From marzari at MIT.EDU Mon Oct 1 06:12:41 2007 From: marzari at MIT.EDU (Nicola Marzari) Date: Mon, 01 Oct 2007 00:12:41 -0400 Subject: [Pw_forum] benchmark calculations for parallel PWSCF In-Reply-To: <20070928113526.5vxbqd2r9mo0ww0s@mail.ph.utexas.edu> References: <20070928113526.5vxbqd2r9mo0ww0s@mail.ph.utexas.edu> Message-ID: <470073B9.1010801@mit.edu> Dear Sahu, I have mostly CP scaling data here, on small machines: http://quasiamore.mit.edu/pmwiki/index.php?n=Main.CP90Timings The bottom line is that provided that you use a recent MPI implementation, scaling is certainly very good using gigabit ethernet up to 12 processors. We haven't tested anything larger. Of course, gigabit ethernet is a slow connection. I've seen tests done on the Cray XT4 that went up to 5000 processors, with excellent scaling. Some notes on hyperparallelization can be found on the wiki http://www.quantum-espresso.org/wiki/index.php/Running_on_parallel_machines I do not have data for PWSCF - of course scaling on k-points or NEB images would be perfect, but also on G-vectors should go reasonably well with hundreds of CPUs. Maybe someone else has data to share ? nicola brsahu at physics.utexas.edu wrote: > Dear PWSCF users, > > Is it possibe to get a info on benchmark PWSCF SCF parallel > calculations (CPU time versus number of processors) for a particular > physical system on any computing machines (linux clusters, IBM (Power > series), SGI, HP etc. > > Is it possible to share the numbers with me if you have such numbers? > I am aware that lot depends on what type of processors, what > communication channel, what libraries etc. But at this stage I am not > looking at a particular set of hardware/software set-up but only a > rough idea of how SCF parallel run scales with > number of processors for a given system size > > Bhagawan Sahu > Microelectronics Research Center > University of Texas at Austin > 10100 Burnet Road, Bldg. 160 > MER 1.606H, Mail code R9900, TX 78758-4445 > e-mail: brsahu at physics.utexas.edu > Phone: (512)-471-1344 FAX: (512)-471-8575 > _______________________________________________ > 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 Daniele.Passerone at empa.ch Mon Oct 1 12:15:04 2007 From: Daniele.Passerone at empa.ch (Daniele Passerone) Date: Mon, 01 Oct 2007 12:15:04 +0200 Subject: [Pw_forum] Intermediate images in NEB In-Reply-To: References: Message-ID: <4700E4C8.11F0.001D.0@empa.ch> Dear forum members We noticed a small bug in the neb capabilities of pwscf, or maybe we are missing something. Indeed, the program seems to set always a linear interpolation between first a last image, even when the intermediate images are given. The origin seems to be in the subroutine initial_guess (module path_base.f90) where an array pos_n with the linearly interpolated position is built. The purpose should be to copy pos_n(:,:) in the pos(:,:) vector only if the intermediate images given by the user are absent or unreasonable. Unfortunately, there is a line pos(:,:) = pos_n(:,:) that always copies the linear guess into the position array. For the moment i modified this line into if (input_images .ne. num_of_images) then pos(:,:) = pos_n(:,:) endif And that should do the job. Best regards, Daniele Passerone From akohlmey at cmm.chem.upenn.edu Mon Oct 1 12:26:27 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 1 Oct 2007 06:26:27 -0400 (EDT) Subject: [Pw_forum] Intermediate images in NEB In-Reply-To: <4700E4C8.11F0.001D.0@empa.ch> Message-ID: On Mon, 1 Oct 2007, Daniele Passerone wrote: dear daniele, please complete your bug report by stating which version of quantum espresso you are using, and if you have the time, you could also check whether the bug still exists in the cvs version... ciao, axel. DP> Dear forum members DP> DP> We noticed a small bug in the neb capabilities of pwscf, or maybe we DP> are missing something. DP> Indeed, the program seems to set always a linear interpolation between DP> first a last image, even when the DP> intermediate images are given. DP> DP> The origin seems to be in the subroutine initial_guess (module DP> path_base.f90) DP> where an array pos_n with the linearly interpolated position is built. DP> DP> The purpose should be to copy pos_n(:,:) in the pos(:,:) vector only if DP> the intermediate images given by the user are absent or DP> unreasonable. DP> Unfortunately, DP> there is a line DP> DP> pos(:,:) = pos_n(:,:) DP> DP> that always copies the linear guess into the position array. DP> DP> For the moment i modified this line into DP> DP> if (input_images .ne. num_of_images) then DP> pos(:,:) = pos_n(:,:) DP> endif DP> DP> And that should do the job. DP> DP> DP> Best regards, DP> DP> Daniele Passerone DP> DP> _______________________________________________ DP> Pw_forum mailing list DP> Pw_forum at pwscf.org DP> http://www.democritos.it/mailman/listinfo/pw_forum DP> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From tone.kokalj at ijs.si Mon Oct 1 14:04:36 2007 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 01 Oct 2007 14:04:36 +0200 Subject: [Pw_forum] Intermediate images in NEB In-Reply-To: <4700E4C8.11F0.001D.0@empa.ch> References: <4700E4C8.11F0.001D.0@empa.ch> Message-ID: <1191240276.2580.11.camel@localhost.localdomain> On Mon, 2007-10-01 at 12:15 +0200, Daniele Passerone wrote: > > The purpose should be to copy pos_n(:,:) in the pos(:,:) vector only if > the intermediate images given by the user are absent or > unreasonable. > Unfortunately, > there is a line > > pos(:,:) = pos_n(:,:) This is not a bug ! The way the intermediate images are used is the following: (1) the initial path is constructed by linear segments between initial--intermedite1--intermediate2--....--final image. (2) then "num_of_images" equispaced images are constructed from this linear-segmented path. The pos(:,:) = pos_n(:,:) just copies this equispaced generate images. Hence the intermediate images are used to "steer" the initial path, but are actually not used. Note also that the number of initermediate_images does not need to be num_of_images - 2. Regards, Tone From giannozz at nest.sns.it Mon Oct 1 14:54:47 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 1 Oct 2007 14:54:47 +0200 Subject: [Pw_forum] benchmark calculations for parallel PWSCF In-Reply-To: <20070928113526.5vxbqd2r9mo0ww0s@mail.ph.utexas.edu> References: <20070928113526.5vxbqd2r9mo0ww0s@mail.ph.utexas.edu> Message-ID: On Sep 28, 2007, at 18:35 , brsahu at physics.utexas.edu wrote: > Is it possibe to get a info on benchmark PWSCF SCF parallel > calculations (CPU time versus number of processors) for a particular > physical system on any computing machines (linux clusters, IBM > (Power series), SGI, HP etc. once upon a time Carlo Sbraccia wrote and sent me a benchmark script. It never percolated to the web site, so I put it here: http://www.fisica.uniud.it/~giannozz/public/benchmark.tgz It contains a table of results as well. It is quite old, so it may require some modifications in order to run with recent versions of the code. 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 Daniele.Passerone at empa.ch Mon Oct 1 15:07:50 2007 From: Daniele.Passerone at empa.ch (Daniele Passerone) Date: Mon, 01 Oct 2007 15:07:50 +0200 Subject: [Pw_forum] Intermediate images in NEB Message-ID: <47010D46.11F0.001D.0@empa.ch> Tone wrote: > This is not a bug ! Dear Tone, Thanks a lot for your clarification (I refer to 3.2.2 version of the code). I inspected the code and you are completely right. However, there are case when it would be desirable to use EXACTLY that initial guess, for example in case of interpolation through intermediate values of a torsional angle... That's the origin of my concern. Maybe it would not be a bad idea to add this option... Thanks for your help Daniele From giannozz at nest.sns.it Mon Oct 1 22:18:14 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 1 Oct 2007 22:18:14 +0200 Subject: [Pw_forum] error in the q2r.out In-Reply-To: <703688.33680.qm@web73009.mail.tp2.yahoo.com> References: <703688.33680.qm@web73009.mail.tp2.yahoo.com> Message-ID: <61D114FB-EB09-4113-9967-7B84F92EBD72@nest.sns.it> On Sep 24, 2007, at 19:08 , ? ?? wrote: > The q2r.out error messsage as below > [...] > Does anyone know what it means ? q2r.x, like matdyn.x, dynmat.x, and many other auxiliary codes, is not parallelized and should be run on a single processor. It sort of works in parallel (i.e. only one process is actually executed) but with no advantage at all wrt execution on one processor, and the disadvantage that error handling will cause more errors, and produce confusing error messages 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 Mon Oct 1 22:19:42 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 1 Oct 2007 22:19:42 +0200 Subject: [Pw_forum] about metal and molecular dynamics In-Reply-To: <3e36a8fc0709262009y371fa433w924778ee7f70e1ea@mail.gmail.com> References: <3e36a8fc0709260114g6ab290c9n75acd03b475a958c@mail.gmail.com> <7b6913e90709261950m6b542118of540278d77794a82@mail.gmail.com> <3e36a8fc0709262009y371fa433w924778ee7f70e1ea@mail.gmail.com> Message-ID: On Sep 27, 2007, at 5:09 , Wei Zhou wrote: > thank you for your answer. but I want to know if the pw.x of QE code > can do variable cell dynamics 'npt' using nose to control temperature. no (or not yet) > or the cp of QE code can do this yes > .or both of them can do this . no .AND. yes = no 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 Mon Oct 1 22:27:22 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 1 Oct 2007 22:27:22 +0200 Subject: [Pw_forum] error in the calculation of mpirun ph.x. In-Reply-To: <390639747.23084@nudt.edu.cn> References: <390639747.23084@nudt.edu.cn> Message-ID: On Sep 24, 2007, at 15:15 , ??? wrote: > When i use mpirun -np 4 ph.x -npool 2 < *.ph.in > *.ph.out, > it is OK at the beginning (including the mpirun -np 4 pw.x > calculation). But when it began to calculate the dynamic > matrix of second q point, it stopped. there were a few problems in the calculation of phonons with pools. They have been fixed only in the latest stable version, soon to be available from the download page 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 chenhanghuipwscf at gmail.com Tue Oct 2 17:16:57 2007 From: chenhanghuipwscf at gmail.com (alan chen) Date: Tue, 2 Oct 2007 11:16:57 -0400 Subject: [Pw_forum] Internal MPI error Message-ID: <22ae3ca40710020816h64cae9e5sfbc529b12f9e67c7@mail.gmail.com> Dear Forum Members, We have encountered an Internal MPI error in a couple of jobs. The jobs are of medium size (around 60 atoms in the unit cell) . When they had run after some time (one or two days) they were automatically killed due to the following error: Fatal error in MPI_Alltoallv: Internal MPI error!, error stack: MPI_Alltoallv(407).: MPI_Alltoallv(sbuf=0x2a96197010, scnts=0x7fbfffdaf0, sdispls=0x7fbfffdb70, MPI_DOUBLE_COMPLEX, rbuf=0x2ad32ce010, rcnts=0x7fbfffdbf0, rdispls=0x7fbfffdc70, MPI_DOUBLE_COMPLEX, comm=0x84000002) failed MPI_Waitall(242)..........................: MPI_Waitall(count=64, req_array=0x3391b40, status_array=0x3391630) failed MPIDI_CH3_Progress_wait(212)..............: an error occurred while handling an event returned by MPIDU_Sock_Wait() MPIDI_CH3I_Progress_handle_sock_event(413): MPIDU_Socki_handle_read(633)..............: connection failure (set=0,sock=8,errno=104:Connection reset by peer) [cli_30]: aborting job: Fatal error in MPI_Alltoallv: Other MPI error, error stack: MPI_Alltoallv(407)........................: MPI_Alltoallv(sbuf=0x2a96197010, scnts=0x7fbfffdaf0, sdispls=0x7fbfffdb70, MPI_DOUBLE_COMPLEX, rbuf=0x2aac72a010, rcnts=0x7fbfffdbf0, rdispls=0x7fbfffdc70, MPI_DOUBLE_COMPLEX, comm=0x84000002) failed MPI_Waitall(242)..........................: MPI_Waitall(count=64, req_array=0x3382f50, status_array=0x3263c60) failed Does anyone have this problem before? How can I avoid this problem? Thank you very much. Hanghui -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071002/bacc9346/attachment.htm From fratesi at mater.unimib.it Tue Oct 2 17:57:28 2007 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Tue, 2 Oct 2007 17:57:28 +0200 (CEST) Subject: [Pw_forum] Intermediate images in NEB In-Reply-To: <47010D46.11F0.001D.0@empa.ch> References: <47010D46.11F0.001D.0@empa.ch> Message-ID: Dear Daniele, | However, there are case when it would be desirable to use EXACTLY that | initial guess, for example in case of interpolation | through intermediate values of a torsional angle... | That's the origin of my concern. Maybe it would not be a bad idea to | add this option... at once I was also in the need of specifying EXACTLY a given initial path. The reason, in my case, was that I wanted to merge two paths from different calculations in a single one. Of course, I didn't want a re-interpolation to spoil the accuracy already reached. Then, I build the path file "by hand" (but awk or the like is helpful). That's not that hard. One possibility for you could be to edit the interpolated path file which you get with nstep=0, and replace the coordinate of some images with the ones you want. Then you can restart from this path file. The real problem, in my opinion, is that a path build up this way will generally have images not at the right spacing, therefore feeling too much the springs in the direction parallel to the path. This could require a few additional optimization steps, and possibly compensate the advantages. Another solution could be to generate a set of path files linking the various intermediate images, to merge them, and finally to start the optimization of this merged path. I feel that could work better than my previous suggestion, because possibly no image would feel to strong springs, if the initial spacings of the various paths is comparable. Hope this helps more than confuses Guido -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli studi di Milano-Bicocca via Cozzi 53, 20125 Milano, Italy From giannozz at nest.sns.it Tue Oct 2 18:23:12 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 2 Oct 2007 18:23:12 +0200 Subject: [Pw_forum] Internal MPI error In-Reply-To: <22ae3ca40710020816h64cae9e5sfbc529b12f9e67c7@mail.gmail.com> References: <22ae3ca40710020816h64cae9e5sfbc529b12f9e67c7@mail.gmail.com> Message-ID: <2C847032-E1E9-4087-ABE9-EB7A35A58DBD@nest.sns.it> On Oct 2, 2007, at 17:16 , alan chen wrote: > [mysterious error messages] > ...connection failure... > [more mysterious error messages] are you sure about the quality of your connection hardware? 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 vparkash at mtu.edu Tue Oct 2 20:58:59 2007 From: vparkash at mtu.edu (Vidur Parkash) Date: Tue, 2 Oct 2007 11:58:59 -0700 (PDT) Subject: [Pw_forum] Another SCF convergence problem Message-ID: <458702.46424.qm@web35410.mail.mud.yahoo.com> Hi I'm trying to perform a SCf calculation on a carbon nanotube cluster (metallic system), and no matter what i do the results do not converge. I've tried changing the mixing factor, add a smearing, tried a different type of charge mixing, change number of k points etc. The input file I've attached is the closest it ever reached towards convergence with accuracy better than 0.1 Ry...but ultimately failing to converge. Can you please suggest some solutions Thanks Vidur -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071002/4f50c6d3/attachment.htm From giannozz at nest.sns.it Tue Oct 2 22:11:57 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 2 Oct 2007 22:11:57 +0200 Subject: [Pw_forum] Another SCF convergence problem In-Reply-To: <458702.46424.qm@web35410.mail.mud.yahoo.com> References: <458702.46424.qm@web35410.mail.mud.yahoo.com> Message-ID: <4BF58114-C88A-4EC9-BC30-36E11825BBE8@nest.sns.it> On Oct 2, 2007, at 20:58 , Vidur Parkash wrote: > The input file I've attached have you? Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From vparkash at mtu.edu Tue Oct 2 22:51:16 2007 From: vparkash at mtu.edu (Vidur Parkash) Date: Tue, 2 Oct 2007 13:51:16 -0700 (PDT) Subject: [Pw_forum] Another SCF convergence problem Message-ID: <731585.75368.qm@web35414.mail.mud.yahoo.com> Hi I'm trying to perform a SCf calculation on a carbon nanotube cluster (metallic system), and no matter what i do the results do not converge. I've tried changing the mixing factor, add a smearing, tried a different type of charge mixing, change number of k points etc. The input file I've attached is the closest it ever reached towards convergence with accuracy better than 0.1 Ry...but ultimately failing to converge. Can you please suggest some solutions. The input file is attached this time. Thanks Vidur Parkash Michigan Tech University 716 EERC, 1400 Townsend Drive Houghton MI-49931, USA Tel: 1-906-487-0023 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071002/4a48e966/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: swnt_bndl.pw.inp Type: application/octet-stream Size: 3588 bytes Desc: 658068986-swnt_bndl.pw.inp Url : http://www.democritos.it/pipermail/pw_forum/attachments/20071002/4a48e966/attachment.obj From chen_shao_hua197 at yahoo.com.tw Tue Oct 2 23:15:35 2007 From: chen_shao_hua197 at yahoo.com.tw (=?big5?q?=B3=AF=20=A4=D6=B5=D8?=) Date: Wed, 3 Oct 2007 05:15:35 +0800 (CST) Subject: [Pw_forum] How to get the phonon frequency logarithmic average In-Reply-To: <40FB3043-FB49-4DE9-A613-58F68FAEA099@nest.sns.it> Message-ID: <913059.39514.qm@web73001.mail.tp2.yahoo.com> Dear Paolo, I had compiled lambda.x from pwtools/lambda.f90 for calculating the "phonon frequency logarithmic averag" and alpha^2F(omega). I tried to write down its input file refer to lambda.f90 as below ! INPUT from standard input: ! emax degaussq ngaussq ! nks ! q(1,1) q(2,1) q(3,1) wk(1) ! ... ... ... ... ! q(1,nks) q(2,nks) q(3,nks) wk(nks) ! filelph(1) ! ... ! filelph(nks) ! ! emax (THz) : alpha2F is plotted from 0 to "emax" in "nex" steps ! degaussq (THz): gaussian smearing for sum over q ! NB: not the same used in phonon ! ! ngaussq : 0 for simple gaussian, 1 for Methfessel-Paxton etc. ! nks : number of q-points used in the sum ! q, wk : q-points and weights ! filelph : output files from phonon, one for each q-point ! May contain "nsig" calculations done with different ! broadenings for the sum over k - all of them are used ! ! OUTPUT in xmgr-readable format: files 'lambda.dat' and 'alpha2F.dat' ! The only part I don't get it is "filelph" . It say "output files from phonon" ,what does it mean ? *.ph.out (produced by ph.x) or others ? Best Regards max Physics Department,National Taiwan University,Taiwan --- Paolo Giannozzi ?? > > On Aug 13, 2007, at 3:42 , clie wrote: > > > recently, i use pwscf to caliculate > electron-phonon couple constance, > > but i want to get Tc and i need the phonon > frequency logarithmic > > average. Could you tell me how to get the value? > > pwtools/lambda.f90 should calculate it. > Unfortunately it has > never been updated to read the new file formats > produced > by the electron-phonon calculation, so it will > require some > work > > 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 > ____________________________________________________________________________________ ????????????? - ???? Yahoo!??????http://tw.info.yahoo.com/seal/index.html From tgrassma at ucsd.edu Tue Oct 2 23:28:37 2007 From: tgrassma at ucsd.edu (Tyler Grassman) Date: Tue, 2 Oct 2007 14:28:37 -0700 Subject: [Pw_forum] General pseudopotential generation questions (using ld1) Message-ID: <002501c8053b$3242ff40$6300a8c0@Crom> Hello all. I'm currently trying to generate some norm-conserving pseudopotentials for use in some calculations I want to try (and they are not available for download). I've read Paolo Giannozzi's guide a few dozen times, in addition to the basic pseudopotential literature, and it's been extremely helpful so far, but I still have some questions. I've managed to generate a number of NC-PPs (RRKJ, PBE) for Ge, H, and O so far, and have been trying to thoroughly test them... For testing I'm comparing the AE vs PS wavefunctions, the logarithmic derivatives, the transferability tests using different electronic configurations using the ld1 code, as well as the Bessell function basis tests. After the PPs pass these tests I'm performing bulk convergence tests and checking for lattice paramter and density of states and that sort of thing (for Ge), and diatomic bond lengths and such for H2 and O2. Pretty standard stuff, I would think. And I think I've managed to generate some decent (I think) PPs from a combination of my own experimentation, as well as utilizing some of the input values used in the VASP pseudopotential library (the NC parts of the US-PPs). However, at this point, I've run into a few questions regarding some of the parameters available for PP generation. First, the potential mixing paramter, "beta." The default is 0.2, but I found in some of the examples in the atomic_doc directory values of 0.5. How does this paramter effect the PP? I tried playing with it a little with my O potentials, but didn't really see a difference. So, what does it do, exactly, and how important is it? Second... Choice of local potential (i.e. lloc=-1 vs. lloc>-1). I think I understand, in principle, what the difference is between these two approaches, but I'm not quite sure that I understand the end result. So, for the O potentials, nothing weird happens, but using lloc=-1 tends to produce PPs that give me an O2 bond length closer to the experimental value with a smaller cutoff energy than do similar potentials (e.g. 2s2 2p4 with lloc=1, 2s2 2p4 3d-1 with lloc=2). With Ge, however, the results *is* weird. The potentials produced with lloc=-1 (4s2 4p2, no semicore d) give a lattice parameter that is actually smaller than experimental (10.60 vs 10.69 Bohr, which definitely seems funny for a GGA calc), while potentials using 4s2 4p2 4d-1 (lloc=2) and 4s2 4p2 4d-1 4f-1 (lloc=3), give values larger than experimental, as would be expected. The lloc=3 case, which is the same used in the VASP US-PPs, gives the best results (10.91 Bohr). Any suggestions as to why this might be occuring? And does anyone have any pointers as to when using the lloc=-1 vs lloc>-1 is or is not appropriate? Finally... rcore values for non-linear core correction... I find that the core charge calculation depends upon what I set rcore to (as well it should). If rcore is set in the input file, the local potential and core charge radii are equal. However, if rcore is not explicitly set in the input file the core radius chosen for the local potential vs. that chosen for the core pseudo-charge are different; the local potential rcore is chosen as the largest rcut, and the core pseudo-charge radius is chosen by some other method (and, at least for Ge, it tends to be quite small compared to the rcut values). Is this perhaps a bug? It seems like it would be safest just to make sure to set rcore by hand, but I just wanted to check. Well, sorry for such a large e-mail, but hopefully someone will be willing to answer these questions (and hopefully such answers will be helpful to more than just myself). I realize that I did not attach the pseudo-generation inputs, mostly just because I felt these questions were of a more general nature, but I would be happy to provide the inputs should anyone feel they are necessary. Thank you very much! Regards, Tyler Grassman Dept. of Chemistry/Biochemistry, Materials Science and Engineering University of California, San Diego From matteo at umn.edu Wed Oct 3 01:20:14 2007 From: matteo at umn.edu (Matteo Cococcioni) Date: Tue, 02 Oct 2007 18:20:14 -0500 Subject: [Pw_forum] Another SCF convergence problem In-Reply-To: <731585.75368.qm@web35414.mail.mud.yahoo.com> References: <731585.75368.qm@web35414.mail.mud.yahoo.com> Message-ID: <4702D22E.4020003@umn.edu> Dear Vidur I gave a look to your input and also to the crystal structure of your system (xcrysden --pwi swnt_bndl.pw.inp). I noticed few things that could give troubles and it looks like some of the input parameters probably were not converged. are you sure that 20 Ry is enough for a NC pseudopotential? degauss = 0.5 looks to me like a large number. even if your calculation were converged it would have converged to a wrong result. Keep in mind this is Ry. your k-point mesh is probably too small. Though your system is quite large on the xy plane I don't think 1 point is enough. two points in z directions are definitely too few. In your case also the second point looks equivalent to the first one to me. I'm not 100% sure actually because you gave it in tpiba units and I'm not sure what the code uses as a in this case (probably celldm(1)). Anyhow if the second point is not equivalent to the first one it is in a very weird position. I would go for an automatically generated mesh (e.g. 228 or 448). Matteo Vidur Parkash wrote: > Hi > > I'm trying to perform a SCf calculation on a carbon nanotube cluster > (metallic system), and no matter what i do the results do not > converge. > I've tried changing the mixing factor, add a smearing, tried a > different type of charge mixing, change number of k points etc. > > The input file I've attached is the closest it ever reached towards > convergence with accuracy better than 0.1 Ry...but ultimately failing > to converge. > > > Can you please suggest some solutions. The input file is attached > this time. > > Thanks > > Vidur Parkash > > Michigan Tech University > 716 EERC, 1400 Townsend Drive > Houghton MI-49931, USA > Tel: 1-906-487-0023 > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- 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/20071002/44e45abc/attachment.vcf From akohlmey at cmm.chem.upenn.edu Wed Oct 3 01:22:55 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 2 Oct 2007 19:22:55 -0400 (EDT) Subject: [Pw_forum] Internal MPI error In-Reply-To: <22ae3ca40710020816h64cae9e5sfbc529b12f9e67c7@mail.gmail.com> Message-ID: On Tue, 2 Oct 2007, alan chen wrote: AC> Dear Forum Members, AC> We have encountered an Internal MPI error in a couple of jobs. The jobs AC> are of medium size (around 60 atoms in the unit cell) . When they had run AC> after some time (one or two days) they were automatically killed due to the AC> following error: AC> AC> Fatal error in MPI_Alltoallv: Internal MPI error!, error stack: AC> MPI_Alltoallv(407).: MPI_Alltoallv(sbuf=0x2a96197010, scnts=0x7fbfffdaf0, AC> sdispls=0x7fbfffdb70, MPI_DOUBLE_COMPLEX, rbuf=0x2ad32ce010, AC> rcnts=0x7fbfffdbf0, rdispls=0x7fbfffdc70, MPI_DOUBLE_COMPLEX, AC> comm=0x84000002) failed AC> MPI_Waitall(242)..........................: MPI_Waitall(count=64, AC> req_array=0x3391b40, status_array=0x3391630) failed AC> MPIDI_CH3_Progress_wait(212)..............: an error occurred while handling AC> an event returned by MPIDU_Sock_Wait() AC> MPIDI_CH3I_Progress_handle_sock_event(413): AC> MPIDU_Socki_handle_read(633)..............: connection failure AC> (set=0,sock=8,errno=104:Connection reset by peer) this looks like an ethernet timeout. have you checked whether your switch can handle the load that the job creates? i assume you are running on top of gigabit ethernet. have you tried the same input on a different machine or serially? what version of the code are you using? please keep in mind, that the more specifics you can provide about what happened, the better the help people can give you. cheers, axel. AC> Does anyone have this problem before? How can I avoid this problem? AC> Thank you very much. AC> AC> Hanghui AC> -- ======================================================================= 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 Wed Oct 3 09:36:50 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 3 Oct 2007 09:36:50 +0200 Subject: [Pw_forum] General pseudopotential generation questions (using ld1) In-Reply-To: <002501c8053b$3242ff40$6300a8c0@Crom> References: <002501c8053b$3242ff40$6300a8c0@Crom> Message-ID: On Oct 2, 2007, at 23:28 , Tyler Grassman wrote: > First, the potential mixing paramter, "beta." The default is 0.2, > but I > found in some of the examples in the atomic_doc directory values of > 0.5. > How does this paramter effect the PP? it doesn't. It affects only how fast scf convergence is achieved. 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 Oct 3 10:06:57 2007 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 03 Oct 2007 10:06:57 +0200 Subject: [Pw_forum] Another SCF convergence problem In-Reply-To: <731585.75368.qm@web35414.mail.mud.yahoo.com> References: <731585.75368.qm@web35414.mail.mud.yahoo.com> Message-ID: <47034DA1.3050307@sissa.it> This may not be totally relevant but ... have you checked that the configuration you are using makes sense ? By visualizing it with xcrysden it appear that the carbon-carbon distances are all larger than 3 angstrom ... so your system is a collection of weakly interacting atoms, probably with very narrow bands. Technically this may be the origin of the instability, but ...is this the system you want to study ? Hpe it helps stefano Stefano de Gironcoli - SISSA and DEMOCRITOS Vidur Parkash wrote: > Hi > > I'm trying to perform a SCf calculation on a carbon nanotube cluster > (metallic system), and no matter what i do the results do not > converge. > I've tried changing the mixing factor, add a smearing, tried a > different type of charge mixing, change number of k points etc. > > The input file I've attached is the closest it ever reached towards > convergence with accuracy better than 0.1 Ry...but ultimately failing > to converge. > > > Can you please suggest some solutions. The input file is attached > this time. > > Thanks > > Vidur Parkash > > Michigan Tech University > 716 EERC, 1400 Townsend Drive > Houghton MI-49931, USA > Tel: 1-906-487-0023 > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at nest.sns.it Wed Oct 3 10:16:44 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 3 Oct 2007 10:16:44 +0200 Subject: [Pw_forum] Another SCF convergence problem In-Reply-To: <731585.75368.qm@web35414.mail.mud.yahoo.com> References: <731585.75368.qm@web35414.mail.mud.yahoo.com> Message-ID: <323BCE2F-F014-42BA-BED6-F865BB337A81@nest.sns.it> On Oct 2, 2007, at 22:51 , Vidur Parkash wrote: > I'm trying to perform a SCf calculation on a carbon nanotube cluster > (metallic system), and no matter what i do the results do not > converge. there is a small utility pwtools/dist.x (documentation in the header of file pwtools/dist.f) that gives you atomic distances and neighbors. It is not fancy but it accepts input data in a format (see below) that is very similar to the format of input data for pw.x . What I get with your data is a C-C distance of 2.45A. Is this what you want? -------------- next part -------------- A non-text attachment was scrubbed... Name: swnt_bndl.pw.inp Type: application/octet-stream Size: 2501 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20071003/53029a1c/attachment.obj -------------- next part -------------- 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 eyvaz_isaev at yahoo.com Wed Oct 3 10:47:32 2007 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 3 Oct 2007 01:47:32 -0700 (PDT) Subject: [Pw_forum] Another SCF convergence problem In-Reply-To: <731585.75368.qm@web35414.mail.mud.yahoo.com> Message-ID: <589705.45619.qm@web60313.mail.yahoo.com> Dear Vidur, Just some comments that might be useful. 1. Increase ecutrho up to 40Ry, 20Ry for norm-conserving type pseudopotential looks small, and unreasonable. 2. degauss is unreasonably large, reduce down to 0.025. Presumably, before you used VASP, if specify 0.5. 3.Try Gamma-point only algorithm. 4. It might be that atomic positions are given in Angstrom, but not in alat units. Bests, Eyvaz. --- Vidur Parkash wrote: > > Hi > > I'm trying to perform a SCf calculation on a carbon > nanotube cluster > (metallic system), and no matter what i do the > results do not > converge. > I've tried changing the mixing factor, add a > smearing, tried a > different type of charge mixing, change number of k > points etc. > > The input file I've attached is the closest it ever > reached towards > convergence with accuracy better than 0.1 Ry...but > ultimately failing > to converge. > > > Can you please suggest some solutions. The input > file is attached > this time. > > Thanks > > Vidur Parkash > > Michigan Tech University > 716 EERC, 1400 Townsend Drive > Houghton MI-49931, USA > Tel: 1-906-487-0023 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, and Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com ____________________________________________________________________________________ Catch up on fall's hot new shows on Yahoo! TV. Watch previews, get listings, and more! http://tv.yahoo.com/collections/3658 From chaohao.mse at gmail.com Wed Oct 3 17:13:39 2007 From: chaohao.mse at gmail.com (Chaohao Hu) Date: Wed, 3 Oct 2007 17:13:39 +0200 Subject: [Pw_forum] A strange problem during testing the examples Message-ID: <6502ee650710030813i28c38a70q248756b3a32ff6ed@mail.gmail.com> Dear Pwscf users, During testing the examples of espresso32, I encounter a strange problem. For example01, when I run the test on example01 using the excutable files compiled by ifort + icc (or gcc), the calculations seem to be stopped once the information as "running the symmetry analysis for Si bands..." appears. For example02, the Gamma-point phonon calculations is also stopped. But using the binary files produced by G95 compiler, all examples run very well. Maybe some compiling optitions should be modified. For ifort + icc, I just configure the enviroment like " ./configure F90=ifort F77=ifort FFLAGS="-O2 -assume byterecl" CC=icc CFLAGS=-O3 LDFLAGS=-static". Any hint is appreciated! The version of fortran compiler I used is intel90 or intel91. Best regards, C.H. Hu -- ============================ C.H. Hu Postdoctoral fellow Chimie et Physico-Chimie appliquees Institut Francais du Petrole (IFP) Rueil-Malmaison, France E_mail: chaohao.mse at gmail.com ============================ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071003/70e53e03/attachment.htm From giannozz at nest.sns.it Wed Oct 3 17:39:53 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 3 Oct 2007 17:39:53 +0200 Subject: [Pw_forum] General pseudopotential generation questions (using ld1) In-Reply-To: <002501c8053b$3242ff40$6300a8c0@Crom> References: <002501c8053b$3242ff40$6300a8c0@Crom> Message-ID: On Oct 2, 2007, at 23:28 , Tyler Grassman wrote: > Finally... rcore values for non-linear core correction... I find > that the > core charge calculation depends upon what I set rcore to (as well it > should). If rcore is set in the input file, the local potential > and core > charge radii are equal. are you sure? the following is the correct and expected behavior: rcloc = matching radius (a.u.) for local pseudo-potential (no default) Must be specified only if lloc=-1, otherwise the corresponding value of rcut is used. rcore= matching radius (a.u.) for the smoothing of the core charge If not specified, the matching radius is determined by the condition rho_core(rcore) = 2*rho_valence(rcore) P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at nest.sns.it Wed Oct 3 17:43:45 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 3 Oct 2007 17:43:45 +0200 Subject: [Pw_forum] General pseudopotential generation questions (using ld1) In-Reply-To: <002501c8053b$3242ff40$6300a8c0@Crom> References: <002501c8053b$3242ff40$6300a8c0@Crom> Message-ID: On Oct 2, 2007, at 23:28 , Tyler Grassman wrote: > With Ge, however, the results *is* weird. The potentials produced > with > lloc=-1 (4s2 4p2, no semicore d) give a lattice parameter that is > actually > smaller than experimental (10.60 vs 10.69 Bohr, which definitely seems > funny for a GGA calc), while potentials using 4s2 4p2 4d-1 (lloc=2) > and > 4s2 4p2 4d-1 4f-1 (lloc=3), give values larger than experimental, > as would > be expected. The lloc=3 case, which is the same used in the VASP > US-PPs, gives the best results (10.91 Bohr). in diamond and zincblende semiconductors, the lattice parameter depends a lot on the quality of the d-channel pseudopotential 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 vparkash at mtu.edu Wed Oct 3 17:44:00 2007 From: vparkash at mtu.edu (Vidur Parkash) Date: Wed, 3 Oct 2007 08:44:00 -0700 (PDT) Subject: [Pw_forum] Another SCF convergence problem In-Reply-To: <47034DA1.3050307@sissa.it> Message-ID: <835417.98286.qm@web35414.mail.mud.yahoo.com> Thank you everybody for finding a very critical bug in my setup, yes The distances are actually double of what they're supposed to be Will try to fix that!...another thing ....how does changing the number of gamma points help the system to converge?...and is there any thumb rule for choosing the number of gamma points? Vidur Stefano de Gironcoli wrote: This may not be totally relevant but ... have you checked that the configuration you are using makes sense ? By visualizing it with xcrysden it appear that the carbon-carbon distances are all larger than 3 angstrom ... so your system is a collection of weakly interacting atoms, probably with very narrow bands. Technically this may be the origin of the instability, but ...is this the system you want to study ? Hpe it helps stefano Stefano de Gironcoli - SISSA and DEMOCRITOS Vidur Parkash wrote: > Hi > > I'm trying to perform a SCf calculation on a carbon nanotube cluster > (metallic system), and no matter what i do the results do not > converge. > I've tried changing the mixing factor, add a smearing, tried a > different type of charge mixing, change number of k points etc. > > The input file I've attached is the closest it ever reached towards > convergence with accuracy better than 0.1 Ry...but ultimately failing > to converge. > > > Can you please suggest some solutions. The input file is attached > this time. > > Thanks > > Vidur Parkash > > Michigan Tech University > 716 EERC, 1400 Townsend Drive > Houghton MI-49931, USA > Tel: 1-906-487-0023 > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > Vidur Parkash Michigan Technological University 716 EERC, 1400 Townsend Drive Houghton, MI-49931, USA Tel: 1-906-487-0023 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071003/f598337f/attachment.htm From tgrassma at ucsd.edu Wed Oct 3 18:07:40 2007 From: tgrassma at ucsd.edu (Tyler Grassman) Date: Wed, 3 Oct 2007 09:07:40 -0700 Subject: [Pw_forum] General pseudopotential generation questions (using ld1) In-Reply-To: Message-ID: <001701c805d7$869ca720$6300a8c0@Crom> Paolo, Thank you for your answers to some of my questions. With regard to the issue concerning the non-linear core correction and rcore values... My apologies, I think I see where I went wrong. I was slightly confusing the meanings of rcore and rcloc (due to slightly different definitions in different PP generation codes I was looking at). Thanks again. Regards, Tyler Grassman Dept. of Chemistry, Materials Science and Engineering University of California, San Diego > -----Original Message----- > From: pw_forum-bounces at pwscf.org > [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi > Sent: Wednesday, October 03, 2007 8:40 AM > To: PWSCF Forum > Subject: Re: [Pw_forum] General pseudopotential generation > questions (usingld1) > > > > On Oct 2, 2007, at 23:28 , Tyler Grassman wrote: > > > Finally... rcore values for non-linear core correction... I find > > that the > > core charge calculation depends upon what I set rcore to (as well it > > should). If rcore is set in the input file, the local potential > > and core > > charge radii are equal. > > are you sure? the following is the correct and expected behavior: > > rcloc = matching radius (a.u.) for local pseudo-potential (no > default) > Must be specified only if lloc=-1, otherwise the > corresponding value of rcut is used. > rcore= matching radius (a.u.) for the smoothing of the core > charge > If not specified, the matching radius is determined > by the condition rho_core(rcore) = 2*rho_valence(rcore) > > P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at nest.sns.it Wed Oct 3 18:48:35 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 3 Oct 2007 18:48:35 +0200 Subject: [Pw_forum] A strange problem during testing the examples In-Reply-To: <6502ee650710030813i28c38a70q248756b3a32ff6ed@mail.gmail.com> References: <6502ee650710030813i28c38a70q248756b3a32ff6ed@mail.gmail.com> Message-ID: <281C9D20-65FB-4802-856B-3E2AE3380D4A@nest.sns.it> On Oct 3, 2007, at 17:13 , Chaohao Hu wrote: > Any hint is appreciated! there is plenty of hints in the user guide, in particular here: http://www.quantum-espresso.org/wiki/index.php/ Installation#Installation_issues and here (1.9-1.11): http://www.quantum-espresso.org/wiki/index.php/Troubleshooting_% 28PWscf%29 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 eyvaz_isaev at yahoo.com Wed Oct 3 19:09:42 2007 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 3 Oct 2007 10:09:42 -0700 (PDT) Subject: [Pw_forum] Another SCF convergence problem In-Reply-To: <835417.98286.qm@web35414.mail.mud.yahoo.com> Message-ID: <662635.10240.qm@web60323.mail.yahoo.com> --- Vidur Parkash wrote: > Thank you everybody for finding a very critical bug > in my setup, yes The distances are actually double > of what they're supposed to be > > Will try to fix that!...another thing ....how does > changing the number of gamma points help the system > to converge?...and is there any thumb rule for > choosing the number of gamma points? Can you please explain what do you mean "gamma points"? If you mean K_POINTS, then their number will not help if atomic positions are wrong (usually poor convergency). Bests, Eyvaz. > > Vidur > > > > > Stefano de Gironcoli wrote: This > may not be totally relevant but ... have you checked > that the > configuration you are using makes sense ? > By visualizing it with xcrysden it appear that the > carbon-carbon > distances are all larger than 3 angstrom ... so > your system is a > collection of weakly interacting atoms, probably > with very narrow bands. > Technically this may be the origin of the > instability, but ...is this > the system you want to study ? > Hpe it helps > stefano > Stefano de Gironcoli - SISSA and DEMOCRITOS > > > > Vidur Parkash wrote: > > Hi > > > > I'm trying to perform a SCf calculation on a > carbon nanotube cluster > > (metallic system), and no matter what i do the > results do not > > converge. > > I've tried changing the mixing factor, add a > smearing, tried a > > different type of charge mixing, change number of > k points etc. > > > > The input file I've attached is the closest it > ever reached towards > > convergence with accuracy better than 0.1 Ry...but > ultimately failing > > to converge. > > > > > > Can you please suggest some solutions. The input > file is attached > > this time. > > > > Thanks > > > > Vidur Parkash > > > > Michigan Tech University > > 716 EERC, 1400 Townsend Drive > > Houghton MI-49931, USA > > Tel: 1-906-487-0023 > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > Vidur Parkash > > Michigan Technological University > 716 EERC, 1400 Townsend Drive > Houghton, MI-49931, USA > Tel: 1-906-487-0023 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, and Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com ____________________________________________________________________________________ Need a vacation? Get great deals to amazing places on Yahoo! Travel. http://travel.yahoo.com/ From vparkash at mtu.edu Wed Oct 3 19:51:36 2007 From: vparkash at mtu.edu (Vidur Parkash) Date: Wed, 3 Oct 2007 10:51:36 -0700 (PDT) Subject: [Pw_forum] Another SCF convergence problem In-Reply-To: <662635.10240.qm@web60323.mail.yahoo.com> Message-ID: <530637.29903.qm@web35404.mail.mud.yahoo.com> Dear Eyvaz Sorry bout that....yes I meant K_POINTS, is there any thumb rule for deciding how many K-points are good for convergence. Is it dependent on the nature of the system, or on the number of atoms or something else Pardon me for my newbie like questions... Vidur Eyvaz Isaev wrote: --- Vidur Parkash wrote: > Thank you everybody for finding a very critical bug > in my setup, yes The distances are actually double > of what they're supposed to be > > Will try to fix that!...another thing ....how does > changing the number of gamma points help the system > to converge?...and is there any thumb rule for > choosing the number of gamma points? Can you please explain what do you mean "gamma points"? If you mean K_POINTS, then their number will not help if atomic positions are wrong (usually poor convergency). Bests, Eyvaz. > > Vidur > > > > > Stefano de Gironcoli wrote: This > may not be totally relevant but ... have you checked > that the > configuration you are using makes sense ? > By visualizing it with xcrysden it appear that the > carbon-carbon > distances are all larger than 3 angstrom ... so > your system is a > collection of weakly interacting atoms, probably > with very narrow bands. > Technically this may be the origin of the > instability, but ...is this > the system you want to study ? > Hpe it helps > stefano > Stefano de Gironcoli - SISSA and DEMOCRITOS > > > > Vidur Parkash wrote: > > Hi > > > > I'm trying to perform a SCf calculation on a > carbon nanotube cluster > > (metallic system), and no matter what i do the > results do not > > converge. > > I've tried changing the mixing factor, add a > smearing, tried a > > different type of charge mixing, change number of > k points etc. > > > > The input file I've attached is the closest it > ever reached towards > > convergence with accuracy better than 0.1 Ry...but > ultimately failing > > to converge. > > > > > > Can you please suggest some solutions. The input > file is attached > > this time. > > > > Thanks > > > > Vidur Parkash > > > > Michigan Tech University > > 716 EERC, 1400 Townsend Drive > > Houghton MI-49931, USA > > Tel: 1-906-487-0023 > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > Vidur Parkash > > Michigan Technological University > 716 EERC, 1400 Townsend Drive > Houghton, MI-49931, USA > Tel: 1-906-487-0023 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, and Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com ____________________________________________________________________________________ Need a vacation? Get great deals to amazing places on Yahoo! Travel. http://travel.yahoo.com/ Vidur Parkash Michigan Technological University 716 EERC, 1400 Townsend Drive Houghton, MI-49931, USA Tel: 1-906-487-0023 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071003/b8dc4a0e/attachment.htm From akohlmey at cmm.chem.upenn.edu Wed Oct 3 20:07:17 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 3 Oct 2007 14:07:17 -0400 (EDT) Subject: [Pw_forum] Another SCF convergence problem In-Reply-To: <530637.29903.qm@web35404.mail.mud.yahoo.com> Message-ID: On Wed, 3 Oct 2007, Vidur Parkash wrote: dear vidur, VP> Sorry bout that....yes I meant K_POINTS, is there any thumb rule for VP> deciding how many K-points are good for convergence. Is it dependent VP> on the nature of the system, or on the number of atoms or something VP> else how about picking up a text book about condensed matter electron structure calculations and answering that question yourself? look for BZ-sampling... you might find the answers to some other (future) problems, too. :) VP> Pardon me for my newbie like questions... nothing bad about that in general, but if you use a computational tool, it is usually helpful to know - at least to some degree - what you are doing. this way you can mostly avoid asking newbie like questions altogether. we all understand that when starting fresh with a new software, it takes a while to get used to the technical problems of running the software and figuring out all the little technical details. the whole process is much less painful, if you have some pre-existing knowledge about the underlying theoretical framework. best regards, axel. VP> VP> Vidur VP> VP> VP> Vidur Parkash VP> VP> Michigan Technological University VP> 716 EERC, 1400 Townsend Drive VP> Houghton, MI-49931, USA VP> Tel: 1-906-487-0023 VP> -- ======================================================================= 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 tgrassma at ucsd.edu Wed Oct 3 21:00:17 2007 From: tgrassma at ucsd.edu (Tyler Grassman) Date: Wed, 3 Oct 2007 12:00:17 -0700 Subject: [Pw_forum] Questions regarding EXX implementation Message-ID: <002401c805ef$a58fda90$6300a8c0@Crom> Hello all. I have some questions regarding the hybrid functionals implementation in PWscf. First of all, how "experimental" is it, exactly? The "DO NOT USE IT FOR ANY PRODUCTION RUN" warning is definitely strong, but I've been doing some of my own testing with it (PBE0 for Ge, bulk and slab, so far), and the results look pretty good, definitely in-line with other EXX-based results in the literature; the calculated lattice paramter is quite good, and there is a band gap (slightly overestimated, but according to the literature, this is normal for Ge). Is there anything in particular about the implementation that is suspect and should be specifically watched out for? Also, does the implementation still only support NC-PPs? The last mention of this I was able to find in the forums is from 2005, and the README file in the EXX_example also says this, so I wondering if this was still the case, or if perhaps this had changed in a more recent (perhaps CVS) version. The calculations are indeed extremely slow compared to "normal" SCF runs; fortunatunately, the R-and-G parallelization seems to be quite efficient, even for the EXX stuff, so the scaling is good (at least up to 32 CPUs), which helps. But, with US-PPs, the lower cutoff energy would certainly help a good deal, as well. If anyone has some experience with the hybrid functional implementation here in PWscf and has found any sort of parameters that really help improve the efficiency of these jobs, I'd love to hear about it. Thank you very much. Regards, Tyler Grassman Dept. of Chemistry/Biochemistry, Dept. of Materials Science & Engineering University of California, San Diego From baroni at sissa.it Wed Oct 3 21:35:17 2007 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 3 Oct 2007 21:35:17 +0200 Subject: [Pw_forum] Another SCF convergence problem In-Reply-To: References: Message-ID: On Oct 3, 2007, at 8:07 PM, Axel Kohlmeyer wrote: > On Wed, 3 Oct 2007, Vidur Parkash wrote: > > dear vidur, > > VP> Sorry bout that....yes I meant K_POINTS, is there any thumb > rule for > VP> deciding how many K-points are good for convergence. Is it > dependent > VP> on the nature of the system, or on the number of atoms or > something > VP> else > > how about picking up a text book about condensed matter electron > structure calculations and answering that question yourself? > look for BZ-sampling... > > you might find the answers to some other (future) problems, too. :) Vidur: as an "old-style" professor, I tend to sympathize with Axel's viewpoint (who, by the way, is much younger than me!). If you choose to trust Axel's advice, a very good starting point is Richard Martin's textbook on electronic structure. Richard has been kind enough (and smart enough with the publishing company) to make a few selected chapters of his textbook available on the net. Vidur: you are very lucky! What you need can be downloaded for free from here: http://electronicstructure.org/Selected_Chapters/Martin-ch04.pdf Of course, the free download wil not save you from a few afternoons of hard study. If you like it, please do not refrain from downloading (and studying!) the other chapters too. Good luck! Stefano --- 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/20071003/33ae2b0a/attachment-0001.htm From giannozz at nest.sns.it Wed Oct 3 22:59:51 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 3 Oct 2007 22:59:51 +0200 Subject: [Pw_forum] Questions regarding EXX implementation In-Reply-To: <002401c805ef$a58fda90$6300a8c0@Crom> References: <002401c805ef$a58fda90$6300a8c0@Crom> Message-ID: On Oct 3, 2007, at 21:00 , Tyler Grassman wrote: > Hello all. I have some questions regarding the hybrid functionals > implementation in PWscf. First of all, how "experimental" is it, > exactly? > The "DO NOT USE IT FOR ANY PRODUCTION RUN" warning is > definitely strong, but I've been doing some of my own testing with it > (PBE0 for Ge, bulk and slab, so far), and the results look pretty good "experimental" = "able to