[Pw_forum] Hi, how to generate the pseudopotentials of I element?
On Wed, 24 Jan 2007, yupiaofei(SDU) wrote: YP> for example, i want to generate the pseudopotentials of I elements? What should i do? YP> YP> This is USPP of I used in CASTEP. Can we obtain some help from these datas? those are parameters for a vanderbilt uspp. it should be rather straightforward to recreate the potential with the vanderbilt code and then convert them to UPF with uspp2upf.x. regardless of how well the reproduction of those parameters work, i would recommend to do careful transferability tests. axel. YP> YP> Ultrasoft potential generated using the setting YP> suggested by Prof. Lee group (I_sml_01). YP> YP> YP> | pseudopotential report: version 7.2.1 date 6-11-1998 | YP> YP> | I ceperley-alder exchange-corr | YP> | z = 53.zv = 7.exfact =.0 | YP> |etot = -23.02217 | YP> | indexorbital occupationenergy | YP> |1500 2.00 -1.30 | YP> |2510 5.00-.53 | YP> | keyps = 3 ifpcor = 0| YP> | rinner = 1.60 for L=1 | YP> | rinner = 1.60 for L=2 | YP> | rinner = 1.60 for L=3 | YP> |new generation scheme:| YP> |nbeta = 4 kkbeta = 645 rcloc =2.| YP> |ibetal epsilon rcut | YP> | 1 0 -1.30 2.00 | YP> | 2 0.00 2.00 | YP> | 3 1 -.53 2.00 | YP> | 4 1.00 2.00 | YP> | lloc = 2 eloc =.000| YP> | ifqopt = 3 nqf= 8 qtryc = 10.000 | YP> | all electron calculation used koelling-harmon equation | YP> | logarithmic mesh | YP> YP> YP> Convergence test YP> YP> I2 dimer, orthorombic cell, a=6.05, b=5.95, c=6.00 Angstrom, LDA YP> Fractional coordinates: YP> (0.71102 0.72156 0.71658) and (0.44630 0.45485 0.44986) YP> YP> = YP> Ecut Etot dEForce on atom 1 YP> (eV) (eV)(eV/atom)(eV/A) YP> - YP> 150 (COARSE) -628.946 0.225 -0.82947 -0.98877 -0.42398 YP> 175 (MEDIUM) -628.985 0.206 -0.69620 -0.68307 -0.60302 YP> 200 -629.167 0.115 -0.72123 -0.71046 -0.62692 YP> 210 (FINE)-629.231 0.083 -1.11127 -0.71342 -0.63400 YP> 230 -629.325 0.036 -0.92169 -0.94618 -1.05568 YP> 240 (PRECISE) -629.348 0.024 -0.95878 -0.89582 -0.93315 YP> 280 -629.376 0.010 -0.95180 -0.90413 -0.92772 YP> 320 -629.383 0.006 -0.95300 -0.90585 -0.92960 YP> 400 -629.395 0.001 -0.96039 -0.92010 -0.95487 YP> 450 -629.395 0.000 -0.96071 -0.92041 -0.95521 YP> 800 -629.396 -0.94534 -0.90747 -0.92607 YP> = YP> ??j)b? b?+?o??? ?i?zj ?+hf??f??X??)???p??+ YP> -- === 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] Question about Example10
:), thank you ! Actually, I read your recommandation about mailing-list. And i do reply the mail to the forum, not directly to you ! Thank you for your suggestion. I then test it , and report to the forum . Best wishes, Hai-Ping On 1/23/07, Paolo Giannozzi wrote: > > On Jan 21, 2007, at 10:10 , lan haiping wrote: > > > Dear Paolo > > you didn't read my recommandation not to address messages to me, > did you? > > > The born effetive charge tensors obtained are greatly consistent > > with published results in Zhong et al (PRL.72.3618) , for O sites > > (-5.81,-2.57,-2.57) , for Pb sites (3.92,3.92,3.92) (all are > > diagonal elements of E-U tensors). > > > > I then recalculated with Berry Phase method, and still cannot find > > satisfactory results for O sites. A typical resulted tensor is > > (-5.84, -1.90,-1.98). > > actually, results from Berry phase and from linear response methods > coincide only at k-point convergence > > 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 > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 -- next part -- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070123/d28e773d/attachment.htm
[Pw_forum] Problem in pp.x
