From nkxirainbow at gmail.com Tue Feb 1 04:22:19 2011 From: nkxirainbow at gmail.com (xirainbow) Date: Tue, 1 Feb 2011 11:22:19 +0800 Subject: [Pw_forum] help with /examples/example03 In-Reply-To: References: Message-ID: Dear Amin: > 1 I understand that the task of this example is to find the minimum > geometry. but how does it decide to to put the molecule in a box of side 12 > bohr? where does 12 come from? > You have to do a convergence test to decide the length of box. In my experience, keeping the nearest neighbor atoms between period image above 10 angstrom is ok. However, if you are dealing with dipole moleculor, you have to pay much attention. > Do we have to assign ibrav to zero whenever we want to optimize the > geometry of an electronic system? > It is up to the symmetry of your meleculor. > > 2 How do you decide to set ecutwfc to 24? /Doc/INPUT_PW.txt just says that > it is a cutoff energy for wavefunctions. I have no clue how much it should > be > You have to do a convergence test to decide it. > > 3 How do you set the x-component of the atomic position of carbon to be at > 2.256 and all the other one to be zero? > 2.256 0 0 > > If you can guide me to a file or a link which explains these kind of > questions, it would be great > http://www.quantum-espresso.org/wiki/index.php/QESB09 DFT in Practice:Some?Fundae? > > Thanks > Amin > -- ____________________________________ Hui Wang School of physics, Fudan University, Shanghai, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110201/2506810b/attachment.htm From ac.rain at inbox.com Wed Feb 2 03:54:35 2011 From: ac.rain at inbox.com (ac.rain at inbox.com) Date: Tue, 1 Feb 2011 18:54:35 -0800 Subject: [Pw_forum] QE and mpich2, Linux In-Reply-To: References: <2535d195-ac71-4965-8379-243a44a796b0@sissa.it> <4d074755.3020701@democritos.it> <47bd3257d74.00000656ac.rain@inbox.com> <9179582e6fa.00000849ac.rain@inbox.com> <60b257887fc.000006d5ac.rain@inbox.com> Message-ID: <0589A8D7D96.00000508ac.rain@inbox.com> I reviewed that doc thank you, I wonder if it is a little out of date, mpirun redirects to mpiexec which does not support options "-nimage" and "-npool" , those are mentioned for Plane-wave tasks on page10. I am running it now in blocks of 4 cpus to match the number-combination requirement. 4 cores on the same system completes in 1h47m , 16 cores on the same system completes in 2h19m. Is this not going to get faster on a single system until we add more memory to the system? or perhaps to drop the number of cpus specified in mpiMachinefile.txt so it spreads a fewer number of jobs over a greater number of systems? or is the bottleneck to do with the local hard drives not being fast enough? I am not familiar with the maths equations/terminology mentioned in the document. thanks, nick > -----Original Message----- > From: giannozz at democritos.it > Sent: Mon, 31 Jan 2011 11:16:06 +0100 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] QE and mpich2, Linux > > in order to take advantage of parallelization, some understanding of > how parallelization works in QE is needed. The user guide and this > document: > http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_para.pdf > contain some info. Throwing in more processors will not by itself do > the job. > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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 ____________________________________________________________ Send your photos by email in seconds... TRY FREE IM TOOLPACK at http://www.imtoolpack.com/default.aspx?rc=if3 Works in all emails, instant messengers, blogs, forums and social networks. From giannozz at democritos.it Wed Feb 2 08:48:46 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 2 Feb 2011 08:48:46 +0100 Subject: [Pw_forum] QE and mpich2, Linux In-Reply-To: <0589A8D7D96.00000508ac.rain@inbox.com> References: <2535d195-ac71-4965-8379-243a44a796b0@sissa.it> <4d074755.3020701@democritos.it> <47bd3257d74.00000656ac.rain@inbox.com> <9179582e6fa.00000849ac.rain@inbox.com> <60b257887fc.000006d5ac.rain@inbox.com> <0589A8D7D96.00000508ac.rain@inbox.com> Message-ID: <572E1D7F-D1FE-4ACA-B2C1-880540AD8A50@democritos.it> On Feb 2, 2011, at 3:54 , ac.rain at inbox.com wrote: > mpirun redirects to mpiexec which does not support > options "-nimage" and "-npool" these options are interpreted by pw.x, not by mpirun or mpiexec P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From sclauzer at sissa.it Wed Feb 2 09:24:40 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 2 Feb 2011 09:24:40 +0100 Subject: [Pw_forum] QE and mpich2, Linux In-Reply-To: <0589A8D7D96.00000508ac.rain@inbox.com> References: <2535d195-ac71-4965-8379-243a44a796b0@sissa.it> <4d074755.3020701@democritos.it> <47bd3257d74.00000656ac.rain@inbox.com> <9179582e6fa.00000849ac.rain@inbox.com> <60b257887fc.000006d5ac.rain@inbox.com> <0589A8D7D96.00000508ac.rain@inbox.com> Message-ID: <7D796F81-94F4-458D-B486-E84CCD479F82@sissa.it> Il giorno 02/feb/2011, alle ore 03.54, ac.rain at inbox.com ha scritto: > > I am running it now in blocks of 4 cpus to match the number-combination requirement. > 4 cores on the same system completes in 1h47m , 16 cores on the same system completes in 2h19m. > > Is this not going to get faster on a single system until we add more memory to the system? or perhaps to drop the number of cpus specified in mpiMachinefile.txt so it spreads a fewer number of jobs over a greater number of systems? > or is the bottleneck to do with the local hard drives not being fast enough? This should be easy to test, by changing the value in disk_io > > I am not familiar with the maths equations/terminology mentioned in the document. Also your terminology is not familiar to us and is not easy to understand what you are saying... what is the "number-combination requirement"? And what does it mean "it spreads a fewer number of jobs over a greater number of systems"? Please make an effort to adopt more clear statements (reading some reviews or following a small tutorial on parallel/high-performance computing might help), otherwise we can only continue to guess what you mean. In order to improve the speed up you should understand (at least broadly) the different levels of parallelization implemented in the code. Another important thing is to understand the timings at the end of the output. Try to compare those numbers for the two different runs. GS > > thanks, > > nick > >> -----Original Message----- >> From: giannozz at democritos.it >> Sent: Mon, 31 Jan 2011 11:16:06 +0100 >> To: pw_forum at pwscf.org >> Subject: Re: [Pw_forum] QE and mpich2, Linux >> >> in order to take advantage of parallelization, some understanding of >> how parallelization works in QE is needed. The user guide and this >> document: >> http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_para.pdf >> contain some info. Throwing in more processors will not by itself do >> the job. >> >> P. >> --- >> Paolo Giannozzi, Dept of Chemistry&Physics&Environment, >> Univ. 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 > > ____________________________________________________________ > Send your photos by email in seconds... > TRY FREE IM TOOLPACK at http://www.imtoolpack.com/default.aspx?rc=if3 > Works in all emails, instant messengers, blogs, forums and social networks. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110202/d9b36202/attachment.htm From elie.moujaes at hotmail.co.uk Wed Feb 2 19:40:34 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Wed, 2 Feb 2011 18:40:34 +0000 Subject: [Pw_forum] computing electron phonon coefficients Message-ID: Dear all , I am trying to compute the electron phonon coefficients for monolayer graphene (using the options elph=.true. and trans=.true.) in the ph.in file. I am using Espresso-4.2. The ph.x executable is stopping after some time with the message: At line 378 of file elphon.f90 (Unit 40 "/tmp/results-MOUJAES/elphomonograph.a2Fsave") Traceback is not availabe, compile with -ftrace=frame or -ftrace=full Fortran runtime error : End of file Can anyone tell me how to fix this problem ? Regards Elie Moujaes University of nottingham NottinghamNG7 2RD uk -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110202/202debc6/attachment.htm From giannozz at democritos.it Thu Feb 3 07:38:58 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 3 Feb 2011 07:38:58 +0100 Subject: [Pw_forum] computing electron phonon coefficients In-Reply-To: References: Message-ID: <02027A35-FCC9-4724-ACB2-89B77455583F@democritos.it> On Feb 2, 2011, at 19:40 , Elie Moujaes wrote: > I am trying to compute the electron phonon coefficients for > monolayer graphene (using the options elph=.true. and trans=.true.) > in the ph.in file. I am using Espresso-4.2. The ph.x executable is > stopping after some time with the message: > > At line 378 of file elphon.f90 (Unit 40 "/tmp/results-MOUJAES/ > elphomonograph.a2Fsave") > Traceback is not availabe, compile with -ftrace=frame or -ftrace=full > Fortran runtime error : End of file before running the electron-phonon calculation, you have to run a non- scf calculation with an option (la2f or something like this) that produces the required file (the one that is missing here) P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From zhaohscas at yahoo.com.cn Thu Feb 3 12:00:56 2011 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Thu, 3 Feb 2011 19:00:56 +0800 Subject: [Pw_forum] About the optical absorption edge juded from the absorption coefficient spectrum graph. Message-ID: <622607416.20110203190056@yahoo.com.cn> Dear all, I'm a newbie on optical peroperties calculations and have some confusions on the optical absorption edge juded from the absorption coefficient spectrum graph. For detail, I'm reading the following paper: First Principles Calculations of Electronic Band Structure and Optical Properties of Cr-Doped ZnO The corresponding doi is as follows: http://pubs.acs.org/doi/abs/10.1021/jp811507r On the 3rd page of this paper, the author said: ------------------ the optical absorption edge of Cr-doped ZnO will shift to the high-energy region compared with pure ZnO, which will be discussed carefully below. ------------------ Then on the 4th page, the author said: ------------------ On the other hand, the absorption edge of the Cr-doped ZnO systems shifts slightly to higher energy with increasing Cr doping concentration. ------------------ Corresponding to all of the above informations, the author give the results by their group in Fig. 6 of that paper. I post here the Fig. 6 of that paper for your information. Could someone please give me some hints on the above analysis based on the Fig. 6, especially how determine the optical absorption edge from the absorption coefficient spectrum graph. Thanks in advance. -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China GnuPG DSA: 0xD108493 2011-2-3 -------------- next part -------------- A non-text attachment was scrubbed... Name: fig6.jpg Type: image/jpeg Size: 55409 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110203/f72f9b4c/attachment-0001.jpg From elie.moujaes at hotmail.co.uk Thu Feb 3 13:32:35 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Thu, 3 Feb 2011 12:32:35 +0000 Subject: [Pw_forum] computing electron phonon coefficients In-Reply-To: <02027A35-FCC9-4724-ACB2-89B77455583F@democritos.it> References: , <02027A35-FCC9-4724-ACB2-89B77455583F@democritos.it> Message-ID: Dear Prof. Giannozzi, Thanks very much for your reply. Regards Elie > From: giannozz at democritos.it > Date: Thu, 3 Feb 2011 07:38:58 +0100 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] computing electron phonon coefficients > > > On Feb 2, 2011, at 19:40 , Elie Moujaes wrote: > > > I am trying to compute the electron phonon coefficients for > > monolayer graphene (using the options elph=.true. and trans=.true.) > > in the ph.in file. I am using Espresso-4.2. The ph.x executable is > > stopping after some time with the message: > > > > At line 378 of file elphon.f90 (Unit 40 "/tmp/results-MOUJAES/ > > elphomonograph.a2Fsave") > > Traceback is not availabe, compile with -ftrace=frame or -ftrace=full > > Fortran runtime error : End of file > > before running the electron-phonon calculation, you have to run a non- > scf calculation > with an option (la2f or something like this) that produces the > required file (the one > that is missing here) > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110203/261f814d/attachment.htm From elie.moujaes at hotmail.co.uk Thu Feb 3 13:52:37 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Thu, 3 Feb 2011 12:52:37 +0000 Subject: [Pw_forum] computing electron phonon coefficients In-Reply-To: <02027A35-FCC9-4724-ACB2-89B77455583F@democritos.it> References: , <02027A35-FCC9-4724-ACB2-89B77455583F@democritos.it> Message-ID: One more question regarding the electron-phonon implementation in QE. Is it possible to plot the band structure and the DOS including the electron phonon interaction in the calculations? Regards Elie Moujaes University of Nottingham NOttingham NG7 2RD UK > From: giannozz at democritos.it > Date: Thu, 3 Feb 2011 07:38:58 +0100 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] computing electron phonon coefficients > > > On Feb 2, 2011, at 19:40 , Elie Moujaes wrote: > > > I am trying to compute the electron phonon coefficients for > > monolayer graphene (using the options elph=.true. and trans=.true.) > > in the ph.in file. I am using Espresso-4.2. The ph.x executable is > > stopping after some time with the message: > > > > At line 378 of file elphon.f90 (Unit 40 "/tmp/results-MOUJAES/ > > elphomonograph.a2Fsave") > > Traceback is not availabe, compile with -ftrace=frame or -ftrace=full > > Fortran runtime error : End of file > > before running the electron-phonon calculation, you have to run a non- > scf calculation > with an option (la2f or something like this) that produces the > required file (the one > that is missing here) > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110203/4ae7566d/attachment.htm From jafernandes at ua.pt Thu Feb 3 19:22:20 2011 From: jafernandes at ua.pt (=?iso-8859-1?Q?Jos=E9?= Alberto Pires Fernandes) Date: Thu, 03 Feb 2011 18:22:20 +0000 Subject: [Pw_forum] location of kpoints Message-ID: Hello As I have explained before I am doing a structural optimization in a large cell with no symmetry. Most of the atoms in the cell are fixed, and I'm trying to optimise the position of two small molecules enclosed in a fixed cavity. The present question is the following: "Can I situate only two kpoints in the approximate centers of these small molecules, instead of a regular distribution?" Best regards Jose Jos? Fernandes Departamento de Quimica Universidade de Aveiro 3810-193 Aveiro Portugal Tel: +351234370720 Fax: +351234370084 From giannozz at democritos.it Thu Feb 3 21:08:13 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 3 Feb 2011 21:08:13 +0100 Subject: [Pw_forum] location of kpoints In-Reply-To: References: Message-ID: <69757F62-0EC4-4151-A37D-BD0DBFDCFC0E@democritos.it> On Feb 3, 2011, at 19:22 , Jos? Alberto Pires Fernandes wrote: > "Can I situate only two kpoints in the approximate centers > of these small molecules, instead of a regular distribution?" ??? k-points live in reciprocal space P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From jafernandes at ua.pt Thu Feb 3 23:20:08 2011 From: jafernandes at ua.pt (=?iso-8859-1?Q?Jos=E9?= Alberto Pires Fernandes) Date: Thu, 03 Feb 2011 22:20:08 +0000 Subject: [Pw_forum] location of kpoints In-Reply-To: <69757F62-0EC4-4151-A37D-BD0DBFDCFC0E@democritos.it> References: <69757F62-0EC4-4151-A37D-BD0DBFDCFC0E@democritos.it> Message-ID: Hello A strange thought, even for a beginner. Sorry! Em Thu, 3 Feb 2011 21:08:13 +0100 Paolo Giannozzi escreveu: > > On Feb 3, 2011, at 19:22 , Jos? Alberto Pires Fernandes >wrote: > >> "Can I situate only two kpoints in the approximate >>centers >> of these small molecules, instead of a regular >>distribution?" > > ??? k-points live in reciprocal space > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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 Jos? Fernandes Departamento de Quimica Universidade de Aveiro 3810-193 Aveiro Portugal Tel: +351234370720 Fax: +351234370084 From ac.rain at inbox.com Fri Feb 4 00:14:38 2011 From: ac.rain at inbox.com (ac.rain at inbox.com) Date: Thu, 3 Feb 2011 15:14:38 -0800 Subject: [Pw_forum] QE and mpich2, Linux In-Reply-To: <572E1D7F-D1FE-4ACA-B2C1-880540AD8A50@democritos.it> References: <47bd3257d74.00000656ac.rain@inbox.com> <0589a8d7d96.00000508ac.rain@inbox.com> <9179582e6fa.00000849ac.rain@inbox.com> <2535d195-ac71-4965-8379-243a44a796b0@sissa.it> <4d074755.3020701@democritos.it> <60b257887fc.000006d5ac.rain@inbox.com> Message-ID: <1CC35B794CC.000002F1ac.rain@inbox.com> the -nimage and -npool were accepted as valid options when I put them at the end of the mpi command, as part of the espresso command. thanks for your help so far, I will keep trying to get this to work properly. Nick > -----Original Message----- > From: giannozz at democritos.it > Sent: Wed, 2 Feb 2011 08:48:46 +0100 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] QE and mpich2, Linux > > > On Feb 2, 2011, at 3:54 , ac.rain at inbox.com wrote: > >> mpirun redirects to mpiexec which does not support >> options "-nimage" and "-npool" > > these options are interpreted by pw.x, not by mpirun or mpiexec > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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 ____________________________________________________________ FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop! Check it out at http://www.inbox.com/earth From elie.moujaes at hotmail.co.uk Fri Feb 4 01:38:42 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Fri, 4 Feb 2011 00:38:42 +0000 Subject: [Pw_forum] problems with q2r.x executable Message-ID: Dear all, I am having problems with the ph.x command in the calculation of the electron-phonon coefficients for graphene. Some of the files produced are of the type a2Fq2r. In my case there are 10 of these a2Fq2r.51, a2Fq2r.52, a2Fq2r.53, a2Fq2r.54, a2Fq2r.55, a2Fq2r.56, a2Fq2r.57, a2Fq2r.58, a2Fq2r.59, a2Fq2r.60. The problem is the {a2Fq2r.51, a2Fq2r.52, a2Fq2r.53} are all appearing as a2Fq2r so that when the q2r.x executable is applied, it complains that the files .51, .52 and ,53 are missing. Can anyone point out what the problem might be? Thanks Elie Moujaes University of Nottingham NG72RD UK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110204/2cd4dea4/attachment.htm From padmaja_patnaik at yahoo.co.uk Fri Feb 4 06:28:59 2011 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Fri, 4 Feb 2011 05:28:59 +0000 (GMT) Subject: [Pw_forum] Error in runing example Message-ID: <277220.33590.qm@web26108.mail.ukl.yahoo.com> Hi I am using QE 4.2.1. while running example02 I obtained the following error message. running the scf calculation for Si... done ? running the phonon calculation at Gamma for Si..../run_example: line 138: 17980 Segmentation fault????? $PH_COMMAND < si.phG.in > si.phG.out ?done ? running the phonon calculation at X for Si..../run_example: line 154: 17983 Segmentation fault????? $PH_COMMAND < si.phX.in > si.phX.out Error condition encountered during test: exit status = 139 Aborting while the same example runs successfully in a previous version on the same machine. Please advise. Thanking in advance Regards Padmaja Patnaik Research Scholar Dept of Physics IIT Bombay Mumbai, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110204/6b883aaa/attachment.htm From wang.riping.81 at gmail.com Fri Feb 4 08:03:04 2011 From: wang.riping.81 at gmail.com (Riping WANG) Date: Fri, 4 Feb 2011 16:03:04 +0900 Subject: [Pw_forum] temph and fnoseh in cp.x Message-ID: Dear forum, Is it necessary to control temph in cp.x. At first, I did not control temph, and ignored fnoseh, I can keep the phonon temperature at target value very well. But later, I try to set fnoseh to control temph, it breaks during elevating phonon temperature. So, is anyone can give me some guide about temph and fnoseh? Is any good reference paper? Thanks very much. WANG Riping 2010.2.4 -- ****************************************************************************** WANG Riping Ph.D student, Institute for Study of the Earth's Interior,Okayama University, 827 Yamada, Misasa, Tottori-ken 682-0193, Japan Tel: +81-858-43-3739(Office), 1215(Inst) E-mail: wang.riping.81 at gmail.com ****************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110204/e717fa40/attachment-0001.htm From giannozz at democritos.it Fri Feb 4 08:46:22 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 4 Feb 2011 08:46:22 +0100 Subject: [Pw_forum] Error in runing example In-Reply-To: <277220.33590.qm@web26108.mail.ukl.yahoo.com> References: <277220.33590.qm@web26108.mail.ukl.yahoo.com> Message-ID: <466390E6-1C46-466B-91F1-3B460619F9F3@democritos.it> On Feb 4, 2011, at 6:28 , Padmaja Patnaik wrote: > running the phonon calculation at Gamma for Si..../run_example: > line 138: 17980 Segmentation fault $PH_COMMAND < si.phG.in > > si.phG.out as explained no less than 1001 times: - you should look INSIDE the output files (si.phG.out in results/, in this case) to see what has happened - this kind of mysterious errors in the provided examples almost invariably means that the code was miscompiled P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Fri Feb 4 08:55:57 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 4 Feb 2011 08:55:57 +0100 Subject: [Pw_forum] problems with q2r.x executable In-Reply-To: References: Message-ID: <4D117B79-C2C7-4A94-816E-014E03E5948A@democritos.it> On Feb 4, 2011, at 1:38 , Elie Moujaes wrote: > The problem is the {a2Fq2r.51, a2Fq2r.52, a2Fq2r.53} are all appearing > as a2Fq2r what do you mean? I have never heard that file X "appears" as Y P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Fri Feb 4 09:00:53 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 4 Feb 2011 09:00:53 +0100 Subject: [Pw_forum] temph and fnoseh in cp.x In-Reply-To: References: Message-ID: <26637FA1-B9F6-48B3-9E41-900843E32944@democritos.it> On Feb 4, 2011, at 8:03 , Riping WANG wrote: > Is it necessary to control temph in cp.x. necessary, no. It might be useful under some circumstances. > Not sure which ones, though: "temph" is the temperature for the fictitious degrees of freedom controlling the variable-cell dynamics, not to be confused with the "true" temperature (tempw). P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From no-reply at dropboxmail.com Fri Feb 4 13:21:04 2011 From: no-reply at dropboxmail.com (Dropbox) Date: Fri, 04 Feb 2011 12:21:04 +0000 Subject: [Pw_forum] Mohammad Saghayezhian invited you to Dropbox Message-ID: <20110204122104.2B7B53F5179@mailman-2.dropboxmail.com> Mohammad Saghayezhian wants you to use Dropbox to sync and share files online and across computers. Get started here: http://www.dropbox.com/link/20.CuZtMe53tq/NjY0NzcwNDE3Nw?src=referrals_bulk9 - The Dropbox Team ____________________________________________________ To stop receiving invites from Dropbox, please go to http://www.dropbox.com/bl/5db3c2c9df42/pw_forum%40pwscf.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110204/239b31e1/attachment.htm From elie.moujaes at hotmail.co.uk Fri Feb 4 14:38:29 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Fri, 4 Feb 2011 13:38:29 +0000 Subject: [Pw_forum] problems with q2r.x executable In-Reply-To: <4D117B79-C2C7-4A94-816E-014E03E5948A@democritos.it> References: , <4D117B79-C2C7-4A94-816E-014E03E5948A@democritos.it> Message-ID: When I execute ph.x , amongst the other files I get (.dyn0, .dyn1,..), I get those a2Fq2r files. it is strange that the first three which should be .51, .52 and .53 files are all produced with the same name a2Fq2r and they appear as WORD files whilst the others are ok. I have also tried deleting everything from the .tmp folder but in vain. ph.x still produces the same strain of files so that when i execute q2r.x, the code complains that a2Fq2r.51 is missing! Regards Elie > From: giannozz at democritos.it > Date: Fri, 4 Feb 2011 08:55:57 +0100 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] problems with q2r.x executable > > > On Feb 4, 2011, at 1:38 , Elie Moujaes wrote: > > > The problem is the {a2Fq2r.51, a2Fq2r.52, a2Fq2r.53} are all appearing > > as a2Fq2r > > what do you mean? I have never heard that file X "appears" as Y > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110204/aa550983/attachment.htm From giannozz at democritos.it Fri Feb 4 22:14:33 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 4 Feb 2011 22:14:33 +0100 Subject: [Pw_forum] problems with q2r.x executable In-Reply-To: References: , <4D117B79-C2C7-4A94-816E-014E03E5948A@democritos.it> Message-ID: <0B9B734C-40D9-4FB9-B16C-387BC0D455C7@democritos.it> On Feb 4, 2011, at 14:38 , Elie Moujaes wrote: > the first three which should be .51, .52 and .53 files > are all produced with the same name a2Fq2r and they > appear as WORD files whilst the others are ok. you need to go into the code where it opens those files and see what happens. There is no way anybody else can find an explanation for such an unlikely event without looking more closely. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From c.sun1 at uq.edu.au Fri Feb 4 23:23:10 2011 From: c.sun1 at uq.edu.au (Chenghua Sun) Date: Sat, 5 Feb 2011 08:23:10 +1000 Subject: [Pw_forum] an error with do_ee Message-ID: <953CBB350E1B83419677AF023AF7CBF5031DD782@UQEXMB4.soe.uq.edu.au> Dear All, Recently I tried to do the Makov-Payne correction on a charged system. I set: do_ee = .true. In the &SYSTEM section, and I also set: which_compensation = 'dcc', in &EE. But I got the error message: from read_namelists : error # 19 reading namelist system The version is 4.0.5. If I delete the setting 'do_ee = .true.', it works well, but without the Makov-Payne correction. Could you help me and give me some ideas? Thanks in advance. Coy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110205/c9335a05/attachment.htm From germaneau at gucas.ac.cn Sat Feb 5 16:04:12 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Sat, 05 Feb 2011 10:04:12 -0500 Subject: [Pw_forum] gibbs free energy Message-ID: <4D4D66EC.5020008@gucas.ac.cn> Dear all, I'm new in using DFT codes and especially pwscf. I'd like to calculate the Gibbs free energy of a crystal as function of temperature in order to study it's stability. How would you proceed? I thank you in advance, Eric. -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of ChineseAcademy of Sciences Yuquan Road 19A Beijing 100049 China /Please consider the environment before printing this email. Consid?rez svp l'environnement avant d'imprimer cet email. / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110205/83c6138f/attachment.htm From kucukben at sissa.it Sat Feb 5 13:21:54 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Sat, 05 Feb 2011 13:21:54 +0100 Subject: [Pw_forum] an error with do_ee In-Reply-To: <953CBB350E1B83419677AF023AF7CBF5031DD782@UQEXMB4.soe.uq.edu.au> References: <953CBB350E1B83419677AF023AF7CBF5031DD782@UQEXMB4.soe.uq.edu.au> Message-ID: <20110205132154.fznks0nqosgkwwsw@webmail.sissa.it> Dear Coy Is there any particular reason why you are using 4.0.5 ? If not, please update the code to the latest version. then you can use the "assume_isolated" key to get the makov payne corrected energies. EE is another story. cheers, emine kucukbenli, phd student, sissa, italy Quoting Chenghua Sun : > Dear All, > > Recently I tried to do the Makov-Payne correction on a charged system. I set: > do_ee = .true. > In the &SYSTEM section, and I also set: > which_compensation = 'dcc', > in &EE. > > But I got the error message: > from read_namelists : error # 19 > reading namelist system > > The version is 4.0.5. > > If I delete the setting 'do_ee = .true.', it works well, but without > the Makov-Payne correction. > > Could you help me and give me some ideas? Thanks in advance. > > Coy > > > > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From nicola.marzari at materials.ox.ac.uk Sat Feb 5 14:31:27 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Sat, 05 Feb 2011 13:31:27 +0000 Subject: [Pw_forum] gibbs free energy In-Reply-To: <4D4D66EC.5020008@gucas.ac.cn> References: <4D4D66EC.5020008@gucas.ac.cn> Message-ID: <4D4D512F.7090207@materials.ox.ac.uk> On 2/5/11 3:04 PM, Eric Germaneau wrote: > Dear all, > > I'm new in using DFT codes and especially pwscf. > I'd like to calculate the Gibbs free energy of a crystal as function of > temperature in order to study it's stability. > How would you proceed? > I thank you in advance, > > Eric. > Hi Eric, Gibbs is E+PV-TS - the enthalpy term is easy (pwscf deals e.g. with constant pressure calculations, or you could just calculate the equation of state and from that the enthalpy), and for the entropy the most relevant part is the vibrational entropy, that you could e.g. calculate in the harmonic or quasiharmonic approximations. Have a look at e.g. the papers of Dario Alfe and Mike Gillan (~1998-2005) - some of them deal with the more complex problem of calculating the free energies of liquid and solid iron, but I believe there was one dealing just with solid-solid transformations. A brief tutorial on quasiharmonic is also in our PRB 71, 205214 (2005) Best, nicola -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From c.sun1 at uq.edu.au Sun Feb 6 00:46:06 2011 From: c.sun1 at uq.edu.au (Chenghua Sun) Date: Sun, 6 Feb 2011 09:46:06 +1000 Subject: [Pw_forum] an error with do_ee References: <953CBB350E1B83419677AF023AF7CBF5031DD782@UQEXMB4.soe.uq.edu.au> <20110205132154.fznks0nqosgkwwsw@webmail.sissa.it> Message-ID: <953CBB350E1B83419677AF023AF7CBF5031DD785@UQEXMB4.soe.uq.edu.au> Dear Emine, Thanks a lot. The keyword assume_isolated does work, as you suggested. I also tested the EE approach (six jobs), and all of those have the convergence problem. So I will use the 'assume_isolated' to do the correction. Just one more thing: I can only use the above key words (both assume_isolated and EE), I can only run 'scf' job, and fail to run 'relax' for version 4.0, 4.1 and 4.2. Is it normal? Thanks again. Coy PhD, Australia ________________________________ From: pw_forum-bounces at pwscf.org on behalf of Emine Kucukbenli Sent: Sat 2011-2-5 22:21 To: pw_forum at pwscf.org Subject: Re: [Pw_forum] an error with do_ee Dear Coy Is there any particular reason why you are using 4.0.5 ? If not, please update the code to the latest version. then you can use the "assume_isolated" key to get the makov payne corrected energies. EE is another story. cheers, emine kucukbenli, phd student, sissa, italy Quoting Chenghua Sun : > Dear All, > > Recently I tried to do the Makov-Payne correction on a charged system. I set: > do_ee = .true. > In the &SYSTEM section, and I also set: > which_compensation = 'dcc', > in &EE. > > But I got the error message: > from read_namelists : error # 19 > reading namelist system > > The version is 4.0.5. > > If I delete the setting 'do_ee = .true.', it works well, but without > the Makov-Payne correction. > > Could you help me and give me some ideas? Thanks in advance. > > Coy > > > > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 5783 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110206/34fefde6/attachment.bin From c.sun1 at uq.edu.au Sun Feb 6 00:56:43 2011 From: c.sun1 at uq.edu.au (Chenghua Sun) Date: Sun, 6 Feb 2011 09:56:43 +1000 Subject: [Pw_forum] an error with do_ee References: <953CBB350E1B83419677AF023AF7CBF5031DD782@UQEXMB4.soe.uq.edu.au> <20110205132154.fznks0nqosgkwwsw@webmail.sissa.it> Message-ID: <953CBB350E1B83419677AF023AF7CBF5031DD786@UQEXMB4.soe.uq.edu.au> Dear Emine, I also noticed the 'assume_isolated' can only work for cubic lattice. Can I extend it to other systems? In my case the model is a two-dimension system, and it is not cubic. Thanks at advance. Coy ________________________________ From: pw_forum-bounces at pwscf.org on behalf of Emine Kucukbenli Sent: Sat 2011-2-5 22:21 To: pw_forum at pwscf.org Subject: Re: [Pw_forum] an error with do_ee Dear Coy Is there any particular reason why you are using 4.0.5 ? If not, please update the code to the latest version. then you can use the "assume_isolated" key to get the makov payne corrected energies. EE is another story. cheers, emine kucukbenli, phd student, sissa, italy Quoting Chenghua Sun : > Dear All, > > Recently I tried to do the Makov-Payne correction on a charged system. I set: > do_ee = .true. > In the &SYSTEM section, and I also set: > which_compensation = 'dcc', > in &EE. > > But I got the error message: > from read_namelists : error # 19 > reading namelist system > > The version is 4.0.5. > > If I delete the setting 'do_ee = .true.', it works well, but without > the Makov-Payne correction. > > Could you help me and give me some ideas? Thanks in advance. > > Coy > > > > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 5235 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110206/af388c20/attachment.bin From w2agz at w2agz.com Sun Feb 6 08:16:36 2011 From: w2agz at w2agz.com (W2AGZ) Date: Sat, 5 Feb 2011 23:16:36 -0800 Subject: [Pw_forum] Lunch Yesterday with Walter Kohn Message-ID: <05ad01cbc5cd$cbb33cc0$6319b640$@w2agz.com> To All Within the PWscf Community: Yesterday I was honored to be invited to have lunch with Walter Kohn, one of four in the company of Ted Geballe, Steve Kivelson and Mac Beasley of the Applied Physics Faculty of Stanford. I believe the QE community would enjoy knowing that Walter, at age 88, is very active and engaged, especially in promoting wind and solar as the future energy scenario of the US (not one I totally agree with, BTW). I first met Walter in the late 1970s when I was at IBM and collaborating with Doug Scalapino on Monte Carlo simulations of low dimensional fermion Hubbard-like models. We did get a few minutes to discuss the future of DFT as well, and agree that our community would benefit greatly from the extension of LDA+U, particularly to electron-phonon interactions. Nicola? Mateo? Eyvaz? -Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110205/7f3ff036/attachment-0001.htm From kucukben at sissa.it Sun Feb 6 10:38:56 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Sun, 06 Feb 2011 10:38:56 +0100 Subject: [Pw_forum] an error with do_ee In-Reply-To: <953CBB350E1B83419677AF023AF7CBF5031DD785@UQEXMB4.soe.uq.edu.au> References: <953CBB350E1B83419677AF023AF7CBF5031DD782@UQEXMB4.soe.uq.edu.au> <20110205132154.fznks0nqosgkwwsw@webmail.sissa.it> <953CBB350E1B83419677AF023AF7CBF5031DD785@UQEXMB4.soe.uq.edu.au> Message-ID: <20110206103856.ksdxy8mf40cs8k04@webmail.sissa.it> Dear Coy, > I also tested the EE approach (six jobs), and all of those have the > convergence problem. Have you put your system in the middle of the cell? The charge density should be fairly small at the boundaries for DCC to work. If this is not your case, we need to check your input and output to understand better. > Just one more thing: I can only use the above key words (both > assume_isolated and EE), I can only run 'scf' job, and fail to run > 'relax' for version 4.0, 4.1 and 4.2. Is it normal? I dont think it is normal, especially in the case of MP correction, as the correction is just on the energy. Post more details so we can look into it. Btw, have you tried martyna-tuckerman? cheers, emine kucukbenli, phd student, sissa, italy > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From c.sun1 at uq.edu.au Sun Feb 6 12:18:17 2011 From: c.sun1 at uq.edu.au (Chenghua Sun) Date: Sun, 6 Feb 2011 21:18:17 +1000 Subject: [Pw_forum] an error with do_ee References: <953CBB350E1B83419677AF023AF7CBF5031DD782@UQEXMB4.soe.uq.edu.au><20110205132154.fznks0nqosgkwwsw@webmail.sissa.it><953CBB350E1B83419677AF023AF7CBF5031DD785@UQEXMB4.soe.uq.edu.au> <20110206103856.ksdxy8mf40cs8k04@webmail.sissa.it> Message-ID: <953CBB350E1B83419677AF023AF7CBF5031DD789@UQEXMB4.soe.uq.edu.au> Dear Emine, The optimized structure used in my work is: Mn 0.000084580 0.139307868 15.221554432 Mn -2.663136985 4.752155376 15.221514785 Mn 5.567587322 0.000140707 14.977486470 Mn 2.663321146 4.752154342 15.221590927 O 0.000079739 3.214534101 17.469943271 O -2.818078799 8.016256977 16.820461708 O 5.567618105 3.254298111 16.820496706 O 2.818266725 8.016258532 16.820492041 O 2.761895432 1.620036457 13.178651487 O 0.000108628 6.403594576 13.178620118 O 8.373256671 1.619981921 13.178625538 The above coordinates were obtained without any correction. &CONTROL calculation = 'scf', pseudo_dir = '/home/uqcsun1/code/pseudo/', outdir = './tmp', restart_mode = 'restart', !max_seconds = 85000, prefix = 'Mn4O7' etot_conv_thr = 1d-6, forc_conv_thr = 1d-4, nstep = 2000, / &SYSTEM ibrav = 4, celldm(1) = 11.135, celldm(2) = 1.0, celldm(3) = 2.70, nat = 11, ntyp = 2, ecutwfc = 25.0, ecutrho = 300.0, nspin = 2, starting_magnetization(1)= 0.0, starting_magnetization(2)= 0.5, tot_charge = -1, occupations= 'smearing', smearing= 'methfessel-paxton', degauss= 0.01, lda_plus_u = .true., Hubbard_U(1)= 1.d-8, Hubbard_U(2)= 4.0, assume_isolated = .true. / &ELECTRONS conv_thr = 1.0d-8, mixing_mode = 'plain', mixing_beta = 0.1, electron_maxstep = 1000, / K_POINTS {automatic} 5 5 1 0 0 0 ATOMIC_SPECIES O 16.0 O-PBE.UPF Mn 54.938 Mn-PBE.UPF If possible, could you please help me and run a calculation with the Makov-Payne correction? Thank you. (I runned with assume_isolated = .true., and the calculated energy is exactly same as that without the correction. it is indicated that the correction is only applied for cubic lattice) Cheers, Coy ------------------------------------------------------------------------- Chenghua Sun, PhD ARC Centre of Excellence for Functional Nanomaterials Centre for Computational Molecular Science Australian Institute for Bioengineering and Nanotechnology, AIBN Building 75, The University of Queensland Qld 4072, Brisbane, Australia Tel (617) 33463972; Fax (617) 33463992 email: c.sun1 at uq.edu.au Web: http://web.aibn.uq.edu.au/cbn -------------------------------------------------------------------------- ________________________________ From: pw_forum-bounces at pwscf.org on behalf of Emine Kucukbenli Sent: Sun 2011-2-6 19:38 To: pw_forum at pwscf.org Subject: Re: [Pw_forum] an error with do_ee Dear Coy, > I also tested the EE approach (six jobs), and all of those have the > convergence problem. Have you put your system in the middle of the cell? The charge density should be fairly small at the boundaries for DCC to work. If this is not your case, we need to check your input and output to understand better. > Just one more thing: I can only use the above key words (both > assume_isolated and EE), I can only run 'scf' job, and fail to run > 'relax' for version 4.0, 4.1 and 4.2. Is it normal? I dont think it is normal, especially in the case of MP correction, as the correction is just on the energy. Post more details so we can look into it. Btw, have you tried martyna-tuckerman? cheers, emine kucukbenli, phd student, sissa, italy > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 8891 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110206/0fb2cc51/attachment.bin From amar.shugani at gmail.com Sun Feb 6 12:30:19 2011 From: amar.shugani at gmail.com (amar shugani) Date: Sun, 6 Feb 2011 03:30:19 -0800 Subject: [Pw_forum] please sir, tell me my input file is correct or not, please give me path Message-ID: ---------- Forwarded message ---------- From: amar shugani Date: Fri, Feb 4, 2011 at 4:56 AM Subject: To: pw_forum-request at pwscf.org Respected sir Iam new to pwscf and working on Molybdenium disilicide. I have made the following input file and visualised the structure in xcrysden but it is not the same as given in crystal structure site ,please sir tell me whether the input file is correct or not , where i am wrong -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110206/467f3632/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: mosi2.scf.in Type: application/octet-stream Size: 1076 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110206/467f3632/attachment.obj From eyvaz_isaev at yahoo.com Sun Feb 6 21:11:53 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sun, 6 Feb 2011 12:11:53 -0800 (PST) Subject: [Pw_forum] Lunch Yesterday with Walter Kohn In-Reply-To: <05ad01cbc5cd$cbb33cc0$6319b640$@w2agz.com> References: <05ad01cbc5cd$cbb33cc0$6319b640$@w2agz.com> Message-ID: <137195.41127.qm@web65706.mail.ac4.yahoo.com> Hello Paul, It is great to know that Walter is still active. My personal respect. As we are aware, LDA_U plus phonons (and may be electron-phonon, as well) is mostly implemented and we just are waiting when Matteo C. releases it . Bests, Eyvaz. From: W2AGZ To: pw_forum at pwscf.org Sent: Sun, February 6, 2011 8:16:36 AM Subject: [Pw_forum] Lunch Yesterday with Walter Kohn To All Within the PWscf Community: Yesterday I was honored to be invited to have lunch with Walter Kohn, one of four in the company of Ted Geballe, Steve Kivelson and Mac Beasley of the Applied Physics Faculty of Stanford. I believe the QE community would enjoy knowing that Walter, at age 88, is very active and engaged, especially in promoting wind and solar as the future energy scenario of the US (not one I totally agree with, BTW). I first met Walter in the late 1970s when I was at IBM and collaborating with Doug Scalapino on Monte Carlo simulations of low dimensional fermion Hubbard-like models. We did get a few minutes to discuss the future of DFT as well, and agree that our community would benefit greatly from the extension of LDA+U, particularly to electron-phonon interactions. Nicola? Mateo? Eyvaz? -Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110206/872aed9c/attachment-0001.htm From ddubey at purdue.edu Sun Feb 6 22:35:59 2011 From: ddubey at purdue.edu (Devendra Kumar Dubey) Date: Sun, 6 Feb 2011 16:35:59 -0500 (EST) Subject: [Pw_forum] Error using cppp.x Message-ID: <609229450.87542.1297028159979.JavaMail.root@mailhub019.itcs.purdue.edu> Dear Users, I am getting an error while post processing using cppp.x (car parinello post processing executable) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from cppp : error # 1 Cannot open file /scratch/......mypath...../cp_51.save/data-file.xml %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% So I searched in the QE forum about this and found out that Paolo has already given a solution for this in the following post http://www.democritos.it/pipermail/pw_forum/2008-May/009022.html where he provides a modified version of fpmdpp.f90 file I noticed that this was posted in May 2008. Currently I am using the version 4.2.1, which is installed on a computational cluster and unfortunately I do not have permissions there to edit files. It seems unlikely that this bug is not fixed in the newer versions of espresso. However the error I am getting is same as discussed in the above post. I am not sure what other reason might be for this error. Any ideas? has anybody else come across this kind of error recently? Before I go ahead and request the computational resource team to recompile espresso with modified code, I thought it would be better to confirm the reason for this error. Thank you for your time and attention, ~Devendra - Graduate Research Student School of Aeronautics & Astronautics Purdue University From mehrnooshhazrati at gmail.com Mon Feb 7 10:03:44 2011 From: mehrnooshhazrati at gmail.com (Mehrnoosh Hazrati) Date: Mon, 7 Feb 2011 12:33:44 +0330 Subject: [Pw_forum] Brillouin zone of a Orthorhombic In-Reply-To: References: Message-ID: Hi Dear I need to find the first Brillouin zone of a Orthorhombic lattice ( Sheet ), with high symmetry K points marked. any help will be highly appreciated. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110207/91cd6088/attachment.htm From kucukben at sissa.it Mon Feb 7 11:14:15 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Mon, 07 Feb 2011 11:14:15 +0100 Subject: [Pw_forum] an error with do_ee In-Reply-To: <953CBB350E1B83419677AF023AF7CBF5031DD789@UQEXMB4.soe.uq.edu.au> References: <953CBB350E1B83419677AF023AF7CBF5031DD782@UQEXMB4.soe.uq.edu.au><20110205132154.fznks0nqosgkwwsw@webmail.sissa.it><953CBB350E1B83419677AF023AF7CBF5031DD785@UQEXMB4.soe.uq.edu.au> <20110206103856.ksdxy8mf40cs8k04@webmail.sissa.it> <953CBB350E1B83419677AF023AF7CBF5031DD789@UQEXMB4.soe.uq.edu.au> Message-ID: <20110207111415.uv8jwybjvowccckg@webmail.sissa.it> Dear Coy, > (I runned with assume_isolated = .true., and the calculated energy > is exactly same as that without the correction. it is indicated that > the correction is only applied for cubic lattice) I am now looking at the 4.2.1 version of the code. If you realized, there is a Doc directory in it, which holds a file called INPUT_PW.txt (or html), Please take a look at that file to see how assume_isolated variable works (now it is a character variable). There is also some minimal explanation on different methods that can be employed and references. Please take a look at the theory papers there to decide which option to use, as what they do (just a shift in the energy or corrected potential etc) are different. Makov Payne correction requires the madelung constant for a given bravais lattice, and it is only implemented for cubic lattices (ibrav 1, 2, 3).Theoretically it is possible to extend it to other kinds of lattices as well. It is also possible practically, if you are willing to calculate the analytical integrals and plug them in the code. cheers, emine ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From davide.ceresoli at materials.ox.ac.uk Mon Feb 7 11:18:36 2011 From: davide.ceresoli at materials.ox.ac.uk (Davide Ceresoli) Date: Mon, 07 Feb 2011 10:18:36 +0000 Subject: [Pw_forum] an error with do_ee In-Reply-To: <953CBB350E1B83419677AF023AF7CBF5031DD789@UQEXMB4.soe.uq.edu.au> References: <953CBB350E1B83419677AF023AF7CBF5031DD782@UQEXMB4.soe.uq.edu.au><20110205132154.fznks0nqosgkwwsw@webmail.sissa.it><953CBB350E1B83419677AF023AF7CBF5031DD785@UQEXMB4.soe.uq.edu.au> <20110206103856.ksdxy8mf40cs8k04@webmail.sissa.it> <953CBB350E1B83419677AF023AF7CBF5031DD789@UQEXMB4.soe.uq.edu.au> Message-ID: <4D4FC6FC.7050500@materials.ox.ac.uk> Your system is a 2D slab, not an isolated molecule. D. On 02/06/2011 11:18 AM, Chenghua Sun wrote: > *Dear Emine,* > ** > *The optimized structure used in my work is:* > Mn 0.000084580 0.139307868 15.221554432 > Mn -2.663136985 4.752155376 15.221514785 > Mn 5.567587322 0.000140707 14.977486470 > Mn 2.663321146 4.752154342 15.221590927 > O 0.000079739 3.214534101 17.469943271 > O -2.818078799 8.016256977 16.820461708 > O 5.567618105 3.254298111 16.820496706 > O 2.818266725 8.016258532 16.820492041 > O 2.761895432 1.620036457 13.178651487 > O 0.000108628 6.403594576 13.178620118 > O 8.373256671 1.619981921 13.178625538 > *The above coordinates were obtained without any correction. * > ** > &CONTROL > calculation = 'scf', > pseudo_dir = '/home/uqcsun1/code/pseudo/', > outdir = './tmp', > restart_mode = 'restart', > !max_seconds = 85000, > prefix = 'Mn4O7' > etot_conv_thr = 1d-6, > forc_conv_thr = 1d-4, > nstep = 2000, > / > &SYSTEM > ibrav = 4, > celldm(1) = 11.135, > celldm(2) = 1.0, > celldm(3) = 2.70, > nat = 11, > ntyp = 2, > ecutwfc = 25.0, > ecutrho = 300.0, > nspin = 2, > starting_magnetization(1)= 0.0, > starting_magnetization(2)= 0.5, > tot_charge = -1, > occupations= 'smearing', > smearing= 'methfessel-paxton', > degauss= 0.01, > lda_plus_u = .true., Hubbard_U(1)= 1.d-8, Hubbard_U(2)= 4.0, > assume_isolated = .true. > / > &ELECTRONS > conv_thr = 1.0d-8, > mixing_mode = 'plain', > mixing_beta = 0.1, > electron_maxstep = 1000, > / > K_POINTS {automatic} > 5 5 1 0 0 0 > ATOMIC_SPECIES > O 16.0 O-PBE.UPF > Mn 54.938 Mn-PBE.UPF > If possible, could you please help me and run a calculation with the Makov-Payne > correction? > Thank you. > (I runned with assume_isolated = .true., and the calculated energy is exactly > same as that without the correction. it is indicated that the correction is only > applied for cubic lattice) > Cheers, > Coy From eyvaz_isaev at yahoo.com Mon Feb 7 11:44:26 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 7 Feb 2011 02:44:26 -0800 (PST) Subject: [Pw_forum] Brillouin zone of a Orthorhombic In-Reply-To: References: Message-ID: <388898.51364.qm@web65710.mail.ac4.yahoo.com> Hi, Which one you need? There are several type of Orthorhombic lattice. For which program you need BZ? Please provide your affiliation. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: Mehrnoosh Hazrati To: pw_forum at pwscf.org Sent: Mon, February 7, 2011 10:03:44 AM Subject: [Pw_forum] Brillouin zone of a Orthorhombic Hi Dear I need to find the first Brillouin zone of a Orthorhombic lattice ( Sheet ), with high symmetry K points marked. any help will be highly appreciated. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110207/29572edc/attachment.htm From c.sun1 at uq.edu.au Mon Feb 7 11:58:23 2011 From: c.sun1 at uq.edu.au (Chenghua Sun) Date: Mon, 7 Feb 2011 20:58:23 +1000 Subject: [Pw_forum] an error with do_ee References: <953CBB350E1B83419677AF023AF7CBF5031DD782@UQEXMB4.soe.uq.edu.au><20110205132154.fznks0nqosgkwwsw@webmail.sissa.it><953CBB350E1B83419677AF023AF7CBF5031DD785@UQEXMB4.soe.uq.edu.au><20110206103856.ksdxy8mf40cs8k04@webmail.sissa.it><953CBB350E1B83419677AF023AF7CBF5031DD789@UQEXMB4.soe.uq.edu.au> <20110207111415.uv8jwybjvowccckg@webmail.sissa.it> Message-ID: <953CBB350E1B83419677AF023AF7CBF5031DD790@UQEXMB4.soe.uq.edu.au> Dear Emine, Thank you very much. I have read those papers, and it seems it is not easy for solids with non-cubic lattice. Best Regards, Coy ------------------------------------------------------------------------- Chenghua Sun, PhD ARC Centre of Excellence for Functional Nanomaterials Centre for Computational Molecular Science Australian Institute for Bioengineering and Nanotechnology, AIBN Building 75, The University of Queensland Qld 4072, Brisbane, Australia Tel (617) 33463972; Fax (617) 33463992 email: c.sun1 at uq.edu.au Web: http://web.aibn.uq.edu.au/cbn -------------------------------------------------------------------------- ________________________________ From: pw_forum-bounces at pwscf.org on behalf of Emine Kucukbenli Sent: Mon 2011-2-7 20:14 To: pw_forum at pwscf.org Subject: Re: [Pw_forum] an error with do_ee Dear Coy, > (I runned with assume_isolated = .true., and the calculated energy > is exactly same as that without the correction. it is indicated that > the correction is only applied for cubic lattice) I am now looking at the 4.2.1 version of the code. If you realized, there is a Doc directory in it, which holds a file called INPUT_PW.txt (or html), Please take a look at that file to see how assume_isolated variable works (now it is a character variable). There is also some minimal explanation on different methods that can be employed and references. Please take a look at the theory papers there to decide which option to use, as what they do (just a shift in the energy or corrected potential etc) are different. Makov Payne correction requires the madelung constant for a given bravais lattice, and it is only implemented for cubic lattices (ibrav 1, 2, 3).Theoretically it is possible to extend it to other kinds of lattices as well. It is also possible practically, if you are willing to calculate the analytical integrals and plug them in the code. cheers, emine ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 6351 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110207/0140ef01/attachment.bin From mehrnooshhazrati at gmail.com Mon Feb 7 12:01:10 2011 From: mehrnooshhazrati at gmail.com (Mehrnoosh Hazrati) Date: Mon, 7 Feb 2011 14:31:10 +0330 Subject: [Pw_forum] Brillouin zone of a Orthorhombic In-Reply-To: <388898.51364.qm@web65710.mail.ac4.yahoo.com> References: <388898.51364.qm@web65710.mail.ac4.yahoo.com> Message-ID: Hi dear Eyvaz, I need K-point set for 'orthorhombic P' lattice for bands calculations. regards, Mehrnoosh. On Mon, Feb 7, 2011 at 2:14 PM, Eyvaz Isaev wrote: > Hi, > > Which one you need? There are several type of Orthorhombic lattice. > For which program you need BZ? > > Please provide your affiliation. > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > ------------------------------ > *From:* Mehrnoosh Hazrati > *To:* pw_forum at pwscf.org > *Sent:* Mon, February 7, 2011 10:03:44 AM > *Subject:* [Pw_forum] Brillouin zone of a Orthorhombic > > > > Hi Dear > > I need to find the first Brillouin zone of a Orthorhombic lattice ( Sheet > ), with high symmetry K points marked. > any help will be highly appreciated. > > > > > > > _______________________________________________ > 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/20110207/fc6b0988/attachment-0001.htm From c.sun1 at uq.edu.au Mon Feb 7 12:00:14 2011 From: c.sun1 at uq.edu.au (Chenghua Sun) Date: Mon, 7 Feb 2011 21:00:14 +1000 Subject: [Pw_forum] an error with do_ee References: <953CBB350E1B83419677AF023AF7CBF5031DD782@UQEXMB4.soe.uq.edu.au><20110205132154.fznks0nqosgkwwsw@webmail.sissa.it><953CBB350E1B83419677AF023AF7CBF5031DD785@UQEXMB4.soe.uq.edu.au> <20110206103856.ksdxy8mf40cs8k04@webmail.sissa.it> <953CBB350E1B83419677AF023AF7CBF5031DD789@UQEXMB4.soe.uq.edu.au> <4D4FC6FC.7050500@materials.ox.ac.uk> Message-ID: <953CBB350E1B83419677AF023AF7CBF5031DD791@UQEXMB4.soe.uq.edu.au> Yes, you are right and it seems I can do such correction. I will use a bigger lattice to reduce the electrostatic interaction. Thanks anyway. ------------------------------------------------------------------------- Chenghua Sun, PhD ARC Centre of Excellence for Functional Nanomaterials Centre for Computational Molecular Science Australian Institute for Bioengineering and Nanotechnology, AIBN Building 75, The University of Queensland Qld 4072, Brisbane, Australia Tel (617) 33463972; Fax (617) 33463992 email: c.sun1 at uq.edu.au Web: http://web.aibn.uq.edu.au/cbn -------------------------------------------------------------------------- ________________________________ From: pw_forum-bounces at pwscf.org on behalf of Davide Ceresoli Sent: Mon 2011-2-7 20:18 To: PWSCF Forum Subject: Re: [Pw_forum] an error with do_ee Your system is a 2D slab, not an isolated molecule. D. On 02/06/2011 11:18 AM, Chenghua Sun wrote: > *Dear Emine,* > ** > *The optimized structure used in my work is:* > Mn 0.000084580 0.139307868 15.221554432 > Mn -2.663136985 4.752155376 15.221514785 > Mn 5.567587322 0.000140707 14.977486470 > Mn 2.663321146 4.752154342 15.221590927 > O 0.000079739 3.214534101 17.469943271 > O -2.818078799 8.016256977 16.820461708 > O 5.567618105 3.254298111 16.820496706 > O 2.818266725 8.016258532 16.820492041 > O 2.761895432 1.620036457 13.178651487 > O 0.000108628 6.403594576 13.178620118 > O 8.373256671 1.619981921 13.178625538 > *The above coordinates were obtained without any correction. * > ** > &CONTROL > calculation = 'scf', > pseudo_dir = '/home/uqcsun1/code/pseudo/', > outdir = './tmp', > restart_mode = 'restart', > !max_seconds = 85000, > prefix = 'Mn4O7' > etot_conv_thr = 1d-6, > forc_conv_thr = 1d-4, > nstep = 2000, > / > &SYSTEM > ibrav = 4, > celldm(1) = 11.135, > celldm(2) = 1.0, > celldm(3) = 2.70, > nat = 11, > ntyp = 2, > ecutwfc = 25.0, > ecutrho = 300.0, > nspin = 2, > starting_magnetization(1)= 0.0, > starting_magnetization(2)= 0.5, > tot_charge = -1, > occupations= 'smearing', > smearing= 'methfessel-paxton', > degauss= 0.01, > lda_plus_u = .true., Hubbard_U(1)= 1.d-8, Hubbard_U(2)= 4.0, > assume_isolated = .true. > / > &ELECTRONS > conv_thr = 1.0d-8, > mixing_mode = 'plain', > mixing_beta = 0.1, > electron_maxstep = 1000, > / > K_POINTS {automatic} > 5 5 1 0 0 0 > ATOMIC_SPECIES > O 16.0 O-PBE.UPF > Mn 54.938 Mn-PBE.UPF > If possible, could you please help me and run a calculation with the Makov-Payne > correction? > Thank you. > (I runned with assume_isolated = .true., and the calculated energy is exactly > same as that without the correction. it is indicated that the correction is only > applied for cubic lattice) > Cheers, > Coy _______________________________________________ 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: not available Type: application/ms-tnef Size: 7207 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110207/84a413e9/attachment.bin From eyvaz_isaev at yahoo.com Mon Feb 7 12:15:55 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 7 Feb 2011 03:15:55 -0800 (PST) Subject: [Pw_forum] Brillouin zone of a Orthorhombic In-Reply-To: References: <388898.51364.qm@web65710.mail.ac4.yahoo.com> Message-ID: <256064.99345.qm@web65713.mail.ac4.yahoo.com> I asked you provide your affiliation, but you did not. Therefore, no reply to your e-mail. Bests, Eyvaz ________________________________ From: Mehrnoosh Hazrati To: PWSCF Forum Sent: Mon, February 7, 2011 12:01:10 PM Subject: Re: [Pw_forum] Brillouin zone of a Orthorhombic Hi dear Eyvaz, I need K-point set for 'orthorhombic P' lattice for bands calculations. regards, Mehrnoosh. On Mon, Feb 7, 2011 at 2:14 PM, Eyvaz Isaev wrote: Hi, > >Which one you need? There are several type of Orthorhombic lattice. >For which program you need BZ? > >Please provide your affiliation. > >Bests, >Eyvaz. > > ------------------------------------------------------------------- >Prof. Eyvaz Isaev, >Department of Physics, Chemistry, and Biology (IFM), Linkoping University, >Sweden > >Theoretical Physics Department, Moscow State Institute of Steel & Alloys, >Russia, > >isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > > > ________________________________ From: Mehrnoosh Hazrati >To: pw_forum at pwscf.org >Sent: Mon, February 7, 2011 10:03:44 AM >Subject: [Pw_forum] Brillouin zone of a Orthorhombic > > > > > > >Hi Dear > >I need to find the first Brillouin zone of a Orthorhombic lattice ( Sheet ), >with high symmetry K points marked. > > >any help will be highly appreciated. > > > > > > >_______________________________________________ >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/20110207/43ccc663/attachment.htm From saqib.javaid at ipcms.u-strasbg.fr Mon Feb 7 13:48:07 2011 From: saqib.javaid at ipcms.u-strasbg.fr (saqib.javaid at ipcms.u-strasbg.fr) Date: Mon, 07 Feb 2011 13:48:07 +0100 Subject: [Pw_forum] question about order of PDOS in fully relativistic case In-Reply-To: <256064.99345.qm@web65713.mail.ac4.yahoo.com> References: <388898.51364.qm@web65710.mail.ac4.yahoo.com> <256064.99345.qm@web65713.mail.ac4.yahoo.com> Message-ID: <1297082887.4d4fea0723757@ipcms.u-strasbg.fr> Dear PWSCF users, I have a question regarding the order in which PDOS is written in fully relativistic case. As per documentation, it is E LDOS(E) PDOS_1(E) ... PDOS_2j+1(E) Does PDOS_1(E) corresponds to -mj and '2j+1' to +mj. e.g. in case of P orbital, the order would corresponds to mj='-3/2,-1/2,1/2,3/2' for 4 columns printed or something else??? I would appreciate a clarification Saqib Javaid University of strasbourg. ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From elie.moujaes at hotmail.co.uk Mon Feb 7 14:06:25 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Mon, 7 Feb 2011 13:06:25 +0000 Subject: [Pw_forum] problems with q2r.x executable In-Reply-To: <0B9B734C-40D9-4FB9-B16C-387BC0D455C7@democritos.it> References: , , <4D117B79-C2C7-4A94-816E-014E03E5948A@democritos.it>, , <0B9B734C-40D9-4FB9-B16C-387BC0D455C7@democritos.it> Message-ID: Prof. Giannozzi, Thanks very much for your reply. I just repeated the calculations and it worked quite well. Regards Elie Moujaes University of Nottingham NG7 2RD UK > From: giannozz at democritos.it > Date: Fri, 4 Feb 2011 22:14:33 +0100 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] problems with q2r.x executable > > > On Feb 4, 2011, at 14:38 , Elie Moujaes wrote: > > > the first three which should be .51, .52 and .53 files > > are all produced with the same name a2Fq2r and they > > appear as WORD files whilst the others are ok. > > you need to go into the code where it opens those files > and see what happens. There is no way anybody else > can find an explanation for such an unlikely event without > looking more closely. > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110207/011ee552/attachment-0001.htm From wonvein at gmail.com Mon Feb 7 14:07:19 2011 From: wonvein at gmail.com (WANG Wei) Date: Mon, 7 Feb 2011 22:07:19 +0900 Subject: [Pw_forum] bands.x can not work as the vdW-DF is activated Message-ID: Dear all, I find the bands.x can not work as the vdW-DF is activated. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% bands.x 000000000051E0A4 vdw_df_mp_get_the 1102 xc_vdW_DF.f90 bands.x 0000000000521E35 vdw_df_mp_xc_vdw_ 348 xc_vdW_DF.f90 bands.x 0000000000509E1C v_xc_ 484 v_of_rho.f90 bands.x 00000000005075A9 v_of_rho_ 58 v_of_rho.f90 bands.x 00000000004D8BA6 read_file_ 246 read_file.f90 bands.x 000000000040609C MAIN__ 92 bands.f90 bands.x 0000000000405DC2 Unknown Unknown Unknown libc.so.6 00000037F521D994 Unknown Unknown Unknown bands.x 0000000000405CE9 Unknown Unknown Unknown %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Thank you! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110207/6fc42b94/attachment.htm From amar.shugani at gmail.com Mon Feb 7 14:47:38 2011 From: amar.shugani at gmail.com (amar shugani) Date: Mon, 7 Feb 2011 05:47:38 -0800 Subject: [Pw_forum] (no subject) Message-ID: sir ,molybdenium disilicide input file is attached pleace tell me file is correct or not give me guide line -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110207/70a0d622/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: mosi2.scf.in Type: application/octet-stream Size: 1076 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110207/70a0d622/attachment.obj From Silvia.Bahmann at physik.tu-freiberg.de Mon Feb 7 14:47:49 2011 From: Silvia.Bahmann at physik.tu-freiberg.de (Silvia Bahmann) Date: Mon, 07 Feb 2011 14:47:49 +0100 Subject: [Pw_forum] Band structure of non-metallic antiferromagnet In-Reply-To: References: Message-ID: <20110207144749.195959uqble1nith@webmail.tu-freiberg.de> Hi, of course, I read the input documentation and tried without tot_magnetization. ( nspin = 2, starting_magnetization(1) = 1, starting_magnetization(2) = -1) But when starting pw.x the following error message appeared: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from iosys : error # 1 fixed occupations and lsda need tot_magnetization %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% This caused me to use tot_magnetization. Any suggestions? Silvia Bahmann Institute for Theoretical Physics TU Bergakademie Freiberg Germany > From: Paolo Giannozzi > > On Dec 17, 2010, at 15:06 , Silvia Bahmann wrote: > >> In v. 4.2.1 of QE one has to define antiferromagnetism in >> an insulator like this: >> >> starting_magnetization(1) = 1, >> starting_magnetization(2) = -1, >> tot_magnetization = 0 > > actually the input documentation says > If you fix the magnetization with "tot_magnetization", > you should not specify starting_magnetization. > Setting starting_magnetization should be sufficient to produce an AFM > state (if the systems wants to go there) > >> Is there another way to define the antiferromagnetism since nelup and >> neldw are not available anymore? > > tot_magnetization does exactly the same as nelup, neldw. Too many > ways to specify the same thing are a source of confusion. > >> And why is the bands code not working? > > maybe it is just an overzealous check (always preferrable to > insufficient > checks allowing to produce meaningless results). You may try to locate > the error message and to disable it if you think that there is no > good reason > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 From Lorenzo.Paulatto at impmc.upmc.fr Mon Feb 7 16:21:29 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Mon, 07 Feb 2011 16:21:29 +0100 Subject: [Pw_forum] Band structure of non-metallic antiferromagnet In-Reply-To: <1D209BB4-9BDE-4581-954F-8634A9464CE0@democritos.it> References: <20101217150635.1214218gsecpwv3f@webmail.tu-freiberg.de> <1D209BB4-9BDE-4581-954F-8634A9464CE0@democritos.it> Message-ID: On Wed, 22 Dec 2010 23:04:46 +0100, Paolo Giannozzi wrote: > actually the input documentation says > If you fix the magnetization with "tot_magnetization", > you should not specify starting_magnetization. > Setting starting_magnetization should be sufficient to produce an AFM > state (if the systems wants to go there) The documentation is wrong: unfortunately a check slipped in the code which requires a starting_magnetization to be specified even when the magnetization is constrained IF AND ONLY IF the constraint is specified with constrained_magnetization='total', fixed_magnetization(3)=XXX. Workaround: use tot_magnetization instead. I.e. change: constrained_magnetization='total' fixed_magnetization(3)=XXX to tot_magnetization=XXX best regards -- Lorenzo Paulatto (IdR) IMPMC - CNRS UMR 7590 & Universit? P&M Curie T23-C13/23-5e27 - 4 place Jussieu - 75252 Paris Cedex5 phone: +33 (0)144 27 5211 www: http://www-int.impmc.upmc.fr/~paulatto/ From sclauzer at sissa.it Mon Feb 7 16:50:03 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 7 Feb 2011 16:50:03 +0100 Subject: [Pw_forum] (no subject) In-Reply-To: References: Message-ID: <0B7712AC-F35D-4452-9D63-9B2D08697CFC@sissa.it> Il giorno 07/feb/2011, alle ore 14.47, amar shugani ha scritto: > sir ,molybdenium disilicide input file is attached pleace tell me file is correct or not Do you have any reason to believe that it is not correct? > give me guide line 1. Specify a meaningful subject in your post 2. Try to address a specific problem 3. Please sign your letters and provide your affiliation GS > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110207/d69337ef/attachment.htm From elie.moujaes at hotmail.co.uk Mon Feb 7 16:51:07 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Mon, 7 Feb 2011 15:51:07 +0000 Subject: [Pw_forum] error ephsum using ph.x Message-ID: Dear all, (1) First of all sorry to bombard you with a lot of questions but I am trying to perform the electron phonon calculation of monolayer graphene and I am facing some problems. when performing the ph.x command, after some time, I get an error: from elphsum : error # 2 q is not a vector in the dense grid %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... This is when trying to do calculations for one particular point. my input file is the following: Electron-Phonon interaction for monolayer graphene &inputph tr2_ph=1.0d-14, prefix='elphmonograph', fildvscf='mgraphdv', amass(1)=12.0107, outdir='/tmp/results_MOUJAES/', fildyn='elphmgraph.dyn', elph=.true., trans=.true., ldisp=.true. nq1=8, nq2=8, nq3=1 / I have tried with lesser points like say nq1=2, nq2=2, nq3=1 and I did not get such an error. (2) My second question is about lambda.x .I have read the example in the QE package but have not really understood it fully. Can anyone briefly explain to me or just point out where there is more explanation about this executable..I fully understtod what it does though.. Regards and thanks for your time Elie Moujaes University of Nottingham NG7 2RD UK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110207/bba46afb/attachment.htm From sclauzer at sissa.it Mon Feb 7 17:05:56 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 7 Feb 2011 17:05:56 +0100 Subject: [Pw_forum] question about order of PDOS in fully relativistic case In-Reply-To: <1297082887.4d4fea0723757@ipcms.u-strasbg.fr> References: <388898.51364.qm@web65710.mail.ac4.yahoo.com> <256064.99345.qm@web65713.mail.ac4.yahoo.com> <1297082887.4d4fea0723757@ipcms.u-strasbg.fr> Message-ID: <75C883CB-70ED-434B-91C8-2E9163ADE62C@sissa.it> Il giorno 07/feb/2011, alle ore 13.48, saqib.javaid at ipcms.u-strasbg.fr ha scritto: > > Dear PWSCF users, > > I have a question regarding the order in which PDOS is written in fully > relativistic case. As per documentation, it is > > E LDOS(E) PDOS_1(E) ... PDOS_2j+1(E) > > Does PDOS_1(E) corresponds to -mj and '2j+1' to +mj. e.g. in case of P orbital, > the order would corresponds to mj='-3/2,-1/2,1/2,3/2' for 4 columns printed or If I remember well it should be as you state here above. Moreover it sounds like the most reasonable choice. For the p orbital (if the corresponding pseudopotential has the SO coupling) you should have two files, one for j=1/2 (which will contain columns corresponding to m_j=-1/2 and +1/2) another for j=3/2 with the values of m_j that you've already listed. HTH GS > something else??? > I would appreciate a clarification > Saqib Javaid > University of strasbourg. > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110207/e2a0c00a/attachment-0001.htm From eyvaz_isaev at yahoo.com Mon Feb 7 17:09:21 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 7 Feb 2011 08:09:21 -0800 (PST) Subject: [Pw_forum] error ephsum using ph.x In-Reply-To: References: Message-ID: <111121.98859.qm@web65704.mail.ac4.yahoo.com> Dear Elie, >from elphsum : error # 2 > q is not a vector in the dense grid That means k-points set used in the first scf step and what you specified in elph.in file are incompatible, i.e. nq1,nq2,nq3 are not divisors of that numbers used to generate dense k-points set. Regarding lambda.x, I guess, there was an example file (an input file) where an explanation was done. If you can not find it (please search before) then contact me. Besides, all info calculated via lambda.x can now be obtained using matdyn.x Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: Elie Moujaes To: pw_forum at pwscf.org Sent: Mon, February 7, 2011 4:51:07 PM Subject: [Pw_forum] error ephsum using ph.x Dear all, (1) First of all sorry to bombard you with a lot of questions but I am trying to perform the electron phonon calculation of monolayer graphene and I am facing some problems. when performing the ph.x command, after some time, I get an error: from elphsum : error # 2 q is not a vector in the dense grid %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... This is when trying to do calculations for one particular point. my input file is the following: Electron-Phonon interaction for monolayer graphene &inputph tr2_ph=1.0d-14, prefix='elphmonograph', fildvscf='mgraphdv', amass(1)=12.0107, outdir='/tmp/results_MOUJAES/', fildyn='elphmgraph.dyn', elph=.true., trans=.true., ldisp=.true. nq1=8, nq2=8, nq3=1 / I have tried with lesser points like say nq1=2, nq2=2, nq3=1 and I did not get such an error. (2) My second question is about lambda.x .I have read the example in the QE package but have not really understood it fully. Can anyone briefly explain to me or just point out where there is more explanation about this executable..I fully understtod what it does though.. Regards and thanks for your time Elie Moujaes University of Nottingham NG7 2RD UK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110207/7ab3f121/attachment.htm From saqib.javaid at ipcms.u-strasbg.fr Mon Feb 7 17:23:55 2011 From: saqib.javaid at ipcms.u-strasbg.fr (saqib.javaid at ipcms.u-strasbg.fr) Date: Mon, 07 Feb 2011 17:23:55 +0100 Subject: [Pw_forum] question about order of PDOS in fully relativistic case In-Reply-To: <75C883CB-70ED-434B-91C8-2E9163ADE62C@sissa.it> References: <388898.51364.qm@web65710.mail.ac4.yahoo.com> <256064.99345.qm@web65713.mail.ac4.yahoo.com> <1297082887.4d4fea0723757@ipcms.u-strasbg.fr> <75C883CB-70ED-434B-91C8-2E9163ADE62C@sissa.it> Message-ID: <1297095835.4d501c9bf29b8@ipcms.u-strasbg.fr> Dear Gabrielle, I was bit concerned because if you are right, the order to PDOS for Spin-orbit, non-collinear case would be different from collinear, scaler relativistic case where order is sorted out according to magnitude of Ml i.e. 0,+-1, +-2 .. thanks a lot for the clarification. best regard saqib javaid University of strasbourg. Selon Gabriele Sclauzero : > > Il giorno 07/feb/2011, alle ore 13.48, saqib.javaid at ipcms.u-strasbg.fr ha > scritto: > > > > > Dear PWSCF users, > > > > I have a question regarding the order in which PDOS is written in fully > > relativistic case. As per documentation, it is > > > > E LDOS(E) PDOS_1(E) ... PDOS_2j+1(E) > > > > Does PDOS_1(E) corresponds to -mj and '2j+1' to +mj. e.g. in case of P > orbital, > > the order would corresponds to mj='-3/2,-1/2,1/2,3/2' for 4 columns printed > or > > If I remember well it should be as you state here above. Moreover it sounds > like the most reasonable choice. > > For the p orbital (if the corresponding pseudopotential has the SO coupling) > you should have two files, > one for j=1/2 (which will contain columns corresponding to m_j=-1/2 and +1/2) > another for j=3/2 with the values of m_j that you've already listed. > > > HTH > > GS > > > > > something else??? > > I would appreciate a clarification > > Saqib Javaid > > University of strasbourg. > > > > ---------------------------------------------------------------- > > This message was sent using IMP, the Internet Messaging Program. > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > PH H2 462, Station 3, CH-1015 Lausanne > > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From sclauzer at sissa.it Mon Feb 7 17:30:15 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 7 Feb 2011 17:30:15 +0100 Subject: [Pw_forum] question about order of PDOS in fully relativistic case In-Reply-To: <1297095835.4d501c9bf29b8@ipcms.u-strasbg.fr> References: <388898.51364.qm@web65710.mail.ac4.yahoo.com> <256064.99345.qm@web65713.mail.ac4.yahoo.com> <1297082887.4d4fea0723757@ipcms.u-strasbg.fr> <75C883CB-70ED-434B-91C8-2E9163ADE62C@sissa.it> <1297095835.4d501c9bf29b8@ipcms.u-strasbg.fr> Message-ID: <071D6090-CA30-496D-A3BC-A4ECE9B07607@sissa.it> Il giorno 07/feb/2011, alle ore 17.23, saqib.javaid at ipcms.u-strasbg.fr ha scritto: > Dear Gabrielle, Dear Saqib, I'm a male, although in French speaking countries my name does strongly suggest the opposite... already tested... > > I was bit concerned because if you are right, the order to PDOS for Spin-orbit, > non-collinear case would be different from collinear, scaler relativistic case > where order is sorted out according to magnitude of Ml i.e. 0,+-1, +-2 .. You can make a test. In system with +/-m_j degeneracy (i.e., a linear chain of atoms without magnetic fields), you should find that the data in the +/-mj columns are identical. Regards, Gabriele > thanks a lot for the clarification. > best regard > saqib javaid > University of strasbourg. > > Selon Gabriele Sclauzero : > >> >> Il giorno 07/feb/2011, alle ore 13.48, saqib.javaid at ipcms.u-strasbg.fr ha >> scritto: >> >>> >>> Dear PWSCF users, >>> >>> I have a question regarding the order in which PDOS is written in fully >>> relativistic case. As per documentation, it is >>> >>> E LDOS(E) PDOS_1(E) ... PDOS_2j+1(E) >>> >>> Does PDOS_1(E) corresponds to -mj and '2j+1' to +mj. e.g. in case of P >> orbital, >>> the order would corresponds to mj='-3/2,-1/2,1/2,3/2' for 4 columns printed >> or >> >> If I remember well it should be as you state here above. Moreover it sounds >> like the most reasonable choice. >> >> For the p orbital (if the corresponding pseudopotential has the SO coupling) >> you should have two files, >> one for j=1/2 (which will contain columns corresponding to m_j=-1/2 and +1/2) >> another for j=3/2 with the values of m_j that you've already listed. >> >> >> HTH >> >> GS >> >> >> >>> something else??? >>> I would appreciate a clarification >>> Saqib Javaid >>> University of strasbourg. >>> >>> ---------------------------------------------------------------- >>> This message was sent using IMP, the Internet Messaging Program. >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> ? Gabriele Sclauzero, EPFL SB ITP CSEA >> PH H2 462, Station 3, CH-1015 Lausanne >> >> > > > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110207/4780dff3/attachment.htm From elie.moujaes at hotmail.co.uk Mon Feb 7 17:33:33 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Mon, 7 Feb 2011 16:33:33 +0000 Subject: [Pw_forum] error ephsum using ph.x In-Reply-To: <111121.98859.qm@web65704.mail.ac4.yahoo.com> References: , <111121.98859.qm@web65704.mail.ac4.yahoo.com> Message-ID: Dera Prof. Isaev, Thanks a lot for the info. I have read the example which is I guess Example 7 in the guide but did not quite understand it.Anyhow will look out other examples . regards Elie Date: Mon, 7 Feb 2011 08:09:21 -0800 From: eyvaz_isaev at yahoo.com To: pw_forum at pwscf.org Subject: Re: [Pw_forum] error ephsum using ph.x Dear Elie, >from elphsum : error # 2 > q is not a vector in the dense grid That means k-points set used in the first scf step and what you specified in elph.in file are incompatible, i.e. nq1,nq2,nq3 are not divisors of that numbers used to generate dense k-points set. Regarding lambda.x, I guess, there was an example file (an input file) where an explanation was done. If you can not find it (please search before) then contact me. Besides, all info calculated via lambda.x can now be obtained using matdyn.x Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From: Elie Moujaes To: pw_forum at pwscf.org Sent: Mon, February 7, 2011 4:51:07 PM Subject: [Pw_forum] error ephsum using ph.x Dear all, (1) First of all sorry to bombard you with a lot of questions but I am trying to perform the electron phonon calculation of monolayer graphene and I am facing some problems. when performing the ph.x command, after some time, I get an error: from elphsum : error # 2 q is not a vector in the dense grid %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... This is when trying to do calculations for one particular point. my input file is the following: Electron-Phonon interaction for monolayer graphene &inputph tr2_ph=1.0d-14, prefix='elphmonograph', fildvscf='mgraphdv', amass(1)=12.0107, outdir='/tmp/results_MOUJAES/', fildyn='elphmgraph.dyn', elph=.true., trans=.true., ldisp=.true. nq1=8, nq2=8, nq3=1 / I have tried with lesser points like say nq1=2, nq2=2, nq3=1 and I did not get such an error. (2) My second question is about lambda.x .I have read the example in the QE package but have not really understood it fully. Can anyone briefly explain to me or just point out where there is more explanation about this executable..I fully understtod what it does though.. Regards and thanks for your time Elie Moujaes University of Nottingham NG7 2RD UK _______________________________________________ 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/20110207/f0fed174/attachment-0001.htm From matteo at umn.edu Mon Feb 7 18:38:54 2011 From: matteo at umn.edu (Matteo Cococcioni) Date: Mon, 7 Feb 2011 11:38:54 -0600 Subject: [Pw_forum] Lunch Yesterday with Walter Kohn In-Reply-To: <137195.41127.qm@web65706.mail.ac4.yahoo.com> References: <05ad01cbc5cd$cbb33cc0$6319b640$@w2agz.com> <137195.41127.qm@web65706.mail.ac4.yahoo.com> Message-ID: Dear Paul and Eyvaz, here is an update on the phonon +U code. The implementation has been recently completed and the code seems to work although, sometimes, calculations with finite U seem more problematic to converge than with the standard (uncorrected) DFT functionals. we are finishing the testing and producing some results for selected systems. We are interested in porting the implementation on the latest version of QE and in releasing it as soon as possible. However, at the moment, Andrea Floris, who did the implementation and is the only person who knows the details of it, cannot work on this personally. Hopefully soon we will have someone learning the implementation (and the phonon code too) who will be able to to release the code to the QE distribution with proper documentation. Best regards, Matteo On Sun, Feb 6, 2011 at 2:11 PM, Eyvaz Isaev wrote: > Hello Paul, > > It is great to know that Walter is still active. My personal respect. > As we are aware, LDA_U plus phonons (and may be electron-phonon, as well) > is mostly implemented and we just are waiting when Matteo C. releases it . > > Bests, > Eyvaz. > > *From:* W2AGZ > *To:* pw_forum at pwscf.org > *Sent:* Sun, February 6, 2011 8:16:36 AM > *Subject:* [Pw_forum] Lunch Yesterday with Walter Kohn > > To All Within the PWscf Community: > > > > Yesterday I was honored to be invited to have lunch with Walter Kohn, one > of four in the company of Ted Geballe, Steve Kivelson and Mac Beasley of the > Applied Physics Faculty of Stanford. I believe the QE community would enjoy > knowing that Walter, at age 88, is very active and engaged, especially in > promoting wind and solar as the future energy scenario of the US (not one I > totally agree with, BTW). I first met Walter in the late 1970s when I was > at IBM and collaborating with Doug Scalapino on Monte Carlo simulations of > low dimensional fermion Hubbard-like models. > > > > We did get a few minutes to discuss the future of DFT as well, and agree > that our community would benefit greatly from the extension of LDA+U, > particularly to electron-phonon interactions. Nicola? Mateo? Eyvaz? > > > > -Paul > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 Fax +1 612 626 7246 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110207/d9119878/attachment.htm From eyvaz_isaev at yahoo.com Mon Feb 7 18:55:06 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 7 Feb 2011 09:55:06 -0800 (PST) Subject: [Pw_forum] error ephsum using ph.x In-Reply-To: References: , <111121.98859.qm@web65704.mail.ac4.yahoo.com> Message-ID: <560594.12149.qm@web65705.mail.ac4.yahoo.com> Yes, lambda.in in example07 is really that you need, if you prefer lambda.x. Bests, Eyvaz. ________________________________ From: Elie Moujaes To: pw_forum at pwscf.org Sent: Mon, February 7, 2011 5:33:33 PM Subject: Re: [Pw_forum] error ephsum using ph.x Dera Prof. Isaev, Thanks a lot for the info. I have read the example which is I guess Example 7 in the guide but did not quite understand it.Anyhow will look out other examples . regards Elie ________________________________ Date: Mon, 7 Feb 2011 08:09:21 -0800 From: eyvaz_isaev at yahoo.com To: pw_forum at pwscf.org Subject: Re: [Pw_forum] error ephsum using ph.x Dear Elie, >from elphsum : error # 2 > q is not a vector in the dense grid That means k-points set used in the first scf step and what you specified in elph.in file are incompatible, i.e. nq1,nq2,nq3 are not divisors of that numbers used to generate dense k-points set. Regarding lambda.x, I guess, there was an example file (an input file) where an explanation was done. If you can not find it (please search before) then contact me. Besides, all info calculated via lambda.x can now be obtained using matdyn.x Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: Elie Moujaes To: pw_forum at pwscf.org Sent: Mon, February 7, 2011 4:51:07 PM Subject: [Pw_forum] error ephsum using ph.x Dear all, (1) First of all sorry to bombard you with a lot of questions but I am trying to perform the electron phonon calculation of monolayer graphene and I am facing some problems. when performing the ph.x command, after some time, I get an error: from elphsum : error # 2 q is not a vector in the dense grid %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... This is when trying to do calculations for one particular point. my input file is the following: Electron-Phonon interaction for monolayer graphene &inputph tr2_ph=1.0d-14, prefix='elphmonograph', fildvscf='mgraphdv', amass(1)=12.0107, outdir='/tmp/results_MOUJAES/', fildyn='elphmgraph.dyn', elph=.true., trans=.true., ldisp=.true. nq1=8, nq2=8, nq3=1 / I have tried with lesser points like say nq1=2, nq2=2, nq3=1 and I did not get such an error. (2) My second question is about lambda.x .I have read the example in the QE package but have not really understood it fully. Can anyone briefly explain to me or just point out where there is more explanation about this executable..I fully understtod what it does though.. Regards and thanks for your time Elie Moujaes University of Nottingham NG7 2RD UK _______________________________________________ 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/20110207/964688ab/attachment.htm From eyvaz_isaev at yahoo.com Mon Feb 7 19:00:01 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 7 Feb 2011 10:00:01 -0800 (PST) Subject: [Pw_forum] Lunch Yesterday with Walter Kohn In-Reply-To: References: <05ad01cbc5cd$cbb33cc0$6319b640$@w2agz.com> <137195.41127.qm@web65706.mail.ac4.yahoo.com> Message-ID: <109684.3792.qm@web65701.mail.ac4.yahoo.com> Hi Matteo, Thanks sharing with the info regarding the current status of LDA+U and phonons. By the way, if you need more tests, I can. Very bests, Eyvaz. ________________________________ From: Matteo Cococcioni To: PWSCF Forum Sent: Mon, February 7, 2011 6:38:54 PM Subject: Re: [Pw_forum] Lunch Yesterday with Walter Kohn Dear Paul and Eyvaz, here is an update on the phonon +U code. The implementation has been recently completed and the code seems to work although, sometimes, calculations with finite U seem more problematic to converge than with the standard (uncorrected) DFT functionals. we are finishing the testing and producing some results for selected systems. We are interested in porting the implementation on the latest version of QE and in releasing it as soon as possible. However, at the moment, Andrea Floris, who did the implementation and is the only person who knows the details of it, cannot work on this personally. Hopefully soon we will have someone learning the implementation (and the phonon code too) who will be able to to release the code to the QE distribution with proper documentation. Best regards, Matteo On Sun, Feb 6, 2011 at 2:11 PM, Eyvaz Isaev wrote: Hello Paul, > >It is great to know that Walter is still active. My personal respect. >As we are aware, LDA_U plus phonons (and may be electron-phonon, as well) is >mostly implemented and we just are waiting when Matteo C. releases it . > >Bests, >Eyvaz. > > >From: W2AGZ >To: pw_forum at pwscf.org >Sent: Sun, February 6, 2011 8:16:36 AM >Subject: [Pw_forum] Lunch Yesterday with Walter Kohn > > >To All Within the PWscf Community: > >Yesterday I was honored to be invited to have lunch with Walter Kohn, one of >four in the company of Ted Geballe, Steve Kivelson and Mac Beasley of the >Applied Physics Faculty of Stanford. I believe the QE community would enjoy >knowing that Walter, at age 88, is very active and engaged, especially in >promoting wind and solar as the future energy scenario of the US (not one I >totally agree with, BTW). I first met Walter in the late 1970s when I was at >IBM and collaborating with Doug Scalapino on Monte Carlo simulations of low >dimensional fermion Hubbard-like models. > >We did get a few minutes to discuss the future of DFT as well, and agree that >our community would benefit greatly from the extension of LDA+U, particularly to >electron-phonon interactions. Nicola? Mateo? Eyvaz? > >-Paul > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > -- Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 Fax +1 612 626 7246 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110207/5c37d867/attachment-0001.htm From giannozz at democritos.it Tue Feb 8 08:41:39 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 8 Feb 2011 08:41:39 +0100 Subject: [Pw_forum] bands.x can not work as the vdW-DF is activated In-Reply-To: References: Message-ID: On Feb 7, 2011, at 14:07 , WANG Wei wrote: > I find the bands.x can not work as the vdW-DF is activated. which version of the code are you referreing to? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Tue Feb 8 09:14:50 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 8 Feb 2011 09:14:50 +0100 Subject: [Pw_forum] Error using cppp.x In-Reply-To: <609229450.87542.1297028159979.JavaMail.root@mailhub019.itcs.purdue.edu> References: <609229450.87542.1297028159979.JavaMail.root@mailhub019.itcs.purdue.edu> Message-ID: On Feb 6, 2011, at 22:35 , Devendra Kumar Dubey wrote: > from cppp : error # 1 > Cannot open file /scratch/......mypath...../cp_51.save/data- > file.xml "cannot open" = "is not there", in most cases > http://www.democritos.it/pipermail/pw_forum/2008-May/009022.html > [...] the error I am getting is same as discussed in the above post it isn't P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From wonvein at gmail.com Tue Feb 8 09:53:11 2011 From: wonvein at gmail.com (WANG Wei) Date: Tue, 8 Feb 2011 17:53:11 +0900 Subject: [Pw_forum] bands.x can not work as the vdW-DF is activated In-Reply-To: References: Message-ID: Dear Giannozzi, I am using the CVS (4.3.a) to make some tests within vdW-DF. Thank your. Best Regrads, WANG On 8 February 2011 16:41, Paolo Giannozzi wrote: > > On Feb 7, 2011, at 14:07 , WANG Wei wrote: > > > I find the bands.x can not work as the vdW-DF is activated. > > which version of the code are you referreing to? > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110208/1870c241/attachment.htm From claudial.81 at gmail.com Tue Feb 8 18:42:02 2011 From: claudial.81 at gmail.com (Claudia Loyola) Date: Tue, 8 Feb 2011 11:42:02 -0600 Subject: [Pw_forum] Wrong ELF values Message-ID: Dear Q-Espresso team, I have a problem with ELF calculation. Let me explain it, I calculated the ELF (electron localization function), for four different structures, in different planes of the structure, and with Xcrysden I visualized them, the problem is that the ELF values are between -0.2092 and 1.2504 for one case and for the others is like the same, and not between 0 and 1 as the theory goes. I do not understand what I am doing wrong... The charge density and the ELF calculation looks really good in each plane, but the values of the ELF are incorrect. What do you think is the problem? If you can help me, I will be very grateful! :D Thanks in advance! Claudia Loyola -- Claudia Loyola Canales Postdoc in Computational Physics Iowa State University Iowa, USA www.lpmd.cl/claudial www.lpmd.cl http://cosmic.mse.iastate.edu/ www.gnm.cl -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110208/c2019c8c/attachment.htm From jdburton1 at gmail.com Tue Feb 8 19:06:23 2011 From: jdburton1 at gmail.com (J. D. Burton) Date: Tue, 8 Feb 2011 12:06:23 -0600 Subject: [Pw_forum] Why does dos.x look for evc.dat files? Message-ID: <01f101cbc7ba$e79ef570$b6dce050$@gmail.com> Greetings, I'm trying to run dos.x (using v4.2.1) but it keeps coming up with an iotk error that it can't find any evc.dat files in the K* directories of prefix.save. Since the cell is pretty big I deleted the evc.dat files some time ago (after I calculated the projected LDOS) so my admin wouldn't complain about using so much hard-drive space. I just wanted to do a quick calculation of the total DOS calculation with a smaller degauss. 1. Why would a calculation of the *total* DOS, not projected LDOS, want the eigenvectors?? The total DOS should only depend on the eigenvalues, k-point weights and a gaussian smearing factor. 2. Is there a way to get around this without having to recalculate the eigenvectors? I thought I could just delete any references to the evc.dat files in data-file.xml, but that just came up with another iotk read error. I know I can just grab the eigenvalues and weights and do this myself (just add up a series of properly weighted gaussians, one at each eigenvalue) . but that seems to defeat the purpose of having a standardized code. J Cheers, J. D. ************************************ J. D. Burton, Ph.D. jdburton1 at gmail.com University of Nebraska Lincoln Physics and Astronomy Office Ph. (402) 472 2499 Mobile Ph. (402) 419 9918 310A Jorgensen Hall CV: http://tinyurl.com/2avltsc ************************************ "The job of a scientist is to generate wrong ideas as fast as possible." -- Murray Gell-Mann -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110208/e52c7137/attachment.htm From ferretti at mit.edu Tue Feb 8 19:52:43 2011 From: ferretti at mit.edu (Andrea Ferretti) Date: Tue, 8 Feb 2011 18:52:43 +0000 (GMT) Subject: [Pw_forum] Why does dos.x look for evc.dat files? In-Reply-To: <01f101cbc7ba$e79ef570$b6dce050$@gmail.com> References: <01f101cbc7ba$e79ef570$b6dce050$@gmail.com> Message-ID: Dear J.D., in principles you are right, the wfcs would not be needed. Anyway, since dos.f90 is started according to all the postprocessing codes, it does some operations on wfcs. In particular, at the end of the routine ~espresso/PW/read_file.f90 you would find CALL pw_readfile( 'wave', ierr ) which is probably where the error is issued. The possibility to restart without reading the wfcs could be added (maybe a simple flag in pw_restart that comments out the above lines would work, but it may be also much more involved)... deleting lines from data_file.xml makes it probably unreadable and is not a good idea in general. For your specific case, in order not to re-run the calculation you can try (no guarantee) the following quick and dirty procedure: * put the correct data_file.xml back in place (if you do not have this file I would start considering re-running the calculation or computing the DOS by yourself (I probably have a stupid f90 code for that, anyway) ) * comment out the line CALL pw_readfile( 'wave', ierr ) in PW/read_file.f90 recompile and try to run it... * immediatly after remove the comment and re-compile !!! andrea BTW: if it takes more then 5 minutes to try all the above, I would go for a direct calculation of the DOS from the eigenvalues written in the output file. (let me know, in case) > > I?m trying to run dos.x (using v4.2.1) but it keeps coming up with an > iotk error that it can?t find any evc.dat files in the K* directories of > prefix.save. Since the cell is pretty big I deleted the evc.dat files > some time ago (after I calculated the > projected LDOS) so my admin wouldn?t complain about using so much > hard-drive space. I just wanted to do a quick calculation of the total > DOS calculation with a smaller degauss. > > ? > > 1.?????? Why would a calculation of the *total* DOS, not projected LDOS, want the eigenvectors?? The total DOS should only depend on the eigenvalues, k-point weights and a gaussian > smearing factor. > > 2.?????? Is there a way to get around this without having to recalculate the eigenvectors? I thought I could just delete any references to the evc.dat files in data-file.xml, but > that just came up with another iotk read error. > > ? > > I know I can just grab the eigenvalues and weights and do this myself (just add up a series of properly weighted gaussians, one at each eigenvalue) ? but that seems to defeat the > purpose of having a standardized code. J > > ? > > Cheers, > > J. D. > > ? > > ************************************ > > J. D. Burton, Ph.D. > > jdburton1 at gmail.com > > University of Nebraska Lincoln > > Physics and Astronomy > > Office Ph. (402) 472 2499 > > Mobile Ph. (402) 419 9918 > > 310A Jorgensen Hall > > CV: http://tinyurl.com/2avltsc > > ************************************ > > "The job of a scientist is to generate wrong ideas as fast as possible." > > -- Murray Gell-Mann > > ? > > > -- Andrea Ferretti Oxford University, Department of Materials Parks Road, Oxford OX1 3PH, UK Tel: +44 (0)1865 612792; Skype: andrea_ferretti URL: http://quasiamore.mit.edu Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html From giannozz at democritos.it Tue Feb 8 20:43:44 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 8 Feb 2011 20:43:44 +0100 Subject: [Pw_forum] Wrong ELF values In-Reply-To: References: Message-ID: On Feb 8, 2011, at 18:42 , Claudia Loyola wrote: > the problem is that the ELF values are between -0.2092 and 1.2504 > for one case and for the others is like the same, and not between 0 > and 1 as the theory goes. I do not understand what I am doing wrong... maybe nothing: there have been other reports of funny results with elf. In particular: http://www.democritos.it/pipermail/pw_forum/2010-October/018460.html So, who is right: 0 References: Message-ID: <270733.96497.qm@web65713.mail.ac4.yahoo.com> Dear Pari, > I have been sending emails for months to all the QE email address, but nobody >sent a reply yet, > > although I subscribed for the forum. Please just let me tell you that nobody from the forum is obliged to answer any question, there are only volunteers. If one has time and have an experience with the similar problem then he can share with this info. Regarding the problem: have you tried using a smaller k-points set? How big is your structure? Have you tried different compilers? Bests, Eyvaz ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: pari shok To: q-e-developers at qe-forge.org Cc: eyvaz_isaev at yahoo.com Sent: Tue, February 8, 2011 5:11:54 PM Subject: pp.x and dos.x crashes with "memory allocation" Dear All, I have a problem and I really really appreciate if anybody could help me. I downloaded QE in two machines: intel (R) pentium (R) 4 cpu 3 GHz with total memory 2GB, and intel (R) core (TM) i7 cpu 870 @2.93 GHz, with 4GB total memory. everything is working perfectly well with the first machine (with espresso-4.1.2), but dos.x and pp.x both crash with "out of memory/ memory allocation" error in the second machine for big structures (espresso-4.2.1 and espresso-4.2). It should be noted that pw.x works properly and the "memory allocation" error happens just for dos and post processing. I downloaded ATLAS and modified "make.sys" accordingly but it didn't help. I used "ulimit -s unlimited" command, it didn't help either. I have been sending emails for months to all the QE email address, but nobody sent a reply yet, although I subscribed for the forum. I would be thankful if anyone of you could help me in this regard. Thanks a lot. Pari Shok, PhD candidate UMD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110208/1da46f46/attachment-0001.htm From giannozz at democritos.it Tue Feb 8 21:16:41 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 8 Feb 2011 21:16:41 +0100 Subject: [Pw_forum] Why does dos.x look for evc.dat files? In-Reply-To: <01f101cbc7ba$e79ef570$b6dce050$@gmail.com> References: <01f101cbc7ba$e79ef570$b6dce050$@gmail.com> Message-ID: <9A3AE6EC-81CE-49F4-A881-D7BBD1D5A27C@democritos.it> On Feb 8, 2011, at 19:06 , J. D. Burton wrote: > 1. Why would a calculation of the *total* DOS, not projected > LDOS, want the eigenvectors?? > because the postprocessing codes need some serious cleanup but nobody has (yet) found the time .and. the will .and. the knowledge to do it. In the distribution under development there is a TODO file, like in all self-respecting software projects. Inside it: === 4.4 Cleanup [...] 4.4.2 Avoid monster routines that do too many things at the same time depending on the value of too many variables. An example: read_file [...] === A recent problem with postprocessing and nonlocal DFT belongs to the same category, by the way. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From yukihiro_okuno at fujifilm.co.jp Wed Feb 9 02:01:13 2011 From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp) Date: Wed, 9 Feb 2011 10:01:13 +0900 Subject: [Pw_forum] vdW force in mm_dispersion.f90 and Van der Waals functional Message-ID: Dear PWSCF developers. I want to evaluate the force from vdW interaction and compare the DFT-D and vdW functional implemented in PWSCF. Then, I saw the source code of mm_dispersion.f90, the implementation of DFT-D. I found in force_london in mm_dispersion Modules, a condition IF (ata /= atb) THEN .... ENDIF But, if ata ==atb ( same atom in the system), there must be a contribution of vdW force from the periodic images of the same atom (index =ata=atb) within the cutoff radius of vdW, I think the condition (if ata/=atb) drops such a contribution. And in CVS version of PWSCF implementation of vdW functional in vDW_DF Modules, it seems there is a stress calculation function, but still no force calculation function within non-local vdW functional. Are there plan to implement the force from vdW interaction within SCF scheme. Sincerely. Yukihiro Okuno. From kucukben at sissa.it Wed Feb 9 02:31:46 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Wed, 09 Feb 2011 02:31:46 +0100 Subject: [Pw_forum] vdW force in mm_dispersion.f90 and Van der Waals functional In-Reply-To: References: Message-ID: <20110209023146.6vnallw2s0oo4cgo@webmail.sissa.it> Dear Yukihiro Okuno, I don't know about the mm_dispersion part, however, as far as I know, reliable force&stress calculations with the vdW-DF are implemented in the CVS version. emine kucukbenli, phd student, sissa, italy Quoting yukihiro_okuno at fujifilm.co.jp: > > > And in CVS version of PWSCF implementation of vdW functional in vDW_DF > Modules, > > it seems there is a stress calculation function, but still no force > calculation function > > within non-local vdW functional. Are there plan to implement the force > from vdW > > interaction within SCF scheme. > > > Sincerely. > > Yukihiro Okuno. > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From germaneau at gucas.ac.cn Wed Feb 9 14:29:53 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Wed, 09 Feb 2011 08:29:53 -0500 Subject: [Pw_forum] gibbs free energy In-Reply-To: <496908022.18617@test1.gucas.ac.cn> References: <4D4D66EC.5020008@gucas.ac.cn> <496908022.18617@test1.gucas.ac.cn> Message-ID: <4D5296D1.2080909@gucas.ac.cn> Dear Professor Marzari, Thank you so much for your reply. The references you suggested to me are very helpful. Best, Eric. On 02/05/2011 08:31 AM, Nicola Marzari wrote: > On 2/5/11 3:04 PM, Eric Germaneau wrote: >> Dear all, >> >> I'm new in using DFT codes and especially pwscf. >> I'd like to calculate the Gibbs free energy of a crystal as function of >> temperature in order to study it's stability. >> How would you proceed? >> I thank you in advance, >> >> Eric. >> > > > Hi Eric, > > Gibbs is E+PV-TS - the enthalpy term is easy (pwscf deals e.g. > with constant pressure calculations, or you could just calculate the > equation of state and from that the enthalpy), and for the entropy > the most relevant part is the vibrational entropy, that you could > e.g. calculate in the harmonic or quasiharmonic approximations. > > Have a look at e.g. the papers of Dario Alfe and Mike Gillan > (~1998-2005) - some of them deal with the more complex problem of > calculating the free energies of liquid and solid iron, but I > believe there was one dealing just with solid-solid transformations. > > A brief tutorial on quasiharmonic is also in our PRB 71, 205214 (2005) > > Best, > > nicola > -- /Be the change you wish to see in the world / ? Mahatma Gandhi ? Dr. ?ric Germaneau College of Physical Sciences Graduate University of ChineseAcademy of Sciences Yuquan Road 19A Beijing 100049 China /Please consider the environment before printing this email. Consid?rez svp l'environnement avant d'imprimer cet email. / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110209/c1be5ef1/attachment.htm From glawe at mpi-halle.mpg.de Wed Feb 9 08:23:07 2011 From: glawe at mpi-halle.mpg.de (Henning Glawe) Date: Wed, 9 Feb 2011 08:23:07 +0100 Subject: [Pw_forum] pp.x ILDOS plots with ultrasoft pseudopotentials Message-ID: <20110209072307.GB10648@ford.simpsons.bogus> Moin, I discovered a problem in the calculation of the ILDOS (plot_num=10) in pp.x, version 4.2.1, when ultrasoft pseudopotentials are used. In principle, setting emin to -\infty and emax to E_{Fermi}, the ILDOS should be identical to the total charge density (except for small differences due to the smeared occupations around E_Fermi in the density). This is true if one uses norm-conserving pseudopotentials. In the case of ultrasoft pseudopotentials, the resulting ILDOS values are of an unreasonable range (-41 to +240), while the density is in good agreement with the ncpp-case (only differences coming from the differnces in valence/core partition). Is this a known problem? -- Mit freundlichen Gr??en Henning Glawe Max-Planck-Institut f?r Mikrostrukturphysik Weinberg 2, 06120 Halle (Saale), Germany http://www.mpi-halle.de/~theory Phone: +49-345-5582-613 Fax: +49-345-5511223 Email: glawe at mpi-halle.de From degironc at sissa.it Wed Feb 9 09:02:29 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 09 Feb 2011 09:02:29 +0100 Subject: [Pw_forum] vdW force in mm_dispersion.f90 and Van der Waals functional In-Reply-To: <20110209023146.6vnallw2s0oo4cgo@webmail.sissa.it> References: <20110209023146.6vnallw2s0oo4cgo@webmail.sissa.it> Message-ID: <4D524A15.9070109@sissa.it> Dear Yukihiro Okuno, by symmetry the DFT-D contribution to the forces on atom na due to its periodic images is zero. As said previously forces and stress are implemented within vdW-DF. Actually forces need no specific implementation as via Hellmann-Feynman theorem only derivatives of the external potential is needed. Stress has been implemented (by Riccardo Sabatini in SISSA) and is currently in the cvs version. stefano On 02/09/2011 02:31 AM, Emine Kucukbenli wrote: > Dear Yukihiro Okuno, > I don't know about the mm_dispersion part, however, as far as I know, > reliable force&stress calculations with the vdW-DF are implemented in > the CVS version. > > emine kucukbenli, phd student, sissa, italy > > Quoting yukihiro_okuno at fujifilm.co.jp: > >> >> And in CVS version of PWSCF implementation of vdW functional in vDW_DF >> Modules, >> >> it seems there is a stress calculation function, but still no force >> calculation function >> >> within non-local vdW functional. Are there plan to implement the force >> from vdW >> >> interaction within SCF scheme. >> >> >> Sincerely. >> >> Yukihiro Okuno. >> > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by Horde http://www.horde.org/ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From eariel99 at gmail.com Wed Feb 9 09:25:38 2011 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Wed, 9 Feb 2011 05:25:38 -0300 Subject: [Pw_forum] Wrong ELF values Message-ID: * Hi, 0 z what happens is that 1 and 0.5 are values with interpretation, and values close to 0 not, as far (rather near) as I know. Paolo Giannozzi* giannozz at democritos.it *Tue Feb 8 20:43:44 CET 2011* - Previous message: [Pw_forum] Wrong ELF values - Next message: [Pw_forum] Why does dos.x look for evc.dat files? - *Messages sorted by:* [ date ] [ thread ] [ subject ] [ author ] ------------------------------ On Feb 8, 2011, at 18:42 , Claudia Loyola wrote: >* the problem is that the ELF values are between -0.2092 and 1.2504*>* for one case and for the others is like the same, and not between 0*>* and 1 as the theory goes. I do not understand what I am doing wrong...* maybe nothing: there have been other reports of funny results with elf. In particular:http://www.democritos.it/pipermail/pw_forum/2010-October/018460.html So, who is right: 0 References: Message-ID: <4D5263FD.90000@sissa.it> this is very strange because the elf code define it as d = fac / rho%of_r(i,1)**(5d0/3d0) * (kkin(i)-0.25d0*tbos(i)/rho%of_r(i,1)) elf (i) = 1.0d0 / (1.0d0 + d**2) which is by definition 0 Dear Q-Espresso team, > > I have a problem with ELF calculation. Let me explain it, I calculated the > ELF (electron localization function), for four different structures, in > different planes of the structure, and with Xcrysden I visualized them, the > problem is that the ELF values are between -0.2092 and 1.2504 for one case > and for the others is like the same, and not between 0 and 1 as the theory > goes. I do not understand what I am doing wrong... > The charge density and the ELF calculation looks really good in each plane, > but the values of the ELF are incorrect. > What do you think is the problem? > If you can help me, I will be very grateful! :D > > Thanks in advance! > Claudia Loyola > > > _______________________________________________ > 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/20110209/b572fc8d/attachment.htm From gyalcin at sakarya.edu.tr Wed Feb 9 12:48:28 2011 From: gyalcin at sakarya.edu.tr (Battal Gazi =?ISO-8859-9?Q?YAL=C7IN?=) Date: Wed, 09 Feb 2011 13:48:28 +0200 Subject: [Pw_forum] help electronic band structure of GaAsN Message-ID: Hello all, I have tried to calculate band structure of GaAsN, but my calculation is always giving the same energy values at Gamma and X point, my program is as follow, I change lots of expression in program, but the results are always same, energy values of Gamma and X same. #!/bin/tcsh set DIR = "$HOME/espresso-4.2.1/WORK/Paper_2010/ZB_GaAsN/GaAs_25_N_75/ELECTRONIC/" cd $DIR cat > scf.in << EOF GaAsN GaAsN &control calculation='scf' restart_mode='from_scratch', tstress = .true. tprnfor = .true. prefix='GaAsN', pseudo_dir ='$HOME/espresso-4.2.1/pseudo/', outdir='$HOME/bgyx/GaAsN_el25/' / &system ibrav= 1, celldm(1)= 9.030, nat=8, ntyp=3, ecutwfc =40.00, / &electrons conv_thr = 1.0d-12, mixing_beta = 0.700, / ATOMIC_SPECIES Ga 69.723 Ga.pz-bhs.UPF As 74.922 As.pz-bhs.UPF N 14.007 N.pz-van_ak.UPF ATOMIC_POSITIONS Ga 0.00 0.00 0.00 As 0.25 0.25 0.25 Ga 0.50 0.50 0.00 N 0.75 0.75 0.25 Ga 0.50 0.00 0.50 N 0.75 0.25 0.75 Ga 0.00 0.50 0.50 N 0.25 0.75 0.75 K_POINTS {automatic} 12 12 12 0 0 0 EOF $HOME/espresso-4.2.1/bin/./pw.x $HOME/espresso-4.2.1/WORK/Paper_2010/ZB_GaAsN/GaAs_25_N_75/ELECTRONIC/P.out cat > nscf.in << EOF GaAsN GaAsN &control calculation='nscf' restart_mode='from_scratch', prefix='GaAsN', pseudo_dir ='$HOME/espresso-4.2.1/pseudo/', outdir='$HOME/bgyx/GaAsN_el25/' / &system ibrav= 1, celldm(1)= 9.030, nat=8, ntyp=3, ecutwfc =40.0, nbnd=20, / &electrons conv_thr = 1.0d-12, mixing_beta = 0.700, / ATOMIC_SPECIES Ga 69.723 Ga.pz-bhs.UPF As 74.922 As.pz-bhs.UPF N 14.007 N.pz-van_ak.UPF ATOMIC_POSITIONS Ga 0.00 0.00 0.00 As 0.25 0.25 0.25 Ga 0.50 0.50 0.00 N 0.75 0.75 0.25 Ga 0.50 0.00 0.50 N 0.75 0.25 0.75 Ga 0.00 0.50 0.50 N 0.25 0.75 0.75 K_POINTS 101 0.000000 0.000000 0.000000 8.000000 0.025000 0.025000 0.000000 8.000000 0.050000 0.050000 0.000000 8.000000 ...................................................... ...................................................... ...................................................... ...................................................... 0.475000 0.475000 0.475000 8.000000 0.500000 0.500000 0.500000 8.000000 EOF $HOME/espresso-4.2.1/bin/./pw.x $HOME/espresso-4.2.1/WORK/Paper_2010/ZB_GaAsN/GaAs_25_N_75/ELECTRONIC/ELEC.out I will wait your help. Thanks Best regards, Res. As. Battal Gazi Yal??n Sakarya Uni. Phys. Dep. Turkiye ___________________________________________________________________________________________ Bu e-posta, SA? CAWIS WebMail kullan?larak g?nderilmi?tir : http://www.mail.sakarya.edu.tr/ Sakarya ?niversitesi ile ilgili bilgi, haber ve duyurular i?in : http://www.sakarya.edu.tr/ ___________________________________________________________________________________________ From elie.moujaes at hotmail.co.uk Wed Feb 9 15:12:00 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Wed, 9 Feb 2011 14:12:00 +0000 Subject: [Pw_forum] Fortran Runtime error: bad real number in item 1 of list input Message-ID: Guys, I am sorry to bother you with my electron phonon calculations again. I am trying to do my calculations for a different system of bilayer graphene but I get errors like: At line 356 of file q2r.f90 (Unit 51 "a2Fq2r.51") Traceback: not available, compile with -ftrace=frame or -ftrace=full Fortran Runtime error: bad real number in item 1 of list input when running q2r.x and At line 1659 of file matdyn.f90 (Unit 51 "a2Fmatdyn.61") Traceback: not available, compile with -ftrace=frame or -ftrace=full Fortran Runtime error: End of File when running matdyn.x I do not know what is going on. I tried the same calculations with a smaller grid before and everything went fine Regards Elie Moujaes University of Nottingham NG7 2RD UK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110209/81944919/attachment.htm From baris.malcioglu at gmail.com Wed Feb 9 15:18:38 2011 From: baris.malcioglu at gmail.com (O. Baris Malcioglu) Date: Wed, 9 Feb 2011 15:18:38 +0100 Subject: [Pw_forum] pp.x and dos.x crashes with "memory allocation" In-Reply-To: <270733.96497.qm@web65713.mail.ac4.yahoo.com> References: <270733.96497.qm@web65713.mail.ac4.yahoo.com> Message-ID: Try seeing if your memory is actually being used using something like vmstat -a -S M 5 5 ignore the first line and check for active memory, which is more meaningful in this case for virtual memory kernels. If it is too big, you'll start swapping, if you run out of swap you'll see that kind of errors. And this forum is definitely not the place to ask this question. Best, Baris 2011/2/8 Eyvaz Isaev > Dear Pari, > > > > I have been sending emails for months to all the QE email address, but > nobody sent a reply yet, > > although I subscribed for the forum. > > Please just let me tell you that nobody from the forum is obliged to > answer any question, there are only volunteers. If one has time and have an > experience with the similar problem then he can share with this info. > > Regarding the problem: have you tried using a smaller k-points set? How big > is your structure? Have you tried different compilers? > > Bests, > Eyvaz > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > ------------------------------ > *From:* pari shok > *To:* q-e-developers at qe-forge.org > *Cc:* eyvaz_isaev at yahoo.com > *Sent:* Tue, February 8, 2011 5:11:54 PM > *Subject:* pp.x and dos.x crashes with "memory allocation" > > Dear All, > I have a problem and I really really appreciate if anybody could help me. > I downloaded QE in two machines: > intel (R) pentium (R) 4 cpu 3 GHz with total memory 2GB, and > intel (R) core (TM) i7 cpu 870 @2.93 GHz, with 4GB total memory. > everything is working perfectly well with the first machine (with > espresso-4.1.2), but dos.x and pp.x both crash with "out of memory/ memory > allocation" error in the second machine for big structures (espresso-4.2.1 > and espresso-4.2). It should be noted that pw.x works properly and the > "memory allocation" error happens just for dos and post processing. > I downloaded ATLAS and modified "make.sys" accordingly but it didn't help. > I used "ulimit -s unlimited" command, it didn't help either. > I have been sending emails for months to all the QE email address, but > nobody sent a reply yet, although I subscribed for the forum. > I would be thankful if anyone of you could help me in this regard. > Thanks a lot. > Pari Shok, > PhD candidate > UMD > > > _______________________________________________ > 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/20110209/65db605d/attachment.htm From wibarrah at gmail.com Wed Feb 9 17:15:07 2011 From: wibarrah at gmail.com (Wilfredo Ibarra Hernandez) Date: Wed, 09 Feb 2011 10:15:07 -0600 Subject: [Pw_forum] Specific Heat Message-ID: <4D52BD8B.5080304@gmail.com> Dear all pwscf users I'm new in QE package. I want to ask if it is possible calculate a specific heat whit QE? I looking in the Manual and in the examples and I can't found anything about this property. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Ibarra Hern?ndez Wilfredo Master student in Materials Science Cinvestav Unidad Qu?retaro Qu?retaro, M?xico -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110209/0d764089/attachment.htm From nicola.marzari at materials.ox.ac.uk Wed Feb 9 17:20:15 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Wed, 09 Feb 2011 16:20:15 +0000 Subject: [Pw_forum] Specific Heat In-Reply-To: <4D52BD8B.5080304@gmail.com> References: <4D52BD8B.5080304@gmail.com> Message-ID: <4D52BEBF.4050801@materials.ox.ac.uk> On 2/9/11 4:15 PM, Wilfredo Ibarra Hernandez wrote: > Dear all pwscf users > > I'm new in QE package. I want to ask if it is possible calculate a > specific heat whit QE? > > I looking in the Manual and in the examples and I can't found anything > about this property. > Dear Wilfredo, if you google specific heat quantum espresso , you get everything you could possibly want, including QHA in the QE-Forge, and http://www.fisica.uniud.it/~giannozz/Papers/QHA.pdf nicola ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From wibarrah at gmail.com Wed Feb 9 17:24:49 2011 From: wibarrah at gmail.com (Wilfredo Ibarra Hernandez) Date: Wed, 09 Feb 2011 10:24:49 -0600 Subject: [Pw_forum] Specific Heat In-Reply-To: <4D52BEBF.4050801@materials.ox.ac.uk> References: <4D52BD8B.5080304@gmail.com> <4D52BEBF.4050801@materials.ox.ac.uk> Message-ID: <4D52BFD1.4020700@gmail.com> Thanks you for your quick answer and sorry for than obvious questions. I'll looking better the next time before write. Thanks again. On 09/02/11 10:20, Nicola Marzari wrote: > On 2/9/11 4:15 PM, Wilfredo Ibarra Hernandez wrote: >> Dear all pwscf users >> >> I'm new in QE package. I want to ask if it is possible calculate a >> specific heat whit QE? >> >> I looking in the Manual and in the examples and I can't found anything >> about this property. >> > > > Dear Wilfredo, > > > if you google specific heat quantum espresso , you get everything > you could possibly want, including QHA in the QE-Forge, and > http://www.fisica.uniud.it/~giannozz/Papers/QHA.pdf > > > nicola > > > ---------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials University of Oxford > Chair of Materials Modelling Director, Materials Modelling Laboratory > nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM -- Ibarra Hern?ndez Wilfredo Master student in Materials Science Cinvestav Unidad Qu?retaro Qu?retaro, M?xico From giannozz at democritos.it Wed Feb 9 19:27:19 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 9 Feb 2011 19:27:19 +0100 Subject: [Pw_forum] Fortran Runtime error: bad real number in item 1 of list input In-Reply-To: References: Message-ID: <32A22F7D-73FF-40EC-8E3E-37BEBEE279F4@democritos.it> On Feb 9, 2011, at 15:12 , Elie Moujaes wrote: > At line 356 of file q2r.f90 (Unit 51 "a2Fq2r.51") > [...] Fortran Runtime error: bad real number in item 1 of list input this tells you which line of which code has trouble reading which line of which file. What about having a look ? --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed Feb 9 19:30:46 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 9 Feb 2011 19:30:46 +0100 Subject: [Pw_forum] help electronic band structure of GaAsN In-Reply-To: References: Message-ID: On Feb 9, 2011, at 12:48 , Battal Gazi YAL?IN wrote: > my calculation is always giving the same energy values > at Gamma and X point than I would first of all check if what you call the "X point" is really the X point or if it is equivalent to Gamma... P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From eyvaz_isaev at yahoo.com Wed Feb 9 19:31:16 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 9 Feb 2011 10:31:16 -0800 (PST) Subject: [Pw_forum] Specific Heat In-Reply-To: <4D52BFD1.4020700@gmail.com> References: <4D52BD8B.5080304@gmail.com> <4D52BEBF.4050801@materials.ox.ac.uk> <4D52BFD1.4020700@gmail.com> Message-ID: <548802.71127.qm@web65711.mail.ac4.yahoo.com> Hi, In addition to Nicola's reply, just have a look at QHA suite in QE 4.2. Any questions/comments, please contact me. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ----- Original Message ---- From: Wilfredo Ibarra Hernandez To: Nicola Marzari Cc: PWSCF Forum Sent: Wed, February 9, 2011 5:24:49 PM Subject: Re: [Pw_forum] Specific Heat Thanks you for your quick answer and sorry for than obvious questions. I'll looking better the next time before write. Thanks again. On 09/02/11 10:20, Nicola Marzari wrote: > On 2/9/11 4:15 PM, Wilfredo Ibarra Hernandez wrote: >> Dear all pwscf users >> >> I'm new in QE package. I want to ask if it is possible calculate a >> specific heat whit QE? >> >> I looking in the Manual and in the examples and I can't found anything >> about this property. >> > > > Dear Wilfredo, > > > if you google specific heat quantum espresso , you get everything > you could possibly want, including QHA in the QE-Forge, and > http://www.fisica.uniud.it/~giannozz/Papers/QHA.pdf > > > nicola > > > ---------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials University of Oxford > Chair of Materials Modelling Director, Materials Modelling Laboratory > nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM -- Ibarra Hern?ndez Wilfredo Master student in Materials Science Cinvestav Unidad Qu?retaro Qu?retaro, M?xico _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum ____________________________________________________________________________________ Expecting? Get great news right away with email Auto-Check. Try the Yahoo! Mail Beta. http://advision.webevents.yahoo.com/mailbeta/newmail_tools.html From wibarrah at gmail.com Wed Feb 9 19:38:30 2011 From: wibarrah at gmail.com (Wilfredo Ibarra Hernandez) Date: Wed, 09 Feb 2011 12:38:30 -0600 Subject: [Pw_forum] Specific Heat In-Reply-To: <548802.71127.qm@web65711.mail.ac4.yahoo.com> References: <4D52BD8B.5080304@gmail.com> <4D52BEBF.4050801@materials.ox.ac.uk> <4D52BFD1.4020700@gmail.com> <548802.71127.qm@web65711.mail.ac4.yahoo.com> Message-ID: <4D52DF26.3030906@gmail.com> Thanks I'm watching this now, looks very well Then I'll run it, I will let you know if I have any question or comments. And thanks for your disposition. On 09/02/11 12:31, Eyvaz Isaev wrote: > Hi, > > In addition to Nicola's reply, just have a look at QHA suite in QE 4.2. > > Any questions/comments, please contact me. > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > > Theoretical Physics Department, Moscow State Institute of Steel& Alloys, > Russia, > > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > > ----- Original Message ---- > From: Wilfredo Ibarra Hernandez > To: Nicola Marzari > Cc: PWSCF Forum > Sent: Wed, February 9, 2011 5:24:49 PM > Subject: Re: [Pw_forum] Specific Heat > > Thanks you for your quick answer and sorry for than obvious questions. > > I'll looking better the next time before write. > > Thanks again. > > > > > On 09/02/11 10:20, Nicola Marzari wrote: > >> On 2/9/11 4:15 PM, Wilfredo Ibarra Hernandez wrote: >> >>> Dear all pwscf users >>> >>> I'm new in QE package. I want to ask if it is possible calculate a >>> specific heat whit QE? >>> >>> I looking in the Manual and in the examples and I can't found anything >>> about this property. >>> >>> >> >> Dear Wilfredo, >> >> >> if you google specific heat quantum espresso , you get everything >> you could possibly want, including QHA in the QE-Forge, and >> http://www.fisica.uniud.it/~giannozz/Papers/QHA.pdf >> >> >> nicola >> >> >> ---------------------------------------------------------------------- >> Prof Nicola Marzari Department of Materials University of Oxford >> Chair of Materials Modelling Director, Materials Modelling Laboratory >> nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM >> > > -- Ibarra Hern?ndez Wilfredo Master student in Materials Science Cinvestav Unidad Qu?retaro Qu?retaro, M?xico From trambui at u.boisestate.edu Wed Feb 9 20:39:57 2011 From: trambui at u.boisestate.edu (Tram Bui) Date: Wed, 9 Feb 2011 12:39:57 -0700 Subject: [Pw_forum] Energy calculation for single carbon atom Message-ID: Hi Everyone, I'm trying to run the total energy calculation for a simple cubic of carbon, in which i'm using the lattice constant of 40 Bohrs (a.u) and the E cut off of 30 Ryd. this should be a very simple calculation. when I used K-points of 10x10x10, the calculation worked fine. However, I then wanna try with the K point of {gamma} and it kept giving me the error of " 1 eigensvalue is not converged". So my question is would you look at the input file and the (not-finished) out put file and let me know what might have been my mistakes? Thank you and have a great week, -- Tram Bui M.S. Materials Science & Engineering trambui at u.boisestate.