reproduce experimental results" :-) P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From tgrassma at ucsd.edu Wed Oct 3 23:18:15 2007 From: tgrassma at ucsd.edu (Tyler Grassman) Date: Wed, 3 Oct 2007 14:18:15 -0700 Subject: [Pw_forum] Questions regarding EXX implementation -- follow-up In-Reply-To: Message-ID: <002d01c80602$e96cc4e0$6300a8c0@Crom> Hello again. I actually just checked out the current CVS version. Unfortunately, it won't compile all the way due to a problem with the "lexx" variable in the paw_xc.f90 file... However, it looks like the EXX stuff if being implemented into the PAW stuff, which is very exciting. Is maybe US-PP/EXX integration being skipped in order to concentrate on integrating it with PAW? And what's the status of both the PAW and PAW/EXX stutf? I see there is now a PAW example, so I'm guessing that's getting closer to be "producting worthy." Anyway, any information on this stuff will be appreciated (sorry, I don't mean to nag, I'm just very interested in the potential applications all of this stuff opens up). Thanks again for the great software and all the hard work! Regards, Tyler Grassman Dept. of Chemistry/Biochemistry, Dept. of Materials Science and Engineering University of California, San Diego > -----Original Message----- > From: pw_forum-bounces at pwscf.org > [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi > Sent: Wednesday, October 03, 2007 2:00 PM > To: PWSCF Forum > Subject: Re: [Pw_forum] Questions regarding EXX implementation > > > > On Oct 3, 2007, at 21:00 , Tyler Grassman wrote: > > > Hello all. I have some questions regarding the hybrid functionals > > implementation in PWscf. First of all, how "experimental" is it, > > exactly? > > The "DO NOT USE IT FOR ANY PRODUCTION RUN" warning is > > definitely strong, but I've been doing some of my own > testing with it > > (PBE0 for Ge, bulk and slab, so far), and the results look > pretty good > > "experimental" = "able to reproduce experimental results" :-) > > P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum > From yueqin at mail.ustc.edu.cn Thu Oct 4 09:53:25 2007 From: yueqin at mail.ustc.edu.cn (yueqin at mail.ustc.edu.cn) Date: Thu, 04 Oct 2007 15:53:25 +0800 Subject: [Pw_forum] (no subject) Message-ID: <391484405.04869@ustc.edu.cn> Hi,All. I want to calculate the DOS of one metal system. In nscf step,the number of 'nbnd' can give very different plot of dos. How can I define nbnd? Is it can define it equal to nbnds (in scf)? I need you help ,thanks! ????????????????Y.Q. Wang ????????????????yueqin at mail.ustc.edu.cn ????????????????????2007-10-04 From paulatto at sissa.it Thu Oct 4 10:02:04 2007 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 4 Oct 2007 10:02:04 +0200 (CEST) Subject: [Pw_forum] Questions regarding EXX implementation -- follow-up In-Reply-To: <002d01c80602$e96cc4e0$6300a8c0@Crom> References: <002d01c80602$e96cc4e0$6300a8c0@Crom> Message-ID: <18652.147.122.5.202.1191484924.squirrel@webmail.sissa.it> On Wed, October 3, 2007 23:18, Tyler Grassman wrote: > Unfortunately, it won't compile all the way due to a problem with the > "lexx" > variable in the paw_xc.f90 file... This is my fault, thank you for reporting. I will fixed in the next week: the file paw_xc.f90 is a temporary hack that will be removed very soon. In the meanwhile, as you are not going to use the paw part anyway, you can replace all the functions in the file with a single "return". Goodbye -- Lorenzo Paulatto +39 040 3787 312 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 Oct 4 10:33:34 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 4 Oct 2007 10:33:34 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: <391484405.04869@ustc.edu.cn> References: <391484405.04869@ustc.edu.cn> Message-ID: On Oct 4, 2007, at 9:53 , wrote: > I want to calculate the DOS of one metal system. In nscf step, > the number of 'nbnd' can give very different plot of dos. > How can I define nbnd? define it as the number of electron states you need to calculate a DOS in the energy range you want > Is it can define it equal to nbnds (in scf)? no, it is typically larger. In scf calculations you need only occupied states 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 Giovanni.Cantele at na.infn.it Thu Oct 4 10:35:12 2007 From: Giovanni.Cantele at na.infn.it (Giovanni Cantele) Date: Thu, 04 Oct 2007 10:35:12 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: <391484405.04869@ustc.edu.cn> References: <391484405.04869@ustc.edu.cn> Message-ID: <4704A5C0.2040607@na.infn.it> yueqin at mail.ustc.edu.cn wrote: > Hi,All. > I want to calculate the DOS of one metal system. In nscf step,the number of > 'nbnd' can give very different plot of dos. How can I define nbnd? Is it can > define it equal to nbnds (in scf)? I need you help ,thanks! > > > ????????????????Y.Q. Wang > ????????????????yueqin at mail.ustc.edu.cn > ????????????????????2007-10-04 > from espresso-3.2/examples/README example08: This example shows how to use pw.x to calculate the DOS of Ni and how to plot the Fermi Surface using XCrysDen If you have a look to the example08 directory, an example of a DOS calculation is given, than can help you to understand how to do it. The variable nbnd is, as far as I know, the same variable for both scf and nscf calculation, with the only difference that in the nscf calculation you may want to increase nbnd to see what happens with 'unoccupied' bands. Of course, the larger nbnd, the wider the energy range your calculation will span. Thus, unless something strange is happening with you input file, the reason why the DOS changes with nbnd is just that you are sampling higher energy bands as you increase nbnd. Of course, this should not affect the 'lower energy' part of the DOS. Giovanni -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: Giovanni.Cantele at na.infn.it Web: http://people.na.infn.it/~cantele From halim_said04 at yahoo.fr Thu Oct 4 11:22:03 2007 From: halim_said04 at yahoo.fr (halim said) Date: Thu, 4 Oct 2007 11:22:03 +0200 (CEST) Subject: [Pw_forum] problem compiling espresso with cmkl libraries In-Reply-To: <391484405.04869@ustc.edu.cn> Message-ID: <232662.82929.qm@web23301.mail.ird.yahoo.com> Dear All, I am trying to compile espresso3.2 in serial version, with ifort compiler and cmkl library in cluster machine. When compiling pw alone as test I got the errors messages, could you please help me in order to solve my problem. First: ./configure F90=ifort Second make pw these the errors messages that I got, I do not know if the origin is from linking with cmkl library or related to some think else. ----------------------------------------- ../Modules/ptoolkit.o ../Modules/random_numbers.o ../Modules/read_cards.o ../Modules/read_namelists.o ../Modules/read_upf.o ../Modules/read_uspp.o ../Modules/recvec.o ../Modules/shmem_include.o ../Modules/splinelib.o ../Modules/stick_base.o ../Modules/task_groups.o ../Modules/timestep.o ../Modules/uspp.o ../Modules/version.o ../Modules/wavefunctions.o ../Modules/wave_base.o ../Modules/xml_io_base.o libpw.a ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a -lmkl_lapack -L/opt/intel/cmkl/8.0/lib/em64t -lmkl_em64t -lguide -lpthread IPO Error: unresolved : __svml_cos2 Referenced in clib.a(fft_stick.o) IPO Error: unresolved : __svml_sin2 Referenced in clib.a(fft_stick.o) .../clib/clib.a(fft_stick.o)(.text+0x37044): In function `complete_twiddle': : undefined reference to `__svml_cos2' .../clib/clib.a(fft_stick.o)(.text+0x37062): In function `complete_twiddle': : undefined reference to `__svml_sin2' .../clib/clib.a(fft_stick.o)(.text+0x3713c): In function `complete_twiddle': : undefined reference to `__svml_cos2' .../clib/clib.a(fft_stick.o)(.text+0x37152): In function `complete_twiddle': : undefined reference to `__svml_sin2' .../clib/clib.a(fft_stick.o)(.text+0x37394): In function `complete_twiddle': : undefined reference to `__svml_cos2' .../clib/clib.a(fft_stick.o)(.text+0x373b2): In function `complete_twiddle': : undefined reference to `__svml_sin2' .../clib/clib.a(fft_stick.o)(.text+0x3740a): In function `complete_twiddle': : undefined reference to `__svml_cos2' .../clib/clib.a(fft_stick.o)(.text+0x37420): In function `complete_twiddle': : undefined reference to `__svml_sin2' .../clib/clib.a(fft_stick.o)(.text+0x380f4): In function `fftw_create_twiddle': : undefined reference to `__svml_cos2' .../clib/clib.a(fft_stick.o)(.text+0x38112): In function `fftw_create_twiddle': : undefined reference to `__svml_sin2' .../clib/clib.a(fft_stick.o)(.text+0x381dc): In function `fftw_create_twiddle': : undefined reference to `__svml_cos2' .../clib/clib.a(fft_stick.o)(.text+0x381f3): In function `fftw_create_twiddle': : undefined reference to `__svml_sin2' .../clib/clib.a(fft_stick.o)(.text+0x390f4): In function `planner_normal': : undefined reference to `__svml_cos2' .../clib/clib.a(fft_stick.o)(.text+0x39111): In function `planner_normal': : undefined reference to `__svml_sin2' .../clib/clib.a(fft_stick.o)(.text+0x3919b): In function `planner_normal': : undefined reference to `__svml_cos2' .../clib/clib.a(fft_stick.o)(.text+0x391b1): In function `planner_normal': : undefined reference to `__svml_sin2' .../clib/clib.a(fft_stick.o)(.text+0x3af43): In function `planner': : undefined reference to `__svml_cos2' .../clib/clib.a(fft_stick.o)(.text+0x3af60): In function `planner': : undefined reference to `__svml_sin2' .../clib/clib.a(fft_stick.o)(.text+0x3afea): In function `planner': : undefined reference to `__svml_cos2' .../clib/clib.a(fft_stick.o)(.text+0x3b000): In function `planner': : undefined reference to `__svml_sin2' .../clib/clib.a(fft_stick.o)(.text+0x3b809): In function `make_node_twiddle': : undefined reference to `__svml_cos2' .../clib/clib.a(fft_stick.o)(.text+0x3b827): In function `make_node_twiddle': : undefined reference to `__svml_sin2' .../clib/clib.a(fft_stick.o)(.text+0x3b901): In function `make_node_twiddle': : undefined reference to `__svml_cos2' .../clib/clib.a(fft_stick.o)(.text+0x3b917): In function `make_node_twiddle': : undefined reference to `__svml_sin2' make[1]: *** [pw.x] Error 1 ------------------------------------------------------------------- Your advices and help are appreciated. Yours sincerely, Halim Said, dept of Phys, Univ Soussa, Tunisi --------------------------------- Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071004/0931146d/attachment.htm From akohlmey at cmm.chem.upenn.edu Thu Oct 4 11:52:41 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 4 Oct 2007 05:52:41 -0400 (EDT) Subject: [Pw_forum] problem compiling espresso with cmkl libraries In-Reply-To: <232662.82929.qm@web23301.mail.ird.yahoo.com> Message-ID: On Thu, 4 Oct 2007, halim said wrote: HS> HS> Dear All, dear halim, HS> I am trying to compile espresso3.2 in serial version, with ifort HS> compiler and cmkl library in cluster machine. HS> When compiling pw alone as test I got the errors messages, could HS> you please help me in order to solve my problem. first off, thanks for providing a complete problem report with all relevant information. HS> First: HS> HS> ./configure F90=ifort HS> HS> Second HS> HS> make pw HS> HS> these the errors messages that I got, I do not know if the origin is from linking with cmkl library or related to some think else. HS> HS> ----------------------------------------- HS> ../Modules/ptoolkit.o ../Modules/random_numbers.o ../Modules/read_cards.o HS> ../Modules/read_namelists.o ../Modules/read_upf.o ../Modules/read_uspp.o HS> ../Modules/recvec.o ../Modules/shmem_include.o ../Modules/splinelib.o HS> ../Modules/stick_base.o ../Modules/task_groups.o ../Modules/timestep.o HS> ../Modules/uspp.o ../Modules/version.o ../Modules/wavefunctions.o HS> ../Modules/wave_base.o ../Modules/xml_io_base.o libpw.a ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a -lmkl_lapack -L/opt/intel/cmkl/8.0/lib/em64t -lmkl_em64t -lguide -lpthread HS> HS> IPO Error: unresolved : __svml_cos2 HS> Referenced in clib.a(fft_stick.o) HS> IPO Error: unresolved : __svml_sin2 HS> Referenced in clib.a(fft_stick.o) HS> .../clib/clib.a(fft_stick.o)(.text+0x37044): In function `complete_twiddle': HS> : undefined reference to `__svml_cos2' HS> .../clib/clib.a(fft_stick.o)(.text+0x37062): In function `complete_twiddle': HS> : undefined reference to `__svml_sin2' this means, that your compiler optimized to use the SSE version of sine, cosine etc. those are in the SVML library. just edit your make.sys file to append '-lsvml' after '-lguide' cheers, axel. HS> ------------------------------------------------------------------- HS> HS> Your advices and help are appreciated. HS> HS> Yours sincerely, HS> HS> Halim Said, HS> dept of Phys, Univ Soussa, HS> Tunisi HS> HS> HS> --------------------------------- HS> Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail -- ======================================================================= 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 Steven.Kirk at hv.se Thu Oct 4 15:41:10 2007 From: Steven.Kirk at hv.se (Steven Kirk) Date: Thu, 04 Oct 2007 15:41:10 +0200 Subject: [Pw_forum] Seeking positive Laplacians in carbon nanotubes Message-ID: <4704ED76.2060507@hv.se> Hello, I am using Quantum Espresso to try to see if I can find metallic (e.g. (3,3)) carbon nanotubes with positive values of the Laplacian of the charge density at the bond critical points (using RFW Bader's AIM approach). I am extracting Laplacians from gridded charge density data exported to the Integrity package. So far I am finding that the corresponding Laplacians are negative, which is not in line with what they are supposed to be for a metal, and simply increasing the number of grid points in the unit cell and increasing the ecutrho parameter do not seem to help the situation. I have looked at some of Nicola Marzari's publications for guidance on possible input parameters, and searched the mailing list archives for advice. I would therefore be very grateful if you have any advice on how I might change my input parameters (for a single point calculation on a (3,3) SWNT): &CONTROL title='N3_M3 calculation', calculation='scf', restart_mode='from_scratch', prefix='N3_M3', pseudo_dir='.' / &SYSTEM ibrav = 4, celldm(1)= 14.0125, celldm(3)= 0.33169, nat = 12, ntyp = 1, ecutwfc = 30, ecutrho = 240, occupations = 'smearing', degauss = 0.03, smearing = 'mv', nbnd = 36 / &ELECTRONS / ATOMIC_SPECIES C 12.0107 C.pbe-rrkjus.UPF ATOMIC_POSITIONS {crystal} C 0.68812 0.81475 0.16090 C 0.48031 0.76393 0.16090 C 0.37337 0.68812 0.66090 C 0.76393 0.78362 0.66090 C 0.18525 0.37337 0.16090 C 0.21638 0.48031 0.66090 C 0.62663 0.31188 0.16090 C 0.23607 0.21638 0.16090 C 0.31188 0.18525 0.66090 C 0.78362 0.51969 0.16090 C 0.81475 0.62663 0.66090 C 0.51969 0.23607 0.66090 K_POINTS automatic 1 1 8 0 0 0 Many thanks in advance, Steve Kirk -- Dr. Steven R. Kirk Dept. of Technology, Mathematics & Computer Science (P)+46 520 223215 University West (F)+46 520 223299 P.O. Box 957 Trollhattan 461 29 SWEDEN http://taconet.webhop.org From marzari at MIT.EDU Thu Oct 4 19:17:46 2007 From: marzari at MIT.EDU (Nicola Marzari) Date: Thu, 04 Oct 2007 13:17:46 -0400 Subject: [Pw_forum] Seeking positive Laplacians in carbon nanotubes In-Reply-To: <4704ED76.2060507@hv.se> References: <4704ED76.2060507@hv.se> Message-ID: <4705203A.3060305@mit.edu> Hi Steve, presuming the calculation converged successfully, and your geometry is correct, what does your charge density look like ? EMetallic nanotubes are very different from a traditional metal, and in particular there is not going to be, in my opinion, any qualitative difference in the charge density of a metallic nanotube from that of a semiconducting nanotube having the same diameter (a part from the obvious ocmment that the bonds will be oriented differently depending on chirality). Another way to say this is that the transverse polarizability is independent of chirality - along a transverse cut, there is no difference in the response between a metal CNT and an insulating one. Would be very interested to see if you find any difference. nicola Steven Kirk wrote: > Hello, > > I am using Quantum Espresso to try to see if I can find metallic (e.g. > (3,3)) carbon nanotubes with positive values of the Laplacian of the > charge density at the bond critical points (using RFW Bader's AIM > approach). I am extracting Laplacians from gridded charge density data > exported to the Integrity package. So far I am finding that the > corresponding Laplacians are negative, which is not in line with what > they are supposed to be for a metal, and simply increasing the number of > grid points in the unit cell and increasing the ecutrho parameter do not > seem to help the situation. I have looked at some of Nicola Marzari's > publications for guidance on possible input parameters, and searched the > mailing list archives for advice. I would therefore be very grateful if > you have any advice on how I might change my input parameters (for a > single point calculation on a (3,3) SWNT): --------------------------------------------------------------------- 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 wlyim at puccini.che.pitt.edu Thu Oct 4 22:44:35 2007 From: wlyim at puccini.che.pitt.edu (William Yim) Date: Thu, 4 Oct 2007 16:44:35 -0400 (EDT) Subject: [Pw_forum] Seeking positive Laplacians in carbon nanotubes In-Reply-To: <4704ED76.2060507@hv.se> Message-ID: Hello, This sounds an interesting issue. I couldn't see any obvious problem in your input. Instead, I want to know what's the reason for a metallic nanotuube to have a positive Laplacian at bond critical point. The C-C or C=C BCP usually have negative Laplacian. Besides, if your expected BCP falls within the cutoff radius, you will not be able to locate it using planewave DFT, as AIM is an all-electron analysis. Best regards, William On Thu, 4 Oct 2007, Steven Kirk wrote: > Hello, > > I am using Quantum Espresso to try to see if I can find metallic (e.g. > (3,3)) carbon nanotubes with positive values of the Laplacian of the > charge density at the bond critical points (using RFW Bader's AIM > approach). I am extracting Laplacians from gridded charge density data > exported to the Integrity package. So far I am finding that the > corresponding Laplacians are negative, which is not in line with what > they are supposed to be for a metal, and simply increasing the number of > grid points in the unit cell and increasing the ecutrho parameter do not > seem to help the situation. I have looked at some of Nicola Marzari's > publications for guidance on possible input parameters, and searched the > mailing list archives for advice. I would therefore be very grateful if > you have any advice on how I might change my input parameters (for a > single point calculation on a (3,3) SWNT): > > > &CONTROL > title='N3_M3 calculation', > calculation='scf', > restart_mode='from_scratch', > prefix='N3_M3', > pseudo_dir='.' > / > &SYSTEM > ibrav = 4, > celldm(1)= 14.0125, > celldm(3)= 0.33169, > nat = 12, > ntyp = 1, > ecutwfc = 30, > ecutrho = 240, > occupations = 'smearing', > degauss = 0.03, > smearing = 'mv', > nbnd = 36 > / > &ELECTRONS > / > ATOMIC_SPECIES > C 12.0107 C.pbe-rrkjus.UPF > ATOMIC_POSITIONS {crystal} > C 0.68812 0.81475 0.16090 > C 0.48031 0.76393 0.16090 > C 0.37337 0.68812 0.66090 > C 0.76393 0.78362 0.66090 > C 0.18525 0.37337 0.16090 > C 0.21638 0.48031 0.66090 > C 0.62663 0.31188 0.16090 > C 0.23607 0.21638 0.16090 > C 0.31188 0.18525 0.66090 > C 0.78362 0.51969 0.16090 > C 0.81475 0.62663 0.66090 > C 0.51969 0.23607 0.66090 > K_POINTS automatic > 1 1 8 0 0 0 > > Many thanks in advance, > Steve Kirk > -- Dr. Wai-Leung Yim Institut fuer Reine und Angewandte Chemie, Theoretische Chemie, Carl von Ossietzky Universtaet Oldenburg, 26129 Oldenburg, Germany Email: wlyim at puccini.che.pitt.edu Phone: +49-441-798-3950 (office) Fax: +49-441-798-3964 From mkychan at MIT.EDU Fri Oct 5 05:14:07 2007 From: mkychan at MIT.EDU (Maria K Chan) Date: Thu, 04 Oct 2007 23:14:07 -0400 Subject: [Pw_forum] Compilation error on IBM Power4 P690 under AIX 5.2 Message-ID: <4705ABFF.4050105@mit.edu> Hi everybody, I am trying to compile pwscf on the San Diego Supercomputing Center's DataStar, which consists of IBM P690's and P655's with AIX5.2, using Axel Kohlmeyer's Make.power5-aix-parallel/serial. A series of iotk_**.f90 compile successfully, and then the error message below is given: ar: 0707-101 k is not a valid flag. Google doesn't know about this error. Can someone give some pointers? Much obliged, Maria Chan --------- (successful iotk_** compilation output omitted) 1501-510 Compilation successful for file iotk_xtox.f90. ar libiotk.a iotk_attr+CHARACTER1_0.o iotk_attr+COMPLEX1_0.o iotk_attr+COMPLEX1_3.o iotk_attr+COMPLEX2_0.o iotk_attr+COMPLEX2_3.o iotk_attr+INTEGER1_0.o iotk_attr+INTEGER1_3.o iotk_attr+INTEGER2_0.o iotk_attr+INTEGER2_3.o iotk_attr+LOGICAL1_0.o iotk_attr+LOGICAL1_3.o iotk_attr+LOGICAL2_0.o iotk_attr+LOGICAL2_3.o iotk_attr+REAL1_0.o iotk_attr+REAL1_3.o iotk_attr+REAL2_0.o iotk_attr+REAL2_3.o iotk_attr.o iotk_attr_interf.o iotk_base.o iotk_dat+CHARACTER1_0.o iotk_dat+CHARACTER1_3.o iotk_dat+COMPLEX1_0.o iotk_dat+COMPLEX1_3.o iotk_dat+COMPLEX2_0.o iotk_dat+COMPLEX2_3.o iotk_dat+INTEGER1_0.o iotk_dat+INTEGER1_3.o iotk_dat+INTEGER2_0.o iotk_dat+INTEGER2_3.o iotk_dat+LOGICAL1_0.o iotk_dat+LOGICAL1_3.o iotk_dat+LOGICAL2_0.o iotk_dat+LOGICAL2_3.o iotk_dat+REAL1_0.o iotk_dat+REAL1_3.o iotk_dat+REAL2_0.o iotk_dat+REAL2_3.o iotk_dat.o iotk_dat_interf.o iotk_error.o iotk_error_interf.o iotk_files.o iotk_files_interf.o iotk_fmt.o iotk_fmt_interf.o iotk_misc.o iotk_misc_interf.o iotk_module.o iotk_scan.o iotk_scan_interf.o iotk_str.o iotk_str_interf.o iotk_unit.o iotk_unit_interf.o iotk_write.o iotk_write_interf.o iotk_xtox.o iotk_xtox_interf.o ar: 0707-101 k is not a valid flag. make: 1254-004 The error code from the last command is 1. Stop. make: 1254-004 The error code from the last command is 2. Stop. make: 1254-004 The error code from the last command is 2. From akohlmey at cmm.chem.upenn.edu Fri Oct 5 05:49:21 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 4 Oct 2007 23:49:21 -0400 (EDT) Subject: [Pw_forum] Compilation error on IBM Power4 P690 under AIX 5.2 In-Reply-To: <4705ABFF.4050105@mit.edu> Message-ID: On Thu, 4 Oct 2007, Maria K Chan wrote: MC> Hi everybody, hi maria, MC> I am trying to compile pwscf on the San Diego Supercomputing Center's please always state which version of the code you are using, when reporting a problem. thanks. MC> DataStar, which consists of IBM P690's and P655's with AIX5.2, using MC> Axel Kohlmeyer's Make.power5-aix-parallel/serial. A series of MC> iotk_**.f90 compile successfully, and then the error message below is given: MC> MC> ar: 0707-101 k is not a valid flag. MC> MC> Google doesn't know about this error. it should. :) this has been discussed here a while ago. please add a line: ARFLAGS_DYNAMIC=$(ARFLAGS) to your make.sys file and it should magically work (knocking on wood). greetings from sunny tsukuba, axel. MC> MC> Can someone give some pointers? MC> MC> Much obliged, MC> Maria Chan MC> MC> _______________________________________________ MC> Pw_forum mailing list MC> Pw_forum at pwscf.org MC> http://www.democritos.it/mailman/listinfo/pw_forum MC> -- ======================================================================= 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 mkychan at MIT.EDU Fri Oct 5 07:31:11 2007 From: mkychan at MIT.EDU (Maria K Chan) Date: Fri, 05 Oct 2007 01:31:11 -0400 Subject: [Pw_forum] Compilation error on IBM Power4 P690 under AIX 5.2 In-Reply-To: References: Message-ID: <4705CC1F.3010201@mit.edu> Hi Axel, Thank you very much for your prompt reply! > please always state which version of the code you are using > Apologies. It's 3.2. > MC> Google doesn't know about this error. > > it should. :) this has been discussed here a while ago. > Sorry I missed the discussion. > please add a line: > > ARFLAGS_DYNAMIC=$(ARFLAGS) > > to your make.sys file and it should magically work (knocking on wood). Yes! It's magic! Compiles now. Enjoy the sunshine. Many thanks, Maria Axel Kohlmeyer wrote: > On Thu, 4 Oct 2007, Maria K Chan wrote: > > MC> Hi everybody, > > hi maria, > > MC> I am trying to compile pwscf on the San Diego Supercomputing Center's > > please always state which version of the code you are using, > when reporting a problem. thanks. > > MC> DataStar, which consists of IBM P690's and P655's with AIX5.2, using > MC> Axel Kohlmeyer's Make.power5-aix-parallel/serial. A series of > MC> iotk_**.f90 compile successfully, and then the error message below is given: > MC> > MC> ar: 0707-101 k is not a valid flag. > MC> > MC> Google doesn't know about this error. > > it should. :) this has been discussed here a while ago. > > please add a line: > > ARFLAGS_DYNAMIC=$(ARFLAGS) > > to your make.sys file and it should magically > work (knocking on wood). > > greetings from sunny tsukuba, > axel. > > MC> > MC> Can someone give some pointers? > MC> > MC> Much obliged, > MC> Maria Chan > MC> > MC> _______________________________________________ > MC> Pw_forum mailing list > MC> Pw_forum at pwscf.org > MC> http://www.democritos.it/mailman/listinfo/pw_forum > MC> > > From yueqin at mail.ustc.edu.cn Fri Oct 5 10:00:15 2007 From: yueqin at mail.ustc.edu.cn (yueqin at mail.ustc.edu.cn) Date: Fri, 05 Oct 2007 16:00:15 +0800 Subject: [Pw_forum] How to get the phonon frequency logarithmic average Message-ID: <391571215.19042@ustc.edu.cn> On Aug 13, 2007, at 3:42 , clie wrote: > recently, i use pwscf to caliculate electron-phonon couple constance, > but i want to get Tc and i need the phonon frequency logarithmic > average. Could you tell me how to get the value? pwtools/lambda.f90 should calculate it. Unfortunately it has never been updated to read the new file formats produced by the electron-phonon calculation, so it will require some work. Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy -------------------------------------------------------------- Hi??Paolo?? it has never been updated to read the new file formats? is it mean we must modify inputfile(which lambda.f90 read from)? or modify anyother? I don't understand what you mean. please give more details.thank you. ?????????????? ????????????????Y.Q. Wang ????????????????yueqin at mail.ustc.edu.cn ????????????????????2007-10-05 From halim_said04 at yahoo.fr Fri Oct 5 10:19:50 2007 From: halim_said04 at yahoo.fr (halim said) Date: Fri, 5 Oct 2007 10:19:50 +0200 (CEST) Subject: [Pw_forum] RE : Re: problem compiling espresso with cmkl libraries In-Reply-To: Message-ID: <363164.50354.qm@web23304.mail.ird.yahoo.com> Dear Axel, Thanks lot for your quick response, I have edited the make.sys and added '-lsvml' after '-lguide' and make clean before recompiling again, the error message is the same as without adding '-lsvml' after '-lguide'. The compiler that I use is intel fortran 9.0, is there other alternative way to success compiling the code. Your help and advice are very appreciate. PS: I have also linked the code by blas and lapack of esspresso.3.2 code but the errors messages appear also for linking. Yours sincerely, Halim Axel Kohlmeyer a ?crit : On Thu, 4 Oct 2007, halim said wrote: HS> HS> Dear All, dear halim, HS> I am trying to compile espresso3.2 in serial version, with ifort HS> compiler and cmkl library in cluster machine. HS> When compiling pw alone as test I got the errors messages, could HS> you please help me in order to solve my problem. first off, thanks for providing a complete problem report with all relevant information. HS> First: HS> HS> ./configure F90=ifort HS> HS> Second HS> HS> make pw HS> HS> these the errors messages that I got, I do not know if the origin is from linking with cmkl library or related to some think else. HS> HS> ----------------------------------------- HS> ../Modules/ptoolkit.o ../Modules/random_numbers.o ../Modules/read_cards.o HS> ../Modules/read_namelists.o ../Modules/read_upf.o ../Modules/read_uspp.o HS> ../Modules/recvec.o ../Modules/shmem_include.o ../Modules/splinelib.o HS> ../Modules/stick_base.o ../Modules/task_groups.o ../Modules/timestep.o HS> ../Modules/uspp.o ../Modules/version.o ../Modules/wavefunctions.o HS> ../Modules/wave_base.o ../Modules/xml_io_base.o libpw.a ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a -lmkl_lapack -L/opt/intel/cmkl/8.0/lib/em64t -lmkl_em64t -lguide -lpthread HS> HS> IPO Error: unresolved : __svml_cos2 HS> Referenced in clib.a(fft_stick.o) HS> IPO Error: unresolved : __svml_sin2 HS> Referenced in clib.a(fft_stick.o) HS> .../clib/clib.a(fft_stick.o)(.text+0x37044): In function `complete_twiddle': HS> : undefined reference to `__svml_cos2' HS> .../clib/clib.a(fft_stick.o)(.text+0x37062): In function `complete_twiddle': HS> : undefined reference to `__svml_sin2' this means, that your compiler optimized to use the SSE version of sine, cosine etc. those are in the SVML library. just edit your make.sys file to append '-lsvml' after '-lguide' cheers, axel. HS> ------------------------------------------------------------------- HS> HS> Your advices and help are appreciated. HS> HS> Yours sincerely, HS> HS> Halim Said, HS> dept of Phys, Univ Soussa, HS> Tunisi HS> HS> HS> --------------------------------- HS> Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail -- ======================================================================= 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 --------------------------------- Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071005/af05a099/attachment.htm From giannozz at nest.sns.it Fri Oct 5 10:58:05 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 5 Oct 2007 10:58:05 +0200 Subject: [Pw_forum] How to get the phonon frequency logarithmic average In-Reply-To: <391571215.19042@ustc.edu.cn> References: <391571215.19042@ustc.edu.cn> Message-ID: <526D8FC8-9007-4E70-91F3-CD7E2E15BAFF@nest.sns.it> On Oct 5, 2007, at 10:00 , wrote: > it has never been updated to read the new file formats? is it mean we > must modify inputfile(which lambda.f90 read from)? or modify anyother? > I don't understand what you mean. please give more details.thank you. the electron-phonon calculation is provided "as is", like everything else, but right now it is in an unsatisfactory state. If you want to perform electron-phonon calculations, you can - use an earlier version (2.1.5 I think) for which the lambda.f90 code was written - use the current version and write your own code(s) to interpret the results, or update the existing one(s) - wait until somebody makes a better electron-phonon code 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 Fri Oct 5 11:08:25 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 5 Oct 2007 11:08:25 +0200 Subject: [Pw_forum] RE : Re: problem compiling espresso with cmkl libraries In-Reply-To: <363164.50354.qm@web23304.mail.ird.yahoo.com> References: <363164.50354.qm@web23304.mail.ird.yahoo.com> Message-ID: On Oct 5, 2007, at 10:19 , halim said wrote: > the error message is the same as without adding '-lsvml' after '- > lguide'. > The compiler that I use is intel fortran 9.0 never trust anything whose version ends with a zero... > , is there other alternative way to success compiling the code. there are at least 1001 alternative ways of compiling the code, but please note: --- Quantum-ESPRESSO compiles and works ***on all non-buggy, properly con?gured hardware and software combinations*** --- (from the user guide). If you compile something and a system library is missing, either you have to add it (in which case you have to discover which library and where it is located), or the system should load it but it doesn't, in which case your software configuration is buggy. 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 akohlmey at cmm.chem.upenn.edu Fri Oct 5 11:20:15 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 5 Oct 2007 05:20:15 -0400 (EDT) Subject: [Pw_forum] RE : Re: problem compiling espresso with cmkl libraries In-Reply-To: <363164.50354.qm@web23304.mail.ird.yahoo.com> Message-ID: On Fri, 5 Oct 2007, halim said wrote: HS> Dear Axel, HS> HS> Thanks lot for your quick response, I have edited the make.sys and added '-lsvml' after '-lguide' HS> HS> and make clean before recompiling again, the error message is the HS> same as without adding HS> '-lsvml' after '-lguide'. The compiler that I use is intel HS> fortran 9.0, is there other alternative way to success compiling the HS> code. i am not convinced. but here is one alternative. please change FFLAGS to: FFLAGS = -O2 -tpp6 -assume byterecl ...and as paolo indicated, please also make sure that you have the latest patchlevel of the intel compiler. ever since version 7.x all initial releases of the intel compilers had some serious deficiencies, that were only resolved after multiple patches. the finaly 9.0 patchlevel was quite ok, but both, 8.1 and 9.1 are more reliable. HS> Your help and advice are very appreciate. HS> HS> PS: I have also linked the code by blas and lapack of HS> esspresso.3.2 code but the errors messages appear also for linking. those errors have nothing to do with blas/lapack. cheers, axel. HS> HS> Yours sincerely, HS> HS> Halim HS> HS> Axel Kohlmeyer a ?crit : HS> On Thu, 4 Oct 2007, halim said wrote: HS> HS> HS> HS> HS> Dear All, HS> HS> dear halim, HS> HS> HS> I am trying to compile espresso3.2 in serial version, with ifort HS> HS> compiler and cmkl library in cluster machine. HS> HS> When compiling pw alone as test I got the errors messages, could HS> HS> you please help me in order to solve my problem. HS> HS> first off, thanks for providing a complete problem report HS> with all relevant information. HS> HS> HS> First: HS> HS> HS> HS> ./configure F90=ifort HS> HS> HS> HS> Second HS> HS> HS> HS> make pw HS> HS> HS> HS> these the errors messages that I got, I do not know if the origin is from linking with cmkl library or related to some think else. HS> HS> HS> HS> ----------------------------------------- HS> HS> ../Modules/ptoolkit.o ../Modules/random_numbers.o ../Modules/read_cards.o HS> HS> ../Modules/read_namelists.o ../Modules/read_upf.o ../Modules/read_uspp.o HS> HS> ../Modules/recvec.o ../Modules/shmem_include.o ../Modules/splinelib.o HS> HS> ../Modules/stick_base.o ../Modules/task_groups.o ../Modules/timestep.o HS> HS> ../Modules/uspp.o ../Modules/version.o ../Modules/wavefunctions.o HS> HS> ../Modules/wave_base.o ../Modules/xml_io_base.o libpw.a ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a -lmkl_lapack -L/opt/intel/cmkl/8.0/lib/em64t -lmkl_em64t -lguide -lpthread HS> HS> HS> HS> IPO Error: unresolved : __svml_cos2 HS> HS> Referenced in clib.a(fft_stick.o) HS> HS> IPO Error: unresolved : __svml_sin2 HS> HS> Referenced in clib.a(fft_stick.o) HS> HS> .../clib/clib.a(fft_stick.o)(.text+0x37044): In function `complete_twiddle': HS> HS> : undefined reference to `__svml_cos2' HS> HS> .../clib/clib.a(fft_stick.o)(.text+0x37062): In function `complete_twiddle': HS> HS> : undefined reference to `__svml_sin2' HS> HS> HS> this means, that your compiler optimized to use the SSE HS> version of sine, cosine etc. those are in the SVML library. HS> HS> just edit your make.sys file to append '-lsvml' after '-lguide' HS> HS> cheers, HS> axel. HS> HS> HS> ------------------------------------------------------------------- HS> HS> HS> HS> Your advices and help are appreciated. HS> HS> HS> HS> Yours sincerely, HS> HS> HS> HS> Halim Said, HS> HS> dept of Phys, Univ Soussa, HS> HS> Tunisi HS> HS> HS> HS> HS> HS> --------------------------------- HS> HS> Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail HS> HS> -- ======================================================================= 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 mpayami at aeoi.org.ir Sat Oct 6 13:00:35 2007 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Sat, 6 Oct 2007 14:30:35 +0330 Subject: [Pw_forum] Problem arising in fc_10.0.023+mkl_9.1.023 Message-ID: <0c0f01c80808$1f45fc60$206510ac@aeoi.org.ir> Dear PW users, I am testing the Intel fc_10.0.023 + mkl_9.1.023 on espresso_3.2. The compiler does not support the "-tpp6" switch but instead it is replaced by "-mtune=pentium4". The compilation is ok. I have also compiled and installed mpich2. In running example_1, say, I encounter the message: ``running the symmetry analysis for Cu bands...[cli_0]: aborting job: application called MPI_Abort(MPI_COMM_WORLD,0) -process 1...'' A crash file is also appeared containing the mewssage: ``from bands: error # 2 pools not implemented''. However, the pools are checked and they work without any problem. Also the distribution of job over the nodes is ok. I would be grateful for any comments. Bests, mahmoud payami CTPM, AEOI, Tehran-Iran. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071006/8f66c0c1/attachment.htm From Xiangqian.Hu at duke.edu Mon Oct 8 15:59:45 2007 From: Xiangqian.Hu at duke.edu (xqhu@duke.edu) Date: Mon, 8 Oct 2007 09:59:45 -0400 Subject: [Pw_forum] Does PWSCF have a bug when optimizing the structure in one electric field? Message-ID: <045d01c809b3$7c170ae0$6600a8c0@HLHXQ> Hi, Dear Users, I tried to optimize the molecular structure in a saw-like electric field using espresso-3.2. However, the optimization is always failed. I checked the forces through the numerical method. It seems that the forces in a electic field are wrong. Maybe the version I used is old. Does anybody have the same problem? Thanks for your help. Xiangqian -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071008/9479a998/attachment.htm From Giovanni.Cantele at na.infn.it Mon Oct 8 16:55:39 2007 From: Giovanni.Cantele at na.infn.it (Giovanni Cantele) Date: Mon, 08 Oct 2007 16:55:39 +0200 Subject: [Pw_forum] Does PWSCF have a bug when optimizing the structure in one electric field? In-Reply-To: <045d01c809b3$7c170ae0$6600a8c0@HLHXQ> References: <045d01c809b3$7c170ae0$6600a8c0@HLHXQ> Message-ID: <470A44EB.3090405@na.infn.it> xqhu at duke.edu wrote: > Hi, Dear Users, > I tried to optimize the molecular structure in a saw-like electric > field using espresso-3.2. However, the optimization is always failed. > I checked the forces through the numerical method. It seems that the > forces in a electic field are wrong. > Does anybody have the same problem? > I'm not sure if I remember well, but some time ago I tried to use the utility for a sample system, a water molecule in an orthorhombic supercell. The point was that if the molecule were placed in the middle of the supercell, weird result came out, in particular concerning the total force. The problem seemed to disappear after centering the molecule around (0,0,0). In this last case, the total force was much more realistic. Just to show you what happened, I used ibrav=6 a=3.0 b=3.0 c=10.0 and edir=3 eamp=0.D0 eopreg=0.1 in both runs. But with emaxpos=0.9 and ATOMIC_POSITIONS { Angstrom } O 1.5 1.5 4.69 H 2.268 1.5 5.31 H 0.732 1.5 5.31 the result was: ! total energy = 235.03525091 ryd Total force = 17.072620 whereas, with emaxpos=0.5 and ATOMIC_POSITIONS { Angstrom } O 0.0 0.0 0.0 H 0.77 0.0 0.62 H -0.77 0.0 0.62 the result was: ! total energy = -34.22828551 ryd Total force = 0.063638 Anyway, I'm not very sure if this is the point. > Maybe the version I used is old. I think 3.2 (+patches for 3.2.1 and 3.2.2) is the latest. Giovanni -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: Giovanni.Cantele at na.infn.it Web: http://people.na.infn.it/~cantele From ganster at crmcn.univ-mrs.fr Mon Oct 8 17:21:10 2007 From: ganster at crmcn.univ-mrs.fr (Patrick GANSTER) Date: Mon, 08 Oct 2007 17:21:10 +0200 Subject: [Pw_forum] problem in compiling cp.x in espresso Message-ID: <470A4AE6.6090500@crmcn.univ-mrs.fr> Dear all, When I compile espresso on AMD Opteron x86_64 with open mpif90 (v9.1), i get this error in the cp part , /opt/mpich/intel/bin/mpif90 -O2 -assume byterecl -nomodule -fpp -D__INTEL -D__FFTW -D__USE_INTERNAL_FFTW -I../include -I./ -I../Modules -I../iotk/src -I../PW -I../PH -I../CPV -c restart_sub.f90 fortcom: Severe: **Internal compiler error: segmentation violation signal raised** Please report this error along with the circumstances in which it occurred in a Software Problem Report. Note: File and line given may not be explicit cause of this error. compilation aborted for restart_sub.f90 (code 3) has anyone reported this problem ?? Patrick Patrick GANSTER Centre de Recherche en Mati?re Condens?e et Nanosciences (CRMCN) CNRS, UPR 7251, case 913 13288 Marseille cedex 9 France t?l : +33 6 62 90 38 50 fax : +33 4 91 41 89 16 From akohlmey at cmm.chem.upenn.edu Mon Oct 8 18:30:05 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 8 Oct 2007 12:30:05 -0400 (EDT) Subject: [Pw_forum] problem in compiling cp.x in espresso In-Reply-To: <470A4AE6.6090500@crmcn.univ-mrs.fr> Message-ID: On Mon, 8 Oct 2007, Patrick GANSTER wrote: PG> Dear all, dear patrick, PG> When I compile espresso on AMD Opteron x86_64 with open mpif90 (v9.1), PG> i get this error in the cp part , please make sure you provide the correct version info. from the compile messages below it looks like you are using the intel compiler version 9.1 with mpich. there is no openmpi version 9.1. the laters version of open mpi is 1.2.3, IIRC. PG> PG> /opt/mpich/intel/bin/mpif90 -O2 -assume byterecl -nomodule -fpp PG> -D__INTEL -D__FFTW -D__USE_INTERNAL_FFTW -I../include -I./ PG> -I../Modules -I../iotk/src -I../PW -I../PH -I../CPV -c restart_sub.f90 PG> fortcom: Severe: **Internal compiler error: segmentation violation PG> signal raised** Please report this error along with the circumstances in PG> which it occurred in a Software Problem Report. Note: File and line PG> given may not be explicit cause of this error. PG> compilation aborted for restart_sub.f90 (code 3) PG> PG> has anyone reported this problem ?? this is a problem of the intel compiler (all internal compiler errors are just that, compiler bugs) and has been fixed long ago. please update the intel compiler to the latest patchlevel. cheers, axel. PG> PG> Patrick PG> PG> Patrick GANSTER PG> PG> Centre de Recherche en Mati?re Condens?e et Nanosciences (CRMCN) PG> CNRS, UPR 7251, case 913 PG> 13288 Marseille cedex 9 France PG> t?l : +33 6 62 90 38 50 PG> fax : +33 4 91 41 89 16 PG> PG> PG> PG> _______________________________________________ PG> Pw_forum mailing list PG> Pw_forum at pwscf.org PG> http://www.democritos.it/mailman/listinfo/pw_forum PG> -- ======================================================================= 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 nazari at iasbs.ac.ir Tue Oct 9 14:06:37 2007 From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir) Date: Tue, 9 Oct 2007 13:06:37 +0100 (BST) Subject: [Pw_forum] error Message-ID: <10894.213.176.122.3.1191931597.squirrel@mail.iasbs.ac.ir> Dear Users, I have tried to compile espresso on pc with linux operating system. I have faced with the following error in make pw step. Would you please let me know how I can solve this problem. Regards Fariba Nazari IASBS pwscf.o ../Modules/atom.o ../Modules/autopilot.o ../Modules/basic_algebra_routines.o ../Modules/berry_phase.o ../Modules/bfgs_module.o ../Modules/cell_base.o ../Modules/check_stop.o ../Modules/clocks.o ../Modules/constants.o ../Modules/constraints_module.o ../Modules/control_flags.o ../Modules/electrons_base.o ../Modules/fft_base.o ../Modules/fft_scalar.o ../Modules/fft_types.o ../Modules/functionals.o ../Modules/input_parameters.o ../Modules/io_files.o ../Modules/io_global.o ../Modules/ions_base.o ../Modules/ions_nose.o ../Modules/kind.o ../Modules/mp_global.o ../Modules/mp_wave.o ../Modules/mp.o ../Modules/metadyn_base.o ../Modules/metadyn_io.o ../Modules/metadyn_vars.o ../Modules/path_base.o ../Modules/path_formats.o ../Modules/path_variables.o ../Modules/path_opt_routines.o ../Modules/path_io_routines.o ../Modules/path_reparametrisation.o ../Modules/parallel_include.o ../Modules/parameters.o ../Modules/parser.o ../Modules/printout_base.o ../Modules/pseudo_types.o ../Modules/ptoolkit.o ../Modules/random_numbers.o ../Modules/read_cards.o ../Modules/read_namelists.o ../Modules/read_upf.o ../Modules/read_uspp.o ../Modules/recvec.o ../Modules/shmem_include.o ../Modules/splinelib.o ../Modules/stick_base.o ../Modules/task_groups.o ../Modules/timestep.o ../Modules/uspp.o ../Modules/version.o ../Modules/wavefunctions.o ../Modules/wave_base.o ../Modules/xml_io_base.o libpw.a ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a -lmkl_lapack -L/opt/intel/mkl/9.1.023/lib/32 -lmkl_ia32 -lguide -lpthread /usr/local/bin/fftw-wisdom /usr/local/bin/fftw-wisdom: In function `_start': (.text+0x0): multiple definition of `_start' /usr/lib/gcc/i386-redhat-linux/4.1.1/../../../crt1.o:(.text+0x0): first defined here /usr/local/bin/fftw-wisdom:(.rodata+0x0): multiple definition of `_fp_hw' /usr/lib/gcc/i386-redhat-linux/4.1.1/../../../crt1.o:(.rodata+0x0): first defined here /usr/local/bin/fftw-wisdom: In function `_fini': (.fini+0x0): multiple definition of `_fini' /usr/lib/gcc/i386-redhat-linux/4.1.1/../../../crti.o:(.fini+0x0): first defined here /usr/local/bin/fftw-wisdom:(.rodata+0x4): multiple definition of `_IO_stdin_used' /usr/lib/gcc/i386-redhat-linux/4.1.1/../../../crt1.o:(.rodata.cst4+0x0): first defined here /usr/local/bin/fftw-wisdom: In function `__data_start': (.data+0x0): multiple definition of `__data_start' /usr/lib/gcc/i386-redhat-linux/4.1.1/../../../crt1.o:(.data+0x0): first defined here /usr/local/bin/fftw-wisdom:(.rodata+0x8): multiple definition of `__dso_handle' /usr/lib/gcc/i386-redhat-linux/4.1.1/crtbegin.o:(.rodata+0x0): first defined here /usr/local/bin/fftw-wisdom: In function `_edata': (*ABS*+0x80d48a4): multiple definition of `__bss_start' /usr/local/bin/fftw-wisdom: In function `_end': (*ABS*+0x80d4af8): multiple definition of `_end' /usr/local/bin/fftw-wisdom: In function `_edata': (*ABS*+0x80d48a4): multiple definition of `_edata' /usr/local/bin/fftw-wisdom: In function `_init': (.init+0x0): multiple definition of `_init' /usr/lib/gcc/i386-redhat-linux/4.1.1/../../../crti.o:(.init+0x0): first defined here ../Modules/berry_phase.o: In function `__berry_phase__ln_setup': berry_phase.f90:(.text+0x33): undefined reference to `ln_alloc_' berry_phase.f90:(.text+0x92): undefined reference to `ln_set_' berry_phase.f90:(.text+0xa5): undefined reference to `ln_activate_' ../Modules/berry_phase.o: In function `__berry_phase__indi_of_ig': berry_phase.f90:(.text+0x21e): undefined reference to `ln_ind_' berry_phase.f90:(.text+0x250): undefined reference to `ln_ind_' berry_phase.f90:(.text+0x286): undefined reference to `ln_ind_' berry_phase.f90:(.text+0x30c): undefined reference to `ln_ind_' berry_phase.f90:(.text+0x335): undefined reference to `ln_ind_' ../Modules/berry_phase.o:berry_phase.f90:(.text+0x379): more undefined references to `ln_ind_' follow ../Modules/berry_phase.o: In function `__berry_phase__ln_closeup': berry_phase.f90:(.text+0xe2): undefined reference to `ln_dealloc_' ../Modules/fft_scalar.o: In function `__fft_scalar__cft_1z': fft_scalar.f90:(.text+0xf2): undefined reference to `create_plan_1d_' fft_scalar.f90:(.text+0x118): undefined reference to `create_plan_1d_' fft_scalar.f90:(.text+0x1f0): undefined reference to `fft_z_stick_' fft_scalar.f90:(.text+0x258): undefined reference to `destroy_plan_1d_' fft_scalar.f90:(.text+0x26c): undefined reference to `destroy_plan_1d_' fft_scalar.f90:(.text+0x295): undefined reference to `fft_z_stick_' ../Modules/fft_scalar.o: In function `__fft_scalar__cft_2xy': fft_scalar.f90:(.text+0x49c): undefined reference to `create_plan_1d_' fft_scalar.f90:(.text+0x4c2): undefined reference to `create_plan_1d_' fft_scalar.f90:(.text+0x516): undefined reference to `create_plan_1d_' fft_scalar.f90:(.text+0x53c): undefined reference to `create_plan_1d_' fft_scalar.f90:(.text+0x633): undefined reference to `fft_x_stick_' fft_scalar.f90:(.text+0x6cb): undefined reference to `destroy_plan_1d_' fft_scalar.f90:(.text+0x6df): undefined reference to `destroy_plan_1d_' fft_scalar.f90:(.text+0x6f3): undefined reference to `destroy_plan_1d_' fft_scalar.f90:(.text+0x707): undefined reference to `destroy_plan_1d_' fft_scalar.f90:(.text+0x785): undefined reference to `fft_x_stick_' fft_scalar.f90:(.text+0x86e): undefined reference to `fft_y_stick_' fft_scalar.f90:(.text+0x8d3): undefined reference to `fft_y_stick_' ../Modules/fft_scalar.o: In function `__fft_scalar__cfft3d': fft_scalar.f90:(.text+0x9c2): undefined reference to `create_plan_3d_' fft_scalar.f90:(.text+0x9f0): undefined reference to `create_plan_3d_' fft_scalar.f90:(.text+0xa7a): undefined reference to `fftw_inplace_drv_3d_' fft_scalar.f90:(.text+0xab0): undefined reference to `destroy_plan_3d_' fft_scalar.f90:(.text+0xacb): undefined reference to `destroy_plan_3d_' fft_scalar.f90:(.text+0xb7a): undefined reference to `fftw_inplace_drv_3d_' ../Modules/fft_scalar.o: In function `__fft_scalar__cfft3ds': fft_scalar.f90:(.text+0xd1c): undefined reference to `create_plan_1d_' fft_scalar.f90:(.text+0xd45): undefined reference to `create_plan_1d_' fft_scalar.f90:(.text+0xd6e): undefined reference to `create_plan_1d_' fft_scalar.f90:(.text+0xd97): undefined reference to `create_plan_1d_' fft_scalar.f90:(.text+0xdc0): undefined reference to `create_plan_1d_' ../Modules/fft_scalar.o:fft_scalar.f90:(.text+0xde9): more undefined references to `create_plan_1d_' follow ../Modules/fft_scalar.o: In function `__fft_scalar__cfft3ds': fft_scalar.f90:(.text+0xee1): undefined reference to `fftw_inplace_drv_1d_' fft_scalar.f90:(.text+0xfa9): undefined reference to `fftw_inplace_drv_1d_' fft_scalar.f90:(.text+0xfe7): undefined reference to `fftw_inplace_drv_1d_' fft_scalar.f90:(.text+0x1025): undefined reference to `destroy_plan_1d_' fft_scalar.f90:(.text+0x104c): undefined reference to `destroy_plan_1d_' fft_scalar.f90:(.text+0x1073): undefined reference to `destroy_plan_1d_' fft_scalar.f90:(.text+0x109a): undefined reference to `destroy_plan_1d_' fft_scalar.f90:(.text+0x10c1): undefined reference to `destroy_plan_1d_' ../Modules/fft_scalar.o:fft_scalar.f90:(.text+0x10e8): more undefined references to `destroy_plan_1d_' follow ../Modules/fft_scalar.o: In function `__fft_scalar__cfft3ds': fft_scalar.f90:(.text+0x11dd): undefined reference to `fftw_inplace_drv_1d_' fft_scalar.f90:(.text+0x126a): undefined reference to `fftw_inplace_drv_1d_' fft_scalar.f90:(.text+0x1317): undefined reference to `fftw_inplace_drv_1d_' ../Modules/fft_scalar.o: In function `__fft_scalar__cft_b': fft_scalar.f90:(.text+0x148e): undefined reference to `create_plan_1d_' fft_scalar.f90:(.text+0x14cf): undefined reference to `create_plan_2d_' fft_scalar.f90:(.text+0x1574): undefined reference to `fftw_inplace_drv_1d_' fft_scalar.f90:(.text+0x15b6): undefined reference to `fftw_inplace_drv_2d_' fft_scalar.f90:(.text+0x15db): undefined reference to `destroy_plan_1d_' fft_scalar.f90:(.text+0x15ef): undefined reference to `destroy_plan_2d_' ../Modules/xml_io_base.o: In function `__xml_io_base__create_directory': xml_io_base.f90:(.text+0x20a): undefined reference to `c_mkdir_' libpw.a(input.o): In function `verify_tmpdir_': input.f90:(.text+0x60a): undefined reference to `c_mkdir_' libpw.a(bp_c_phase.o): In function `c_phase_': bp_c_phase.f90:(.text+0x103a): undefined reference to `ylm_q_' libpw.a(bp_radin.o): In function `radlg_': bp_radin.f:(.text+0x17a): undefined reference to `s_wsle' bp_radin.f:(.text+0x190): undefined reference to `do_lio' bp_radin.f:(.text+0x198): undefined reference to `e_wsle' bp_radin.f:(.text+0x1a5): undefined reference to `s_wsle' bp_radin.f:(.text+0x1bb): undefined reference to `do_lio' bp_radin.f:(.text+0x1d0): undefined reference to `do_lio' bp_radin.f:(.text+0x1d5): undefined reference to `e_wsle' bp_radin.f:(.text+0x1e3): undefined reference to `s_stop' libpw.a(bp_radin.o): In function `radlg1_': bp_radin.f:(.text+0x2b5): undefined reference to `s_wsle' bp_radin.f:(.text+0x2cb): undefined reference to `do_lio' bp_radin.f:(.text+0x2d3): undefined reference to `e_wsle' bp_radin.f:(.text+0x2e0): undefined reference to `s_wsle' bp_radin.f:(.text+0x2f6): undefined reference to `do_lio' bp_radin.f:(.text+0x30b): undefined reference to `do_lio' bp_radin.f:(.text+0x310): undefined reference to `e_wsle' bp_radin.f:(.text+0x31e): undefined reference to `s_stop' libpw.a(c_phase_field.o): In function `c_phase_field_': c_phase_field.f90:(.text+0x2008): undefined reference to `ylm_q_' libpw.a(h_epsi_her.o): In function `h_epsi_her_': h_epsi_her.f90:(.text+0xd9e): undefined reference to `ylm_q_' h_epsi_her.f90:(.text+0x1292): undefined reference to `ylm_q_' collect2: ld returned 1 exit status make[1]: *** [pw.x] Error 1 make[1]: Leaving directory `/root/fariba/espresso-3.2.3/PW' make: *** [pw] Error 2 From zucco at dipteris.unige.it Tue Oct 9 16:13:21 2007 From: zucco at dipteris.unige.it (Marino Vetuschi Zuccolini) Date: Tue, 9 Oct 2007 16:13:21 +0200 Subject: [Pw_forum] Different behavior in relax tasks Message-ID: <3D5FCD86-A9F7-497C-B1E5-787B329561BD@dipteris.unige.it> Dear all, sorry if the question was already posted and the answer done, but I didn't found a good one. Does the if_pos syntax for ATOMIC_POSITION block > MUST < runs in "calculation='vc-relax'" jobs AS in "calculation='relax'" ? I'm using 3.2 and 3.2cvs versions and pw.x "relax" seems to run well instead of "vc-relax", where apparently nothing change in coordinate position. Thanks m. ******************************************************* Marino Vetuschi Zuccolini zucco at dipteris.unige.it Researcher / Geochemist Laboratory of Geochemistry DIPartimento per lo studio della TErra e delle sue RISorse - Universit? di Genova Tel. ++39 010 3538136 Fax. ++39 010 352169 Corso Europa 26, 16132 - Genova - Italy From whitley3 at llnl.gov Wed Oct 10 18:17:40 2007 From: whitley3 at llnl.gov (Heather Whitley) Date: Wed, 10 Oct 2007 09:17:40 -0700 Subject: [Pw_forum] error In-Reply-To: References: Message-ID: <470CFB24.6000202@llnl.gov> Dear Fariba, I encountered this problem as well when trying to compile the CVS version of Espresso. It occurs because the linker defaults to "ld" rather than the compiler. You can likely fix it by setting the variable "LD" in your make.sys file to the name of whichever compiler you are using (like mpiifort, mpipgf90, etc.) Regards, Heather > Message: 1 > Date: Tue, 9 Oct 2007 13:06:37 +0100 (BST) > From: nazari at iasbs.ac.ir > Subject: [Pw_forum] error > To: pw_forum at pwscf.org > Message-ID: <10894.213.176.122.3.1191931597.squirrel at mail.iasbs.ac.ir> > Content-Type: text/plain;charset=utf-8 > > > > Dear Users, > > I have tried to compile espresso on pc with linux operating system. > I have faced with the following error in make pw step. Would you > > please let me know how I can solve this problem. > > Regards > Fariba Nazari > IASBS > pwscf.o ../Modules/atom.o ../Modules/autopilot.o > ../Modules/basic_algebra_routines.o ../Modules/berry_phase.o > ../Modules/bfgs_module.o ../Modules/cell_base.o ../Modules/check_stop.o > ../Modules/clocks.o ../Modules/constants.o > ../Modules/constraints_module.o ../Modules/control_flags.o > ../Modules/electrons_base.o ../Modules/fft_base.o > ../Modules/fft_scalar.o ../Modules/fft_types.o ../Modules/functionals.o > ../Modules/input_parameters.o ../Modules/io_files.o > ../Modules/io_global.o ../Modules/ions_base.o ../Modules/ions_nose.o > ../Modules/kind.o ../Modules/mp_global.o ../Modules/mp_wave.o > ../Modules/mp.o ../Modules/metadyn_base.o ../Modules/metadyn_io.o > ../Modules/metadyn_vars.o ../Modules/path_base.o > ../Modules/path_formats.o ../Modules/path_variables.o > ../Modules/path_opt_routines.o ../Modules/path_io_routines.o > ../Modules/path_reparametrisation.o ../Modules/parallel_include.o > ../Modules/parameters.o ../Modules/parser.o ../Modules/printout_base.o > ../Modules/pseudo_types.o ../Modules/ptoolkit.o > ../Modules/random_numbers.o ../Modules/read_cards.o > ../Modules/read_namelists.o ../Modules/read_upf.o ../Modules/read_uspp.o > ../Modules/recvec.o ../Modules/shmem_include.o ../Modules/splinelib.o > ../Modules/stick_base.o ../Modules/task_groups.o ../Modules/timestep.o > ../Modules/uspp.o ../Modules/version.o ../Modules/wavefunctions.o > ../Modules/wave_base.o ../Modules/xml_io_base.o libpw.a ../flib/ptools.a > ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a -lmkl_lapack > -L/opt/intel/mkl/9.1.023/lib/32 -lmkl_ia32 -lguide -lpthread > /usr/local/bin/fftw-wisdom > /usr/local/bin/fftw-wisdom: In function `_start': > (.text+0x0): multiple definition of `_start' > /usr/lib/gcc/i386-redhat-linux/4.1.1/../../../crt1.o:(.text+0x0): first > defined here > /usr/local/bin/fftw-wisdom:(.rodata+0x0): multiple definition of `_fp_hw' > /usr/lib/gcc/i386-redhat-linux/4.1.1/../../../crt1.o:(.rodata+0x0): first > defined here > /usr/local/bin/fftw-wisdom: In function `_fini': > (.fini+0x0): multiple definition of `_fini' > /usr/lib/gcc/i386-redhat-linux/4.1.1/../../../crti.o:(.fini+0x0): first > defined here > /usr/local/bin/fftw-wisdom:(.rodata+0x4): multiple definition of > `_IO_stdin_used' > /usr/lib/gcc/i386-redhat-linux/4.1.1/../../../crt1.o:(.rodata.cst4+0x0): > first defined here > /usr/local/bin/fftw-wisdom: In function `__data_start': > (.data+0x0): multiple definition of `__data_start' > /usr/lib/gcc/i386-redhat-linux/4.1.1/../../../crt1.o:(.data+0x0): first > defined here > /usr/local/bin/fftw-wisdom:(.rodata+0x8): multiple definition of > `__dso_handle' > /usr/lib/gcc/i386-redhat-linux/4.1.1/crtbegin.o:(.rodata+0x0): first > defined here > /usr/local/bin/fftw-wisdom: In function `_edata': > (*ABS*+0x80d48a4): multiple definition of `__bss_start' > /usr/local/bin/fftw-wisdom: In function `_end': > (*ABS*+0x80d4af8): multiple definition of `_end' > /usr/local/bin/fftw-wisdom: In function `_edata': > (*ABS*+0x80d48a4): multiple definition of `_edata' > /usr/local/bin/fftw-wisdom: In function `_init': > (.init+0x0): multiple definition of `_init' > /usr/lib/gcc/i386-redhat-linux/4.1.1/../../../crti.o:(.init+0x0): first > defined here > ../Modules/berry_phase.o: In function `__berry_phase__ln_setup': > berry_phase.f90:(.text+0x33): undefined reference to `ln_alloc_' > berry_phase.f90:(.text+0x92): undefined reference to `ln_set_' > berry_phase.f90:(.text+0xa5): undefined reference to `ln_activate_' > ../Modules/berry_phase.o: In function `__berry_phase__indi_of_ig': > berry_phase.f90:(.text+0x21e): undefined reference to `ln_ind_' > berry_phase.f90:(.text+0x250): undefined reference to `ln_ind_' > berry_phase.f90:(.text+0x286): undefined reference to `ln_ind_' > berry_phase.f90:(.text+0x30c): undefined reference to `ln_ind_' > berry_phase.f90:(.text+0x335): undefined reference to `ln_ind_' > ../Modules/berry_phase.o:berry_phase.f90:(.text+0x379): more undefined > references to `ln_ind_' follow > ../Modules/berry_phase.o: In function `__berry_phase__ln_closeup': > berry_phase.f90:(.text+0xe2): undefined reference to `ln_dealloc_' > ../Modules/fft_scalar.o: In function `__fft_scalar__cft_1z': > fft_scalar.f90:(.text+0xf2): undefined reference to `create_plan_1d_' > fft_scalar.f90:(.text+0x118): undefined reference to `create_plan_1d_' > fft_scalar.f90:(.text+0x1f0): undefined reference to `fft_z_stick_' > fft_scalar.f90:(.text+0x258): undefined reference to `destroy_plan_1d_' > fft_scalar.f90:(.text+0x26c): undefined reference to `destroy_plan_1d_' > fft_scalar.f90:(.text+0x295): undefined reference to `fft_z_stick_' > ../Modules/fft_scalar.o: In function `__fft_scalar__cft_2xy': > fft_scalar.f90:(.text+0x49c): undefined reference to `create_plan_1d_' > fft_scalar.f90:(.text+0x4c2): undefined reference to `create_plan_1d_' > fft_scalar.f90:(.text+0x516): undefined reference to `create_plan_1d_' > fft_scalar.f90:(.text+0x53c): undefined reference to `create_plan_1d_' > fft_scalar.f90:(.text+0x633): undefined reference to `fft_x_stick_' > fft_scalar.f90:(.text+0x6cb): undefined reference to `destroy_plan_1d_' > fft_scalar.f90:(.text+0x6df): undefined reference to `destroy_plan_1d_' > fft_scalar.f90:(.text+0x6f3): undefined reference to `destroy_plan_1d_' > fft_scalar.f90:(.text+0x707): undefined reference to `destroy_plan_1d_' > fft_scalar.f90:(.text+0x785): undefined reference to `fft_x_stick_' > fft_scalar.f90:(.text+0x86e): undefined reference to `fft_y_stick_' > fft_scalar.f90:(.text+0x8d3): undefined reference to `fft_y_stick_' > ../Modules/fft_scalar.o: In function `__fft_scalar__cfft3d': > fft_scalar.f90:(.text+0x9c2): undefined reference to `create_plan_3d_' > fft_scalar.f90:(.text+0x9f0): undefined reference to `create_plan_3d_' > fft_scalar.f90:(.text+0xa7a): undefined reference to > `fftw_inplace_drv_3d_' > fft_scalar.f90:(.text+0xab0): undefined reference to `destroy_plan_3d_' > fft_scalar.f90:(.text+0xacb): undefined reference to `destroy_plan_3d_' > fft_scalar.f90:(.text+0xb7a): undefined reference to > `fftw_inplace_drv_3d_' > ../Modules/fft_scalar.o: In function `__fft_scalar__cfft3ds': > fft_scalar.f90:(.text+0xd1c): undefined reference to `create_plan_1d_' > fft_scalar.f90:(.text+0xd45): undefined reference to `create_plan_1d_' > fft_scalar.f90:(.text+0xd6e): undefined reference to `create_plan_1d_' > fft_scalar.f90:(.text+0xd97): undefined reference to `create_plan_1d_' > fft_scalar.f90:(.text+0xdc0): undefined reference to `create_plan_1d_' > ../Modules/fft_scalar.o:fft_scalar.f90:(.text+0xde9): more undefined > references to `create_plan_1d_' follow > ../Modules/fft_scalar.o: In function `__fft_scalar__cfft3ds': > fft_scalar.f90:(.text+0xee1): undefined reference to > `fftw_inplace_drv_1d_' > fft_scalar.f90:(.text+0xfa9): undefined reference to > `fftw_inplace_drv_1d_' > fft_scalar.f90:(.text+0xfe7): undefined reference to > `fftw_inplace_drv_1d_' > fft_scalar.f90:(.text+0x1025): undefined reference to `destroy_plan_1d_' > fft_scalar.f90:(.text+0x104c): undefined reference to `destroy_plan_1d_' > fft_scalar.f90:(.text+0x1073): undefined reference to `destroy_plan_1d_' > fft_scalar.f90:(.text+0x109a): undefined reference to `destroy_plan_1d_' > fft_scalar.f90:(.text+0x10c1): undefined reference to `destroy_plan_1d_' > ../Modules/fft_scalar.o:fft_scalar.f90:(.text+0x10e8): more undefined > references to `destroy_plan_1d_' follow > ../Modules/fft_scalar.o: In function `__fft_scalar__cfft3ds': > fft_scalar.f90:(.text+0x11dd): undefined reference to > `fftw_inplace_drv_1d_' > fft_scalar.f90:(.text+0x126a): undefined reference to > `fftw_inplace_drv_1d_' > fft_scalar.f90:(.text+0x1317): undefined reference to > `fftw_inplace_drv_1d_' > ../Modules/fft_scalar.o: In function `__fft_scalar__cft_b': > fft_scalar.f90:(.text+0x148e): undefined reference to `create_plan_1d_' > fft_scalar.f90:(.text+0x14cf): undefined reference to `create_plan_2d_' > fft_scalar.f90:(.text+0x1574): undefined reference to > `fftw_inplace_drv_1d_' > fft_scalar.f90:(.text+0x15b6): undefined reference to > `fftw_inplace_drv_2d_' > fft_scalar.f90:(.text+0x15db): undefined reference to `destroy_plan_1d_' > fft_scalar.f90:(.text+0x15ef): undefined reference to `destroy_plan_2d_' > ../Modules/xml_io_base.o: In function `__xml_io_base__create_directory': > xml_io_base.f90:(.text+0x20a): undefined reference to `c_mkdir_' > libpw.a(input.o): In function `verify_tmpdir_': > input.f90:(.text+0x60a): undefined reference to `c_mkdir_' > libpw.a(bp_c_phase.o): In function `c_phase_': > bp_c_phase.f90:(.text+0x103a): undefined reference to `ylm_q_' > libpw.a(bp_radin.o): In function `radlg_': > bp_radin.f:(.text+0x17a): undefined reference to `s_wsle' > bp_radin.f:(.text+0x190): undefined reference to `do_lio' > bp_radin.f:(.text+0x198): undefined reference to `e_wsle' > bp_radin.f:(.text+0x1a5): undefined reference to `s_wsle' > bp_radin.f:(.text+0x1bb): undefined reference to `do_lio' > bp_radin.f:(.text+0x1d0): undefined reference to `do_lio' > bp_radin.f:(.text+0x1d5): undefined reference to `e_wsle' > bp_radin.f:(.text+0x1e3): undefined reference to `s_stop' > libpw.a(bp_radin.o): In function `radlg1_': > bp_radin.f:(.text+0x2b5): undefined reference to `s_wsle' > bp_radin.f:(.text+0x2cb): undefined reference to `do_lio' > bp_radin.f:(.text+0x2d3): undefined reference to `e_wsle' > bp_radin.f:(.text+0x2e0): undefined reference to `s_wsle' > bp_radin.f:(.text+0x2f6): undefined reference to `do_lio' > bp_radin.f:(.text+0x30b): undefined reference to `do_lio' > bp_radin.f:(.text+0x310): undefined reference to `e_wsle' > bp_radin.f:(.text+0x31e): undefined reference to `s_stop' > libpw.a(c_phase_field.o): In function `c_phase_field_': > c_phase_field.f90:(.text+0x2008): undefined reference to `ylm_q_' > libpw.a(h_epsi_her.o): In function `h_epsi_her_': > h_epsi_her.f90:(.text+0xd9e): undefined reference to `ylm_q_' > h_epsi_her.f90:(.text+0x1292): undefined reference to `ylm_q_' > collect2: ld returned 1 exit status > make[1]: *** [pw.x] Error 1 > make[1]: Leaving directory `/root/fariba/espresso-3.2.3/PW' > make: *** [pw] Error 2 > > -- *********************************************** Heather D. Whitley Quantum Simulations Group Lawrence Livermore National Laboratory Livermore, CA 94551 whitley3 at llnl.gov http://www.llnl.gov/qsg From cesards at msi.umn.edu Thu Oct 11 01:03:36 2007 From: cesards at msi.umn.edu (Cesar R.S. da Silva) Date: Wed, 10 Oct 2007 18:03:36 -0500 (CDT) Subject: [Pw_forum] Different behavior in relax tasks (Marino Vetuschi Zuccolini) Message-ID: <63981.128.101.191.226.1192057416.squirrel@www.msi.umn.edu> Hi Marino, please, send your input file. Cesar. From nazari at iasbs.ac.ir Thu Oct 11 10:43:04 2007 From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir) Date: Thu, 11 Oct 2007 09:43:04 +0100 (BST) Subject: [Pw_forum] error -intel-fast-memset Message-ID: <25692.213.176.122.3.1192092184.squirrel@mail.iasbs.ac.ir> Dear All, I have compiled espresso-3.2 on machine which have Linux operating system gcc, ifort9.0, MKL8.0, fftw.3.1.2. But when I want to run example02 I faced with the following error: Running the scf calculation .../root/fariba/expresso-3-2/bin/pw.x:symbole lookup....... error: undefined symbol: -intel-fast-memset Would you please give me a comment? Regards fariba nazari IASBS From zucco at dipteris.unige.it Thu Oct 11 10:52:04 2007 From: zucco at dipteris.unige.it (Marino Vetuschi Zuccolini) Date: Thu, 11 Oct 2007 10:52:04 +0200 Subject: [Pw_forum] Different behavior in relax tasks (Marino Vetuschi Zuccolini) In-Reply-To: <63981.128.101.191.226.1192057416.squirrel@www.msi.umn.edu> References: <63981.128.101.191.226.1192057416.squirrel@www.msi.umn.edu> Message-ID: <245A58C9-30A6-42E1-B47B-8D690DD8C6A9@dipteris.unige.it> Hi Cesar, > Hi Marino, > > please, send your input file. here the two simple input files I try to use to simulate the displacement of the Oxygen in ringwoodite mimicking your very recent paper (L. Li,1 R. M. Wentzcovitch, D.J. Weidner, and Cesar R. S. Da Silva - JGR 112, B05206, doi:10.1029/2006JB004546, 2007). The parameters for sensitive variables are far from the good values but the result I obtain now are deriving probably from a misusing of the available options. All suggestion are welcomed, m. &control calculation='vc-relax' restart_mode='from_scratch', disk_io = 'minimal', tprnfor = .true., tstress = .true., prefix='ringwoodite.opt', pseudo_dir = '/sh/PWSCF_pseudo', outdir='./tmp/', verbosity = 'high', / &system ibrav=2, celldm(1)=15.9251789, nat=3, ntyp=3, nspin= 1, ecutwfc = 70.0, ecutrho = 280.0, / &electrons conv_thr = 1.0d-8 mixing_beta = 0.7 / &IONS tempw = 300., / &CELL cell_dynamics = 'damp-w' , press = 0.0 , wmass = 0.01 , / ATOMIC_SPECIES Mg 24.305 Mg.pz-n-vbc.UPF O 15.999 O.pz-mt.UPF Si 28.085 Si.pz-vbc.UPF ATOMIC_POSITIONS crystal Si 0.12500 0.12500 0.12500 0 0 0 Mg 0.50000 0.50000 0.50000 0 0 0 O 0.24410 0.24410 0.24410 K_POINTS automatic 4 4 4 0.5 0.5 0.5 &control calculation='relax' restart_mode='from_scratch', disk_io = 'minimal', tprnfor = .true., tstress = .true., prefix='ringwoodite.opt', pseudo_dir = '/sh/PWSCF_pseudo', outdir='./tmp/', verbosity = 'high', / &system ibrav=2, celldm(1)=15.9251789, nat=3, ntyp=3, nspin= 1, ecutwfc = 70.0, ecutrho = 280.0, / &electrons conv_thr = 1.0d-8 mixing_beta = 0.7 / &IONS tempw = 300., / ATOMIC_SPECIES Mg 24.305 Mg.pz-n-vbc.UPF O 15.999 O.pz-mt.UPF Si 28.085 Si.pz-vbc.UPF ATOMIC_POSITIONS crystal Si 0.12500 0.12500 0.12500 0 0 0 Mg 0.50000 0.50000 0.50000 0 0 0 O 0.24410 0.24410 0.24410 K_POINTS gamma On 11 Oct 2007, at 1:03, Cesar R.S. da Silva wrote: > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ******************************************************* Marino Vetuschi Zuccolini zucco at dipteris.unige.it Researcher / Geochemist Laboratory of Geochemistry DIPartimento per lo studio della TErra e delle sue RISorse - Universit? di Genova Tel. ++39 010 3538136 Fax. ++39 010 352169 Corso Europa 26, 16132 - Genova - Italy From giannozz at nest.sns.it Thu Oct 11 12:48:44 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 11 Oct 2007 12:48:44 +0200 Subject: [Pw_forum] Problem arising in fc_10.0.023+mkl_9.1.023 In-Reply-To: <0c0f01c80808$1f45fc60$206510ac@aeoi.org.ir> References: <0c0f01c80808$1f45fc60$206510ac@aeoi.org.ir> Message-ID: <4281A352-D398-4A09-B290-E758945FE8F3@nest.sns.it> On Oct 6, 2007, at 13:00 , Mahmoud Payami wrote: > Dear PW users, > > I am testing the Intel fc_10.0.023 + mkl_9.1.023 on espresso_3.2. > [...] > In running example_1, say, I encounter the message: > > ``running the symmetry analysis for Cu bands...[cli_0]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD,0) -process 1...'' > A crash file is also appeared containing the mewssage: > ``from bands: error # 2 > pools not implemented''. > > However, the pools are checked and they work without any problem. pools work without any problem where properly implemented, but in some codes, pools are not implemented. More exactly: the parallelization over k-points (requiring partition of processors into the so-called pools) is not implemented. All codes call the same initialization routine that partitions processes into pools if required to do so with the appopriate command line option (-npool 2 for instance), but unless somebody has programmed how to partition the tasks and how to collect the results, pools will not work by themselves. The code "bands.x" stops if run with pools because unpredictable behavior may result. Apparently it doesn't stop in a gracious manner, but it manages anyway to spread the message why it is stopping. 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 Oct 11 12:49:00 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 11 Oct 2007 12:49:00 +0200 Subject: [Pw_forum] Does PWSCF have a bug when optimizing the structure in one electric field? In-Reply-To: <470A44EB.3090405@na.infn.it> References: <045d01c809b3$7c170ae0$6600a8c0@HLHXQ> <470A44EB.3090405@na.infn.it> Message-ID: <6ACCFEBC-2441-4ED8-B6D4-5B5C399C082E@nest.sns.it> On Oct 8, 2007, at 16:55 , Giovanni Cantele wrote: >> Maybe the version I used is old. > I think 3.2 (+patches for 3.2.1 and 3.2.2) is the latest. actually the latest "stable" is 3.2.3 and it is already available from the download page of www.pwscf.org (it hasn't been announced because the web sites haven't yet been updated). It doesn't fix, to the best of my knowledge, any problem in calculations under an electric field, though. Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at nest.sns.it Thu Oct 11 13:07:26 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 11 Oct 2007 13:07:26 +0200 Subject: [Pw_forum] error In-Reply-To: <470CFB24.6000202@llnl.gov> References: <470CFB24.6000202@llnl.gov> Message-ID: <3CA7DEBA-7AA7-4744-8253-F577E4033B4E@nest.sns.it> On Oct 10, 2007, at 18:17 , Heather Whitley wrote: > I encountered this problem as well when trying to compile > the CVS version of Espresso. It occurs because the linker > defaults to "ld" rather than the compiler. I don't think it does, unless you explicitly set the environment variable LD to "ld". Could you please provide some evidence (i.e. config.log 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 giannozz at nest.sns.it Thu Oct 11 13:18:37 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 11 Oct 2007 13:18:37 +0200 Subject: [Pw_forum] error -intel-fast-memset In-Reply-To: <25692.213.176.122.3.1192092184.squirrel@mail.iasbs.ac.ir> References: <25692.213.176.122.3.1192092184.squirrel@mail.iasbs.ac.ir> Message-ID: <195A303E-D324-4D84-BAC2-AC5D434F1E1E@nest.sns.it> On Oct 11, 2007, at 10:43 , nazari at iasbs.ac.ir wrote: > Running the scf calculation .../root/fariba/expresso-3-2/bin/ > pw.x:symbole > lookup....... error: undefined symbol: -intel-fast-memset more likely, "_intel_fast_memset". It is a compiler library. Either you are not correctly linking the object files (you should use the same for compiling and linking), or you are using strange compiler options, or you have a bad installation of the compiler 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 ceresoli at sissa.it Thu Oct 11 16:46:42 2007 From: ceresoli at sissa.it (Davide Ceresoli) Date: Thu, 11 Oct 2007 16:46:42 +0200 Subject: [Pw_forum] Different behavior in relax tasks (Marino Vetuschi Zuccolini) In-Reply-To: <245A58C9-30A6-42E1-B47B-8D690DD8C6A9@dipteris.unige.it> References: <63981.128.101.191.226.1192057416.squirrel@www.msi.umn.edu> <245A58C9-30A6-42E1-B47B-8D690DD8C6A9@dipteris.unige.it> Message-ID: <470E3752.7060204@sissa.it> Marino Vetuschi Zuccolini wrote: > Hi Cesar, > >> Hi Marino, >> >> please, send your input file. > Hi all, yesterday I run into the same problem. It's a bug in the variable cell routines (vsinit and vcmove). Try to put movable atoms first: ATOMIC_POSITIONS crystal O 0.24410 0.24410 0.24410 Si 0.12500 0.12500 0.12500 0 0 0 Mg 0.50000 0.50000 0.50000 0 0 0 Best regards, Davide -- +----------------------------------------------------------+ Davide Ceresoli Scuola Internazionale Superiore di Studi Avanzati (SISSA) via Beirut 2-4 I-34014 Trieste, Italy Phone: +39-040-3787-448 Fax: +39-040-3787-528 Mobile: +39-347-1001570 Skype: dceresoli Homepage: http://people.sissa.it/~ceresoli +----------------------------------------------------------+ From whitley3 at llnl.gov Thu Oct 11 20:10:18 2007 From: whitley3 at llnl.gov (Heather Whitley) Date: Thu, 11 Oct 2007 11:10:18 -0700 Subject: [Pw_forum] error Message-ID: <470E670A.7020407@llnl.gov> />I don't think it does, unless you explicitly set the environment >variable LD to "ld". Could you please provide some evidence >(i.e. config.log file)? / Sure, here is the relevant line from the config.log: ac_cv_env_LDFLAGS_set= ac_cv_env_LDFLAGS_value= This doesn't show the problem, however. The problem lies in the Makefiles, where $LD is specified as the linker. If your system uses ld as the default linker, then you will end up using it in the compilation. Here's an example: pw.x : pwscf.o libpw.a $(LIBOBJS) $(LD) $(LDFLAGS) -o $@ \ pwscf.o $(MODULES) libpw.a $(LIBOBJS) $(LIBS) - ( cd ../bin; ln -fs ../PW/$@ . ) In the non-CVS version of Espresso, this Makefile has this instead: pw.x : pwscf.o libpw.a $(LIBOBJS) $(MPIF90) $(LDFLAGS) -o $@ \ pwscf.o $(MODULES) libpw.a $(LIBOBJS) $(LIBS) - ( cd ../bin; ln -fs ../PW/$@ . ) I was able to compile Espresso-3.2, but not the CVS version, and eventually found this difference with the help of computing support. I am not sure if I replied to this message in the correct way. I'm not sure how to make the messages go into the proper thread. If someone wants to privately email me that information, since it's not related to the code, I would appreciate it. Thanks! Best regards, Heather -- *********************************************** Heather D. Whitley Quantum Simulations Group Lawrence Livermore National Laboratory, L-415 Livermore, CA 94551 whitley3 at llnl.gov http://www.llnl.gov/qsg From mpayami at aeoi.org.ir Thu Oct 11 20:45:30 2007 From: mpayami at aeoi.org.ir (Mahmoud Payami Shabestari) Date: Thu, 11 Oct 2007 22:15:30 +0330 Subject: [Pw_forum] Problem arising in fc_10.0.023+mkl_9.1.023 In-Reply-To: <4281A352-D398-4A09-B290-E758945FE8F3@nest.sns.it> References: <0c0f01c80808$1f45fc60$206510ac@aeoi.org.ir> <4281A352-D398-4A09-B290-E758945FE8F3@nest.sns.it> Message-ID: Dear Paolo, Thank you very much. My question was a stupid one. Bests, mahmoud payami > pools work without any problem where properly implemented, but > in some codes, pools are not implemented. More exactly: the > parallelization over k-points (requiring partition of processors into > the so-called pools) is not implemented. All codes call the same > initialization routine that partitions processes into pools if required > to do so with the appopriate command line option (-npool 2 for > instance), but unless somebody has programmed how to partition > the tasks and how to collect the results, pools will not work by > themselves. The code "bands.x" stops if run with pools because > unpredictable behavior may result. Apparently it doesn't stop in a > gracious manner, but it manages anyway to spread the message > why it is stopping. > > 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 giannozz at nest.sns.it Thu Oct 11 22:00:30 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 11 Oct 2007 22:00:30 +0200 Subject: [Pw_forum] error In-Reply-To: <470E670A.7020407@llnl.gov> References: <470E670A.7020407@llnl.gov> Message-ID: <024229F0-D48B-4D22-9D9A-2696F4C3818E@nest.sns.it> On Oct 11, 2007, at 20:10 , Heather Whitley wrote: > Sure, here is the relevant line from the config.log: > > ac_cv_env_LDFLAGS_set= > ac_cv_env_LDFLAGS_value= it looks to me completely irrelevant... > This doesn't show the problem, however. The problem lies in the > Makefiles, where $LD is specified as the linker. If your system uses > ld as the default linker, then you will end up using it in the > compilation. I don't think so: configure should generate a make.sys that explicitly defines LD=something, typically the same as the compiler. Unless, of course, you are re-using an old make.sys 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 whitley3 at llnl.gov Thu Oct 11 23:12:41 2007 From: whitley3 at llnl.gov (Heather Whitley) Date: Thu, 11 Oct 2007 14:12:41 -0700 Subject: [Pw_forum] error Message-ID: <470E91C9.5020609@llnl.gov> On Oct 11, 2007, at 20:10 , Heather Whitley wrote: >/ Sure, here is the relevant line from the config.log: />/ />/ ac_cv_env_LDFLAGS_set= />/ ac_cv_env_LDFLAGS_value= / it looks to me completely irrelevant... Yes, it is. I realized that and sent an updated email, but it bounced and is awaiting approval due to size. It contains the entire config.log file. >I don't think so: configure should generate a make.sys that explicitly >defines LD=something, typically the same as the compiler. Unless, >of course, you are re-using an old make.sys No, I used the created make.sys. The line with the LD specification is commented out if I don't change it by hand after running configure: # Linker and linker-specific flags (if any) # Typically LD coincides with F90 or MPIF90 - not actually used # LD = mpif90 LDFLAGS = Heather -- *********************************************** Heather D. Whitley, Quantum Simulations Group Lawrence Livermore National Laboratory, L-415 Livermore, CA 94551 whitley3 at llnl.gov http://www.llnl.gov/qsg From bopengchemist at gmail.com Fri Oct 12 07:13:54 2007 From: bopengchemist at gmail.com (Bo Peng) Date: Fri, 12 Oct 2007 13:13:54 +0800 Subject: [Pw_forum] problem on k points and ecutwfc test Message-ID: <3faf0730710112213k39bd6aatcd2414ec369581d9@mail.gmail.com> Hi Dear user, I have tried to test the k-points and ecutwfc convergence for a Mg(002) slab which contains 7 layers and the middle 5 layers have been fixed. PROBLEM I: I have tested (1x1x1, 2x2x1, 4x4x1, 5x5x1, 7x7x1, 8x8x1, 10x10x1) M-P k-points grids for one input file, other parameters are the same(see below). For 2x2x1, 5x5x1 and 8x8x1, I have got "The maximum number of steps has been reached. End of BFGS Geometry Optimization" However, for others, say, (1x1x1, 4x4x1, 7x7x1, 10x10x1)I have got "bfgs converged in xx scf cycles and xx bfgs steps End of BFGS Geometry Optimization" For the latter cases, the convergences have completed successfully, but for the former cases, they seemed not finished. I wonder, if just for k-points test, whether it is worth to restart the jobs to make the optimization converged? Or, choosing new K sampling, such as (3x3x1, 6x6x1, 9x9x1, etc.)? PROBLEM II when testing ecutwfc convergence, I have chosen 10, 14, 18, 22, 26, 30 Ry as the value of the ecutwfc. It works well for ecutwfc=18, 26 and 30. When ecutwfc=14 or 22, the following errors occured: ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from bfgs : error # 1 bfgs history already reset at previous step %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... I have checked the mailing list archives, like: http://www.democritos.it/pipermail/pw_forum/2006-November/005331.html suggested that restarting the jobs to make the geometry optimization converged. However, I wonder why the optimizaition is failed for certain lower values of ecutwfc which seems would be more easily to be completed. In PROBLEM I, ecutwfc=24Ry; In PROBLEM II, K_POINTS are 5 5 1 0 0 0 the following is the input file: &CONTROL calculation = 'relax', prefix = 'Mgrelax', pseudo_dir = '/....../pseudo/', outdir = '/....../tmp/', tstress=.true. tprnfor=.true. / &SYSTEM ibrav = 14, a = 3.149307D0, b = 3.149307D0, c = 32.624496, cosab = 0.5D0, cosac = 0.D0, cosbc = 0.D0, nat = 7, ntyp = 1, ecutwfc = xx.D0, occupations = "smearing", smearing = "methfessel-paxton", degauss = 0.05D0, / &ELECTRONS / &IONS ion_dynamics='bfgs', pot_extrapolation = "second_order", wfc_extrapolation = "second_order", / ATOMIC_SPECIES Mg 24.305 Mg.pw91-np-van.UPF ATOMIC_POSITIONS {angstrom} Mg 2.099538 2.099538 0.000000 Mg 1.049769 1.049769 2.718708 0 0 0 Mg 2.099538 2.099538 5.437416 0 0 0 Mg 1.049769 1.049769 8.156124 0 0 0 Mg 2.099538 2.099538 10.874832 0 0 0 Mg 1.049769 1.049769 13.59354 0 0 0 Mg 2.099538 2.099538 16.312248 K_POINTS {automatic} nk1 nk2 nk3 0 0 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071012/56fd0019/attachment-0001.htm From bopengchemist at gmail.com Fri Oct 12 07:21:14 2007 From: bopengchemist at gmail.com (Bo Peng) Date: Fri, 12 Oct 2007 13:21:14 +0800 Subject: [Pw_forum] problem on k points and ecutwfc test Message-ID: <3faf0730710112221k337aec18kc6b1ef774875be92@mail.gmail.com> Hi there, Thank you in advance, sorry for neglecting my affiliation. Bo Peng Ph D candidate Institude of New Energy and Materials NKU Tientsin CHN, bopengchemist at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071012/553b6bdf/attachment.htm From zucco at dipteris.unige.it Fri Oct 12 08:58:13 2007 From: zucco at dipteris.unige.it (Marino Vetuschi Zuccolini) Date: Fri, 12 Oct 2007 08:58:13 +0200 Subject: [Pw_forum] Different behavior in relax tasks (Marino Vetuschi Zuccolini) In-Reply-To: <470E3752.7060204@sissa.it> References: <63981.128.101.191.226.1192057416.squirrel@www.msi.umn.edu> <245A58C9-30A6-42E1-B47B-8D690DD8C6A9@dipteris.unige.it> <470E3752.7060204@sissa.it> Message-ID: <2FB5578C-27CE-430C-AF1C-50175AC30163@dipteris.unige.it> Davide, thanks for the suggestion. Now it works. m. On 11 Oct 2007, at 16:46, Davide Ceresoli wrote: > Marino Vetuschi Zuccolini wrote: >> Hi Cesar, >> >>> Hi Marino, >>> >>> please, send your input file. >> > Hi all, > yesterday I run into the same problem. It's a bug in the > variable cell > routines (vsinit and vcmove). Try to put movable atoms first: > > ATOMIC_POSITIONS crystal > O 0.24410 0.24410 0.24410 > Si 0.12500 0.12500 0.12500 0 0 0 > Mg 0.50000 0.50000 0.50000 0 0 0 > > Best regards, > Davide > > > -- > +----------------------------------------------------------+ > Davide Ceresoli > Scuola Internazionale Superiore di Studi Avanzati (SISSA) > via Beirut 2-4 > I-34014 Trieste, Italy > Phone: +39-040-3787-448 Fax: +39-040-3787-528 > Mobile: +39-347-1001570 > Skype: dceresoli > Homepage: http://people.sissa.it/~ceresoli > +----------------------------------------------------------+ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ******************************************************* Marino Vetuschi Zuccolini zucco at dipteris.unige.it Researcher / Geochemist Laboratory of Geochemistry DIPartimento per lo studio della TErra e delle sue RISorse - Universit? di Genova Tel. ++39 010 3538136 Fax. ++39 010 352169 Corso Europa 26, 16132 - Genova - Italy From giannozz at nest.sns.it Fri Oct 12 09:58:48 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 12 Oct 2007 09:58:48 +0200 Subject: [Pw_forum] error In-Reply-To: <470E91C9.5020609@llnl.gov> References: <470E91C9.5020609@llnl.gov> Message-ID: On Oct 11, 2007, at 23:12 , Heather Whitley wrote: >> I don't think so: configure should generate a make.sys that >> explicitly >> defines LD=something, typically the same as the compiler. Unless, >> of course, you are re-using an old make.sys > > No, I used the created make.sys. The line with the LD > specification is commented out if I don't change it by hand after > running configure: > > # Linker and linker-specific flags (if any) > # Typically LD coincides with F90 or MPIF90 - not actually used > > # LD = mpif90 ok, thank you, now I see. It should have been fixed in CVS versions later than Dec. 18 2006: http://www.democritos.it:8888/O-sesame/chngview?cn=4363 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 Xiangqian.Hu at duke.edu Fri Oct 12 17:39:31 2007 From: Xiangqian.Hu at duke.edu (xqhu@duke.edu) Date: Fri, 12 Oct 2007 11:39:31 -0400 Subject: [Pw_forum] Does PWSCF have a bug when optimizing the structure in electric field References: Message-ID: <01ec01c80ce6$154146b0$4c990398@HLHXQ> Dear users, I just checked the PWSCF codes of 3.2.3. Only setlocal.f90 and v_of_rho.f90 call add_efield. If you look at the codes carefully, you will see the add_efield is called only once! Obviously, when you optimze the structure in an electric field, the etot_efield is never updated! I guess something must be wrong. Good luck! Best, Xiangqian From sassmannshausen at tugraz.at Fri Oct 12 21:19:22 2007 From: sassmannshausen at tugraz.at (=?iso-8859-15?q?J=F6rg_Sa=DFmannshausen?=) Date: Fri, 12 Oct 2007 21:19:22 +0200 Subject: [Pw_forum] Problems with example05 Message-ID: <200710122119.22641.sassmannshausen@tugraz.at> Dear all, I have downloaded the latest (espresso-3.2.3) version of espresso and I am currently trying to install it on my AMD x2 machine, running Debian Etch (64bit). I am using the Intel Fortran Compiler (build 9.1 20060925) and gcc (build 4.1.2 20061115) for the compilation, mpich2-1.0.6 (build with above compilers) and acml3.6.0 as math library. For FFTW I am using fftw3.2 (build with above compilers). Compilation is going well (after I changed the make.sys so my libraries are acutally used) and the example jobs are running ok in seriel mode. However, in parallel mode some examples are stalling. Top shows me 100% cpu, with 2 cups being used. However, I notice a rather high load of sys (around 70%sy) and only the remaing part being user (around 30%us). Following Axel Kohlmeyer's suggestion I tried: - using OpenMPI instead of MPICH (did not solve the problem, but here I get 100%us) - changing the flags to O2 -unroll -tpp6 -pc64 (problem still persists) - changing the flags to O2 -unroll -pc64 (same) I have the same problems on my Intel P4 dual Xeon machine (using icc instead of gcc, also using ATLAS and the intern lapack, as the mkl was ok during compilation, but on execution of the programs produced: "undefined symbol: __intel_cpu_indicator" and google told me that the mkl is the culprit here. Note: ldd did not show any missing libraries). As the run_example script does not really gives much insight of what is happening when the program is running, I did it sequentielly. Here is the way I started it and the output: zeus:/usr/local/src/espresso-3.2.3/examples/example05/test# /opt/mpich2-1.0.5_icc_ifc/bin/mpiexec -n 4 ../../../bin/pp.x < si.pp_rho.in Program POST-PROC v.3.2.2 starts ... Today is 12Oct2007 at 20:40: 3 Parallel version (MPI) Number of processors in use: 4 R & G space division: proc/pool = 4 Planes per process (thick) : nr3 = 20 npp = 5 ncplane = 400 Proc/ planes cols G planes cols G columns G Pool (dense grid) (smooth grid) (wavefct grid) 1 5 63 683 5 63 683 22 135 2 5 64 686 5 64 686 21 132 3 5 63 682 5 63 682 21 132 4 5 63 682 5 63 682 21 132 0 20 253 2733 20 253 2733 85 531 nbndx = 4 nbnd = 4 natomwfc = 8 npwx = 90 nelec = 8.00 nkb = 8 ngl = 61 Calling punch_plot, plot_num = 0 Writing data to file sicharge Reading header from file sicharge Reading data from file sicharge Writing data to be plotted to file si.rho.dat and here the program simply stalls. Running it with strace gives (last lines only) recv(5, " Writing data to be plotted "..., 1024, 0) = 51 write(1, " Writing data to be plotted "..., 51 Writing data to be plotted to file si.rho.dat ) = 51 select(7, [4 5 6], [], [], {1, 0}) = 0 (Timeout) select(7, [4 5 6], [], [], {1, 0}) = 0 (Timeout) So I am stuck here; 2 machines, different CPU and versions of MPI (MPICH and OpenMPI), same problem. Also, some other example jobs show the same problem: ok in serial mode, stalling in parallel mode. Has anybody a good idea? I somehow doubt that the problem is with MPICH as other programs are working and also OpenMPI produces the same problem, so I conclude it is not the underlying MPI. Any (useful) comments are apreciated. Many thanks J?rg P.S. The same happens if I am using the internal BLAS/LAPACK :-( -- ************************************************************* J?rg Sa?mannshausen Institut f?r chemische Technologie organischer Stoffe TU-Graz Stremayrgasse 16 8010 Graz Austria phone: +43 (0)316 873 8954 fax: +43 (0)316 873 4959 homepage: http://sassy.formativ.net/ From giannozz at nest.sns.it Fri Oct 12 23:16:41 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 12 Oct 2007 23:16:41 +0200 Subject: [Pw_forum] Problems with example05 In-Reply-To: <200710122119.22641.sassmannshausen@tugraz.at> References: <200710122119.22641.sassmannshausen@tugraz.at> Message-ID: <6D2C062C-3D22-4693-9CB6-DF87778B81BE@nest.sns.it> On Oct 12, 2007, at 21:19 , J?rg Sa?mannshausen wrote: > However, in parallel mode some examples are stalling not all examples work in parallel execution (they should, but your case demonstrate that they don't). The reason is that only the most important codes: scf, phonon, MD calculations, are parallelized. Smaller codes, auxiliary codes are mostly not parallelized, for obvious reasons. From http://www.quantum-espresso.org/wiki/index.php/ Running_on_parallel_machines: "Please note that all postprocessing codes not reading data ?les produced by pw.x ? that is, average.x, voronoy.x, dos.x ? the plotting codes plotrho.x, plotband.x, and all executables in pwtools/, should be executed on just one processor. Unpredictable results may follow if those codes are run on more than one processor." In reality nothing unpredictable should happen, because all nonparallel codes run serially on one processor while all others do nothing. It is however likely that there are cases, notably in the pp.x code, where something goes wrong. It is typically something really stupid, like a call to a routine that performs some hidden communications and waits for an answer from other processors that are instead idling. All such cases should have been fixed in the CVS version, I think. In any case: if the problem is limited to a few nonparallelized post-processing codes stalling in parallel execution, you can safely ignore it 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 nazari at iasbs.ac.ir Sat Oct 13 12:42:59 2007 From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir) Date: Sat, 13 Oct 2007 11:42:59 +0100 (BST) Subject: [Pw_forum] error -intel-fast-memset In-Reply-To: <195A303E-D324-4D84-BAC2-AC5D434F1E1E@nest.sns.it> References: <25692.213.176.122.3.1192092184.squirrel@mail.iasbs.ac.ir> <195A303E-D324-4D84-BAC2-AC5D434F1E1E@nest.sns.it> Message-ID: <52881.213.176.122.3.1192272179.squirrel@mail.iasbs.ac.ir> Dear Paolo, I checked LD and I ahve used the same for compiling and linking, and The compiler ia installed properly. Would you please let me know what do you mean by "using strange compiler options" becuse I just follow the User's guide. Regards Fariba Nazari IASBS > > On Oct 11, 2007, at 10:43 , nazari at iasbs.ac.ir wrote: > >> Running the scf calculation .../root/fariba/expresso-3-2/bin/ >> pw.x:symbole >> lookup....... error: undefined symbol: -intel-fast-memset > > more likely, "_intel_fast_memset". It is a compiler library. Either > you are not correctly linking the object files (you should use the > same for compiling and linking), or you are using strange compiler > options, or you have a bad installation of the compiler > > 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 giannozz at nest.sns.it Sat Oct 13 21:29:55 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Sat, 13 Oct 2007 21:29:55 +0200 Subject: [Pw_forum] error -intel-fast-memset In-Reply-To: <52881.213.176.122.3.1192272179.squirrel@mail.iasbs.ac.ir> References: <25692.213.176.122.3.1192092184.squirrel@mail.iasbs.ac.ir> <195A303E-D324-4D84-BAC2-AC5D434F1E1E@nest.sns.it> <52881.213.176.122.3.1192272179.squirrel@mail.iasbs.ac.ir> Message-ID: On Oct 13, 2007, at 12:42 , nazari at iasbs.ac.ir wrote: > I checked LD and I have used the same for compiling and linking, > and The compiler is installed properly. > > Would you please let me know what do you mean by "using strange > compiler options" becuse I just follow the User's guide. optimization for the incorrect machine type, or IPO (interprocedural optimization or whatever it means), or any of those fancy optimizations that after a week of compilation produce an executable that is 1% faster (and sometimes slower) than the executable produced using simple optimization. Try first of all to use the internal copy of FFTW : add -D__USE_INTERNAL_FFTW to DFLAGS, recompile (you actually need to recompile only clib/fft_stick.c); use the internal copy of blas and lapack: BLAS_LIBS = ../flib/blas.a LAPACK_LIBS = ../flib/lapack.a If there are still missing system libraries, there is a problem with your compiler or system libraries. If it works, replace BLAS_LIBS and LAPACK_LIBS with what is needed for mkl (no need to recompile). If there are again missing system libraries, there is a problem with mkl. Otherwise, remove -D__USE_INTERNAL_FFTW from DFLAGS, specify the fftw library in FFT_LIBS, recompile clib/fft_stick.c . If the missing libraries show up again, your fftw library is compiled in a strange way, or in any event, in a way that is incompatible with the rest 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 hashem.yamani at gmail.com Sun Oct 14 19:14:57 2007 From: hashem.yamani at gmail.com (Hashem Al-Yamani) Date: Sun, 14 Oct 2007 19:14:57 +0200 Subject: [Pw_forum] Putting band structure symbols on the x-axis Message-ID: <82a593400710141014t799e45c4jfbc5b726077e1a2e@mail.gmail.com> Dear All ; I wounder how can I put the symbols of gamma, X, R ..... on the X axis when or after plotting the band structure . Any ideas ?? Thanks alot . Best Regards ; Hashem Jordan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071014/585b1aff/attachment.htm From eyvaz_isaev at yahoo.com Mon Oct 15 00:16:07 2007 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sun, 14 Oct 2007 15:16:07 -0700 (PDT) Subject: [Pw_forum] Putting band structure symbols on the x-axis In-Reply-To: <82a593400710141014t799e45c4jfbc5b726077e1a2e@mail.gmail.com> Message-ID: <328865.19963.qm@web60315.mail.yahoo.com> Hi, --- Hashem Al-Yamani wrote: > Dear All ; > > I wounder how can I put the symbols of gamma, X, R > ..... on the X axis when > or after plotting the band structure . > > Any ideas ?? > Use a file to extract bands structure from output file I spreaded some time ago via the forum and additional gnuplot script. Of course, you can do that editing a postscipt file, but this way suggests that you are familiar with Postscript. If you can not find any of these files please let me know. Bests, Eyvaz. > Thanks alot . > > > > Best Regards ; > > Hashem > > Jordan University > > _______________________________________________ > 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, and Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com ____________________________________________________________________________________ Catch up on fall's hot new shows on Yahoo! TV. Watch previews, get listings, and more! http://tv.yahoo.com/collections/3658 From mbaris at metu.edu.tr Mon Oct 15 09:26:36 2007 From: mbaris at metu.edu.tr (mbaris at metu.edu.tr) Date: Mon, 15 Oct 2007 10:26:36 +0300 Subject: [Pw_forum] Putting band structure symbols on the x-axis In-Reply-To: <328865.19963.qm@web60315.mail.yahoo.com> References: <328865.19963.qm@web60315.mail.yahoo.com> Message-ID: <20071015102636.s1qaij8vw8cmc448@webmail2.metu.edu.tr> Hi, You can find a simple script I have written for this purpose here: http://www.obm.cc/piled/?page_id=176 this script uses the same algorithm used in plotband in deciding the turning points, but produces a gnuplot script. What you need is the -labels flag, when added the script will ask you the label of each turning point it finds. You can edit the output gnuplot batch in any way you like. Details on how to use are on the page. A recent version of tcl and gnuplot is recommended. Be advised, this script is in "works for my case, hope it works for you too??? stage. Best, O. Baris Malcioglu METU Physics Ankara Turkey Alinti Eyvaz Isaev > Hi, > --- Hashem Al-Yamani wrote: > >> Dear All ; >> >> I wounder how can I put the symbols of gamma, X, R >> ..... on the X axis when >> or after plotting the band structure . >> >> Any ideas ?? >> > > Use a file to extract bands structure from output file > I spreaded some time ago via the forum and additional > gnuplot script. Of course, you can do that editing a > postscipt file, but this way suggests that you are > familiar with Postscript. > > If you can not find any of these files please let me > know. > > Bests, > Eyvaz. > > > >> Thanks alot . >> >> >> >> Best Regards ; >> >> Hashem >> >> Jordan University >> > _______________________________________________ >> 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, and > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com > > > > ____________________________________________________________________________________ > Catch up on fall's hot new shows on Yahoo! TV. Watch previews, get > listings, and more! > http://tv.yahoo.com/collections/3658 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From helen at fh.huji.ac.il Mon Oct 15 13:47:32 2007 From: helen at fh.huji.ac.il (Helen) Date: Mon, 15 Oct 2007 13:47:32 +0200 Subject: [Pw_forum] Ge band-gap Message-ID: <001401c80f21$2c2dde00$cd604084@fh.huji.ac.il> I have tried calculating the band-gap of Ge in a similar way to example01 for Si, and obtained a direct band-gap=0.75, indirect band-gap=0.46 at a lattice constant=10.614 (optimized lattice constant, converged ecutwfc). At the experimental lattice constant the direct band-gap=0.51, indirect band-gap=0.38. In literature the band-gaps for LDA are quoted as being negative. Why am I getting positive results? Is there a problem with the pseudopotential? I noticed from the archives that in July 2004 this issue was raised, but an answer wasn't really given. Thank you very much for your help, Dr. Helen Eisenberg, Post-doctoral researcher, The Fritz Haber Center for Molecular Dynamics, The Hebrew University of Jerusalem, Jerusalem 91904 Israel INPUT: &control calculation = 'scf' restart_mode='from_scratch', prefix='ge', tstress = .true. tprnfor = .true. pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' / &system ibrav= 2, celldm(1) =10.6769, nat= 2, ntyp= 1, ecutwfc =27.0, / &electrons diagonalization=cg mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES Ge 72.59 Ge.pz_bhs.UPF ATOMIC_POSITIONS Ge 0.00 0.00 0.00 Ge 0.25 0.25 0.25 K_POINTS 10 0.1250000 0.1250000 0.1250000 1.00 0.1250000 0.1250000 0.3750000 3.00 0.1250000 0.1250000 0.6250000 3.00 0.1250000 0.1250000 0.8750000 3.00 0.1250000 0.3750000 0.3750000 3.00 0.1250000 0.3750000 0.6250000 6.00 0.1250000 0.3750000 0.8750000 6.00 0.1250000 0.6250000 0.6250000 3.00 0.3750000 0.3750000 0.3750000 1.00 0.3750000 0.3750000 0.6250000 3.00 EOF $ECHO " running the scf calculation for Si...\c" $PW_COMMAND < ge.scf.cg.in > ge.scf.cg.out $ECHO " done" # band structure calculation along delta, sigma and lambda lines cat > ge.band.cg.in << EOF &control calculation='bands' pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/', prefix='ge' / &system ibrav= 2, celldm(1) =10.6769, nat= 2, ntyp= 1, ecutwfc =27.0, nbnd = 8, / &electrons diagonalization=cg / ATOMIC_SPECIES Ge 72.59 Ge.pz_bhs.UPF ATOMIC_POSITIONS Ge 0.00 0.00 0.00 Ge 0.25 0.25 0.25 K_POINTS 6 0.0 0.0 0.0 1.0 0.1 0.1 0.1 1.0 0.2 0.2 0.2 1.0 0.3 0.3 0.3 1.0 0.4 0.4 0.4 1.0 0.5 0.5 0.5 1.0 EOF: RESULTS: k = 0.0000 0.0000 0.0000 band energies (ev): -7.1507 5.4288 5.4288 5.4288 5.9790 8.0294 8.0294 8.0294 k = 0.1000 0.1000 0.1000 band energies (ev): -7.0370 3.6667 5.2082 5.2082 6.8127 8.3334 8.3334 8.6989 k = 0.2000 0.2000 0.2000 band energies (ev): -6.7011 1.6617 4.7838 4.7838 6.5618 8.8874 8.8874 10.4632 k = 0.3000 0.3000 0.3000 band energies (ev): -6.1690 -0.1311 4.4065 4.4065 6.1730 9.1840 9.1840 12.2437 k = 0.4000 0.4000 0.4000 band energies (ev): -5.5394 -1.5375 4.1640 4.1640 5.9087 9.1822 9.1822 12.7544 k = 0.5000 0.5000 0.5000 band energies (ev): -5.1829 -2.1557 4.0814 4.0814 5.8180 9.1444 9.1444 12.6631 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071015/172e8fe4/attachment.htm From marzari at MIT.EDU Mon Oct 15 14:12:37 2007 From: marzari at MIT.EDU (Nicola Marzari) Date: Mon, 15 Oct 2007 08:12:37 -0400 Subject: [Pw_forum] Putting band structure symbols on the x-axis In-Reply-To: <20071015102636.s1qaij8vw8cmc448@webmail2.metu.edu.tr> References: <328865.19963.qm@web60315.mail.yahoo.com> <20071015102636.s1qaij8vw8cmc448@webmail2.metu.edu.tr> Message-ID: <47135935.8080708@mit.edu> Dear All, Xmgrace would also work very well, for this and a lot of 2-d plotting problems: http://plasma-gate.weizmann.ac.il/Grace/ It allows you to define symbols at specific positions on the axis, and it has greek (and other) alphabets. nicola --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From giannozz at nest.sns.it Mon Oct 15 17:54:49 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 15 Oct 2007 17:54:49 +0200 Subject: [Pw_forum] Ge band-gap In-Reply-To: <001401c80f21$2c2dde00$cd604084@fh.huji.ac.il> References: <001401c80f21$2c2dde00$cd604084@fh.huji.ac.il> Message-ID: <5E7E0DE9-BA09-4F71-8070-5C96D9204EA7@nest.sns.it> On Oct 15, 2007, at 13:47 , Helen wrote: > I have tried calculating the band-gap of Ge in a similar way to > example01 > for Si, and obtained a direct band-gap=0.75, indirect band-gap=0.46 > at a > lattice constant=10.614 (optimized lattice constant, converged > ecutwfc). > At the experimental lattice constant the direct band-gap=0.51, > indirect > band-gap=0.38. In literature the band-gaps for LDA are quoted as being > negative. the exact value of the band gap in Ge (in GaAs as well) is sensitive to everything: the lattice parameter, the pseudopotential, the spin-orbit splitting, the phase of the moon,... If I remember correctly, all- electron LDA results give zero direct gap. Then you have the PP approximation; moreover norm-conserving PPs are converted to the "separable" form by choosing a l channel ("local") and transforming the difference between the other channels and the local one into a sum of projectors. Results are very close to, but not exactly equal to, those for the original ("semilocal") form, and they depend upon the choice of the local part. So unless you have evidence that different codes yield different results for exactly the same system, I don't see any reason to doubt about your results. 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 szs_naghavi at yahoo.com Tue Oct 16 08:47:29 2007 From: szs_naghavi at yahoo.com (zahra sadat naghavi) Date: Mon, 15 Oct 2007 23:47:29 -0700 (PDT) Subject: [Pw_forum] problem with defining zigzag nanotube Message-ID: <59630.43160.qm@web63014.mail.re1.yahoo.com> hi i want to define the single zigzag nanotube to the code, but it does not recognize the symmetries i'd like(2 instead of 10). what may be the problem? ofcourse i am using the Supercell appaoach in Hexagonal Bravais Lattice. and these are the atomic positions( in Angstrom) i use: 1.1750 0.0000 0.7105 0.5875 1.0176 1.4210 -0.5875 1.0176 0.7105 -1.1750 0.0000 1.4210 -0.5875 -1.0176 0.7105 0.5875 -1.0176 1.4210 1.1750 0.0000 -0.7105 0.5875 1.0176 -1.4210 -0.5875 1.0176 -0.7105 -1.1750 0.0000 -1.4210 -0.5875 -1.0176 -0.7105 0.5875 -1.0176 -1.4210 thanx for any suggestion --------------------------------- Be a better Heartthrob. Get better relationship answers from someone who knows. Yahoo! Answers - Check it out. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071015/2a24b167/attachment.htm From wyanchao at gmail.com Tue Oct 16 12:24:19 2007 From: wyanchao at gmail.com (wang yanchao) Date: Tue, 16 Oct 2007 18:24:19 +0800 Subject: [Pw_forum] Ask question? Message-ID: <55639d30710160324k52b58dd4ie55993984438063a@mail.gmail.com> Dear users. I want to mix the pseudopotential used the virtual.x . but it can't finish.I read the code of virtual.f90 in the uptools,then I think the codes which is related with the problem is following " if (mesh(1).ne.mesh(2) ) then interpolate = .true. end if capel = 0.d0 do i=1,upf_mesh capel = capel + abs(r(i,1)-r(i,2)) + abs(rab(i,1)-rab(i,2)) end do if (capel.gt.1.d-6) then write (*,*) " pseudopotentials have different mesh " interpolate = .true. end if write (*,*) "INTERPOLATE =", interpolate if (interpolate) call errore ("virtual", & "grid interpolation is not working yet",1) " If mesh(1) isn't equal mesh(2) ,the value of interpolate is set to True. if interpolate =true, the error must happen. This seem showed that two pseudopotentials can't mix if they have different mesh grid. But the message of error which "grid interpolation is not working yet" seems indicates that a subroutine which is used to interpolate should be called before the error. So I am confused. If someone know how to deal with it , Please tell me.Thanks a lot! -- Yanchao Wang National lab of Superhard Materials,JiLin Univ.Changchun 130012,P.R.China Email:wyanchao at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071016/6dcf52cc/attachment.htm From giannozz at nest.sns.it Tue Oct 16 19:07:05 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 16 Oct 2007 19:07:05 +0200 Subject: [Pw_forum] problem with defining zigzag nanotube In-Reply-To: <59630.43160.qm@web63014.mail.re1.yahoo.com> References: <59630.43160.qm@web63014.mail.re1.yahoo.com> Message-ID: On Oct 16, 2007, at 8:47 , zahra sadat naghavi wrote: > i want to define the single zigzag nanotube to the code, but it > does not > recognize the symmetries i'd like(2 instead of 10). what may be the > problem? the problem is that you (like everybody else) didn't read the instructions... See the User Guide, http://www.quantum-espresso.org/wiki/index.php/ Main_Page chapter 8 "Troubleshooting", item 1.22 "pw.x doesn?t ?nd all the symmetries you expected" 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 Tue Oct 16 19:07:16 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 16 Oct 2007 19:07:16 +0200 Subject: [Pw_forum] Ask question? In-Reply-To: <55639d30710160324k52b58dd4ie55993984438063a@mail.gmail.com> References: <55639d30710160324k52b58dd4ie55993984438063a@mail.gmail.com> Message-ID: <29EDB1B1-2DAE-4448-A9DC-EA2A814E84E2@nest.sns.it> On Oct 16, 2007, at 12:24 , wang yanchao wrote: > I want to mix the pseudopotential used the virtual.x . you too? see the following message: http://www.democritos.it/pipermail/pw_forum/2007-September/007288.html 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 cao at qtp.ufl.edu Tue Oct 16 22:02:25 2007 From: cao at qtp.ufl.edu (Chao Cao) Date: Tue, 16 Oct 2007 16:02:25 -0400 Subject: [Pw_forum] DFT+U: about how to get U Message-ID: <471518D1.7020605@qtp.ufl.edu> Hi there, I read about M. Cococcioni's paper and thesis on how to get the U parameter, and have the following question on mind: Does the procedure of perturbing atomic occupation go through every single atom or just "hubbard" atoms? In the latter case, does the response matrix chi include elements related with hubbard atoms only ( i.e. chi(m,n) m and n are both hubbard atoms ), or it has to include everything? If it includes everything, what do we do about elements related to non-hubbard atoms (maybe set them to 0 (?))? Thanks in advance. Chao Cao -- Chao Cao Quantum Theory Project and Department of Physics University of Florida, Gainesville, FL 32611 U.S.A. From matteo at umn.edu Tue Oct 16 22:50:03 2007 From: matteo at umn.edu (Matteo Cococcioni) Date: Tue, 16 Oct 2007 15:50:03 -0500 Subject: [Pw_forum] DFT+U: about how to get U In-Reply-To: <471518D1.7020605@qtp.ufl.edu> References: <471518D1.7020605@qtp.ufl.edu> Message-ID: <503FB608-55AA-4DEB-86AF-60649E0F7642@umn.edu> Dear Chao Cao, the linear response procedure is repeated only for non-equivalent Hubbard atoms. Regards, Matteo %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Matteo Cococcioni Department of Chemical Engineering and Materials Science University of Minnesota 151 Amundson Hall 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 Fax +1 612 626 7246 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% On Oct 16, 2007, at 3:02 PM, Chao Cao wrote: > Hi there, > I read about M. Cococcioni's paper and thesis on how to get the U > parameter, and have the following question on mind: > Does the procedure of perturbing atomic occupation go through every > single atom or just "hubbard" atoms? In the latter case, does the > response matrix chi include elements related with hubbard atoms only ( > i.e. chi(m,n) m and n are both hubbard atoms ), or it has to include > everything? If it includes everything, what do we do about elements > related to non-hubbard atoms (maybe set them to 0 (?))? > > Thanks in advance. > > Chao Cao > > -- > Chao Cao > > Quantum Theory Project and Department of Physics > University of Florida, Gainesville, FL 32611 > U.S.A. > > _______________________________________________ > 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/20071016/955556bc/attachment.htm From cao at qtp.ufl.edu Wed Oct 17 05:33:47 2007 From: cao at qtp.ufl.edu (Chao Cao) Date: Tue, 16 Oct 2007 23:33:47 -0400 Subject: [Pw_forum] DFT+U: about how to get U In-Reply-To: <503FB608-55AA-4DEB-86AF-60649E0F7642@umn.edu> References: <471518D1.7020605@qtp.ufl.edu> <503FB608-55AA-4DEB-86AF-60649E0F7642@umn.edu> Message-ID: <4715829B.9010409@qtp.ufl.edu> Dear Matteo, Thanks for this fast response. I have two more questions. I am assuming that by "non-equivalent" you mean non-equivalent site instead of non-equivalent type, i.e. if I have two Fe atoms within 1 unit cell, I'll have to treat them individually, therefore they might have different U number? Also, it looks to me that this method is not restricted to d-electrons, and practically it also applies to p and f electrons, am I right? Chao Cao Matteo Cococcioni wrote: > Dear Chao Cao, > > the linear response procedure is repeated only for non-equivalent > Hubbard atoms. > > Regards, > > Matteo > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > Matteo Cococcioni > Department of Chemical Engineering and Materials Science > University of Minnesota > 151 Amundson Hall > 421 Washington Av. SE > Minneapolis, MN 55455 > Tel. +1 612 624 9056 Fax +1 612 626 7246 > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > On Oct 16, 2007, at 3:02 PM, Chao Cao wrote: > >> Hi there, >> I read about M. Cococcioni's paper and thesis on how to get the U >> parameter, and have the following question on mind: >> Does the procedure of perturbing atomic occupation go through every >> single atom or just "hubbard" atoms? In the latter case, does the >> response matrix chi include elements related with hubbard atoms only ( >> i.e. chi(m,n) m and n are both hubbard atoms ), or it has to include >> everything? If it includes everything, what do we do about elements >> related to non-hubbard atoms (maybe set them to 0 (?))? >> >> Thanks in advance. >> >> Chao Cao >> >> -- >> Chao Cao >> >> Quantum Theory Project and Department of Physics >> University of Florida, Gainesville, FL 32611 >> U.S.A. >> >> _______________________________________________ >> 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 > -- Chao Cao Quantum Theory Project and Department of Physics University of Florida, Gainesville, FL 32611 U.S.A. From naser_zd2000 at yahoo.com Wed Oct 17 14:50:34 2007 From: naser_zd2000 at yahoo.com (naser zare) Date: Wed, 17 Oct 2007 05:50:34 -0700 (PDT) Subject: [Pw_forum] Relaxation of Na(100) Message-ID: <280374.44155.qm@web32904.mail.mud.yahoo.com> Dear all Hello I am studying about relaxation of Na(100) .I use "GGA(PBE)" for XC .I have worked on that issue(relaxation) with k-point mesh equal 32??32??1 ,and Ecut range of 25 to 35Ry for wavefunction and Ecut=140Ry up to 350 Ry for charge density .I run program based on presented ranges ,and also used two smearing model(gauss and methfessel-paxton). However,forces had not been reach below 0.0001 Ry/a.u ,but approximately 0.0005 Ry/a.u . It should be stated that I reduced dt from 20.DO to 2.D0 step by step in relaxation ,but I have not reached forces below 0.0001 Ry/a.u yet. I should state that I have this difficult for slab with 7 layers and more, that number of atoms in supercell is more than 7 atoms. I should state that my main question is about reaching 0.0001 Ry/a.u and what can I do for that?, and I was wondering if you could help me. Thank you for your attention. Best regards, Nasser Zare Dehnavi __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071017/00589588/attachment.htm From degironc at sissa.it Wed Oct 17 15:05:36 2007 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 17 Oct 2007 15:05:36 +0200 Subject: [Pw_forum] Relaxation of Na(100) In-Reply-To: <280374.44155.qm@web32904.mail.mud.yahoo.com> References: <280374.44155.qm@web32904.mail.mud.yahoo.com> Message-ID: <471608A0.3040002@sissa.it> on the basis of the forces you have reached and an estimate of the first-nearest neihgbour interatomic force constant (that you can infer from Na typical phonon frequencies) could you please post an estimate of the effect that a residual force of 0.0005 Ry/a.u. makes on a) the interatomic distance b) the total energy of the system ? thanks stefano de Gironcoli - SISSA and DEMOCRITOS naser zare wrote: > Dear all > Hello > I am studying about relaxation of Na(100) .I use "GGA(PBE)" for XC .I > have worked on that issue(relaxation) with k-point mesh equal > 32??32??1 ,and Ecut range of 25 to 35Ry for wavefunction and > Ecut=140Ry up to 350 Ry for charge density .I run program based on > presented ranges ,and also used two smearing model(gauss and > methfessel-paxton). However,forces had not been reach below 0.0001 > Ry/a.u ,but approximately 0.0005 Ry/a.u . It should be stated that I > reduced dt from 20.DO to 2.D0 step by step in relaxation ,but I have > not reached forces below 0.0001 Ry/a.u yet. > I should state that I have this difficult for slab with 7 layers and > more, that number of atoms in supercell is more than 7 atoms. > I should state that my main question is about reaching 0.0001 Ry/a.u > and what can I do for that?, and I was wondering if you could help me. > Thank you for your attention. > Best regards, > Nasser Zare Dehnavi > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From matteo at umn.edu Wed Oct 17 17:29:57 2007 From: matteo at umn.edu (Matteo Cococcioni) Date: Wed, 17 Oct 2007 10:29:57 -0500 Subject: [Pw_forum] DFT+U: about how to get U In-Reply-To: <4715829B.9010409@qtp.ufl.edu> References: <471518D1.7020605@qtp.ufl.edu> <503FB608-55AA-4DEB-86AF-60649E0F7642@umn.edu> <4715829B.9010409@qtp.ufl.edu> Message-ID: <47162A75.7080508@umn.edu> Dear Chao Cao, Chao Cao wrote: > Dear Matteo, > Thanks for this fast response. I have two more questions. > I am assuming that by "non-equivalent" you mean non-equivalent site > instead of non-equivalent type, i.e. if I have two Fe atoms within 1 > unit cell, I'll have to treat them individually, therefore they might > have different U number? > > Yes, I meant non equivalent sites. two atoms of the same kind but on non-equivalent sites may have different U. > Also, it looks to me that this method is not restricted to d-electrons, > and practically it also applies to p and f electrons, am I right? > > formally it's possible to apply it to p or s electrons. however the LDA+U was designed for localized orbitals. also with extended orbitals you may need to orthogonalize them because you may have significant overlaps bewteen different atoms. no problem with f states. Matteo > Chao Cao > > Matteo Cococcioni wrote: > >> Dear Chao Cao, >> >> the linear response procedure is repeated only for non-equivalent >> Hubbard atoms. >> >> Regards, >> >> Matteo >> >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> Matteo Cococcioni >> Department of Chemical Engineering and Materials Science >> University of Minnesota >> 151 Amundson Hall >> 421 Washington Av. SE >> Minneapolis, MN 55455 >> Tel. +1 612 624 9056 Fax +1 612 626 7246 >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> >> On Oct 16, 2007, at 3:02 PM, Chao Cao wrote: >> >> >>> Hi there, >>> I read about M. Cococcioni's paper and thesis on how to get the U >>> parameter, and have the following question on mind: >>> Does the procedure of perturbing atomic occupation go through every >>> single atom or just "hubbard" atoms? In the latter case, does the >>> response matrix chi include elements related with hubbard atoms only ( >>> i.e. chi(m,n) m and n are both hubbard atoms ), or it has to include >>> everything? If it includes everything, what do we do about elements >>> related to non-hubbard atoms (maybe set them to 0 (?))? >>> >>> Thanks in advance. >>> >>> Chao Cao >>> >>> -- >>> Chao Cao >>> >>> Quantum Theory Project and Department of Physics >>> University of Florida, Gainesville, FL 32611 >>> U.S.A. >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -------------- next part -------------- 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/20071017/c0ce1562/attachment.vcf From amigliore at cmm.upenn.edu Wed Oct 17 19:00:21 2007 From: amigliore at cmm.upenn.edu (Agostino Migliore) Date: Wed, 17 Oct 2007 13:00:21 -0400 (EDT) Subject: [Pw_forum] DFT+U: about how to get U In-Reply-To: <47162A75.7080508@umn.edu> References: <471518D1.7020605@qtp.ufl.edu> <503FB608-55AA-4DEB-86AF-60649E0F7642@umn.edu> <4715829B.9010409@qtp.ufl.edu> <47162A75.7080508@umn.edu> Message-ID: <35715.130.91.67.172.1192640421.squirrel@cmm.upenn.edu> Hello I am working on electron transfer in a solvated Fe2+/Fe3+ system. The electron is (or "should be") always (i.e. for each water configuration) essentially localized on one site, but a small portion (increasing near the transition state) must be on the other site, just because of a nonzero (although small) electronic coupling between the two sites. So, I wonder if I should use two different U numbers for the two ions (e.g., that obtained for the isolated oxidized (3+) site and the one for the reduced site (2+), after check, without U, about the site that should turn out to be essentially reduced/oxidized) or if I should use an average U for both (neglecting the differences due to different water arrangements) and "leave the transferring electron to reach its state", without biasing its localization through different U's. Regards, Agostino Migliore From amigliore at cmm.upenn.edu Wed Oct 17 21:38:46 2007 From: amigliore at cmm.upenn.edu (Agostino Migliore) Date: Wed, 17 Oct 2007 15:38:46 -0400 (EDT) Subject: [Pw_forum] how to get U in DFT+Hubbard U Message-ID: <35947.130.91.67.172.1192649926.squirrel@cmm.upenn.edu> Hello I am working on electron transfer in a solvated Fe2+/Fe3+ system. The electron is (or "should be") always (i.e. for each water configuration) essentially localized on one site, but a small portion (increasing near the transition state) must be on the other site, just because of a nonzero (although small) electronic coupling between the two sites. So, I wonder and ask if I should use two different U numbers for the two ions (e.g., that obtained for the isolated oxidized (3+) site and the one for the reduced site (2+), after check, without U, about the site that should turn out to be essentially reduced/oxidized) or if I should use an average U for both (neglecting the differences due to different water arrangements) and "leave the transferring electron to reach its state", without biasing its localization through different U's. Regards, Agostino Migliore From cao at qtp.ufl.edu Wed Oct 17 21:42:13 2007 From: cao at qtp.ufl.edu (Chao Cao) Date: Wed, 17 Oct 2007 15:42:13 -0400 Subject: [Pw_forum] how to get U in DFT+Hubbard U In-Reply-To: <35947.130.91.67.172.1192649926.squirrel@cmm.upenn.edu> References: <35947.130.91.67.172.1192649926.squirrel@cmm.upenn.edu> Message-ID: <47166595.4030009@qtp.ufl.edu> Based on what Matteo told me in his reply, I would guess you should use two different values... And they are not even equivalent in my opinion... Anyway, I'm also a newbie on LDA+U, let's listen to what pro says... :) Chao Cao Agostino Migliore wrote: > Hello > > I am working on electron transfer in a solvated Fe2+/Fe3+ system. The > electron is (or "should be") always (i.e. for each water configuration) > essentially localized on one site, but a small portion (increasing near > the transition state) must be on the other site, just because of a nonzero > (although small) electronic coupling between the two sites. So, I wonder > and ask > if I should use two different U numbers for the two ions (e.g., that > obtained for the isolated oxidized (3+) site and the one for the reduced > site (2+), after check, without U, about the site that should turn out to > be essentially reduced/oxidized) or if I should use an average U for both > (neglecting the differences due to different water arrangements) and > "leave the transferring electron to reach its state", without biasing its > localization through different U's. > > Regards, > Agostino Migliore > _______________________________________________ > 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 stewart at cnf.cornell.edu Wed Oct 17 22:44:31 2007 From: stewart at cnf.cornell.edu (stewart at cnf.cornell.edu) Date: Wed, 17 Oct 2007 16:44:31 -0400 Subject: [Pw_forum] 3rd Annual CNF Fall Workshop on Nanoscience and Geology In-Reply-To: <6D2C062C-3D22-4693-9CB6-DF87778B81BE@nest.sns.it> References: <200710122119.22641.sassmannshausen@tugraz.at> <6D2C062C-3D22-4693-9CB6-DF87778B81BE@nest.sns.it> Message-ID: <20071017204431.51074.qmail@mail.spidergraphics.com> Dear Quantum Espresso users and developers, I would like to draw your attention to the 3rd Annual Cornell Nanoscale Facility Fall Workshop, "Defining the Interface between Nanoscience and Geology" to be held at Cornell University from Nov. 12-13th. This year, we will examine how nanoscale simulation tools can impact research in geology. Areas of focus include modeling high pressure materials, phonon dispersions and seismology, biomineralization, and fluid-mineral interactions. This workshop will provide morning lectures on the theory and afternoon hands-on sessions where participants work directly with the codes. The Quantum Espresso package will be covered in tutorial sessions. For more details and to register, please visit: http://www.cnf.cornell.edu/cnf_fallworkshop2007.html Thanks to the Kavli Institute for Nanoscience, we will have funding to help a limited number of graduate and post-doctoral students attend the workshop. The number of participants is limited so register early. Please do not hesitate to contact me if you have any questions. I hope you can join us! Best regards, Derek ** This workshop is made possible through funding from the Kavli Institute for Nanoscience, the National Nanotechnology Infrastructure Network (NNIN), and the National Science Foundation ** ################################ Derek Stewart, Ph. D. Scientific Computation Associate 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 From matteo at umn.edu Thu Oct 18 00:50:45 2007 From: matteo at umn.edu (Matteo Cococcioni) Date: Wed, 17 Oct 2007 17:50:45 -0500 Subject: [Pw_forum] how to get U in DFT+Hubbard U In-Reply-To: <35947.130.91.67.172.1192649926.squirrel@cmm.upenn.edu> References: <35947.130.91.67.172.1192649926.squirrel@cmm.upenn.edu> Message-ID: <471691C5.2000209@umn.edu> Dear Agostino, I will try to answer to your questions. the fact that the electron never localized is not due to a "real" electronic coupling between the two Fe (which are important at short distances of course), but mostly to self-interaction. Yes, you should use two different U ideally self-consistently computed with the water molecules relaxed in the configuration with the electron localized on the 2+ Fe. However it may turn out difficult to get this result with LDA+U only because LDA+U is not designed to cure self-interaction problems. You may need Us as large as 10 eV to get that result. It could be useful for you to read this paper: Phys. Rev. Lett. 97, 028303 (2006) Hope this will help. Matteo Agostino Migliore wrote: > Hello > > I am working on electron transfer in a solvated Fe2+/Fe3+ system. The > electron is (or "should be") always (i.e. for each water configuration) > essentially localized on one site, but a small portion (increasing near > the transition state) must be on the other site, just because of a nonzero > (although small) electronic coupling between the two sites. So, I wonder > and ask > if I should use two different U numbers for the two ions (e.g., that > obtained for the isolated oxidized (3+) site and the one for the reduced > site (2+), after check, without U, about the site that should turn out to > be essentially reduced/oxidized) or if I should use an average U for both > (neglecting the differences due to different water arrangements) and > "leave the transferring electron to reach its state", without biasing its > localization through different U's. > > Regards, > Agostino Migliore > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- A non-text attachment was scrubbed... Name: matteo.vcf Type: text/x-vcard Size: 294 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20071017/364bc49d/attachment.vcf From baroni at sissa.it Thu Oct 18 08:08:35 2007 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 18 Oct 2007 08:08:35 +0200 Subject: [Pw_forum] 3rd Annual CNF Fall Workshop on Nanoscience and Geology In-Reply-To: <20071017204431.51074.qmail@mail.spidergraphics.com> References: <200710122119.22641.sassmannshausen@tugraz.at> <6D2C062C-3D22-4693-9CB6-DF87778B81BE@nest.sns.it> <20071017204431.51074.qmail@mail.spidergraphics.com> Message-ID: <3C954185-D27B-493B-91E1-BAFEF1A9A9A1@sissa.it> Dear Derek: this is really great news. I wish I could attend! best wishes - Stefano On Oct 17, 2007, at 10:44 PM, stewart at cnf.cornell.edu wrote: > Dear Quantum Espresso users and developers, > > I would like to draw your attention to the 3rd Annual Cornell > Nanoscale > Facility Fall Workshop, "Defining the Interface between Nanoscience > and > Geology" to be held at Cornell University from Nov. 12-13th. > > This year, we will examine how nanoscale simulation tools can impact > research in geology. Areas of focus include modeling high pressure > materials, phonon dispersions and seismology, biomineralization, and > fluid-mineral interactions. This workshop will provide morning > lectures on > the theory and afternoon hands-on sessions where participants work > directly > with the codes. The Quantum Espresso package will be covered in > tutorial > sessions. > > For more details and to register, please visit: > > http://www.cnf.cornell.edu/cnf_fallworkshop2007.html > > Thanks to the Kavli Institute for Nanoscience, we will have funding > to help > a limited number of graduate and post-doctoral students attend the > workshop. > The number of participants is limited so register early. > > Please do not hesitate to contact me if you have any questions. I > hope you > can join us! > > Best regards, > > Derek > > ** This workshop is made possible through funding from the Kavli > Institute > for Nanoscience, the National Nanotechnology Infrastructure Network > (NNIN), > and the National Science Foundation ** > > > ################################ > Derek Stewart, Ph. D. > Scientific Computation Associate > 250 Duffield Hall > Cornell Nanoscale Facility (CNF) > Ithaca, NY 14853 > stewart (at) cnf.cornell.edu > (607) 255-2856 > _______________________________________________ > 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/20071018/819e4507/attachment-0001.htm From cao at qtp.ufl.edu Thu Oct 18 22:38:45 2007 From: cao at qtp.ufl.edu (Chao Cao) Date: Thu, 18 Oct 2007 16:38:45 -0400 Subject: [Pw_forum] DFT+U: about how to get U In-Reply-To: <47162A75.7080508@umn.edu> References: <471518D1.7020605@qtp.ufl.edu> <503FB608-55AA-4DEB-86AF-60649E0F7642@umn.edu> <4715829B.9010409@qtp.ufl.edu> <47162A75.7080508@umn.edu> Message-ID: <4717C455.5020503@qtp.ufl.edu> Dear Matteo, Just out of curiosity, I tried to calculate U parameter for 2p-electron of oxygen in a NiO cluster following the procedure you suggested. Before the calculation, I was guessing that the out for oxygen would be very small, however... it turned out to be ~6 eV for Ni (which I guess is still reasonable) and ~11 eV for O... So I guess either my procedure was wrong or there was something fundamentally wrong so that practically I should not try to calculate U for 2p electrons? I am really newbie in this LDA+U thing, sorry about these naive questions... And this is the input file, and for perturbation calculations I just change Hubbard_alpha value and put "diago_thr_init = 1.0d-12", "startingwfc='file' " and "startingpot='file' "s in there. Thanks a lot &control calculation = 'scf' restart_mode = 'from_scratch' prefix = 'test' outdir = './' / &system ibrav = 0, celldm(1) = 1.88972687777, nat = 8, ntyp = 2, ecutwfc = 40, ecutrho = 400 occupations = 'tetrahedra' nspin = 2, multiplicity = 9 lda_plus_u = .true., Hubbard_alpha(1) = 0.00 Hubbard_U(1) = 1.0d-20, Hubbard_U(2) = 1.0d-20, / &electrons mixing_beta = 0.2 conv_thr = 1.0d-8 / ATOMIC_SPECIES Ni 58.6934 Ni.pbe-van_bm.UPF O 15.9994 O.pbe-van_bm.UPF ATOMIC_POSITIONS alat Ni 1.044490324 1.227039735 1.098575578 Ni 1.227039735 -1.044490324 -1.098575578 Ni -1.044490324 -1.227039735 1.098575578 Ni -1.227039735 1.044490324 -1.098575578 O -0.830714207 -1.049403843 -0.960644686 O -1.049403843 0.830714207 0.960644686 O 0.830714207 1.049403843 -0.960644686 O 1.049403843 -0.830714207 0.960644686 K_POINTS automatic 1,1,1,0,0,0 CELL_PARAMETERS 14.000000000 0.000000000 0.000000000 0.000000000 14.000000000 0.000000000 0.000000000 0.000000000 14.000000000 Chao Cao Matteo Cococcioni wrote: > > Dear Chao Cao, > > Chao Cao wrote: >> Dear Matteo, >> Thanks for this fast response. I have two more questions. >> I am assuming that by "non-equivalent" you mean non-equivalent site >> instead of non-equivalent type, i.e. if I have two Fe atoms within 1 >> unit cell, I'll have to treat them individually, therefore they might >> have different U number? >> >> > > Yes, I meant non equivalent sites. two atoms of the same kind but on > non-equivalent sites may have different U. > >> Also, it looks to me that this method is not restricted to d-electrons, >> and practically it also applies to p and f electrons, am I right? >> >> > > formally it's possible to apply it to p or s electrons. however the > LDA+U was designed for localized orbitals. > also with extended orbitals you may need to orthogonalize them because > you may have significant overlaps bewteen different atoms. > no problem with f states. > > Matteo > >> Chao Cao >> >> Matteo Cococcioni wrote: >> >>> Dear Chao Cao, >>> >>> the linear response procedure is repeated only for non-equivalent >>> Hubbard atoms. >>> >>> Regards, >>> >>> Matteo >>> >>> >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> Matteo Cococcioni >>> Department of Chemical Engineering and Materials Science >>> University of Minnesota >>> 151 Amundson Hall >>> 421 Washington Av. SE >>> Minneapolis, MN 55455 >>> Tel. +1 612 624 9056 Fax +1 612 626 7246 >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> >>> >>> On Oct 16, 2007, at 3:02 PM, Chao Cao wrote: >>> >>> >>>> Hi there, >>>> I read about M. Cococcioni's paper and thesis on how to get the U >>>> parameter, and have the following question on mind: >>>> Does the procedure of perturbing atomic occupation go through every >>>> single atom or just "hubbard" atoms? In the latter case, does the >>>> response matrix chi include elements related with hubbard atoms only ( >>>> i.e. chi(m,n) m and n are both hubbard atoms ), or it has to include >>>> everything? If it includes everything, what do we do about elements >>>> related to non-hubbard atoms (maybe set them to 0 (?))? >>>> >>>> Thanks in advance. >>>> >>>> Chao Cao >>>> >>>> -- >>>> Chao Cao >>>> >>>> Quantum Theory Project and Department of Physics >>>> University of Florida, Gainesville, FL 32611 >>>> U.S.A. >>>> >>>> _______________________________________________ >>>> Pw_forum mailing list >>>> Pw_forum at pwscf.org >>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>> >>> ------------------------------------------------------------------------ >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >> >> >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Chao Cao Quantum Theory Project and Department of Physics University of Florida, Gainesville, FL 32611 U.S.A. From sohrab.ismail-beigi at yale.edu Fri Oct 19 05:01:35 2007 From: sohrab.ismail-beigi at yale.edu (Sohrab Ismail-Beigi) Date: Thu, 18 Oct 2007 23:01:35 -0400 Subject: [Pw_forum] Problems with Polarization calculations Message-ID: Dear PWSCF forum, I've been having a problem running PWSCF for the Berry phase calculations of polarization for elements with f (l=3) and higher pseudopotentials (i.e. any lanthanides, etc.) My system is an oxide that has La in it, and my pseudopotential is norm conserving and has lmax=3. Here is the error that the program produces upon entering the Berry phase code (bp_c_phase.f90): %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from ylm_q : error # 181312304 not programmed for L> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% OK, that is a bit cryptic. The error is coming from the "ylm_q" subroutine inside the file "bp_ylm_q.f". The ylm_q subroutine just calculates (real) spherical harmonics and has code for doing so up to l=4 (impressive actually). ylm_q exists with the error above if one tries to calculate higher angular momenta than l=4. The routine is given an integer index which it decodes into (l,m): e.g. index=1 means l=0; index=4 -> l=1; index = 9 -> l=2, etc. It is coded up to index=25. Now, the problem is cause by ylm_q being called on being called on line 400 of bp_c_phase.f90: CALL ylm_q(lmaxq*lmaxq,dk,dkmod,ylm_dk) It is being asked to compute the angular momentum ylm for a very large index lmaxq*lmaxq. lmaxq itself is set when reading the pseudopotential in "allocate_nlpot.f90" where it is set to "lmaxq = 2*lmaxkb+1". For lmaxkb=2 (i.e. up to angular momentum l=2), lmaxq=5 so lmaxq*lmaxq=25 and ylm_q just manages to work. But for any atom with f projectors, lmax=3 -> lmaxq=7, and lmaxq*lmaxq=49 which causes the error and failure. My questions are two-fold: (1) First, this is clearly an unintentional bug of some sort. Apparently no elements with f projectors (e.g. transition metals) were ever used for Berry phase...!??! Personally, I don't understand the "lmaxq*lmaxq" bit at all in this code; it is mysterious. In fact, as far as I can see, the output from ylm_q is being sent to "qvan3" which only needs something like lmaxq entries rather lmaxq*lmaxq.... But it is hard to be sure without more comments. (2) On a more global and physics-related point, there are segments of the code in bp_c_phase.f90 (in particular the ylm_q calls and related quantities) that don't seem to make sense for norm conserving pseudopotentials. Namely, the Berry phase calculation for standard orthonormal wavefunctions (from norm-conserving psps) only depends on the inner product of Bloch states and neighboring k-points: one shouldn't be needing any angular momentum operators at all! The ylm_q and related codes, from what I can gather from the code, seem to be designed to add a contribution to the electronic part of the Berry phase that has the form of some type of non-local atomic pseudopotential, which makes me think this is appropriate for ultra- soft psps where norm-conservation has been relaxed so one has to have some non-local projectors in the augmentation region to fix this up when calculating Berry phases. Therefore, does the bp_c_phase.f90 code implicitly assume ultra-soft psps? Any help you can provide is great --- as it is, there is no way to proceed forward unless one finds the real representations of Ylm up to some very high l!!! Thanks, --Sohrab --------------------------------------------- Sohrab Ismail-Beigi Associate Professor of Applied Physics and Physics Dept. of Applied Physics Yale University P.O. Box 208284 New Haven, CT 06520 Phone: 203.432.2107 Fax: 203.432.4283 Email: sohrab.ismail-beigi at yale.edu http://volga.eng.yale.edu/ - group home page http://www.eng.yale.edu/aphy/ - dept. page w/ links http://www.eng.yale.edu/graduate -- info about graduate studies in AP and brochures From shrek_826 at yahoo.com.cn Fri Oct 19 05:17:27 2007 From: shrek_826 at yahoo.com.cn (Fan Yang) Date: Fri, 19 Oct 2007 11:17:27 +0800 (CST) Subject: [Pw_forum] error information Message-ID: <523656.98285.qm@web15311.mail.cnb.yahoo.com> Dear users, I have encountered a simple question about using this programme, and the error information is as follows: =============================== from data_structure: error # too many sticks =============================== and I don't know what is the reason. Can anyone help me,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 ====================================== --------------------------------- ?????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071019/7d30b013/attachment.htm From akohlmey at cmm.chem.upenn.edu Fri Oct 19 07:58:24 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 19 Oct 2007 01:58:24 -0400 (EDT) Subject: [Pw_forum] error information In-Reply-To: <523656.98285.qm@web15311.mail.cnb.yahoo.com> References: <523656.98285.qm@web15311.mail.cnb.yahoo.com> Message-ID: On Fri, 19 Oct 2007, Fan Yang wrote: FY> Dear users, FY> I have encountered a simple question about using this FY> programme, and the error information is as follows: FY> =============================== FY> FY> from data_structure: error # FY> FY> too many sticks FY> FY> =============================== FY> and I don't know what is the reason. this is most likely due an error in your input file. FY> Can anyone help me,thanks in advance! first you have to help people to help you. please read and follow the advice of point 4. at: http://www.quantum-espresso.org/wiki/index.php/Developer_Manual#How_to_Contribute_to_Quantum-ESPRESSO cheers, axel. FY> FY> FY> FY> ====================================== FY> Fan Yang FY> PH.D Candidate in Electrochemistry FY> College of Chemistry and Molecular Science FY> Wuhan University,430072,Hubei Province,China FY> E-mail:shrek_826 at yahoo.com.cn FY> ====================================== FY> FY> FY> --------------------------------- FY> ???????????????????? -- ======================================================================= 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 Fri Oct 19 10:24:18 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 19 Oct 2007 10:24:18 +0200 Subject: [Pw_forum] Problems with Polarization calculations In-Reply-To: References: Message-ID: <2575FD3A-927C-4AB6-A22B-A38485BE1F3B@nest.sns.it> On Oct 19, 2007, at 5:01 , Sohrab Ismail-Beigi wrote: > from ylm_q : error # 181312304 > not programmed for L> > OK, that is a bit cryptic. it depends for whom :-) It means that spherical harmonics for N > M, M=what is printed, are not programmed. Actually Nmax =(Lmax+1)**2 because spherical harmonics are calculated and stored with a combined index (l,m), running from 1 to (Lmax+1)**2 . This is done consistently everywhere, even if sometimes it is not reflected in the name of variables (for instance, "lmax" in PW/bp_ylm_q.f is misleading). Spherical harmonics used in the Berry phase calculation are implemented only up to L=4 (i.e. projectors up to l=2): see PW/bp_ylm_q.f, unlike those used in the rest of the code (see flib/ylmr2.f90) that work for any L. It shouldn't be difficult to use the same spherical harmonics everywhere, though. The message would have been less cryptic if N was a sensible number (like 49=(2*3+1)**2...) instead of a funny number. The likely reason is that something is going out of bounds BEFORE the check in ylm_q is performed. This is obviously a bug. You can verify this by compiling with bound check enabled (-g -C on most compilers, -g -fbounds-check on gfortran). > Apparently no elements with f projectors (e.g. transition metals) > were ever used for Berry phase...!??! apparently not. I would try to avoid f projectors in transition metals: they are a mess even without them. > Therefore, does the bp_c_phase.f90 code implicitly assume ultra-soft > psps? coming from David Vanderbilt's group, I guess so! Norm-conserving pseudopotentials in the separable form are a special case of ultrasoft pseudopotentials, so if it works for the latter, it works for the former as well. 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 oulihui666 at 126.com Fri Oct 19 15:20:24 2007 From: oulihui666 at 126.com (oulihui666) Date: Fri, 19 Oct 2007 21:20:24 +0800 (CST) Subject: [Pw_forum] How to calculate the properties of pt Bulk and the pt(111) surface Message-ID: <5080304.558351192800024339.JavaMail.coremail@bj126app81.126.com> Dear pwscf users: Because of the need of research, I tried to calculate the properties of pt Bulk and the pt(111) surface containing 20 pt atoms with pwscf, however,when calculating, error information was found, it displayed:======================================================= "from data_structure: error # 1 too many sticks"======================================================= I am really newbie in this thing, sorry about these naive questions...And this is the input file: Thanks a lot &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , outdir = '/home/olh/tmp/' , wfcdir = '/home/olh/work/' , pseudo_dir = '/home/olh/pseudo/' , prefix = 'Pt(111)_20' , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 0, A = 5.549 , B = 5.549 , C = 21.062 , cosAB = -0.5 , cosAC = 0 , cosBC = 0 , nat = 20, ntyp = 1, ecutwfc = 40 , ecutrho = 160 , occupations = 'smearing' , degauss = 0.02 , smearing = 'gaussian' , nr1 = 1 , nr2 = 1 , nr3 = 1 , / &ELECTRONS conv_thr = 1.0D-8 , mixing_beta = 0.7D0 , diagonalization = 'david' , / CELL_PARAMETERS cubic 10.486467456 0.000000000 0.000000000 -5.243233728 9.081547213 0.000000000 0.000000000 0.000000000 39.801219799 ATOMIC_SPECIES Pt 195.09000 Pt.pz-rrkjus.linux.UPF ATOMIC_POSITIONS angstrom Pt -0.000000000 0.000000000 -9.062000000 0 0 0 Pt -0.000000000 2.775000000 -9.062000000 0 0 0 Pt 2.403000000 -1.387000000 -9.062000000 0 0 0 Pt 2.403000000 1.387000000 -9.062000000 0 0 0 Pt -0.000000000 -0.000000000 -2.265000000 0 0 0 Pt -0.000000000 2.775000000 -2.265000000 0 0 0 Pt 2.403000000 -1.387000000 -2.265000000 0 0 0 Pt 2.403000000 1.387000000 -2.265000000 0 0 0 Pt 1.602000000 0.000000000 -4.531000000 0 0 0 Pt 1.602000000 2.775000000 -4.531000000 0 0 0 Pt 4.005000000 -1.387000000 -4.531000000 0 0 0 Pt 4.005000000 1.387000000 -4.531000000 0 0 0 Pt 0.801000000 1.387000000 -6.796000000 1 1 1 Pt 0.801000000 4.162000000 -6.796000000 1 1 1 Pt 3.204000000 0.000000000 -6.796000000 1 1 1 Pt 3.204000000 2.775000000 -6.796000000 1 1 1 Pt 0.801000000 1.387000000 -0.000000000 1 1 1 Pt 0.801000000 4.162000000 -0.000000000 1 1 1 Pt 3.204000000 -0.000000000 -0.000000000 1 1 1 Pt 3.204000000 2.775000000 -0.000000000 1 1 1 K_POINTS automatic 2 2 2 1 1 1 Lihui Ou -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071019/43dada79/attachment.htm From nedward at MIT.EDU Fri Oct 19 16:30:08 2007 From: nedward at MIT.EDU (Nicholas E. Singh-Miller) Date: Fri, 19 Oct 2007 10:30:08 -0400 (EDT) Subject: [Pw_forum] How to calculate the properties of pt Bulk and the pt(111) surface In-Reply-To: <5080304.558351192800024339.JavaMail.coremail@bj126app81.126.com> References: <5080304.558351192800024339.JavaMail.coremail@bj126app81.126.com> Message-ID: Hi Lihui, Glacing at your input file, one issue is imeadiately apparent. nr1, nr2, nr3 are set to one, when they should probably be bigger (or not set at all and allowed to be determined by ecutrho). From the the doc INPUT_PW nr1,nr2,nr3 INTEGER three-dimensional FFT mesh (hard grid) for charge density (and scf potential). If not specified the grid is calculated based on the cutoff for charge density (see also "ecutrho") this doc can be found in ~/espresso-3.2.3/Doc/ hope that helps. Nick On Fri, 19 Oct 2007, oulihui666 wrote: > Dear pwscf users: Because of the need of research, I tried to calculate the properties of pt Bulk and the pt(111) surface containing 20 pt atoms with pwscf, however,when calculating, error information was found, it displayed:======================================================= "from data_structure: error # 1 too many sticks"======================================================= I am really newbie in this thing, sorry about these naive questions...And this is the input file: Thanks a lot > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > outdir = '/home/olh/tmp/' , > wfcdir = '/home/olh/work/' , > pseudo_dir = '/home/olh/pseudo/' , > prefix = 'Pt(111)_20' , > tstress = .true. , > tprnfor = .true. , > / > &SYSTEM > ibrav = 0, > A = 5.549 , > B = 5.549 , > C = 21.062 , > cosAB = -0.5 , > cosAC = 0 , > cosBC = 0 , > nat = 20, > ntyp = 1, > ecutwfc = 40 , > ecutrho = 160 , > occupations = 'smearing' , > degauss = 0.02 , > smearing = 'gaussian' , > nr1 = 1 , > nr2 = 1 , > nr3 = 1 , > / > &ELECTRONS > conv_thr = 1.0D-8 , > mixing_beta = 0.7D0 , > diagonalization = 'david' , > / > CELL_PARAMETERS cubic > 10.486467456 0.000000000 0.000000000 > -5.243233728 9.081547213 0.000000000 > 0.000000000 0.000000000 39.801219799 > ATOMIC_SPECIES > Pt 195.09000 Pt.pz-rrkjus.linux.UPF > ATOMIC_POSITIONS angstrom > Pt -0.000000000 0.000000000 -9.062000000 0 0 0 > Pt -0.000000000 2.775000000 -9.062000000 0 0 0 > Pt 2.403000000 -1.387000000 -9.062000000 0 0 0 > Pt 2.403000000 1.387000000 -9.062000000 0 0 0 > Pt -0.000000000 -0.000000000 -2.265000000 0 0 0 > Pt -0.000000000 2.775000000 -2.265000000 0 0 0 > Pt 2.403000000 -1.387000000 -2.265000000 0 0 0 > Pt 2.403000000 1.387000000 -2.265000000 0 0 0 > Pt 1.602000000 0.000000000 -4.531000000 0 0 0 > Pt 1.602000000 2.775000000 -4.531000000 0 0 0 > Pt 4.005000000 -1.387000000 -4.531000000 0 0 0 > Pt 4.005000000 1.387000000 -4.531000000 0 0 0 > Pt 0.801000000 1.387000000 -6.796000000 1 1 1 > Pt 0.801000000 4.162000000 -6.796000000 1 1 1 > Pt 3.204000000 0.000000000 -6.796000000 1 1 1 > Pt 3.204000000 2.775000000 -6.796000000 1 1 1 > Pt 0.801000000 1.387000000 -0.000000000 1 1 1 > Pt 0.801000000 4.162000000 -0.000000000 1 1 1 > Pt 3.204000000 -0.000000000 -0.000000000 1 1 1 > Pt 3.204000000 2.775000000 -0.000000000 1 1 1 > K_POINTS automatic > 2 2 2 1 1 1 > Lihui Ou ***************************************** Nicholas E. Singh-Miller Ph.D. Candidate Prof. Marzari Group (quasiamore.mit.edu) Materials Science and Engineering Massachusetts Institute of Technology 13-4066 (617)324-0372 ***************************************** From nazari at iasbs.ac.ir Sat Oct 20 18:59:15 2007 From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir) Date: Sat, 20 Oct 2007 17:59:15 +0100 (BST) Subject: [Pw_forum] g95/cfft3d Message-ID: <23731.213.176.122.3.1192899555.squirrel@mail.iasbs.ac.ir> Dear Paolo, Thank you the error "-intel-fast-memset" was solved with your prevouis comment. Now there exist another error for run_example: "from cfft3d, error# no scalar fft driver specified, I have run the example in two different machine one with ifort 9.0 compiler and the other one has g95.In user guide it is mentioned that the error is related to ifort 9.0 compiler but I have checked two different compiler. Would you please let me know is there any solution. Regards Fariba Nazari IASBS > > On Oct 11, 2007, at 10:43 , nazari at iasbs.ac.ir wrote: > >> Running the scf calculation .../root/fariba/expresso-3-2/bin/ >> pw.x:symbole >> lookup....... error: undefined symbol: -intel-fast-memset > > more likely, "_intel_fast_memset". It is a compiler library. Either > you are not correctly linking the object files (you should use the > same for compiling and linking), or you are using strange compiler > options, or you have a bad installation of the compiler > > 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 sassmannshausen at tugraz.at Sun Oct 21 13:26:28 2007 From: sassmannshausen at tugraz.at (=?iso-8859-1?q?J=F6rg_Sa=DFmannshausen?=) Date: Sun, 21 Oct 2007 13:26:28 +0200 Subject: [Pw_forum] g95/cfft3d In-Reply-To: References: Message-ID: <200710211326.29014.sassmannshausen@tugraz.at> Dear Fariba, I have used the intel 9.1.039 compiler and I did not have that problem (on AMDx2, running Debian Etch). Maybe updating to it might solve it? As for your previous error (-intel-fast-memset), I have noticed that there is a difference in the order in /etc/ld.so.conf: If I move the line for the mkl _after_ the lines for the intel compiler, the libguide from the compiler will be used instead of the libguide for the mkl. Reversing the order (i.e. mkl line before intel lines) everything is ok. Alternatively, use static linking which make the binaries more portable as well. My to cents to the problem. Best wishes J?rg > ?Dear Paolo, > ?Thank you the ?error "-intel-fast-memset" was solved with ?your ?prevouis > ?comment. > ?Now there exist another error for ?run_example: "from cfft3d, error# > ?no scalar fft driver specified, I have run the example in two different > ?machine one with ?ifort 9.0 compiler and the other one has g95.In user > guide it is mentioned that the error is related to ifort 9.0 compiler but > I have checked two different compiler. Would you please let me know is > there any solution. > ?Regards > ?Fariba Nazari > ?IASBS > > > > > > ?> > > > On Oct 11, 2007, at 10:43 , nazari at iasbs.ac.ir wrote: > >> ?Running the scf calculation .../root/fariba/expresso-3-2/bin/ > >> pw.x:symbole > >> lookup....... ? error: undefined symbol: -intel-fast-memset > > > > more likely, "_intel_fast_memset". It is a compiler library. Either > > you are not correctly linking the object files (you should use the > > same for compiling and linking), or you are using strange compiler > > options, or you have a bad installation of the compiler > > > > Paolo > > --- > > Paolo Giannozzi, Dept of Physics, University of Udine > > via delle Scienze 208, 33100 Udine, Italy > > Phone +39-0432-558216, fax +39-0432-558222 -- ************************************************************* J?rg Sa?mannshausen Institut f?r chemische Technologie organischer Stoffe TU-Graz Stremayrgasse 16 8010 Graz Austria phone: +43 (0)316 873 8954 fax: +43 (0)316 873 4959 homepage: http://sassy.formativ.net/ From yuhailin_79 at msn.com Mon Oct 22 04:23:30 2007 From: yuhailin_79 at msn.com (hailin yu) Date: Mon, 22 Oct 2007 10:23:30 +0800 Subject: [Pw_forum] Help! phonon calculation at G point. Message-ID: From: yuhailin_79 at msn.comTo: pw_users at pwscf.orgSubject: Help! phonon calculation at G point.Date: Wed, 17 Oct 2007 11:08:51 +0800 Dear all: I have some trouble with phonon calculation at G point. Recently, I have calculated two kinds of PtC, rosksalt structure and zinc-blende structure. Firstly, I have fully relaxed the lattice constants and atomic positions using quantum-espressso3.2.3. The results we attained is well agreement with these results using by VASP and CASTEP. Following, I calculate the phonon frequency at G point of the two structures. For zinc-blende structure, we attained the phonon frequency as follows: q = ( 0.000000000 0.000000000 0.000000000 ) ************************************************************************** omega( 1) = 1.086480 [THz] = 36.241319 [cm-1] ( 0.340996 0.000000 0.272050 0.000000 -0.549845 0.000000 ) ( 0.346068 0.000000 0.276096 0.000000 -0.558022 0.000000 ) omega( 2) = 1.086480 [THz] = 36.241319 [cm-1] ( -0.191604 0.000000 -0.550378 0.000000 -0.391141 0.000000 ) ( -0.194454 0.000000 -0.558563 0.000000 -0.396958 0.000000 ) omega( 3) = 1.086480 [THz] = 36.241319 [cm-1] ( 0.582777 0.000000 -0.340135 0.000000 0.193129 0.000000 ) ( 0.591444 0.000000 -0.345194 0.000000 0.196001 0.000000 ) omega( 4) = 16.225674 [THz] = 541.233828 [cm-1] ( -0.026894 0.000000 0.048005 0.000000 0.029340 0.000000 ) ( 0.430439 0.000000 -0.768321 0.000000 -0.469592 0.000000 ) omega( 5) = 16.225674 [THz] = 541.233828 [cm-1] ( -0.036407 0.000000 0.009944 0.000000 -0.049641 0.000000 ) ( 0.582692 0.000000 -0.159157 0.000000 0.794513 0.000000 ) omega( 6) = 16.225674 [THz] = 541.233828 [cm-1] ( 0.042894 0.000000 0.038539 0.000000 -0.023738 0.000000 ) ( -0.686516 0.000000 -0.616817 0.000000 0.379926 0.000000 ) **************************************************************************I don't know why omega(1), omega(2) and omega(3) are not equal to zero? while the optic modes is well agreement with the results attained by VASP. I want to know how to improve the accuracy. Can you tell me? Thanks a lot! For roskslt structure, we attained the phonon frequency as follows: q = ( 0.000000000 0.000000000 0.000000000 ) ************************************************************************** omega( 1) = -16.323420 [THz] = -544.494287 [cm-1] ( 0.057067 0.000000 0.023583 0.000000 0.002155 0.000000 ) ( -0.921868 0.000000 -0.380961 0.000000 -0.034805 0.000000 ) omega( 2) = -16.323420 [THz] = -544.494287 [cm-1] ( -0.015312 0.000000 0.032457 0.000000 0.050295 0.000000 ) ( 0.247345 0.000000 -0.524309 0.000000 -0.812467 0.000000 ) omega( 3) = -16.323420 [THz] = -544.494287 [cm-1] ( 0.018065 0.000000 -0.046988 0.000000 0.035822 0.000000 ) ( -0.291827 0.000000 0.759046 0.000000 -0.578678 0.000000 ) omega( 4) = 0.284260 [THz] = 9.481955 [cm-1] ( 0.369808 0.000000 -0.578558 0.000000 0.160509 0.000000 ) ( 0.371847 0.000000 -0.581748 0.000000 0.161394 0.000000 ) omega( 5) = 0.284260 [THz] = 9.481955 [cm-1] ( 0.598650 0.000000 0.340881 0.000000 -0.150560 0.000000 ) ( 0.601951 0.000000 0.342761 0.000000 -0.151390 0.000000 ) omega( 6) = 0.284260 [THz] = 9.481955 [cm-1] ( -0.045937 0.000000 -0.215223 0.000000 -0.669940 0.000000 ) ( -0.046191 0.000000 -0.216410 0.000000 -0.673634 0.000000 ) **************************************************************************Why the phonon frequency is negative? As a test, I have caculated the elastic constants of this structure and find it satisfy formula:C44>0, C11>|C12|,C11+2C12>0. So we don't know what was wrong. Can you tell me? Thanks!The input file as shown in the follow:RS.scf.in: &control calculation='scf' restart_mode='from_scratch' tstress = .true. tprnfor = .true. prefix='RS' etot_conv_thr=1.0D-5 forc_conv_thr=1.0D-4 pseudo_dir = '/home/yhl/espresso-3.0/pseudo/' outdir='/home/yhl/tmp/' / &system ibrav= 2, celldm(1) =8.98, nat= 2, ntyp= 2 ecutwfc =100.0 ecutrho =500.0 degauss =0.02 smearing='mp' occupations ='smearing' / &electrons conv_thr = 1.0d-12 mixing_beta = 0.7 /ATOMIC_SPECIES Pt 195.08 Pt.pbe-nd-rrkjus.UPF C 12.01 C.pbe-rrkjus.UPFATOMIC_POSITIONS Pt 0.00 0.00 0.00 C 0.5 0.5 0.5K_POINTS AUTOMATIC 12 12 12 1 1 1RS.ph.in phonon of PtC&inputph tr2_ph=1.0d-14, prefix='RS', ldisp=.true., nq1=4,nq2=4,nq3=4 amass(1)=195.08, amass(2)=12.01, outdir='/home/yhl/tmp/', fildyn='RS.dyn', / Discover the new Windows Vista Learn more! _________________________________________________________________ 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/20071022/4d6d7a47/attachment.htm From baroni at sissa.it Mon Oct 22 08:51:18 2007 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 22 Oct 2007 08:51:18 +0200 Subject: [Pw_forum] Help! phonon calculation at G point. In-Reply-To: References: Message-ID: Dear Hailin Yu: didn?t you know that Quantum Espresso comes with a users' guide? Well, it is probably not as good as one can expect, and as we would like it to be, but it does contain the answer to ypur questions. See: http://www.pwscf.org/guide/3.1.1/other/users-guide-3.1.1.pdf The above link was found by googling the following keywords: "negative frequencies " site:pwscf.org This being said, the first calculation seems to be just affected by accuracy issues (that are briefly discussed in the users' guide referenced above). The second calculation, instead, seems to signal an instability of the optical modes 9such as a ferroelectric instability) that is not necessarily related to any elastic instability. Hope this helps Stefano On Oct 22, 2007, at 4:23 AM, hailin yu wrote: > > > From: yuhailin_79 at msn.com > To: pw_users at pwscf.org > Subject: Help! phonon calculation at G point. > Date: Wed, 17 Oct 2007 11:08:51 +0800 > > Dear all: > > I have some trouble with phonon calculation at G point. > Recently, I have calculated two kinds of PtC, rosksalt structure > and zinc-blende structure. Firstly, I have fully relaxed the > lattice constants and atomic positions using quantum- > espressso3.2.3. The results we attained is well agreement with > these results using by VASP and CASTEP. Following, I calculate the > phonon frequency at G point of the two structures. > For zinc-blende structure, we attained the phonon frequency as > follows: > q = ( 0.000000000 0.000000000 0.000000000 ) > > ********************************************************************** > **** > omega( 1) = 1.086480 [THz] = 36.241319 [cm-1] > ( 0.340996 0.000000 0.272050 0.000000 -0.549845 0.000000 ) > ;( 0.346068 0.000000 0.276096 0.000000 -0.558022 0.000000 ) > omega( 2) = 1.086480 [THz] = 36.241319 [cm-1] > ( -0.191604 0.000000 -0.550378 0.000000 -0.391141 0.000000 ) > ( -0.194454 0.000000 -0.558563 0.000000 -0.396958 0.000000 ) > omega( 3) = 1.086480 [THz] = 36.241319 [cm-1] > ( 0.582777 0.000000 -0.340135 0.000000 0.193129 0.000000 ) > ( 0.591444 0.000000 -0.345194 0.000000 0.196001 0.000000 ) > omega( 4) = 16.225674 [THz] = 541.233828 [cm-1] > ( -0.026894 0.000000 0.048005 0.000000 0.029340 0.000000 ) > ( 0. 