the post-processing for band structure..../run_example: > line 237: 15828 Segmentation fault (core dumped) > $BANDS_COMMAND < si.bands.in > si.bands.out > [...] Could anyone guide me... if you look for 'segmentation fault' in the archive of the mailing list and in the wiki, you will find several messages. This is short but says basically everything: http://www.democritos.it/pipermail/pw_forum/2004-September/001362.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 willykohn at gmail.com Wed Apr 2 22:43:03 2008 From: willykohn at gmail.com (willy kohn) Date: Wed, 2 Apr 2008 16:43:03 -0400 Subject: [Pw_forum] question pertaining to subroutine regterg Message-ID: <8a1b6d820804021343x4d72ee8dt879614ac064f1aa@mail.gmail.com> Hi, there: I was stucked again in the subroutine regterg in the file regterg.f90 when I read the pwscf code. There are two things bothering me. One is in the subroutine, the variables psi and hpsi are declared as complex(dp), however, they are used as parameters to call the Lapack subroutine DGEMM, which requires real numbers. For example, in the line 136, CALL DGEMM( 'T', 'N', nbase, nbase, ndim2, 2.D0 , & psi, ndmx2, hpsi, ndmx2, 0.D0, hr, nvecx ) The other one is about the diagonalization of the reduced hamiltonian hr, which is declared as a real symmetric matrix in the subroutine. But in general, the wavefunction psi is complex, how can we guarentee all the elements in the matrix is real? Can the matrix hr be a Hermitian one? Best, Wei -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080402/705ea27b/attachment.htm From yccheng.nju at gmail.com Thu Apr 3 09:46:07 2008 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Thu, 3 Apr 2008 15:46:07 +0800 Subject: [Pw_forum] The results of DOS calculation! Message-ID: Dear pwscf users: I have a problem when I analyze the results of DOS calculation. The first line of the result of *.dos always is "# E (eV) dos(E) Int dos(E)" or "# E (eV) dosup(E) dosdw(E) Int dos(E)". What does "Int dos(E)" stand for? Regards? -- Y. C. Cheng Department of Phyics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080403/1d6235d4/attachment.htm From miguel.martinez at ehu.es Thu Apr 3 09:55:46 2008 From: miguel.martinez at ehu.es (=?UTF-8?B?TWlndWVsIE1hcnTDrW5leiBDYW5hbGVz?=) Date: Thu, 03 Apr 2008 09:55:46 +0200 Subject: [Pw_forum] The results of DOS calculation! In-Reply-To: References: Message-ID: <47F48D82.9000002@ehu.es> Dear ???, ??? escribi?: > What does "Int dos(E)" stand for? From my experience, Int dos(E) is nothing but the integrated density of states. Check its number at the fermi energy and compare to total number of electrons. I hope this helps, Miguel -- ---------------------------------------- Miguel Mart?nez Canales Dto. F?sica de la Materia Condensada UPV/EHU Facultad de Ciencia y Tecnolog?a Apdo. 644 48080 Bilbao (Spain) Fax: +34 94 601 3500 Tlf: +34 94 601 5326 ---------------------------------------- "If you have an apple and I have an apple and we exchange these apples then you and I will still each have one apple. But if you have an idea and I have an idea and we exchange these ideas, then each of us will have two ideas." George Bernard Shaw From kyin.cn at gmail.com Thu Apr 3 11:28:23 2008 From: kyin.cn at gmail.com (Kun Yin) Date: Thu, 3 Apr 2008 17:28:23 +0800 Subject: [Pw_forum] matdyn.x input file problem Message-ID: <000301c8956d$126211d0$2100a8c0@snowwolf> Dear Users, Does matdyn.x have a q-vector number limit? The followings are two matdyn.x input file. The difference is one has 96 q-vectors and the other one has 97 q-vectors, their front 96 vectors are the same. The first one runs OK with output after a while. But the second one runs without any output even error message, the CPU utilization of matdyn.x is zero. ------->> first matdyn.in file with 96 q points <<--------------------- &input asr='simple', amass(1)=24.305, amass(2)=26.981, amass(3)=15.999, flfrc='mgal2o4-0.88v0_444.fc', flfrq='frequency' / 96 0.50000 0.50000 0.50000 1.00000 0.45833 0.45833 0.45833 1.00000 0.52083 0.52083 0.45833 1.00000 0.54167 0.50000 0.45833 1.00000 0.41667 0.41667 0.41667 1.00000 0.47917 0.47917 0.41667 1.00000 0.50000 0.45833 0.41667 1.00000 0.54167 0.54167 0.41667 1.00000 0.56250 0.52083 0.41667 1.00000 0.58333 0.50000 0.41667 1.00000 0.37500 0.37500 0.37500 1.00000 0.43750 0.43750 0.37500 1.00000 0.45833 0.41667 0.37500 1.00000 0.50000 0.50000 0.37500 1.00000 0.52083 0.47917 0.37500 1.00000 0.54167 0.45833 0.37500 1.00000 0.56250 0.56250 0.37500 1.00000 0.58333 0.54167 0.37500 1.00000 0.60417 0.52083 0.37500 1.00000 0.62500 0.50000 0.37500 1.00000 0.33333 0.33333 0.33333 1.00000 0.39583 0.39583 0.33333 1.00000 0.41667 0.37500 0.33333 1.00000 0.45833 0.45833 0.33333 1.00000 0.47917 0.43750 0.33333 1.00000 0.50000 0.41667 0.33333 1.00000 0.52083 0.52083 0.33333 1.00000 0.54167 0.50000 0.33333 1.00000 0.56250 0.47917 0.33333 1.00000 0.58333 0.45833 0.33333 1.00000 0.58333 0.58333 0.33333 1.00000 0.60417 0.56250 0.33333 1.00000 0.62500 0.54167 0.33333 1.00000 0.64583 0.52083 0.33333 1.00000 0.66667 0.50000 0.33333 1.00000 0.29167 0.29167 0.29167 1.00000 0.35417 0.35417 0.29167 1.00000 0.37500 0.33333 0.29167 1.00000 0.41667 0.41667 0.29167 1.00000 0.43750 0.39583 0.29167 1.00000 0.45833 0.37500 0.29167 1.00000 0.47917 0.47917 0.29167 1.00000 0.50000 0.45833 0.29167 1.00000 0.52083 0.43750 0.29167 1.00000 0.54167 0.41667 0.29167 1.00000 0.54167 0.54167 0.29167 1.00000 0.56250 0.52083 0.29167 1.00000 0.58333 0.50000 0.29167 1.00000 0.60417 0.47917 0.29167 1.00000 0.62500 0.45833 0.29167 1.00000 0.60417 0.60417 0.29167 1.00000 0.62500 0.58333 0.29167 1.00000 0.64583 0.56250 0.29167 1.00000 0.66667 0.54167 0.29167 1.00000 0.68750 0.52083 0.29167 1.00000 0.70833 0.50000 0.29167 1.00000 0.25000 0.25000 0.25000 1.00000 0.31250 0.31250 0.25000 1.00000 0.33333 0.29167 0.25000 1.00000 0.37500 0.37500 0.25000 1.00000 0.39583 0.35417 0.25000 1.00000 0.41667 0.33333 0.25000 1.00000 0.43750 0.43750 0.25000 1.00000 0.45833 0.41667 0.25000 1.00000 0.47917 0.39583 0.25000 1.00000 0.50000 0.37500 0.25000 1.00000 0.50000 0.50000 0.25000 1.00000 0.52083 0.47917 0.25000 1.00000 0.54167 0.45833 0.25000 1.00000 0.56250 0.43750 0.25000 1.00000 0.58333 0.41667 0.25000 1.00000 0.56250 0.56250 0.25000 1.00000 0.58333 0.54167 0.25000 1.00000 0.60417 0.52083 0.25000 1.00000 0.62500 0.50000 0.25000 1.00000 0.64583 0.47917 0.25000 1.00000 0.66667 0.45833 0.25000 1.00000 0.62500 0.62500 0.25000 1.00000 0.64583 0.60417 0.25000 1.00000 0.66667 0.58333 0.25000 1.00000 0.68750 0.56250 0.25000 1.00000 0.70833 0.54167 0.25000 1.00000 0.72917 0.52083 0.25000 1.00000 0.75000 0.50000 0.25000 1.00000 0.20833 0.20833 0.20833 1.00000 0.27083 0.27083 0.20833 1.00000 0.29167 0.25000 0.20833 1.00000 0.33333 0.33333 0.20833 1.00000 0.35417 0.31250 0.20833 1.00000 0.37500 0.29167 0.20833 1.00000 0.39583 0.39583 0.20833 1.00000 0.41667 0.37500 0.20833 1.00000 0.43750 0.35417 0.20833 1.00000 0.45833 0.33333 0.20833 1.00000 0.45833 0.45833 0.20833 1.00000 0.47917 0.43750 0.20833 1.00000 ------->> second matdyn.in file with 97 q points <<--------------------- &input asr='simple', amass(1)=24.305, amass(2)=26.981, amass(3)=15.999, flfrc='mgal2o4-0.88v0_444.fc', flfrq='frequency' / 97 0.50000 0.50000 0.50000 1.00000 0.45833 0.45833 0.45833 1.00000 0.52083 0.52083 0.45833 1.00000 0.54167 0.50000 0.45833 1.00000 0.41667 0.41667 0.41667 1.00000 0.47917 0.47917 0.41667 1.00000 0.50000 0.45833 0.41667 1.00000 0.54167 0.54167 0.41667 1.00000 0.56250 0.52083 0.41667 1.00000 0.58333 0.50000 0.41667 1.00000 0.37500 0.37500 0.37500 1.00000 0.43750 0.43750 0.37500 1.00000 0.45833 0.41667 0.37500 1.00000 0.50000 0.50000 0.37500 1.00000 0.52083 0.47917 0.37500 1.00000 0.54167 0.45833 0.37500 1.00000 0.56250 0.56250 0.37500 1.00000 0.58333 0.54167 0.37500 1.00000 0.60417 0.52083 0.37500 1.00000 0.62500 0.50000 0.37500 1.00000 0.33333 0.33333 0.33333 1.00000 0.39583 0.39583 0.33333 1.00000 0.41667 0.37500 0.33333 1.00000 0.45833 0.45833 0.33333 1.00000 0.47917 0.43750 0.33333 1.00000 0.50000 0.41667 0.33333 1.00000 0.52083 0.52083 0.33333 1.00000 0.54167 0.50000 0.33333 1.00000 0.56250 0.47917 0.33333 1.00000 0.58333 0.45833 0.33333 1.00000 0.58333 0.58333 0.33333 1.00000 0.60417 0.56250 0.33333 1.00000 0.62500 0.54167 0.33333 1.00000 0.64583 0.52083 0.33333 1.00000 0.66667 0.50000 0.33333 1.00000 0.29167 0.29167 0.29167 1.00000 0.35417 0.35417 0.29167 1.00000 0.37500 0.33333 0.29167 1.00000 0.41667 0.41667 0.29167 1.00000 0.43750 0.39583 0.29167 1.00000 0.45833 0.37500 0.29167 1.00000 0.47917 0.47917 0.29167 1.00000 0.50000 0.45833 0.29167 1.00000 0.52083 0.43750 0.29167 1.00000 0.54167 0.41667 0.29167 1.00000 0.54167 0.54167 0.29167 1.00000 0.56250 0.52083 0.29167 1.00000 0.58333 0.50000 0.29167 1.00000 0.60417 0.47917 0.29167 1.00000 0.62500 0.45833 0.29167 1.00000 0.60417 0.60417 0.29167 1.00000 0.62500 0.58333 0.29167 1.00000 0.64583 0.56250 0.29167 1.00000 0.66667 0.54167 0.29167 1.00000 0.68750 0.52083 0.29167 1.00000 0.70833 0.50000 0.29167 1.00000 0.25000 0.25000 0.25000 1.00000 0.31250 0.31250 0.25000 1.00000 0.33333 0.29167 0.25000 1.00000 0.37500 0.37500 0.25000 1.00000 0.39583 0.35417 0.25000 1.00000 0.41667 0.33333 0.25000 1.00000 0.43750 0.43750 0.25000 1.00000 0.45833 0.41667 0.25000 1.00000 0.47917 0.39583 0.25000 1.00000 0.50000 0.37500 0.25000 1.00000 0.50000 0.50000 0.25000 1.00000 0.52083 0.47917 0.25000 1.00000 0.54167 0.45833 0.25000 1.00000 0.56250 0.43750 0.25000 1.00000 0.58333 0.41667 0.25000 1.00000 0.56250 0.56250 0.25000 1.00000 0.58333 0.54167 0.25000 1.00000 0.60417 0.52083 0.25000 1.00000 0.62500 0.50000 0.25000 1.00000 0.64583 0.47917 0.25000 1.00000 0.66667 0.45833 0.25000 1.00000 0.62500 0.62500 0.25000 1.00000 0.64583 0.60417 0.25000 1.00000 0.66667 0.58333 0.25000 1.00000 0.68750 0.56250 0.25000 1.00000 0.70833 0.54167 0.25000 1.00000 0.72917 0.52083 0.25000 1.00000 0.75000 0.50000 0.25000 1.00000 0.20833 0.20833 0.20833 1.00000 0.27083 0.27083 0.20833 1.00000 0.29167 0.25000 0.20833 1.00000 0.33333 0.33333 0.20833 1.00000 0.35417 0.31250 0.20833 1.00000 0.37500 0.29167 0.20833 1.00000 0.39583 0.39583 0.20833 1.00000 0.41667 0.37500 0.20833 1.00000 0.43750 0.35417 0.20833 1.00000 0.45833 0.33333 0.20833 1.00000 0.45833 0.45833 0.20833 1.00000 0.47917 0.43750 0.20833 1.00000 0.50000 0.41667 0.20833 1.00000 Have you ever found this problem? Why? Please help me to analyze it, thank you! ============================ Kun Yin Department of Earth Sciences, Nanjing University, Jiangsu, Nanjing 210093, People's Republic of China. Email:kyin.cn at gmail.com ============================ From giannozz at nest.sns.it Thu Apr 3 11:46:03 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 3 Apr 2008 11:46:03 +0200 Subject: [Pw_forum] matdyn.x input file problem In-Reply-To: <000301c8956d$126211d0$2100a8c0@snowwolf> References: <000301c8956d$126211d0$2100a8c0@snowwolf> Message-ID: <34BA566D-AD49-4F34-9468-4E4D3E935C4D@nest.sns.it> On Apr 3, 2008, at 11:28 , Kun Yin wrote: > Does matdyn.x have a q-vector number limit? no > The followings are two matdyn.x input file. The difference is > one has 96 q-vectors > and the other one has 97 q-vectors, their front 96 vectors are the > same. The first one > runs OK with output after a while. But the second one runs without > any output even error > message, the CPU utilization of matdyn.x is zero. the second one is not running, but waiting for input --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From kyin.cn at gmail.com Thu Apr 3 12:22:34 2008 From: kyin.cn at gmail.com (Kun Yin) Date: Thu, 3 Apr 2008 18:22:34 +0800 Subject: [Pw_forum] matdyn.x input file problem References: <000301c8956d$126211d0$2100a8c0@snowwolf> <34BA566D-AD49-4F34-9468-4E4D3E935C4D@nest.sns.it> Message-ID: <001d01c89574$a3892c00$2100a8c0@snowwolf> Dear Paolo Giannozzi, You said matdyn.x is waiting for input, I don't understand what kind of 'input' you refered to. I have posted the input file of matdyn.in for the second one in last mail. Can you tell me how to modify it to make it run but wait? Best regards, Kun Yin ----- Original Message ----- From: "Paolo Giannozzi" To: "PWSCF Forum" Sent: Thursday, April 03, 2008 5:46 PM Subject: Re: [Pw_forum] matdyn.x input file problem > > On Apr 3, 2008, at 11:28 , Kun Yin wrote: > >> Does matdyn.x have a q-vector number limit? > > no > >> The followings are two matdyn.x input file. The difference is >> one has 96 q-vectors >> and the other one has 97 q-vectors, their front 96 vectors are the >> same. The first one >> runs OK with output after a while. But the second one runs without >> any output even error >> message, the CPU utilization of matdyn.x is zero. > > the second one is not running, but waiting for input > --- > 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 h.zhang at ifw-dresden.de Thu Apr 3 13:55:21 2008 From: h.zhang at ifw-dresden.de (Hongbin Zhang) Date: Thu, 3 Apr 2008 13:55:21 +0200 (CEST) Subject: [Pw_forum] A question about relaxing interfaces Message-ID: Dear all PWSCF users, I am trying to do some relaxation calc. of interfaces with PWSCF, but these's a question wrt relaxations: Suppose we have a supercell without vacuum layers and only one interface (i.f.), which might look like this: ------- | | |bulk1| | | | i.f.| | | |bulk2| | | ------ There are strong inplane constraints, so we only relax distances between atomic layers at the interface. So here comes my problem: if we use "relax", the atomic layers at the interface will be relaxed, but since the whole z lattice constant won't change, the structure is supposed to be not fully relaxed. Is this right? Otherwise, if we use "vcrelax", how could one set up inplane constraints? Thanks a lot. Bests From peressi at ts.infn.it Thu Apr 3 15:11:39 2008 From: peressi at ts.infn.it (peressi at ts.infn.it) Date: Thu, 3 Apr 2008 15:11:39 +0200 (CEST) Subject: [Pw_forum] A question about relaxing interfaces In-Reply-To: References: Message-ID: <53099.140.105.192.194.1207228299.squirrel@dftmail.ts.infn.it> Due to periodic boundary conditions, you have 2 interfaces (repeat your cell along the growth direction and you will see immediately), that may be equivalent or not according to their details (crystalline structure, crystallographic direction, composition of the interface itself...). Coming to your question: If the in-plane lattice constant is fixed, you should optimize c (='whole z lattice constant'). A good starting point is determined by calculating the z lattice constant separately of bulk1 and bulk2 constrained on that in-plane lattice constant , using the macroscopic theory of elasticity and using the average at the interface region. Then, you calculate the corresponding stress and if the z-component is non negligible you will slightly modify c (rescaling the internal atomic position; check forces on the atoms; if they increase too much, you will need also to re-relax them) and recalculate the stress. The optimal c could be found by linear interpolation. You could look at a review article and references therein: M. Peressi, N. Binggeli, and A. Baldereschi, Band engineering at interfaces: theory and numerical experiments. Phys. D: Appl. Phys. 31, 1273 (1998). Maria > > Dear all PWSCF users, > > I am trying to do some relaxation calc. of interfaces with PWSCF, but > these's a question wrt relaxations: > > Suppose we have a supercell without vacuum layers and only one > interface (i.f.), which might look like this: > > ------- > | | > |bulk1| > | | > | i.f.| > | | > |bulk2| > | | > ------ > There are strong inplane constraints, so we only relax distances between > atomic layers at the interface. So here comes my problem: if we use > "relax", the atomic layers at the interface will be relaxed, but since the > whole z lattice constant won't change, the structure is supposed to be not > fully relaxed. Is this right? > > Otherwise, if we use "vcrelax", how could one set up inplane constraints? > > Thanks a lot. > > Bests > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From baroni at sissa.it Thu Apr 3 16:46:16 2008 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 3 Apr 2008 16:46:16 +0200 Subject: [Pw_forum] question pertaining to subroutine regterg In-Reply-To: <8a1b6d820804021343x4d72ee8dt879614ac064f1aa@mail.gmail.com> References: <8a1b6d820804021343x4d72ee8dt879614ac064f1aa@mail.gmail.com> Message-ID: <85F2320C-EE43-4182-80D8-EAD992FF8BE1@sissa.it> Hi Wei. I know little of the routine regter, as it is now, but I know very well what it used to be, because I wrote a routine with this name long, long, ago. The routine name is a kind of awkward acronym, where the first "R" stands for real (as opposed to Cegter: guess why); TER stands for iTERative, and EG for EiGen ... Admittedly, not a very informative name 1) a real matrix can be stored in a complex array: the computer will never know, because fortran arguments are passed to subprograms by reference (i.e. the compiler passes just the memory address of the first element of the array: it is the programmer's responsibility to make sure that what the subroutine receives is what the he/she intends). It is admittedly not good programming practice to pass a complex array instead of a real one (or vice versa), but I can assure that this was common practice when I was young (long, long ago). 2) the eigenvectors of a real symmetric matrix can ALWAYS be chosen to be real, as you can easily convince yourself by simply thinking of the definition of eiegenvectors. Hope this helps the peace of your mind. Cheers - Stefano Baroni PS: I do appreciate that some people take the luxury of digging into the codes. This is the only way to learn the art of scientific computing. Bravo! On Apr 2, 2008, at 10:43 PM, willy kohn wrote: > Hi, there: > > I was stucked again in the subroutine regterg in the file > regterg.f90 when I read the pwscf code. There are two things > bothering me. > > One is in the subroutine, the variables psi and hpsi are declared as > complex(dp), however, they are used as parameters to call the > Lapack subroutine DGEMM, which requires real numbers. For example, > in the line 136, > > CALL DGEMM( 'T', 'N', nbase, nbase, ndim2, 2.D0 , & > psi, ndmx2, hpsi, ndmx2, 0.D0, hr, nvecx ) > > The other one is about the diagonalization of the reduced > hamiltonian hr, which is declared as a real symmetric matrix in the > subroutine. But in general, the wavefunction psi is complex, how can > we guarentee all the elements in the matrix is real? Can the matrix > hr be a Hermitian one? > > > Best, > > Wei > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) 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/20080403/9d18ccd0/attachment.htm From giannozz at nest.sns.it Thu Apr 3 16:53:24 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 3 Apr 2008 16:53:24 +0200 Subject: [Pw_forum] question pertaining to subroutine regterg In-Reply-To: <8a1b6d820804021343x4d72ee8dt879614ac064f1aa@mail.gmail.com> References: <8a1b6d820804021343x4d72ee8dt879614ac064f1aa@mail.gmail.com> Message-ID: On Apr 2, 2008, at 22:43 , willy kohn wrote: > One is in the subroutine, the variables psi and hpsi are declared > as complex(dp), > however, they are used as parameters to call the Lapack subroutine > DGEMM, > which requires real numbers. a vector of N complex numbers is equivalent to a vector of 2N real numbers > The other one is about the diagonalization of the reduced > hamiltonian hr, which is > declared as a real symmetric matrix in the subroutine. But in > general, the > wavefunction psi is complex, how can we guarentee all the elements > in the matrix > is real? at k=0 the wavefunctions are real in real space, so the hamiltonian is also real Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at nest.sns.it Thu Apr 3 21:40:48 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 3 Apr 2008 21:40:48 +0200 Subject: [Pw_forum] matdyn.x input file problem In-Reply-To: <001d01c89574$a3892c00$2100a8c0@snowwolf> References: <000301c8956d$126211d0$2100a8c0@snowwolf> <34BA566D-AD49-4F34-9468-4E4D3E935C4D@nest.sns.it> <001d01c89574$a3892c00$2100a8c0@snowwolf> Message-ID: On Apr 3, 2008, at 12:22 , Kun Yin wrote: > You said matdyn.x is waiting for input, I don't understand > what kind of 'input' you refered to. I have posted the input > file of matdyn.in for the second one in last mail. Can you > tell me how to modify it to make it run but wait? what makes you think that the problem is in the input file? If you say that the code does nothing and uses no cpu, most likely it is waiting for input from terminal. Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From shrek_826 at yahoo.com.cn Fri Apr 4 05:20:37 2008 From: shrek_826 at yahoo.com.cn (Fan Yang) Date: Fri, 4 Apr 2008 11:20:37 +0800 (CST) Subject: [Pw_forum] How to calculate the d-band center? Message-ID: <940919.78701.qm@web15312.mail.cnb.yahoo.com> Dear everyone, Does anyone know how to calculate the d-band center of transition metals? According to the Friedel Model, the d-band is treated as a rectangular density of states centred on energy a with width W . However, the PDOS we obtained from calculation is usually irregular with sharp peaks, not a rectangular. Then comes to the question: how to decide the range of d-band energy by applying rectangular model ? how to get the d-band center from PDOS? Thanks inadvance. ====================================== Fan Yang PH.D Candidate in Electrochemistry College of Chemistry and Molecular Science Wuhan University,430072,Hubei Province,China E-mail:shrek_826 at yahoo.com.cn ====================================== ____________________________________________________________________________________ You rock. That's why Blockbuster's offering you one month of Blockbuster Total Access, No Cost. http://tc.deals.yahoo.com/tc/blockbuster/text5.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080404/33998653/attachment.htm From baroni at sissa.it Fri Apr 4 12:17:24 2008 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 4 Apr 2008 12:17:24 +0200 Subject: [Pw_forum] How to calculate the d-band center? In-Reply-To: <940919.78701.qm@web15312.mail.cnb.yahoo.com> References: <940919.78701.qm@web15312.mail.cnb.yahoo.com> Message-ID: calculate the first moment of the DOS, using some arbitrary cutoff at the low- and high-energy sides of the d bands, as assigned by visual inspection. The second moment would give the width (kind of). SB On Apr 4, 2008, at 5:20 AM, Fan Yang wrote: > > Dear everyone, > Does anyone know how to calculate the d-band center of > transition metals? According to the Friedel Model, the d-band is > treated as a rectangular density of states centred on energy a with > width W . However, the PDOS we obtained from calculation is usually > irregular with sharp peaks, not a rectangular. Then comes to the > question: how to decide the range of d-band energy by applying > rectangular model ? how to get the d-band center from PDOS? > Thanks inadvance. > ====================================== > Fan Yang > PH.D Candidate in Electrochemistry > College of Chemistry and Molecular Science > Wuhan University,430072,Hubei Province,China > E-mail:shrek_826 at yahoo.com.cn > ====================================== > > You rock. That's why Blockbuster's offering you one month of > Blockbuster Total Access, No > Cost._______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) 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/20080404/439b2427/attachment.htm From min0220 at postech.ac.kr Sat Apr 5 10:32:02 2008 From: min0220 at postech.ac.kr (Min Seung Kyu) Date: Sat, 5 Apr 2008 17:32:02 +0900 (KST) Subject: [Pw_forum] compile error on Xeon with intel fortran Message-ID: Dear users and developers, I compiled espresso3.2.3 on Xeon machine with Intel fortran 10.1.012 and MKL 10.0.1.014 version. Whenever I run pw.x, however, I get segementation fault message at the beginning. Program PWSCF v.3.2.3 starts ... Today is 4Apr2008 at 21:35:35 Ultrasoft (Vanderbilt) Pseudopotentials Current dimensions of program pwscf are: ntypx = 10 npk = 40000 lmax = 3 nchix = 6 ndmx = 2000 nbrx = 14 nqfx = 8 forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source pw.x 0000000000DF55B7 Unknown Unknown Unknown libpthread.so.0 0000003A0550C4F0 Unknown Unknown Unknown pw.x 0000000000DF5593 Unknown Unknown Unknown libpthread.so.0 0000003A0550C4F0 Unknown Unknown Unknown My maks.sys file contains BLAS_LIBS = -L/opt/intel/mkl/10.0.1.014/lib/em64t -lmkl_em64t -lmkl_core -lguide -lpthread Please let me know what I should do. Sincerely, Min. From lanhaiping at gmail.com Sat Apr 5 11:29:56 2008 From: lanhaiping at gmail.com (lan haiping) Date: Sat, 5 Apr 2008 11:29:56 +0200 Subject: [Pw_forum] compile error on Xeon with intel fortran In-Reply-To: References: Message-ID: Dear Min, Some one else told me before that ifort v10 is not a stable compiler.. You can try to install ifort v9.1 with some mkl math lib. Best, On Sat, Apr 5, 2008 at 10:32 AM, Min Seung Kyu wrote: > Dear users and developers, > > I compiled espresso3.2.3 on Xeon machine with Intel fortran 10.1.012 and > > MKL 10.0.1.014 version. Whenever I run pw.x, however, I get segementation > > fault message at the beginning. > > Program PWSCF v.3.2.3 starts ... > Today is 4Apr2008 at 21:35:35 > > Ultrasoft (Vanderbilt) Pseudopotentials > > Current dimensions of program pwscf are: > > ntypx = 10 npk = 40000 lmax = 3 > nchix = 6 ndmx = 2000 nbrx = 14 nqfx = 8 > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image PC Routine Line Source > pw.x 0000000000DF55B7 Unknown Unknown > Unknown > libpthread.so.0 0000003A0550C4F0 Unknown Unknown > Unknown > pw.x 0000000000DF5593 Unknown Unknown > Unknown > libpthread.so.0 0000003A0550C4F0 Unknown Unknown > Unknown > > My maks.sys file contains > > BLAS_LIBS = -L/opt/intel/mkl/10.0.1.014/lib/em64t -lmkl_em64t > -lmkl_core -lguide -lpthread > > Please let me know what I should do. > > Sincerely, Min. > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080405/3e27af6a/attachment.htm From hashem.yamani at gmail.com Sat Apr 5 15:21:29 2008 From: hashem.yamani at gmail.com (Hashem Al-Yamani) Date: Sat, 5 Apr 2008 13:21:29 +0000 Subject: [Pw_forum] charge density landscape Message-ID: <82a593400804050621t565b3cabn56b4d50e3e95aeed@mail.gmail.com> Dear Everyone; Does any one knows how to get the charge density distribution on a landscape paper orientation so that non of the numbers on the right side of the paper are cut ???? thanx alot Best regards ; H. Al-Yamani Physics Department Jordan Univ. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080405/544af473/attachment.htm From akohlmey at cmm.chem.upenn.edu Sat Apr 5 15:19:16 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sat, 5 Apr 2008 09:19:16 -0400 (EDT) Subject: [Pw_forum] compile error on Xeon with intel fortran In-Reply-To: References: Message-ID: On Sat, 5 Apr 2008, lan haiping wrote: IH> Dear Min, IH> Some one else told me before that ifort v10 is not a stable compiler.. this is not correct. newer patchlevels of 10.1 are quite reliable. 10.1.012 should be ok. the original 10.0 release was bad, like almost all intel x.0 releases. cheers, axel. IH> You can try to install ifort v9.1 with some mkl math lib. IH> Best, IH> IH> On Sat, Apr 5, 2008 at 10:32 AM, Min Seung Kyu IH> wrote: IH> IH> > Dear users and developers, IH> > IH> > I compiled espresso3.2.3 on Xeon machine with Intel fortran 10.1.012 and IH> > IH> > MKL 10.0.1.014 version. Whenever I run pw.x, however, I get segementation IH> > IH> > fault message at the beginning. IH> > IH> > Program PWSCF v.3.2.3 starts ... IH> > Today is 4Apr2008 at 21:35:35 IH> > IH> > Ultrasoft (Vanderbilt) Pseudopotentials IH> > IH> > Current dimensions of program pwscf are: IH> > IH> > ntypx = 10 npk = 40000 lmax = 3 IH> > nchix = 6 ndmx = 2000 nbrx = 14 nqfx = 8 IH> > forrtl: severe (174): SIGSEGV, segmentation fault occurred IH> > Image PC Routine Line Source IH> > pw.x 0000000000DF55B7 Unknown Unknown IH> > Unknown IH> > libpthread.so.0 0000003A0550C4F0 Unknown Unknown IH> > Unknown IH> > pw.x 0000000000DF5593 Unknown Unknown IH> > Unknown IH> > libpthread.so.0 0000003A0550C4F0 Unknown Unknown IH> > Unknown IH> > IH> > My maks.sys file contains IH> > IH> > BLAS_LIBS = -L/opt/intel/mkl/10.0.1.014/lib/em64t -lmkl_em64t IH> > -lmkl_core -lguide -lpthread IH> > IH> > Please let me know what I should do. IH> > IH> > Sincerely, Min. IH> > IH> > IH> > IH> > IH> > _______________________________________________ IH> > Pw_forum mailing list IH> > Pw_forum at pwscf.org IH> > http://www.democritos.it/mailman/listinfo/pw_forum IH> > IH> IH> IH> IH> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From akohlmey at cmm.chem.upenn.edu Sat Apr 5 15:27:03 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sat, 5 Apr 2008 09:27:03 -0400 (EDT) Subject: [Pw_forum] compile error on Xeon with intel fortran In-Reply-To: References: Message-ID: On Sat, 5 Apr 2008, Min Seung Kyu wrote: MSK> Dear users and developers, dear min, MSK> I compiled espresso3.2.3 on Xeon machine with Intel fortran 10.1.012 and MSK> MSK> MKL 10.0.1.014 version. Whenever I run pw.x, however, I get segementation what linux version and which release? which type of xeon cpu (check out /proc/cpuinfo)? are you running 32-bit mode or x86_64? MSK> fault message at the beginning. check out the usual recommendations with intel: - increase stack size limit. - disable MKL threads with setting the environment variable OMP_NUM_THREADS to 1. (as of version 10 MKL always tries to run multiple threads on multi cpu/core machines, regardless whether you also are running MPI or just don't want it) - try compiling with reduced optimization. MSK> Program PWSCF v.3.2.3 starts ... MSK> Today is 4Apr2008 at 21:35:35 MSK> MSK> Ultrasoft (Vanderbilt) Pseudopotentials MSK> MSK> Current dimensions of program pwscf are: MSK> MSK> ntypx = 10 npk = 40000 lmax = 3 MSK> nchix = 6 ndmx = 2000 nbrx = 14 nqfx = 8 MSK> forrtl: severe (174): SIGSEGV, segmentation fault occurred MSK> Image PC Routine Line Source MSK> pw.x 0000000000DF55B7 Unknown Unknown Unknown MSK> libpthread.so.0 0000003A0550C4F0 Unknown Unknown Unknown MSK> pw.x 0000000000DF5593 Unknown Unknown Unknown MSK> libpthread.so.0 0000003A0550C4F0 Unknown Unknown Unknown MSK> MSK> My maks.sys file contains MSK> MSK> BLAS_LIBS = -L/opt/intel/mkl/10.0.1.014/lib/em64t -lmkl_em64t -lmkl_core -lguide -lpthread where are the rest of the settings? they matter as much as the BLAS lib. what makes you think that MKL is the culprit? MSK> MSK> Please let me know what I should do. the most important thing you should do is to report problems in a way, that somebody can reproduce it. you provide some information, but it is not complete... cheers, axel. MSK> Sincerely, Min. MSK> MSK> MSK> MSK> MSK> _______________________________________________ MSK> Pw_forum mailing list MSK> Pw_forum at pwscf.org MSK> http://www.democritos.it/mailman/listinfo/pw_forum MSK> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From giannozz at nest.sns.it Sun Apr 6 08:59:54 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Sun, 6 Apr 2008 08:59:54 +0200 Subject: [Pw_forum] compile error on Xeon with intel fortran In-Reply-To: References: Message-ID: <4E14D60C-3EEB-4216-9B63-30A1D54295EE@nest.sns.it> On Apr 5, 2008, at 10:32 , Min Seung Kyu wrote: > Please let me know what I should do. try the "configure" of the new cvs version: it has better support for recent intel compilers and mkl Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From mpayami at aeoi.org.ir Sun Apr 6 22:16:14 2008 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Sun, 6 Apr 2008 13:16:14 -0700 Subject: [Pw_forum] I do not receive messages since 28-March References: Message-ID: <001001c89823$10972f80$546b10ac@ctpm> Dear PW mailing Administrator, Because of misfunctioning of our E-mail service for a few days, I have not received any messages from PW since 28-March-08. I would be grateful if you please help me to fix it. For your information, I have checked it that my name exists in the mailing list. Best regards, Mahmoud Payami From min0220 at postech.ac.kr Sun Apr 6 09:34:32 2008 From: min0220 at postech.ac.kr (Min Seung Kyu) Date: Sun, 6 Apr 2008 16:34:32 +0900 (KST) Subject: [Pw_forum] compile error on Xeon with intel fortran In-Reply-To: <4E14D60C-3EEB-4216-9B63-30A1D54295EE@nest.sns.it> References: <4E14D60C-3EEB-4216-9B63-30A1D54295EE@nest.sns.it> Message-ID: Thank you all for your reply. It works fine if I use new "configure" of the cvs version. Sincerely, Min. On Sun, 6 Apr 2008, Paolo Giannozzi wrote: > > On Apr 5, 2008, at 10:32 , Min Seung Kyu wrote: > >> Please let me know what I should do. > > try the "configure" of the new cvs version: it has better > support for recent intel compilers and mkl > > 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 > > > > From baroni at sissa.it Sun Apr 6 13:51:50 2008 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 6 Apr 2008 13:51:50 +0200 Subject: [Pw_forum] I do not receive messages since 28-March In-Reply-To: <001001c89823$10972f80$546b10ac@ctpm> References: <001001c89823$10972f80$546b10ac@ctpm> Message-ID: Dear Mohmoud: we are a bit confused. You say that the malfunction is YOURS, and then you ask US to help. How could we? Cheers - SB On Apr 6, 2008, at 10:16 PM, Mahmoud Payami wrote: > Dear PW mailing Administrator, > > Because of misfunctioning of our E-mail service for a few days, > I have > not received any messages from PW since 28-March-08. I would be > grateful if > you please help me to fix it. For your information, I have checked > it that > my name exists in the mailing list. > > Best regards, > > Mahmoud Payami > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080406/55d2a01e/attachment.htm From giannozz at nest.sns.it Sun Apr 6 16:43:36 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Sun, 6 Apr 2008 16:43:36 +0200 Subject: [Pw_forum] I do not receive messages since 28-March In-Reply-To: References: <001001c89823$10972f80$546b10ac@ctpm> Message-ID: On Apr 6, 2008, at 13:51 , Stefano Baroni wrote: > Dear Mohmoud: we are a bit confused. You say that the malfunction > is YOURS, and then you ask US to help. How could we? yes we can :-) After a given number of bounces, the mailing list software disables an e-mail. I have re-enabled it (last bounce: April 1st, so now it should be fine). Mahmoud (and everybody else): I am quite sure that this operation (and others) can be done directly by you via the web interface, http://www.democritos.it/mailman/listinfo/pw_forum by registering with your e-mail and mailing list password (that nobody, me included, keeps, but it can be required via the same interface) Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From mpayami at aeoi.org.ir Sun Apr 6 22:05:25 2008 From: mpayami at aeoi.org.ir (Mahmoud Payami Shabestari) Date: Sun, 06 Apr 2008 23:35:25 +0330 Subject: [Pw_forum] I do not receive messages since 28-March In-Reply-To: References: <001001c89823$10972f80$546b10ac@ctpm> Message-ID: Dear Paolo, Thank you so much. Now it works. Best Regards, Mahmoud Theoretical Physics Group Atomic Energy Organization of Iran P. O. Box 11365-8486 Tehran-Iran Phone: ?+98 (21) 82064393 Fax: ? ?+98 (21) 88003793 E-mail(1): mpayami at aeoi.org.ir E-mail(2): mpayami at acnet.ir -------------------------------------------------- -----Original Message----- From: Paolo Giannozzi To: PWSCF Forum Date: Sun, 6 Apr 2008 16:43:36 +0200 Subject: Re: [Pw_forum] I do not receive messages since 28-March > > On Apr 6, 2008, at 13:51 , Stefano Baroni wrote: > > > Dear Mohmoud: we are a bit confused. You say that the malfunction > > is YOURS, and then you ask US to help. How could we? > > yes we can :-) After a given number of bounces, the mailing list > software > disables an e-mail. I have re-enabled it (last bounce: April 1st, so > now it > should be fine). > > Mahmoud (and everybody else): I am quite sure that this operation > (and others) can be done directly by you via the web interface, > http://www.democritos.it/mailman/listinfo/pw_forum > by registering with your e-mail and mailing list password (that nobody, > me included, keeps, but it can be required via the same interface) > > 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 From hqzhou at nju.edu.cn Mon Apr 7 04:14:23 2008 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Mon, 7 Apr 2008 10:14:23 +0800 Subject: [Pw_forum] compile error on Xeon with intel fortran References: Message-ID: <006101c89855$18be83c0$1d00a8c0@solarflare> Axel, 9.0 (build 20050809) seems an exception. I have been using this version of Intel compiler since its release and successfully compiled all prevailing DFT code. Huiqun Zhou @Nanjing University, China ----- Original Message ----- From: "Axel Kohlmeyer" To: "lan haiping" Cc: "PWSCF Forum" Sent: Saturday, April 05, 2008 9:19 PM Subject: Re: [Pw_forum] compile error on Xeon with intel fortran > On Sat, 5 Apr 2008, lan haiping wrote: > > IH> Dear Min, > IH> Some one else told me before that ifort v10 is not a stable > compiler.. > > this is not correct. newer patchlevels of 10.1 are quite > reliable. 10.1.012 should be ok. the original 10.0 release > was bad, like almost all intel x.0 releases. > > cheers, > axel. > From akohlmey at cmm.chem.upenn.edu Mon Apr 7 07:32:04 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 7 Apr 2008 01:32:04 -0400 Subject: [Pw_forum] compile error on Xeon with intel fortran In-Reply-To: <006101c89855$18be83c0$1d00a8c0@solarflare> References: <006101c89855$18be83c0$1d00a8c0@solarflare> Message-ID: <7b6913e90804062232h42b79162mac250eb02e19eed9@mail.gmail.com> On Sun, Apr 6, 2008 at 10:14 PM, Huiqun Zhou wrote: > Axel, > > 9.0 (build 20050809) seems an exception. I have been using > this version of Intel compiler since its release and successfully > compiled all prevailing DFT code. nope that one's broken as well. it miscompiles several codes. you have to have a newer patchlevel to have a working 9.0 compiler. i had moderate success with the 20051020 build, but the correspondingly late patchlevels of 8.1 and 9.1 have been much more reliable. the issue with miscompiled code is that the code not always crashes on you, but sometimes just gives the wrong result... cheers, axel. > > Huiqun Zhou > @Nanjing University, China > > > > ----- Original Message ----- > From: "Axel Kohlmeyer" > To: "lan haiping" > Cc: "PWSCF Forum" > Sent: Saturday, April 05, 2008 9:19 PM > Subject: Re: [Pw_forum] compile error on Xeon with intel fortran > > > > On Sat, 5 Apr 2008, lan haiping wrote: > > > > IH> Dear Min, > > IH> Some one else told me before that ifort v10 is not a stable > > compiler.. > > > > this is not correct. newer patchlevels of 10.1 are quite > > reliable. 10.1.012 should be ok. the original 10.0 release > > was bad, like almost all intel x.0 releases. > > > > cheers, > > axel. > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From sks.jnc at gmail.com Mon Apr 7 09:00:34 2008 From: sks.jnc at gmail.com (S. K. S.) Date: Mon, 7 Apr 2008 12:30:34 +0530 Subject: [Pw_forum] format UPF Message-ID: Dear All, Is there any already exits converter to convert a pseudopotential, generated by Octopus, into UPF format?????? regards, SKS JNCASR India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080407/a7fb9ae2/attachment.htm From ezadshojaee at hotmail.com Mon Apr 7 09:24:40 2008 From: ezadshojaee at hotmail.com (Ezad Shojaee) Date: Mon, 7 Apr 2008 07:24:40 +0000 Subject: [Pw_forum] problem with calculating elastic constants in AlAs Message-ID: Hi i tried to use the linear relation between omega(k)/k (near Gamma point in TA branch of phonon band structure of AlAs) in the [000]-[100] direction, to calculate the sound velocity along [100] and finally estimate the elastic constant C_44 of it(AlAs): v_transverse[100]=sqrt(C_44/density) but i have orders difference with the experimental value(56.6 Gpa). I wonder if anyone(tried the same) could tell me what may be wrong in my calculation? I calculated the desired velocity as 506m/s (by the mean of the 6th example's results) Thanx for any comment _________________________________________________________________ Explore the seven wonders of the world http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en-US&form=QBRE -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080407/4dc21f42/attachment.htm From hqzhou at nju.edu.cn Mon Apr 7 09:34:04 2008 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Mon, 7 Apr 2008 15:34:04 +0800 Subject: [Pw_forum] compile error on Xeon with intel fortran References: <006101c89855$18be83c0$1d00a8c0@solarflare> <7b6913e90804062232h42b79162mac250eb02e19eed9@mail.gmail.com> Message-ID: <00e201c89881$c195eb10$1d00a8c0@solarflare> I used PWscf, Siesta and Wien2k quite often and checked the examples and my own which gave comparable results to the experiments although I didn't try other DFT code heavily. I only found that linking to fftw 3.x when using 9.0 compiler could crash ph.x (and may be others, but not pw.x). Maybe, compiler options used and OS version (?) make difference ("o") Huiqun ----- Original Message ----- From: "Axel Kohlmeyer" To: "PWSCF Forum" Cc: "lan haiping" Sent: Monday, April 07, 2008 1:32 PM Subject: Re: [Pw_forum] compile error on Xeon with intel fortran > On Sun, Apr 6, 2008 at 10:14 PM, Huiqun Zhou wrote: >> Axel, >> >> 9.0 (build 20050809) seems an exception. I have been using >> this version of Intel compiler since its release and successfully >> compiled all prevailing DFT code. > > nope that one's broken as well. it miscompiles several codes. > you have to have a newer patchlevel to have a working 9.0 > compiler. i had moderate success with the 20051020 build, > but the correspondingly late patchlevels of 8.1 and 9.1 have > been much more reliable. > > the issue with miscompiled code is that the code not always > crashes on you, but sometimes just gives the wrong result... > > cheers, > axel. > >> >> Huiqun Zhou >> @Nanjing University, China >> >> >> >> ----- Original Message ----- >> From: "Axel Kohlmeyer" >> To: "lan haiping" >> Cc: "PWSCF Forum" >> Sent: Saturday, April 05, 2008 9:19 PM >> Subject: Re: [Pw_forum] compile error on Xeon with intel fortran >> >> >> > On Sat, 5 Apr 2008, lan haiping wrote: >> > >> > IH> Dear Min, >> > IH> Some one else told me before that ifort v10 is not a stable >> > compiler.. >> > >> > this is not correct. newer patchlevels of 10.1 are quite >> > reliable. 10.1.012 should be ok. the original 10.0 release >> > was bad, like almost all intel x.0 releases. >> > >> > cheers, >> > axel. >> > >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> >> >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From baroni at sissa.it Mon Apr 7 10:24:04 2008 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 7 Apr 2008 10:24:04 +0200 Subject: [Pw_forum] Fwd: How to calculate the d-band center? References: <40550.13240.qm@web15305.mail.cnb.yahoo.com> Message-ID: <5FF78EC8-9DD2-44E8-8D2E-4C96E48FF504@sissa.it> Dear Yang: please always address your correspondence to the pw_forum list, rather than to its individual members Begin forwarded message: > From: Fan Yang > Date: April 7, 2008 5:29:40 AM GMT+02:00 > To: Stefano Baroni > Subject: Re: [Pw_forum] How to calculate the d-band center? > Reply-To: Fan Yang > > Dear sir, > > Thanks for your reply, but I'm not sure whether I've got > your words. > > First, an arbitrary cutoff should be choosed, then each > interval (abscissa of PDOS, X-coordinate) located in this slected > region would have a height (ordinate of PDOS, Y-coordinate). The d- > band center should be defined as the sum of the product of internal > multiplied by height divided by the total number of heights, namely, > (X1*Y1+X2*Y2+...+Xn*Yn)/(Y1+Y2+...+Yn). Am I right? > I am confused, in turn. It should simply be integral: $ \int_{E_1}^{E_2} E n(E) dE$, where $E_1$ and $E_2$ are the lowe and upper cutoffs. > Another question, whether the using of arbitrary cutoff > would affect the value of d-band center? > of course, it will. this simply reflects the fact that the very concept of "d-band center" is (slightly) ill defined. The more isolated the band is, the less sensitive the value of the integral will be on the choice of the cutoffs, the more well defined the concept of "d-band center" ... If I may dare to give you a suggestion, never try to implement any formula, before you think you understand to some degree of confidence the concepts on which the formula is based. simple drwaing by hands, drafts notes, trila-and-error will help ... I know it may be hard, but it is the only path to learning ... cheers - SB > Best Regards, > > Fan > > > > > ====================================== > Fan Yang > PH.D Candidate in Electrochemistry > College of Chemistry and Molecular Science > Wuhan University,430072,Hubei Province,China > E-mail:shrek_826 at yahoo.com.cn > ====================================== > > > ----- Original Message ---- > From: Stefano Baroni > To: Fan Yang ; PWSCF Forum > > Sent: Friday, April 4, 2008 6:17:24 PM > Subject: Re: [Pw_forum] How to calculate the d-band center? > > calculate the first moment of the DOS, using some arbitrary cutoff > at the low- and high-energy sides of the d bands, as assigned by > visual inspection. The second moment would give the width (kind of). > SB > > On Apr 4, 2008, at 5:20 AM, Fan Yang wrote: >> >> Dear everyone, >> Does anyone know how to calculate the d-band center of >> transition metals? According to the Friedel Model, the d-band is >> treated as a rectangular density of states centred on energy a with >> width W . However, the PDOS we obtained from calculation is usually >> irregular with sharp peaks, not a rectangular. Then comes to the >> question: how to decide the range of d-band energy by applying >> rectangular model ? how to get the d-band center from PDOS? >> Thanks inadvance. >> ====================================== >> Fan Yang >> PH.D Candidate in Electrochemistry >> College of Chemistry and Molecular Science >> Wuhan University,430072,Hubei Province,China >> E-mail:shrek_826 at yahoo.com.cn >> ====================================== >> >> You rock. That's why Blockbuster's offering you one month of >> Blockbuster Total Access, No >> Cost._______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - > Trieste > [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > You rock. That's why Blockbuster's offering you one month of > Blockbuster Total Access, No Cost. --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080407/12f01422/attachment-0001.htm From ferretti.andrea at unimore.it Mon Apr 7 10:30:23 2008 From: ferretti.andrea at unimore.it (Andrea Ferretti) Date: Mon, 7 Apr 2008 10:30:23 +0200 (CEST) Subject: [Pw_forum] format UPF In-Reply-To: References: Message-ID: Dear Jncasr, > > Is there any already > exits converter to > convert a pseudopotential, > generated by Octopus, > into UPF format?????? > at the web page of ETSF (european theoretical spectroscopy facility), http://www.etsf.eu/index.php?page=tools you can find a converter among pseudopotential formats which should be able to do the work.. andrea -- Andrea Ferretti National Research Center S3, CNR-INFM ( http://s3.infm.it ) Dip. Fisica, Univ. di Modena e Reggio E. (Italy) Tel: +39 059 2055301; Fax: +39 059 374794; Skype: andrea_ferretti URL: http://www.nanoscience.unimo.it Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html From hqzhou at nju.edu.cn Mon Apr 7 13:47:44 2008 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Mon, 7 Apr 2008 19:47:44 +0800 Subject: [Pw_forum] parallel run of phonon calculation (ph.x) Message-ID: <01de01c898a5$317583f0$1d00a8c0@solarflare> list-users, I'm trying to run ph.x in the mode of q-point parallelization, using 4 compute nodes with 4 cpu cores in each. The command is sort of following mpiexec -n 16 ph.x -npool 4 < input > output Say, it determined there are 8 q points according to the q-mesh I set. I'm expecting it could parallelly compute 4 q points per time (so get *.dyn1-4 simultaneously), but I saw it still compute q point one by one. Is my understanding of q point parallelization wrong? Thanks! Huiqun Zhou @Earth Sciences, Nanjing University, China From giannozz at nest.sns.it Mon Apr 7 15:00:32 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 07 Apr 2008 15:00:32 +0200 Subject: [Pw_forum] parallel run of phonon calculation (ph.x) In-Reply-To: <01de01c898a5$317583f0$1d00a8c0@solarflare> References: <01de01c898a5$317583f0$1d00a8c0@solarflare> Message-ID: <47FA1AF0.5070602@nest.sns.it> Huiqun Zhou wrote: > Is my understanding of q point parallelization wrong? it is. You can have parallelization on plane waves, parallelization on the k-points (those used in the calculation of the self-consistent charge density) but there are no other parallelization levels in the phonon code. In particular, there is no parallelization on either the node patterns or the q-points (those used to calculate the phonon dispersions). It is relatively easy to implement them and sooner or later it will be done, since it is very useful for execution on the so-called "grid" (large clusters of loosely coupled machines that appear as a single machine to the user) Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From vero at qi.fcen.uba.ar Mon Apr 7 21:08:35 2008 From: vero at qi.fcen.uba.ar (Veronica Muriel Sanchez) Date: Mon, 07 Apr 2008 16:08:35 -0300 Subject: [Pw_forum] question about nose-hoover thermostat-PWscf Message-ID: <1207595315.5665.13.camel@pbt.q1.fcen.uba.ar> Hello, My name is Veronica Sanchez, I'm doing my PhD study on material science. I want to perform a dynamic calculation using the Nose-Hoover thermostat implemented in the Quantum Espresso code, using a Car-Parinello dynamic. I read your question (and the answer) in the PWscf forum. I have the same question as you did. You wrote this: "(2) fnosep As mentioned in the Doc/input_CP, fnosep means the oscillation freq. of the nose thermostat. While in the Doc/INPUT.HOWTO, I was told QNP=2*g*Kb/Omega^2, where Omega is the typical ionic frequency. Dose fnosep and Omega represent the same thing?" I know from the answer that is not the same, but I still don't know how to determine the fnosep parameter. If you have understood how to do it, I will be very greatful if you can help me. Thanks in advanced, Best regards, Ver?nica S?nchez From konstantin_kudin at yahoo.com Mon Apr 7 22:30:27 2008 From: konstantin_kudin at yahoo.com (Konstantin Kudin) Date: Mon, 7 Apr 2008 13:30:27 -0700 (PDT) Subject: [Pw_forum] question about nose-hoover thermostat-PWscf In-Reply-To: <1207595315.5665.13.camel@pbt.q1.fcen.uba.ar> Message-ID: <665759.28095.qm@web57706.mail.re3.yahoo.com> Hi Veronica, The CP code only requires the frequency of the thermostat in THz, and Doc/INPUT.HOWTO is not applicable in this case. As a rough guidance, 3 terahertz = 100 cm^-1 . So, suppose you are simulating heavy water where low frequencies are around 200 cm^-1, and high frequencies near 2500 cm^-1. Then thermostat frequency could be around 800 cm^-1, resulting in "fnosep=24.0" for the CP code. You could also use chains, and make frequencies in the chain vary. Then you can set: nhpcl = 4 fnosep = 12.0 9.0 6.0 3.0 and you'll have a chain of thermostats with 400, 300, 200, 100 cm^-1. I hope this helps a bit. Kostya Kostya --- Veronica Muriel Sanchez wrote: > Hello, > > My name is Veronica Sanchez, I'm doing my PhD study on material > science. > I want to perform a dynamic calculation using the Nose-Hoover > thermostat > implemented in the Quantum Espresso code, using a Car-Parinello > dynamic. > > I read your question (and the answer) in the PWscf forum. I have the > same question as you did. You wrote this: > > > "(2) fnosep > As mentioned in the