Sorry for repeating the e-mail, but the subject was not correct... I have performed a parallel calculation for relaxing a dithiol, and the results came out fine. Now I want to plot |psi|^2 of the band immediately above the Fermi level (the LUMO). I am running pp.x with the following input: prefix = 'dithiol_relax' outdir = './' filplot = 'dithiol_relax_pp' plot_num = 7 kpoint = 0.000 0.000 0.000 kband = 14 lsign=.false. / iflag = 3 output_format = 5 fileout = 'dithiol.lumo.xsf' / I suspect the problem is in the "kpoint" entry. I have already tried setting it to "Gamma", "1", and last as shown above, but with no success. I am obtaining the following error: Program POST-PROC v.3.0starts ... Today is 23Jan2007 at 19:33:29 Parallel version (MPI) Number of processors in use: 4 R & G space division: proc/pool =4 %% from postproc : error #18 reading inputpp namelist %% stopping ... What is wrong in the inputpp section? Marcos -- Dr. Marcos Verissimo Alves Post-Doctoral Fellow Condensed Matter and Statistical Physics Sector International Centre for Theoretical Physics Trieste, Italy I have become so addicted to vi that I try to exit OpenOffice by typing :wq! ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Marcos Verissimo Alves Post-Doctoral Fellow Condensed Matter and Statistical Physics Sector International Centre for Theoretical Physics Trieste, Italy I have become so addicted to vi that I try to exit OpenOffice by typing :wq!
[Pw_forum] About Pseudo-Potential generation
Dear all, I have serveral questions about PP generation. Please forgive me if there are any stupid question as I am a new in this field. (1) Comparing Rabe-Rappe-Kaxiras-Joannopoulos and Troullier-Martin pseudization, it seems that the former is simpler. But actually which one is better? Do each of them have their particular advantages. (2) What's the difference between using one channel as the local PP and pseudizing the all electron potential. (3) Sometimes, one will use fractional occupation such as [Ne]3s1.5 for Mg. Why's that? (4) If I want to do high pressure calculation later, does it mean that I must use a small core radius. Thanks for helping me! Lawrence ___ YM - ??? http://messenger.yahoo.com.hk -- next part -- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070123/7243f1bc/attachment.htm
[Pw_forum] Problem in pp.x
On Tue, 23 Jan 2007, Marcos Verissimo Alves wrote: hi marcos, greetings from snowy philly! MVA> Sorry for repeating the e-mail, but the subject was not correct... MVA> MVA> I have performed a parallel calculation for relaxing a dithiol, and the MVA> results came out fine. Now I want to plot |psi|^2 of the band immediately MVA> above the Fermi level (the LUMO). I am running pp.x with the following MVA> input: MVA> MVA> MVA> prefix = 'dithiol_relax' MVA> outdir = './' MVA> filplot = 'dithiol_relax_pp' MVA> plot_num = 7 MVA> kpoint = 0.000 0.000 0.000 this kind of input does not make sense in a namelist. i suppose the kpoint value refers to the 'index' number of the k-point in your previous calculation. ciao, axel. ps: our group just got a (new) post doc from bazil... ;-) MVA> kband = 14 MVA> lsign=.false. MVA> / MVA> MVA> iflag = 3 MVA> output_format = 5 MVA> fileout = 'dithiol.lumo.xsf' MVA> / MVA> MVA> I suspect the problem is in the "kpoint" entry. I have already tried MVA> setting it to "Gamma", "1", and last as shown above, but with no success. MVA> I am obtaining the following error: MVA> MVA> Program POST-PROC v.3.0starts ... MVA> Today is 23Jan2007 at 19:33:29 MVA> MVA> Parallel version (MPI) MVA> MVA> Number of processors in use: 4 MVA> R & G space division: proc/pool =4 MVA> MVA> %% MVA> from postproc : error #18 MVA> reading inputpp namelist MVA> %% MVA> MVA> stopping ... MVA> MVA> What is wrong in the inputpp section? MVA> MVA> Marcos MVA> MVA> -- === 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] problem in DOS