430439 0.000000 -0.768321 0.000000 -0.469592 0.000000 ) > omega( 5) = 16.225674 [THz] = 541.233828 [cm-1] > ( -0.036407 0.000000 0.009944 0.000000 -0.049641 0.000000 ) > ( 0.582692 0.000000 -0.159157 0.000000 0.794513 0.000000 ) > omega( 6) = 16.225674 [THz] = 541.233828 [cm-1] > ( 0.042894 0.000000 0.038539 0.000000 -0.023738 0.000000 ) > ( -0.686516 0.000000 -0.616817 0.000000 0.379926 0.000000 ) > > ********************************************************************** > **** > I don't know why omega(1), omega(2) and omega(3) are not equal to > zero? while the optic modes is well agreement with the results > attained by VASP. I want to know how to improve the accuracy. Can > you tell me? Thanks a lot! > > For roskslt structure, we attained the phonon frequency as follows: > > q = ( 0.000000000 0.000000000 0.000000000 ) > > ********************************************************************** > **** > omega( 1) = -16.323420 [THz] = -544.494287 [cm-1] > ( 0.057067 0.000000 0.023583 0.000000 0.002155 0.000000 ) > ( -0.921868 0.000000 -0.380961 0.000000 -0.034805 0.000000 ) > omega( 2) = -16.323420 [THz] = -544.494287 [cm-1] > ( -0.015312 0.000000 0.032457 0.000000 0.050295 0.000000 ) > ( 0.247345 0.000000 -0.524309 0.000000 -0.812467 0.000000 ) > omega( 3) =&nbs p; -16.323420 [THz] = -544.494287 [cm-1] > ( 0.018065 0.000000 -0.046988 0.000000 0.035822 0.000000 ) > ( -0.291827 0.000000 0.759046 0.000000 -0.578678 0.000000 ) > omega( 4) = 0.284260 [THz] = 9.481955 [cm-1] > ( 0.369808 0.000000 -0.578558 0.000000 0.160509 0.000000 ) > ( 0.371847 0.000000 -0.581748 0.000000 0.161394 0.000000 ) > omega( 5) = 0.284260 [THz] = 9.481955 [cm-1] > ( 0.598650 0.000000 0.340881 0.000000 -0.150560 0.000000 ) > ( 0.601951 0.000000 0.342761 0.000000 -0.151390 0.000000 ) > omega( 6) = 0.284260 [THz] = 9.481955 [cm-1] > ( -0.045937 0.000000 -0.215223 0.000000 -0.669940 0.000000 ) > ( -0.046191 0.000000 -0.216410 0.000000 -0.673634 0.000000 ) > > ********************************************************************** > **** > Why the phonon frequency is negative? As a test, I have caculated > the elastic constants of this structure and find it satisfy formula: > C44>0, C11>|C12|,C11+2C12>0. So we don't know what was wrong. Can > you tell me? Thanks! > The input file as shown in the follow: > RS.scf.in: > > &control > calculation='scf' > restart_mode='from_scratch' > tstress = .true. > tprnfor = .true. > prefix='RS' > etot_conv_thr=1.0D-5 > forc_conv_thr=1.0D-4 > & nbsp; pseudo_dir = '/home/yhl/espresso-3.0/pseudo/' > outdir='/home/yhl/tmp/' > / > &system > ibrav= 2, celldm(1) =8.98, nat= 2, ntyp= 2 > ecutwfc =100.0 > ecutrho =500.0 > degauss =0.02 > smearing='mp' > occupations ='smearing' > / > &electrons > conv_thr = 1.0d-12 > mixing_beta = 0.7 > / > ATOMIC_SPECIES > Pt 195.08 Pt.pbe-nd-rrkjus.UPF > C 12.01 C.pbe-rrkjus.UPF > ATOMIC_POSITIONS > Pt 0.00 0.00 0.00 > C 0.5 0.5 0.5 > K_POINTS AUTOMATIC > 12 12 12 1 1 1 > > RS.ph.in > > phonon of PtC > &inputph > tr2_ph=1.0d-14, > prefix='RS', > ldisp=.true., > nq1=4,nq2=4,nq3=4 > amass(1)=195.08, > amass(2)=12.01, > outdir='/home/yhl/tmp/', > fildyn='RS.dyn', > / > > > Discover the new Windows Vista Learn more! > > Discover the new Windows Vista Learn more! > _______________________________________________ > 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/20071022/d13babe1/attachment-0001.htm From giannozz at nest.sns.it Mon Oct 22 09:12:34 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 22 Oct 2007 09:12:34 +0200 Subject: [Pw_forum] g95/cfft3d In-Reply-To: <23731.213.176.122.3.1192899555.squirrel@mail.iasbs.ac.ir> References: <23731.213.176.122.3.1192899555.squirrel@mail.iasbs.ac.ir> Message-ID: <15E14A3B-623F-4A7B-B5BA-83147BE46D27@nest.sns.it> On Oct 20, 2007, at 18:59 , nazari at iasbs.ac.ir wrote: > "from cfft3d, error# no scalar fft driver specified" [...] In user > guide it is mentioned that the error is related to ifort 9.0 compiler it is > but I have checked two different compiler. you should re-run "./configure" and then "make clean" before changing compiler 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 sunshoutian168 at yahoo.com.cn Mon Oct 22 09:08:56 2007 From: sunshoutian168 at yahoo.com.cn (shoutian sun) Date: Mon, 22 Oct 2007 15:08:56 +0800 (CST) Subject: [Pw_forum] q2r.x to calculate force constant,erors hapenned Message-ID: <319990.30466.qm@web92002.mail.cnb.yahoo.com> The results of your email command are provided below. Attached is your original message. - Results: Ignoring non-text/plain MIME parts - Unprocessed: I set kpoints automatic 5 5 8 in self consistent calculation,(pw.x) and set np nq1=2, nq2=2, nq3=4 in the input file of ph.x when i use q2r.x to calculate force constant,erors hapenned. Could anyone of you tell me why? Thank you so much. --------------------------------- ?????????? - Done --------------------------------- ?????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071022/5ba45c98/attachment.htm From eyvaz_isaev at yahoo.com Mon Oct 22 09:32:43 2007 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 22 Oct 2007 00:32:43 -0700 (PDT) Subject: [Pw_forum] q2r.x to calculate force constant,erors hapenned In-Reply-To: <319990.30466.qm@web92002.mail.cnb.yahoo.com> Message-ID: <818596.49185.qm@web60320.mail.yahoo.com> Dear Shoutian, First of all please provide your affiliation. And then nobody can help you unless you provide more information about an error message you have got. Bests, Eyvaz. --- shoutian sun wrote: > The results of your email command are provided > below. Attached is your > original message. > > - Results: > Ignoring non-text/plain MIME parts > > - Unprocessed: > I set kpoints automatic 5 5 8 in self > consistent > calculation,(pw.x) > and set np nq1=2, nq2=2, nq3=4 in the input > file of ph.x > when i use q2r.x to calculate force > constant,erors hapenned. > Could anyone of you tell me why? > Thank you so much. > --------------------------------- > ???????????????????? > > - Done > > > > --------------------------------- > ???????????????????? > _______________________________________________ > 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, and Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From chaohao.mse at gmail.com Mon Oct 22 10:10:19 2007 From: chaohao.mse at gmail.com (Chaohao Hu) Date: Mon, 22 Oct 2007 10:10:19 +0200 Subject: [Pw_forum] how to setup the dt flag in vc-relax calculations Message-ID: <6502ee650710220110y2e891e44ve29566c041c73137@mail.gmail.com> Dear Pwscf users, I want to perform a vc-relax calculation for a low-symmetry structure (P-1), but the calculation is not always convergenced. Maybe this structure is far away from its equilibrium. From the help files I know the time step flag "dt" is a important parameter for variable cell relaxing calculation. In the manual, it is said the good values of "dt" is 50/70 or 100/150, but the default value in INPUT_PW file is 20.0D0. How to understand them? Here, a part of input file is attached. The initial atomic position is determined by performing "relax" calculation. &CONTROL calculation = "vc-relax" , restart_mode = 'from_scratch' , outdir='~/tmp/' , pseudo_dir = '~/espresso32/pseudo' , disk_io = 'default' , verbosity = 'default' , tstress = .true. , tprnfor = .true. , nstep = 55 , etot_conv_thr = 1.0E-5 , forc_conv_thr = 1.0D-4 , dt = 50 , / &SYSTEM ibrav = 0, celldm(1) = 12.2409, nosym = .true., nat = 30, ntyp = 3, ecutwfc = 25.D0, ecutrho = 150.D0, / &ELECTRONS electron_maxstep = 500, conv_thr = 1.D-7, mixing_beta = 0.7D0, diagonalization = 'david' , / &IONS / &CELL cell_dynamics = 'damp-w', press = 0.00, wmass = 0.007, / ... ... K_POINTS automatic 5 5 5 1 1 1 -- ============================ C.H. Hu Postdoctoral fellow Chimie et Physico-Chimie appliquees Institut Francais du Petrole (IFP) Rueil-Malmaison, France E_mail: chaohao.mse at gmail.com ============================ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071022/44f9a8c1/attachment.htm From wangjunjie1981_0 at 163.com Mon Oct 22 12:51:36 2007 From: wangjunjie1981_0 at 163.com (wangjunjie1981_0) Date: Mon, 22 Oct 2007 18:51:36 +0800 (CST) Subject: [Pw_forum] how to determine mass of mixing pseudopotential by virtual.x Message-ID: <1027070235.1012091193050296360.JavaMail.coremail@bj163app104.163.com> Dear all Recently, i generate mixing pseudopotential by virtual.x, and i intend to test it. But i do not know how to determine the mass of virtual-atom pseudopotential. Thank you for your advance. Best regards. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071022/319ad00c/attachment.htm From baroni at sissa.it Mon Oct 22 12:55:49 2007 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 22 Oct 2007 12:55:49 +0200 Subject: [Pw_forum] how to determine mass of mixing pseudopotential by virtual.x In-Reply-To: <1027070235.1012091193050296360.JavaMail.coremail@bj163app104.163.com> References: <1027070235.1012091193050296360.JavaMail.coremail@bj163app104.163.com> Message-ID: <3F477A28-7273-4C46-BB77-8799ECE9D422@sissa.it> The atomic mass is only used for calculating phonon frequencies, for which the VCA may or may not be a good approximation. If you do not calculate phonon frequencies, you can input whatever value you want. SB PS: please, if possible, sign your posts and also add your affiliation - thanks On Oct 22, 2007, at 12:51 PM, wangjunjie1981_0 wrote: > > Dear all > > Recently, i generate mixing pseudopotential by virtual.x, and i > intend to test it. But i do not know how to determine the mass of > virtual-atom pseudopotential. > Thank you for your advance. > > Best regards. > > > > > ???????????????? > ?????????????? > _______________________________________________ > 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/20071022/d63507d4/attachment.htm From oulihui666 at 126.com Mon Oct 22 14:51:47 2007 From: oulihui666 at 126.com (oulihui666) Date: Mon, 22 Oct 2007 20:51:47 +0800 (CST) Subject: [Pw_forum] How to calculate the properties of free OH Message-ID: <14449068.355251193057507364.JavaMail.coremail@bj126app52.126.com> Dear pwscf users: Because of the need of research, I tried to calculate the properties of free OH with pwscf, however,when calculating, error information was found, it displayed: ============================================== from electrons : error # 1 charge is wrong ============================================== I am really newbie in this thing, sorry about these naive questions... Can you please suggest some solutions? And this is the input file: Thanks a lot best regards Lihui Ou &CONTROL calculation = 'relax' , restart_mode = 'from_scratch' , outdir = '/home/olh/tmp/' , pseudo_dir = '/home/olh/pseudo/' , prefix = 'OH' , forc_conv_thr = 1.0D-4 , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 14, A = 10.000 , B = 10.000 , C = 10.000 , cosAB = 0 , cosAC = 0 , cosBC = 0 , nat = 2, ntyp = 2, ecutwfc = 60 , ecutrho = 240 , / &ELECTRONS conv_thr = 1.D-7 , mixing_beta = 0.7D0 , / &IONS ion_dynamics = 'bfgs' , pot_extrapolation = 'second_order' , wfc_extrapolation = 'second_order' , / ATOMIC_SPECIES O 16.00000 O.pz-rrkjus.UPF H 1.00000 Cu.pz-d-rrkjus.UPF ATOMIC_POSITIONS angstrom O 5.000000000 5.000000000 5.000000000 H 5.000000000 5.000000000 6.000000000 K_POINTS automatic 3 3 1 1 1 1 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071022/27f0a849/attachment-0001.htm From paulatto at sissa.it Mon Oct 22 15:29:54 2007 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 22 Oct 2007 15:29:54 +0200 (CEST) Subject: [Pw_forum] How to calculate the properties of free OH In-Reply-To: <14449068.355251193057507364.JavaMail.coremail@bj126app52.126.com> References: <14449068.355251193057507364.JavaMail.coremail@bj126app52.126.com> Message-ID: <19066.147.122.5.202.1193059794.squirrel@webmail.sissa.it> On Mon, October 22, 2007 14:51, oulihui666 wrote: > H 1.00000 Cu.pz-d-rrkjus.UPF Are you sure that using a Copper pseudopotential for Hydrogen is a good idea ;-). And please, specify your name and affiliation! Goodbye -- Lorenzo Paulatto +39 040 3787 312 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From stewart at cnf.cornell.edu Mon Oct 22 15:30:25 2007 From: stewart at cnf.cornell.edu (stewart at cnf.cornell.edu) Date: Mon, 22 Oct 2007 09:30:25 -0400 Subject: [Pw_forum] How to calculate the properties of free OH In-Reply-To: <14449068.355251193057507364.JavaMail.coremail@bj126app52.126.com> References: <14449068.355251193057507364.JavaMail.coremail@bj126app52.126.com> Message-ID: <20071022133025.36977.qmail@mail.spidergraphics.com> Dear Lihui Ou, From the input file, you are calling the copper pseudopotential, Cu.pz-d-rrkjus.UPF, for your hydrogen atom. Switch this to a hydrogen pseudopotential and this should fix the problem. Also, please include your affiliation in future emails to the pwscf forum. Best regards, Derek oulihui666 writes: > > Dear pwscf users: > Because of the need of research, I tried to calculate the properties of free OH with pwscf, however,when calculating, error information was found, it displayed: > ============================================== > from electrons : error # 1 > charge is wrong > ============================================== > I am really newbie in this thing, sorry about these naive questions... > Can you please suggest some solutions? > And this is the input file: > Thanks a lot > best regards > Lihui Ou > > &CONTROL > calculation = 'relax' , > restart_mode = 'from_scratch' , > outdir = '/home/olh/tmp/' , > pseudo_dir = '/home/olh/pseudo/' , > prefix = 'OH' , > forc_conv_thr = 1.0D-4 , > tstress = .true. , > tprnfor = .true. , > / > &SYSTEM > ibrav = 14, > A = 10.000 , > B = 10.000 , > C = 10.000 , > cosAB = 0 , > cosAC = 0 , > cosBC = 0 , > nat = 2, > ntyp = 2, > ecutwfc = 60 , > ecutrho = 240 , > / > &ELECTRONS > conv_thr = 1.D-7 , > mixing_beta = 0.7D0 , > / > &IONS > ion_dynamics = 'bfgs' , > pot_extrapolation = 'second_order' , > wfc_extrapolation = 'second_order' , > / > ATOMIC_SPECIES > O 16.00000 O.pz-rrkjus.UPF > H 1.00000 Cu.pz-d-rrkjus.UPF > ATOMIC_POSITIONS angstrom > O 5.000000000 5.000000000 5.000000000 > H 5.000000000 5.000000000 6.000000000 > K_POINTS automatic > 3 3 1 1 1 1 > ################################ Derek Stewart, Ph. D. Scientific Computation Associate 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 From marcel at physik.tu-berlin.de Mon Oct 22 15:32:22 2007 From: marcel at physik.tu-berlin.de (Marcel Mohr) Date: Mon, 22 Oct 2007 15:32:22 +0200 (CEST) Subject: [Pw_forum] How to calculate the properties of free OH In-Reply-To: <14449068.355251193057507364.JavaMail.coremail@bj126app52.126.com> References: <14449068.355251193057507364.JavaMail.coremail@bj126app52.126.com> Message-ID: <20071022153051.T43881@rosa.physik-pool.tu-berlin.de> Hi, I think this is easy: From marzari at MIT.EDU Mon Oct 22 15:38:32 2007 From: marzari at MIT.EDU (Nicola Marzari) Date: Mon, 22 Oct 2007 09:38:32 -0400 Subject: [Pw_forum] How to calculate the properties of free OH In-Reply-To: <20071022153051.T43881@rosa.physik-pool.tu-berlin.de> References: <14449068.355251193057507364.JavaMail.coremail@bj126app52.126.com> <20071022153051.T43881@rosa.physik-pool.tu-berlin.de> Message-ID: <471CA7D8.7050907@mit.edu> One more comment - if you study an isolated molecule, you do not need to use k-point sampling - the bands are perfectly flat for a supercell that is large enough, and using just one k-points will suffice. If anything, you can use Gamma, and if you use the Gamma code exploit explicitly the fact that at Gamma the wavefunctions can be chosen as real (speeding up your calculation, decreasing your memory. Very relevant if you are doing molecular calculations in large systems). Did anyone mention adding the affiliation :-) ? nicola -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From chaohao.mse at gmail.com Mon Oct 22 15:56:16 2007 From: chaohao.mse at gmail.com (Chaohao Hu) Date: Mon, 22 Oct 2007 15:56:16 +0200 Subject: [Pw_forum] how to consider the "dt" flag during vc-relax calculations Message-ID: <6502ee650710220656o5c8ac9b4s29eda137dc8d5686@mail.gmail.com> Dear Pwscf users, I want to perform a vc-relax calculation for a low-symmetry structure (P-1), but the calculation is not always convergenced. Maybe this structure is far away from its equilibrium. From the help files I know the time step flag "dt" is a important parameter for variable cell relaxing calculation. In the manual, it is said the good values of "dt" is 50/70 or 100/150, but the default value in INPUT_PW file is 20.0D0. How to understand them? Here, a part of my input file is attached. The initial atomic position is determined by performing "relax" calculation. &CONTROL calculation = "vc-relax" , restart_mode = 'from_scratch' , outdir='~/tmp/' , pseudo_dir = '~/espresso32/pseudo' , disk_io = 'default' , verbosity = 'default' , tstress = .true. , tprnfor = .true. , nstep = 55 , etot_conv_thr = 1.0E-5 , forc_conv_thr = 1.0D-4 , dt = 50 , / &SYSTEM ibrav = 0, celldm(1) = 12.2409, nosym = .true., nat = 30, ntyp = 3, ecutwfc = 25.D0, ecutrho = 150.D0, / &ELECTRONS electron_maxstep = 500, conv_thr = 1.D-7, mixing_beta = 0.7D0, diagonalization = 'david' , / &IONS / &CELL cell_dynamics = 'damp-w', press = 0.00, wmass = 0.007, / ... ... K_POINTS automatic 5 5 5 1 1 1 Best regards, C. H. Hu -- ============================ C.H. Hu Postdoctoral fellow Chimie et Physico-Chimie appliquees Institut Francais du Petrole (IFP) Rueil-Malmaison, France E_mail: chaohao.mse at gmail.com ============================ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071022/e9b4550a/attachment.htm From chaohao.mse at gmail.com Mon Oct 22 16:08:37 2007 From: chaohao.mse at gmail.com (Chaohao Hu) Date: Mon, 22 Oct 2007 16:08:37 +0200 Subject: [Pw_forum] how to consider the "dt" flag during vc-relax calculations In-Reply-To: <6502ee650710220656o5c8ac9b4s29eda137dc8d5686@mail.gmail.com> References: <6502ee650710220656o5c8ac9b4s29eda137dc8d5686@mail.gmail.com> Message-ID: <6502ee650710220708gb4d71aftb8dedd39ab37a46e@mail.gmail.com> I am very sorry for sending this mail again. But I am still awaiting your response. Regards, C. H. Hu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071022/82d63c6f/attachment.htm From ding at sissa.it Mon Oct 22 16:23:50 2007 From: ding at sissa.it (Xunlei Ding) Date: Mon, 22 Oct 2007 16:23:50 +0200 Subject: [Pw_forum] How to calculate the properties of free OH In-Reply-To: <14449068.355251193057507364.JavaMail.coremail@bj126app52.126.com> References: <14449068.355251193057507364.JavaMail.coremail@bj126app52.126.com> Message-ID: <471CB276.7060900@sissa.it> Dear Ou, I think you need to use nspin=2 for HO calculation, because it has 7 electrons. So I think you need to add these in &SYSTEM section: nspin = 2, starting_magnetization(1)=0.1, occupations='fixed', nelup=4, neldw=3, nelec=7 And as others have said, you need also decide: 1. whether to use pseudo of Cu for H 2. Use Gamma kpoint instead of what you used now. Best wishes, Ding oulihui666 wrote: > Dear pwscf users: > > Because of the need of research, I tried to calculate the properties > of free OH with pwscf, however,when calculating, error information was > found, it displayed: > > ============================================== > > * **from electrons : error # 1* > > * charge is wrong* > > ============================================== > > I am really newbie in this thing, sorry about these naive questions... > > Can you please suggest some solutions? > > And this is the input file: > > Thanks a lot > > best regards > > Lihui Ou > > &CONTROL > > calculation = 'relax' , > > restart_mode = 'from_scratch' , > > outdir = '/home/olh/tmp/' , > > pseudo_dir = '/home/olh/pseudo/' , > > prefix = 'OH' , > > forc_conv_thr = 1.0D-4 , > > tstress = .true. , > > tprnfor = .true. , > > / > > &SYSTEM > > ibrav = 14, > > A = 10.000 , > > B = 10.000 , > > C = 10.000 , > > cosAB = 0 , > > cosAC = 0 , > > cosBC = 0 , > > nat = 2, > > ntyp = 2, > > ecutwfc = 60 , > > ecutrho = 240 , > > / > > &ELECTRONS > > conv_thr = 1.D-7 , > > mixing_beta = 0.7D0 , > > / > > &IONS > > ion_dynamics = 'bfgs' , > > pot_extrapolation = 'second_order' , > > wfc_extrapolation = 'second_order' , > > / > > ATOMIC_SPECIES > > O 16.00000 O.pz-rrkjus.UPF > > H 1.00000 Cu.pz-d-rrkjus.UPF > > ATOMIC_POSITIONS angstrom > > O 5.000000000 5.000000000 5.000000000 > > H 5.000000000 5.000000000 6.000000000 > > K_POINTS automatic > > 3 3 1 1 1 1 > > > > ------------------------------------------------------------------------ > ???? Yeah.net ?? ?? ?? ?? ?? ?? ?????? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? > ?? ?? ?? >> > <%20http://event.mail.163.com/chanel/click.htm?from=NO_16&domain=126> > >------------------------------------------------------------------------ > >_______________________________________________ >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 Oct 22 17:23:54 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 22 Oct 2007 11:23:54 -0400 (EDT) Subject: [Pw_forum] how to consider the "dt" flag during vc-relax calculations In-Reply-To: <6502ee650710220708gb4d71aftb8dedd39ab37a46e@mail.gmail.com> References: <6502ee650710220656o5c8ac9b4s29eda137dc8d5686@mail.gmail.com> <6502ee650710220708gb4d71aftb8dedd39ab37a46e@mail.gmail.com> Message-ID: On Mon, 22 Oct 2007, Chaohao Hu wrote: CHH> I am very sorry for sending this mail again. But I am still CHH> awaiting your response. ...and you think that by not even waiting a single day for a response and reposting, you will increase your chances of getting a (useful) reply? hmmmmm... please keep in mind that people responding to questions do this voluntarily and are not getting paid for it (as you didn't have to pay for the code), so nobody is obliged to answer, even more so in a timely fashion. if you don't get an answer to a question right away, can have a lot of reasons. for example: - nobody knows an answer. - nobody understood your question. - nobody feels like answering your question. - a person that would answer is in a different time zone, e.g. 7-8 hours behind you. - a person that would answer feels that you should search the mailing list archive fist. - a person that would answer does not have the time to do it right now. - ... the best chance for you would be to have a closer look at the mailing list archives (there have been a lot of questions about vc-relax) and see if you can find something applicable to you. IIRC, the main reason for non-convergence are too tight convergence criteria on the forces. cheers, axel. CHH> Regards, CHH> C. H. Hu CHH> -- ======================================================================= 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 eyvaz_isaev at yahoo.com Mon Oct 22 19:17:32 2007 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 22 Oct 2007 10:17:32 -0700 (PDT) Subject: [Pw_forum] How to calculate the properties of free OH In-Reply-To: <14449068.355251193057507364.JavaMail.coremail@bj126app52.126.com> Message-ID: <371415.11218.qm@web60313.mail.yahoo.com> Dear newbie, First of all, again, please specify your affiliation. There was lots of good suggestions, as example, change to H potential if you are going to study OH. In fact, the main reason for such a kind messages (errors) is that your system is a metallic, but you did not specify "occupations" keyword and related ones ("degauss", and "smearing" if you choose occupations='smearing', and nothing if you specify occupations='tetrahedra'). As you did not specify "occupations" your system is considered as a semiconducting (insulating) one. As a consequence, you lost some amount of electrons. Besides, please read carefully output file. There is excellent comment of pw.x: from setup : info # -1 the system is metallic, specify occupations This info is sufficient to understand why you received the error message and what you should do. Bests, Eyvaz. --- oulihui666 wrote: > > Dear pwscf users: > Because of the need of research, I tried to > calculate the properties of free OH with pwscf, > however,when calculating, error information was > found, it displayed: > ============================================== > > from electrons : error # > 1 > charge is wrong > ============================================== > I am really newbie in this thing, sorry about these > naive questions... > Can you please suggest some solutions? > And this is the input file: > Thanks a lot > best regards > Lihui Ou > > &CONTROL > calculation = 'relax' , > restart_mode = 'from_scratch' , > outdir = '/home/olh/tmp/' , > pseudo_dir = '/home/olh/pseudo/' , > prefix = 'OH' , > forc_conv_thr = 1.0D-4 , > tstress = .true. , > tprnfor = .true. , > / > &SYSTEM > ibrav = 14, > A = 10.000 , > B = 10.000 , > C = 10.000 , > cosAB = 0 , > cosAC = 0 , > cosBC = 0 , > nat = 2, > ntyp = 2, > ecutwfc = 60 , > ecutrho = 240 , > / > &ELECTRONS > conv_thr = 1.D-7 , > mixing_beta = 0.7D0 , > / > &IONS > ion_dynamics = 'bfgs' , > pot_extrapolation = 'second_order' , > wfc_extrapolation = 'second_order' , > / > ATOMIC_SPECIES > O 16.00000 O.pz-rrkjus.UPF > H 1.00000 Cu.pz-d-rrkjus.UPF > ATOMIC_POSITIONS angstrom > O 5.000000000 5.000000000 5.000000000 > H 5.000000000 5.000000000 6.000000000 > K_POINTS automatic > 3 3 1 1 1 1 > > _______________________________________________ > 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, and Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From cesards at msi.umn.edu Tue Oct 23 00:21:26 2007 From: cesards at msi.umn.edu (Cesar R.S. da Silva) Date: Mon, 22 Oct 2007 17:21:26 -0500 (CDT) Subject: [Pw_forum] how to consider the "dt" flag during vc-relax In-Reply-To: References: Message-ID: <58593.128.101.191.226.1193091686.squirrel@www.msi.umn.edu> Dear Chao, Your dt setting should work OK. wmass could be reduced to somthing like 0.002, provided atomic masses are all set to the average mass (amu), but your value is not that bad. The only thing I think could produce convergence problems is your conv_thr. Try conv_thr = 1e-9. Variable cell requires precise stress calculation, and a more stringent convergence criteria for the SCF cycle is required. Cesar. > ------------------------------ > > Message: 5 > Date: Mon, 22 Oct 2007 15:56:16 +0200 > From: "Chaohao Hu" > Subject: [Pw_forum] how to consider the "dt" flag during vc-relax > calculations > To: "PWSCF Forum" > Message-ID: > <6502ee650710220656o5c8ac9b4s29eda137dc8d5686 at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Pwscf users, > > I want to perform a vc-relax calculation for a low-symmetry structure > (P-1), > but the calculation is not always convergenced. Maybe this structure is > far > away from its equilibrium. From the help files I know the time step flag > "dt" is a important parameter for variable cell relaxing calculation. In > the manual, it is said the good values of "dt" is 50/70 or 100/150, but > the > default value in INPUT_PW file is 20.0D0. How to understand them? Here, a > part of my input file is attached. The initial atomic position is > determined > by performing "relax" calculation. > > &CONTROL > calculation = "vc-relax" , > restart_mode = 'from_scratch' , > outdir='~/tmp/' , > pseudo_dir = '~/espresso32/pseudo' , > disk_io = 'default' , > verbosity = 'default' , > tstress = .true. , > tprnfor = .true. , > nstep = 55 , > etot_conv_thr = 1.0E-5 , > forc_conv_thr = 1.0D-4 , > dt = 50 , > / > &SYSTEM > ibrav = 0, > celldm(1) = 12.2409, > nosym = .true., > nat = 30, > ntyp = 3, > ecutwfc = 25.D0, > ecutrho = 150.D0, > / > &ELECTRONS > electron_maxstep = 500, > conv_thr = 1.D-7, > mixing_beta = 0.7D0, > diagonalization = 'david' , > / > &IONS > / > &CELL > cell_dynamics = 'damp-w', > press = 0.00, > wmass = 0.007, > / > ... > ... > K_POINTS automatic > 5 5 5 1 1 1 > > Best regards, > C. H. Hu > > -- > ============================ > C.H. Hu > Postdoctoral fellow > Chimie et Physico-Chimie appliquees > Institut Francais du Petrole (IFP) > Rueil-Malmaison, France > E_mail: chaohao.mse at gmail.com > ============================ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20071022/e9b4550a/attachment-0001.htm > > ------------------------------ > > Message: 6 > Date: Mon, 22 Oct 2007 16:08:37 +0200 > From: "Chaohao Hu" > Subject: Re: [Pw_forum] how to consider the "dt" flag during vc-relax > calculations > To: "PWSCF Forum" > Message-ID: > <6502ee650710220708gb4d71aftb8dedd39ab37a46e at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > I am very sorry for sending this mail again. But I am still awaiting your > response. > > Regards, > C. H. Hu > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20071022/82d63c6f/attachment-0001.htm > > ------------------------------ > > Message: 7 > Date: Mon, 22 Oct 2007 16:23:50 +0200 > From: Xunlei Ding > Subject: Re: [Pw_forum] How to calculate the properties of free OH > To: PWSCF Forum > Message-ID: <471CB276.7060900 at sissa.it> > Content-Type: text/plain; charset=x-gbk; format=flowed > > Dear Ou, > > I think you need to use nspin=2 for HO calculation, because it has 7 > electrons. > So I think you need to add these in &SYSTEM section: > nspin = 2, starting_magnetization(1)=0.1, > occupations='fixed', > nelup=4, neldw=3, nelec=7 > > And as others have said, you need also decide: > 1. whether to use pseudo of Cu for H > 2. Use Gamma kpoint instead of what you used now. > > Best wishes, > Ding > > oulihui666 wrote: > >> Dear pwscf users: >> >> Because of the need of research, I tried to calculate the properties >> of free OH with pwscf, however,when calculating, error information was >> found, it displayed: >> >> ============================================== >> >> * **from electrons : error # 1* >> >> * charge is wrong* >> >> ============================================== >> >> I am really newbie in this thing, sorry about these naive questions... >> >> Can you please suggest some solutions? >> >> And this is the input file: >> >> Thanks a lot >> >> best regards >> >> Lihui Ou >> >> &CONTROL >> >> calculation = 'relax' , >> >> restart_mode = 'from_scratch' , >> >> outdir = '/home/olh/tmp/' , >> >> pseudo_dir = '/home/olh/pseudo/' , >> >> prefix = 'OH' , >> >> forc_conv_thr = 1.0D-4 , >> >> tstress = .true. , >> >> tprnfor = .true. , >> >> / >> >> &SYSTEM >> >> ibrav = 14, >> >> A = 10.000 , >> >> B = 10.000 , >> >> C = 10.000 , >> >> cosAB = 0 , >> >> cosAC = 0 , >> >> cosBC = 0 , >> >> nat = 2, >> >> ntyp = 2, >> >> ecutwfc = 60 , >> >> ecutrho = 240 , >> >> / >> >> &ELECTRONS >> >> conv_thr = 1.D-7 , >> >> mixing_beta = 0.7D0 , >> >> / >> >> &IONS >> >> ion_dynamics = 'bfgs' , >> >> pot_extrapolation = 'second_order' , >> >> wfc_extrapolation = 'second_order' , >> >> / >> >> ATOMIC_SPECIES >> >> O 16.00000 O.pz-rrkjus.UPF >> >> H 1.00000 Cu.pz-d-rrkjus.UPF >> >> ATOMIC_POSITIONS angstrom >> >> O 5.000000000 5.000000000 5.000000000 >> >> H 5.000000000 5.000000000 6.000000000 >> >> K_POINTS automatic >> >> 3 3 1 1 1 1 >> >> >> >> ------------------------------------------------------------------------ >> ???? Yeah.net ?? ?? ?? ?? ?? ?? ?????? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? >> ?? ?? ?? >> >> <%20http://event.mail.163.com/chanel/click.htm?from=NO_16&domain=126> >> >>------------------------------------------------------------------------ >> >>_______________________________________________ >>Pw_forum mailing list >>Pw_forum at pwscf.org >>http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > ------------------------------ > > Message: 8 > Date: Mon, 22 Oct 2007 11:23:54 -0400 (EDT) > From: Axel Kohlmeyer > Subject: Re: [Pw_forum] how to consider the "dt" flag during vc-relax > calculations > To: Chaohao Hu > Cc: PWSCF Forum > Message-ID: > Content-Type: TEXT/PLAIN; charset=US-ASCII > > On Mon, 22 Oct 2007, Chaohao Hu wrote: > > CHH> I am very sorry for sending this mail again. But I am still > CHH> awaiting your response. > > ...and you think that by not even waiting a single day for > a response and reposting, you will increase your chances of > getting a (useful) reply? hmmmmm... > > please keep in mind that people responding to questions do > this voluntarily and are not getting paid for it (as you > didn't have to pay for the code), so nobody is obliged to > answer, even more so in a timely fashion. > > if you don't get an answer to a question right away, > can have a lot of reasons. for example: > - nobody knows an answer. > - nobody understood your question. > - nobody feels like answering your question. > - a person that would answer is in a different time zone, > e.g. 7-8 hours behind you. > - a person that would answer feels that you should search > the mailing list archive fist. > - a person that would answer does not have the time to do > it right now. > - ... > > the best chance for you would be to have a closer look at > the mailing list archives (there have been a lot of questions > about vc-relax) and see if you can find something applicable > to you. IIRC, the main reason for non-convergence are too > tight convergence criteria on the forces. > > cheers, > axel. > > > CHH> Regards, > CHH> C. H. Hu > CHH> > > -- > ======================================================================= > 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 > > > End of Pw_forum Digest, Vol 4, Issue 29 > *************************************** > From amos at errno.com Tue Oct 23 06:47:04 2007 From: amos at errno.com (Amos Leffler) Date: Mon, 22 Oct 2007 21:47:04 -0700 Subject: [Pw_forum] Problems with CPMD Program Message-ID: <471D7CC8.8010709@errno.com> Dear Forum, I am having trouble running the first stage of the CPMD program for CO. I should state that I was able to run the example21 program successfully so I know the compilation was successful. I copied the input for that program and made what I think are the proper changes to run CO using the INPUT_HOWTO file. The output is shown below. /home/amos/Desktop/espresso-3.2/examples/example40 : starting This example shows how to use cp.x to perform molecular dynamics simulation of medium to large systems. executables directory: /home/amos/Desktop/espresso-3.2/bin pseudo directory: /home/amos/Desktop/espresso-3.2/pseudo temporary directory: /home/amos/tmp checking that needed directories and files exist... done running cp.x as: /home/amos/Desktop/espresso-3.2/bin/cp.x cleaning /home/amos/tmp... done /home/amos/Desktop/espresso-3.2/examples/example40 : done where example40 is a new example. Note that the program simply ignores all of the input data and terminates. It should be noted that line 69 had to be changed to FPMD_COMMAND from CP_COMMAND to get the "running cp.x to give an output. Hopefully someone will see something missing or incorrect. With thanks Amos Leffler unaffiliated ------------------------------------------------------------------------ CPMD Input File #!/bin/sh # run from directory where this script is cd `echo $0 | sed 's/\(.*\)\/.*/\1/'` # extract pathname EXAMPLE_DIR=`pwd` # check whether echo has the -e option if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi $ECHO $ECHO "$EXAMPLE_DIR : starting" $ECHO $ECHO "This example shows how to use cp.x to perform molecular dynamics" $ECHO "simulation of medium to large systems." # set the needed environment variables . ../environment_variables # required executables and pseudopotentials BIN_LIST="cp.x" PSEUDO_LIST="O.pz-rrkjus.UPF C.pz-vbc.UPF" $ECHO $ECHO " executables directory: $BIN_DIR" $ECHO " pseudo directory: $PSEUDO_DIR" $ECHO " temporary directory: $TMP_DIR" $ECHO " checking that needed directories and files exist...\c" # check for directories for DIR in "$BIN_DIR" "$PSEUDO_DIR" ; do if test ! -d $DIR ; then $ECHO $ECHO "ERROR: $DIR not existent or not a directory" $ECHO "Aborting" exit 1 fi done for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do if test ! -d $DIR ; then mkdir $DIR fi done cd $EXAMPLE_DIR/results # check for executables for FILE in $BIN_LIST ; do if test ! -x $BIN_DIR/$FILE ; then $ECHO $ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable" $ECHO "Aborting" exit 1 fi done # check for pseudopotentials for FILE in $PSEUDO_LIST ; do if test ! -r $PSEUDO_DIR/$FILE ; then $ECHO $ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable" $ECHO "Aborting" exit 1 fi done $ECHO " done" # how to run executables FPMD_COMMAND="$PARA_PREFIX $BIN_DIR/cp.x $PARA_POSTFIX" $ECHO $ECHO " running cp.x as: $FPMD_COMMAND" $ECHO # clean TMP_DIR $ECHO " cleaning $TMP_DIR...\c" rm -rf $TMP_DIR/* $ECHO " done" # molecular dynamics calculation cat > co-14.in << EOF &control title = ' CO 14 molecules ', calculation = 'cp', restart_mode = 'from_scratch', ! 'restart', ndr = 50, ndw = -1, nstep = 10, iprint = 10, isave = 100, tstress = .TRUE., tprnfor = .TRUE., dt = 5.0d0, etot_conv_thr = 1.d-8, prefix = 'cp', pseudo_dir='$PSEUDO_DIR/', outdir='$TMP_DIR/', / &system ibrav = 2, celldm(1) = 6.244, celldm(2) = 0.0, celldm(3) = 0.0, celldm(4) = 0.0, celldm(5) = 0.0, celldm(6) = 0.0, nat = 28, ntyp = 2, nbnd = 70, nelec = 140, ecutwfc = 40.0, ecfixed = 68.0, qcutz = 68.0, q2sigma = 8.0, xc_type = 'PZ', / &electrons emass = 400.d0, emass_cutoff = 2.5d0, orthogonalization = 'ortho', ortho_eps = 5.d-8, ortho_max = 20, electron_dynamics = 'sd', electron_velocities = 'zero', electron_temperature = 'not_controlled', TFOR=.false, TNOSEP=.false, DELTAT=10, EMAEC=2, FRICE=0.05, / &ions ion_dynamics = 'none', ! ion_radius(1) = 0.8d0, ! ion_radius(2) = 0.5d0, ! ion_velocities = 'zero', ion_temperature = 'not_controlled' / &cell cell_dynamics = 'none', cell_velocities = 'zero', press = 0.0d0, wmass = 70000.0d0 / ATOMIC_SPECIES C 12.0d0 C.pz-vbc.UPF O 16.0d0 O.pz-rrkjus.UPF ATOMIC_POSITIONS (Angstroms) C -0.307 -0.307 -0.307 C 5.323 -0.307 -0.307 C -0.307 5.323 -0.307 C 5.323 5.323 -0.307 C -0.307 -0.307 5.323 C 5.323 -0.307 5.323 C -0.307 5.323 5.323 C 5.323 5.323 5.323 C 3.122 0.307 2.815 C 3.122 5.937 2.815 C 0.307 2.508 3.122 C 5.937 2.508 3.122 C 2.508 2.508 5.937 C 2.508 2.508 0.307 O 0.307 0.307 0.307 O 5.937 0.307 0.307 O 0.307 5.937 0.307 O 5.937 5.937 0.307 O 0.307 0.307 5.937 O 5.937 0.307 5.937 O 0.307 5.937 5.937 O 5.937 5.937 5.937 O 2.508 -0.307 3.122 O 2.508 5.323 3.122 O -0.307 3.122 2.508 O 5.937 3.122 2.508 O 3.122 3.122 5.323 O 3.122 3.122 -0.307 EOF $ECHO $ECHO "$EXAMPLE_DIR : done" From giannozz at nest.sns.it Tue Oct 23 09:10:36 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 23 Oct 2007 09:10:36 +0200 Subject: [Pw_forum] Problems with CPMD Program In-Reply-To: <471D7CC8.8010709@errno.com> References: <471D7CC8.8010709@errno.com> Message-ID: On Oct 23, 2007, at 6:47 , Amos Leffler wrote: > I am having trouble running the first stage of the CPMD program please note that "CPMD" is the name of a different Car-Parrinello code (http://www.cpmd.org/) > # molecular dynamics calculation > cat > co-14.in << EOF > ... > EOF > > $ECHO > $ECHO "$EXAMPLE_DIR : done" done what? 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 chaohao.mse at gmail.com Tue Oct 23 09:29:12 2007 From: chaohao.mse at gmail.com (Chaohao Hu) Date: Tue, 23 Oct 2007 09:29:12 +0200 Subject: [Pw_forum] how to consider the "dt" flag during vc-relax In-Reply-To: <58593.128.101.191.226.1193091686.squirrel@www.msi.umn.edu> References: <58593.128.101.191.226.1193091686.squirrel@www.msi.umn.edu> Message-ID: <6502ee650710230029l12ee5e17y94a969d73faa5038@mail.gmail.com> Dear Cesar, Thank you for your reply. According to your suggestion, I change "dt" and conv_thr to 80 and 1.D-10, the convergence is not improved, although the calculation is running. The calculated total force and stress is given here as a attachment because it is too long. As you can see from this file, the final cell parameters is changed largely, which also affects the k-points meshing during my calculation. Another point added here is that my systems only contain some light elements like H, Li. How to further optimize these parameters? Regards, C.H. On 10/23/07, Cesar R.S. da Silva wrote: > > Dear Chao, > > Your dt setting should work OK. wmass could be reduced to somthing like > 0.002, provided atomic masses are all set to the average mass (amu), but > your value is not that bad. The only thing I think could produce > convergence problems is your conv_thr. Try conv_thr = 1e-9. Variable cell > requires precise stress calculation, and a more stringent convergence > criteria for the SCF cycle is required. > > Cesar. > > -- ============================ C.H. Hu Postdoctoral fellow Chimie et Physico-Chimie appliquees Institut Francais du Petrole (IFP) Rueil-Malmaison, France E_mail: chaohao.mse at gmail.com ============================ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071023/f6af0ce9/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: vc_relax_problem Type: application/octet-stream Size: 15091 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20071023/f6af0ce9/attachment.obj From sunshoutian168 at yahoo.com.cn Tue Oct 23 09:36:37 2007 From: sunshoutian168 at yahoo.com.cn (shoutian sun) Date: Tue, 23 Oct 2007 15:36:37 +0800 (CST) Subject: [Pw_forum] How to calculate the properties of free OH Message-ID: <210388.2553.qm@web92006.mail.cnb.yahoo.com> > Dear Ou, >Your problem is >> ============================================== >> >> * **from electrons : error # 1* >> >> * charge is wrong* >> >> ============================================== >I have met this problem before,please set nelec=... in the NAMELIST&SYSTEM in the inputfile of pw.x.At the same time set dt smaller maybe dt=50 or 40 or 30 is OK. one more thing, do set max_second as default,or do not set it. Best wishes sun, from east china normal university. --------------------------------- @yahoo.cn ????????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071023/e8a8e453/attachment-0001.htm From hqzhou at nju.edu.cn Tue Oct 23 09:48:56 2007 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Tue, 23 Oct 2007 15:48:56 +0800 Subject: [Pw_forum] Problems with CPMD Program References: <471D7CC8.8010709@errno.com> Message-ID: <002401c81549$2b5cff50$1d00a8c0@solarflare> Amos, Your script just created an input file, co-14.in. You should add one line something like: $FPMD_COMMAND < co-14.in > co-14.out after EOF. Dr. Huiqun Zhou Earth Sciences Nanjing University, China ----- Original Message ----- From: "Amos Leffler" To: "PWSCF Forum" Sent: Tuesday, October 23, 2007 12:47 PM Subject: [Pw_forum] Problems with CPMD Program > Dear Forum, > I am having trouble running the first stage of the CPMD program > for CO. I should state that I was able to run the example21 program > successfully so I know the compilation was successful. > I copied the input for that program and made what I think are the proper > changes to run CO using the INPUT_HOWTO file. > The output is shown below. > > > /home/amos/Desktop/espresso-3.2/examples/example40 : starting > > This example shows how to use cp.x to perform molecular dynamics > simulation of medium to large systems. > > executables directory: /home/amos/Desktop/espresso-3.2/bin > pseudo directory: /home/amos/Desktop/espresso-3.2/pseudo > temporary directory: /home/amos/tmp > checking that needed directories and files exist... done > > running cp.x as: /home/amos/Desktop/espresso-3.2/bin/cp.x > > cleaning /home/amos/tmp... done > > /home/amos/Desktop/espresso-3.2/examples/example40 : done > > where example40 is a new example. Note that the program simply ignores > all of the input data and terminates. It should be noted that line 69 > had to be changed to FPMD_COMMAND > from CP_COMMAND to get the "running cp.x to give an output. > Hopefully someone will see something missing or incorrect. > > With thanks > > Amos Leffler > > > unaffiliated > > ------------------------------------------------------------------------ > CPMD Input File > > #!/bin/sh > > # run from directory where this script is > cd `echo $0 | sed 's/\(.*\)\/.*/\1/'` # extract pathname > EXAMPLE_DIR=`pwd` > > # check whether echo has the -e option > if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi > > $ECHO > $ECHO "$EXAMPLE_DIR : starting" > $ECHO > $ECHO "This example shows how to use cp.x to perform molecular dynamics" > $ECHO "simulation of medium to large systems." > > # set the needed environment variables > . ../environment_variables > > # required executables and pseudopotentials > BIN_LIST="cp.x" > PSEUDO_LIST="O.pz-rrkjus.UPF C.pz-vbc.UPF" > > $ECHO > $ECHO " executables directory: $BIN_DIR" > $ECHO " pseudo directory: $PSEUDO_DIR" > $ECHO " temporary directory: $TMP_DIR" > $ECHO " checking that needed directories and files exist...\c" > > # check for directories > for DIR in "$BIN_DIR" "$PSEUDO_DIR" ; do > if test ! -d $DIR ; then > $ECHO > $ECHO "ERROR: $DIR not existent or not a directory" > $ECHO "Aborting" > exit 1 > fi > done > for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do > if test ! -d $DIR ; then > mkdir $DIR > fi > done > cd $EXAMPLE_DIR/results > > # check for executables > for FILE in $BIN_LIST ; do > if test ! -x $BIN_DIR/$FILE ; then > $ECHO > $ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable" > $ECHO "Aborting" > exit 1 > fi > done > > # check for pseudopotentials > for FILE in $PSEUDO_LIST ; do > if test ! -r $PSEUDO_DIR/$FILE ; then > $ECHO > $ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable" > $ECHO "Aborting" > exit 1 > fi > done > $ECHO " done" > > # how to run executables > FPMD_COMMAND="$PARA_PREFIX $BIN_DIR/cp.x $PARA_POSTFIX" > $ECHO > $ECHO " running cp.x as: $FPMD_COMMAND" > $ECHO > > # clean TMP_DIR > $ECHO " cleaning $TMP_DIR...\c" > rm -rf $TMP_DIR/* > $ECHO " done" > > # molecular dynamics calculation > cat > co-14.in << EOF > &control > title = ' CO 14 molecules ', > calculation = 'cp', > restart_mode = 'from_scratch', ! 