Doc/input_CP, fnosep means the oscillation > freq. of > the nose thermostat. While in the Doc/INPUT.HOWTO, I was told > QNP=2*g*Kb/Omega^2, where Omega is the typical ionic frequency. Dose > fnosep > and Omega represent the same thing?" > > I know from the answer that is not the same, but I still don't know > how to determine the fnosep parameter. > If you have understood how to do it, I will be very greatful if you > can help me. > > Thanks in advanced, > Best regards, > > Ver?nica S?nchez > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ____________________________________________________________________________________ You rock. That's why Blockbuster's offering you one month of Blockbuster Total Access, No Cost. http://tc.deals.yahoo.com/tc/blockbuster/text5.com From vero at qi.fcen.uba.ar Mon Apr 7 23:18:19 2008 From: vero at qi.fcen.uba.ar (Veronica Muriel Sanchez) Date: Mon, 07 Apr 2008 18:18:19 -0300 Subject: [Pw_forum] question about nose-hoover thermostat-PWscf In-Reply-To: <665759.28095.qm@web57706.mail.re3.yahoo.com> References: <665759.28095.qm@web57706.mail.re3.yahoo.com> Message-ID: <1207603100.5665.36.camel@pbt.q1.fcen.uba.ar> Hi Kostya, Thanks for your response, it was very helpful. Veronica El lun, 07-04-2008 a las 13:30 -0700, Konstantin Kudin escribi?: > Hi Veronica, > > The CP code only requires the frequency of the thermostat in THz, and > Doc/INPUT.HOWTO is not applicable in this case. > > As a rough guidance, 3 terahertz = 100 cm^-1 . > > So, suppose you are simulating heavy water where low frequencies are > around 200 cm^-1, and high frequencies near 2500 cm^-1. Then thermostat > frequency could be around 800 cm^-1, resulting in "fnosep=24.0" for the > CP code. > > You could also use chains, and make frequencies in the chain vary. > Then you can set: > nhpcl = 4 > fnosep = 12.0 9.0 6.0 3.0 > and you'll have a chain of thermostats with 400, 300, 200, 100 cm^-1. > > I hope this helps a bit. > > Kostya > > > Kostya > > --- Veronica Muriel Sanchez wrote: > > > Hello, > > > > My name is Veronica Sanchez, I'm doing my PhD study on material > > science. > > I want to perform a dynamic calculation using the Nose-Hoover > > thermostat > > implemented in the Quantum Espresso code, using a Car-Parinello > > dynamic. > > > > I read your question (and the answer) in the PWscf forum. I have the > > same question as you did. You wrote this: > > > > > > "(2) fnosep > > As mentioned in the Doc/input_CP, fnosep means the oscillation > > freq. of > > the nose thermostat. While in the Doc/INPUT.HOWTO, I was told > > QNP=2*g*Kb/Omega^2, where Omega is the typical ionic frequency. Dose > > fnosep > > and Omega represent the same thing?" > > > > I know from the answer that is not the same, but I still don't know > > how to determine the fnosep parameter. > > If you have understood how to do it, I will be very greatful if you > > can help me. > > > > Thanks in advanced, > > Best regards, > > > > Ver?nica S?nchez > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ____________________________________________________________________________________ > You rock. That's why Blockbuster's offering you one month of Blockbuster Total Access, No Cost. > http://tc.deals.yahoo.com/tc/blockbuster/text5.com > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From akohlmey at cmm.chem.upenn.edu Mon Apr 7 23:12:46 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 7 Apr 2008 17:12:46 -0400 (EDT) Subject: [Pw_forum] question about nose-hoover thermostat-PWscf In-Reply-To: <1207603100.5665.36.camel@pbt.q1.fcen.uba.ar> References: <665759.28095.qm@web57706.mail.re3.yahoo.com> <1207603100.5665.36.camel@pbt.q1.fcen.uba.ar> Message-ID: On Mon, 7 Apr 2008, Veronica Muriel Sanchez wrote: hi veronica, please let me commend you for giving an almost perfect example of how a question should be asked on a user forum. - you introduce yourself and the nature of the system that you want to investigate - you have read the documentation and researched the mailing list archives - you clearly describe your problem and in that also give a hint how the documentation can be improved - you give feedback on whether the answer was useful. to see this every once in a while is very motivating. congratulations and thanks, axel. VMS> Hi Kostya, VMS> VMS> Thanks for your response, it was very helpful. VMS> VMS> Veronica VMS> VMS> El lun, 07-04-2008 a las 13:30 -0700, Konstantin Kudin escribi?: VMS> > Hi Veronica, VMS> > VMS> > The CP code only requires the frequency of the thermostat in THz, and VMS> > Doc/INPUT.HOWTO is not applicable in this case. VMS> > VMS> > As a rough guidance, 3 terahertz = 100 cm^-1 . VMS> > VMS> > So, suppose you are simulating heavy water where low frequencies are VMS> > around 200 cm^-1, and high frequencies near 2500 cm^-1. Then thermostat VMS> > frequency could be around 800 cm^-1, resulting in "fnosep=24.0" for the VMS> > CP code. VMS> > VMS> > You could also use chains, and make frequencies in the chain vary. VMS> > Then you can set: VMS> > nhpcl = 4 VMS> > fnosep = 12.0 9.0 6.0 3.0 VMS> > and you'll have a chain of thermostats with 400, 300, 200, 100 cm^-1. VMS> > VMS> > I hope this helps a bit. VMS> > VMS> > Kostya VMS> > VMS> > VMS> > Kostya VMS> > VMS> > --- Veronica Muriel Sanchez wrote: VMS> > VMS> > > Hello, VMS> > > VMS> > > My name is Veronica Sanchez, I'm doing my PhD study on material VMS> > > science. VMS> > > I want to perform a dynamic calculation using the Nose-Hoover VMS> > > thermostat VMS> > > implemented in the Quantum Espresso code, using a Car-Parinello VMS> > > dynamic. VMS> > > VMS> > > I read your question (and the answer) in the PWscf forum. I have the VMS> > > same question as you did. You wrote this: VMS> > > VMS> > > VMS> > > "(2) fnosep VMS> > > As mentioned in the Doc/input_CP, fnosep means the oscillation VMS> > > freq. of VMS> > > the nose thermostat. While in the Doc/INPUT.HOWTO, I was told VMS> > > QNP=2*g*Kb/Omega^2, where Omega is the typical ionic frequency. Dose VMS> > > fnosep VMS> > > and Omega represent the same thing?" VMS> > > VMS> > > I know from the answer that is not the same, but I still don't know VMS> > > how to determine the fnosep parameter. VMS> > > If you have understood how to do it, I will be very greatful if you VMS> > > can help me. VMS> > > VMS> > > Thanks in advanced, VMS> > > Best regards, VMS> > > VMS> > > Ver?nica S?nchez VMS> > > VMS> > > _______________________________________________ VMS> > > Pw_forum mailing list VMS> > > Pw_forum at pwscf.org VMS> > > http://www.democritos.it/mailman/listinfo/pw_forum VMS> > > VMS> > VMS> > VMS> > VMS> > ____________________________________________________________________________________ VMS> > You rock. That's why Blockbuster's offering you one month of Blockbuster Total Access, No Cost. VMS> > http://tc.deals.yahoo.com/tc/blockbuster/text5.com VMS> > _______________________________________________ VMS> > Pw_forum mailing list VMS> > Pw_forum at pwscf.org VMS> > http://www.democritos.it/mailman/listinfo/pw_forum VMS> > VMS> VMS> _______________________________________________ VMS> Pw_forum mailing list VMS> Pw_forum at pwscf.org VMS> http://www.democritos.it/mailman/listinfo/pw_forum VMS> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From colonel.sreekar at gmail.com Tue Apr 8 17:45:05 2008 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Tue, 8 Apr 2008 21:15:05 +0530 Subject: [Pw_forum] pseudopotential file format Message-ID: Dear PWSCF users, I want to compute a spherically averaged pseudopotential of a configuration. Could anyone guide me as to what are all the values in the pseudopotential file in the UPF format. A link to related tutorial would also be helpful. Regards, Sreekar Guddeti -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080408/5e3ce320/attachment.htm From paulatto at sissa.it Tue Apr 8 18:21:38 2008 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 8 Apr 2008 18:21:38 +0200 (CEST) Subject: [Pw_forum] pseudopotential file format In-Reply-To: References: Message-ID: <2328.147.122.5.182.1207671698.squirrel@webmail.sissa.it> On Mar, Aprile 8, 2008 17:45, sreekar guddeti wrote: > Dear PWSCF users, > I want to compute a spherically averaged pseudopotential of a > configuration. > Could anyone guide me as to what are all the values in the pseudopotential > file in the UPF format. A link to related tutorial would also be helpful. The UPF format have been restyled in prevision of QE 4.0 version (which will come shortly). I have finished writing the specifications of the new format less then 2 hours ago, so they are still in a draft state. The *old* version spefication (which will be supported by QE for at least 20 more years) are located here: http://www.pwscf.org/format.txt I am also preparing (this is almlost ready) a little library that would allow you to write an UPF file (new format) without the need to worry about the output formatting. You would have to fill a fortran derived type and then feed it to the library. I don't know which approach you prefer, but I will be glad to provide you all the material as soon as it is ready. In the meanwhile I can provide you a copy privately, but keep in mind that it is still a work in progress and may change a bit in the next few weeks. Regards, LP P.s. please provide your formal affiliation when writing in this mailing list. -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) +39 040 3787 511 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From wangxinquan at tju.edu.cn Wed Apr 9 05:50:07 2008 From: wangxinquan at tju.edu.cn (wangxinquan at tju.edu.cn) Date: Wed, 09 Apr 2008 11:50:07 +0800 Subject: [Pw_forum] "MPI_COMM_RANK : Null communicator..." error through Platform LSF system Message-ID: <407713007.16944@tju.edu.cn> Dear users and developers, Recently I have done a test on Nankai Stars HPC. The error message "MPI_COMM_RANK : Null communicator??Aborting program !"appeared when I did a scf calculation through 2 cpu (2nodes). To solve this problem, I have found some hints from google, such as??please make sure that you used the same version of MPI for compiling and running, and included the corresponding header file mpi.h in your code.?? (http://www.ncsa.edu/UserInfo/Resources/Hardware/XeonCluster/FAQ/XeonJobs.html) According to the pwscf mailing list,"dynamic port number used in mpi intercommunication is not working. This is most probably an installation issue regarding LSF." may be a problem. (http://www.democritos.it/pipermail/pw_forum/2007-June/006689.html) According to the pwscf manual,"Your machine might be configured so as to disallow interactive execution" may be another problem. My question is: To solve ??MPI_COMM_RANK???? problem, do I need to modify pwscf code, mpich_gm code or LSF system? Calculation Details are as follows: --------------------------------------------------------------------------------- HPC background: Nankai Stars (http://202.113.29.200/introduce.htm) 800 Xeon 3.06 Ghz CPU (400 nodes) 800 GB Memory 53T High-Speed Storage Myrinet Parallel jobs are run and debuged through Platform LSF system. Mpich_gm driver:1.2.6..13a Espresso-3.2.3 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Installation: /configure CC=mpicc F77=mpif77 F90=mpif90 make all --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Submit script : #!/bin/bash #BSUB -q normal #BSUB -J test.icymoon #BSUB -c 3:00 #BSUB -a "mpich_gm" #BSUB -o %J.log #BSUB -n 2 cd /nfs/s04r2p1/wangxq_tj echo "test icymoon" mpirun.lsf /nfs/s04r2p1/wangxq_tj/espresso-3.2.3/bin/pw.x < /nfs/s04r2p1/wangxq_tj/cu.scf.in > cu.scf.out echo "test icymoon end" --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Output file (%J.log): ?? ?? The output (if any) follows: test icymoon 0 - MPI_COMM_RANK : Null communicator [0] Aborting program ! [0] Aborting program! test icymoon end --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- &control calculation='scf' restart_mode='from_scratch', pseudo_dir = '/nfs/s04r2p1/wangxq_tj/espresso-3.2.3/pseudo/', outdir='/nfs/s04r2p1/wangxq_tj/', prefix='cu' / &system ibrav = 2, celldm(1) =6.73, nat= 1, ntyp= 1, ecutwfc = 25.0, ecutrho = 300.0 occupations='smearing', smearing='methfessel-paxton', degauss=0.02 noncolin = .true. starting_magnetization(1) = 0.5 angle1(1) = 90.0 angle2(1) = 0.0 / &electrons conv_thr = 1.0e-8 mixing_beta = 0.7 / ATOMIC_SPECIES Cu 63.55 Cu.pz-d-rrkjus.UPF ATOMIC_POSITIONS Cu 0.0 0.0 0.0 K_POINTS (automatic) 8 8 8 0 0 0 -------------------------------------------------------------------------------- --------------------------------------------------------------------------------- cu.scf.out 1 - MPI_COMM_RANK : Null communicator [1] Aborting program ! [1] Aborting program! TID HOST_NAME COMMAND_LINE STATUS TERMINATION_TIME ==== ========== ================ ======================= =================== 0001 node333 Exit (255) 04/08/2008 19:36:59 0002 node284 Exit (255) 04/08/2008 19:36:59 --------------------------------------------------------------------------------- Any help will be deeply appreciated! Best regards, ===================================== X.Q. Wang wangxinquan at tju.edu.cn School of Chemical Engineering and Technology Tianjin University 92 Weijin Road, Tianjin, P. R. China tel:86-22-27890268, fax: 86-22-27892301 ===================================== From akohlmey at cmm.chem.upenn.edu Wed Apr 9 12:57:11 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 9 Apr 2008 06:57:11 -0400 (EDT) Subject: [Pw_forum] "MPI_COMM_RANK : Null communicator..." error through Platform LSF system In-Reply-To: <407713007.16944@tju.edu.cn> References: <407713007.16944@tju.edu.cn> Message-ID: On Wed, 9 Apr 2008, wangxinquan at tju.edu.cn wrote: WX> Dear users and developers, WX> WX> Recently I have done a test on Nankai Stars HPC. The error message WX> "MPI_COMM_RANK : Null communicator??Aborting program !"appeared when I did WX> a scf calculation through 2 cpu (2nodes). this is not a quantum espresso problem, but a problem of your local machine. please contact your system adminimstrator to investigate. you may want to try a simpler, "hello world"-style MPI program first to verify this. cheers, axel. WX> WX> To solve this problem, I have found some hints from google, such as??please WX> make sure that you used the same version of MPI for compiling and running, and WX> included the corresponding header file mpi.h in your code.?? WX> (http://www.ncsa.edu/UserInfo/Resources/Hardware/XeonCluster/FAQ/XeonJobs.html) WX> WX> According to the pwscf mailing list,"dynamic port number used in mpi WX> intercommunication is not working. This is most probably an installation issue WX> regarding LSF." may be a problem. WX> (http://www.democritos.it/pipermail/pw_forum/2007-June/006689.html) WX> WX> According to the pwscf manual,"Your machine might be configured so as to WX> disallow interactive execution" may be another problem. WX> WX> My question is: WX> To solve ??MPI_COMM_RANK???? problem, do I need to modify pwscf code, WX> mpich_gm code or LSF system? WX> WX> Calculation Details are as follows: WX> --------------------------------------------------------------------------------- WX> HPC background: WX> Nankai Stars (http://202.113.29.200/introduce.htm) WX> 800 Xeon 3.06 Ghz CPU (400 nodes) WX> 800 GB Memory WX> 53T High-Speed Storage WX> Myrinet WX> Parallel jobs are run and debuged through Platform LSF system. WX> Mpich_gm driver:1.2.6..13a WX> Espresso-3.2.3 WX> --------------------------------------------------------------------------------- WX> WX> --------------------------------------------------------------------------------- WX> Installation: WX> /configure CC=mpicc F77=mpif77 F90=mpif90 WX> make all WX> --------------------------------------------------------------------------------- WX> WX> --------------------------------------------------------------------------------- WX> Submit script : WX> #!/bin/bash WX> #BSUB -q normal WX> #BSUB -J test.icymoon WX> #BSUB -c 3:00 WX> #BSUB -a "mpich_gm" WX> #BSUB -o %J.log WX> #BSUB -n 2 WX> WX> cd /nfs/s04r2p1/wangxq_tj WX> echo "test icymoon" WX> WX> mpirun.lsf /nfs/s04r2p1/wangxq_tj/espresso-3.2.3/bin/pw.x < WX> /nfs/s04r2p1/wangxq_tj/cu.scf.in > cu.scf.out WX> WX> echo "test icymoon end" WX> --------------------------------------------------------------------------------- WX> WX> --------------------------------------------------------------------------------- WX> Output file (%J.log): WX> WX> ?? ?? WX> The output (if any) follows: WX> WX> test icymoon WX> 0 - MPI_COMM_RANK : Null communicator WX> [0] Aborting program ! WX> [0] Aborting program! WX> test icymoon end WX> --------------------------------------------------------------------------------- WX> WX> --------------------------------------------------------------------------------- WX> WX> &control WX> WX> calculation='scf' WX> restart_mode='from_scratch', WX> pseudo_dir = '/nfs/s04r2p1/wangxq_tj/espresso-3.2.3/pseudo/', WX> outdir='/nfs/s04r2p1/wangxq_tj/', WX> prefix='cu' WX> / WX> WX> &system WX> WX> ibrav = 2, celldm(1) =6.73, nat= 1, ntyp= 1, WX> ecutwfc = 25.0, ecutrho = 300.0 WX> occupations='smearing', smearing='methfessel-paxton', degauss=0.02 WX> noncolin = .true. WX> starting_magnetization(1) = 0.5 WX> angle1(1) = 90.0 WX> angle2(1) = 0.0 WX> / WX> WX> &electrons WX> WX> conv_thr = 1.0e-8 WX> mixing_beta = 0.7 WX> / WX> WX> ATOMIC_SPECIES WX> Cu 63.55 Cu.pz-d-rrkjus.UPF WX> ATOMIC_POSITIONS WX> Cu 0.0 0.0 0.0 WX> K_POINTS (automatic) WX> 8 8 8 0 0 0 WX> -------------------------------------------------------------------------------- WX> WX> --------------------------------------------------------------------------------- WX> cu.scf.out WX> WX> 1 - MPI_COMM_RANK : Null communicator WX> [1] Aborting program ! WX> [1] Aborting program! WX> WX> TID HOST_NAME COMMAND_LINE STATUS TERMINATION_TIME WX> WX> ==== ========== ================ ======================= =================== WX> WX> 0001 node333 Exit (255) 04/08/2008 19:36:59 WX> WX> 0002 node284 Exit (255) 04/08/2008 19:36:59 WX> WX> --------------------------------------------------------------------------------- WX> WX> Any help will be deeply appreciated! WX> WX> Best regards, WX> WX> ===================================== WX> WX> X.Q. Wang WX> WX> wangxinquan at tju.edu.cn WX> WX> School of Chemical Engineering and Technology WX> WX> Tianjin University WX> WX> 92 Weijin Road, Tianjin, P. R. China WX> WX> tel:86-22-27890268, fax: 86-22-27892301 WX> WX> ===================================== WX> WX> WX> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From janos.kiss at theochem.ruhr-uni-bochum.de Wed Apr 9 15:12:45 2008 From: janos.kiss at theochem.ruhr-uni-bochum.de (Janos Kiss) Date: Wed, 9 Apr 2008 14:12:45 +0100 Subject: [Pw_forum] Band structure calculation HOWTO Message-ID: <200804091512.46010.janos.kiss@theochem.ruhr-uni-bochum.de> Dear PWSCF mailing list members, I am a novice user of this code, and i intend to do some band structure calculations on a metallic O-terminated polar wurtzite ZnO surface, represented with a periodically repeated H-doped hexagonal slab. I have found a nice tutorial on the band structure calculation of bulk Si: http://people.sissa.it/~degironc/QE-Tutorial/tutorial_pwscf_ex.pdf http://people.sissa.it/~degironc/QE-Tutorial/examples_pwscf_ex.tgz Although i have followed the instructions in the tutorial very carefully, once i try to plot the band structure with the plotband.x it is clear that the minimum/maximum energy values and the Fermi energy is different (with more than an eV) compared with the values presented in this tutorial. Beside this problem the band structure also shows a feature in the Sigma to Gamma point path not present in the tutorial's plot. I'm just wonderind where this discrepancy is coming from. Did i miscompile the code, or eventually the tutorial was done by mistake with different settings/pseudopotential? Because i have a metallic system, besides the cutoff i should converge with respect to degauss/smearing as well. On which quantities should i keep my eye on, when i try to converge with the degauss/smearing? Is there eventually a preferred smearing scheme which is easier to converge/handle? Is there a sample k-point path implemented in the code? (i would like to have a k-point path along the Gamma to M, M to K, K to Gamma high symmetry points). In what extent will be affected the band structure by the smearing scheme if eventually the system changes from the metallic state to a semiconductor by some adsorbates/surface defects? Also some other usefull hints/tricks/explanations on what to do or not to do in a band structure calculation with PWSCF would be greatly appreciated. I apologize if these questions are obsolete/redundant, but i could not find a straightforward way to search trough the whole content of the mailing list. Best regards, Janos. ================================================================== Janos Kiss e-mail: janos.kiss at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: +49 (0)234/32-26485 NC 03/297 +49 (0)234 32 26754 Ruhr-Universitaet Bochum Fax: +49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de ================================================================== From colonel.sreekar at gmail.com Wed Apr 9 18:40:50 2008 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Wed, 9 Apr 2008 22:10:50 +0530 Subject: [Pw_forum] UPF file format Message-ID: Dear PWSCF users, One naive question... why is the rab(mesh) != r(mesh + 1) - r(mesh) in the UPF format -- Sreekar Guddeti 3rd year Engineering Physics Student Indian Institute of Technology (Bombay) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080409/ce199ae3/attachment.htm From wangxinquan at tju.edu.cn Thu Apr 10 04:47:07 2008 From: wangxinquan at tju.edu.cn (wangxinquan) Date: Thu, 10 Apr 2008 10:47:07 +0800 Subject: [Pw_forum] "MPI_COMM_RANK : Null communicator..." error through Platform LSF system References: <407724357.20843@tju.edu.cn> Message-ID: <407796782.27088@eyou.net> Dear all, To solve "MPI_COMM_RANK..." problem, I have modified make.sys. IFLAGS=-I../include -I/usr/local/mpich/1.2.6..13a/gm-2.1.3aa2nks3/smp/intel32/ssh/include MPI_LIBS=/usr/local/mpich/1.2.6..13a/gm-2.1.3aa2nks3/smp/intel32/ssh/lib/libmpichf90.a For IFLAGS parameter, the path of mpif.h was included. Finally, the "MPI_COMM_RANK..." problem has been solved. Unfortunately, a new error appeared. The output (if any) follows: test icymoon [0] MPI Abort by user Aborting program! [0] Aborting program! test icymoon end CRASH file: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 0 from read_namelists : error # 1 reading namelist control %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 1 from read_namelists : error # 1 reading namelist control %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% The input file is as follow: ------------------------------------------------------------------ &control calculation='scf' restart_mode='from_scratch', pseudo_dir='/nfs/s04r2p1/wangxq_tj/espresso-3.2.3/pseudo/', outdir='/nfs/s04r2p1/wangxq_tj/', prefix='cu' / &system ... ... ------------------------------------------------------------------ I have checked "control" section. But I can not find any error in it. It confused me that whether it is an input file error or a mpich error? Any help will be deeply appreciated! Best regards, XQ Wang ------------------------------ Message: 3 Date: Wed, 09 Apr 2008 11:50:07 +0800 From: "" Subject: [Pw_forum] "MPI_COMM_RANK : Null communicator..." error through Platform LSF system To: pw_forum at pwscf.org Message-ID: <407713007.16944 at tju.edu.cn > Content-Type: text/plain Dear users and developers, Recently I have done a test on Nankai Stars HPC. The error message "MPI_COMM_RANK : Null communicator?Aborting program !"appeared when I did a scf calculation through 2 cpu (2nodes). To solve this problem, I have found some hints from google, such as?please make sure that you used the same version of MPI for compiling and running, and included the corresponding header file mpi.h in your code.? (http://www.ncsa.edu/UserInfo/Resources/Hardware/XeonCluster/FAQ/XeonJobs.html) According to the pwscf mailing list,"dynamic port number used in mpi intercommunication is not working. This is most probably an installation issue regarding LSF." may be a problem. (http://www.democritos.it/pipermail/pw_forum/2007-June/006689.html) According to the pwscf manual,"Your machine might be configured so as to disallow interactive execution" may be another problem. My question is: To solve ?MPI_COMM_RANK?? problem, do I need to modify pwscf code, mpich_gm code or LSF system? Calculation Details are as follows: --------------------------------------------------------------------------------- HPC background: Nankai Stars (http://202.113.29.200/introduce.htm) 800 Xeon 3.06 Ghz CPU (400 nodes) 800 GB Memory 53T High-Speed Storage Myrinet Parallel jobs are run and debuged through Platform LSF system. Mpich_gm driver:1.2.6..13a Espresso-3.2.3 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Installation: /configure CC=mpicc F77=mpif77 F90=mpif90 make all --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Submit script : #!/bin/bash #BSUB -q normal #BSUB -J test.icymoon #BSUB -c 3:00 #BSUB -a "mpich_gm" #BSUB -o %J.log #BSUB -n 2 cd /nfs/s04r2p1/wangxq_tj echo "test icymoon" mpirun.lsf /nfs/s04r2p1/wangxq_tj/espresso-3.2.3/bin/pw.x < /nfs/s04r2p1/wangxq_tj/cu.scf.in > cu.scf.out echo "test icymoon end" --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Output file (%J.log): ? ? The output (if any) follows: test icymoon 0 - MPI_COMM_RANK : Null communicator [0] Aborting program ! [0] Aborting program! test icymoon end --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- &control calculation='scf' restart_mode='from_scratch', pseudo_dir = '/nfs/s04r2p1/wangxq_tj/espresso-3.2.3/pseudo/', outdir='/nfs/s04r2p1/wangxq_tj/', prefix='cu' / &system ibrav = 2, celldm(1) =6.73, nat= 1, ntyp= 1, ecutwfc = 25.0, ecutrho = 300.0 occupations='smearing', smearing='methfessel-paxton', degauss=0.02 noncolin = .true. starting_magnetization(1) = 0.5 angle1(1) = 90.0 angle2(1) = 0.0 / &electrons conv_thr = 1.0e-8 mixing_beta = 0.7 / ATOMIC_SPECIES Cu 63.55 Cu.pz-d-rrkjus.UPF ATOMIC_POSITIONS Cu 0.0 0.0 0.0 K_POINTS (automatic) 8 8 8 0 0 0 -------------------------------------------------------------------------------- --------------------------------------------------------------------------------- cu.scf.out 1 - MPI_COMM_RANK : Null communicator [1] Aborting program ! [1] Aborting program! TID HOST_NAME COMMAND_LINE STATUS TERMINATION_TIME ==== ========== ================ ======================= =================== 0001 node333 Exit (255) 04/08/2008 19:36:59 0002 node284 Exit (255) 04/08/2008 19:36:59 --------------------------------------------------------------------------------- Any help will be deeply appreciated! Best regards, ===================================== X.Q. Wang wangxinquan at tju.edu.cn School of Chemical Engineering and Technology Tianjin University 92 Weijin Road, Tianjin, P. R. China tel:86-22-27890268, fax: 86-22-27892301 ===================================== ------------------------------ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum End of Pw_forum Digest, Vol 10, Issue 13 **************************************** ===================================== X.Q. Wang wangxinquan at tju.edu.cn Schoolof Chemical Engineeringand Technology TianjinUniversity 92 Weijin Road, Tianjin, P. R. China tel:86-22-27890268, fax: 86-22-27892301 ===================================== From hande at newton.physics.metu.edu.tr Thu Apr 10 09:05:30 2008 From: hande at newton.physics.metu.edu.tr (Hande Ustunel) Date: Thu, 10 Apr 2008 10:05:30 +0300 (EEST) Subject: [Pw_forum] inconsistent number of sticks in nscf calculation Message-ID: Dear PWSCF users and developers, We are trying to calculate the band structure of a 1x1 surface slab of TiO2 in the anatase structure using espresso-3.2.3. We are working on a 64-bit HP Quad-Core machine and the code has been compiled using Intel BLAS and LAPACK libraries and ifort. Our initial relaxation run where take an automatic kpoint set of 6x6x1 ran smoothly without problems. When we try to run a subsequent nscf calculation with manually chosen kpoints however, we get the following error : %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from fft_dlay_set : error # 7 inconsistent number of sticks %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% This error doesn't occur when we run the nscf calculation with an automatic set of kpoints. In order to eliminate corruption of the tmp directory, we keep a fresh copy and update every time before we make an attempt to run the nscf calculation. We have also searched the archive and tried what Paolo suggested http://www.democritos.it/pipermail/pw_forum/2007-September/007170.html which doesn't seem to solve the problem for us. But since the espresso-3.2.3 was released later than the date of the post this was expected I suppose. We have tried decreasing the z direction of the problem in order to perhaps prevent the integer overflow mentioned by Paolo in the above post but as you will notice this already yields a vacuum that's too small and there really isn't much room for decreasing it any further. Our input and output (or what little there is of it) is in the attachment. The associated piece of code seems to be in fft_types.f90 IF( ANY( nsp( 1:nproc ) /= ncpw( 1:nproc ) ) ) THEN DO ip = 1, nproc WRITE( stdout,*) ' * ', ip, ' * ', nsp( ip ), ' /= ', ncpw( ip ) END DO CALL errore( ' fft_dlay_set ', ' inconsistent number of sticks ', 7 ) END IF if that's of any help. We would very much appreciate help on how we could fix the matter or even information on whether this is a system- or code-related issue. Thank you very much in advance. Best wishes, Hande -- Hande Ustunel Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande -------------- next part -------------- &control calculation='nscf', restart_mode='from_scratch', pseudo_dir='/scratch/hande/anataz-stick/pseudo', outdir='./anatazsurface-bak/', prefix='surface', / &system ibrav=0, celldm(1)=1, nat=28, ntyp=2, ecutwfc=25 ecutrho=250 occupations='smearing' smearing='gaussian' degauss=0.02 / &electrons diagonalization='david', conv_thr=1.0e-8, mixing_beta=0.5 mixing_mode='local-TF' mixing_ndim=12 / ATOMIC_SPECIES Ti 1.0 Ti.pw91-nsp-van.UPF O 1.0 O.pw91-van_ak.UPF ATOMIC_POSITIONS {alat} Ti 0.012289003 0.002385732 5.312372086 Ti 0.010515557 3.501949373 10.312267075 Ti 3.507124013 3.502871881 15.018187602 Ti 3.619900000 0.000018864 19.778000000 Ti -0.000056513 0.000034504 24.240000000 Ti -0.000048957 3.619900000 28.686000000 Ti 3.506015098 3.500017061 33.397709005 Ti 3.515462875 0.002929990 38.111219986 Ti 0.019783649 0.002052877 42.803045745 Ti 0.004896346 3.494235430 47.791195016 O 0.016875058 3.504922706 4.571575256 O 0.026699044 -0.001699333 8.800200308 O 3.512994083 3.493776671 10.917730847 O 0.014371887 3.509065579 13.921202821 O 3.547320848 0.004245743 15.798858910 O 3.498849231 3.502774827 18.766217420 O -0.000015280 0.000026656 20.465000000 O 3.619800000 0.000028710 23.508000000 O -0.000562640 3.619900000 24.918000000 O -0.000683690 0.000054602 28.010000000 O 3.503918449 3.483907511 29.626411131 O 0.006267445 3.536093437 32.584847059 O 3.504778818 0.007228710 34.403498142 O 3.536168358 3.506140770 37.359754547 O 0.020653913 0.019321273 39.200777922 O 3.520271916 -0.004927238 42.221271587 O 0.019169951 3.499125661 44.309771072 O 0.015502800 -0.006762498 48.523621768 K_POINTS 61 0.00000 0.00000 0.00000 1.00000 0.05000 0.00000 0.00000 1.00000 0.10000 0.00000 0.00000 1.00000 0.15000 0.00000 0.00000 1.00000 0.20000 0.00000 0.00000 1.00000 0.25000 0.00000 0.00000 1.00000 0.30000 0.00000 0.00000 1.00000 0.35000 0.00000 0.00000 1.00000 0.40000 0.00000 0.00000 1.00000 0.45000 0.00000 0.00000 1.00000 0.50000 0.00000 0.00000 1.00000 0.55000 0.00000 0.00000 1.00000 0.60000 0.00000 0.00000 1.00000 0.65000 0.00000 0.00000 1.00000 0.70000 0.00000 0.00000 1.00000 0.75000 0.00000 0.00000 1.00000 0.80000 0.00000 0.00000 1.00000 0.85000 0.00000 0.00000 1.00000 0.90000 0.00000 0.00000 1.00000 0.95000 0.00000 0.00000 1.00000 1.00000 0.00000 0.00000 1.00000 1.00000 0.05000 0.00000 1.00000 1.00000 0.10000 0.00000 1.00000 1.00000 0.15000 0.00000 1.00000 1.00000 0.20000 0.00000 1.00000 1.00000 0.25000 0.00000 1.00000 1.00000 0.30000 0.00000 1.00000 1.00000 0.35000 0.00000 1.00000 1.00000 0.40000 0.00000 1.00000 1.00000 0.45000 0.00000 1.00000 1.00000 0.50000 0.00000 1.00000 1.00000 0.55000 0.00000 1.00000 1.00000 0.60000 0.00000 1.00000 1.00000 0.65000 0.00000 1.00000 1.00000 0.70000 0.00000 1.00000 1.00000 0.75000 0.00000 1.00000 1.00000 0.80000 0.00000 1.00000 1.00000 0.85000 0.00000 1.00000 1.00000 0.90000 0.00000 1.00000 1.00000 0.95000 0.00000 1.00000 1.00000 1.00000 0.00000 1.00000 0.95000 0.95000 0.00000 1.00000 0.90000 0.90000 0.00000 1.00000 0.85000 0.85000 0.00000 1.00000 0.80000 0.80000 0.00000 1.00000 0.75000 0.75000 0.00000 1.00000 0.70000 0.70000 0.00000 1.00000 0.65000 0.65000 0.00000 1.00000 0.60000 0.60000 0.00000 1.00000 0.55000 0.55000 0.00000 1.00000 0.50000 0.50000 0.00000 1.00000 0.45000 0.45000 0.00000 1.00000 0.40000 0.40000 0.00000 1.00000 0.35000 0.35000 0.00000 1.00000 0.30000 0.30000 0.00000 1.00000 0.25000 0.25000 0.00000 1.00000 0.20000 0.20000 0.00000 1.00000 0.15000 0.15000 0.00000 1.00000 0.10000 0.10000 0.00000 1.00000 0.05000 0.05000 0.00000 1.00000 0.00000 0.00000 0.00000 1.00000 CELL_PARAMETERS 7.0000 0.00000 0.00000 0.00000 7.00000 0.00000 0.00000 0.00000 60.0000 -------------- next part -------------- Program PWSCF v.3.2.3 starts ... Today is 10Apr2008 at 9:47:10 Parallel version (MPI) Number of processors in use: 1 Ultrasoft (Vanderbilt) Pseudopotentials Current dimensions of program pwscf are: ntypx = 10 npk = 40000 lmax = 3 nchix = 6 ndmx = 2000 nbrx = 14 nqfx = 8 * 1 * 204 /= 749 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from fft_dlay_set : error # 7 inconsistent number of sticks %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... job aborted: rank: node: exit code[: error message] 0: nazli: -2: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 From giannozz at nest.sns.it Thu Apr 10 11:04:30 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 10 Apr 2008 11:04:30 +0200 Subject: [Pw_forum] "MPI_COMM_RANK : Null communicator..." error through Platform LSF system In-Reply-To: <407796782.27088@eyou.net> References: <407724357.20843@tju.edu.cn> <407796782.27088@eyou.net> Message-ID: <557150E5-62F9-40F6-9ABA-7F1BA895F5A1@nest.sns.it> On Apr 10, 2008, at 4:47 , wangxinquan wrote: > from read_namelists : error # 1 > reading namelist control http://www.quantum-espresso.org/wiki/index.php/ Frequently_Asked_Questions#The_code_stops_with_an_. 22error_reading_namelist_xxxx.22 --- 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 nest.sns.it Thu Apr 10 15:15:07 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 10 Apr 2008 15:15:07 +0200 Subject: [Pw_forum] inconsistent number of sticks in nscf calculation In-Reply-To: References: Message-ID: Hi Hande > Our initial relaxation run where take an automatic kpoint set of > 6x6x1 ran > smoothly without problems. When we try to run a subsequent nscf > calculation > with manually chosen kpoints however, we get the following error : > > from fft_dlay_set : error # 7 > inconsistent number of sticks this is a bug, or more exactly, a case of inability to cope with weird input data. The problem is not present in serial execution, or if k- points are automatically calculated; it is present only in parallel execution (even on a single processor) and if k-points are given as a list, and if they are way beyond the first Brillouin Zone. If you give a list of "good" k-points the error disappears. Remember that k-points are by default in units of 2pi/a, where a = lattice parameter, but you set a=1! this is perfectly legitimate as long as everything is consistent with this defintion, in particular atomic positions and k-points. The serial and parallel-on-a-processor cases use different FFTs and different algorithms to distribute the "sticks" (columns in G-space). Apparently the serial algorithm is more robust and better tolerates strange k-points in input. Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From hande at newton.physics.metu.edu.tr Thu Apr 10 15:25:52 2008 From: hande at newton.physics.metu.edu.tr (Hande Ustunel) Date: Thu, 10 Apr 2008 16:25:52 +0300 (EEST) Subject: [Pw_forum] inconsistent number of sticks in nscf calculation In-Reply-To: Message-ID: Dear Paolo, > they are way beyond the first Brillouin Zone. If you give a list of > "good" > k-points the error disappears. Remember that k-points are by default in > units of 2pi/a, where a = lattice parameter, but you set a=1! this is Thank you very much for the explanation. In fact, if I decrease the range of the kpoints, it works which means that I was exceeding the edge of the BZ earlier. I'll do a sanity check on the kpoints then. Best wishes, Hande -- Hande Ustunel Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande From giannozz at nest.sns.it Thu Apr 10 15:34:19 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 10 Apr 2008 15:34:19 +0200 Subject: [Pw_forum] UPF file format In-Reply-To: References: Message-ID: On Apr 9, 2008, at 18:40 , sreekar guddeti wrote: > One naive question... why is the rab(mesh) != r(mesh + 1) - r(mesh) > in the UPF format rab(i)= dF/dx dx, where r(i), the nonuniform grid used in atomic codes, is defined as r(i) = F(x(i)), with x(i) a uniform grid spaced dx, F(x) a mapping function. In the "atomic" code, F(x) = r_0 e^x, so rab(i) = r(i) dx. The "rab" grid is useful for the calculation of numerical integrals Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From yccheng.nju at gmail.com Thu Apr 10 16:00:11 2008 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Thu, 10 Apr 2008 22:00:11 +0800 Subject: [Pw_forum] (no subject) Message-ID: Dear PWscf users: I am trying to test the IR and Raman properties of silicon. I followed the instruction of the user's manual(scf, phonon at gamma, dynmat.x) and got diagonalizing the dynamical matrix. I am shame that I can't understand the dynamical matrix. The matrix is list as follows: ================================================================================================================================= q = 0.0000 0.0000 0.0000 ************************************************************************** omega( 1) = 0.000000 [THz] = 0.000005 [cm-1] ( 0.000000 0.000000 -0.707107 0.000000 0.000000 0.000000 ) ( 0.000000 0.000000 -0.707107 0.000000 0.000000 0.000000 ) omega( 2) = 0.000000 [THz] = 0.000005 [cm-1] ( -0.707107 0.000000 0.000000 0.000000 0.000000 0.000000 ) ( -0.707107 0.000000 0.000000 0.000000 0.000000 0.000000 ) omega( 3) = 0.000000 [THz] = 0.000005 [cm-1] ( 0.000000 0.000000 0.000000 0.000000 -0.707107 0.000000 ) ( 0.000000 0.000000 0.000000 0.000000 -0.707107 0.000000 ) omega( 4) = 15.294056 [THz] = 510.158172 [cm-1] ( 0.000000 0.000000 0.707107 0.000000 0.000000 0.000000 ) ( 0.000000 0.000000 -0.707107 0.000000 0.000000 0.000000 ) omega( 5) = 15.294056 [THz] = 510.158172 [cm-1] ( 0.000000 0.000000 0.000000 0.000000 -0.707107 0.000000 ) ( 0.000000 0.000000 0.000000 0.000000 0.707107 0.000000 ) omega( 6) = 15.294056 [THz] = 510.158172 [cm-1] ( -0.707107 0.000000 0.000000 0.000000 0.000000 0.000000 ) ( 0.707107 0.000000 0.000000 0.000000 0.000000 0.000000 ) ************************************************************************** ================================================================================================================================== How can I get the IR and Raman mode and the intensity? Thanks in advance! Best regards. -- Y. C. Cheng Department of Phyics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080410/e2682695/attachment-0001.htm From baroni at sissa.it Thu Apr 10 16:10:19 2008 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 10 Apr 2008 16:10:19 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: References: Message-ID: <6BD1A49E-64F1-4C88-BE9D-A8EEBF537C27@sissa.it> Dear YC Cheng, I am afraid it will take a bit longer to you to understand how to calculate infrared and Raman intensities, than just reading the QE users' manual. Please, make sure you undrestand first how IR and Raman intensities are given in terms of the Born effective charges and derivatives of the polarizability tensor, respectively. This information is NOT contained in the dynamical matrix. Any standard advanced texbook on lattice dynamics would do. You may want to browse for references in our RMP paper first: see: S. Baroni et al. Rev. Mod. Phys. 73, 515 (2001). Hope this helps Stefano Baroni On Apr 10, 2008, at 4:00 PM, ??? wrote: > Dear PWscf users: > I am trying to test the IR and Raman properties of silicon. > I followed the instruction of the user's manual(scf, phonon at > gamma, dynmat.x) and got diagonalizing the dynamical matrix. I am > shame that I can't understand the dynamical matrix. The matrix is > list as follows: > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > ====================================================================== > q = 0.0000 0.0000 0.0000 > > ************************************************************************** > omega( 1) = 0.000000 [THz] = 0.000005 [cm-1] > ( 0.000000 0.000000 -0.707107 0.000000 0.000000 > 0.000000 ) > ( 0.000000 0.000000 -0.707107 0.000000 0.000000 > 0.000000 ) > omega( 2) = 0.000000 [THz] = 0.000005 [cm-1] > ( -0.707107 0.000000 0.000000 0.000000 0.000000 > 0.000000 ) > ( -0.707107 0.000000 0.000000 0.000000 0.000000 > 0.000000 ) > omega( 3) = 0.000000 [THz] = 0.000005 [cm-1] > ( 0.000000 0.000000 0.000000 0.000000 -0.707107 > 0.000000 ) > ( 0.000000 0.000000 0.000000 0.000000 -0.707107 > 0.000000 ) > omega( 4) = 15.294056 [THz] = 510.158172 [cm-1] > ( 0.000000 0.000000 0.707107 0.000000 0.000000 > 0.000000 ) > ( 0.000000 0.000000 -0.707107 0.000000 0.000000 > 0.000000 ) > omega( 5) = 15.294056 [THz] = 510.158172 [cm-1] > ( 0.000000 0.000000 0.000000 0.000000 -0.707107 > 0.000000 ) > ( 0.000000 0.000000 0.000000 0.000000 0.707107 > 0.000000 ) > omega( 6) = 15.294056 [THz] = 510.158172 [cm-1] > ( -0.707107 0.000000 0.000000 0.000000 0.000000 > 0.000000 ) > ( 0.707107 0.000000 0.000000 0.000000 0.000000 > 0.000000 ) > > ************************************************************************** > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > = > ====================================================================== > How can I get the IR and Raman mode and the intensity? > Thanks in advance! > > Best regards. > > -- > Y. C. Cheng > Department of Phyics > Nanjing University > Nanjing 210093 > P. R. China > Tel: 86-25-83592907 > Email: yccheng.nju at gmail.com > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080410/85b4f642/attachment.htm From polynmr at physics.unc.edu Thu Apr 10 19:51:38 2008 From: polynmr at physics.unc.edu (Charles Chen) Date: Thu, 10 Apr 2008 13:51:38 -0400 Subject: [Pw_forum] Resource usage on Single CPU vs MPI Message-ID: <47FE53AA.90903@physics.unc.edu> Dear pwscf users, I am using CVS2 on IA64+linux cluster, complied with MPICH. I can have some tutorial sample (si.scf.in) done but frequently get warning from our administrator on using too much resources. Is this difference reasonable? Here is the resources usage excerpt from the output file: for single processor: > Resource usage summary: > > CPU time : 1680.30 sec. > Max Memory : 4 MB > Max Swap : 12 MB > > Max Processes : 1 > Max Threads : 1 for two processors used: > Resource usage summary: > > CPU time : 11781.85 sec. > Max Memory : 110 MB > Max Swap : 59562 MB > > Max Processes : 6 > Max Threads : 6 Thanks! Charles Chen -- NMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMR NMR Dr. Qiang "Charles" Chen NMR NMR Department of Physics and Astronomy NMR NMR University of North Carolina NMR NMR Phillips Hall, CB#3255 NMR NMR Chapel Hill, NC 27599-3255 NMR NMR Tel: 919-962-1571 (O) NMR NMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMR From marzari at MIT.EDU Thu Apr 10 20:31:19 2008 From: marzari at MIT.EDU (Nicola Marzari) Date: Thu, 10 Apr 2008 14:31:19 -0400 Subject: [Pw_forum] Resource usage on Single CPU vs MPI In-Reply-To: <47FE53AA.90903@physics.unc.edu> References: <47FE53AA.90903@physics.unc.edu> Message-ID: <47FE5CF7.5080308@mit.edu> si.scf.in should take at most a few seconds to execute. nicola Charles Chen wrote: > Dear pwscf users, > > I am using CVS2 on IA64+linux cluster, complied with MPICH. > > I can have some tutorial sample (si.scf.in) done but frequently get > warning from our administrator on using too much resources. > > Is this difference reasonable? > > Here is the resources usage excerpt from the output file: > > for single processor: > >> Resource usage summary: >> >> CPU time : 1680.30 sec. >> Max Memory : 4 MB >> Max Swap : 12 MB >> >> Max Processes : 1 >> Max Threads : 1 > for two processors used: >> Resource usage summary: >> >> CPU time : 11781.85 sec. >> Max Memory : 110 MB >> Max Swap : 59562 MB >> >> Max Processes : 6 >> Max Threads : 6 > Thanks! > > Charles Chen > -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From giannozz at nest.sns.it Thu Apr 10 23:26:32 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 10 Apr 2008 23:26:32 +0200 Subject: [Pw_forum] Resource usage on Single CPU vs MPI In-Reply-To: <47FE53AA.90903@physics.unc.edu> References: <47FE53AA.90903@physics.unc.edu> Message-ID: <5825B4E1-FD7E-45AA-A0B9-E7ACD153373E@nest.sns.it> On Apr 10, 2008, at 19:51 , Charles Chen wrote: > Is this difference reasonable? the difference between what and what? > for single processor: > >> Resource usage summary: >> >> CPU time : 1680.30 sec. >> Max Memory : 4 MB >> Max Swap : 12 MB >> >> Max Processes : 1 >> Max Threads : 1 > for two processors used: >> Resource usage summary: >> >> CPU time : 11781.85 sec. >> Max Memory : 110 MB >> Max Swap : 59562 MB >> >> Max Processes : 6 >> Max Threads : 6 for the same job? this is absurd. Either you are doing something very weird, or your machine is very weird --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From yccheng.nju at gmail.com Fri Apr 11 10:02:15 2008 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Fri, 11 Apr 2008 16:02:15 +0800 Subject: [Pw_forum] Thanks Message-ID: Dear Stefano Baroni: Thank you for your suggestion. Best regards. -- Y. C. Cheng Department of Phyics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080411/942f62ea/attachment.htm From lanhaiping at gmail.com Fri Apr 11 10:12:44 2008 From: lanhaiping at gmail.com (lan haiping) Date: Fri, 11 Apr 2008 16:12:44 +0800 Subject: [Pw_forum] Thanks In-Reply-To: References: Message-ID: Suggestion : Donot break topic threads for discussing ! On Fri, Apr 11, 2008 at 4:02 PM, ??? wrote: > Dear Stefano Baroni: > Thank you for your suggestion. > Best regards. > -- > Y. C. Cheng > Department of Phyics > Nanjing University > Nanjing 210093 > P. R. China > Tel: 86-25-83592907 > Email: yccheng.nju at gmail.com > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080411/9b672cc1/attachment.htm From cao at qtp.ufl.edu Sat Apr 12 00:01:52 2008 From: cao at qtp.ufl.edu (Chao Cao) Date: Fri, 11 Apr 2008 18:01:52 -0400 Subject: [Pw_forum] Zero-norm error during PP generation Message-ID: <47FFDFD0.4070900@qtp.ufl.edu> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Lorenzo and PWSCF users: I was using ld1.x to generate PAW dataset for Lanthanum, where I encountered a puzzling problem of "zero norm error". The input file is as follows, and the error is right after the 2nd round of AE calculation: Message from routine normalize: zero norm: not a true US PP ? Message from routine normalize: zero norm: not a true US PP ? The input file is as follows: &input title='La' prefix='La/ld1', zed=57, config='[Xe] 5d1 4f0 6s2 6p0' iswitch=3, dft='PBE' / &inputp pseudotype=3, nlcc=.true., ! rcore=1.4 lloc= 3, rcloc = 2.4 file_pseudopw='La.pbe-paw.UPF' zval = 9.0 lpaw=.true. which_augfun ='BESSEL' !'PSQ' rmatch_augfun= 2.2 tm = .true. file_screen='La/ld1.scr' file_beta ='La/ld1.beta' file_wfcusgen ='La/ld1.usc' file_wfcaegen ='La/ld1.aec' !nX n l occ nrg rmin rcut / 7 5P 2 1 6.00 0.00 2.00 2.40 5P 2 1 0.00 1.60 2.00 2.40 5D 3 2 1.00 0.00 2.20 2.60 5D 3 2 0.00 0.20 2.20 2.60 6S 1 0 2.00 0.00 2.20 2.60 6S 1 0 0.00 1.20 2.20 2.60 4F 4 3 0.00 0.00 2.40 2.40 &test ecutmin = 36 ecutmax = 48 decut=2 configts(1) = '5p6 5d1 6s2' / I guess I made some stupid mistake in the input file, but I simply cannot find it... Any hints/suggestions? Thanks in advance. Chao Cao - -- Chao Cao Quantum Theory Project and Department of Physics University of Florida, Gainesville, FL 32611 U.S.A. -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.7 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFH/9/QFfX+kymy7P4RAp3EAKCFxnFr5N3QmPGZfdXsLXkr6RXLdwCbBk+v XhLaToGqugWQY/NHuUBD81w= =rOtv -----END PGP SIGNATURE----- From wangxinquan at tju.edu.cn Sat Apr 12 06:12:19 2008 From: wangxinquan at tju.edu.cn (wangxinquan) Date: Sat, 12 Apr 2008 12:12:19 +0800 Subject: [Pw_forum] "MPI_COMM_RANK : Null communicator..." error through Platform LSF system References: <407836057.19314@tju.edu.cn> Message-ID: <407974715.06673@eyou.net> Dear Paolo, According to your suggestion, the job has been completed:) (the submit script should be: mpirun.lsf /nfs/s04r2p1/wangxq_tj/espresso-3.2.3/bin/pw.x \ -in /nfs/s04r2p1/wangxq_tj/cu.scf.in > cu.scf.out) Thank you very much for the help! Cheers, Wang Message: 2 Date: Thu, 10 Apr 2008 11:04:30 +0200 From: Paolo Giannozzi Subject: Re: [Pw_forum] "MPI_COMM_RANK : Null communicator..." error through Platform LSF system To: PWSCF Forum Message-ID: <557150E5-62F9-40F6-9ABA-7F1BA895F5A1 at nest.sns.it > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed On Apr 10, 2008, at 4:47 , wangxinquan wrote: > from read_namelists : error # 1 > reading namelist control http://www.quantum-espresso.org/wiki/index.php/ Frequently_Asked_Questions#The_code_stops_with_an_. 22error_reading_namelist_xxxx.22 --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ------------------------------ ===================================== X.Q. Wang wangxinquan at tju.edu.cn Schoolof Chemical Engineeringand Technology TianjinUniversity 92 Weijin Road, Tianjin, P. R. China tel:86-22-27890268, fax: 86-22-27892301 ===================================== From paulatto at sissa.it Sat Apr 12 13:02:19 2008 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sat, 12 Apr 2008 13:02:19 +0200 (CEST) Subject: [Pw_forum] Zero-norm error during PP generation In-Reply-To: <47FFDFD0.4070900@qtp.ufl.edu> References: <47FFDFD0.4070900@qtp.ufl.edu> Message-ID: <10156.82.49.215.112.1207998139.squirrel@webmail.sissa.it> On Sab, Aprile 12, 2008 00:01, Chao Cao wrote: > Message from routine normalize: > zero norm: not a true US PP ? Dear Chao Cao, this error message is triggereed when self-consistency has a difficult time to converge. If the solver cannot find a solution for a certain wfc it sets it to zero and try with the next one, as a consequence normalization routine willcomplain. Sometimes on the next iteration it can find a solution for all wfcs, but the error ususally hint the presence of some ghost state. Yes, we will try to make the error clearer for the next release. > I guess I made some stupid mistake in the input file, but I simply > cannot find it... Any hints/suggestions? Thanks in advance. There are not many pseudopotential libraries that have a Lanthanide pseudopotential. There is one from N. Holzwarth, here: http://www.wfu.edu/~natalie/papers/pwpaw/periodictable/atoms/LaN/La_GGA_input and it has radiuses dramatically different from yours. Actually I'm as lost as you in this matter, I can only suggest to start with an all-electron calculation (no inputp namelist) and see what the radiuses (average, square average, maximum) are. I hope it helps, goodbye. -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) +39 040 3787 511 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From wangxinquan at tju.edu.cn Tue Apr 15 02:51:02 2008 From: wangxinquan at tju.edu.cn (wangxinquan) Date: Tue, 15 Apr 2008 08:51:02 +0800 Subject: [Pw_forum] Is 24cpu enough for 96 atoms relaxation? Message-ID: <408221868.02883@eyou.net> Dear all, Recently, I'm doing a vc-relax calculation of 96 atom system(2*2*2 supercell,24cpu). The load for each node is as follow: node(2cpu work/node)? 