No, it seems that it does not work for any case even for example 8. Would you please give some comments about possible compiler or library problems and the way it should be solved. Many thanks in advance Javad Hashemifar On 1/23/07, Paolo Giannozzi wrote: > > On Jan 23, 2007, at 14:02 , Javad hashemifar wrote: > > > Sorry, I forgot to say that "dos.x -inp inputfile" command also > > did not work! > > does it work in at least some cases (for instance, example 8)? > if not, it may be something related to your compiler or libraries. > If it does, please provide a test job for a case that doesn't 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 > -- == Seyed Javad Hashemifar,Ph.D. [current:] Tel:+49-203-3794743Fax:+49-203-3794742 Fachbereich Physik (AG Kratzer), Universitat Duisburg-Essen 47048 Dusiburg, Germany [permanent:] Tel: +98-311-3912375 Fax: +98-311-3912376 Physics Department, Isfahan University of Technology 84156 Isfahan, Iran ---
[Pw_forum] problem in DOS
On Jan 23, 2007, at 14:02 , Javad hashemifar wrote: > Sorry, I forgot to say that "dos.x -inp inputfile" command also > did not work! does it work in at least some cases (for instance, example 8)? if not, it may be something related to your compiler or libraries. If it does, please provide a test job for a case that doesn't work Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] problem in DOS
Sorry, I forgot to say that "dos.x -inp inputfile" command also did not work! Javad Hashemifar On 1/23/07, Javad hashemifar wrote: > Thanks for your reply. > It happens in both parallel and serial execution. In fact I tested > several possibilities: running in parallel on the same number of nodes > that pw.x ran, running in serial after a parallel ran of pw.x, running > a serial after a serial ran of pw.x, and in all cases the same problem > happens. > We are using the latest version of Espresso (released on Nov. 2006) > > Bests > Javad Hashemifar > > On 1/23/07, Paolo Giannozzi wrote: > > > > On Jan 23, 2007, at 11:43 , Javad hashemifar wrote > > > > > When I run dos.x < inputfile it seems that the program doesn't do > > > any thing [...] we have installed pwscf in parallel version using the > > > MPI libraries. > > > > does it happen in parallel execution or also in serail execution? > > does "dos.x -inp inputfile" 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 > > > > > -- > == > Seyed Javad Hashemifar,Ph.D. > [current:] > Tel:+49-203-3794743Fax:+49-203-3794742 > Fachbereich Physik (AG Kratzer), Universitat Duisburg-Essen > 47048 Dusiburg, Germany > [permanent:] > Tel: +98-311-3912375 Fax: +98-311-3912376 > Physics Department, Isfahan University of Technology > 84156 Isfahan, Iran > --- > -- == Seyed Javad Hashemifar,Ph.D. [current:] Tel:+49-203-3794743Fax:+49-203-3794742 Fachbereich Physik (AG Kratzer), Universitat Duisburg-Essen 47048 Dusiburg, Germany [permanent:] Tel: +98-311-3912375 Fax: +98-311-3912376 Physics Department, Isfahan University of Technology 84156 Isfahan, Iran ---
[Pw_forum] bug in atlas
Atlas has recently (20Nov06) reported an error in computation of complex GEMM (C = A*B +C) for the special case B = Atransp. ( http://sourceforge.net/mailarchive/forum.php?thread_id=31031975_id=434) How serious is this error and would this affect pwscf calculations? -- Prashant Shevgaonkar, Chemical Engineering Department, Vishwakarma Institute of Technology, Pune, India 411 037 Email: shevgaonkar at gmail.com -- next part -- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070123/ecceb4d5/attachment.htm
[Pw_forum] problem in DOS