'restart', > ndr = 50, > ndw = -1, > nstep = 10, > iprint = 10, > isave = 100, > tstress = .TRUE., > tprnfor = .TRUE., > dt = 5.0d0, > etot_conv_thr = 1.d-8, > prefix = 'cp', > pseudo_dir='$PSEUDO_DIR/', > outdir='$TMP_DIR/', > / > &system > ibrav = 2, > celldm(1) = 6.244, > celldm(2) = 0.0, > celldm(3) = 0.0, > celldm(4) = 0.0, > celldm(5) = 0.0, > celldm(6) = 0.0, > nat = 28, > ntyp = 2, > nbnd = 70, > nelec = 140, > ecutwfc = 40.0, > ecfixed = 68.0, > qcutz = 68.0, > q2sigma = 8.0, > xc_type = 'PZ', > / > &electrons > emass = 400.d0, > emass_cutoff = 2.5d0, > orthogonalization = 'ortho', > ortho_eps = 5.d-8, > ortho_max = 20, > electron_dynamics = 'sd', > electron_velocities = 'zero', > electron_temperature = 'not_controlled', > TFOR=.false, > TNOSEP=.false, > DELTAT=10, > EMAEC=2, > FRICE=0.05, > / > &ions > ion_dynamics = 'none', > ! ion_radius(1) = 0.8d0, > ! ion_radius(2) = 0.5d0, > ! ion_velocities = 'zero', > ion_temperature = 'not_controlled' > / > &cell > cell_dynamics = 'none', > cell_velocities = 'zero', > press = 0.0d0, > wmass = 70000.0d0 > / > ATOMIC_SPECIES > C 12.0d0 C.pz-vbc.UPF > O 16.0d0 O.pz-rrkjus.UPF > > ATOMIC_POSITIONS (Angstroms) > C -0.307 -0.307 -0.307 > C 5.323 -0.307 -0.307 > C -0.307 5.323 -0.307 > C 5.323 5.323 -0.307 > C -0.307 -0.307 5.323 > C 5.323 -0.307 5.323 > C -0.307 5.323 5.323 > C 5.323 5.323 5.323 > C 3.122 0.307 2.815 > C 3.122 5.937 2.815 > C 0.307 2.508 3.122 > C 5.937 2.508 3.122 > C 2.508 2.508 5.937 > C 2.508 2.508 0.307 > O 0.307 0.307 0.307 > O 5.937 0.307 0.307 > O 0.307 5.937 0.307 > O 5.937 5.937 0.307 > O 0.307 0.307 5.937 > O 5.937 0.307 5.937 > O 0.307 5.937 5.937 > O 5.937 5.937 5.937 > O 2.508 -0.307 3.122 > O 2.508 5.323 3.122 > O -0.307 3.122 2.508 > O 5.937 3.122 2.508 > O 3.122 3.122 5.323 > O 3.122 3.122 -0.307 > EOF > > $ECHO > $ECHO "$EXAMPLE_DIR : done" > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From naser_zd2000 at yahoo.com Tue Oct 23 12:53:33 2007 From: naser_zd2000 at yahoo.com (naser zare) Date: Tue, 23 Oct 2007 03:53:33 -0700 (PDT) Subject: [Pw_forum] How to plot with dashed line in two-dimensional plot of density? Message-ID: <80893.67635.qm@web32907.mail.mud.yahoo.com> Dear all Hello I want to use dashed line in two-dimensional plot of density when I use from plotrho.x . How can I do it? Thank you very much. Best Regards Zare Dehnavi __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071023/fb4dc7b8/attachment.htm From chaohao.mse at gmail.com Tue Oct 23 13:57:23 2007 From: chaohao.mse at gmail.com (Chaohao Hu) Date: Tue, 23 Oct 2007 13:57:23 +0200 Subject: [Pw_forum] how to consider the "dt" flag during vc-relax In-Reply-To: <6502ee650710230029l12ee5e17y94a969d73faa5038@mail.gmail.com> References: <58593.128.101.191.226.1193091686.squirrel@www.msi.umn.edu> <6502ee650710230029l12ee5e17y94a969d73faa5038@mail.gmail.com> Message-ID: <6502ee650710230457o41e46389y470105e1c1bb4995@mail.gmail.com> Wow, the convergence is good when the "dt" flag is further reduced to 30 considering my special system in which it only contains some light elements. Thanks Dr. Axel and Cesar again for your suggestion -:) ========== total stress (Ry/bohr**3) (kbar) P= - 7.01 total stress (Ry/bohr**3) (kbar) P= - 6.21 total stress (Ry/bohr**3) (kbar) P= - 5.28 total stress (Ry/bohr**3) (kbar) P= - 4.38 total stress (Ry/bohr**3) (kbar) P= - 3.39 total stress (Ry/bohr**3) (kbar) P= - 2.40 total stress (Ry/bohr**3) (kbar) P= - 1.49 total stress (Ry/bohr**3) (kbar) P= - 0.61 total stress (Ry/bohr**3) (kbar) P= 0.24 total stress (Ry/bohr**3) (kbar) P= 0.59 total stress (Ry/bohr**3) (kbar) P= - 0.00 total stress (Ry/bohr**3) (kbar) P= 0.14 total stress (Ry/bohr**3) (kbar) P= 0.15 total stress (Ry/bohr**3) (kbar) P= 0.21 total stress (Ry/bohr**3) (kbar) P= 0.24 total stress (Ry/bohr**3) (kbar) P= 0.19 total stress (Ry/bohr**3) (kbar) P= 0.15 total stress (Ry/bohr**3) (kbar) P= 0.13 total stress (Ry/bohr**3) (kbar) P= 0.10 total stress (Ry/bohr**3) (kbar) P= 0.07 total stress (Ry/bohr**3) (kbar) P= 0.07 total stress (Ry/bohr**3) (kbar) P= 0.07 total stress (Ry/bohr**3) (kbar) P= 0.07 total stress (Ry/bohr**3) (kbar) P= 0.03 ... Total force = 0.001176 Total SCF correction = 0.000004 Total force = 0.001374 Total SCF correction = 0.000004 Total force = 0.001858 Total SCF correction = 0.000006 Total force = 0.001973 Total SCF correction = 0.000003 Total force = 0.001762 Total SCF correction = 0.000004 Total force = 0.001475 Total SCF correction = 0.000004 Total force = 0.001355 Total SCF correction = 0.000004 Total force = 0.001877 Total SCF correction = 0.000005 Total force = 0.001823 Total SCF correction = 0.000003 Total force = 0.001150 Total SCF correction = 0.000005 Total force = 0.000929 Total SCF correction = 0.000003 Total force = 0.000917 Total SCF correction = 0.000002 Total force = 0.000931 Total SCF correction = 0.000003 Total force = 0.001003 Total SCF correction = 0.000003 Total force = 0.000736 Total SCF correction = 0.000002 Total force = 0.000728 Total SCF correction = 0.000002 Total force = 0.000749 Total SCF correction = 0.000001 Total force = 0.000747 Total SCF correction = 0.000002 Total force = 0.000692 Total SCF correction = 0.000003 Total force = 0.000751 Total SCF correction = 0.000002 Total force = 0.000872 Total SCF correction = 0.000002 Total force = 0.000671 Total SCF correction = 0.000003 Total force = 0.000723 Total SCF correction = 0.000002 Total force = 0.000715 Total SCF correction = 0.000003 Total force = 0.000620 Total SCF correction = 0.000002 ... Best regards, C.H. -- ============================ C.H. Hu Postdoctoral fellow Chimie et Physico-Chimie appliquees Institut Francais du Petrole (IFP) Rueil-Malmaison, France E_mail: chaohao.mse at gmail.com ============================ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071023/a4bdd1fb/attachment.htm From akohlmey at cmm.chem.upenn.edu Tue Oct 23 16:17:43 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 23 Oct 2007 10:17:43 -0400 (EDT) Subject: [Pw_forum] how to consider the "dt" flag during vc-relax In-Reply-To: <6502ee650710230457o41e46389y470105e1c1bb4995@mail.gmail.com> References: <58593.128.101.191.226.1193091686.squirrel@www.msi.umn.edu> <6502ee650710230029l12ee5e17y94a969d73faa5038@mail.gmail.com> <6502ee650710230457o41e46389y470105e1c1bb4995@mail.gmail.com> Message-ID: On Tue, 23 Oct 2007, Chaohao Hu wrote: CH> Wow, the convergence is good when the "dt" flag is further reduced to 30 CH> considering my special system in which it only contains some light elements. CH> Thanks Dr. Axel and Cesar again for your suggestion -:) ...and you should also consider cesar's suggestion of setting the atomic masses all to the same value. with light elements the relative differences between the atom masses and thus the speed with which those atoms move differs the most. for the purpose of getting the right structure the masses don't matter. cheers, axel. CH> CH> ========== CH> total stress (Ry/bohr**3) (kbar) P= - CH> 7.01 CH> total stress (Ry/bohr**3) (kbar) P= - CH> 6.21 CH> total stress (Ry/bohr**3) (kbar) P= - CH> 5.28 CH> total stress (Ry/bohr**3) (kbar) P= - CH> 4.38 CH> total stress (Ry/bohr**3) (kbar) P= - CH> 3.39 CH> total stress (Ry/bohr**3) (kbar) P= - CH> 2.40 CH> total stress (Ry/bohr**3) (kbar) P= - CH> 1.49 CH> total stress (Ry/bohr**3) (kbar) P= - CH> 0.61 CH> total stress (Ry/bohr**3) (kbar) P= CH> 0.24 CH> total stress (Ry/bohr**3) (kbar) P= CH> 0.59 CH> total stress (Ry/bohr**3) (kbar) P= - CH> 0.00 CH> total stress (Ry/bohr**3) (kbar) P= CH> 0.14 CH> total stress (Ry/bohr**3) (kbar) P= CH> 0.15 CH> total stress (Ry/bohr**3) (kbar) P= CH> 0.21 CH> total stress (Ry/bohr**3) (kbar) P= CH> 0.24 CH> total stress (Ry/bohr**3) (kbar) P= CH> 0.19 CH> total stress (Ry/bohr**3) (kbar) P= CH> 0.15 CH> total stress (Ry/bohr**3) (kbar) P= CH> 0.13 CH> total stress (Ry/bohr**3) (kbar) P= CH> 0.10 CH> total stress (Ry/bohr**3) (kbar) P= CH> 0.07 CH> total stress (Ry/bohr**3) (kbar) P= CH> 0.07 CH> total stress (Ry/bohr**3) (kbar) P= CH> 0.07 CH> total stress (Ry/bohr**3) (kbar) P= CH> 0.07 CH> total stress (Ry/bohr**3) (kbar) P= CH> 0.03 CH> ... CH> Total force = 0.001176 Total SCF correction = 0.000004 CH> Total force = 0.001374 Total SCF correction = 0.000004 CH> Total force = 0.001858 Total SCF correction = 0.000006 CH> Total force = 0.001973 Total SCF correction = 0.000003 CH> Total force = 0.001762 Total SCF correction = 0.000004 CH> Total force = 0.001475 Total SCF correction = 0.000004 CH> Total force = 0.001355 Total SCF correction = 0.000004 CH> Total force = 0.001877 Total SCF correction = 0.000005 CH> Total force = 0.001823 Total SCF correction = 0.000003 CH> Total force = 0.001150 Total SCF correction = 0.000005 CH> Total force = 0.000929 Total SCF correction = 0.000003 CH> Total force = 0.000917 Total SCF correction = 0.000002 CH> Total force = 0.000931 Total SCF correction = 0.000003 CH> Total force = 0.001003 Total SCF correction = 0.000003 CH> Total force = 0.000736 Total SCF correction = 0.000002 CH> Total force = 0.000728 Total SCF correction = 0.000002 CH> Total force = 0.000749 Total SCF correction = 0.000001 CH> Total force = 0.000747 Total SCF correction = 0.000002 CH> Total force = 0.000692 Total SCF correction = 0.000003 CH> Total force = 0.000751 Total SCF correction = 0.000002 CH> Total force = 0.000872 Total SCF correction = 0.000002 CH> Total force = 0.000671 Total SCF correction = 0.000003 CH> Total force = 0.000723 Total SCF correction = 0.000002 CH> Total force = 0.000715 Total SCF correction = 0.000003 CH> Total force = 0.000620 Total SCF correction = 0.000002 CH> ... CH> CH> Best regards, CH> C.H. CH> CH> -- ======================================================================= 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 chaohao.mse at gmail.com Tue Oct 23 17:24:28 2007 From: chaohao.mse at gmail.com (Chaohao Hu) Date: Tue, 23 Oct 2007 17:24:28 +0200 Subject: [Pw_forum] how to consider the "dt" flag during vc-relax In-Reply-To: References: <58593.128.101.191.226.1193091686.squirrel@www.msi.umn.edu> <6502ee650710230029l12ee5e17y94a969d73faa5038@mail.gmail.com> <6502ee650710230457o41e46389y470105e1c1bb4995@mail.gmail.com> Message-ID: <6502ee650710230824u297cdfa8i8369b8d89ac7a2c0@mail.gmail.com> OK, I will further optimize the speed of the convergence. On this issue, these suggestions are valuable for me... Regards, C.H. On 10/23/07, Axel Kohlmeyer wrote: > > On Tue, 23 Oct 2007, Chaohao Hu wrote: > > CH> Wow, the convergence is good when the "dt" flag is further reduced to > 30 > CH> considering my special system in which it only contains some light > elements. > CH> Thanks Dr. Axel and Cesar again for your suggestion -:) > > ...and you should also consider cesar's suggestion of setting > the atomic masses all to the same value. with light elements > the relative differences between the atom masses and thus the > speed with which those atoms move differs the most. for the > purpose of getting the right structure the masses don't matter. > > cheers, > axel. > > -- ============================ C.H. Hu Postdoctoral fellow Chimie et Physico-Chimie appliquees Institut Francais du Petrole (IFP) Rueil-Malmaison, France E_mail: chaohao.mse at gmail.com ============================ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071023/7d3189c2/attachment.htm From giannozz at nest.sns.it Tue Oct 23 17:25:57 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 23 Oct 2007 17:25:57 +0200 Subject: [Pw_forum] How to calculate the properties of free OH In-Reply-To: <210388.2553.qm@web92006.mail.cnb.yahoo.com> References: <210388.2553.qm@web92006.mail.cnb.yahoo.com> Message-ID: <29C69215-B256-43D1-BAC3-0DAFD4AB6027@nest.sns.it> On Oct 23, 2007, at 9:36 , shoutian sun wrote: > please set nelec=... in the NAMELIST&SYSTEM in the input > file of pw.x. this is not needed, unless one wants to make a calculation for a non neutral system. 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 Tue Oct 23 17:29:26 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 23 Oct 2007 17:29:26 +0200 Subject: [Pw_forum] How to plot with dashed line in two-dimensional plot of density? In-Reply-To: <80893.67635.qm@web32907.mail.mud.yahoo.com> References: <80893.67635.qm@web32907.mail.mud.yahoo.com> Message-ID: <696AEB03-95E1-4582-8E5F-74923AAF335D@nest.sns.it> On Oct 23, 2007, at 12:53 , naser zare wrote: > I want to use dashed line in two-dimensional plot of density when I > use from plotrho.x . How can I do it? modify PP/plotrho.f90 following the instructions: ! uncomment the call to "cplot" if you want contour lines, ! plus gray levels and shading for negative values call cplot (rhoo, nx, ny, x, xmin, xmax, nx, y, ymin, ymax, & ny, nlevels, z, xdim, ydim, xs, ys, filename, fileout) ! uncomment the call to "psplot" if you want contour lines ! of various kinds: solid, dashed, etc ! call psplot ( rhoo, nx, x, nx, y, ny, nlevels, z, xdim, ydim, & ! xs, ys, fileout) No warranty: last time I tried it it was sort of working, but it was several years ago. Otherwise you can use a plotting program like gnuplot or xmgrace. 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 ghaderyan at gmail.com Tue Oct 23 23:00:48 2007 From: ghaderyan at gmail.com (saman ghaderyan) Date: Wed, 24 Oct 2007 00:30:48 +0330 Subject: [Pw_forum] ev.x Message-ID: hi i want to use EV.X for hexagonal structure, how can i tidy my input file. thanx saman ghaderyan bu ali sina university iran -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071024/f42b7c24/attachment.htm From eyvaz_isaev at yahoo.com Wed Oct 24 00:01:30 2007 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 23 Oct 2007 15:01:30 -0700 (PDT) Subject: [Pw_forum] ev.x In-Reply-To: Message-ID: <821776.35415.qm@web60313.mail.yahoo.com> Dear Saman, If you mean a fitting procedure with ev.x, for this purpose you need only (Volume, Energy) pairs. Just take the right cell from the list suggested by ev.x. I suggest Volume in a.u.^3 is preferable, and Energy usually in Ry. If you like very much Ang^3, use it, but then the bulk modulus has to be recalculated (think about, how?). Bests, Eyvaz. --- saman ghaderyan wrote: > hi > i want to use EV.X for hexagonal structure, how can > i tidy my input file. > thanx > saman ghaderyan > bu ali sina university > iran > > _______________________________________________ > 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, and Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From sunshoutian168 at yahoo.com.cn Wed Oct 24 03:21:10 2007 From: sunshoutian168 at yahoo.com.cn (shoutian sun) Date: Wed, 24 Oct 2007 09:21:10 +0800 (CST) Subject: [Pw_forum] A small thing about phonon. Message-ID: <428072.21706.qm@web92005.mail.cnb.yahoo.com> >Dear all, > >I have met a problem in calculation of phonon,my code as follows: >&CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > outdir='/home/user/ecnuphyk/SUN/tmp/tmp-p1/' , > pseudo_dir = '/home/user/ecnuphyk/SUN/pseudo/' , > prefix='...' , > tstress = .true. , > tprnfor = .true. , > etot_conv_thr = 1.0E-5 , > forc_conv_thr = 1.0D-4 , > / > &SYSTEM > ibrav = 0 , > celldm(1) = 1.889725988578923203102406997093 , > nat = 16 , > ntyp = 2 , > nspin = 1 > ecutwfc = 37.0 , > / > &ELECTRONS > conv_thr = 1.0d-7 , > mixing_beta = 0.7 , > / >CELL_PARAMETERS (alat) >... >ATOMIC_SPECIES >... >ATOMIC_POSITIONS {crystal} >... >K_POINTS automatic > 5 5 8 1 1 0 > >phonons of ... >&inputph > tr2_ph=1.0d-12, > prefix='', > ldisp=.true., > nq1=3, nq2=3, nq3=4 > epsil=.true. , > amass(1)=..., > amass(2)=..., > outdir= '/home/user/ecnuphyk/SUN/tmp/tmp-p4/' , > fildyn='....dyn', > / *********************************** please pay attention to K_POINTS automatic and nq1=3, nq2=3, nq3=4 should I have to set nq in &inputph in proportion to the mesh of K_POINTS automatic? Thanks regards, --------------------------------- ?????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071024/97255f8d/attachment.htm From yanyan1110_2 at yahoo.cn Wed Oct 24 04:36:41 2007 From: yanyan1110_2 at yahoo.cn (Yanyan) Date: Wed, 24 Oct 2007 10:36:41 +0800 (CST) Subject: [Pw_forum] how to determine the mass of mixing pseudopotential by virtual.x Message-ID: <479927.72626.qm@web92206.mail.cnh.yahoo.com> Dear Stefano de Gironcoli Recently, i am testing the virtual-atom pseudopotential generated by virtual.x. I want to ask if the testing results of the virtual pseudo made by 0% pseudo1 + 100% pseudo2 are in same agreement with the results calculated directly with pseudo2. If both values are different, only the convergence trend is equal. Is the virtual-pseudo OK? While i want to calculate phonon frequencies, how can I do to obtain the mass of virtual-atom pseudopotential. Because of the mixing pseudopotential as (1-x) pseudopotential1 + x pseudopotential2, whether the mass of virtual-atom pseudopotential can be determined by (1-x) mass of potential1 + x mass of potential2. Thank you for your advice. Best regards Junjie Wang --------------------------------- ?????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071024/edc33d2f/attachment.htm From baroni at sissa.it Wed Oct 24 08:23:56 2007 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 24 Oct 2007 08:23:56 +0200 Subject: [Pw_forum] how to determine the mass of mixing pseudopotential by virtual.x In-Reply-To: <479927.72626.qm@web92206.mail.cnh.yahoo.com> References: <479927.72626.qm@web92206.mail.cnh.yahoo.com> Message-ID: <17A5C144-1338-4879-879B-E119DE29A995@sissa.it> On Oct 24, 2007, at 4:36 AM, Yanyan wrote: > Dear Stefano de Gironcoli > Recently, i am testing the virtual-atom pseudopotential > generated by virtual.x. > I want to ask if the testing results of the virtual pseudo made by > 0% pseudo1 + 100% pseudo2 > are in same agreement with the results calculated directly with > pseudo2. They should, as far as I understand, but others may have something more to add. > If both > values are different, only the convergence trend is equal. Is the > virtual-pseudo OK? > While i want to calculate phonon frequencies, how can I do to > obtain the mass > of virtual-atom pseudopotential. Because of the mixing > pseudopotential as (1-x) > pseudopotential1 + x pseudopotential2, whether the mass of virtual- > atom > pseudopotential can be determined by (1-x) mass of potential1 + x > mass of potential2. As already said in this forum a few days ago, it depends on the application. To be (a little bit) more specific: the weighted mass gives reasonable results for acoustic phonons, where atoms of different mass vibrate in phase. For the optic branches, instead, different atoms vibrate out of phase, so that taking the average mass is only meaningful when the optic branches of the pure compounds overlap considerably (which in turn implies that the masses are close enough). Beware, though, that the time-consuming part of any phonon calculation is the computation of the interatomic force constants, which do not depend on mass. Once these calculated, the calculation and diagonalization of the dynamical matrices is a relatively minor task. It may make sense therefore to calculate the interatomic force constants using the VCA, and then to calculate the dynamical matrices using real masses. This procedure has been followed successfully since the eve of DFPT. Examples of its application can be found, e.g., in Rev. Mod. Phys. 73, 515 (2001). Hope this helps. Stefano (Baroni) > Thank you for your advice. > Best regards > Junjie Wang > > ?????????? > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+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/20071024/99d33808/attachment.htm From w2agz at pacbell.net Wed Oct 24 08:36:11 2007 From: w2agz at pacbell.net (Paul M. Grant) Date: Tue, 23 Oct 2007 23:36:11 -0700 Subject: [Pw_forum] kubuntu+gfortran+configure+make all=no executables Message-ID: <000001c81608$2ba210d0$82e63270$@net> Up to yesterday I've run PWscf on several openSUSE distos with consistent success. Over the weekend, I experimented with Kubuntu 7.10. Intel fortran compiler installs gave floating point exceptions (well duplicated by others), so switched to gfortran and lapack3 packages. Configure followed by make all seems to go smoothly, but /.espresso./bin contains only links to no (visible) executables! Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford University EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071023/f9cc61fe/attachment-0001.htm From ghaderyan at gmail.com Wed Oct 24 09:06:40 2007 From: ghaderyan at gmail.com (saman ghaderyan) Date: Wed, 24 Oct 2007 10:36:40 +0330 Subject: [Pw_forum] thanks Message-ID: Thanx Dear Eyvaz I get my answer. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071024/515b6da8/attachment.htm From giannozz at nest.sns.it Wed Oct 24 09:42:48 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 24 Oct 2007 09:42:48 +0200 Subject: [Pw_forum] A small thing about phonon. In-Reply-To: <428072.21706.qm@web92005.mail.cnb.yahoo.com> References: <428072.21706.qm@web92005.mail.cnb.yahoo.com> Message-ID: On Oct 24, 2007, at 3:21 , shoutian sun wrote: > please pay attention to K_POINTS automatic and nq1=3, nq2=3, nq3=4 > should I have to set nq in &inputph in proportion to the mesh of > K_POINTS automatic? no: the two grids serve different purposes 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 Oct 24 09:51:10 2007 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 24 Oct 2007 09:51:10 +0200 Subject: [Pw_forum] how to determine the mass of mixing pseudopotential by virtual.x In-Reply-To: <479927.72626.qm@web92206.mail.cnh.yahoo.com> References: <479927.72626.qm@web92206.mail.cnh.yahoo.com> Message-ID: <471EF96E.7050502@sissa.it> If the interpolation works correctly the two pseudos should give the same properties. For numerical reasons they will not be *identical* but they should be two different representations of the SAME pseudopotential ... therefore energies, forces, structural properties and everything should be basically the same. stefano Yanyan wrote: > Dear Stefano de Gironcoli > Recently, i am testing the virtual-atom pseudopotential generated by virtual.x. > I want to ask if the testing results of the virtual pseudo made by 0% pseudo1 + 100% pseudo2 > are in same agreement with the results calculated directly with pseudo2. If both > values are different, only the convergence trend is equal. Is the virtual-pseudo OK? > While i want to calculate phonon frequencies, how can I do to obtain the mass > of virtual-atom pseudopotential. Because of the mixing pseudopotential as (1-x) > pseudopotential1 + x pseudopotential2, whether the mass of virtual-atom > pseudopotential can be determined by (1-x) mass of potential1 + x mass of potential2. > Thank you for your advice. > Best regards > Junjie Wang > > ------------------------------------------------------------------------ > ?????????? > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From lanhaiping at gmail.com Wed Oct 24 13:09:00 2007 From: lanhaiping at gmail.com (lan haiping) Date: Wed, 24 Oct 2007 19:09:00 +0800 Subject: [Pw_forum] How to deal with semicore states with Norm conserving PP? Message-ID: Dear All, I just found that opium package cannot generate ncpp for elements including semicore states . Is there any other scheme for norm conserving pseudopentials can take semicore states into account for pwscf calculation ? Bests, Hai-Ping -- 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/20071024/91e02a9c/attachment.htm From sassmannshausen at tugraz.at Wed Oct 24 14:40:51 2007 From: sassmannshausen at tugraz.at (=?iso-8859-1?q?J=F6rg_Sa=DFmannshausen?=) Date: Wed, 24 Oct 2007 14:40:51 +0200 Subject: [Pw_forum] kubuntu+gfortran+configure+make all=no executables In-Reply-To: References: Message-ID: <200710241440.52268.sassmannshausen@tugraz.at> Dear Paul, I am running Debian (Etch) which is similar to Kubuntu. I have had no problems compiling PWscf on both my AMD x2 (64bit) and my Intel dual Xeon (32bit) machines. The ifort compiler flags I used were: -O2 -unroll -tpp7 -pc64 for both machines and I don't have any problems with the build stage. Testjobs were ok. I used the Intel fortran compiler 9.1.x on both machines and gcc 4.1.2. I did not see any floating point exeptions during compilation (unless I overlooked them). I think it would help a bit if you tell us what kind of machine you have (32bit/64bit, intel, amd) as I cannot see right now where the problem might be. All the best J?rg Am Mittwoch 24 Oktober 2007 08:43 schrieb pw_forum-request at pwscf.org: > Message: 2 > Date: Tue, 23 Oct 2007 23:36:11 -0700 > From: "Paul M. Grant" > Subject: [Pw_forum] kubuntu+gfortran+configure+make all=no executables > To: > Message-ID: <000001c81608$2ba210d0$82e63270$@net> > Content-Type: text/plain; charset="us-ascii" > > Up to yesterday I've run PWscf on several openSUSE distos with consistent > success. ?Over the weekend, I experimented with Kubuntu 7.10. ?Intel > fortran compiler installs gave floating point exceptions (well duplicated > by others), so switched to gfortran and lapack3 packages. ?Configure > followed by make all seems to go smoothly, but /.espresso./bin contains > only links to no (visible) executables! > > ? > > Paul M. Grant, PhD > > Principal, W2AGZ Technologies > > Visiting Scholar, Applied Physics, Stanford University > > EPRI Science Fellow (Retired) > > IBM Research Staff Member Emeritus > > ? w2agz at pacbell.net > > ? http://www.w2agz.com -- ************************************************************* J?rg Sa?mannshausen Institut f?r chemische Technologie organischer Stoffe TU-Graz Stremayrgasse 16 8010 Graz Austria phone: +43 (0)316 873 8954 fax: +43 (0)316 873 4959 homepage: http://sassy.formativ.net/ From mbaris at metu.edu.tr Wed Oct 24 15:04:39 2007 From: mbaris at metu.edu.tr (mbaris at metu.edu.tr) Date: Wed, 24 Oct 2007 16:04:39 +0300 Subject: [Pw_forum] kubuntu+gfortran+configure+make all=no executables Message-ID: <20071024160439.g6li189v2uosows0@webmail2.metu.edu.tr> Dear Paul, some quick checks/reminders: 1) are you sure your fftw and lapack (especially lapack) libs are also compiled with the same gcc/glibc? (I often encounter some very weird errors linking libraries compiled with different compilers, especially between the 10.x series intel and gcc) 2) Have you distcleaned the pwscf distrubution after switching to gcc? 3) If you are sure your build environment is supported by INTEL (i.e. you have a supported glibc/kernel), Floating point exceptions tend to be caused by incorrect linker related environment variables such as LD_LIBRARY_PATH in my experience. 4) Have you tried intel mkl+fftw using the Intel compiler? MKL also has a non commercial version that can be installed in userspace (be sure to crop non-required libraries to reduce disk usage). Best, Baris Malcioglu METU Physics From giannozz at nest.sns.it Wed Oct 24 15:13:09 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 24 Oct 2007 15:13:09 +0200 Subject: [Pw_forum] kubuntu+gfortran+configure+make all=no executables In-Reply-To: <000001c81608$2ba210d0$82e63270$@net> References: <000001c81608$2ba210d0$82e63270$@net> Message-ID: <20CDB52F-DEF1-4551-982E-F698F4452601@nest.sns.it> On Oct 24, 2007, at 8:36 , Paul M. Grant wrote: > [...] switched to gfortran and lapack3 packages. Configure > followed by make all seems to go smoothly, but /?espresso?/bin > contains only links to no (visible) executables! a recent version of gfortran works (almost) perfectly on Mac OS-X and I am using it all the time. It gives a warning (errno=2) during load: /usr/bin/ld: warning can't open dynamic library: etc. etc. but it produces a working executable (it has obscure problems with the system blas that disappear if the fortran blas are used). If no executable is produced, there must be an error or a warning somewhere. On some machines, depending on configuration, a harmless warning like the above may be sufficient to stop loading. If this is the case, try to add the following to LDFLAGS: -Xlinker --noinhibit-exec 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 Oct 24 15:15:57 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 24 Oct 2007 15:15:57 +0200 Subject: [Pw_forum] How to deal with semicore states with Norm conserving PP? In-Reply-To: References: Message-ID: <48ED2D3C-610A-4319-B39E-B7330606DF1A@nest.sns.it> On Oct 24, 2007, at 13:09 , lan haiping wrote: > I just found that opium package cannot generate ncpp for elements > including semicore states . > Is there any other scheme for norm conserving pseudopentials can > take semicore states into account for pwscf calculation ? the pseudopotential code of quantum-espresso (in atomic/ subdir) can do this. It is a little bit tricky, though Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From martina.dellangela at elettra.trieste.it Wed Oct 24 15:58:52 2007 From: martina.dellangela at elettra.trieste.it (Martina Dell'Angela) Date: Wed, 24 Oct 2007 15:58:52 +0200 Subject: [Pw_forum] problem ph.x Message-ID: Dear All, I'm having some troubles in running some examples contained in the example directory. All of them using ph.x did not work. The message I got is for example for example 2: ---- running the phonon calculation at Gamma... 7 [main] ph.x 3144_ctgtls::handle_exceptions: Error while dumping state (probably corrupted stack) ./runexample: line 137: 3144 Segmentation fault (core dumped) $PH_COMMAND$ ---------- What happens? Thanks Martina From naser_zd2000 at yahoo.com Wed Oct 24 17:07:18 2007 From: naser_zd2000 at yahoo.com (naser zare) Date: Wed, 24 Oct 2007 08:07:18 -0700 (PDT) Subject: [Pw_forum] How to plot with dashed line in two-dimensional plot of density? In-Reply-To: <696AEB03-95E1-4582-8E5F-74923AAF335D@nest.sns.it> Message-ID: <138280.41394.qm@web32901.mail.mud.yahoo.com> Dear Prof Giannozzi Hello At first ,Thank you very much for your kindness. I did it successfully. But I need to plot the difference of densities and it is negative in some points. " plotrho.x" canot plot negative values in both cases (cplo and psplot), so I wonder how I can use solid line for positive values and dashed line for negative ones. I would be grateful if you kindly guide me. Best Regards Nasser Zare Dehnavi Paolo Giannozzi wrote: On Oct 23, 2007, at 12:53 , naser zare wrote: > I want to use dashed line in two-dimensional plot of density when I > use from plotrho.x . How can I do it? modify PP/plotrho.f90 following the instructions: ! uncomment the call to "cplot" if you want contour lines, ! plus gray levels and shading for negative values call cplot (rhoo, nx, ny, x, xmin, xmax, nx, y, ymin, ymax, & ny, nlevels, z, xdim, ydim, xs, ys, filename, fileout) ! uncomment the call to "psplot" if you want contour lines ! of various kinds: solid, dashed, etc ! call psplot ( rhoo, nx, x, nx, y, ny, nlevels, z, xdim, ydim, & ! xs, ys, fileout) No warranty: last time I tried it it was sort of working, but it was several years ago. Otherwise you can use a plotting program like gnuplot or xmgrace. 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 __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071024/5d471e93/attachment.htm From giannozz at nest.sns.it Wed Oct 24 18:17:44 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 24 Oct 2007 18:17:44 +0200 Subject: [Pw_forum] How to plot with dashed line in two-dimensional plot of density? In-Reply-To: <138280.41394.qm@web32901.mail.mud.yahoo.com> References: <138280.41394.qm@web32901.mail.mud.yahoo.com> Message-ID: <99CFA7C6-4065-4118-840A-C5E3B37097FA@nest.sns.it> On Oct 24, 2007, at 17:07 , naser zare wrote: > I need to plot the difference of densities and it is negative in > some points. > " plotrho.x" canot plot negative values in both cases (cplo and > psplot), so > I wonder how I can use solid line for positive values and dashed > line for > negative ones. you can edit the postscript file (look for lines like "[...] 0 setdash ...") ; or modify the fortran file (look for variable "linetype": this is what determines the type of contour) P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at nest.sns.it Wed Oct 24 18:18:59 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 24 Oct 2007 18:18:59 +0200 Subject: [Pw_forum] problem ph.x In-Reply-To: References: Message-ID: <39CC802D-6880-4485-ABA8-D209ED4297CD@nest.sns.it> On Oct 24, 2007, at 15:58 , Martina Dell'Angela wrote: > I'm having some troubles in running some examples > contained in the example directory. > All of them using ph.x did not work. > The message I got is for example for example 2: > ---- > running the phonon calculation at Gamma... 7 [main] ph.x > 3144_ctgtls::handle_exceptions: Error while dumping state > (probably > corrupted stack) > ./runexample: line 137: 3144 Segmentation fault (core > dumped) $PH_COMMAND$ > ---------- > What happens? something that cannot be explained on the basis of so little information. Machine, compiler, code version? 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 martina.dellangela at elettra.trieste.it Wed Oct 24 18:34:44 2007 From: martina.dellangela at elettra.trieste.it (Martina Dell'Angela) Date: Wed, 24 Oct 2007 18:34:44 +0200 Subject: [Pw_forum] problem ph.x In-Reply-To: <39CC802D-6880-4485-ABA8-D209ED4297CD@nest.sns.it> References: <39CC802D-6880-4485-ABA8-D209ED4297CD@nest.sns.it> Message-ID: I hope this is enough: I am working on a windows xp machine with cygwin version 1.5.24 the gcc compiler version is 3.4.4 expresso code version is 3.2.3 On Wed, 24 Oct 2007 18:18:59 +0200 Paolo Giannozzi wrote: > > On Oct 24, 2007, at 15:58 , Martina Dell'Angela wrote: > >> I'm having some troubles in running some examples >> contained in the example directory. >> All of them using ph.x did not work. >> The message I got is for example for example 2: >> ---- >> running the phonon calculation at Gamma... 7 [main] >>ph.x >> 3144_ctgtls::handle_exceptions: Error while dumping >>state >> (probably >> corrupted stack) >> ./runexample: line 137: 3144 Segmentation fault (core >> dumped) $PH_COMMAND$ >> ---------- >> What happens? > > something that cannot be explained on the basis of so >little > information. Machine, compiler, code version? > > P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at nest.sns.it Wed Oct 24 18:55:05 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 24 Oct 2007 18:55:05 +0200 Subject: [Pw_forum] problem ph.x In-Reply-To: References: <39CC802D-6880-4485-ABA8-D209ED4297CD@nest.sns.it> Message-ID: <4C48CEF1-1C87-4331-99B9-D7ACF90B1759@nest.sns.it> On Oct 24, 2007, at 18:34 , Martina Dell'Angela wrote: > I am working on a windows xp machine with cygwin version 1.5.24 wow! so it works on windows... > the gcc compiler version is 3.4.4 > expresso code version is 3.2.3 f90 compiler: ifort, g95, gfortran? some versions of ifort are buggy; others have known problem with too much allocated stack. See here: http://www.quantum-espresso.org/wiki/index.php/ Installation#Installation_issues and here http://www.quantum-espresso.org/wiki/index.php/Troubleshooting_% 28PWscf%29 G95 is very stable; only recent versions of gfortran work well. 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 w2agz at pacbell.net Wed Oct 24 19:35:46 2007 From: w2agz at pacbell.net (Paul M. Grant) Date: Wed, 24 Oct 2007 10:35:46 -0700 Subject: [Pw_forum] kubuntu+gfortran+configure+make all=no executables Message-ID: <009601c81664$50167990$f0436cb0$@net> First of all, thanks to Baris, Joerg and Paolo for getting back so fast.you guys are great. I will answer your questions in detail later. I ran into this problem last night around midnight and I apologize for my rather cryptic posting, but I was half asleep. I'm digging into this a little more deeply, so let me pass on the latest.it's very strange.it may be a "permissions" or file type matter or some sort of flag that needs to be fed to gfortran. I think I can claim to be a wizard on the XP-SP2 registry and file system, but Linux is still strange to me. I'm in a directory ~/espresso-3.2.3/bin console window, and when I type "ls -lsh pw.x" I get 0 lrwxrwxrwx 1 pmpgrant pmpgrant 10 2007-10-23 23:09 pw.x -> ../PW/pw.x Now there is no pw.x in PW (only holds .o and .f90 files) and I think what this is saying that Linux thinks the pw.x in ~/bin is a "0-byte link" to an executable "somewhere." Yet when I open ~/bin in Dolphin (the new KDE file manager), the Details view shows that the file pw.x is 2.7 MB in size! At the bottom of the window, Dophin reports (I wish screenshots could be sent to the forum) "pw.x -> ../PW/pw.x Executable File (Link)" It's as if the Linux "Link Editor (that's old IBM jargon.what's it called here? make.x?)" got confused and assigned a link attribute to what is really an executable binary file. The same pattern holds true for all the QE .x files to be found in ~/bin. I'll bet if the "l" attribute can be removed, I'll have an executable (how can I do this.chmod?). Thanks again, and I will get back with details on the problems installing Intel compiler is having with Ubuntu 7.10 which I think is a bug in the former. -Paul Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford University EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071024/320c2e13/attachment.htm From akohlmey at cmm.chem.upenn.edu Wed Oct 24 20:57:12 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 24 Oct 2007 14:57:12 -0400 (EDT) Subject: [Pw_forum] kubuntu+gfortran+configure+make all=no executables In-Reply-To: <009601c81664$50167990$f0436cb0$@net> References: <009601c81664$50167990$f0436cb0$@net> Message-ID: On Wed, 24 Oct 2007, Paul M. Grant wrote: hi paul, PG> First of all, thanks to Baris, Joerg and Paolo for getting back so fast.you PG> guys are great. yep. they are. it is nice to see a forum, where there are many people answering questions and not just one or two. ;-) [...] PG> I'm in a directory ~/espresso-3.2.3/bin console window, and when I type "ls PG> -lsh pw.x" I get PG> PG> PG> PG> 0 lrwxrwxrwx 1 pmpgrant pmpgrant 10 2007-10-23 23:09 pw.x -> ../PW/pw.x PG> ok. this is the way QE works. you have a collection of so-called symbolic links in the bin directory pointing to the corresponding executables. compared to windows a symbolic link is like those .lnk files, i.e. an entry in a directory the redirects elsewhere. only that in the linux/unix case it is most transparent. PG> Now there is no pw.x in PW (only holds .o and .f90 files) and I think what PG> this is saying that Linux thinks the pw.x in ~/bin is a "0-byte link" to an PG> executable "somewhere." are you sure of that? PG> Yet when I open ~/bin in Dolphin (the new KDE file manager), the Details PG> view shows that the file pw.x is 2.7 MB in size! At the bottom of the that means, that the symbolic link is actually pointing somewhere. you can verify this very easily by doing: file bin/pw.x this will tell you whether the link works or is 'broken'. PG> window, Dophin reports (I wish screenshots could be sent to the forum) "pw.x PG> -> ../PW/pw.x Executable File (Link)" It's as if the Linux "Link Editor PG> (that's old IBM jargon.what's it called here? make.x?)" got confused and PG> assigned a link attribute to what is really an executable binary file. The PG> same pattern holds true for all the QE .x files to be found in ~/bin. I'll PG> bet if the "l" attribute can be removed, I'll have an executable (how can I PG> do this.chmod?). nope this attribute cannot be removed and it is not an artefact of the linker (its name is ld, btw). a symbolic link, like a directory, a fifo, a socket or a device node is a special filesystem entry with special semantics and those cannot be changed with chmod. if the linker fails it usually deletes the resulting partial object, or (and this is what might have happened) it will leave a file without executable permissions. PG> PG> Thanks again, and I will get back with details on the problems installing PG> Intel compiler is having with Ubuntu 7.10 which I think is a bug in the PG> former. it is actually about as likely, that ubuntu 7.10 is using a very new glibc that introduces yet another quirkiness which results in backward incompabibility of binaries. it would not be the first time. please note, that the intel compilers (which version are you using btw) are only verified on a subset of linux machines, and particularly putting it on a new release is always risky. there may be some changes in libraries, and/or linker that are not handled by the linker/runtime of the intel compilers. cheers, axel. PG> PG> PG> PG> -Paul PG> PG> PG> PG> Paul M. Grant, PhD PG> PG> Principal, W2AGZ Technologies PG> PG> Visiting Scholar, Applied Physics, Stanford University PG> PG> EPRI Science Fellow (Retired) PG> PG> IBM Research Staff Member Emeritus PG> PG> w2agz at pacbell.net PG> PG> http://www.w2agz.com PG> PG> PG> PG> PG> PG> PG> PG> -- ======================================================================= 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 w2agz at pacbell.net Wed Oct 24 21:05:37 2007 From: w2agz at pacbell.net (Paul M. Grant) Date: Wed, 24 Oct 2007 12:05:37 -0700 Subject: [Pw_forum] kubuntu+gfortran+configure+make all=no executables In-Reply-To: References: <009601c81664$50167990$f0436cb0$@net> Message-ID: <00ba01c81670$de33e3f0$9a9babd0$@net> Axel, just before opening your note, I was able to run example01! This shows you how little I understand bash and pathing (that's what's it called in DOS...and OS/2 Warp) in Linux. I then went to my /home and typed in the full path to pw.x and it ran...well, sort of...no input, of course. Thanks, and I'll now read the rest of your note! Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford University EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com ? ? -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Axel Kohlmeyer Sent: Wednesday, October 24, 2007 11:57 AM To: Paul M. Grant Cc: pw_forum at pwscf.org Subject: Re: [Pw_forum] kubuntu+gfortran+configure+make all=no executables On Wed, 24 Oct 2007, Paul M. Grant wrote: hi paul, PG> First of all, thanks to Baris, Joerg and Paolo for getting back so fast.you PG> guys are great. yep. they are. it is nice to see a forum, where there are many people answering questions and not just one or two. ;-) [...] PG> I'm in a directory ~/espresso-3.2.3/bin console window, and when I type "ls PG> -lsh pw.x" I get PG> PG> PG> PG> 0 lrwxrwxrwx 1 pmpgrant pmpgrant 10 2007-10-23 23:09 pw.x -> ../PW/pw.x PG> ok. this is the way QE works. you have a collection of so-called symbolic links in the bin directory pointing to the corresponding executables. compared to windows a symbolic link is like those .lnk files, i.e. an entry in a directory the redirects elsewhere. only that in the linux/unix case it is most transparent. PG> Now there is no pw.x in PW (only holds .o and .f90 files) and I think what PG> this is saying that Linux thinks the pw.x in ~/bin is a "0-byte link" to an PG> executable "somewhere." are you sure of that? PG> Yet when I open ~/bin in Dolphin (the new KDE file manager), the Details PG> view shows that the file pw.x is 2.7 MB in size! At the bottom of the that means, that the symbolic link is actually pointing somewhere. you can verify this very easily by doing: file bin/pw.x this will tell you whether the link works or is 'broken'. PG> window, Dophin reports (I wish screenshots could be sent to the forum) "pw.x PG> -> ../PW/pw.x Executable File (Link)" It's as if the Linux "Link Editor PG> (that's old IBM jargon.what's it called here? make.x?)" got confused and PG> assigned a link attribute to what is really an executable binary file. The PG> same pattern holds true for all the QE .x files to be found in ~/bin. I'll PG> bet if the "l" attribute can be removed, I'll have an executable (how can I PG> do this.chmod?). nope this attribute cannot be removed and it is not an artefact of the linker (its name is ld, btw). a symbolic link, like a directory, a fifo, a socket or a device node is a special filesystem entry with special semantics and those cannot be changed with chmod. if the linker fails it usually deletes the resulting partial object, or (and this is what might have happened) it will leave a file without executable permissions. PG> PG> Thanks again, and I will get back with details on the problems installing PG> Intel compiler is having with Ubuntu 7.10 which I think is a bug in the PG> former. it is actually about as likely, that ubuntu 7.10 is using a very new glibc that introduces yet another quirkiness which results in backward incompabibility of binaries. it would not be the first time. please note, that the intel compilers (which version are you using btw) are only verified on a subset of linux machines, and particularly putting it on a new release is always risky. there may be some changes in libraries, and/or linker that are not handled by the linker/runtime of the intel compilers. cheers, axel. PG> PG> PG> PG> -Paul PG> PG> PG> PG> Paul M. Grant, PhD PG> PG> Principal, W2AGZ Technologies PG> PG> Visiting Scholar, Applied Physics, Stanford University PG> PG> EPRI Science Fellow (Retired) PG> PG> IBM Research Staff Member Emeritus PG> PG> w2agz at pacbell.net PG> PG> http://www.w2agz.com PG> PG> PG> PG> PG> PG> PG> PG> -- ======================================================================= 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 akohlmey at cmm.chem.upenn.edu Wed Oct 24 21:43:52 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 24 Oct 2007 15:43:52 -0400 (EDT) Subject: [Pw_forum] kubuntu+gfortran+configure+make all=no executables In-Reply-To: <00ba01c81670$de33e3f0$9a9babd0$@net> References: <009601c81664$50167990$f0436cb0$@net> <00ba01c81670$de33e3f0$9a9babd0$@net> Message-ID: On Wed, 24 Oct 2007, Paul M. Grant wrote: PG> Axel, just before opening your note, I was able to run example01! This PG> shows you how little I understand bash and pathing (that's what's it called PG> in DOS...and OS/2 Warp) in Linux. I then went to my /home and typed in the PG> full path to pw.x and it ran...well, sort of...no input, of course. a-ha. you are just another 'victim' of the 'dot-first' strategy in dos (and related OS'es). if you do not use an absolute path, the current working directory is search for a matching executable first. on unix/linux machines, this is considered a security risk. say, some bad co-user of your machine finds a way to have you cd into one of his directories and that directory contains an executable called 'ls'. now you are likely to type ls to see what is in this directory, but with the 'dot-first' strategy, you would execute the local ls and not the one in the system path. and that local 'ls' can be modified to installa trojan and/or keylogger into your account and then all your passwords can be looked up. this is all the more dangerous when it happens to a root user. now if you do not have the current working directory (or '.') in your path, you are safe(r) from that problem, but you have to type './pw.x' instead of 'pw.x'. you can emulate the DOS-like behavior by changing your path, e.g. with export PATH=.:${PATH}, but that can be very confusing. an acceptable compromise would be to set 'export PATH=${PATH}:.' in which local directories are examined _after_ the system directories. PG> PG> Thanks, and I'll now read the rest of your note! don't know whether there is much else to learn. i think with your comment, you have found an explanation (and also demonstrated to me that graphical file managers are inferior to the command line in 99% of the cases. ;-) ). cheers, axel. PG> PG> Paul M. Grant, PhD PG> Principal, W2AGZ Technologies PG> Visiting Scholar, Applied Physics, Stanford University PG> EPRI Science Fellow (Retired) PG> IBM Research Staff Member Emeritus PG> w2agz at pacbell.net PG> http://www.w2agz.com PG> ? PG> ? PG> PG> -----Original Message----- PG> From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On PG> Behalf Of Axel Kohlmeyer PG> Sent: Wednesday, October 24, 2007 11:57 AM PG> To: Paul M. Grant PG> Cc: pw_forum at pwscf.org PG> Subject: Re: [Pw_forum] kubuntu+gfortran+configure+make all=no executables PG> PG> On Wed, 24 Oct 2007, Paul M. Grant wrote: PG> PG> hi paul, PG> PG> PG> First of all, thanks to Baris, Joerg and Paolo for getting back so PG> fast.you PG> PG> guys are great. PG> PG> yep. they are. it is nice to see a forum, where there are PG> many people answering questions and not just one or two. ;-) PG> PG> [...] PG> PG> PG> I'm in a directory ~/espresso-3.2.3/bin console window, and when I type PG> "ls PG> PG> -lsh pw.x" I get PG> PG> PG> PG> PG> PG> PG> PG> 0 lrwxrwxrwx 1 pmpgrant pmpgrant 10 2007-10-23 23:09 pw.x -> ../PW/pw.x PG> PG> PG> PG> ok. this is the way QE works. you have a collection of so-called PG> symbolic links in the bin directory pointing to the corresponding PG> executables. compared to windows a symbolic link is like those PG> .lnk files, i.e. an entry in a directory the redirects elsewhere. PG> only that in the linux/unix case it is most transparent. PG> PG> PG> Now there is no pw.x in PW (only holds .o and .f90 files) and I think PG> what PG> PG> this is saying that Linux thinks the pw.x in ~/bin is a "0-byte link" to PG> an PG> PG> executable "somewhere." PG> PG> are you sure of that? PG> PG> PG> Yet when I open ~/bin in Dolphin (the new KDE file manager), the Details PG> PG> view shows that the file pw.x is 2.7 MB in size! At the bottom of the PG> PG> that means, that the symbolic link is actually pointing somewhere. PG> you can verify this very easily by doing: file bin/pw.x PG> this will tell you whether the link works or is 'broken'. PG> PG> PG> window, Dophin reports (I wish screenshots could be sent to the forum) PG> "pw.x PG> PG> -> ../PW/pw.x Executable File (Link)" It's as if the Linux "Link Editor PG> PG> (that's old IBM jargon.what's it called here? make.x?)" got confused and PG> PG> assigned a link attribute to what is really an executable binary file. PG> The PG> PG> same pattern holds true for all the QE .x files to be found in ~/bin. PG> I'll PG> PG> bet if the "l" attribute can be removed, I'll have an executable (how PG> can I PG> PG> do this.chmod?). PG> PG> nope this attribute cannot be removed and it is not an artefact of the PG> linker (its name is ld, btw). a symbolic link, like a directory, a fifo, PG> a socket or a device node is a special filesystem entry with special PG> semantics and those cannot be changed with chmod. if the linker fails PG> it usually deletes the resulting partial object, or (and this is what PG> might have happened) it will leave a file without executable PG> permissions. PG> PG> PG> PG> PG> Thanks again, and I will get back with details on the problems PG> installing PG> PG> Intel compiler is having with Ubuntu 7.10 which I think is a bug in the PG> PG> former. PG> PG> it is actually about as likely, that ubuntu 7.10 is using a very new PG> glibc that introduces yet another quirkiness which results in PG> backward incompabibility of binaries. it would not be the first time. PG> PG> please note, that the intel compilers (which version are you using btw) PG> are only verified on a subset of linux machines, and particularly PG> putting it on a new release is always risky. there may be some changes PG> in libraries, and/or linker that are not handled by the linker/runtime PG> of the intel compilers. PG> PG> cheers, PG> axel. PG> PG> PG> PG> PG> PG> PG> PG> PG> -Paul PG> PG> PG> PG> PG> PG> PG> PG> Paul M. Grant, PhD PG> PG> PG> PG> Principal, W2AGZ Technologies PG> PG> PG> PG> Visiting Scholar, Applied Physics, Stanford University PG> PG> PG> PG> EPRI Science Fellow (Retired) PG> PG> PG> PG> IBM Research Staff Member Emeritus PG> PG> PG> PG> w2agz at pacbell.net PG> PG> PG> PG> http://www.w2agz.com PG> PG> PG> PG> PG> PG> PG> PG> PG> PG> PG> PG> PG> PG> PG> PG> PG> PG> -- ======================================================================= 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 w2agz at pacbell.net Thu Oct 25 01:39:12 2007 From: w2agz at pacbell.net (Paul M. Grant) Date: Wed, 24 Oct 2007 16:39:12 -0700 Subject: [Pw_forum] kubuntu+gfortran+configure+make all=no executables Message-ID: <00bb01c81697$155d54d0$4017fe70$@net> Baris, Joerg, Paolo and Axel: I apologize for the commotion the entire issue was due to a blunder on my part. I had mistakenly ?source-d? instead of ?export-ed? the path to the QE binaries in .bashrc! Grrr. When I tried to execute the QE binaries in the bin directory, bash reported it couldn?t find the files. That?s when I saw the executables had the ?l? attribute set and got thoroughly confused by the nomenclature which I still don?t completely understand why the ?make? routine does this the ?link? seems somewhat ?recursive? (incestuous?) in that the executable code is buried in what seems to be a ?link.? In Windows, a .lnk really does point to a separate file. BTW, Axel, if you do a ?cp pw.x xpw.x?, xpw.x loses the ?l? attribute and actually does ?look and feel like? an executable in ls ?l and a KDE file manager and it does run when you have the pathing right. For newbies the best advice is to run example01 if they think they?ve got a successful build the run_example scripts ?look around? and make sure everything is found and pathed and more or less ignores .bashrc. Incidentally, whoever wrote the ?configure? script deserves a case or two of pinot grigio from the QE development staff. I did take Axel?s advice and ran ?file? against both pw.x and xpw.x and got the following (respectively): pw.x: symbolic link to ?../PW/pw.x? (Weird my comment do they really mean ?..PW/pw.o??) xpw.x: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), for GNU/Linux 2.6.8, dynamically linked (uses shared libs), not stripped. OK, now on to agonies with the Intel compiler and (K)Ubuntu 7.10. Axel, please go to the following posting: http://ubuntuforums.org/showthread.php?p=3603521. This is exactly the error that occurred with me on attempting an install of 10.0.023. You can see from the responses that apparently someone was able with a tour de force effort to hack a fix. (BTW, the Intel install complained as usual it couldn?t find g++ and I had to go get the distro for that first.). I then tried backing off to 9.1.045 and got the same error message at a different line in ./install.sh. So Axel, you may be right the problem could be in the new Ubuntu distro. Incidentally, the install docs for the Intel Fortran compiler do not mention Ubuntu as a tested platform nor Debian, which is really wild only Red Hat and SUSE derivatives. Re glibc, I don?t really know where it sits in the directory structure (this is a issue I?ve always had with Unix-derived OS?s vis-?-vis DOS/Windows, and the location seems to change with the distro). The Ubuntu repository doc lists it as 2.6.1-1ubuntu9. Gcc and g++ seem to be around the GNU 4.2 level. I?ve had success on several of my machines using openSUSE with Intel Fortran and the LAPACK/BLAS distributed with QE. More about that in a separate post. Given all this new grief with Intel Fortran and Ubuntu (which I will post to the respective user groups), I decided to try one of the GNU distributions. My understanding is that a ?divorce? or ?forking? occurred several years ago between g95 and gfortran and the latter became the ?official? GNU release (I have no idea which of the three ifort, g95 or gfortran is ?best? for QE can someone out there advise?). Since I was changing compilers, I thought I would also change math libraries (there is a very cryptic remark in the QE UG that ? vendor-optimized libraries can be used: this often yields huge gains.? Axel, I think you?re the keeper of the libraries which one(s) give the ?hugest gains.?) . Because Intel Fortran install bombed, I was leery of trying Intel MLK. I did notice the Ubuntu repositories contained a package called lapack3 and refblas3, so I downloaded and installed them. I don?t think configure found them, though, since a quick scan on config.log only picked up the flib .a archives for lapack and blas. If I can figure out how to point configure to the lapack3 and refblas3 libs, I?ll test them against my favorite QE benchmark example07. Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford University EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071024/ae275505/attachment.htm From akohlmey at cmm.chem.upenn.edu Thu Oct 25 02:29:04 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 24 Oct 2007 20:29:04 -0400 Subject: [Pw_forum] kubuntu+gfortran+configure+make all=no executables In-Reply-To: <00bb01c81697$155d54d0$4017fe70$@net> References: <00bb01c81697$155d54d0$4017fe70$@net> Message-ID: <7b6913e90710241729g681a72dapec71a489f771c182@mail.gmail.com> On 10/24/07, Paul M. Grant wrote: paul, > Baris, Joerg, Paolo and Axel: I apologize for the commotion?the entire > issue was due to a blunder on my part. I had mistakenly "source-d" instead > of "export-ed" the path to the QE binaries in .bashrc! Grrr. When I tried > to execute the QE binaries in the bin directory, bash reported it couldn't no problem. > find the files. That's when I saw the executables had the "l" attribute set > and got thoroughly confused by the nomenclature?which I still don't > completely understand why the "make" routine does this?the "link" seems > somewhat "recursive" (incestuous?) in that the executable code is buried in > what seems to be a "link." In Windows, a .lnk really does point to a no. the purpose of a (symbolic) link is to give you access to a file without having to copy it (and saving disk space in the process). the make program loops over the subdirectories and compiles the various executables there, but for convenience, they are then 'collected' in bin through symlinks. for details, check out, e.g., http://en.wikipedia.org/wiki/Symbolic_Link the symbolic link in unix is superior to windows in that if you copy it, you don't copy the link, but the object it points to. > separate file. BTW, Axel, if you do a "cp pw.x xpw.x", xpw.x loses the "l" > attribute and actually does "look and feel like" an executable in ls ?l and yes. that is the expected behavior and you create a real copy, since the symlink redirects you to the real binary. probably what is most confusing to you is the fact, that the 'link' part of a symlink has nothing to do with the linking (or binding) of an executable. [...] > > I did take Axel's advice and ran "file" against both pw.x and xpw.x and got > the following (respectively): > > pw.x: symbolic link to '../PW/pw.x' (Weird?my comment?do they really mean > '..PW/pw.o'?) no that is correct. the real executable is built in ../PW/pw.x, seen relative from bin. so executing ./bin/pw.x actually will execute ./bin/../PW/pw.x does that make sense to you? [...] > OK, now on to agonies with the Intel compiler and (K)Ubuntu 7.10. Axel, > please go to the following posting: > http://ubuntuforums.org/showthread.php?p=3603521. This is > exactly the error that occurred with me on attempting an install of > 10.0.023. You can see from the responses that apparently someone was able > with a tour de force effort to hack a fix. (BTW, the Intel install > complained as usual it couldn't find g++ and I had to go get the distro for > that first.). I then tried backing off to 9.1.045 and got the same error > message at a different line in ./install.sh. So Axel, you may be right?the > problem could be in the new Ubuntu distro. Incidentally, the install docs ha ha. this is funny. i should have run into the same problem when intalling intel 10 on my (fresh installed) fedora 7.92 laptop, but since i don't like the the intel installer messing with my installations, and since i hate having to set environment variables with for LD_LIBRARY_PATH globally, i always avoided the install.sh script and used rpm directly and was using my own wrapper in /usr/local/bin, e.g. for ifort #!/bin/sh PATH="/opt/intel/fc/10.0.026/bin:${PATH}" INTEL_LICENSE_FILE=${HOME}/licenses:/opt/intel/licenses export INTEL_LICENSE_FILE PATH exec -a "/opt/intel/fc/10.0.026/bin/ifort" /opt/intel/fc/10.0.026/bin/ifortbin "$@" this has been working very well for me since intel 8.0. lesson: sometimes paranoia about automated tools guessing wrong can help you avoid a lot of trouble. ;-) > for the Intel Fortran compiler do not mention Ubuntu as a tested > platform?nor Debian, which is really wild?only Red Hat and SUSE derivatives. > Re glibc, I don't really know where it sits in the directory structure > (this is a issue I've always had with Unix-derived OS's vis-?-vis > DOS/Windows, and the location seems to change with the distro). The Ubuntu > repository doc lists it as 2.6.1-1ubuntu9. Gcc and g++ seem to be around > the GNU 4.2 level. fedora 7.92 has gcc-4.1.2 and glibc 2.7 hmm,.... > I've had success on several of my machines using openSUSE with Intel Fortran > and the LAPACK/BLAS distributed with QE. More about that in a separate > post. > Given all this new grief with Intel Fortran and Ubuntu (which I will post to > the respective user groups), I decided to try one of the GNU distributions. > My understanding is that a "divorce" or "forking" occurred several years ago > between g95 and gfortran and the latter became the "official" GNU release (I > have no idea which of the three?ifort, g95 or gfortran?is "best" for QE?can > someone out there advise?). Since I was changing compilers, I thought I i think a lot of people use intel. on many x86 machines it produces the fastest code, but one has to stay up-to-date with the patches. g95 is more complete as a fortran95 compiler as gfortran, which still has a few more quirks, but is continously getting better. > would also change math libraries (there is a very cryptic remark in the QE > UG that "?vendor-optimized libraries can be used: this often yields huge > gains." Axel, I think you're the keeper of the libraries?which one(s) give > the "hugest gains.") . Because Intel Fortran install bombed, I was leery of the default fortran implementations of LAPACK and BLAS are usually the slowest, and those are the ones that most distributions ship. fedora now offers ATLAS rpms as drop-in. ATLAS is a re-implementation of BLAS and some parts of LAPACK in a ways that it can automatically adapt to the cpu/hardware during compilation. for distributions (or commercial packages) this is not feasable, so they ship alternate versions for different hardware combinations or some generic optimization. the major jump is from the (cpu cache ignorant) fortran versions to the (cpu cache aware) versions (e.g. ATLAS, MKL, ACML, GOTO). the rest is usually a minor contribution. with MKL it seems to me that recently, intel is optimizing MKL in a way that it assumes the (2x larger) cache size of the xeon versions of processors, which means that desktops don't perform as well as the corresponding xeon of the same or lower clock (which is usually much more expensive). there are now also ACML versions that work with intel, and recent intels (woodcrest, clovertown and co) are much more similar to opterons than the (netburst) pentium4, so that this is an alternative. in the end, you have to test on your hardware with several options and pick the one that works best. i usually go for something convenient (= MKL). i rather spend my time on thinking about the most efficient strategy of calculations then fighting for the last half percent of optimal speed. you lose more time in doing useless calculations. so even if you can do those a little bit faster does not help you as much as knowing that they are useless _before_ you do them. > trying Intel MLK. I did notice the Ubuntu repositories contained a package > called lapack3 and refblas3, so I downloaded and installed them. I don't > think configure found them, though, since a quick scan on config.log only > picked up the flib .a archives for lapack and blas. those are probably even slower than the blas/lapack shipped with QE, since they are likely to be compiled as shared libraries (shared libraries are up to 10% slower). not worth the effort for the reasons from above. cheers, axel. > If I can figure out how to point configure to the lapack3 and refblas3 libs, > I'll test them against my favorite QE benchmark?example07. > > > > Paul M. Grant, PhD > > Principal, W2AGZ Technologies > > Visiting Scholar, Applied Physics, Stanford University > > EPRI Science Fellow (Retired) > > IBM Research Staff Member Emeritus > > w2agz at pacbell.net > > http://www.w2agz.com > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From sunshoutian168 at yahoo.com.cn Thu Oct 25 03:12:33 2007 From: sunshoutian168 at yahoo.com.cn (shoutian sun) Date: Thu, 25 Oct 2007 09:12:33 +0800 (CST) Subject: [Pw_forum] A problem K_POINTS nq and q2r.x in calculation of dispersion curve and DOS. Message-ID: <909104.65924.qm@web92006.mail.cnb.yahoo.com> >Dear all, >I set 5 5 5 1 1 1 in K_POINTS {automatic} and nq1=3, nq2=2, nq3=2 in &inputph,then I got a series of al.dyn...,after that I calculate >force constants with q2r.x,and the errors appeared in q2r.in.out. > >If set 5 5 5 1 1 1 inK_POINTS {automatic} and nq1=3, nq2=3, nq3=3 in &inputph everything is OK, so can anyone tell me the reasons? > >Thank you so much. > >&control > calculation='scf' > restart_mode='from_scratch', > tstress = .true. > tprnfor = .true. > prefix='al', > etot_conv_thr = 1.0E-6 , > forc_conv_thr = 1.0D-5 , > pseudo_dir = '/home/user/ecnuphyk/SUN/pseudo/', > outdir='/home/user/ecnuphyk/SUN/tmp/tmp4/' > / > &system > ibrav= 2, celldm(1) =7.6197064734844, nat= 1, ntyp= 1, > ecutwfc =25.0, > occupations='smearing', smearing='methfessel-paxton', degauss=0.005, > / > &electrons > conv_thr = 1.0d-8 > mixing_beta = 0.7 > / >ATOMIC_SPECIES > Al 26.98 Al.pw91-n-van.UPF >ATOMIC_POSITIONS > Al 0.00 0.00 0.00 >K_POINTS {automatic} > 5 5 5 1 1 1 >************************************************* >phonons of Al > &inputph > tr2_ph=1.0d-14, > prefix='al', > ldisp=.true., > trans=.true., > nq1=3, nq2=2, nq3=2 , > amass(1)=26.98, > outdir='/home/user/ecnuphyk/SUN/tmp/tmp4/', > fildyn='al.dyn', > / >********************************************************* >[ecnuphyk at access001 a]$ more q2r.in.out > reading grid info from file al.dyn0 > reading force constants from file al.dyn1 > Dielectric Tensor not found > nqs= 1 > q= 0.00000000 0.00000000 0.00000000 > reading force constants from file al.dyn2 > nqs= 4 > q= 0.50000000 -0.50000000 0.50000000 > q= -0.50000000 0.50000000 0.50000000 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from init : error # 1 > q not allowed > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... >******************************************************* --------------------------------- ?????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071025/a094c308/attachment.htm From w2agz at pacbell.net Thu Oct 25 03:20:56 2007 From: w2agz at pacbell.net (Paul M. Grant) Date: Wed, 24 Oct 2007 18:20:56 -0700 Subject: [Pw_forum] kubuntu+gfortran+configure+make all=no executables In-Reply-To: References: <009601c81664$50167990$f0436cb0$@net> <00ba01c81670$de33e3f0$9a9babd0$@net> Message-ID: <00d601c816a5$4b6d5350$e247f9f0$@net> Axel, thanks for the dialog. Naively I thought dot-slash first replied only to executing bash scripts, not executables. Between this note and the last, I sent an "mea culpa" to all...you'll find it amusing I hope! Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford University EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com ? ? -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Axel Kohlmeyer Sent: Wednesday, October 24, 2007 12:44 PM To: PWSCF Forum Subject: Re: [Pw_forum] kubuntu+gfortran+configure+make all=no executables On Wed, 24 Oct 2007, Paul M. Grant wrote: PG> Axel, just before opening your note, I was able to run example01! PG> This shows you how little I understand bash and pathing (that's PG> what's it called in DOS...and OS/2 Warp) in Linux. I then went to PG> my /home and typed in the full path to pw.x and it ran...well, sort of...no input, of course. a-ha. you are just another 'victim' of the 'dot-first' strategy in dos (and related OS'es). if you do not use an absolute path, the current working directory is search for a matching executable first. on unix/linux machines, this is considered a security risk. say, some bad co-user of your machine finds a way to have you cd into one of his directories and that directory contains an executable called 'ls'. now you are likely to type ls to see what is in this directory, but with the 'dot-first' strategy, you would execute the local ls and not the one in the system path. and that local 'ls' can be modified to installa trojan and/or keylogger into your account and then all your passwords can be looked up. this is all the more dangerous when it happens to a root user. now if you do not have the current working directory (or '.') in your path, you are safe(r) from that problem, but you have to type './pw.x' instead of 'pw.x'. you can emulate the DOS-like behavior by changing your path, e.g. with export PATH=.:${PATH}, but that can be very confusing. an acceptable compromise would be to set 'export PATH=${PATH}:.' in which local directories are examined _after_ the system directories. PG> PG> Thanks, and I'll now read the rest of your note! don't know whether there is much else to learn. i think with your comment, you have found an explanation (and also demonstrated to me that graphical file managers are inferior to the command line in 99% of the cases. ;-) ). cheers, axel. PG> PG> Paul M. Grant, PhD PG> Principal, W2AGZ Technologies PG> Visiting Scholar, Applied Physics, Stanford University EPRI Science PG> Fellow (Retired) IBM Research Staff Member Emeritus PG> w2agz at pacbell.net http://www.w2agz.com PG> ? PG> ? PG> PG> -----Original Message----- PG> From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On PG> Behalf Of Axel Kohlmeyer PG> Sent: Wednesday, October 24, 2007 11:57 AM PG> To: Paul M. Grant PG> Cc: pw_forum at pwscf.org PG> Subject: Re: [Pw_forum] kubuntu+gfortran+configure+make all=no executables PG> PG> On Wed, 24 Oct 2007, Paul M. Grant wrote: PG> PG> hi paul, PG> PG> PG> First of all, thanks to Baris, Joerg and Paolo for getting back so PG> fast.you PG> PG> guys are great. PG> PG> yep. they are. it is nice to see a forum, where there are PG> many people answering questions and not just one or two. ;-) PG> PG> [...] PG> PG> PG> I'm in a directory ~/espresso-3.2.3/bin console window, and when I type PG> "ls PG> PG> -lsh pw.x" I get PG> PG> PG> PG> PG> PG> PG> PG> 0 lrwxrwxrwx 1 pmpgrant pmpgrant 10 2007-10-23 23:09 pw.x -> ../PW/pw.x PG> PG> PG> PG> ok. this is the way QE works. you have a collection of so-called PG> symbolic links in the bin directory pointing to the corresponding PG> executables. compared to windows a symbolic link is like those PG> .lnk files, i.e. an entry in a directory the redirects elsewhere. PG> only that in the linux/unix case it is most transparent. PG> PG> PG> Now there is no pw.x in PW (only holds .o and .f90 files) and I think PG> what PG> PG> this is saying that Linux thinks the pw.x in ~/bin is a "0-byte link" to PG> an PG> PG> executable "somewhere." PG> PG> are you sure of that? PG> PG> PG> Yet when I open ~/bin in Dolphin (the new KDE file manager), the Details PG> PG> view shows that the file pw.x is 2.7 MB in size! At the bottom of the PG> PG> that means, that the symbolic link is actually pointing somewhere. PG> you can verify this very easily by doing: file bin/pw.x PG> this will tell you whether the link works or is 'broken'. PG> PG> PG> window, Dophin reports (I wish screenshots could be sent to the forum) PG> "pw.x PG> PG> -> ../PW/pw.x Executable File (Link)" It's as if the Linux "Link Editor PG> PG> (that's old IBM jargon.what's it called here? make.x?)" got confused and PG> PG> assigned a link attribute to what is really an executable binary file. PG> The PG> PG> same pattern holds true for all the QE .x files to be found in ~/bin. PG> I'll PG> PG> bet if the "l" attribute can be removed, I'll have an executable (how PG> can I PG> PG> do this.chmod?). PG> PG> nope this attribute cannot be removed and it is not an artefact of the PG> linker (its name is ld, btw). a symbolic link, like a directory, a fifo, PG> a socket or a device node is a special filesystem entry with special PG> semantics and those cannot be changed with chmod. if the linker fails PG> it usually deletes the resulting partial object, or (and this is what PG> might have happened) it will leave a file without executable PG> permissions. PG> PG> PG> PG> PG> Thanks again, and I will get back with details on the problems PG> installing PG> PG> Intel compiler is having with Ubuntu 7.10 which I think is a bug in the PG> PG> former. PG> PG> it is actually about as likely, that ubuntu 7.10 is using a very new PG> glibc that introduces yet another quirkiness which results in PG> backward incompabibility of binaries. it would not be the first time. PG> PG> please note, that the intel compilers (which version are you using btw) PG> are only verified on a subset of linux machines, and particularly PG> putting it on a new release is always risky. there may be some changes PG> in libraries, and/or linker that are not handled by the linker/runtime PG> of the intel compilers. PG> PG> cheers, PG> axel. PG> PG> PG> PG> PG> PG> PG> PG> PG> -Paul PG> PG> PG> PG> PG> PG> PG> PG> Paul M. Grant, PhD PG> PG> PG> PG> Principal, W2AGZ Technologies PG> PG> PG> PG> Visiting Scholar, Applied Physics, Stanford University PG> PG> PG> PG> EPRI Science Fellow (Retired) PG> PG> PG> PG> IBM Research Staff Member Emeritus PG> PG> PG> PG> w2agz at pacbell.net PG> PG> PG> PG> http://www.w2agz.com PG> PG> PG> PG> PG> PG> PG> PG> PG> PG> PG> PG> PG> PG> PG> PG> PG> PG> -- ======================================================================= 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 lanhaiping at gmail.com Thu Oct 25 07:42:25 2007 From: lanhaiping at gmail.com (lan haiping) Date: Thu, 25 Oct 2007 13:42:25 +0800 Subject: [Pw_forum] How to deal with semicore states with Norm conserving PP? In-Reply-To: <48ED2D3C-610A-4319-B39E-B7330606DF1A@nest.sns.it> References: <48ED2D3C-610A-4319-B39E-B7330606DF1A@nest.sns.it> Message-ID: Thank you, Paolo. I will try it . I want to generate a ncpp for Ti atom, is it possible test the generated pp with ultrasoft one ? cheers , Hai.Ping On 10/24/07, Paolo Giannozzi wrote: > > > On Oct 24, 2007, at 13:09 , lan haiping wrote: > > > I just found that opium package cannot generate ncpp for elements > > including semicore states . > > Is there any other scheme for norm conserving pseudopentials can > > take semicore states into account for pwscf calculation ? > > the pseudopotential code of quantum-espresso (in atomic/ subdir) > can do this. It is a little bit tricky, though > > Paolo > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- 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/20071025/78da1c7b/attachment.htm From eyvaz_isaev at yahoo.com Thu Oct 25 10:13:52 2007 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 25 Oct 2007 01:13:52 -0700 (PDT) Subject: [Pw_forum] How to deal with semicore states with Norm conserving PP? In-Reply-To: Message-ID: <332362.62142.qm@web60316.mail.yahoo.com> Dear Hai Ping, --- lan haiping wrote: > Thank you, Paolo. I will try it . > I want to generate a ncpp for Ti atom, is it > possible test the generated pp with ultrasoft one ? > You can compare (test???) ground state parameters, as lattice parameters, and bulk modulus, but not total energies calculated using different pseudopotentials. If you mean something different I suggested, my apologies. Bests, Eyvaz. > cheers , > Hai.Ping > > > On 10/24/07, Paolo Giannozzi > wrote: > > > > > > On Oct 24, 2007, at 13:09 , lan haiping wrote: > > > > > I just found that opium package cannot generate > ncpp for elements > > > including semicore states . > > > Is there any other scheme for norm conserving > pseudopentials can > > > take semicore states into account for pwscf > calculation ? > > > > the pseudopotential code of quantum-espresso (in > atomic/ subdir) > > can do this. It is a little bit tricky, though > > > > Paolo > > --- > > Paolo Giannozzi, Dept of Physics, University of > Udine > > via delle Scienze 208, 33100 Udine, Italy > > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > 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 > ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, and Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From chaohao.mse at gmail.com Thu Oct 25 10:30:37 2007 From: chaohao.mse at gmail.com (C.H. Hu) Date: Thu, 25 Oct 2007 10:30:37 +0200 Subject: [Pw_forum] negative frequencies during phonon calculations Message-ID: <6502ee650710250130t2523ac87ic6e2cbc759fbf5d4@mail.gmail.com> Dear Pwscf users, I performed gamma-point phonon calculation for my system only including some light elements. Some negative frequencies appear as following. The structure has been optimized first and the nscf calculation was also performed. Does the negative frequencies indicate the structural instability? or how to eliminate these imaginary frequencies during my following calculations? ========= q = ( 0.000000000 0.000000000 0.000000000 ) ************************************************************************** omega( 1) = -3.014004 [THz] = -100.537026 [cm-1] omega( 2) = -1.833969 [THz] = -61.175042 [cm-1] omega( 3) = -1.568539 [THz] = -52.321189 [cm-1] omega( 4) = -1.362118 [THz] = -45.435661 [cm-1] omega( 5) = -0.979698 [THz] = -32.679419 [cm-1] omega( 6) = 3.631786 [THz] = 121.144148 [cm-1] omega( 7) = 4.565661 [THz] = 152.295057 [cm-1] omega( 8) = 4.870748 [THz] = 162.471753 [cm-1] omega( 9) = 5.926574 [THz] = 197.690558 [cm-1] omega(10) = 6.692205 [THz] = 223.229420 [cm-1] omega(11) = 6.751437 [THz] = 225.205202 [cm-1] omega(12) = 7.152446 [THz] = 238.581500 [cm-1] omega(13) = 7.290775 [THz] = 243.195689 [cm-1] omega(14) = 7.583548 [THz] = 252.961623 [cm-1] omega(15) = 7.848509 [THz] = 261.799816 [cm-1] omega(16) = 8.216032 [THz] = 274.059149 [cm-1] omega(17) = 8.450907 [THz] = 281.893782 [cm-1] omega(18) = 8.617843 [THz] = 287.462209 [cm-1] omega(19) = 8.874576 [THz] = 296.025963 [cm-1] omega(20) = 9.106260 [THz] = 303.754152 [cm-1] omega(21) = 9.776634 [THz] = 326.115571 [cm-1] omega(22) = 9.846084 [THz] = 328.432188 [cm-1] omega(23) = 10.441744 [THz] = 348.301414 [cm-1] omega(24) = 10.901272 [THz] = 363.629712 [cm-1] omega(25) = 11.120174 [THz] = 370.931537 [cm-1] omega(26) = 11.296950 [THz] = 376.828190 [cm-1] omega(27) = 11.744897 [THz] = 391.770187 [cm-1] omega(28) = 11.823415 [THz] = 394.389308 [cm-1] omega(29) = 12.284723 [THz] = 409.776965 [cm-1] omega(30) = 12.879001 [THz] = 429.600078 [cm-1] omega(31) = 13.104238 [THz] = 437.113223 [cm-1] omega(32) = 13.295358 [THz] = 443.488354 [cm-1] omega(33) = 13.386218 [THz] = 446.519146 [cm-1] omega(34) = 13.536055 [THz] = 451.517199 [cm-1] omega(35) = 13.571174 [THz] = 452.688634 [cm-1] omega(36) = 14.064683 [THz] = 469.150452 [cm-1] omega(37) = 14.556450 [THz] = 485.554120 [cm-1] omega(38) = 14.667300 [THz] = 489.251729 [cm-1] omega(39) = 15.110352 [THz] = 504.030430 [cm-1] omega(40) = 15.395285 [THz] = 513.534849 [cm-1] omega(41) = 16.043631 [THz] = 535.161476 [cm-1] omega(42) = 16.936124 [THz] = 564.932033 [cm-1] omega(43) = 18.733204 [THz] = 624.876561 [cm-1] omega(44) = 18.876424 [THz] = 629.653928 [cm-1] omega(45) = 19.992373 [THz] = 666.878205 [cm-1] omega(46) = 21.505666 [THz] = 717.356559 [cm-1] omega(47) = 21.617840 [THz] = 721.098322 [cm-1] omega(48) = 22.309307 [THz] = 744.163333 [cm-1] omega(49) = 23.662551 [THz] = 789.303000 [cm-1] omega(50) = 24.061062 [THz] = 802.595969 [cm-1] omega(51) = 24.064277 [THz] = 802.703198 [cm-1] omega(52) = 25.648159 [THz] = 855.536168 [cm-1] omega(53) = 26.862084 [THz] = 896.028637 [cm-1] omega(54) = 26.984089 [THz] = 900.098318 [cm-1] omega(55) = 28.413367 [THz] = 947.774196 [cm-1] omega(56) = 28.483349 [THz] = 950.108578 [cm-1] omega(57) = 28.903442 [THz] = 964.121470 [cm-1] omega(58) = 29.425892 [THz] = 981.548629 [cm-1] omega(59) = 29.797340 [THz] = 993.938893 [cm-1] omega(60) = 30.194172 [THz] = 1007.175875 [cm-1] omega(61) = 30.533468 [THz] = 1018.493632 [cm-1] omega(62) = 30.805908 [THz] = 1027.581303 [cm-1] omega(63) = 31.041973 [THz] = 1035.455634 [cm-1] omega(64) = 32.094778 [THz] = 1070.573675 [cm-1] omega(65) = 33.759643 [THz] = 1126.107965 [cm-1] omega(66) = 33.969486 [THz] = 1133.107616 [cm-1] omega(67) = 36.434092 [THz] = 1215.318565 [cm-1] omega(68) = 36.726631 [THz] = 1225.076683 [cm-1] omega(69) = 39.522021 [THz] = 1318.321478 [cm-1] omega(70) = 39.623203 [THz] = 1321.696562 [cm-1] omega(71) = 40.034020 [THz] = 1335.400026 [cm-1] omega(72) = 40.044563 [THz] = 1335.751729 [cm-1] omega(73) = 50.292137 [THz] = 1677.576257 [cm-1] omega(74) = 50.298606 [THz] = 1677.792065 [cm-1] omega(75) = 51.050051 [THz] = 1702.857719 [cm-1] omega(76) = 51.176742 [THz] = 1707.083716 [cm-1] omega(77) = 53.131701 [THz] = 1772.294552 [cm-1] omega(78) = 53.564853 [THz] = 1786.743033 [cm-1] omega(79) = 53.946325 [THz] = 1799.467683 [cm-1] omega(80) = 54.547644 [THz] = 1819.525644 [cm-1] omega(81) = 55.855114 [THz] = 1863.138433 [cm-1] omega(82) = 56.009839 [THz] = 1868.299538 [cm-1] omega(83) = 56.878920 [THz] = 1897.289172 [cm-1] omega(84) = 56.962499 [THz] = 1900.077075 [cm-1] omega(85) = 57.147227 [THz] = 1906.238980 [cm-1] omega(86) = 57.294672 [THz] = 1911.157244 [cm-1] omega(87) = 58.113524 [THz] = 1938.471399 [cm-1] omega(88) = 58.186280 [THz] = 1940.898280 [cm-1] omega(89) = 60.420046 [THz] = 2015.409202 [cm-1] omega(90) = 60.431210 [THz] = 2015.781574 [cm-1] ************************************************************************** ========= Regards, C.H. -- ============================ C.H. Hu Postdoctoral fellow Chimie et Physico-Chimie appliquees Institut Francais du Petrole (IFP) Rueil-Malmaison, France E_mail: chaohao.mse at gmail.com ============================ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071025/1d291bcd/attachment.htm From giannozz at nest.sns.it Thu Oct 25 11:01:25 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 25 Oct 2007 11:01:25 +0200 Subject: [Pw_forum] A problem K_POINTS nq and q2r.x in calculation of dispersion curve and DOS. In-Reply-To: <909104.65924.qm@web92006.mail.cnb.yahoo.com> References: <909104.65924.qm@web92006.mail.cnb.yahoo.com> Message-ID: <14FB2DB7-767D-4AC4-9C6E-3B5DEB86F6E3@nest.sns.it> On Oct 25, 2007, at 3:12 , shoutian sun wrote: > > ibrav= 2, celldm(1) =7.6197064734844, nat= 1, ntyp= 1 this is a cubic (fcc) lattice, with full cubic (O_h) symmetry > > nq1=3, nq2=2, nq3=2 this grid does not have cubic symmetry, so... > > q not allowed 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 lanhaiping at gmail.com Thu Oct 25 11:04:08 2007 From: lanhaiping at gmail.com (lan haiping) Date: Thu, 25 Oct 2007 17:04:08 +0800 Subject: [Pw_forum] How to deal with semicore states with Norm conserving PP? In-Reply-To: <332362.62142.qm@web60316.mail.yahoo.com> References: <332362.62142.qm@web60316.mail.yahoo.com> Message-ID: Thank you , Prof Isaev. I just surveyed atomic_doc, and found the '&test' process could take other pseudopotentials as configuration. So i wonder is it possible for a ncpp to take uspp as reference configuration? Is such process necessary for pseudopotential testing ? :), i will do the testing you mentioned for generated pseudopotentials, and thank you for your suggestion. Regards, Hai-Ping On 10/25/07, Eyvaz Isaev wrote: > > Dear Hai Ping, > > --- lan haiping wrote: > > > Thank you, Paolo. I will try it . > > I want to generate a ncpp for Ti atom, is it > > possible test the generated pp with ultrasoft one ? > > > > You can compare (test???) ground state parameters, as > lattice parameters, and bulk modulus, but not total > energies calculated using different pseudopotentials. > > If you mean something different I suggested, my > apologies. > > Bests, > Eyvaz. > > > cheers , > > Hai.Ping > > > > > > On 10/24/07, Paolo Giannozzi > > wrote: > > > > > > > > > On Oct 24, 2007, at 13:09 , lan haiping wrote: > > > > > > > I just found that opium package cannot generate > > ncpp for elements > > > > including semicore states . > > > > Is there any other scheme for norm conserving > > pseudopentials can > > > > take semicore states into account for pwscf > > calculation ? > > > > > > the pseudopotential code of quantum-espresso (in > > atomic/ subdir) > > > can do this. It is a little bit tricky, though > > > > > > Paolo > > > --- > > > Paolo Giannozzi, Dept of Physics, University of > > Udine > > > via delle Scienze 208, 33100 Udine, Italy > > > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > > > > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > > -- > > 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 > > > > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, and > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.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/20071025/579853d4/attachment-0001.htm From katalin.gaal-nagy at physik.uni-regensburg.de Thu Oct 25 10:45:22 2007 From: katalin.gaal-nagy at physik.uni-regensburg.de (Katalin Gaal-Nagy) Date: Thu, 25 Oct 2007 10:45:22 +0200 (CEST) Subject: [Pw_forum] negative frequencies during phonon calculations In-Reply-To: <6502ee650710250130t2523ac87ic6e2cbc759fbf5d4@mail.gmail.com> References: <6502ee650710250130t2523ac87ic6e2cbc759fbf5d4@mail.gmail.com> Message-ID: Dear C. H. Hu, it depends on your system. If you treat, e.g., a molecule, the first six frequencies should vanish. However, due to convergence (number of plane waves, size of the supercell, etc. ) they often appear as imaginary or small real, even if all other frequencies are converged with respect to ecut and celldm. If you have a bulk structure, then imaginary frequencies indicate a lattice instability. However, they can appear also as a result of a non-converged groundstate (Ecut, #k, ...). Recently I also found that the parameters tr2_ph for the phonons and conv_thr for the groundstate can affect the quality of the phonon calculation, especially the "vanishing" frequencies for molecules. I hope it helps. All the best, Katalin On Thu, 25 Oct 2007, C.H. Hu wrote: > Dear Pwscf users, > > I performed gamma-point phonon calculation for my system only including some > light elements. Some negative frequencies appear as following. The > structure has been optimized first and the nscf calculation was also > performed. Does the negative frequencies indicate the structural > instability? or how to eliminate these imaginary frequencies during my > following calculations? > > ========= > q = ( 0.000000000 0.000000000 0.000000000 ) > > ************************************************************************** > omega( 1) = -3.014004 [THz] = -100.537026 [cm-1] > omega( 2) = -1.833969 [THz] = -61.175042 [cm-1] > omega( 3) = -1.568539 [THz] = -52.321189 [cm-1] > omega( 4) = -1.362118 [THz] = -45.435661 [cm-1] > omega( 5) = -0.979698 [THz] = -32.679419 [cm-1] > omega( 6) = 3.631786 [THz] = 121.144148 [cm-1] > omega( 7) = 4.565661 [THz] = 152.295057 [cm-1] > omega( 8) = 4.870748 [THz] = 162.471753 [cm-1] > omega( 9) = 5.926574 [THz] = 197.690558 [cm-1] > omega(10) = 6.692205 [THz] = 223.229420 [cm-1] > omega(11) = 6.751437 [THz] = 225.205202 [cm-1] > omega(12) = 7.152446 [THz] = 238.581500 [cm-1] > omega(13) = 7.290775 [THz] = 243.195689 [cm-1] > omega(14) = 7.583548 [THz] = 252.961623 [cm-1] > omega(15) = 7.848509 [THz] = 261.799816 [cm-1] > omega(16) = 8.216032 [THz] = 274.059149 [cm-1] > omega(17) = 8.450907 [THz] = 281.893782 [cm-1] > omega(18) = 8.617843 [THz] = 287.462209 [cm-1] > omega(19) = 8.874576 [THz] = 296.025963 [cm-1] > omega(20) = 9.106260 [THz] = 303.754152 [cm-1] > omega(21) = 9.776634 [THz] = 326.115571 [cm-1] > omega(22) = 9.846084 [THz] = 328.432188 [cm-1] > omega(23) = 10.441744 [THz] = 348.301414 [cm-1] > omega(24) = 10.901272 [THz] = 363.629712 [cm-1] > omega(25) = 11.120174 [THz] = 370.931537 [cm-1] > omega(26) = 11.296950 [THz] = 376.828190 [cm-1] > omega(27) = 11.744897 [THz] = 391.770187 [cm-1] > omega(28) = 11.823415 [THz] = 394.389308 [cm-1] > omega(29) = 12.284723 [THz] = 409.776965 [cm-1] > omega(30) = 12.879001 [THz] = 429.600078 [cm-1] > omega(31) = 13.104238 [THz] = 437.113223 [cm-1] > omega(32) = 13.295358 [THz] = 443.488354 [cm-1] > omega(33) = 13.386218 [THz] = 446.519146 [cm-1] > omega(34) = 13.536055 [THz] = 451.517199 [cm-1] > omega(35) = 13.571174 [THz] = 452.688634 [cm-1] > omega(36) = 14.064683 [THz] = 469.150452 [cm-1] > omega(37) = 14.556450 [THz] = 485.554120 [cm-1] > omega(38) = 14.667300 [THz] = 489.251729 [cm-1] > omega(39) = 15.110352 [THz] = 504.030430 [cm-1] > omega(40) = 15.395285 [THz] = 513.534849 [cm-1] > omega(41) = 16.043631 [THz] = 535.161476 [cm-1] > omega(42) = 16.936124 [THz] = 564.932033 [cm-1] > omega(43) = 18.733204 [THz] = 624.876561 [cm-1] > omega(44) = 18.876424 [THz] = 629.653928 [cm-1] > omega(45) = 19.992373 [THz] = 666.878205 [cm-1] > omega(46) = 21.505666 [THz] = 717.356559 [cm-1] > omega(47) = 21.617840 [THz] = 721.098322 [cm-1] > omega(48) = 22.309307 [THz] = 744.163333 [cm-1] > omega(49) = 23.662551 [THz] = 789.303000 [cm-1] > omega(50) = 24.061062 [THz] = 802.595969 [cm-1] > omega(51) = 24.064277 [THz] = 802.703198 [cm-1] > omega(52) = 25.648159 [THz] = 855.536168 [cm-1] > omega(53) = 26.862084 [THz] = 896.028637 [cm-1] > omega(54) = 26.984089 [THz] = 900.098318 [cm-1] > omega(55) = 28.413367 [THz] = 947.774196 [cm-1] > omega(56) = 28.483349 [THz] = 950.108578 [cm-1] > omega(57) = 28.903442 [THz] = 964.121470 [cm-1] > omega(58) = 29.425892 [THz] = 981.548629 [cm-1] > omega(59) = 29.797340 [THz] = 993.938893 [cm-1] > omega(60) = 30.194172 [THz] = 1007.175875 [cm-1] > omega(61) = 30.533468 [THz] = 1018.493632 [cm-1] > omega(62) = 30.805908 [THz] = 1027.581303 [cm-1] > omega(63) = 31.041973 [THz] = 1035.455634 [cm-1] > omega(64) = 32.094778 [THz] = 1070.573675 [cm-1] > omega(65) = 33.759643 [THz] = 1126.107965 [cm-1] > omega(66) = 33.969486 [THz] = 1133.107616 [cm-1] > omega(67) = 36.434092 [THz] = 1215.318565 [cm-1] > omega(68) = 36.726631 [THz] = 1225.076683 [cm-1] > omega(69) = 39.522021 [THz] = 1318.321478 [cm-1] > omega(70) = 39.623203 [THz] = 1321.696562 [cm-1] > omega(71) = 40.034020 [THz] = 1335.400026 [cm-1] > omega(72) = 40.044563 [THz] = 1335.751729 [cm-1] > omega(73) = 50.292137 [THz] = 1677.576257 [cm-1] > omega(74) = 50.298606 [THz] = 1677.792065 [cm-1] > omega(75) = 51.050051 [THz] = 1702.857719 [cm-1] > omega(76) = 51.176742 [THz] = 1707.083716 [cm-1] > omega(77) = 53.131701 [THz] = 1772.294552 [cm-1] > omega(78) = 53.564853 [THz] = 1786.743033 [cm-1] > omega(79) = 53.946325 [THz] = 1799.467683 [cm-1] > omega(80) = 54.547644 [THz] = 1819.525644 [cm-1] > omega(81) = 55.855114 [THz] = 1863.138433 [cm-1] > omega(82) = 56.009839 [THz] = 1868.299538 [cm-1] > omega(83) = 56.878920 [THz] = 1897.289172 [cm-1] > omega(84) = 56.962499 [THz] = 1900.077075 [cm-1] > omega(85) = 57.147227 [THz] = 1906.238980 [cm-1] > omega(86) = 57.294672 [THz] = 1911.157244 [cm-1] > omega(87) = 58.113524 [THz] = 1938.471399 [cm-1] > omega(88) = 58.186280 [THz] = 1940.898280 [cm-1] > omega(89) = 60.420046 [THz] = 2015.409202 [cm-1] > omega(90) = 60.431210 [THz] = 2015.781574 [cm-1] > ************************************************************************** > ========= > > Regards, > C.H. > > -- > ============================ > C.H. Hu > Postdoctoral fellow > Chimie et Physico-Chimie appliquees > Institut Francais du Petrole (IFP) > Rueil-Malmaison, France > E_mail: chaohao.mse at gmail.com > ============================ > ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, , >>>>>>> Katalin Gaal-Nagy <<<<<<< , , Phys.Dept./INFM , , University of Milan , , Via Celoria 16 , , +39 02 50317377 , ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, , >>>>>>> katalin.gaal-nagy at physik.uni-regensburg.de <<<<<<< , ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, , >>>>>>> Don't dream your life, live your dream <<<<<<< , ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, From eyvaz_isaev at yahoo.com Thu Oct 25 12:18:45 2007 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 25 Oct 2007 03:18:45 -0700 (PDT) Subject: [Pw_forum] How to deal with semicore states with Norm conserving PP? In-Reply-To: Message-ID: <931126.609.qm@web60320.mail.yahoo.com> Hi again, OK, now it is more clear what do you mean "test". I used ld1 for a while ago, and forgot about this one. If I understand correctly &test section in the code (ld1) means "take a pseudopotential generated and test atomic configurations specified, i.e. compare energy levels calculated using all-electron method and a pseudopotential shown as file_pseudo." This serves as a transferability test. As example, for Al there are four configurations to be tested and in ./references you can find al.out file and see how Al.rrkj3 pseudopotential reproduces all-electron energies for these valence states. So, to me it seems very strange generate a pseudopotential, and then take another one for test purpose. Bests, Eyvaz. --- lan haiping wrote: > Thank you , Prof Isaev. > I just surveyed atomic_doc, > and found the '&test' process could take other > pseudopotentials as configuration. > So i wonder is it possible for a ncpp to take uspp > as reference > configuration? > Is such process necessary for pseudopotential > testing ? > :), i will do the testing you mentioned for > generated pseudopotentials, and > thank you for your > suggestion. > > Regards, > Hai-Ping > > > > On 10/25/07, Eyvaz Isaev > wrote: > > > > Dear Hai Ping, > > > > --- lan haiping wrote: > > > > > Thank you, Paolo. I will try it . > > > I want to generate a ncpp for Ti atom, is it > > > possible test the generated pp with ultrasoft > one ? > > > > > > > You can compare (test???) ground state parameters, > as > > lattice parameters, and bulk modulus, but not > total > > energies calculated using different > pseudopotentials. > > > > If you mean something different I suggested, my > > apologies. > > > > Bests, > > Eyvaz. > > > > > cheers , > > > Hai.Ping > > > > > > > > > On 10/24/07, Paolo Giannozzi > > > > wrote: > > > > > > > > > > > > On Oct 24, 2007, at 13:09 , lan haiping wrote: > > > > > > > > > I just found that opium package cannot > generate > > > ncpp for elements > > > > > including semicore states . > > > > > Is there any other scheme for norm > conserving > > > pseudopentials can > > > > > take semicore states into account for pwscf > > > calculation ? > > > > > > > > the pseudopotential code of quantum-espresso > (in > > > atomic/ subdir) > > > > can do this. It is a little bit tricky, though > > > > > > > > Paolo > > > > --- > > > > Paolo Giannozzi, Dept of Physics, University > of > > > Udine > > > > via delle Scienze 208, 33100 Udine, Italy > > > > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > > > > > > > > > > > _______________________________________________ > > > > Pw_forum mailing list > > > > Pw_forum at pwscf.org > > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > > > > > > > -- > > > 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 > > > > > > > > > > ------------------------------------------------------------------- > > Prof. Eyvaz Isaev, > > Theoretical Physics Department, Moscow State > Institute of Steel & Alloys, > > Russia, and > > Condensed Matter Theory Group, Uppsala University, > Sweden > > Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com > > > > __________________________________________________ > > Do You Yahoo!? > > Tired of spam? Yahoo! Mail has the best spam > protection around > > http://mail.yahoo.com > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > Hai-Ping Lan > Department of Electronics , > Peking University , Bejing, 100871 > lanhaiping at gmail.com, hplan at pku.edu.cn > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, and Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From lanhaiping at gmail.com Thu Oct 25 12:30:46 2007 From: lanhaiping at gmail.com (lan haiping) Date: Thu, 25 Oct 2007 18:30:46 +0800 Subject: [Pw_forum] How to deal with semicore states with Norm conserving PP? In-Reply-To: <931126.609.qm@web60320.mail.yahoo.com> References: <931126.609.qm@web60320.mail.yahoo.com> Message-ID: Thanks for your clarification to me , Professor Isaev. I am new to pseudopotential generation, which seems needing much experience to obtain a 'good' pp. i will try to dig more about this subject. Cheers? Hai-Ping On 10/25/07, Eyvaz Isaev wrote: > > Hi again, > > OK, now it is more clear what do you mean "test". > I used ld1 for a while ago, and forgot about this one. > > > If I understand correctly &test section in the code > (ld1) means "take a pseudopotential generated and test > atomic configurations specified, i.e. compare energy > levels calculated using all-electron method and a > pseudopotential shown as file_pseudo." This serves as > a transferability test. > As example, for Al there are four configurations to be > tested and in ./references you can find al.out file > and see how Al.rrkj3 pseudopotential reproduces > all-electron energies for these valence states. > > So, to me it seems very strange generate a > pseudopotential, and then take another one for test > purpose. > > Bests, > Eyvaz. > > --- lan haiping wrote: > > > Thank you , Prof Isaev. > > I just surveyed atomic_doc, > > and found the '&test' process could take other > > pseudopotentials as configuration. > > So i wonder is it possible for a ncpp to take uspp > > as reference > > configuration? > > Is such process necessary for pseudopotential > > testing ? > > :), i will do the testing you mentioned for > > generated pseudopotentials, and > > thank you for your > > suggestion. > > > > Regards, > > Hai-Ping > > > > > > > > On 10/25/07, Eyvaz Isaev > > wrote: > > > > > > Dear Hai Ping, > > > > > > --- lan haiping wrote: > > > > > > > Thank you, Paolo. I will try it . > > > > I want to generate a ncpp for Ti atom, is it > > > > possible test the generated pp with ultrasoft > > one ? > > > > > > > > > > You can compare (test???) ground state parameters, > > as > > > lattice parameters, and bulk modulus, but not > > total > > > energies calculated using different > > pseudopotentials. > > > > > > If you mean something different I suggested, my > > > apologies. > > > > > > Bests, > > > Eyvaz. > > > > > > > cheers , > > > > Hai.Ping > > > > > > > > > > > > On 10/24/07, Paolo Giannozzi > > > > > > wrote: > > > > > > > > > > > > > > > On Oct 24, 2007, at 13:09 , lan haiping wrote: > > > > > > > > > > > I just found that opium package cannot > > generate > > > > ncpp for elements > > > > > > including semicore states . > > > > > > Is there any other scheme for norm > > conserving > > > > pseudopentials can > > > > > > take semicore states into account for pwscf > > > > calculation ? > > > > > > > > > > the pseudopotential code of quantum-espresso > > (in > > > > atomic/ subdir) > > > > > can do this. It is a little bit tricky, though > > > > > > > > > > Paolo > > > > > --- > > > > > Paolo Giannozzi, Dept of Physics, University > > of > > > > Udine > > > > > via delle Scienze 208, 33100 Udine, Italy > > > > > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > Pw_forum mailing list > > > > > Pw_forum at pwscf.org > > > > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > > > > > > > > > > > > -- > > > > 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 > > > > > > > > > > > > > > > > ------------------------------------------------------------------- > > > Prof. Eyvaz Isaev, > > > Theoretical Physics Department, Moscow State > > Institute of Steel & Alloys, > > > Russia, and > > > Condensed Matter Theory Group, Uppsala University, > > Sweden > > > Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com > > > > > > __________________________________________________ > > > Do You Yahoo!? > > > Tired of spam? Yahoo! Mail has the best spam > > protection around > > > http://mail.yahoo.com > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > > -- > > Hai-Ping Lan > > Department of Electronics , > > Peking University , Bejing, 100871 > > lanhaiping at gmail.com, hplan at pku.edu.cn > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, and > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.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/20071025/12b9f26f/attachment-0001.htm From lanhaiping at gmail.com Thu Oct 25 12:40:43 2007 From: lanhaiping at gmail.com (lan haiping) Date: Thu, 25 Oct 2007 18:40:43 +0800 Subject: [Pw_forum] too many nodes for 1d1.x code Message-ID: Hi, I am looking through the ld1.x code to generate a ncpp for Ti element . Taking the pseudo-configuration from the opium package, and suggestion of Paolo's PP notation, my calculations alway complain "too many nodes". I have tried to change the rcut for the channels , and also set rho0 to nozero value to use 4 bessel functions . All these settings seem no success . I also tried to set tm as true to use TM pseudo scheme , but the code complains 'too many attempts' this time . Would you please give me some suggestion to deal with these situation ? any comments are appreciated. my input is below! cheers, hai-ping cat > ti.in < Message-ID: <370830.34280.qm@web60312.mail.yahoo.com> Please follow the Netiquette accepted in the forum: no official call, just first name. Besides, > config='[Ar] 3d1 4s0 4p0' looks strange. For Ti one has to treat semicore states (3s^2 3p^6) as valence, too. Bests, Eyvaz. --- lan haiping wrote: > Hi, > I am looking through the ld1.x code to generate a > ncpp for Ti element . > Taking the pseudo-configuration from the opium > package, and suggestion of > Paolo's PP notation, my calculations > alway complain "too many nodes". I have tried to > change the rcut for the > channels , and also set rho0 to nozero value to use > 4 bessel functions . All these settings seem no > success . I also tried to > set tm as true to use TM pseudo scheme , but the > code > complains 'too many attempts' this time . Would you > please give me some > suggestion to deal with these situation ?? any > comments > are appreciated. my input is below! > cheers, > hai-ping > > cat > ti.in < &input > title='Ti', > zed=22., > rel=1, > rlderiv=2.50, > eminld=-4.0, > emaxld=4.0, > deld=0.02, > nld= 2, > iswitch=3, > config='[Ar] 3d1 4s0 4p0' > dft='PBE', > / > &inputp > pseudotype=2, > lloc= 1, > rho0=0.01, > file_pseudopw='Ti.RRKJ3.UPF', > / > 5 > 3S 1 0 2.00 0.00 1.80 2.00 > 3P 2 1 6.00 0.00 2.00 2.00 > 3D 3 2 1.00 0.00 2.00 2.00 > 4S 4 0 0.00 0.00 1.80 2.10 > 4P 5 1 0.00 0.00 2.20 2.20 > EOF > > -- > 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 > ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, and Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From wangjunjie1981_0 at 163.com Thu Oct 25 15:41:45 2007 From: wangjunjie1981_0 at 163.com (wangjunjie1981_0) Date: Thu, 25 Oct 2007 21:41:45 +0800 (CST) Subject: [Pw_forum] how to determine the mass of virtual-atom generated by virtual.x Message-ID: <13199058.519561193319705775.JavaMail.coremail@bj163app47.163.com> Dear StefanoThank you for your answer.I have another question that how to determine the mass of virtual-atom potential generated by virtual.x. it is equal to the mass of the main atom, or (1-x) M1+x M2, M1 is mass of potential1 and M2 is mass of potential2. Thank you for your adviceBest regardsJunjie Wang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071025/a9447eb3/attachment.htm From lanhaiping at gmail.com Thu Oct 25 15:50:16 2007 From: lanhaiping at gmail.com (lan haiping) Date: Thu, 25 Oct 2007 21:50:16 +0800 Subject: [Pw_forum] too many nodes for 1d1.x code In-Reply-To: <370830.34280.qm@web60312.mail.yahoo.com> References: <370830.34280.qm@web60312.mail.yahoo.com> Message-ID: thank you , Eyvaz ! On 10/25/07, Eyvaz Isaev wrote: > > Please follow the Netiquette accepted in the forum: no > official call, just first name. > > Besides, > > config='[Ar] 3d1 4s0 4p0' > looks strange. For Ti one has to treat semicore states > (3s^2 3p^6) as valence, too. i just thought the code would take the setting card of &inputp as valence reference configuration. I then changed the config setting to '[Ne] 3s2 3p6 3d1 4s0 4p0' , while the code complained again. i also tried to add more projector channels, such as 7 3S 1 0 2.00 0.00 1.80 2.00 3S 1 0 0.00 0.05 1.80 2.00 3P 2 1 6.00 0.00 2.00 2.00 3P 2 1 0.00 0.05 2.00 2.00 3D 3 2 1.00 0.00 2.00 2.00 4S 4 0 0.00 0.00 1.80 2.10 4P 5 1 0.00 0.00 2.20 2.20 it behaved as before, also gave me "too many nodes" . Such work is indeed tricky. Bests, > Eyvaz. > > --- lan haiping wrote: > > > Hi, > > I am looking through the ld1.x code to generate a > > ncpp for Ti element . > > Taking the pseudo-configuration from the opium > > package, and suggestion of > > Paolo's PP notation, my calculations > > alway complain "too many nodes". I have tried to > > change the rcut for the > > channels , and also set rho0 to nozero value to use > > 4 bessel functions . All these settings seem no > > success . I also tried to > > set tm as true to use TM pseudo scheme , but the > > code > > complains 'too many attempts' this time . Would you > > please give me some > > suggestion to deal with these situation ?(c) any > > comments > > are appreciated. my input is below! > > cheers, > > hai-ping > > > > cat > ti.in < > &input > > title='Ti', > > zed=22., > > rel=1, > > rlderiv=2.50, > > eminld=-4.0, > > emaxld=4.0, > > deld=0.02, > > nld= 2, > > iswitch=3, > > config='[Ar] 3d1 4s0 4p0' > > dft='PBE', > > / > > &inputp > > pseudotype=2, > > lloc= 1, > > rho0=0.01, > > file_pseudopw='Ti.RRKJ3.UPF', > > / > > 5 > > 3S 1 0 2.00 0.00 1.80 2.00 > > 3P 2 1 6.00 0.00 2.00 2.00 > > 3D 3 2 1.00 0.00 2.00 2.00 > > 4S 4 0 0.00 0.00 1.80 2.10 > > 4P 5 1 0.00 0.00 2.20 2.20 > > EOF > > > > -- > > 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 > > > > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, and > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.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/20071025/e3ccccc6/attachment.htm From eyvaz_isaev at yahoo.com Thu Oct 25 16:01:14 2007 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 25 Oct 2007 07:01:14 -0700 (PDT) Subject: [Pw_forum] how to determine the mass of virtual-atom generated by virtual.x In-Reply-To: <13199058.519561193319705775.JavaMail.coremail@bj163app47.163.com> Message-ID: <323217.3395.qm@web60314.mail.yahoo.com> Dear Wang, Please read carefully Stefano's excellent reply on this issue posted just a few days ago to the forum. Quite briefly, yes. Bests, Eyvaz. --- wangjunjie1981_0 wrote: > Dear StefanoThank you for your answer.I have another > question that how to determine the mass of > virtual-atom potential generated by virtual.x. it is > equal to the mass of the main atom, or (1-x) M1+x > M2, M1 is mass of potential1 and M2 is mass of > potential2. Thank you for your adviceBest > regardsJunjie Wang > _______________________________________________ > 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, and Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From murda at sissa.it Thu Oct 25 16:04:21 2007 From: murda at sissa.it (Garold Murdachaew) Date: Thu, 25 Oct 2007 16:04:21 +0200 (CEST) Subject: [Pw_forum] pw.x runtime error on ibm sp5 In-Reply-To: References: Message-ID: Dear Pwscf forum members, I am having a runtime error in pw.x related to fft on the cineca sp5. I am using the recommended essl library to supply the fft routines. If someone could please give me some idea of how to resolve this problem, I would appreciate it. Thank you. The details are below. Best regards, Garold Murdachaew Postdoctoral Fellow - Condensed Matter Sector SISSA-ISAS (International School for Advanced Studies) email : murda at sissa.it New Building, Room 208 Via Beirut 2-4, 34014 Trieste, Italy tel : +39 040 3787 477 fax : +39 040 3787 528 Details: I downloaded the cvs version of espresso3.2.3. pw.x works fine under linux. I also configured and compiled without problems on the cineca sp5 using: ./configure BLAS_LIBS="-lessl" LAPACK_LIBS="-lessl -L/cineca/lib -llapack" The result of configure was: The following libraries have been found: BLAS_LIBS=-lessl LAPACK_LIBS=-lessl -L/cineca/lib -llapack FFT_LIBS=-lessl MASS_LIBS= -lmassvp4 -lmass (Note that I had used exactly the same settings to compile a trouble-free version of espresso3.0 some time ago.) This was followed by "make all" and the compilation appeared to be trouble-free. However, when I ran pw.x I there was an immediate crash with the error message: from cft_1z : error # 1 no scalar fft driver specified From degironc at sissa.it Thu Oct 25 17:19:23 2007 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 25 Oct 2007 17:19:23 +0200 Subject: [Pw_forum] how to determine the mass of virtual-atom generated by virtual.x In-Reply-To: <13199058.519561193319705775.JavaMail.coremail@bj163app47.163.com> References: <13199058.519561193319705775.JavaMail.coremail@bj163app47.163.com> Message-ID: <4720B3FB.70403@sissa.it> A virtual atom is a ficticious object that you introduce with some purpouse... Which mass (if any) is more appropriate depends on what is your purpouse. If you want to relax the system any mass is good since it is not used. If you plan to calculate phonons of a material then you should use the mass appropriate for it. In certain cases (GaAlAs alloys or superlattices for instance) it is a very good approximation to calculate the interatomic force constants with ana average atom and then study the big systems introducing the disorder by assigning the "true" Ga and Al masses to electronically equivalent virtual atoms (this approximation is called Mass Approximation) [see for instance S.~Baroni, S.~de~Gironcoli, and P.~Giannozzi, {\sl Phonon dispersions in Ga$_{x}$Al$_{1-x}$As alloys}, Phys.\ Rev.\ Lett.\ {\bf 65}, 84 (1990) ; E.~Molinari, S.~Baroni, P.~Giannozzi, and S.~de~Gironcoli, {\sl Effects of disorder on the Raman spectra of GaAs/AlAs superlattices}, Phys.