281:98% 325:84% 337:73% 280:87% 307:77% 276:64% 318:55% 351:64% 341:50% 329:23% node(1cpu work/node)? 322:93% 269:100% 343:76% 300:99% node329 and node341 are inefficient. My questions are: 1. What are the ways to improve efficiency of node? 2. By now 8 iterations have been taken 10 hours. I'm afraid it is a little slow. Is 24cpu enough for 96 atoms relaxation? PS: ------------------------------------------------------------ HPC background: Nankai Stars (http://202.113.29.200/introduce.htm) 800 Xeon 3.06 Ghz CPU (400 nodes) 800 GB Memory 53T High-Speed Storage Myrinet Parallel jobs are run and debuged through Platform LSF system. Mpich_gm driver:1.2.6..13a Test package: Espresso-3.2.3 ------------------------------------------------------------- Any hints will be deeply appreciated! Best regards, Wang ===================================== X.Q. Wang wangxinquan at tju.edu.cn Schoolof Chemical Engineeringand Technology TianjinUniversity 92 Weijin Road, Tianjin, P. R. China tel:86-22-27890268, fax: 86-22-27892301 ===================================== From cao at qtp.ufl.edu Tue Apr 15 18:21:13 2008 From: cao at qtp.ufl.edu (Chao Cao) Date: Tue, 15 Apr 2008 12:21:13 -0400 Subject: [Pw_forum] ld1.x bug in 4.0 CVS3 Message-ID: <4804D5F9.6090106@qtp.ufl.edu> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 When I try to do AE calculation for Fe, it fails. Reproducible with both intel and pgf compilers. INPUT File: &input title='Fe' prefix='ld1', zed=26, config='[Ar] 3d7.0 4s1.0 4p0.0' iswitch=1, dft='PBE' / OUTPUT: --------------------------- All-electron run - ---------------------------- Fe scalar relativistic calculation atomic number is 26.00 dft =PBE lsd =0 sic =0 latt =0 beta=0.20 tr2=1.0E-14 mesh =1983 r(mesh) = 99.27596 xmin = -8.00 dx = 0.00800 1 Ry = 13.60569193 eV, c = 137.03599966 n l nl e(Ry) e(Ha) e(eV) 1 0 1S 1( 2.00) -513.4596 -256.7298 -6985.9733 2 0 2S 1( 2.00) -58.9316 -29.4658 -801.8052 2 1 2P 1( 6.00) -50.1027 -25.0514 -681.6822 3 0 3S 1( 2.00) -5.7136 -2.8568 -77.7370 3 1 3P 1( 6.00) -3.2678 -1.6339 -44.4603 3 2 3D 1( 7.00) -0.0007 -0.0003 -0.0091 4 0 4S 1( 1.00) -0.1838 -0.0919 -2.5006 4 1 4P 1( 0.00) -0.0162 -0.0081 -0.2201 eps = NaN iter = 3 Etot = NaN Ry, NaN Ha, NaN eV Ekin = NaN Ry, NaN Ha, NaN eV Encl = NaN Ry, NaN Ha, NaN eV Eh = NaN Ry, NaN Ha, NaN eV Exc = NaN Ry, NaN Ha, NaN eV Evxt = NaN Ry, NaN Ha, NaN eV normalization and overlap integrals s(1S/1S) = 1.000000 = 0.0585 = 0.0046 r(max) = 0.0382 s(1S/2S) = -0.003174 s(1S/3S) = -0.001140 s(1S/4S) = -0.000207 s(2S/2S) = 1.000000 = 0.2666 = 0.0839 r(max) = 0.2218 s(2S/3S) = -0.000652 s(2S/4S) = -0.000116 s(2P/2P) = 1.000000 = 0.2350 = 0.0679 r(max) = 0.1801 s(2P/3P) = -0.000509 s(2P/4P) = -0.000043 s(3S/3S) = 1.000000 = 0.8281 = 0.7954 r(max) = 0.7074 s(3S/4S) = -0.000065 s(3P/3P) = 1.000000 = 0.8908 = 0.9457 r(max) = 0.7246 s(3P/4P) = -0.000025 s(3D/3D) = NaN = NaN = NaN r(max) = 99.2760 s(4S/4S) = 1.000000 = 3.8362 = 17.4827 r(max) = 2.9621 s(4P/4P) = 1.000000 = 7.6899 = 78.5634 r(max) = 5.0224 ------------------------ End of All-electron run - ------------------------ - -- Chao Cao Quantum Theory Project and Department of Physics University of Florida, Gainesville, FL 32611 U.S.A. -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.7 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFIBNX5FfX+kymy7P4RAvDgAKCFGd53tjMsWp4RiwswzzR5rnVkyACfQ79t wFni4KEfpGk5+2NQjewlKuM= =4KP9 -----END PGP SIGNATURE----- From giannozz at nest.sns.it Tue Apr 15 18:42:37 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 15 Apr 2008 18:42:37 +0200 Subject: [Pw_forum] ld1.x bug in 4.0 CVS3 In-Reply-To: <4804D5F9.6090106@qtp.ufl.edu> References: <4804D5F9.6090106@qtp.ufl.edu> Message-ID: <4804DAFD.4010100@nest.sns.it> Chao Cao wrote: > When I try to do AE calculation for Fe, it fails. > Reproducible with both intel and pgf compilers. thank you, but it is irreproducible on my PC, with both intel and gfortran compilers Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From akohlmey at cmm.chem.upenn.edu Tue Apr 15 18:33:49 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 15 Apr 2008 12:33:49 -0400 (EDT) Subject: [Pw_forum] ld1.x bug in 4.0 CVS3 In-Reply-To: <4804D5F9.6090106@qtp.ufl.edu> References: <4804D5F9.6090106@qtp.ufl.edu> Message-ID: On Tue, 15 Apr 2008, Chao Cao wrote: CC> -----BEGIN PGP SIGNED MESSAGE----- CC> Hash: SHA1 CC> CC> When I try to do AE calculation for Fe, it fails. Reproducible with both CC> intel and pgf compilers. ...but not with the intel compilers on my machine. (platform: x86_64, intel 10.1.015, mkl 10.0.1.014) perhaps you don't have the latest patchlevel or are overoptimizing. PGI compilers are notorious for miscompilations and with the intel compilers you always have to update to the latest patchlevel... cheers, axel. CC> CC> CC> INPUT File: CC> CC> &input CC> title='Fe' CC> prefix='ld1', CC> zed=26, CC> config='[Ar] 3d7.0 4s1.0 4p0.0' CC> iswitch=1, CC> dft='PBE' CC> / CC> CC> CC> OUTPUT: CC> CC> --------------------------- All-electron run CC> - ---------------------------- CC> CC> Fe CC> CC> scalar relativistic calculation CC> CC> atomic number is 26.00 CC> dft =PBE lsd =0 sic =0 latt =0 beta=0.20 tr2=1.0E-14 CC> mesh =1983 r(mesh) = 99.27596 xmin = -8.00 dx = 0.00800 CC> 1 Ry = 13.60569193 eV, c = 137.03599966 CC> CC> n l nl e(Ry) e(Ha) e(eV) CC> 1 0 1S 1( 2.00) -513.4596 -256.7298 -6985.9733 CC> 2 0 2S 1( 2.00) -58.9316 -29.4658 -801.8052 CC> 2 1 2P 1( 6.00) -50.1027 -25.0514 -681.6822 CC> 3 0 3S 1( 2.00) -5.7136 -2.8568 -77.7370 CC> 3 1 3P 1( 6.00) -3.2678 -1.6339 -44.4603 CC> 3 2 3D 1( 7.00) -0.0007 -0.0003 -0.0091 CC> 4 0 4S 1( 1.00) -0.1838 -0.0919 -2.5006 CC> 4 1 4P 1( 0.00) -0.0162 -0.0081 -0.2201 CC> CC> eps = NaN iter = 3 CC> CC> Etot = NaN Ry, NaN Ha, NaN eV CC> CC> Ekin = NaN Ry, NaN Ha, NaN eV CC> Encl = NaN Ry, NaN Ha, NaN eV CC> Eh = NaN Ry, NaN Ha, NaN eV CC> Exc = NaN Ry, NaN Ha, NaN eV CC> Evxt = NaN Ry, NaN Ha, NaN eV CC> CC> CC> normalization and overlap integrals CC> CC> s(1S/1S) = 1.000000 = 0.0585 = 0.0046 r(max) = CC> 0.0382 CC> s(1S/2S) = -0.003174 CC> s(1S/3S) = -0.001140 CC> s(1S/4S) = -0.000207 CC> s(2S/2S) = 1.000000 = 0.2666 = 0.0839 r(max) = CC> 0.2218 CC> s(2S/3S) = -0.000652 CC> s(2S/4S) = -0.000116 CC> s(2P/2P) = 1.000000 = 0.2350 = 0.0679 r(max) = CC> 0.1801 CC> s(2P/3P) = -0.000509 CC> s(2P/4P) = -0.000043 CC> s(3S/3S) = 1.000000 = 0.8281 = 0.7954 r(max) = CC> 0.7074 CC> s(3S/4S) = -0.000065 CC> s(3P/3P) = 1.000000 = 0.8908 = 0.9457 r(max) = CC> 0.7246 CC> s(3P/4P) = -0.000025 CC> s(3D/3D) = NaN = NaN = NaN r(max) = CC> 99.2760 CC> s(4S/4S) = 1.000000 = 3.8362 = 17.4827 r(max) = CC> 2.9621 CC> s(4P/4P) = 1.000000 = 7.6899 = 78.5634 r(max) = CC> 5.0224 CC> CC> ------------------------ End of All-electron run CC> - ------------------------ CC> CC> - -- CC> Chao Cao CC> CC> Quantum Theory Project and Department of Physics CC> University of Florida, Gainesville, FL 32611 CC> U.S.A. CC> -----BEGIN PGP SIGNATURE----- CC> Version: GnuPG v2.0.7 (GNU/Linux) CC> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org CC> CC> iD8DBQFIBNX5FfX+kymy7P4RAvDgAKCFGd53tjMsWp4RiwswzzR5rnVkyACfQ79t CC> wFni4KEfpGk5+2NQjewlKuM= CC> =4KP9 CC> -----END PGP SIGNATURE----- CC> _______________________________________________ CC> Pw_forum mailing list CC> Pw_forum at pwscf.org CC> http://www.democritos.it/mailman/listinfo/pw_forum CC> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From akohlmey at cmm.chem.upenn.edu Tue Apr 15 19:00:29 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 15 Apr 2008 13:00:29 -0400 (EDT) Subject: [Pw_forum] prerelease "feature" in CPV Message-ID: hi, FYI, i just noticed, that the codes in the CPV directory don't have a call to remove_stack_limit() (ifdef'd to __INTEL) to make the live of those tolerable who are troubled by paranoid or lazy and uncooperative sysadmins that don't want to adjust the default stacksize to acommodate the stack size requirements of the intel compilers. cheers, axel. -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From penghua8503 at 163.com Wed Apr 16 03:09:22 2008 From: penghua8503 at 163.com (penghua8503) Date: Wed, 16 Apr 2008 09:09:22 +0800 (CST) Subject: [Pw_forum] d3.x Message-ID: <5055180.777861208308162713.JavaMail.coremail@bj163app33.163.com> Dear All, I use d3.x in PWscf to calculate phonon life of Si. But I do not understand the results of it. I want to know which data is the phonon life. And I what to get an idea of how d3.x works (its flow).could you give me some reference article? I really appreciate your help. Thank you. Sincerely yours Hua PENG Hua PENG School of Physics ShandongUniversity, Jinan 25100 People' Republic of China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080416/a9df1462/attachment.htm From willykohn at gmail.com Wed Apr 16 03:31:23 2008 From: willykohn at gmail.com (willy kohn) Date: Tue, 15 Apr 2008 21:31:23 -0400 Subject: [Pw_forum] question pertaining to subroutine regterg In-Reply-To: <85F2320C-EE43-4182-80D8-EAD992FF8BE1@sissa.it> References: <8a1b6d820804021343x4d72ee8dt879614ac064f1aa@mail.gmail.com> <85F2320C-EE43-4182-80D8-EAD992FF8BE1@sissa.it> Message-ID: <8a1b6d820804151831h1c1833fej179fc6d90eb1d083@mail.gmail.com> Hi, baroni: Thank you very much! It took me quite a while to straight things out. It is a honor to get your and Paolo's kindly help. If permitted, I might keep bothering you guys about the code :) cheers, Wei On Thu, Apr 3, 2008 at 10:46 AM, Stefano Baroni wrote: > Hi Wei. > I know little of the routine regter, as it is now, but I know very well > what it used to be, because I wrote a routine with this name long, long, > ago. The routine name is a kind of awkward acronym, where the first "R" > stands for real (as opposed to Cegter: guess why); TER stands for iTERative, > and EG for EiGen ... Admittedly, not a very informative name > 1) a real matrix can be stored in a complex array: the computer will never > know, because fortran arguments are passed to subprograms by reference (i.e. > the compiler passes just the memory address of the first element of the > array: it is the programmer's responsibility to make sure that what the > subroutine receives is what the he/she intends). It is admittedly not good > programming practice to pass a complex array instead of a real one (or vice > versa), but I can assure that this was common practice when I was young > (long, long ago). > > 2) the eigenvectors of a real symmetric matrix can ALWAYS be chosen to be > real, as you can easily convince yourself by simply thinking of the > definition of eiegenvectors. > > Hope this helps the peace of your mind. > > Cheers - Stefano Baroni > > PS: I do appreciate that some people take the luxury of digging into the > codes. This is the only way to learn the art of scientific computing. Bravo! > > On Apr 2, 2008, at 10:43 PM, willy kohn wrote: > > Hi, there: > > I was stucked again in the subroutine regterg in the file regterg.f90 when > I read the pwscf code. There are two things bothering me. > > One is in the subroutine, the variables psi and hpsi are declared as > complex(dp), however, they are used as parameters to call the Lapack > subroutine DGEMM, which requires real numbers. For example, in the line 136, > > > CALL DGEMM( 'T', 'N', nbase, nbase, ndim2, 2.D0 , & > psi, ndmx2, hpsi, ndmx2, 0.D0, hr, nvecx ) > > The other one is about the diagonalization of the reduced hamiltonian hr, > which is declared as a real symmetric matrix in the subroutine. But in > general, the wavefunction psi is complex, how can we guarentee all the > elements in the matrix is real? Can the matrix hr be a Hermitian one? > > > Best, > > Wei > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) > > 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/20080415/760bfc27/attachment-0001.htm From s305igun at mail.chem.itb.ac.id Wed Apr 16 05:11:49 2008 From: s305igun at mail.chem.itb.ac.id (s305igun at mail.chem.itb.ac.id) Date: Wed, 16 Apr 2008 10:11:49 +0700 (WIT) Subject: [Pw_forum] Quantum Espresso Lab using cp.x In-Reply-To: <8a1b6d820804151831h1c1833fej179fc6d90eb1d083@mail.gmail.com> References: <8a1b6d820804021343x4d72ee8dt879614ac064f1aa@mail.gmail.com> <85F2320C-EE43-4182-80D8-EAD992FF8BE1@sissa.it> <8a1b6d820804151831h1c1833fej179fc6d90eb1d083@mail.gmail.com> Message-ID: <35842.167.205.72.169.1208315509.squirrel@mail.chem.itb.ac.id> Dear all, I have problem when I run some example from examples_cp (Quantum Espresso Lab using cp.x v.5). The problem is cppp.x, and output report give comment: ######################################################################################################################## # UNRECOVERABLE ERROR (ierr=1) # ERROR IN: iotk_open_read (iotk_files.spp:479) # CVS Revision: 1.2 # unit file=.//h2o_mol_51.save/data-file.xml binary=F iostat=29 ######################################################################################################################## Do the people can help this problem? Thanks verry much Good luck for your research Rahmat Gunawan PhD Student Lab. Theoretical and Computational Chemistry Department of Chemistry Institut Teknologi Bandung West Java Indonesia From giannozz at nest.sns.it Wed Apr 16 10:37:56 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 16 Apr 2008 10:37:56 +0200 Subject: [Pw_forum] Quantum Espresso Lab using cp.x In-Reply-To: <35842.167.205.72.169.1208315509.squirrel@mail.chem.itb.ac.id> References: <8a1b6d820804021343x4d72ee8dt879614ac064f1aa@mail.gmail.com> <85F2320C-EE43-4182-80D8-EAD992FF8BE1@sissa.it> <8a1b6d820804151831h1c1833fej179fc6d90eb1d083@mail.gmail.com> <35842.167.205.72.169.1208315509.squirrel@mail.chem.itb.ac.id> Message-ID: <4805BAE4.8090804@nest.sns.it> s305igun at mail.chem.itb.ac.id wrote: > I have problem when I run some example from examples_cp > (Quantum Espresso Lab using cp.x v.5) never heard about "Quantum Espresso Lab", even less about v.5 ... > ######################################################################################################################## > # UNRECOVERABLE ERROR (ierr=1) > # ERROR IN: iotk_open_read (iotk_files.spp:479) > # CVS Revision: 1.2 > # unit > file=.//h2o_mol_51.save/data-file.xml > binary=F > iostat=29 > ######################################################################################################################## file ./h2o_mol_51.save/data-file.xml is not there Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Wed Apr 16 10:43:42 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 16 Apr 2008 10:43:42 +0200 Subject: [Pw_forum] Is 24cpu enough for 96 atoms relaxation? In-Reply-To: <408221868.02883@eyou.net> References: <408221868.02883@eyou.net> Message-ID: <4805BC3E.1030502@nest.sns.it> wangxinquan wrote: > The load for each node is as follow: [...] > 1. What are the ways to improve efficiency of node? sending two processes on some nodes and one on some other nodes is a sure way to worsen efficiency > Is 24cpu enough for 96 atoms relaxation? it depends on the system, on the kind of parallelization... There is no general answer to questions about parallelism, especially if they are ill-posed Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From s305igun at mail.chem.itb.ac.id Wed Apr 16 19:23:45 2008 From: s305igun at mail.chem.itb.ac.id (s305igun at mail.chem.itb.ac.id) Date: Thu, 17 Apr 2008 00:23:45 +0700 (WIT) Subject: [Pw_forum] Quantum Espresso Lab using cp.x In-Reply-To: <4805BAE4.8090804@nest.sns.it> References: <8a1b6d820804021343x4d72ee8dt879614ac064f1aa@mail.gmail.com> <85F2320C-EE43-4182-80D8-EAD992FF8BE1@sissa.it> <8a1b6d820804151831h1c1833fej179fc6d90eb1d083@mail.gmail.com> <35842.167.205.72.169.1208315509.squirrel@mail.chem.itb.ac.id> <4805BAE4.8090804@nest.sns.it> Message-ID: <50732.167.205.72.169.1208366625.squirrel@mail.chem.itb.ac.id> Dear Profesor Paolo Giannozzi, Thanks for your reply. I was studied the "Quantum Espresso Lab" from: http://cms.mcc.uiuc.edu/wiki/display/ss2006/Quantum+Espresso+Lab+using+cp.x It is true that the file ./h2o_mol_51.save/data-file.xml is not there. So I try again to run cppp.x with edit "outdir" in h2o_mol.cppp-dens.in and done Thank you Prof. Paolo Giannozzi Best Regards rahmat gunawan PhD student Lab. of Theoretical and Computational Chemistry Department of Chemistry Institut Teknologi Bandung West Java > s305igun at mail.chem.itb.ac.id wrote: > >> I have problem when I run some example from examples_cp >> (Quantum Espresso Lab using cp.x v.5) > > never heard about "Quantum Espresso Lab", even less about v.5 ... > >> ######################################################################################################################## >> # UNRECOVERABLE ERROR (ierr=1) >> # ERROR IN: iotk_open_read (iotk_files.spp:479) >> # CVS Revision: 1.2 >> # unit >> file=.//h2o_mol_51.save/data-file.xml >> binary=F >> iostat=29 >> ######################################################################################################################## > > file ./h2o_mol_51.save/data-file.xml is not there > > Paolo > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From janos.kiss at theochem.ruhr-uni-bochum.de Wed Apr 16 20:58:57 2008 From: janos.kiss at theochem.ruhr-uni-bochum.de (Janos Kiss) Date: Wed, 16 Apr 2008 20:58:57 +0200 Subject: [Pw_forum] Problem with NEB Message-ID: <200804162058.57988.janos.kiss@theochem.ruhr-uni-bochum.de> Dear PWSCF mailing list members, i try to do a nudged elastic band calculation with PWSCF 3.2.3 compiled as a parallel 64-bit executable with ifc 10.1, MKL 8.1 and Open MPI 1.2.4 on a Xeon cluster. Each node has 8 CPU cores, 16G physical memory and they use Gigabit LAN for communication between nodes. I use the R- and G-space parallelization for a single image (over 8 CPU in one node), and the parallelization on the number of NEB images on top of that. The problem is that the configurations after the linear interpolation between reactant end product are often 'unchemical' even if i include some intermediate images. The WF convergence for these images can be particularly problematic in the very first scf step. If the WF is not converged within the given maximum number of steps (set to 250 in my case) for one of the images the code stops for that given image complaining that ' convergence NOT achieved, stopping'. The executables keep running on all nodes apparently doing nothing, so i have to kill the job by hand. Although i have the write_save and wf_collect flags set to true if i try to restart the calculation the code stops immediately complaining that: from control_checkin : error # 1 calculation 'restart' not allowed I naively thought that it checks the images, and it gonna reiterate those which were not converged. The restart is not working because of the parallelization upon NEB images, because the forces are not available for all images, or because it was killed and some files were not written out properly? What is the minimum requirement for a stopped/killed NEB calculation to be suitable for restart? Most of the time the problematic configurations are far away from the reactant or product and they would have large forces acting on them anyway. Is there a way to relax the tightness of the WF convergence relative to the number of scf steps? Is it possible to print out the forces in an NEB calculation at the end of the WF optimization no matter how bad the estimated energy error is? These forces should be still good enough for the first 1-2 NEB relaxation steps. For the new configurations convergence could be achieved within the maximum number of steps. I know that there are some ways around (using less tight threshold on all images and so on) but those are not so straightforward. All which popped in my mind would affect the convergence of the low energy images as well, where more accuracy is really needed, or would substantially increase the overall execution/setup speed. All the best, Janos. ================================================================== Janos Kiss e-mail: janos.kiss at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: +49 (0)234/32-26485 NC 03/297 +49 (0)234 32 26754 Ruhr-Universitaet Bochum Fax: +49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de ================================================================== From yrehem at mac.com Wed Apr 16 21:37:21 2008 From: yrehem at mac.com (Yaser Rehem) Date: Wed, 16 Apr 2008 12:37:21 -0700 Subject: [Pw_forum] Fortran runtime error during scf in 4.0cvs3 Message-ID: <7B6E59F0-BEE8-4C9A-AB0E-A810C5E90387@mac.com> I got the following runtime error will attempting a scf on my system: Cut & Paste from my Shell below: >At line 1288 of file cegterg.f90 >Traceback: not available, compile with -ftrace=frame or -ftrace=full >At line 1288 of file cegterg.f90 >Traceback: not available, compile with -ftrace=frame or -ftrace=full >Fortran runtime error: Array section out of bounds >Fortran runtime error: Array section out of bounds >* I'm running pwscf 4cvs3 on OS X 10.5.2 (9C7010), openmpi 1.2.4. I was running the input file below on 6 procs, 1 pool, when I got the above error msg in my shell, and 2 of the 6 pw.x instances quit. P.s. I realize I've got a ridiculously large number of k-points---I'm in in the process of converging the stress tensor with respect to ecutwfc and ecutrho, and wanted to ensure k-points were absolutely not an issue. My plan was to converge k-points next. Input File: &control calculation = 'scf' restart_mode='from_scratch' prefix='ConvTest' outdir = './ConvergenceTests' pseudo_dir = '../pseudo' tstress = .true. tprnfor = .true. / &system ibrav= 0 celldm(1) = 8.207702028 nat= 14 ntyp= 2 ecutwfc = 38 ecutrho = 380 occupations = 'smearing' degauss = 0.03 smearing = 'cold' / &electrons mixing_beta = 0.7 conv_thr = 1.0d-8 / CELL_PARAMETERS {alat} 1.010363552 0.000000012 0.000000000 0.000000021 1.750048386 -0.000024105 0.000000000 -0.000012933 0.925 ATOMIC_SPECIES C 12.0107 C.pz-rrkjus.UPF.txt Li 6.941 Li_VDB_LDA_SEMI.UPF.txt ATOMIC_POSITIONS {angstrom} Li 0.000000030 2.506788198 -0.000140635 Li 2.171198117 6.271103089 -0.000356521 C 1.467363622 2.526363526 2.006309099 C 0.733070280 1.265423702 2.006682218 C 0.738585262 3.794292056 2.006616072 C 1.464475654 0.009242556 2.006460051 C 2.923841993 0.009242573 2.006460051 C 3.649732475 3.794292091 2.006616072 C 3.655247398 1.265423737 2.006682218 C 2.920954087 2.526363543 2.006309099 C 3.657326610 6.344930347 2.006451947 C 0.730991187 6.344930313 2.006451947 C 1.464091389 5.063798994 2.006936383 C 2.924226378 5.063799011 2.006936383 K_POINTS {automatic} 14 8 16 0 0 0 -Yaser Rehem Rehem Research & Consulting -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080416/faf74b66/attachment.htm From yrehem at mac.com Wed Apr 16 22:27:40 2008 From: yrehem at mac.com (Yaser Rehem) Date: Wed, 16 Apr 2008 13:27:40 -0700 Subject: [Pw_forum] Fortran runtime error during scf in 4.0cvs3 In-Reply-To: <7B6E59F0-BEE8-4C9A-AB0E-A810C5E90387@mac.com> References: <7B6E59F0-BEE8-4C9A-AB0E-A810C5E90387@mac.com> Message-ID: An additional piece of information: I don't get this error when I run the same input on one processor. On Apr 16, 2008, at 12:37 PM, Yaser Rehem wrote: > I got the following runtime error will attempting a scf on my system: > > Cut & Paste from my Shell below: > >At line 1288 of file cegterg.f90 > >Traceback: not available, compile with -ftrace=frame or -ftrace=full > >At line 1288 of file cegterg.f90 > >Traceback: not available, compile with -ftrace=frame or -ftrace=full > >Fortran runtime error: Array section out of bounds > >Fortran runtime error: Array section out of bounds > >* > > I'm running pwscf 4cvs3 on OS X 10.5.2 (9C7010), openmpi 1.2.4. > > I was running the input file below on 6 procs, 1 pool, when I got > the above error msg in my shell, and 2 of the 6 pw.x instances quit. > > P.s. I realize I've got a ridiculously large number of k-points--- > I'm in in the process of converging the stress tensor with respect > to ecutwfc and ecutrho, and wanted to ensure k-points were > absolutely not an issue. My plan was to converge k-points next. > > Input File: > > &control > calculation = 'scf' > restart_mode='from_scratch' > prefix='ConvTest' > outdir = './ConvergenceTests' > pseudo_dir = '../pseudo' > tstress = .true. > tprnfor = .true. > / > &system > ibrav= 0 > celldm(1) = 8.207702028 > nat= 14 > ntyp= 2 > ecutwfc = 38 > ecutrho = 380 > occupations = 'smearing' > degauss = 0.03 > smearing = 'cold' > / > &electrons > mixing_beta = 0.7 > conv_thr = 1.0d-8 > / > CELL_PARAMETERS {alat} > 1.010363552 0.000000012 0.000000000 > 0.000000021 1.750048386 -0.000024105 > 0.000000000 -0.000012933 0.925 > ATOMIC_SPECIES > C 12.0107 C.pz-rrkjus.UPF.txt > Li 6.941 Li_VDB_LDA_SEMI.UPF.txt > ATOMIC_POSITIONS {angstrom} > Li 0.000000030 2.506788198 -0.000140635 > Li 2.171198117 6.271103089 -0.000356521 > C 1.467363622 2.526363526 2.006309099 > C 0.733070280 1.265423702 2.006682218 > C 0.738585262 3.794292056 2.006616072 > C 1.464475654 0.009242556 2.006460051 > C 2.923841993 0.009242573 2.006460051 > C 3.649732475 3.794292091 2.006616072 > C 3.655247398 1.265423737 2.006682218 > C 2.920954087 2.526363543 2.006309099 > C 3.657326610 6.344930347 2.006451947 > C 0.730991187 6.344930313 2.006451947 > C 1.464091389 5.063798994 2.006936383 > C 2.924226378 5.063799011 2.006936383 > K_POINTS {automatic} > 14 8 16 0 0 0 > > -Yaser Rehem > Rehem Research & Consulting > > _______________________________________________ > 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/20080416/8ba0a419/attachment-0001.htm From janos.kiss at theochem.ruhr-uni-bochum.de Wed Apr 16 22:25:51 2008 From: janos.kiss at theochem.ruhr-uni-bochum.de (Janos Kiss) Date: Wed, 16 Apr 2008 22:25:51 +0200 Subject: [Pw_forum] Problem with NEB half solved Message-ID: <200804162225.51530.janos.kiss@theochem.ruhr-uni-bochum.de> OK, really carefully inspecting the input files, i just realized that accidentally i put the restart flag in the calculation control sequence, so that part of the problem was sitting between the keyboard and the chair (as one of my revered group members would say). Of course with the same buggy input the crash was reproduced several times :) I would be still interested in the other question send in my previous email. All the best, Janos. ================================================================== Janos Kiss e-mail: janos.kiss at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: +49 (0)234/32-26485 NC 03/297 +49 (0)234 32 26754 Ruhr-Universitaet Bochum Fax: +49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de ================================================================== From akohlmey at cmm.chem.upenn.edu Wed Apr 16 23:12:09 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 16 Apr 2008 17:12:09 -0400 (EDT) Subject: [Pw_forum] Fortran runtime error during scf in 4.0cvs3 In-Reply-To: <7B6E59F0-BEE8-4C9A-AB0E-A810C5E90387@mac.com> References: <7B6E59F0-BEE8-4C9A-AB0E-A810C5E90387@mac.com> Message-ID: On Wed, 16 Apr 2008, Yaser Rehem wrote: hi yaser, YR> I got the following runtime error will attempting a scf on my system: YR> YR> Cut & Paste from my Shell below: YR> >At line 1288 of file cegterg.f90 YR> >Traceback: not available, compile with -ftrace=frame or -ftrace=full YR> >At line 1288 of file cegterg.f90 YR> >Traceback: not available, compile with -ftrace=frame or -ftrace=full YR> >Fortran runtime error: Array section out of bounds YR> >Fortran runtime error: Array section out of bounds YR> >* what compiler? what version? when _exactly_ does this happen? this looks a lot like a miscompiled file. that array is dynamically allocated after all. i'm currently running your input on my desktop and it has already completed the two iterations... does it change when you use 6 pools instead (should be much more efficient unless you run out of memory). cheers, axel. YR> YR> I'm running pwscf 4cvs3 on OS X 10.5.2 (9C7010), openmpi 1.2.4. YR> YR> I was running the input file below on 6 procs, 1 pool, when I got the above YR> error msg in my shell, and 2 of the 6 pw.x instances quit. YR> YR> P.s. I realize I've got a ridiculously large number of k-points---I'm in in YR> the process of converging the stress tensor with respect to ecutwfc and YR> ecutrho, and wanted to ensure k-points were absolutely not an issue. My YR> plan was to converge k-points next. YR> YR> Input File: YR> YR> &control YR> calculation = 'scf' YR> restart_mode='from_scratch' YR> prefix='ConvTest' YR> outdir = './ConvergenceTests' YR> pseudo_dir = '../pseudo' YR> tstress = .true. YR> tprnfor = .true. YR> / YR> &system YR> ibrav= 0 YR> celldm(1) = 8.207702028 YR> nat= 14 YR> ntyp= 2 YR> ecutwfc = 38 YR> ecutrho = 380 YR> occupations = 'smearing' YR> degauss = 0.03 YR> smearing = 'cold' YR> / YR> &electrons YR> mixing_beta = 0.7 YR> conv_thr = 1.0d-8 YR> / YR> CELL_PARAMETERS {alat} YR> 1.010363552 0.000000012 0.000000000 YR> 0.000000021 1.750048386 -0.000024105 YR> 0.000000000 -0.000012933 0.925 YR> ATOMIC_SPECIES YR> C 12.0107 C.pz-rrkjus.UPF.txt YR> Li 6.941 Li_VDB_LDA_SEMI.UPF.txt YR> ATOMIC_POSITIONS {angstrom} YR> Li 0.000000030 2.506788198 -0.000140635 YR> Li 2.171198117 6.271103089 -0.000356521 YR> C 1.467363622 2.526363526 2.006309099 YR> C 0.733070280 1.265423702 2.006682218 YR> C 0.738585262 3.794292056 2.006616072 YR> C 1.464475654 0.009242556 2.006460051 YR> C 2.923841993 0.009242573 2.006460051 YR> C 3.649732475 3.794292091 2.006616072 YR> C 3.655247398 1.265423737 2.006682218 YR> C 2.920954087 2.526363543 2.006309099 YR> C 3.657326610 6.344930347 2.006451947 YR> C 0.730991187 6.344930313 2.006451947 YR> C 1.464091389 5.063798994 2.006936383 YR> C 2.924226378 5.063799011 2.006936383 YR> K_POINTS {automatic} YR> 14 8 16 0 0 0 YR> YR> -Yaser Rehem YR> Rehem Research & Consulting YR> YR> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From yrehem at mac.com Wed Apr 16 23:42:42 2008 From: yrehem at mac.com (Yaser Rehem) Date: Wed, 16 Apr 2008 14:42:42 -0700 Subject: [Pw_forum] Fortran runtime error during scf in 4.0cvs3 In-Reply-To: References: <7B6E59F0-BEE8-4C9A-AB0E-A810C5E90387@mac.com> Message-ID: <898F7757-F995-4FAD-9AB0-FF100AE8F863@mac.com> Sorry for forgetting to specify the compiler, it's: g95-0.90 On Apr 16, 2008, at 2:12 PM, Axel Kohlmeyer wrote: > On Wed, 16 Apr 2008, Yaser Rehem wrote: > > hi yaser, > > YR> I got the following runtime error will attempting a scf on my > system: > YR> > YR> Cut & Paste from my Shell below: > YR> >At line 1288 of file cegterg.f90 > YR> >Traceback: not available, compile with -ftrace=frame or - > ftrace=full > YR> >At line 1288 of file cegterg.f90 > YR> >Traceback: not available, compile with -ftrace=frame or - > ftrace=full > YR> >Fortran runtime error: Array section out of bounds > YR> >Fortran runtime error: Array section out of bounds > YR> >* > > what compiler? what version? > when _exactly_ does this happen? > > this looks a lot like a miscompiled file. > that array is dynamically allocated after all. > > i'm currently running your input on my desktop and it has > already completed the two iterations... > > does it change when you use 6 pools instead (should be > much more efficient unless you run out of memory). > > cheers, > axel. > > YR> > YR> I'm running pwscf 4cvs3 on OS X 10.5.2 (9C7010), openmpi 1.2.4. > YR> > YR> I was running the input file below on 6 procs, 1 pool, when I > got the above > YR> error msg in my shell, and 2 of the 6 pw.x instances quit. > YR> > YR> P.s. I realize I've got a ridiculously large number of k- > points---I'm in in > YR> the process of converging the stress tensor with respect to > ecutwfc and > YR> ecutrho, and wanted to ensure k-points were absolutely not an > issue. My > YR> plan was to converge k-points next. > YR> > YR> Input File: > YR> > YR> &control > YR> calculation = 'scf' > YR> restart_mode='from_scratch' > YR> prefix='ConvTest' > YR> outdir = './ConvergenceTests' > YR> pseudo_dir = '../pseudo' > YR> tstress = .true. > YR> tprnfor = .true. > YR> / > YR> &system > YR> ibrav= 0 > YR> celldm(1) = 8.207702028 > YR> nat= 14 > YR> ntyp= 2 > YR> ecutwfc = 38 > YR> ecutrho = 380 > YR> occupations = 'smearing' > YR> degauss = 0.03 > YR> smearing = 'cold' > YR> / > YR> &electrons > YR> mixing_beta = 0.7 > YR> conv_thr = 1.0d-8 > YR> / > YR> CELL_PARAMETERS {alat} > YR> 1.010363552 0.000000012 0.000000000 > YR> 0.000000021 1.750048386 -0.000024105 > YR> 0.000000000 -0.000012933 0.925 > YR> ATOMIC_SPECIES > YR> C 12.0107 C.pz-rrkjus.UPF.txt > YR> Li 6.941 Li_VDB_LDA_SEMI.UPF.txt > YR> ATOMIC_POSITIONS {angstrom} > YR> Li 0.000000030 2.506788198 -0.000140635 > YR> Li 2.171198117 6.271103089 -0.000356521 > YR> C 1.467363622 2.526363526 2.006309099 > YR> C 0.733070280 1.265423702 2.006682218 > YR> C 0.738585262 3.794292056 2.006616072 > YR> C 1.464475654 0.009242556 2.006460051 > YR> C 2.923841993 0.009242573 2.006460051 > YR> C 3.649732475 3.794292091 2.006616072 > YR> C 3.655247398 1.265423737 2.006682218 > YR> C 2.920954087 2.526363543 2.006309099 > YR> C 3.657326610 6.344930347 2.006451947 > YR> C 0.730991187 6.344930313 2.006451947 > YR> C 1.464091389 5.063798994 2.006936383 > YR> C 2.924226378 5.063799011 2.006936383 > YR> K_POINTS {automatic} > YR> 14 8 16 0 0 0 > YR> > YR> -Yaser Rehem > YR> Rehem Research & Consulting > YR> > YR> > > -- > = > ====================================================================== > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http:// > www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA > 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > = > ====================================================================== > If you make something idiot-proof, the universe creates a better > idiot. From akohlmey at cmm.chem.upenn.edu Wed Apr 16 23:20:41 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 16 Apr 2008 17:20:41 -0400 (EDT) Subject: [Pw_forum] Fortran runtime error during scf in 4.0cvs3 In-Reply-To: <898F7757-F995-4FAD-9AB0-FF100AE8F863@mac.com> References: <7B6E59F0-BEE8-4C9A-AB0E-A810C5E90387@mac.com> <898F7757-F995-4FAD-9AB0-FF100AE8F863@mac.com> Message-ID: On Wed, 16 Apr 2008, Yaser Rehem wrote: YR> Sorry for forgetting to specify the compiler, it's: g95-0.90 version 0.91 is the current stable version as of march 2008... a. YR> On Apr 16, 2008, at 2:12 PM, Axel Kohlmeyer wrote: YR> YR> > On Wed, 16 Apr 2008, Yaser Rehem wrote: YR> > YR> > hi yaser, YR> > YR> > YR> I got the following runtime error will attempting a scf on my YR> > system: YR> > YR> YR> > YR> Cut & Paste from my Shell below: YR> > YR> >At line 1288 of file cegterg.f90 YR> > YR> >Traceback: not available, compile with -ftrace=frame or - YR> > ftrace=full YR> > YR> >At line 1288 of file cegterg.f90 YR> > YR> >Traceback: not available, compile with -ftrace=frame or - YR> > ftrace=full YR> > YR> >Fortran runtime error: Array section out of bounds YR> > YR> >Fortran runtime error: Array section out of bounds YR> > YR> >* YR> > YR> > what compiler? what version? YR> > when _exactly_ does this happen? YR> > YR> > this looks a lot like a miscompiled file. YR> > that array is dynamically allocated after all. YR> > YR> > i'm currently running your input on my desktop and it has YR> > already completed the two iterations... YR> > YR> > does it change when you use 6 pools instead (should be YR> > much more efficient unless you run out of memory). YR> > YR> > cheers, YR> > axel. YR> > YR> > YR> YR> > YR> I'm running pwscf 4cvs3 on OS X 10.5.2 (9C7010), openmpi 1.2.4. YR> > YR> YR> > YR> I was running the input file below on 6 procs, 1 pool, when I YR> > got the above YR> > YR> error msg in my shell, and 2 of the 6 pw.x instances quit. YR> > YR> YR> > YR> P.s. I realize I've got a ridiculously large number of k- YR> > points---I'm in in YR> > YR> the process of converging the stress tensor with respect to YR> > ecutwfc and YR> > YR> ecutrho, and wanted to ensure k-points were absolutely not an YR> > issue. My YR> > YR> plan was to converge k-points next. YR> > YR> YR> > YR> Input File: YR> > YR> YR> > YR> &control YR> > YR> calculation = 'scf' YR> > YR> restart_mode='from_scratch' YR> > YR> prefix='ConvTest' YR> > YR> outdir = './ConvergenceTests' YR> > YR> pseudo_dir = '../pseudo' YR> > YR> tstress = .true. YR> > YR> tprnfor = .true. YR> > YR> / YR> > YR> &system YR> > YR> ibrav= 0 YR> > YR> celldm(1) = 8.207702028 YR> > YR> nat= 14 YR> > YR> ntyp= 2 YR> > YR> ecutwfc = 38 YR> > YR> ecutrho = 380 YR> > YR> occupations = 'smearing' YR> > YR> degauss = 0.03 YR> > YR> smearing = 'cold' YR> > YR> / YR> > YR> &electrons YR> > YR> mixing_beta = 0.7 YR> > YR> conv_thr = 1.0d-8 YR> > YR> / YR> > YR> CELL_PARAMETERS {alat} YR> > YR> 1.010363552 0.000000012 0.000000000 YR> > YR> 0.000000021 1.750048386 -0.000024105 YR> > YR> 0.000000000 -0.000012933 0.925 YR> > YR> ATOMIC_SPECIES YR> > YR> C 12.0107 C.pz-rrkjus.UPF.txt YR> > YR> Li 6.941 Li_VDB_LDA_SEMI.UPF.txt YR> > YR> ATOMIC_POSITIONS {angstrom} YR> > YR> Li 0.000000030 2.506788198 -0.000140635 YR> > YR> Li 2.171198117 6.271103089 -0.000356521 YR> > YR> C 1.467363622 2.526363526 2.006309099 YR> > YR> C 0.733070280 1.265423702 2.006682218 YR> > YR> C 0.738585262 3.794292056 2.006616072 YR> > YR> C 1.464475654 0.009242556 2.006460051 YR> > YR> C 2.923841993 0.009242573 2.006460051 YR> > YR> C 3.649732475 3.794292091 2.006616072 YR> > YR> C 3.655247398 1.265423737 2.006682218 YR> > YR> C 2.920954087 2.526363543 2.006309099 YR> > YR> C 3.657326610 6.344930347 2.006451947 YR> > YR> C 0.730991187 6.344930313 2.006451947 YR> > YR> C 1.464091389 5.063798994 2.006936383 YR> > YR> C 2.924226378 5.063799011 2.006936383 YR> > YR> K_POINTS {automatic} YR> > YR> 14 8 16 0 0 0 YR> > YR> YR> > YR> -Yaser Rehem YR> > YR> Rehem Research & Consulting YR> > YR> YR> > YR> YR> > YR> > -- YR> > = YR> > ====================================================================== YR> > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http:// YR> > www.cmm.upenn.edu YR> > Center for Molecular Modeling -- University of Pennsylvania YR> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA YR> > 19104-6323 YR> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 YR> > = YR> > ====================================================================== YR> > If you make something idiot-proof, the universe creates a better YR> > idiot. YR> YR> _______________________________________________ YR> Pw_forum mailing list YR> Pw_forum at pwscf.org YR> http://www.democritos.it/mailman/listinfo/pw_forum YR> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From cao at qtp.ufl.edu Thu Apr 17 02:57:23 2008 From: cao at qtp.ufl.edu (Chao Cao) Date: Wed, 16 Apr 2008 20:57:23 -0400 Subject: [Pw_forum] PAW in 4.0CVS3 Message-ID: <4806A073.7060401@qtp.ufl.edu> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Lorenzo, Is there any major change or bug fix for PAW method between CVS2 and CVS3? I used exactly the same set of PP-generation input and PW input, but somehow got very different result in total energy and force (differs by several eV). Also, if I do structural relaxation using PAW in 4.0cvs3, and use the relaxed structure to do another SCF, the total energy/stress/force from SCF calculation can be substantially different from the final step in structural relaxation calculation. For example, I used the PAW dataset provided in pseudo/ directory to calculate Cu2O bulk, and the last step of relaxation gives me a total energy of -592.22777692 Ry and P=-0.03 kbar; but if I start from the final structure and do one SCF, the result is -592.22732012 Ry and P=-0.42 kbar. Since I set conv_thr to be 1.0d-7, a 0.0004 Ry difference in total energy looks really big to me... - -- Chao Cao Quantum Theory Project and Department of Physics University of Florida, Gainesville, FL 32611 U.S.A. -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.7 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFIBqBzFfX+kymy7P4RArAhAJ9Lp9H8kQykEbHi5P4FodimdVHSFgCfVFyO Quu1E1XTCoWIKWhoPS9iBCA= =JTOk -----END PGP SIGNATURE----- From akohlmey at cmm.chem.upenn.edu Thu Apr 17 02:40:59 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 16 Apr 2008 20:40:59 -0400 (EDT) Subject: [Pw_forum] PAW in 4.0CVS3 In-Reply-To: <4806A073.7060401@qtp.ufl.edu> References: <4806A073.7060401@qtp.ufl.edu> Message-ID: On Wed, 16 Apr 2008, Chao Cao wrote: CC> -----BEGIN PGP SIGNED MESSAGE----- CC> Hash: SHA1 CC> CC> Dear Lorenzo, CC> Is there any major change or bug fix for PAW method between CVS2 and CC> CVS3? I used exactly the same set of PP-generation input and PW input, CC> but somehow got very different result in total energy and force (differs CC> by several eV). lorenzo is probably (hopefully) asleep, so i'll give it a shot... the fundamental constants and unit conversions were updated to the latest CODATA 2006 recommended values. if you enter data that needs to be converted to internal units, e.g. coodinates or cell dimensions in angstrom, that may have the effect that you see. i've seen even larger discrepancies in some cases where the code (not QE) was even further off. makes you think about the real accuracy of what we are doing here, don't it? cheers, axel. CC> Also, if I do structural relaxation using PAW in 4.0cvs3, and use the CC> relaxed structure to do another SCF, the total energy/stress/force from CC> SCF calculation can be substantially different from the final step in CC> structural relaxation calculation. For example, I used the PAW dataset CC> provided in pseudo/ directory to calculate Cu2O bulk, and the last step CC> of relaxation gives me a total energy of -592.22777692 Ry and P=-0.03 CC> kbar; but if I start from the final structure and do one SCF, the result CC> is -592.22732012 Ry and P=-0.42 kbar. Since I set conv_thr to be 1.0d-7, CC> a 0.0004 Ry difference in total energy looks really big to me... CC> CC> - -- CC> Chao Cao CC> CC> Quantum Theory Project and Department of Physics CC> University of Florida, Gainesville, FL 32611 CC> U.S.A. CC> -----BEGIN PGP SIGNATURE----- CC> Version: GnuPG v2.0.7 (GNU/Linux) CC> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org CC> CC> iD8DBQFIBqBzFfX+kymy7P4RArAhAJ9Lp9H8kQykEbHi5P4FodimdVHSFgCfVFyO CC> Quu1E1XTCoWIKWhoPS9iBCA= CC> =JTOk CC> -----END PGP SIGNATURE----- CC> _______________________________________________ CC> Pw_forum mailing list CC> Pw_forum at pwscf.org CC> http://www.democritos.it/mailman/listinfo/pw_forum CC> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From cao at qtp.ufl.edu Thu Apr 17 03:27:43 2008 From: cao at qtp.ufl.edu (Chao Cao) Date: Wed, 16 Apr 2008 21:27:43 -0400 Subject: [Pw_forum] PAW in 4.0CVS3 In-Reply-To: References: <4806A073.7060401@qtp.ufl.edu> Message-ID: <4806A78F.4000700@qtp.ufl.edu> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Axel Kohlmeyer wrote: > On Wed, 16 Apr 2008, Chao Cao wrote: > > Dear Lorenzo, > Is there any major change or bug fix for PAW method between CVS2 and > CVS3? I used exactly the same set of PP-generation input and PW input, > but somehow got very different result in total energy and force (differs > by several eV). > >> lorenzo is probably (hopefully) asleep, so i'll give it a shot... > >> the fundamental constants and unit conversions were updated to the >> latest CODATA 2006 recommended values. if you enter data that needs >> to be converted to internal units, e.g. coodinates or cell dimensions >> in angstrom, that may have the effect that you see. Well, that IS the problem that I actually have no unit conversion, unless "bohr" is also changed...:p And about the discrepancy between SCF/relaxation, I was giving an easy example since everyone has Cu/O PAW data in distribution. I have a case that gives me ~0.1 eV difference, which makes me very uncomfortable... Chao Cao > >> i've seen even larger discrepancies in some cases where the code >> (not QE) was even further off. makes you think about the real >> accuracy of what we are doing here, don't it? > >> cheers, >> axel. > > > Also, if I do structural relaxation using PAW in 4.0cvs3, and use the > relaxed structure to do another SCF, the total energy/stress/force from > SCF calculation can be substantially different from the final step in > structural relaxation calculation. For example, I used the PAW dataset > provided in pseudo/ directory to calculate Cu2O bulk, and the last step > of relaxation gives me a total energy of -592.22777692 Ry and P=-0.03 > kbar; but if I start from the final structure and do one SCF, the result > is -592.22732012 Ry and P=-0.42 kbar. Since I set conv_thr to be 1.0d-7, > a 0.0004 Ry difference in total energy looks really big to me... > _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum - -- Chao Cao Quantum Theory Project and Department of Physics University of Florida, Gainesville, FL 32611 U.S.A. -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.7 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFIBqePFfX+kymy7P4RAouJAJ4vwlSXD0W/6pVQuz7a85EU8bGZ9gCfZzrO Ah5ynUHN712l+fg2HkK5rT0= =Bvr7 -----END PGP SIGNATURE----- From penghua8503 at 163.com Thu Apr 17 04:43:27 2008 From: penghua8503 at 163.com (penghua8503) Date: Thu, 17 Apr 2008 10:43:27 +0800 (CST) Subject: [Pw_forum] d3.x phonon life Message-ID: <30727171.159241208400207129.JavaMail.coremail@bj163app15.163.com> Dear All, I use d3.x in PWscf to calculate phonon life of Si. But I do not understand the results of it. I want to know which data is the phonon life. And I what to get an idea of how d3.x works (its flow).could you give me some reference article? I really appreciate your help. Thank you. Sincerely yours Hua PENG Hua PENG School of Physics ShandongUniversity, Jinan 25100 People' Republic of China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080417/f4852292/attachment.htm From giannozz at nest.sns.it Thu Apr 17 09:51:41 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 17 Apr 2008 09:51:41 +0200 Subject: [Pw_forum] Fortran runtime error during scf in 4.0cvs3 In-Reply-To: <7B6E59F0-BEE8-4C9A-AB0E-A810C5E90387@mac.com> References: <7B6E59F0-BEE8-4C9A-AB0E-A810C5E90387@mac.com> Message-ID: <9C570655-9889-45C6-862A-D18B602F6DEC@nest.sns.it> On Apr 16, 2008, at 21:37 , Yaser Rehem wrote: > >At line 1288 of file cegterg.f90 > >Traceback: not available, compile with -ftrace=frame or -ftrace=full > >At line 1288 of file cegterg.f90 > >Traceback: not available, compile with -ftrace=frame or -ftrace=full > >Fortran runtime error: Array section out of bounds > >Fortran runtime error: Array section out of bounds unlike most other compilers, g95 has the good habit of producing meaningful error reports instead of "segmentation violation" or "assertion failed" . This is actually a bug, although harmless, because the array section that is out of bound (only on those processors that do not perform parallel diagonalization) is never used (on those processors; on the others, everything is correct). Still, some compilers may complain, or worse. It will be fixed soon. Thank you for reporting this. > Li 6.941 Li_VDB_LDA_SEMI.UPF.txt note that this potential was removed from the pseudotential table because there were reports that phonon calculations were yielding strange results. Axel says that he got good results instead for structural and electronic properties. Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From paulatto at sissa.it Thu Apr 17 10:12:12 2008 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 17 Apr 2008 10:12:12 +0200 (CEST) Subject: [Pw_forum] PAW in 4.0CVS3 In-Reply-To: <4806A073.7060401@qtp.ufl.edu> References: <4806A073.7060401@qtp.ufl.edu> Message-ID: <26652.82.56.170.239.1208419932.squirrel@webmail.sissa.it> On Gio, Aprile 17, 2008 02:57, Chao Cao wrote: > Is there any major change or bug fix for PAW method between CVS2 and > CVS3? As far as I remember, there should be exactly zero of them. > I used exactly the same set of PP-generation input and PW input, > but somehow got very different result in total energy and force (differs > by several eV). I think you should regenerate your pseudopotentials files, as I have revised the format, maybe the new version is misreading the old files. > [cut] > Since I set conv_thr to be 1.0d-7, > a 0.0004 Ry difference in total energy looks really big to me... It definitely is, but I never had such a problem. Unless you have done some serious mistake in you input (i.e. cutoff far too low) it should not happen. There is a very stupid bug in the CVS3 version, it may cause random data to be used for augmentation charge. If you want to fix it by hand, you have to actually set to zero the "zeros" array in read_nonlocal routine, in Modules/read_upf_v2.f90. I hope whis will fix your problems, but if they persist, please report. bye -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) +39 040 3787 511 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From giannozz at nest.sns.it Thu Apr 17 10:41:08 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 17 Apr 2008 10:41:08 +0200 Subject: [Pw_forum] Problem with NEB In-Reply-To: <200804162058.57988.janos.kiss@theochem.ruhr-uni-bochum.de> References: <200804162058.57988.janos.kiss@theochem.ruhr-uni-bochum.de> Message-ID: <0A84650E-EEE9-49DA-81BB-BD88B844BC20@nest.sns.it> On Apr 16, 2008, at 20:58 , Janos Kiss wrote: > > The problem is that the configurations after the linear > interpolation between > reactant end product are often 'unchemical' even if i include some > intermediate images. The WF convergence for these images can be > particularly > problematic in the very first scf step. If the WF is not converged > within the > given maximum number of steps (set to 250 in my case) for one of > the images > the code stops for that given image complaining that ' convergence NOT > achieved, stopping'. which convergence is not achieved? scf convergence, or iterative diagonalization convergence ? in the former case, a simple solution might be to set conv_elec to .true. at the last iteration in PW/electrons.f90 (just after the call to mix_rho: if (idum == niter) conv_elec = .true. ) and leave the code go on with whatever forces it can calculate. In the latter case, things are more complicated. It is not difficult to add yet another option to produce such behaviour, but there are already too many, and I think it is not wise to make it the default behavior. Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at nest.sns.it Thu Apr 17 10:59:31 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 17 Apr 2008 10:59:31 +0200 Subject: [Pw_forum] Band structure calculation HOWTO In-Reply-To: <200804091512.46010.janos.kiss@theochem.ruhr-uni-bochum.de> References: <200804091512.46010.janos.kiss@theochem.ruhr-uni-bochum.de> Message-ID: <3500935F-65BD-4FF6-A250-268DF2F4F450@nest.sns.it> On Apr 9, 2008, at 15:12 , Janos Kiss wrote: > I have found a nice tutorial on the band structure calculation of > bulk Si: > http://people.sissa.it/~degironc/QE-Tutorial/tutorial_pwscf_ex.pdf > http://people.sissa.it/~degironc/QE-Tutorial/examples_pwscf_ex.tgz nice but very old. There is a newer version which for obscure reasons never percolated to the web site. > I'm just wondering where this discrepancy is coming from. Did i > miscompile > the code, or eventually the tutorial was done by mistake with > different settings/pseudopotential? different pseudopotentials is the likely answer. Absolute values of Kohn-Sham states vary with the pseudopotentials > In what extent will be affected the band structure by the smearing > scheme if > eventually the system changes from the metallic state to a > semiconductor by > some adsorbates/surface defects? if the smearing is small wrt the gap, results will be affected very little Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From phill.english at gmail.com Thu Apr 17 13:48:26 2008 From: phill.english at gmail.com (Phillip English) Date: Thu, 17 Apr 2008 19:48:26 +0800 Subject: [Pw_forum] Query about restarting vc-relax Message-ID: <48073915.15528c0a.64f1.4bb1@mx.google.com> Dear users and developers, I'm new to using PWscf, and I've been attempting to run some basic calculations of TiO2 and its two predominant polymorphs, rutile and anatase. I'm having no trouble running 'scf', 'relax', and 'vc-relax' calculations for the rutile polymorph, as it finishes within one period of the time allocated to me on our supercomputers. However, anatase takes a little bit longer, so it is being cut off mid-calculation by the queueing system. From what I understand, this is what the restart_mode='restart' flag is for, so I have tried using that to restart my calculation. Before I restarted the calculation, the energy was converging nicely towards a value I expected. However as soon as I restarted, the energy blew out. Looking at the cell parameters, they too blew out, and visualising the structure showed that the cell was indeed expanding quite rapidly. When I looked at the output more closely, it seemed like the starting cell parameters for the restarted calculation were still being calculated by the program according to the specified 'ibrav' and 'celldm' values, rather than restarting with the cell parameters that had relaxed from the previous calculation. This is what I supposed caused the 'explosion'. It seems strange to me that while the atomic positions are read in correctly, the cell parameters are not. So, my question after that long preamble; do you need to manually re-enter the cell parameters using the 'CELL_PARAMETERS' flag when restarting a vc-relax calculation? If this isn't the case, does anyone have any ideas about what might have caused the behaviour described. Apologies if this has been covered before, I used the search function and a google search on the mailing list archives to try and find the answer but couldn't. Cheers, Phillip English PhD Student Curtin University, Perth Western Australia Australia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080417/4ed78bba/attachment.htm From akohlmey at cmm.chem.upenn.edu Thu Apr 17 13:42:55 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 17 Apr 2008 07:42:55 -0400 (EDT) Subject: [Pw_forum] Query about restarting vc-relax In-Reply-To: <48073915.15528c0a.64f1.4bb1@mx.google.com> References: <48073915.15528c0a.64f1.4bb1@mx.google.com> Message-ID: On Thu, 17 Apr 2008, Phillip English wrote: PE> Dear users and developers, PE> PE> PE> PE> I'm new to using PWscf, and I've been attempting to run some basic PE> calculations of TiO2 and its two predominant polymorphs, rutile and anatase. PE> I'm having no trouble running 'scf', 'relax', and 'vc-relax' calculations PE> for the rutile polymorph, as it finishes within one period of the time PE> allocated to me on our supercomputers. However, anatase takes a little bit PE> longer, so it is being cut off mid-calculation by the queueing system. From phillip, please consider setting the 'max_seconds' flag to a value of, say, 15 mins less than the maximum run time of your batch job. this way you make sure that the job stops cleanly and is thus cleanly restartable. i don't know whether this will solve your problem, but it might cure future problems when you jobs get randomly killed in the middle of writing a restart for example. cheers, axel. p.s.: if this is a real bug, it would be nice to know which OS/compiler/QE-version this relates to. perhaps it has been found and fixed already in the cvs version? PE> what I understand, this is what the restart_mode='restart' flag is for, so I PE> have tried using that to restart my calculation. PE> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From giannozz at nest.sns.it Thu Apr 17 15:44:34 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 17 Apr 2008 15:44:34 +0200 Subject: [Pw_forum] Query about restarting vc-relax In-Reply-To: <48073915.15528c0a.64f1.4bb1@mx.google.com> References: <48073915.15528c0a.64f1.4bb1@mx.google.com> Message-ID: <233DBC61-1A58-4DEF-ACDE-2ECEF8024FB5@nest.sns.it> On Apr 17, 2008, at 13:48 , Phillip English wrote: > However as soon as I restarted, the energy blew out. Looking at the > cell parameters, they too blew out, and visualising the structure > showed that the cell was indeed expanding quite rapidly. When I > looked at the output more closely, it seemed like the starting cell > parameters for the restarted calculation were still being > calculated by the program according to the specified ?ibrav? and > ?celldm? values, rather than restarting with the cell parameters > that had relaxed from the previous calculation. This is what I > supposed caused the ?explosion?. It seems strange to me that while > the atomic positions are read in correctly, the cell parameters are > not. > restarting from a variable-cell optimization / molecular dynamics run ? not sure it works properly. If nobody has ever verified it, it is unlikely that it works. The only parts of the distribution that typically work are either the most frequently used, or those used by people willing to, and able to, improve the code. > So, my question after that long preamble; do you need to manually > re-enter the cell parameters using the ?CELL_PARAMETERS? flag when > restarting a vc-relax calculation? > not unlikely, but it might not be sufficient Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From yrehem at mac.com Thu Apr 17 20:13:41 2008 From: yrehem at mac.com (Yaser Rehem) Date: Thu, 17 Apr 2008 11:13:41 -0700 Subject: [Pw_forum] Fortran runtime error during scf in 4.0cvs3 In-Reply-To: References: <7B6E59F0-BEE8-4C9A-AB0E-A810C5E90387@mac.com> <898F7757-F995-4FAD-9AB0-FF100AE8F863@mac.com> Message-ID: <9CC5C278-6340-482F-8D80-1F5609614CD3@mac.com> Axel- I upgraded to g95-0.91 and recompiled pwscf. I still get the same error messages when attempted the scf with 6 processors. I played a little and discovered that it runs fine with upto 4 processors, but fails when I attempt to use more than 4. On Apr 16, 2008, at 2:20 PM, Axel Kohlmeyer wrote: > On Wed, 16 Apr 2008, Yaser Rehem wrote: > > YR> Sorry for forgetting to specify the compiler, it's: g95-0.90 > > version 0.91 is the current stable version as of march 2008... > > a. > > YR> On Apr 16, 2008, at 2:12 PM, Axel Kohlmeyer wrote: > YR> > YR> > On Wed, 16 Apr 2008, Yaser Rehem wrote: > YR> > > YR> > hi yaser, > YR> > > YR> > YR> I got the following runtime error will attempting a scf on > my > YR> > system: > YR> > YR> > YR> > YR> Cut & Paste from my Shell below: > YR> > YR> >At line 1288 of file cegterg.f90 > YR> > YR> >Traceback: not available, compile with -ftrace=frame or - > YR> > ftrace=full > YR> > YR> >At line 1288 of file cegterg.f90 > YR> > YR> >Traceback: not available, compile with -ftrace=frame or - > YR> > ftrace=full > YR> > YR> >Fortran runtime error: Array section out of bounds > YR> > YR> >Fortran runtime error: Array section out of bounds > YR> > YR> >* > YR> > > YR> > what compiler? what version? > YR> > when _exactly_ does this happen? > YR> > > YR> > this looks a lot like a miscompiled file. > YR> > that array is dynamically allocated after all. > YR> > > YR> > i'm currently running your input on my desktop and it has > YR> > already completed the two iterations... > YR> > > YR> > does it change when you use 6 pools instead (should be > YR> > much more efficient unless you run out of memory). > YR> > > YR> > cheers, > YR> > axel. > YR> > > YR> > YR> > YR> > YR> I'm running pwscf 4cvs3 on OS X 10.5.2 (9C7010), openmpi > 1.2.4. > YR> > YR> > YR> > YR> I was running the input file below on 6 procs, 1 pool, > when I > YR> > got the above > YR> > YR> error msg in my shell, and 2 of the 6 pw.x instances quit. > YR> > YR> > YR> > YR> P.s. I realize I've got a ridiculously large number of k- > YR> > points---I'm in in > YR> > YR> the process of converging the stress tensor with respect to > YR> > ecutwfc and > YR> > YR> ecutrho, and wanted to ensure k-points were absolutely not > an > YR> > issue. My > YR> > YR> plan was to converge k-points next. > YR> > YR> > YR> > YR> Input File: > YR> > YR> > YR> > YR> &control > YR> > YR> calculation = 'scf' > YR> > YR> restart_mode='from_scratch' > YR> > YR> prefix='ConvTest' > YR> > YR> outdir = './ConvergenceTests' > YR> > YR> pseudo_dir = '../pseudo' > YR> > YR> tstress = .true. > YR> > YR> tprnfor = .true. > YR> > YR> / > YR> > YR> &system > YR> > YR> ibrav= 0 > YR> > YR> celldm(1) = 8.207702028 > YR> > YR> nat= 14 > YR> > YR> ntyp= 2 > YR> > YR> ecutwfc = 38 > YR> > YR> ecutrho = 380 > YR> > YR> occupations = 'smearing' > YR> > YR> degauss = 0.03 > YR> > YR> smearing = 'cold' > YR> > YR> / > YR> > YR> &electrons > YR> > YR> mixing_beta = 0.7 > YR> > YR> conv_thr = 1.0d-8 > YR> > YR> / > YR> > YR> CELL_PARAMETERS {alat} > YR> > YR> 1.010363552 0.000000012 0.000000000 > YR> > YR> 0.000000021 1.750048386 -0.000024105 > YR> > YR> 0.000000000 -0.000012933 0.925 > YR> > YR> ATOMIC_SPECIES > YR> > YR> C 12.0107 C.pz-rrkjus.UPF.txt > YR> > YR> Li 6.941 Li_VDB_LDA_SEMI.UPF.txt > YR> > YR> ATOMIC_POSITIONS {angstrom} > YR> > YR> Li 0.000000030 2.506788198 -0.000140635 > YR> > YR> Li 2.171198117 6.271103089 -0.000356521 > YR> > YR> C 1.467363622 2.526363526 2.006309099 > YR> > YR> C 0.733070280 1.265423702 2.006682218 > YR> > YR> C 0.738585262 3.794292056 2.006616072 > YR> > YR> C 1.464475654 0.009242556 2.006460051 > YR> > YR> C 2.923841993 0.009242573 2.006460051 > YR> > YR> C 3.649732475 3.794292091 2.006616072 > YR> > YR> C 3.655247398 1.265423737 2.006682218 > YR> > YR> C 2.920954087 2.526363543 2.006309099 > YR> > YR> C 3.657326610 6.344930347 2.006451947 > YR> > YR> C 0.730991187 6.344930313 2.006451947 > YR> > YR> C 1.464091389 5.063798994 2.006936383 > YR> > YR> C 2.924226378 5.063799011 2.006936383 > YR> > YR> K_POINTS {automatic} > YR> > YR> 14 8 16 0 0 0 > YR> > YR> > YR> > YR> -Yaser Rehem > YR> > YR> Rehem Research & Consulting > YR> > YR> > YR> > YR> > YR> > > YR> > -- > YR> > = > YR> > > ====================================================================== > YR> > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http:// > YR> > www.cmm.upenn.edu > YR> > Center for Molecular Modeling -- University of > Pennsylvania > YR> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA > YR> > 19104-6323 > YR> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: > 1-215-898-5425 > YR> > = > YR> > > ====================================================================== > YR> > If you make something idiot-proof, the universe creates a better > YR> > idiot. > YR> > YR> _______________________________________________ > YR> Pw_forum mailing list > YR> Pw_forum at pwscf.org > YR> http://www.democritos.it/mailman/listinfo/pw_forum > YR> > > -- > = > ====================================================================== > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http:// > www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA > 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > = > ====================================================================== > If you make something idiot-proof, the universe creates a better > idiot. From giannozz at nest.sns.it Thu Apr 17 20:25:33 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 17 Apr 2008 20:25:33 +0200 Subject: [Pw_forum] Fortran runtime error during scf in 4.0cvs3 In-Reply-To: <9CC5C278-6340-482F-8D80-1F5609614CD3@mac.com> References: <7B6E59F0-BEE8-4C9A-AB0E-A810C5E90387@mac.com> <898F7757-F995-4FAD-9AB0-FF100AE8F863@mac.com> <9CC5C278-6340-482F-8D80-1F5609614CD3@mac.com> Message-ID: On Apr 17, 2008, at 20:13 , Yaser Rehem wrote: > I upgraded to g95-0.91 and recompiled pwscf. I still get the same > error messages when attempted the scf with 6 processors. I played a > little and discovered that it runs fine with upto 4 processors, but > fails when I attempt to use more than 4. the problem exists only of the number of processors used in the parallel subspace diagonalization (must be the square of an integer) is not the same as the number of processor for R- and G-space parallelization. So 4=2x2 is fine, 16=4x4 is also, 6 is not Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From yrehem at mac.com Thu Apr 17 20:34:00 2008 From: yrehem at mac.com (Yaser Rehem) Date: Thu, 17 Apr 2008 11:34:00 -0700 Subject: [Pw_forum] Fortran runtime error during scf in 4.0cvs3 In-Reply-To: References: <7B6E59F0-BEE8-4C9A-AB0E-A810C5E90387@mac.com> <898F7757-F995-4FAD-9AB0-FF100AE8F863@mac.com> <9CC5C278-6340-482F-8D80-1F5609614CD3@mac.com> Message-ID: <7DB95B51-5866-4043-BDEF-B942590535B3@mac.com> It ran fine with 2 and 3 processors as well. Is there some upper limit when the square of an integer issue kicks in? On Apr 17, 2008, at 11:25 AM, Paolo Giannozzi wrote: > > On Apr 17, 2008, at 20:13 , Yaser Rehem wrote: > >> I upgraded to g95-0.91 and recompiled pwscf. I still get the same >> error messages when attempted the scf with 6 processors. I played a >> little and discovered that it runs fine with upto 4 processors, but >> fails when I attempt to use more than 4. > > the problem exists only of the number of processors used in the > parallel subspace diagonalization (must be the square of an integer) > is not the same as the number of processor for R- and G-space > parallelization. So 4=2x2 is fine, 16=4x4 is also, 6 is not > > Paolo > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > From yrehem at mac.com Thu Apr 17 20:54:14 2008 From: yrehem at mac.com (Yaser Rehem) Date: Thu, 17 Apr 2008 11:54:14 -0700 Subject: [Pw_forum] Fortran runtime error during scf in 4.0cvs3 In-Reply-To: <9C570655-9889-45C6-862A-D18B602F6DEC@nest.sns.it> References: <7B6E59F0-BEE8-4C9A-AB0E-A810C5E90387@mac.com> <9C570655-9889-45C6-862A-D18B602F6DEC@nest.sns.it> Message-ID: I just noticed this response now. Thank you Paolo! On Apr 17, 2008, at 12:51 AM, Paolo Giannozzi wrote: > > On Apr 16, 2008, at 21:37 , Yaser Rehem wrote: > >>> At line 1288 of file cegterg.f90 >>> Traceback: not available, compile with -ftrace=frame or -ftrace=full >>> At line 1288 of file cegterg.f90 >>> Traceback: not available, compile with -ftrace=frame or -ftrace=full >>> Fortran runtime error: Array section out of bounds >>> Fortran runtime error: Array section out of bounds > > unlike most other compilers, g95 has the good habit of producing > meaningful > error reports instead of "segmentation violation" or "assertion > failed" . This is > actually a bug, although harmless, because the array section that is > out of > bound (only on those processors that do not perform parallel > diagonalization) > is never used (on those processors; on the others, everything is > correct). > Still, some compilers may complain, or worse. It will be fixed soon. > Thank you > for reporting this. > >> Li 6.941 Li_VDB_LDA_SEMI.UPF.txt > > note that this potential was removed from the pseudotential table > because > there were reports that phonon calculations were yielding strange > results. > Axel says that he got good results instead for structural and > electronic properties. > > 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 From cesards at msi.umn.edu Fri Apr 18 03:39:31 2008 From: cesards at msi.umn.edu (Cesar R.S. da Silva) Date: Thu, 17 Apr 2008 20:39:31 -0500 (CDT) Subject: [Pw_forum] Query about restarting vc-relax (Cesar R.S. da Silva) Message-ID: <58476.128.101.191.226.1208482771.squirrel@www.msi.umn.edu> Dear Phillip, I have used vc-relax for several years and never faced this problem. Please, send me your input file and pseudo-potentials. I'll try to reproduce your error, and fix it. Cesar. ---------------------------------------------------- Cesar R.S. da Silva, PhD. Minnesota Supercomputing Institute, University of Minnesota. Phone: (612)-624-7425 e-mail: cesards at msi.umn.edu ---------------------------------------------------- From iphyboy at hotmail.com Fri Apr 18 11:12:07 2008 From: iphyboy at hotmail.com (=?gb2312?B?w/fOxMPA?=) Date: Fri, 18 Apr 2008 17:12:07 +0800 Subject: [Pw_forum] fixed magnetic moment calculation Message-ID: Dear users: I know that PWSCF cam carry out calculation of fixed moment in a cell as well as its direction, but now I want to do a fixed magnetic moment AFM calculation for the sake of model Hamiliton investigation,i.e. the magnetic moment of the neighboring atom has the same value but in the opposite direction. Any suggestion is highly appreciated. Wenmei _________________________________________________________________ Windows Live Photo gallery ????????????????????????????? http://get.live.cn/product/photo.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080418/2947f431/attachment.htm From yccheng.nju at gmail.com Fri Apr 18 13:10:23 2008 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Fri, 18 Apr 2008 19:10:23 +0800 Subject: [Pw_forum] Raman Intensity Message-ID: Dear pwscf users: I am trying to use the v3.2.3 to study Raman properties. In the "INPUT_PH", it mentions literature "M. Lazzeri and F. Mauri, Phys. Rev. Lett. 90, 036401 (2003)". In this paper, Lazzeri computed the raman intensities form the second order derivative of the electronic density matrix with respect to a uniform electric field. Moreover, another paper "J. Sun and et. al. , Phys. Rev. B 74, 193101" discussed the raman spectrum via Lazzeri's method. I think this method, which has been implented int pwscf code, is different from the linear response method (1.S. Baroni et al. Rev. Mod. Phys. 73, 515 (2001), 2.P. Umari and et. al. Phys. Rev. B 63, 094305), which get the raman intensities by polarizability tensors. However, I cannot understant the results of example15(AlAs)which study the raman tensor of AlAs. The results of Raman tensor are showed as below: ======================================================================================================= Raman tensor (A^2) atom # 1 pol. 1 -0.201910099100E-14 -0.540966680608E-15 -0.190481225566E-15 -0.145527656333E-14 -0.739067155197E-15 -0.517081932644E+01 -0.556205178654E-15 -0.517081932644E+01 0.906690633696E-15 atom # 1 pol. 2 ... atom # 1 pol. 3 ... atom # 2 pol. 1 ... atom # 2 pol. 2 ... atom # 2 pol. 3 ... ======================================================================================================= My questions: what does A^2 mean? what does pol. * mean? I have another question about the alas.dynG. 1.Do omega 1, 2, 3 stand for the acoustic mode? 2.How can I get the Raman intensities?(the last but not the least!) ************************************************************************** omega( 1) = 0.043635 [THz] = 1.455501 [cm-1] ( -0.499893 0.000000 0.432764 0.000000 -0.250591 0.000000 ) ( -0.499920 0.000000 0.432787 0.000000 -0.250604 0.000000 ) omega( 2) = 0.043635 [THz] = 1.455501 [cm-1] ( 0.189458 0.000000 -0.164016 0.000000 -0.661194 0.000000 ) ( 0.189468 0.000000 -0.164025 0.000000 -0.661229 0.000000 ) omega( 3) = 0.043635 [THz] = 1.455501 [cm-1] ( -0.462802 0.000000 -0.534591 0.000000 0.000000 0.000000 ) ( -0.462827 0.000000 -0.534620 0.000000 0.000000 0.000000 ) omega( 4) = 10.686462 [THz] = 356.464369 [cm-1] ( -0.105298 0.000000 0.234486 0.000000 0.253351 0.000000 ) ( 0.272091 0.000000 -0.605913 0.000000 -0.654659 0.000000 ) omega( 5) = 10.686462 [THz] = 356.464369 [cm-1] ( 0.329240 0.000000 0.147848 0.000000 0.000000 0.000000 ) ( -0.850757 0.000000 -0.382040 0.000000 0.000000 0.000000 ) omega( 6) = 10.686462 [THz] = 356.464369 [cm-1] ( -0.103785 0.000000 0.231118 0.000000 -0.257044 0.000000 ) ( 0.268182 0.000000 -0.597208 0.000000 0.664201 0.000000 ) ************************************************************************** -- Y. C. Cheng Department of Phyics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080418/6c97389e/attachment.htm From giannozz at nest.sns.it Fri Apr 18 13:38:43 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 18 Apr 2008 13:38:43 +0200 Subject: [Pw_forum] Raman Intensity In-Reply-To: References: Message-ID: <48088843.1030805@nest.sns.it> ??? wrote: > My questions: what does A^2 mean? Angstrom square > what does pol. * mean? polarization: x, y, z -- Paolo Giannozzi, Democritos and University of Udine, Italy From eyvaz_isaev at yahoo.com Fri Apr 18 14:00:19 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 18 Apr 2008 05:00:19 -0700 (PDT) Subject: [Pw_forum] Raman Intensity In-Reply-To: Message-ID: <759773.18299.qm@web65714.mail.ac4.yahoo.com> Hi, > I have another question about the alas.dynG. > 1.Do omega 1, 2, 3 stand for the acoustic mode? Yes, of course. > 2.How can I get the Raman intensities?(the last but > not the least!) As far as I remember you should use dynmat.x to get such a kind information. Bests, Eyvaz. > > ************************************************************************** > omega( 1) = 0.043635 [THz] = > 1.455501 [cm-1] > ( -0.499893 0.000000 0.432764 0.000000 -0.250591 > 0.000000 ) > ( -0.499920 0.000000 0.432787 0.000000 -0.250604 > 0.000000 ) > omega( 2) = 0.043635 [THz] = > 1.455501 [cm-1] > ( 0.189458 0.000000 -0.164016 0.000000 -0.661194 > 0.000000 ) > ( 0.189468 0.000000 -0.164025 0.000000 -0.661229 > 0.000000 ) > omega( 3) = 0.043635 [THz] = > 1.455501 [cm-1] > ( -0.462802 0.000000 -0.534591 0.000000 0.000000 > 0.000000 ) > ( -0.462827 0.000000 -0.534620 0.000000 0.000000 > 0.000000 ) > omega( 4) = 10.686462 [THz] = > 356.464369 [cm-1] > ( -0.105298 0.000000 0.234486 0.000000 0.253351 > 0.000000 ) > ( 0.272091 0.000000 -0.605913 0.000000 -0.654659 > 0.000000 ) > omega( 5) = 10.686462 [THz] = > 356.464369 [cm-1] > ( 0.329240 0.000000 0.147848 0.000000 0.000000 > 0.000000 ) > ( -0.850757 0.000000 -0.382040 0.000000 0.000000 > 0.000000 ) > omega( 6) = 10.686462 [THz] = > 356.464369 [cm-1] > ( -0.103785 0.000000 0.231118 0.000000 -0.257044 > 0.000000 ) > ( 0.268182 0.000000 -0.597208 0.000000 0.664201 > 0.000000 ) > > ************************************************************************** > > > -- > Y. C. Cheng > Department of Phyics > Nanjing University > Nanjing 210093 > P. R. China > Tel: 86-25-83592907 > Email: yccheng.nju at gmail.com > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, IFM, Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ From lily_physics at yahoo.com.sg Fri Apr 18 14:06:05 2008 From: lily_physics at yahoo.com.sg (Lily Anh) Date: Fri, 18 Apr 2008 20:06:05 +0800 (SGT) Subject: [Pw_forum] symmetry operation not allowed Message-ID: <442610.77801.qm@web76105.mail.sg1.yahoo.com> Dear all, I know this is a old question and I also read the previous answer about this. I test with different ecutwfc , ecutrho (until 30 times of ecutwfc) , and K-grid. However, the problem still exists. Since the calculation expense is always in concern, so I want to use symmetry during the calculation. I attach the output and input file here for reference. Output file: Current dimensions of program pwscf are: ntypx =10 npk =40000 lmax = 3 nchix = 6 ndmx = 2000 nbrx =14 nqfx = 8 warning: symmetry operation # 2 not allowed. fractional translation: -0.4999900 -0.4999400 -0.5000000 in crystal coordinates warning: symmetry operation # 3 not allowed. fractional translation: 0.0000100 -0.5000000 -0.2498700 in crystal coordinates warning: symmetry operation # 4 not allowed. fractional translation: -0.5000000 0.0000600 0.2501300 in crystal coordinates Planes per process (thick) : nr3 = 90 npp = 8 ncplane =32400 Planes per process (smooth): nr3s= 32 npps= 3 ncplanes= 4096 Proc/ planes cols G planes cols G columns G Pool (dense grid) (smooth grid) (wavefct grid) 1 8 1960 109526 3 261 5323 76 838 2 8 1961 109525 3 261 5333 75 837 3 8 1961 109525 3 261 5325 75 837 4 8 1961 109525 3 261 5321 75 837 5 8 1961 109525 3 261 5321 77 837 6 8 1961 109525 3 261 5321 77 837 7 7 1960 109524 3 262 5338 77 837 8 7 1960 109524 3 261 5339 77 837 9 7 1960 109524 2 261 5337 77 837 10 7 1960 109524 2 261 5337 77 837 11 7 1960 109524 2 261 5335 77 837 12 7 1960 109524 2 261 5325 77 837 0 90 235251314295 32 3133 63955 917 10045 bravais-lattice index = 8 lattice parameter (a_0) = 15.6923 a.u. unit-cell volume = 1872.5343 (a.u.)^3 number of atoms/cell = 36 number of atomic types = 2 kinetic-energy cutoff = 40.0000 Ry charge density cutoff = 1200.0000 Ry convergence threshold = 1.0E-08 beta = 0.7000 number of iterations used = 8 plain mixing Exchange-correlation = SLA PW PBE PBE (1434) iswitch = 0 celldm(1)= 15.692292 celldm(2)= 1.000000 celldm(3)= 0.484586 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) = ( 0.000000 1.000000 0.000000 ) a(3) = ( 0.000000 0.000000 0.484586 ) reciprocal axes: (cart.. coord. in units 2 pi/a_0) b(1) = ( 1.000000 0.000000 0.000000 ) b(2) = ( 0.000000 1.000000 0.000000 ) b(3) = ( 0.000000 0.000000 2.063618 ) PSEUDO 1 is O (US) zval = 6.0 lmax= 2 lloc= 0 Version 0 0 0 of US pseudo code Using log mesh of 1269 points The pseudopotential has 4 beta functions with: l(1) = 0 l(2) = 0 l(3) = 1 l(4) = 1 Q(r) pseudized with 0 coefficients, rinner = 0.000 0.000 0.000 0.000 0.000 PSEUDO 2 is H (US) zval = 1.0 lmax= 1 lloc= 0 Version 0 0 0 of US pseudo code Using log mesh of 1061 points The pseudopotential has 2 beta functions with: l(1) = 0 l(2) = 0 Q(r) pseudized with 0 coefficients, rinner = 0.000 0.000 0.000 atomic species valence mass pseudopotential O 6.00 15.99940 O ( 1.00) H 1.00 1.00790 H ( 1.00) No symmetry! INPTU file: &control calculation='scf', restart_mode='from_scratch', prefix='h2o' pseudo_dir = '/pwwork/pseudo/', outdir=/pwwork/tmp/tmp1/' tstress=.t.., tprnfor=.t. / &system ibrav = 8, celldm(1) = 15.69229199303824618227,celldm(2) =1.00,celldm(3) =.48458574181117533718,nat= 36, ntyp= 2, ecutwfc=40,ecutrho=1200 / &electrons mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES O 15.9994 O.pbe-rrkjus.UPF H 1.0079 H.pbe-rrkjus.UPF ATOMIC_POSITIONS {crystal} O -0.00178 0.00473 0.00365 O 0..00177 0.50473 0.24622 O 0.13861 0.25239 0.61888 O 0.25932 0.63953 0.89389 O 0.24067 0.86042 0.39389 O 0.36138 0..24756 0.11888 O 0.49822 -0.00479 0.74622 O 0.50177 0.49521 0.50365 O 0.63861 0.74756 0.13098 O 0.74067 0.13953 0.35598 O 0.75932 0.36042 0.85598 O 0.86138 0.75239 0.63098 H 0.71747 0.77486 0.30843 H 0.78252 0.72509 0.80843 H 0.77591 0.21514 0.53383 H 0.72409 0.28481 1.03383 H 0.21747 0.22509 0.44143 H 0.28252 0.27486 -0.05857 H 0.22409 0.71514 0.71603 H 0.27591 0.78481 0.21603 H 0.42227 0.15633 0..02004 H 0.45437 0.40953 0.36230 H 0.83871 0.08712 0.26341 H 0.54563 -0.09047 0.88757 H 0.58770 0.03448 0.60370 H 0.57773 0.65633 0.22982 H 0.66128 0.41283 0.76341 H 0.04563 0.09042 -0.13770 H 0.08770 -0.03453 0.14616 H 0.92227 0.84362 0.72982 H -0.08771 0.46547 0.10370 H -0.04563 0.59042 0..38757 H 0.07773 0.34362 0.52004 H 0.16128 0.58712 0.98645 H 0.41229 0.53448 0.64616 H 0.33871 0.91283 0.48645 K_POINTS { automatic } 2 2 4 0 0 0 Any reply is appreciated! Regards Lily __________________________________________________________________ Yahoo! Singapore Answers Real people. Real questions. Real answers. Share what you know at http://answers.yahoo.com.sg -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080418/ec93fe8f/attachment-0001.htm From yccheng.nju at gmail.com Fri Apr 18 14:44:05 2008 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Fri, 18 Apr 2008 20:44:05 +0800 Subject: [Pw_forum] Raman Intensity In-Reply-To: <759773.18299.qm@web65714.mail.ac4.yahoo.com> References: <759773.18299.qm@web65714.mail.ac4.yahoo.com> Message-ID: Thank you for your reply! I use the dynmat.x to calculate alas.dynG, and have some questions about the results. *************************************************************************************************** # mode [cm-1] [THz] IR Raman depol 1 0.00 0.0000 0.0000 0.0006 0.7500 2 0.00 0.0000 0.0000 0.0006 0.7500 3 0.00 0.0000 0.0000 0.0006 0.7500 4 356.47 10.6866 5.4447 29.3043 0.7500 5 356.47 10.6866 5.4447 29.3043 0.7500 6 356.47 10.6866 5.4447 29.3043 0.7500 *************************************************************************************************** Do the column "IR" and "Raman" stand for the IR intensity and Raman intensity? And what does depol stand for? 2008/4/18, Eyvaz Isaev : > > Hi, > > > I have another question > about the alas.dynG. > > 1.Do omega 1, 2, 3 > stand for the acoustic mode? > > Yes, > of course. > > > 2.How can I get the > Raman intensities?(the last but > > not the > least!) > > As far as I remember you > should use dynmat.x to get such a kind > information. > > Bests, > Eyvaz. > > > > > > > ************************************************************************** > > > omega( 1) = 0.043635 [THz] = > > > 1.455501 [cm-1] > > ( -0.499893 > 0.000000 0.432764 0.000000 -0.250591 > > > 0.000000 ) > > ( -0.499920 0.000000 0.432787 > 0.000000 -0.250604 > > 0.000000 ) > > > omega( 2) = 0.043635 [THz] = > > > 1.455501 [cm-1] > > ( 0.189458 > 0.000000 -0.164016 0.000000 -0.661194 > > > 0.000000 ) > > ( 0.189468 0.000000 -0.164025 > 0.000000 -0.661229 > > 0.000000 ) > > > omega( 3) = 0.043635 [THz] = > > > 1.455501 [cm-1] > > ( -0.462802 > 0.000000 -0.534591 0.000000 0.000000 > > > 0.000000 ) > > ( -0.462827 0.000000 -0.534620 > 0.000000 0.000000 > > 0.000000 ) > > > omega( 4) = 10.686462 [THz] = > > > 356.464369 [cm-1] > > ( -0.105298 0.000000 > 0.234486 0.000000 0.253351 > > 0.000000 > ) > > ( 0.272091 0.000000 -0.605913 > 0.000000 -0.654659 > > 0.000000 ) > > > omega( 5) = 10.686462 [THz] = > > > 356.464369 [cm-1] > > ( 0.329240 0.000000 > 0.147848 0.000000 0.000000 > > 0.000000 > ) > > ( -0.850757 0.000000 -0.382040 > 0.000000 0.000000 > > 0.000000 ) > > > omega( 6) = 10.686462 [THz] = > > > 356.464369 [cm-1] > > ( -0.103785 0.000000 > 0.231118 0.000000 -0.257044 > > 0.000000 > ) > > ( 0.268182 0.000000 -0.597208 > 0.000000 0.664201 > > 0.000000 ) > > > > > > ************************************************************************** > > > > > > > -- > > Y. C. > Cheng > > Department of Phyics > > > Nanjing University > > Nanjing > 210093 > > P. R. China > > Tel: > 86-25-83592907 > > Email: > yccheng.nju at gmail.com > > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > IFM, Linkoping University, Sweden > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com > > > > ____________________________________________________________________________________ > Be a better friend, newshound, and > know-it-all with Yahoo! Mobile. Try it now. > http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Y. C. Cheng Department of Phyics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080418/b616f6bd/attachment.htm From yccheng.nju at gmail.com Fri Apr 18 14:44:46 2008 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Fri, 18 Apr 2008 20:44:46 +0800 Subject: [Pw_forum] Raman Intensity In-Reply-To: <48088843.1030805@nest.sns.it> References: <48088843.1030805@nest.sns.it> Message-ID: Thank you for your reply! 2008/4/18, Paolo Giannozzi : > > ??? wrote: > > > My questions: what does A^2 mean? > > Angstrom square > > > what does pol. * mean? > > polarization: x, y, z > -- > 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 > -- Y. C. Cheng Department of Phyics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080418/59bba707/attachment.htm From lanhaiping at gmail.com Fri Apr 18 14:59:43 2008 From: lanhaiping at gmail.com (lan haiping) Date: Fri, 18 Apr 2008 14:59:43 +0200 Subject: [Pw_forum] symmetry operation not allowed In-Reply-To: <442610.77801.qm@web76105.mail.sg1.yahoo.com> References: <442610.77801.qm@web76105.mail.sg1.yahoo.com> Message-ID: what is your problem ? On Fri, Apr 18, 2008 at 2:06 PM, Lily Anh wrote: > Dear all, > > I know this is a old question and I also read the previous answer about > this. > > I test with different ecutwfc , ecutrho (until 30 times of ecutwfc) , and > K-grid. However, the problem still exists. Since the calculation expense > is always in concern, so I want to use symmetry during the calculation. > > I attach the output and input file here for reference. > > Output file: > > Current dimensions of program pwscf are: > > ntypx =10 npk =40000 lmax = 3 > > nchix = 6 ndmx = 2000 nbrx =14 nqfx = 8 > > warning: symmetry operation # 2 not allowed. fractional > translation: > > -0.4999900 -0.4999400 -0.5000000 in crystal coordinates > > warning: symmetry operation # 3 not allowed. fractional > translation: > > 0.0000100 -0.5000000 -0.2498700 in crystal coordinates > > warning: symmetry operation # 4 not allowed. fractional > translation: > > -0.5000000 0.0000600 0.2501300 in crystal coordinates > > > > Planes per process (thick) : nr3 = 90 npp = 8 ncplane =32400 > > > > Planes per process (smooth): nr3s= 32 npps= 3 ncplanes= 4096 > > > > Proc/ planes cols G planes cols G columns G > > Pool (dense grid) (smooth grid) (wavefct grid) > > 1 8 1960 109526 3 261 5323 76 838 > > 2 8 1961 109525 3 261 5333 75 837 > > 3 8 1961 109525 3 261 5325 75 837 > > 4 8 1961 109525 3 261 5321 75 837 > > 5 8 1961 109525 3 261 5321 77 837 > > 6 8 1961 109525 3 261 5321 77 837 > > 7 7 1960 109524 3 262 5338 77 837 > > 8 7 1960 109524 3 261 5339 77 837 > > 9 7 1960 109524 2 261 5337 77 837 > > 10 7 1960 109524 2 261 5337 77 837 > > 11 7 1960 109524 2 261 5335 77 837 > > 12 7 1960 109524 2 261 5325 77 837 > > 0 90 235251314295 32 3133 63955 917 10045 > > > > > > > > bravais-lattice index = 8 > > lattice parameter (a_0) = 15.6923 a.u. > > unit-cell volume = 1872.5343 (a.u.)^3 > > number of atoms/cell = 36 > > number of atomic types = 2 > > kinetic-energy cutoff = 40.0000 Ry > > charge density cutoff = 1200.0000 Ry > > convergence threshold = 1.0E-08 > > beta = 0.7000 > > number of iterations used = 8 plain mixing > > Exchange-correlation = SLA PW PBE PBE (1434) > > iswitch = 0 > > > > celldm(1)= 15.692292 celldm(2)= 1.000000 celldm(3)= 0.484586 > > 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) = ( 0.000000 1.000000 0.000000 ) > > a(3) = ( 0.000000 0.000000 0.484586 ) > > > > reciprocal axes: (cart. coord. in units 2 pi/a_0) > > b(1) = ( 1.000000 0.000000 0.000000 ) > > b(2) = ( 0.000000 1.000000 0.000000 ) > > b(3) = ( 0.000000 0.000000 2.063618 ) > > > > > > PSEUDO 1 is O (US) zval = 6.0 lmax= 2 lloc= 0 > > Version 0 0 0 of US pseudo code > > Using log mesh of 1269 points > > The pseudopotential has 4 beta functions with: > > l(1) = 0 > > l(2) = 0 > > l(3) = 1 > > l(4) = 1 > > Q(r) pseudized with 0 coefficients, rinner = 0.000 0.000 > 0.000 > > 0.000 0.000 > > > > PSEUDO 2 is H (US) zval = 1.0 lmax= 1 lloc= 0 > > Version 0 0 0 of US pseudo code > > Using log mesh of 1061 points > > The pseudopotential has 2 beta functions with: > > l(1) = 0 > > l(2) = 0 > > Q(r) pseudized with 0 coefficients, rinner = 0.000 0.000 > 0.000 > > > > > > atomic species valence mass pseudopotential > > O 6.00 15.99940 O ( 1.00) > > H 1.00 1.00790 H ( 1.00) > > > > No symmetry! > > INPTU file: > > &control > > calculation='scf', > > restart_mode='from_scratch', > > prefix='h2o' > > pseudo_dir = '/pwwork/pseudo/', > > outdir=/pwwork/tmp/tmp1/' > > tstress=.t., > > tprnfor=.t. > > / > > &system > > ibrav = 8, celldm(1) = 15.69229199303824618227,celldm(2) > =1.00,celldm(3) =.48458574181117533718,nat= 36, ntyp= 2, > > ecutwfc=40,ecutrho=1200 > > / > > &electrons > > mixing_beta = 0.7 > > conv_thr = 1.0d-8 > > / > > ATOMIC_SPECIES > > O 15.9994 O.pbe-rrkjus.UPF > > H 1.0079 H.pbe-rrkjus.UPF > > ATOMIC_POSITIONS {crystal} > > O -0.00178 0.00473 0.00365 > > O 0.00177 0.50473 0.24622 > > O 0.13861 0.25239 0.61888 > > O 0.25932 0.63953 0.89389 > > O 0.24067 0.86042 0.39389 > > O 0.36138 0.24756 0.11888 > > O 0.49822 -0.00479 0.74622 > > O 0.50177 0.49521 0.50365 > > O 0.63861 0.74756 0.13098 > > O 0.74067 0.13953 0.35598 > > O 0.75932 0.36042 0.85598 > > O 0.86138 0.75239 0.63098 > > H 0.71747 0.77486 0.30843 > > H 0.78252 0.72509 0.80843 > > H 0.77591 0.21514 0.53383 > > H 0.72409 0.28481 1.03383 > > H 0.21747 0.22509 0.44143 > > H 0.28252 0.27486 -0.05857 > > H 0.22409 0.71514 0.71603 > > H 0.27591 0.78481 0.21603 > > H 0.42227 0.15633 0.02004 > > H 0.45437 0.40953 0.36230 > > H 0.83871 0.08712 0.26341 > > H 0.54563 -0.09047 0.88757 > > H 0.58770 0.03448 0.60370 > > H 0.57773 0.65633 0.22982 > > H 0.66128 0.41283 0.76341 > > H 0.04563 0.09042 -0.13770 > > H 0.08770 -0.03453 0.14616 > > H 0.92227 0.84362 0.72982 > > H -0.08771 0.46547 0.10370 > > H -0.04563 0.59042 0.38757 > > H 0.07773 0.34362 0.52004 > > H 0.16128 0.58712 0.98645 > > H 0.41229 0.53448 0.64616 > > H 0.33871 0.91283 0.48645 > > K_POINTS { automatic } > > 2 2 4 0 0 0 > > Any reply is appreciated! > > Regards > > Lily > > > > ------------------------------ > > *Real people. Real questions. Real answers. Share what you know > *. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080418/5c31c5f2/attachment-0001.htm From giannozz at nest.sns.it Fri Apr 18 15:05:04 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 18 Apr 2008 15:05:04 +0200 Subject: [Pw_forum] Raman Intensity In-Reply-To: References: <759773.18299.qm@web65714.mail.ac4.yahoo.com> Message-ID: <48089C80.1020904@nest.sns.it> ??? wrote: > I use the dynmat.x to calculate alas.dynG note that dynmat.f90 assumes a specific scattering geometry. You need to modify dynmat.f90 if you want the results for a different scattering geometry. > Do the column "IR" and "Raman" stand for the IR intensity and Raman > intensity? for what else should they stand for???? > And what does depol stand for? depolarization ratio -- Paolo Giannozzi, Democritos and University of Udine, Italy From eyvaz_isaev at yahoo.com Fri Apr 18 15:10:38 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 18 Apr 2008 06:10:38 -0700 (PDT) Subject: [Pw_forum] symmetry operation not allowed In-Reply-To: <442610.77801.qm@web76105.mail.sg1.yahoo.com> Message-ID: <944613.31632.qm@web65715.mail.ac4.yahoo.com> Hi, You can set up nr1, nr2, and nr3 manually. Or change ecutrho gradually. Also provide your affiliation, please. Bests,` Eyvaz. --- Lily Anh wrote: > Dear all, > I know this is a old question and I also read the > previous > answer about this. > I test with different ecutwfc , ecutrho (until 30 > times of ecutwfc) , and > K-grid. However, the problem still exists. Since > the calculation expense is always in > concern, so I want to use symmetry during the > calculation. > I attach the output and input file here for > reference. > Output file: > Current > dimensions of program pwscf are: > ntypx =10 npk =40000 lmax = 3 > nchix = 6 ndmx = 2000 nbrx =14 nqfx = 8 > warning: symmetry > operation # 2 not allowed. fractional > translation: > -0.4999900 > -0.4999400 -0.5000000 in crystal > coordinates > warning: symmetry > operation # 3 not allowed. fractional > translation: > 0.0000100 > -0.5000000 -0.2498700 in crystal > coordinates > warning: symmetry > operation # 4 not allowed. fractional > translation: > -0.5000000 0.0000600 0.2501300 in crystal > coordinates > > Planes per > process (thick) : nr3 = 90 npp = 8 > ncplane =32400 > > Planes per > process (smooth): nr3s= 32 npps= 3 > ncplanes= 4096 > > Proc/ planes cols G planes cols G > columns G > Pool (dense grid) (smooth grid) > (wavefct grid) > 1 8 1960 109526 3 261 5323 76 > 838 > 2 8 1961 109525 3 261 5333 75 > 837 > 3 8 1961 109525 3 261 5325 75 > 837 > 4 8 1961 109525 3 261 5321 75 > 837 > 5 8 1961 109525 3 261 5321 77 > 837 > 6 8 1961 109525 3 261 5321 77 > 837 > 7 7 1960 109524 3 262 5338 77 > 837 > 8 7 1960 109524 3 261 5339 77 > 837 > 9 7 1960 109524 2 261 5337 77 > 837 > 10 7 1960 > 109524 2 261 5337 77 837 > 11 7 1960 109524 2 261 5335 77 > 837 > 12 7 1960 109524 2 261 5325 77 > 837 > 0 90 235251314295 32 3133 63955 917 > 10045 > > > > bravais-lattice > index = 8 > lattice parameter > (a_0) = 15.6923 a.u. > unit-cell > volume = 1872.5343 (a.u.)^3 > number of > atoms/cell = 36 > number of atomic > types = 2 > kinetic-energy > cutoff = 40.0000 Ry > charge density > cutoff = 1200.0000 Ry > convergence > threshold = 1.0E-08 > beta = 0.7000 > number of > iterations used = 8 plain mixing > Exchange-correlation = SLA PW PBE PBE > (1434) > iswitch = 0 > > celldm(1)= 15.692292 celldm(2)= 1.000000 > celldm(3)= 0.484586 > 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) = > ( 0.000000 1.000000 0.000000 ) > a(3) = > ( 0.000000 0.000000 0.484586 ) > > reciprocal axes: > (cart.. coord. in units 2 pi/a_0) > b(1) = ( 1.000000 0.000000 > 0.000000 ) > b(2) = > ( 0.000000 1.000000 0.000000 ) > b(3) = > ( 0.000000 0.000000 2.063618 ) > > > PSEUDO 1 is > O (US) zval = 6.0 lmax= 2 lloc= 0 > Version 0 0 0 of US pseudo code > Using log mesh > of 1269 points > The > pseudopotential has 4 beta functions > with: > l(1) > = 0 > l(2) > = 0 > l(3) > = 1 > l(4) > = 1 > Q(r) pseudized > with 0 coefficients, rinner = 0.000 0.000 > 0.000 > > 0.000 0.000 > > PSEUDO 2 is > H (US) zval = 1.0 lmax= 1 lloc= 0 > Version 0 0 0 of US pseudo code > Using log mesh > of 1061 points > The > pseudopotential has 2 beta functions > with: > l(1) > = 0 > l(2) > = 0 > Q(r) pseudized > with 0 coefficients, rinner = 0.000 0.000 > 0.000 > > > atomic > species valence mass pseudopotential > O 6.00 15.99940 O ( > 1.00) > H 1.00 1.00790 H ( > 1.00) > > No symmetry! > INPTU file: > &control > calculation='scf', > restart_mode='from_scratch', > prefix='h2o' > pseudo_dir = '/pwwork/pseudo/', > outdir=/pwwork/tmp/tmp1/' > tstress=.t.., > tprnfor=.t. > / > &system > ibrav = 8, > celldm(1) = 15.69229199303824618227,celldm(2) > =1.00,celldm(3) > =.48458574181117533718,nat= 36, ntyp= 2, > ecutwfc=40,ecutrho=1200 > / > &electrons > mixing_beta = 0.7 > conv_thr = 1.0d-8 > / > ATOMIC_SPECIES > O 15.9994 O.pbe-rrkjus.UPF > H 1.0079 H.pbe-rrkjus.UPF > ATOMIC_POSITIONS {crystal} > O -0.00178 0.00473 0.00365 > O 0..00177 0.50473 0.24622 > O 0.13861 0.25239 0.61888 > O 0.25932 0.63953 0.89389 > O 0.24067 0.86042 0.39389 > O 0.36138 0..24756 0.11888 > === message truncated ===> _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, IFM, Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ From yccheng.nju at gmail.com Fri Apr 18 15:18:23 2008 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Fri, 18 Apr 2008 21:18:23 +0800 Subject: [Pw_forum] Raman Intensity In-Reply-To: <48089C80.1020904@nest.sns.it> References: <759773.18299.qm@web65714.mail.ac4.yahoo.com> <48089C80.1020904@nest.sns.it> Message-ID: Thank you for your reply! Because I am not familiar with the fortran language, I am shame that it will take me some time to understand the dynmat.f90. note that dynmat.f90 assumes a specific scattering geometry. > You need to modify dynmat.f90 if you want the results for a > different scattering geometry. > > > Do the column "IR" and "Raman" stand for the IR intensity and Raman > > intensity? > > for what else should they stand for???? > > > And what does depol stand for? > > depolarization ratio > -- > 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 > -- Y. C. Cheng Department of Phyics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080418/58e50f31/attachment.htm From giannozz at nest.sns.it Fri Apr 18 15:20:01 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 18 Apr 2008 15:20:01 +0200 Subject: [Pw_forum] Raman Intensity In-Reply-To: References: <759773.18299.qm@web65714.mail.ac4.yahoo.com> <48089C80.1020904@nest.sns.it> Message-ID: <4808A001.9020703@nest.sns.it> ??? wrote: > Because I am not familiar with the fortran language, I am shame that it > will take me some time to understand the dynmat.f90. Raman scattering is much more difficult to understand than fortran -- Paolo Giannozzi, Democritos and University of Udine, Italy From yccheng.nju at gmail.com Fri Apr 18 15:25:39 2008 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Fri, 18 Apr 2008 21:25:39 +0800 Subject: [Pw_forum] Raman Intensity In-Reply-To: <4808A001.9020703@nest.sns.it> References: <759773.18299.qm@web65714.mail.ac4.yahoo.com> <48089C80.1020904@nest.sns.it> <4808A001.9020703@nest.sns.it> Message-ID: Thank you! 2008/4/18, Paolo Giannozzi : > > ??? wrote: > > > Because I am not familiar with the fortran language, I am shame that it > > will take me some time to understand the dynmat.f90. > > Raman scattering is much more difficult to understand than fortran > > -- > 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 > -- Y. C. Cheng Department of Phyics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080418/8e808e68/attachment.htm From degironc at sissa.it Fri Apr 18 16:16:40 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 18 Apr 2008 16:16:40 +0200 Subject: [Pw_forum] symmetry operation not allowed In-Reply-To: <442610.77801.qm@web76105.mail.sg1.yahoo.com> References: <442610.77801.qm@web76105.mail.sg1.yahoo.com> Message-ID: <4808AD48.1010503@sissa.it> Dear Lily Anh, the fractional translations that are discarded by the code have all coordinates very close to multiples of 0.25, 0.5 or 0.0 but not exactly 0.25, 0.5, 0.0. I think it will be very difficult to get rid of these warning messages by playing with nr1,nr2,nr3 only... You should instead see if by rigidly translating your configuration (so that, for instance, one of the atoms is exactly at the origin) you can obtain exactly 0.25 0.5 and 0.0 fractional translations. In that case it will be sufficient to take some nr1, nr2,nr3 that are multiple of 4 in order to eliminate the warnings. Hope this helps, stefano Lily Anh wrote: > > Dear all, > > I know this is a old question and I also read the previous answer > about this. > > I test with different ecutwfc , ecutrho (until 30 times of ecutwfc) , > and K-grid. However, the problem still exists. Since the calculation > expense is always in concern, so I want to use symmetry during the > calculation. > > I attach the output and input file here for reference. > > Output file: > > Current dimensions of program pwscf are: > > ntypx =10 npk =40000 lmax = 3 > > nchix = 6 ndmx = 2000 nbrx =14 nqfx = 8 > > warning: symmetry operation # 2 not allowed. fractional > translation: > > -0.4999900 -0.4999400 -0.5000000 in crystal coordinates > > warning: symmetry operation # 3 not allowed. fractional > translation: > > 0.0000100 -0.5000000 -0.2498700 in crystal coordinates > > warning: symmetry operation # 4 not allowed. fractional > translation: > > -0.5000000 0.0000600 0.2501300 in crystal coordinates > From lily_physics at yahoo.com.sg Fri Apr 18 16:14:06 2008 From: lily_physics at yahoo.com.sg (Lily Anh) Date: Fri, 18 Apr 2008 22:14:06 +0800 (SGT) Subject: [Pw_forum] symmetry operation not allowed Message-ID: <201158.79538.qm@web76114.mail.sg1.yahoo.com> Thanks for your suggestion. I have changed ecutwfc (from 20-50Ry every 5 Ry), ecutrho (200-1200 every 50), k grid. But nothing works. How to change nr1 nr2 nr3, larger or smaller? The structure should have 4 symmetry operations while the code can not find any symmetry. I want to reduce the calculation time. That's why I want to remove the message like warning: symmetry operation # 2 not allowed. fractional translation: -0.4999900 -0.4999400 -0.5000000 in crystal coordinates warning: symmetry operation # 3 not allowed. fractional translation: 0.0000100 -0.5000000 -0.2498700 in crystal coordinates warning: symmetry operation # 4 not allowed. fractional translation: -0.5000000 0.0000600 0.2501300 in crystal coordinates Planes per process (thick) : nr3 = 45 npp = 4 ncplane = 8100 my input file is &control calculation='scf', restart_mode='from_scratch', prefix='h2o' pseudo_dir = '/work/pwwork/pseudo/', outdir='/work/pwwork/tmp/tmp1/' tstress=.t., tprnfor=.t. / &system ibrav = 8, celldm(1) = 15.69229199303824618227,celldm(2) =1.00,celldm(3) =.48458574181117533718,nat= 36, ntyp= 2, ecutwfc=40,ecutrho=1200 / &electrons mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES O 15.9994 O.pbe-rrkjus..UPF H 1.0079 H.pbe-rrkjus.UPF ATOMIC_POSITIONS {crystal} O -0.00178 0.00473 0.00365 O 0.00177 0.50473 0.24622 O 0.13861 0.25239 0.61888 O 0.25932 0.63953 0.89389 O 0.24067 0.86042 0.39389 O 0.36138 0.24756 0.11888 O 0.49822 -0.00479 0.74622 O 0.50177 0.49521 0.50365 O 0.63861 0.74756 0.13098 O 0.74067 0.13953 0.35598 O 0.75932 0.36042 0.85598 O 0.86138 0.75239 0.63098 H 0.71747 0.77486 0.30843 H 0.78252 0.72509 0.80843 H 0.77591 0.21514 0.53383 H 0.72409 0.28481 1.03383 H 0.21747 0.22509 0.44143 H 0.28252 0..27486 -0.05857 H 0.22409 0.71514 0.71603 H 0.27591 0.78481 0.21603 H 0.42227 0.15633 0.02004 H 0.45437 0.40953 0.36230 H 0.83871 0.08712 0.26341 H 0.54563 -0.09047 0.88757 H 0.58770 0.03448 0.60370 H 0.57773 0.65633 0.22982 H 0.66128 0.41283 0.76341 H 0.04563 0.09042 -0.13770 H 0.08770 -0.03453 0.14616 H 0.92227 0.84362 0.72982 H -0.08771 0.46547 0.10370 H -0.04563 0.59042 0.38757 H 0.07773 0.34362 0.52004 H 0.16128 0.58712 0.98645 H 0.41229 0.53448 0.64616 H 0.33871 0.91283 0.48645 K_POINTS { automatic } 2 2 4 0 0 0 __________________________________________________________________ Yahoo! Singapore Answers Real people. Real questions. Real answers. Share what you know at http://answers.yahoo.com.sg -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080418/6a2d8f87/attachment-0001.htm From degironc at sissa.it Fri Apr 18 16:30:11 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 18 Apr 2008 16:30:11 +0200 Subject: [Pw_forum] symmetry operation not allowed In-Reply-To: <201158.79538.qm@web76114.mail.sg1.yahoo.com> References: <201158.79538.qm@web76114.mail.sg1.yahoo.com> Message-ID: <4808B073.3040400@sissa.it> Lily Anh wrote: > Thanks for your suggestion. > I have changed ecutwfc (from 20-50Ry every 5 Ry), ecutrho (200-1200 > every 50), k grid. But nothing works. How to change nr1 nr2 nr3, > larger or smaller? nr1, nr2 and nr3 are input parameters in the &control namelist that usually take a default value on the basis of ecutrho but can be specified directly when needed (as in this case) . > The structure should have 4 symmetry operations while the code can not > find any symmetry. I want to reduce the calculation time. the code finds correctly all 4 symmetry operations but discards them (except the trivial identity) because of the incompatibility of the required fractional translation with the FFT grid. By choosing a different origin for your system it could be possible to make the fractional translations simple fractions of the fundamental lattice vectors. Hope it helps, stefano From giannozz at nest.sns.it Fri Apr 18 16:36:24 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 18 Apr 2008 16:36:24 +0200 Subject: [Pw_forum] symmetry operation not allowed In-Reply-To: <201158.79538.qm@web76114.mail.sg1.yahoo.com> References: <201158.79538.qm@web76114.mail.sg1.yahoo.com> Message-ID: <4808B1E8.30707@nest.sns.it> Lily Anh wrote: > I have changed ecutwfc (from 20-50Ry every 5 Ry), ecutrho (200-1200 > every 50), k grid. But nothing works. of course nothing works: your system does not have the symmetry you pretend it has. The code follows some rather strict criteria to decide whether a symmetry operation is present or not. This is explained in detail in the user guide, and has been explained in this mailing list no less than 36000 times Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From akohlmey at cmm.chem.upenn.edu Fri Apr 18 16:14:57 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 18 Apr 2008 10:14:57 -0400 (EDT) Subject: [Pw_forum] symmetry operation not allowed In-Reply-To: <201158.79538.qm@web76114.mail.sg1.yahoo.com> References: <201158.79538.qm@web76114.mail.sg1.yahoo.com> Message-ID: On Fri, 18 Apr 2008, Lily Anh wrote: LA> Thanks for your suggestion. LA> I have changed ecutwfc (from 20-50Ry every 5 Ry), ecutrho (200-1200 LA> every 50), k grid. But nothing works. How to change nr1 nr2 nr3, LA> larger or smaller? lily, as stefano wrote, you are trying to solve the wrong problem! your input coordinates are only near symmetric. symmetrize them and _then_ adjust the grid, if you still see warnings. for that you have to keep in mind that the values chosen by the program are always the smallest possible (i.e. supported by the fast fourier transform library), so you have to increase them (at additional computational cost!) to make them match the symmetry of your system. cheers, axel. -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From kazempoor2000 at yahoo.com Fri Apr 18 16:41:18 2008 From: kazempoor2000 at yahoo.com (ali kazempoor) Date: Fri, 18 Apr 2008 07:41:18 -0700 (PDT) Subject: [Pw_forum] warning Message-ID: <554685.54721.qm@web33106.mail.mud.yahoo.com> Dear all during band structure calculation i have these warnings: WARNING: 1 eigenvalues not converged WARNING: 2 eigenvalues not converged WARNING: 2 eigenvalues not converged what is the reason? thanks ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ From paulatto at sissa.it Fri Apr 18 17:20:07 2008 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 18 Apr 2008 17:20:07 +0200 (CEST) Subject: [Pw_forum] warning In-Reply-To: <554685.54721.qm@web33106.mail.mud.yahoo.com> References: <554685.54721.qm@web33106.mail.mud.yahoo.com> Message-ID: <6356.147.122.5.183.1208532007.squirrel@webmail.sissa.it> On Ven, Aprile 18, 2008 16:41, ali kazempoor wrote: > what is the reason? Dear Ali, please read this entry in the wiki: http://quantum-espresso.org/wiki/index.php/Troubleshooting_%28PWscf%29#.27warning_:_N_eigenvectors_not_converged_....27 bye -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) +39 040 3787 511 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From cristian.degliesposti at unibo.it Fri Apr 18 18:11:05 2008 From: cristian.degliesposti at unibo.it (Cristian Degli Esposti Boschi) Date: Fri, 18 Apr 2008 18:11:05 +0200 Subject: [Pw_forum] Choice of pseudpotential (d orbitals for Fe) Message-ID: Dear users and developers, I'm using Quantum Espresso 3.2 and would like to reproduce some of the DFT results of C. Rovira et al., J. Phys. Chem. A 101, 8914 (1997) regarding the equilibrium geometries of Iron-Porphyrin (FeP) complexes. However, I find some significant discrepancies: in particular in our equilibrium structure of FeP(Im)(CO), where Im denotes the imidazole group, the FeP plane gets considerably more "domed" with respect to what reported in the above-mentioned reference. Of course there could be several reasons for this, but in particular I noted that they use XC functional of Becke (exchange) and Perdew (corr) type. They also mention a comparison with BLYP-type functionals. However, since orbital energy structure of the ground state involves d orbitals of Fe, initially I chose the pseudopotentials (in the pwscf site) that include the d orbitals contribution, namely Fe.pbe-nd-rrkjus.UPF or Fe.pz-nd-rrkjus.UPF For the sake of uniformness I used PBE- or PZ-type pseudopotentials also for C, O and N. Now, I wonder if the problem of excessive doming could be due to the use of wrong pseudopotential ... I would like to try with BLYP's but the one for Fe does not seem to include explicitly d orbitals. Are there other sources of pseudopotentials? Thanks in advance for any help. Cristian ___________________________________________________ Cristian Degli Esposti Boschi CNR, CNISM, Unita' di Ricerca di Bologna, c/o Dipartimento di Fisica, Universita' di Bologna viale Berti-Pichat, 6/2, 40127, Bologna, Italia tel. ++39 051 2095114 fax ++39 051 2095113 e-mail: cristian.degliesposti -AT- unibo.it web: http://www.df.unibo.it/fismat/theory ___________________________________________________ From ylli at theory.issp.ac.cn Sat Apr 19 06:09:08 2008 From: ylli at theory.issp.ac.cn (Li yan-ling) Date: Sat, 19 Apr 2008 12:09:08 +0800 (CST) Subject: [Pw_forum] cannot remap grid on k-point list Message-ID: <53745.137.189.4.2.1208578148.squirrel@210.73.16.4> Dear all users, When I perform the el-ph interaction calculation, I meet a error as follows in ph.out file. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from lint : error # 91 cannot remap grid on k-point list %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... [3] MPI Abort by user Aborting program ! [3] Aborting program! forrtl: error (76): IOT trap signal xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx I search the mailing. But I can't find the methods to solve this error. My input file as follows. %%%The fit.in is &control calculation='scf' restart_mode='from_scratch' pseudo_dir = '../', outdir='./tmp/' prefix='mgb4' / &system ibrav= 8, a = 3.562310106, b = 8.047763193, c = 3.29005963,nat= 20, ntyp= 2, ecutwfc =28.0, ecutrho =300.0, occupations='smearing',smearing='mp', degauss=0.03,la2F=.true., / &electrons conv_thr = 1.0d-12 mixing_beta = 0.7 / ATOMIC_SPECIES Mg 24.305 Mg.UPF B 10.811 B.UPF ATOMIC_POSITIONS angstrom Mg 0.00000000 0.00000000 0.08164318 Mg 0.00000000 4.02388160 1.72667300 Mg 1.78115505 4.02388160 0.08164318 Mg 1.78115505 0.00000000 1.72667300 B 2.12172031 6.56075530 0.08171232 B 1.28305471 6.28121132 1.72679415 B 2.12172031 2.53687371 1.72674204 B 1.28305471 2.25732972 0.08176433 B 1.44058974 1.48700801 0.08171232 B 2.27925540 1.76655176 1.72679415 B 1.44058974 5.51088949 1.72674204 B 2.27925540 5.79043347 0.08176433 B 0.34056526 5.51088949 0.08171232 B 3.06420976 5.79043347 1.72679415 B 0.34056526 1.48700801 1.72674204 B 3.06420976 1.76655176 0.08176433 B 3.22174484 2.53687371 0.08171232 B 0.49810035 2.25732972 1.72679415 B 0.49810035 6.28121132 0.08176433 K_POINTS {automatic} 16 8 16 0 0 0 %%%% %%The scf.in is ...... ...... K_POINTS {automatic} 8 4 8 0 0 0 %%%%%%%% The ph.in is Electron-phonon coefficients &inputph tr2_ph=1.0d-13, prefix='mgb4', fildvscf='geh4dv', amass(1)=24.305,amass(2)=10.811, outdir='./tmp/', fildyn='mgb4.dyn', elph=.true., trans=.true., ldisp=.true., nq1=4,nq2=2,nq3=4 / %%%%%%%%%%%%%%%%%%%%%%%% All suggestions are welcome. Thanks a lot. Yanling Li, Institute of solid states physics,CAS, China From kazempoor2000 at yahoo.com Sat Apr 19 07:13:49 2008 From: kazempoor2000 at yahoo.com (ali kazempoor) Date: Fri, 18 Apr 2008 22:13:49 -0700 (PDT) Subject: [Pw_forum] pp Message-ID: <114003.43510.qm@web33106.mail.mud.yahoo.com> Dear All I want to plot local density of state at fermi level,but durin the running pp.x ,this error take place: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from davcio : error # 10 i/o error in davcio and the input file is as below: &inputpp prefix = ' MnAs-1-3' outdir = '/scratch/akbarzadeh/' filplot = 'MnAs1-1fermidos' plot_num=3 spin_component = 0 , / &plot nfile = 1 filepp(1) = 'MnAs1-3fermidos' weight(1) = 1.0 iflag = 3 output_format =5 fileout = 'MnAs1-3.fermidos.dat' / can anyone help me? thanks ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ From paulatto at sissa.it Sat Apr 19 15:18:16 2008 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sat, 19 Apr 2008 15:18:16 +0200 (CEST) Subject: [Pw_forum] pp In-Reply-To: <114003.43510.qm@web33106.mail.mud.yahoo.com> References: <114003.43510.qm@web33106.mail.mud.yahoo.com> Message-ID: <29961.80.183.42.90.1208611096.squirrel@webmail.sissa.it> On Sab, Aprile 19, 2008 07:13, ali kazempoor wrote: > filplot = 'MnAs1-1fermidos' > filepp(1) = 'MnAs1-3fermidos' Dear ali, I think you miss typed the filename in one of the rows, as they are not equal. It is not necessary an error, but it's very unlikely for you to do it on purpose. Furthermore, the default value for filepp(1) is filplot, so you need not specify it 90% of the times. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) +39 040 3787 511 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From iphyboy at hotmail.com Sun Apr 20 17:55:49 2008 From: iphyboy at hotmail.com (=?gb2312?B?w/fOxMPA?=) Date: Sun, 20 Apr 2008 23:55:49 +0800 Subject: [Pw_forum] el_ph_mat value in elphsum ? Message-ID: Dear users; I want to modfiy the phonon code in /PH to obtain transport a2F function in PWSCF-3.2.3, now I have already known that I should mainly modify the code in file elphsum subroutine in elphon.f90, transport a2F function is firmly realted to the electron-phonon interaction matrix elements. I carefully read the Subroutine elphsum, but I have a very confusing question: in elphsum, how el_ph_mat is calculated? although another subroutine elphel can calculate el_ph_mat, the elphsum does not call elphel subroutine at all. So , how the values of el_ph_mat are coming into being ? Any suggestion is appreciated. Best. Wenmei _________________________________________________________________ ?????????????MSN????TA????? http://im.live.cn/emoticons/?ID=18 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080420/84ea05c9/attachment.htm From subhra at iitg.ernet.in Mon Apr 21 04:01:44 2008 From: subhra at iitg.ernet.in (Subhradip Ghosh) Date: Mon, 21 Apr 2008 07:31:44 +0530 (IST) Subject: [Pw_forum] warning in q2r.x Message-ID: <53196.202.141.81.5.1208743304.squirrel@webmail.iitg.ernet.in> I am doing phonon calculations on a L10 structure. The output of q2r.x produces the following warning: "fft-check warning: sum of imaginary terms = .2454409E-06" How serious is this warning and what could be the consequences? Also, what could be the possible reasons? Regards, Subhradip ************************************************************************ Dr. Subhradip Ghosh Assistant Professor Department of Physics Indian Institute of Technology Guwahati,Assam-781039 India E-mail:subhra at iitg.ernet.in Phone: +91 361 2582717(O) +91 361 2584717(R) Fax: +91 361 2582749 (Physics) +91 361 2690762 (General) ************************************************************************ From shrek_826 at yahoo.com.cn Mon Apr 21 14:49:24 2008 From: shrek_826 at yahoo.com.cn (Fan Yang) Date: Mon, 21 Apr 2008 20:49:24 +0800 (CST) Subject: [Pw_forum] about lattice basis vectors? Message-ID: <642258.38683.qm@web15309.mail.cnb.yahoo.com> Dear everyone, ???????? I?have a simple question about the setting of PWGUI,?namely, does the lattice basis vectors in "CELL_PARAMETERS" refer to real lattice or reciprocal lattice?? and what does the lattice type mean, since it has only two?choices-cubic and hexagpnal? ???????? Thanks in advance. ? ====================================== Fan Yang PH.D Candidate?in Electrochemistry????????????????????? College of Chemistry and Molecular Science??????????? Wuhan University,430072,Hubei Province,China? E-mail:shrek_826 at yahoo.com.cn ====================================== ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080421/09010cfd/attachment.htm From degironc at sissa.it Mon Apr 21 15:05:20 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 21 Apr 2008 15:05:20 +0200 Subject: [Pw_forum] about lattice basis vectors? In-Reply-To: <642258.38683.qm@web15309.mail.cnb.yahoo.com> References: <642258.38683.qm@web15309.mail.cnb.yahoo.com> Message-ID: <480C9110.5070303@sissa.it> Fan Yang wrote: > Dear everyone, > I have a simple question about the setting of PWGUI, namely, > does the lattice basis vectors in "CELL_PARAMETERS" refer to real > lattice or reciprocal lattice? and what does the lattice type mean, > since it has only two choices-cubic and hexagpnal? > Thanks in advance. 1) The real lattice. 2) cubic/hexagonal refer to whether the symmetry group of the lattice has to be searched among the subgroups of cubic or simple hexagonal groups. stefano > > ====================================== > Fan Yang > PH.D Candidate in Electrochemistry > College of Chemistry and Molecular Science > Wuhan University,/430072/,Hubei Province,China > /E-mail:shrek_826 at yahoo.com.cn/ > ====================================== > > ------------------------------------------------------------------------ > Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try > it now. > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at nest.sns.it Mon Apr 21 15:39:21 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 21 Apr 2008 15:39:21 +0200 Subject: [Pw_forum] Choice of pseudpotential (d orbitals for Fe) In-Reply-To: References: Message-ID: <480C9909.4020708@nest.sns.it> Cristian Degli Esposti Boschi wrote: > initially I chose the pseudopotentials (in the pwscf site) that > include the d orbitals contribution, namely > > Fe.pbe-nd-rrkjus.UPF or > Fe.pz-nd-rrkjus.UPF The notation is misleading in this case: the d states are in no way "semicore" states for Fe, they are valence states, like them or not. Note that LDA results ("pz") are unlikely to get a warm reception in the chemical community: don't spend too much time on it. > Now, I wonder if the problem of excessive doming could be due > to the use of wrong pseudopotential ... did you make any tests on small molecules? Sometimes 3d transition metals require 3s and 3p "semicore" states into the valence for good results in difficult cases like the one you are dealing with. Those pseudopotentials are not "wrong" for sure, but they have been tested in solid-state systems like crystalline Fe, not in (notoriously nasty) organometallic systems. You may give a try to Fe.pbe-sp-van.UPF, that has semicore 3s and 3p (in addition to 3d, of course) in valence. Note that more electrons == more cpu time. > I would like to try with BLYP's but the one for Fe > does not seem to include explicitly d orbitals. Are there > other sources of pseudopotentials? it depends on your definition of "sources of pseudopotentials". If it includes pseudopotential generation codes, there is plenty of them, not necessarily easy to use. The pseudopotentials download page and the wiki section on pseudpotentials contains a fair amount of information. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Mon Apr 21 15:57:26 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 21 Apr 2008 15:57:26 +0200 Subject: [Pw_forum] warning in q2r.x In-Reply-To: <53196.202.141.81.5.1208743304.squirrel@webmail.iitg.ernet.in> References: <53196.202.141.81.5.1208743304.squirrel@webmail.iitg.ernet.in> Message-ID: <480C9D46.8080506@nest.sns.it> Subhradip Ghosh wrote: > "fft-check warning: sum of imaginary terms = .2454409E-06" > > How serious is this warning and what could be the consequences? since the sum of imaginary terms is so small, I wouldn't mind too much > Also, what could be the possible reasons? numerical noise in the dynamical matrices, which could come from inperfect convergence of the phonon calculation Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Mon Apr 21 16:06:30 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 21 Apr 2008 16:06:30 +0200 Subject: [Pw_forum] el_ph_mat value in elphsum ? In-Reply-To: References: Message-ID: <480C9F66.5000301@nest.sns.it> ??? wrote: > in elphsum, how el_ph_mat is calculated? although another subroutine > elphel can calculate el_ph_mat, the elphsum does not call elphel > subroutine at all. it is called by other subroutines: $ grep -i 'call elphel' espresso/PH/*f90 espresso/PH/elphon.f90: CALL elphel (npert (irr), imode0, dvscfins) espresso/PH/solve_linter.f90: if (elph) call elphel (npe, imode0, dvscfins) Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From shrek_826 at yahoo.com.cn Tue Apr 22 04:30:20 2008 From: shrek_826 at yahoo.com.cn (Fan Yang) Date: Tue, 22 Apr 2008 10:30:20 +0800 (CST) Subject: [Pw_forum] about lattice basis vectors? Message-ID: <937427.50901.qm@web15308.mail.cnb.yahoo.com> Thanks for stefano's reply, and I'm also confused the?"lattice specification" in PWGUI, which could be descripted?either by celldm() or by A,B,C,cosAB,cosAC,cosBC, but?not both.? If the former method is selected, there?has no problem. However, if I use the latter,?the structure?could not be displayed properly in XCrySDen. It seems that the angles between vector A and B, A and C, B and C?are defined as alpha, beta, and gamma respectively, which?is different?from?the widely-used definition (the angles between vector?B and C, A and C,?A and?B?are defined as alpha, beta, and gamma respectively). There?may be?a small?bug about specifying lattice, either in PWscf or in XCrySDen. ? ====================================== Fan Yang PH.D Candidate?in Electrochemistry????????????????????? College of Chemistry and Molecular Science??????????? Wuhan University,430072,Hubei Province,China? E-mail:shrek_826 at yahoo.com.cn ====================================== ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080422/5bf2c7a5/attachment.htm From shrek_826 at yahoo.com.cn Tue Apr 22 04:30:22 2008 From: shrek_826 at yahoo.com.cn (Fan Yang) Date: Tue, 22 Apr 2008 10:30:22 +0800 (CST) Subject: [Pw_forum] about lattice basis vectors? Message-ID: <826465.44921.qm@web15311.mail.cnb.yahoo.com> Thanks for stefano's reply, and I'm also confused the?"lattice specification" in PWGUI, which could be descripted?either by celldm() or by A,B,C,cosAB,cosAC,cosBC, but?not both.? If the former method is selected, there?has no problem. However, if I use the latter,?the structure?could not be displayed properly in XCrySDen. It seems that the angles between vector A and B, A and C, B and C?are defined as alpha, beta, and gamma respectively, which?is different?from?the widely-used definition (the angles between vector?B and C, A and C,?A and?B?are defined as alpha, beta, and gamma respectively). There?may be?a small?bug about specifying lattice, either in PWscf or in XCrySDen. ? ====================================== Fan Yang PH.D Candidate?in Electrochemistry????????????????????? College of Chemistry and Molecular Science??????????? Wuhan University,430072,Hubei Province,China? E-mail:shrek_826 at yahoo.com.cn ====================================== ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080422/a09babe2/attachment.htm From tone.kokalj at ijs.si Tue Apr 22 09:08:28 2008 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 22 Apr 2008 09:08:28 +0200 Subject: [Pw_forum] about lattice basis vectors? In-Reply-To: <937427.50901.qm@web15308.mail.cnb.yahoo.com> References: <937427.50901.qm@web15308.mail.cnb.yahoo.com> Message-ID: <1208848108.18970.5.camel@walk.ijs.si> On Tue, 2008-04-22 at 10:30 +0800, Fan Yang wrote: > > Thanks for stefano's reply, and I'm also confused the "lattice > specification" in PWGUI, which could be descripted either by celldm() > or by A,B,C,cosAB,cosAC,cosBC, but not both. Which is ok. It's like walking or driving a car: can't do both at the same time. > If the former method is selected, there has no problem. However, if I > use the latter, the structure could not be displayed properly in > XCrySDen. It seems that the angles between vector A and B, A and C, B > and C are defined as alpha, beta, and gamma respectively, which is > different from the widely-used definition (the angles between vector B > and C, A and C, A and B are defined as alpha, beta, and gamma > respectively). There may be a small bug about specifying lattice, > either in PWscf or in XCrySDen. You are right. Thanks! There was a typo in xcrysden's pw.x-input to xsf filter, i.e.: celldm(1) = a / bohr celldm(2) = b / a celldm(3) = c / a celldm(4) = cosab celldm(5) = cosac celldm(6) = cosbc Of course it should be: celldm(1) = a / bohr celldm(2) = b / a celldm(3) = c / a celldm(4) = cosbc celldm(5) = cosac celldm(6) = cosab You may use the celldm() for the time being to display the structure. Regards, Tone -- Tone Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) From sagarambavale at yahoo.co.in Tue Apr 22 11:09:17 2008 From: sagarambavale at yahoo.co.in (ambavale sagar) Date: Tue, 22 Apr 2008 14:39:17 +0530 (IST) Subject: [Pw_forum] wrong nrztot Message-ID: <641625.13560.qm@web94606.mail.in2.yahoo.com> i am running complex band calculation for al bulk in 100 direction (for 001 direction it is given in example 12) using espresso4.0cvs2 . But it gives error as "wrong nrztot" the output is: from in init_cond : error # 1626817 wrong nrztot the input file for band calculation is &inputcond outdir='/db/sagar/tmp/' prefixl='al_bulk' band_file ='bands.albulk' ikind=0 energy0=10.d0 denergy=-0.4d0 ewind=1.d0 epsproj=1.d-3 delgep = 1.d-12 cutplot = 3.d0 / 1 0.0 0.0 1.0 60 Bring your gang together. Do your thing. Find your favourite Yahoo! group at http://in.promos.yahoo.com/groups/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080422/963f13e6/attachment.htm From sagarambavale at yahoo.co.in Tue Apr 22 11:24:21 2008 From: sagarambavale at yahoo.co.in (ambavale sagar) Date: Tue, 22 Apr 2008 14:54:21 +0530 (IST) Subject: [Pw_forum] wrong nrztot Message-ID: <276093.49340.qm@web94613.mail.in2.yahoo.com> sorry, i forgot to attach scf file and my signature. so resending the entire mail. i am using espresso 4.0cvs2 for calculating complex band structure of al bulk in 100 direction( for 001 it is given in example 12). this gives me following errror: from in init_cond : error # 1626817 wrong nrztot %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... the input file for complex band is : &inputcond outdir='/db/sagar/tmp/' prefixl='al_bulk' band_file ='bands.albulk' ikind=0 energy0=10.d0 denergy=-0.4d0 ewind=1.d0 epsproj=1.d-3 delgep = 1.d-12 cutplot = 3.d0 / 1 0.0 0.0 1.0 60 while the file for scf calculation is: &control calculation='scf' restart_mode='from_scratch', pseudo_dir = '/db/espresso4.0cvs2/pseudo/', outdir='/db/sagar/tmp/', prefix='al_bulk' tprnfor = .true. tstress = .true. / &system ibrav= 2, celldm(1) =7.50, nat= 1, ntyp= 1, ecutwfc =15.0, occupations='smearing', smearing='marzari-vanderbilt', degauss=0.05 / &electrons diagonalization='david' mixing_beta = 0.7 / ATOMIC_SPECIES Al 26.98 Al.vbc.UPF ATOMIC_POSITIONS Al 0.00 0.00 0.00 K_POINTS (automatic) 2 2 2 1 1 1 Sagar Ambavale PhD student The M.S.University of Baroda Inida From Chandigarh to Chennai - find friends all over India. Go to http://in.promos.yahoo.com/groups/citygroups/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080422/63b0ce9f/attachment.htm From s305igun at mail.chem.itb.ac.id Tue Apr 22 12:12:27 2008 From: s305igun at mail.chem.itb.ac.id (s305igun at mail.chem.itb.ac.id) Date: Tue, 22 Apr 2008 17:12:27 +0700 (WIT) Subject: [Pw_forum] cp.x for graphite In-Reply-To: <276093.49340.qm@web94613.mail.in2.yahoo.com> References: <276093.49340.qm@web94613.mail.in2.yahoo.com> Message-ID: <49755.167.205.72.169.1208859147.squirrel@mail.chem.itb.ac.id> Dear PW user, Thanks for all discussions, but I have problem when I tried some cp.x calculation for graphite. This is output comment: * Physical Quantities at step: 55 cg_sub: missed minimum, case 1, iteration 1 cg_sub: missed minimum, case 1, iteration 2 cg_sub: missed minimum, case 1, iteration 3 cg_sub: missed minimum, case 1, iteration 4 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from dspev_drv : error # 7 diagonalization failed %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... So I need your help, how I can solved this case Thanks very much Best Regards Rahmat Gunawan Lab. of Theoretical and Computational Chemistry Faculty of Mathematics and natural Sciences Institut Teknologi Bandung West Java From smogunov at sissa.it Tue Apr 22 10:51:46 2008 From: smogunov at sissa.it (Alexander) Date: Tue, 22 Apr 2008 09:51:46 +0100 Subject: [Pw_forum] wrong nrztot In-Reply-To: <276093.49340.qm@web94613.mail.in2.yahoo.com> References: <276093.49340.qm@web94613.mail.in2.yahoo.com> Message-ID: <200804221051.46901.smogunov@sissa.it> Dear Sagar. This is because you should use the tetragonal unit cell with two atoms per cell like in the example 12. Regards, Alexander On Tuesday 22 April 2008 11:24, ambavale sagar wrote: > sorry, i forgot to attach scf file and my signature. so resending the > entire mail. i am using espresso 4.0cvs2 for calculating complex band > structure of al bulk in 100 direction( for 001 it is given in example 12). > this gives me following errror: > > from in init_cond : error # 1626817 > wrong nrztot > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >%%% > > stopping ... > > the input file for complex band is : > > &inputcond > outdir='/db/sagar/tmp/' > prefixl='al_bulk' > band_file ='bands.albulk' > ikind=0 > energy0=10.d0 > denergy=-0.4d0 > ewind=1.d0 > epsproj=1.d-3 > delgep = 1.d-12 > cutplot = 3.d0 > / > 1 > 0.0 0.0 1.0 > 60 > > while the file for scf calculation is: > > &control > calculation='scf' > restart_mode='from_scratch', > pseudo_dir = '/db/espresso4.0cvs2/pseudo/', > outdir='/db/sagar/tmp/', > prefix='al_bulk' > tprnfor = .true. > tstress = .true. > / > &system > ibrav= 2, celldm(1) =7.50, nat= 1, ntyp= 1, ecutwfc =15.0, > occupations='smearing', smearing='marzari-vanderbilt', degauss=0.05 > / > &electrons > diagonalization='david' > mixing_beta = 0.7 > / > ATOMIC_SPECIES > Al 26.98 Al.vbc.UPF > ATOMIC_POSITIONS > Al 0.00 0.00 0.00 > K_POINTS (automatic) > 2 2 2 1 1 1 > > > Sagar Ambavale > PhD student > The M.S.University of Baroda > Inida > > > > From Chandigarh to Chennai - find friends all over India. Go to > http://in.promos.yahoo.com/groups/citygroups/ From vormar at gmail.com Tue Apr 22 13:13:31 2008 From: vormar at gmail.com (Marci) Date: Tue, 22 Apr 2008 13:13:31 +0200 Subject: [Pw_forum] carbon pseudopotential Message-ID: <34ad5960804220413s69eaeb50u9ca3413cc3b65c3f@mail.gmail.com> Dear all, I'm searching for a norm-conserving pbe type pseudo for C. Can someone send me one? I'd really appreciate it. Anyway, is there a way to convert Siesta pseudo to UPF format? I've checked the forum archive but didn't get the answer. Thanks a lot, Marton Voros -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080422/a60f026b/attachment.htm From giannozz at nest.sns.it Tue Apr 22 13:27:46 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 22 Apr 2008 13:27:46 +0200 Subject: [Pw_forum] carbon pseudopotential In-Reply-To: <34ad5960804220413s69eaeb50u9ca3413cc3b65c3f@mail.gmail.com> References: <34ad5960804220413s69eaeb50u9ca3413cc3b65c3f@mail.gmail.com> Message-ID: <480DCBB2.4000305@nest.sns.it> Marci wrote: > I'm searching for a norm-conserving pbe type pseudo for C. I have this one, of unknown origin, sitting on my disk since several years. No warranty. > is there a way to convert Siesta pseudo to UPF format? of course there is, but it has to be implemented. There is a template in upftools/any2upf.f90 Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Cpbe.mt Url: http://www.democritos.it/pipermail/pw_forum/attachments/20080422/075b37a3/attachment-0001.txt From sabatini at sissa.it Tue Apr 22 15:18:34 2008 From: sabatini at sissa.it (Riccardo Sabatini) Date: Tue, 22 Apr 2008 15:18:34 +0200 Subject: [Pw_forum] OpenMPI on mac Message-ID: <20080422151834.9g2e9ns1ogscccs4@webmail.sissa.it> Hi everyone, i'm starting in these days to setup a little cluster (well, just two intel mac dual core, osx 10.5.2) to learn how parallel processing works. I'm working with the espresso version 4.0 and i have Intel Fortran compiler (v10) and gcc from the developers tools (xcode 2.5, gcc 4.01) on both the machines. I downloaded and compiled OpenMPI and i'm pretty sure it works fine on both computer (i tried with a very simple program from the openmpi website). Now i tried to compile QE with all the wrappers (mpif90, mpicc, mpicxx, mpif77) in the make.sys, at least that's what the openmpi suggests to do in their FAQ. The compilation runs perfectly but when i try to run a simple simulation the programs fails with this error message *** An error occurred in MPI_Comm_f2c *** before MPI was initialized *** MPI_ERRORS_ARE_FATAL (goodbye) [rikis-macbook.local:56606] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed! The command i use is mpirun -np 2 $PWROOT/bin/pw.x < si.scf.in and i run it on just one mac (my laptop). To be precise i can see two times the error, as if both the processes break for the same problem. I understood the problem is the fortran-c handler but i really have no idea how to fix this. I haven't worked yet on the real cluster but i think if it's not working with the dual core alone no hope with the rest.... Waiting for your news, thanks a lot for the help. Kind regards, Riccardo ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From yrehem at mac.com Tue Apr 22 18:48:57 2008 From: yrehem at mac.com (Yaser Rehem) Date: Tue, 22 Apr 2008 09:48:57 -0700 Subject: [Pw_forum] OpenMPI on mac In-Reply-To: <20080422151834.9g2e9ns1ogscccs4@webmail.sissa.it> References: <20080422151834.9g2e9ns1ogscccs4@webmail.sissa.it> Message-ID: <2ECF143F-B8BD-4D10-8CB9-169DB7DB78DE@mac.com> Ricardo- I don't have experience with your configuration, however, I can tell you that openmpi 1.2.4 installed via macports worked fine when I compiled 4.0 with g95 on my Mac. If all else fails you can try that configuration. Cheers, -Yaser Rehem Rehem Research & Consulting On Apr 22, 2008, at 6:18 AM, Riccardo Sabatini wrote: > Hi everyone, > > i'm starting in these days to setup a little cluster (well, just > two intel mac dual > core, osx 10.5.2) to learn how parallel processing works. I'm working > with the espresso > version 4.0 and i have Intel Fortran compiler (v10) and gcc from the > developers tools > (xcode 2.5, gcc 4.01) on both the machines. > > I downloaded and compiled OpenMPI and i'm pretty sure it works > fine on both computer > (i tried with a very simple program from the openmpi website). Now i > tried to compile QE > with all the wrappers (mpif90, mpicc, mpicxx, mpif77) in the make.sys, > at least that's > what the openmpi suggests to do in their FAQ. The compilation runs > perfectly but when i > try to run a simple simulation the programs fails with this error > message > > *** An error occurred in MPI_Comm_f2c > *** before MPI was initialized > *** MPI_ERRORS_ARE_FATAL (goodbye) > [rikis-macbook.local:56606] Abort before MPI_INIT completed > successfully; not able to > guarantee that all other processes were killed! > > The command i use is > > mpirun -np 2 $PWROOT/bin/pw.x < si.scf.in > > and i run it on just one mac (my laptop). To be precise i can see > two times the > error, as if both the processes break for the same problem. I > understood the problem is > the fortran-c handler but i really have no idea how to fix this. I > haven't worked yet on > the real cluster but i think if it's not working with the dual core > alone no hope with > the rest.... > > Waiting for your news, thanks a lot for the help. Kind regards, > > Riccardo > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by Horde http://www.horde.org/ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From oulihui666 at 126.com Wed Apr 23 04:16:55 2008 From: oulihui666 at 126.com (oulihui666) Date: Wed, 23 Apr 2008 10:16:55 +0800 (CST) Subject: [Pw_forum] About lattice parameter Message-ID: <19806605.56661208917016342.JavaMail.coremail@bj126app81.126.com> Dear pwscf users, Recently, I have a problem about lattice parameter, and I search the whole email list, I do not find the answer, so I hope I could everyone's help. In many literatures, I found that many people have calculated theoretical lattice parameters, and then constructed various adsorption model according to theoretical lattice parameters. Here, I feel confused why people do not use experimental lattice parameters during the calculation? In my opinion, using experimental lattice parameters should be more appropriate. Any suggestion will be appreciated. Thank you in advance best wishes Lihui Ou -- ====================================== Lihui Ou PH.D Candidate in Electrochemistry College of Chemistry and Molecular Science Wuhan University,430072,Hubei Province,China E-mail:oulihui666 at 126.com ====================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080423/38536ee9/attachment.htm From akohlmey at cmm.chem.upenn.edu Wed Apr 23 04:31:03 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 22 Apr 2008 22:31:03 -0400 (EDT) Subject: [Pw_forum] About lattice parameter In-Reply-To: <19806605.56661208917016342.JavaMail.coremail@bj126app81.126.com> References: <19806605.56661208917016342.JavaMail.coremail@bj126app81.126.com> Message-ID: On Wed, 23 Apr 2008, oulihui666 wrote: LO> Dear pwscf users, LO> lattice parameters during the calculation? In my opinion, using LO> experimental lattice parameters should be more appropriate. Any LO> suggestion will be appreciated. if you use a lattice parameter that is not consistent with the theoretical method you are using, you calculate a strained surface. do you think this will give a better result? cheers, axel. LO> LO> Thank you in advance LO> best wishes LO> Lihui Ou LO> LO> LO> -- LO> LO> ====================================== LO> Lihui Ou LO> PH.D Candidate in Electrochemistry LO> College of Chemistry and Molecular Science LO> Wuhan University,430072,Hubei Province,China LO> E-mail:oulihui666 at 126.com LO> ====================================== -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From penghua8503 at 163.com Wed Apr 23 10:06:58 2008 From: penghua8503 at 163.com (penghua8503) Date: Wed, 23 Apr 2008 16:06:58 +0800 (CST) Subject: [Pw_forum] phonon life calculation (third-order expansion coefficients) ? Message-ID: <9178570.541351208938018245.JavaMail.coremail@bj163app125.163.com> Dear All, I use d3.x in PWscf to calculate phonon life of Si. But I do not understand the results of it. I want to know which data is related to the phonon life. The data below is in the si.anh_G and si.d3G.out. what do the datas stand for? Derivative of the force constants(si.anh_G) 1 2 2 10.2000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 1 'Si ' 28.0860000000000 1 1 0.0000000 0.0000000 0.0000000 2 1 0.2500000 0.2500000 0.2500000 Third derivative in cartesian axes q = ( 0.000000000 0.000000000 0.000000000 ) modo: 1 1 1 -0.194289029309E-15 0.000000000000E+00 -0.124900090270E-15 0.000000000000E+00 -0.416333634234E-16 0.000000000000E+00 -0.832667268469E-16 0.000000000000E+00 0.693889390391E-16 0.000000000000E+00 0.383186572412E+00 0.000000000000E+00 -0.971445146547E-16 0.000000000000E+00 0.383186572412E+00 0.000000000000E+00 0.138777878078E-16 0.000000000000E+00 1 2 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -0.277555756156E-16 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -0.385633147861E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 -0.385633147861E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 2 1 -0.416333634234E-16 0.000000000000E+00 0.277555756156E-16 0.000000000000E+00 0.277555756156E-16 0.000000000000E+00 -0.555111512313E-16 0.000000000000E+00 0.832667268469E-16 0.000000000000E+00 -0.385633147861E+00 0.000000000000E+00 -0.111022302463E-15 0.000000000000E+00 -0.385633147861E+00 0.000000000000E+00 -0.277555756156E-16 0.000000000000E+00 2 2 0.277555756156E-16 0.000000000000E+00 -0.416333634234E-16 0.000000000000E+00 0.416333634234E-16 0.000000000000E+00 -0.277555756156E-16 0.000000000000E+00 -0.693889390391E-16 0.000000000000E+00 0.385633147861E+00 0.000000000000E+00 0.277555756156E-16 0.000000000000E+00 0.385633147861E+00 0.000000000000E+00 0.416333634234E-16 0.000000000000E+00 modo: 2 .......... .......... ******************************** Calculating the matrix elements (si.d3G.out) calling drhod2v 1 0.000000 0.000000 0.000000 0.000000 0.650919 0.000000 0.000000 0.000000 0.000000 0.000000 0.325460 0.000000 0.650919 0.000000 0.325460 0.000000 0.000000 0.000000 2 0.000000 0.000000 0.000000 0.000000 0.650919 0.000000 0.000000 0.000000 0.000000 0.000000 0.325460 0.000000 0.650919 0.000000 0.325460 0.000000 0.000000 0.000000 1 0.000000 0.000000 0.727750 0.000000 0.000000 0.000000 0.727750 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 2 0.000000 0.000000 0.727750 0.000000 0.000000 0.000000 0.727750 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ..... ..... I really appreciate your help. Best wishes for you! Thank you. Hua PENG People' Republic of China penghua8503 at 163.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080423/62b50ace/attachment.htm From kazempoor2000 at yahoo.com Wed Apr 23 12:58:26 2008 From: kazempoor2000 at yahoo.com (ali kazempoor) Date: Wed, 23 Apr 2008 03:58:26 -0700 (PDT) Subject: [Pw_forum] ewald Message-ID: <345198.26069.qm@web33107.mail.mud.yahoo.com> Dear all I have two question? 1-the contribution of ion-ion interaction is only participate in ewald energy or not?because in calculation of isolated atom energy ,we see that the ewald energy is not equal to 0. 2-ono electron energy is only kinetic energy or not? thanks ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ From degironc at sissa.it Wed Apr 23 13:03:00 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 23 Apr 2008 13:03:00 +0200 Subject: [Pw_forum] ewald In-Reply-To: <345198.26069.qm@web33107.mail.mud.yahoo.com> References: <345198.26069.qm@web33107.mail.mud.yahoo.com> Message-ID: <480F1764.60301@sissa.it> ali kazempoor wrote: > Dear all > I have two question? > 1-the contribution of ion-ion interaction is only > participate in ewald energy or not?because in > calculation of isolated atom energy ,we see that the > ewald energy is not equal to 0. > it is the electrostatic energy per cell of an infinite array of ionic point charges in an uniform compensating background... > 2-ono electron energy is only kinetic energy or not? > kinetic energy + local and non-local external potential. ... that is the one electron operators in the system. regards, stefano > thanks > > > ____________________________________________________________________________________ > Be a better friend, newshound, and > know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From costanzo at ms.fci.unibo.it Wed Apr 23 14:06:59 2008 From: costanzo at ms.fci.unibo.it (Francesca Costanzo) Date: Wed, 23 Apr 2008 14:06:59 +0200 (CEST) Subject: [Pw_forum] "charge is wrong" In-Reply-To: <480F1764.60301@sissa.it> References: <345198.26069.qm@web33107.mail.mud.yahoo.com> <480F1764.60301@sissa.it> Message-ID: Dear all, I have a problem when I run the optimization geometry of terthiophene on Si(001). The error looks like: ------------------------------------------------------------------------- WARNING: integrated charge= 476.79997686, expected= 490.00000000 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from electrons : error # 1 charge is wrong %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... -------------------------------------------------------------- I have read in your forum that this error can be generated by a wrong pseudopotential. I don't think is that the problem since I have already optimized with the same conditions and the same pseudopotentials the dithiophene molecule on the Si(001) surface and the surface Si(001) such as. May you suggest to me what should I pay attention to ? best regards, Francesca Costanzo -- Francesca Costanzo, Ph.D. Dipartimento di Chimica Fisica ed Inorganica Viale Risorgimento 4 40136 Bologna tel.0039-051-2093710 fax 0039-051-2093690 From kazempoor2000 at yahoo.com Wed Apr 23 15:14:34 2008 From: kazempoor2000 at yahoo.com (ali kazempoor) Date: Wed, 23 Apr 2008 06:14:34 -0700 (PDT) Subject: [Pw_forum] ELF Message-ID: <160057.78670.qm@web33103.mail.mud.yahoo.com> Dear all We are working on MnAs(Mn is a transition metal) nanowire and plot the electron localization function in pp part. But for larger value we have not isovalue around Mn.why? second question is what is the meaning of ELF? is its concept close to the wannier function? thanks ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ From giannozz at nest.sns.it Wed Apr 23 15:18:39 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 23 Apr 2008 15:18:39 +0200 Subject: [Pw_forum] "charge is wrong" In-Reply-To: References: <345198.26069.qm@web33107.mail.mud.yahoo.com> <480F1764.60301@sissa.it> Message-ID: <480F372F.5020004@nest.sns.it> Francesca Costanzo wrote: > The error looks like: > ------------------------------------------------------------------------- > WARNING: integrated charge= 476.79997686, expected= 490.00000000 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from electrons : error # 1 > charge is wrong > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > -------------------------------------------------------------- some errors are self-explaining, others are not and may originate from errors in data or peculiar conditions that are impossible to locate and pinpoint on the basis of the error mesage alone. This error belong to the second case, so more information is required Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Wed Apr 23 15:21:46 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 23 Apr 2008 15:21:46 +0200 Subject: [Pw_forum] ELF In-Reply-To: <160057.78670.qm@web33103.mail.mud.yahoo.com> References: <160057.78670.qm@web33103.mail.mud.yahoo.com> Message-ID: <480F37EA.1000008@nest.sns.it> ali kazempoor wrote: > We are working on MnAs(Mn is a transition metal) > nanowire and plot the electron localization function > in pp part. But for larger value we have not isovalue > around Mn.why? > second question is what is the meaning of ELF? is its > concept close to the wannier function? if you do not know what ELF means, why are you complaining that "for larger value" (of what?) "we have not isovalue around Mn" ? Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From costanzo at ms.fci.unibo.it Wed Apr 23 15:49:30 2008 From: costanzo at ms.fci.unibo.it (Francesca Costanzo) Date: Wed, 23 Apr 2008 15:49:30 +0200 (CEST) Subject: [Pw_forum] "charge is wrong" In-Reply-To: <480F372F.5020004@nest.sns.it> References: <345198.26069.qm@web33107.mail.mud.yahoo.com> <480F1764.60301@sissa.it> <480F372F.5020004@nest.sns.it> Message-ID: Thank you Paolo for your quick answer, may be the input file can be more self explaining. By the way the machine where the job is running is the sp5 at Cineca. --------------------------------------------------- # self-consistent calculation cat > si-large-t3.in << EOF &control max_seconds = 12000 calculation='relax' prefix='si', tstress = .true. tprnfor = .true. restart_mode= 'from_scratch', pseudo_dir ='/sfs/sanfs/home/userincm/incbo407/PWscf/pseudo/', outdir='/scratch/incbo407/au-PWscf/test-3/', etot_conv_thr = 1.d-4 nstep= 200 / &system ibrav = 8, celldm(1) = 29.02243, celldm(2) = 1.0, celldm(3)= 0.89771, nat=151, ntyp=4, ecutwfc=25.0, ecutrho =150.0 / &electrons mixing_mode = 'plain' mixing_beta = 0.1 conv_thr = 1.0d-6 / &ions upscale = 100.D0 / ATOMIC_SPECIES C 12.0107 C.pw91-van_ak.UPF S 32.066 S.pw91-van_ak.UPF Si 28.086 Si.pw91-n-van.UPF H 1.00794 H.pw91-van_ak.UPF ATOMIC_POSITIONS {angstrom} C 6.323650155 1.945078917 1.942084640 1 1 1 C 4.985668179 2.145241151 1.908512881 1 1 1 C 7.070612552 0.658816882 1.880463439 1 1 1 C 4.095635106 3.335729482 1.712456076 1 1 1 C 8.335549051 0.851620731 2.591437070 1 1 1 C 2.789704215 3.003130118 2.349365500 1 1 1 C 2.564179766 1.679800841 2.532646946 1 1 1 C 8.796543791 2.142383776 2.590638952 1 1 1 C 10.596966037 3.807722785 2.209610013 1 1 1 C 11.932582810 3.847106050 1.632135869 1 1 1 C 12.621210230 2.572450605 1.823957122 1 1 1 C 10.162049375 2.552383486 2.512288015 1 1 1 S 11.491577580 1.333197439 2.166171201 1 1 1 S 3.939462625 0.693654418 1.999470582 1 1 1 S 7.495754331 3.283820690 2.003311263 1 1 1 Si -0.025458690 0.578077012 0.212317046 1 1 1 Si -0.004095184 2.805979901 -0.577632902 1 1 1 Si -0.012464715 8.317146922 0.197311075 1 1 1 Si -0.010166785 10.525788261 -0.639504802 1 1 1 Si 3.742398541 0.811087438 -0.433554906 1 1 1 Si 3.840497867 3.192970034 -0.263154075 1 1 1 Si 3.820010046 8.707761278 -0.653146160 1 1 1 Si 3.825401546 10.912982215 0.173089839 1 1 1 Si 7.566244166 0.715578013 -0.172518628 1 1 1 Si 7.715668688 3.075042380 -0.455669890 1 1 1 Si 7.663284193 8.313847847 0.172107233 1 1 1 Si 7.669250544 10.521630467 -0.653840380 1 1 1 Si 11.399656452 0.880142457 -0.256213627 1 1 1 Si 11.606233646 3.270986863 -0.342190601 1 1 1 Si 11.515219587 8.706224746 -0.649959230 1 1 1 Si 11.519315521 10.909865275 0.181585107 1 1 1 Si 1.733991281 0.087139576 -1.335025290 1 1 1 Si 1.899706795 3.844207758 -1.383064548 1 1 1 Si 1.788404924 7.824466165 -1.299397549 1 1 1 Si 2.011898191 11.423909440 -1.305474548 1 1 1 Si 5.719323806 0.084506663 -1.445404999 1 1 1 Si 5.747106383 3.819883863 -1.466863573 1 1 1 Si 5.852062580 7.827307603 -1.311526041 1 1 1 Si 5.639188874 11.411099120 -1.305030585 1 1 1 Si 9.496576315 0.050684040 -1.365756480 1 1 1 Si 9.631649626 3.876980764 -1.476073080 1 1 1 Si 9.481240311 7.831908335 -1.304628797 1 1 1 Si 9.704384413 11.405951019 -1.298119558 1 1 1 Si 13.488916508 0.145662378 -1.270785947 1 1 1 Si 13.518286278 3.856930210 -1.498335979 1 1 1 Si 13.546969595 7.828865664 -1.302717477 1 1 1 Si 13.325170521 11.425900779 -1.305690991 1 1 1 Si 1.928794839 1.935631174 -2.816368782 1 1 1 Si 1.903015360 5.856544012 -2.623544612 1 1 1 Si 1.910252703 9.622227600 -2.833834705 1 1 1 Si 1.902564806 13.423206056 -2.588637771 1 1 1 Si 5.764947952 1.938838768 -2.906677641 1 1 1 Si 5.755850841 5.869037091 -2.646163508 1 1 1 Si 5.756126116 9.618251816 -2.845372988 1 1 1 Si 5.746927556 13.385834763 -2.617002944 1 1 1 Si 9.557988586 1.928794265 -2.831589665 1 1 1 Si 9.574641759 5.900158856 -2.670826884 1 1 1 Si 9.596291600 9.619686826 -2.838054333 1 1 1 Si 9.575129529 13.378351513 -2.606953682 1 1 1 Si 13.438269672 1.922429563 -2.844702276 1 1 1 Si 13.456927720 5.889563844 -2.667358157 1 1 1 Si 13.432406374 9.625624451 -2.834683722 1 1 1 Si 13.423819273 13.449905751 -2.556467349 1 1 1 Si 0.003993115 1.918472534 -4.160541912 1 1 1 Si 0.008812095 5.788767480 -4.044515669 1 1 1 Si -0.006256380 9.604384862 -4.149176784 1 1 1 Si -0.016165869 13.425104639 -3.988847549 1 1 1 Si 3.831309097 1.936584114 -4.184775749 1 1 1 Si 3.825457270 5.806591786 -4.015090913 1 1 1 Si 3.830667539 9.619463962 -4.148709049 1 1 1 Si 3.820682728 13.452230978 -3.998580292 1 1 1 Si 7.689282144 1.924833656 -4.207601619 1 1 1 Si 7.664043631 5.791769734 -4.047164251 1 1 1 Si 7.677981583 9.605638594 -4.152240006 1 1 1 Si 7.667996338 13.411472052 -4.007396250 1 1 1 Si 11.502265161 1.927851866 -4.148648209 1 1 1 Si 11.516429852 5.808318797 -4.025335694 1 1 1 Si 11.515754131 9.618965790 -4.150926406 1 1 1 Si 11.516598061 13.461707996 -3.988204540 1 1 1 Si 0.004516669 -0.039550550 -5.437703631 1 1 1 Si 0.000710101 3.873463623 -5.446311522 1 1 1 Si 0.004862419 7.673495411 -5.462160638 1 1 1 Si -0.003131150 11.544916747 -5.447998083 1 1 1 Si 3.837941197 -0.027281489 -5.451757548 1 1 1 Si 3.836493404 3.898425643 -5.446530286 1 1 1 Si 3.837293937 7.683349298 -5.457596121 1 1 1 Si 3.835808961 11.559981099 -5.444452634 1 1 1 Si 7.679408716 -0.047227212 -5.448822898 1 1 1 Si 7.678278727 3.887025773 -5.461385616 1 1 1 Si 7.674423050 7.675865823 -5.465088887 1 1 1 Si 7.675452021 11.537889569 -5.458660907 1 1 1 Si 11.515174947 -0.018506642 -5.444439779 1 1 1 Si 11.513139299 3.885349183 -5.435430684 1 1 1 Si 11.518512872 7.682748486 -5.461111142 1 1 1 Si 11.518802734 11.565220239 -5.440600617 1 1 1 Si 1.920000583 0.000000000 -6.787005141 0 0 0 Si 1.920000583 3.840001695 -6.787005141 0 0 0 Si 1.920000583 7.679002187 -6.787005141 0 0 0 Si 1.920000583 11.519003354 -6.787005141 0 0 0 Si 5.759004250 0.000000000 -6.787005141 0 0 0 Si 5.759004250 3.840001695 -6.787005141 0 0 0 Si 5.759004250 7.679002187 -6.787005141 0 0 0 Si 5.759004250 11.519003354 -6.787005141 0 0 0 Si 9.599005416 0.000000000 -6.787005141 0 0 0 Si 9.599005416 3.840001695 -6.787005141 0 0 0 Si 9.599005416 7.679002187 -6.787005141 0 0 0 Si 9.599005416 11.519003354 -6.787005141 0 0 0 Si 13.439006583 0.000000000 -6.787005141 0 0 0 Si 13.439006583 3.840001695 -6.787005141 0 0 0 Si 13.439006583 7.679002187 -6.787005141 0 0 0 Si 13.439006583 11.519003354 -6.787005141 0 0 0 H 12.529065981 4.760266317 1.683438182 0 0 0 H 9.966561700 4.705072497 2.289501202 1 1 1 H 13.664446286 2.298383667 1.926092211 1 1 1 H 6.432753586 -0.237462585 2.045455167 1 1 1 H 4.541701287 4.303625762 1.990744173 1 1 1 H 8.945620008 0.011821173 2.925131269 1 1 1 H 2.044200744 3.761126301 2.582349855 1 1 1 H 1.676812571 1.164499388 2.876654725 1 1 1 H 1.921800844 -1.178600503 -7.731501862 0 0 0 H 1.920601199 1.182700568 -7.726104254 0 0 0 H 1.920300627 2.663400954 -7.734205958 0 0 0 H 1.921500801 5.020302445 -7.729104689 0 0 0 H 1.918400880 6.498201366 -7.728305632 0 0 0 H 1.919200996 8.855506090 -7.734401754 0 0 0 H 1.920300627 10.335905903 -7.725500992 0 0 0 H 1.918300866 12.697407002 -7.731702950 0 0 0 H 5.757803018 -1.179300604 -7.729602116 0 0 0 H 5.759602221 1.180000176 -7.729702660 0 0 0 H 5.760401278 2.659601461 -7.729305777 0 0 0 H 5.757601931 5.018002640 -7.732004581 0 0 0 H 5.758501532 6.499302054 -7.729803203 0 0 0 H 5.759803308 8.858204894 -7.730305922 0 0 0 H 5.759205338 10.338403619 -7.728406175 0 0 0 H 5.758300444 12.697608090 -7.730401174 0 0 0 H 9.597301466 -1.179000561 -7.729104689 0 0 0 H 9.598502698 1.179600648 -7.730104834 0 0 0 H 9.598603242 2.658401287 -7.727400739 0 0 0 H 9.597703640 5.017602582 -7.732401464 0 0 0 H 9.600603532 6.500603831 -7.731300775 0 0 0 H 9.600201357 8.859903553 -7.727802913 0 0 0 H 9.599005416 10.339006881 -7.728803058 0 0 0 H 9.600905163 12.697205915 -7.730004291 0 0 0 H 13.439906184 -1.179200590 -7.729702660 0 0 0 H 13.438207525 1.180300749 -7.729205233 0 0 0 H 13.437307924 2.660401048 -7.730004291 0 0 0 H 13.439805640 5.018801698 -7.730903892 0 0 0 H 13.439805640 6.500101112 -7.730803348 0 0 0 H 13.437805350 8.858702320 -7.729903747 0 0 0 H 13.439006583 10.338504163 -7.728702515 0 0 0 H 13.439705097 12.697703342 -7.730501717 0 0 0 K_POINTS {automatic} 1 1 1 0 0 0 EOF ------------------------------------------------------------------------------ Best reagrds, Francesca On Wed, 23 Apr 2008, Paolo Giannozzi wrote: > Francesca Costanzo wrote: > >> The error looks like: >> ------------------------------------------------------------------------- >> WARNING: integrated charge= 476.79997686, expected= 490.00000000 >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> from electrons : error # 1 >> charge is wrong >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> stopping ... >> -------------------------------------------------------------- > > some errors are self-explaining, others are not and may originate > from errors in data or peculiar conditions that are impossible to > locate and pinpoint on the basis of the error mesage alone. This > error belong to the second case, so more information is required > > Paolo > From fenghongjian at ss.buaa.edu.cn Wed Apr 23 15:27:39 2008 From: fenghongjian at ss.buaa.edu.cn (Hong-Jian Feng) Date: Wed, 23 Apr 2008 21:27:39 +0800 Subject: [Pw_forum] "charge is wrong" References: <345198.26069.qm@web33107.mail.mud.yahoo.com>, <480F1764.60301@sissa.it>, Message-ID: <200804232122513385957@ss.buaa.edu.cn> Dear Francesca Costanzo, I have just encountered the same problems couple days ago, and I found it had been caused by not turning the spin polarization on with odd electrons in my system. So I recommend you to have a check on the number of electrons on your system in order to avoid the case. Best regards, Hong-Jian Feng school of science Beijing University of Aeronautics & Astronautics ???? Francesca Costanzo ????? 