Thanks for your reply. It happens in both parallel and serial execution. In fact I tested several possibilities: running in parallel on the same number of nodes that pw.x ran, running in serial after a parallel ran of pw.x, running a serial after a serial ran of pw.x, and in all cases the same problem happens. We are using the latest version of Espresso (released on Nov. 2006) Bests Javad Hashemifar On 1/23/07, Paolo Giannozzi wrote: > > On Jan 23, 2007, at 11:43 , Javad hashemifar wrote > > > When I run dos.x < inputfile it seems that the program doesn't do > > any thing [...] we have installed pwscf in parallel version using the > > MPI libraries. > > does it happen in parallel execution or also in serail execution? > does "dos.x -inp inputfile" 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 > -- == Seyed Javad Hashemifar,Ph.D. [current:] Tel:+49-203-3794743Fax:+49-203-3794742 Fachbereich Physik (AG Kratzer), Universitat Duisburg-Essen 47048 Dusiburg, Germany [permanent:] Tel: +98-311-3912375 Fax: +98-311-3912376 Physics Department, Isfahan University of Technology 84156 Isfahan, Iran ---
[Pw_forum] Question about Example10
On Jan 21, 2007, at 10:10 , lan haiping wrote: > Dear Paolo you didn't read my recommandation not to address messages to me, did you? > The born effetive charge tensors obtained are greatly consistent > with published results in Zhong et al (PRL.72.3618) , for O sites > (-5.81,-2.57,-2.57) , for Pb sites (3.92,3.92,3.92) (all are > diagonal elements of E-U tensors). > > I then recalculated with Berry Phase method, and still cannot find > satisfactory results for O sites. A typical resulted tensor is > (-5.84, -1.90,-1.98). actually, results from Berry phase and from linear response methods coincide only at k-point convergence Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] bug in atlas
On Tue, 23 Jan 2007, Konstantin Kudin wrote: KK> Dear Prashant, KK> KK> The question you are asking should be straightforward to figure out on KK> your own. Just grep through the source code (it is GPL and is KK> available), find all the instances of complex GEMM, and find those that KK> utilize the special case. KK> KK> Then you can report your findings back to the list. good idea! and very useful, too. but sadly, that is only (the easy) half of the job. you also have to check the LAPACK subroutines that QE uses for the use of that problematic call, which is a bit messy since there are quite a few cross-calls from within lapack, so best is to check all of it. cheers, axel. KK> KK> Regards, KK> Kostya KK> KK> KK> --- Prashant Shevgaonkar wrote: KK> KK> > Atlas has recently (20Nov06) reported an error in computation of KK> > complex KK> > GEMM (C = A*B +C) for the special case B = Atransp. KK> > ( KK> > KK> http://sourceforge.net/mailarchive/forum.php?thread_id=31031975_id=434) KK> > How serious is this error and would this affect pwscf calculations? KK> > KK> > -- KK> > Prashant Shevgaonkar, KK> > Chemical Engineering Department, KK> > Vishwakarma Institute of Technology, KK> > Pune, India 411 037 KK> > Email: shevgaonkar at gmail.com KK> > KK> KK> KK> KK> KK> KK> Yahoo! Music Unlimited KK> Access over 1 million songs. KK> http://music.yahoo.com/unlimited KK> ___ KK> Pw_forum mailing list KK> Pw_forum at pwscf.org KK> http://www.democritos.it/mailman/listinfo/pw_forum KK> -- === 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] problem in DOS
On Jan 23, 2007, at 11:43 , Javad hashemifar wrote > When I run dos.x < inputfile it seems that the program doesn't do > any thing [...] we have installed pwscf in parallel version using the > MPI libraries. does it happen in parallel execution or also in serail execution? does "dos.x -inp inputfile" work? Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] problem in relaxation by using bfgs