\ Rev.\ B {\bf 45}, 4280 (1992); G.~Scamarcio, L.~Tapfer, W.~K\"onig, A.~Fisher, K.~Ploog, E.~Molinari, S.~Baroni, P.~Giannozzi, and S.~de~Gironcoli, {\sl Infrared reflectivity by TO phonons in (GaAs)$_{m}$(AlAs)$_{n}$ ultrathin superlattices}, Phys.\ Rev.\ B (RC) {\bf 43}, 14754 (1991); C.~Bungaro, and S.~de~Gironcoli, {\sl Ab initio study of phonons in Al$_x$Ga$_{1-x}$N alloys}, Appl.\ Phys.\ Lett.\ {\bf 76}, 2101 (2000). ] I'm sure that there are systems where no choice is reasonable. stefano wangjunjie1981_0 wrote: > Dear Stefano > Thank you for your answer. > I have another question that how to determine the mass of virtual-atom potential generated by virtual.x. it is equal to the mass of the main atom, or (1-x) M1+x M2, M1 is mass of potential1 and M2 is mass of potential2. > Thank you for your advice > Best regards > Junjie Wang From giannozz at nest.sns.it Thu Oct 25 23:22:31 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 25 Oct 2007 23:22:31 +0200 Subject: [Pw_forum] too many nodes for 1d1.x code In-Reply-To: <370830.34280.qm@web60312.mail.yahoo.com> References: <370830.34280.qm@web60312.mail.yahoo.com> Message-ID: <934B7557-DD59-42D8-96D0-BBE11A7D1ECB@nest.sns.it> On Oct 25, 2007, at 15:01 , Eyvaz Isaev wrote: >> config='[Ar] 3d1 4s0 4p0' > looks strange. For Ti one has to treat semicore states > (3s^2 3p^6) as valence, too. it is not needed to explicitly list all valence states, though, as long as the electronic configuration is a valid one. 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 Oct 25 23:27:31 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 25 Oct 2007 23:27:31 +0200 Subject: [Pw_forum] too many nodes for 1d1.x code In-Reply-To: References: Message-ID: On Oct 25, 2007, at 12:40 , lan haiping wrote: > pseudotype=2, multiprojector PP are much trickier than single-projector PP (i.e. those derived from semilocal Hamann-Schlueter-Chiang PP). Try first single projector PP, pseudizing 3s and 3p states and not 4s and 4p 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 hyello25 at gmail.com Fri Oct 26 07:14:30 2007 From: hyello25 at gmail.com (hyello25 Qgrui) Date: Fri, 26 Oct 2007 13:14:30 +0800 Subject: [Pw_forum] help for convergence in "Computing Second order response" Message-ID: hi everyone, When I do raman calculation of Li2O, I found the "second order response" process is not convergent. The log is below: iter # 1 av.it.: 8.1 thresh= 0.100E-01 alpha_mix = 0.700|ddv_scf|^2 = 0.208E-03 iter # 2 av.it.: 13.1 thresh= 0.144E-02 alpha_mix = 0.700|ddv_scf|^2 = 0.905E-01 iter # 3 av.it.: 11.0 thresh= 0.100E-01 alpha_mix = 0.700|ddv_scf|^2 = 0.228E-03 iter # 4 av.it.: 8.8 thresh= 0.151E-02 alpha_mix = 0.700|ddv_scf|^2 = 0.178E-03 iter # 5 av.it.: 10.9 thresh= 0.133E-02 alpha_mix = 0.700|ddv_scf|^2 = 0.118E-08 iter # 6 av.it.: 12.6 thresh= 0.343E-05 alpha_mix = 0.700|ddv_scf|^2 = 0.155E-07 iter # 7 av.it.: 9.6 thresh= 0.124E-04 alpha_mix = 0.700|ddv_scf|^2 = 0.279E-08 iter # 8 av.it.: 11.9 thresh= 0.529E-05 alpha_mix = 0.700|ddv_scf|^2 = 0.191E-08 iter # 9 av.it.: 11.9 thresh= 0.437E-05 alpha_mix = 0.700|ddv_scf|^2 = 0.402E-07 iter # 10 av.it.: 10.9 thresh= 0.201E-04 alpha_mix = 0.700|ddv_scf|^2 = 0.437E-08 .............................(omitted) iter # 42 av.it.: 10.7 thresh= 0.855E-07 alpha_mix = 0.700|ddv_scf|^2 = 0.201E-11 iter # 43 av.it.: 11.9 thresh= 0.142E-06 alpha_mix = 0.700|ddv_scf|^2 = 0.181E-12 iter # 44 av.it.: 13.6 thresh= 0.425E-07 alpha_mix = 0.700|ddv_scf|^2 = 0.546E-10 iter # 45 av.it.: 10.2 thresh= 0.739E-06 alpha_mix = 0.700|ddv_scf|^2 = 0.190E-11 iter # 46 av.it.: 11.0 thresh= 0.138E-06 alpha_mix = 0.700|ddv_scf|^2 = 0.111E-11 and the ph input file as: &inputph tr2_ph=1.0d-14, prefix='li2O', amass(1)= 6.941, amass(2)=15.999, fildyn='li2O.dynG', epsil=.true., trans=.true., lraman=.true., outdir='/home/qgr/_work_/li2O/raman/temp', / 0 0 0 And in the scf input file, conv_thr = 1.0d-12 with my own Li and O PPs generated using fhi98PP code. How can I solve the problem? What is more wried, this situation never happened days before when using the exactly same input file and PPs. That is , I cannot repeat the result again with all the same input file though I check all the input file carefully. The scf result are the same, but the ph.x gave different convergence process. Besides, I got different raman frequencies. Thanks in advance. Bests, Qian -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071026/67fcb15d/attachment.htm From giannozz at nest.sns.it Fri Oct 26 10:05:51 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 26 Oct 2007 10:05:51 +0200 Subject: [Pw_forum] pw.x runtime error on ibm sp5 In-Reply-To: References: Message-ID: <66CD3D36-0FC1-47C5-9DE3-80C71DF6C08D@nest.sns.it> On Oct 25, 2007, at 16:04 , Garold Murdachaew wrote: > ./configure BLAS_LIBS="-lessl" LAPACK_LIBS="-lessl -L/cineca/lib - > llapack" use "./configure" with no options 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 shang.yi at hotmail.com Fri Oct 26 10:32:43 2007 From: shang.yi at hotmail.com (shangyi) Date: Fri, 26 Oct 2007 16:32:43 +0800 Subject: [Pw_forum] cp trouble! Message-ID: _________________________________________________________________ MSN ???????????????????? http://cn.msn.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071026/4f12d1b1/attachment.htm From giannozz at nest.sns.it Fri Oct 26 10:50:47 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 26 Oct 2007 10:50:47 +0200 Subject: [Pw_forum] cp trouble! In-Reply-To: References: Message-ID: <08BAF379-9746-4675-9C32-14E717C19247@nest.sns.it> On Oct 26, 2007, at 10:32 , shangyi wrote: > > ???????????????? Windows Live > Mail? ????? if this it the output of cp, there is some serious trouble for sure :-) 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 shang.yi at hotmail.com Fri Oct 26 12:13:52 2007 From: shang.yi at hotmail.com (shangyi) Date: Fri, 26 Oct 2007 18:13:52 +0800 Subject: [Pw_forum] cp trouble! real one :-) Message-ID: Dear all: I was troubled by using cp.x need your help.(It is real one this time :-) ) Firstly, I failed to minize the the electronic system, the Ekinc converged slowly. Though I tested different Emass, dt parameters and 'sd' 'damp' strategies, the Ekinc couldn't approach the ground state after hundreds nstep. In this calculation, the initio geometry was optimized by pw.x precesily and using one processor! Secondly, The above work crashed when I using two processor, with the error " %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from gfftindex : error # 1 wrong index: ism %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from gfftindex : error # 1 wrong index: ism %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ..." . It must be something wrong with my input file, because the example18 completed well with mpirun 2 processor. I tracked the error in cpmd_fpmd.f90, but I didn't understand it clearly! And suggestion are appreciated! Thanks in advance! Best wishes! shangyi Graduate shool of China academcy of Science The flowlling is my input file:++++++++++++++++++++++++++++++++++++++++++++++ &CONTROL calculation = 'cp' restart_mode = 'from_scratch' dt = 5 pseudo_dir = '$PSEUDO_DIR/' outdir = '$TMP_DIR/' prefix = 'B_s-Si_td' tprnfor = .true. tstress = .true. etot_conv_thr = 1.0D-6 forc_conv_thr = 1.0D-4 nstep = 300 iprint = 10 isave = 10 ndr = 50 ndw = 51 /&SYSTEM ibrav = 1 celldm(1) = 20.70 nat = 65 ntyp = 2 ecutwfc = 18 nr1b=10, nr2b=10, nr3b=10/&ELECTRONS electron_dynamics='sd' startingwfc='random' ampre=0.01 emass=600 emass_cutoff=3.0/&IONS ion_dynamics = 'none'/ATOMIC_SPECIES B 10.81 B.pbe-n-van.UPF Si 28.0855 Si.pbe-rrkj.UPFATOMIC_POSITIONS (crystal)B 0.372493954 0.372493954 0.622473845Si 0.000331891 0.000331891 0.000946865Si 0.002913283 0.002913284 0.500839406Si 0.000919037 0.500401244 -0.000381662Si 0.000173022 0.500341220 0.499240295Si 0.500401246 0.000919038 -0.000381660Si 0.500341221 0.000173023 0.499240296Si 0.499975918 0.499975919 0.002224618Si 0.489333946 0.489333946 0.499848759Si 0.002910338 0.250843813 0.252910663Si 0.000173550 0.249235559 0.750344627Si 0.000333283 0.750949140 0.250333167Si 0.000917203 0.749622296 0.750399197Si 0.500340453 0.249236195 0.250175949Si 0.489330885 0.249854369 0.739330048Si 0.500402256 0.749625754 0.250913139Si 0.499973752 0.752221367 0.749979717Si 0.250843814 0.002910337 0.252910662Si 0.249235561 0.000173551 0.750344627Si 0.249236196 0.500340453 0.250175948Si 0.249854368 0.489330884 0.739330049Si 0.750949140 0.000333283 0.250333167Si 0.749622295 0.000917202 0.750399197Si 0.749625754 0.500402256 0.250913138Si 0.752221368 0.499973751 0.749979716Si 0.250363127 0.250363127 0.001841796Si 0.262077433 0.262077433 0.512080768Si 0.246966242 0.752641749 0.002646383Si 0.250364014 0.751839999 0.500362867Si 0.752641749 0.246966242 0.002646384Si 0.751840001 0.250364014 0.500362867Si 0.750628968 0.750628969 0.000627019Si 0.752641348 0.752641349 0.496970004Si 0.375392624 0.129570822 0.379575878Si 0.373038049 0.125910178 0.875062322Si 0.373040969 0.625067600 0.375903522Si 0.371891094 0.625058543 0.875063368Si 0.876228492 0.125387574 0.375385685Si 0.875772547 0.124270774 0.875164451Si 0.875775796 0.625163899 0.374271807Si 0.875585609 0.625607971 0.875605748Si 0.125384885 0.125384884 0.126230457Si 0.129571510 0.129571510 0.625394353Si 0.124270382 0.625161615 0.125778192Si 0.125908857 0.625063579 0.623037908Si 0.625161615 0.124270382 0.125778195Si 0.625063581 0.125908857 0.623037909Si 0.625608658 0.625608659 0.125585610Si 0.625058363 0.625058363 0.621896724Si 0.129570823 0.375392624 0.379575877Si 0.125910178 0.373038048 0.875062322Si 0.125387574 0.876228492 0.375385687Si 0.124270774 0.875772548 0.875164451Si 0.625067599 0.373040969 0.375903522Si 0.625058543 0.371891095 0.875063369Si 0.625163898 0.875775798 0.374271805Si 0.625607971 0.875585610 0.875605748Si 0.375145402 0.375145402 0.126663266Si 0.375283840 0.876599210 0.126595465Si 0.375144062 0.876660413 0.625147125Si 0.876599211 0.375283840 0.126595465Si 0.876660413 0.375144062 0.625147125Si 0.875334356 0.875334356 0.125335899Si 0.876598990 0.876598990 0.625278802Si 0.480066718 0.480066718 0.730070074K_POINTS (automatic)2 2 2 0 0 0++++++++++++++++++++++++++++++++++++++++++++++++++ _________________________________________________________________ Windows Live Custom Domain?????????? https://domains.live.com/default.aspx -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071026/40c0e6d6/attachment.htm From giannozz at nest.sns.it Fri Oct 26 18:32:28 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 26 Oct 2007 18:32:28 +0200 Subject: [Pw_forum] cp trouble! real one :-) In-Reply-To: References: Message-ID: <4BD7A7EB-1B3A-4D4E-AF7C-9C977B468462@nest.sns.it> On Oct 26, 2007, at 12:13 , shangyi wrote: > from gfftindex : error # 1 > wrong index: ism never heard about the "ISM index", published by the Institute for Supply Management, giving an estimate of economic activity? maybe it is a bad idea to believe all those indexes :-) Seriously: this is a bug, activated by inappropriate input data > K_POINTS (automatic) > 2 2 2 0 0 0 cp.x doesn't know about k-points: it uses the Gamma point (k=0) no matter what. Unfortunately it looks like the presence of the above instructions confuses cp.x in some serious way (hint: look at the electronic charge printed on output, it is approx. half what it should be). Just remove the two cards above. This is already fixed in the version under development. 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 oulihui666 at 126.com Sat Oct 27 05:20:41 2007 From: oulihui666 at 126.com (oulihui666) Date: Sat, 27 Oct 2007 11:20:41 +0800 (CST) Subject: [Pw_forum] A simple problem about display Message-ID: <6706523.122501193455241461.JavaMail.coremail@bj126app104.126.com> Dear pwscf users: I want to ask a simple problem about display: How to display the curve of change of energy and change of molecular structure in the process of optimization with pwscf?I am really newbie in this thing, sorry about these naive questions...Thanks a lot best regards Lihui Ou -- ======================================Lihui OuPH.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/20071027/4347e1a2/attachment-0001.htm From baroni at sissa.it Sat Oct 27 09:18:59 2007 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 27 Oct 2007 09:18:59 +0200 Subject: [Pw_forum] A simple problem about display In-Reply-To: <6706523.122501193455241461.JavaMail.coremail@bj126app104.126.com> References: <6706523.122501193455241461.JavaMail.coremail@bj126app104.126.com> Message-ID: <32D652E7-7D5B-498D-A371-A25ABF485FF0@sissa.it> Dear Ou, I do not think there is any canned tool to do that. I am not sure that such a plot would be really meaningful, because it would depend a lot on the details of the optimization algorithm. In any event, if you really need it, it should not be difficult to cook it up yourself. Just extract the relevant data (energies, atomic positions - either by hands or using awk/perl), and plot them as functions of a fictitious integer "coordinate" (the "optimization step": 1,2,3 ...). To plot energies you can use gnuplot, xmgr, or a similar program, whereas to plot the structure you can use xcrysden ... If you do not know how awk/perl or the like work, be assured: neither do I. Just do what I would: either browse the intenet for one of the many available on-line guides, or tease a serviceable and knowledgeable colleague of yours. Please, keep us informed of your progresses. Cheers - SB On Oct 27, 2007, at 5:20 AM, oulihui666 wrote: > Dear pwscf users: > I want to ask a simple problem about display: How to display > the curve of change of energy and change of molecular structure in > the process of optimization with pwscf? I am really newbie in this > thing, sorry about these naive questions... > Thanks a lot > best regards > 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 > ====================================== > _______________________________________________ > 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/20071027/8fee2c95/attachment.htm From shang.yi at hotmail.com Sat Oct 27 09:34:01 2007 From: shang.yi at hotmail.com (shangyi) Date: Sat, 27 Oct 2007 15:34:01 +0800 Subject: [Pw_forum] cp trouble! real one :-) In-Reply-To: <4BD7A7EB-1B3A-4D4E-AF7C-9C977B468462@nest.sns.it> References: <4BD7A7EB-1B3A-4D4E-AF7C-9C977B468462@nest.sns.it> Message-ID: Dear Paolo: Thank you! It seems that the problems are solved with your suggestions! > > > K_POINTS (automatic)> > 2 2 2 0 0 0> > cp.x doesn't know about k-points: it uses the Gamma> point (k=0) no matter what. Unfortunately it looks like> the presence of the above instructions confuses cp.x> in some serious way (hint: look at the electronic charge> printed on output, it is approx. half what it should be). The system I concerned is Si64B, which has 259 electrons. The electron information printed in output is"Number of Electron 259, of States 130". So I don't know how to understand your hints? Some confusion happens on me again? > Just remove the two cards above. I did it. The cp.x works well.> This is already fixed in the version under development. As a cp novice, I benfit much from your humor :-) and your advice! I will contiune the next step on cp learning and calculation! Thanks again! Best wishes! shangyi Graduate school of China academy of science _________________________________________________________________ ? Live Search ??????? http://www.live.com/?searchOnly=true -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071027/571633f1/attachment.htm From ding at sissa.it Sat Oct 27 10:36:58 2007 From: ding at sissa.it (Xunlei Ding) Date: Sat, 27 Oct 2007 10:36:58 +0200 Subject: [Pw_forum] A simple problem about display In-Reply-To: <6706523.122501193455241461.JavaMail.coremail@bj126app104.126.com> References: <6706523.122501193455241461.JavaMail.coremail@bj126app104.126.com> Message-ID: <4722F8AA.6040604@sissa.it> Hi, Ou, As suggested by Prof. Baroni, here are some details: Supposing your output file is test.out (even if the optimization is not finished, but only done for some optimization steps): $grep ! test.out You will get like ------------------ ! total energy = -2728.47867910 ryd ! total energy = -2728.47877935 ryd ! total energy = -2728.47893365 ryd ! total energy = -2728.47914358 ryd ! total energy = -2728.47940321 ryd ! total energy = -2728.47969828 ryd ! total energy = -2728.47992015 ryd ! total energy = -2728.48000760 ryd .... Then you can modify it to 1 -2728.47867910 2 -2728.47877935 3 -2728.47893365 4 -2728.47914358 ... Then you can use gnuplot to plot this data. Also, I write a little script "plot_energy" to do this job: Just to use command like: ./plot_energy test.out ---------below is the script "plot_energy"----------------------------------- #!/bin/bash awk '/!/{i++; print "\t",i,"\t\t" $5}' $1 >plot.temp gnuplot < Dear pwscf users: > I want to ask a simple problem about display: How to display the curve > of change of energy and change of molecular structure in the process > of optimization with pwscf? I am really newbie in this thing, sorry > about these naive questions... > >Thanks a lot > >best regards > > 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 / > ====================================== > >------------------------------------------------------------------------ > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > From lanhaiping at gmail.com Sat Oct 27 11:13:42 2007 From: lanhaiping at gmail.com (lan haiping) Date: Sat, 27 Oct 2007 17:13:42 +0800 Subject: [Pw_forum] too many nodes for 1d1.x code In-Reply-To: References: Message-ID: Thank you ,Paolo. Your suggestion really works well. Bests H.P On 10/26/07, Paolo Giannozzi wrote: > > > On Oct 25, 2007, at 12:40 , lan haiping wrote: > > > pseudotype=2, > > multiprojector PP are much trickier than single-projector PP > (i.e. those derived from semilocal Hamann-Schlueter-Chiang > PP). Try first single projector PP, pseudizing 3s and 3p states > and not 4s and 4p > > 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 > -- 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/20071027/a65026ad/attachment.htm From giannozz at nest.sns.it Sat Oct 27 19:30:04 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Sat, 27 Oct 2007 19:30:04 +0200 Subject: [Pw_forum] cp trouble! real one :-) In-Reply-To: References: <4BD7A7EB-1B3A-4D4E-AF7C-9C977B468462@nest.sns.it> Message-ID: <4F6435A7-C787-432A-9D81-E49F5944E479@nest.sns.it> On Oct 27, 2007, at 9:34 , shangyi wrote: > > (hint: look at the electronic charge > > printed on output, it is approx. half what it should be). > The system I concerned is Si64B, which has 259 electrons. > The electron information printed in output is > "Number of Electron 259, of States 130". I was referring to single-processor execution with the two unnecessary cards in the data. In that particular case, the code doesn't crash but if you look carefully it prints "charge density in G-space: ..., in R-space: ...." The two numbers must coincide (and they do) but the numbers that are printed in the "bad" case is something like 127.9 instead of 259 as it should be. So no panic, everything is under control! 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 akohlmey at cmm.chem.upenn.edu Sat Oct 27 23:19:01 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sat, 27 Oct 2007 17:19:01 -0400 Subject: [Pw_forum] cp trouble! real one :-) In-Reply-To: References: <4BD7A7EB-1B3A-4D4E-AF7C-9C977B468462@nest.sns.it> Message-ID: <7b6913e90710271419o39289602lfa3e08de6610edf1@mail.gmail.com> On 10/27/07, shangyi wrote: > > dear shangyi, > The system I concerned is Si64B, which has 259 electrons. The electron > information printed in output is > "Number of Electron 259, of States 130". So I don't know how to understand > your hints? Some confusion happens on me again? don't worry about that one. the problem here is that you are running a system with an odd number of electrons, but don't do a spin polarized calculation, i.e. you have to set nspin=2 and multiplicity according to what you need (probably 2). > > Just remove the two cards above. > I did it. The cp.x works well. but your results are probably bogus because of the fact that you "force" your system to have two half-occupied orbitals. (with nspin=1 full spin symmetry is assumed and only one wavefunction computed for both spin-up and spin-down). cheers, axel. > > This is already fixed in the version under development. > As a cp novice, I benfit much from your humor :-) and your advice! I will > contiune the next step on cp learning and calculation! > > Thanks again! > Best wishes! > > shangyi > Graduate school of China academy of science > > > ________________________________ > ????? Hotmail???????????????? ????? > _______________________________________________ > 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 shang.yi at hotmail.com Sun Oct 28 09:06:06 2007 From: shang.yi at hotmail.com (shangyi) Date: Sun, 28 Oct 2007 16:06:06 +0800 Subject: [Pw_forum] cp trouble! real one :-) In-Reply-To: <7b6913e90710271419o39289602lfa3e08de6610edf1@mail.gmail.com> References: <4BD7A7EB-1B3A-4D4E-AF7C-9C977B468462@nest.sns.it> <7b6913e90710271419o39289602lfa3e08de6610edf1@mail.gmail.com> Message-ID: Dear Paolo and axel: I get your messgaes and benefit much from them! Thanks! Best wishes! shangyi Graduate school of China academy of science _________________________________________________________________ Windows Live Custom Domain?????????? https://domains.live.com/default.aspx -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071028/ca8ec88f/attachment.htm From szs_naghavi at yahoo.com Mon Oct 29 13:16:18 2007 From: szs_naghavi at yahoo.com (zahra sadat naghavi) Date: Mon, 29 Oct 2007 05:16:18 -0700 (PDT) Subject: [Pw_forum] phonon Message-ID: <426671.70958.qm@web63011.mail.re1.yahoo.com> what should i do if i want to calculat phonon frequencies at gama point for a metal? __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071029/92844577/attachment.htm From degironc at sissa.it Mon Oct 29 13:22:22 2007 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 29 Oct 2007 13:22:22 +0100 Subject: [Pw_forum] phonon In-Reply-To: <426671.70958.qm@web63011.mail.re1.yahoo.com> References: <426671.70958.qm@web63011.mail.re1.yahoo.com> Message-ID: <4725D07E.4060400@sissa.it> have a look to example02 Stefano de Gironcoli - SISSA and DEMOCRITOS zahra sadat naghavi wrote: > what should i do if i want to calculat phonon frequencies at gama > point for a metal? > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From Giovanni.Cantele at na.infn.it Mon Oct 29 13:21:35 2007 From: Giovanni.Cantele at na.infn.it (Giovanni Cantele) Date: Mon, 29 Oct 2007 13:21:35 +0100 Subject: [Pw_forum] phonon In-Reply-To: <426671.70958.qm@web63011.mail.re1.yahoo.com> References: <426671.70958.qm@web63011.mail.re1.yahoo.com> Message-ID: <4725D04F.5060300@na.infn.it> zahra sadat naghavi wrote: > what should i do if i want to calculat phonon frequencies at gama > point for a metal? perhaps it could be helpful starting browsing the code documentation and examples: http://www.quantum-espresso.org/wiki/index.php/Using_PWscf#Phonon_calculations espresso-3.2/examples/example02 example 02 shows you "how to use pw.x and ph.x to calculate phonon frequencies at Gamma and X for Si and C in the diamond structure and for fcc-Ni." Giovanni -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: Giovanni.Cantele at na.infn.it Web: http://people.na.infn.it/~cantele From baroni at sissa.it Mon Oct 29 13:24:03 2007 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 29 Oct 2007 21:24:03 +0900 Subject: [Pw_forum] phonon In-Reply-To: <4725D07E.4060400@sissa.it> References: <426671.70958.qm@web63011.mail.re1.yahoo.com> <4725D07E.4060400@sissa.it> Message-ID: also, be so kind as to sign your posts, please - SB On Oct 29, 2007, at 9:22 PM, Stefano de Gironcoli wrote: > have a look to example02 > Stefano de Gironcoli - SISSA and DEMOCRITOS > > zahra sadat naghavi wrote: >> what should i do if i want to calculat phonon frequencies at gama >> point for a metal? >> >> __________________________________________________ >> Do You Yahoo!? >> Tired of spam? Yahoo! Mail has the best spam protection around >> http://mail.yahoo.com >> >> --------------------------------------------------------------------- >> --- >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- 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/20071029/115b7ae2/attachment.htm From baroni at sissa.it Mon Oct 29 13:36:29 2007 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 29 Oct 2007 21:36:29 +0900 Subject: [Pw_forum] phonon In-Reply-To: <4725D04F.5060300@na.infn.it> References: <426671.70958.qm@web63011.mail.re1.yahoo.com> <4725D04F.5060300@na.infn.it> Message-ID: <8936D75F-345A-46D8-AC44-74B1C73D9E7F@sissa.it> Unless Zahra wanted to know how to obtain phonons from the electronic structure calculate by sampling only the gamma point of the Brillouin zone (BZ). Beware that the k-points used to sample the BZ (which i like to call "k points") have nothing to do with the k-points at which phonon frequencies are calculated (which I like to call "q points"). If you quant to calculate phonons at q-point=gamma, then please follow the suggestions by Giovanni Cantele and Stefano de Gironcoli. Otherwise, please make sure that you understand the difference between "k points" and "q points" (see my sloppy definition above). If you don't, please revert to us before proceeding. Good luck - SB On Oct 29, 2007, at 9:21 PM, Giovanni Cantele wrote: > zahra sadat naghavi wrote: >> what should i do if i want to calculat phonon frequencies at gama >> point for a metal? > perhaps it could be helpful starting browsing the code > documentation and > examples: > > http://www.quantum-espresso.org/wiki/index.php/ > Using_PWscf#Phonon_calculations > > espresso-3.2/examples/example02 > > example 02 shows you "how to use pw.x and ph.x to calculate phonon > frequencies at Gamma and X for Si and C in the diamond structure and > for fcc-Ni." > > > Giovanni > > -- > > > > Dr. Giovanni Cantele > Coherentia CNR-INFM and Dipartimento di Scienze Fisiche > Universita' di Napoli "Federico II" > Complesso Universitario di Monte S. Angelo - Ed. 6 > Via Cintia, I-80126, Napoli, Italy > Phone: +39 081 676910 > Fax: +39 081 676346 > E-mail: Giovanni.Cantele at na.infn.it > Web: http://people.na.infn.it/~cantele > > _______________________________________________ > 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/20071029/17ba1f1c/attachment-0001.htm From chenhanghuipwscf at gmail.com Mon Oct 29 15:41:18 2007 From: chenhanghuipwscf at gmail.com (alan chen) Date: Mon, 29 Oct 2007 09:41:18 -0500 Subject: [Pw_forum] about 'relax' calculation for a large job Message-ID: <22ae3ca40710290741k4e897d74me372bc64c80f9d96@mail.gmail.com> To whom it may concern, I am now doing a large job of 'relax' calculation. The unit cell contains 80 atoms and vacuum. The job has been running for two weeks. While the total energy is decreasing, the amount it decreases is approximately a constant, around 0.005 Ry after each self-consistent calculation and the total force is fluctuating around '0.02 Ry/au'. I use 'bfgs' for ion dynamics and 'first extrapolation' for both pot_extrapolation and wfc_extrapolation. Has anyone encounted such a problem before and how did you solve it? Thank you very much. Hanghui -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071029/816b538b/attachment.htm From hashem.yamani at gmail.com Mon Oct 29 19:36:50 2007 From: hashem.yamani at gmail.com (Hashem Al-Yamani) Date: Mon, 29 Oct 2007 20:36:50 +0200 Subject: [Pw_forum] Plotting band structure using the xmgr file Message-ID: <82a593400710291136u32f1948dhd5ea8629ddb3cf69@mail.gmail.com> Dear All .... I did successfully plot the band structure using xmgrace on the file ".xmgr" ..... any idea how can I put the k-points on it on the x-axis (i.e. gamma, A, X, R, Z, ........ ) . Any one knows the steps and I would be greatful . Thanks in advance . Best regards . Hashem Jordan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071029/af299929/attachment.htm From njuxuyuehua at gmail.com Tue Oct 30 04:11:52 2007 From: njuxuyuehua at gmail.com (xu yuehua) Date: Tue, 30 Oct 2007 11:11:52 +0800 Subject: [Pw_forum] a question about whether the phonon calculation can continue when the machine is shut down suddenly Message-ID: hello ,everyone: my calculation cost much time,so i want to go on the calculation at the stop . but i do not know whether it can achieve the aim and how to deal with it i need your help. thanks a lot -- Xu Yuehua physics Department of Nanjing university China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071030/78465437/attachment.htm From lanhaiping at gmail.com Tue Oct 30 05:52:13 2007 From: lanhaiping at gmail.com (lan haiping) Date: Tue, 30 Oct 2007 12:52:13 +0800 Subject: [Pw_forum] a question about whether the phonon calculation can continue when the machine is shut down suddenly In-Reply-To: References: Message-ID: Dear yuehua Referring to $ESPRESSO/Doc/INPUT_PH, keyword 'recover' can reach your goal. Bests, Hai-Ping On 10/30/07, xu yuehua wrote: > > > hello ,everyone: > my calculation cost much time,so i want to go on the calculation at the > stop . > but i do not know whether it can achieve the aim and how to deal with > it > i need your help. > thanks a lot > -- > Xu Yuehua > physics Department of Nanjing university > China > > _______________________________________________ > 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/20071030/d7c9613d/attachment.htm From njuxuyuehua at gmail.com Tue Oct 30 06:54:06 2007 From: njuxuyuehua at gmail.com (xu yuehua) Date: Tue, 30 Oct 2007 13:54:06 +0800 Subject: [Pw_forum] a question about whether the phonon calculation can continue when the machine is shut down suddenly In-Reply-To: References: Message-ID: hi ,Hai-Ping THANKS for your help.it saves me a lot of time. bests 2007/10/30, lan haiping : > > Dear yuehua > > Referring to $ESPRESSO/Doc/INPUT_PH, keyword 'recover' can reach your > goal. > > Bests, > Hai-Ping > > On 10/30/07, xu yuehua wrote: > > > > > hello ,everyone: > > my calculation cost much time,so i want to go on the calculation at the > > stop . > > but i do not know whether it can achieve the aim and how to deal with > > it > > i need your help. > > thanks a lot > > -- > > Xu Yuehua > > physics Department of Nanjing university > > China > > > > _______________________________________________ > > 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 > > -- Xu Yuehua physics Department of Nanjing university China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071030/60c18c77/attachment.htm From Giovanni.Cantele at na.infn.it Tue Oct 30 08:11:07 2007 From: Giovanni.Cantele at na.infn.it (Giovanni Cantele) Date: Tue, 30 Oct 2007 08:11:07 +0100 Subject: [Pw_forum] Plotting band structure using the xmgr file In-Reply-To: <82a593400710291136u32f1948dhd5ea8629ddb3cf69@mail.gmail.com> References: <82a593400710291136u32f1948dhd5ea8629ddb3cf69@mail.gmail.com> Message-ID: <4726D90B.1090705@na.infn.it> Hashem Al-Yamani wrote: > Dear All .... > > I did successfully plot the band structure using xmgrace on the file > ".xmgr" ..... any idea how can I put the k-points on it on the x-axis > (i.e. gamma, A, X, R, Z, ........ ) . Any one knows the steps and I > would be greatful . > > > Thanks in advance . > > > Best regards . > > Hashem > > Jordan University > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > Plot -> Axis Properties on the top choose X axis than go to the "Special" tab from "Special ticks:" choose "Tick marks and labels" (default is "None") then select the number of ticks, e.g. 5 finally, in the first 5 rows below "Tick location - Label:" input the x coordinates of your points and the labels (for Gamma label the string is "\xG" ) Hope this helps, Giovanni -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: Giovanni.Cantele at na.infn.it Web: http://people.na.infn.it/~cantele From giannozz at nest.sns.it Tue Oct 30 09:34:02 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 30 Oct 2007 09:34:02 +0100 Subject: [Pw_forum] Problems with Polarization calculations In-Reply-To: References: Message-ID: <62D1DA28-3008-4A0E-8DDC-1615276CC65B@nest.sns.it> On Oct 19, 2007, at 5:01 , Sohrab Ismail-Beigi wrote: > from ylm_q : error # 181312304 > not programmed for L> the reason for the funny number is really dumb: the error message is wrong! the printed value of L was never set. So nothing is going out-of-bounds as I was saying in my previous message. There were however other problems in the Berry's phase calculation (only for the US case, though). I hope they are fixed now in the CVS version. The CVS version should work also for l=3 . 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 marcel at physik.tu-berlin.de Tue Oct 30 10:10:12 2007 From: marcel at physik.tu-berlin.de (Marcel Mohr) Date: Tue, 30 Oct 2007 10:10:12 +0100 (CET) Subject: [Pw_forum] a question about whether the phonon calculation can continue when the machine is shut down suddenly In-Reply-To: References: Message-ID: <20071030100616.T27396@rosa.physik-pool.tu-berlin.de> Hi both of you, >> Referring to $ESPRESSO/Doc/INPUT_PH, keyword 'recover' can reach your >> goal. >> at least it's what the manual says. Last time I did a recover, after a crash I obtained the following message Representation # 6 mode # 6 Self-consistent Calculation %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from broyden : error # 4 factorization %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from broyden : error # 4 factorization %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from broyden : error # 4 factorization %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from broyden : error # 4 factorization %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... job aborted: rank: node: exit code[: error message] 0: david012: -2 1: david012: -2: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 1 2: david012: -2 3: david012: -2 and in the CRASH file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 1 from broyden : error # 4 factorization %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Cheers Marcel On Tue, 30 Oct 2007, xu yuehua wrote: > hi ,Hai-Ping > THANKS for your help.it saves me a lot of time. > bests > > > > 2007/10/30, lan haiping : >> >> Hai-Ping >> >> On 10/30/07, xu yuehua wrote: >> >>> >>> hello ,everyone: >>> my calculation cost much time,so i want to go on the calculation at the >>> stop . >>> but i do not know whether it can achieve the aim and how to deal with >>> it >>> i need your help. >>> thanks a lot >>> -- >>> Xu Yuehua >>> physics Department of Nanjing university >>> China >>> >>> _______________________________________________ >>> 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 >> >> > > > -- > Xu Yuehua > physics Department of Nanjing university > China > From umari at democritos.it Tue Oct 30 12:31:29 2007 From: umari at democritos.it (umari at democritos.it) Date: Tue, 30 Oct 2007 12:31:29 +0100 Subject: [Pw_forum] about 'relax' calculation for a large job (alan chen) Message-ID: <20071030123129.nh1usgj5wk0skwk4@mail.democritos.it> Dear Alan Could you indicate your affiliation when posting on the mailing list? If your system is treated only at the gamma point I suggest to relax it through a damped molecular dynamics through the cp code. You can perform both Car-Parrinello and Born_Oppenheimer MD. It can treat also metallic systems through ensemble DFT. Regards, Paolo ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From lanhaiping at gmail.com Tue Oct 30 13:20:53 2007 From: lanhaiping at gmail.com (lan haiping) Date: Tue, 30 Oct 2007 20:20:53 +0800 Subject: [Pw_forum] a question about whether the phonon calculation can continue when the machine is shut down suddenly In-Reply-To: <20071030100616.T27396@rosa.physik-pool.tu-berlin.de> References: <20071030100616.T27396@rosa.physik-pool.tu-berlin.de> Message-ID: Dear Marcel I just look through the codes, and found this error information is due to matrix factorization, i.e. it means your calculation would give some singular values during the mix_pot/rho calculation. bests, hai-ping On 10/30/07, Marcel Mohr wrote: > > Hi both of you, > > >> Referring to $ESPRESSO/Doc/INPUT_PH, keyword 'recover' can reach > your > >> goal. > >> > > at least it's what the manual says. Last time I did a recover, after a > crash I obtained the following message > > Representation # 6 mode # 6 > > Self-consistent Calculation > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from broyden : error # 4 > factorization > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from broyden : error # 4 > factorization > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from broyden : error # 4 > factorization > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from broyden : error # 4 > factorization > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > job aborted: > rank: node: exit code[: error message] > 0: david012: -2 > 1: david012: -2: application called MPI_Abort(MPI_COMM_WORLD, 0) - process > 1 > 2: david012: -2 > 3: david012: -2 > > > > and in the CRASH file > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > task # 1 > from broyden : error # 4 > factorization > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > Cheers Marcel > > > > On Tue, 30 Oct 2007, xu yuehua wrote: > > > hi ,Hai-Ping > > THANKS for your help.it saves me a lot of time. > > bests > > > > > > > > 2007/10/30, lan haiping : > >> > >> Hai-Ping > >> > >> On 10/30/07, xu yuehua wrote: > >> > >>> > >>> hello ,everyone: > >>> my calculation cost much time,so i want to go on the calculation at > the > >>> stop . > >>> but i do not know whether it can achieve the aim and how to deal > with > >>> it > >>> i need your help. > >>> thanks a lot > >>> -- > >>> Xu Yuehua > >>> physics Department of Nanjing university > >>> China > >>> > >>> _______________________________________________ > >>> 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 > >> > >> > > > > > > -- > > Xu Yuehua > > physics Department of Nanjing university > > China > > > > _______________________________________________ > 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/20071030/a933c4c9/attachment.htm From njuxuyuehua at gmail.com Tue Oct 30 13:28:40 2007 From: njuxuyuehua at gmail.com (xu yuehua) Date: Tue, 30 Oct 2007 20:28:40 +0800 Subject: [Pw_forum] a question about whether the phonon calculation can continue when the machine is shut down suddenly In-Reply-To: <20071030100616.T27396@rosa.physik-pool.tu-berlin.de> References: <20071030100616.T27396@rosa.physik-pool.tu-berlin.de> Message-ID: hi Marcel just now ,i looked over my calculation ,and everything is OK .there is no such problem as yours. so i think it is not the recover problem,maybe 2007/10/30, Marcel Mohr : > > Hi both of you, > > >> Referring to $ESPRESSO/Doc/INPUT_PH, keyword 'recover' can reach > your > >> goal. > >> > > > at least it's what the manual says. Last time I did a recover, after a > crash I obtained the following message > > Representation # 6 mode # 6 > > Self-consistent Calculation > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from broyden : error # 4 > factorization > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > stopping ... > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from broyden : error # 4 > factorization > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > stopping ... > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from broyden : error # 4 > factorization > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > stopping ... > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from broyden : error # 4 > factorization > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > stopping ... > > job aborted: > rank: node: exit code[: error message] > 0: david012: -2 > 1: david012: -2: application called MPI_Abort(MPI_COMM_WORLD, 0) - process > 1 > 2: david012: -2 > 3: david012: -2 > > > > and in the CRASH file > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > task # 1 > from broyden : error # 4 > factorization > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > Cheers Marcel > > > > On Tue, 30 Oct 2007, xu yuehua wrote: > > > hi ,Hai-Ping > > THANKS for your help.it saves me a lot of time. > > bests > > > > > > > > 2007/10/30, lan haiping : > >> > >> Hai-Ping > >> > >> On 10/30/07, xu yuehua < njuxuyuehua at gmail.com > wrote: > >> > >>> > >>> hello ,everyone: > >>> my calculation cost much time,so i want to go on the calculation at > the > >>> stop . > >>> but i do not know whether it can achieve the aim and how to deal > with > >>> it > >>> i need your help. > >>> thanks a lot > >>> -- > >>> Xu Yuehua > >>> physics Department of Nanjing university > >>> China > >>> > >>> _______________________________________________ > >>> 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 > >> > >> > > > > > > -- > > Xu Yuehua > > physics Department of Nanjing university > > China > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Xu Yuehua physics Department of Nanjing university China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071030/35e5b5a5/attachment-0001.htm From szs_naghavi at yahoo.com Tue Oct 30 14:06:14 2007 From: szs_naghavi at yahoo.com (zahra sadat naghavi) Date: Tue, 30 Oct 2007 06:06:14 -0700 (PDT) Subject: [Pw_forum] (no subject) Message-ID: <734718.12973.qm@web63002.mail.re1.yahoo.com> can espresso understand along-diameter vibrations of a nanotube that their k's are along the circomfrence ?(we put the nanotube in Hexagonal lattice) __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071030/401d1923/attachment.htm From marcel at physik.tu-berlin.de Tue Oct 30 14:06:15 2007 From: marcel at physik.tu-berlin.de (Marcel Mohr) Date: Tue, 30 Oct 2007 14:06:15 +0100 (CET) Subject: [Pw_forum] a question about whether the phonon calculation can continue when the machine is shut down suddenly In-Reply-To: References: <20071030100616.T27396@rosa.physik-pool.tu-berlin.de> Message-ID: <20071030135827.U29770@rosa.physik-pool.tu-berlin.de> Hi ok. Thats good to know for the next time. Marcel On Tue, 30 Oct 2007, xu yuehua wrote: > hi Marcel > > just now ,i looked over my calculation ,and everything is OK .there is no > such problem as yours. > so i think it is not the recover problem,maybe > > > > > 2007/10/30, Marcel Mohr : >> >> Hi both of you, >> >>>> Referring to $ESPRESSO/Doc/INPUT_PH, keyword 'recover' can reach >> your >>>> goal. >>>> >> >> >> at least it's what the manual says. Last time I did a recover, after a >> crash I obtained the following message >> >> Representation # 6 mode # 6 >> >> Self-consistent Calculation >> >> >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> from broyden : error # 4 >> factorization >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> >> stopping ... >> >> >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> from broyden : error # 4 >> factorization >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> >> stopping ... >> >> >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> from broyden : error # 4 >> factorization >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> >> stopping ... >> >> >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> from broyden : error # 4 >> factorization >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> >> stopping ... >> >> job aborted: >> rank: node: exit code[: error message] >> 0: david012: -2 >> 1: david012: -2: application called MPI_Abort(MPI_COMM_WORLD, 0) - process >> 1 >> 2: david012: -2 >> 3: david012: -2 >> >> >> >> and in the CRASH file >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> task # 1 >> from broyden : error # 4 >> factorization >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> >> >> Cheers Marcel >> >> >> >> On Tue, 30 Oct 2007, xu yuehua wrote: >> >>> hi ,Hai-Ping >>> THANKS for your help.it saves me a lot of time. >>> bests >>> >>> >>> >>> 2007/10/30, lan haiping : >>>> >>>> Hai-Ping >>>> >>>> On 10/30/07, xu yuehua < njuxuyuehua at gmail.com > wrote: >>>> >>>>> >>>>> hello ,everyone: >>>>> my calculation cost much time,so i want to go on the calculation at >> the >>>>> stop . >>>>> but i do not know whether it can achieve the aim and how to deal >> with >>>>> it >>>>> i need your help. >>>>> thanks a lot >>>>> -- >>>>> Xu Yuehua >>>>> physics Department of Nanjing university >>>>> China >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>> >>> >>> -- >>> Xu Yuehua >>> physics Department of Nanjing university >>> China >>> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > Xu Yuehua > physics Department of Nanjing university > China > From baroni at sissa.it Tue Oct 30 14:10:37 2007 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 30 Oct 2007 22:10:37 +0900 Subject: [Pw_forum] (no subject) In-Reply-To: <734718.12973.qm@web63002.mail.re1.yahoo.com> References: <734718.12973.qm@web63002.mail.re1.yahoo.com> Message-ID: <975E783F-2FD4-4FDE-9BDE-EA6AA5BD563D@sissa.it> yes - can you please sign your posta with name/affiliation? thanks S. On Oct 30, 2007, at 10:06 PM, zahra sadat naghavi wrote: > can espresso understand along-diameter vibrations of a nanotube > that their k's are along the circomfrence ?(we put the nanotube in > Hexagonal lattice) > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.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) 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/20071030/639519a6/attachment.htm From oulihui666 at 126.com Tue Oct 30 13:45:25 2007 From: oulihui666 at 126.com (oulihui666) Date: Tue, 30 Oct 2007 20:45:25 +0800 (CST) Subject: [Pw_forum] some simple problems Message-ID: <25223785.1249551193748325042.JavaMail.coremail@bj126app75.126.com> Dear Prof. Baroni, The problem about display, I have solved, thank you very much. Recently, I encounter some problems, pwscf only do periodic hybrid density functional theory calculation, it could do any other general density functional theory calculation? Is there any principle about settings of k-point and cut-off energy? Thanks 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/20071030/b38f7237/attachment-0001.htm From giannozz at nest.sns.it Tue Oct 30 21:36:19 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 30 Oct 2007 21:36:19 +0100 Subject: [Pw_forum] a question about whether the phonon calculation can continue when the machine is shut down suddenly In-Reply-To: <20071030100616.T27396@rosa.physik-pool.tu-berlin.de> References: <20071030100616.T27396@rosa.physik-pool.tu-berlin.de> Message-ID: <637AA336-F1E7-45BD-A121-B4BF8F308484@nest.sns.it> On Oct 30, 2007, at 10:10 , Marcel Mohr wrote: > [...] Last time I did a recover, after a crash I obtained the > following message > [...] > from broyden : error # 4 > factorization restarting from a crash may or may not work. If the needed files are corrupted, it doesn't work. There might be other reasons such as a problem in the way the calculation is restarted, but it is hard to say more in absence of a reproducible problem, and this kind of problems tend to be erratic. 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 Tue Oct 30 21:50:42 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 30 Oct 2007 21:50:42 +0100 Subject: [Pw_forum] about 'relax' calculation for a large job In-Reply-To: <22ae3ca40710290741k4e897d74me372bc64c80f9d96@mail.gmail.com> References: <22ae3ca40710290741k4e897d74me372bc64c80f9d96@mail.gmail.com> Message-ID: On Oct 29, 2007, at 15:41 , alan chen wrote: > I am now doing a large job of 'relax' calculation. The unit > cell contains 80 atoms and vacuum. The job has been running for two > weeks. While the total energy is decreasing, > the amount it decreases is approximately a constant, around 0.005 > Ry after each self-consistent calculation and the total force is > fluctuating around '0.02 Ry/au'. I use 'bfgs' for ion dynamics and > 'first extrapolation' for both pot_extrapolation and > wfc_extrapolation. > Has anyone encounted such a problem before lots of people: it is one of the most frequently asked questions > and how did you solve it? search the mailing list and see here for some hints: http://www.quantum-espresso.org/wiki/index.php/Troubleshooting_% 28PWscf%29 item 1.28 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 Tue Oct 30 21:54:28 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 30 Oct 2007 21:54:28 +0100 Subject: [Pw_forum] help for convergence in "Computing Second order response" In-Reply-To: References: Message-ID: On Oct 26, 2007, at 7:14 , hyello25 Qgrui wrote: > When I do raman calculation of Li2O, I found the "second order > response" > process is not convergent. try to reduce the alpha_mix parameter > What is more wried, this situation never happened days before when > using the exactly same input file and PPs. That is , I cannot > repeat the > result again with all the same input file though I check all the > input file > carefully. The scf result are the same, but the ph.x gave different > convergence process. Besides, I got different raman frequencies. you are not doing the same calculation. Computers are deterministic, even if it often happens that they look like random number generators 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 sunshoutian168 at yahoo.com.cn Wed Oct 31 03:17:55 2007 From: sunshoutian168 at yahoo.com.cn (shoutian sun) Date: Wed, 31 Oct 2007 10:17:55 +0800 (CST) Subject: [Pw_forum] The negative frequencies in the calculation of phonon. Message-ID: <675605.14027.qm@web92005.mail.cnb.yahoo.com> >Dear all, >I have a problem in calculating phonons of a material.I think the ecutwfc = 44.0982(600eV) >and the K_POINTS is enough(in vc-relax I set it 10 10 8). The forces of atoms is also list >below. But the frequencies in *.dyn1 is negative(about -1.67895THz). &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , outdir='/home/user/ecnuphyk/SUN/tmp/tmp-p4/' , pseudo_dir = '/home/user/ecnuphyk/SUN/pseudo/' , prefix='...' , tstress = .true. , tprnfor = .true. , etot_conv_thr = 1.0D-5 , forc_conv_thr = 1.0D-4 , / &SYSTEM ibrav = 0 , celldm(1) = ... , nat = 16 , ntyp = 2 , nspin = 1 , ecutwfc = 44.0982 ,#about 600eV / &ELECTRONS conv_thr = 1.0d-7 , mixing_beta = 0.7 , / CELL_PARAMETERS (alat) ... ATOMIC_SPECIES ... ATOMIC_POSITIONS (crystal) ... K_POINTS automatic 8 8 6 0 0 0 *************The forces of the atoms in the self-consistent calculation: atom 1 type 1 force = 0.00000085 -0.00000187 -0.00000180 atom 2 type 1 force = -0.00000200 0.00000092 0.00000220 atom 3 type 1 force = 0.00000200 -0.00000092 -0.00000220 atom 4 type 1 force = -0.00000085 0.00000187 0.00000180 atom 5 type 2 force = -0.00002835 0.00003010 -0.00000078 atom 6 type 2 force = -0.00002239 -0.00001414 0.00000083 atom 7 type 2 force = 0.00001800 0.00001850 0.00000131 atom 8 type 2 force = 0.00000012 -0.00000010 -0.00000065 atom 9 type 2 force = 0.00002757 -0.00002933 -0.00000124 atom 10 type 2 force = -0.00000019 -0.00000006 0.00000066 atom 11 type 2 force = 0.00000019 0.00000006 -0.00000066 atom 12 type 2 force = -0.00002757 0.00002933 0.00000124 atom 13 type 2 force = -0.00000012 0.00000010 0.00000065 atom 14 type 2 force = -0.00001800 -0.00001850 -0.00000131 atom 15 type 2 force = 0.00002239 0.00001414 -0.00000083 atom 16 type 2 force = 0.00002835 -0.00003010 0.00000078 ********************ph.in phonons of ... &inputph tr2_ph=1.0d-12, prefix='...', ldisp=.true., nq1=4, nq2=4, nq3=3 epsil=.true. , ... outdir= '/home/user/ecnuphyk/SUN/tmp/tmp-p4/' , fildyn='....dyn', / >********************************* --------------------------------- ?????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071031/91e44523/attachment.htm From giannozz at nest.sns.it Wed Oct 31 16:06:26 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 31 Oct 2007 16:06:26 +0100 Subject: [Pw_forum] The negative frequencies in the calculation of phonon. In-Reply-To: <675605.14027.qm@web92005.mail.cnb.yahoo.com> References: <675605.14027.qm@web92005.mail.cnb.yahoo.com> Message-ID: <3CCB9EB6-1285-47A7-BA46-1BF41AE9B357@nest.sns.it> On Oct 31, 2007, at 3:17 , shoutian sun wrote: > the frequencies in *.dyn1 is negative(about -1.67895THz). see http://www.quantum-espresso.org/wiki/index.php, chapter "Troubleshooting", items 1.34 and 1.35 Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222