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110209/8a2df1d6/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: C.in Type: application/octet-stream Size: 545 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110209/8a2df1d6/attachment.obj From crma at sissa.it Wed Feb 9 20:56:32 2011 From: crma at sissa.it (Changru Ma) Date: Wed, 9 Feb 2011 20:56:32 +0100 (CET) Subject: [Pw_forum] Energy calculation for single carbon atom In-Reply-To: References: Message-ID: <56130.79.45.239.115.1297281392.squirrel@webmail.sissa.it> Hi Tram, Please have a look at the User's Guide first: http://www.quantum-espresso.org/user_guide/node50.html#SECTION0001110240000000000000 Best wishes, Changru > Hi Everyone, > I'm trying to run the total energy calculation for a simple cubic of > carbon, in which i'm using the lattice constant of 40 Bohrs (a.u) and the > E > cut off of 30 Ryd. this should be a very simple calculation. when I used > K-points of 10x10x10, the calculation worked fine. However, I then wanna > try > with the K point of {gamma} and it kept giving me the error of " 1 > eigensvalue is not converged". So my question is would you look at the > input > file and the (not-finished) out put file and let me know what might have > been my mistakes? > > Thank you and have a great week, > > > > -- > Tram Bui > > M.S. Materials Science & Engineering > trambui at u.boisestate.edu > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Changru Ma, PhD Student SISSA and Theory at Elettra Group email: crma at sissa.it ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From ttduyle at gmail.com Wed Feb 9 21:03:13 2011 From: ttduyle at gmail.com (Duy Le) Date: Wed, 9 Feb 2011 15:03:13 -0500 Subject: [Pw_forum] Energy calculation for single carbon atom In-Reply-To: <56130.79.45.239.115.1297281392.squirrel@webmail.sissa.it> References: <56130.79.45.239.115.1297281392.squirrel@webmail.sissa.it> Message-ID: for isolated atom, you need to perform spin-polarized DFT, and also you need to fix occupation number by using Hund's rule(use occupations card). -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Wed, Feb 9, 2011 at 2:56 PM, Changru Ma wrote: > Hi Tram, > > Please have a look at the User's Guide first: > > http://www.quantum-espresso.org/user_guide/node50.html#SECTION0001110240000000000000 > > Best wishes, > Changru > >> Hi Everyone, >> ? ? ?I'm trying to run the total energy calculation for a simple cubic of >> carbon, in which i'm using the lattice constant of 40 Bohrs (a.u) and the >> E >> cut off of 30 Ryd. ?this should be a very simple calculation. when I used >> K-points of 10x10x10, the calculation worked fine. However, I then wanna >> try >> with the K point of {gamma} and it kept giving me the error of " 1 >> eigensvalue is not converged". So my question is would you look at the >> input >> file and the (not-finished) out put file and let me know what might have >> been my mistakes? >> >> Thank you and have a great week, >> >> >> >> -- >> Tram Bui >> >> M.S. Materials Science & Engineering >> trambui at u.boisestate.edu >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > -- > Changru Ma, PhD Student > SISSA and Theory at Elettra Group > email: crma at sissa.it > > > ---------------------------------------------------------------- > ?SISSA Webmail https://webmail.sissa.it/ > ?Powered by SquirrelMail http://www.squirrelmail.org/ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From claudial.81 at gmail.com Wed Feb 9 23:43:48 2011 From: claudial.81 at gmail.com (Claudia Loyola) Date: Wed, 9 Feb 2011 16:43:48 -0600 Subject: [Pw_forum] Wrong ELF values In-Reply-To: <4D5263FD.90000@sissa.it> References: <4D5263FD.90000@sissa.it> Message-ID: Hello, First, thanks for your answers. I tried in another machine (with the same version 4.2.1) and the result are different, but are still out of range, first I obtained: [-0.2092:1.2504] and now [-0.1951:0.981], I ran the same scf and elf input file, but in different machines. The range is the "thermometer" that shows xcrysden?, right? maybe I am missing something... :( Thanks a lot! Claudia Loyola On Wed, Feb 9, 2011 at 3:53 AM, Stefano de Gironcoli wrote: > this is very strange because the elf code define it as > > d = fac / rho%of_r(i,1)**(5d0/3d0) * > (kkin(i)-0.25d0*tbos(i)/rho%of_r(i,1)) > elf (i) = 1.0d0 / (1.0d0 + d**2) > > which is by definition 0 are your results reproducible ? have you tried on another machine. > please provide a simple test case. > > stefano > > > > On 02/08/2011 06:42 PM, Claudia Loyola wrote: > > Dear Q-Espresso team, > > I have a problem with ELF calculation. Let me explain it, I calculated the > ELF (electron localization function), for four different structures, in > different planes of the structure, and with Xcrysden I visualized them, the > problem is that the ELF values are between -0.2092 and 1.2504 for one case > and for the others is like the same, and not between 0 and 1 as the theory > goes. I do not understand what I am doing wrong... > The charge density and the ELF calculation looks really good in each plane, > but the values of the ELF are incorrect. > What do you think is the problem? > If you can help me, I will be very grateful! :D > > Thanks in advance! > Claudia Loyola > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Claudia Loyola Canales Postdoc in Computational Physics Iowa State University Iowa, USA http://www.lpmd.cl/claudial http://www.lpmd.cl http://cosmic.mse.iastate.edu/ http://www.gnm.cl -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110209/99e6cc0f/attachment-0001.htm From giannozz at democritos.it Thu Feb 10 07:31:01 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 10 Feb 2011 07:31:01 +0100 Subject: [Pw_forum] pp.x ILDOS plots with ultrasoft pseudopotentials In-Reply-To: <20110209072307.GB10648@ford.simpsons.bogus> References: <20110209072307.GB10648@ford.simpsons.bogus> Message-ID: <3CC8F50E-8BD4-41D9-A8C6-E0F26799A102@democritos.it> On Feb 9, 2011, at 8:23 , Henning Glawe wrote: > Is this a known problem? no, it isn't. Please provide a (small) test showing this behavior P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From glapenna at iccom.cnr.it Thu Feb 10 08:55:43 2011 From: glapenna at iccom.cnr.it (Giovanni La Penna) Date: Thu, 10 Feb 2011 08:55:43 +0100 (CET) Subject: [Pw_forum] Wrong ELF values In-Reply-To: References: <4D5263FD.90000@sissa.it> Message-ID: On Wed, 9 Feb 2011, Claudia Loyola wrote: > first I obtained: [-0.2092:1.2504] ?and now [-0.1951:0.981], I ran the same > scf and elf input file, but in different machines. > The range is the "thermometer" that shows xcrysden?, right? maybe I am > missing something... :( Please, check the data in the file (pp or cube), because the range provided by visualization packages is due to interpolations. Giovanni ============================================================ Giovanni La Penna - National research council (Cnr) Institute for chemistry of organo-metallic compounds (Iccom) via Madonna del Piano 10, I-50019 Sesto Fiorentino, Firenze, Italy tel.: +39 055 522-5264, fax: +39 055 522-5203 e-mail: glapenna at iccom.cnr.it - http://www.iccom.cnr.it/lapenna skype: giovannilapenna ============================================================ From baris.malcioglu at gmail.com Thu Feb 10 11:10:56 2011 From: baris.malcioglu at gmail.com (O. Baris Malcioglu) Date: Thu, 10 Feb 2011 11:10:56 +0100 Subject: [Pw_forum] iotk error - again In-Reply-To: <02c401cb96e3$b7039900$250acb00$@w2agz.com> References: <01bd01cb95e1$14f67ef0$3ee37cd0$@w2agz.com> <02c401cb96e3$b7039900$250acb00$@w2agz.com> Message-ID: Dear all, I've also started getting a lot of IOTK errors recently using the CVS version. I've got two possible candidates, 1)highly asynchronous file system (i.e. a parallel system that is not robust in the sense of NFS, and highly overloaded) 2) a conspiracy going on with the newest intel compilers running in an environment that is not-so-new. Since this error is annoyingly frequent but not replicable at will, could you please contact me if you are using a asynchronous file system with the compilers you are using? , Best, Baris Malcioglu P.S. The parallel file systems optimized for performance tend to be asynchronous, full list can be found here: http://en.wikipedia.org/wiki/List_of_file_systems ################################################################################ ######################################## # FROM IOTK LIBRARY, VERSION 1.2.0 # UNRECOVERABLE ERROR (ierr=1) # ERROR IN: iotk_scan_tag (iotk_scan.spp:468) # CVS Revision: 1.23 # iostat=67 # ERROR IN: iotk_scan (iotk_scan.spp:743) # CVS Revision: 1.23 # ERROR IN: iotk_scan_end (iotk_scan.spp:233) # CVS Revision: 1.23 # foundl # ERROR IN: iotk_close_read (iotk_files.spp:645) # CVS Revision: 1.20 ################################################################################ ######################################## 2010/12/8 W2AGZ > Thanks, Paolo. I'll look into it ths week. -Paul > > -----Original Message----- > From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On > Behalf Of Paolo Giannozzi > Sent: Wednesday, December 08, 2010 1:49 AM > To: PWSCF Forum > Subject: Re: [Pw_forum] iotk error - again > > On Dec 7, 2010, at 8:33 , W2AGZ wrote: > > > "replace q_real by q_real_space." Is this the fix? > > > > > no. This is the fix for a very specific case, and the only one I remember > in > which an error was issued by iotk for a good reason (i.e. a variable was > written with one name and read with another). All other instances of iotk > errors I remember are related to miscompilation. > > Try first of all to compile iotk with reduced optimization (e.g. using > $(MAKE) FFLAGS="$(FFLAGS_NOOPT)" ) > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics, Univ. 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 > > > _______________________________________________ > 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/20110210/1fa89f53/attachment.htm From Lorenzo.Paulatto at impmc.upmc.fr Thu Feb 10 12:08:58 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Thu, 10 Feb 2011 12:08:58 +0100 Subject: [Pw_forum] iotk error - again In-Reply-To: References: <01bd01cb95e1$14f67ef0$3ee37cd0$@w2agz.com> <02c401cb96e3$b7039900$250acb00$@w2agz.com> Message-ID: Are you using the most recent version of intel fortran compiler (it's called XE, or 11.0)? It has a lot of problem, we've been discussing the issue some time ago: it definitely is a miscompilation problem. I have a stinky workaround, but the best solution is to downgrade the compiler. cheers On Thu, 10 Feb 2011 11:10:56 +0100, O. Baris Malcioglu wrote: > Dear all, > I've also started getting a lot of IOTK errors recently using the CVS > version. > I've got two possible candidates, > 1)highly asynchronous file system (i.e. a parallel system that is not > robust > in the sense of NFS, and highly overloaded) > 2) a conspiracy going on with the newest intel compilers running in an > environment that is not-so-new. > Since this error is annoyingly frequent but not replicable at will, could > you please contact me if you are using a asynchronous file system with > the > compilers you are using? , > Best, > Baris Malcioglu > P.S. The parallel file systems optimized for performance tend to be > asynchronous, full list can be found here: > http://en.wikipedia.org/wiki/List_of_file_systems > > > ################################################################################ > ######################################## > # FROM IOTK LIBRARY, VERSION 1.2.0 > # UNRECOVERABLE ERROR (ierr=1) > # ERROR IN: iotk_scan_tag (iotk_scan.spp:468) > # CVS Revision: 1.23 > # > iostat=67 > # ERROR IN: iotk_scan (iotk_scan.spp:743) > # CVS Revision: 1.23 > # ERROR IN: iotk_scan_end (iotk_scan.spp:233) > # CVS Revision: 1.23 > # foundl > # ERROR IN: iotk_close_read (iotk_files.spp:645) > # CVS Revision: 1.20 > ################################################################################ > ######################################## > > > 2010/12/8 W2AGZ > >> Thanks, Paolo. I'll look into it ths week. -Paul >> >> -----Original Message----- >> From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On >> Behalf Of Paolo Giannozzi >> Sent: Wednesday, December 08, 2010 1:49 AM >> To: PWSCF Forum >> Subject: Re: [Pw_forum] iotk error - again >> >> On Dec 7, 2010, at 8:33 , W2AGZ wrote: >> >> > "replace q_real by q_real_space." Is this the fix? >> > >> >> >> no. This is the fix for a very specific case, and the only one I >> remember >> in >> which an error was issued by iotk for a good reason (i.e. a variable was >> written with one name and read with another). All other instances of >> iotk >> errors I remember are related to miscompilation. >> >> Try first of all to compile iotk with reduced optimization (e.g. using >> $(MAKE) FFLAGS="$(FFLAGS_NOOPT)" ) >> >> P. >> --- >> Paolo Giannozzi, Dept of Chemistry&Physics, Univ. 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 >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> -- Lorenzo Paulatto (IdR) IMPMC - CNRS UMR 7590 & Universit? P&M Curie T23-C13/23-5e27 - 4 place Jussieu - 75252 Paris Cedex5 phone: +33 (0)144 27 5211 www: http://www-int.impmc.upmc.fr/~paulatto/ From davide.ceresoli at materials.ox.ac.uk Thu Feb 10 12:31:00 2011 From: davide.ceresoli at materials.ox.ac.uk (Davide Ceresoli) Date: Thu, 10 Feb 2011 11:31:00 +0000 Subject: [Pw_forum] iotk error - again In-Reply-To: References: <01bd01cb95e1$14f67ef0$3ee37cd0$@w2agz.com> <02c401cb96e3$b7039900$250acb00$@w2agz.com> Message-ID: <4D53CC74.90906@materials.ox.ac.uk> On 02/10/2011 11:08 AM, Lorenzo Paulatto wrote: > Are you using the most recent version of intel fortran compiler (it's > called XE, or 11.0)? It has a lot of problem, we've been discussing the > issue some time ago: it definitely is a miscompilation problem. I have a > stinky workaround, but the best solution is to downgrade the compiler. Or to upgrade it: the latest Intel compiler (12.0.2, named XE 2011.2.137) works ok with iotk. From Lorenzo.Paulatto at impmc.upmc.fr Thu Feb 10 12:32:30 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Thu, 10 Feb 2011 12:32:30 +0100 Subject: [Pw_forum] iotk error - again In-Reply-To: <4D53CC74.90906@materials.ox.ac.uk> References: <01bd01cb95e1$14f67ef0$3ee37cd0$@w2agz.com> <02c401cb96e3$b7039900$250acb00$@w2agz.com> <4D53CC74.90906@materials.ox.ac.uk> Message-ID: On Thu, 10 Feb 2011 12:31:00 +0100, Davide Ceresoli wrote: > Or to upgrade it: the latest Intel compiler (12.0.2, named XE 2011.2.137) I did a mistake before, the one that gives problems is XE (12.0.0), I know nothing about 12.0.x with x>0. If you have experienced no problems, I strongly encourage to upgrade. -- Lorenzo Paulatto (IdR) IMPMC - CNRS UMR 7590 & Universit? P&M Curie T23-C13/23-5e27 - 4 place Jussieu - 75252 Paris Cedex5 phone: +33 (0)144 27 5211 www: http://www-int.impmc.upmc.fr/~paulatto/ From davide.ceresoli at materials.ox.ac.uk Thu Feb 10 13:00:06 2011 From: davide.ceresoli at materials.ox.ac.uk (Davide Ceresoli) Date: Thu, 10 Feb 2011 12:00:06 +0000 Subject: [Pw_forum] iotk error - again In-Reply-To: References: <01bd01cb95e1$14f67ef0$3ee37cd0$@w2agz.com> <02c401cb96e3$b7039900$250acb00$@w2agz.com> <4D53CC74.90906@materials.ox.ac.uk> Message-ID: <4D53D346.30606@materials.ox.ac.uk> On 02/10/2011 11:32 AM, Lorenzo Paulatto wrote: > On Thu, 10 Feb 2011 12:31:00 +0100, Davide Ceresoli > wrote: >> Or to upgrade it: the latest Intel compiler (12.0.2, named XE 2011.2.137) > > I did a mistake before, the one that gives problems is XE (12.0.0), I know > nothing about 12.0.x with x>0. If you have experienced no problems, I > strongly encourage to upgrade. > One simple rule I've learned in the past: avoid ".0" releases of the Intel compiler! Cheers. From hannu.komsa at epfl.ch Thu Feb 10 14:31:14 2011 From: hannu.komsa at epfl.ch (hannu.komsa at epfl.ch) Date: Thu, 10 Feb 2011 14:31:14 +0100 Subject: [Pw_forum] help electronic band structure of GaAsN In-Reply-To: References: Message-ID: <20110210143114.903936qxt5328u5e@webmail.epfl.ch> Both Gamma and X-point are already included in the k-point set that you are using in the scf-calculation. With the input file you provided, I got the energies which are clearly not the same: k = 0.0000 0.0000 0.0000 ( 3119 PWs) bands (ev): -8.8751 -6.6653 -6.6653 -5.8658 -0.8107 -0.8107 -0.8107 3.1632 3.1632 3.1632 3.2952 3.2952 3.2952 5.6642 5.6642 5.6642 k = 0.0000 0.0000-0.5000 ( 3178 PWs) bands (ev): -7.9545 -7.8977 -6.6043 -6.0557 -0.3493 -0.3493 1.0219 2.0320 2.0320 2.3674 2.4642 2.7178 4.2172 4.2172 4.2869 4.2869 So, most likely it's as Paolo said. By the way, usually if you want to get correct results for GaAsN you should have Ga-3d electrons included in the calculations, although it seems that such pseudos are available only for PBE in the QE homepage. Hannu-Pekka Komsa EPFL, Switzerland > Hello all, I have tried to calculate band structure of GaAsN, but my > calculation is always giving the same energy values at Gamma and X > point, my program is as follow, I change lots of expression in > program, but the results are always same, energy values of Gamma and > X same. > From dabrowski at ihp-microelectronics.com Thu Feb 10 16:18:41 2011 From: dabrowski at ihp-microelectronics.com (Dabrowski Jaroslaw) Date: Thu, 10 Feb 2011 16:18:41 +0100 Subject: [Pw_forum] B3LYP in PWscf Message-ID: The list of functionals available for PWscf, posted (e.g.) on the QE home page includes B3LYP and several other hybrid potentials. Still, attempts to use BL3YP with pw.x from versions 4.1.1 or 4.2.1 of QE and with calculation="scf" result in the error message from setup.f90: "HYBRID XC not implemented in PWscf". Was B3LYP removed from recent distributions, or I miss something else? I could not find any information on this subject. But I found several remarks indicating that people used PWscf with B3LYP, and this confuses me even more. Cheers -- Jarek _____________________________________________ Dr.rer.nat. Jaroslaw Dabrowski Scientist Materials Research IHP Fon: +49 (335) 5625-316 Fax: +49 (335) 5625-681 E-Mail: dabrowski at ihp-microelectronics.com Website: http://www.ihp-microelectronics.com _____________________________________________ IHP GmbH Innovations for High Performance Microelectronics Leibniz-Institut f?r innovative Mikroelektronik Im Technologiepark 25 15236 Frankfurt (Oder) Germany Gesch?ftsf?hrer: Prof. Dr. Wolfgang Mehr, Manfred St?cker, Vorsitzende des Aufsichtsrates: Konstanze Pistor Handelsregister: HRB 1982 Amtsgericht Frankfurt (Oder) , Steuernummer: 061/12500152, Umsatzsteuer-ID: DE 138996546 Die IHP GmbH ist Mitglied der Leibniz-Gemeinschaft und wird von der Bundesrepublik Deutschland und dem Land Brandenburg institutionell finanziert. Diese E-Mail enth?lt vertrauliche und / oder rechtlich gesch?tzte Informationen. Wenn Sie nicht der richtige Adressat sind oder diese E-Mail irrt?mlich erhalten haben, informieren Sie bitte sofort den Absender und vernichten Sie diese Mail. Das unerlaubte Kopieren sowie die unbefugte Weitergabe dieser Mail sind nicht gestattet. This e-mail contains confidential and / or privileged information. If you are not the intended recipient or have received this e-mail in error, please notify the sender immediately and destroy this e-mail. Any unauthorized copying, disclosure or distribution of the material in this e-mail is strictly forbidden. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110210/1d4cace2/attachment-0001.htm From giuseppe.mattioli at mlib.ism.cnr.it Thu Feb 10 12:25:19 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Thu, 10 Feb 2011 12:25:19 +0100 Subject: [Pw_forum] B3LYP in PWscf In-Reply-To: References: Message-ID: <201102101225.20044.giuseppe.mattioli@mlib.ism.cnr.it> Have you compiled the code with the -DEXX flag, as explained in the $yourespresso/examples/EXX_example/README file? Yours Giuseppe On Thursday 10 February 2011 16:18:41 Dabrowski Jaroslaw wrote: > The list of functionals available for PWscf, posted (e.g.) on the QE home > page includes B3LYP and several other hybrid potentials. Still, attempts to > use BL3YP with pw.x from versions 4.1.1 or 4.2.1 of QE and with > calculation="scf" result in the error message from setup.f90: "HYBRID XC > not implemented in PWscf". Was B3LYP removed from recent distributions, or > I miss something else? I could not find any information on this subject. > But I found several remarks indicating that people used PWscf with B3LYP, > and this confuses me even more. > > Cheers -- Jarek > > > > _____________________________________________ > > Dr.rer.nat. Jaroslaw Dabrowski > Scientist > Materials Research > IHP > > Fon: +49 (335) 5625-316 > Fax: +49 (335) 5625-681 > E-Mail: dabrowski at ihp-microelectronics.com > Website: > http://www.ihp-microelectronics.com > > _____________________________________________ > > IHP GmbH > Innovations for High Performance Microelectronics > Leibniz-Institut f?r innovative Mikroelektronik > Im Technologiepark 25 > 15236 Frankfurt (Oder) > Germany > > Gesch?ftsf?hrer: Prof. Dr. Wolfgang Mehr, Manfred St?cker, Vorsitzende des > Aufsichtsrates: Konstanze Pistor Handelsregister: HRB 1982 Amtsgericht > Frankfurt (Oder) , Steuernummer: 061/12500152, Umsatzsteuer-ID: DE > 138996546 > > Die IHP GmbH ist Mitglied der Leibniz-Gemeinschaft und wird von der > Bundesrepublik Deutschland und dem Land Brandenburg institutionell > finanziert. > > Diese E-Mail enth?lt vertrauliche und / oder rechtlich gesch?tzte > Informationen. Wenn Sie nicht der richtige Adressat sind oder diese E-Mail > irrt?mlich erhalten haben, informieren Sie bitte sofort den Absender und > vernichten Sie diese Mail. Das unerlaubte Kopieren sowie die unbefugte > Weitergabe dieser Mail sind nicht gestattet. > > This e-mail contains confidential and / or privileged information. If you > are not the intended recipient or have received this e-mail in error, > please notify the sender immediately and destroy this e-mail. Any > unauthorized copying, disclosure or distribution of the material in this > e-mail is strictly forbidden. -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From degironc at sissa.it Thu Feb 10 17:02:50 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 10 Feb 2011 17:02:50 +0100 Subject: [Pw_forum] B3LYP in PWscf In-Reply-To: References: Message-ID: <4D540C2A.2000607@sissa.it> One needs to recompile the code switching on the exact exchange feature. have a look at the README example in EXX_example Stefano de Gironcoli On 02/10/2011 04:18 PM, Dabrowski Jaroslaw wrote: > The list of functionals available for PWscf, posted (e.g.) on the QE home page includes B3LYP and several other hybrid potentials. Still, attempts to use BL3YP with pw.x from versions 4.1.1 or 4.2.1 of QE and with calculation="scf" result in the error message from setup.f90: "HYBRID XC not implemented in PWscf". Was B3LYP removed from recent distributions, or I miss something else? I could not find any information on this subject. But I found several remarks indicating that people used PWscf with B3LYP, and this confuses me even more. > > Cheers -- Jarek > > > > _____________________________________________ > > Dr.rer.nat. Jaroslaw Dabrowski > Scientist > Materials Research > IHP > > Fon: +49 (335) 5625-316 > Fax: +49 (335) 5625-681 > E-Mail: dabrowski at ihp-microelectronics.com > Website: http://www.ihp-microelectronics.com > > _____________________________________________ > > IHP GmbH > Innovations for High Performance Microelectronics > Leibniz-Institut f?r innovative Mikroelektronik > Im Technologiepark 25 > 15236 Frankfurt (Oder) > Germany > > Gesch?ftsf?hrer: Prof. Dr. Wolfgang Mehr, Manfred St?cker, Vorsitzende des Aufsichtsrates: Konstanze Pistor > Handelsregister: HRB 1982 Amtsgericht Frankfurt (Oder) , Steuernummer: 061/12500152, Umsatzsteuer-ID: DE 138996546 > > Die IHP GmbH ist Mitglied der Leibniz-Gemeinschaft und wird von der Bundesrepublik Deutschland und dem Land Brandenburg institutionell finanziert. > > Diese E-Mail enth?lt vertrauliche und / oder rechtlich gesch?tzte Informationen. Wenn Sie nicht der richtige Adressat sind oder diese E-Mail irrt?mlich erhalten haben, informieren Sie bitte sofort den Absender und vernichten Sie diese Mail. Das unerlaubte Kopieren sowie die unbefugte Weitergabe dieser Mail sind nicht gestattet. > > This e-mail contains confidential and / or privileged information. If you are not the intended recipient or have received this e-mail in error, please notify the sender immediately and destroy this e-mail. Any unauthorized copying, disclosure or distribution of the material in this e-mail is strictly forbidden. > > > > > > _______________________________________________ > 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/20110210/aeeadb8a/attachment.htm From wparker at anl.gov Thu Feb 10 16:53:22 2011 From: wparker at anl.gov (William Parker) Date: Thu, 10 Feb 2011 09:53:22 -0600 Subject: [Pw_forum] B3LYP in PWscf In-Reply-To: References: Message-ID: <34465F4E-9E70-454F-8591-8CA6B21972D1@anl.gov> Dear Jarek, On Feb 10, 2011, at 9:18 AM, Dabrowski Jaroslaw wrote: > The list of functionals available for PWscf, posted (e.g.) on the QE home page includes B3LYP and several other hybrid potentials. Still, attempts to use BL3YP with pw.x from versions 4.1.1 or 4.2.1 of QE and with calculation=?scf? result in the error message from setup.f90: ?HYBRID XC not implemented in PWscf?. Was B3LYP removed from recent distributions, or I miss something else? I could not find any information on this You need to compile Q/E with -DEXX in the DFLAGS of your make.sys file. Then, all of the implemented hybrid functionals will be open to you, and you can experience the joys of converging the k-point mesh for the Fock integral. See examples/EXX_example/README for more information. --William ********************************************************* William D. Parker phone: (630) 252-1775 Computational Postdoctoral Fellow fax: (630) 252-4798 MSD-212, Rm. C-215 Argonne National Laboratory 9700 S. Cass Ave. Argonne, IL 60439 ********************************************************* From m_pazoki at physics.sharif.edu Thu Feb 10 18:05:48 2011 From: m_pazoki at physics.sharif.edu (meysam pazoki) Date: Thu, 10 Feb 2011 20:35:48 +0330 Subject: [Pw_forum] Fermi energy shift Message-ID: Dear Quantum Espresso users I have a question about shifting the fermi energy of semiconductors. After adsorbtion of oxygen atoms on the surface of ZnO slab,the calculated fermi energy was shifted. My question is that "Can i trust on this shift of fermi energy or i should consider the shift of local orbital DOS relative to fermi energi?" We know that DFT results for semiconductor gaps is wrong ,can i use DFT for this discussions or i should use GW? Thanks alot for your help Best Regards meysam pazoki Ph.D student of physics SUT -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110210/0b23e55b/attachment.htm From dabrowski at ihp-microelectronics.com Thu Feb 10 19:09:36 2011 From: dabrowski at ihp-microelectronics.com (Dabrowski Jaroslaw) Date: Thu, 10 Feb 2011 19:09:36 +0100 Subject: [Pw_forum] B3LYP in PWscf In-Reply-To: References: Message-ID: > "HYBRID XC not implemented in PWscf". Sorry. Stupid me. The solution is: before compiling, edit make.sys and add the option -DEXX to the line DFLAGS defining the preprocessing options... Cheers -- Jarek ________________________________________ Dr.rer.nat. Jaroslaw Dabrowski Scientist Materials Research IHP Fon: +49 (335) 5625-316 Fax: +49 (335) 5625-681 E-Mail: dabrowski at ihp-microelectronics.com Website: ________________________________________ IHP GmbH Innovations for High Performance Microelectronics Leibniz-Institut fuer innovative Mikroelektronik Im Technologiepark 25 15236 Frankfurt (Oder) Germany Geschaeftsfuehrer: Prof. Dr. Wolfgang Mehr, Manfred Stoecker, Vorsitzende des Aufsichtsrates: Konstanze Pistor Handelsregister: HRB 1982 Amtsgericht Frankfurt (Oder) , Steuernummer: 061/12500152, Umsatzsteuer-ID: DE 138996546 Die IHP GmbH ist Mitglied der Leibniz-Gemeinschaft und wird von der Bundesrepublik Deutschland und dem Land Brandenburg institutionell finanziert. Diese E-Mail enthaelt vertrauliche und / oder rechtlich geschuetzte Informationen. Wenn Sie nicht der richtige Adressat sind oder diese E-Mail irrtuemlich erhalten haben, informieren Sie bitte sofort den Absender und vernichten Sie diese Mail. Das unerlaubte Kopieren sowie die unbefugte Weitergabe dieser Mail sind nicht gestattet. This e-mail contains confidential and / or privileged information. If you are not the intended recipient or have received this e-mail in error, please notify the sender immediately and destroy this e-mail. Any unauthorized copying, disclosure or distribution of the material in this e-mail is strictly forbidden. From eyvaz_isaev at yahoo.com Thu Feb 10 19:54:49 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 10 Feb 2011 10:54:49 -0800 (PST) Subject: [Pw_forum] B3LYP in PWscf In-Reply-To: References: Message-ID: <276904.50330.qm@web65713.mail.ac4.yahoo.com> Hi, Let me add the next info from setup.f90" IF ( okvan .OR. okpaw ) CALL errore( 'setup ', & 'HYBRID XC not implemented for USPP or PAW', 1 ) Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ----- Original Message ---- From: Dabrowski Jaroslaw To: "pw_forum at pwscf.org" Sent: Thu, February 10, 2011 7:09:36 PM Subject: Re: [Pw_forum] B3LYP in PWscf > "HYBRID XC not implemented in PWscf". Sorry. Stupid me. The solution is: before compiling, edit make.sys and add the option -DEXX to the line DFLAGS defining the preprocessing options... Cheers -- Jarek ________________________________________ Dr.rer.nat. Jaroslaw Dabrowski Scientist Materials Research IHP Fon: +49 (335) 5625-316 Fax: +49 (335) 5625-681 E-Mail: dabrowski at ihp-microelectronics.com Website: ________________________________________ IHP GmbH Innovations for High Performance Microelectronics Leibniz-Institut fuer innovative Mikroelektronik Im Technologiepark 25 15236 Frankfurt (Oder) Germany Geschaeftsfuehrer: Prof. Dr. Wolfgang Mehr, Manfred Stoecker, Vorsitzende des Aufsichtsrates: Konstanze Pistor Handelsregister: HRB 1982 Amtsgericht Frankfurt (Oder) , Steuernummer: 061/12500152, Umsatzsteuer-ID: DE 138996546 Die IHP GmbH ist Mitglied der Leibniz-Gemeinschaft und wird von der Bundesrepublik Deutschland und dem Land Brandenburg institutionell finanziert. Diese E-Mail enthaelt vertrauliche und / oder rechtlich geschuetzte Informationen. Wenn Sie nicht der richtige Adressat sind oder diese E-Mail irrtuemlich erhalten haben, informieren Sie bitte sofort den Absender und vernichten Sie diese Mail. Das unerlaubte Kopieren sowie die unbefugte Weitergabe dieser Mail sind nicht gestattet. This e-mail contains confidential and / or privileged information. If you are not the intended recipient or have received this e-mail in error, please notify the sender immediately and destroy this e-mail. Any unauthorized copying, disclosure or distribution of the material in this e-mail is strictly forbidden. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From bongani.ngwenya at gmail.com Fri Feb 11 08:20:56 2011 From: bongani.ngwenya at gmail.com (Bongani Ngwenya) Date: Fri, 11 Feb 2011 02:20:56 -0500 Subject: [Pw_forum] BN problem Message-ID: Dear all, I'm trying to do an SCF calculation in quantum espresso. The program runs for a few minutes and then stops, giving the following error message "from davcio : error # 10 error while reading from file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... " The following is the input file I used: &control pseudo_dir = '.', calculation = 'scf', prefix = 'BN_5X5', restart_mode = 'restart', / &system ibrav = 0, celldm(1) = 23.73887, nat = 50, ntyp = 2, ecutwfc = 38, ecutrho = 304, occupations='smearing', degauss=0.003, smearing='mp', / &electrons conv_thr = 1.D-7, mixing_beta = 0.8, / &ions ion_dynamics = 'damp', \ ATOMIC_SPECIES B 10.811 B.pbe-n-van_ak.UPF N 14.007 N.pbe-van_ak.UPF ATOMIC_POSITIONS {alat} B 0.00000 0.00000 0.50000 N 0.11547 0.00000 0.50000 B 0.17321 0.10000 0.50000 B 0.17321 -0.10000 0.50000 N 0.28868 0.10000 0.50000 N 0.28868 -0.10000 0.50000 B 0.34641 0.00000 0.50000 B 0.34641 -0.20000 0.50000 B 0.34641 0.20000 0.50000 N 0.46188 0.00000 0.50000 N 0.46188 0.20000 0.50000 N 0.46188 -0.20000 0.50000 B 0.51962 0.10000 0.50000 B 0.51962 -0.10000 0.50000 B 0.51962 0.30000 0.50000 B 0.51962 -0.30000 0.50000 N 0.63509 0.10000 0.50000 N 0.63509 -0.10000 0.50000 N 0.63509 0.30000 0.50000 N 0.63509 -0.30000 0.50000 B 0.69282 0.00000 0.50000 B 0.69282 0.20000 0.50000 B 0.69282 -0.20000 0.50000 B 0.69282 0.40000 0.50000 B 0.69282 -0.40000 0.50000 N 0.80829 0.00000 0.50000 N 0.80829 0.20000 0.50000 N 0.80829 -0.20000 0.50000 N 0.80829 0.40000 0.50000 N 0.80829 -0.40000 0.50000 B 0.86603 0.10000 0.50000 B 0.86603 -0.10000 0.50000 B 0.86603 0.30000 0.50000 B 0.86603 -0.30000 0.50000 N 0.98149 0.10000 0.50000 N 0.98149 -0.10000 0.50000 N 0.98149 0.30000 0.50000 N 0.98149 -0.30000 0.50000 B 1.03923 0.00000 0.50000 B 1.03923 0.20000 0.50000 B 1.03923 -0.20000 0.50000 N 1.15470 0.00000 0.50000 N 1.15470 0.20000 0.50000 N 1.15470 -0.20000 0.50000 B 1.21244 0.10000 0.50000 B 1.21244 -0.10000 0.50000 N 1.32791 0.10000 0.50000 N 1.32791 -0.10000 0.50000 B 1.38564 0.00000 0.50000 N 1.50111 0.00000 0.50000 K_POINTS {automatic} 10 10 1 0 0 0 CELL_PARAMETERS {hexagonal} 0.866025404 0.50000 0.00000 0.866025404 -0.50000 0.00000 0.00000 0.00000 1.94071 Please help me do a successful calculation. Regards, Bongani Ngwenya Cell: 0027 84 429 5399 Office: 0027 12 420 3114 Fax: 0027 86 517 6293 bongani.ngwenya at gmail.com mabotho at yahoo.co.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110211/b2729002/attachment-0001.htm From baris.malcioglu at gmail.com Fri Feb 11 11:31:47 2011 From: baris.malcioglu at gmail.com (O. Baris Malcioglu) Date: Fri, 11 Feb 2011 11:31:47 +0100 Subject: [Pw_forum] iotk error - again In-Reply-To: <4D53D346.30606@materials.ox.ac.uk> References: <01bd01cb95e1$14f67ef0$3ee37cd0$@w2agz.com> <02c401cb96e3$b7039900$250acb00$@w2agz.com> <4D53CC74.90906@materials.ox.ac.uk> <4D53D346.30606@materials.ox.ac.uk> Message-ID: If everyone was experiencing the same error with Intel compilers before 12.0.2, then the cluster file system seems not to be the source of error, I also concur 12.0.2 seems to be working fine in this cluster after various tests... Best, Baris P.S. I have at least two test cases where 12.0.0 was working fine with iotk, possibly some absurd fight over industry standards going on somewhere, which I couldn't care less. 2011/2/10 Davide Ceresoli > On 02/10/2011 11:32 AM, Lorenzo Paulatto wrote: > > On Thu, 10 Feb 2011 12:31:00 +0100, Davide Ceresoli > > wrote: > >> Or to upgrade it: the latest Intel compiler (12.0.2, named XE > 2011.2.137) > > > > I did a mistake before, the one that gives problems is XE (12.0.0), I > know > > nothing about 12.0.x with x>0. If you have experienced no problems, I > > strongly encourage to upgrade. > > > One simple rule I've learned in the past: avoid ".0" releases of the Intel > compiler! > > Cheers. > _______________________________________________ > 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/20110211/bd98f316/attachment.htm From baris.malcioglu at gmail.com Fri Feb 11 11:34:07 2011 From: baris.malcioglu at gmail.com (O. Baris Malcioglu) Date: Fri, 11 Feb 2011 11:34:07 +0100 Subject: [Pw_forum] Fortran Runtime error: bad real number in item 1 of list input In-Reply-To: References: Message-ID: Are you sure your file was written to the disk correctly (Quotas, run crashing before file is completed, etc.) ? 2011/2/9 Elie Moujaes > Guys, > > I am sorry to bother you with my electron phonon calculations again. I am > trying to do my calculations for a different system of bilayer graphene but > I get errors like: > > At line 356 of file q2r.f90 (Unit 51 "a2Fq2r.51") > Traceback: not available, compile with -ftrace=frame or -ftrace=full > Fortran Runtime error: bad real number in item 1 of list input > > when running q2r.x > > and > > At line 1659 of file matdyn.f90 (Unit 51 "a2Fmatdyn.61") > Traceback: not available, compile with -ftrace=frame or -ftrace=full > Fortran Runtime error: End of File > > when running matdyn.x > > I do not know what is going on. I tried the same calculations with a > smaller grid before and everything went fine > > Regards > > Elie Moujaes > University of Nottingham > NG7 2RD > UK > > _______________________________________________ > 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/20110211/fecb82f3/attachment.htm From eyvaz_isaev at yahoo.com Fri Feb 11 11:50:34 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 11 Feb 2011 02:50:34 -0800 (PST) Subject: [Pw_forum] BN problem In-Reply-To: References: Message-ID: <492053.78136.qm@web65702.mail.ac4.yahoo.com> Hi, Have you searched the forum archive or seen the User Guide in /Doc before posting your message? Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: Bongani Ngwenya To: pw_forum at pwscf.org Sent: Fri, February 11, 2011 8:20:56 AM Subject: [Pw_forum] BN problem Dear all, I'm trying to do an SCF calculation in quantum espresso. The program runs for a few minutes and then stops, giving the following error message "from davcio : error # 10 error while reading from file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... " The following is the input file I used: &control pseudo_dir = '.', calculation = 'scf', prefix = 'BN_5X5', restart_mode = 'restart', / &system ibrav = 0, celldm(1) = 23.73887, nat = 50, ntyp = 2, ecutwfc = 38, ecutrho = 304, occupations='smearing', degauss=0.003, smearing='mp', / &electrons conv_thr = 1.D-7, mixing_beta = 0.8, / &ions ion_dynamics = 'damp', \ ATOMIC_SPECIES B 10.811 B.pbe-n-van_ak.UPF N 14.007 N.pbe-van_ak.UPF ATOMIC_POSITIONS {alat} B 0.00000 0.00000 0.50000 N 0.11547 0.00000 0.50000 B 0.17321 0.10000 0.50000 B 0.17321 -0.10000 0.50000 N 0.28868 0.10000 0.50000 N 0.28868 -0.10000 0.50000 B 0.34641 0.00000 0.50000 B 0.34641 -0.20000 0.50000 B 0.34641 0.20000 0.50000 N 0.46188 0.00000 0.50000 N 0.46188 0.20000 0.50000 N 0.46188 -0.20000 0.50000 B 0.51962 0.10000 0.50000 B 0.51962 -0.10000 0.50000 B 0.51962 0.30000 0.50000 B 0.51962 -0.30000 0.50000 N 0.63509 0.10000 0.50000 N 0.63509 -0.10000 0.50000 N 0.63509 0.30000 0.50000 N 0.63509 -0.30000 0.50000 B 0.69282 0.00000 0.50000 B 0.69282 0.20000 0.50000 B 0.69282 -0.20000 0.50000 B 0.69282 0.40000 0.50000 B 0.69282 -0.40000 0.50000 N 0.80829 0.00000 0.50000 N 0.80829 0.20000 0.50000 N 0.80829 -0.20000 0.50000 N 0.80829 0.40000 0.50000 N 0.80829 -0.40000 0.50000 B 0.86603 0.10000 0.50000 B 0.86603 -0.10000 0.50000 B 0.86603 0.30000 0.50000 B 0.86603 -0.30000 0.50000 N 0.98149 0.10000 0.50000 N 0.98149 -0.10000 0.50000 N 0.98149 0.30000 0.50000 N 0.98149 -0.30000 0.50000 B 1.03923 0.00000 0.50000 B 1.03923 0.20000 0.50000 B 1.03923 -0.20000 0.50000 N 1.15470 0.00000 0.50000 N 1.15470 0.20000 0.50000 N 1.15470 -0.20000 0.50000 B 1.21244 0.10000 0.50000 B 1.21244 -0.10000 0.50000 N 1.32791 0.10000 0.50000 N 1.32791 -0.10000 0.50000 B 1.38564 0.00000 0.50000 N 1.50111 0.00000 0.50000 K_POINTS {automatic} 10 10 1 0 0 0 CELL_PARAMETERS {hexagonal} 0.866025404 0.50000 0.00000 0.866025404 -0.50000 0.00000 0.00000 0.00000 1.94071 Please help me do a successful calculation. Regards, Bongani Ngwenya Cell: 0027 84 429 5399 Office: 0027 12 420 3114 Fax: 0027 86 517 6293 bongani.ngwenya at gmail.com mabotho at yahoo.co.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110211/680e898b/attachment.htm From dabrowski at ihp-microelectronics.com Fri Feb 11 12:54:23 2011 From: dabrowski at ihp-microelectronics.com (Dabrowski Jaroslaw) Date: Fri, 11 Feb 2011 12:54:23 +0100 Subject: [Pw_forum] B3LYP in PWscf In-Reply-To: References: Message-ID: Many thanks for all the replies! I did not realize that this is an experimental feature that needs to be enabled by special pre-compiler settings. It is really encouraging that even such a silly question gets answered on the forum, and that fast. It really helps, because anyone can overlook something simple but important, and then it sometimes becomes difficult to find the way out all by oneself. My regards! Of course, it works like a charm. Cheers -- Jarek ________________________________________ Dr.rer.nat. Jaroslaw Dabrowski Scientist Materials Research IHP Fon: +49 (335) 5625-316 Fax: +49 (335) 5625-681 E-Mail: dabrowski at ihp-microelectronics.com Website: ________________________________________ IHP GmbH Innovations for High Performance Microelectronics Leibniz-Institut fuer innovative Mikroelektronik Im Technologiepark 25 15236 Frankfurt (Oder) Germany Geschaeftsfuehrer: Prof. Dr. Wolfgang Mehr, Manfred Stoecker, Vorsitzende des Aufsichtsrates: Konstanze Pistor Handelsregister: HRB 1982 Amtsgericht Frankfurt (Oder) , Steuernummer: 061/12500152, Umsatzsteuer-ID: DE 138996546 Die IHP GmbH ist Mitglied der Leibniz-Gemeinschaft und wird von der Bundesrepublik Deutschland und dem Land Brandenburg institutionell finanziert. Diese E-Mail enthaelt vertrauliche und / oder rechtlich geschuetzte Informationen. Wenn Sie nicht der richtige Adressat sind oder diese E-Mail irrtuemlich erhalten haben, informieren Sie bitte sofort den Absender und vernichten Sie diese Mail. Das unerlaubte Kopieren sowie die unbefugte Weitergabe dieser Mail sind nicht gestattet. This e-mail contains confidential and / or privileged information. If you are not the intended recipient or have received this e-mail in error, please notify the sender immediately and destroy this e-mail. Any unauthorized copying, disclosure or distribution of the material in this e-mail is strictly forbidden. From giuseppe.mattioli at mlib.ism.cnr.it Fri Feb 11 08:27:48 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Fri, 11 Feb 2011 08:27:48 +0100 Subject: [Pw_forum] B3LYP in PWscf In-Reply-To: References: Message-ID: <201102110827.48870.giuseppe.mattioli@mlib.ism.cnr.it> One last warning! Remember that hybrid calculations with pw.x are VERY HEAVY... Yours Giuseppe On Friday 11 February 2011 12:54:23 Dabrowski Jaroslaw wrote: > Many thanks for all the replies! I did not realize that this is an > experimental feature that needs to be enabled by special pre-compiler > settings. It is really encouraging that even such a silly question gets > answered on the forum, and that fast. It really helps, because anyone can > overlook something simple but important, and then it sometimes becomes > difficult to find the way out all by oneself. My regards! > > Of course, it works like a charm. > > Cheers -- Jarek > > > ________________________________________ > > Dr.rer.nat. Jaroslaw Dabrowski > Scientist > Materials Research > IHP > > Fon: +49 (335) 5625-316 > Fax: +49 (335) 5625-681 > E-Mail: dabrowski at ihp-microelectronics.com > Website: > ________________________________________ > > IHP GmbH > Innovations for High Performance Microelectronics > Leibniz-Institut fuer innovative Mikroelektronik > Im Technologiepark 25 > 15236 Frankfurt (Oder) > Germany > > Geschaeftsfuehrer: Prof. Dr. Wolfgang Mehr, Manfred Stoecker, Vorsitzende > des Aufsichtsrates: Konstanze Pistor Handelsregister: HRB 1982 Amtsgericht > Frankfurt (Oder) , Steuernummer: 061/12500152, Umsatzsteuer-ID: DE > 138996546 > > Die IHP GmbH ist Mitglied der Leibniz-Gemeinschaft und wird von der > Bundesrepublik Deutschland und dem Land Brandenburg institutionell > finanziert. > > Diese E-Mail enthaelt vertrauliche und / oder rechtlich geschuetzte > Informationen. Wenn Sie nicht der richtige Adressat sind oder diese E-Mail > irrtuemlich erhalten haben, informieren Sie bitte sofort den Absender und > vernichten Sie diese Mail. Das unerlaubte Kopieren sowie die unbefugte > Weitergabe dieser Mail sind nicht gestattet. > > This e-mail contains confidential and / or privileged information. If you > are not the intended recipient or have received this e-mail in error, > please notify the sender immediately and destroy this e-mail. Any > unauthorized copying, disclosure or distribution of the material in this > e-mail is strictly forbidden. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From padmaja_patnaik at yahoo.co.uk Fri Feb 11 13:13:19 2011 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Fri, 11 Feb 2011 12:13:19 +0000 (GMT) Subject: [Pw_forum] doubt in starting magnetization variable Message-ID: <842727.56189.qm@web26102.mail.ukl.yahoo.com> Hi All I have the following doubt. I have done the scf calculations for both spins with certain values of starting magnetization on different atoms of the compound. Next for calculating the density of states is it correct to mention only nspin = 2 in the input? Or do I have to mention the same (same as the scf input) starting magnetization values in DOS input also? Thanks and regards, Padmaja Patnaik Research Scholar Dept of Physics IIT Bombay Mumbai, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110211/2d860fb5/attachment.htm From faccin.giovani at gmail.com Fri Feb 11 17:09:11 2011 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Fri, 11 Feb 2011 12:09:11 -0400 Subject: [Pw_forum] A question on atomic magnetic moments Message-ID: Dear QE users, My first post on this list! Given the daily flow of messages, I'm glad to see that this is an active community! I'm trying to setup a simulation of a system containing iron. In order to do it, first I'm first testing the dimer and bulk, in order to see if they are being calculated correctly. I'm using the Fe.pbe-nd-rrkjus.UPF pseudo from the online database, with a 3d74s1 valence configuration and +1 magnetization. I've obtained a dimer equilibrium bond length of 2.05 angstroms (experiment: 2.02) and a vibrational frequency of 330 cm^-1 (experiment: 300). I'm happy with these results! Using another DFT code (OpenMX), also with GGA, I've obtained 2.10 angstroms for the equilibrium bond length and also 330 cm^-1 for the vibrational frequency. What puzzles me is the system magnetization. These are the results I'm getting (in units of Bohr mag.): Openmx - scalar relativistic: 6.62 Openmx - full relativistic, non collinear: 6.86 Quantum Espresso - : 7.14 Theoretical DFT literacy values: 6.00 Experiment: 6.5 +/- 1 My question: shouldn't those numbers be integers? If so, what could be causing this? Any information you need, just ask. Thank you! -- Giovani M. Faccin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110211/7bf35850/attachment.htm From giannozz at democritos.it Fri Feb 11 22:44:10 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 11 Feb 2011 22:44:10 +0100 Subject: [Pw_forum] doubt in starting magnetization variable In-Reply-To: <842727.56189.qm@web26102.mail.ukl.yahoo.com> References: <842727.56189.qm@web26102.mail.ukl.yahoo.com> Message-ID: <944D25DB-A4E4-49BB-9818-143E69113831@democritos.it> On Feb 11, 2011, at 13:13 , Padmaja Patnaik wrote: > for calculating the density of states is it correct to mention only > nspin = 2 in the input? > Or do I have to mention the same (same as the scf input) starting > magnetization values in DOS input also? I think starting_magnetization is ignored in all non-scf calculations P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From jcconesa at icp.csic.es Sat Feb 12 13:46:26 2011 From: jcconesa at icp.csic.es (CONESA CEGARRA, JOSE CARLOS) Date: Sat, 12 Feb 2011 13:46:26 +0100 Subject: [Pw_forum] combining vdW-DF and hybrids? In-Reply-To: <276904.50330.qm@web65713.mail.ac4.yahoo.com> References: <276904.50330.qm@web65713.mail.ac4.yahoo.com> Message-ID: <20110212134626.42751btldoq8dvky@webmail.csic.es> hi, I am doing some tests with the cvs version of Q-E. I wonder, could one combine the HSE06 functional (that refers only to exchange) with the vdw-DF correlation? I tried a line such as input_dft='nox+pw+hse+vdw' but got a message of incompatibility of functionals. Also, some question to the developers: a) is there work for allowing soon the use of hybrid functionals with USPP or PAW potentials? b) will the vdW-DF2 functional be available (with both ions and cell relaxation, if possible) in the 4.3 version? All the best, -- Jos? C. Conesa Instituto de Cat?lisis y Petroleoqu?mica, CSIC Marie Curie 2, Cantoblanco, 28049 Madrid, Spain Telef. +34-915854766 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110212/1e879e8d/attachment.htm From mehrnooshhazrati at gmail.com Sat Feb 12 14:51:09 2011 From: mehrnooshhazrati at gmail.com (Mehrnoosh Hazrati) Date: Sat, 12 Feb 2011 17:21:09 +0330 Subject: [Pw_forum] ibrav=8 Message-ID: Dear QE users, I want to calculate the band structures for a orthorhombic P lattice ( ibrav=8 ), which K-point set should i choose ? best regards, Mehrnoosh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110212/afb996b2/attachment.htm From jdai3 at mail.ustc.edu.cn Sat Feb 12 15:05:20 2011 From: jdai3 at mail.ustc.edu.cn (=?utf-8?B?RGFpIEp1bg==?=) Date: Sat, 12 Feb 2011 22:05:20 +0800 Subject: [Pw_forum] =?utf-8?q?ibrav=3D8?= References: Message-ID: <201102122205179192706@mail.ustc.edu.cn> Dear Hazrati, take a look at http://www.cryst.ehu.es/cryst/get_kvec.html; choose the space group, and then you can see the k-vectors. Best regards, 2011-02-12 Jun DAI Room3016, Hefei National Laboratory for Physical Sciences at the Microscale University of Science & Technology of China Hefei, Anhui 230026, P.R. China Tel. :+86-551-3606428 ???? Mehrnoosh Hazrati ????? 2011-02-12 21:51:36 ???? pw_forum ??? ??? [Pw_forum] ibrav=8 Dear QE users, I want to calculate the band structures for a orthorhombic P lattice ( ibrav=8 ), which K-point set should i choose ? best regards, Mehrnoosh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110212/cdf97af9/attachment.htm From mehrnooshhazrati at gmail.com Sat Feb 12 15:23:57 2011 From: mehrnooshhazrati at gmail.com (Mehrnoosh Hazrati) Date: Sat, 12 Feb 2011 17:53:57 +0330 Subject: [Pw_forum] ibrav=8 In-Reply-To: <201102122205179192706@mail.ustc.edu.cn> References: <201102122205179192706@mail.ustc.edu.cn> Message-ID: Dear Jun DAI, Thank you so much for your suggestion. Yours sincerely Mehrnoosh On Sat, Feb 12, 2011 at 5:35 PM, Dai Jun wrote: > Dear Hazrati, > take a look at http://www.cryst.ehu.es/cryst/get_kvec.html; > choose the space group, and then you can see the k-vectors. > > Best regards, > > 2011-02-12 > ------------------------------ > Jun DAI > Room3016, Hefei National Laboratory for Physical Sciences at the Microscale > University of Science & Technology of China > Hefei, Anhui 230026, P.R. China > Tel. :+86-551-3606428 > ------------------------------ > *????* Mehrnoosh Hazrati > *?????* 2011-02-12 21:51:36 > *????* pw_forum > *???* > *???* [Pw_forum] ibrav=8 > Dear QE users, > > I want to calculate the band structures for a orthorhombic P lattice ( > ibrav=8 ), which K-point set should i choose ? > > best regards, > Mehrnoosh > > _______________________________________________ > 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/20110212/41c0c15d/attachment.htm From giannozz at democritos.it Sat Feb 12 16:30:04 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 12 Feb 2011 16:30:04 +0100 Subject: [Pw_forum] frequencies using finite differences instead of perturbation theory? In-Reply-To: <4D343EDD.70908@nano.ku.dk> References: <4D343EDD.70908@nano.ku.dk> Message-ID: <92565AF6-7492-40DE-80F6-4B1098655AAA@democritos.it> On Jan 17, 2011, at 14:06 , Martin Andersson wrote: > I am looking into the effects of empirical dispersion, and as far as I > can see from the phonon output file, the effect from dispersion isn't > included when the frequencies are calculated using ph.x. Is there a > way > to use finite differences in the QE suite as opposed to perturbation > theory in order to get frequencies with empirical dispersion included? there is for sure more than one way, but none currently implemented and ready to use, AFAIK. Once upon a time there used to be a frozen-phonon code, but nobody was maintaining it so it has been removed. In the Gamma/ subdirectory there is a piece of code that evaluates Raman coefficients using finite differences on the dielectic tensors. It was written for testing purposes several years ago and could be easily adapted to frozen-phonon calculations, but it will need some work. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sat Feb 12 16:35:50 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 12 Feb 2011 16:35:50 +0100 Subject: [Pw_forum] volume discrepancy when adjusting (ecfixed, q2sigma, qcurtz) In-Reply-To: References: Message-ID: On Jan 7, 2011, at 11:59 , Riping WANG wrote: > What is the criteria to select the best (ecfixed,q2sigma,qcurtz) > value? I think you should consult the original reference to the method: number 3 in http://www.quantum-espresso.org/wiki/index.php/Ref:_Variable-cell_MD P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sat Feb 12 16:41:27 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 12 Feb 2011 16:41:27 +0100 Subject: [Pw_forum] A question on atomic magnetic moments In-Reply-To: References: Message-ID: <80982012-517C-4A53-A0E1-6975EF5CE89E@democritos.it> On Feb 11, 2011, at 17:09 , Giovani Faccin wrote: > My question: shouldn't those numbers be integers? only in finite systems, if you neglect spin-orbit. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sat Feb 12 16:46:04 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 12 Feb 2011 16:46:04 +0100 Subject: [Pw_forum] combining vdW-DF and hybrids? In-Reply-To: <20110212134626.42751btldoq8dvky@webmail.csic.es> References: <276904.50330.qm@web65713.mail.ac4.yahoo.com> <20110212134626.42751btldoq8dvky@webmail.csic.es> Message-ID: <386CB571-BF9E-4BCD-BFED-B38F81B8CB5C@democritos.it> On Feb 12, 2011, at 13:46 , CONESA CEGARRA, JOSE CARLOS wrote: > a) is there work for allowing soon the use of hybrid functionals > with USPP or PAW potentials? > it is on the list of things that it would be nice to have, but it is unlikely that it will be available "soon" > b) will the vdW-DF2 functional be available (with both ions and > cell relaxation, if possible) in the 4.3 version? > the 4.3 version will be more or less a snapshot of the current CVS tree P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From faccin.giovani at gmail.com Sun Feb 13 07:16:02 2011 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Sun, 13 Feb 2011 02:16:02 -0400 Subject: [Pw_forum] A question on atomic magnetic moments In-Reply-To: <80982012-517C-4A53-A0E1-6975EF5CE89E@democritos.it> References: <80982012-517C-4A53-A0E1-6975EF5CE89E@democritos.it> Message-ID: Dear Paolo, Thanks for the reply. Just to make sure that the simulation cell size is not an issue (so that the system is really finite), I've tested different possibilities, including some quite big cells. Still, after a certain size the value of the magnetization is converging to 6.82 instead of the expected 6. So something else is causing this. Unfortunately I've got no clue as to what could it be. Should it be of any help, this is my input file: &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , wf_collect = .true. , outdir = './output' , pseudo_dir = '../pseudo/' , prefix = 'fe' , etot_conv_thr = 1.0D-9 , forc_conv_thr = 1.0D-6 , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 1, celldm(1) = 43, nat = 2, ntyp = 1, ecutwfc = 100 , ecutrho = 300 , occupations = 'smearing' , degauss = 0.02 , smearing = 'methfessel-paxton' , nspin = 2 , starting_magnetization(1) = 1.0, / &ELECTRONS conv_thr = 1.0e-9 , mixing_beta = 0.7 , diagonalization = 'david' , / ATOMIC_SPECIES Fe 58.69000 Fe.pbe-nd-rrkjus.UPF ATOMIC_POSITIONS angstrom Fe 0.000000000 0.000000000 0.000000000 Fe 2.047510 0.000000000 0.000000000 K_POINTS automatic 1 1 1 1 1 1 Any suggestions are highly welcome. Giovani 2011/2/12 Paolo Giannozzi > > On Feb 11, 2011, at 17:09 , Giovani Faccin wrote: > > > My question: shouldn't those numbers be integers? > > only in finite systems, if you neglect spin-orbit. > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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 > -- Giovani -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110213/45bbd38d/attachment.htm From cyrille.barreteau at cea.fr Sun Feb 13 08:52:18 2011 From: cyrille.barreteau at cea.fr (BARRETEAU Cyrille) Date: Sun, 13 Feb 2011 08:52:18 +0100 Subject: [Pw_forum] =?iso-8859-1?q?RE=A0=3A__A_question_on_atomic_magnetic?= =?iso-8859-1?q?_moments?= References: <80982012-517C-4A53-A0E1-6975EF5CE89E@democritos.it> Message-ID: <18E4AC9C2FAC504E994A6759DE5ABE8DE3153D@DIODON.extra.cea.fr> Dear Giovani Try to decrease the degauss value of your smearing.. and see what happens. cyrille ================================================================== Cyrille Barreteau phone : +33 (0)1 69 08 29 51 CEA Saclay fax : +33 (0)1 69 08 84 46 IRAMIS, SPCSI, Batiment 462 email cyrille.barreteau at cea.fr 91191 Gif sur Yvette Cedex FRANCE ~~~~~~~~~~~~~~~~~~~~~~~~ Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/ ================================================================== ________________________________ De: pw_forum-bounces at pwscf.org de la part de Giovani Faccin Date: dim. 13/02/2011 07:16 ?: PWSCF Forum Objet : Re: [Pw_forum] A question on atomic magnetic moments Dear Paolo, Thanks for the reply. Just to make sure that the simulation cell size is not an issue (so that the system is really finite), I've tested different possibilities, including some quite big cells. Still, after a certain size the value of the magnetization is converging to 6.82 instead of the expected 6. So something else is causing this. Unfortunately I've got no clue as to what could it be. Should it be of any help, this is my input file: &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , wf_collect = .true. , outdir = './output' , pseudo_dir = '../pseudo/' , prefix = 'fe' , etot_conv_thr = 1.0D-9 , forc_conv_thr = 1.0D-6 , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 1, celldm(1) = 43, nat = 2, ntyp = 1, ecutwfc = 100 , ecutrho = 300 , occupations = 'smearing' , degauss = 0.02 , smearing = 'methfessel-paxton' , nspin = 2 , starting_magnetization(1) = 1.0, / &ELECTRONS conv_thr = 1.0e-9 , mixing_beta = 0.7 , diagonalization = 'david' , / ATOMIC_SPECIES Fe 58.69000 Fe.pbe-nd-rrkjus.UPF ATOMIC_POSITIONS angstrom Fe 0.000000000 0.000000000 0.000000000 Fe 2.047510 0.000000000 0.000000000 K_POINTS automatic 1 1 1 1 1 1 Any suggestions are highly welcome. Giovani 2011/2/12 Paolo Giannozzi On Feb 11, 2011, at 17:09 , Giovani Faccin wrote: > My question: shouldn't those numbers be integers? only in finite systems, if you neglect spin-orbit. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. 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 -- Giovani -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 10302 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110213/fda2a2fb/attachment.bin From david.grifith at gmail.com Sun Feb 13 13:56:57 2011 From: david.grifith at gmail.com (David Grifith) Date: Sun, 13 Feb 2011 16:26:57 +0330 Subject: [Pw_forum] atomic orbitals Message-ID: Dear QE Users Is it possible that we visualize the atomic orbitals, hybrid orbitals, and the overlap between bond orbitals by the Quantum Espresso and its side programs like XCrysden ? I appreciate your helpful comments in advance. Best Wisehs -- Sincerely Yours David G. JCU -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110213/5839f097/attachment.htm From nicola.marzari at materials.ox.ac.uk Sun Feb 13 18:53:36 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Sun, 13 Feb 2011 17:53:36 +0000 Subject: [Pw_forum] atomic orbitals In-Reply-To: References: Message-ID: <4D581AA0.3070804@materials.ox.ac.uk> On 2/13/11 12:56 PM, David Grifith wrote: > Dear QE Users > > Is it possible that we visualize the atomic orbitals, hybrid orbitals, > and the overlap between bond orbitals by the Quantum Espresso and its > side programs like XCrysden ? > I appreciate your helpful comments in advance. Best Wisehs QE calculates eigenstates of the Hamiltonian, that you can certainly visualize. The orbitals you mention are a conceptualization of what happens as a chemical bond is formed, and there are no formal definitions (a part, of course, for atomic orbitals in isolated atoms, that are eigenstates of the atomic Hamiltonian). If you perform unitary transformations on the eigenstates that make them more local (and not eigenstates any more, but leaving the total energy and total charge density unchanged - the occupied manifold is not affected by unitary transformations) you get orbitals that are reminiscent of those approximate concepts above - see www.wannier.org and early biblio. That code works with QE. As often mentioned in the mailing list, please do sign in full your posts (i.e. not with acronyms). Thanks! nicola -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From ttduyle at gmail.com Sun Feb 13 20:52:49 2011 From: ttduyle at gmail.com (Duy Le) Date: Sun, 13 Feb 2011 14:52:49 -0500 Subject: [Pw_forum] A question on atomic magnetic moments In-Reply-To: References: <80982012-517C-4A53-A0E1-6975EF5CE89E@democritos.it> Message-ID: You should be able to fix magneticmoment of system at the desired value (say 6, 6.5, 7) to see which one give you the lowest energy. -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Sun, Feb 13, 2011 at 1:16 AM, Giovani Faccin wrote: > Dear Paolo, > > Thanks for the reply. > > Just to make sure that the simulation cell size is not an issue (so that the > system is really finite), I've tested different possibilities, including > some quite big cells. Still, after a certain size the value of the > magnetization is converging to 6.82 instead of the expected 6. > > So something else is causing this. Unfortunately I've got no clue as to what > could it be. > > Should it be of any help, this is my input file: > > > ?&CONTROL > ???????????????? calculation = 'scf' , > ??????????????? restart_mode = 'from_scratch' , > ????????????????? wf_collect = .true. , > ????????????????????? outdir = './output' , > ????????????????? pseudo_dir = '../pseudo/' , > ????????????????????? prefix = 'fe' , > ?????????????? etot_conv_thr = 1.0D-9 , > ?????????????? forc_conv_thr = 1.0D-6 , > ???????????????????? tstress = .true. , > ???????????????????? tprnfor = .true. , > ?/ > ?&SYSTEM > ?????????????????????? ibrav = 1, > ?????????????????? celldm(1) = 43, > ???????????????????????? nat = 2, > ??????????????????????? ntyp = 1, > ???????????????????? ecutwfc = 100 , > ???????????????????? ecutrho = 300 , > ???????????????? occupations = 'smearing' , > ???????????????????? degauss = 0.02 , > ??????????????????? smearing = 'methfessel-paxton' , > ?????????????????????? nspin = 2 , > ?? starting_magnetization(1) = 1.0, > ?/ > ?&ELECTRONS > ??????????????????? conv_thr = 1.0e-9 , > ???????????????? mixing_beta = 0.7 , > ???????????? diagonalization = 'david' , > ?/ > ATOMIC_SPECIES > ?? Fe?? 58.69000? Fe.pbe-nd-rrkjus.UPF > ATOMIC_POSITIONS angstrom > ?? Fe????? 0.000000000??? 0.000000000??? 0.000000000 > ?? Fe????? 2.047510?????? 0.000000000??? 0.000000000 > K_POINTS automatic > ? 1 1 1?? 1 1 1 > > Any suggestions are highly welcome. > > Giovani > > > 2011/2/12 Paolo Giannozzi >> >> On Feb 11, 2011, at 17:09 , Giovani Faccin wrote: >> >> > My question: shouldn't those numbers be integers? >> >> only in finite systems, if you neglect spin-orbit. >> >> P. >> --- >> Paolo Giannozzi, Dept of Chemistry&Physics&Environment, >> Univ. 