Many thanks Dr Giannozzi for your kind attention. I found that if I use bfgs_ndim= 2 then the mentioned problem will not appear at all. If you find any reason behind this error please keep us (users) informed. Kind regards Javad Hashemifar On 1/16/07, Paolo Giannozzi wrote: > > On Dec 22, 2006, at 9:20 , Javad hashemifar wrote: > > > I am trying to relax a tetragonal interface supercell at different > > values of vertical lattice parameter (celldm(3)). I am using > > calculation=relax and the namelist IONS is as follows: > > > > ion_dynamic = bfgs > > bfgs_ndim= 3, > > pot_extrapolation = "second_order", > > wfc_extrapolation = "second_order", > > > > [...] For some values of celldm(3) every thing is OK and the system > > relax well and both etot_conv_thr and forc_conv_thr satisfies. But in > > some other values of celldm(3) the calculation stops with the > > following error: > > > > from checkallsym : error # 1 > > some of the original symmetry operations not satisfied > > we tried your test and actually there is a problem, but we don't > know what the problem is. Could you please verify if the error > happens also if you remove the line > bfgs_ndim= 3 > ? 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 > -- == Seyed Javad Hashemifar,Ph.D. [current:] Tel:+49-203-3794743Fax:+49-203-3794742 Fachbereich Physik (AG Kratzer), Universitat Duisburg-Essen 47048 Dusiburg, Germany [permanent:] Tel: +98-311-3912375 Fax: +98-311-3912376 Physics Department, Isfahan University of Technology 84156 Isfahan, Iran ---
[Pw_forum] problem in DOS
Dear Espresso users During DOS calculation I encountered a strange problem. When I run dos.x < inputfile it seems that the program doesn't do any thing. First I thought that probably dos.x did not realize the input file but when I modified some of the parameters in the input file, dos.x got error. After further check I found that the same problem occures for pp.x while there is no problem for pw.x in both scf and nscf calculation. Let me to note that we have installed pwscf in parallel version using the MPI libraries. I will appreciate your kind helps and comments. Javad Hashemifar
[Pw_forum] problem in DOS
On Tue, 23 Jan 2007, Javad hashemifar wrote: please try running in serial to make sure your input is correct. with some MPI implementations (e.g. MPICH and derived), you do not see any error output, since the connection is terminated before that text can be forwarded. axel. JH> No, it seems that it does not work for any case even for example 8. JH> Would you please give some comments about possible compiler or library JH> problems and the way it should be solved. JH> JH> Many thanks in advance JH> Javad Hashemifar JH> JH> On 1/23/07, Paolo Giannozzi wrote: JH> > JH> > On Jan 23, 2007, at 14:02 , Javad hashemifar wrote: JH> > JH> > > Sorry, I forgot to say that "dos.x -inp inputfile" command also JH> > > did not work! JH> > JH> > does it work in at least some cases (for instance, example 8)? JH> > if not, it may be something related to your compiler or libraries. JH> > If it does, please provide a test job for a case that doesn't work JH> > JH> > Paolo JH> > --- JH> > Paolo Giannozzi, Democritos and University of Udine, Italy JH> > JH> > JH> > ___ JH> > Pw_forum mailing list JH> > Pw_forum at pwscf.org JH> > http://www.democritos.it/mailman/listinfo/pw_forum JH> > JH> JH> JH> -- === 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] bug in atlas
Dear Prashant, The question you are asking should be straightforward to figure out on your own. Just grep through the source code (it is GPL and is available), find all the instances of complex GEMM, and find those that utilize the special case. Then you can report your findings back to the list. Regards, Kostya --- Prashant Shevgaonkar wrote: > Atlas has recently (20Nov06) reported an error in computation of > complex > GEMM (C = A*B +C) for the special case B = Atransp. > ( > http://sourceforge.net/mailarchive/forum.php?thread_id=31031975_id=434) > How serious is this error and would this affect pwscf calculations? > > -- > Prashant Shevgaonkar, > Chemical Engineering Department, > Vishwakarma Institute of Technology, > Pune, India 411 037 > Email: shevgaonkar at gmail.com > Yahoo! Music Unlimited Access over 1 million songs. http://music.yahoo.com/unlimited