2008-04-23 21:03:15 ???? PWSCF Forum ??? ??? [Pw_forum] "charge is wrong" Dear all, I have a problem when I run the optimization geometry of terthiophene on Si(001). The error looks like: ------------------------------------------------------------------------- WARNING: integrated charge= 476.79997686, expected= 490.00000000 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from electrons : error # 1 charge is wrong %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... -------------------------------------------------------------- I have read in your forum that this error can be generated by a wrong pseudopotential. I don't think is that the problem since I have already optimized with the same conditions and the same pseudopotentials the dithiophene molecule on the Si(001) surface and the surface Si(001) such as. May you suggest to me what should I pay attention to ? best regards, Francesca Costanzo -- Francesca Costanzo, Ph.D. Dipartimento di Chimica Fisica ed Inorganica Viale Risorgimento 4 40136 Bologna tel.0039-051-2093710 fax 0039-051-2093690 _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080423/0b97164b/attachment.htm From akohlmey at cmm.chem.upenn.edu Wed Apr 23 15:44:14 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 23 Apr 2008 09:44:14 -0400 (EDT) Subject: [Pw_forum] ELF In-Reply-To: <160057.78670.qm@web33103.mail.mud.yahoo.com> References: <160057.78670.qm@web33103.mail.mud.yahoo.com> Message-ID: On Wed, 23 Apr 2008, ali kazempoor wrote: AK> Dear all AK> We are working on MnAs(Mn is a transition metal) AK> nanowire and plot the electron localization function AK> in pp part. But for larger value we have not isovalue AK> around Mn.why? AK> second question is what is the meaning of ELF? is its AK> concept close to the wannier function? no. http://www.cpfs.mpg.de/ELF/ axel. AK> thanks AK> AK> AK> ____________________________________________________________________________________ AK> Be a better friend, newshound, and AK> know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ AK> _______________________________________________ AK> Pw_forum mailing list AK> Pw_forum at pwscf.org AK> http://www.democritos.it/mailman/listinfo/pw_forum AK> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From baris.malcioglu at gmail.com Wed Apr 23 15:16:37 2008 From: baris.malcioglu at gmail.com (O. Baris Malcioglu) Date: Wed, 23 Apr 2008 16:16:37 +0300 Subject: [Pw_forum] "charge is wrong" In-Reply-To: References: <345198.26069.qm@web33107.mail.mud.yahoo.com> <480F1764.60301@sissa.it> <480F372F.5020004@nest.sns.it> Message-ID: <480F36B5.8050404@gmail.com> Dear Francesca, I have encountered this error once. Did you try increasing ecutrho? Sometimes this solves the problem, (Yours seem particularly low to me) In my case, it turned out to be something going wrong in the parametrization of USPP I have used, however. hope this helps, O. Baris Malcioglu SISSA Trieste, Italy Francesca Costanzo wrote: > Thank you Paolo > for your quick answer, > may be the input file can be more self explaining. > By the way the machine where the job is running is the sp5 at Cineca. > > > --------------------------------------------------- > # self-consistent calculation > cat > si-large-t3.in << EOF > &control > max_seconds = 12000 > calculation='relax' > prefix='si', > tstress = .true. > tprnfor = .true. > restart_mode= 'from_scratch', > pseudo_dir ='/sfs/sanfs/home/userincm/incbo407/PWscf/pseudo/', > outdir='/scratch/incbo407/au-PWscf/test-3/', > etot_conv_thr = 1.d-4 > nstep= 200 > / > &system > ibrav = 8, celldm(1) = 29.02243, celldm(2) = 1.0, celldm(3)= 0.89771, > nat=151, ntyp=4, ecutwfc=25.0, ecutrho =150.0 > / > &electrons > mixing_mode = 'plain' > mixing_beta = 0.1 > conv_thr = 1.0d-6 > / > &ions > upscale = 100.D0 > / > ATOMIC_SPECIES > C 12.0107 C.pw91-van_ak.UPF > S 32.066 S.pw91-van_ak.UPF > Si 28.086 Si.pw91-n-van.UPF > H 1.00794 H.pw91-van_ak.UPF > ATOMIC_POSITIONS {angstrom} > C 6.323650155 1.945078917 1.942084640 1 1 1 > C 4.985668179 2.145241151 1.908512881 1 1 1 > C 7.070612552 0.658816882 1.880463439 1 1 1 > C 4.095635106 3.335729482 1.712456076 1 1 1 > C 8.335549051 0.851620731 2.591437070 1 1 1 > C 2.789704215 3.003130118 2.349365500 1 1 1 > C 2.564179766 1.679800841 2.532646946 1 1 1 > C 8.796543791 2.142383776 2.590638952 1 1 1 > C 10.596966037 3.807722785 2.209610013 1 1 1 > C 11.932582810 3.847106050 1.632135869 1 1 1 > C 12.621210230 2.572450605 1.823957122 1 1 1 > C 10.162049375 2.552383486 2.512288015 1 1 1 > S 11.491577580 1.333197439 2.166171201 1 1 1 > S 3.939462625 0.693654418 1.999470582 1 1 1 > S 7.495754331 3.283820690 2.003311263 1 1 1 > Si -0.025458690 0.578077012 0.212317046 1 1 1 > Si -0.004095184 2.805979901 -0.577632902 1 1 1 > Si -0.012464715 8.317146922 0.197311075 1 1 1 > Si -0.010166785 10.525788261 -0.639504802 1 1 1 > Si 3.742398541 0.811087438 -0.433554906 1 1 1 > Si 3.840497867 3.192970034 -0.263154075 1 1 1 > Si 3.820010046 8.707761278 -0.653146160 1 1 1 > Si 3.825401546 10.912982215 0.173089839 1 1 1 > Si 7.566244166 0.715578013 -0.172518628 1 1 1 > Si 7.715668688 3.075042380 -0.455669890 1 1 1 > Si 7.663284193 8.313847847 0.172107233 1 1 1 > Si 7.669250544 10.521630467 -0.653840380 1 1 1 > Si 11.399656452 0.880142457 -0.256213627 1 1 1 > Si 11.606233646 3.270986863 -0.342190601 1 1 1 > Si 11.515219587 8.706224746 -0.649959230 1 1 1 > Si 11.519315521 10.909865275 0.181585107 1 1 1 > Si 1.733991281 0.087139576 -1.335025290 1 1 1 > Si 1.899706795 3.844207758 -1.383064548 1 1 1 > Si 1.788404924 7.824466165 -1.299397549 1 1 1 > Si 2.011898191 11.423909440 -1.305474548 1 1 1 > Si 5.719323806 0.084506663 -1.445404999 1 1 1 > Si 5.747106383 3.819883863 -1.466863573 1 1 1 > Si 5.852062580 7.827307603 -1.311526041 1 1 1 > Si 5.639188874 11.411099120 -1.305030585 1 1 1 > Si 9.496576315 0.050684040 -1.365756480 1 1 1 > Si 9.631649626 3.876980764 -1.476073080 1 1 1 > Si 9.481240311 7.831908335 -1.304628797 1 1 1 > Si 9.704384413 11.405951019 -1.298119558 1 1 1 > Si 13.488916508 0.145662378 -1.270785947 1 1 1 > Si 13.518286278 3.856930210 -1.498335979 1 1 1 > Si 13.546969595 7.828865664 -1.302717477 1 1 1 > Si 13.325170521 11.425900779 -1.305690991 1 1 1 > Si 1.928794839 1.935631174 -2.816368782 1 1 1 > Si 1.903015360 5.856544012 -2.623544612 1 1 1 > Si 1.910252703 9.622227600 -2.833834705 1 1 1 > Si 1.902564806 13.423206056 -2.588637771 1 1 1 > Si 5.764947952 1.938838768 -2.906677641 1 1 1 > Si 5.755850841 5.869037091 -2.646163508 1 1 1 > Si 5.756126116 9.618251816 -2.845372988 1 1 1 > Si 5.746927556 13.385834763 -2.617002944 1 1 1 > Si 9.557988586 1.928794265 -2.831589665 1 1 1 > Si 9.574641759 5.900158856 -2.670826884 1 1 1 > Si 9.596291600 9.619686826 -2.838054333 1 1 1 > Si 9.575129529 13.378351513 -2.606953682 1 1 1 > Si 13.438269672 1.922429563 -2.844702276 1 1 1 > Si 13.456927720 5.889563844 -2.667358157 1 1 1 > Si 13.432406374 9.625624451 -2.834683722 1 1 1 > Si 13.423819273 13.449905751 -2.556467349 1 1 1 > Si 0.003993115 1.918472534 -4.160541912 1 1 1 > Si 0.008812095 5.788767480 -4.044515669 1 1 1 > Si -0.006256380 9.604384862 -4.149176784 1 1 1 > Si -0.016165869 13.425104639 -3.988847549 1 1 1 > Si 3.831309097 1.936584114 -4.184775749 1 1 1 > Si 3.825457270 5.806591786 -4.015090913 1 1 1 > Si 3.830667539 9.619463962 -4.148709049 1 1 1 > Si 3.820682728 13.452230978 -3.998580292 1 1 1 > Si 7.689282144 1.924833656 -4.207601619 1 1 1 > Si 7.664043631 5.791769734 -4.047164251 1 1 1 > Si 7.677981583 9.605638594 -4.152240006 1 1 1 > Si 7.667996338 13.411472052 -4.007396250 1 1 1 > Si 11.502265161 1.927851866 -4.148648209 1 1 1 > Si 11.516429852 5.808318797 -4.025335694 1 1 1 > Si 11.515754131 9.618965790 -4.150926406 1 1 1 > Si 11.516598061 13.461707996 -3.988204540 1 1 1 > Si 0.004516669 -0.039550550 -5.437703631 1 1 1 > Si 0.000710101 3.873463623 -5.446311522 1 1 1 > Si 0.004862419 7.673495411 -5.462160638 1 1 1 > Si -0.003131150 11.544916747 -5.447998083 1 1 1 > Si 3.837941197 -0.027281489 -5.451757548 1 1 1 > Si 3.836493404 3.898425643 -5.446530286 1 1 1 > Si 3.837293937 7.683349298 -5.457596121 1 1 1 > Si 3.835808961 11.559981099 -5.444452634 1 1 1 > Si 7.679408716 -0.047227212 -5.448822898 1 1 1 > Si 7.678278727 3.887025773 -5.461385616 1 1 1 > Si 7.674423050 7.675865823 -5.465088887 1 1 1 > Si 7.675452021 11.537889569 -5.458660907 1 1 1 > Si 11.515174947 -0.018506642 -5.444439779 1 1 1 > Si 11.513139299 3.885349183 -5.435430684 1 1 1 > Si 11.518512872 7.682748486 -5.461111142 1 1 1 > Si 11.518802734 11.565220239 -5.440600617 1 1 1 > Si 1.920000583 0.000000000 -6.787005141 0 0 0 > Si 1.920000583 3.840001695 -6.787005141 0 0 0 > Si 1.920000583 7.679002187 -6.787005141 0 0 0 > Si 1.920000583 11.519003354 -6.787005141 0 0 0 > Si 5.759004250 0.000000000 -6.787005141 0 0 0 > Si 5.759004250 3.840001695 -6.787005141 0 0 0 > Si 5.759004250 7.679002187 -6.787005141 0 0 0 > Si 5.759004250 11.519003354 -6.787005141 0 0 0 > Si 9.599005416 0.000000000 -6.787005141 0 0 0 > Si 9.599005416 3.840001695 -6.787005141 0 0 0 > Si 9.599005416 7.679002187 -6.787005141 0 0 0 > Si 9.599005416 11.519003354 -6.787005141 0 0 0 > Si 13.439006583 0.000000000 -6.787005141 0 0 0 > Si 13.439006583 3.840001695 -6.787005141 0 0 0 > Si 13.439006583 7.679002187 -6.787005141 0 0 0 > Si 13.439006583 11.519003354 -6.787005141 0 0 0 > H 12.529065981 4.760266317 1.683438182 0 0 0 > H 9.966561700 4.705072497 2.289501202 1 1 1 > H 13.664446286 2.298383667 1.926092211 1 1 1 > H 6.432753586 -0.237462585 2.045455167 1 1 1 > H 4.541701287 4.303625762 1.990744173 1 1 1 > H 8.945620008 0.011821173 2.925131269 1 1 1 > H 2.044200744 3.761126301 2.582349855 1 1 1 > H 1.676812571 1.164499388 2.876654725 1 1 1 > H 1.921800844 -1.178600503 -7.731501862 0 0 0 > H 1.920601199 1.182700568 -7.726104254 0 0 0 > H 1.920300627 2.663400954 -7.734205958 0 0 0 > H 1.921500801 5.020302445 -7.729104689 0 0 0 > H 1.918400880 6.498201366 -7.728305632 0 0 0 > H 1.919200996 8.855506090 -7.734401754 0 0 0 > H 1.920300627 10.335905903 -7.725500992 0 0 0 > H 1.918300866 12.697407002 -7.731702950 0 0 0 > H 5.757803018 -1.179300604 -7.729602116 0 0 0 > H 5.759602221 1.180000176 -7.729702660 0 0 0 > H 5.760401278 2.659601461 -7.729305777 0 0 0 > H 5.757601931 5.018002640 -7.732004581 0 0 0 > H 5.758501532 6.499302054 -7.729803203 0 0 0 > H 5.759803308 8.858204894 -7.730305922 0 0 0 > H 5.759205338 10.338403619 -7.728406175 0 0 0 > H 5.758300444 12.697608090 -7.730401174 0 0 0 > H 9.597301466 -1.179000561 -7.729104689 0 0 0 > H 9.598502698 1.179600648 -7.730104834 0 0 0 > H 9.598603242 2.658401287 -7.727400739 0 0 0 > H 9.597703640 5.017602582 -7.732401464 0 0 0 > H 9.600603532 6.500603831 -7.731300775 0 0 0 > H 9.600201357 8.859903553 -7.727802913 0 0 0 > H 9.599005416 10.339006881 -7.728803058 0 0 0 > H 9.600905163 12.697205915 -7.730004291 0 0 0 > H 13.439906184 -1.179200590 -7.729702660 0 0 0 > H 13.438207525 1.180300749 -7.729205233 0 0 0 > H 13.437307924 2.660401048 -7.730004291 0 0 0 > H 13.439805640 5.018801698 -7.730903892 0 0 0 > H 13.439805640 6.500101112 -7.730803348 0 0 0 > H 13.437805350 8.858702320 -7.729903747 0 0 0 > H 13.439006583 10.338504163 -7.728702515 0 0 0 > H 13.439705097 12.697703342 -7.730501717 0 0 0 > K_POINTS {automatic} > 1 1 1 0 0 0 > EOF > > ------------------------------------------------------------------------------ > > > > Best reagrds, > Francesca > > > On Wed, 23 Apr 2008, Paolo Giannozzi wrote: > > >> Francesca Costanzo wrote: >> >> >>> The error looks like: >>> ------------------------------------------------------------------------- >>> WARNING: integrated charge= 476.79997686, expected= 490.00000000 >>> >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> from electrons : error # 1 >>> charge is wrong >>> >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> >>> stopping ... >>> -------------------------------------------------------------- >>> >> some errors are self-explaining, others are not and may originate >> from errors in data or peculiar conditions that are impossible to >> locate and pinpoint on the basis of the error mesage alone. This >> error belong to the second case, so more information is required >> >> Paolo >> >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From cao at qtp.ufl.edu Wed Apr 23 16:42:07 2008 From: cao at qtp.ufl.edu (Chao Cao) Date: Wed, 23 Apr 2008 10:42:07 -0400 Subject: [Pw_forum] "charge is wrong" In-Reply-To: References: <345198.26069.qm@web33107.mail.mud.yahoo.com> <480F1764.60301@sissa.it> <480F372F.5020004@nest.sns.it> Message-ID: <480F4ABF.6020706@qtp.ufl.edu> One other possibility is that your system is metallic but you did not specify occupation and smearing. Best, Chao Cao Francesca Costanzo wrote: > Thank you Paolo > for your quick answer, > may be the input file can be more self explaining. > By the way the machine where the job is running is the sp5 at Cineca. > > > --------------------------------------------------- > # self-consistent calculation > cat > si-large-t3.in << EOF > &control > max_seconds = 12000 > calculation='relax' > prefix='si', > tstress = .true. > tprnfor = .true. > restart_mode= 'from_scratch', > pseudo_dir ='/sfs/sanfs/home/userincm/incbo407/PWscf/pseudo/', > outdir='/scratch/incbo407/au-PWscf/test-3/', > etot_conv_thr = 1.d-4 > nstep= 200 > / > &system > ibrav = 8, celldm(1) = 29.02243, celldm(2) = 1.0, celldm(3)= 0.89771, > nat=151, ntyp=4, ecutwfc=25.0, ecutrho =150.0 > / > &electrons > mixing_mode = 'plain' > mixing_beta = 0.1 > conv_thr = 1.0d-6 > / > &ions > upscale = 100.D0 > / > ATOMIC_SPECIES > C 12.0107 C.pw91-van_ak.UPF > S 32.066 S.pw91-van_ak.UPF > Si 28.086 Si.pw91-n-van.UPF > H 1.00794 H.pw91-van_ak.UPF > ATOMIC_POSITIONS {angstrom} > C 6.323650155 1.945078917 1.942084640 1 1 1 > C 4.985668179 2.145241151 1.908512881 1 1 1 > C 7.070612552 0.658816882 1.880463439 1 1 1 > C 4.095635106 3.335729482 1.712456076 1 1 1 > C 8.335549051 0.851620731 2.591437070 1 1 1 > C 2.789704215 3.003130118 2.349365500 1 1 1 > C 2.564179766 1.679800841 2.532646946 1 1 1 > C 8.796543791 2.142383776 2.590638952 1 1 1 > C 10.596966037 3.807722785 2.209610013 1 1 1 > C 11.932582810 3.847106050 1.632135869 1 1 1 > C 12.621210230 2.572450605 1.823957122 1 1 1 > C 10.162049375 2.552383486 2.512288015 1 1 1 > S 11.491577580 1.333197439 2.166171201 1 1 1 > S 3.939462625 0.693654418 1.999470582 1 1 1 > S 7.495754331 3.283820690 2.003311263 1 1 1 > Si -0.025458690 0.578077012 0.212317046 1 1 1 > Si -0.004095184 2.805979901 -0.577632902 1 1 1 > Si -0.012464715 8.317146922 0.197311075 1 1 1 > Si -0.010166785 10.525788261 -0.639504802 1 1 1 > Si 3.742398541 0.811087438 -0.433554906 1 1 1 > Si 3.840497867 3.192970034 -0.263154075 1 1 1 > Si 3.820010046 8.707761278 -0.653146160 1 1 1 > Si 3.825401546 10.912982215 0.173089839 1 1 1 > Si 7.566244166 0.715578013 -0.172518628 1 1 1 > Si 7.715668688 3.075042380 -0.455669890 1 1 1 > Si 7.663284193 8.313847847 0.172107233 1 1 1 > Si 7.669250544 10.521630467 -0.653840380 1 1 1 > Si 11.399656452 0.880142457 -0.256213627 1 1 1 > Si 11.606233646 3.270986863 -0.342190601 1 1 1 > Si 11.515219587 8.706224746 -0.649959230 1 1 1 > Si 11.519315521 10.909865275 0.181585107 1 1 1 > Si 1.733991281 0.087139576 -1.335025290 1 1 1 > Si 1.899706795 3.844207758 -1.383064548 1 1 1 > Si 1.788404924 7.824466165 -1.299397549 1 1 1 > Si 2.011898191 11.423909440 -1.305474548 1 1 1 > Si 5.719323806 0.084506663 -1.445404999 1 1 1 > Si 5.747106383 3.819883863 -1.466863573 1 1 1 > Si 5.852062580 7.827307603 -1.311526041 1 1 1 > Si 5.639188874 11.411099120 -1.305030585 1 1 1 > Si 9.496576315 0.050684040 -1.365756480 1 1 1 > Si 9.631649626 3.876980764 -1.476073080 1 1 1 > Si 9.481240311 7.831908335 -1.304628797 1 1 1 > Si 9.704384413 11.405951019 -1.298119558 1 1 1 > Si 13.488916508 0.145662378 -1.270785947 1 1 1 > Si 13.518286278 3.856930210 -1.498335979 1 1 1 > Si 13.546969595 7.828865664 -1.302717477 1 1 1 > Si 13.325170521 11.425900779 -1.305690991 1 1 1 > Si 1.928794839 1.935631174 -2.816368782 1 1 1 > Si 1.903015360 5.856544012 -2.623544612 1 1 1 > Si 1.910252703 9.622227600 -2.833834705 1 1 1 > Si 1.902564806 13.423206056 -2.588637771 1 1 1 > Si 5.764947952 1.938838768 -2.906677641 1 1 1 > Si 5.755850841 5.869037091 -2.646163508 1 1 1 > Si 5.756126116 9.618251816 -2.845372988 1 1 1 > Si 5.746927556 13.385834763 -2.617002944 1 1 1 > Si 9.557988586 1.928794265 -2.831589665 1 1 1 > Si 9.574641759 5.900158856 -2.670826884 1 1 1 > Si 9.596291600 9.619686826 -2.838054333 1 1 1 > Si 9.575129529 13.378351513 -2.606953682 1 1 1 > Si 13.438269672 1.922429563 -2.844702276 1 1 1 > Si 13.456927720 5.889563844 -2.667358157 1 1 1 > Si 13.432406374 9.625624451 -2.834683722 1 1 1 > Si 13.423819273 13.449905751 -2.556467349 1 1 1 > Si 0.003993115 1.918472534 -4.160541912 1 1 1 > Si 0.008812095 5.788767480 -4.044515669 1 1 1 > Si -0.006256380 9.604384862 -4.149176784 1 1 1 > Si -0.016165869 13.425104639 -3.988847549 1 1 1 > Si 3.831309097 1.936584114 -4.184775749 1 1 1 > Si 3.825457270 5.806591786 -4.015090913 1 1 1 > Si 3.830667539 9.619463962 -4.148709049 1 1 1 > Si 3.820682728 13.452230978 -3.998580292 1 1 1 > Si 7.689282144 1.924833656 -4.207601619 1 1 1 > Si 7.664043631 5.791769734 -4.047164251 1 1 1 > Si 7.677981583 9.605638594 -4.152240006 1 1 1 > Si 7.667996338 13.411472052 -4.007396250 1 1 1 > Si 11.502265161 1.927851866 -4.148648209 1 1 1 > Si 11.516429852 5.808318797 -4.025335694 1 1 1 > Si 11.515754131 9.618965790 -4.150926406 1 1 1 > Si 11.516598061 13.461707996 -3.988204540 1 1 1 > Si 0.004516669 -0.039550550 -5.437703631 1 1 1 > Si 0.000710101 3.873463623 -5.446311522 1 1 1 > Si 0.004862419 7.673495411 -5.462160638 1 1 1 > Si -0.003131150 11.544916747 -5.447998083 1 1 1 > Si 3.837941197 -0.027281489 -5.451757548 1 1 1 > Si 3.836493404 3.898425643 -5.446530286 1 1 1 > Si 3.837293937 7.683349298 -5.457596121 1 1 1 > Si 3.835808961 11.559981099 -5.444452634 1 1 1 > Si 7.679408716 -0.047227212 -5.448822898 1 1 1 > Si 7.678278727 3.887025773 -5.461385616 1 1 1 > Si 7.674423050 7.675865823 -5.465088887 1 1 1 > Si 7.675452021 11.537889569 -5.458660907 1 1 1 > Si 11.515174947 -0.018506642 -5.444439779 1 1 1 > Si 11.513139299 3.885349183 -5.435430684 1 1 1 > Si 11.518512872 7.682748486 -5.461111142 1 1 1 > Si 11.518802734 11.565220239 -5.440600617 1 1 1 > Si 1.920000583 0.000000000 -6.787005141 0 0 0 > Si 1.920000583 3.840001695 -6.787005141 0 0 0 > Si 1.920000583 7.679002187 -6.787005141 0 0 0 > Si 1.920000583 11.519003354 -6.787005141 0 0 0 > Si 5.759004250 0.000000000 -6.787005141 0 0 0 > Si 5.759004250 3.840001695 -6.787005141 0 0 0 > Si 5.759004250 7.679002187 -6.787005141 0 0 0 > Si 5.759004250 11.519003354 -6.787005141 0 0 0 > Si 9.599005416 0.000000000 -6.787005141 0 0 0 > Si 9.599005416 3.840001695 -6.787005141 0 0 0 > Si 9.599005416 7.679002187 -6.787005141 0 0 0 > Si 9.599005416 11.519003354 -6.787005141 0 0 0 > Si 13.439006583 0.000000000 -6.787005141 0 0 0 > Si 13.439006583 3.840001695 -6.787005141 0 0 0 > Si 13.439006583 7.679002187 -6.787005141 0 0 0 > Si 13.439006583 11.519003354 -6.787005141 0 0 0 > H 12.529065981 4.760266317 1.683438182 0 0 0 > H 9.966561700 4.705072497 2.289501202 1 1 1 > H 13.664446286 2.298383667 1.926092211 1 1 1 > H 6.432753586 -0.237462585 2.045455167 1 1 1 > H 4.541701287 4.303625762 1.990744173 1 1 1 > H 8.945620008 0.011821173 2.925131269 1 1 1 > H 2.044200744 3.761126301 2.582349855 1 1 1 > H 1.676812571 1.164499388 2.876654725 1 1 1 > H 1.921800844 -1.178600503 -7.731501862 0 0 0 > H 1.920601199 1.182700568 -7.726104254 0 0 0 > H 1.920300627 2.663400954 -7.734205958 0 0 0 > H 1.921500801 5.020302445 -7.729104689 0 0 0 > H 1.918400880 6.498201366 -7.728305632 0 0 0 > H 1.919200996 8.855506090 -7.734401754 0 0 0 > H 1.920300627 10.335905903 -7.725500992 0 0 0 > H 1.918300866 12.697407002 -7.731702950 0 0 0 > H 5.757803018 -1.179300604 -7.729602116 0 0 0 > H 5.759602221 1.180000176 -7.729702660 0 0 0 > H 5.760401278 2.659601461 -7.729305777 0 0 0 > H 5.757601931 5.018002640 -7.732004581 0 0 0 > H 5.758501532 6.499302054 -7.729803203 0 0 0 > H 5.759803308 8.858204894 -7.730305922 0 0 0 > H 5.759205338 10.338403619 -7.728406175 0 0 0 > H 5.758300444 12.697608090 -7.730401174 0 0 0 > H 9.597301466 -1.179000561 -7.729104689 0 0 0 > H 9.598502698 1.179600648 -7.730104834 0 0 0 > H 9.598603242 2.658401287 -7.727400739 0 0 0 > H 9.597703640 5.017602582 -7.732401464 0 0 0 > H 9.600603532 6.500603831 -7.731300775 0 0 0 > H 9.600201357 8.859903553 -7.727802913 0 0 0 > H 9.599005416 10.339006881 -7.728803058 0 0 0 > H 9.600905163 12.697205915 -7.730004291 0 0 0 > H 13.439906184 -1.179200590 -7.729702660 0 0 0 > H 13.438207525 1.180300749 -7.729205233 0 0 0 > H 13.437307924 2.660401048 -7.730004291 0 0 0 > H 13.439805640 5.018801698 -7.730903892 0 0 0 > H 13.439805640 6.500101112 -7.730803348 0 0 0 > H 13.437805350 8.858702320 -7.729903747 0 0 0 > H 13.439006583 10.338504163 -7.728702515 0 0 0 > H 13.439705097 12.697703342 -7.730501717 0 0 0 > K_POINTS {automatic} > 1 1 1 0 0 0 > EOF > > ------------------------------------------------------------------------------ > > > > Best reagrds, > Francesca > > > On Wed, 23 Apr 2008, Paolo Giannozzi wrote: > >> Francesca Costanzo wrote: >> >>> The error looks like: >>> ------------------------------------------------------------------------- >>> WARNING: integrated charge= 476.79997686, expected= 490.00000000 >>> >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> from electrons : error # 1 >>> charge is wrong >>> >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> >>> stopping ... >>> -------------------------------------------------------------- >> some errors are self-explaining, others are not and may originate >> from errors in data or peculiar conditions that are impossible to >> locate and pinpoint on the basis of the error mesage alone. This >> error belong to the second case, so more information is required >> >> Paolo >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Chao Cao Quantum Theory Project and Department of Physics University of Florida, Gainesville, FL 32611 U.S.A. From eyvaz_isaev at yahoo.com Wed Apr 23 17:15:35 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 23 Apr 2008 08:15:35 -0700 (PDT) Subject: [Pw_forum] "charge is wrong" In-Reply-To: Message-ID: <606941.54240.qm@web65703.mail.ac4.yahoo.com> Hi Francesca, As you can see you got charge deficieny, meaning that bands number is not sufficient. You did not specify any occupations keyword, so your system is considered as insulator (or semiconducting) for which only nbnd=(number of valence electros divided by 2) is used. It might be that during relaxation process your system turns to be metallic for which one should use more bands number. So, try nbnd=490/2 + 10= 255 (in &system) Hope this helps. Bests, Eyvaz. --- Francesca Costanzo wrote: > Thank you Paolo > for your quick answer, > may be the input file can be more self explaining. > By the way the machine where the job is running is > the sp5 at Cineca. > > > --------------------------------------------------- > # self-consistent calculation > cat > si-large-t3.in << EOF > &control > max_seconds = 12000 > calculation='relax' > prefix='si', > tstress = .true. > tprnfor = .true. > restart_mode= 'from_scratch', > pseudo_dir > ='/sfs/sanfs/home/userincm/incbo407/PWscf/pseudo/', > outdir='/scratch/incbo407/au-PWscf/test-3/', > etot_conv_thr = 1.d-4 > nstep= 200 > / > &system > ibrav = 8, celldm(1) = 29.02243, celldm(2) = > 1.0, celldm(3)= 0.89771, > nat=151, ntyp=4, ecutwfc=25.0, ecutrho =150.0 > / > &electrons > mixing_mode = 'plain' > mixing_beta = 0.1 > conv_thr = 1.0d-6 > / > &ions > upscale = 100.D0 > / > ATOMIC_SPECIES > C 12.0107 C.pw91-van_ak.UPF > S 32.066 S.pw91-van_ak.UPF > Si 28.086 Si.pw91-n-van.UPF > H 1.00794 H.pw91-van_ak.UPF > ATOMIC_POSITIONS {angstrom} > C 6.323650155 1.945078917 1.942084640 > 1 1 1 > C 4.985668179 2.145241151 1.908512881 > 1 1 1 > C 7.070612552 0.658816882 1.880463439 > 1 1 1 > C 4.095635106 3.335729482 1.712456076 > 1 1 1 > C 8.335549051 0.851620731 2.591437070 > 1 1 1 > C 2.789704215 3.003130118 2.349365500 > 1 1 1 > C 2.564179766 1.679800841 2.532646946 > 1 1 1 > C 8.796543791 2.142383776 2.590638952 > 1 1 1 > C 10.596966037 3.807722785 2.209610013 > 1 1 1 > C 11.932582810 3.847106050 1.632135869 > 1 1 1 > C 12.621210230 2.572450605 1.823957122 > 1 1 1 > C 10.162049375 2.552383486 2.512288015 > 1 1 1 > S 11.491577580 1.333197439 2.166171201 > 1 1 1 > S 3.939462625 0.693654418 1.999470582 > 1 1 1 > S 7.495754331 3.283820690 2.003311263 > 1 1 1 > Si -0.025458690 0.578077012 0.212317046 > 1 1 1 > Si -0.004095184 2.805979901 -0.577632902 > 1 1 1 > Si -0.012464715 8.317146922 0.197311075 > 1 1 1 > Si -0.010166785 10.525788261 -0.639504802 > 1 1 1 > Si 3.742398541 0.811087438 -0.433554906 > 1 1 1 > Si 3.840497867 3.192970034 -0.263154075 > 1 1 1 > Si 3.820010046 8.707761278 -0.653146160 > 1 1 1 > Si 3.825401546 10.912982215 0.173089839 > 1 1 1 > Si 7.566244166 0.715578013 -0.172518628 > 1 1 1 > Si 7.715668688 3.075042380 -0.455669890 > 1 1 1 > Si 7.663284193 8.313847847 0.172107233 > 1 1 1 > Si 7.669250544 10.521630467 -0.653840380 > 1 1 1 > Si 11.399656452 0.880142457 -0.256213627 > 1 1 1 > Si 11.606233646 3.270986863 -0.342190601 > 1 1 1 > Si 11.515219587 8.706224746 -0.649959230 > 1 1 1 > Si 11.519315521 10.909865275 0.181585107 > 1 1 1 > Si 1.733991281 0.087139576 -1.335025290 > 1 1 1 > Si 1.899706795 3.844207758 -1.383064548 > 1 1 1 > Si 1.788404924 7.824466165 -1.299397549 > 1 1 1 > Si 2.011898191 11.423909440 -1.305474548 > 1 1 1 > Si 5.719323806 0.084506663 -1.445404999 > 1 1 1 > Si 5.747106383 3.819883863 -1.466863573 > 1 1 1 > Si 5.852062580 7.827307603 -1.311526041 > 1 1 1 > Si 5.639188874 11.411099120 -1.305030585 > 1 1 1 > Si 9.496576315 0.050684040 -1.365756480 > 1 1 1 > Si 9.631649626 3.876980764 -1.476073080 > 1 1 1 > Si 9.481240311 7.831908335 -1.304628797 > 1 1 1 > Si 9.704384413 11.405951019 -1.298119558 > 1 1 1 > Si 13.488916508 0.145662378 -1.270785947 > 1 1 1 > Si 13.518286278 3.856930210 -1.498335979 > 1 1 1 > Si 13.546969595 7.828865664 -1.302717477 > 1 1 1 > Si 13.325170521 11.425900779 -1.305690991 > 1 1 1 > Si 1.928794839 1.935631174 -2.816368782 > 1 1 1 > Si 1.903015360 5.856544012 -2.623544612 > 1 1 1 > Si 1.910252703 9.622227600 -2.833834705 > 1 1 1 > Si 1.902564806 13.423206056 -2.588637771 > 1 1 1 > Si 5.764947952 1.938838768 -2.906677641 > 1 1 1 > Si 5.755850841 5.869037091 -2.646163508 > 1 1 1 > Si 5.756126116 9.618251816 -2.845372988 > 1 1 1 > Si 5.746927556 13.385834763 -2.617002944 > 1 1 1 > Si 9.557988586 1.928794265 -2.831589665 > 1 1 1 > Si 9.574641759 5.900158856 -2.670826884 > 1 1 1 > Si 9.596291600 9.619686826 -2.838054333 > 1 1 1 > Si 9.575129529 13.378351513 -2.606953682 > 1 1 1 > Si 13.438269672 1.922429563 -2.844702276 > 1 1 1 > Si 13.456927720 5.889563844 -2.667358157 > 1 1 1 > Si 13.432406374 9.625624451 -2.834683722 > 1 1 1 > Si 13.423819273 13.449905751 -2.556467349 > 1 1 1 > Si 0.003993115 1.918472534 -4.160541912 > 1 1 1 > Si 0.008812095 5.788767480 -4.044515669 > 1 1 1 > Si -0.006256380 9.604384862 -4.149176784 > 1 1 1 > Si -0.016165869 13.425104639 -3.988847549 > 1 1 1 > Si 3.831309097 1.936584114 -4.184775749 > 1 1 1 > Si 3.825457270 5.806591786 -4.015090913 > 1 1 1 > Si 3.830667539 9.619463962 -4.148709049 > 1 1 1 > Si 3.820682728 13.452230978 -3.998580292 > 1 1 1 > Si 7.689282144 1.924833656 -4.207601619 > 1 1 1 > Si 7.664043631 5.791769734 -4.047164251 > 1 1 1 > Si 7.677981583 9.605638594 -4.152240006 > 1 1 1 > Si 7.667996338 13.411472052 -4.007396250 > 1 1 1 > Si 11.502265161 1.927851866 -4.148648209 > 1 1 1 > Si 11.516429852 5.808318797 -4.025335694 > 1 1 1 > Si 11.515754131 9.618965790 -4.150926406 > 1 1 1 > Si 11.516598061 13.461707996 -3.988204540 > 1 1 1 > Si 0.004516669 -0.039550550 -5.437703631 > === message truncated === ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, IFM, Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ From degironc at sissa.it Wed Apr 23 17:52:05 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 23 Apr 2008 17:52:05 +0200 Subject: [Pw_forum] "charge is wrong" In-Reply-To: References: <345198.26069.qm@web33107.mail.mud.yahoo.com> <480F1764.60301@sissa.it> Message-ID: <480F5B25.2000009@sissa.it> Dear Framcesca, when does the error occurs ? before/after the first scf iteration? just after an ionic move ? after restarting an interrupted run ? stefano Francesca Costanzo wrote: > Dear all, > I have a problem when I run the optimization geometry of > terthiophene on Si(001). > > The error looks like: > ------------------------------------------------------------------------- > WARNING: integrated charge= 476.79997686, expected= 490.00000000 > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from electrons : error # 1 > charge is wrong > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > -------------------------------------------------------------- > I have read in your forum that this error can be generated by a wrong > pseudopotential. > I don't think is that the problem > since I have already optimized with the same conditions and the > same pseudopotentials the dithiophene molecule on the Si(001) surface > and the surface Si(001) such as. > May you suggest to me what should I pay attention to ? > best regards, > Francesca Costanzo > > From costanzo at ms.fci.unibo.it Wed Apr 23 18:15:58 2008 From: costanzo at ms.fci.unibo.it (Francesca Costanzo) Date: Wed, 23 Apr 2008 18:15:58 +0200 (CEST) Subject: [Pw_forum] "charge is wrong" In-Reply-To: <480F5B25.2000009@sissa.it> References: <345198.26069.qm@web33107.mail.mud.yahoo.com> <480F1764.60301@sissa.it> <480F5B25.2000009@sissa.it> Message-ID: Dear Stefano, after number of scf cycles = 14 number of bfgs steps = 12 where the energy were going down the run was interrupted without error. Then, I took the last optimized geometry starting "from_scratch" and the error "charge is wrong" appears after number of scf cycles = 1 number of bfgs steps = 0 the only possibility that I see is that it took the old si.save file without overwrite on it, although I used the keyword "from_scratch". Is it possible? Thanks anywyay, Francesca On Wed, 23 Apr 2008, Stefano de Gironcoli wrote: > Dear Framcesca, > when does the error occurs ? > before/after the first scf iteration? just after an ionic move ? > after restarting an interrupted run ? > stefano > > Francesca Costanzo wrote: >> Dear all, >> I have a problem when I run the optimization geometry of >> terthiophene on Si(001). >> >> The error looks like: >> ------------------------------------------------------------------------- >> WARNING: integrated charge= 476.79997686, expected= 490.00000000 >> >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> from electrons : error # 1 >> charge is wrong >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> stopping ... >> -------------------------------------------------------------- >> I have read in your forum that this error can be generated by a wrong >> pseudopotential. >> I don't think is that the problem >> since I have already optimized with the same conditions and the >> same pseudopotentials the dithiophene molecule on the Si(001) surface >> and the surface Si(001) such as. >> May you suggest to me what should I pay attention to ? >> best regards, >> Francesca Costanzo >> >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From degironc at sissa.it Wed Apr 23 18:34:22 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 23 Apr 2008 18:34:22 +0200 Subject: [Pw_forum] "charge is wrong" In-Reply-To: References: <345198.26069.qm@web33107.mail.mud.yahoo.com> <480F1764.60301@sissa.it> <480F5B25.2000009@sissa.it> Message-ID: <480F650E.6020800@sissa.it> Francesca Costanzo wrote: > Dear Stefano, > after > number of scf cycles = 14 > number of bfgs steps = 12 > where the energy were going down the run was interrupted without error. > > Then, I took the last optimized geometry starting "from_scratch" and > the error "charge is wrong" appears after > number of scf cycles = 1 > number of bfgs steps = 0 > > so it completed one full scf cycle starting from_scratch with the new configuration.... is the starting (superposition of atomic) charge at the beginning of the run ok ? are the forces very large ? is the new configuration reasonable, the total energy as expected? after how many iteration of the second scf cycle does the code crash ? Something to try is to clean manually the scratch area and see if the error appears again. stefano stefano From mark.kosmowski at gmail.com Wed Apr 23 18:46:29 2008 From: mark.kosmowski at gmail.com (Mark Kosmowski) Date: Wed, 23 Apr 2008 12:46:29 -0400 Subject: [Pw_forum] "charge is wrong" Message-ID: You have 12 carbons, 3 sulfurs, 96 silicons and 40 hydrogens. Is this correct? For this many atoms I would expect to see (I do molecular solids) either the number of hydrogens divisible by 3 or that there be 4 sulfurs. I am not familiar with your system, but it might not hurt to double check your &ions section. Mark Kosmowski Syracuse University Syracuse, NY US > Message: 1 > Date: Wed, 23 Apr 2008 16:16:37 +0300 > From: "O. Baris Malcioglu" > Subject: Re: [Pw_forum] "charge is wrong" > To: PWSCF Forum > Message-ID: <480F36B5.8050404 at gmail.com> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Francesca, > > I have encountered this error once. > > Did you try increasing ecutrho? Sometimes this solves the problem, > (Yours seem particularly low to me) > > In my case, it turned out to be something going wrong in the > parametrization of USPP I have used, however. > > hope this helps, > > > O. Baris Malcioglu > SISSA Trieste, Italy > > Francesca Costanzo wrote: > > Thank you Paolo > > for your quick answer, > > may be the input file can be more self explaining. > > By the way the machine where the job is running is the sp5 at Cineca. > > > > > > --------------------------------------------------- > > # self-consistent calculation > > cat > si-large-t3.in << EOF > > &control > > max_seconds = 12000 > > calculation='relax' > > prefix='si', > > tstress = .true. > > tprnfor = .true. > > restart_mode= 'from_scratch', > > pseudo_dir ='/sfs/sanfs/home/userincm/incbo407/PWscf/pseudo/', > > outdir='/scratch/incbo407/au-PWscf/test-3/', > > etot_conv_thr = 1.d-4 > > nstep= 200 > > / > > &system > > ibrav = 8, celldm(1) = 29.02243, celldm(2) = 1.0, celldm(3)= 0.89771, > > nat=151, ntyp=4, ecutwfc=25.0, ecutrho =150.0 > > / > > &electrons > > mixing_mode = 'plain' > > mixing_beta = 0.1 > > conv_thr = 1.0d-6 > > / > > &ions > > upscale = 100.D0 > > / > > ATOMIC_SPECIES > > C 12.0107 C.pw91-van_ak.UPF > > S 32.066 S.pw91-van_ak.UPF > > Si 28.086 Si.pw91-n-van.UPF > > H 1.00794 H.pw91-van_ak.UPF > > ATOMIC_POSITIONS {angstrom} > > C 6.323650155 1.945078917 1.942084640 1 1 1 > > C 4.985668179 2.145241151 1.908512881 1 1 1 > > C 7.070612552 0.658816882 1.880463439 1 1 1 > > C 4.095635106 3.335729482 1.712456076 1 1 1 > > C 8.335549051 0.851620731 2.591437070 1 1 1 > > C 2.789704215 3.003130118 2.349365500 1 1 1 > > C 2.564179766 1.679800841 2.532646946 1 1 1 > > C 8.796543791 2.142383776 2.590638952 1 1 1 > > C 10.596966037 3.807722785 2.209610013 1 1 1 > > C 11.932582810 3.847106050 1.632135869 1 1 1 > > C 12.621210230 2.572450605 1.823957122 1 1 1 > > C 10.162049375 2.552383486 2.512288015 1 1 1 > > S 11.491577580 1.333197439 2.166171201 1 1 1 > > S 3.939462625 0.693654418 1.999470582 1 1 1 > > S 7.495754331 3.283820690 2.003311263 1 1 1 > > Si -0.025458690 0.578077012 0.212317046 1 1 1 > > Si -0.004095184 2.805979901 -0.577632902 1 1 1 > > Si -0.012464715 8.317146922 0.197311075 1 1 1 > > Si -0.010166785 10.525788261 -0.639504802 1 1 1 > > Si 3.742398541 0.811087438 -0.433554906 1 1 1 > > Si 3.840497867 3.192970034 -0.263154075 1 1 1 > > Si 3.820010046 8.707761278 -0.653146160 1 1 1 > > Si 3.825401546 10.912982215 0.173089839 1 1 1 > > Si 7.566244166 0.715578013 -0.172518628 1 1 1 > > Si 7.715668688 3.075042380 -0.455669890 1 1 1 > > Si 7.663284193 8.313847847 0.172107233 1 1 1 > > Si 7.669250544 10.521630467 -0.653840380 1 1 1 > > Si 11.399656452 0.880142457 -0.256213627 1 1 1 > > Si 11.606233646 3.270986863 -0.342190601 1 1 1 > > Si 11.515219587 8.706224746 -0.649959230 1 1 1 > > Si 11.519315521 10.909865275 0.181585107 1 1 1 > > Si 1.733991281 0.087139576 -1.335025290 1 1 1 > > Si 1.899706795 3.844207758 -1.383064548 1 1 1 > > Si 1.788404924 7.824466165 -1.299397549 1 1 1 > > Si 2.011898191 11.423909440 -1.305474548 1 1 1 > > Si 5.719323806 0.084506663 -1.445404999 1 1 1 > > Si 5.747106383 3.819883863 -1.466863573 1 1 1 > > Si 5.852062580 7.827307603 -1.311526041 1 1 1 > > Si 5.639188874 11.411099120 -1.305030585 1 1 1 > > Si 9.496576315 0.050684040 -1.365756480 1 1 1 > > Si 9.631649626 3.876980764 -1.476073080 1 1 1 > > Si 9.481240311 7.831908335 -1.304628797 1 1 1 > > Si 9.704384413 11.405951019 -1.298119558 1 1 1 > > Si 13.488916508 0.145662378 -1.270785947 1 1 1 > > Si 13.518286278 3.856930210 -1.498335979 1 1 1 > > Si 13.546969595 7.828865664 -1.302717477 1 1 1 > > Si 13.325170521 11.425900779 -1.305690991 1 1 1 > > Si 1.928794839 1.935631174 -2.816368782 1 1 1 > > Si 1.903015360 5.856544012 -2.623544612 1 1 1 > > Si 1.910252703 9.622227600 -2.833834705 1 1 1 > > Si 1.902564806 13.423206056 -2.588637771 1 1 1 > > Si 5.764947952 1.938838768 -2.906677641 1 1 1 > > Si 5.755850841 5.869037091 -2.646163508 1 1 1 > > Si 5.756126116 9.618251816 -2.845372988 1 1 1 > > Si 5.746927556 13.385834763 -2.617002944 1 1 1 > > Si 9.557988586 1.928794265 -2.831589665 1 1 1 > > Si 9.574641759 5.900158856 -2.670826884 1 1 1 > > Si 9.596291600 9.619686826 -2.838054333 1 1 1 > > Si 9.575129529 13.378351513 -2.606953682 1 1 1 > > Si 13.438269672 1.922429563 -2.844702276 1 1 1 > > Si 13.456927720 5.889563844 -2.667358157 1 1 1 > > Si 13.432406374 9.625624451 -2.834683722 1 1 1 > > Si 13.423819273 13.449905751 -2.556467349 1 1 1 > > Si 0.003993115 1.918472534 -4.160541912 1 1 1 > > Si 0.008812095 5.788767480 -4.044515669 1 1 1 > > Si -0.006256380 9.604384862 -4.149176784 1 1 1 > > Si -0.016165869 13.425104639 -3.988847549 1 1 1 > > Si 3.831309097 1.936584114 -4.184775749 1 1 1 > > Si 3.825457270 5.806591786 -4.015090913 1 1 1 > > Si 3.830667539 9.619463962 -4.148709049 1 1 1 > > Si 3.820682728 13.452230978 -3.998580292 1 1 1 > > Si 7.689282144 1.924833656 -4.207601619 1 1 1 > > Si 7.664043631 5.791769734 -4.047164251 1 1 1 > > Si 7.677981583 9.605638594 -4.152240006 1 1 1 > > Si 7.667996338 13.411472052 -4.007396250 1 1 1 > > Si 11.502265161 1.927851866 -4.148648209 1 1 1 > > Si 11.516429852 5.808318797 -4.025335694 1 1 1 > > Si 11.515754131 9.618965790 -4.150926406 1 1 1 > > Si 11.516598061 13.461707996 -3.988204540 1 1 1 > > Si 0.004516669 -0.039550550 -5.437703631 1 1 1 > > Si 0.000710101 3.873463623 -5.446311522 1 1 1 > > Si 0.004862419 7.673495411 -5.462160638 1 1 1 > > Si -0.003131150 11.544916747 -5.447998083 1 1 1 > > Si 3.837941197 -0.027281489 -5.451757548 1 1 1 > > Si 3.836493404 3.898425643 -5.446530286 1 1 1 > > Si 3.837293937 7.683349298 -5.457596121 1 1 1 > > Si 3.835808961 11.559981099 -5.444452634 1 1 1 > > Si 7.679408716 -0.047227212 -5.448822898 1 1 1 > > Si 7.678278727 3.887025773 -5.461385616 1 1 1 > > Si 7.674423050 7.675865823 -5.465088887 1 1 1 > > Si 7.675452021 11.537889569 -5.458660907 1 1 1 > > Si 11.515174947 -0.018506642 -5.444439779 1 1 1 > > Si 11.513139299 3.885349183 -5.435430684 1 1 1 > > Si 11.518512872 7.682748486 -5.461111142 1 1 1 > > Si 11.518802734 11.565220239 -5.440600617 1 1 1 > > Si 1.920000583 0.000000000 -6.787005141 0 0 0 > > Si 1.920000583 3.840001695 -6.787005141 0 0 0 > > Si 1.920000583 7.679002187 -6.787005141 0 0 0 > > Si 1.920000583 11.519003354 -6.787005141 0 0 0 > > Si 5.759004250 0.000000000 -6.787005141 0 0 0 > > Si 5.759004250 3.840001695 -6.787005141 0 0 0 > > Si 5.759004250 7.679002187 -6.787005141 0 0 0 > > Si 5.759004250 11.519003354 -6.787005141 0 0 0 > > Si 9.599005416 0.000000000 -6.787005141 0 0 0 > > Si 9.599005416 3.840001695 -6.787005141 0 0 0 > > Si 9.599005416 7.679002187 -6.787005141 0 0 0 > > Si 9.599005416 11.519003354 -6.787005141 0 0 0 > > Si 13.439006583 0.000000000 -6.787005141 0 0 0 > > Si 13.439006583 3.840001695 -6.787005141 0 0 0 > > Si 13.439006583 7.679002187 -6.787005141 0 0 0 > > Si 13.439006583 11.519003354 -6.787005141 0 0 0 > > H 12.529065981 4.760266317 1.683438182 0 0 0 > > H 9.966561700 4.705072497 2.289501202 1 1 1 > > H 13.664446286 2.298383667 1.926092211 1 1 1 > > H 6.432753586 -0.237462585 2.045455167 1 1 1 > > H 4.541701287 4.303625762 1.990744173 1 1 1 > > H 8.945620008 0.011821173 2.925131269 1 1 1 > > H 2.044200744 3.761126301 2.582349855 1 1 1 > > H 1.676812571 1.164499388 2.876654725 1 1 1 > > H 1.921800844 -1.178600503 -7.731501862 0 0 0 > > H 1.920601199 1.182700568 -7.726104254 0 0 0 > > H 1.920300627 2.663400954 -7.734205958 0 0 0 > > H 1.921500801 5.020302445 -7.729104689 0 0 0 > > H 1.918400880 6.498201366 -7.728305632 0 0 0 > > H 1.919200996 8.855506090 -7.734401754 0 0 0 > > H 1.920300627 10.335905903 -7.725500992 0 0 0 > > H 1.918300866 12.697407002 -7.731702950 0 0 0 > > H 5.757803018 -1.179300604 -7.729602116 0 0 0 > > H 5.759602221 1.180000176 -7.729702660 0 0 0 > > H 5.760401278 2.659601461 -7.729305777 0 0 0 > > H 5.757601931 5.018002640 -7.732004581 0 0 0 > > H 5.758501532 6.499302054 -7.729803203 0 0 0 > > H 5.759803308 8.858204894 -7.730305922 0 0 0 > > H 5.759205338 10.338403619 -7.728406175 0 0 0 > > H 5.758300444 12.697608090 -7.730401174 0 0 0 > > H 9.597301466 -1.179000561 -7.729104689 0 0 0 > > H 9.598502698 1.179600648 -7.730104834 0 0 0 > > H 9.598603242 2.658401287 -7.727400739 0 0 0 > > H 9.597703640 5.017602582 -7.732401464 0 0 0 > > H 9.600603532 6.500603831 -7.731300775 0 0 0 > > H 9.600201357 8.859903553 -7.727802913 0 0 0 > > H 9.599005416 10.339006881 -7.728803058 0 0 0 > > H 9.600905163 12.697205915 -7.730004291 0 0 0 > > H 13.439906184 -1.179200590 -7.729702660 0 0 0 > > H 13.438207525 1.180300749 -7.729205233 0 0 0 > > H 13.437307924 2.660401048 -7.730004291 0 0 0 > > H 13.439805640 5.018801698 -7.730903892 0 0 0 > > H 13.439805640 6.500101112 -7.730803348 0 0 0 > > H 13.437805350 8.858702320 -7.729903747 0 0 0 > > H 13.439006583 10.338504163 -7.728702515 0 0 0 > > H 13.439705097 12.697703342 -7.730501717 0 0 0 > > K_POINTS {automatic} > > 1 1 1 0 0 0 > > EOF > > > > ------------------------------------------------------------------------------ > > > > > > > > Best reagrds, > > Francesca > > > > > > On Wed, 23 Apr 2008, Paolo Giannozzi wrote: > > > > > >> Francesca Costanzo wrote: > >> > >> > >>> The error looks like: > >>> ------------------------------------------------------------------------- > >>> WARNING: integrated charge= 476.79997686, expected= 490.00000000 > >>> > >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > >>> from electrons : error # 1 > >>> charge is wrong > >>> > >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > >>> > >>> stopping ... > >>> -------------------------------------------------------------- > >>> > >> some errors are self-explaining, others are not and may originate > >> from errors in data or peculiar conditions that are impossible to > >> locate and pinpoint on the basis of the error mesage alone. This > >> error belong to the second case, so more information is required > >> > >> Paolo > >> > >> > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > ------------------------------ > From giannozz at nest.sns.it Wed Apr 23 19:08:57 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 23 Apr 2008 19:08:57 +0200 Subject: [Pw_forum] "charge is wrong" In-Reply-To: <606941.54240.qm@web65703.mail.ac4.yahoo.com> References: <606941.54240.qm@web65703.mail.ac4.yahoo.com> Message-ID: <480F6D29.9000506@nest.sns.it> Eyvaz Isaev wrote: > As you can see you got charge deficieny, meaning that > bands number is not sufficient. You did not specify > any occupations keyword, so your system is considered > as insulator (or semiconducting) for which only > nbnd=(number of valence electros divided by 2) is > used. It might be that during relaxation process your > system turns to be metallic for which one should use > more bands number. > So, try nbnd=490/2 + 10= 255 (in &system) this might be a good suggestion, and one that is valid in any case: having a few more bands and a small broadening is a a good insurance against nasty phenomena such as bad or no convergence. However: I run the same job (using gamma instead of 0,0,0 so that it runs faster) with the current development version: it seems to work. So it might also be a problem with the previous version of the parallel subspace diagonalization. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From sagarambavale at yahoo.co.in Thu Apr 24 08:21:42 2008 From: sagarambavale at yahoo.co.in (ambavale sagar) Date: Thu, 24 Apr 2008 11:51:42 +0530 (IST) Subject: [Pw_forum] wrong nrztot Message-ID: <446216.58363.qm@web94602.mail.in2.yahoo.com> Dear Smogunov sir, Sorry but i can'at understand that why only tetragonal must be used as electrode bulk geometry? can't we use FCC? and how to define this(fcc) geometry using tetragonal unit cell with only two atoms? sagar %%%%%%%%%%%%%%%%%%%%%%%%%% Dear Sagar. This is because you should use the tetragonal unit cell with two atoms per cell like in the example 12. Regards, Alexander On Tuesday 22 April 2008 11:24, ambavale sagar wrote: > sorry, i forgot to attach scf file and my signature. so resending the > entire mail. i am using espresso 4.0cvs2 for calculating complex band > structure of al bulk in 100 direction( for 001 it is given in example 12). > this gives me following errror: > > from in init_cond : error # 1626817 > wrong nrztot > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >%%% > > stopping ... > > the input file for complex band is : > > &inputcond > outdir='/db/sagar/tmp/' > prefixl='al_bulk' > band_file ='bands.albulk' > ikind=0 > energy0=10.d0 > denergy=-0.4d0 > ewind=1.d0 > epsproj=1.d-3 > delgep = 1.d-12 > cutplot = 3.d0 > / > 1 > 0.0 0.0 1.0 > 60 > > while the file for scf calculation is: > > &control > calculation='scf' > restart_mode='from_scratch', > pseudo_dir = '/db/espresso4.0cvs2/pseudo/', > outdir='/db/sagar/tmp/', > prefix='al_bulk' > tprnfor = .true. > tstress = .true. > / > &system > ibrav= 2, celldm(1) =7.50, nat= 1, ntyp= 1, ecutwfc =15.0, > occupations='smearing', smearing='marzari-vanderbilt', degauss=0.05 > / > &electrons > diagonalization='david' > mixing_beta = 0.7 > / > ATOMIC_SPECIES > Al 26.98 Al.vbc.UPF > ATOMIC_POSITIONS > Al 0.00 0.00 0.00 > K_POINTS (automatic) > 2 2 2 1 1 1 > > > Sagar Ambavale > PhD student > The M.S.University of Baroda > Inida Best Jokes, Best Friends, Best Food and more. Go to http://in.promos.yahoo.com/groups/bestofyahoo/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080424/32599a5e/attachment.htm From smogunov at sissa.it Thu Apr 24 09:15:19 2008 From: smogunov at sissa.it (Alexander) Date: Thu, 24 Apr 2008 08:15:19 +0100 Subject: [Pw_forum] wrong nrztot In-Reply-To: <446216.58363.qm@web94602.mail.in2.yahoo.com> References: <446216.58363.qm@web94602.mail.in2.yahoo.com> Message-ID: <200804240915.19855.smogunov@sissa.it> Dear Sagar. You can describe the fcc structure with tetragonal unit cell: a1=(a/2,-a/2,0) a2=(a/2,a/2,0) a3=(0,0,a) having two atoms at 0 and at 0.5*(a1+a2+a3). Of course, you can use fcc as the leads but as it is implemented in pwcond now your unit cell should be monoclinic (tetragonal is a particular case of monoclinic), i.e. such that a3 is perpendicular to both a1 and a2 and the direction of transport is a3. The one-dimensional complex bands are calculated at fixed (k1,k2) along the k3 direction which will coincide with a3. In the setup above with k1=k2=0 they will be complex bands in [001] direction. Anyway, [100] (what you want to calculate) and [001] (what is presented in the example 12) are equivalent directions in fcc. Best regards, Alexander On Thursday 24 April 2008 08:21, ambavale sagar wrote: > Dear Smogunov sir, > Sorry but i can'at understand that why only tetragonal must be used as > electrode bulk geometry? can't we use FCC? > and how to define this(fcc) geometry using tetragonal unit cell with only > two atoms? > > sagar > > %%%%%%%%%%%%%%%%%%%%%%%%%% > Dear Sagar. > This is because you should use the tetragonal > unit cell with two atoms per cell like in the example 12. > Regards, > Alexander > > On Tuesday 22 April 2008 11:24, ambavale sagar wrote: > > sorry, i forgot to attach scf file and my signature. so resending the > > entire mail. i am using espresso 4.0cvs2 for calculating complex band > > structure of al bulk in 100 direction( for 001 it is given in example > > 12). this gives me following errror: > > > > from in init_cond : error # 1626817 > > wrong nrztot > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > >%% %%% > > > > stopping ... > > > > the input file for complex band is : > > > > &inputcond > > outdir='/db/sagar/tmp/' > > prefixl='al_bulk' > > band_file ='bands.albulk' > > ikind=0 > > energy0=10.d0 > > denergy=-0.4d0 > > ewind=1.d0 > > epsproj=1.d-3 > > delgep = 1.d-12 > > cutplot = 3.d0 > > / > > 1 > > 0.0 0.0 1.0 > > 60 > > > > while the file for scf calculation is: > > > > &control > > calculation='scf' > > restart_mode='from_scratch', > > pseudo_dir = '/db/espresso4.0cvs2/pseudo/', > > outdir='/db/sagar/tmp/', > > prefix='al_bulk' > > tprnfor = .true. > > tstress = .true. > > / > > &system > > ibrav= 2, celldm(1) =7.50, nat= 1, ntyp= 1, ecutwfc =15.0, > > occupations='smearing', smearing='marzari-vanderbilt', degauss=0.05 > > / > > &electrons > > diagonalization='david' > > mixing_beta = 0.7 > > / > > ATOMIC_SPECIES > > Al 26.98 Al.vbc.UPF > > ATOMIC_POSITIONS > > Al 0.00 0.00 0.00 > > K_POINTS (automatic) > > 2 2 2 1 1 1 > > > > > > Sagar Ambavale > > PhD student > > The M.S.University of Baroda > > Inida > > Best Jokes, Best Friends, Best Food and more. Go to > http://in.promos.yahoo.com/groups/bestofyahoo/ From costanzo at ms.fci.unibo.it Thu Apr 24 14:17:54 2008 From: costanzo at ms.fci.unibo.it (Francesca Costanzo) Date: Thu, 24 Apr 2008 14:17:54 +0200 (CEST) Subject: [Pw_forum] "charge is wrong" In-Reply-To: <480F6D29.9000506@nest.sns.it> References: <606941.54240.qm@web65703.mail.ac4.yahoo.com> <480F6D29.9000506@nest.sns.it> Message-ID: Thank you to everybody for your accurate answers. I am trying some of your suggestions. best regards, Francesca On Wed, 23 Apr 2008, Paolo Giannozzi wrote: > Eyvaz Isaev wrote: > >> As you can see you got charge deficieny, meaning that >> bands number is not sufficient. You did not specify >> any occupations keyword, so your system is considered >> as insulator (or semiconducting) for which only >> nbnd=(number of valence electros divided by 2) is >> used. It might be that during relaxation process your >> system turns to be metallic for which one should use >> more bands number. >> So, try nbnd=490/2 + 10= 255 (in &system) > > this might be a good suggestion, and one that is valid in > any case: having a few more bands and a small broadening > is a a good insurance against nasty phenomena such as bad > or no convergence. > > However: I run the same job (using gamma instead of 0,0,0 > so that it runs faster) with the current development version: > it seems to work. So it might also be a problem with the > previous version of the parallel subspace diagonalization. > > Paolo > -- Francesca Costanzo, Ph.D. Dipartimento di Chimica Fisica ed Inorganica Viale Risorgimento 4 40136 Bologna tel.0039-051-2093710 fax 0039-051-2093690 From jtmullen at ncsu.edu Thu Apr 24 17:52:28 2008 From: jtmullen at ncsu.edu (jtmullen at ncsu.edu) Date: Thu, 24 Apr 2008 11:52:28 -0400 (EDT) Subject: [Pw_forum] Compiling ESPRESSO 3.2.3 on Mac OS X PPC Message-ID: <51085.152.14.74.99.1209052348.squirrel@webmail.ncsu.edu> Greetings, I am attempting to compile ESPRESSO 3.2.3 on my Mac in debug mode so that I can step through the code to become familiar with various function implementations. I cannot get it to compile, though I can compile my own fortran programs with the compiler configuration. I confess that though I can follow MAKE somewhat, I am very unfamiliar with autoconf, so I hope that the solution is obvious and I am just missing it. Details of machine configuration Max OS X 10.4 PPC GCC 4.0 installed via Fink using gfortran installed at /sw/bin/gfortran Command line configure ./configure F90=/sw/bin/gfortran F77=/sw/bin/gfortran (I tried only setting F90, but this caused more problems) Output ---------------------------------------------------------- checking build system type... powerpc-apple-darwin8.11.0 checking architecture... macppc checking for Fortran 77 compiler default output file name... a.out checking whether the Fortran 77 compiler works... yes checking whether we are cross compiling... yes checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU Fortran 77 compiler... yes checking whether /sw/bin/gfortran accepts -g... yes checking for mpxlf90... no checking for mpf90... no checking for /sw/bin/gfortran... no checking whether we are using the GNU Fortran 77 compiler... no checking whether accepts -g... no setting F90... /sw/bin/gfortran setting MPIF90... ..... DELETED SUCCESSFUL HEADER FILE CHECKS FOR BREVITY...... checking size of int *... 