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 > > > > -- > Giovani > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From elie.moujaes at hotmail.co.uk Mon Feb 14 03:36:58 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Mon, 14 Feb 2011 02:36:58 +0000 Subject: [Pw_forum] band structure of a 60 Carbon atom system Message-ID: Dear all, I am trying to get the band structure of a 60 Carbon atom system. i have done the scf calculations and the band structure calculation. I am comparing my results to other ones. I have realised that in my calculations even after setting the Fermi energy to zero, Two of the bands that are supposed to cross at the zero level in others calculations crossed below the zero reference in my calculations. The shape of the curves are similar though. I am trying to figure out the origin of this difference. Could anyone tell me what might be going wrong? Is this a pseudopotential related problem? Thanks Elie Moujaes University of nottingham NG7 2RD UK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110214/024f0309/attachment.htm From faccin.giovani at gmail.com Mon Feb 14 05:31:52 2011 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Mon, 14 Feb 2011 00:31:52 -0400 Subject: [Pw_forum] A question on atomic magnetic moments In-Reply-To: References: <80982012-517C-4A53-A0E1-6975EF5CE89E@democritos.it> Message-ID: Hi Duy Le, Thanks for the idea. Tried it, and this is what I got: Imposed Magnetization | Total Energy (Hartree) 5.0 5.2 5.4 5.6 -55.527688685 5.8 -55.533921200 6.0 -55.540351250 6.2 -55.540980910 6.4 -55.541296415 6.6 6.8 7.0 7.2 Values in blank are simulations that didn't execute, with the following error message: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 0 from set_nelup_neldw : error # 2 tot_magnetization is inconsistent with total number of electrons %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% So two interesting facts appeared here: 1 - The energy minimum does not converge to 6, as it should do; 2 - When an unconstrained magnetization is used, the magnetization converges to a value around 6.82. However, If I try to impose this value as a fixed magnetization from start, pw.x won't even begin the calculation. Weird, isn't it? I'm posting below a sample input file used for this battery of tests. I've used a smaller cell size here to speed things up a little. If celldm(1) is increased say to 40 instead of 25, you'll get a change in magnetic moment of about 0.05 mB. This is probably irrelevant as far as finding the cause of these results is concerned. Any other suggestions, just tell me; I'll try it and report back. ====================== &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , wf_collect = .true. , outdir = './output' , pseudo_dir = '../pseudo/' , prefix = 'fe' , etot_conv_thr = 1.0D-9 , forc_conv_thr = 1.0D-6 , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 1, celldm(1) = 25, nat = 2, ntyp = 1, ecutwfc = 100 , ecutrho = 300 , occupations = 'smearing' , degauss = 0.005 , smearing = 'methfessel-paxton' , nspin = 2 , starting_magnetization(1) = 1.0, tot_magnetization = 6.0 , / &ELECTRONS conv_thr = 1.0e-9 , mixing_beta = 0.7 ,I diagonalization = 'david' , / ATOMIC_SPECIES Fe 58.69000 Fe.pbe-nd-rrkjus.UPF ATOMIC_POSITIONS angstrom Fe 0.000000000 0.000000000 0.000000000 Fe 2.048000000 0.000000000 0.000000000 K_POINTS automatic 1 1 1 1 1 1 ====================== Giovani 2011/2/13 Duy Le > You should be able to fix magneticmoment of system at the desired > value (say 6, 6.5, 7) to see which one give you the lowest energy. > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > > "Men don't need hand to do things" > > > > On Sun, Feb 13, 2011 at 1:16 AM, Giovani Faccin > wrote: > > Dear Paolo, > > > > Thanks for the reply. > > > > Just to make sure that the simulation cell size is not an issue (so that > the > > system is really finite), I've tested different possibilities, including > > some quite big cells. Still, after a certain size the value of the > > magnetization is converging to 6.82 instead of the expected 6. > > > > So something else is causing this. Unfortunately I've got no clue as to > what > > could it be. > > > > Should it be of any help, this is my input file: > > > > > > &CONTROL > > calculation = 'scf' , > > restart_mode = 'from_scratch' , > > wf_collect = .true. , > > outdir = './output' , > > pseudo_dir = '../pseudo/' , > > prefix = 'fe' , > > etot_conv_thr = 1.0D-9 , > > forc_conv_thr = 1.0D-6 , > > tstress = .true. , > > tprnfor = .true. , > > / > > &SYSTEM > > ibrav = 1, > > celldm(1) = 43, > > nat = 2, > > ntyp = 1, > > ecutwfc = 100 , > > ecutrho = 300 , > > occupations = 'smearing' , > > degauss = 0.02 , > > smearing = 'methfessel-paxton' , > > nspin = 2 , > > starting_magnetization(1) = 1.0, > > / > > &ELECTRONS > > conv_thr = 1.0e-9 , > > mixing_beta = 0.7 , > > diagonalization = 'david' , > > / > > ATOMIC_SPECIES > > Fe 58.69000 Fe.pbe-nd-rrkjus.UPF > > ATOMIC_POSITIONS angstrom > > Fe 0.000000000 0.000000000 0.000000000 > > Fe 2.047510 0.000000000 0.000000000 > > K_POINTS automatic > > 1 1 1 1 1 1 > > > > Any suggestions are highly welcome. > > > > Giovani > > > > > > 2011/2/12 Paolo Giannozzi > >> > >> On Feb 11, 2011, at 17:09 , Giovani Faccin wrote: > >> > >> > My question: shouldn't those numbers be integers? > >> > >> only in finite systems, if you neglect spin-orbit. > >> > >> P. > >> --- > >> Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > >> Univ. 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 > > > > > > > > -- > > Giovani > > > > _______________________________________________ > > 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 > -- Giovani -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110214/914e77a3/attachment-0001.htm From faccin.giovani at gmail.com Mon Feb 14 05:50:36 2011 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Mon, 14 Feb 2011 00:50:36 -0400 Subject: [Pw_forum] RE : A question on atomic magnetic moments In-Reply-To: References: <80982012-517C-4A53-A0E1-6975EF5CE89E@democritos.it> Message-ID: Dear Cyrille, First of all, thanks for the reply on my post. Following your suggestion, I've run a few calculations with lower degauss values. In particular, the ones reported on the message for Duy Le were made with a much smaller value ( 0.005 ) than the original 0.02 from the first message. Besides that, I've tried degauss values as low as 0.002 without any significant improvement on the final magnetization. I'm still wondering how do people find 6.00 so easily for the magnetization. I'm trying with 2 different DFT codes and no way I'm reaching those results, even though bulk/dimer equilibrium distances and force constants appear to be ok. Any other ideas, just tell me, I'll try it and report back on the list. Thanks again, Giovani 2011/2/13 BARRETEAU Cyrille > Dear Giovani > Try to decrease the degauss value of your smearing.. and see what happens. > > cyrille > > > ================================================================== > Cyrille Barreteau > phone : +33 (0)1 69 08 29 51 > CEA Saclay fax > : +33 (0)1 69 08 84 46 > IRAMIS, SPCSI, Batiment 462 email > cyrille.barreteau at cea.fr > 91191 Gif sur Yvette Cedex > FRANCE > ~~~~~~~~~~~~~~~~~~~~~~~~ > Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/ > ================================================================== > > ________________________________ > > De: pw_forum-bounces at pwscf.org de la part de Giovani Faccin > Date: dim. 13/02/2011 07:16 > ?: PWSCF Forum > Objet : Re: [Pw_forum] A question on atomic magnetic moments > > > Dear Paolo, > > Thanks for the reply. > > Just to make sure that the simulation cell size is not an issue (so that > the system is really finite), I've tested different possibilities, including > some quite big cells. Still, after a certain size the value of the > magnetization is converging to 6.82 instead of the expected 6. > > So something else is causing this. Unfortunately I've got no clue as to > what could it be. > > Should it be of any help, this is my input file: > > > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > wf_collect = .true. , > outdir = './output' , > pseudo_dir = '../pseudo/' , > prefix = 'fe' , > etot_conv_thr = 1.0D-9 , > forc_conv_thr = 1.0D-6 , > tstress = .true. , > tprnfor = .true. , > / > &SYSTEM > ibrav = 1, > celldm(1) = 43, > nat = 2, > ntyp = 1, > ecutwfc = 100 , > ecutrho = 300 , > occupations = 'smearing' , > degauss = 0.02 , > smearing = 'methfessel-paxton' , > nspin = 2 , > starting_magnetization(1) = 1.0, > / > &ELECTRONS > conv_thr = 1.0e-9 , > mixing_beta = 0.7 , > diagonalization = 'david' , > / > ATOMIC_SPECIES > Fe 58.69000 Fe.pbe-nd-rrkjus.UPF > ATOMIC_POSITIONS angstrom > Fe 0.000000000 0.000000000 0.000000000 > Fe 2.047510 0.000000000 0.000000000 > K_POINTS automatic > 1 1 1 1 1 1 > > Any suggestions are highly welcome. > > Giovani > > > > 2011/2/12 Paolo Giannozzi > > > > On Feb 11, 2011, at 17:09 , Giovani Faccin wrote: > > > My question: shouldn't those numbers be integers? > > > only in finite systems, if you neglect spin-orbit. > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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 > > > > > > -- > Giovani > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Giovani -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110214/6b387d96/attachment.htm From prasenjit.jnc at gmail.com Mon Feb 14 06:22:30 2011 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Mon, 14 Feb 2011 10:52:30 +0530 Subject: [Pw_forum] RE : A question on atomic magnetic moments In-Reply-To: References: <80982012-517C-4A53-A0E1-6975EF5CE89E@democritos.it> Message-ID: A small suggestion, try changing the smearing type, instead of using mp, try using m-v or even simple gaussian is fine for small clusters. Also, you should check the value of the contribution to total energy from smearing (printed in the output after your calculations have converged).......ideally for small clusters as yours, this should be zero. This tells you that your smearing is physically small enough so that the spurious effect of broadening becomes negligible. With regards, Prasenjit On 14 February 2011 10:20, Giovani Faccin wrote: > Dear Cyrille, > > First of all, thanks for the reply on my post. > > Following your suggestion, I've run a few calculations with lower degauss > values. In particular, the ones reported on the message for Duy Le were made > with a much smaller value ( 0.005 ) than the original 0.02 from the first > message. Besides that, I've tried degauss values as low as 0.002 without any > significant improvement on the final magnetization. > > I'm still wondering how do people find 6.00 so easily for the magnetization. > I'm trying with 2 different DFT codes and no way I'm reaching those results, > even though bulk/dimer equilibrium distances and force constants appear to > be ok. > > Any other ideas, just tell me, I'll try it and report back on the list. > > Thanks again, > > Giovani > > > 2011/2/13 BARRETEAU Cyrille >> >> Dear Giovani >> Try to decrease the degauss value of your smearing.. and see what happens. >> >> ?cyrille >> >> >> ================================================================== >> Cyrille Barreteau >> ?phone : +33 (0)1 69 08 29 51 >> CEA Saclay ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? fax >> : ? ? ?+33 (0)1 69 08 84 46 >> IRAMIS, SPCSI, ? ?Batiment 462 ? ? ? ? ? ? ? ? ? ? ? ? ? ?email >> cyrille.barreteau at cea.fr >> 91191 Gif sur Yvette Cedex >> FRANCE >> ~~~~~~~~~~~~~~~~~~~~~~~~ >> Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/ >> ================================================================== >> >> ________________________________ >> >> De: pw_forum-bounces at pwscf.org de la part de Giovani Faccin >> Date: dim. 13/02/2011 07:16 >> ?: PWSCF Forum >> Objet : Re: [Pw_forum] A question on atomic magnetic moments >> >> >> Dear Paolo, >> >> Thanks for the reply. >> >> Just to make sure that the simulation cell size is not an issue (so that >> the system is really finite), I've tested different possibilities, including >> some quite big cells. Still, after a certain size the value of the >> magnetization is converging to 6.82 instead of the expected 6. >> >> So something else is causing this. Unfortunately I've got no clue as to >> what could it be. >> >> Should it be of any help, this is my input file: >> >> >> ?&CONTROL >> ? ? ? ? ? ? ? ? calculation = 'scf' , >> ? ? ? ? ? ? ? ?restart_mode = 'from_scratch' , >> ? ? ? ? ? ? ? ? ?wf_collect = .true. , >> ? ? ? ? ? ? ? ? ? ? ?outdir = './output' , >> ? ? ? ? ? ? ? ? ?pseudo_dir = '../pseudo/' , >> ? ? ? ? ? ? ? ? ? ? ?prefix = 'fe' , >> ? ? ? ? ? ? ? etot_conv_thr = 1.0D-9 , >> ? ? ? ? ? ? ? forc_conv_thr = 1.0D-6 , >> ? ? ? ? ? ? ? ? ? ? tstress = .true. , >> ? ? ? ? ? ? ? ? ? ? tprnfor = .true. , >> ?/ >> ?&SYSTEM >> ? ? ? ? ? ? ? ? ? ? ? ibrav = 1, >> ? ? ? ? ? ? ? ? ? celldm(1) = 43, >> ? ? ? ? ? ? ? ? ? ? ? ? nat = 2, >> ? ? ? ? ? ? ? ? ? ? ? ?ntyp = 1, >> ? ? ? ? ? ? ? ? ? ? ecutwfc = 100 , >> ? ? ? ? ? ? ? ? ? ? ecutrho = 300 , >> ? ? ? ? ? ? ? ? occupations = 'smearing' , >> ? ? ? ? ? ? ? ? ? ? degauss = 0.02 , >> ? ? ? ? ? ? ? ? ? ?smearing = 'methfessel-paxton' , >> ? ? ? ? ? ? ? ? ? ? ? nspin = 2 , >> ? starting_magnetization(1) = 1.0, >> ?/ >> ?&ELECTRONS >> ? ? ? ? ? ? ? ? ? ?conv_thr = 1.0e-9 , >> ? ? ? ? ? ? ? ? mixing_beta = 0.7 , >> ? ? ? ? ? ? diagonalization = 'david' , >> ?/ >> ATOMIC_SPECIES >> ? Fe ? 58.69000 ?Fe.pbe-nd-rrkjus.UPF >> ATOMIC_POSITIONS angstrom >> ? Fe ? ? ?0.000000000 ? ?0.000000000 ? ?0.000000000 >> ? Fe ? ? ?2.047510 ? ? ? 0.000000000 ? ?0.000000000 >> K_POINTS automatic >> ?1 1 1 ? 1 1 1 >> >> Any suggestions are highly welcome. >> >> Giovani >> >> >> >> 2011/2/12 Paolo Giannozzi >> >> >> >> ? ? ? ?On Feb 11, 2011, at 17:09 , Giovani Faccin wrote: >> >> ? ? ? ?> My question: shouldn't those numbers be integers? >> >> >> ? ? ? ?only in finite systems, if you neglect spin-orbit. >> >> ? ? ? ?P. >> ? ? ? ?--- >> ? ? ? ?Paolo Giannozzi, Dept of Chemistry&Physics&Environment, >> ? ? ? ?Univ. 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 >> >> >> >> >> >> -- >> Giovani >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > Giovani > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- PRASENJIT GHOSH, Assistant Professor, IISER Pune, First floor, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan Pune, Maharashtra 411021, India Phone: +91 (20) 2590 8203 Fax: +91 (20) 2589 9790 From cyrille.barreteau at cea.fr Mon Feb 14 09:14:27 2011 From: cyrille.barreteau at cea.fr (BARRETEAU Cyrille) Date: Mon, 14 Feb 2011 09:14:27 +0100 Subject: [Pw_forum] =?iso-8859-1?q?RE=A0=3A__RE_=3A_A_question_on_atomic_m?= =?iso-8859-1?q?agnetic_moments?= References: <80982012-517C-4A53-A0E1-6975EF5CE89E@democritos.it> Message-ID: <18E4AC9C2FAC504E994A6759DE5ABE8DE3153F@DIODON.extra.cea.fr> Dear Giovani I personnaly did calculations on Fe clusters some time ago. I always found "almost integer" magnetic moments. However I once encoutered some difficulties with the default value of "nbnd". I had to increase it. Try to set nbnd=20 for example... Magnetic clusters can be very tricky.. It also very common to find several magnetic solutions.. good luck cyrille ================================================================== Cyrille Barreteau phone : +33 (0)1 69 08 29 51 CEA Saclay fax : +33 (0)1 69 08 84 46 IRAMIS, SPCSI, Batiment 462 email cyrille.barreteau at cea.fr 91191 Gif sur Yvette Cedex FRANCE ~~~~~~~~~~~~~~~~~~~~~~~~ Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/ ================================================================== ________________________________ De: pw_forum-bounces at pwscf.org de la part de Giovani Faccin Date: lun. 14/02/2011 05:50 ?: PWSCF Forum Objet : Re: [Pw_forum] RE : A question on atomic magnetic moments Dear Cyrille, First of all, thanks for the reply on my post. Following your suggestion, I've run a few calculations with lower degauss values. In particular, the ones reported on the message for Duy Le were made with a much smaller value ( 0.005 ) than the original 0.02 from the first message. Besides that, I've tried degauss values as low as 0.002 without any significant improvement on the final magnetization. I'm still wondering how do people find 6.00 so easily for the magnetization. I'm trying with 2 different DFT codes and no way I'm reaching those results, even though bulk/dimer equilibrium distances and force constants appear to be ok. Any other ideas, just tell me, I'll try it and report back on the list. Thanks again, Giovani 2011/2/13 BARRETEAU Cyrille Dear Giovani Try to decrease the degauss value of your smearing.. and see what happens. cyrille ================================================================== Cyrille Barreteau phone : +33 (0)1 69 08 29 51 CEA Saclay fax : +33 (0)1 69 08 84 46 IRAMIS, SPCSI, Batiment 462 email cyrille.barreteau at cea.fr 91191 Gif sur Yvette Cedex FRANCE ~~~~~~~~~~~~~~~~~~~~~~~~ Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/ ================================================================== ________________________________ De: pw_forum-bounces at pwscf.org de la part de Giovani Faccin Date: dim. 13/02/2011 07:16 ?: PWSCF Forum Objet : Re: [Pw_forum] A question on atomic magnetic moments Dear Paolo, Thanks for the reply. Just to make sure that the simulation cell size is not an issue (so that the system is really finite), I've tested different possibilities, including some quite big cells. Still, after a certain size the value of the magnetization is converging to 6.82 instead of the expected 6. So something else is causing this. Unfortunately I've got no clue as to what could it be. Should it be of any help, this is my input file: &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , wf_collect = .true. , outdir = './output' , pseudo_dir = '../pseudo/' , prefix = 'fe' , etot_conv_thr = 1.0D-9 , forc_conv_thr = 1.0D-6 , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 1, celldm(1) = 43, nat = 2, ntyp = 1, ecutwfc = 100 , ecutrho = 300 , occupations = 'smearing' , degauss = 0.02 , smearing = 'methfessel-paxton' , nspin = 2 , starting_magnetization(1) = 1.0, / &ELECTRONS conv_thr = 1.0e-9 , mixing_beta = 0.7 , diagonalization = 'david' , / ATOMIC_SPECIES Fe 58.69000 Fe.pbe-nd-rrkjus.UPF ATOMIC_POSITIONS angstrom Fe 0.000000000 0.000000000 0.000000000 Fe 2.047510 0.000000000 0.000000000 K_POINTS automatic 1 1 1 1 1 1 Any suggestions are highly welcome. Giovani 2011/2/12 Paolo Giannozzi On Feb 11, 2011, at 17:09 , Giovani Faccin wrote: > My question: shouldn't those numbers be integers? only in finite systems, if you neglect spin-orbit. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. 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 -- Giovani _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Giovani -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 12291 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110214/7f73a8d3/attachment.bin From davide.sangalli at gmail.com Mon Feb 14 10:59:05 2011 From: davide.sangalli at gmail.com (Davide Sangalli) Date: Mon, 14 Feb 2011 10:59:05 +0100 Subject: [Pw_forum] k-points parallelization in pwscf 4.2.1 Message-ID: <4D58FCE8.3040002@gmail.com> Dear forum, I did some check on the pwscf parallelization (version 4.2.1). Here the results for the same calculations: 1 - serial 2 - np=6, npool=1 (i.e. fft grid parallelization) 3 - np=6, npool=6 (i.e. kpts parallelization) (all processoros belong to the same node) The fft parallelization is quite efficient. It takes 1m56.75s vs 7m19.59s in the serial run. On the other hand the kpts parallelization is not working. It takes more than the serial run: 11m14.40s vs 7m19.59s What could my problem be? Best regards, Davide Here you can find some more details: ************************************** 1 - serial: Parallel version (MPI), running on 1 processors ... Proc/ planes cols G planes cols G columns G Pool (dense grid) (smooth grid) (wavefct grid) 1 80 4469 230753 48 1633 51175 457 7513 ... number of k points= 6 gaussian broad. (Ry)= 0.0200 ngauss = 0 cart. coord. in units 2pi/a_0 k( 1) = ( 0.1250000 0.1250000 0.1213003), wk = 0.2500000 k( 2) = ( 0.1250000 0.1250000 0.3639010), wk = 0.2500000 k( 3) = ( 0.1250000 0.3750000 0.1213003), wk = 0.5000000 k( 4) = ( 0.1250000 0.3750000 0.3639010), wk = 0.5000000 k( 5) = ( 0.3750000 0.3750000 0.1213003), wk = 0.2500000 k( 6) = ( 0.3750000 0.3750000 0.3639010), wk = 0.2500000 ... PWSCF : 7m16.35s CPU time, 7m19.59s WALL time ******************************************************************************* 2 - fft parallelization: Parallel version (MPI), running on 6 processors R & G space division: proc/pool = 6 ... Proc/ planes cols G planes cols G columns G Pool (dense grid) (smooth grid) (wavefct grid) 1 14 744 38458 8 272 8538 77 1253 2 14 745 38459 8 272 8544 76 1252 3 13 745 38459 8 273 8525 76 1252 4 13 745 38459 8 272 8516 76 1252 5 13 745 38459 8 272 8520 76 1252 6 13 745 38459 8 272 8532 76 1252 tot 80 4469 230753 48 1633 51175 457 7513 ... number of k points= 6 gaussian broad. (Ry)= 0.0200 ngauss = 0 cart. coord. in units 2pi/a_0 k( 1) = ( 0.1250000 0.1250000 0.1213003), wk = 0.2500000 k( 2) = ( 0.1250000 0.1250000 0.3639010), wk = 0.2500000 k( 3) = ( 0.1250000 0.3750000 0.1213003), wk = 0.5000000 k( 4) = ( 0.1250000 0.3750000 0.3639010), wk = 0.5000000 k( 5) = ( 0.3750000 0.3750000 0.1213003), wk = 0.2500000 k( 6) = ( 0.3750000 0.3750000 0.3639010), wk = 0.2500000 ... PWSCF : 1m49.61s CPU time, 1m56.75s WALL time 3 - kpts parallelization Parallel version (MPI), running on 6 processors K-points division: npool = 6 ... Proc/ planes cols G planes cols G columns G Pool (dense grid) (smooth grid) (wavefct grid) 1 80 4469 230753 48 1633 51175 457 7513 ... number of k points= 6 gaussian broad. (Ry)= 0.0200 ngauss = 0 cart. coord. in units 2pi/a_0 k( 1) = ( 0.1250000 0.1250000 0.1213003), wk = 0.2500000 k( 2) = ( 0.1250000 0.1250000 0.3639010), wk = 0.2500000 k( 3) = ( 0.1250000 0.3750000 0.1213003), wk = 0.5000000 k( 4) = ( 0.1250000 0.3750000 0.3639010), wk = 0.5000000 k( 5) = ( 0.3750000 0.3750000 0.1213003), wk = 0.2500000 k( 6) = ( 0.3750000 0.3750000 0.3639010), wk = 0.2500000 ... PWSCF : 10m57.44s CPU time, 11m14.40s WALL time From giannozz at democritos.it Mon Feb 14 11:34:54 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 14 Feb 2011 11:34:54 +0100 Subject: [Pw_forum] k-points parallelization in pwscf 4.2.1 In-Reply-To: <4D58FCE8.3040002@gmail.com> References: <4D58FCE8.3040002@gmail.com> Message-ID: <4D59054E.7030302@democritos.it> Davide Sangalli wrote: > What could my problem be? the only reason I can think of is that k-point parallelization doesn't (and cannot) distribute memory, so the total memory requirement will be npools*(size of serial execution). If you run on the same node six instances of a large executable, memory conflicts may slow down more than parallelization can speed up. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Mon Feb 14 11:40:28 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 14 Feb 2011 11:40:28 +0100 Subject: [Pw_forum] A question on atomic magnetic moments In-Reply-To: References: <80982012-517C-4A53-A0E1-6975EF5CE89E@democritos.it> Message-ID: <4D59069C.4000102@democritos.it> Giovani Faccin wrote: > from set_nelup_neldw : error # 2 > tot_magnetization is inconsistent with total number of electrons this check was written having in mind integer values of the magnetization. It is meaningless with non-integer magnetization values. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Mon Feb 14 11:52:39 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 14 Feb 2011 11:52:39 +0100 Subject: [Pw_forum] band structure of a 60 Carbon atom system In-Reply-To: References: Message-ID: <4D590977.6030408@democritos.it> Elie Moujaes wrote: > Is this a pseudopotential related problem? No, it is related to the phase of the moon. When the moon is in the seventh house and Jupiter aligns with Mars, the Fermi energy will be correct. Seriously: I can't stand any longer this attitude of blaming pseudopotentials for everything. Anyway: it is related to the way Fermi energy is calculated and to the peculiar form of the Fermi surface in graphene. -- Paolo Giannozzi, Democritos and University of Udine, Italy From wonvein at gmail.com Mon Feb 14 11:53:24 2011 From: wonvein at gmail.com (WANG Wei) Date: Mon, 14 Feb 2011 19:53:24 +0900 Subject: [Pw_forum] k-points parallelization in pwscf 4.2.1 In-Reply-To: <4D59054E.7030302@democritos.it> References: <4D58FCE8.3040002@gmail.com> <4D59054E.7030302@democritos.it> Message-ID: Dear all, How to run pwscf in a fft grid parallelization mode? Thank you. +---------------------------------------------------------+ Vei WANG Kawazoe's Lab Institute for Materials Research (IMR), Tohoku University2-1-1 Katahira, Aoba-ku, Sendai, Japan Phone: +81-022-215-2057 Fax: +81-022-215-2052 +---------------------------------------------------------+ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110214/48bf8d25/attachment.htm From davide.sangalli at gmail.com Mon Feb 14 12:15:10 2011 From: davide.sangalli at gmail.com (Davide Sangalli) Date: Mon, 14 Feb 2011 12:15:10 +0100 Subject: [Pw_forum] k-points parallelization in pwscf 4.2.1 In-Reply-To: References: <4D58FCE8.3040002@gmail.com> <4D59054E.7030302@democritos.it> Message-ID: <4D590EBE.3030204@gmail.com> An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110214/72e7dda1/attachment.htm From srijan.india at gmail.com Mon Feb 14 12:15:45 2011 From: srijan.india at gmail.com (Srijan Kumar Saha) Date: Mon, 14 Feb 2011 12:15:45 +0100 Subject: [Pw_forum] A question on atomic magnetic moments In-Reply-To: References: Message-ID: Dear QE users, QE is able to find the correct symmetry for the input file, added at the end of this email. Here is the proof: 48 Sym.Ops. (with inversion). However, during vc-relax it breaks the symmetry. Proof goes here: 0.000000000 0.000000000 0.000000000 0.250189867 0.250189867 0.250189867 0.000000000 0.250189689 0.250189689 0.250189689 0.000000000 0.250189689 0.250189689 0.250189689 0.000000000 0.500379494 0.000000000 0.000000000 0.750569121 0.250189867 0.250189867 0.500379494 0.250189728 0.250189728 0.750569299 0.000000000 0.250189689 0.750569299 0.250189689 0.000000000 0.000000000 0.500379494 0.000000000 0.250189867 0.750569121 0.250189867 0.000000000 0.750569299 0.250189689 0.250189728 0.500379494 0.250189728 0.250189689 0.750569299 0.000000000 0.500379494 0.500379494 0.000000000 0.750569121 0.750569121 0.250189867 0.500379494 0.750569260 0.250189728 0.750569260 0.500379494 0.250189728 0.750569299 0.750569299 0.000000000 0.000000000 0.000000000 0.500379494 0.250189867 0.250189867 0.750569121 0.000000000 0.250189689 0.750569299 0.250189689 0.000000000 0.750569299 0.250189728 0.250189728 0.500379494 0.500379494 0.000000000 0.500379494 0.750569121 0.250189867 0.750569121 0.500379494 0.250189728 0.750569260 0.750569299 0.000000000 0.750569299 0.750569260 0.250189728 0.500379494 0.000000000 0.500379494 0.500379494 0.250189867 0.750569121 0.750569121 0.000000000 0.750569299 0.750569299 0.250189728 0.500379494 0.750569260 0.250189728 0.750569260 0.500379494 0.500379494 0.500379494 0.500379494 0.750569121 0.750569121 0.750569121 0.500379494 0.750569260 0.750569260 0.750569260 0.500379494 0.750569260 0.750569260 0.750569260 0.500379494 Is this possible to keep symmetry of the initial system conserved during vc-relax with BFGS ? Input file: &control calculation='vc-relax' restart_mode='from_scratch', prefix='pbmno', tstress = .true. tprnfor = .true. wf_collect=.true. verbosity='high' etot_conv_thr=1.0D-5, forc_conv_thr=1.0D-4, / &system ibrav = 1, nat = 40, ntyp=3, celldm(1)=20.70 nosym=.FALSE. ecutwfc = 30.0, ecutrho = 240.0, occupations='smearing', smearing='fd', degauss=0.005d0, nspin=2 starting_magnetization(2)=1.0, / &electrons diagonalization = 'david' conv_thr = 1.0d-9 mixing_beta = 0.7 / &ions / &cell / ATOMIC_SPECIES Pb 1.0 Pb.UPF Mn 1.0 Mn.UPF O 1.0 O.UPF ATOMIC_POSITIONS (alat) Pb 0.00 0.00 0.00 Mn 0.25 0.25 0.25 O 0.00 0.25 0.25 O 0.25 0.00 0.25 O 0.25 0.25 0.00 Pb 0.50 0.00 0.00 Mn 0.75 0.25 0.25 O 0.50 0.25 0.25 O 0.75 0.00 0.25 O 0.75 0.25 0.00 Pb 0.00 0.50 0.00 Mn 0.25 0.75 0.25 O 0.00 0.75 0.25 O 0.25 0.50 0.25 O 0.25 0.75 0.00 Pb 0.50 0.50 0.00 Mn 0.75 0.75 0.25 O 0.50 0.75 0.25 O 0.75 0.50 0.25 O 0.75 0.75 0.00 Pb 0.00 0.00 0.50 Mn 0.25 0.25 0.75 O 0.00 0.25 0.75 O 0.25 0.00 0.75 O 0.25 0.25 0.50 Pb 0.50 0.00 0.50 Mn 0.75 0.25 0.75 O 0.50 0.25 0.75 O 0.75 0.00 0.75 O 0.75 0.25 0.50 Pb 0.00 0.50 0.50 Mn 0.25 0.75 0.75 O 0.00 0.75 0.75 O 0.25 0.50 0.75 O 0.25 0.75 0.50 Pb 0.50 0.50 0.50 Mn 0.75 0.75 0.75 O 0.50 0.75 0.75 O 0.75 0.50 0.75 O 0.75 0.75 0.50 K_POINTS {automatic} 2 2 2 0 0 0 Thanking you and with my best regards, Srijan K CCMT Indian Institute of Science India 560012 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110214/55419f44/attachment.htm From davide.sangalli at gmail.com Mon Feb 14 12:18:37 2011 From: davide.sangalli at gmail.com (Davide Sangalli) Date: Mon, 14 Feb 2011 12:18:37 +0100 Subject: [Pw_forum] k-points parallelization in pwscf 4.2.1 In-Reply-To: <4D59054E.7030302@democritos.it> References: <4D58FCE8.3040002@gmail.com> <4D59054E.7030302@democritos.it> Message-ID: <4D590F8D.8000500@gmail.com> Thank you for the answer. I did a check to be sure, but these jobs use only few MB of memory. The serial run uses just 2.5% of my node memory (so around 15% for the run on 6 CPUs). It does not seems to me that this could be the problem. Moreover in the fft parallelization the memory was not distributed neither. Is it possible that pwscf is not properly compiled? Is there any other check that you would suggest to do? Best regards, Davide ************************************* Largest allocated arrays est. size (Mb) dimensions Kohn-Sham Wavefunctions 5.68 Mb ( 6422, 58) NL pseudopotentials 13.33 Mb ( 6422, 136) Each V/rho on FFT grid 7.81 Mb ( 512000) Each G-vector array 1.76 Mb ( 230753) G-vector shells 0.09 Mb ( 12319) Largest temporary arrays est. size (Mb) dimensions Auxiliary wavefunctions 22.73 Mb ( 6422, 232) Each subspace H/S matrix 0.82 Mb ( 232, 232) Each matrix 0.12 Mb ( 136, 58) Arrays for rho mixing 62.50 Mb ( 512000, 8) writing wfc files to a dedicated directory On 02/14/2011 11:34 AM, Paolo Giannozzi wrote: > Davide Sangalli wrote: > >> What could my problem be? > the only reason I can think of is that k-point parallelization doesn't > (and cannot) distribute memory, so the total memory requirement will > be npools*(size of serial execution). If you run on the same node six > instances of a large executable, memory conflicts may slow down more > than parallelization can speed up. > > P. From wonvein at gmail.com Mon Feb 14 12:23:26 2011 From: wonvein at gmail.com (WANG Wei) Date: Mon, 14 Feb 2011 20:23:26 +0900 Subject: [Pw_forum] k-points parallelization in pwscf 4.2.1 In-Reply-To: <4D590EBE.3030204@gmail.com> References: <4D58FCE8.3040002@gmail.com> <4D59054E.7030302@democritos.it> <4D590EBE.3030204@gmail.com> Message-ID: Dear Davide, Thank you for your reply. Best Regards, WANG -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110214/2b92e2ff/attachment.htm From Lorenzo.Paulatto at impmc.upmc.fr Mon Feb 14 12:26:11 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Mon, 14 Feb 2011 12:26:11 +0100 Subject: [Pw_forum] k-points parallelization in pwscf 4.2.1 In-Reply-To: <4D590EBE.3030204@gmail.com> References: <4D58FCE8.3040002@gmail.com> <4D59054E.7030302@democritos.it> <4D590EBE.3030204@gmail.com> Message-ID: On Mon, 14 Feb 2011 12:15:10 +0100, Davide Sangalli wrote: > (if properly compiled) I wish to stress that if the code is NOT properly compiled this will probably cause a mysterious input/output error (because two instances of pw.x running with the same input will try to read/write the same files grossly at the same time). -- Lorenzo Paulatto (IdR) IMPMC - CNRS UMR 7590 & Universit? P&M Curie T23-C13/23-5e27 - 4 place Jussieu - 75252 Paris Cedex5 phone: +33 (0)144 27 5211 www: http://www-int.impmc.upmc.fr/~paulatto/ From pcj994 at bham.ac.uk Mon Feb 14 12:33:30 2011 From: pcj994 at bham.ac.uk (Paul Jennings) Date: Mon, 14 Feb 2011 11:33:30 +0000 Subject: [Pw_forum] DOS for Molecules and clusters Message-ID: <4D59130A.9080704@bham.ac.uk> Dear PWSCF Users! Is it possible to do a Gamma-point DOS and/or pDOS calculation? I have performed DOS and pDOS calculations for solid Ni and it seems to work well for a 12 12 12 0 0 0 k-point grid. Now I try to calculate the DOS at the Gamma point for a small cluster say Au6. By performing the same calculations ( scf nscf) the dos.x module runs without a problem but only produces a empty output file. Best wishes Paul Here are my input files: !! &CONTROL calculation = "nscf", !!or!! "scf", prefix = "Au6_dos", pseudo_dir = " . ", outdir = "X", / &SYSTEM ibrav = 0, nat = 6, ntyp = 1, ecutwfc = 40.D0, occupations = "smearing", smearing = "mp", degauss = 0.005, / &ELECTRONS conv_thr = 1.D-6, mixing_beta = 0.5D0, / &IONS / CELL_PARAMETERS cubic 25.55 0.00 0.00 0.00 25.55 0.00 0.00 0.00 25.55 ATOMIC_SPECIES Au 196.97 Au.pbe-nd-rrkjus.UPF ATOMIC_POSITIONS {bohr} Au 7.776772195 10.628086166 12.775000000 Au 12.775000000 10.457400704 12.775000000 Au 17.773227805 10.628086166 12.775000000 Au 10.128705068 15.041410031 12.775000000 Au 15.421294932 15.041410031 12.775000000 Au 12.775000000 19.284606902 12.775000000 K_POINTS {Gamma} !! &inputpp outdir="/scratch/heiless/" prefix="Au6_dos" fildos="Au6.dos" Emin=1.0, Emax=25.0, DeltaE=0.1 / -- ****************************************************** Paul Jennings Centre for Hydrogen and Fuel Cell Research PEMFC Research group School of Chemical Engineering The University of Birmingham Edgbaston, Birmingham B15 2TT (U.K.) E: PCJ994 at bham.ac.uk T: 07816644583 W: www.fuelcells.bham.ac.uk ****************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110214/4bfa0f4f/attachment.htm From sclauzer at sissa.it Mon Feb 14 13:42:43 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 14 Feb 2011 13:42:43 +0100 Subject: [Pw_forum] A question on atomic magnetic moments In-Reply-To: References: Message-ID: <00A49709-A6A9-4E18-B47E-AFB94204E9F3@sissa.it> Dear Srijan, First, why do you post you request within an existing thread that has nothing to do with your problem? Where is the proof that the final symmetry is different from the initial one? I believe that the relaxation procedure will keep the same initial symmetry since forces and stress tensor are symmetrized according to it. I think that you should not pay attention to differences of the order of 10^-9, since there will be always some sort of numerical/roundoff errors in the calculation. GS Il giorno 14/feb/2011, alle ore 12.15, Srijan Kumar Saha ha scritto: > > Dear QE users, > > QE is able to find the correct symmetry for the input file, added at the end of this email. > Here is the proof: > 48 Sym.Ops. (with inversion). > > However, during vc-relax it breaks the symmetry. > Proof goes here: > 0.000000000 0.000000000 0.000000000 > 0.250189867 0.250189867 0.250189867 > 0.000000000 0.250189689 0.250189689 > 0.250189689 0.000000000 0.250189689 > 0.250189689 0.250189689 0.000000000 > 0.500379494 0.000000000 0.000000000 > 0.750569121 0.250189867 0.250189867 > 0.500379494 0.250189728 0.250189728 > 0.750569299 0.000000000 0.250189689 > 0.750569299 0.250189689 0.000000000 > 0.000000000 0.500379494 0.000000000 > 0.250189867 0.750569121 0.250189867 > 0.000000000 0.750569299 0.250189689 > 0.250189728 0.500379494 0.250189728 > 0.250189689 0.750569299 0.000000000 > 0.500379494 0.500379494 0.000000000 > 0.750569121 0.750569121 0.250189867 > 0.500379494 0.750569260 0.250189728 > 0.750569260 0.500379494 0.250189728 > 0.750569299 0.750569299 0.000000000 > 0.000000000 0.000000000 0.500379494 > 0.250189867 0.250189867 0.750569121 > 0.000000000 0.250189689 0.750569299 > 0.250189689 0.000000000 0.750569299 > 0.250189728 0.250189728 0.500379494 > 0.500379494 0.000000000 0.500379494 > 0.750569121 0.250189867 0.750569121 > 0.500379494 0.250189728 0.750569260 > 0.750569299 0.000000000 0.750569299 > 0.750569260 0.250189728 0.500379494 > 0.000000000 0.500379494 0.500379494 > 0.250189867 0.750569121 0.750569121 > 0.000000000 0.750569299 0.750569299 > 0.250189728 0.500379494 0.750569260 > 0.250189728 0.750569260 0.500379494 > 0.500379494 0.500379494 0.500379494 > 0.750569121 0.750569121 0.750569121 > 0.500379494 0.750569260 0.750569260 > 0.750569260 0.500379494 0.750569260 > 0.750569260 0.750569260 0.500379494 > > > Is this possible to keep symmetry of the initial system conserved during vc-relax with BFGS ? > > Input file: > &control > calculation='vc-relax' > restart_mode='from_scratch', > prefix='pbmno', > tstress = .true. > tprnfor = .true. > wf_collect=.true. > verbosity='high' > etot_conv_thr=1.0D-5, > forc_conv_thr=1.0D-4, > / > &system > ibrav = 1, > nat = 40, > ntyp=3, > celldm(1)=20.70 > nosym=.FALSE. > ecutwfc = 30.0, > ecutrho = 240.0, > occupations='smearing', > smearing='fd', > degauss=0.005d0, > nspin=2 > starting_magnetization(2)=1.0, > / > &electrons > diagonalization = 'david' > conv_thr = 1.0d-9 > mixing_beta = 0.7 > / > &ions > / > &cell > / > ATOMIC_SPECIES > Pb 1.0 Pb.UPF > Mn 1.0 Mn.UPF > O 1.0 O.UPF > ATOMIC_POSITIONS (alat) > Pb 0.00 0.00 0.00 > Mn 0.25 0.25 0.25 > O 0.00 0.25 0.25 > O 0.25 0.00 0.25 > O 0.25 0.25 0.00 > Pb 0.50 0.00 0.00 > Mn 0.75 0.25 0.25 > O 0.50 0.25 0.25 > O 0.75 0.00 0.25 > O 0.75 0.25 0.00 > Pb 0.00 0.50 0.00 > Mn 0.25 0.75 0.25 > O 0.00 0.75 0.25 > O 0.25 0.50 0.25 > O 0.25 0.75 0.00 > Pb 0.50 0.50 0.00 > Mn 0.75 0.75 0.25 > O 0.50 0.75 0.25 > O 0.75 0.50 0.25 > O 0.75 0.75 0.00 > Pb 0.00 0.00 0.50 > Mn 0.25 0.25 0.75 > O 0.00 0.25 0.75 > O 0.25 0.00 0.75 > O 0.25 0.25 0.50 > Pb 0.50 0.00 0.50 > Mn 0.75 0.25 0.75 > O 0.50 0.25 0.75 > O 0.75 0.00 0.75 > O 0.75 0.25 0.50 > Pb 0.00 0.50 0.50 > Mn 0.25 0.75 0.75 > O 0.00 0.75 0.75 > O 0.25 0.50 0.75 > O 0.25 0.75 0.50 > Pb 0.50 0.50 0.50 > Mn 0.75 0.75 0.75 > O 0.50 0.75 0.75 > O 0.75 0.50 0.75 > O 0.75 0.75 0.50 > K_POINTS {automatic} > 2 2 2 0 0 0 > > Thanking you and with my best regards, > Srijan K > CCMT > Indian Institute of Science > India 560012 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110214/8e777cef/attachment.htm From srijan.india at gmail.com Mon Feb 14 14:18:34 2011 From: srijan.india at gmail.com (Srijan Kumar Saha) Date: Mon, 14 Feb 2011 14:18:34 +0100 Subject: [Pw_forum] vc-relax with BFGS Message-ID: Dear Gabriele, Thanks a lot for your quick response. > First, why do you post you request within an existing thread that has nothing to do with your problem? < Sorry, for this mistake. It was an oversight on my side. > Where is the proof that the final symmetry is different from the initial one? < Here goes more direct proof: Initial symmetry : 48 Sym.Ops. (with inversion). Final symmetry : 6 Sym.Ops. (no inversion). > I think that you should not pay attention to differences of the order of 10^-9, < If we compare the final & initial positions given in my previous email, then we can see that the differences are quite large. These differences go away if we use Wentzcovitch Damped Dynamics, instead of BFGS. However, Damped Dynamics stops without convergence (50 iterations completed, stopping). Since this dynamics converge very slowly, I would like to know whether VC-RELAX with BFGS has the above capability of respecting the symmetry. Thanks & regards, Srijan K. CCMT Indian Institute of Science India 560012 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110214/38c1bf32/attachment-0001.htm From sclauzer at sissa.it Mon Feb 14 14:49:20 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 14 Feb 2011 14:49:20 +0100 Subject: [Pw_forum] k-points parallelization in pwscf 4.2.1 In-Reply-To: <4D590F8D.8000500@gmail.com> References: <4D58FCE8.3040002@gmail.com> <4D59054E.7030302@democritos.it> <4D590F8D.8000500@gmail.com> Message-ID: <50807287-9445-4387-890A-C72DDD91F789@sissa.it> Dear Davide, it might be a memory-contention problem, since CPU cache sizes are of the order of a few MB. Please provide the detailed timings at the end of the runs (that are the first thing one should look at in order to interpret these kind of speedup tests). Next time please take a few seconds to sign your post using full name and affiliation. Regards, GS Il giorno 14/feb/2011, alle ore 12.18, Davide Sangalli ha scritto: > Thank you for the answer. > > I did a check to be sure, but these jobs use only few MB of memory. > The serial run uses just 2.5% of my node memory (so around 15% for the > run on 6 CPUs). > It does not seems to me that this could be the problem. > Moreover in the fft parallelization the memory was not distributed neither. > > Is it possible that pwscf is not properly compiled? > Is there any other check that you would suggest to do? > > Best regards, > Davide > > ************************************* > Largest allocated arrays est. size (Mb) dimensions > Kohn-Sham Wavefunctions 5.68 Mb ( 6422, 58) > NL pseudopotentials 13.33 Mb ( 6422, 136) > Each V/rho on FFT grid 7.81 Mb ( 512000) > Each G-vector array 1.76 Mb ( 230753) > G-vector shells 0.09 Mb ( 12319) > Largest temporary arrays est. size (Mb) dimensions > Auxiliary wavefunctions 22.73 Mb ( 6422, 232) > Each subspace H/S matrix 0.82 Mb ( 232, 232) > Each matrix 0.12 Mb ( 136, 58) > Arrays for rho mixing 62.50 Mb ( 512000, 8) > writing wfc files to a dedicated directory > > > On 02/14/2011 11:34 AM, Paolo Giannozzi wrote: >> Davide Sangalli wrote: >> >>> What could my problem be? >> the only reason I can think of is that k-point parallelization doesn't >> (and cannot) distribute memory, so the total memory requirement will >> be npools*(size of serial execution). If you run on the same node six >> instances of a large executable, memory conflicts may slow down more >> than parallelization can speed up. >> >> P. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110214/d15028b2/attachment.htm From sclauzer at sissa.it Mon Feb 14 15:18:15 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 14 Feb 2011 15:18:15 +0100 Subject: [Pw_forum] vc-relax with BFGS In-Reply-To: References: Message-ID: <68F299F3-4727-4ECE-8742-747311CC7544@sissa.it> Il giorno 14/feb/2011, alle ore 14.18, Srijan Kumar Saha ha scritto: > > > Where is the proof that the final symmetry is different from the initial one? < > > Here goes more direct proof: > > Initial symmetry : 48 Sym.Ops. (with inversion). > Final symmetry : 6 Sym.Ops. (no inversion). Where did you get this information from? Was it printed by the code? I never saw a printout of the "Final symmetry", but maybe I am wrong and the code computes and prints it. Which version of the code are you using? > > > I think that you should not pay attention to differences of the order of 10^-9, < > > If we compare the final & initial positions given in my previous email, then we can see that > the differences are quite large. From your previous email it looks to me that the atoms are still in the original arrangement with cubic symmetry. I can guess that the volume of the cell has increased a bit (less than 1%) and so the atomic positions, which are always expressed in terms of the INITIAL celldm(1), will scale accordingly on the final output. The largest deviations I can spot out are below 10^-8. Moreover, I don't understand why you want to perform such kind of expensive calculation on a supercell. Have you tried with the fundamental unit cell first? GS > These differences go away if we use > Wentzcovitch Damped Dynamics, instead of BFGS. However, Damped Dynamics stops > without convergence (50 iterations completed, stopping). Since this dynamics converge very > slowly, I would like to know whether VC-RELAX with BFGS has the above capability of respecting the > symmetry. > > Thanks & regards, > Srijan K. > CCMT > Indian Institute of Science > India 560012 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110214/9b1511a5/attachment.htm From srijan.india at gmail.com Mon Feb 14 15:54:03 2011 From: srijan.india at gmail.com (Srijan Kumar Saha) Date: Mon, 14 Feb 2011 15:54:03 +0100 Subject: [Pw_forum] vc-relax with BFGS In-Reply-To: <68F299F3-4727-4ECE-8742-747311CC7544@sissa.it> References: <68F299F3-4727-4ECE-8742-747311CC7544@sissa.it> Message-ID: Dear Gabriele, Thank you very much for your kind reply. > Where did you get this information from? Was it printed by the code? I never saw a printout of the "Final symmetry", but maybe I am wrong and the code computes and prints it. Which version of the code are you using? I am using the 4.2 version of the QE code and I have obtained the Final symmetry simply feeding back the final positions and final cell parameters in a brand new relax calculation. Then, in the beginning of this new run, the QE prints the symmetry again. Moreover, I have cross-checked the above symmetry with another symmetry tool called ISOTROPY. Thanks and regards, Srijan K. CCMT Indian Institute of Science India 560012 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110214/9382f6ef/attachment.htm From davide.sangalli at gmail.com Mon Feb 14 16:21:30 2011 From: davide.sangalli at gmail.com (Davide Sangalli) Date: Mon, 14 Feb 2011 16:21:30 +0100 Subject: [Pw_forum] k-points parallelization in pwscf 4.2.1 In-Reply-To: <50807287-9445-4387-890A-C72DDD91F789@sissa.it> References: <4D58FCE8.3040002@gmail.com> <4D59054E.7030302@democritos.it> <4D590F8D.8000500@gmail.com> <50807287-9445-4387-890A-C72DDD91F789@sissa.it> Message-ID: <4D59487A.7000900@gmail.com> An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110214/58563f17/attachment-0001.htm From Lorenzo.Paulatto at impmc.upmc.fr Mon Feb 14 16:41:29 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Mon, 14 Feb 2011 16:41:29 +0100 Subject: [Pw_forum] vc-relax with BFGS In-Reply-To: References: <68F299F3-4727-4ECE-8742-747311CC7544@sissa.it> Message-ID: Could you please post both complete outputs? In private, if you prefer On Mon, 14 Feb 2011 15:54:03 +0100, Srijan Kumar Saha wrote: > I am using the 4.2 version of the QE code and I have obtained the Final > symmetry > simply feeding back the final positions and final cell parameters in a > brand > new relax calculation. > Then, in the beginning of this new run, the QE prints the symmetry again. > Moreover, I have cross-checked the above symmetry with another symmetry > tool > called ISOTROPY. > > Thanks and regards, > Srijan K. > CCMT > Indian Institute of Science > India 560012 -- Lorenzo Paulatto (IdR) IMPMC - CNRS UMR 7590 & Universit? P&M Curie T23-C13/23-5e27 - 4 place Jussieu - 75252 Paris Cedex5 phone: +33 (0)144 27 5211 www: http://www-int.impmc.upmc.fr/~paulatto/ From prayerz.omo at gmail.com Mon Feb 14 18:03:43 2011 From: prayerz.omo at gmail.com (Omololu Akin-Ojo) Date: Mon, 14 Feb 2011 18:03:43 +0100 Subject: [Pw_forum] DOS for Molecules and clusters In-Reply-To: <4D59130A.9080704@bham.ac.uk> References: <4D59130A.9080704@bham.ac.uk> Message-ID: Check Emin & Emax in your dos input; maybe they are outside the range of the energy levels of the cluster. o. On Mon, Feb 14, 2011 at 12:33 PM, Paul Jennings wrote: > Dear PWSCF Users! > > Is it possible to do a Gamma-point DOS and/or pDOS calculation? I have > performed DOS and pDOS calculations for solid Ni and it seems to work well > for a 12 12 12 0 0 0 k-point grid. > Now I try to calculate the DOS at the Gamma point for a small cluster say > Au6. By performing the same calculations ( scf nscf) the dos.x module runs > without a problem but only > produces a empty output file. > > Best wishes > > Paul > > Here are my input files: > !! > &CONTROL > calculation = "nscf", !!or!! "scf", > prefix = "Au6_dos", > pseudo_dir = " . ", > outdir = "X", > / > &SYSTEM > ibrav = 0, > nat = 6, > ntyp = 1, > ecutwfc = 40.D0, > occupations = "smearing", > smearing = "mp", > degauss = 0.005, > / > &ELECTRONS > conv_thr = 1.D-6, > mixing_beta = 0.5D0, > / > &IONS > / > CELL_PARAMETERS cubic > 25.55 0.00 0.00 > 0.00 25.55 0.00 > 0.00 0.00 25.55 > ATOMIC_SPECIES > Au 196.97 Au.pbe-nd-rrkjus.UPF > ATOMIC_POSITIONS {bohr} > Au 7.776772195 10.628086166 12.775000000 > Au 12.775000000 10.457400704 12.775000000 > Au 17.773227805 10.628086166 12.775000000 > Au 10.128705068 15.041410031 12.775000000 > Au 15.421294932 15.041410031 12.775000000 > Au 12.775000000 19.284606902 12.775000000 > K_POINTS {Gamma} > !! > &inputpp > outdir="/scratch/heiless/" > prefix="Au6_dos" > fildos="Au6.dos" > Emin=1.0, Emax=25.0, DeltaE=0.1 > / > > -- > ****************************************************** > Paul Jennings > > Centre for Hydrogen and Fuel Cell Research > PEMFC Research group > School of Chemical Engineering > The University of Birmingham > Edgbaston, Birmingham B15 2TT (U.K.) > > E: PCJ994 at bham.ac.uk > T: 07816644583 > W: www.fuelcells.bham.ac.uk > > ****************************************************** > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ***************** Seek GOD! ************* From sclauzer at sissa.it Mon Feb 14 18:13:30 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 14 Feb 2011 18:13:30 +0100 Subject: [Pw_forum] k-points parallelization in pwscf 4.2.1 In-Reply-To: <4D59487A.7000900@gmail.com> References: <4D58FCE8.3040002@gmail.com> <4D59054E.7030302@democritos.it> <4D590F8D.8000500@gmail.com> <50807287-9445-4387-890A-C72DDD91F789@sissa.it> <4D59487A.7000900@gmail.com> Message-ID: <4D5962BA.6050006@sissa.it> On 02/14/2011 04:21 PM, Davide Sangalli wrote: > OK. I think it could be a "memory - cache" related problem. > > I did the same test with lower cut-off (still 6 CPUs). > Now my serial run used 0.2 % of the memory and my parallel around 1.3% > > The parallelization over the fft grid is still faster, but the kpts > parallelization now is faster than the serial run. > Serial: PWSCF : 1m 3.14s CPU > time, 1m 4.05s WALL time > fft grid parallelization: PWSCF : 15.46s CPU time, > 16.36s WALL time > kpts parallelization: PWSCF : 35.98s CPU time, > 36.47s WALL time > > Thank you and best regards, > Davide Maybe I didn't explain myself. I was referring to the complete timings, also with the separate contribution from all the subroutines. GS > > > On 02/14/2011 02:49 PM, Gabriele Sclauzero wrote: >> Dear Davide, >> >> it might be a memory-contention problem, since CPU cache sizes are >> of the order of a few MB. Please provide the detailed timings at the >> end of the runs (that are the first thing one should look at in order >> to interpret these kind of speedup tests). >> >> Next time please take a few seconds to sign your post using full name >> and affiliation. >> >> Regards, >> >> GS >> >> >> Il giorno 14/feb/2011, alle ore 12.18, Davide Sangalli ha scritto: >> >>> Thank you for the answer. >>> >>> I did a check to be sure, but these jobs use only few MB of memory. >>> The serial run uses just 2.5% of my node memory (so around 15% for the >>> run on 6 CPUs). >>> It does not seems to me that this could be the problem. >>> Moreover in the fft parallelization the memory was not distributed >>> neither. >>> >>> Is it possible that pwscf is not properly compiled? >>> Is there any other check that you would suggest to do? >>> >>> Best regards, >>> Davide >>> >>> ************************************* >>> Largest allocated arrays est. size (Mb) dimensions >>> Kohn-Sham Wavefunctions 5.68 Mb ( 6422, 58) >>> NL pseudopotentials 13.33 Mb ( 6422, 136) >>> Each V/rho on FFT grid 7.81 Mb ( 512000) >>> Each G-vector array 1.76 Mb ( 230753) >>> G-vector shells 0.09 Mb ( 12319) >>> Largest temporary arrays est. size (Mb) dimensions >>> Auxiliary wavefunctions 22.73 Mb ( 6422, 232) >>> Each subspace H/S matrix 0.82 Mb ( 232, 232) >>> Each matrix 0.12 Mb ( 136, 58) >>> Arrays for rho mixing 62.50 Mb ( 512000, 8) >>> writing wfc files to a dedicated directory >>> >>> >>> On 02/14/2011 11:34 AM, Paolo Giannozzi wrote: >>>> Davide Sangalli wrote: >>>> >>>>> What could my problem be? >>>> the only reason I can think of is that k-point parallelization doesn't >>>> (and cannot) distribute memory, so the total memory requirement will >>>> be npools*(size of serial execution). If you run on the same node six >>>> instances of a large executable, memory conflicts may slow down more >>>> than parallelization can speed up. >>>> >>>> P. >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> ? Gabriele Sclauzero, EPFL SB ITP CSEA >> / PH H2 462, Station 3, CH-1015 Lausanne/ >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > Davide Sangalli > MDM labs, IMM, CNR. > Agrate (MI) Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110214/6d7a75c2/attachment.htm From giannozz at democritos.it Mon Feb 14 18:22:24 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 14 Feb 2011 18:22:24 +0100 Subject: [Pw_forum] k-points parallelization in pwscf 4.2.1 In-Reply-To: <4D590F8D.8000500@gmail.com> References: <4D58FCE8.3040002@gmail.com> <4D59054E.7030302@democritos.it> <4D590F8D.8000500@gmail.com> Message-ID: <4D5964D0.6090400@democritos.it> Also notice that parallelization on k-points has (in principle) a linear speedup on the diagonalization of H and related operations depending on the number of k-points, but not for other operations depending upon the charge density such as calculation of V[n(r)]. The latter are typically small in comparison with the former, but it depends a lot upon the specific system. FFT parallelization distributes both calculations (and yes, it distributes most memory, I stand by my statement) P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From sclauzer at sissa.it Mon Feb 14 18:46:10 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 14 Feb 2011 18:46:10 +0100 Subject: [Pw_forum] vc-relax with BFGS In-Reply-To: References: <68F299F3-4727-4ECE-8742-747311CC7544@sissa.it> Message-ID: <4D596A62.6000609@sissa.it> On 02/14/2011 03:54 PM, Srijan Kumar Saha wrote: > > > Dear Gabriele, > > Thank you very much for your kind reply. > > > Where did you get this information from? Was it printed by the code? > I never saw a printout of the "Final symmetry", but maybe I am wrong > and the code computes and prints it. Which version of the code are you > using? > > I am using the 4.2 version of the QE code and I have obtained the > Final symmetry > simply feeding back the final positions and final cell parameters in a > brand new relax calculation. > Then, in the beginning of this new run, the QE prints the symmetry again. OK, but how are you building the new input? If you want to use the atomic positions as supplied in your previous email e.g. 0.000000000 0.000000000 0.000000000 0.250189867 0.250189867 0.250189867 0.000000000 0.250189689 0.250189689 0.250189689 0.000000000 0.250189689 0.250189689 0.250189689 0.000000000 ... you have to use CELL_PARAMETERS as supplied from the output of vc-relax, and ibrav =0 For me it works using: CELL_PARAMETERS 1.000758849 0.0 0.0 0.0 1.000758849 0.0 0.0 0.0 1.000758849 guessing the celldm expansion from your final positions. Another solution would be to use the final celldm(1) and rescale the atomic positions. BTW, during relaxations the code checks at each step if the initial symmetry is conserved. If the symmetry had changed during the run the code would have stopped with an error message. Regards, GS > Moreover, I have cross-checked the above symmetry with another > symmetry tool called ISOTROPY. > > Thanks and regards, > Srijan K. > CCMT > Indian Institute of Science > India 560012 > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110214/99e3e1f8/attachment-0001.htm From claudial.81 at gmail.com Mon Feb 14 18:57:04 2011 From: claudial.81 at gmail.com (Claudia Loyola) Date: Mon, 14 Feb 2011 11:57:04 -0600 Subject: [Pw_forum] Wrong ELF values In-Reply-To: References: <4D5263FD.90000@sissa.it> Message-ID: Dear all, well I think that I am really missing something because I don't understand what is the pp file that you mentioned. I am doing ELF in planes, so cube file do not work here. I check the *.out file but with the xcrysden output_format, I mean I have 3 files *.out, *.charge and *.xsf. In the *.out file I have, of course, the same range that the visualization part (*.xsf). When you told me about pp file, I really did not understand what you mean by this, because I know that with the pp.x executable I can obtain 3 different output_format files: contour.x (I made, and I obtained this range: -0.173535, 0.879845, for plotting with contour.x executable), plotrho (I made, and I obtained this range:-0.173535, 0.879845 for plotting with plotrho.x executable) and finally XCRYSDEN. I am sure that you do not mean pseudopotential file with pp file... Well, this is one of the input file: &inputpp prefix = 'Ba-apt' , outdir = './restore' , filplot = 'Ba38_33_10.charge' , plot_num= 8 , / &plot nfile = 1 , filepp(1) = 'Ba38_33_10.charge' , weight(1) = 1.0 , iflag = 2 , output_format = 3 , fileout = 'ba.rho38_33_10.xsf' , x0(1) =0.0, x0(2)=0.0, x0(3) = 10.602, e1(1) =38.218, e1(2)=0.0, e1(3) = 0.0, e2(1) =0.0, e2(2)=33.108, e2(3) = 0.0, nx=100, ny=100 / So for the output_format I used: 1, 2, 3 and of course the fileout with different names.. Whit this I obtain *.charge, output_format_file_name and *.out (from pp.x). Please I really want understand what I am doing wrong or what I'm not understanding... :( if you can be more specific I really appreciate!! :D Thanks in advance, Claudia Loyola On Thu, Feb 10, 2011 at 1:55 AM, Giovanni La Penna wrote: > > On Wed, 9 Feb 2011, Claudia Loyola wrote: > >> first I obtained: [-0.2092:1.2504] and now [-0.1951:0.981], I ran the >> same >> scf and elf input file, but in different machines. >> The range is the "thermometer" that shows xcrysden?, right? maybe I am >> missing something... :( >> > > Please, check the data in the file (pp or cube), because > the range provided by visualization packages is due to interpolations. > > Giovanni > > ============================================================ > Giovanni La Penna - National research council (Cnr) > Institute for chemistry of organo-metallic compounds (Iccom) > via Madonna del Piano 10, > I-50019 Sesto Fiorentino, Firenze, Italy > tel.: +39 055 522-5264, fax: +39 055 522-5203 > e-mail: glapenna at iccom.cnr.it - http://www.iccom.cnr.it/lapenna > skype: giovannilapenna > ============================================================ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Claudia Loyola Canales Postdoc in Computational Physics Iowa State University Iowa, USA http://www.lpmd.cl/claudial http://www.lpmd.cl http://cosmic.mse.iastate.edu/ http://www.gnm.cl -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110214/2b44343e/attachment.htm From giannozz at democritos.it Mon Feb 14 19:24:54 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 14 Feb 2011 19:24:54 +0100 Subject: [Pw_forum] Wrong ELF values In-Reply-To: References: <4D5263FD.90000@sissa.it> Message-ID: <887CD207-034D-4CC2-AB91-F5617FDE3DAE@democritos.it> On Feb 14, 2011, at 18:57 , Claudia Loyola wrote: > Well, this is one of the input file: not very useful without the scf part > filplot = 'Ba38_33_10.charge' > filepp(1) = 'Ba38_33_10.charge' this is the "pp" file: the one containing raw data to be plotted P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From srijan.india at gmail.com Mon Feb 14 20:21:53 2011 From: srijan.india at gmail.com (Srijan Kumar Saha) Date: Mon, 14 Feb 2011 20:21:53 +0100 Subject: [Pw_forum] vc-relax with BFGS In-Reply-To: <4D596A62.6000609@sissa.it> References: <68F299F3-4727-4ECE-8742-747311CC7544@sissa.it> <4D596A62.6000609@sissa.it> Message-ID: Dear Gabriele, > Another solution would be to use the final celldm(1) and rescale the atomic positions. I did not rescale the atomic positions simply thinking that it has been already done by QE. Sorry for this. After rescaling, symmetry is OK. Thank you very much once again. With best regards, Srijan K. CCMT Indian Institute of Science India 560012 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110214/62b17bc5/attachment.htm From lli14 at binghamton.edu Mon Feb 14 22:44:35 2011 From: lli14 at binghamton.edu (Liang Li) Date: Mon, 14 Feb 2011 16:44:35 -0500 Subject: [Pw_forum] davcio error while running pdos calculation: davcio error # 10 error while reading from file Message-ID: Dear QE users: A davcio error came up when I was doing Lowdin analysis using projwfc.x. I first carried out a scf calculation followed by nscf with a extended k-mesh and everything went smoothly. But when it comes to pdos calculation, the program crashed and kept saying the following error message: Calling projwave .... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from davcio : error # 10 error while reading from file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I understand that davcio error is usually related to an I/O problem, but I do have appropriate permissions over all necessary files, and there is plenty of space on the disk. There was no problem when I was running example08 (the pdos example come with the PWscf package), so probably there are some problems caused by my own system. This problem is killing me these days, and I will highly appreciate it if someone would take a look at it. By the way, I am taking care of a Cu-O system with a total atom number of 42, and I am using 4.2 version (parallel) PWscf. Thanks a ton! Liang Li PhD student Dept. of Mechanical Engineering State university of New York@ Binghamton NY, USA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110214/21beb3f6/attachment.htm From giannozz at democritos.it Tue Feb 15 08:36:03 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 15 Feb 2011 08:36:03 +0100 Subject: [Pw_forum] davcio error while running pdos calculation: davcio error # 10 error while reading from file In-Reply-To: References: Message-ID: <625277D1-47FF-4C57-8C06-FF581BC08109@democritos.it> On Feb 14, 2011, at 22:44 , Liang Li wrote: > I will highly appreciate it if someone would take a look at it. a look at...what? the error message says that either a file that should be there is not there, or it doesn't have the correct size. In 99.9999% of the cases, either you did not specify the correct location of the files (variables prefix and outdir) or you run the pDOS calculation on a number of processors that is not the same used to produce the files, without specifying the appropriate option (wf_collect) P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From degironc at sissa.it Tue Feb 15 09:01:45 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 15 Feb 2011 09:01:45 +0100 Subject: [Pw_forum] Wrong ELF values In-Reply-To: References: <4D5263FD.90000@sissa.it> Message-ID: <4D5A32E9.3090505@sissa.it> Dear Claudia, I may not remember correctly what the format adopted by pp.x to define planes is... but i think it is Cartesian coordinates in unit of alat (aka celldm(1)). so when you write e1(1) =38.218, e1(2)=0.0, e1(3) = 0.0, e2(1) =0.0, e2(2)=33.108, e2(3) = 0.0, this means presumably 38 x 33 UNIT CELLS, sampled with 100x100 points (that is about 2-3 points in each unit cell). No surprise the FFT interpolation used gets confused. I think you should use more sensible values for e1(1) and e2(2)... what is your value of celldm(1)? At least this is my guess. stefano On 02/14/2011 06:57 PM, Claudia Loyola wrote: > Well, this is one of the input file: > > &inputpp > &plot > nfile = 1 , > filepp(1) = 'Ba38_33_10.charge' , > weight(1) = 1.0 , > iflag = 2 , > output_format = 3 , > fileout = 'ba.rho38_33_10.xsf' , > x0(1) =0.0, x0(2)=0.0, x0(3) = 10.602, > e1(1) =38.218, e1(2)=0.0, e1(3) = 0.0, > e2(1) =0.0, e2(2)=33.108, e2(3) = 0.0, > nx=100, ny=100 > / From giannozz at democritos.it Tue Feb 15 09:18:45 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 15 Feb 2011 09:18:45 +0100 Subject: [Pw_forum] DOS for Molecules and clusters In-Reply-To: References: <4D59130A.9080704@bham.ac.uk> Message-ID: <4D5A36E5.6010902@democritos.it> Omololu Akin-Ojo wrote: > Check Emin & Emax in your dos input; maybe they are outside > the range of the energy levels of the cluster. correct: eigenvalues are between -9.6541 to 0.0310, while Emin=1, Emax=25. In case of doubt, better not to specify Emin and Emax: the code will plot the DOS on the available energy range P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From glawe at mpi-halle.mpg.de Tue Feb 15 07:29:51 2011 From: glawe at mpi-halle.mpg.de (Henning Glawe) Date: Tue, 15 Feb 2011 07:29:51 +0100 Subject: [Pw_forum] pp.x ILDOS plots with ultrasoft pseudopotentials In-Reply-To: <3CC8F50E-8BD4-41D9-A8C6-E0F26799A102@democritos.it> References: <20110209072307.GB10648@ford.simpsons.bogus> <3CC8F50E-8BD4-41D9-A8C6-E0F26799A102@democritos.it> Message-ID: <20110215062951.GC744@ford.simpsons.bogus> On Thu, Feb 10, 2011 at 07:31:01AM +0100, Paolo Giannozzi wrote: > On Feb 9, 2011, at 8:23 , Henning Glawe wrote: > > Is this a known problem? > > no, it isn't. Please provide a (small) test showing this behavior You'll find one attached to this mail (both pw.x scf input, pp.x ildos and pp.x density input). I did some further investigations: for a set of espresso versions, I tried different compiler versions in order to exclude a possible mis-compilation problem (gfortran-debian-4.4.5-8, ifort-11.1, ifort-12.0.2, all on amd64 architecture systems). Details of the problem: - use USPP - calculate ildos for emin=-\infty, emax=E_{Fermi} and compare to \rho Observations: - in faulty versions, the range of values is [-41,+240], while in working versions, it is [0,0.76] Affected quantum espresso versions: >=4.2 Espresso versions up to 4.1.3 are OK, the calculated ildos \approx \rho if integration range is -\infty to E_{Fermi} (the smearing contibutes only in the scf density, but not in the ildos, which causes small differences). I could observe these proboblem only when using ultrasoft pseudopotentials, results with norm-conserving pseudos seem to be ok. -- Mit freundlichen Gr??en Henning Glawe Max-Planck-Institut f?r Mikrostrukturphysik Weinberg 2, 06120 Halle (Saale), Germany http://www.mpi-halle.de/~theory Phone: +49-345-5582-613 Fax: +49-345-5511223 Email: glawe at mpi-halle.de -------------- next part -------------- &control calculation = 'scf' restart_mode = 'from_scratch' prefix = 'CaC6' pseudo_dir = '../pseudo' outdir = 'scratch/' verbosity = 'high' ! tstress = .true. ! tprnfor = .true. ! etot_conv_thr = 1.0d-5 ! forc_conv_thr = 1.0d-4 wf_collect = .true. / &system ibrav = 5 celldm(1) = 9.6963160 celldm(4) = 0.64213864405089686974 nat = 7 ntyp = 2 ecutwfc = 30 ecutrho = 300 occupations = 'smearing' smearing = 'methfessel-paxton' degauss=0.06 / &electrons diagonalization = 'david' mixing_beta = 0.2 conv_thr = 1.0d-10 mixing_beta = 0.3 / ATOMIC_SPECIES Ca 40.078 Ca.pw91-nsp-van.UPF C 12.011 C.pw91-van_ak.UPF ATOMIC_POSITIONS crystal Ca 0.000000000 0.000000000 0.000000000 C 0.166666667 0.833333333 0.500000000 C 0.500000000 0.166666667 0.833333333 C 0.833333333 0.500000000 0.166666667 C 0.833333333 0.166666667 0.500000000 C 0.500000000 0.833333333 0.166666667 C 0.166666667 0.500000000 0.833333333 K_POINTS AUTOMATIC 8 8 8 0 0 0 -------------- next part -------------- &inputPP outdir = 'scratch/', prefix = 'CaC6' plot_num = 10 filplot = 'CaC6.all.ildos' emin = -50 emax = 9.8040 ! emin = 9.7540 ! emax = 9.8540 / &plot iflag=3, output_format=6 fileout='CaC6.all.ildos.cube' / -------------- next part -------------- &inputPP outdir = 'scratch/', prefix = 'CaC6' plot_num = 0 filplot = 'CaC6.density' emin = -50 emax = 9.6261 / &plot iflag=3, output_format=6 fileout='CaC6.density.cube' / From rose1988.mary at gmail.com Tue Feb 15 10:22:47 2011 From: rose1988.mary at gmail.com (Rose Mary) Date: Tue, 15 Feb 2011 09:22:47 +0000 Subject: [Pw_forum] Basic question on Band structure Message-ID: Hi all, I need to ask all a very question,I am a new user of espresso, also I am a very new in solid state Physics ,how shall I predict that my calculated band structure is correct?Also it will be helpful if I can get some theory of fundamentals of band structure calculation . Regards Rose Mary University of Kent Brussel -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110215/862c04bd/attachment.htm From degironc at sissa.it Tue Feb 15 10:26:14 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 15 Feb 2011 10:26:14 +0100 Subject: [Pw_forum] Basic question on Band structure In-Reply-To: References: Message-ID: <4D5A46B6.6060107@sissa.it> M. Martin, Electronic Structure: basic theory and practical methods, Cambridge University Press (2004) On 02/15/2011 10:22 AM, Rose Mary wrote: > Hi all, > > I need to ask all a very question,I am a new user of espresso, also I am a > very new in solid state Physics ,how shall I predict that my calculated band > structure is correct?Also it will be helpful if I can get some theory of > fundamentals of band structure calculation . > > Regards > > Rose Mary > > University of Kent > > Brussel > > > > _______________________________________________ > 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/20110215/5d2f192c/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Tue Feb 15 06:06:12 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Tue, 15 Feb 2011 06:06:12 +0100 Subject: [Pw_forum] combining vdW-DF and hybrids? In-Reply-To: <20110212134626.42751btldoq8dvky@webmail.csic.es> References: <276904.50330.qm@web65713.mail.ac4.yahoo.com> <20110212134626.42751btldoq8dvky@webmail.csic.es> Message-ID: <201102150606.12911.giuseppe.mattioli@mlib.ism.cnr.it> I would only add a perhaps useless suggestion. If you are dealing with molecules and your main interest is in using the HSE06 functional, then try to use the london=.true. keyword. The semiempirical london correction behaves well with molecules and could fit to your system. HTH Giuseppe On Saturday 12 February 2011 13:46:26 CONESA CEGARRA, JOSE CARLOS wrote: > hi, > > I am doing some tests with the cvs version of Q-E. I wonder, could one > combine the HSE06 functional (that refers only to exchange) with the vdw-DF > correlation? I tried a line such as input_dft='nox+pw+hse+vdw' > > but got a message of incompatibility of functionals. > > Also, some question to the developers: > > a) is there work for allowing soon the use of hybrid functionals with USPP > or PAW potentials? > > b) will the vdW-DF2 functional be available (with both ions and cell > relaxation, if possible) in the 4.3 version? > > All the best, -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From giuseppe.mattioli at mlib.ism.cnr.it Tue Feb 15 06:11:42 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Tue, 15 Feb 2011 06:11:42 +0100 Subject: [Pw_forum] A question on atomic magnetic moments In-Reply-To: <4D59069C.4000102@democritos.it> References: <4D59069C.4000102@democritos.it> Message-ID: <201102150611.42366.giuseppe.mattioli@mlib.ism.cnr.it> Dear all More a further question than an answer. Why should we obtain integer magnetic moments? Does not the infamous correlation error spread electrons among degenerate (or almost degenerate) electronic states, as in the case of the H2+ molecular ion? Yours Giuseppe On Monday 14 February 2011 11:40:28 Paolo Giannozzi wrote: > Giovani Faccin wrote: > > from set_nelup_neldw : error # 2 > > tot_magnetization is inconsistent with total number of electrons > > this check was written having in mind integer values of the > magnetization. It is meaningless with non-integer magnetization values. > > P. -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From davide.sangalli at gmail.com Tue Feb 15 11:37:40 2011 From: davide.sangalli at gmail.com (Davide Sangalli) Date: Tue, 15 Feb 2011 11:37:40 +0100 Subject: [Pw_forum] k-points parallelization in pwscf 4.2.1 In-Reply-To: <4D5964D0.6090400@democritos.it> References: <4D58FCE8.3040002@gmail.com> <4D59054E.7030302@democritos.it> <4D590F8D.8000500@gmail.com> <4D5964D0.6090400@democritos.it> Message-ID: <4D5A5774.4030700@gmail.com> Dear Paolo and Gabriele, thanks a lot for all your comments. For Gabriele, in case you are still interested, I post the details of my calculations. Best regards and thank you again, Davide **************************************************************** TEST 1: Serial run init_run : 24.83s CPU 25.13s WALL ( 1 calls) electrons : 349.01s CPU 351.40s WALL ( 1 calls) forces : 17.99s CPU 18.04s WALL ( 1 calls) stress : 44.14s CPU 44.30s WALL ( 1 calls) Called by init_run: wfcinit : 10.50s CPU 10.64s WALL ( 1 calls) potinit : 1.93s CPU 1.97s WALL ( 1 calls) Called by electrons: c_bands : 209.73s CPU 211.25s WALL ( 10 calls) sum_band : 65.96s CPU 66.35s WALL ( 10 calls) v_of_rho : 8.64s CPU 8.82s WALL ( 11 calls) newd : 70.57s CPU 70.81s WALL ( 11 calls) mix_rho : 0.79s CPU 0.79s WALL ( 10 calls) Called by c_bands: init_us_2 : 1.45s CPU 1.46s WALL ( 138 calls) cegterg : 205.73s CPU 206.86s WALL ( 60 calls) Called by *egterg: h_psi : 119.93s CPU 119.97s WALL ( 217 calls) s_psi : 24.87s CPU 24.88s WALL ( 217 calls) g_psi : 1.04s CPU 1.03s WALL ( 151 calls) cdiaghg : 3.98s CPU 4.07s WALL ( 211 calls) Called by h_psi: add_vuspsi : 24.87s CPU 24.87s WALL ( 217 calls) General routines calbec : 39.51s CPU 39.52s WALL ( 289 calls) cft3s : 64.52s CPU 65.52s WALL ( 22216 calls) interpolate : 0.79s CPU 0.79s WALL ( 21 calls) davcio : 0.01s CPU 0.63s WALL ( 198 calls) Parallel routines PWSCF : 7m16.35s CPU time, 7m19.59s WALL time **************************************************************** TEST 1: kpts parallelization init_run : 29.99s CPU 30.29s WALL ( 1 calls) electrons : 441.37s CPU 453.52s WALL ( 1 calls) forces : 51.92s CPU 52.91s WALL ( 1 calls) stress : 133.94s CPU 137.38s WALL ( 1 calls) Called by init_run: wfcinit : 2.64s CPU 2.68s WALL ( 1 calls) potinit : 1.92s CPU 2.02s WALL ( 1 calls) Called by electrons: c_bands : 40.54s CPU 42.66s WALL ( 10 calls) sum_band : 177.87s CPU 182.15s WALL ( 10 calls) v_of_rho : 11.17s CPU 11.74s WALL ( 11 calls) newd : 228.49s CPU 229.61s WALL ( 11 calls) mix_rho : 2.67s CPU 2.68s WALL ( 10 calls) Called by c_bands: init_us_2 : 0.64s CPU 0.68s WALL ( 21 calls) cegterg : 39.15s CPU 40.36s WALL ( 10 calls) Called by *egterg: h_psi : 34.15s CPU 34.19s WALL ( 37 calls) s_psi : 1.64s CPU 1.64s WALL ( 37 calls) g_psi : 0.22s CPU 0.22s WALL ( 26 calls) cdiaghg : 0.48s CPU 0.48s WALL ( 36 calls) Called by h_psi: add_vuspsi : 1.67s CPU 1.67s WALL ( 37 calls) General routines calbec : 2.83s CPU 2.83s WALL ( 49 calls) cft3s : 25.51s CPU 25.77s WALL ( 3904 calls) interpolate : 1.57s CPU 1.58s WALL ( 21 calls) davcio : 0.00s CPU 0.09s WALL ( 10 calls) Parallel routines PWSCF : 10m57.44s CPU time, 11m14.40s WALL time **************************************************************** TEST 1: FFT parallelization init_run : 7.12s CPU 8.04s WALL ( 1 calls) electrons : 71.85s CPU 77.28s WALL ( 1 calls) forces : 8.49s CPU 8.68s WALL ( 1 calls) stress : 21.95s CPU 22.46s WALL ( 1 calls) Called by init_run: wfcinit : 1.61s CPU 2.06s WALL ( 1 calls) potinit : 0.74s CPU 0.79s WALL ( 1 calls) Called by electrons: c_bands : 35.48s CPU 38.71s WALL ( 11 calls) sum_band : 16.47s CPU 17.71s WALL ( 11 calls) v_of_rho : 2.59s CPU 2.75s WALL ( 12 calls) newd : 18.12s CPU 18.81s WALL ( 12 calls) mix_rho : 0.42s CPU 0.44s WALL ( 11 calls) Called by c_bands: init_us_2 : 0.65s CPU 0.66s WALL ( 150 calls) cegterg : 34.41s CPU 37.31s WALL ( 66 calls) Called by *egterg: h_psi : 23.01s CPU 25.34s WALL ( 239 calls) s_psi : 1.95s CPU 1.94s WALL ( 239 calls) g_psi : 0.23s CPU 0.23s WALL ( 167 calls) cdiaghg : 2.90s CPU 3.18s WALL ( 233 calls) Called by h_psi: add_vuspsi : 1.91s CPU 1.91s WALL ( 239 calls) General routines calbec : 3.54s CPU 3.81s WALL ( 317 calls) cft3s : 12.24s CPU 15.25s WALL ( 24298 calls) interpolate : 0.35s CPU 0.37s WALL ( 23 calls) davcio : 0.00s CPU 0.54s WALL ( 216 calls) Parallel routines fft_scatter : 4.34s CPU 6.95s WALL ( 24298 calls) PWSCF : 1m49.61s CPU time, 1m56.75s WALL time On 02/14/2011 06:22 PM, Paolo Giannozzi wrote: > Also notice that parallelization on k-points has (in principle) > a linear speedup on the diagonalization of H and related operations > depending on the number of k-points, but not for other operations > depending upon the charge density such as calculation of V[n(r)]. > The latter are typically small in comparison with the former, but > it depends a lot upon the specific system. FFT parallelization > distributes both calculations (and yes, it distributes most memory, > I stand by my statement) > > P. Davide Sangalli MDM Lab, IMM, CNR Agrate (MI), Italy From sclauzer at sissa.it Tue Feb 15 12:10:58 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 15 Feb 2011 12:10:58 +0100 Subject: [Pw_forum] k-points parallelization in pwscf 4.2.1 In-Reply-To: <4D5A5774.4030700@gmail.com> References: <4D58FCE8.3040002@gmail.com> <4D59054E.7030302@democritos.it> <4D590F8D.8000500@gmail.com> <4D5964D0.6090400@democritos.it> <4D5A5774.4030700@gmail.com> Message-ID: <543F7419-B956-4A54-956A-E52C357F4F15@sissa.it> OK, thanks. It is as Paolo suggested: some parts of the code are not parallelized over k-points. This said, I don't see why these parts of the code show a much larger timing when going from the serial run to the run with k-point parallelization. For instance, I would expect that newd has the same timing more or less, but it takes 3 times more. Also the timing of sum_band looks quite higher. Maybe there is a communication overhead between MPI processes, or the memory contention problem that was mentioned before (since the volume of data between cores and main memory largely increases when passing from 1 to 6 pools). GS Il giorno 15/feb/2011, alle ore 11.37, Davide Sangalli ha scritto: > Dear Paolo and Gabriele, > thanks a lot for all your comments. > > For Gabriele, in case you are still interested, I post the details of my > calculations. > > Best regards and thank you again, > Davide > > **************************************************************** > TEST 1: Serial run > init_run : 24.83s CPU 25.13s WALL ( 1 calls) > electrons : 349.01s CPU 351.40s WALL ( 1 calls) > forces : 17.99s CPU 18.04s WALL ( 1 calls) > stress : 44.14s CPU 44.30s WALL ( 1 calls) > > Called by init_run: > wfcinit : 10.50s CPU 10.64s WALL ( 1 calls) > potinit : 1.93s CPU 1.97s WALL ( 1 calls) > > Called by electrons: > c_bands : 209.73s CPU 211.25s WALL ( 10 calls) > sum_band : 65.96s CPU 66.35s WALL ( 10 calls) > v_of_rho : 8.64s CPU 8.82s WALL ( 11 calls) > newd : 70.57s CPU 70.81s WALL ( 11 calls) > mix_rho : 0.79s CPU 0.79s WALL ( 10 calls) > > Called by c_bands: > init_us_2 : 1.45s CPU 1.46s WALL ( 138 calls) > cegterg : 205.73s CPU 206.86s WALL ( 60 calls) > > Called by *egterg: > h_psi : 119.93s CPU 119.97s WALL ( 217 calls) > s_psi : 24.87s CPU 24.88s WALL ( 217 calls) > g_psi : 1.04s CPU 1.03s WALL ( 151 calls) > cdiaghg : 3.98s CPU 4.07s WALL ( 211 calls) > > Called by h_psi: > add_vuspsi : 24.87s CPU 24.87s WALL ( 217 calls) > > General routines > calbec : 39.51s CPU 39.52s WALL ( 289 calls) > cft3s : 64.52s CPU 65.52s WALL ( 22216 calls) > interpolate : 0.79s CPU 0.79s WALL ( 21 calls) > davcio : 0.01s CPU 0.63s WALL ( 198 calls) > > Parallel routines > > PWSCF : 7m16.35s CPU time, 7m19.59s WALL time > > **************************************************************** > TEST 1: kpts parallelization > init_run : 29.99s CPU 30.29s WALL ( 1 calls) > electrons : 441.37s CPU 453.52s WALL ( 1 calls) > forces : 51.92s CPU 52.91s WALL ( 1 calls) > stress : 133.94s CPU 137.38s WALL ( 1 calls) > > Called by init_run: > wfcinit : 2.64s CPU 2.68s WALL ( 1 calls) > potinit : 1.92s CPU 2.02s WALL ( 1 calls) > > Called by electrons: > c_bands : 40.54s CPU 42.66s WALL ( 10 calls) > sum_band : 177.87s CPU 182.15s WALL ( 10 calls) > v_of_rho : 11.17s CPU 11.74s WALL ( 11 calls) > newd : 228.49s CPU 229.61s WALL ( 11 calls) > mix_rho : 2.67s CPU 2.68s WALL ( 10 calls) > > Called by c_bands: > init_us_2 : 0.64s CPU 0.68s WALL ( 21 calls) > cegterg : 39.15s CPU 40.36s WALL ( 10 calls) > > Called by *egterg: > h_psi : 34.15s CPU 34.19s WALL ( 37 calls) > s_psi : 1.64s CPU 1.64s WALL ( 37 calls) > g_psi : 0.22s CPU 0.22s WALL ( 26 calls) > cdiaghg : 0.48s CPU 0.48s WALL ( 36 calls) > > Called by h_psi: > add_vuspsi : 1.67s CPU 1.67s WALL ( 37 calls) > > General routines > calbec : 2.83s CPU 2.83s WALL ( 49 calls) > cft3s : 25.51s CPU 25.77s WALL ( 3904 calls) > interpolate : 1.57s CPU 1.58s WALL ( 21 calls) > davcio : 0.00s CPU 0.09s WALL ( 10 calls) > > Parallel routines > > PWSCF : 10m57.44s CPU time, 11m14.40s WALL time > > **************************************************************** > TEST 1: FFT parallelization > > init_run : 7.12s CPU 8.04s WALL ( 1 calls) > electrons : 71.85s CPU 77.28s WALL ( 1 calls) > forces : 8.49s CPU 8.68s WALL ( 1 calls) > stress : 21.95s CPU 22.46s WALL ( 1 calls) > > Called by init_run: > wfcinit : 1.61s CPU 2.06s WALL ( 1 calls) > potinit : 0.74s CPU 0.79s WALL ( 1 calls) > > Called by electrons: > c_bands : 35.48s CPU 38.71s WALL ( 11 calls) > sum_band : 16.47s CPU 17.71s WALL ( 11 calls) > v_of_rho : 2.59s CPU 2.75s WALL ( 12 calls) > newd : 18.12s CPU 18.81s WALL ( 12 calls) > mix_rho : 0.42s CPU 0.44s WALL ( 11 calls) > > Called by c_bands: > init_us_2 : 0.65s CPU 0.66s WALL ( 150 calls) > cegterg : 34.41s CPU 37.31s WALL ( 66 calls) > > Called by *egterg: > h_psi : 23.01s CPU 25.34s WALL ( 239 calls) > s_psi : 1.95s CPU 1.94s WALL ( 239 calls) > g_psi : 0.23s CPU 0.23s WALL ( 167 calls) > cdiaghg : 2.90s CPU 3.18s WALL ( 233 calls) > > Called by h_psi: > add_vuspsi : 1.91s CPU 1.91s WALL ( 239 calls) > > General routines > calbec : 3.54s CPU 3.81s WALL ( 317 calls) > cft3s : 12.24s CPU 15.25s WALL ( 24298 calls) > interpolate : 0.35s CPU 0.37s WALL ( 23 calls) > davcio : 0.00s CPU 0.54s WALL ( 216 calls) > > Parallel routines > fft_scatter : 4.34s CPU 6.95s WALL ( 24298 calls) > > PWSCF : 1m49.61s CPU time, 1m56.75s WALL time > > > > > On 02/14/2011 06:22 PM, Paolo Giannozzi wrote: >> Also notice that parallelization on k-points has (in principle) >> a linear speedup on the diagonalization of H and related operations >> depending on the number of k-points, but not for other operations >> depending upon the charge density such as calculation of V[n(r)]. >> The latter are typically small in comparison with the former, but >> it depends a lot upon the specific system. FFT parallelization >> distributes both calculations (and yes, it distributes most memory, >> I stand by my statement) >> >> P. > > Davide Sangalli > MDM Lab, IMM, CNR > Agrate (MI), Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110215/a196e46a/attachment-0001.htm From nicola.marzari at materials.ox.ac.uk Tue Feb 15 12:29:46 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Tue, 15 Feb 2011 11:29:46 +0000 Subject: [Pw_forum] RE : A question on atomic magnetic moments In-Reply-To: References: <80982012-517C-4A53-A0E1-6975EF5CE89E@democritos.it> Message-ID: <4D5A63AA.5080706@materials.ox.ac.uk> Thanks Prasenjit - a further comment, to be careful about. In molecules/clusters, you could end up with a situation where the HOMO is degenerate, and you have fractional occupations, so the entropy term S is constant, and -TS is linear (T is deguass); this supposing the other states below the homo are separated from the HOMO by at least 2 or 3 times degauss. What you want is the total energy - that is obtained by subtracting the term "-TS" to the "total energy" printed by the code (since the "total energy" printed by the code, when you use a smearing, is not the total energy, but the total free energy E-TS). nicola On 2/14/11 5:22 AM, Prasenjit Ghosh wrote: > A small suggestion, try changing the smearing type, instead of using > mp, try using m-v or even simple gaussian is fine for small clusters. > Also, you should check the value of the contribution to total energy > from smearing (printed in the output after your calculations have > converged).......ideally for small clusters as yours, this should be > zero. This tells you that your smearing is physically small enough so > that the spurious effect of broadening becomes negligible. > > With regards, > > Prasenjit > -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From nicola.marzari at materials.ox.ac.uk Tue Feb 15 12:33:34 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Tue, 15 Feb 2011 11:33:34 +0000 Subject: [Pw_forum] Basic question on Band structure In-Reply-To: References: Message-ID: <4D5A648E.40208@materials.ox.ac.uk> Hi Rose Mary, in addition to the book by Richard Martin, suggested by Stefano, you could listen to all the relevant lectures from the QE Santa Barbara school, in the learn/multimedia section of the quantum-espresso page, as well as everything else that is in the learn section. nicola On 2/15/11 9:22 AM, Rose Mary wrote: > Hi all, > > I need to ask all a very question,I am a new user of espresso, also I am > a very new in solid state Physics ,how shall I predict that my > calculated band structure is correct?Also it will be helpful if I can > get some theory of fundamentals of band structure calculation . > > Regards > > Rose Mary > > University of Kent > > Brussel -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From claudial.81 at gmail.com Tue Feb 15 16:42:23 2011 From: claudial.81 at gmail.com (Claudia Loyola) Date: Tue, 15 Feb 2011 09:42:23 -0600 Subject: [Pw_forum] Wrong ELF values In-Reply-To: <4D5A32E9.3090505@sissa.it> References: <4D5263FD.90000@sissa.it> <4D5A32E9.3090505@sissa.it> Message-ID: Hello! yes, you are right if I define the vectors in function of "a" and I define alat=a , but let me show you how I define the vectors in the scf input file: &SYSTEM ibrav = 0 , celldm(1) =1.0 , . . . CELL_PARAMETERS (alat=1.0) 19.109476287 -0.014917030 0.000000953 -9.542147268 16.554932043 0.000000170 0.000000706 0.000000344 14.136501037 so in this case the vector basis are the real large in bohr, and the alat is 1.0 like celldm(1). Indeed, the value of the vectors for pp.x are in function of alat, but my alat is 1.0, so I can write directly in bohr the values of the planes that I take, in fact I take "two replicates" in each direction. I think this is correct too. Thank you very much for your comments :) regards, Claudia Loyola On Tue, Feb 15, 2011 at 2:01 AM, Stefano de Gironcoli wrote: > Dear Claudia, > I may not remember correctly what the format adopted by pp.x to > define planes is... but i think it is Cartesian coordinates in unit of > alat (aka celldm(1)). > > so when you write > e1(1) =38.218, e1(2)=0.0, e1(3) = 0.0, > e2(1) =0.0, e2(2)=33.108, e2(3) = 0.0, > this means presumably 38 x 33 UNIT CELLS, sampled with 100x100 points > (that is about 2-3 points in each unit cell). No surprise the FFT > interpolation used gets confused. > > I think you should use more sensible values for e1(1) and e2(2)... what > is your value of celldm(1)? > > At least this is my guess. > > stefano > > > On 02/14/2011 06:57 PM, Claudia Loyola wrote: > > Well, this is one of the input file: > > > > &inputpp > > &plot > > nfile = 1 , > > filepp(1) = 'Ba38_33_10.charge' , > > weight(1) = 1.0 , > > iflag = 2 , > > output_format = 3 , > > fileout = 'ba.rho38_33_10.xsf' , > > x0(1) =0.0, x0(2)=0.0, x0(3) = 10.602, > > e1(1) =38.218, e1(2)=0.0, e1(3) = 0.0, > > e2(1) =0.0, e2(2)=33.108, e2(3) = 0.0, > > nx=100, ny=100 > > / > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Claudia Loyola Canales Postdoc in Computational Physics Iowa State University Iowa, USA http://www.lpmd.cl/claudial http://www.lpmd.cl http://cosmic.mse.iastate.edu/ http://www.gnm.cl -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110215/e508c14c/attachment.htm From jcconesa at icp.csic.es Tue Feb 15 16:57:59 2011 From: jcconesa at icp.csic.es (Jose C. Conesa) Date: Tue, 15 Feb 2011 16:57:59 +0100 Subject: [Pw_forum] combining vdW-DF and hybrids? In-Reply-To: <201102150606.12911.giuseppe.mattioli@mlib.ism.cnr.it> References: <276904.50330.qm@web65713.mail.ac4.yahoo.com> <20110212134626.42751btldoq8dvky@webmail.csic.es> <201102150606.12911.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <4D5AA287.8080109@icp.csic.es> Hi, Thanks for the suggestion, but it does not help me. I'm not concerned only with molecules, but with oxide layer compounds and surfaces as well; and for these the standard Grimme's parameters are not adequate (see J Phys Chem C _114_(2010)22718). For this I should like to try hse06 and vdW-DF together, but it's not clear if Q-E allows it. Jos?-Carlos El 15/02/2011 6:06, Giuseppe Mattioli escribi?: > I would only add a perhaps useless suggestion. > If you are dealing with molecules and your main interest is in using the HSE06 > functional, then try to use the london=.true. keyword. The semiempirical > london correction behaves well with molecules and could fit to your system. > HTH > > Giuseppe > > On Saturday 12 February 2011 13:46:26 CONESA CEGARRA, JOSE CARLOS wrote: >> hi, >> >> I am doing some tests with the cvs version of Q-E. I wonder, could one >> combine the HSE06 functional (that refers only to exchange) with the vdw-DF >> correlation? I tried a line such as input_dft='nox+pw+hse+vdw' >> >> but got a message of incompatibility of functionals. >> >> Also, some question to the developers: >> >> a) is there work for allowing soon the use of hybrid functionals with USPP >> or PAW potentials? >> >> b) will the vdW-DF2 functional be available (with both ions and cell >> relaxation, if possible) in the 4.3 version? >> >> All the best, > > -- Jos? C. Conesa Instituto de Cat?lisis y Petroleoqu?mica, CSIC Marie Curie 2, Cantoblanco 28049 Madrid, Spain Tel. +34-915854766 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110215/992771f4/attachment.htm From faccin.giovani at gmail.com Tue Feb 15 17:03:21 2011 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Tue, 15 Feb 2011 12:03:21 -0400 Subject: [Pw_forum] Basic question on Band structure In-Reply-To: References: Message-ID: Hi Rose Mary, See if you can find this book: V. L. Moruzzi, J. F. Janak, A. R. Williams; Calculated Electronic Properties of Metals. It's a kind of handbook containing calculated DOS and other properties for many elements. Then you just have to plot your calculated DOS e compare with the book's plot. Regards, Giovani Faccin 2011/2/15 Rose Mary > Hi all, > > I need to ask all a very question,I am a new user of espresso, also I am a > very new in solid state Physics ,how shall I predict that my calculated band > structure is correct?Also it will be helpful if I can get some theory of > fundamentals of band structure calculation . > > Regards > > Rose Mary > > University of Kent > > Brussel > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Giovani -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110215/89c2e849/attachment.htm From faccin.giovani at gmail.com Tue Feb 15 17:15:37 2011 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Tue, 15 Feb 2011 12:15:37 -0400 Subject: [Pw_forum] RE : A question on atomic magnetic moments In-Reply-To: <4D5A63AA.5080706@materials.ox.ac.uk> References: <80982012-517C-4A53-A0E1-6975EF5CE89E@democritos.it> <4D5A63AA.5080706@materials.ox.ac.uk> Message-ID: Dear Prasenjit and Nicola, Thank you for the comment on smearing. I was not paying attention to it. A quick look on some logs I have here show that this contribution is not that much negligible in some calculations (around 0.00364895 Ry, for example). Thus I'll evaluate the total energy as "! total energy - smearing contribution(-TS)" from now on and see what I get. I'm finishing a test battery based on another suggestion from the forum. Once I report it, I'll take the best result from there and experiment with smearing to see what we get from it. Thanks again! Giovani 2011/2/15 Nicola Marzari > > > Thanks Prasenjit - a further comment, to be careful about. > > In molecules/clusters, you could end up with a situation where > the HOMO is degenerate, and you have fractional occupations, > so the entropy term S is constant, and -TS is linear (T is deguass); > this supposing the other states below the homo are separated > from the HOMO by at least 2 or 3 times degauss. > > What you want is the total energy - that is obtained by > subtracting the term "-TS" to the "total energy" printed > by the code (since the "total energy" printed by the code, > when you use a smearing, is not the total energy, but the > total free energy E-TS). > > nicola > > > > On 2/14/11 5:22 AM, Prasenjit Ghosh wrote: > > A small suggestion, try changing the smearing type, instead of using > > mp, try using m-v or even simple gaussian is fine for small clusters. > > Also, you should check the value of the contribution to total energy > > from smearing (printed in the output after your calculations have > > converged).......ideally for small clusters as yours, this should be > > zero. This tells you that your smearing is physically small enough so > > that the spurious effect of broadening becomes negligible. > > > > With regards, > > > > Prasenjit > > > > > -- > ---------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials University of Oxford > Chair of Materials Modelling Director, Materials Modelling Laboratory > nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Giovani -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110215/f91a0db6/attachment-0001.htm From degironc at sissa.it Tue Feb 15 17:16:39 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 15 Feb 2011 17:16:39 +0100 Subject: [Pw_forum] Wrong ELF values In-Reply-To: References: <4D5263FD.90000@sissa.it> <4D5A32E9.3090505@sissa.it> Message-ID: <4D5AA6E7.2030404@sissa.it> I see... how large is your calculation? if it is not too big, would you mind send me (at my email) one set of input and output to have a look ? stefano On 02/15/2011 04:42 PM, Claudia Loyola wrote: > Hello! > > yes, you are right if I define the vectors in function of "a" and I define > alat=a , but let me show you how I define the vectors in the scf input file: > > &SYSTEM > ibrav = 0 , > celldm(1) =1.0 , > . > . > . > CELL_PARAMETERS (alat=1.0) > 19.109476287 -0.014917030 0.000000953 > -9.542147268 16.554932043 0.000000170 > 0.000000706 0.000000344 14.136501037 > > so in this case the vector basis are the real large in bohr, and the alat is > 1.0 like celldm(1). Indeed, the value of the vectors for pp.x are in > function of alat, but my alat is 1.0, so I can write directly in bohr the > values of the planes that I take, in fact I take "two replicates" in each > direction. I think this is correct too. > > Thank you very much for your comments :) > > regards, > Claudia Loyola > > On Tue, Feb 15, 2011 at 2:01 AM, Stefano de Gironcoliwrote: > >> Dear Claudia, >> I may not remember correctly what the format adopted by pp.x to >> define planes is... but i think it is Cartesian coordinates in unit of >> alat (aka celldm(1)). >> >> so when you write >> e1(1) =38.218, e1(2)=0.0, e1(3) = 0.0, >> e2(1) =0.0, e2(2)=33.108, e2(3) = 0.0, >> this means presumably 38 x 33 UNIT CELLS, sampled with 100x100 points >> (that is about 2-3 points in each unit cell). No surprise the FFT >> interpolation used gets confused. >> >> I think you should use more sensible values for e1(1) and e2(2)... what >> is your value of celldm(1)? >> >> At least this is my guess. >> >> stefano >> >> >> On 02/14/2011 06:57 PM, Claudia Loyola wrote: >>> Well, this is one of the input file: >>> >>> &inputpp >>> &plot >>> nfile = 1 , >>> filepp(1) = 'Ba38_33_10.charge' , >>> weight(1) = 1.0 , >>> iflag = 2 , >>> output_format = 3 , >>> fileout = 'ba.rho38_33_10.xsf' , >>> x0(1) =0.0, x0(2)=0.0, x0(3) = 10.602, >>> e1(1) =38.218, e1(2)=0.0, e1(3) = 0.0, >>> e2(1) =0.0, e2(2)=33.108, e2(3) = 0.0, >>> nx=100, ny=100 >>> / >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110215/a4a739f0/attachment.htm From wibarrah at gmail.com Tue Feb 15 17:29:53 2011 From: wibarrah at gmail.com (=?ISO-8859-1?Q?Wilfredo_Ibarra_Hern=E1ndez?=) Date: Tue, 15 Feb 2011 10:29:53 -0600 Subject: [Pw_forum] [Pw_Forum] specific heat Message-ID: Dear all. In the past I was asked if someone worked with the calculation of specific heat. I'm working with QHA, but I have a question. The temperature for this calculation, It's necessary be integer? because I modify the Edit_me file, but when I put delta_T with values like 0.1 the calculation not write anything in the "system.QHA.out" and I need this values because I want make a graphic "Cv/T^3 Vs. T". And the important values are near to zero. Thanks for you help. ~~~~~~~~~~~~~~~~~~~~~~~~~~~ Ibarra Hern?ndez Wilfredo Master student in materials science Cinvestav unidad Qu?retaro Qu?retaro, M?xico. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110215/77543d23/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Tue Feb 15 13:29:22 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Tue, 15 Feb 2011 13:29:22 +0100 Subject: [Pw_forum] combining vdW-DF and hybrids? In-Reply-To: <4D5AA287.8080109@icp.csic.es> References: <201102150606.12911.giuseppe.mattioli@mlib.ism.cnr.it> <4D5AA287.8080109@icp.csic.es> Message-ID: <201102151329.22712.giuseppe.mattioli@mlib.ism.cnr.it> Dear Jos?-Carlos I'm involved in studies of molecules interacting with metal oxide surfaces too, so I face problem similar to yours. I know that the Grimme trick is not the best thing, but you can change by hand the C6 coefficients following some molecular mechanics force field (AMBER, CHARMM...). Anyway your calculations will be VERY cpu-consuming, even if you sample the BZ with gamma only... Yours Giuseppe On Tuesday 15 February 2011 16:57:59 Jose C. Conesa wrote: > Hi, > Thanks for the suggestion, but it does not help me. I'm not concerned > only with molecules, but with oxide layer compounds and surfaces as > well; and for these the standard Grimme's parameters are not adequate > (see J Phys Chem C _114_(2010)22718). For this I should like to try > hse06 and vdW-DF together, but it's not clear if Q-E allows it. > > Jos?-Carlos > > El 15/02/2011 6:06, Giuseppe Mattioli escribi?: > > I would only add a perhaps useless suggestion. > > If you are dealing with molecules and your main interest is in using the > > HSE06 functional, then try to use the london=.true. keyword. The > > semiempirical london correction behaves well with molecules and could fit > > to your system. HTH > > > > Giuseppe > > > > On Saturday 12 February 2011 13:46:26 CONESA CEGARRA, JOSE CARLOS wrote: > >> hi, > >> > >> I am doing some tests with the cvs version of Q-E. I wonder, could one > >> combine the HSE06 functional (that refers only to exchange) with the > >> vdw-DF correlation? I tried a line such as input_dft='nox+pw+hse+vdw' > >> > >> but got a message of incompatibility of functionals. > >> > >> Also, some question to the developers: > >> > >> a) is there work for allowing soon the use of hybrid functionals with > >> USPP or PAW potentials? > >> > >> b) will the vdW-DF2 functional be available (with both ions and cell > >> relaxation, if possible) in the 4.3 version? > >> > >> All the best, -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From faccin.giovani at gmail.com Tue Feb 15 18:42:10 2011 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Tue, 15 Feb 2011 13:42:10 -0400 Subject: [Pw_forum] RE : RE : A question on atomic magnetic moments Message-ID: Dear Cyrille, I recalculated the dimer with different values of nbnd. Now some interesting changes appeared: Value of nbnd | Magnetization 10 4.00 12 6.88 14 6.49 16 6.49 18 6.49 20 6.49 22 6.88 24 6.88 26 6.49 28 6.49 Also we dimer is now no longer at the equilibrium position; taking for example for nbnd=20: Forces acting on atoms (Ry/au): atom 1 type 1 force = 0.02342880 0.00000000 0.00000000 atom 2 type 1 force = -0.02342880 0.00000000 0.00000000 For the record, the smearing contribution on these calculations goes like this : smearing contrib. (-TS) = -0.00101846 Ry which were made using degauss = 0.005, with 'methfessel-paxton' smearing type. So looks like there are two things to improve: reduce the smearing contribution and also use a high nbnd. Peharps those high values of magnetization at nbnd=22, 24 could be due to smearing? I'll test it and report back on the list. Any other suggestions, just say it, I'll give it a try. Thanks, Giovani Faccin 2011/2/14 BARRETEAU Cyrille > Dear Giovani > > I personnaly did calculations on Fe clusters some time ago. I always found > "almost integer" magnetic moments. > However I once encoutered some difficulties with the default value of > "nbnd". I had to increase it. Try to set nbnd=20 for example... > > Magnetic clusters can be very tricky.. It also very common to find several > magnetic solutions.. > > good luck > > cyrille > > ================================================================== > Cyrille Barreteau > phone : +33 (0)1 69 08 29 51 > CEA Saclay fax > : +33 (0)1 69 08 84 46 > IRAMIS, SPCSI, Batiment 462 email > cyrille.barreteau at cea.fr > 91191 Gif sur Yvette Cedex > FRANCE > ~~~~~~~~~~~~~~~~~~~~~~~~ > Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/ > ================================================================== > > ________________________________ > > De: pw_forum-bounces at pwscf.org de la part de Giovani Faccin > Date: lun. 14/02/2011 05:50 > ?: PWSCF Forum > Objet : Re: [Pw_forum] RE : A question on atomic magnetic moments > > > Dear Cyrille, > > First of all, thanks for the reply on my post. > > Following your suggestion, I've run a few calculations with lower degauss > values. In particular, the ones reported on the message for Duy Le were made > with a much smaller value ( 0.005 ) than the original 0.02 from the first > message. Besides that, I've tried degauss values as low as 0.002 without any > significant improvement on the final magnetization. > > I'm still wondering how do people find 6.00 so easily for the > magnetization. I'm trying with 2 different DFT codes and no way I'm reaching > those results, even though bulk/dimer equilibrium distances and force > constants appear to be ok. > > Any other ideas, just tell me, I'll try it and report back on the list. > > Thanks again, > > Giovani > > > > 2011/2/13 BARRETEAU Cyrille > > > Dear Giovani > Try to decrease the degauss value of your smearing.. and see what > happens. > > cyrille > > > ================================================================== > Cyrille Barreteau > phone : +33 (0)1 69 08 29 51 > CEA Saclay > fax : +33 (0)1 69 08 84 46 > IRAMIS, SPCSI, Batiment 462 email > cyrille.barreteau at cea.fr > 91191 Gif sur Yvette Cedex > FRANCE > ~~~~~~~~~~~~~~~~~~~~~~~~ > Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/ > ================================================================== > > ________________________________ > > De: pw_forum-bounces at pwscf.org de la part de Giovani Faccin > Date: dim. 13/02/2011 07:16 > ?: PWSCF Forum > Objet : Re: [Pw_forum] A question on atomic magnetic moments > > > Dear Paolo, > > Thanks for the reply. > > Just to make sure that the simulation cell size is not an issue (so > that the system is really finite), I've tested different possibilities, > including some quite big cells. Still, after a certain size the value of the > magnetization is converging to 6.82 instead of the expected 6. > > So something else is causing this. Unfortunately I've got no clue as > to what could it be. > > Should it be of any help, this is my input file: > > > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > wf_collect = .true. , > outdir = './output' , > pseudo_dir = '../pseudo/' , > prefix = 'fe' , > etot_conv_thr = 1.0D-9 , > forc_conv_thr = 1.0D-6 , > tstress = .true. , > tprnfor = .true. , > / > &SYSTEM > ibrav = 1, > celldm(1) = 43, > nat = 2, > ntyp = 1, > ecutwfc = 100 , > ecutrho = 300 , > occupations = 'smearing' , > degauss = 0.02 , > smearing = 'methfessel-paxton' , > nspin = 2 , > starting_magnetization(1) = 1.0, > / > &ELECTRONS > conv_thr = 1.0e-9 , > mixing_beta = 0.7 , > diagonalization = 'david' , > / > ATOMIC_SPECIES > Fe 58.69000 Fe.pbe-nd-rrkjus.UPF > ATOMIC_POSITIONS angstrom > Fe 0.000000000 0.000000000 0.000000000 > Fe 2.047510 0.000000000 0.000000000 > K_POINTS automatic > 1 1 1 1 1 1 > > Any suggestions are highly welcome. > > Giovani > > > > 2011/2/12 Paolo Giannozzi > > > > On Feb 11, 2011, at 17:09 , Giovani Faccin wrote: > > > My question: shouldn't those numbers be integers? > > > only in finite systems, if you neglect spin-orbit. > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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 > > > > > > -- > Giovani > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > -- > Giovani > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Giovani -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110215/b8203d44/attachment-0001.htm From nicola.marzari at materials.ox.ac.uk Tue Feb 15 19:03:32 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Tue, 15 Feb 2011 18:03:32 +0000 Subject: [Pw_forum] RE : RE : A question on atomic magnetic moments In-Reply-To: References: Message-ID: <4D5ABFF4.1060501@materials.ox.ac.uk> Dear Giovanni, Cyrille, the iron dimer has a very complex electronic structure (see e.g. our PRL 2006 Kulik et al) - different multiplets, and for each multiplet, different symmetries. In principle, there is no way to guess to which of the many self-consistent states you'll converge to, and I suppose that what you have here is that you have converged to different states. You'll need to look at the total energy, kohn-sham eigenstates, and the symmetry of those to understand what you are looking at (also, there is no point in having more bands than efermi + 3*degauss - empty bands above that threshold are useless). There is no easy way to force the code into one state or the other - you could try using GGA+U - some U's will stabilize reliably one state, and then by reducing smoothly the U (or increasing it) you might be able to have (as a function of U) the energy of your preferred electronic configuration. Last - for a cluster or a molecule smearing is used, somewhat inappropriately, to help a calculation converge when using iterative approaches - it keeps you company during the voyage, but shouldn't share your bed (the real reason d'etre for smearing is to improve k-point integrations in metals). nicola On 2/15/11 5:42 PM, Giovani Faccin wrote: > Dear Cyrille, > > I recalculated the dimer with different values of nbnd. Now some > interesting changes appeared: > > Value of nbnd | Magnetization > > 10 4.00 > 12 6.88 > 14 6.49 > 16 6.49 > 18 6.49 > 20 6.49 > 22 6.88 > 24 6.88 > 26 6.49 > 28 6.49 > -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From parishok at gmail.com Tue Feb 15 19:48:04 2011 From: parishok at gmail.com (pari shok) Date: Tue, 15 Feb 2011 13:48:04 -0500 Subject: [Pw_forum] problem with pp.x and dos and a question about vectors in ILDOS calculation Message-ID: Dear All, problem with pp.x and dos and a question about vectors in ILDOS calculation. Firstly, the problem with pp.x and dos.x: I downloaded QE in two machines: intel (R) pentium (R) 4 cpu 3 GHz with total memory 2GB, uses gfortran and intel (R) core (TM) i7 cpu 870 @2.93 GHz, with 4GB total memory, uses gfortran. everything is working perfectly well with the first machine (with espresso-4.1.2), but dos.x and pp.x both crash with "out of memory/ memory allocation" error in the second machine for big structures (espresso-4.2.1 and espresso-4.2). It should be noted that pw.x works properly and the "memory allocation" error happens just for dos and post processing. Sometimes, it seems that both pp.x and dos.x are frozen. In this case, nothing is written to output file and the programs don't even send any memory messages. I downloaded ATLAS and modified "make.sys" accordingly but it didn't help. I used "ulimit -s unlimited" command, it didn't help either. I should emphasise that dos.x and pp.x in the old machine work properly for the same inputs. Therefore, the input files don't have any problems. I am really obsessed with it. I would really be grateful if anybody who had experienced the same problem could help me somehow. Secondly, a couple of questions about vectors in ILDOS: 1. If the origin of ILDOS calculation is set to (000) and the vector is set to (001), does the ILDOS calculations spans the whole slab in "z" direction? 2. Does ILDOS in one direction (along one vector) gives the LDOS on the plane perpendicular to that vector in each point? I really appreciate your help. This is the second time that I've subscribed for the forum in the hope that this time my subscription would be successful. Yours P Shok PhD at UMD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110215/6caa6e5f/attachment.htm From saqib.javaid at ipcms.u-strasbg.fr Tue Feb 15 20:09:59 2011 From: saqib.javaid at ipcms.u-strasbg.fr (saqib.javaid at ipcms.u-strasbg.fr) Date: Tue, 15 Feb 2011 20:09:59 +0100 Subject: [Pw_forum] RE : RE : A question on atomic magnetic moments In-Reply-To: <4D5ABFF4.1060501@materials.ox.ac.uk> References: <4D5ABFF4.1060501@materials.ox.ac.uk> Message-ID: <1297796999.4d5acf870120c@ipcms.u-strasbg.fr> Dear Nicola, with regards to your comments "it keeps you company during the voyage, > but shouldn't share your bed...", does this mean that smearing contribution print as "-TS" should be less than convergence criteria (typically 1mry) with regards to increase in no. of K points and KE cut-off for a SCF calculation? I would appreciate a clarification with best regards saqib javaid University of strasbourg. Selon Nicola Marzari : > > > Dear Giovanni, Cyrille, > > > the iron dimer has a very complex electronic structure (see e.g. our > PRL 2006 Kulik et al) - different multiplets, and for each multiplet, > different symmetries. > > In principle, there is no way to guess to which of the many > self-consistent states you'll converge to, and I suppose that what > you have here is that you have converged to different states. > You'll need to look at the total energy, kohn-sham eigenstates, and the > symmetry of those to understand what you are looking at > (also, there is no point in having more bands than efermi + 3*degauss - > empty bands above that threshold are useless). > > There is no easy way to force the code into one state or the other - > you could try using GGA+U - some U's will stabilize reliably one state, > and then by reducing smoothly the U (or increasing it) you might be able > to have (as a function of U) the energy of your preferred electronic > configuration. > > Last - for a cluster or a molecule smearing is used, somewhat > inappropriately, to help a calculation converge when using > iterative approaches - it keeps you company during the voyage, > but shouldn't share your bed (the real reason d'etre for > smearing is to improve k-point integrations in metals). > > nicola > > > On 2/15/11 5:42 PM, Giovani Faccin wrote: > > Dear Cyrille, > > > > I recalculated the dimer with different values of nbnd. Now some > > interesting changes appeared: > > > > Value of nbnd | Magnetization > > > > 10 4.00 > > 12 6.88 > > 14 6.49 > > 16 6.49 > > 18 6.49 > > 20 6.49 > > 22 6.88 > > 24 6.88 > > 26 6.49 > > 28 6.49 > > > > > -- > ---------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials University of Oxford > Chair of Materials Modelling Director, Materials Modelling Laboratory > nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From giannozz at democritos.it Tue Feb 15 20:19:25 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 15 Feb 2011 20:19:25 +0100 Subject: [Pw_forum] problem with pp.x and dos and a question about vectors in ILDOS calculation In-Reply-To: References: Message-ID: <076C4EE8-5BC7-4101-BCFE-92DB97E842E6@democritos.it> On Feb 15, 2011, at 19:48 , pari shok wrote: > I downloaded ATLAS this is completely irrelevant to your problem > I should emphasise that dos.x and pp.x in the old > machine work properly for the same inputs. so why don't you use the old machine? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From sclauzer at sissa.it Tue Feb 15 22:54:54 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 15 Feb 2011 22:54:54 +0100 Subject: [Pw_forum] problem with pp.x and dos and a question about vectors in ILDOS calculation In-Reply-To: References: Message-ID: <9AAB9B85-62B3-4AAC-B0B5-3C8FEFB81599@sissa.it> Some hints: 1) buggy compiler? which versions of gfortran are you using? is it the same on both machines? Have you tried with a different compiler? 2) try to define better the configuration giving problem: which compiler, which QE version? If you compare different compilers/QE versions on the two machines it is more difficult to spot out where is the problem. 3) monitor memory usage (with top command for instance: you can execute it on the background and print to file snapshots of system usage) 4) try to understand at which point of execution the code stops. open the source files of the code that crashes, put some print instructions. Better, use a debugger... GS Il giorno 15/feb/2011, alle ore 19.48, pari shok ha scritto: > Dear All, > problem with pp.x and dos and a question about vectors in ILDOS calculation. > Firstly, the problem with pp.x and dos.x: > I downloaded QE in two machines: > intel (R) pentium (R) 4 cpu 3 GHz with total memory 2GB, uses gfortran and > intel (R) core (TM) i7 cpu 870 @2.93 GHz, with 4GB total memory, uses gfortran. > everything is working perfectly well with the first machine (with espresso-4.1.2), but dos.x and pp.x both crash with "out of memory/ memory allocation" error in the second machine for big structures (espresso-4.2.1 and espresso-4.2). It should be noted that pw.x works properly and the "memory allocation" error happens just for dos and post processing. Sometimes, it seems that both pp.x and dos.x are frozen. In this case, nothing is written to output file and the programs don't even send any memory messages. > I downloaded ATLAS and modified "make.sys" accordingly but it didn't help. I used "ulimit -s unlimited" command, it didn't help either. > I should emphasise that dos.x and pp.x in the old machine work properly for the same inputs. Therefore, the input files don't have any problems. > I am really obsessed with it. I would really be grateful if anybody who had experienced the same problem could help me somehow. > > Secondly, a couple of questions about vectors in ILDOS: > 1. If the origin of ILDOS calculation is set to (000) and the vector is set to (001), does the ILDOS calculations spans the whole slab in "z" direction? > 2. Does ILDOS in one direction (along one vector) gives the LDOS on the plane perpendicular to that vector in each point? > > I really appreciate your help. > This is the second time that I've subscribed for the forum in the hope that this time my subscription would be successful. > Yours > P Shok > PhD at UMD > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110215/ee60d727/attachment.htm From faccin.giovani at gmail.com Wed Feb 16 05:58:46 2011 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Wed, 16 Feb 2011 00:58:46 -0400 Subject: [Pw_forum] RE : RE : A question on atomic magnetic moments In-Reply-To: <4D5ABFF4.1060501@materials.ox.ac.uk> References: <4D5ABFF4.1060501@materials.ox.ac.uk> Message-ID: Dear Nicola, Just read your article. Indeed, this dimer is not as easy as I first thought! I'm running a GGA+U study with U=3.1 eV (took that value from your article, hope I understood it correctly). It's interesting that with GGA+U, integer values are now appearing for the magnetization. For example, the first scf interactions reported this: interaction 1: 12.00 interaction 2: 4.00 interaction 3: 6.00 . . . last interaction: 8.00 Although the value everyone gets is 6.00, the fact that integer numbers are now showing up looks like progress. Smearing interference on the total energy is not happening anymore (I'm using degauss = 0.0005 - thanks Cyrille!) Example 25 on the QE distribution talks about setting the "starting_ns_eigenvalue" to explore different initial states on the energy landscape. I'm wondering if, perhaps, that parameter could be the path to reach a final 6.00 magnetization. I'll try to map different values of this variable along with the system's total energy and see what shows up; if something interesting is found, it'll be reported back here. Unfortunately I've got no prior experience with some aspects of electronic structure calculations. In particular, about the Kohn-Sham eigenstates analysis you mentioned, I'm not sure what to look for there. If I'm not being too much abusive, may I ask for some learning directions on this? (a book or article suggestion, or perhaps an example?) Thanks a lot! Giovani Faccin 2011/2/15 Nicola Marzari > > > Dear Giovanni, Cyrille, > > > the iron dimer has a very complex electronic structure (see e.g. our > PRL 2006 Kulik et al) - different multiplets, and for each multiplet, > different symmetries. > > In principle, there is no way to guess to which of the many > self-consistent states you'll converge to, and I suppose that what > you have here is that you have converged to different states. > You'll need to look at the total energy, kohn-sham eigenstates, and the > symmetry of those to understand what you are looking at > (also, there is no point in having more bands than efermi + 3*degauss - > empty bands above that threshold are useless). > > There is no easy way to force the code into one state or the other - > you could try using GGA+U - some U's will stabilize reliably one state, and > then by reducing smoothly the U (or increasing it) you might be able > to have (as a function of U) the energy of your preferred electronic > configuration. > > Last - for a cluster or a molecule smearing is used, somewhat > inappropriately, to help a calculation converge when using > iterative approaches - it keeps you company during the voyage, > but shouldn't share your bed (the real reason d'etre for > smearing is to improve k-point integrations in metals). > > nicola > > > > On 2/15/11 5:42 PM, Giovani Faccin wrote: > >> Dear Cyrille, >> >> I recalculated the dimer with different values of nbnd. Now some >> interesting changes appeared: >> >> Value of nbnd | Magnetization >> >> 10 4.00 >> 12 6.88 >> 14 6.49 >> 16 6.49 >> 18 6.49 >> 20 6.49 >> 22 6.88 >> 24 6.88 >> 26 6.49 >> 28 6.49 >> >> > > -- > ---------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials University of Oxford > Chair of Materials Modelling Director, Materials Modelling Laboratory > nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM > -- Giovani -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110216/f761310a/attachment-0001.htm From priyankagoud8 at gmail.com Wed Feb 16 08:29:04 2011 From: priyankagoud8 at gmail.com (priyanka goud) Date: Wed, 16 Feb 2011 12:59:04 +0530 Subject: [Pw_forum] Need Pseudo potentials Message-ID: Dear PWSCF users, I need pseudo potentials for Rb( Rubidium) metal. I have gone through this website (http://www.quantum-espresso.org/pseudo.php) for the same. But there are some elements(eg:Rb,Fr etc) for which pseudo potentials has not been defined. Is there any way to retrieve pseudo potentials for such elements(My case is Rubidium-Rb). Thanks in Advance. From yukihiro_okuno at fujifilm.co.jp Wed Feb 16 08:33:02 2011 From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp) Date: Wed, 16 Feb 2011 16:33:02 +0900 Subject: [Pw_forum] momentum matrix element calculation in PWSCF Message-ID: Dear PWSCF developers. I want to calculate absorption or dielectric (\epsion' or \epsilon'' ) of materials I know in order to get optical properties of materials accurately, Bethe Salpieter equation is recommended, but for saving calculation time, we want to do more simple calculation. Then, if the momentum operator matrix element ( or transition matrix element <\phi_{c} | r| \phi_{v} > ) <\phi_{c}|p|\phi_{v}> (where \phi_{c} , \phi_{v} is conduction and valence wave functions, respectively. and p is the momentum operator ) can be calculated, I think dielectric function can be estimated. Then, are there subroutine in PWSCF to calculate momentum matrix element in order to estimate the absorption or dielectric function. Can XSpectra be used to estimate the absorption or dielectric function of the materials ? Sincerely, Yukihiro Okuno. From degironc at sissa.it Wed Feb 16 09:21:39 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 16 Feb 2011 09:21:39 +0100 Subject: [Pw_forum] momentum matrix element calculation in PWSCF In-Reply-To: References: Message-ID: <4D5B8913.8050503@sissa.it> Dear yukihiro_okuno, did you take the time to read some literature/documentation/maiing list archive before posting your enquire ? please do. stefano On 02/16/2011 08:33 AM, yukihiro_okuno at fujifilm.co.jp wrote: > Dear PWSCF developers. > > I want to calculate absorption or dielectric (\epsion' or \epsilon'' ) of > materials > > I know in order to get optical properties of materials accurately, > > Bethe Salpieter equation is recommended, but for saving calculation > time, > > we want to do more simple calculation. > > Then, if the momentum operator matrix element ( or transition matrix > element<\phi_{c} | r| \phi_{v}> ) > > > <\phi_{c}|p|\phi_{v}> (where \phi_{c} , \phi_{v} is conduction and valence > wave functions, respectively. > > and p is the momentum operator ) > > can be calculated, I think dielectric function can be estimated. > > Then, are there subroutine in PWSCF to calculate momentum matrix element in > order to estimate the > > absorption or dielectric function. > > Can XSpectra be used to estimate the absorption or dielectric function of > the materials ? > > > Sincerely, Yukihiro Okuno. > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From sks.jnc at gmail.com Wed Feb 16 09:41:55 2011 From: sks.jnc at gmail.com (S. K. S.) Date: Wed, 16 Feb 2011 09:41:55 +0100 Subject: [Pw_forum] Ge LDA USPP Message-ID: Dear QE Friends, Does any one have LDA-USPP for Ge ? Thanking you, Saha SK RA JNCASR Bangalore-560012 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110216/bbb31d29/attachment.htm From kirtinandan07 at gmail.com Wed Feb 16 10:38:57 2011 From: kirtinandan07 at gmail.com (vicky singh) Date: Wed, 16 Feb 2011 15:08:57 +0530 Subject: [Pw_forum] not able to visualize the optimized coordinate of the output file with xcrysden Message-ID: Dear friends I want to visualize the optimized coordinate or latest coordinate of the output file for pw.x with xcrysden but it gives an error. For optimized coordinate error is ERROR: While executing exec sh /home/XCrySDen-1.4.1bin-static/scripts/pwo2xsf.sh -optcoor for latest coordinate the error is Error: ERROR: wrong number of fields (6) in atomic coordinates, should be 4 or 7. Thanks in advance vicky singh research student Bangalore -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110216/c81be2bf/attachment.htm From nicola.marzari at materials.ox.ac.uk Wed Feb 16 11:13:08 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Wed, 16 Feb 2011 10:13:08 +0000 Subject: [Pw_forum] Need Pseudo potentials In-Reply-To: References: Message-ID: <4D5BA334.6010301@materials.ox.ac.uk> Dear Priyanka, there are a few projects that make their pseudopotentials available - if you go to http://quantum-espresso.org/pseudo.php and click on the left ("Notes") you'll see the links. The Fritz-Haber package, in particular, has a Troullier-Martin pseudopotential for Rubidium, that could be converted into UPF using the converter fhi2upf (in upftools). Once you have generated/converted the pseudo, test it. Does the atom come out with PWSCF as it does in the pseudo code (same pseudoeigenvalues, once you take into account that the zero of energy is different)? Are there other calculations you can compare yourself to? nicola On 2/16/11 7:29 AM, priyanka goud wrote: > Dear PWSCF users, > > I need pseudo potentials for Rb( > Rubidium) metal. > I have gone through this website > (http://www.quantum-espresso.org/pseudo.php) for the same. > But there are some elements(eg:Rb,Fr etc) for which pseudo potentials > has not been defined. > > Is there any way to retrieve pseudo potentials for such elements(My > case is Rubidium-Rb). > > Thanks in Advance. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From nicola.marzari at materials.ox.ac.uk Wed Feb 16 11:35:51 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Wed, 16 Feb 2011 10:35:51 +0000 Subject: [Pw_forum] momentum matrix element calculation in PWSCF In-Reply-To: References: Message-ID: <4D5BA887.1040705@materials.ox.ac.uk> Dear Yukihiro, epsil.f90 (in QE) does what you ask, but probably it would be worth investing in YAMBO or SaX (both public and interfaced with QE). Note that the reconstruction of the AE wavefunction might be relevant. Maybe others can comment on that ? nicola On 2/16/11 7:33 AM, yukihiro_okuno at fujifilm.co.jp wrote: > > Dear PWSCF developers. > > I want to calculate absorption or dielectric (\epsion' or \epsilon'' ) of > materials > > I know in order to get optical properties of materials accurately, > > Bethe Salpieter equation is recommended, but for saving calculation > time, > > we want to do more simple calculation. > > Then, if the momentum operator matrix element ( or transition matrix > element<\phi_{c} | r| \phi_{v}> ) > > > <\phi_{c}|p|\phi_{v}> (where \phi_{c} , \phi_{v} is conduction and valence > wave functions, respectively. > > and p is the momentum operator ) > > can be calculated, I think dielectric function can be estimated. > > Then, are there subroutine in PWSCF to calculate momentum matrix element in > order to estimate the > > absorption or dielectric function. > > Can XSpectra be used to estimate the absorption or dielectric function of > the materials ? > > > Sincerely, Yukihiro Okuno. > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From sclauzer at sissa.it Wed Feb 16 11:42:07 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 16 Feb 2011 11:42:07 +0100 Subject: [Pw_forum] not able to visualize the optimized coordinate of the output file with xcrysden In-Reply-To: References: Message-ID: <14FC3DDF-F291-4D95-A797-92BF97264F74@sissa.it> Please redirect the question to the xcrysden forum. Il giorno 16/feb/2011, alle ore 10.38, vicky singh ha scritto: > Dear friends > I want to visualize the optimized coordinate or latest coordinate of the output file for pw.x with xcrysden but it gives an error. > > For optimized coordinate error is > ERROR: While executing exec sh > /home/XCrySDen-1.4.1bin-static/scripts/pwo2xsf.sh -optcoor Try to update to the latest version XCrySDen/1.5.17-bin/xcrysden > > for latest coordinate the error is > Error: ERROR: wrong number of fields (6) in atomic coordinates, should be 4 or 7. How do your final coordinates look like in the the PWscf output file? Have you had a look inside? GS > > Thanks in advance > > vicky singh > research student Bangalore > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110216/cedad79a/attachment.htm From faccin.giovani at gmail.com Wed Feb 16 13:03:47 2011 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Wed, 16 Feb 2011 08:03:47 -0400 Subject: [Pw_forum] RE : RE : A question on atomic magnetic moments In-Reply-To: <4D5BA8F3.9000203@materials.ox.ac.uk> References: <4D5ABFF4.1060501@materials.ox.ac.uk> <4D5BA8F3.9000203@materials.ox.ac.uk> Message-ID: Nicola, Now I understand it! :P Thanks again! Giovani 2011/2/16 Nicola Marzari > > > Ciao Giovanni, > > I was suggesting just to plot them, using Xcryden, and look at their > symmetries - then you understand we you have say, a sigma, pi or > delta molecular orbital, etc... > > nicola > > > Unfortunately I've got no prior experience with some aspects of >> electronic structure calculations. In particular, about the Kohn-Sham >> eigenstates analysis you mentioned, I'm not sure what to look for there. >> If I'm not being too much abusive, may I ask for some learning >> directions on this? (a book or article suggestion, or perhaps an example?) >> >> > > -- > ---------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials University of Oxford > Chair of Materials Modelling Director, Materials Modelling Laboratory > nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM > -- Giovani -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110216/8a1a5c49/attachment.htm From neto.baldini at gmail.com Wed Feb 16 14:18:41 2011 From: neto.baldini at gmail.com (Ettore Baldini Neto) Date: Wed, 16 Feb 2011 11:18:41 -0200 Subject: [Pw_forum] Problems with 'relax' calculations Message-ID: Dear users, I'm trying to relax a 32C graphene layer with a Ti atom and the calculation simply stops without any error messages. I'm attaching my input in order to get some insight in what's going on. Is there any parameter badly defined? Although I know I must include spin polarization, for now I'm not considering it. But what would it be a good value for starting_magnetization for Ti?? I have no experience in performing such calculations. Thanks for your help Bests Ettore PS. The last thing it writes in the output is: ..... iteration # 4 ecut= 40.00 Ry beta=0.70 CG style diagonalization ethr = 1.95E-07, avg # of iterations = 3.2 negative rho (up, down): 0.369E-02 0.000E+00 total cpu time spent up to now is 8905.97 secs total energy = -481.99306649 Ry Harris-Foulkes estimate = -481.99307188 Ry estimated scf accuracy < 0.00002695 Ry iteration # 5 ecut= 40.00 Ry beta=0.70 CG style diagonalization .......... ********************************************************************** Dr. Ettore Baldini-Neto Researcher W.von Braun Center for Advanced Research, Campinas, Brazil ********************************************************************** -------------- next part -------------- A non-text attachment was scrubbed... Name: 1MLG_Ti.inp.rtf Type: text/rtf Size: 1661 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110216/7297aae3/attachment.bin From faccin.giovani at gmail.com Wed Feb 16 14:28:25 2011 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Wed, 16 Feb 2011 09:28:25 -0400 Subject: [Pw_forum] Problems with 'relax' calculations In-Reply-To: References: Message-ID: Ettore, One thing that can make pw.x freeze is bad behaviour from the MPI implementation. I've experienced random freezes myself when using QE with openmpi on a single node, multicore computer. If you are running your calculation in parallel, give it a try in serial just to see if it can pass the point where this error is occuring. Giovani Faccin CPPP-UFMS/IFGW-Unicamp - Brazil 2011/2/16 Ettore Baldini Neto > Dear users, > > I'm trying to relax a 32C graphene layer with a Ti atom and the calculation > simply stops without any error messages. > I'm attaching my input in order to get some insight in what's going on. Is > there any parameter badly defined? > Although I know I must include spin polarization, for now I'm not > considering it. But what would it be a good value > for starting_magnetization for Ti?? I have no experience in performing such > calculations. > > Thanks for your help > > Bests > > Ettore > > PS. The last thing it writes in the output is: > > ..... > iteration # 4 ecut= 40.00 Ry beta=0.70 > CG style diagonalization > ethr = 1.95E-07, avg # of iterations = 3.2 > > negative rho (up, down): 0.369E-02 0.000E+00 > > total cpu time spent up to now is 8905.97 secs > > total energy = -481.99306649 Ry > Harris-Foulkes estimate = -481.99307188 Ry > estimated scf accuracy < 0.00002695 Ry > > iteration # 5 ecut= 40.00 Ry beta=0.70 > CG style diagonalization > .......... > > > ********************************************************************** > Dr. Ettore Baldini-Neto > Researcher > W.von Braun Center for Advanced Research, Campinas, Brazil > ********************************************************************** > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Giovani -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110216/d01ff9e7/attachment-0001.htm From neto.baldini at gmail.com Wed Feb 16 14:37:06 2011 From: neto.baldini at gmail.com (Ettore Baldini Neto) Date: Wed, 16 Feb 2011 11:37:06 -0200 Subject: [Pw_forum] Problems with 'relax' calculations In-Reply-To: References: Message-ID: Giovani, I was running it in parallel, mainly using -npool. ( I did perform this kind of calculation before and all went well). Now I'm doing a serial calculation, let's see. Thanks and best regards, Ettore On Feb 16, 2011, at 11:28 AM, Giovani Faccin wrote: > Ettore, > > One thing that can make pw.x freeze is bad behaviour from the MPI implementation. I've experienced random freezes myself when using QE with openmpi on a single node, multicore computer. > > If you are running your calculation in parallel, give it a try in serial just to see if it can pass the point where this error is occuring. > > Giovani Faccin > > CPPP-UFMS/IFGW-Unicamp - Brazil > > > > 2011/2/16 Ettore Baldini Neto > Dear users, > > I'm trying to relax a 32C graphene layer with a Ti atom and the calculation simply stops without any error messages. > I'm attaching my input in order to get some insight in what's going on. Is there any parameter badly defined? > Although I know I must include spin polarization, for now I'm not considering it. But what would it be a good value > for starting_magnetization for Ti?? I have no experience in performing such calculations. > > Thanks for your help > > Bests > > Ettore > > PS. The last thing it writes in the output is: > > ..... > iteration # 4 ecut= 40.00 Ry beta=0.70 > CG style diagonalization > ethr = 1.95E-07, avg # of iterations = 3.2 > > negative rho (up, down): 0.369E-02 0.000E+00 > > total cpu time spent up to now is 8905.97 secs > > total energy = -481.99306649 Ry > Harris-Foulkes estimate = -481.99307188 Ry > estimated scf accuracy < 0.00002695 Ry > > iteration # 5 ecut= 40.00 Ry beta=0.70 > CG style diagonalization > .......... > > > ********************************************************************** > Dr. Ettore Baldini-Neto > Researcher > W.von Braun Center for Advanced Research, Campinas, Brazil > ********************************************************************** > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Giovani > _______________________________________________ > 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/20110216/4b415d6d/attachment.htm From xrhino at gmail.com Wed Feb 16 17:04:28 2011 From: xrhino at gmail.com (YY) Date: Wed, 16 Feb 2011 11:04:28 -0500 Subject: [Pw_forum] problems computing cholesky decomposition Message-ID: Dear All, I meet a "problems computing cholesky decomposition" problem while doing the parallel calculations. I checked the archives of this mailing list and din't find a proper solution. So I write here for further help. I am doing the relaxation/scf calculation. When I submitted the job on a blue-gene machine with " -np 512 -npool 2" , it works but too slow (1000 sec per electron step). So I tried a higher level parallel calculation with "-np 512 -npool 2 -ntg 4 -ndiag 16", and it gave a CRASH report as: from pdpotrf : error # 23 problems computing cholesky decomposition I checked the memory usage, and it is not the reason. Here is the input file and thanks for your help! &control calculation='scf' restart_mode='from_scratch', pseudo_dir = '/gpfs/small/STED/home/STEDzhyy/pseudo/pwscf' outdir='./tmp' prefix='pbe' tprnfor = .true. tstress = .false. disk_io='none' / &system ibrav= 0, celldm(1)=1.8897, nat= 249, ntyp= 4, ecutwfc =25,ecutrho=150 occupations='smearing', smearing='gaussian', degauss=0.0072, nspin = 2, starting_magnetization(1)=0 starting_magnetization(2)=0 starting_magnetization(3)=0.01 starting_magnetization(4)=0.05 / &electrons / CELL_PARAMETERS cubic 17.8076000000000008 -10.2812000000000001 0.0000000000000000 0.0000000000000000 20.5624000000000002 0.0000000000000000 0.0000000000000000 0.0000000000000000 25.0000000000000000 ATOMIC_SPECIES C 12.0107 C.pbe-van_ak.UPF H 1.00794 H.pbe-van_ak.UPF N 14.007 N.pbe-van_ak.UPF Cu 63.546 Cu.pbe-n-van_ak.UPF ATOMIC_POSITIONS {crystal} C 0.6877770687760563 0.7285346962446679 0.5652978667315952 1 1 1 C 0.6645003128091277 0.7848711188927444 0.5642487594707469 1 1 1 *********** Cu 0.0416700000000034 0.9583299999999966 0.2518400000000014 0 0 0 Cu 0.0416700000000034 0.4583299999999966 0.2518400000000014 0 0 0 K_POINTS {gamma} Yuyang Zhang Nanoscale Physics and Devices Laboratory Institute of Physics, Chinese Academy of Sciences Beijing 100190, P. R. China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110216/3ae8e426/attachment.htm From claudial.81 at gmail.com Wed Feb 16 18:10:53 2011 From: claudial.81 at gmail.com (Claudia Loyola) Date: Wed, 16 Feb 2011 11:10:53 -0600 Subject: [Pw_forum] Wrong ELF values In-Reply-To: <4D5AA6E7.2030404@sissa.it> References: <4D5263FD.90000@sissa.it> <4D5A32E9.3090505@sissa.it> <4D5AA6E7.2030404@sissa.it> Message-ID: Hello! I am sorry, I did not answer before! well I saw the "pp" file (the *.charge in my case) and how it is a large file I have to use a big command line for see what are the minimum an maximum values for the elf calculation, and the range was from 0 to 1, so they are right! :) . How said Giovanni, xcrysden interpolates the data, for this reason, the values were out of range. Probably contour and plotrho output_format do the same. Thanks for help me! :) best regards, Claudia Loyola On Tue, Feb 15, 2011 at 10:16 AM, Stefano de Gironcoli wrote: > I see... > how large is your calculation? if it is not too big, would you mind send me > (at my email) one set of input and output to have a look ? > stefano > > > On 02/15/2011 04:42 PM, Claudia Loyola wrote: > > Hello! > > yes, you are right if I define the vectors in function of "a" and I define > alat=a , but let me show you how I define the vectors in the scf input file: > > &SYSTEM > ibrav = 0 , > celldm(1) =1.0 , > . > . > . > CELL_PARAMETERS (alat=1.0) > 19.109476287 -0.014917030 0.000000953 > -9.542147268 16.554932043 0.000000170 > 0.000000706 0.000000344 14.136501037 > > so in this case the vector basis are the real large in bohr, and the alat is > 1.0 like celldm(1). Indeed, the value of the vectors for pp.x are in > function of alat, but my alat is 1.0, so I can write directly in bohr the > values of the planes that I take, in fact I take "two replicates" in each > direction. I think this is correct too. > > Thank you very much for your comments :) > > regards, > Claudia Loyola > > On Tue, Feb 15, 2011 at 2:01 AM, Stefano de Gironcoli wrote: > > > Dear Claudia, > I may not remember correctly what the format adopted by pp.x to > define planes is... but i think it is Cartesian coordinates in unit of > alat (aka celldm(1)). > > so when you write > e1(1) =38.218, e1(2)=0.0, e1(3) = 0.0, > e2(1) =0.0, e2(2)=33.108, e2(3) = 0.0, > this means presumably 38 x 33 UNIT CELLS, sampled with 100x100 points > (that is about 2-3 points in each unit cell). No surprise the FFT > interpolation used gets confused. > > I think you should use more sensible values for e1(1) and e2(2)... what > is your value of celldm(1)? > > At least this is my guess. > > stefano > > > On 02/14/2011 06:57 PM, Claudia Loyola wrote: > > Well, this is one of the input file: > > &inputpp > &plot > nfile = 1 , > filepp(1) = 'Ba38_33_10.charge' , > weight(1) = 1.0 , > iflag = 2 , > output_format = 3 , > fileout = 'ba.rho38_33_10.xsf' , > x0(1) =0.0, x0(2)=0.0, x0(3) = 10.602, > e1(1) =38.218, e1(2)=0.0, e1(3) = 0.0, > e2(1) =0.0, e2(2)=33.108, e2(3) = 0.0, > nx=100, ny=100 > / > > _______________________________________________ > Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > _______________________________________________ > Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Claudia Loyola Canales Postdoc in Computational Physics Iowa State University Iowa, USA http://www.lpmd.cl/claudial http://www.lpmd.cl http://cosmic.mse.iastate.edu/ http://www.gnm.cl -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110216/81260be9/attachment.htm From eyvaz_isaev at yahoo.com Wed Feb 16 20:15:22 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 16 Feb 2011 11:15:22 -0800 (PST) Subject: [Pw_forum] [Pw_Forum] specific heat In-Reply-To: References: Message-ID: <684991.94316.qm@web65713.mail.ac4.yahoo.com> Dear Wilfredo, Yes, T_start, T_end, T_step are integers. If you like use small T_step, just go to /QHA/SRC/F_QHA.f90 and edit the line 65: integer :: T_start, T_end, T_step just change the line to real (kind=8) :: T_start, T_end, T_step Then recompile QHA. What is the temperature range you are interested in? Any problem, please let me know. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: Wilfredo Ibarra Hern?ndez To: Pw_forum at pwscf.org Sent: Tue, February 15, 2011 7:29:53 PM Subject: [Pw_forum] [Pw_Forum] specific heat Dear all. In the past I was asked if someone worked with the calculation of specific heat. I'm working with QHA, but I have a question. The temperature for this calculation, It's necessary be integer? because I modify the Edit_me file, but when I put delta_T with values like 0.1 the calculation not write anything in the "system.QHA.out" and I need this values because I want make a graphic "Cv/T^3 Vs. T". And the important values are near to zero. Thanks for you help. ~~~~~~~~~~~~~~~~~~~~~~~~~~~ Ibarra Hern?ndez Wilfredo Master student in materials science Cinvestav unidad Qu?retaro Qu?retaro, M?xico. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110216/a11d81e8/attachment-0001.htm From parishok at gmail.com Wed Feb 16 22:27:55 2011 From: parishok at gmail.com (pari shok) Date: Wed, 16 Feb 2011 16:27:55 -0500 Subject: [Pw_forum] DOS on the planes in the middle of slab Message-ID: Dear All, I need to calculate DOS on different planes in the middle of the slab that I made. I should mention that I put vacuum on the top of whole structure as well. This is why - I need to know more information about the output file of ILDOS on a plane. - Moreover, according to the LDOS formula, the LDOS in each point of z direction is the average LDOS on the plane perpendicular to it (x,y). I was wondering whether ILDOS on on the z vector from (000) to (001): 1. spans the whole slab height, 2. gives the plane average of LDOS on the plane perpendicular to each point on the vector (of course in that specified min and max energy). Any kind of help would be greatly appreciated. Thank you. P Shokri -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110216/6a4b4d49/attachment.htm From degironc at sissa.it Wed Feb 16 22:48:00 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 16 Feb 2011 22:48:00 +0100 Subject: [Pw_forum] Wrong ELF values In-Reply-To: References: <4D5263FD.90000@sissa.it> <4D5A32E9.3090505@sissa.it> <4D5AA6E7.2030404@sissa.it> Message-ID: <4D5C4610.8070905@sissa.it> yet... if plotrho interpolates data in a crazy way it would be better to see on what it depends... can you send me the "pp" file and the input to plotrho ? is the one you posted earlier? regards, stefano On 02/16/2011 06:10 PM, Claudia Loyola wrote: > Hello! > > I am sorry, I did not answer before! > well I saw the "pp" file (the *.charge in my case) and how it is a large > file I have to use a big command line for see what are the minimum an > maximum values for the elf calculation, and the range was from 0 to 1, so > they are right! :) . How said Giovanni, xcrysden interpolates the data, for > this reason, the values were out of range. Probably contour and > plotrho output_format > do the same. > > Thanks for help me! :) > best regards, > Claudia Loyola > > On Tue, Feb 15, 2011 at 10:16 AM, Stefano de Gironcoliwrote: > >> I see... >> how large is your calculation? if it is not too big, would you mind send me >> (at my email) one set of input and output to have a look ? >> stefano >> >> >> On 02/15/2011 04:42 PM, Claudia Loyola wrote: >> >> Hello! >> >> yes, you are right if I define the vectors in function of "a" and I define >> alat=a , but let me show you how I define the vectors in the scf input file: >> >> &SYSTEM >> ibrav = 0 , >> celldm(1) =1.0 , >> . >> . >> . >> CELL_PARAMETERS (alat=1.0) >> 19.109476287 -0.014917030 0.000000953 >> -9.542147268 16.554932043 0.000000170 >> 0.000000706 0.000000344 14.136501037 >> >> so in this case the vector basis are the real large in bohr, and the alat is >> 1.0 like celldm(1). Indeed, the value of the vectors for pp.x are in >> function of alat, but my alat is 1.0, so I can write directly in bohr the >> values of the planes that I take, in fact I take "two replicates" in each >> direction. I think this is correct too. >> >> Thank you very much for your comments :) >> >> regards, >> Claudia Loyola >> >> On Tue, Feb 15, 2011 at 2:01 AM, Stefano de Gironcoli wrote: >> >> >> Dear Claudia, >> I may not remember correctly what the format adopted by pp.x to >> define planes is... but i think it is Cartesian coordinates in unit of >> alat (aka celldm(1)). >> >> so when you write >> e1(1) =38.218, e1(2)=0.0, e1(3) = 0.0, >> e2(1) =0.0, e2(2)=33.108, e2(3) = 0.0, >> this means presumably 38 x 33 UNIT CELLS, sampled with 100x100 points >> (that is about 2-3 points in each unit cell). No surprise the FFT >> interpolation used gets confused. >> >> I think you should use more sensible values for e1(1) and e2(2)... what >> is your value of celldm(1)? >> >> At least this is my guess. >> >> stefano >> >> >> On 02/14/2011 06:57 PM, Claudia Loyola wrote: >> >> Well, this is one of the input file: >> >> &inputpp >> &plot >> nfile = 1 , >> filepp(1) = 'Ba38_33_10.charge' , >> weight(1) = 1.0 , >> iflag = 2 , >> output_format = 3 , >> fileout = 'ba.rho38_33_10.xsf' , >> x0(1) =0.0, x0(2)=0.0, x0(3) = 10.602, >> e1(1) =38.218, e1(2)=0.0, e1(3) = 0.0, >> e2(1) =0.0, e2(2)=33.108, e2(3) = 0.0, >> nx=100, ny=100 >> / >> >> _______________________________________________ >> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum >> >> >> _______________________________________________ >> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110216/52988fd0/attachment.htm From wibarrah at gmail.com Wed Feb 16 23:45:19 2011 From: wibarrah at gmail.com (=?ISO-8859-1?Q?Wilfredo_Ibarra_Hern=E1ndez?=) Date: Wed, 16 Feb 2011 16:45:19 -0600 Subject: [Pw_forum] [Pw_Forum] specific heat In-Reply-To: <684991.94316.qm@web65713.mail.ac4.yahoo.com> References: <684991.94316.qm@web65713.mail.ac4.yahoo.com> Message-ID: thanks for the answer. I want to look Cv at 0.5 ?K or less near to zero, but I worked with my values after 1 ?K and I things are very good the graphic looks amazing. And the QHA works great. Congratulations for the implementation 2011/2/16 Eyvaz Isaev > Dear Wilfredo, > > Yes, T_start, T_end, T_step are integers. If you like use small T_step, > just go to /QHA/SRC/F_QHA.f90 and edit the line 65: > > integer :: T_start, T_end, T_step > > just change the line to real (kind=8) :: T_start, T_end, T_step > > Then recompile QHA. > What is the temperature range you are interested in? Any problem, please > let me know. > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > ------------------------------ > *From:* Wilfredo Ibarra Hern?ndez > *To:* Pw_forum at pwscf.org > *Sent:* Tue, February 15, 2011 7:29:53 PM > *Subject:* [Pw_forum] [Pw_Forum] specific heat > > Dear all. > > In the past I was asked if someone worked with the calculation of specific > heat. I'm working with QHA, but I have a question. > > The temperature for this calculation, It's necessary be integer? because I > modify the Edit_me file, but when I put delta_T with values like 0.1 the > calculation not write anything in the "system.QHA.out" and I need this > values because I want make a graphic "Cv/T^3 Vs. T". And the important > values are near to zero. > > Thanks for you help. > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Ibarra Hern?ndez Wilfredo > Master student in materials science > Cinvestav unidad Qu?retaro > Qu?retaro, M?xico. > > > _______________________________________________ > 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/20110216/2bea67fc/attachment.htm From nicola.marzari at materials.ox.ac.uk Thu Feb 17 00:00:43 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Wed, 16 Feb 2011 23:00:43 +0000 Subject: [Pw_forum] [Pw_Forum] specific heat In-Reply-To: References: <684991.94316.qm@web65713.mail.ac4.yahoo.com> Message-ID: <4D5C571B.8080701@materials.ox.ac.uk> On 2/16/11 10:45 PM, Wilfredo Ibarra Hern?ndez wrote: > thanks for the answer. > I want to look Cv at 0.5 ?K or less near to zero, but I worked with my > values after 1 ?K and I things are very good the graphic looks amazing. > And the QHA works great. Congratulations for the implementation > BTW, at those temperature you can calculate it analytically (maybe with the help of mathematica), just assuming linear dispersion relations (since the only modes that matter are the acoustic modes near gamma). The dynamical matrix will be determined by the total mass of the unit cell, and by the elastic constants of the material (that you can take from experiments or calculate with finite strains). nicola ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From wang.riping.81 at gmail.com Thu Feb 17 06:47:31 2011 From: wang.riping.81 at gmail.com (Riping WANG) Date: Thu, 17 Feb 2011 14:47:31 +0900 Subject: [Pw_forum] record for quantum espresso installation on 64bit fedora-14 on intel computer Message-ID: Dear forum, I attached my record for quantum espresso installation on 64bit fedora-14 on intel computer. Hope it can save somebody's time. WANG Riping 2010.2.17 ####################################################################################### #!/bin/bash #quantum espresso installation on 64 bit fedora-14 at intel computer #Please follow this record carefully. Many small error takes a newer a lot of time. #1. system installation. when partition the disk, select the first one to use all the hard disk. #2. set IP and DNS. #IP: 150.46.48.xxx #Netmask: 255.255.255.0 #Gateway: 150.46.48.4 #DNS: 150.46.44.4 #3. set some global setting. This step must be done before install software. su echo "wang ALL=(ALL) ALL" >> /etc/sudoers && sed -i '1,10s/SELINUX=enforcing/SELINUX=permissive/' /etc/selinux/config exit #add PATH and LD_LIBRARY_PATH in /etc/profile. #It is better to add by gedit or vi. Such as: sudo gedit /etc/profile #If add by the way like "echo ... >> /etc/profile", #It may be in root: echo "export LD_LIBRARY_PATH=/opt/intel/bin/intel64/:/opt/intel/composerxe-2011.2.137/compiler/lib/intel64/:/usr/local/lib" >> /etc/profile #But it is not recommended. I have may times to have error in this way. #intel (icc,ifort and MKL) is automatically installed /opt/intel/ #/usr/local/ is for openmpi # So for other version, it is necessary to adjust coresponding numbers when adding PATH and LD_LIBRARY_PATH. export PATH=$PATH:/opt/intel/bin/:/opt/intel/composerxe-2011.2.137/compiler/bin/intel64:/tmp/espresso-4.2.1/bin/:/usr/local/bin/ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/intel/bin/intel64/:/opt/intel/composerxe-2011.2.137/compiler/lib/intel64/:/usr/local/lib/ exit # You have to restart the computer here. #4. install software #Install c++ before install icc and ifort. yum -y install gcc-c++ #MKL is contained automatically. #Download ifort from http://software.intel.com/en-us/articles/non-commercial-software-download/ #It is better to install purely 64 bit code, which can be selected from official download web. #my series number for icc: N5D5-G5HV9WX2 #my series number for ifort: VW5G-KXG4S6MM #For detail, following http://conquer-ur-computer.blogspot.com/2010/12/install-intel-fortran-c-ifort-icc-in.html # Install openmpi,fftw,espresso # It is better to download from http://www.open-mpi.org/ . # If use yum install openmpi, it can not recognize gfortran instead of ifort. # For cc when installing openmpi, I use gcc as default; I try to use icc, but failed. # install fftw. Download fftw from http://www.fftw.org/index.html # install quantum espresso. Download from http://qe-forge.org/frs/?group_id=10 # when configure, /opt/intel/mkl/lib/intel64 are diretory where MKL is installed. Do not miss -L in this line. /home/wang/espresso/install are espress to be installed. Do not miss -lmkl_em64t_nothread. # All is installed in root usr. # For espresso, for my case, the pseudopotential files must be stored in /home/wang/espreso/pseudo/, otherwise the cp.x can not find pseudo potential files. cp.x do do recoganize PSEUDO_DIR in the input file. su yum -y install preupgrade && yum -y update && yum -y install gcc-c++ gnuplot octave tigervnc serviceconf wget yum -y groupinstall "Office/Productivity" && yum list openoffice* && yum -y install openoffice.org-langpack-zh_CN # install openoffice. cd openmpi-1.4.3 ./configure --prefix=/usr/local F77=ifort FC=ifort make all install cd .. cd fftw-3.2.2 ./configure --enable-threads make make install cd .. cd espresso-4.2.1 ./configure BLAS_LIBS="-L/tmp/espresso-4.2.1/install -L/opt/intel/mkl/lib/intel64 -lmkl_em64t_nothread" LAPACK_LIBS="-L/tmp/espresso-4.2.1/install -L/opt/intel/mkl/lib/intel64" make all cd .. exit #5 set ssh and farewall, It is better to set this step after su sudo sed -i 's/GSSAPIAuthentication yes/#GSSAPIAuthentication yes/g' /etc/ssh/sshd_config sudo sed -i 's/GSSAPICleanupCredentials yes/#GSSAPICleanupCredentials yes/g' /etc/ssh/sshd_config sudo sed -i 's/#RSAAuthentication yes/RSAAuthentication yes/g' /etc/ssh/sshd_config sudo sed -i 's/#PubkeyAuthentication yes/PubkeyAuthentication yes/g' /etc/ssh/sshd_config sudo sed -i 's/#AuthorizedKeysFile/AuthorizedKeysFile/g' /etc/ssh/sshd_config ssh-agent /etc/init.d/sshd start /etc/init.d/iptables save /etc/init.d/iptables stop chkconfig sshd on exit ####################################################################################### -- ****************************************************************************** WANG Riping Ph.D student, Institute for Study of the Earth's Interior,Okayama University, 827 Yamada, Misasa, Tottori-ken 682-0193, Japan Tel: +81-858-43-3739(Office), 1215(Inst) E-mail: wang.riping.81 at gmail.com ****************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110217/2f8f9cab/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: quantum espresso installation on 64bit fedora-14 on intel computer Type: application/octet-stream Size: 4353 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110217/2f8f9cab/attachment-0001.obj From germaneau at gucas.ac.cn Thu Feb 17 21:00:55 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Thu, 17 Feb 2011 15:00:55 -0500 Subject: [Pw_forum] compilation error Message-ID: <4D5D7E77.1080405@gucas.ac.cn> Dear QE users, when I compile (make all) QE on a x86_64 mahine with gfortran 4.4.4 I got the follwing error: /metadyn_io.f90:18.17: USE iotk_module 1 Fatal Error: Parse error when checking module version for file 'iotk_module.mod' opened at (1) make[1]: *** [metadyn_io.o] Error 1 make[1]: Leaving directory `/home/germaneau/soft/science/DFT-codes/quantum_expresso/espresso-4.2.1/Modules' make: *** [mods] Error 2/ When I compile on my i686 laptop with gfortran 4.3.3 it goes just fine. Can you please tell me whether you experienced this issue and how did you solve it? Thanks in advance, Eric. -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of ChineseAcademy of Sciences Yuquan Road 19A Beijing 100049 China /Please consider the environment before printing this email. Consid?rez svp l'environnement avant d'imprimer cet email. / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110217/04264343/attachment.htm From giannozz at democritos.it Thu Feb 17 09:29:12 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 17 Feb 2011 09:29:12 +0100 Subject: [Pw_forum] compilation error In-Reply-To: <4D5D7E77.1080405@gucas.ac.cn> References: <4D5D7E77.1080405@gucas.ac.cn> Message-ID: <1B760E5F-76BC-449D-95B9-365F491821C4@democritos.it> On Feb 17, 2011, at 21:00 , Eric Germaneau wrote: > USE iotk_module > 1 > Fatal Error: Parse error when checking module version for file > 'iotk_module.mod' opened at (1) rm iotk/src/iotk_module.o iotk/src/iotk_module.mod Please specify the QE version when reporting compilation problems P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From Lorenzo.Paulatto at impmc.upmc.fr Thu Feb 17 10:36:42 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Thu, 17 Feb 2011 10:36:42 +0100 Subject: [Pw_forum] compilation error In-Reply-To: <4D5D7E77.1080405@gucas.ac.cn> References: <4D5D7E77.1080405@gucas.ac.cn> Message-ID: Dear Eric, Apparently you started to compile with a certain compiler, than you reconfigured for another one (or another version of the same) and continued. Issue a "make clean" before recompiling. On Thu, 17 Feb 2011 21:00:55 +0100, Eric Germaneau wrote: > Dear QE users, > > when I compile (make all) QE on a x86_64 mahine with gfortran 4.4.4 I > got the follwing error: > > /metadyn_io.f90:18.17: > > USE iotk_module > 1 > Fatal Error: Parse error when checking module version for file > 'iotk_module.mod' opened at (1) > make[1]: *** [metadyn_io.o] Error 1 > make[1]: Leaving directory > `/home/germaneau/soft/science/DFT-codes/quantum_expresso/espresso-4.2.1/Modules' > make: *** [mods] Error 2/ > > When I compile on my i686 laptop with gfortran 4.3.3 it goes just fine. > Can you please tell me whether you experienced this issue and how did > you solve it? > Thanks in advance, > > > Eric. > -- Lorenzo Paulatto (IdR) IMPMC - CNRS UMR 7590 & Universit? P&M Curie T23-C13/23-5e27 - 4 place Jussieu - 75252 Paris Cedex5 phone: +33 (0)144 27 5211 www: http://www-int.impmc.upmc.fr/~paulatto/ From germaneau at gucas.ac.cn Fri Feb 18 03:20:38 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Thu, 17 Feb 2011 21:20:38 -0500 Subject: [Pw_forum] compilation error In-Reply-To: <497926617.03978@test1.gucas.ac.cn> References: <4D5D7E77.1080405@gucas.ac.cn> <497926617.03978@test1.gucas.ac.cn> Message-ID: <4D5DD776.4010003@gucas.ac.cn> Dear Professor Giannozzi, Dear Professor Paulatto, Thank you so much for your prompt answer. You are right I forgot to write the QE version I have, it is the realize 4.2.1. I always do a "make clean" before a make. So, I tried to compiled in a fresh gunziped/untared directory and it compiled with "make all". But I noticed it does not seems to work with make -j4 all for instance. Best, Eric. On 02/17/2011 03:29 AM, Paolo Giannozzi wrote: > On Feb 17, 2011, at 21:00 , Eric Germaneau wrote: > >> USE iotk_module >> 1 >> Fatal Error: Parse error when checking module version for file >> 'iotk_module.mod' opened at (1) > rm iotk/src/iotk_module.o iotk/src/iotk_module.mod > > Please specify the QE version when reporting compilation problems > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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 > -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of ChineseAcademy of Sciences Yuquan Road 19A Beijing 100049 China /Please consider the environment before printing this email. Consid?rez svp l'environnement avant d'imprimer cet email. / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110217/1c921b8e/attachment.htm From giannozz at democritos.it Thu Feb 17 15:15:11 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 17 Feb 2011 15:15:11 +0100 Subject: [Pw_forum] compilation error In-Reply-To: <4D5DD776.4010003@gucas.ac.cn> References: <4D5D7E77.1080405@gucas.ac.cn> <497926617.03978@test1.gucas.ac.cn> <4D5DD776.4010003@gucas.ac.cn> Message-ID: <266866F3-A496-4426-8E5F-D42AC3AE3C5D@democritos.it> On Feb 18, 2011, at 3:20 , Eric Germaneau wrote: > But I noticed it does not seems to work with make -j4 all for > instance. make -j4 ??? --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From Lorenzo.Paulatto at impmc.upmc.fr Thu Feb 17 19:08:04 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Thu, 17 Feb 2011 19:08:04 +0100 Subject: [Pw_forum] compilation error In-Reply-To: <4D5DD776.4010003@gucas.ac.cn> References: <4D5D7E77.1080405@gucas.ac.cn> <497926617.03978@test1.gucas.ac.cn> <4D5DD776.4010003@gucas.ac.cn> Message-ID: On Fri, 18 Feb 2011 03:20:38 +0100, Eric Germaneau wrote: > I always do a "make clean" before a make. So, I tried to compiled in a > fresh gunziped/untared directory and it compiled with "make all". > But I noticed it does not seems to work with make -j4 all for instance. > Best, Indeed, "make -jN" does not work, because the source sub-directories are inter-dependents. I Axel Kohlmeyer (if i remember correctly) suggested once to do "make MFLAGS=-j4" which does work work. Personally, I prefer to go take cup of coffee while it compiles. regards -- Lorenzo Paulatto (IdR) IMPMC - CNRS UMR 7590 & Universit? P&M Curie T23-C13/23-5e27 - 4 place Jussieu - 75252 Paris Cedex5 phone: +33 (0)144 27 5211 www: http://www-int.impmc.upmc.fr/~paulatto/ From jiachen at princeton.edu Thu Feb 17 21:44:23 2011 From: jiachen at princeton.edu (jia chen) Date: Thu, 17 Feb 2011 15:44:23 -0500 Subject: [Pw_forum] My wish about cp code: empty states Message-ID: Dear developers, Firstly, I would like to thank all developers' hard work which makes my current work possible. Then I would like to write down my wish about cp code. I hope cp can recover the implementation of empty states, or implement the occupation method. I know we can do that by nscf calculations in pwscf, but It would be really nice that this feather is in cp. I could do that in earlier version, but it is beyond my capability in 4.2.1. I simply hope I can get someone's attention. Really appreciate it. Best Wishes -- Jia Chen -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110217/832aea26/attachment.htm From giannozz at democritos.it Thu Feb 17 22:23:38 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 17 Feb 2011 22:23:38 +0100 Subject: [Pw_forum] My wish about cp code: empty states In-Reply-To: References: Message-ID: On Feb 17, 2011, at 21:44 , jia chen wrote: > I hope cp can recover the implementation of empty states [...] > I know we can do that by nscf calculations in pwscf > what is wrong with that approach? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From jiachen at princeton.edu Thu Feb 17 22:44:23 2011 From: jiachen at princeton.edu (jiachen at princeton.edu) Date: Thu, 17 Feb 2011 16:44:23 -0500 Subject: [Pw_forum] My wish about cp code: empty states Message-ID: <54896.1297979063@princeton.edu> Nothing wrong about this method, native empty states of cp are necessary for wannier functions and pbe0 code based on that. On Thu 17/02/11 4:23 PM , Paolo Giannozzi wrote: > On Feb 17, 2011, at 21:44 , jia chen wrote: > > > I hope cp can recover the implementation of empty states [...] > > I know we can do that by nscf calculations in pwscf > > > > > what is wrong with that approach? > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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 [1] > > > > Links: > ------ > [1] > http://webmail.princeton.edu/parse.php?redirect=http://www.democritos.it/ma > ilman/listinfo/pw_forum > From jiachen at princeton.edu Thu Feb 17 22:52:35 2011 From: jiachen at princeton.edu (jiachen at princeton.edu) Date: Thu, 17 Feb 2011 16:52:35 -0500 Subject: [Pw_forum] My wish about cp code: empty states Message-ID: <54947.1297979555@princeton.edu> On Thu 17/02/11 4:23 PM , Paolo Giannozzi wrote: > On Feb 17, 2011, at 21:44 , jia chen wrote: > > > I hope cp can recover the implementation of empty states [...] > > I know we can do that by nscf calculations in pwscf > > > > > what is wrong with that approach? > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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 [1] > > > > Links: > ------ > [1] > http://webmail.princeton.edu/parse.php?redirect=http://www.democritos.it/ma > ilman/listinfo/pw_forum > From nicola.marzari at materials.ox.ac.uk Fri Feb 18 01:13:47 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Fri, 18 Feb 2011 00:13:47 +0000 Subject: [Pw_forum] My wish about cp code: empty states In-Reply-To: References: Message-ID: <4D5DB9BB.3050406@materials.ox.ac.uk> Dear Jia Chen, as Paolo mentioned, you could do cp, and then restart pwscf nscf. You can also use ensemble-DFT in cp - that should work (we recently run some large metallic slab calculations) although it is probably not optimized as the rest of cp. nicola On 2/17/11 8:44 PM, jia chen wrote: > Dear developers, > > Firstly, I would like to thank all developers' hard work which makes > my current work possible. Then I would like to write down my wish about > cp code. I hope cp can recover the implementation of empty states, or > implement the occupation method. I know we can do that by nscf > calculations in pwscf, but It would be really nice that this feather is > in cp. I could do that in earlier version, but it is beyond my > capability in 4.2.1. I simply hope I can get someone's attention. Really > appreciate it. > > Best Wishes > -- > Jia Chen > > -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From w2agz at w2agz.com Fri Feb 18 08:06:08 2011 From: w2agz at w2agz.com (W2AGZ) Date: Thu, 17 Feb 2011 23:06:08 -0800 Subject: [Pw_forum] ibrav=12 Message-ID: <057501cbcf3a$528100f0$f78302d0$@w2agz.com> To All (especially Eyvaz): I would like to create a file for PlotPhon/Include to support general monoclinic structures. Below is the Include file for orthorhombic as an example "kick off:" # Simple Orthorhombic lattice (X=b/a, Y=c/a) 1.0 0.0 0 0.0 XX 0 0.0 0.0 YY # With respect to basis vectors 1 0.00000 0.00000 0.50000 Z 50 0.00000 0.00000 0.00000 G 50 0.500000 0.00000 0.00000 X 50 0.500000 0.50000 0.00000 S 50 0.000000 0.50000 0.00000 Y 50 0.000000 0.00000 0.00000 G 50 0.500000 0.50000 0.50000 R Now, the "popular" cell convention for monoclinic structures is either "b-axis-unique," or "c-axis-unique." PWgui and PWscf prefer the latter, but that's OK, since it's a simple transformation, as least in direct space, between the two. But, what is the appropiate "include" for ibrav=12 "c-axis unique?" I've been to "BILBOA," and the Bouchaert-Smoluchowski-Wigner path I want is gamma-a-u-e-z-lambda-gamma for both electrons and phonons. Incidentally, when I was a graduate student, the legend was that the BSW notation was invented by physicists to purposely confuse chemists. So, please tell me how to construct the appropriate "scripts/lines" and "include" files accordingly. Grazi, Paul Grant IBM Research Staff Member Emeritus www.w2agz.com Addenda...I include the following at the risk of angering Santo Paolo who may excommunicate me from the forum on the basis of "topic out of bounds." "Mea culpa...dominus noster..." Therefore I apologize for this posting and to those for whom English is not their native language, especially Americans, Australians, Kiwis, Irish, Scots, Welsh, Cornish, Indians and particularly Quebecois (British Columbians excepted). 2011 is the 100th anniversary of the discovery of superconductivity and the 25th of above liquid nitrogen in copper oxide perovskites. I will be giving one of the plenary talks at the upcoming APS March Meeting in Dallas...go here for the epitome. And later a reprise at the MRS April Meeting in San Francisco. But, in addition, I will also present a contributed talk at each meeting on "proxy" CuO structures based entirely on Quantum Espresso resources...go here to see. I would love to see and meet members of the QE community at each event...and offer a "real espresso" beverage. Look for me outside any of the superconductivity sessions, or inquire in the press room. I'm reasonably identifiable...an old guy with long white hair and beard. Hmm...well...maybe not that unique! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110217/bac55d1d/attachment.htm From m_pazoki at physics.sharif.edu Fri Feb 18 11:08:07 2011 From: m_pazoki at physics.sharif.edu (meysam pazoki) Date: Fri, 18 Feb 2011 13:38:07 +0330 Subject: [Pw_forum] Fermi energy Calculation Message-ID: Dear PWSCF users I have a problem with calculation of exact fermi level for my system. My system is 64 atom ZnO supercell and espresso gives a positive fermi energy for this system. As i know this is not exact fermi level,how can i calculate the exact fermi energy? Thanks in advance Meysam Pazoki Ph.D student of physics SUT -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110218/0db56acd/attachment.htm From nkxirainbow at gmail.com Fri Feb 18 11:25:04 2011 From: nkxirainbow at gmail.com (xirainbow) Date: Fri, 18 Feb 2011 18:25:04 +0800 Subject: [Pw_forum] Fermi energy Calculation In-Reply-To: References: Message-ID: Dear *Meysam Pazoki*: Fermi energy indicate that:Below it, all the states is occupied by electrons, whereas no electron is above it. In my view, Fermi energy can below or above zero. And, in pseudopotential method, the absolute value of fermi energy has no physical meaning. If i am wrong, please point it out ?? On Fri, Feb 18, 2011 at 6:08 PM, meysam pazoki wrote: > Dear PWSCF users > I have a problem with calculation of exact fermi level for my system. > My system is 64 atom ZnO supercell and espresso gives a positive fermi > energy for this system. > As i know this is not exact fermi level,how can i calculate the exact fermi > energy? > Thanks in advance > Meysam Pazoki > Ph.D student of physics > SUT > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ____________________________________ Hui Wang School of physics, Fudan University, Shanghai, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110218/fd3434e1/attachment.htm From m_pazoki at physics.sharif.edu Fri Feb 18 12:12:10 2011 From: m_pazoki at physics.sharif.edu (meysam pazoki) Date: Fri, 18 Feb 2011 14:42:10 +0330 Subject: [Pw_forum] ZnO(1010) surface BandGap Message-ID: Dear PWSCF users In scf calculations of my 64 atom ZnO supercell(wich is relaxed by bfgs method),the band gap of ZnO (1010) surface approximately disapear. Espresso gives a 0.2 eV gap for this system in GGA functional.The surface consist of 4 layers of ZnO bulk unit cell. Is it due to surface states or not?how can i improve my calculations? Thanks in advance Best Regards Meysam Pazoki Ph.D student of physics SUT -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110218/5caa192b/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Fri Feb 18 07:37:16 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Fri, 18 Feb 2011 07:37:16 +0100 Subject: [Pw_forum] ZnO(1010) surface BandGap In-Reply-To: References: Message-ID: <201102180737.16217.giuseppe.mattioli@mlib.ism.cnr.it> Dear Meysam You cannot (easily) improve your calculation... Due to static correlation error, there is a strong interaction between the Zn 3d band and the O 2p band which push up the valence band maximum. It does not depend on the slab or bulk geometry. Your weapons could be some hybrid functional or a SIC scheme... HTH Giuseppe On Friday 18 February 2011 12:12:10 meysam pazoki wrote: > Dear PWSCF users > In scf calculations of my 64 atom ZnO supercell(wich is relaxed by bfgs > method),the band gap of ZnO (1010) surface approximately disapear. > Espresso gives a 0.2 eV gap for this system in GGA functional.The surface > consist of 4 layers of ZnO bulk unit cell. > Is it due to surface states or not?how can i improve my calculations? > Thanks in advance > Best Regards > Meysam Pazoki > Ph.D student of physics > SUT -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From eyvaz_isaev at yahoo.com Fri Feb 18 18:04:35 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 18 Feb 2011 09:04:35 -0800 (PST) Subject: [Pw_forum] ibrav=12 In-Reply-To: <057501cbcf3a$528100f0$f78302d0$@w2agz.com> References: <057501cbcf3a$528100f0$f78302d0$@w2agz.com> Message-ID: <778960.59485.qm@web65713.mail.ac4.yahoo.com> Dear Paul, In fact, I am working on this problem in order to support in PlotPhon almost all lattice types. I will let you know soon, hopefully. Best regards, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: W2AGZ To: pw_forum at pwscf.org Sent: Fri, February 18, 2011 10:06:08 AM Subject: [Pw_forum] ibrav=12 To All (especially Eyvaz): I would like to create a file for PlotPhon/Include to support general monoclinic structures. Below is the Include file for orthorhombic as an example ?kick off:? # Simple Orthorhombic lattice (X=b/a, Y=c/a) 1.0 0.0 0 0.0 XX 0 0.0 0.0 YY # With respect to basis vectors 1 0.00000 0.00000 0.50000 Z 50 0.00000 0.00000 0.00000 G 50 0.500000 0.00000 0.00000 X 50 0.500000 0.50000 0.00000 S 50 0.000000 0.50000 0.00000 Y 50 0.000000 0.00000 0.00000 G 50 0.500000 0.50000 0.50000 R Now, the ?popular? cell convention for monoclinic structures is either ?b-axis-unique,? or ?c-axis-unique.? PWgui and PWscf prefer the latter, but that?s OK, since it?s a simple transformation, as least in direct space, between the two. But, what is the appropiate ?include? for ibrav=12 ?c-axis unique?? I?ve been to ?BILBOA,? and the Bouchaert-Smoluchowski-Wigner path I want is gamma-a-u-e-z-lambda-gamma for both electrons and phonons. Incidentally, when I was a graduate student, the legend was that the BSW notation was invented by physicists to purposely confuse chemists. So, please tell me how to construct the appropriate ?scripts/lines? and ?include? files accordingly. Grazi, Paul Grant IBM Research Staff Member Emeritus www.w2agz.com Addenda...I include the following at the risk of angering Santo Paolo who may excommunicate me from the forum on the basis of ?topic out of bounds.? ?Mea culpa...dominus noster...? Therefore I apologize for this posting and to those for whom English is not their native language, especially Americans, Australians, Kiwis, Irish, Scots, Welsh, Cornish, Indians and particularly Quebecois (British Columbians excepted). 2011 is the 100th anniversary of the discovery of superconductivity and the 25th of above liquid nitrogen in copper oxide perovskites. I will be giving one of the plenary talks at the upcoming APS March Meeting in Dallas...go here for the epitome. And later a reprise at the MRS April Meeting in San Francisco. But, in addition, I will also present a contributed talk at each meeting on ?proxy? CuO structures based entirely on Quantum Espresso resources...go here to see. I would love to see and meet members of the QE community at each event...and offer a ?real espresso? beverage. Look for me outside any of the superconductivity sessions, or inquire in the press room. I?m reasonably identifiable...an old guy with long white hair and beard. Hmm...well...maybe not that unique! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110218/144556be/attachment.htm From w2agz at w2agz.com Fri Feb 18 20:43:14 2011 From: w2agz at w2agz.com (W2AGZ) Date: Fri, 18 Feb 2011 11:43:14 -0800 Subject: [Pw_forum] ibrav=12 In-Reply-To: <778960.59485.qm@web65713.mail.ac4.yahoo.com> References: <057501cbcf3a$528100f0$f78302d0$@w2agz.com> <778960.59485.qm@web65713.mail.ac4.yahoo.com> Message-ID: <060f01cbcfa4$1657cc70$43076550$@w2agz.com> Thanks, Eyvaz. The space group I?m interested in is P21/c (14). 8 atoms per unit cell, 24 IRs. If you need a beta tester, just ask. -Paul From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Eyvaz Isaev Sent: Friday, February 18, 2011 9:05 AM To: PWSCF Forum Subject: Re: [Pw_forum] ibrav=12 Dear Paul, In fact, I am working on this problem in order to support in PlotPhon almost all lattice types. I will let you know soon, hopefully. Best regards, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com _____ From: W2AGZ To: pw_forum at pwscf.org Sent: Fri, February 18, 2011 10:06:08 AM Subject: [Pw_forum] ibrav=12 To All (especially Eyvaz): I would like to create a file for PlotPhon/Include to support general monoclinic structures. Below is the Include file for orthorhombic as an example ?kick off:? # Simple Orthorhombic lattice (X=b/a, Y=c/a) 1.0 0.0 0 0.0 XX 0 0.0 0.0 YY # With respect to basis vectors 1 0.00000 0.00000 0.50000 Z 50 0.00000 0.00000 0.00000 G 50 0.500000 0.00000 0.00000 X 50 0.500000 0.50000 0.00000 S 50 0.000000 0.50000 0.00000 Y 50 0.000000 0.00000 0.00000 G 50 0.500000 0.50000 0.50000 R Now, the ?popular? cell convention for monoclinic structures is either ?b-axis-unique,? or ?c-axis-unique.? PWgui and PWscf prefer the latter, but that?s OK, since it?s a simple transformation, as least in direct space, between the two. But, what is the appropiate ?include? for ibrav=12 ?c-axis unique?? I?ve been to ?BILBOA,? and the Bouchaert-Smoluchowski-Wigner path I want is gamma-a-u-e-z-lambda-gamma for both electrons and phonons. Incidentally, when I was a graduate student, the legend was that the BSW notation was invented by physicists to purposely confuse chemists. So, please tell me how to construct the appropriate ?scripts/lines? and ?include? files accordingly. Grazi, Paul Grant IBM Research Staff Member Emeritus www.w2agz.com Addenda...I include the following at the risk of angering Santo Paolo who may excommunicate me from the forum on the basis of ?topic out of bounds.? ?Mea culpa...dominus noster...? Therefore I apologize for this posting and to those for whom English is not their native language, especially Americans, Australians, Kiwis, Irish, Scots, Welsh, Cornish, Indians and particularly Quebecois (British Columbians excepted). 2011 is the 100th anniversary of the discovery of superconductivity and the 25th of above liquid nitrogen in copper oxide perovskites. I will be giving one of the plenary talks at the upcoming APS March Meeting in Dallas...go here for the epitome. And later a reprise at the MRS April Meeting in San Francisco. But, in addition, I will also present a contributed talk at each meeting on ?proxy? CuO structures based entirely on Quantum Espresso resources...go here to see. I would love to see and meet members of the QE community at each event...and offer a ?real espresso? beverage. Look for me outside any of the superconductivity sessions, or inquire in the press room. I?m reasonably identifiable...an old guy with long white hair and beard. Hmm...well...maybe not that unique! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110218/a37556f2/attachment-0001.htm From persakthi at gmail.com Sat Feb 19 07:28:17 2011 From: persakthi at gmail.com (sakthi kumaran) Date: Sat, 19 Feb 2011 11:58:17 +0530 Subject: [Pw_forum] classical potential MD simulation Message-ID: Dear all, Is it possible to compute the interaction between two capped nanotubes facing each other using classical LJ12 potential using Molecular dynamics technique in Quantum espresso.If possible what is the procedure for doing so. Thank you guys in advance -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110219/7028bae6/attachment.htm From crma at sissa.it Sat Feb 19 08:16:09 2011 From: crma at sissa.it (Changru Ma) Date: Sat, 19 Feb 2011 08:16:09 +0100 Subject: [Pw_forum] classical potential MD simulation In-Reply-To: References: Message-ID: <2F1F1527-47E2-443D-AC4B-0B2E79A38BC1@sissa.it> Dear sakthi kumaran, It's not possible to perform classical molecular dynamics in Quantum Espresso now. QE can do ab-initio molecular dynamics: Car-Parrinello Molecular Dynamics and Born-Oppenheimer Molecular Dynamics. PS. Next time please take a few seconds to sign your post with your affiliation. Best wishes, Changru On 19 Feb, 2011, at 07:28, sakthi kumaran wrote: > Dear all, > Is it possible to compute the interaction between two capped nanotubes facing each other using classical LJ12 potential using Molecular dynamics technique in Quantum espresso.If possible what is the procedure for doing so. > > Thank you guys in advance > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 375 8713 (Elettra) +39 040 378 7870 (SISSA) http://www.sissa.it/~crma --- From m_pazoki at physics.sharif.edu Sat Feb 19 14:04:46 2011 From: m_pazoki at physics.sharif.edu (meysam pazoki) Date: Sat, 19 Feb 2011 16:34:46 +0330 Subject: [Pw_forum] Fermi Energy Caculation In-Reply-To: References: Message-ID: ---------- Forwarded message ---------- From: meysam pazoki Date: Sat, Feb 19, 2011 at 4:33 PM Subject: Re: Fermi Energy Caculation To: pw_forum at pwscf.org Dear xirainbow Thanks for your comment. Each semiconductor have a fermi energy level. The exact value of fermi energy (relative to vaccum level) depicts that the contact of this semiconductor with Au(for example) is *Schottky* or ohmic. Or for example when this semiconductor is in contact with a Red/Ox electrolyte ,what is the length of double layer ? This is duo to when a metal and a semiconductor are in contact, in equilibrium the fermi energy of two systems should be identical(Fermi energy (with good approximation) is equal to chemical potential. Chemical potential is energy of adding 1 electron to the system.In equilibrium there is no electronic current between two parts. ) But when you work with two samples in contact to each other you need to know the value of fermi energy relative to vaccum. Best wishes meysam -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110219/574535da/attachment.htm From m_pazoki at physics.sharif.edu Sat Feb 19 14:11:06 2011 From: m_pazoki at physics.sharif.edu (meysam pazoki) Date: Sat, 19 Feb 2011 16:41:06 +0330 Subject: [Pw_forum] ZnO(1010) surface BandGap Message-ID: Dear Giuseppe Thanks for your reply. In Bulk ZnO with GGA ,i have 1.2 eV Gap but in the slab it is approximately disappeared. What is wrong with ZnO surface?I dont know why in calculation of surface ,the gap is disappeared. Best Regards meysam -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110219/31f2f585/attachment.htm From glapenna at iccom.cnr.it Sat Feb 19 14:55:14 2011 From: glapenna at iccom.cnr.it (Giovanni La Penna) Date: Sat, 19 Feb 2011 14:55:14 +0100 (CET) Subject: [Pw_forum] classical potential MD simulation In-Reply-To: <2F1F1527-47E2-443D-AC4B-0B2E79A38BC1@sissa.it> References: <2F1F1527-47E2-443D-AC4B-0B2E79A38BC1@sissa.it> Message-ID: It may be possible to make QM/MM with QE and some empirical MD package. Some years ago a sort of plugin was build for DLPOLY/Siesta: J. Torras et al., PUPIL: a systematic approach to software integration in multi-scale simulations Comp. Phys. Commun. 177, 265 (2007). Maybe, with a limited amount of work, additional software, etc.. There is a big problem with PBC for QM area merged into a classical system larger than QM boundaries. Giovanni ============================================================ Giovanni La Penna - National research council (Cnr) Institute for chemistry of organo-metallic compounds (Iccom) via Madonna del Piano 10, I-50019 Sesto Fiorentino, Firenze, Italy tel.: +39 055 522-5264, fax: +39 055 522-5203 e-mail: glapenna at iccom.cnr.it - http://www.iccom.cnr.it/lapenna skype: giovannilapenna ============================================================ From carlo.nervi at unito.it Sat Feb 19 15:55:26 2011 From: carlo.nervi at unito.it (Carlo Nervi) Date: Sat, 19 Feb 2011 15:55:26 +0100 (CET) Subject: [Pw_forum] ibrav=12 In-Reply-To: <060f01cbcfa4$1657cc70$43076550$@w2agz.com> References: <057501cbcf3a$528100f0$f78302d0$@w2agz.com><778960.59485.qm@web65713.mail.ac4.yahoo.com> <060f01cbcfa4$1657cc70$43076550$@w2agz.com> Message-ID: <43095.127.0.0.1.1298127326.squirrel@mail.unito.it> Dear Paul, commenting your note, and as a chemist, I've been confused by the convenction used in quantum espresso. I'm using a, b, c, alpha, beta and gamma, but not always I've been able to directly translate the content of cif files into QE input... Here is an example about monoclinic input: http://www.democritos.it/pipermail/pw_forum/2010-February/015993.html I had to switch (b, c) in the cell and (y, z) in the data.... Finally i decided to use only triclinic for all input files, regardless of the real ibrav... Just my 2c... Carlo -- ------------------------------------------------------ Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 Fax: +39 011 6707855 - Dipartimento di Chimica IFM via P. Giuria 7, 10125 Torino, Italy http://lem.ch.unito.it/ > > > ------------------ Messaggio originale ------------------- > Oggetto: Re: [Pw_forum] ibrav=12 > Da: "W2AGZ" > Data: Ven, 18 Febbraio 2011, 8:43 pm > A: "'PWSCF Forum'" > ---------------------------------------------------------- > > Thanks, Eyvaz. The space group I???m interested in is > P21/c (14). 8 atoms per unit cell, 24 IRs. If you need > a beta tester, just ask. -Paul > > > > From: pw_forum-bounces at pwscf.org > [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Eyvaz > Isaev > Sent: Friday, February 18, 2011 9:05 AM > To: PWSCF Forum > Subject: Re: [Pw_forum] ibrav=12 > > > > Dear Paul, > > In fact, I am working on this problem in order to support > in PlotPhon almost all lattice types. I will let you know > soon, hopefully. > > > Best regards, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), > Linkoping University, Sweden > Theoretical Physics Department, Moscow State Institute of > Steel & Alloys, Russia, > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > > > > _____ > > From: W2AGZ > To: pw_forum at pwscf.org > Sent: Fri, February 18, 2011 10:06:08 AM > Subject: [Pw_forum] ibrav=12 > > To All (especially Eyvaz): > > > > I would like to create a file for PlotPhon/Include to > support general monoclinic structures. Below is the > Include file for orthorhombic as an example ???kick > off:??� > > > > # Simple Orthorhombic lattice (X=b/a, Y=c/a) > > 1.0 0.0 0 > > 0.0 XX 0 > > 0.0 0.0 YY > > # With respect to basis vectors > > 1 0.00000 0.00000 0.50000 Z > > 50 0.00000 0.00000 0.00000 G > > 50 0.500000 0.00000 0.00000 X > > 50 0.500000 0.50000 0.00000 S > > 50 0.000000 0.50000 0.00000 Y > > 50 0.000000 0.00000 0.00000 G > > 50 0.500000 0.50000 0.50000 R > > > > Now, the ???popular??� cell convention for monoclinic > structures is either ???b-axis-unique,??� or > ???c-axis-unique.??� PWgui and PWscf prefer the latter, > but that???s OK, since it???s a simple transformation, as > least in direct space, between the two. But, what is the > appropiate ???include??� for ibrav=12 ???c-axis unique???� > I???ve been to ???BILBOA,??� and the > Bouchaert-Smoluchowski-Wigner path I want is > gamma-a-u-e-z-lambda-gamma for both electrons and phonons. > Incidentally, when I was a graduate student, the legend > was that the BSW notation was invented by physicists to > purposely confuse chemists. So, please tell me how to > construct the appropriate ???scripts/lines??� and > ???include??� files accordingly. > > > > Grazi, Paul Grant > > IBM Research Staff Member Emeritus > > www.w2agz.com > > > > Addenda...I include the following at the risk of angering > Santo Paolo who may excommunicate me from the forum on the > basis of ???topic out of bounds.??� ???Mea culpa...dominus > noster...??� Therefore I apologize for this posting and > to those for whom English is not their native language, > especially Americans, Australians, Kiwis, Irish, Scots, > Welsh, Cornish, Indians and particularly Quebecois > (British Columbians excepted). > > > > 2011 is the 100th anniversary of the discovery of > superconductivity and the 25th of above liquid nitrogen in > copper oxide perovskites. I will be giving one of the > plenary talks at the upcoming APS March Meeting in > Dallas...go here > for > the epitome. And later a reprise at the MRS April Meeting > in San Francisco. But, in addition, I will also present a > contributed talk at each meeting on ???proxy??� CuO > structures based entirely on Quantum Espresso > resources...go here > to > see. > > > > I would love to see and meet members of the QE community > at each event...and offer a ???real espresso??� beverage. > Look for me outside any of the superconductivity > sessions, or inquire in the press room. I???m reasonably > identifiable...an old guy with long white hair and beard. > Hmm...well...maybe not that unique! > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From jiachen at princeton.edu Sat Feb 19 18:39:45 2011 From: jiachen at princeton.edu (jia chen) Date: Sat, 19 Feb 2011 12:39:45 -0500 Subject: [Pw_forum] Fermi Energy Caculation In-Reply-To: References: Message-ID: Dear Pazoki, You can calculate work function for certain surfaces in pp. Best Wishes Jia On Sat, Feb 19, 2011 at 8:04 AM, meysam pazoki wrote: > > > ---------- Forwarded message ---------- > From: meysam pazoki > Date: Sat, Feb 19, 2011 at 4:33 PM > Subject: Re: Fermi Energy Caculation > To: pw_forum at pwscf.org > > > Dear xirainbow > Thanks for your comment. Each semiconductor have a fermi energy level. > The exact value of fermi energy (relative to vaccum level) depicts that the contact of this semiconductor with Au(for example) is Schottky or ohmic. > Or for example when this semiconductor is in contact with a Red/Ox electrolyte ,what is the length of double layer ? > This is duo to when a metal and a semiconductor are in contact, in equilibrium the fermi energy of two systems should be identical(Fermi energy? (with good approximation) is equal to chemical potential. Chemical potential is energy of adding 1 electron to the system.In equilibrium there is no electronic current between two parts. ) > But when you work with two samples in contact to each other you need to know the value of fermi energy relative to vaccum. > Best wishes > meysam > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Jia Chen From giannozz at democritos.it Sat Feb 19 20:30:10 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 19 Feb 2011 20:30:10 +0100 Subject: [Pw_forum] ibrav=12 In-Reply-To: <43095.127.0.0.1.1298127326.squirrel@mail.unito.it> References: <057501cbcf3a$528100f0$f78302d0$@w2agz.com><778960.59485.qm@web65713.mail.ac4.yahoo.com> <060f01cbcfa4$1657cc70$43076550$@w2agz.com> <43095.127.0.0.1.1298127326.squirrel@mail.unito.it> Message-ID: On Feb 19, 2011, at 15:55 , Carlo Nervi wrote: > I've been confused by the convenction used in quantum espresso. the conventions used in QE for lattices are explained in detail in the documentation. They may not be the smartest or the "more standard" choice, though (not sure what is considered "standard" in crystallography). Any proposal for improvement is welcome, as long as - it is written in fortran and ready to be plugged into the code, and - it is backward-compatible (does not affect existing input data). An ugly but safe and straightforward way to achieve this is to define more values of "ibrav". The relevant parts of code are the 30 lines or so starting from IF ( celldm_(1) == 0.D0 .and. a /= 0.D0 ) THEN in PW/input.f90, plus flib/latgen.f90 P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sat Feb 19 21:34:15 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 19 Feb 2011 21:34:15 +0100 Subject: [Pw_forum] Fermi Energy Caculation In-Reply-To: References: Message-ID: <71BB5D8A-6EA8-47A9-A516-F0A3C45486B7@democritos.it> Please see items 11.7.0.8, 11.7.0.9 and 11.7.0.11 of the user guide: http://www.quantum-espresso.org/user_guide/ node60.html#SECTION000127080000000000000 P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From vinothrece at gmail.com Sun Feb 20 04:13:27 2011 From: vinothrece at gmail.com (vinoth r) Date: Sun, 20 Feb 2011 08:43:27 +0530 Subject: [Pw_forum] DOS calculation Message-ID: Dear pwscf user, i want to calculate DOS for Graphene Nanoribbon.I optimized my GNR using relax calculation.i finished my SCFcalculation also.while doing NSCF calculation i got like (last few lines of my nscf output) negative rho (up, down): 0.227E-02 0.000E+00 Starting wfc are 132 atomic wfcs total cpu time spent up to now is 90.08 secs per-process dynamical memory: 730.3 Mb Band Structure Calculation. After 5 hours also it doesnt calculate any thing & it doesnt show any error.Could you help me to rectify the problem. with regards Abenano -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110220/79024311/attachment.htm From lyue at gmx.net Mon Feb 21 00:45:24 2011 From: lyue at gmx.net (Lun Yue) Date: Mon, 21 Feb 2011 00:45:24 +0100 Subject: [Pw_forum] Strange band structure diagram Message-ID: <20110220234524.184840@gmx.net> Dear pwscf users, I did some calculations about bulk TiO2 rutile and got a really strange band structure diagram: http://img840.imageshack.us/i/rutilebands.png/ I checked the input files but could not find the problem, please help me in figuring out it. Best regards, Lun Yue My input files: ======= rutile.scf.in =============== &control calculation = 'scf', prefix = 'rutile_scf', verbosity = 'default', / &system ibrav = 6, celldm(1) = 8.680890966, celldm(3) = 0.64394729330137, nat = 6, ntyp = 2, ecutwfc = 40, ecutrho = 400, occupations = 'fixed', nbnd = 40, / &electrons conv_thr = 1.0e-09, electron_maxstep = 100, mixing_beta = 0.3, conv_thr = 1.0e-08, mixing_mode = 'plain', / ATOMIC_SPECIES O 15.999 O.pbe-van_ak.UPF Ti 47.867 Ti.pbe-sp-van_ak.UPF ATOMIC_POSITIONS (angstrom) Ti 0.00000000 0.00000000 0.00000000 Ti 2.29686500 2.29686500 1.47906000 O 1.40246577 1.40246577 0.00000000 O -1.40246577 -1.40246577 0.00000000 O 3.69933077 0.89439923 1.47906000 O 0.89439923 3.69933077 1.47906000 K_POINTS (automatic) 6 6 6 0 0 0 ========= rutile.bands.in ============= &control calculation = 'bands', prefix = 'rutile_scf', verbosity = 'default', / &system ibrav = 6, celldm(1) = 8.680890966, celldm(3) = 0.64394729330137, nat = 6, ntyp = 2, ecutwfc = 40, ecutrho = 400, occupations = 'fixed', nbnd = 40, / &electrons conv_thr = 1.0e-09, electron_maxstep = 100, mixing_beta = 0.3, conv_thr = 1.0e-08, mixing_mode = 'plain', / ATOMIC_SPECIES O 15.999 O.pbe-van_ak.UPF Ti 47.867 Ti.pbe-sp-van_ak.UPF ATOMIC_POSITIONS (angstrom) Ti 0.00000000 0.00000000 0.00000000 Ti 2.29686500 2.29686500 1.47906000 O 1.40246577 1.40246577 0.00000000 O -1.40246577 -1.40246577 0.00000000 O 3.69933077 0.89439923 1.47906000 O 0.89439923 3.69933077 1.47906000 K_POINTS crystal 60 0.5000000000 0.0000000000 0.5000000000 1.0 0.4750000000 0.0000000000 0.4750000000 1.0 0.4500000000 0.0000000000 0.4500000000 1.0 0.4250000000 0.0000000000 0.4250000000 1.0 0.4000000000 0.0000000000 0.4000000000 1.0 0.3750000000 0.0000000000 0.3750000000 1.0 0.3500000000 0.0000000000 0.3500000000 1.0 0.3250000000 0.0000000000 0.3250000000 1.0 0.3000000000 0.0000000000 0.3000000000 1.0 0.2750000000 0.0000000000 0.2750000000 1.0 0.2500000000 0.0000000000 0.2500000000 1.0 0.2250000000 0.0000000000 0.2250000000 1.0 0.2000000000 0.0000000000 0.2000000000 1.0 0.1750000000 0.0000000000 0.1750000000 1.0 0.1500000000 0.0000000000 0.1500000000 1.0 0.1250000000 0.0000000000 0.1250000000 1.0 0.1000000000 0.0000000000 0.1000000000 1.0 0.0750000000 0.0000000000 0.0750000000 1.0 0.0500000000 0.0000000000 0.0500000000 1.0 0.0250000000 0.0000000000 0.0250000000 1.0 0.0000000000 0.0000000000 0.0000000000 1.0 0.0000000000 0.0454545455 0.0000000000 1.0 0.0000000000 0.0909090909 0.0000000000 1.0 0.0000000000 0.1363636364 0.0000000000 1.0 0.0000000000 0.1818181818 0.0000000000 1.0 0.0000000000 0.2272727273 0.0000000000 1.0 0.0000000000 0.2727272727 0.0000000000 1.0 0.0000000000 0.3181818182 0.0000000000 1.0 0.0000000000 0.3636363636 0.0000000000 1.0 0.0000000000 0.4090909091 0.0000000000 1.0 0.0000000000 0.4545454545 0.0000000000 1.0 0.0000000000 0.5000000000 0.0000000000 1.0 0.0454545455 0.5000000000 0.0000000000 1.0 0.0909090909 0.5000000000 0.0000000000 1.0 0.1363636364 0.5000000000 0.0000000000 1.0 0.1818181818 0.5000000000 0.0000000000 1.0 0.2272727273 0.5000000000 0.0000000000 1.0 0.2727272727 0.5000000000 0.0000000000 1.0 0.3181818182 0.5000000000 0.0000000000 1.0 0.3636363636 0.5000000000 0.0000000000 1.0 0.4090909091 0.5000000000 0.0000000000 1.0 0.4545454545 0.5000000000 0.0000000000 1.0 0.5000000000 0.5000000000 0.0000000000 1.0 0.5000000000 0.5000000000 0.0294117647 1.0 0.5000000000 0.5000000000 0.0588235294 1.0 0.5000000000 0.5000000000 0.0882352941 1.0 0.5000000000 0.5000000000 0.1176470588 1.0 0.5000000000 0.5000000000 0.1470588235 1.0 0.5000000000 0.5000000000 0.1764705882 1.0 0.5000000000 0.5000000000 0.2058823529 1.0 0.5000000000 0.5000000000 0.2352941176 1.0 0.5000000000 0.5000000000 0.2647058824 1.0 0.5000000000 0.5000000000 0.2941176471 1.0 0.5000000000 0.5000000000 0.3235294118 1.0 0.5000000000 0.5000000000 0.3529411765 1.0 0.5000000000 0.5000000000 0.3823529412 1.0 0.5000000000 0.5000000000 0.4117647059 1.0 0.5000000000 0.5000000000 0.4411764706 1.0 0.5000000000 0.5000000000 0.4705882353 1.0 0.5000000000 0.5000000000 0.5000000000 1.0 -- NEU: FreePhone - kostenlos mobil telefonieren und surfen! Jetzt informieren: http://www.gmx.net/de/go/freephone From claudial.81 at gmail.com Mon Feb 21 01:33:00 2011 From: claudial.81 at gmail.com (Claudia Loyola) Date: Sun, 20 Feb 2011 18:33:00 -0600 Subject: [Pw_forum] Strange band structure diagram In-Reply-To: <20110220234524.184840@gmx.net> References: <20110220234524.184840@gmx.net> Message-ID: Hi, if your question is for the overlap between the bands, in the input file for band.x executable, add this line: no_overlap=.true., regards, Claudia Loyola On Sun, Feb 20, 2011 at 5:45 PM, Lun Yue wrote: > Dear pwscf users, > > I did some calculations about bulk TiO2 rutile and got a really strange > band structure diagram: > http://img840.imageshack.us/i/rutilebands.png/ > > I checked the input files but could not find the problem, please help me in > figuring out it. > > > Best regards, > Lun Yue > > My input files: > > ======= rutile.scf.in =============== > > &control > calculation = 'scf', > prefix = 'rutile_scf', > verbosity = 'default', > / > &system > ibrav = 6, > celldm(1) = 8.680890966, > celldm(3) = 0.64394729330137, > nat = 6, > ntyp = 2, > ecutwfc = 40, > ecutrho = 400, > occupations = 'fixed', > nbnd = 40, > / > &electrons > conv_thr = 1.0e-09, > electron_maxstep = 100, > mixing_beta = 0.3, > conv_thr = 1.0e-08, > mixing_mode = 'plain', > / > > ATOMIC_SPECIES > O 15.999 O.pbe-van_ak.UPF > Ti 47.867 Ti.pbe-sp-van_ak.UPF > ATOMIC_POSITIONS (angstrom) > Ti 0.00000000 0.00000000 0.00000000 > Ti 2.29686500 2.29686500 1.47906000 > O 1.40246577 1.40246577 0.00000000 > O -1.40246577 -1.40246577 0.00000000 > O 3.69933077 0.89439923 1.47906000 > O 0.89439923 3.69933077 1.47906000 > K_POINTS (automatic) > 6 6 6 0 0 0 > > > > ========= rutile.bands.in ============= > > &control > calculation = 'bands', > prefix = 'rutile_scf', > verbosity = 'default', > / > &system > ibrav = 6, > celldm(1) = 8.680890966, > celldm(3) = 0.64394729330137, > nat = 6, > ntyp = 2, > ecutwfc = 40, > ecutrho = 400, > occupations = 'fixed', > nbnd = 40, > / > &electrons > conv_thr = 1.0e-09, > electron_maxstep = 100, > mixing_beta = 0.3, > conv_thr = 1.0e-08, > mixing_mode = 'plain', > / > > ATOMIC_SPECIES > O 15.999 O.pbe-van_ak.UPF > Ti 47.867 Ti.pbe-sp-van_ak.UPF > ATOMIC_POSITIONS (angstrom) > Ti 0.00000000 0.00000000 0.00000000 > Ti 2.29686500 2.29686500 1.47906000 > O 1.40246577 1.40246577 0.00000000 > O -1.40246577 -1.40246577 0.00000000 > O 3.69933077 0.89439923 1.47906000 > O 0.89439923 3.69933077 1.47906000 > K_POINTS crystal > 60 > 0.5000000000 0.0000000000 0.5000000000 1.0 > 0.4750000000 0.0000000000 0.4750000000 1.0 > 0.4500000000 0.0000000000 0.4500000000 1.0 > 0.4250000000 0.0000000000 0.4250000000 1.0 > 0.4000000000 0.0000000000 0.4000000000 1.0 > 0.3750000000 0.0000000000 0.3750000000 1.0 > 0.3500000000 0.0000000000 0.3500000000 1.0 > 0.3250000000 0.0000000000 0.3250000000 1.0 > 0.3000000000 0.0000000000 0.3000000000 1.0 > 0.2750000000 0.0000000000 0.2750000000 1.0 > 0.2500000000 0.0000000000 0.2500000000 1.0 > 0.2250000000 0.0000000000 0.2250000000 1.0 > 0.2000000000 0.0000000000 0.2000000000 1.0 > 0.1750000000 0.0000000000 0.1750000000 1.0 > 0.1500000000 0.0000000000 0.1500000000 1.0 > 0.1250000000 0.0000000000 0.1250000000 1.0 > 0.1000000000 0.0000000000 0.1000000000 1.0 > 0.0750000000 0.0000000000 0.0750000000 1.0 > 0.0500000000 0.0000000000 0.0500000000 1.0 > 0.0250000000 0.0000000000 0.0250000000 1.0 > 0.0000000000 0.0000000000 0.0000000000 1.0 > 0.0000000000 0.0454545455 0.0000000000 1.0 > 0.0000000000 0.0909090909 0.0000000000 1.0 > 0.0000000000 0.1363636364 0.0000000000 1.0 > 0.0000000000 0.1818181818 0.0000000000 1.0 > 0.0000000000 0.2272727273 0.0000000000 1.0 > 0.0000000000 0.2727272727 0.0000000000 1.0 > 0.0000000000 0.3181818182 0.0000000000 1.0 > 0.0000000000 0.3636363636 0.0000000000 1.0 > 0.0000000000 0.4090909091 0.0000000000 1.0 > 0.0000000000 0.4545454545 0.0000000000 1.0 > 0.0000000000 0.5000000000 0.0000000000 1.0 > 0.0454545455 0.5000000000 0.0000000000 1.0 > 0.0909090909 0.5000000000 0.0000000000 1.0 > 0.1363636364 0.5000000000 0.0000000000 1.0 > 0.1818181818 0.5000000000 0.0000000000 1.0 > 0.2272727273 0.5000000000 0.0000000000 1.0 > 0.2727272727 0.5000000000 0.0000000000 1.0 > 0.3181818182 0.5000000000 0.0000000000 1.0 > 0.3636363636 0.5000000000 0.0000000000 1.0 > 0.4090909091 0.5000000000 0.0000000000 1.0 > 0.4545454545 0.5000000000 0.0000000000 1.0 > 0.5000000000 0.5000000000 0.0000000000 1.0 > 0.5000000000 0.5000000000 0.0294117647 1.0 > 0.5000000000 0.5000000000 0.0588235294 1.0 > 0.5000000000 0.5000000000 0.0882352941 1.0 > 0.5000000000 0.5000000000 0.1176470588 1.0 > 0.5000000000 0.5000000000 0.1470588235 1.0 > 0.5000000000 0.5000000000 0.1764705882 1.0 > 0.5000000000 0.5000000000 0.2058823529 1.0 > 0.5000000000 0.5000000000 0.2352941176 1.0 > 0.5000000000 0.5000000000 0.2647058824 1.0 > 0.5000000000 0.5000000000 0.2941176471 1.0 > 0.5000000000 0.5000000000 0.3235294118 1.0 > 0.5000000000 0.5000000000 0.3529411765 1.0 > 0.5000000000 0.5000000000 0.3823529412 1.0 > 0.5000000000 0.5000000000 0.4117647059 1.0 > 0.5000000000 0.5000000000 0.4411764706 1.0 > 0.5000000000 0.5000000000 0.4705882353 1.0 > 0.5000000000 0.5000000000 0.5000000000 1.0 > > -- > NEU: FreePhone - kostenlos mobil telefonieren und surfen! > Jetzt informieren: http://www.gmx.net/de/go/freephone > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Claudia Loyola Canales Postdoc in Computational Physics Iowa State University Iowa, USA www.lpmd.cl/claudial www.lpmd.cl http://cosmic.mse.iastate.edu/ www.gnm.cl -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110220/5bc31a5f/attachment.htm From priyankagoud8 at gmail.com Mon Feb 21 05:55:36 2011 From: priyankagoud8 at gmail.com (priyanka goud) Date: Mon, 21 Feb 2011 10:25:36 +0530 Subject: [Pw_forum] selection of k-path Message-ID: Dear PWSCF users, Iam trying to calculate the band structure of a crystal. So for the selection of k-path points Iam using XCRYSDEN software. According to the CIF file of the crystal ,symmetry_space_group is : Pc symmetry type is : Monoclinic The same I gave as input for the crystal and visualized thriugh XCRYSDEN for k-path. It is showing that The Guessed Bravice Lattice not supported . But Pc symmetry group is presnt in Bilbao Crystallographic Server (http://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-kv-list) Now which points can i take for the crystal and what labelling I can give. Here Iam attaching some data of CIF file and the pwscf input . Please provide me some solutions for this. Thanks in advance. Priyanka, Ph.D Student, IICT, INDIA. -------------- next part -------------- A non-text attachment was scrubbed... Name: cif-file-inputpw.doc Type: application/msword Size: 34816 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110221/85c13a23/attachment-0001.doc From sharat_c at yahoo.com Mon Feb 21 07:33:35 2011 From: sharat_c at yahoo.com (Sharat Chandra) Date: Sun, 20 Feb 2011 22:33:35 -0800 (PST) Subject: [Pw_forum] pseudopotential for Uranium Message-ID: <157156.17374.qm@web33101.mail.mud.yahoo.com> Hi I am trying to generate a pseudopotential for Uranium for use in my calculations for UFe2 compound. I have tried converting the fhi PPs available from the ABINIT web site, as well as generating the TM PP based on the publication by Crocombette etal, Phys. Rev. B, 64, 104107, 2001, and also trying to generate the ultrasoft PP, using the atom code. I have checked the mailing list and did not find any discussion with emphasis on this topic. The fhi PPs have 6 electrons, while the PPs generated using the PRB data have 12 electrons. I have not been able to get the proper lattice parameter and bulk modulus of U in fcc phase, published in the same paper, which are 134.3 a.u.^3 and 154 GPa. I either get too large values, or too small values, based on the number of electrons in the PPs. Can some one please tell me what I am doing wrong? If any one can tell me what are the proper values for rcore and rcloc, I will be very grateful. I have put below the different inputs that I have used to generate the PPs. -------------- SR, Ultrasoft, 6 electrons --------------------------------- ?&input ??????? title='U', ??????? zed=92.0, ??????? rel=1, ??????? iswitch=3, ??????? rlderiv=2.50, ??????? eminld=-4.0, ??????? emaxld=4.0, ??????? deld=0.02, ??????? nld=5, ??????? config='[Rn] 5f3 6d1 7s2', ??????? dft='PBE' ?/ ?&inputp ??????? pseudotype=3, ??????? lloc=0, ??????? file_pseudopw='Urel.SR.PBE.UPF', ??????? nlcc=.true., ??????? rcore=1.5, ??????? rcloc=2.5, ?/ 3 5F? 4? 3? 3.00? 0.00? 2.90? 2.90? 3.50 6D? 3? 2? 1.00? 0.00? 3.50? 3.50? 2.50 7S? 1? 0? 2.00? 0.00? 2.80? 2.80? 0.00 ------------------------------------------------------------------------- ---------------- SR, TM, 12 electrons, PRB inputs --------------------- ?&input ??????? title='U', ??????? zed=92.0, ??????? rel=1, ??????? iswitch=3, ??????? rlderiv=2.50, ??????? eminld=-4.0, ??????? emaxld=4.0, ??????? deld=0.02, ??????? nld=5, ??????? dft='PBE' ?/ 5 6S? 6? 0? 2.00? 0.50 6P? 6? 1? 6.00? 1.50 6D? 6? 2? 1.00? 2.50 5F? 5? 3? 3.00? 3.50 7S? 7? 0? 2.00? 0.50 ?&inputp ??????? pseudotype=2, ??????? lloc=-1, ??????? file_pseudopw='Urel.SR.PBE.TM2.UPF', ??????? nlcc=.true., ??????? tm=.true., ??????? rcore=1.2, ??????? rcloc=1.9, ?/ 4 5F? 4? 3? 3.00? 0.00? 1.26? 1.26 6P? 2? 1? 6.00? 0.00? 1.52? 1.52 6D? 3? 2? 1.00? 0.00? 2.20? 2.20 6S? 1? 0? 2.00? 0.00? 1.26? 1.26 -------------------------------------------------------------------- Regards and thanks for your time. Dr. Sharat Chandra Materials Science Division Indira Gandhi Centre for Atomic Research Kalpakkam 603 102, TN, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110220/d202c315/attachment.htm From sclauzer at sissa.it Mon Feb 21 09:09:58 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 21 Feb 2011 09:09:58 +0100 Subject: [Pw_forum] DOS calculation In-Reply-To: References: Message-ID: <156590C4-B6F7-4C26-8744-2AE8F505579A@sissa.it> Maybe your calculation is heavy (many many bands and k-points) and is actually going on (slowly), but you can't see it. To understand if the program is stuck or is just proceeding silently, use verbosity='high' (it will display additional printout each time a k-point has been completed) or look at the time stamps of the .wfc file(s). HTH GS Il giorno 20/feb/2011, alle ore 04.13, vinoth r ha scritto: > Dear pwscf user, > i want to calculate DOS for Graphene Nanoribbon.I optimized my GNR using relax calculation.i finished my SCFcalculation also.while doing NSCF calculation i got like (last few lines of my nscf output) > > negative rho (up, down): 0.227E-02 0.000E+00 > Starting wfc are 132 atomic wfcs > > total cpu time spent up to now is 90.08 secs > > per-process dynamical memory: 730.3 Mb > > Band Structure Calculation. > > After 5 hours also it doesnt calculate any thing & it doesnt show any error.Could you help me to rectify the problem. > > with regards > Abenano > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110221/2c093503/attachment.htm From pcj994 at bham.ac.uk Mon Feb 21 13:00:15 2011 From: pcj994 at bham.ac.uk (Paul Jennings) Date: Mon, 21 Feb 2011 12:00:15 +0000 Subject: [Pw_forum] Phonones Message-ID: <4D6253CF.90409@bham.ac.uk> Dear QE users I try to do a gamma point phonon calculations for say Au6. After doing a SCF calculation (at the gamme point) and using the input file for ph.x of the form: Phonons of Au6 at Gamma &inputph tr2_ph=1.0d-14, amass(1)=196.97, prefix="Au6_dos", outdir="/scratch/heiless", fildyn="Au6.dynG", / 0.0 0.0 0.0 the program comes up with the following error message: from phq_readin : error # 1 cannot start from pw.x data file using Gamma-point tricks The procedure I used works well for solid Si but unfortunately I don't know what the problem for this small cluster is. Any help would be appreciated. Many thanks, Paul -- ****************************************************** Paul Jennings Centre for Hydrogen and Fuel Cell Research PEMFC Research group School of Chemical Engineering The University of Birmingham Edgbaston, Birmingham B15 2TT (U.K.) E: PCJ994 at bham.ac.uk T: 07816644583 W: www.fuelcells.bham.ac.uk ****************************************************** From lyue at gmx.net Mon Feb 21 13:01:53 2011 From: lyue at gmx.net (Lun Yue) Date: Mon, 21 Feb 2011 13:01:53 +0100 Subject: [Pw_forum] Strange band structure diagram In-Reply-To: References: <20110220234524.184840@gmx.net> Message-ID: <20110221120153.80730@gmx.net> Hello Claudia: It works. Thanks a lot! Best regards, Lun Yue -------- Original-Nachricht -------- > Datum: Sun, 20 Feb 2011 18:33:00 -0600 > Von: Claudia Loyola > An: PWSCF Forum > Betreff: Re: [Pw_forum] Strange band structure diagram > Hi, > > if your question is for the overlap between the bands, in the input file > for > band.x executable, add this line: > > no_overlap=.true., > > regards, > Claudia Loyola > > On Sun, Feb 20, 2011 at 5:45 PM, Lun Yue wrote: > > > Dear pwscf users, > > > > I did some calculations about bulk TiO2 rutile and got a really strange > > band structure diagram: > > http://img840.imageshack.us/i/rutilebands.png/ > > > > I checked the input files but could not find the problem, please help me > in > > figuring out it. > > > > > > Best regards, > > Lun Yue > > > > My input files: > > > > ======= rutile.scf.in =============== > > > > &control > > calculation = 'scf', > > prefix = 'rutile_scf', > > verbosity = 'default', > > / > > &system > > ibrav = 6, > > celldm(1) = 8.680890966, > > celldm(3) = 0.64394729330137, > > nat = 6, > > ntyp = 2, > > ecutwfc = 40, > > ecutrho = 400, > > occupations = 'fixed', > > nbnd = 40, > > / > > &electrons > > conv_thr = 1.0e-09, > > electron_maxstep = 100, > > mixing_beta = 0.3, > > conv_thr = 1.0e-08, > > mixing_mode = 'plain', > > / > > > > ATOMIC_SPECIES > > O 15.999 O.pbe-van_ak.UPF > > Ti 47.867 Ti.pbe-sp-van_ak.UPF > > ATOMIC_POSITIONS (angstrom) > > Ti 0.00000000 0.00000000 0.00000000 > > Ti 2.29686500 2.29686500 1.47906000 > > O 1.40246577 1.40246577 0.00000000 > > O -1.40246577 -1.40246577 0.00000000 > > O 3.69933077 0.89439923 1.47906000 > > O 0.89439923 3.69933077 1.47906000 > > K_POINTS (automatic) > > 6 6 6 0 0 0 > > > > > > > > ========= rutile.bands.in ============= > > > > &control > > calculation = 'bands', > > prefix = 'rutile_scf', > > verbosity = 'default', > > / > > &system > > ibrav = 6, > > celldm(1) = 8.680890966, > > celldm(3) = 0.64394729330137, > > nat = 6, > > ntyp = 2, > > ecutwfc = 40, > > ecutrho = 400, > > occupations = 'fixed', > > nbnd = 40, > > / > > &electrons > > conv_thr = 1.0e-09, > > electron_maxstep = 100, > > mixing_beta = 0.3, > > conv_thr = 1.0e-08, > > mixing_mode = 'plain', > > / > > > > ATOMIC_SPECIES > > O 15.999 O.pbe-van_ak.UPF > > Ti 47.867 Ti.pbe-sp-van_ak.UPF > > ATOMIC_POSITIONS (angstrom) > > Ti 0.00000000 0.00000000 0.00000000 > > Ti 2.29686500 2.29686500 1.47906000 > > O 1.40246577 1.40246577 0.00000000 > > O -1.40246577 -1.40246577 0.00000000 > > O 3.69933077 0.89439923 1.47906000 > > O 0.89439923 3.69933077 1.47906000 > > K_POINTS crystal > > 60 > > 0.5000000000 0.0000000000 0.5000000000 1.0 > > 0.4750000000 0.0000000000 0.4750000000 1.0 > > 0.4500000000 0.0000000000 0.4500000000 1.0 > > 0.4250000000 0.0000000000 0.4250000000 1.0 > > 0.4000000000 0.0000000000 0.4000000000 1.0 > > 0.3750000000 0.0000000000 0.3750000000 1.0 > > 0.3500000000 0.0000000000 0.3500000000 1.0 > > 0.3250000000 0.0000000000 0.3250000000 1.0 > > 0.3000000000 0.0000000000 0.3000000000 1.0 > > 0.2750000000 0.0000000000 0.2750000000 1.0 > > 0.2500000000 0.0000000000 0.2500000000 1.0 > > 0.2250000000 0.0000000000 0.2250000000 1.0 > > 0.2000000000 0.0000000000 0.2000000000 1.0 > > 0.1750000000 0.0000000000 0.1750000000 1.0 > > 0.1500000000 0.0000000000 0.1500000000 1.0 > > 0.1250000000 0.0000000000 0.1250000000 1.0 > > 0.1000000000 0.0000000000 0.1000000000 1.0 > > 0.0750000000 0.0000000000 0.0750000000 1.0 > > 0.0500000000 0.0000000000 0.0500000000 1.0 > > 0.0250000000 0.0000000000 0.0250000000 1.0 > > 0.0000000000 0.0000000000 0.0000000000 1.0 > > 0.0000000000 0.0454545455 0.0000000000 1.0 > > 0.0000000000 0.0909090909 0.0000000000 1.0 > > 0.0000000000 0.1363636364 0.0000000000 1.0 > > 0.0000000000 0.1818181818 0.0000000000 1.0 > > 0.0000000000 0.2272727273 0.0000000000 1.0 > > 0.0000000000 0.2727272727 0.0000000000 1.0 > > 0.0000000000 0.3181818182 0.0000000000 1.0 > > 0.0000000000 0.3636363636 0.0000000000 1.0 > > 0.0000000000 0.4090909091 0.0000000000 1.0 > > 0.0000000000 0.4545454545 0.0000000000 1.0 > > 0.0000000000 0.5000000000 0.0000000000 1.0 > > 0.0454545455 0.5000000000 0.0000000000 1.0 > > 0.0909090909 0.5000000000 0.0000000000 1.0 > > 0.1363636364 0.5000000000 0.0000000000 1.0 > > 0.1818181818 0.5000000000 0.0000000000 1.0 > > 0.2272727273 0.5000000000 0.0000000000 1.0 > > 0.2727272727 0.5000000000 0.0000000000 1.0 > > 0.3181818182 0.5000000000 0.0000000000 1.0 > > 0.3636363636 0.5000000000 0.0000000000 1.0 > > 0.4090909091 0.5000000000 0.0000000000 1.0 > > 0.4545454545 0.5000000000 0.0000000000 1.0 > > 0.5000000000 0.5000000000 0.0000000000 1.0 > > 0.5000000000 0.5000000000 0.0294117647 1.0 > > 0.5000000000 0.5000000000 0.0588235294 1.0 > > 0.5000000000 0.5000000000 0.0882352941 1.0 > > 0.5000000000 0.5000000000 0.1176470588 1.0 > > 0.5000000000 0.5000000000 0.1470588235 1.0 > > 0.5000000000 0.5000000000 0.1764705882 1.0 > > 0.5000000000 0.5000000000 0.2058823529 1.0 > > 0.5000000000 0.5000000000 0.2352941176 1.0 > > 0.5000000000 0.5000000000 0.2647058824 1.0 > > 0.5000000000 0.5000000000 0.2941176471 1.0 > > 0.5000000000 0.5000000000 0.3235294118 1.0 > > 0.5000000000 0.5000000000 0.3529411765 1.0 > > 0.5000000000 0.5000000000 0.3823529412 1.0 > > 0.5000000000 0.5000000000 0.4117647059 1.0 > > 0.5000000000 0.5000000000 0.4411764706 1.0 > > 0.5000000000 0.5000000000 0.4705882353 1.0 > > 0.5000000000 0.5000000000 0.5000000000 1.0 > > > > -- > > NEU: FreePhone - kostenlos mobil telefonieren und surfen! > > Jetzt informieren: http://www.gmx.net/de/go/freephone > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > Claudia Loyola Canales > Postdoc in Computational Physics > Iowa State University > Iowa, USA > www.lpmd.cl/claudial > www.lpmd.cl > http://cosmic.mse.iastate.edu/ > www.gnm.cl -- GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit gratis Handy-Flat! http://portal.gmx.net/de/go/dsl From eyvaz_isaev at yahoo.com Mon Feb 21 13:37:53 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 21 Feb 2011 04:37:53 -0800 (PST) Subject: [Pw_forum] Phonones In-Reply-To: <4D6253CF.90409@bham.ac.uk> References: <4D6253CF.90409@bham.ac.uk> Message-ID: <454423.44264.qm@web65704.mail.ac4.yahoo.com> Hi, You could try in two ways: 1. K_POINTS automatic 1 1 1 0 0 0 This will give you only Gamma point, and G-point tricky will be avoided (hopefully). 2. You can specify in ph.in file ldisp=.true. nq1=2, nq2=2, nq3=2 start_q=1 last_q=1 G-point is the first in the q-list generated. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ----- Original Message ---- From: Paul Jennings To: pw_forum at pwscf.org Sent: Mon, February 21, 2011 3:00:15 PM Subject: [Pw_forum] Phonones Dear QE users I try to do a gamma point phonon calculations for say Au6. After doing a SCF calculation (at the gamme point) and using the input file for ph.x of the form: Phonons of Au6 at Gamma &inputph tr2_ph=1.0d-14, amass(1)=196.97, prefix="Au6_dos", outdir="/scratch/heiless", fildyn="Au6.dynG", / 0.0 0.0 0.0 the program comes up with the following error message: from phq_readin : error # 1 cannot start from pw.x data file using Gamma-point tricks The procedure I used works well for solid Si but unfortunately I don't know what the problem for this small cluster is. Any help would be appreciated. Many thanks, Paul -- ****************************************************** Paul Jennings Centre for Hydrogen and Fuel Cell Research PEMFC Research group School of Chemical Engineering The University of Birmingham Edgbaston, Birmingham B15 2TT (U.K.) E: PCJ994 at bham.ac.uk T: 07816644583 W: www.fuelcells.bham.ac.uk ****************************************************** _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From cyrille.barreteau at cea.fr Mon Feb 21 13:59:50 2011 From: cyrille.barreteau at cea.fr (Cyrille Barreteau) Date: Mon, 21 Feb 2011 13:59:50 +0100 Subject: [Pw_forum] subtile error for non collinear calculations with a GGA pseudo In-Reply-To: <71BB5D8A-6EA8-47A9-A516-F0A3C45486B7@democritos.it> References: <71BB5D8A-6EA8-47A9-A516-F0A3C45486B7@democritos.it> Message-ID: <1298293190.22838.71.camel@spcsi25169> Dear all I have noticed an usual behavior when doing non collinear calculation with a GGA pseudopotential. During the iteration process there are some NaN appearing in the output file (see below). The strange thing is that the code continues and converges.. iteration # 1 ecut= 35.00 Ry beta=0.30 Davidson diagonalization with overlap ethr = 1.00E-02, avg # of iterations = 2.0 NaN NaN NaN This type of Pb is not present when using a LDA pseudo. Moreover I have tried to do a calculation of a collinear configuration with or without the 'noncolin' option. In principle both should lead to almost the same solution. This is not the case. There are some differences which according to me are larger than just numerical errors.. I guess there is some kind of Pb when performing non collinear calculations with a GGA pseudo. thanks to give me a hint to solve this problem cyrille -- ================================================================== Cyrille Barreteau | phone : +33 (0)1 69 08 29 51 CEA Saclay | fax : +33 (0)1 69 08 84 46 IRAMIS SPCSI Bat 462 | email cyrille.barreteau at cea.fr 91191 Gif sur Yvette FRANCE ~~~~~~~~~~~~~~~~~~~~~~~~ home page: http://iramis.cea.fr/Pisp/cbarreteau/ Lab page: http://iramis.cea.fr/spcsi/ ================================================================== From pc229 at kent.ac.uk Mon Feb 21 14:37:28 2011 From: pc229 at kent.ac.uk (pieremanuele canepa) Date: Mon, 21 Feb 2011 13:37:28 +0000 Subject: [Pw_forum] Jmol and J-ICE can deal with quantumEspresso Message-ID: Dear QuantumEspresso users, I am glad to announce you that Jmol(http://jmol.sourceforge.net/) as well my personal Jmol (interface: J-ICE (http://j-ice.sourceforge.net/) can read quantumESPRESSO outputs. Now we can read simple geometry from SCF job and geometry optimization tasks. The phonon part is still work in progress. As a Jmol developer (and quanumEspresso users) I kindly ask you to provide me more phonon tests you might have (not those available in the example folder). Bests, Piero -- *Please consider the environment before printing this e-mail.* ** Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc229 at kent.ac.uk mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110221/e5bd610d/attachment.htm From vinothrece at gmail.com Mon Feb 21 15:29:10 2011 From: vinothrece at gmail.com (vinoth r) Date: Mon, 21 Feb 2011 19:59:10 +0530 Subject: [Pw_forum] DOS calculation In-Reply-To: <156590C4-B6F7-4C26-8744-2AE8F505579A@sissa.it> References: <156590C4-B6F7-4C26-8744-2AE8F505579A@sissa.it> Message-ID: thank you very much.i will use verbosity='high'. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110221/c2834fb0/attachment.htm From dalcorso at sissa.it Mon Feb 21 18:39:57 2011 From: dalcorso at sissa.it (Andrea Dal Corso) Date: Mon, 21 Feb 2011 18:39:57 +0100 Subject: [Pw_forum] subtile error for non collinear calculations with a GGA pseudo In-Reply-To: <1298293190.22838.71.camel@spcsi25169> References: <71BB5D8A-6EA8-47A9-A516-F0A3C45486B7@democritos.it> <1298293190.22838.71.camel@spcsi25169> Message-ID: <1298309997.11519.8.camel@ulisse.cm.sissa.it> On Mon, 2011-02-21 at 13:59 +0100, Cyrille Barreteau wrote: > Dear all > > I have noticed an usual behavior when doing non collinear calculation > with a GGA pseudopotential. > > During the iteration process there are some NaN appearing in the output > file (see below). The strange thing is that the code continues and > converges.. > > iteration # 1 ecut= 35.00 Ry beta=0.30 > Davidson diagonalization with overlap > ethr = 1.00E-02, avg # of iterations = 2.0 > NaN NaN NaN This error has been already corrected in the cvs version a few months ago. Note however that GGA + noncollinear is less stable than the other parts of QE. HTH, Andrea > > This type of Pb is not present when using a LDA pseudo. > > Moreover I have tried to do a calculation of a collinear configuration > with or without the 'noncolin' option. In principle both should lead to > almost the same solution. This is not the case. There are some > differences which according to me are larger than just numerical > errors.. > > I guess there is some kind of Pb when performing non collinear > calculations with a GGA pseudo. > > thanks to give me a hint to solve this problem > > cyrille > -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Bonomea 265 Fax. 0039-040-3787249 I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it From cyrille.barreteau at cea.fr Mon Feb 21 19:39:13 2011 From: cyrille.barreteau at cea.fr (BARRETEAU Cyrille) Date: Mon, 21 Feb 2011 19:39:13 +0100 Subject: [Pw_forum] =?iso-8859-1?q?RE=A0=3A__subtile_error_for_non_colline?= =?iso-8859-1?q?ar_calculations_witha=09GGA_pseudo?= References: <71BB5D8A-6EA8-47A9-A516-F0A3C45486B7@democritos.it><1298293190.22838.71.camel@spcsi25169> <1298309997.11519.8.camel@ulisse.cm.sissa.it> Message-ID: <18E4AC9C2FAC504E994A6759DE5ABE8DE3154B@DIODON.extra.cea.fr> Andrea, Thanks for your anwer. I will therefore download the CVS version and do some testing. By the way I have also noticed that some pseudopotentials generated by old version of ld1.x (typically older than 4.0.5) are no longer accepted by pw. Does it mean that some errors were found in ld1.x. Or is it due to a modification of the format? thanks cyrille ================================================================== Cyrille Barreteau phone : +33 (0)1 69 08 29 51 CEA Saclay fax : +33 (0)1 69 08 84 46 IRAMIS, SPCSI, Batiment 462 email cyrille.barreteau at cea.fr 91191 Gif sur Yvette Cedex FRANCE ~~~~~~~~~~~~~~~~~~~~~~~~ Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/ ================================================================== ________________________________ De: pw_forum-bounces at pwscf.org de la part de Andrea Dal Corso Date: lun. 21/02/2011 18:39 ?: PWSCF Forum Objet : Re: [Pw_forum] subtile error for non collinear calculations witha GGA pseudo On Mon, 2011-02-21 at 13:59 +0100, Cyrille Barreteau wrote: > Dear all > > I have noticed an usual behavior when doing non collinear calculation > with a GGA pseudopotential. > > During the iteration process there are some NaN appearing in the output > file (see below). The strange thing is that the code continues and > converges.. > > iteration # 1 ecut= 35.00 Ry beta=0.30 > Davidson diagonalization with overlap > ethr = 1.00E-02, avg # of iterations = 2.0 > NaN NaN NaN This error has been already corrected in the cvs version a few months ago. Note however that GGA + noncollinear is less stable than the other parts of QE. HTH, Andrea > > This type of Pb is not present when using a LDA pseudo. > > Moreover I have tried to do a calculation of a collinear configuration > with or without the 'noncolin' option. In principle both should lead to > almost the same solution. This is not the case. There are some > differences which according to me are larger than just numerical > errors.. > > I guess there is some kind of Pb when performing non collinear > calculations with a GGA pseudo. > > thanks to give me a hint to solve this problem > > cyrille > -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Bonomea 265 Fax. 0039-040-3787249 I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 8126 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110221/58905ba3/attachment-0001.bin From giannozz at democritos.it Mon Feb 21 20:55:50 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 21 Feb 2011 20:55:50 +0100 Subject: [Pw_forum] subtile error for non collinear calculations with a GGA pseudo In-Reply-To: <1298293190.22838.71.camel@spcsi25169> References: <71BB5D8A-6EA8-47A9-A516-F0A3C45486B7@democritos.it> <1298293190.22838.71.camel@spcsi25169> Message-ID: <0F053152-FAA9-438C-8E9D-9BC8576F6C64@democritos.it> On Feb 21, 2011, at 13:59 , Cyrille Barreteau wrote: > Moreover I have tried to do a calculation of a collinear > configuration with or without the 'noncolin' option. In > principle both should lead to almost the same solution. in practise, they don't. It is a known problem (Andrea explained it to me some time ago), not related to bad coding but to a more fundamental and subtle problem of how to define the quantization axis P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From cyrille.barreteau at cea.fr Mon Feb 21 21:07:36 2011 From: cyrille.barreteau at cea.fr (BARRETEAU Cyrille) Date: Mon, 21 Feb 2011 21:07:36 +0100 Subject: [Pw_forum] =?iso-8859-1?q?RE=A0=3A__subtile_error_for_non_colline?= =?iso-8859-1?q?ar_calculations_with_aGGA_pseudo?= References: <71BB5D8A-6EA8-47A9-A516-F0A3C45486B7@democritos.it><1298293190.22838.71.camel@spcsi25169> <0F053152-FAA9-438C-8E9D-9BC8576F6C64@democritos.it> Message-ID: <18E4AC9C2FAC504E994A6759DE5ABE8DE3154D@DIODON.extra.cea.fr> Paolo, In fact I have compared collinear and non collinear calculation for a "collinear situation" (bcc Cr AF): both calculations perfectly agree (up to numerical precision) for a LDA pseudo but not for a GGA pseudo. This is probaly due to the error mentionned previously (corrected in the CVS version). Therefore following Andrea's suggestion I will try the last cvs version to check that gga pseudo work also.. good evening cyrille ================================================================== Cyrille Barreteau phone : +33 (0)1 69 08 29 51 CEA Saclay fax : +33 (0)1 69 08 84 46 IRAMIS, SPCSI, Batiment 462 email cyrille.barreteau at cea.fr 91191 Gif sur Yvette Cedex FRANCE ~~~~~~~~~~~~~~~~~~~~~~~~ Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/ ================================================================== ________________________________ De: pw_forum-bounces at pwscf.org de la part de Paolo Giannozzi Date: lun. 21/02/2011 20:55 ?: PWSCF Forum Objet : Re: [Pw_forum] subtile error for non collinear calculations with aGGA pseudo On Feb 21, 2011, at 13:59 , Cyrille Barreteau wrote: > Moreover I have tried to do a calculation of a collinear > configuration with or without the 'noncolin' option. In > principle both should lead to almost the same solution. in practise, they don't. It is a known problem (Andrea explained it to me some time ago), not related to bad coding but to a more fundamental and subtle problem of how to define the quantization axis P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 6786 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110221/3632c891/attachment.bin From giannozz at democritos.it Mon Feb 21 21:24:19 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 21 Feb 2011 21:24:19 +0100 Subject: [Pw_forum] =?iso-8859-1?q?RE=A0=3A__subtile_error_for_non_colline?= =?iso-8859-1?q?ar_calculations_with_aGGA_pseudo?= In-Reply-To: <18E4AC9C2FAC504E994A6759DE5ABE8DE3154D@DIODON.extra.cea.fr> References: <71BB5D8A-6EA8-47A9-A516-F0A3C45486B7@democritos.it><1298293190.22838.71.camel@spcsi25169> <0F053152-FAA9-438C-8E9D-9BC8576F6C64@democritos.it> <18E4AC9C2FAC504E994A6759DE5ABE8DE3154D@DIODON.extra.cea.fr> Message-ID: <2130D5CB-BF12-44A6-A1FB-BA4B4BBBEB90@democritos.it> On Feb 21, 2011, at 21:07 , BARRETEAU Cyrille wrote: > both calculations perfectly agree (up to numerical precision) > for a LDA pseudo but not for a GGA pseudo. This is probably > due to the error mentioned previously (corrected in the CVS > version). I think it is a different problem. It arises only with GGA because you need gradients to calculate the xc functional. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From quantumdft at gmail.com Tue Feb 22 04:16:46 2011 From: quantumdft at gmail.com (vega lew) Date: Tue, 22 Feb 2011 11:16:46 +0800 Subject: [Pw_forum] Jmol and J-ICE can deal with quantumEspresso In-Reply-To: References: Message-ID: <4D632A9E.1080504@gmail.com> Dear Pieremanuele Canepa, Thank you for developing such a convenient tool for us. The second one, J-ICE, could read and display thegeometry from SCF job and geometry optimization tasks of Quantum-Espresso very well. But there is something wrong with the first one, Jmol. It only could directly read .xyz files not the .out files as J-ICE do. I still wonder whether you have a plan to make your tools read geometry from output files of NEB calculation. thank you again for your wonderful and convenient program. Best vega On 02/21/11 21:37, pieremanuele canepa wrote: > Dear QuantumEspresso users, > > I am glad to announce you that Jmol(http://jmol.sourceforge.net/) as > well my personal Jmol (interface: J-ICE (http://j-ice.sourceforge.net/) > can read quantumESPRESSO outputs. > > Now we can read simple geometry from SCF job and geometry > optimization tasks. The phonon part is still work in progress. > As a Jmol developer (and quanumEspresso users) I kindly ask you to > provide me more phonon tests you might have > (not those available in the example folder). > > Bests, Piero > > -- > /Please consider the environment before printing this e-mail./ > > Pieremanuele Canepa > Room 104 > Functional Material Group > School of Physical Sciences, Ingram Building, > University of Kent, Canterbury, Kent, > CT2 7NH > United Kingdom > > e-mail: pc229 at kent.ac.uk > mobile: +44 (0) 7772-9756456 > ----------------------------------------------------------- > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ================================================ Vega Lew ( weijia liu) Graduate student State Key Laboratory of Materials-oriented Chemical Engineering Nanjing University of Technology, 210009, Nanjing, China *************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, China *************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110222/0a717a86/attachment.htm From quantumdft at gmail.com Tue Feb 22 04:22:52 2011 From: quantumdft at gmail.com (vega lew) Date: Tue, 22 Feb 2011 11:22:52 +0800 Subject: [Pw_forum] Jmol and J-ICE can deal with quantumEspresso In-Reply-To: References: Message-ID: <4D632C0C.8080307@gmail.com> I find the Jmol program inside the J-ICE folder could directly read the output file from Q-E. However, the program (Jmol-12.0.33-binary) downloaded from http://jmol.sourceforge.net/ did not. vega On 02/21/11 21:37, pieremanuele canepa wrote: > Dear QuantumEspresso users, > > I am glad to announce you that Jmol(http://jmol.sourceforge.net/) as > well my personal Jmol (interface: J-ICE (http://j-ice.sourceforge.net/) > can read quantumESPRESSO outputs. > > Now we can read simple geometry from SCF job and geometry > optimization tasks. The phonon part is still work in progress. > As a Jmol developer (and quanumEspresso users) I kindly ask you to > provide me more phonon tests you might have > (not those available in the example folder). > > Bests, Piero > > -- > /Please consider the environment before printing this e-mail./ > > Pieremanuele Canepa > Room 104 > Functional Material Group > School of Physical Sciences, Ingram Building, > University of Kent, Canterbury, Kent, > CT2 7NH > United Kingdom > > e-mail: pc229 at kent.ac.uk > mobile: +44 (0) 7772-9756456 > ----------------------------------------------------------- > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ================================================ Vega Lew ( weijia liu) Graduate student State Key Laboratory of Materials-oriented Chemical Engineering Nanjing University of Technology, 210009, Nanjing, China *************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, China *************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110222/b64f9a93/attachment-0001.htm From pc229 at kent.ac.uk Tue Feb 22 09:50:08 2011 From: pc229 at kent.ac.uk (pieremanuele canepa) Date: Tue, 22 Feb 2011 08:50:08 +0000 Subject: [Pw_forum] FW: Jmol and J-ICE can deal with quantumEspresso In-Reply-To: <42054E10C02CD44D81EF510077A30A0738329CC1E8@MAPI.ad.kent.ac.uk> References: <42054E10C02CD44D81EF510077A30A0738329CC1E8@MAPI.ad.kent.ac.uk> Message-ID: Dear Vega, use the developer version. You right about the error in the first geometry. I will fix it. if you want NEB implemented in Jmol send me some outputs. all the best, Piero On Tue, Feb 22, 2011 at 3:23 AM, P.Canepa wrote: > > ------------------------------------------- > From: pw_forum-bounces at pwscf.org on behalf of vega lew[ > SMTP:QUANTUMDFT at GMAIL.COM] > Sent: Tuesday, February 22, 2011 3:22:52 AM > To: PWSCF Forum > Subject: Re: [Pw_forum] Jmol and J-ICE can deal with quantumEspresso > Auto forwarded by a Rule I find the Jmol program inside the J-ICE folder > could directly read the output file from Q-E. > > However, the program (Jmol-12.0.33-binary) downloaded from > http://jmol.sourceforge.net/ did not. > > > vega > > On 02/21/11 21:37, pieremanuele canepa wrote: > > Dear QuantumEspresso users, > > I am glad to announce you that Jmol(http://jmol.sourceforge.net/) as well > my personal Jmol (interface: J-ICE (http://j-ice.sourceforge.net/) > can read quantumESPRESSO outputs. > > Now we can read simple geometry from SCF job and geometry optimization > tasks. The phonon part is still work in progress. > As a Jmol developer (and quanumEspresso users) I kindly ask you to provide > me more phonon tests you might have > (not those available in the example folder). > > Bests, Piero > > -- > *Please consider the environment before printing this e-mail.* > > Pieremanuele Canepa > Room 104 > Functional Material Group > School of Physical Sciences, Ingram Building, > University of Kent, Canterbury, Kent, > CT2 7NH > United Kingdom > > e-mail: pc229 at kent.ac.uk > mobile: +44 (0) 7772-9756456 > ----------------------------------------------------------- > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > -- > > ================================================ > Vega Lew ( weijia liu) > Graduate student > State Key Laboratory of Materials-oriented Chemical Engineering > Nanjing University of Technology, 210009, Nanjing, China > *************************************************************** > Email: vegalew at gmail.com > Office: Room A705, Technical Innovation Building, > Xinmofan Road 5#, Nanjing, China > *************************************************************** > -- *Please consider the environment before printing this e-mail.* ** Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc229 at kent.ac.uk mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110222/612c3e20/attachment.htm From quantumdft at gmail.com Tue Feb 22 12:23:04 2011 From: quantumdft at gmail.com (vega lew) Date: Tue, 22 Feb 2011 19:23:04 +0800 Subject: [Pw_forum] FW: Jmol and J-ICE can deal with quantumEspresso In-Reply-To: References: <42054E10C02CD44D81EF510077A30A0738329CC1E8@MAPI.ad.kent.ac.uk> Message-ID: <4D639C98.8090406@gmail.com> Dear Piero, I just recalled that there is no information about coordinates in output files. Fortunately, the Jmol could read xyz files instead. It is really a convenient tool for our Q-E users. Thank you again for your wonderful program. By the way: when I read the output using Jmol, I find the del(E) map in Geom. tab could update in real time. However, the ForceMax never update at all. Could you please check it? Best vega On 02/22/11 16:50, pieremanuele canepa wrote: > > Dear Vega, > > use the developer version. > > You right about the error in the first geometry. I will fix it. > > if you want NEB implemented in Jmol send me some outputs. > > > all the best, Piero > > > On Tue, Feb 22, 2011 at 3:23 AM, P.Canepa > wrote: > > > ------------------------------------------- > From: pw_forum-bounces at pwscf.org > on behalf of vega > lew[SMTP:QUANTUMDFT at GMAIL.COM ] > Sent: Tuesday, February 22, 2011 3:22:52 AM > To: PWSCF Forum > Subject: Re: [Pw_forum] Jmol and J-ICE can deal with quantumEspresso > Auto forwarded by a Rule I find the Jmol program inside the J-ICE > folder could directly read the output file from Q-E. > > However, the program (Jmol-12.0.33-binary) downloaded from > http://jmol.sourceforge.net/ did not. > > > vega > > On 02/21/11 21:37, pieremanuele canepa wrote: >> Dear QuantumEspresso users, >> >> I am glad to announce you that Jmol(http://jmol.sourceforge.net/) >> as well my personal Jmol (interface: J-ICE >> (http://j-ice.sourceforge.net/) >> can read quantumESPRESSO outputs. >> >> Now we can read simple geometry from SCF job and geometry >> optimization tasks. The phonon part is still work in progress. >> As a Jmol developer (and quanumEspresso users) I kindly ask you >> to provide me more phonon tests you might have >> (not those available in the example folder). >> >> Bests, Piero >> >> -- >> /Please consider the environment before printing this e-mail./ >> >> Pieremanuele Canepa >> Room 104 >> Functional Material Group >> School of Physical Sciences, Ingram Building, >> University of Kent, Canterbury, Kent, >> CT2 7NH >> United Kingdom >> >> e-mail: pc229 at kent.ac.uk >> mobile: +44 (0) 7772-9756456 >> ----------------------------------------------------------- >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > ================================================ > Vega Lew ( weijia liu) > Graduate student > State Key Laboratory of Materials-oriented Chemical Engineering > Nanjing University of Technology, 210009, Nanjing, China > *************************************************************** > Email: vegalew at gmail.com > Office: Room A705, Technical Innovation Building, > Xinmofan Road 5#, Nanjing, China > *************************************************************** > > > > > -- > /Please consider the environment before printing this e-mail./ > > Pieremanuele Canepa > Room 104 > Functional Material Group > School of Physical Sciences, Ingram Building, > University of Kent, Canterbury, Kent, > CT2 7NH > United Kingdom > > e-mail: pc229 at kent.ac.uk > mobile: +44 (0) 7772-9756456 > ----------------------------------------------------------- > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ================================================ Vega Lew ( weijia liu) Graduate student State Key Laboratory of Materials-oriented Chemical Engineering Nanjing University of Technology, 210009, Nanjing, China *************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, China *************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110222/6b706cb3/attachment.htm From cyrille.barreteau at cea.fr Tue Feb 22 16:24:49 2011 From: cyrille.barreteau at cea.fr (BARRETEAU Cyrille) Date: Tue, 22 Feb 2011 16:24:49 +0100 Subject: [Pw_forum] =?iso-8859-1?q?RE=A0=3A__RE=A0=3A__subtile_error_for_n?= =?iso-8859-1?q?on_collinear_calculations_with_aGGA_pseudo?= References: <71BB5D8A-6EA8-47A9-A516-F0A3C45486B7@democritos.it><1298293190.22838.71.camel@spcsi25169><0F053152-FAA9-438C-8E9D-9BC8576F6C64@democritos.it><18E4AC9C2FAC504E994A6759DE5ABE8DE3154D@DIODON.extra.cea.fr> <2130D5CB-BF12-44A6-A1FB-BA4B4BBBEB90@democritos.it> Message-ID: <18E4AC9C2FAC504E994A6759DE5ABE8DE31554@DIODON.extra.cea.fr> I have done some checks on the 4.3a version and now everything seems to work fine for both lda and gga pseudos. In particular I have done calculations of an antiferro bcc chromium with collinear and non collinear option. Now I do not get any "NaN" message and both calculations perfectly agree (up to numerical precision) which was not the case with the 4.2.1 versionfor a gga pseudo.. cyrille ================================================================== Cyrille Barreteau phone : +33 (0)1 69 08 29 51 CEA Saclay fax : +33 (0)1 69 08 84 46 IRAMIS, SPCSI, Batiment 462 email cyrille.barreteau at cea.fr 91191 Gif sur Yvette Cedex FRANCE ~~~~~~~~~~~~~~~~~~~~~~~~ Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/ ================================================================== ________________________________ De: pw_forum-bounces at pwscf.org de la part de Paolo Giannozzi Date: lun. 21/02/2011 21:24 ?: PWSCF Forum Objet : Re: [Pw_forum] RE : subtile error for non collinear calculations with aGGA pseudo On Feb 21, 2011, at 21:07 , BARRETEAU Cyrille wrote: > both calculations perfectly agree (up to numerical precision) > for a LDA pseudo but not for a GGA pseudo. This is probably > due to the error mentioned previously (corrected in the CVS > version). I think it is a different problem. It arises only with GGA because you need gradients to calculate the xc functional. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 6680 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110222/d2b29f1f/attachment-0001.bin From pcj994 at bham.ac.uk Tue Feb 22 18:17:20 2011 From: pcj994 at bham.ac.uk (Paul Jennings) Date: Tue, 22 Feb 2011 17:17:20 +0000 Subject: [Pw_forum] Phonones In-Reply-To: <454423.44264.qm@web65704.mail.ac4.yahoo.com> References: <4D6253CF.90409@bham.ac.uk> <454423.44264.qm@web65704.mail.ac4.yahoo.com> Message-ID: <4D63EFA0.5090701@bham.ac.uk> Thank you very much, It now works. Cheers, Paul On 21/02/2011 12:37, Eyvaz Isaev wrote: > Hi, > > You could try in two ways: > > 1. K_POINTS automatic > 1 1 1 0 0 0 > > This will give you only Gamma point, and G-point tricky will be avoided > (hopefully). > > 2. You can specify in ph.in file > > ldisp=.true. > nq1=2, nq2=2, nq3=2 > start_q=1 > last_q=1 > > G-point is the first in the q-list generated. > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > > Theoretical Physics Department, Moscow State Institute of Steel& Alloys, > Russia, > > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > > ----- Original Message ---- > From: Paul Jennings > To: pw_forum at pwscf.org > Sent: Mon, February 21, 2011 3:00:15 PM > Subject: [Pw_forum] Phonones > > > Dear QE users > > I try to do a gamma point phonon calculations for say Au6. After doing a SCF > calculation (at the gamme point) > and using the input file for ph.x of the form: > > Phonons of Au6 at Gamma > &inputph > tr2_ph=1.0d-14, > amass(1)=196.97, > prefix="Au6_dos", > outdir="/scratch/heiless", > fildyn="Au6.dynG", > / > 0.0 0.0 0.0 > > > the program comes up with the following error message: > > from phq_readin : error # 1 > cannot start from pw.x data file using Gamma-point tricks > > The procedure I used works well for solid Si but unfortunately I don't know what > the problem for this small > cluster is. > > Any help would be appreciated. > Many thanks, > Paul > > -- ****************************************************** Paul Jennings Centre for Hydrogen and Fuel Cell Research PEMFC Research group School of Chemical Engineering The University of Birmingham Edgbaston, Birmingham B15 2TT (U.K.) E: PCJ994 at bham.ac.uk T: 07816644583 W: www.fuelcells.bham.ac.uk ****************************************************** From konda.physics at gmail.com Tue Feb 22 18:16:39 2011 From: konda.physics at gmail.com (kondaiah samudrala) Date: Tue, 22 Feb 2011 22:46:39 +0530 Subject: [Pw_forum] regarding kpoint Message-ID: Dear sir I have a simple question regarding kpoints.will you please explain how to choose kpoints in Band structure calculations( after scf calculation) for different crystal structures.i know the crystal symmetry directions but i am not getting proper band structure. with regards S.Appalkondaiah Research Schlor University of Hyderabad Hyderabad India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110222/8592ebda/attachment.htm From xrhino at gmail.com Wed Feb 23 05:13:19 2011 From: xrhino at gmail.com (YY) Date: Tue, 22 Feb 2011 23:13:19 -0500 Subject: [Pw_forum] projwfc.x error Message-ID: Dear All, After the scf calculation, I try to use projwfc.x to calculate the PDOS, but get an error message like this: Calling projwave .... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from davcio : error # 10 error while reading from file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I am sure the inputfile is right and the related files exists, because I can calculate total DOS by dos.x correctly. I search the archive of this forum, the same problem was report several times, but no clear answer. I compiled pw.x and projwfc.x from the same version source code (v4.2.1). No matter I use 1 CPU or the same number CPUs as used in pw.x, I get the same error message. Does anyone can give some useful information about it? Best wishes. Yuyang Zhang Nanoscale Physics and Devices Laboratory Institute of Physics, Chinese Academy of Sciences Beijing 100190, P. R. China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110222/1ec1611f/attachment.htm From crma at sissa.it Wed Feb 23 08:45:08 2011 From: crma at sissa.it (Changru Ma) Date: Wed, 23 Feb 2011 08:45:08 +0100 Subject: [Pw_forum] projwfc.x error In-Reply-To: References: Message-ID: <12B60D56-FE0A-4128-9809-E00C2C42A8FE@sissa.it> Dear Yuyang, Please read user guide, page 56. On 23 Feb, 2011, at 05:13, YY wrote: > Dear All, > > After the scf calculation, I try to use projwfc.x to calculate the PDOS, but get an error message like this: > Calling projwave .... > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from davcio : error # 10 > error while reading from file > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > I am sure the inputfile is right and the related files exists, because I can calculate total DOS by dos.x correctly. > I search the archive of this forum, the same problem was report several times, but no clear answer. > I compiled pw.x and projwfc.x from the same version source code (v4.2.1). > No matter I use 1 CPU or the same number CPUs as used in pw.x, I get the same error message. Either use wf_collect = .t. or use the same number CPUs as used in pw.x I suggest you to check if outdir and prefix are the same first. Best wishes, Changru --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 375 8713 (Elettra) +39 040 378 7870 (SISSA) http://www.sissa.it/~crma --- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110223/7f34870d/attachment.htm From giannozz at democritos.it Wed Feb 23 09:32:25 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 23 Feb 2011 09:32:25 +0100 Subject: [Pw_forum] pp.x ILDOS plots with ultrasoft pseudopotentials In-Reply-To: <20110215062951.GC744@ford.simpsons.bogus> References: <20110209072307.GB10648@ford.simpsons.bogus> <3CC8F50E-8BD4-41D9-A8C6-E0F26799A102@democritos.it> <20110215062951.GC744@ford.simpsons.bogus> Message-ID: On Feb 15, 2011, at 7:29 , Henning Glawe wrote: > - in faulty versions, the range of values is [-41,+240], while in > working > versions, it is [0,0.76] > > Affected quantum espresso versions: >=4.2 here is what I got: http://www.fisica.uniud.it/~giannozz/CaC6.tar.gz I don't see anything obviously wrong in it P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed Feb 23 09:39:13 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 23 Feb 2011 09:39:13 +0100 Subject: [Pw_forum] projwfc.x error In-Reply-To: References: Message-ID: <53A655A7-C00C-4BB9-A847-468AA58CF129@democritos.it> On Feb 23, 2011, at 5:13 , YY wrote: > the same problem was report several times, but no clear answer. no clear report either. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From glawe at mpi-halle.mpg.de Wed Feb 23 10:25:43 2011 From: glawe at mpi-halle.mpg.de (Henning Glawe) Date: Wed, 23 Feb 2011 10:25:43 +0100 Subject: [Pw_forum] pp.x ILDOS plots with ultrasoft pseudopotentials In-Reply-To: References: <20110209072307.GB10648@ford.simpsons.bogus> <3CC8F50E-8BD4-41D9-A8C6-E0F26799A102@democritos.it> <20110215062951.GC744@ford.simpsons.bogus> Message-ID: <20110223092543.GC15795@ford.simpsons.bogus> On Wed, Feb 23, 2011 at 09:32:25AM +0100, Paolo Giannozzi wrote: > > On Feb 15, 2011, at 7:29 , Henning Glawe wrote: > > > - in faulty versions, the range of values is [-41,+240], while in > > working > > versions, it is [0,0.76] > > > > Affected quantum espresso versions: >=4.2 > > here is what I got: > http://www.fisica.uniud.it/~giannozz/CaC6.tar.gz > I don't see anything obviously wrong in it Strange, your result seems OK. Here is my result, using 4.2.1, compiled with ifort 11.1: users.physik.fu-berlin.de/~glawe/4.2.1-ifort-11.1-debug.tar.gz Looking at your result, there may be 2 reasons for the errors in my case: - my statement 'Affected quantum espresso versions: >=4.2' was referring to released versions, so the problem may be fixed in CVS (I saw a 4.3a version string in your case) - my pp calculations were done using 2 MPI tasks, while yours were running on a single CPU. I will run some tests with a single CPU in order to investigate further. -- Mit freundlichen Gr??en Henning Glawe Max-Planck-Institut f?r Mikrostrukturphysik Weinberg 2, 06120 Halle (Saale), Germany http://www.mpi-halle.de/~theory Phone: +49-345-5582-613 Fax: +49-345-5511223 Email: glawe at mpi-halle.de From kangbugy at lycos.co.kr Wed Feb 23 11:35:10 2011 From: kangbugy at lycos.co.kr (=?UTF-8?B?a2FuZ2J1Z3lAbHljb3MuY28ua3I=?=) Date: Wed, 23 Feb 2011 19:35:10 +0900 Subject: [Pw_forum] =?utf-8?q?about_perovskite_and_AuCu3?= Message-ID: <75825d757782cf4890b9c96071a99ac1$5c67170d@pcmail3.nate.com> An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110223/ac93b271/attachment.htm From pcj994 at bham.ac.uk Wed Feb 23 12:23:52 2011 From: pcj994 at bham.ac.uk (Paul Jennings) Date: Wed, 23 Feb 2011 11:23:52 +0000 Subject: [Pw_forum] Semicore states and Spin-orbit coupling Message-ID: <4D64EE48.3020501@bham.ac.uk> Dear QE users. The research group I am in has started to use the QE package but before the group has used AO based codes. Therefore the concern of my questions is maybe trivial to you. I have two questions and both are connected somehow to the (ultrasoft)pseudopotentials. 1.) What kind of influence a semicore state in the pseudopotential has on the calculation. I found some general information of the comparison of norm-conserving and non norm-conserving (ultrasoft) pseudopotentials but I don't find any good written description of the influence of semicore states. Which properties are altered the most if using semicore states and what are the advantages and disadvantages? 2.) Since the systems I have to deal with contain heavy elements the question arises what kind of influence the spin orbit coupling has on structural and electronic properties. I found one paper and the two corresponding potentials for gold and platinum which incoperate a full relativistic treatment and enable a calculation including spin-orbit coupling for the LDA functional. Perhaps I havn't found the example of tutorial but is there a general procedure to incoperate SO effects on a GGA or a meta-GGA level yet? A third question is dealing with the density cutoff. 3.) In the QEwiki is written that a higher density cutoff should be used in the case of ultrasoft pseudopotentials and it should be checked that all setting have converged. I have done some calculations and changed first of all the Ecutoff and after that the Rhocutoff from four to ten times the Ecutoff. There was no big influence of the Rhocutoff on the structure and energy in my particular case. Just to avoid a problem in the future. What properties are altered the most by using a insufficent Rhocutoff? Best wishes Paul -- ****************************************************** Paul Jennings Centre for Hydrogen and Fuel Cell Research PEMFC Research group School of Chemical Engineering The University of Birmingham Edgbaston, Birmingham B15 2TT (U.K.) E: PCJ994 at bham.ac.uk T: 07816644583 W: www.fuelcells.bham.ac.uk ****************************************************** From ttduyle at gmail.com Wed Feb 23 13:28:16 2011 From: ttduyle at gmail.com (Duy Le) Date: Wed, 23 Feb 2011 07:28:16 -0500 Subject: [Pw_forum] about perovskite and AuCu3 In-Reply-To: <75825d757782cf4890b9c96071a99ac1$5c67170d@pcmail3.nate.com> References: <75825d757782cf4890b9c96071a99ac1$5c67170d@pcmail3.nate.com> Message-ID: It should be cubic perovskite. So Primitive vectors are: a 0 0 0 a 0 0 0 a and coordinates of atoms are: 0. 0. 0. (Au) 0.5 0.5 0. (Cu) 0.0 0.5 0.5 (Cu) 0.5 0.0 0.5 (Cu) -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Wed, Feb 23, 2011 at 5:35 AM, kangbugy at lycos.co.kr wrote: > Hi. > I study QE as graduate student in Korea. > But I have many problems. > One of them is about AuCu3 structure. > This basic structure is perovskite, but there is not a atom at body center. > > i.e., it is fcc structure. > Because I thought fcc structure, I used that 'ibrav = 2'. > Also, > atomic position is > Au 0.00 0.00 0.00 > Cu 0.50 0.50 0.00 > But scf.out's result appeared that 'atomic position #1 and #2 are overlap'. > I don't understand that. > > Another question is scf data of perovskite. > What can I input the data about perovskite? > > &SYSTEM > ibrav = 1, > A = 3.717 , > B = 3.717 , > C = 3.717 , > cosAB = 90 , > cosAC = 90 , > cosBC = 90 , > nat = 5, > ntyp = 3, > ecutwfc = 30, > / > &electrons > / > ATOMIC_SPECIES > Mg 24.305 Mg.pz-n-vbc.UPF > C 16.01 C.pz-rrkjus.UPF > Ni 58.71 Ni.pz-nd-rrkjus.UPF > > ATOMIC_POSITIONS > Mg 0.00 0.00 0.00 > C 0.50 0.50 0.50 > Ni 0.00 0.50 0.50 > Ni 0.50 0.50 0.00 > Ni 0.50 0.00 0.50 > > K_POINTS automatic > 10 10 10 0 0 0 > > Help me please. > > _______________________________________________ > 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/20110223/daa6df9b/attachment.htm From giannozz at democritos.it Wed Feb 23 14:29:07 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 23 Feb 2011 14:29:07 +0100 Subject: [Pw_forum] pp.x ILDOS plots with ultrasoft pseudopotentials In-Reply-To: <20110223092543.GC15795@ford.simpsons.bogus> References: <20110209072307.GB10648@ford.simpsons.bogus> <3CC8F50E-8BD4-41D9-A8C6-E0F26799A102@democritos.it> <20110215062951.GC744@ford.simpsons.bogus> <20110223092543.GC15795@ford.simpsons.bogus> Message-ID: <65A852CE-8B02-4865-9A51-D10F7A91D009@democritos.it> On Feb 23, 2011, at 10:25 , Henning Glawe wrote: > - my statement 'Affected quantum espresso versions: >=4.2' was > referring to > released versions, so the problem may be fixed in CVS (I saw a > 4.3a version > string in your case) it looks like there is a problem with v.4.2.x that has disappeared in the soon-to-be-released 4.3 version. The funny thing is that very little has changed in the affected part of the code P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From a.aezami at gmail.com Wed Feb 23 14:37:05 2011 From: a.aezami at gmail.com (azadeh aezami) Date: Wed, 23 Feb 2011 17:07:05 +0330 Subject: [Pw_forum] about perovskite and AuCu3 In-Reply-To: References: <75825d757782cf4890b9c96071a99ac1$5c67170d@pcmail3.nate.com> Message-ID: hi i'm azadeh.please chek below web site. http://cst-www.nrl.navy.mil/lattice/ On Wed, Feb 23, 2011 at 3:58 PM, Duy Le wrote: > It should be cubic perovskite. So > Primitive vectors are: > a 0 0 > 0 a 0 > 0 0 a > and coordinates of atoms are: > 0. 0. 