4 checking malloc.h usability... no checking malloc.h presence... no checking for malloc.h... no checking for /sw/bin/gfortran... no checking whether we are using the GNU Fortran 77 compiler... no checking whether accepts -g... no setting F77... setting FFLAGS... -O4 -qarch=auto -qtune=auto -qsuffix=cpp=f90 -qdpc -qalias=nointptr setting F90FLAGS... $(FFLAGS) -qfree=f90 setting FFLAGS_NOOPT... -O0 setting CFLAGS... -O3 setting CPP... cpp setting CPPFLAGS... -P -traditional setting LD... setting LDFLAGS... setting AR... libtool setting ARFLAGS... -static -o setting ARFLAGS_DYNAMIC...-dynamic -arch_only ppc -all_load -single_module -L/opt/ibmcmp/xlf/8.1/lib -lxlf90 -lxl -lc -o checking whether make sets $(MAKE)... yes checking whether Fortran files must be preprocessed... no checking how to get verbose linking output from ... configure: WARNING: compilation failed checking for Fortran libraries of ... checking for dummy main to link with Fortran libraries... none checking for Fortran name-mangling scheme... configure: error: cannot compile a simple Fortran program See `config.log' for more details. -------------------------------------------------------- The config.log file is huge, but I can certainly post some of it if someone can make use of it. Has someone compiled the code on a machine configured like mine and, if so, can you point me in the right direction ? Thanks Jeff Mullen Graduate Student Dept of Physics North Carolina State University From giannozz at nest.sns.it Thu Apr 24 18:51:45 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 24 Apr 2008 18:51:45 +0200 Subject: [Pw_forum] Compiling ESPRESSO 3.2.3 on Mac OS X PPC In-Reply-To: <51085.152.14.74.99.1209052348.squirrel@webmail.ncsu.edu> References: <51085.152.14.74.99.1209052348.squirrel@webmail.ncsu.edu> Message-ID: <4810BAA1.8030905@nest.sns.it> jtmullen at ncsu.edu wrote: > I am attempting to compile ESPRESSO 3.2.3 on my Mac please use the cvs cnapshot: it has better support for both Mac and gfortran. Please also note that only recent versions of gfortran are able to produce working executables for at least part of quantum-espresso. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From polynmr at physics.unc.edu Thu Apr 24 21:41:00 2008 From: polynmr at physics.unc.edu (Charles) Date: Thu, 24 Apr 2008 15:41:00 -0400 Subject: [Pw_forum] LSF problem? Message-ID: <4810E24C.1000805@physics.unc.edu> Dear PWSCF users Recently I compiled QE4.0cvs2 on SGI Altix with 128 Itanium2 CPU running Linux. MPI is used. Job need to be submitted to the cluster via LSF, and the cluster also provides 8 CPU for testing jobs. I did some calculation with pw.x on the example silicon system. Here is the strange I found 1. run locally on the 8 CPU cluster, requesting 4 CPUs for the job the reported time used by PWSCF is 4.38s CPU time and 2.02s wall time. It does not look bad to me. 2. run on 128-CPU cluster, requesting 4 CPUs for the job PWSCF reports" Number of processors in use: 4 R & G space division: proc/pool = 4 PWSCF : 35m48.41s CPU time, 3m14.98s wall time This is too slow I guess and the system is overloaded if I run some big system. It looks there is something wrong with the system. But the system administrator can not provide useful support on this case. Could anybody have the similar system tell me how to tweak the compilation? Thanks! Charles From akohlmey at cmm.chem.upenn.edu Thu Apr 24 21:39:58 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 24 Apr 2008 15:39:58 -0400 (EDT) Subject: [Pw_forum] LSF problem? In-Reply-To: <4810E24C.1000805@physics.unc.edu> References: <4810E24C.1000805@physics.unc.edu> Message-ID: On Thu, 24 Apr 2008, Charles wrote: C> Dear PWSCF users dear charles, C> 1. run locally on the 8 CPU cluster, requesting 4 CPUs for the job C> C> the reported time used by PWSCF is 4.38s CPU time and 2.02s wall time. you should keep in mind, that this is a _very_ small job and thus does not parallelize very well. C> It does not look bad to me. C> C> 2. run on 128-CPU cluster, requesting 4 CPUs for the job C> C> PWSCF reports" C> Number of processors in use: 4 C> R & G space division: proc/pool = 4 C> PWSCF : 35m48.41s CPU time, 3m14.98s wall time ahhhh. i know that one. you are most likely another victim of the atomatic multi-threading of intel MKL. your MKL will try to run as many threads as your machine has CPU cores, that is why your CPU time is so much higher than your wall time. since spawning that many threads costs so much time (particularly if the batch system confines you to the number of nodes that you request) your wall time goes up enormously as well. you should do three things: a) you can set up your environment to have the environment variable OMP_NUM_THREADS set to 1. that should make your executable behave reasonably, provided there are no other users on that machine suffering from the same problem and that LSF actually supports and activates processor sets. b) you should have a word with your system admins to forcibly set OMP_NUM_THREADS by default to 1 for everybody. c) you can link QE executables with mkl in a way that you using the non-threaded core libraries. just change your make.sys so that LAPACK_LIBS is empty and BLAS_LIBS BLAS_LIBS = -L$(MKL_PATH) -lmkl_intel_lp64 -lmkl_sequential -lmkl_core you have to set MKL_PATH to the directory of where your MKL is installed. BTW, the same works for opteron/em64t-xeons. C> This is too slow I guess and the system is overloaded if I run some big C> system. C> C> It looks there is something wrong with the system. But the system C> administrator can not provide useful support on this case. get a new sysadmin then. C> Could anybody have the similar system tell me how to tweak the compilation? yep. you can also look up the docs on the altix of the PSC: http://www.psc.edu/machines/sgi/altix/pople.php the _do_ have good sysadmins. ;-) cheers, axel. C> C> Thanks! C> C> Charles C> C> _______________________________________________ C> Pw_forum mailing list C> Pw_forum at pwscf.org C> http://www.democritos.it/mailman/listinfo/pw_forum C> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From polynmr at physics.unc.edu Fri Apr 25 05:41:22 2008 From: polynmr at physics.unc.edu (Charles Chen) Date: Thu, 24 Apr 2008 23:41:22 -0400 Subject: [Pw_forum] GIAPW LSF problem? In-Reply-To: <4810E24C.1000805@physics.unc.edu> References: <4810E24C.1000805@physics.unc.edu> Message-ID: <481152E2.2060406@physics.unc.edu> Dear PWSCF users I have compiled QE4.0cvs2 on SGI Altix with 128 Itanium2 CPU running Linux. MPI is used. Job need to be submitted to the cluster via LSF, and the cluster also provides 8 CPU for testing jobs without LSF. I can run the examples coming with the package when I use the -in tag to read input files during LSF submission. However, I can not use the method to run the GIPAW example. The error message I get is like this when I tried to calculate NMR with gipaw.x: from LSF: > MPI: --------stack traceback------- > line: 2 Unable to parse input as legal command or C expression. > The "backtrace" command has failed because there is no running program. > MPI: Intel(R) Debugger for applications running on IA-64, Version > 10.1-32 , Build 20070829 > > MPI: -----stack traceback ends----- > MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize() > MPI: aborting job from gipaw: > from gipaw_readin : error # 1 > reading inputgipaw namelist So, the gipaw.x does not read the input file. To make sure I have the correct input file, I run the job locally without LSF and I successfully got the NMR result. Is there something I need to specify when I make gipaw.x, so that it can read the input file with -in tag? Or this is a problem purely related to LSF? Thanks in advance! Charles Chen From sabatini at sissa.it Fri Apr 25 12:26:19 2008 From: sabatini at sissa.it (Riccardo Sabatini) Date: Fri, 25 Apr 2008 12:26:19 +0200 Subject: [Pw_forum] OpenMPI problems with espresso 4.0cvs Message-ID: <20080425122619.p09gnvluv4skcgsw@webmail.sissa.it> Hello everyone, i finally compiled espresso with MPI (thanks for the suggestion, with gfortran worked perfectly). I had no problem in the compilation but i can't make it run. I'm trying a super easy run: from the exercise01 the si.scf.cg.in. Now, if i run the file with the espresso 3.2 compiled without mpi obviously runs perfectly but if i try the same file with the mpi version it gives me this error (3 times) --------------------------------------------------------------------------------- Program PWSCF v.4.0cvs starts ... Today is 25Apr2008 at 12:11:35 Ultrasoft (Vanderbilt) Pseudopotentials and 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 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_namelists : error # 1 reading namelist control %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... --------------------------------------------------------------------------------- My launch command is (i'm running on a four cores processor now) mpirun -np 4 ../QE-MPI/bin/pw.x < prova.in Is there something i'm missing ? Maybe a line do add for parallel compilation in the input file ? I've tried the only option in the INPUT_PW about parallel compilation, wf_collect, but nothing changes. Since the compilation gave me 0 errors maybe the problem is the combination openMPI+gfotran+espresso-4.0. Thanks for the help, Riccardo ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From baris.malcioglu at gmail.com Fri Apr 25 12:47:17 2008 From: baris.malcioglu at gmail.com (O. Baris Malcioglu) Date: Fri, 25 Apr 2008 12:47:17 +0200 Subject: [Pw_forum] OpenMPI problems with espresso 4.0cvs In-Reply-To: <20080425122619.p09gnvluv4skcgsw@webmail.sissa.it> References: <20080425122619.p09gnvluv4skcgsw@webmail.sissa.it> Message-ID: Hi, Have you checked whether your shared storage is working properly? Regards, O. Baris Malcioglu, SISSA, Italy On Fri, Apr 25, 2008 at 12:26 PM, Riccardo Sabatini wrote: > Hello everyone, > > i finally compiled espresso with MPI (thanks for the suggestion, > with gfortran worked perfectly). I had no problem in the compilation > but i can't make it run. I'm trying a super easy run: from the > exercise01 the si.scf.cg.in. > > Now, if i run the file with the espresso 3.2 compiled without mpi > obviously runs perfectly but if i try the same file with the mpi > version it gives me this error (3 times) > > --------------------------------------------------------------------------------- > > Program PWSCF v.4.0cvs starts ... > Today is 25Apr2008 at 12:11:35 > > Ultrasoft (Vanderbilt) Pseudopotentials and 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 > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_namelists : error # 1 > reading namelist control > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > --------------------------------------------------------------------------------- > > My launch command is (i'm running on a four cores processor now) > > mpirun -np 4 ../QE-MPI/bin/pw.x < prova.in > > Is there something i'm missing ? Maybe a line do add for parallel > compilation in the input file ? I've tried the only option in the > INPUT_PW about parallel compilation, wf_collect, but nothing changes. > Since the compilation gave me 0 errors maybe the problem is the > combination openMPI+gfotran+espresso-4.0. > > Thanks for the help, > > Riccardo > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by Horde http://www.horde.org/ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From akohlmey at cmm.chem.upenn.edu Fri Apr 25 15:31:25 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 25 Apr 2008 09:31:25 -0400 (EDT) Subject: [Pw_forum] OpenMPI problems with espresso 4.0cvs In-Reply-To: <20080425122619.p09gnvluv4skcgsw@webmail.sissa.it> References: <20080425122619.p09gnvluv4skcgsw@webmail.sissa.it> Message-ID: On Fri, 25 Apr 2008, Riccardo Sabatini wrote: RS> Hello everyone, hi riccardo, RS> RS> i finally compiled espresso with MPI (thanks for the suggestion, RS> with gfortran worked perfectly). I had no problem in the compilation RS> but i can't make it run. I'm trying a super easy run: from the RS> exercise01 the si.scf.cg.in. RS> RS> Now, if i run the file with the espresso 3.2 compiled without mpi RS> obviously runs perfectly but if i try the same file with the mpi RS> version it gives me this error (3 times) doing the same thing 3 times doesn't make it more likely to work... RS> stopping ... RS> --------------------------------------------------------------------------------- RS> RS> My launch command is (i'm running on a four cores processor now) RS> RS> mpirun -np 4 ../QE-MPI/bin/pw.x < prova.in have you tried the -in flag? not all MPI implementations replicate the input across all nodes and i personally think it is in general a bad idea to read an input from stdin. we don't run anything interactively these days anyways and being able to check file status etc. is a bit advantage. cheers, axel. RS> Is there something i'm missing ? Maybe a line do add for parallel RS> compilation in the input file ? I've tried the only option in the RS> INPUT_PW about parallel compilation, wf_collect, but nothing changes. RS> Since the compilation gave me 0 errors maybe the problem is the RS> combination openMPI+gfotran+espresso-4.0. RS> RS> Thanks for the help, RS> RS> Riccardo RS> RS> ---------------------------------------------------------------- RS> SISSA Webmail https://webmail.sissa.it/ RS> Powered by Horde http://www.horde.org/ RS> RS> RS> _______________________________________________ RS> Pw_forum mailing list RS> Pw_forum at pwscf.org RS> http://www.democritos.it/mailman/listinfo/pw_forum RS> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From sabatini at sissa.it Fri Apr 25 16:46:48 2008 From: sabatini at sissa.it (Riccardo Sabatini) Date: Fri, 25 Apr 2008 16:46:48 +0200 Subject: [Pw_forum] OpenMPI problems with espresso 4.0cvs In-Reply-To: References: <20080425122619.p09gnvluv4skcgsw@webmail.sissa.it> Message-ID: <20080425164648.c5iz7a5wusss0c8g@webmail.sissa.it> Hi again, i wrote "3 times" meaning that even if i launch mpirun with 4 processors the error comes out just three times, maybe mpirun launches only three instances of the program,sorry for the misunderstanding. I tried to launch with the direct location to the file instead the std input redirection but nothing still works (i don't usually launch pw interactively, was just the pasted snippet to let the mailing list understand me). I haven't tried anyway the -in flag, seems the openmpi i have doesn't understand that flag but i'll look in the help manual to see if there's something similar, maybe the problem is there. I'll let you know as soon as i try. Thanks for the help, regards Riccardo Quoting Axel Kohlmeyer : > On Fri, 25 Apr 2008, Riccardo Sabatini wrote: > > RS> Hello everyone, > > hi riccardo, > > RS> > RS> i finally compiled espresso with MPI (thanks for the suggestion, > RS> with gfortran worked perfectly). I had no problem in the compilation > RS> but i can't make it run. I'm trying a super easy run: from the > RS> exercise01 the si.scf.cg.in. > RS> > RS> Now, if i run the file with the espresso 3.2 compiled without mpi > RS> obviously runs perfectly but if i try the same file with the mpi > RS> version it gives me this error (3 times) > > doing the same thing 3 times doesn't make it more likely to work... > > RS> stopping ... > RS> > --------------------------------------------------------------------------------- > RS> > RS> My launch command is (i'm running on a four cores processor now) > RS> > RS> mpirun -np 4 ../QE-MPI/bin/pw.x < prova.in > > have you tried the -in flag? not all MPI implementations > replicate the input across all nodes and i personally > think it is in general a bad idea to read an input from > stdin. we don't run anything interactively these days > anyways and being able to check file status etc. is > a bit advantage. > > cheers, > axel. > > RS> Is there something i'm missing ? Maybe a line do add for parallel > RS> compilation in the input file ? I've tried the only option in the > RS> INPUT_PW about parallel compilation, wf_collect, but nothing changes. > RS> Since the compilation gave me 0 errors maybe the problem is the > RS> combination openMPI+gfotran+espresso-4.0. > RS> > RS> Thanks for the help, > RS> > RS> Riccardo > RS> > RS> ---------------------------------------------------------------- > RS> SISSA Webmail https://webmail.sissa.it/ > RS> Powered by Horde http://www.horde.org/ > RS> > RS> > RS> _______________________________________________ > RS> Pw_forum mailing list > RS> Pw_forum at pwscf.org > RS> http://www.democritos.it/mailman/listinfo/pw_forum > RS> > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From sabatini at sissa.it Fri Apr 25 16:48:21 2008 From: sabatini at sissa.it (Riccardo Sabatini) Date: Fri, 25 Apr 2008 16:48:21 +0200 Subject: [Pw_forum] OpenMPI problems with espresso 4.0cvs In-Reply-To: References: <20080425122619.p09gnvluv4skcgsw@webmail.sissa.it> Message-ID: <20080425164821.089vkf1l5wwkkgsc@webmail.sissa.it> Hi, right now i'm working on my local machine, just one pc with one 4-core processor and one hard drive, later on i'll try a little network cluster. I keep on trying, we'll see if i can get out (starting to think about a bug somewhere). Thanks for the help, Riccardo Quoting "O. Baris Malcioglu" : > Hi, > > Have you checked whether your shared storage is working properly? > > Regards, > > O. Baris Malcioglu, > > SISSA, Italy > > > On Fri, Apr 25, 2008 at 12:26 PM, Riccardo Sabatini > wrote: >> Hello everyone, >> >> i finally compiled espresso with MPI (thanks for the suggestion, >> with gfortran worked perfectly). I had no problem in the compilation >> but i can't make it run. I'm trying a super easy run: from the >> exercise01 the si.scf.cg.in. >> >> Now, if i run the file with the espresso 3.2 compiled without mpi >> obviously runs perfectly but if i try the same file with the mpi >> version it gives me this error (3 times) >> >> >> --------------------------------------------------------------------------------- >> >> Program PWSCF v.4.0cvs starts ... >> Today is 25Apr2008 at 12:11:35 >> >> Ultrasoft (Vanderbilt) Pseudopotentials and 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 >> >> >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> from read_namelists : error # 1 >> reading namelist control >> >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> stopping ... >> >> --------------------------------------------------------------------------------- >> >> My launch command is (i'm running on a four cores processor now) >> >> mpirun -np 4 ../QE-MPI/bin/pw.x < prova.in >> >> Is there something i'm missing ? Maybe a line do add for parallel >> compilation in the input file ? I've tried the only option in the >> INPUT_PW about parallel compilation, wf_collect, but nothing changes. >> Since the compilation gave me 0 errors maybe the problem is the >> combination openMPI+gfotran+espresso-4.0. >> >> Thanks for the help, >> >> Riccardo >> >> ---------------------------------------------------------------- >> SISSA Webmail https://webmail.sissa.it/ >> Powered by Horde http://www.horde.org/ >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From sabatini at sissa.it Fri Apr 25 16:52:41 2008 From: sabatini at sissa.it (Riccardo Sabatini) Date: Fri, 25 Apr 2008 16:52:41 +0200 Subject: [Pw_forum] OpenMPI problems with espresso 4.0cvs In-Reply-To: References: <20080425122619.p09gnvluv4skcgsw@webmail.sissa.it> <20080425132345.clx45sda0w0wk8o0@webmail.sissa.it> Message-ID: <20080425165241.gngjfl2egwo4c4g4@webmail.sissa.it> Hi, made some trials but nothing still works :(( I specified the machine both with --host both with a machine file, nothing changes and i tried to run it on just one core mpirun -np 1 ../QE-MPI/pw.x < si.scf.cg.in In this case the program doesn't even start, printing this output ---------------------------------------------------------------------- Program PWSCF v.4.0cvs starts ... Today is 25Apr2008 at 14:37:21 Ultrasoft (Vanderbilt) Pseudopotentials and 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 ---------------------------------------------------------------------- I'll write down all the compilation iformation i have, if anyone wonna try to see if it's a bug in the espresso 4 snapshot. ----------------from make.sys DFLAGS = -D__GFORTRAN -D__FFTW -D__USE_INTERNAL_FFTW FDFLAGS = $(DFLAGS) IFLAGS = -I../include MODFLAGS = -I./ -I../Modules -I../iotk/src \ -I../PW -I../PH MPIF90 = mpif90 #F90 = gfortran CC = cc F77 = gfortran CPP = cpp CPPFLAGS = -P -traditional $(DFLAGS) $(IFLAGS) CFLAGS = -O3 $(DFLAGS) $(IFLAGS) F90FLAGS = $(FFLAGS) -x f95-cpp-input $(FDFLAGS) $(IFLAGS) $(MODFLAGS) FFLAGS = -O3 ----------------------------------------------------------------------------- I use the following compilers, GNU Fortran (GCC) 4.2.1 (Ubuntu 4.2.1-5ubuntu4) cc (GCC) 4.1.3 20070929 (prerelease) (Ubuntu 4.1.2-16ubuntu2) cpp (GCC) 4.1.3 20070929 (prerelease) (Ubuntu 4.1.2-16ubuntu2) OpenMPI 1.1-2.5 ubuntu1 Will see if someone can reproduce the problem, in any case thanks again for the help, Riccardo Quoting "O. Baris Malcioglu" : > Hello again, > > Maybe you should try something like > > mpirun -np 4 --host localhost > > or a machine file explicitly stating you are working on the localhost, > > the reason why you are getting 3 errors but not 4 can be related to > openmpi spawning jobs at other machines. > > You can try running the code you have compiled with mpi serially to > see whether the compilation is broken or not. > > Hope this helps, > Baris Malcioglu > SISSA, Italy > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From baroni at sissa.it Fri Apr 25 17:55:15 2008 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 25 Apr 2008 17:55:15 +0200 Subject: [Pw_forum] Greeting from xingqiu chen In-Reply-To: <1209130953.5666.3.camel@chenx-lin.ornl.gov> References: <1209130953.5666.3.camel@chenx-lin.ornl.gov> Message-ID: <6D2AF414-E9F0-445D-8E26-9D6925ECD91B@sissa.it> Dear Xingqiu Chen, in order to calculate anything (phonon frequencies, as well as any other properties) as a function of pressure, just calculate it as a function of volume, and use the (calculated) equation of state to relate volume with pressure. Also, please notice that the correct way to address this kind of questions is through the pw_forum mailing list to which you can subscribe from the pwscf home page: http://www.democritos.it/mailman/listinfo/pw_users Hope this helps SB On Apr 25, 2008, at 3:42 PM, Chen Xingqiu wrote: > Dear Prof. Baroni, > > I am using the package PWscf to calculate phonon dispersions. But in > my > case, I need to calculate pressure-dependent phonon dispersions. So, > could you please show me how to add pressure factor in my input > file. Do > you have such a input script? > > So many thanks in advance! > Best wishes, Xingqiu Chen --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080425/5f03532d/attachment-0001.htm From paulatto at sissa.it Fri Apr 25 18:16:21 2008 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 25 Apr 2008 18:16:21 +0200 (CEST) Subject: [Pw_forum] GIAPW LSF problem? In-Reply-To: <481152E2.2060406@physics.unc.edu> References: <4810E24C.1000805@physics.unc.edu> <481152E2.2060406@physics.unc.edu> Message-ID: <62313.151.65.45.150.1209140181.squirrel@webmail.sissa.it> On Ven, Aprile 25, 2008 05:41, Charles Chen wrote: > So, the gipaw.x does not read the input file. There is no -in nor -input option in gipaw.x, at the moment the only way to feed it the input is via standard input. > Is there something I need to specify when I make gipaw.x, so that it can > read the input file with -in tag? Yes, you have to program it ;-). > Or this is a problem purely related to LSF? Maybe you can still use mpi + lsf whith input redirection. It usually works, but you need the input file on all nodes. (You can create it in the input script using the "cat << eof ... eof" trick as in the examples) regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) +39 040 3787 511 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From polynmr at physics.unc.edu Fri Apr 25 18:22:26 2008 From: polynmr at physics.unc.edu (Charles) Date: Fri, 25 Apr 2008 12:22:26 -0400 Subject: [Pw_forum] GIAPW LSF problem? In-Reply-To: <62313.151.65.45.150.1209140181.squirrel@webmail.sissa.it> References: <4810E24C.1000805@physics.unc.edu> <481152E2.2060406@physics.unc.edu> <62313.151.65.45.150.1209140181.squirrel@webmail.sissa.it> Message-ID: <48120542.30501@physics.unc.edu> Thanks Lorenzo, I found a easy solution. Basically it is to use -i tag of LSF rather than use -in tag for pw, bands, pp, etc. This also works for gipaw. Maybe this can be added as another note in the user guide for people have to struggle with the input redirection. This works for me with mpi+lsf system Charles Lorenzo Paulatto wrote: > On Ven, Aprile 25, 2008 05:41, Charles Chen wrote: >> So, the gipaw.x does not read the input file. > > There is no -in nor -input option in gipaw.x, at the moment the only way > to feed it the input is via standard input. > >> Is there something I need to specify when I make gipaw.x, so that it can >> read the input file with -in tag? > > Yes, you have to program it ;-). > >> Or this is a problem purely related to LSF? > > Maybe you can still use mpi + lsf whith input redirection. It usually > works, but you need the input file on all nodes. (You can create it in the > input script using the "cat << eof ... eof" trick as in the examples) > > regards > From akohlmey at cmm.chem.upenn.edu Fri Apr 25 18:07:24 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 25 Apr 2008 12:07:24 -0400 (EDT) Subject: [Pw_forum] GIAPW LSF problem? In-Reply-To: <48120542.30501@physics.unc.edu> References: <4810E24C.1000805@physics.unc.edu> <481152E2.2060406@physics.unc.edu> <62313.151.65.45.150.1209140181.squirrel@webmail.sissa.it> <48120542.30501@physics.unc.edu> Message-ID: On Fri, 25 Apr 2008, Charles wrote: charles, the even better solution would be to get rid of LSF. it is creating a lot of problems with typical "cluster usage" _and_ costs a lot of money. PBS/Torque+Maui don't cost you zip and work much better. unfortunately, there are too many sysadmins around that don't understand that something that costs a lot can be worse than something that costs nothing... :-( cheers, axel. CC> Thanks Lorenzo, CC> CC> I found a easy solution. CC> CC> Basically it is to use -i tag of LSF rather than use -in tag for pw, CC> bands, pp, etc. This also works for gipaw. CC> CC> Maybe this can be added as another note in the user guide for people CC> have to struggle with the input redirection. CC> CC> This works for me with mpi+lsf system CC> CC> Charles CC> CC> Lorenzo Paulatto wrote: CC> > On Ven, Aprile 25, 2008 05:41, Charles Chen wrote: CC> >> So, the gipaw.x does not read the input file. CC> > CC> > There is no -in nor -input option in gipaw.x, at the moment the only way CC> > to feed it the input is via standard input. CC> > CC> >> Is there something I need to specify when I make gipaw.x, so that it can CC> >> read the input file with -in tag? CC> > CC> > Yes, you have to program it ;-). CC> > CC> >> Or this is a problem purely related to LSF? CC> > CC> > Maybe you can still use mpi + lsf whith input redirection. It usually CC> > works, but you need the input file on all nodes. (You can create it in the CC> > input script using the "cat << eof ... eof" trick as in the examples) CC> > CC> > regards CC> > CC> CC> _______________________________________________ CC> Pw_forum mailing list CC> Pw_forum at pwscf.org CC> http://www.democritos.it/mailman/listinfo/pw_forum CC> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From yrehem at mac.com Fri Apr 25 20:59:09 2008 From: yrehem at mac.com (Yaser Rehem) Date: Fri, 25 Apr 2008 11:59:09 -0700 Subject: [Pw_forum] First Principles Electrode Capacity Estimation Message-ID: To those using pwscf for first principles electrochemistry: I've been looking through the literature to see if anyone has been able to use DFT to estimate reversible intercalation electrode capacity. I've found DFT applied to the estimation of average voltage, stability, diffusivity,... but not capacity. Can anyone point me to literature that deals with first principles capacity estimation; or is this work still to be done? Thank you, -Yaser Rehem Rehem Research & Consulting From archygu at hotmail.com Sat Apr 26 04:53:55 2008 From: archygu at hotmail.com (=?gb2312?B?ucuzvb3c?=) Date: Sat, 26 Apr 2008 10:53:55 +0800 Subject: [Pw_forum] for help inGaAs Message-ID: Dear pwscf users, i want to calculate the spin Hall Effect in hole doped GaAs. however,we do not know how to set atomic positions. for example,in the GaAs system scf calculation , I set the atomic position as follows: Ga 0 0 0 As 0.25 0.25 0.25 but how can I do if I want to add two vacant( 0.5 0.5 0.5) (0.75 ,0.75 0.75) in the GaAs scf calculation? _________________________________________________________________ Windows Live Photo gallery ????????????????????????????? http://get.live.cn/product/photo.html From archygu at hotmail.com Sat Apr 26 04:53:56 2008 From: archygu at hotmail.com (=?gb2312?B?ucuzvb3c?=) Date: Sat, 26 Apr 2008 10:53:56 +0800 Subject: [Pw_forum] for help inGaAs Message-ID: Dear pwscf users, i want to calculate the spin Hall Effect in hole doped GaAs. however,we do not know how to set atomic positions. for example,in the GaAs system scf calculation , I set the atomic position as follows: Ga 0 0 0 As 0.25 0.25 0.25 but how can I do if I want to add two vacant( 0.5 0.5 0.5) (0.75 ,0.75 0.75) in the GaAs scf calculation? _________________________________________________________________ ???MSN??????????????????? http://mobile.msn.com.cn/ From paulatto at sissa.it Sat Apr 26 09:07:46 2008 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sat, 26 Apr 2008 09:07:46 +0200 (CEST) Subject: [Pw_forum] for help inGaAs In-Reply-To: References: Message-ID: <12630.82.48.217.71.1209193666.squirrel@webmail.sissa.it> On Sab, Aprile 26, 2008 04:53, ?????? wrote: > how can I do if I want to add two vacant( 0.5 0.5 0.5) (0.75 ,0.75 > 0.75) in the GaAs scf calculation? If I have interpreted you question orrectly you have to do the calculation with a simple cubic cell with 8 atoms. Then you may reduce the number of atoms to 6 by removing the ones in (0.5 0.5 0.5) (0.75 0.75 0.75), provided they exist. Use XCrysDen or similar software to check the atomic positions, and remember to check the cell volume versus the number of atoms, to be sure you have set celldm(1) correctly (it should be the same for fcc, sc; the fcc cell volume is 1/4 than for sc) regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) +39 040 3787 511 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From eyvaz_isaev at yahoo.com Sat Apr 26 22:32:28 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sat, 26 Apr 2008 13:32:28 -0700 (PDT) Subject: [Pw_forum] for help inGaAs In-Reply-To: Message-ID: <71506.34206.qm@web65702.mail.ac4.yahoo.com> Dear anonymous QE user, Next time when you put a question, please provide your affiliation as it is accepted in this forum. Bests, Eyvaz. --- ?????? wrote: > > Dear pwscf users, > i want to calculate the spin Hall Effect in hole > doped GaAs. > however,we do not know how to set atomic positions. > for example,in the GaAs system scf calculation , > I set the atomic position as follows: > Ga 0 0 0 > As 0.25 0.25 0.25 > but how can I do if I want to add two vacant( 0.5 > 0.5 0.5) (0.75 ,0.75 0.75) in the GaAs scf > calculation? > > _________________________________________________________________ > ??????MSN?????????????????????????????????????? > http://mobile.msn.com.cn/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, IFM, Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ From lanhaiping at gmail.com Sun Apr 27 08:27:16 2008 From: lanhaiping at gmail.com (lan haiping) Date: Sun, 27 Apr 2008 14:27:16 +0800 Subject: [Pw_forum] [OT] How to identify NFE states ? Message-ID: Dear All, I am wondering about the nearly free electron states . To identify such states, does it mean that its effective mass is very close to free electron ,And we can identify it from bands' dispersion ? Bests H.P -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080427/84f44c16/attachment.htm From marzari at MIT.EDU Sun Apr 27 16:40:56 2008 From: marzari at MIT.EDU (Nicola Marzari) Date: Sun, 27 Apr 2008 10:40:56 -0400 Subject: [Pw_forum] Choice of pseudpotential (d orbitals for Fe) In-Reply-To: References: Message-ID: <48149078.4050009@mit.edu> Dear Cristian, you might also want to have a look at some of our recent literature arguing the relevance of GGA+U for these complexes (a 2006 PRL and a JCP 2007). On the pwscf website we uploaded an ultrasoft Fe with 16 valence electrons that was generated in a 2.5+ oxidation state, to more closely mimic usual conditions in these complexes. Our experience was that is was performing sligtly better than the other PBE ultrasoft 16e on the site, but overall with fairly similar results. nicola Cristian Degli Esposti Boschi wrote: > Dear users and developers, > > I'm using Quantum Espresso 3.2 and would like to reproduce some of the DFT results > of C. Rovira et al., J. Phys. Chem. A 101, 8914 (1997) regarding the > equilibrium geometries of Iron-Porphyrin (FeP) complexes. > However, I find some significant discrepancies: > in particular in our equilibrium structure of FeP(Im)(CO), where Im denotes the > imidazole group, the FeP plane gets considerably more "domed" with respect > to what reported in the above-mentioned reference. > > Of course there could be several reasons for this, but in particular > I noted that they use XC functional of Becke (exchange) and Perdew (corr) > type. They also mention a comparison with BLYP-type functionals. > However, since orbital energy structure of the ground state > involves d orbitals of Fe, initially I chose the pseudopotentials > (in the pwscf site) that include the d orbitals contribution, > namely > > Fe.pbe-nd-rrkjus.UPF or > Fe.pz-nd-rrkjus.UPF > > For the sake of uniformness I used PBE- or PZ-type pseudopotentials also for C, O and N. > > Now, I wonder if the problem of excessive doming could be due to the use > of wrong pseudopotential ... > I would like to try with BLYP's but the one for Fe > does not seem to include explicitly d orbitals. Are there other sources > of pseudopotentials? > > Thanks in advance for any help. Cristian > > ___________________________________________________ > Cristian Degli Esposti Boschi > CNR, CNISM, Unita' di Ricerca di Bologna, c/o > Dipartimento di Fisica, Universita' di Bologna > viale Berti-Pichat, 6/2, 40127, Bologna, Italia > tel. ++39 051 2095114 fax ++39 051 2095113 > e-mail: cristian.degliesposti -AT- unibo.it > web: http://www.df.unibo.it/fismat/theory > ___________________________________________________ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From baroni at sissa.it Sun Apr 27 19:40:38 2008 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 27 Apr 2008 19:40:38 +0200 Subject: [Pw_forum] [OT] How to identify NFE states ? In-Reply-To: References: Message-ID: <4908A727-2A77-4B86-BECE-253200A81949@sissa.it> The higher the energy, the lower the effect of the pseudopotential, so high-energy states are expected to be more free-electron like than low- lying ones. I am afraid that the very ocncept of "effective mass" is not very meaningful for these states. However, I would expect (although I have never verified) that for high-lying states the derivative of the band energy with respect to the wavenumber be linear with respect to the wavenumber, with the coefficient given by the inverse of the free-electron mass. SB On Apr 27, 2008, at 8:27 AM, lan haiping wrote: > Dear All, > > I am wondering about the nearly free electron states . To identify > such states, > does it mean that its effective mass is very close to free > electron ,And we can identify > it from bands' dispersion ? > > Bests > H.P > > -- > Hai-Ping Lan > Department of Electronics , > Peking University , Bejing, 100871 > lanhaiping at gmail.com, hplan at pku.edu.cn > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080427/2806c094/attachment.htm From yrehem at mac.com Sun Apr 27 21:39:26 2008 From: yrehem at mac.com (Yaser Rehem) Date: Sun, 27 Apr 2008 12:39:26 -0700 Subject: [Pw_forum] bfgs vc-relax symmetry breaking Message-ID: Dear Javier et al. I noticed in a previous posting that you were testing the bfgs vc- relax and requested the input file from a user that had seen his symmetry broken during relaxation. I have also encountered this problem when relaxing an LiCoO2 structure. I am using the 4.0cvs3 release. I've pasted my input file below in case it is of use to you. Meanwhile, per your suggestion, I'll try using the nosym flag. Sincerely, -Yaser Rehem Rehem Research & Consulting &control calculation = 'vc-relax' restart_mode='from_scratch' prefix='LiCoO2.lda.16.16.4' tstress = .true. tprnfor = .true. outdir = './output' pseudo_dir = '../pseudo' / &system ibrav= 4 celldm(1) = 5.506963703 celldm(3) = 5.061254424 nat= 12 ntyp= 3 ecutwfc = 40 ecutrho = 400 ecfixed = 35 qcutz = 35 q2sigma = 4 occupations = 'smearing' degauss = 0.03 smearing = 'cold' / &electrons mixing_beta = 0.7 conv_thr = 1.0d-8 / &Ions ion_dynamics = 'bfgs' / &cell cell_dynamics = 'bfgs' / ATOMIC_SPECIES Co 58.9332 Co.pz-nd-rrkjus.UPF.txt Li 6.941 Li_VDB_LDA_SEMI.UPF.txt O 15.9994 O.pz-rrkjus.UPF.txt ATOMIC_POSITIONS Co 0 0.021818463 -0.057337571 O 0.499999999 0.310480668 0.282051193 Li 0 0.60451232 0.785692891 O 0 0.033926343 1.287397609 Co 0.499999999 0.322831271 1.62680675 O 0 0.61186111 1.965217115 Li 0 0.035196846 2.467906226 O 0.499999999 0.322447182 2.970274878 Co 0 0.611145832 3.309737861 O 0 0.033615198 3.648617307 Li 0.499999999 0.313259151 4.157130001 O 0 0.598503748 4.663887786 K_POINTS {automatic} 16 16 4 0 0 0 From giannozz at nest.sns.it Sun Apr 27 21:58:01 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Sun, 27 Apr 2008 21:58:01 +0200 Subject: [Pw_forum] OpenMPI problems with espresso 4.0cvs In-Reply-To: <20080425164648.c5iz7a5wusss0c8g@webmail.sissa.it> References: <20080425122619.p09gnvluv4skcgsw@webmail.sissa.it> <20080425164648.c5iz7a5wusss0c8g@webmail.sissa.it> Message-ID: On Apr 25, 2008, at 16:46 , Riccardo Sabatini wrote: > I haven't tried anyway the -in flag, seems the openmpi i have > doesn't understand that flag it seems that you do not understand that flag: it is the code that scans the command line for "-inp" or "-in" followed by a file name; if found, it opens the named file as standard input unit. All this is independent of mpi (open- or closed-) and hasn't changed since a few versions. Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From j.antonio.montoya at gmail.com Mon Apr 28 01:26:20 2008 From: j.antonio.montoya at gmail.com (Javier Antonio Montoya) Date: Sun, 27 Apr 2008 19:26:20 -0400 Subject: [Pw_forum] OpenMPI problems with espresso 4.0cvs In-Reply-To: <20080425164648.c5iz7a5wusss0c8g@webmail.sissa.it> References: <20080425122619.p09gnvluv4skcgsw@webmail.sissa.it> <20080425164648.c5iz7a5wusss0c8g@webmail.sissa.it> Message-ID: <993c5eba0804271626g614f8f1ci696af76b768d7940@mail.gmail.com> Dear Riccardo, First of all let me clarify that "-in" is not an option for mpirun but for espresso itself, i.e. you should type something like mpirun -np 4 directory/where/espresso/is/pw.x -in file.in > file.out instead of mpirun -np 4 directory/where/espresso/is/pw.x < file.in > file.out That's all. Second, specifying options like "mpirun -np 4 --host localhost" or "mpirun h C ..." are not likely to solve your problem. Now, I don't know how often people explains step by step the configuration for a particular machine but since I got a 4-core Xeon just one week ago I will try to post here all the steps that I have made so far (please: execute the first four steps as root, the symbols ">" that appear starting some of the lines are just there for signaling the terminal prompt, you don't have to write them): 1- I downloaded the latest versions of icc, ifort, and mkl (10.1.015, 10.1.015, and 10.0.2.018 respectively) from Intel's web site as a non-supported version and installed all the packages including idbg (idbg comes twice, with icc and ifort but it is the same package) 2- I copied the files: ifortvars.sh, iccvars.sh, idbvars.sh, and mklvarsem64t.sh (all of this if you are using bash as your shell) that come with the compilers and the mkl libraries, to the directory /etc/profile.d/ (which should already exist assuming that you don't use ubuntu in your Xeon machine). 3- now, you should download the latest version of LAM/MPI (I found this one easier to configure than mpich2 in runlevel2, since it does not require a certain mpd daemon in order to run properly) Let's say that you unpack your lam/mpi inside a directory named /opt/MPI/ then you will have a directory that looks like : /opt/MPI/lam-7.1.4 . Now you can create inside that directory a configure script that looks like: ================================================================== >vi myscript.sh #!/bin/sh cd /opt/MPI/lam-7.1.4 CC=icc CXX=icpc FC=ifort export CC CXX FC # Lam without gm ./configure --prefix=/opt/MPI/lam-7.1.4/lam --with-rpi=usysv --without-threads --disable-tv-queue make make install exit ================================================================= And enable it for execution : > chmod 755 myscript.sh This version of the script is the most basic that you can have in order to compile your lam/mpi, but I do not know what other options could be used in order to enhance our lam/mpi performance for a Xeon machine and the specific compilers that I am using. If somebody who knows how to improve on this posts this information I would be very grateful as well. execute this by typing: > ./myscript.sh IF YOU'VE MANAGED TO MAKE ALL OF THIS TO WORK WITH A DIFFERENT COMPILER YOU DON"T NEED TO DO IT AGAIN UNLESS YOU THINK THAT INTEL COMPILERS CAN DO A BETTER JOB. when the process ends successfully you need to create also a hostfile inside /opt/MPI//lam-7.1.4/lam/etc/ , go inside there and do: =================================================================== >vi hostfile localhost localhost localhost localhost =================================================================== 4- Then, all what you have to do now is to create yet another file inside /etc/profile.d/ : =================================================================== >vi lam.sh #!/bin/sh export LAM=/opt/MPI/lam-7.1.4/lam export OMP_NUM_THREADS=1 PATH=/opt/MPI/lam-7.1.4/lam/include:/opt/MPI/lam-7.1.4/lam/bin:$PATH export PATH LD_LIBRARY_PATH=/opt/MPI/lam-7.1.4/lam/lib:$LD_LIBRARY_PATH export LD_LIBRARY_PATH MANPATH=/opt/MPI/lam-7.1.4/lam/man:$MANPATH export MANPATH export LAMRSH=ssh =================================================================== Note the following: -export OMP_NUM_THREADS=1 ,as recently suggested by Axel Kohlmeyer is there in order to avoid bad behavior from mkl libraries. -PATH=/opt/MPI/lam-7.1.4/lam/include without this piece the espresso's "./configure" command will not properly compile in parallel since the file "mpif.h" with the definitions is inthere. What I observed by running "mpirun -np 4" with a non parallel pw.x in my machine was, that with the "<" option the code collapsed, while with the "-in" option the code seems to run but it does the very same calculation in each core, and therefore, it writes the same output four times inside a single output file, of course, still using the same time that one single processor would use. 5- Now, as normal user (logout from root) go and test that your parallel environment is working (maybe you will want to reboot your machine, or "source" each one of the "xxx.sh" scripts recently created inside /etc/profile.d, or open a new terminal) > laminfo LAM/MPI: 7.1.4 Prefix: /opt/MPI/lam-7.1.4/lam Architecture: x86_64-unknown-linux-gnu Configured by: root Configured on: Sun Apr 27 16:38:22 EDT 2008 Configure host: GiNUx3 Memory manager: ptmalloc2 C bindings: yes C++ bindings: yes Fortran bindings: yes C compiler: icc C++ compiler: icpc Fortran compiler: ifort Fortran symbols: underscore C profiling: yes C++ profiling: yes Fortran profiling: yes C++ exceptions: no Thread support: no ROMIO support: yes IMPI support: no Debug support: no Purify clean: no SSI boot: globus (API v1.1, Module v0.6) SSI boot: rsh (API v1.1, Module v1.1) SSI boot: slurm (API v1.1, Module v1.0) SSI coll: lam_basic (API v1.1, Module v7.1) SSI coll: shmem (API v1.1, Module v1.0) SSI coll: smp (API v1.1, Module v1.2) SSI rpi: crtcp (API v1.1, Module v1.1) SSI rpi: lamd (API v1.0, Module v7.1) SSI rpi: sysv (API v1.0, Module v7.1) SSI rpi: tcp (API v1.0, Module v7.1) SSI rpi: usysv (API v1.0, Module v7.1) >lamboot LAM 7.1.4/MPI 2 C++/ROMIO - Indiana University >lamnodes n0 localhost.localdomain:1:origin,this_node >lamhalt LAM 7.1.4/MPI 2 C++/ROMIO - Indiana University NOW ESPRESSO, 6- After having done the previous steps on my machine the configuration of espresso just worked by doing ./configure , but I had to do the following in order to make espresso understand that the system is a parallel machine, as root: >cp /opt/MPI/lam-7.1.4/lam/bin/mpif77 /opt/MPI/lam-7.1.4/lam/bin/mpif90 In order to make sure that the parallel compiler is named mpif90, mpif77 is just the default name that lam/mpi uses and it is capable of compiling any fortran code. The last part of the output of ./configure then looks like this after execution: -------------------------------------------------------------------- ESPRESSO can take advantage of several optimized numerical libraries (essl, fftw, mkl...). This configure script attempts to find them, but may fail if they have been installed in non-standard locations. If a required library is not found, the local copy will be compiled. The following libraries have been found: BLAS_LIBS= -lmkl_em64t LAPACK_LIBS= -lmkl_em64t FFT_LIBS= Please check if this is what you expect. If any libraries are missing, you may specify a list of directories to search and retry, as follows: ./configure LIBDIRS="list of directories, separated by spaces" Parallel environment detected successfully. Configured for compilation of parallel executables. For more info, read the ESPRESSO User's Guide (Doc/users-guide.tex). -------------------------------------------------------------------- configure: success 7- The make.sys file should NOW contain: ======================================================= DFLAGS = -D__INTEL -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA MPIF90 = mpif90 LD = mpif90 ======================================================= Interestingly enough, with this process I can direct input with "<" instead of using "-in" without getting any error, and then I can run all the examples in parallel. CHEERS, J. A. MONTOYA On Fri, Apr 25, 2008 at 10:46 AM, Riccardo Sabatini wrote: > Hi again, > > i wrote "3 times" meaning that even if i launch mpirun with 4 > processors the error comes out just three times, maybe mpirun launches > only three instances of the program,sorry for the misunderstanding. I > tried to launch with the direct location to the file instead the std > input redirection but nothing still works (i don't usually launch pw > interactively, was just the pasted snippet to let the mailing list > understand me). > > I haven't tried anyway the -in flag, seems the openmpi i have > doesn't understand that flag but i'll look in the help manual to see > if there's something similar, maybe the problem is there. I'll let you > know as soon as i try. > > Thanks for the help, regards > > Riccardo > > Quoting Axel Kohlmeyer : > > > On Fri, 25 Apr 2008, Riccardo Sabatini wrote: > > > > RS> Hello everyone, > > > > hi riccardo, > > > > RS> > > RS> i finally compiled espresso with MPI (thanks for the suggestion, > > RS> with gfortran worked perfectly). I had no problem in the compilation > > RS> but i can't make it run. I'm trying a super easy run: from the > > RS> exercise01 the si.scf.cg.in. > > RS> > > RS> Now, if i run the file with the espresso 3.2 compiled without > mpi > > RS> obviously runs perfectly but if i try the same file with the mpi > > RS> version it gives me this error (3 times) > > > > doing the same thing 3 times doesn't make it more likely to work... > > > > RS> stopping ... > > RS> > > > --------------------------------------------------------------------------------- > > RS> > > RS> My launch command is (i'm running on a four cores processor > now) > > RS> > > RS> mpirun -np 4 ../QE-MPI/bin/pw.x < prova.in > > > > have you tried the -in flag? not all MPI implementations > > replicate the input across all nodes and i personally > > think it is in general a bad idea to read an input from > > stdin. we don't run anything interactively these days > > anyways and being able to check file status etc. is > > a bit advantage. > > > > cheers, > > axel. > > > > RS> Is there something i'm missing ? Maybe a line do add for > parallel > > RS> compilation in the input file ? I've tried the only option in the > > RS> INPUT_PW about parallel compilation, wf_collect, but nothing > changes. > > RS> Since the compilation gave me 0 errors maybe the problem is the > > RS> combination openMPI+gfotran+espresso-4.0. > > RS> > > RS> Thanks for the help, > > RS> > > RS> Riccardo > > RS> > > RS> ---------------------------------------------------------------- > > RS> SISSA Webmail https://webmail.sissa.it/ > > RS> Powered by Horde http://www.horde.org/ > > RS> > > RS> > > RS> _______________________________________________ > > RS> Pw_forum mailing list > > RS> Pw_forum at pwscf.org > > RS> http://www.democritos.it/mailman/listinfo/pw_forum > > RS> > > > > -- > > ======================================================================= > > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > > Center for Molecular Modeling -- University of Pennsylvania > > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > > ======================================================================= > > If you make something idiot-proof, the universe creates a better idiot. > > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by Horde http://www.horde.org/ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080427/0da6666f/attachment-0001.htm From sagarambavale at yahoo.co.in Mon Apr 28 06:47:37 2008 From: sagarambavale at yahoo.co.in (ambavale sagar) Date: Mon, 28 Apr 2008 10:17:37 +0530 (IST) Subject: [Pw_forum] wrong nrztot Message-ID: <609256.86514.qm@web94614.mail.in2.yahoo.com> Good morning, Sorry but i can't understand that why only tetragonal must be used as electrode bulk geometry? can't we use FCC? and how to define this(fcc) geometry using tetragonal unit cell with only two atoms? sagar %%%%%%%%%%%%%%%%%%%%%%%%%% Dear Sagar. This is because you should use the tetragonal unit cell with two atoms per cell like in the example 12. Regards, Alexander On Tuesday 22 April 2008 11:24, ambavale sagar wrote: > sorry, i forgot to attach scf file and my signature. so resending the > entire mail. i am using espresso 4.0cvs2 for calculating complex band > structure of al bulk in 100 direction( for 001 it is given in example 12). > this gives me following errror: > > from in init_cond : error # 1626817 > wrong nrztot > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >%%% > > stopping ... > > the input file for complex band is : > > &inputcond > outdir='/db/sagar/tmp/' > prefixl='al_bulk' > band_file ='bands.albulk' > ikind=0 > energy0=10..d0 > denergy=-0.4d0 > ewind=1.d0 > epsproj=1.d-3 > delgep = 1.d-12 > cutplot = 3.d0 > / > 1 > 0.0 0.0 1.0 > 60 > > while the file for scf calculation is: > > &control > calculation='scf' > restart_mode='from_scratch', > pseudo_dir = '/db/espresso4.0cvs2/pseudo/', > outdir='/db/sagar/tmp/', > prefix='al_bulk' > tprnfor = .true. > tstress = .true. > / > &system > ibrav= 2, celldm(1) =7.50, nat= 1, ntyp= 1, ecutwfc =15.0, > occupations='smearing', smearing='marzari-vanderbilt', degauss=0.05 > / > &electrons > diagonalization='david' > mixing_beta = 0.7 > / > ATOMIC_SPECIES > Al 26.98 Al.vbc.UPF > ATOMIC_POSITIONS > Al 0.00 0.00 0.00 > K_POINTS (automatic) > 2 2 2 1 1 1 > > > Sagar Ambavale > PhD student > The M.S.University of Baroda > Inida Get the freedom to save as many mails as you wish. Click here to know how. Bring your gang together. Do your thing. Find your favourite Yahoo! group at http://in.promos.yahoo.com/groups/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080428/52b00542/attachment.htm From giannozz at nest.sns.it Mon Apr 28 10:26:52 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 28 Apr 2008 10:26:52 +0200 Subject: [Pw_forum] GIAPW LSF problem? In-Reply-To: <62313.151.65.45.150.1209140181.squirrel@webmail.sissa.it> References: <4810E24C.1000805@physics.unc.edu> <481152E2.2060406@physics.unc.edu> <62313.151.65.45.150.1209140181.squirrel@webmail.sissa.it> Message-ID: <48158A4C.6090506@nest.sns.it> Lorenzo Paulatto wrote: > There is no -in nor -input option in gipaw.x no no, it is there and it works >> Or this is a problem purely related to LSF? very likely Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From zhengb at ictp.it Mon Apr 28 10:56:24 2008 From: zhengb at ictp.it (Zheng Bing) Date: Mon, 28 Apr 2008 10:56:24 +0200 (CEST) Subject: [Pw_forum] SCF output information when testing espresso4.0cvs3 Message-ID: Hi, good morning, I tested "espresso4.0cvs3" with a simple scf calculation. I think the information for atomic magnetization in the output aren't reliable. I tried to find where the problem is from but failed. Could you give me some opinions about it? Thanks. The input is as following: ---------------------------------------- &control calculation='scf', pseudo_dir = '$pseudi', outdir='$workdir', prefix='bmo_4.2', disk_io='high', verbosity='high',/ &system ibrav=0,celldm(1)=7.3894,nat=5,ntyp=3,nbnd=30,ecutwfc=35.0, ecutrho=350.0,occupations='smearing',smearing='gaussian', degauss=0.01, starting_magnetization(2)=1.0, constrained_magnetization='atomic', lambda=1.0, nspin=2, &electrons conv_thr = 1.0d-2 / ATOMIC_SPECIES Bi 70.00 Bi.pbe-d-mt.UPF Mn 70.00 Mn.pbe-sp-van.UPF O 70.00 O.pbe-rrkjus.UPF ATOMIC_POSITIONS Bi .000000000 .000000000 .000000000 Mn .500000000 .500000000 .500000000 O .000000000 .500000000 .500000000 O .500000000 .000000000 .500000000 O .500000000 .500000000 .000000000 K_POINTS (automatic) 2 2 2 0 0 0 CELL_PARAMETERS {cubic} 1.