0. (Au) > 0.5 0.5 0. (Cu) > 0.0 0.5 0.5 (Cu) > 0.5 0.0 0.5 (Cu) > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > > "Men don't need hand to do things" > > > On Wed, Feb 23, 2011 at 5:35 AM, kangbugy at lycos.co.kr < > kangbugy at lycos.co.kr> wrote: > >> Hi. >> I study QE as graduate student in Korea. >> But I have many problems. >> One of them is about AuCu3 structure. >> This basic structure is perovskite, but there is not a atom at body >> center. >> i.e., it is fcc structure. >> Because I thought fcc structure, I used that 'ibrav = 2'. >> Also, >> atomic position is >> Au 0.00 0.00 0.00 >> Cu 0.50 0.50 0.00 >> But scf.out's result appeared that 'atomic position #1 and #2 are >> overlap'. >> I don't understand that. >> >> Another question is scf data of perovskite. >> What can I input the data about perovskite? >> >> &SYSTEM >> ibrav = 1, >> A = 3.717 , >> B = 3.717 , >> C = 3.717 , >> cosAB = 90 , >> cosAC = 90 , >> cosBC = 90 , >> nat = 5, >> ntyp = 3, >> ecutwfc = 30, >> / >> &electrons >> / >> ATOMIC_SPECIES >> Mg 24.305 Mg.pz-n-vbc.UPF >> C 16.01 C.pz-rrkjus.UPF >> Ni 58.71 Ni.pz-nd-rrkjus.UPF >> >> ATOMIC_POSITIONS >> Mg 0.00 0.00 0.00 >> C 0.50 0.50 0.50 >> Ni 0.00 0.50 0.50 >> Ni 0.50 0.50 0.00 >> Ni 0.50 0.00 0.50 >> >> K_POINTS automatic >> 10 10 10 0 0 0 >> >> Help me please. >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110223/a3b96b69/attachment-0001.htm From caperott at ucs.br Wed Feb 23 14:41:50 2011 From: caperott at ucs.br (Claudio Perottoni) Date: Wed, 23 Feb 2011 10:41:50 -0300 Subject: [Pw_forum] phcg.x with US PPs Message-ID: <4D650E9E.6000207@ucs.br> Hi, While US PPs can be used in gamma_only scf calculations with pw.x, attempts to run phonon calculations with phcg.x returns the following error message: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from cg_readin : error # 1 ultrasoft pseudopotential not implemented %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Is there somebody working to implement phonon calculations with US PPs in phcg.x? Can we expect this being implemented any time soon? Regards, Claudio -- ****************************************************************** Dr. Cl?udio A. Perottoni Universidade de Caxias do Sul Centro de Ci?ncias Exatas e Tecnologia Rua Francisco Get?lio Vargas, 1130 95070-560 Caxias do Sul - RS - Brazil Phone: +55 54 3218 2607 http://www.ucs.br/ccet/defq/caperott/ ****************************************************************** From giannozz at democritos.it Wed Feb 23 14:59:03 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 23 Feb 2011 14:59:03 +0100 Subject: [Pw_forum] phcg.x with US PPs In-Reply-To: <4D650E9E.6000207@ucs.br> References: <4D650E9E.6000207@ucs.br> Message-ID: <8E0D5B77-1491-4B11-BD1C-B0AB78D07F49@democritos.it> On Feb 23, 2011, at 14:41 , Claudio Perottoni wrote: > Is there somebody working to implement phonon calculations > with US PPs in phcg.x? I wrote that piece of code many years ago. Its extension to USPP require some serious work and I am not aware of anybody working on it P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From weslley at vonbraunlabs.com.br Wed Feb 23 15:24:59 2011 From: weslley at vonbraunlabs.com.br (Weslley Souza Patrocinio) Date: Wed, 23 Feb 2011 11:24:59 -0300 Subject: [Pw_forum] Makov-Payne electrostatic correction for non-cubic lattices Message-ID: Hi, people. I'm initiating the use of this software and I'm interested in use the Quantum-Espresso platform to calculate a charged defect in a dielectric with hexagonal lattice. I found in the QE documentation that the Makov-Payne method of electrostatic interaction correction is implemented. However, the final expression of the correction given in the Makov & Payne work is associated to cubic lattice systems, but the formalism presented in the paper can be expanded to other crystalline lattices. I want to know if QE uses the Makov-Payne approach only for cubic systems or for other lattice types. If doesn't work for hexagonal lattices, I will find some convergence problem in the ground state calculation due the periodic boundary conditions (PBC) interactions ? My bests, Weslley Souza Patrocinio Nanotechnology group Wernher von Braun Center for Advanced Research -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110223/b0b8a3cd/attachment.htm From glawe at mpi-halle.mpg.de Wed Feb 23 15:58:22 2011 From: glawe at mpi-halle.mpg.de (Henning Glawe) Date: Wed, 23 Feb 2011 15:58:22 +0100 Subject: [Pw_forum] pp.x ILDOS plots with ultrasoft pseudopotentials In-Reply-To: <65A852CE-8B02-4865-9A51-D10F7A91D009@democritos.it> References: <20110209072307.GB10648@ford.simpsons.bogus> <3CC8F50E-8BD4-41D9-A8C6-E0F26799A102@democritos.it> <20110215062951.GC744@ford.simpsons.bogus> <20110223092543.GC15795@ford.simpsons.bogus> <65A852CE-8B02-4865-9A51-D10F7A91D009@democritos.it> Message-ID: <20110223145822.GC2323@ford.simpsons.bogus> On Wed, Feb 23, 2011 at 02:29:07PM +0100, Paolo Giannozzi wrote: > On Feb 23, 2011, at 10:25 , Henning Glawe wrote: > > > - my statement 'Affected quantum espresso versions: >=4.2' was > > referring to > > released versions, so the problem may be fixed in CVS (I saw a > > 4.3a version > > string in your case) > > it looks like there is a problem with v.4.2.x that has disappeared in > the > soon-to-be-released 4.3 version. The funny thing is that very little has > changed in the affected part of the code Another funny thing about the 'wrong' results is: they depend on the number of MPI tasks; could the error be related to read-access to uninitialized memory? in any case, I'll give current CVS a try. Thank you for helping! -- Mit freundlichen Gr??en Henning Glawe Max-Planck-Institut f?r Mikrostrukturphysik Weinberg 2, 06120 Halle (Saale), Germany http://www.mpi-halle.de/~theory Phone: +49-345-5582-613 Fax: +49-345-5511223 Email: glawe at mpi-halle.de From giannozz at democritos.it Wed Feb 23 22:10:12 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 23 Feb 2011 22:10:12 +0100 Subject: [Pw_forum] Makov-Payne electrostatic correction for non-cubic lattices In-Reply-To: References: Message-ID: <67EB5CFF-8DC4-4C08-8D1F-648BEF4EB420@democritos.it> On Feb 23, 2011, at 15:24 , Weslley Souza Patrocinio wrote: > However, the final expression of the correction given in the > Makov & Payne work is associated to cubic lattice systems, > but the formalism presented in the paper can be expanded > to other crystalline lattices. are you sure? I vaguely remember quite the opposite > P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From germaneau at gucas.ac.cn Thu Feb 24 12:45:14 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Thu, 24 Feb 2011 06:45:14 -0500 Subject: [Pw_forum] about perovskite and AuCu3 In-Reply-To: <498463289.12938@test1.gucas.ac.cn> References: <75825d757782cf4890b9c96071a99ac1$5c67170d@pcmail3.nate.com> <498463289.12938@test1.gucas.ac.cn> Message-ID: <4D6644CA.3090406@gucas.ac.cn> Hey Azadeh, Take a look to this database. You'll see that there are many form of Perovskite. Hope it can help. Eric. On 02/23/2011 08:37 AM, azadeh aezami wrote: > hi > i'm azadeh.please chek below web site. > > http://cst-www.nrl.navy.mil/lattice/ > > > > > > On Wed, Feb 23, 2011 at 3:58 PM, Duy Le > wrote: > > It should be cubic perovskite. So > Primitive vectors are: > a 0 0 > 0 a 0 > 0 0 a > and coordinates of atoms are: > 0. 0. 0. (Au) > 0.5 0.5 0. (Cu) > 0.0 0.5 0.5 (Cu) > 0.5 0.0 0.5 (Cu) > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > > "Men don't need hand to do things" > > > On Wed, Feb 23, 2011 at 5:35 AM, kangbugy at lycos.co.kr > > wrote: > > Hi. > I study QE as graduate student in Korea. > But I have many problems. > One of them is about AuCu3 structure. > This basic structure is perovskite, but there is not a atom at > body center. > i.e., it is fcc structure. > Because I thought fcc structure, I used that 'ibrav = 2'. > Also, > atomic position is > Au 0.00 0.00 0.00 > Cu 0.50 0.50 0.00 > But scf.out's result appeared that 'atomic position #1 and #2 > are overlap'. > I don't understand that. > > Another question is scf data of perovskite. > What can I input the data about perovskite? > > &SYSTEM > ibrav = 1, > A = 3.717 , > B = 3.717 , > C = 3.717 , > cosAB = 90 , > cosAC = 90 , > cosBC = 90 , > nat = 5, > ntyp = 3, > ecutwfc = 30, > / > &electrons > / > ATOMIC_SPECIES > Mg 24.305 Mg.pz-n-vbc.UPF > C 16.01 C.pz-rrkjus.UPF > Ni 58.71 Ni.pz-nd-rrkjus.UPF > > ATOMIC_POSITIONS > Mg 0.00 0.00 0.00 > C 0.50 0.50 0.50 > Ni 0.00 0.50 0.50 > Ni 0.50 0.50 0.00 > Ni 0.50 0.00 0.50 > > K_POINTS automatic > 10 10 10 0 0 0 > > Help me please. > > > _______________________________________________ > 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 -- /Be the change you wish to see in the world / ? Mahatma Gandhi ? Dr. ?ric Germaneau College of Physical Sciences Graduate University of ChineseAcademy of Sciences Yuquan Road 19A Beijing 100049 China /Please consider the environment before printing this email. Consid?rez svp l'environnement avant d'imprimer cet email. / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110224/15f97262/attachment.htm From weslley at vonbraunlabs.com.br Thu Feb 24 01:31:53 2011 From: weslley at vonbraunlabs.com.br (Weslley Souza Patrocinio) Date: Wed, 23 Feb 2011 21:31:53 -0300 Subject: [Pw_forum] Makov-Payne electrostatic correction for non-cubic lattices In-Reply-To: <67EB5CFF-8DC4-4C08-8D1F-648BEF4EB420@democritos.it> References: <67EB5CFF-8DC4-4C08-8D1F-648BEF4EB420@democritos.it> Message-ID: Hi, Mr. Giannozzi. I'm sure about my words in the previous message. In the article the integral formulas are obtained to the quadripole contribution to the electrostatic correction and the evaluation of the cubic lattice case is done, resulting in the well known formula to correct this energy. The first order correction (Madelung energy) is not associated to a specific lattice although there is the assumption of anisotropy of the dielectric xyz components, but the quadripole correction is evaluated to the cubic lattice. The principal question is about the convergence of the total energy in my system. I'll find any problem to converge the potentials due the charged defect and the hexagonal lattice ? Other ab initio softwares do not advise this type of calculation, and if QE is not capable too I have a huge problem. Thanks for your help. My bests, Weslley. On Wed, Feb 23, 2011 at 6:10 PM, Paolo Giannozzi wrote: > > On Feb 23, 2011, at 15:24 , Weslley Souza Patrocinio wrote: > > > However, the final expression of the correction given in the > > Makov & Payne work is associated to cubic lattice systems, > > but the formalism presented in the paper can be expanded > > to other crystalline lattices. > > are you sure? I vaguely remember quite the opposite > > > > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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 > -- Weslley Souza Patrocinio Pesquisador Departamento de Nanotecnologia Centro de Pesquisas Avan?adas Wernher von Braun e-mail: weslley at vonbraunlabs.com.br skype: weslley.vonbraun -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110223/0ed36815/attachment-0001.htm From cjobrien at ncsu.edu Thu Feb 24 03:50:25 2011 From: cjobrien at ncsu.edu (Christopher O'Brien) Date: Wed, 23 Feb 2011 21:50:25 -0500 Subject: [Pw_forum] Ionic forces not reducing Message-ID: <934A8BF3-C58D-4E31-A8F7-459F63D7730F@ncsu.edu> Below this is a super-cell of an interface of Cu2O and Ti. The problem is simply that the forc_conv_thr is not met within 100 iterations. etot_conv_thr is almost always met first (even decreasing etot_conv_thr to 1.0d-6). Typically, the force in this system decreases to ~0.01 Ry/B with a delta F on the same order of magnitude but fluctuates about this value. This means that I continually get the warning telling me to reduce the convergence threshold. Ideally I would like obtain a maximum force of ~1D-4. Does anyone have any suggestions? I am at a loss. Thanks in advance, Chris O'Brien title = 'Cu2O-Ti-case2' , calculation = 'vc-relax' , restart_mode = 'from_scratch' , wf_collect = .false. , outdir = './', wfcdir = './', pseudo_dir = '/share2/cjobrien/pseudo/', prefix = 'Cu2OTi', disk_io = 'low', verbosity = 'minimal', tstress = .true., tprnfor = .true., forc_conv_thr = 1.0d-4, etot_conv_thr = 1.0d-5, / &SYSTEM ibrav = 0, celldm(1) = 8.1878, nat = 14, ntyp = 3, ecutwfc = 30.0 , ecutrho = 300.0 , occupations = 'smearing' , smearing = 'mv' , degauss = 0.01 , / &ELECTRONS conv_thr = 1.0d-6 , mixing_beta = 0.7 , / &IONS ion_dynamics = 'bfgs', / &CELL cell_dynamics = 'bfgs', press = 0.0, cell_dofree = 'xyz', / CELL_PARAMETERS 0.929429709 0.0 0.0 0.0 0.929429709 0.0 0.0 0.0 2.924945006 ATOMIC_SPECIES Cu 58.70000 Cu.pw91-n-van_ak.UPF Ti 47.88000 Ti.pw91-nsp-van.UPF O 16.00000 O.pw91-van_ak.UPF ATOMIC_POSITIONS alat Cu 0 0 0 Cu 0.504691013 0.504691013 0 Cu 0.484702934 0.019988079 0.553031754 Cu 0.019988079 0.484702934 0.553031754 Cu 0.039976158 0.039976158 1.106063508 Cu 0.464714854 0.464714854 1.106063508 O 0.252345506 0.252345506 0.285738983 O 0.024221288 0.024221288 1.544049139 Ti 0.480469725 0.024221288 1.544049139 Ti 0.024221288 0.480469725 1.544049139 Ti 0.484702934 0.484702934 2.015504257 Ti 0.019988079 0.019988079 2.015504257 Ti 0.01575487 0.488936142 2.486959376 Ti 0.488936142 0.01575487 2.486959376 K_POINTS automatic 8 8 4 0 0 0 =================================================================== Christopher J. O'Brien cjobrien at ncsu.edu https://sites.google.com/a/ncsu.edu/cjobrien/ Ph.D. Candidate Computational Materials Group Department of Materials Science & Engineering North Carolina State University __________________________________________________________________ Please send all documents in PDF. For Word documents: Please use the 'Save as PDF' option before sending. =================================================================== From nicola.marzari at materials.ox.ac.uk Thu Feb 24 04:38:44 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Thu, 24 Feb 2011 03:38:44 +0000 Subject: [Pw_forum] Semicore states and Spin-orbit coupling In-Reply-To: <4D64EE48.3020501@bham.ac.uk> References: <4D64EE48.3020501@bham.ac.uk> Message-ID: <4D65D2C4.2010306@materials.ox.ac.uk> Dear Paul, > 1.) What kind of influence a semicore state in the pseudopotential has on the calculation. I found some general information of > the comparison of norm-conserving and non norm-conserving (ultrasoft) pseudopotentials but I don't find any good > written description of the influence of semicore states. Which properties are altered the > most if using semicore states and what are the advantages and disadvantages? in general you can have semicore states both in the norm-conserving (nc) and ultrasoft approaches (us). The only disadvantage of including them is the additional computational cost (more electrons, and more structured orbitals that require a higher cutoff). sometimes the "non-linear core correction" can be used (e.g. in group I/II) to account for core/valance overlap - see the 1982 Louie PRB, or http://www.tcm.phy.cam.ac.uk/~mds21/thesis/node17.html Let's take Fe: 4s2 3d6 are the valence, while 3s2 3p6 are the semicore. 8-electron pseudos are probably good to describe metallic iron, but not much else - but only a comparison of calculations done with or without semicore can tell you if they are needed (if they make a difference, they are needed). Adding 3p6 (at the cost of 6 more electrons) is probably a very good thing, while adding 3s2 (although customarily done) probably doesn't help that much (they are too low in energy). A critical difference here emerges between us and nc pseudo - nc pseudo have one projector per angular momentum, while us have typically two - hence if you use the 3s semi-core, with us you can have a s projector at 3s energies, and a s projector at 4s energies, while with nc you are forced to have one projector that acts in the same way on the 3s and 4s (a bad idea - better to drop the 3s back in the core). > 2.) Since the systems I have to deal with contain heavy elements the question arises what kind of influence the spin orbit > coupling has on structural and electronic properties. I found one paper and the two corresponding potentials for gold > and platinum which incorporate a full relativistic treatment and enable a calculation including spin-orbit coupling for > the LDA functional. Perhaps I havn't found the example of tutorial but is there a general procedure to incorporate > SO effects on a GGA or a meta-GGA level yet? I'd look at Andrea Dal Corso papers on phonons - probably the effects on structural properties are small, and on electronic properties, ahem, relevant for all properties that are not there without spin-orbit :-). Do keep in mind, though, that the pseudopotentials themselves have been generated with a relativistic calculation for the all electron atom, so a lot of the key effects have been captured there already. > > A third question is dealing with the density cutoff. > > 3.) In the QEwiki is written that a higher density cutoff should be used in the case of ultrasoft pseudopotentials and it should > be checked that all setting have converged. I have done some calculations and changed first of all the Ecutoff and after > that the Rhocutoff from four to ten times the Ecutoff. There was no big influence of the Rhocutoff on the structure and energy > in my particular case. Just to avoid a problem in the future. What properties are altered the most by using a insufficent Rhocutoff? > Best way to think at this is not that a higher density cutoff is needed (density cutoff is fixed by the true physics of the charge density), but a lowe wavefunction cutoff can be used. The end result is the same. 8 times is a good ballpark, and 6 to 12 the common range. Of course, if your Ecutoff is very high, then 4 will work - but the point is that you want to use for both the minimum value that is sufficient. A good check can be optical phonons - do them with energy cutoffs of 10-12-14....-38-40 Ry, using a rhocutoff of 4, 6, 8, 12 times , and compare these curves. nicola > Best wishes > > Paul > > > -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From giuseppe.mattioli at mlib.ism.cnr.it Thu Feb 24 10:10:51 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (giuseppe.mattioli at mlib.ism.cnr.it) Date: Thu, 24 Feb 2011 10:10:51 +0100 Subject: [Pw_forum] Ionic forces not reducing Message-ID: <20110224101051.oi7kp63pc4ww8c8k@webmail.sic.rm.cnr.it> Dear Christopher You should try to reduce conv_thr in &ELECTRONS, in order to have a more accurate calculation of forces and stress. Try, for instance, with conv_thr = 1.0d-9 (and with a lower mixing_beta, 0.2~0.3 or so, if the electronic calculation does not converge). HTH Giuseppe Quoting Christopher O'Brien : > Below this is a super-cell of an interface of Cu2O and Ti. The > problem is simply that the forc_conv_thr is not met within 100 > iterations. etot_conv_thr is almost always met first (even > decreasing etot_conv_thr to 1.0d-6). Typically, the force in this > system decreases to ~0.01 Ry/B with a delta F on the same order of > magnitude but fluctuates about this value. This means that I > continually get the warning telling me to reduce the convergence > threshold. Ideally I would like obtain a maximum force of ~1D-4. > Does anyone have any suggestions? I am at a loss. > > Thanks in advance, > Chris O'Brien > > > title = 'Cu2O-Ti-case2' , > calculation = 'vc-relax' , > restart_mode = 'from_scratch' , > wf_collect = .false. , > outdir = './', > wfcdir = './', > pseudo_dir = '/share2/cjobrien/pseudo/', > prefix = 'Cu2OTi', > disk_io = 'low', > verbosity = 'minimal', > tstress = .true., > tprnfor = .true., > forc_conv_thr = 1.0d-4, > etot_conv_thr = 1.0d-5, > / > &SYSTEM > ibrav = 0, > celldm(1) = 8.1878, > nat = 14, > ntyp = 3, > ecutwfc = 30.0 , > ecutrho = 300.0 , > occupations = 'smearing' , > smearing = 'mv' , > degauss = 0.01 , > / > &ELECTRONS > conv_thr = 1.0d-6 , > mixing_beta = 0.7 , > / > &IONS > ion_dynamics = 'bfgs', > / > &CELL > cell_dynamics = 'bfgs', > press = 0.0, > cell_dofree = 'xyz', > / > CELL_PARAMETERS > 0.929429709 0.0 0.0 > 0.0 0.929429709 0.0 > 0.0 0.0 2.924945006 > ATOMIC_SPECIES > Cu 58.70000 Cu.pw91-n-van_ak.UPF > Ti 47.88000 Ti.pw91-nsp-van.UPF > O 16.00000 O.pw91-van_ak.UPF > ATOMIC_POSITIONS alat > Cu 0 0 0 > Cu 0.504691013 0.504691013 0 > Cu 0.484702934 0.019988079 0.553031754 > Cu 0.019988079 0.484702934 0.553031754 > Cu 0.039976158 0.039976158 1.106063508 > Cu 0.464714854 0.464714854 1.106063508 > O 0.252345506 0.252345506 0.285738983 > O 0.024221288 0.024221288 1.544049139 > Ti 0.480469725 0.024221288 1.544049139 > Ti 0.024221288 0.480469725 1.544049139 > Ti 0.484702934 0.484702934 2.015504257 > Ti 0.019988079 0.019988079 2.015504257 > Ti 0.01575487 0.488936142 2.486959376 > Ti 0.488936142 0.01575487 2.486959376 > K_POINTS automatic > 8 8 4 0 0 0 > > =================================================================== > Christopher J. O'Brien > cjobrien at ncsu.edu > https://sites.google.com/a/ncsu.edu/cjobrien/ > > Ph.D. Candidate > Computational Materials Group > Department of Materials Science & Engineering > North Carolina State University > __________________________________________________________________ > Please send all documents in PDF. > For Word documents: Please use the 'Save as PDF' option before sending. > =================================================================== > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > Giuseppe Mattioli ISM-CNR, Italy From sclauzer at sissa.it Thu Feb 24 10:34:26 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 24 Feb 2011 10:34:26 +0100 Subject: [Pw_forum] Ionic forces not reducing In-Reply-To: <20110224101051.oi7kp63pc4ww8c8k@webmail.sic.rm.cnr.it> References: <20110224101051.oi7kp63pc4ww8c8k@webmail.sic.rm.cnr.it> Message-ID: Il giorno 24/feb/2011, alle ore 10.10, giuseppe.mattioli at mlib.ism.cnr.it ha scritto: > > > Dear Christopher > You should try to reduce conv_thr in &ELECTRONS, in order to have a > more accurate calculation of forces and stress. Try, for instance, > with conv_thr = 1.0d-9 (and with a lower mixing_beta, 0.2~0.3 or so, > if the electronic calculation does not converge). Alternatively you can use upscale=1.D3 in &IONS (the default should be 1.D1, if I remember well). > HTH > > Giuseppe > > Quoting Christopher O'Brien : > >> Below this is a super-cell of an interface of Cu2O and Ti. The >> problem is simply that the forc_conv_thr is not met within 100 >> iterations. etot_conv_thr is almost always met first (even >> decreasing etot_conv_thr to 1.0d-6). Typically, the force in this >> system decreases to ~0.01 Ry/B with a delta F on the same order of >> magnitude but fluctuates about this value. This means that I >> continually get the warning telling me to reduce the convergence >> threshold. Ideally I would like obtain a maximum force of ~1D-4. This threshold looks very tight to me. The default of 1.D-3 is often sufficient. If you really need such a good accuracy, you might also need to increase the cutoffs to get more precise forces. All the elements in your compound are pretty unfriendly to planewaves, even when using ultrasoft pseudos (Cu and Ti have 3d electrons in valence, O has 2p). I suggest you to perform a test on the force convergence w.r.t. ecutwfc. HTH GS >> Does anyone have any suggestions? I am at a loss. >> >> Thanks in advance, >> Chris O'Brien >> >> >> title = 'Cu2O-Ti-case2' , >> calculation = 'vc-relax' , >> restart_mode = 'from_scratch' , >> wf_collect = .false. , >> outdir = './', >> wfcdir = './', >> pseudo_dir = '/share2/cjobrien/pseudo/', >> prefix = 'Cu2OTi', >> disk_io = 'low', >> verbosity = 'minimal', >> tstress = .true., >> tprnfor = .true., >> forc_conv_thr = 1.0d-4, >> etot_conv_thr = 1.0d-5, >> / >> &SYSTEM >> ibrav = 0, >> celldm(1) = 8.1878, >> nat = 14, >> ntyp = 3, >> ecutwfc = 30.0 , >> ecutrho = 300.0 , >> occupations = 'smearing' , >> smearing = 'mv' , >> degauss = 0.01 , >> / >> &ELECTRONS >> conv_thr = 1.0d-6 , >> mixing_beta = 0.7 , >> / >> &IONS >> ion_dynamics = 'bfgs', >> / >> &CELL >> cell_dynamics = 'bfgs', >> press = 0.0, >> cell_dofree = 'xyz', >> / >> CELL_PARAMETERS >> 0.929429709 0.0 0.0 >> 0.0 0.929429709 0.0 >> 0.0 0.0 2.924945006 >> ATOMIC_SPECIES >> Cu 58.70000 Cu.pw91-n-van_ak.UPF >> Ti 47.88000 Ti.pw91-nsp-van.UPF >> O 16.00000 O.pw91-van_ak.UPF >> ATOMIC_POSITIONS alat >> Cu 0 0 0 >> Cu 0.504691013 0.504691013 0 >> Cu 0.484702934 0.019988079 0.553031754 >> Cu 0.019988079 0.484702934 0.553031754 >> Cu 0.039976158 0.039976158 1.106063508 >> Cu 0.464714854 0.464714854 1.106063508 >> O 0.252345506 0.252345506 0.285738983 >> O 0.024221288 0.024221288 1.544049139 >> Ti 0.480469725 0.024221288 1.544049139 >> Ti 0.024221288 0.480469725 1.544049139 >> Ti 0.484702934 0.484702934 2.015504257 >> Ti 0.019988079 0.019988079 2.015504257 >> Ti 0.01575487 0.488936142 2.486959376 >> Ti 0.488936142 0.01575487 2.486959376 >> K_POINTS automatic >> 8 8 4 0 0 0 >> >> =================================================================== >> Christopher J. O'Brien >> cjobrien at ncsu.edu >> https://sites.google.com/a/ncsu.edu/cjobrien/ >> >> Ph.D. Candidate >> Computational Materials Group >> Department of Materials Science & Engineering >> North Carolina State University >> __________________________________________________________________ >> Please send all documents in PDF. >> For Word documents: Please use the 'Save as PDF' option before sending. >> =================================================================== >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > Giuseppe Mattioli > ISM-CNR, Italy > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110224/3c670c38/attachment.htm From wibarrah at gmail.com Fri Feb 25 03:26:56 2011 From: wibarrah at gmail.com (Wilfredo Ibarra Hernandez) Date: Thu, 24 Feb 2011 20:26:56 -0600 Subject: [Pw_forum] [Pw_Forum] heat capacity In-Reply-To: References: <20110224101051.oi7kp63pc4ww8c8k@webmail.sic.rm.cnr.it> Message-ID: <4D671370.3070303@gmail.com> Dear all I'm used the QHA package for Cv calculation in FCC structure and works very well. But now I try to use it for a Trigonal R (ibrav = 5) and it's not implemented yet in QHA, there is another way to calculate that. Thanks all. -- Ibarra Hern?ndez Wilfredo Master student in Materials Science Cinvestav Unidad Qu?retaro Qu?retaro, M?xico From w2agz at w2agz.com Fri Feb 25 05:57:24 2011 From: w2agz at w2agz.com (W2AGZ) Date: Thu, 24 Feb 2011 20:57:24 -0800 Subject: [Pw_forum] Semicore states and Spin-orbit coupling In-Reply-To: <4D65D2C4.2010306@materials.ox.ac.uk> References: <4D64EE48.3020501@bham.ac.uk> <4D65D2C4.2010306@materials.ox.ac.uk> Message-ID: <009501cbd4a8$7fc4f6c0$7f4ee440$@w2agz.com> To All: I noted the thorough and extensive response by Nicola to the subject question. Where were professors like him when I was a graduate student? Speaking of which... Many, many, many...years ago, while I was a PhD candidate in the group of Harvey Brooks and Bill Paul at Harvard, a burning question at the time was, "What's the energy gap of grey tin (the diamond structure of Sn)?" It was thought tin could not be made pure enough so that it could be detected optically or through transport. Bill and his student, Steve Groves (deceased about four years ago), came up with the brilliant idea that the "conduction band" might "sink" below the valence band (the reversal from Si and Ge), and thus, by "k dot p" perturbation, undergo a "reflection of the upper branch" of the lower s-p split valence band, resulting in a "zero-gap" band gap with Ef passing through the gamma point degeneracy. It is now known as the "Groves-Paul" model for the electronic structure of grey tin, and is the forerunner of the now famous "Dirac singularity" in graphene. So...for some time, I've wondered if, given the appopriate pseudopotential, would quantum-espresso be able to yield the Groves-Paul bandstructure? Alas, after a very cursory search, I've not been able to find an appropriate PP which includes the required spin-orbit interaction...at least as far as I can see from the two that are in the QE database. I haven't looked further, but is the QE community aware of such? Does the ld1.x tool in QE provide the necessary resource and ability, should I want to "make one?" Sorry for the long post. I think this exercise would provide a great class lecture presentation or assignment. Ciao, -Paul IBM Research Staff Member Emeritus -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Nicola Marzari Sent: Wednesday, February 23, 2011 7:39 PM To: PWSCF Forum Subject: Re: [Pw_forum] Semicore states and Spin-orbit coupling Dear Paul, > 1.) What kind of influence a semicore state in the pseudopotential has on the calculation. I found some general information of > the comparison of norm-conserving and non norm-conserving (ultrasoft) pseudopotentials but I don't find any good > written description of the influence of semicore states. Which properties are altered the > most if using semicore states and what are the advantages and disadvantages? in general you can have semicore states both in the norm-conserving (nc) and ultrasoft approaches (us). The only disadvantage of including them is the additional computational cost (more electrons, and more structured orbitals that require a higher cutoff). sometimes the "non-linear core correction" can be used (e.g. in group I/II) to account for core/valance overlap - see the 1982 Louie PRB, or http://www.tcm.phy.cam.ac.uk/~mds21/thesis/node17.html Let's take Fe: 4s2 3d6 are the valence, while 3s2 3p6 are the semicore. 8-electron pseudos are probably good to describe metallic iron, but not much else - but only a comparison of calculations done with or without semicore can tell you if they are needed (if they make a difference, they are needed). Adding 3p6 (at the cost of 6 more electrons) is probably a very good thing, while adding 3s2 (although customarily done) probably doesn't help that much (they are too low in energy). A critical difference here emerges between us and nc pseudo - nc pseudo have one projector per angular momentum, while us have typically two - hence if you use the 3s semi-core, with us you can have a s projector at 3s energies, and a s projector at 4s energies, while with nc you are forced to have one projector that acts in the same way on the 3s and 4s (a bad idea - better to drop the 3s back in the core). > 2.) Since the systems I have to deal with contain heavy elements the question arises what kind of influence the spin orbit > coupling has on structural and electronic properties. I found one paper and the two corresponding potentials for gold > and platinum which incorporate a full relativistic treatment and enable a calculation including spin-orbit coupling for > the LDA functional. Perhaps I havn't found the example of tutorial but is there a general procedure to incorporate > SO effects on a GGA or a meta-GGA level yet? I'd look at Andrea Dal Corso papers on phonons - probably the effects on structural properties are small, and on electronic properties, ahem, relevant for all properties that are not there without spin-orbit :-). Do keep in mind, though, that the pseudopotentials themselves have been generated with a relativistic calculation for the all electron atom, so a lot of the key effects have been captured there already. > > A third question is dealing with the density cutoff. > > 3.) In the QEwiki is written that a higher density cutoff should be used in the case of ultrasoft pseudopotentials and it should > be checked that all setting have converged. I have done some calculations and changed first of all the Ecutoff and after > that the Rhocutoff from four to ten times the Ecutoff. There was no big influence of the Rhocutoff on the structure and energy > in my particular case. Just to avoid a problem in the future. What properties are altered the most by using a insufficent Rhocutoff? > Best way to think at this is not that a higher density cutoff is needed (density cutoff is fixed by the true physics of the charge density), but a lowe wavefunction cutoff can be used. The end result is the same. 8 times is a good ballpark, and 6 to 12 the common range. Of course, if your Ecutoff is very high, then 4 will work - but the point is that you want to use for both the minimum value that is sufficient. A good check can be optical phonons - do them with energy cutoffs of 10-12-14....-38-40 Ry, using a rhocutoff of 4, 6, 8, 12 times , and compare these curves. nicola > Best wishes > > Paul > > > -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From weylfang at gmail.com Fri Feb 25 12:09:11 2011 From: weylfang at gmail.com (Weyl Fang) Date: Fri, 25 Feb 2011 19:09:11 +0800 Subject: [Pw_forum] about path_thr setting Message-ID: <000301cbd4dc$74b39190$5e1ab4b0$@gmail.com> Dear all, I am doing some neb calculations on a surface H2S adsorption system with espresso 4.2.1. These calculations have taken me much time. I think If I increase path_thr, I could save some time The default setting of this parameter is 0.0500 eV / A. If I increase the value to 0.1000 eV / A, can I get an accurate result? Any suggestions are welcomed! Thanks Weyl ==================================================================== Weyl Fang Graduate student State Key Laboratory of Materials-oriented Chemical Engineering Nanjing University of Technology, 210009, Nanjing, China ******************************************************************** Email: weylfang at gmail.com / fangwei111 at 163.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, China ******************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110225/06833abc/attachment.htm From eyvaz_isaev at yahoo.com Fri Feb 25 15:12:56 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 25 Feb 2011 06:12:56 -0800 (PST) Subject: [Pw_forum] [Pw_Forum] heat capacity In-Reply-To: <4D671370.3070303@gmail.com> References: <20110224101051.oi7kp63pc4ww8c8k@webmail.sic.rm.cnr.it> <4D671370.3070303@gmail.com> Message-ID: <244314.47955.qm@web65711.mail.ac4.yahoo.com> Dear Wilfredo, Can you, please, send me your input file, so that I can try to build the BZ for your case. You can get phonon DOS by means of matdyn.x and then use it (you shoud add a few additional info, see PHDOS.out file) in combination with F_QHA.x file. This will give you C_v, S and internal energy only. If you are interested in C_v at low temperature limit (~10K and lower) then you can use the analytical expression C_v=234*(T/Theta_D)^3 (in units of R) Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ----- Original Message ---- From: Wilfredo Ibarra Hernandez To: pw_forum at pwscf.org Sent: Fri, February 25, 2011 5:26:56 AM Subject: [Pw_forum] [Pw_Forum] heat capacity Dear all I'm used the QHA package for Cv calculation in FCC structure and works very well. But now I try to use it for a Trigonal R (ibrav = 5) and it's not implemented yet in QHA, there is another way to calculate that. Thanks all. -- Ibarra Hern?ndez Wilfredo Master student in Materials Science Cinvestav Unidad Qu?retaro Qu?retaro, M?xico _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From parishok at gmail.com Fri Feb 25 17:58:22 2011 From: parishok at gmail.com (pari shok) Date: Fri, 25 Feb 2011 11:58:22 -0500 Subject: [Pw_forum] vectors for post processing calculation for hexagonal structure Message-ID: Hello, I was wondering how I could possibly get the STM (or other post processing calculations) on the surface of a hexagonal structure. If I define the vectors as: e1(1):1 e1(2):0 and e1(3):0 e2(1):0 e2(2):1 and e2(3):0 and the origin as: x0(1):0 x0(2):0 x0(3):the slab length (say 20 Angstroms), will it cover the *entire surface* of the hexagonal structure? I appreciate your help. P Shok -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110225/9cc5b84a/attachment.htm From ylli at aps.anl.gov Sat Feb 26 00:08:06 2011 From: ylli at aps.anl.gov (Yuelin Li) Date: Fri, 25 Feb 2011 17:08:06 -0600 (CST) Subject: [Pw_forum] input name empty Message-ID: <1450026687.43329.1298675286926.JavaMail.root@zimbra-mb1.anl.gov> While trying to run the example acetylene.in, have the following error, please help. Yuelin li ylli at ylliVB:~/Documents/temp$ pw.x < acetylene.in > acetylene.out STOP 2 ylli at ylliVB:~/Documents/temp$ cat acetylene.out Program PWSCF v.4.3a starts on 25Feb2011 at 17: 5:53 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please cite "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org", in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO Current dimensions of program PWSCF are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 Waiting for input... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from trimcheck : error # 1 input name empty %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% The full acetylene.in is here ---------------------------------- &CONTROL nstep = 50, dt = 10.D0, calculation = "md", outdir = "", / &SYSTEM nosym = .TRUE., ibrav = 1, celldm(1) = 10.D0, nat = 4, ntyp = 2, ecutwfc = 24.0D0, ecutrho = 144.0D0, occupations = "smearing", degauss = 0.01D0, smearing = "gauss", / &ELECTRONS conv_thr = 1.D-7, mixing_beta = 0.5D0, / &IONS pot_extrapolation = "second_order", wfc_extrapolation = "second_order", / ATOMIC_SPECIES H 1.0 H.US_PBE.RRKJ3.UPF C 12.0 C.US_PBE.RRKJ3.UPF ATOMIC_POSITIONS { bohr } C 0.000000000 0.000000000 0.000000000 0 0 0 C 2.100000000 0.000000000 0.000000000 H -1.600000000 0.400000000 0.000000000 H 3.600000000 -0.400000000 0.000000000 K_POINTS { gamma } From giannozz at democritos.it Sat Feb 26 08:49:50 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 26 Feb 2011 08:49:50 +0100 Subject: [Pw_forum] input name empty In-Reply-To: <1450026687.43329.1298675286926.JavaMail.root@zimbra-mb1.anl.gov> References: <1450026687.43329.1298675286926.JavaMail.root@zimbra-mb1.anl.gov> Message-ID: <5515591D-8200-4531-8C3A-288B13552242@democritos.it> On Feb 26, 2011, at 24:08 , Yuelin Li wrote: > > from trimcheck : error # 1 > input name empty > outdir = "", outdir should be set to something P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From daijiayu at nudt.edu.cn Sat Feb 26 09:51:31 2011 From: daijiayu at nudt.edu.cn (jiayudai) Date: Sat, 26 Feb 2011 16:51:31 +0800 Subject: [Pw_forum] about TDDFPT Message-ID: Dear developers, We are very pleased to see the release of TDDFPT in the new code of QE. However, there is no any explanation about it in the Doc directory. For example, we do not know what's the meaning of the input varables, the treatment for the spectra. So, is there any other files which we can find how to understand the input file and how to get the spectra from the output files? Even in the Examples supplied in the code, there is no any README exaplanation. Thanks a lot. Jiayu ---------------- ------------------------------------------- Jiayu Dai Department of Physics National University of Defense Technology, Changsha, 410073, P R China ----------------------------------------- From metokal at gmail.com Sat Feb 26 10:25:23 2011 From: metokal at gmail.com (Mehmet Topsakal) Date: Sat, 26 Feb 2011 11:25:23 +0200 Subject: [Pw_forum] about TDDFPT In-Reply-To: References: Message-ID: Dear Jiayu, I attended http://www.democritos.it/nanoexcite2010/ and here is some of my files that I collected during workshop http://unam.bilkent.edu.tr/mt2/random/nanoexcite2010/ . They might be helpful. Regards On Sat, Feb 26, 2011 at 10:51 AM, jiayudai wrote: > Dear developers, > > We are very pleased to see the release of TDDFPT in the new code of QE. > However, there is no any explanation about it in the Doc directory. For > example, we do not know what's the meaning of the input varables, the > treatment for the spectra. So, is there any other files which we can find > how to understand the input file and how to get the spectra from the output > files? Even in the Examples supplied in the code, there is no any README > exaplanation. > > Thanks a lot. > > Jiayu > ---------------- > ------------------------------------------- > Jiayu Dai > Department of Physics > National University of Defense Technology, > Changsha, 410073, P R China > ----------------------------------------- > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Mehmet Topsakal (Ph.D. Student) UNAM-Institute of Materials Science and Nanotechnology. Bilkent University. 06800 Bilkent, Ankara/Turkey Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365 http://www.researcherid.com/rid/A-5015-2010 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110226/593065f5/attachment.htm From daijiayu at nudt.edu.cn Sat Feb 26 10:45:18 2011 From: daijiayu at nudt.edu.cn (jiayudai) Date: Sat, 26 Feb 2011 17:45:18 +0800 Subject: [Pw_forum] about TDDFPT Message-ID: Dear Mehmet, Thanks for your quick response, it really helpful. The problem now is that we did not have the explanation of input variables from tddfpt. Besides, there are some different in the released code of QE-4.3a from the files you supplied for the old version. So, i would like to know the details for the input files and the postplot after the calculations. Thanks. Jiayu >From: Mehmet Topsakal >Reply-To: >To: jiayudai , PWSCF Forum >Subject: Re: [Pw_forum] about TDDFPT >Date: Sat, 26 Feb 2011 11:25:23 +0200 > DearJiayu, I attendedhttp://www.democritos.it/nanoexcite2010/and here is some of my files that I collected during workshophttp://unam.bilkent.edu.tr/mt2/random/nanoexcite2010/. They might be helpful. Regards On Sat, Feb 26, 2011 at 10:51 AM, jiayudai wrote: Dear developers, We are very pleased to see the release of TDDFPT in the new code of QE. However, there is no any explanation about it in the Doc directory. For example, we do not know what's the meaning of the input varables, the treatment for the spectra. So, is there any other files which we can find how to understand the input file and how to get the spectra from the output files? Even in the Examples supplied in the code, there is no any README exaplanation. Thanks a lot. Jiayu ---------------- ------------------------------------------- Jiayu Dai Department of Physics National University of Defense Technology, Changsha, 410073, P R China ----------------------------------------- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Mehmet Topsakal (Ph.D. Student) UNAM-Institute of Materials Science and Nanotechnology. Bilkent University. 06800 Bilkent, Ankara/Turkey Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365 http://www.researcherid.com/rid/A-5015-2010 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110226/3f11d908/attachment.htm From germaneau at gucas.ac.cn Sun Feb 27 05:50:55 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Sat, 26 Feb 2011 23:50:55 -0500 Subject: [Pw_forum] Bravais lattices & matrix of cell parameters Message-ID: <4D69D82F.6020003@gucas.ac.cn> Dear all, The program "cp" is able to take into account the Bravais lattices. I'd like to know the relationships between the elements of the matrix of cell parameters for each Bravais lattices. Can you please tell me where I can get it or explain to me how to derive them? Thanks in advance, Eric. -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of ChineseAcademy of Sciences Yuquan Road 19A Beijing 100049 China /Please consider the environment before printing this email. Consid?rez svp l'environnement avant d'imprimer cet email. / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110226/38d2533f/attachment.htm From sumalchandra at gmail.com Sun Feb 27 07:11:24 2011 From: sumalchandra at gmail.com (sumal chandra) Date: Sun, 27 Feb 2011 12:11:24 +0600 Subject: [Pw_forum] pseudopotential Message-ID: Dear all Now I am working on Hf . Pseudopotential is not mention in the Quantum Espresso data base.If you have any pseudopotential of Hf, Plase give me Sumal Chandra Department of physics University of Rajshahi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110227/dd503030/attachment.htm From kangbugy at lycos.co.kr Sun Feb 27 14:49:06 2011 From: kangbugy at lycos.co.kr (=?UTF-8?B?a2FuZ2J1Z3lAbHljb3MuY28ua3I=?=) Date: Sun, 27 Feb 2011 22:49:06 +0900 Subject: [Pw_forum] =?utf-8?q?about_K-point_on_band_calculation?= Message-ID: <0c853afe062ef11a317f0b0d7728b30f$5c67176b@pcmail3.nate.com> An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110227/302abb3b/attachment.htm From mehrnooshhazrati at gmail.com Mon Feb 28 09:31:53 2011 From: mehrnooshhazrati at gmail.com (Mehrnoosh Hazrati) Date: Mon, 28 Feb 2011 12:01:53 +0330 Subject: [Pw_forum] DOS diagram problem In-Reply-To: References: Message-ID: Hi dear QE users, I don't get a correct DOS diagram, what can be the problem with my input ? I attached the incorrect diagram. thank you in advance. Mehrnoosh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110228/28acae43/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: DOS.docx Type: application/vnd.openxmlformats-officedocument.wordprocessingml.document Size: 18363 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110228/28acae43/attachment-0001.bin From hqzhou at nju.edu.cn Mon Feb 28 10:00:37 2011 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Mon, 28 Feb 2011 17:00:37 +0800 Subject: [Pw_forum] temperature rescaling for vc-md Message-ID: <365CBDDE367D4DB7B161F1FB96765E97@solarflare> Hi, I'm trying to run a vc-md simulation of a supercell with 80 atoms at 300 K and 20 GPa, but the SCF convergence is always failed to reach after 20 or so ion steps no matter how I change mixing_beta from 0.5 to 0.05. One thing I noticed is that the temperature controling may be not in effect as the temperature remains as high as 6 digits. I used the 'rescaling' , the only setting available for vc-md, for ion_temperature, the default 100.0 for tolp. Below is part of my input file, any comments are welcome. I would also like to know which source file I need to look at for the rescaling function. The same system is running without any problem using CP dynamics in VASP and CASTEP. &control calculation = 'vc-md', restart_mode = 'from_scratch', prefix = 'mgsio3', tstress = .true., tprnfor = .true., pseudo_dir = '/home/hqzhou/qe_pseudo/', outdir = '/gpfsTMP/hqzhou/tmp/' wf_collect = .true. nstep = 100 dt = 20.0 / &system !ibrav = 0 !celldm(1) = 0.0 ibrav = 14 celldm(1) = 18.0484, celldm(2) = 1.0322, celldm(3) = 0.7221 celldm(4) = 0.0, celldm(5) = 0.0, celldm(6) = 0.0 nat = 80, ntyp = 3, ecutwfc = 40.0, ecutrho = 400.0 nspin = 1 nosym = .true. occupations = 'fixed' / &electrons electron_maxstep = 200 diagonalization = david mixing_mode = 'plain' mixing_beta = 0.1 conv_thr = 1.0d-8 / &ions ion_dynamics = 'beeman' pot_extrapolation = 'second_order' wfc_extrapolation = 'second_order' upscale = 100.0 ion_temperature = 'rescaling' tempw = 300.0 refold_pos = .true. / &cell cell_dynamics = 'pr' press = 200.0 !wmass = 0.05 cell_factor = 1.6 press_conv_thr = 0.2 / ...... Thanks in advance. zhou huiqun @earth sciences, nanjing university, china -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110228/f10dd312/attachment.htm From glapenna at iccom.cnr.it Mon Feb 28 10:31:49 2011 From: glapenna at iccom.cnr.it (Giovanni La Penna) Date: Mon, 28 Feb 2011 10:31:49 +0100 (CET) Subject: [Pw_forum] temperature rescaling for vc-md In-Reply-To: <365CBDDE367D4DB7B161F1FB96765E97@solarflare> References: <365CBDDE367D4DB7B161F1FB96765E97@solarflare> Message-ID: I would suggest to heat the system slowly. restart='from_scratch' means that previous velocities are not loaded. So going from zero (for a hopefully relaxed system) to 300 K, with a time-step of 1 fs (if a remember correctly), may imply a huge time to converge at each time step. Even CP would not work properly this way: it runs, but temperature oscillations become huge and the fake electron kinetic energy would quickly increase, providing an uncontrolled dynamics. Other codes may have hidden controls on temperature, time-steps, etc.. Giovanni ============================================================ Giovanni La Penna - National research council (Cnr) Institute for chemistry of organo-metallic compounds (Iccom) via Madonna del Piano 10, I-50019 Sesto Fiorentino, Firenze, Italy tel.: +39 055 522-5264, fax: +39 055 522-5203 e-mail: glapenna at iccom.cnr.it - http://www.iccom.cnr.it/lapenna skype: giovannilapenna ============================================================ On Mon, 28 Feb 2011, Huiqun Zhou wrote: > ... > but the SCF convergence is always failed to?reach after 20 or so ion steps > no matter > how I change mixing_beta from 0.5 to 0.05. One thing I noticed is that the > temperature > controling may be not in effect as the temperature remains as high as 6 > digits. I used > ... From science35 at gmail.com Mon Feb 28 10:33:53 2011 From: science35 at gmail.com (patriot pershing) Date: Mon, 28 Feb 2011 10:33:53 +0100 Subject: [Pw_forum] how to create SIC PP for Zn Message-ID: dear all i would create a pseudo file with SIC correction for Zn i have prepared an input file and i have set a value for alpha parameters but the ld1.x program don't work so if any one has a suggestion please inform me best regards From sclauzer at sissa.it Mon Feb 28 11:05:33 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 28 Feb 2011 11:05:33 +0100 Subject: [Pw_forum] vectors for post processing calculation for hexagonal structure In-Reply-To: References: Message-ID: <8EDE35D4-57D6-4B53-8C08-E7506871493E@sissa.it> Hello, Il giorno 25/feb/2011, alle ore 17.58, pari shok ha scritto: > Hello, > I was wondering how I could possibly get the STM (or other post processing calculations) on the surface of a hexagonal structure. > If I define the vectors as: > e1(1):1 e1(2):0 and e1(3):0 > e2(1):0 e2(2):1 and e2(3):0 > and the origin as: > x0(1):0 x0(2):0 x0(3):the slab length (say 20 Angstroms), > will it cover the entire surface of the hexagonal structure? I don't think so. The documentation says: !!! x0, e1, e2 are in alat units !!! which usually means that these vectors are in a cartesian frame of reference and in units of celldm(1). Moreover, it also says Variables: e1(i), e2(i), i=1,3 Type: REAL Description: 3D vectors which determine the plotting plane (must be orthogonal) while the vectors which define the basal plane of the hexagonal lattice are obviously not orthogonal. If you need to visualize the charge in planes which are normal to one of the crystal axes you can use iflag=3 and output_format=5. Then open the file with xcrysden, visualize the grid data (menu on the top right) and select the plane you want. Finally you can make nice eps, jpeg, png, ... figures. > I appreciate your help. You're welcome. However we appreciate that you sign with your affiliation too. Thanks! HTH GS > P Shok > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110228/a9c64bfc/attachment.htm From sclauzer at sissa.it Mon Feb 28 11:09:14 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 28 Feb 2011 11:09:14 +0100 Subject: [Pw_forum] how to create SIC PP for Zn In-Reply-To: References: Message-ID: <7584B69B-D7A9-41C5-894E-980FBEFC1F16@sissa.it> Il giorno 28/feb/2011, alle ore 10.33, patriot pershing ha scritto: > dear all > i would create a pseudo file with SIC correction for Zn i have > prepared an input file and i have set a value for alpha parameters alpha parameters? > but > the ld1.x program don't work I don't think that ld1 has this capability yet. From the Doc: Variable: isic Type: INTEGER Description: 0 ... no Self-interaction correction 1 ... apply Self-interaction correction Default: 0 Status: only for all-electron calculation Please notice the last line. > so if any one has a suggestion please inform me Yes, please sign your emails and put your affiliation. Thanks. HTH GS > best regards > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110228/35dddffc/attachment.htm From sclauzer at sissa.it Mon Feb 28 11:13:45 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 28 Feb 2011 11:13:45 +0100 Subject: [Pw_forum] DOS diagram problem In-Reply-To: References: Message-ID: Il giorno 28/feb/2011, alle ore 09.31, Mehrnoosh Hazrati ha scritto: > Hi dear QE users, > > I don't get a correct DOS diagram, what can be the problem with my input ? What is you input??? > I attached the incorrect diagram. I can't visualize it. Please send your plot in a more standard format (eps, pdf, jpg, png, ...) > > thank you in advance. > Mehrnoosh Please supply your affiliation. Thanks. GS > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110228/e176c8bf/attachment-0001.htm From giannozz at democritos.it Mon Feb 28 11:22:33 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 28 Feb 2011 11:22:33 +0100 Subject: [Pw_forum] about TDDFPT In-Reply-To: References: Message-ID: On Feb 26, 2011, at 9:51 , jiayudai wrote: > We are very pleased to see the release of TDDFPT in the new code > of QE. However, there is no any explanation about it in the Doc > directory. > For example, we do not know what's the meaning of the input variables more documentation should be available before the new version is released P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Mon Feb 28 11:24:10 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 28 Feb 2011 11:24:10 +0100 Subject: [Pw_forum] Bravais lattices & matrix of cell parameters In-Reply-To: <4D69D82F.6020003@gucas.ac.cn> References: <4D69D82F.6020003@gucas.ac.cn> Message-ID: On Feb 27, 2011, at 5:50 , Eric Germaneau wrote: > I'd like to know the relationships between the elements of the matrix > of cell parameters for each Bravais lattices. you would like to know...what exactly? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From nicola.marzari at materials.ox.ac.uk Mon Feb 28 11:31:05 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Mon, 28 Feb 2011 10:31:05 +0000 Subject: [Pw_forum] Bravais lattices & matrix of cell parameters In-Reply-To: <4D69D82F.6020003@gucas.ac.cn> References: <4D69D82F.6020003@gucas.ac.cn> Message-ID: <4D6B7969.3040800@materials.ox.ac.uk> On 2/27/11 4:50 AM, Eric Germaneau wrote: > Dear all, > > The program "cp" is able to take into account the Bravais lattices. > I'd like to know the relationships between the elements of the matrix of > cell parameters for each Bravais lattices. > Can you please tell me where I can get it or explain to me how to derive > them? > Thanks in advance, > > Eric. ???? ???????PW????????? Doc/INPUT_PW.txt? ??? ?namelist SYSTEM???????????? ??? ??? -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From hqzhou at nju.edu.cn Mon Feb 28 11:41:01 2011 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Mon, 28 Feb 2011 18:41:01 +0800 Subject: [Pw_forum] temperature rescaling for vc-md References: <365CBDDE367D4DB7B161F1FB96765E97@solarflare> Message-ID: Giovanni, Thanks for your quick response! I'll try to reduce the dt and 'restart' for restart_mode. Thank you. Huiqun ----- Original Message ----- From: "Giovanni La Penna" To: "PWSCF Forum" Sent: Monday, February 28, 2011 5:31 PM Subject: Re: [Pw_forum] temperature rescaling for vc-md > > I would suggest to heat the system slowly. > restart='from_scratch' > means that previous velocities are not loaded. > So going from zero (for a hopefully relaxed system) to 300 K, > with a time-step of 1 fs (if a remember correctly), may imply > a huge time to converge at each time step. > Even CP would not work properly this way: it runs, but temperature > oscillations become huge and the fake electron > kinetic energy would quickly increase, providing > an uncontrolled dynamics. > Other codes may have hidden controls on temperature, > time-steps, etc.. > > Giovanni > > ============================================================ > Giovanni La Penna - National research council (Cnr) > Institute for chemistry of organo-metallic compounds (Iccom) > via Madonna del Piano 10, > I-50019 Sesto Fiorentino, Firenze, Italy > tel.: +39 055 522-5264, fax: +39 055 522-5203 > e-mail: glapenna at iccom.cnr.it - http://www.iccom.cnr.it/lapenna > skype: giovannilapenna > ============================================================ > > On Mon, 28 Feb 2011, Huiqun Zhou wrote: > >> ... >> but the SCF convergence is always failed to reach after 20 or so ion >> steps >> no matter >> how I change mixing_beta from 0.5 to 0.05. One thing I noticed is that >> the >> temperature >> controling may be not in effect as the temperature remains as high as 6 >> digits. I used >> ... -------------------------------------------------------------------------------- > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From srijan.india at gmail.com Mon Feb 28 12:35:00 2011 From: srijan.india at gmail.com (Srijan Kumar Saha) Date: Mon, 28 Feb 2011 12:35:00 +0100 Subject: [Pw_forum] Berry Phase Message-ID: Dear QE USERS, I am facing the following error during polarisation computation with Berry Phase method; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from c_phase : error # 1 Polarization only for insulators and no empty bands %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... even though, I have fixed the occupations which is needed for an insulator ? Does this mean that Berry Phase calculation in QE is only for BAND-INSULATOR, and not for any other insulator ? Does this mean, if one has odd number of electrons in a unit-cell, then QE can not treat the system as insulator, even one forces QE to do so by specifying occupation "fixed" ? Looking forward to your kind reply. Input files are appended below : &control calculation = 'scf' restart_mode = 'from_scratch' pseudo_dir = '/home/pseudo/' outdir = './' tstress=.true. tprnfor=.true. / &system ibrav=1 celldm(1)=6.84, nat=5 ntyp=3 ecutwfc=50.0, ecutrho=400.0, occupations='fixed' tot_magnetization=3.0 nspin=2, / &electrons conv_thr = 1e-7, / ATOMIC_SPECIES Bi 209.0 Bi.pbe-d-mt.UPF Fe 55.85 Fe.pbe-nd-rrkjus.UPF O 16.00 O.pbe-mt.UPF ATOMIC_POSITIONS Bi 0.000 0.000 0.010 Fe 0.500 0.500 0.500 O 0.000 0.500 0.500 O 0.500 0.500 0.000 O 0.500 0.000 0.500 K_POINTS {automatic} 4 4 4 1 1 1 BerryPhase.in: &control calculation = 'nscf' pseudo_dir = '/home/pseudo/' outdir = './' lberry = .true. gdir = 3 nppstr = 7 / &system ibrav = 1 celldm(1) = 6.84 nat = 5 ntyp = 3 ecutwfc = 50.0 ecutrho=400.0, tot_magnetization=3.0, nspin=2 occupations='fixed' / &electrons / ATOMIC_SPECIES Bi 209.0 Bi.pbe-d-mt.UPF Fe 55.85 Fe.pbe-nd-rrkjus.UPF O 16.00 O.pbe-mt.UPF ATOMIC_POSITIONS Bi 0.000 0.000 0.010 Fe 0.500 0.500 0.500 O 0.000 0.500 0.500 O 0.500 0.500 0.000 O 0.500 0.000 0.500 K_POINTS {automatic} 4 4 7 1 1 1 Thanking you and with my best regards, Srijan Kumar R&D Associate, Indian Institute of Science, India, 560012 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110228/60e70851/attachment.htm From degironc at sissa.it Mon Feb 28 16:57:24 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 28 Feb 2011 16:57:24 +0100 Subject: [Pw_forum] Bravais lattices & matrix of cell parameters In-Reply-To: <4D6C6E47.5050902@gucas.ac.cn> References: <4D69D82F.6020003@gucas.ac.cn> <498883713.27999@test1.gucas.ac.cn> <4D6C6E47.5050902@gucas.ac.cn> Message-ID: <4D6BC5E4.50007@sissa.it> look at the description of the ibrav variable to see which parameter are needed in the different cases. stefano On 03/01/2011 04:55 AM, Eric Germaneau wrote: > Well, my question concern more the crystal class than the Bravais > lattice actually. > I was just wondering what the matrix of the cell parameters looks like > in a case of non triclinic cell. > I'm wondering how the fact that a=b for instance is "translated" in > the matrix form of the cell parameters. > One may also have less than six degree of freedom. > Thank you, > > Eric. > > On 02/28/2011 05:24 AM, Paolo Giannozzi wrote: >> On Feb 27, 2011, at 5:50 , Eric Germaneau wrote: >> >>> I'd like to know the relationships between the elements of the matrix >>> of cell parameters for each Bravais lattices. >> you would like to know...what exactly? P. >> --- >> Paolo Giannozzi, Dept of Chemistry&Physics&Environment, >> Univ. 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 >> > > > _______________________________________________ > 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/20110228/7d523cbd/attachment-0001.htm From 1009ukumar at gmail.com Mon Feb 28 17:39:22 2011 From: 1009ukumar at gmail.com (sonu kumar) Date: Mon, 28 Feb 2011 22:09:22 +0530 Subject: [Pw_forum] how to create SIC PP for Zn Message-ID: Dear all QE users, > i would create a pseudo file with SIC correction for Zn i have > > prepared an input file and i have set a value for alpha parameters > > I don't think that ld1 has this capability yet. From the Doc: > > Variable: isic > > Type: INTEGER > Description: 0 ... no Self-interaction correction > 1 ... apply Self-interaction correction > Default: 0 > Status: only for all-electron calculation > > > Please notice the last line. > > Then, what is the use of having this flag for ae calculations? Looking for any hint or explanation... With kind regards, -- Sonu Kumar Phd Student Physics Department Indian Institute of Technology Delhi-110016, India web:-http://www.iitd.ac.in/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110228/c20e5966/attachment.htm From sclauzer at sissa.it Mon Feb 28 18:47:46 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 28 Feb 2011 18:47:46 +0100 Subject: [Pw_forum] how to create SIC PP for Zn In-Reply-To: References: Message-ID: Il giorno 28/feb/2011, alle ore 17.39, sonu kumar ha scritto: > Dear all QE users, > > > i would create a pseudo file with SIC correction for Zn i have > > prepared an input file and i have set a value for alpha parameters > > I don't think that ld1 has this capability yet. From the Doc: > > Variable: isic > > Type: INTEGER > Description: 0 ... no Self-interaction correction > 1 ... apply Self-interaction correction > Default: 0 > Status: only for all-electron calculation > > > Please notice the last line. > > > > Then, what is the use of having this flag for ae calculations? Doing AE atomic calculations with SIC. Regards, GS > Looking for any hint or explanation... > > With kind regards, > > -- > Sonu Kumar > > Phd Student > Physics Department > Indian Institute of Technology > Delhi-110016, India > web:-http://www.iitd.ac.in/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110228/79e3627b/attachment.htm From giannozz at democritos.it Mon Feb 28 18:58:17 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 28 Feb 2011 18:58:17 +0100 Subject: [Pw_forum] how to create SIC PP for Zn In-Reply-To: References: Message-ID: On Feb 28, 2011, at 17:39 , sonu kumar wrote: > Then, what is the use of having this flag for ae calculations? > Looking for any hint or explanation... I think it dates back to the time when dinosaurs roamed the earth and the first SIC was introduced (1980 or so) P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Mon Feb 28 19:52:33 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 28 Feb 2011 19:52:33 +0100 Subject: [Pw_forum] Berry Phase In-Reply-To: References: Message-ID: On Feb 28, 2011, at 12:35 , Srijan Kumar Saha wrote: > I am facing the following error during polarisation computation > with Berry Phase method; > from c_phase : error # 1 > Polarization only for insulators and no empty bands I am not sure that the case you are interested in (spin-polarized insulators) is actually supported. If it isn't, the error message is misleading. If it is, the error message is incorrect. You may try to comment the check in PW/bp_c_phase.f90 and see what happens (no warranty) P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222