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 1.0000 --------------------------------------------------- ---------------------------------------------------- The output which only the atomic magnetization from the last scf step are shown. Notice the No.4 is zero. ============================================================================== atom number 1 relative position : 0.0000 0.0000 0.0000 charge : 9.095727 magnetization : 0.016660 magnetization/charge: 0.001832 constrained moment : 0.000000 ============================================================================== atom number 2 relative position : 0.5000 0.5000 0.5000 charge : 11.952491 magnetization : 0.055621 magnetization/charge: 0.004654 constrained moment : 1.000000 ============================================================================== atom number 3 relative position : 0.0000 0.5000 0.5000 charge : 5.364920 magnetization : -0.784068 magnetization/charge: -0.146147 constrained moment : 0.000000 ============================================================================== atom number 4 relative position : 0.5000 0.0000 0.5000 charge : 5.364920 magnetization : 0.000000 magnetization/charge: 0.000000 constrained moment : 0.000000 ============================================================================== atom number 5 relative position : 0.5000 0.5000 0.0000 charge : 5.364920 magnetization : -0.784027 magnetization/charge: -0.146140 constrained moment : 0.000000 ======================================================= ZHENG Bing - International Center for Theoretical Physics(ICTP) - Strada Costiera 11 - 34014 Trieste, ITALY E-mail: zhengb at ictp.it - Tel : +39 040 224 0459 - Fax : +39 040 224 163 - From xwzhang at uestc.edu.cn Mon Apr 28 10:55:44 2008 From: xwzhang at uestc.edu.cn (xwzhang) Date: Mon, 28 Apr 2008 16:55:44 +0800 Subject: [Pw_forum] Does anyone have Ge ultrasoft-PP for GGA? Message-ID: <200804281655434857996@uestc.edu.cn> Dear pwscf friends, Does any one have PP for Ge suitable in Heusler compounds (Co2MnGe, or Rh2MnGe, magnetic metallic state)? Thank you! Wenxu Zhang 2008-04-28 State Key Lab. of Integrated Devices and Thin Films, University of Electronic Science and Technology, Chengdu 610054 P. R. China Tel: +86-28-83201475 Fax:+86-28-83204938 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080428/d64600be/attachment.htm From xwzhang at uestc.edu.cn Mon Apr 28 10:55:44 2008 From: xwzhang at uestc.edu.cn (xwzhang) Date: Mon, 28 Apr 2008 16:55:44 +0800 Subject: [Pw_forum] Does anyone have Ge ultrasoft-PP for GGA? Message-ID: <200804281655434857996@uestc.edu.cn> Dear pwscf friends, Does any one have PP for Ge suitable in Heusler compounds (Co2MnGe, or Rh2MnGe, magnetic metallic state)? Thank you! Wenxu Zhang 2008-04-28 State Key Lab. of Integrated Devices and Thin Films, University of Electronic Science and Technology, Chengdu 610054 P. R. China Tel: +86-28-83201475 Fax:+86-28-83204938 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080428/d64600be/attachment-0001.htm From paulatto at sissa.it Mon Apr 28 11:07:10 2008 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 28 Apr 2008 11:07:10 +0200 (CEST) Subject: [Pw_forum] GIAPW LSF problem? In-Reply-To: <48158A4C.6090506@nest.sns.it> References: <4810E24C.1000805@physics.unc.edu> <481152E2.2060406@physics.unc.edu> <62313.151.65.45.150.1209140181.squirrel@webmail.sissa.it> <48158A4C.6090506@nest.sns.it> Message-ID: <29401.147.122.5.216.1209373630.squirrel@webmail.sissa.it> On Lun, Aprile 28, 2008 10:26, Paolo Giannozzi wrote: > no no, it is there and it works > You are right, as usual. Now that I now it's there, I can see how it works. bye -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) +39 040 3787 511 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From giannozz at nest.sns.it Mon Apr 28 14:17:12 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 28 Apr 2008 14:17:12 +0200 Subject: [Pw_forum] SCF output information when testing espresso4.0cvs3 In-Reply-To: References: Message-ID: <4815C048.2050701@nest.sns.it> Zheng Bing wrote: > The input is as following: > ---------------------------------------- > &control > calculation='scf', pseudo_dir = '$pseudi', outdir='$workdir', > prefix='bmo_4.2', disk_io='high', verbosity='high',/ > &system > ibrav=0,celldm(1)=7.3894,nat=5,ntyp=3,nbnd=30,ecutwfc=35.0, > ecutrho=350.0,occupations='smearing',smearing='gaussian', > degauss=0.01, starting_magnetization(2)=1.0, > constrained_magnetization='atomic', > lambda=1.0, nspin=2, > &electrons there must be a missing line here > conv_thr = 1.0d-2 too small for meaningful results > ---------------------------------------------------- > The output which only the atomic magnetization from the last > scf step are shown. Notice the No.4 is zero. this is what I get. Please be more specific on how you got your results. ============================================================================== atom number 1 relative position : 0.0000 0.0000 0.0000 charge : 9.095727 magnetization : 0.016660 magnetization/charge: 0.001832 constrained moment : 0.000000 ============================================================================== atom number 2 relative position : 0.5000 0.5000 0.5000 charge : 11.952491 magnetization : 0.055621 magnetization/charge: 0.004654 constrained moment : 1.000000 ============================================================================== atom number 3 relative position : 0.0000 0.5000 0.5000 charge : 5.364920 magnetization : 0.000000 magnetization/charge: 0.000000 constrained moment : 0.000000 ============================================================================== atom number 4 relative position : 0.5000 0.0000 0.5000 charge : 5.364920 magnetization : 0.000000 magnetization/charge: 0.000000 constrained moment : 0.000000 ============================================================================== atom number 5 relative position : 0.5000 0.5000 0.0000 charge : 5.364920 magnetization : 0.000000 magnetization/charge: 0.000000 constrained moment : 0.000000 ============================================================================== -- Paolo Giannozzi, Democritos and University of Udine, Italy From baroni at sissa.it Mon Apr 28 18:58:10 2008 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 28 Apr 2008 18:58:10 +0200 Subject: [Pw_forum] SCF output information when testing espresso4.0cvs3 In-Reply-To: <4815C048.2050701@nest.sns.it> References: <4815C048.2050701@nest.sns.it> Message-ID: <21F55DDB-1D6D-4882-9720-39A86FA05CDC@sissa.it> On Apr 28, 2008, at 2:17 PM, Paolo Giannozzi wrote: > Zheng Bing wrote: > >> The input is as following: >> ---------------------------------------- >> &control >> calculation='scf', pseudo_dir = '$pseudi', outdir='$workdir', >> prefix='bmo_4.2', disk_io='high', verbosity='high',/ >> &system >> ibrav=0,celldm(1)=7.3894,nat=5,ntyp=3,nbnd=30,ecutwfc=35.0, >> ecutrho=350.0,occupations='smearing',smearing='gaussian', >> degauss=0.01, starting_magnetization(2)=1.0, >> constrained_magnetization='atomic', >> lambda=1.0, nspin=2, >> &electrons > > there must be a missing line here > >> conv_thr = 1.0d-2 > > too small for meaningful results you mean "too large", Paolo, don't you? SB --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080428/606c9bfa/attachment-0001.htm From zhengb at ictp.it Mon Apr 28 20:28:46 2008 From: zhengb at ictp.it (Zheng Bing) Date: Mon, 28 Apr 2008 20:28:46 +0200 (CEST) Subject: [Pw_forum] SCF output information when testing espresso4.0cvs3 In-Reply-To: <4815C048.2050701@nest.sns.it> References: <4815C048.2050701@nest.sns.it> Message-ID: Hi, Paolo, Thanks a lot for your reply. I am sorry that I couldn't explain the problem in details. I just did another calculation with larger system and more accurate conv_thr, of which input and output about the atomic magnetization is in the following. In its result, the atomic magnetizations become zero when the atom number is larger than 5. Here the total atom number is 15. I did some other calculations with espresso4.0cvs_01, also containing "constrained_magnetization='atomic'". For 135-atom system, the atomic magnetization became totally zero after atom No.45. For 150-atom system, the atomic magnetization became totally zero after atom No.50. I don't think they are reasonable since such results aren't consistent with the PROJWFC output. I attach the new input here. Thanks. Bing. --------------------------------------- &control calculation='scf' restart_mode='from_scratch' pseudo_dir = '../espresso4.0cvs3/pseudo/', outdir='/scratch/userictp/ictpcm21/BMO/SCRATCH/', prefix='bmo_3' disk_io='high' verbosity='high' tprnfor=.true. / &system ibrav=0, celldm(1)=7.337510, nat=15, ntyp=3, nbnd=100, nspin=2, ecutwfc=35.0, ecutrho=350.0, occupations='smearing', smearing='gaussian', degauss=0.02, starting_magnetization(2)=1.0, constrained_magnetization='atomic', lambda=1.0, / &electrons conv_thr = 1.0d-6 / ATOMIC_SPECIES Bi 70.00 Bi.pbe-d-mt.UPF Mn 70.00 Mn.pbe-sp-van.UPF O 70.00 O.pbe-rrkjus.UPF ATOMIC_POSITIONS Bi .00 .00 .00 Mn .50 .50 .50 O .00 .50 .50 O .50 .00 .50 O .50 .50 .00 Bi .00 .00 1.00 Mn .50 .50 1.50 O .00 .50 1.50 O .50 .00 1.50 O .50 .50 1.00 Bi .00 .00 2.00 Mn .50 .50 2.50 O .00 .50 2.50 O .50 .00 2.50 O .50 .50 2.00 K_POINTS (automatic) 3 3 1 0 0 0 CELL_PARAMETERS {cubic} 1.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 3.0000 --------------------------------------------------- ------------------------------------------------ Results about atomic magnetization: ============================================================================== atom number 1 relative position : 0.0000 0.0000 0.0000 charge : 9.036256 magnetization : 0.009405 magnetization/charge: 0.001041 constrained moment : 0.000000 ============================================================================== atom number 2 relative position : 0.5000 0.5000 0.5000 charge : 11.897526 magnetization : 0.036603 magnetization/charge: 0.003077 constrained moment : 1.000000 ============================================================================== atom number 3 relative position : 0.0000 0.5000 0.5000 charge : 5.328264 magnetization : 2.947166 magnetization/charge: 0.553119 constrained moment : 0.000000 ============================================================================== atom number 4 relative position : 0.5000 0.0000 0.5000 charge : 5.328264 magnetization : 0.036614 magnetization/charge: 0.006872 constrained moment : 0.000000 ============================================================================== atom number 5 relative position : 0.5000 0.5000 0.0000 charge : 5.327783 magnetization : 0.036603 magnetization/charge: 0.006870 constrained moment : 0.000000 ============================================================================== atom number 6 relative position : 0.0000 0.0000 1.0000 charge : 9.036269 magnetization : 0.000000 magnetization/charge: 0.000000 constrained moment : 0.000000 ============================================================================== atom number 7 relative position : 0.5000 0.5000 1.5000 charge : 11.897203 magnetization : 0.000000 magnetization/charge: 0.000000 constrained moment : 1.000000 ============================================================================== atom number 8 relative position : 0.0000 0.5000 1.5000 charge : 5.327862 magnetization : 0.000000 magnetization/charge: 0.000000 constrained moment : 0.000000 ============================================================================ atom number 9 relative position : 0.5000 0.0000 1.5000 charge : 5.327862 magnetization : 0.000000 magnetization/charge: 0.000000 constrained moment : 0.000000 ============================================================================== atom number 10 relative position : 0.5000 0.5000 1.0000 charge : 5.328059 magnetization : 0.000000 magnetization/charge: 0.000000 constrained moment : 0.000000 ============================================================================== atom number 11 relative position : 0.0000 0.0000 2.0000 charge : 9.036269 magnetization : 0.000000 magnetization/charge: 0.000000 constrained moment : 0.000000 ============================================================================== atom number 12 relative position : 0.5000 0.5000 2.5000 charge : 11.897526 magnetization : 0.000000 magnetization/charge: 0.000000 constrained moment : 1.000000 ============================================================================= atom number 13 relative position : 0.0000 0.5000 2.5000 charge : 5.328264 magnetization : 0.000000 magnetization/charge: 0.000000 constrained moment : 0.000000 ============================================================================== atom number 14 relative position : 0.5000 0.0000 2.5000 charge : 5.328264 magnetization : 0.000000 magnetization/charge: 0.000000 constrained moment : 0.000000 ============================================================================== atom number 15 relative position : 0.5000 0.5000 2.0000 charge : 5.328059 magnetization : 0.000000 magnetization/charge: 0.000000 constrained moment : 0.000000 ============================================================================== THE END********* On Mon, 28 Apr 2008, Paolo Giannozzi wrote: > Zheng Bing wrote: > >> The input is as following: >> ---------------------------------------- >> &control >> calculation='scf', pseudo_dir = '$pseudi', outdir='$workdir', >> prefix='bmo_4.2', disk_io='high', verbosity='high',/ >> &system >> ibrav=0,celldm(1)=7.3894,nat=5,ntyp=3,nbnd=30,ecutwfc=35.0, >> ecutrho=350.0,occupations='smearing',smearing='gaussian', >> degauss=0.01, starting_magnetization(2)=1.0, >> constrained_magnetization='atomic', >> lambda=1.0, nspin=2, >> &electrons > > there must be a missing line here > >> conv_thr = 1.0d-2 > > too small for meaningful results > >> ---------------------------------------------------- >> The output which only the atomic magnetization from the last >> scf step are shown. Notice the No.4 is zero. > > this is what I get. Please be more specific on how you got > your results. > > ============================================================================== > atom number 1 relative position : 0.0000 0.0000 0.0000 > charge : 9.095727 > magnetization : 0.016660 > magnetization/charge: 0.001832 > constrained moment : 0.000000 > ============================================================================== > atom number 2 relative position : 0.5000 0.5000 0.5000 > charge : 11.952491 > magnetization : 0.055621 > magnetization/charge: 0.004654 > constrained moment : 1.000000 > ============================================================================== > atom number 3 relative position : 0.0000 0.5000 0.5000 > charge : 5.364920 > magnetization : 0.000000 > magnetization/charge: 0.000000 > constrained moment : 0.000000 > ============================================================================== > atom number 4 relative position : 0.5000 0.0000 0.5000 > charge : 5.364920 > magnetization : 0.000000 > magnetization/charge: 0.000000 > constrained moment : 0.000000 > ============================================================================== > atom number 5 relative position : 0.5000 0.5000 0.0000 > charge : 5.364920 > magnetization : 0.000000 > magnetization/charge: 0.000000 > constrained moment : 0.000000 > ============================================================================== > -- > 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 > ZHENG Bing - International Center for Theoretical Physics(ICTP) - Strada Costiera 11 - 34014 Trieste, ITALY E-mail: zhengb at ictp.it - Tel : +39 040 224 0459 - Fax : +39 040 224 163 - From giannozz at nest.sns.it Tue Apr 29 10:42:40 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 29 Apr 2008 10:42:40 +0200 Subject: [Pw_forum] SCF output information when testing espresso4.0cvs3 In-Reply-To: <21F55DDB-1D6D-4882-9720-39A86FA05CDC@sissa.it> References: <4815C048.2050701@nest.sns.it> <21F55DDB-1D6D-4882-9720-39A86FA05CDC@sissa.it> Message-ID: <4816DF80.2050208@nest.sns.it> Stefano Baroni wrote: >> >>> conv_thr = 1.0d-2 >> >> too small for meaningful results > > you mean "too large", Paolo, don't you? definitely! Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From hushujun at mail.sdu.edu.cn Tue Apr 29 14:55:31 2008 From: hushujun at mail.sdu.edu.cn (=?gb2312?B?uvrK9778IFNodS1qdW4gSHU=?=) Date: Tue, 29 Apr 2008 20:55:31 +0800 Subject: [Pw_forum] A possible bug of pp.x Message-ID: <409473731.03297@mail.sdu.edu.cn> Dear the developers: When i perform the post-processing calculation to obtain the charge and spin density, i found a possible bug. Since the node have a dual core processor, i sequentially started two pp jobs (plot_num = 0 and plot_num = 6) in less than 5 seconds (charge density of plot_num = 0 is earlier). The running time is about 2 minutes. However, the output data of charge and spin density are almost the same. Both are more likely the output of earlier job, although there are still some error data (the xcrysden image is ill). But when i run the later one until the earlier one has been finished, everything is OK. The vesion of the code is 3.2.3 and the parallel compiled pp.x runs in serial model. Shujun Hu ------------------------------ Shujun Hu e-mail: hushujun at 163.com Shandong university Phone: +86/0531-88375097 Jinan, Shandong Province, China, 250100 From polynmr at physics.unc.edu Tue Apr 29 15:26:52 2008 From: polynmr at physics.unc.edu (Charles Chen) Date: Tue, 29 Apr 2008 09:26:52 -0400 Subject: [Pw_forum] A possible bug of pp.x In-Reply-To: <409473731.03297@mail.sdu.edu.cn> References: <409473731.03297@mail.sdu.edu.cn> Message-ID: <4817221C.3020401@physics.unc.edu> Is pp.x supposed to run serial only? correct me if I am wrong. Charles Chen ??? Shu-jun Hu wrote: > Dear the developers: > When i perform the post-processing calculation to obtain the charge and spin > density, i found a possible bug. Since the node have a dual core processor, i > sequentially started two pp jobs (plot_num = 0 and plot_num = 6) in less than 5 > seconds (charge density of plot_num = 0 is earlier). The running time is about 2 > minutes. However, the output data of charge and spin density are almost the same. > Both are more likely the output of earlier job, although there are still some > error data (the xcrysden image is ill). But when i run the later one until the > earlier one has been finished, everything is OK. > The vesion of the code is 3.2.3 and the parallel compiled pp.x runs in serial > model. > > > Shujun Hu > > > > > > > > > > > ------------------------------ > Shujun Hu e-mail: hushujun at 163.com > Shandong university Phone: +86/0531-88375097 > Jinan, Shandong Province, China, 250100 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > -- NMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMR NMR Dr. Qiang "Charles" Chen NMR NMR Department of Physics and Astronomy NMR NMR University of North Carolina NMR NMR Phillips Hall, CB#3255 NMR NMR Chapel Hill, NC 27599-3255 NMR NMR Tel: 919-962-1571 (O) NMR NMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMR From baroni at sissa.it Tue Apr 29 15:54:06 2008 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 29 Apr 2008 15:54:06 +0200 Subject: [Pw_forum] Dear Professor In-Reply-To: <13428159.528771209474323018.JavaMail.coremail@bj163app112.163.com> References: <13428159.528771209474323018.JavaMail.coremail@bj163app112.163.com> Message-ID: Dear Hua Peng: please, refer to the pw_form mailing list that you can subscribe from http://www.pwscf.org The calculation of phonon lifetimes from third-order perturbaton theory is discussed, e.g., in A. Debernardi, S. Baroni, and E. Molinari, Phys. Rev. Lett. 75, 1819 - 1822 (1995) See also Dbernardi's PhD thesis: Anharmonic Properties of Semiconductors from Density Functional Perturbation Theory Best wishes - SB On Apr 29, 2008, at 3:05 PM, penghua8503 wrote: > > > > Dear Professor Baroni, > I am a postgraduate student from Shandong University in China I > run example14 in PWscf to calculate phonon life of Si. I got a > file(si.anh_G)produced by d3.x. But I do not understand the results > of it Are these dates the third derivative of energy? Using the file > in the result, how can I get the phonon life? Could you give me some > reference article? I really appreciate your help. > Thanks again for reading this mail. > Sincerely yours > Hua Peng > > Hua Peng > School of Physics > Shandong University, Jinan 25100 > People' Republic of Chin > > > ??????230????????60692999 --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080429/552f99f6/attachment.htm From giannozz at nest.sns.it Tue Apr 29 15:59:06 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 29 Apr 2008 15:59:06 +0200 Subject: [Pw_forum] SCF output information when testing espresso4.0cvs3 In-Reply-To: References: <4815C048.2050701@nest.sns.it> Message-ID: <481729AA.2060007@nest.sns.it> Zheng Bing wrote: > I don't think they are reasonable since such results aren't consistent > with the PROJWFC output. in fact they aren't. Stefano de Gironcoli justfound why: see http://www.democritos.it:8888/O-sesame/chngview?cn=5827 Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Tue Apr 29 16:02:35 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 29 Apr 2008 16:02:35 +0200 Subject: [Pw_forum] A possible bug of pp.x In-Reply-To: <4817221C.3020401@physics.unc.edu> References: <409473731.03297@mail.sdu.edu.cn> <4817221C.3020401@physics.unc.edu> Message-ID: <48172A7B.2050101@nest.sns.it> Charles Chen wrote: > Is pp.x supposed to run serial only? correct me if I am wrong. the first step (extracting data from files) can be performed either serially or in parallel. The second step (plotting) has to be performed serially. This should be invisible to the user. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From akohlmey at cmm.chem.upenn.edu Tue Apr 29 15:50:09 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 29 Apr 2008 09:50:09 -0400 (EDT) Subject: [Pw_forum] A possible bug of pp.x In-Reply-To: <409473731.03297@mail.sdu.edu.cn> References: <409473731.03297@mail.sdu.edu.cn> Message-ID: On Tue, 29 Apr 2008, ?????? Shu-jun Hu wrote: SH> SH> Dear the developers: SH> When i perform the post-processing calculation to obtain the charge and spin SH> density, i found a possible bug. Since the node have a dual core processor, i SH> sequentially started two pp jobs (plot_num = 0 and plot_num = 6) in less than 5 SH> seconds (charge density of plot_num = 0 is earlier). The running time is about 2 SH> minutes. However, the output data of charge and spin density are almost the same. SH> Both are more likely the output of earlier job, although there are still some SH> error data (the xcrysden image is ill). But when i run the later one until the SH> earlier one has been finished, everything is OK. dear shujun hu, i assume that both pp.x inputs access the same "prefix" directory and intermediate files. in that case you have to make sure that the intermediate files (filplot) that pp.x writes have different names. if they don't you'll get a complete mixup and that would explain the phenomenon you are describing. this would actually be a "shooting yourself in the foot" and thus not a bug. ;-) cheers, axel. SH> The vesion of the code is 3.2.3 and the parallel compiled pp.x runs in serial SH> model. SH> SH> SH> Shujun Hu SH> SH> SH> SH> SH> SH> SH> SH> SH> SH> SH> ------------------------------ SH> Shujun Hu e-mail: hushujun at 163.com SH> Shandong university Phone: +86/0531-88375097 SH> Jinan, Shandong Province, China, 250100 SH> _______________________________________________ SH> Pw_forum mailing list SH> Pw_forum at pwscf.org SH> http://www.democritos.it/mailman/listinfo/pw_forum SH> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From zhengb at ictp.it Tue Apr 29 17:18:54 2008 From: zhengb at ictp.it (Zheng Bing) Date: Tue, 29 Apr 2008 17:18:54 +0200 (CEST) Subject: [Pw_forum] SCF output information when testing espresso4.0cvs3 In-Reply-To: <481729AA.2060007@nest.sns.it> References: <4815C048.2050701@nest.sns.it> <481729AA.2060007@nest.sns.it> Message-ID: It works now. Thanks. On Tue, 29 Apr 2008, Paolo Giannozzi wrote: > Zheng Bing wrote: > >> I don't think they are reasonable since such results aren't consistent >> with the PROJWFC output. > > in fact they aren't. Stefano de Gironcoli justfound why: see > http://www.democritos.it:8888/O-sesame/chngview?cn=5827 > > Paolo > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ZHENG Bing - International Center for Theoretical Physics(ICTP) - Strada Costiera 11 - 34014 Trieste, ITALY E-mail: zhengb at ictp.it - Tel : +39 040 224 0459 - Fax : +39 040 224 163 - From giannozz at nest.sns.it Tue Apr 29 18:56:38 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 29 Apr 2008 18:56:38 +0200 Subject: [Pw_forum] Does anyone have Ge ultrasoft-PP for GGA? In-Reply-To: <200804281655434857996@uestc.edu.cn> References: <200804281655434857996@uestc.edu.cn> Message-ID: <48175346.3080300@nest.sns.it> xwzhang wrote: > Does any one have PP for Ge suitable in Heusler compounds (Co2MnGe, or > Rh2MnGe, magnetic metallic state)? I have a Ge (14e, ultrasoft, PBE) sitting on my disk since 3 years. I don't remember for which purpose it was generated and I have no idea whether it is suitable for Heusler or any other compounds. It is here: http://www.fisica.uniud.it/~giannozz/public/Ge.pbe-d-van.UPF.gz No warranty Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Tue Apr 29 19:20:46 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 29 Apr 2008 19:20:46 +0200 Subject: [Pw_forum] cannot remap grid on k-point list In-Reply-To: <53745.137.189.4.2.1208578148.squirrel@210.73.16.4> References: <53745.137.189.4.2.1208578148.squirrel@210.73.16.4> Message-ID: <481758EE.2030807@nest.sns.it> Li yan-ling wrote: > nat= 20 > ATOMIC_POSITIONS angstrom > Mg 0.00000000 0.00000000 0.08164318 > Mg 0.00000000 4.02388160 1.72667300 > Mg 1.78115505 4.02388160 0.08164318 > Mg 1.78115505 0.00000000 1.72667300 > B 2.12172031 6.56075530 0.08171232 > B 1.28305471 6.28121132 1.72679415 > B 2.12172031 2.53687371 1.72674204 > B 1.28305471 2.25732972 0.08176433 > B 1.44058974 1.48700801 0.08171232 > B 2.27925540 1.76655176 1.72679415 > B 1.44058974 5.51088949 1.72674204 > B 2.27925540 5.79043347 0.08176433 > B 0.34056526 5.51088949 0.08171232 > B 3.06420976 5.79043347 1.72679415 > B 0.34056526 1.48700801 1.72674204 > B 3.06420976 1.76655176 0.08176433 > B 3.22174484 2.53687371 0.08171232 > B 0.49810035 2.25732972 1.72679415 > B 0.49810035 6.28121132 0.08176433 one, two, three, ... nineteen -- Paolo Giannozzi, Democritos and University of Udine, Italy From ylli at theory.issp.ac.cn Wed Apr 30 09:11:00 2008 From: ylli at theory.issp.ac.cn (Li yan-ling) Date: Wed, 30 Apr 2008 15:11:00 +0800 (CST) Subject: [Pw_forum] cannot remap grid on k-point list Message-ID: <12800.137.189.4.2.1209539460.squirrel@210.73.16.4> Dear Paolo and other PWSCF users, The problem is not the case what you said. I'm sorry I miss a line about B atom. Thanks your answer. Can you tell me the other possible reason for this problem? Thanks in advance. Yan Ling Li, Institute of Solid state physics, CAS, China. >Li yan-ling wrote: >> nat= 20 > ATOMIC_POSITIONS angstrom > Mg 0.00000000 0.00000000 0.08164318 > Mg 0.00000000 4.02388160 1.72667300 > Mg 1.78115505 4.02388160 0.08164318 > Mg 1.78115505 0.00000000 1.72667300 > B 2.12172031 6.56075530 0.08171232 > B 1.28305471 6.28121132 1.72679415 > B 2.12172031 2.53687371 1.72674204 > B 1.28305471 2.25732972 0.08176433 > B 1.44058974 1.48700801 0.08171232 > B 2.27925540 1.76655176 1.72679415 > B 1.44058974 5.51088949 1.72674204 > B 2.27925540 5.79043347 0.08176433 > B 0.34056526 5.51088949 0.08171232 > B 3.06420976 5.79043347 1.72679415 > B 0.34056526 1.48700801 1.72674204 > B 3.06420976 1.76655176 0.08176433 > B 3.22174484 2.53687371 0.08171232 > B 0.49810035 2.25732972 1.72679415 > B 0.49810035 6.28121132 0.08176433 >one, two, three, ... nineteen -- >Paolo Giannozzi, Democritos and University of Udine, Italy From degironc at sissa.it Wed Apr 30 10:12:36 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 30 Apr 2008 10:12:36 +0200 Subject: [Pw_forum] cannot remap grid on k-point list In-Reply-To: <12800.137.189.4.2.1209539460.squirrel@210.73.16.4> References: <12800.137.189.4.2.1209539460.squirrel@210.73.16.4> Message-ID: <481829F4.70605@sissa.it> dear Li yan-ling, In the source code I notice the following comment --- ! this failure of the algorithm may indicate that the displaced grid ! (with k1,k2,k3.ne.0) does not have the full symmetry of the lattice call errore('lint','cannot remap grid on k-point list',n) --- Is this your case ? If not, can you please try to reproduce this error in a simpler case and post a complete job script that run in a short time (1-2 minute) ? If it is a problem related to symmetry you should be able to reproduce it reducing significantly the cutoff and the number of atoms. best regards, stefano Li yan-ling wrote: > Dear Paolo and other PWSCF users, > The problem is not the case what you said. I'm sorry I miss a line about > B atom. Thanks your answer. > Can you tell me the other possible reason for this problem? > > Thanks in advance. > > Yan Ling Li, > > Institute of Solid state physics, CAS, China. > > >> Li yan-ling wrote: >> > > >>> nat= 20 >>> > > >> ATOMIC_POSITIONS angstrom >> Mg 0.00000000 0.00000000 0.08164318 >> Mg 0.00000000 4.02388160 1.72667300 >> Mg 1.78115505 4.02388160 0.08164318 >> Mg 1.78115505 0.00000000 1.72667300 >> B 2.12172031 6.56075530 0.08171232 >> B 1.28305471 6.28121132 1.72679415 >> B 2.12172031 2.53687371 1.72674204 >> B 1.28305471 2.25732972 0.08176433 >> B 1.44058974 1.48700801 0.08171232 >> B 2.27925540 1.76655176 1.72679415 >> B 1.44058974 5.51088949 1.72674204 >> B 2.27925540 5.79043347 0.08176433 >> B 0.34056526 5.51088949 0.08171232 >> B 3.06420976 5.79043347 1.72679415 >> B 0.34056526 1.48700801 1.72674204 >> B 3.06420976 1.76655176 0.08176433 >> B 3.22174484 2.53687371 0.08171232 >> B 0.49810035 2.25732972 1.72679415 >> B 0.49810035 6.28121132 0.08176433 >> > > >> one, two, three, ... nineteen >> > > From mitujoshi at gmail.com Wed Apr 30 11:33:18 2008 From: mitujoshi at gmail.com (Joshi Mitesh) Date: Wed, 30 Apr 2008 02:33:18 -0700 Subject: [Pw_forum] Pseudoptential for Rb Message-ID: Dear all, Does anyone have pseudopotential for Rb ( LDA or GGA ) -Mitesh Joshi Department of Physics Sardar Patel University v v nagar, Anand Gujarat, India 388 120 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080430/74e40194/attachment.htm From lanhaiping at gmail.com Wed Apr 30 11:56:18 2008 From: lanhaiping at gmail.com (lan haiping) Date: Wed, 30 Apr 2008 17:56:18 +0800 Subject: [Pw_forum] [OT] How to identify NFE states ? In-Reply-To: <4908A727-2A77-4B86-BECE-253200A81949@sissa.it> References: <4908A727-2A77-4B86-BECE-253200A81949@sissa.it> Message-ID: Thank you ,Stefano! I have misinterpreted the meaning of effective mass. When we talk about NFE states, does it mean that such E-K dispersion should be held between 2 symmetry points, like from X-> Gamma ? On Mon, Apr 28, 2008 at 1:40 AM, Stefano Baroni wrote: > The higher the energy, the lower the effect of the pseudopotential, so > high-energy states are expected to be more free-electron like than low-lying > ones. I am afraid that the very ocncept of "effective mass" is not very > meaningful for these states. However, I would expect (although I have never > verified) that for high-lying states the derivative of the band energy with > respect to the wavenumber be linear with respect to the wavenumber, with the > coefficient given by the inverse of the free-electron mass. SB > On Apr 27, 2008, at 8:27 AM, lan haiping wrote: > > Dear All, > > I am wondering about the nearly free electron states . To identify such > states, > does it mean that its effective mass is very close to free electron ,And > we can identify > it from bands' dispersion ? > > Bests > H.P > > -- > Hai-Ping Lan > Department of Electronics , > Peking University , Bejing, 100871 > lanhaiping at gmail.com, hplan at pku.edu.cn_______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de > la pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080430/f7dfef37/attachment.htm From zhengb at ictp.it Wed Apr 30 12:04:41 2008 From: zhengb at ictp.it (Zheng Bing) Date: Wed, 30 Apr 2008 12:04:41 +0200 (CEST) Subject: [Pw_forum] Restart problem in espresso4.0cvs3 Message-ID: Good morning. I am testing espresso4.0cvs3 and I met some problems when I tried to restart the calculation. The error information is: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 1 from read_config_from_file : error # 1 problems in reading file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% The input is: cat >! bmo.in <<*** BMO cubic &control calculation='scf' pseudo_dir = '$pseudi', outdir='$workdir', prefix='bmo_000_f' disk_io='high' verbosity='high' tprnfor=.true. restart_mode='restart', / &system ibrav=0, celldm(1)=7.3894, nat=5, ntyp=3, nbnd=30, ecutwfc=35.0, ecutrho=350.0, occupations='smearing', smearing='gaussian', degauss=0.01, starting_magnetization(2)=1.0, nspin=2, / &electrons conv_thr = 1.0d-7 / &ions / ATOMIC_SPECIES Bi 70.00 Bi.pbe-d-mt.UPF Mn 70.00 Mn.pbe-sp-van.UPF O 70.00 O.pbe-rrkjus.UPF ATOMIC_POSITIONS Bi .00 .00 .00 Mn .50 .50 .50 O .50 .50 .00 O .50 .00 .50 O .00 .50 .50 K_POINTS (automatic) 24 24 24 0 0 0 CELL_PARAMETERS {cubic} 1.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 1.0000 *** $exec/pw.x -procs 4 -nodes 1 -tasks_per_node 4 < bmo.in >> ./bmo.out ------------------------------------------------------------------------------ It didn't happen when I used espresso4.0cvs01. Does anybody tell me why? Thanks in advance! Best, ZHENG Bing - International Center for Theoretical Physics(ICTP) - Strada Costiera 11 - 34014 Trieste, ITALY E-mail: zhengb at ictp.it - Tel : +39 040 224 0459 - Fax : +39 040 224 163 - From giannozz at nest.sns.it Wed Apr 30 12:15:30 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 30 Apr 2008 12:15:30 +0200 Subject: [Pw_forum] Restart problem in espresso4.0cvs3 In-Reply-To: References: Message-ID: <2AFAC34A-8CF8-4818-828C-30D96B86500A@nest.sns.it> On Apr 30, 2008, at 12:04 , Zheng Bing wrote: > I am testing espresso4.0cvs3 and I met some problems when I > tried to restart the calculation. produced by the same version of the code, or by a previous one? there have been recent changes to the format of data file. They should be backward-compatible, though, but it is important to know whether the code cannot read the previous or the current version of the data file Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From degironc at sissa.it Wed Apr 30 12:52:43 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 30 Apr 2008 12:52:43 +0200 Subject: [Pw_forum] [OT] How to identify NFE states ? In-Reply-To: References: <4908A727-2A77-4B86-BECE-253200A81949@sissa.it> Message-ID: <48184F7B.5020508@sissa.it> Dear Hai-Ping Lan, I think that the idea of NFE is that there are situations in which the effective (pseudo)-potential resulting from e-ion, e-e, and orthogonality to core electrons results to be weak and hence the eigenvalue problem to be solved is close to the free-electron one. Obviously at very high energies the kinetic energy dominates and the potential can be thought to be weak. But early empirical pseudopotential calculations (such Cohen-Bergstressen PhysRev 141, 789 (1966) or similar) show that silicon band structures is also close to FE in a certain sense... especially away from the regions of the BZ where the free electron bands would cross (where the pseudopotential opens gaps there and the dispersion is strongly modified)... But the true potential in silicon IS NOT smooth and valence wave-functions ARE NOT simple plane waves since they are orthogonal to core states and only when things are recast in a way that the effective hamiltonian, acting on some properly defined pseudo-wfc, is weak then the FE features of the dispersion relation can be understood... here come my question: WHY do you want to know which states are NFE-like ? what is the physical property you are interested in and what are the peculiar features of NFE for that property? This would help a great deal in understanding what a NFE should mean for your problem... best regards, Stefano de Gironcoli - SISSA and DEMOCRITOS lan haiping wrote: > Thank you ,Stefano! > I have misinterpreted the meaning of effective mass. > When we talk about NFE states, does it mean that such > E-K dispersion should be held between 2 symmetry points, like from X-> > Gamma ? > > On Mon, Apr 28, 2008 at 1:40 AM, Stefano Baroni > wrote: > > The higher the energy, the lower the effect of the > pseudopotential, so high-energy states are expected to be more > free-electron like than low-lying ones. I am afraid that the very > ocncept of "effective mass" is not very meaningful for these > states. However, I would expect (although I have never verified) > that for high-lying states the derivative of the band energy with > respect to the wavenumber be linear with respect to the > wavenumber, with the coefficient given by the inverse of the > free-electron mass. SB > > On Apr 27, 2008, at 8:27 AM, lan haiping wrote: > >> Dear All, >> >> I am wondering about the nearly free electron states . To >> identify such states, >> does it mean that its effective mass is very close to free >> electron ,And we can identify >> it from bands' dispersion ? >> >> Bests >> H.P >> >> -- >> Hai-Ping Lan >> Department of Electronics , >> Peking University , Bejing, 100871 >> lanhaiping at gmail.com , >> hplan at pku.edu.cn >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - > Trieste > [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une > morale de la pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Hai-Ping Lan > Department of Electronics , > Peking University , Bejing, 100871 > lanhaiping at gmail.com , hplan at pku.edu.cn > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From zhengb at ictp.it Wed Apr 30 13:09:40 2008 From: zhengb at ictp.it (Zheng Bing) Date: Wed, 30 Apr 2008 13:09:40 +0200 (CEST) Subject: [Pw_forum] Restart problem in espresso4.0cvs3 In-Reply-To: <2AFAC34A-8CF8-4818-828C-30D96B86500A@nest.sns.it> References: <2AFAC34A-8CF8-4818-828C-30D96B86500A@nest.sns.it> Message-ID: Hi, Paolo, I calculated it with the same version. I didn't change anything but "restart_mode", which was turned into "restart". Best, Bing On Wed, 30 Apr 2008, Paolo Giannozzi wrote: > > On Apr 30, 2008, at 12:04 , Zheng Bing wrote: > >> I am testing espresso4.0cvs3 and I met some problems when I >> tried to restart the calculation. > > produced by the same version of the code, or by a previous one? > there have been recent changes to the format of data file. They > should be backward-compatible, though, but it is important to know > whether the code cannot read the previous or the current version > of the data file > > 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 > ZHENG Bing - International Center for Theoretical Physics(ICTP) - Strada Costiera 11 - 34014 Trieste, ITALY E-mail: zhengb at ictp.it - Tel : +39 040 224 0459 - Fax : +39 040 224 163 - From giannozz at nest.sns.it Wed Apr 30 16:11:40 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 30 Apr 2008 16:11:40 +0200 Subject: [Pw_forum] Restart problem in espresso4.0cvs3 In-Reply-To: References: Message-ID: <90D5AC1F-BF25-4F0F-9A4C-3E48D68BBA48@nest.sns.it> On Apr 30, 2008, at 12:04 , Zheng Bing wrote: > I met some problems when I tried to restart the calculation. You are restarting from a 'scf' calculation. I am afraid that this case is not implemented right now. In general, restarting from the first scf step of any calculation (MD, structural optimisation, NEB) is not going to work, I am afraid Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From zhengb at ictp.it Wed Apr 30 16:16:09 2008 From: zhengb at ictp.it (Zheng Bing) Date: Wed, 30 Apr 2008 16:16:09 +0200 (CEST) Subject: [Pw_forum] Restart problem in espresso4.0cvs3 In-Reply-To: <90D5AC1F-BF25-4F0F-9A4C-3E48D68BBA48@nest.sns.it> References: <90D5AC1F-BF25-4F0F-9A4C-3E48D68BBA48@nest.sns.it> Message-ID: I see, Thanks. On Wed, 30 Apr 2008, Paolo Giannozzi wrote: > > On Apr 30, 2008, at 12:04 , Zheng Bing wrote: > >> I met some problems when I tried to restart the calculation. > > You are restarting from a 'scf' calculation. I am afraid that > this case is not implemented right now. In general, restarting > from the first scf step of any calculation (MD, structural > optimisation, NEB) is not going to work, I am afraid > > 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 > ZHENG Bing - International Center for Theoretical Physics(ICTP) - Strada Costiera 11 - 34014 Trieste, ITALY E-mail: zhengb at ictp.it - Tel : +39 040 224 0459 - Fax : +39 040 224 163 - From lanhaiping at gmail.com Wed Apr 30 17:14:39 2008 From: lanhaiping at gmail.com (lan haiping) Date: Wed, 30 Apr 2008 23:14:39 +0800 Subject: [Pw_forum] [OT] How to identify NFE states ? In-Reply-To: <48184F7B.5020508@sissa.it> References: <4908A727-2A77-4B86-BECE-253200A81949@sissa.it> <48184F7B.5020508@sissa.it> Message-ID: Thank you very much,Stefano. In fact, I just noticed some discussions on n-type doping on carbon nanotubes systems and graphite intercalated compounds. On these systems, NFE states have particular importance or some particular behaviors, for instance, the occupied NFE states were thought to account for superconducting transition behavior in some GICs. With regard to NFE, there seems no clear definition. I noticed that some discussion denoted band that is not a parabola along two high symmetry points but just a part . Best Best On Wed, Apr 30, 2008 at 6:52 PM, Stefano de Gironcoli wrote: > Dear Hai-Ping Lan, > > I think that the idea of NFE is that there are situations in which the > effective (pseudo)-potential resulting from > e-ion, e-e, and orthogonality to core electrons results to be weak and > hence the eigenvalue problem to be solved > is close to the free-electron one. > Obviously at very high energies the kinetic energy dominates and the > potential can be thought to be weak. > But early empirical pseudopotential calculations (such > Cohen-Bergstressen PhysRev 141, 789 (1966) or similar) > show that silicon band structures is also close to FE in a certain > sense... especially away from the regions > of the BZ where the free electron bands would cross (where the > pseudopotential opens gaps there and the dispersion > is strongly modified)... > But the true potential in silicon IS NOT smooth and valence > wave-functions ARE NOT simple plane waves since > they are orthogonal to core states and only when things are recast in a > way that the effective hamiltonian, acting on > some properly defined pseudo-wfc, is weak then the FE features of the > dispersion relation can be understood... > > here come my question: > > WHY do you want to know which states are NFE-like ? what is the physical > property you are interested in and > what are the peculiar features of NFE for that property? > > This would help a great deal in understanding what a NFE should mean for > your problem... > > best regards, > > Stefano de Gironcoli - SISSA and DEMOCRITOS > > > lan haiping wrote: > > Thank you ,Stefano! > > I have misinterpreted the meaning of effective mass. > > When we talk about NFE states, does it mean that such > > E-K dispersion should be held between 2 symmetry points, like from X-> > > Gamma ? > > > > On Mon, Apr 28, 2008 at 1:40 AM, Stefano Baroni > > wrote: > > > > The higher the energy, the lower the effect of the > > pseudopotential, so high-energy states are expected to be more > > free-electron like than low-lying ones. I am afraid that the very > > ocncept of "effective mass" is not very meaningful for these > > states. However, I would expect (although I have never verified) > > that for high-lying states the derivative of the band energy with > > respect to the wavenumber be linear with respect to the > > wavenumber, with the coefficient given by the inverse of the > > free-electron mass. SB > > > > On Apr 27, 2008, at 8:27 AM, lan haiping wrote: > > > >> Dear All, > >> > >> I am wondering about the nearly free electron states . To > >> identify such states, > >> does it mean that its effective mass is very close to free > >> electron ,And we can identify > >> it from bands' dispersion ? > >> > >> Bests > >> H.P > >> > >> -- > >> Hai-Ping Lan > >> Department of Electronics , > >> Peking University , Bejing, 100871 > >> lanhaiping at gmail.com , > >> hplan at pku.edu.cn > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > --- > > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - > > Trieste > > [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) > > > > La morale est une logique de l'action comme la logique est une > > morale de la pens?e - Jean Piaget > > > > Please, if possible, don't send me MS Word or PowerPoint > attachments > > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > -- > > Hai-Ping Lan > > Department of Electronics , > > Peking University , Bejing, 100871 > > lanhaiping at gmail.com , hplan at pku.edu.cn > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080430/d27fe6ec/attachment.html From giannozz at nest.sns.it Wed Apr 30 21:18:01 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 30 Apr 2008 21:18:01 +0200 Subject: [Pw_forum] Restart problem in espresso4.0cvs3 In-Reply-To: <90D5AC1F-BF25-4F0F-9A4C-3E48D68BBA48@nest.sns.it> References: <90D5AC1F-BF25-4F0F-9A4C-3E48D68BBA48@nest.sns.it> Message-ID: <78181B2F-22C5-4EE8-8323-5A78DE3B765D@nest.sns.it> On Apr 30, 2008, at 16:11 , Paolo Giannozzi wrote: > On Apr 30, 2008, at 12:04 , Zheng Bing wrote: > >> I met some problems when I tried to restart the calculation. > > You are restarting from a 'scf' calculation. I am afraid that > this case is not implemented right now. In general, restarting > from the first scf step of any calculation (MD, structural > optimisation, NEB) is not going to work, I am afraid ...and in fact it didn't, but only in same cases. Anyway: it wasn't that difficult to fix it. The quick fix is to change IF ( ierr == 1 ) THEN into IF ( ierr > 0 ) THEN in PW/read_conf_from_file.f90 . Thank you for the second report of a true bug in a few days! Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at nest.sns.it Wed Apr 30 21:25:25 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 30 Apr 2008 21:25:25 +0200 Subject: [Pw_forum] Pseudoptential for Rb In-Reply-To: References: Message-ID: On Apr 30, 2008, at 11:33 , Joshi Mitesh wrote: > Does anyone have pseudopotential for Rb ( LDA or GGA ) 1-electron or 9-electron ? 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 thonhauser at MIT.EDU Wed Apr 30 22:57:40 2008 From: thonhauser at MIT.EDU (Timo Thonhauser) Date: Wed, 30 Apr 2008 16:57:40 -0400 Subject: [Pw_forum] difference between nr1 and nrx1 Message-ID: <4818DD44.6050807@mit.edu> Dear Developers, What is the difference between nr1, nr2, nr3 and nrx1, nrx2, nrx3 in the code? For all practical purposes they always seem to be the same. In PW/pwcom.f90 we find: nr1, &! fft dimension along x nr2, &! fft dimension along y nr3, &! fft dimension along z nrx1, &! maximum fft dimension along x nrx2, &! maximum fft dimension along y nrx3, &! maximum fft dimension along z But when would nr1 differ from nrx1? Thanks a lot! Timo -- ______________________________________________________________________ Dr. TIMO THONHAUSER Department of Materials Science and Engineering (617) 253 6026 MIT, 13-4084, 77 Massachusetts Avenue thonhauser at mit.edu Cambridge, MA 02139-4307, USA www.mit.edu/~thonhaus ______________________________________________________________________